• Journal of KIISE:Databases
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• v.32 no.3
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• pp.254-262
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• 2005

This paper presents a new sequential indexing method called segment-page indexing (SP-indexing) for multidimensional range queries. The design objectives of SP-indexing are twofold:(1) improving the range query performance of multidimensional indexing methods (MIMs) and (2) providing a compromise between optimal index clustering and the full index reorganization overhead. Although more than ten years of database research has resulted in a great variety of MIMs, most efforts have focused on data-level clustering and there has been less attempt to cluster indexes. As a result, most relevant index nodes are widely scattered on a disk and many random disk accesses are required during the search. SP-indexing avoids such scattering by storing the relevant nodes contiguously in a segment that contains a sequence of contiguous disk pages and improves performance by offering sequential access within a segment. Experimental results demonstrate that SP-indexing improves query performance up to several times compared with traditional MIMs using small disk pages with respect to total elapsed time and it reduces waste of disk bandwidth due to the use of simple large pages.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.91-95
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• 2005

In the multidimensional protein identification technology of high-throughput proteomics, we use one-dimensional gel electrophoresis and after the separation by two-dimensional liquid chromatography, the sample is analyzed by tandem mass spectrometry. In this study, we have analyzed the Pseudomonas Putida KT2440 protein. From the protein identification, the protein database was combined with its reversed sequence database. From the peptide selection whose error rate is less than 1%, the SEQUEST database search for the tandem mass spectral data identified 2,045 proteins. For each protein, we compared the molecular weight calibrated from 1D-gel band position with the theoretical molecular weight computed from the amino acid sequence, by defining a variable MW$_{corr}$ Since the bacterial proteome is simpler than human proteome considering the complexity and modifications, the proteome analysis result for the Pseudomonas Putida KT2440 could suggest a guideline to build the protocol to analyze human proteome data.

• Journal of Industrial Technology
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• v.21 no.A
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• pp.167-179
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• 2001

This paper discusses an index-based subsequence matching that supports time warping in large sequence databases. Time warping enables finding sequences with similar patterns even when they are of different lengths. In earlier work, we suggested an efficient method for whole matching under time warping. This method constructs a multidimensional index on a set of feature vectors, which are invariant to time warping, from data sequences. For filtering at feature space, it also applies a lower-bound function, which consistently underestimates the time warping distance as well as satisfies the triangular inequality. In this paper, we incorporate the prefix-querying approach based on sliding windows into the earlier approach. For indexing, we extract a feature vector from every subsequence inside a sliding window and construct a multi-dimensional index using a feature vector as indexing attributes. For query precessing, we perform a series of index searches using the feature vectors of qualifying query prefixes. Our approach provides effective and scalable subsequence matching even with a large volume of a database. We also prove that our approach does not incur false dismissal. To verily the superiority of our method, we perform extensive experiments. The results reseal that our method achieves significant speedup with real-world S&P 500 stock data and with very large synthetic data.

• Journal of the Korean Magnetic Resonance Society
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• v.2 no.2
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• pp.85-105
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• 1998

Prions cause neurodegenerative diseases in animals and humans. The scrapie prion protein (PrPSc) is the major-possibly only-component of the infectious prion and is generated from the cellular isoform (PrPC) by a conformational change. Limited proteolysis of PrPSc produces an polypeptide comprised primarily of residues 90 to 231, which retains infectivity. The three-dimensional structure of rPrP(90-231), a recombinant protein resembling PrPC with the Syrian hamster (SHa) sequence, was solved using multidimensional NMR. Low-resolution structures of rPrP(90-231), synthetic peptides up to 56 residues, a longer (29-231, full-length) protein with SHa sequence, and a short here further structure refinement of rPrP(90-231) and dynamic features of the protein. Consideration of these features in the context of published data suggests regions of conformational heterogeneity, structural elements involved in the PrPC\longrightarrowPrPSc transformation, and possible structural features related to a species barrier to transmission of prion diseases.

• Journal of KIISE:Databases
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• v.33 no.7
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• pp.693-707
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• 2006

To improve performance using a multidimensional index in similar sequence matching, we transform a high-dimensional sequence to a low-dimensional sequence, and then construct a low-dimensional MBR that contains multiple transformed sequences. In this paper we propose a formal method that transforms a high-dimensional MBR itself to a low-dimensional MBR, and show that this method significantly reduces the number of lower-dimensional transformations. To achieve this goal, we first formally define the new notion of MBR-safe. We say that a transform is MBR-safe if a low-dimensional MBR to which a high-dimensional MBR is transformed by the transform contains every individual low-dimensional sequence to which a high-dimensional sequence is transformed. We then propose two MBR-safe transforms based on DFT and DCT, the most representative lower-dimensional transformations. For this, we prove the traditional DFT and DCT are not MBR-safe, and define new transforms, called mbrDFT and mbrDCT, by extending DFT and DCT, respectively. We also formally prove these mbrDFT and mbrDCT are MBR-safe. Moreover, we show that mbrDFT(or mbrDCT) is optimal among the DFT-based(or DCT-based) MBR-safe transforms that directly convert a high-dimensional MBR itself into a low-dimensional MBR. Analytical and experimental results show that the proposed mbrDFT and mbrDCT reduce the number of lower-dimensional transformations drastically, and improve performance significantly compared with the $na\"{\i}ve$ transforms. These results indicate that our MBR- safe transforms provides a useful framework for a variety of applications that require the lower-dimensional transformation of high-dimensional MBRs.

• Korean Journal of Microbiology
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• v.51 no.1
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• pp.81-85
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• 2015

Since the banning of antibiotic growth promoters (AGPs), the death of livestock has been increased, thus there is a strong demand for AGP-alternatives. Modulation of gut microbiota has been reported to affect host physiological functions and suggested to be a novel approach for developing AGP-alternatives. However, little has been understood about livestock gut microbiota compared to that of humans. We conducted preliminary study provide fundamental information regarding to regional differences in swine gut microbiota. Swine fecal samples were obtained from farms in Jeju (n=40), Gwangju (n=28), and Haenam (n=30). MiSeq was used to sequence 16S rRNA V4 region, and Mothur pipeline (Schloss et al., 2009) was used for data processing. A total of 5,642,125 reads were obtained and 3,868,143 reads were remained after removing erroneous reads. Analysis of taxonomic composition at the phylum level indicated greater abundance of Firmicutes among Jeju swine, and cluster analysis of distribution of operational taxonomic units also showed regional differences among swine gut microbiota. In addition, correlation analysis between non-metric multidimensional scaling and abundance of phyla suggested that the phyla Actinobacter, Verrucomicrobia, Firmicutes, and Fibrobacteres were driving factors for the regional differences. Livestock gut microbiota may be affected by diet and practices in farms. Our results indicated significant regional differences in swine gut microbiota, suggesting that future livestock gut microbiota studies should be designed with the regional differences in mind.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.2
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• pp.56-60
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• 2016

Adenylate kinase (AK) enzyme which acts as the catalyst of reversible high energy phosphorylation reaction between ATP and AMP which associate with energetic metabolism and nucleic acid synthesis and signal transmission. This enzyme has three distinct domains: Core, AMP binding domain (AMPbd) and Lid domain (LID). The primary role of AMPbd and LID is associated with conformational changes due to flexibility of two domains. Three dimensional structure of human AK1 has not been confirmed and various mutation experiments have been done to determine the active sites. In this study, AK1R138A which is changed arginine[138] of LID domain with alanine[138] was made and conducted with NMR experiments, backbone dynamics analysis and mo-lecular docking dynamic simulation to find the cause of structural change and substrate binding site. Synthetic human muscle type adenylate kinase 1 (hAK1) and its mutant (AK1R138A) were re-combinded with E. coli and expressed in M9 cell. Expressed proteins were purified and finally gained at 0.520 mM hAK1 and 0.252 mM AK1R138A. Multinuclear multidimensional NMR experiments including HNCA, HN(CO)CA, were conducted for amino acid sequence analysis and signal assignments of $^1H-^{15}N$ HSQC spectrum. Our chemical shift perturbation data is shown LID domain residues and around alanine[138] and per-turbation value(0.22ppm) of valine[179] is consid-ered as inter-communication effect with LID domain and the structural change between hAK1 and AK1R138A.

• The KIPS Transactions:PartA
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• v.11A no.5
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• pp.383-390
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• 2004

This paper propose a method that controls facial expression of 3D avatar by having the user select a sequence of facial expressions in the space of facial expressions. And we setup its system. The space of expression is created from about 2400 frames consist of motion captured data of facial expressions. To represent the state of each expression, we use the distance matrix that represents the distances between pairs of feature points on the face. The set of distance matrices is used as the space of expressions. But this space is not such a space where one state can go to another state via the straight trajectory between them. We derive trajectories between two states from the captured set of expressions in an approximate manner. First, two states are regarded adjacent if the distance between their distance matrices is below a given threshold. Any two states are considered to have a trajectory between them If there is a sequence of adjacent states between them. It is assumed . that one states goes to another state via the shortest trajectory between them. The shortest trajectories are found by dynamic programming. The space of facial expressions, as the set of distance matrices, is multidimensional. Facial expression of 3D avatar Is controled in real time as the user navigates the space. To help this process, we visualized the space of expressions in 2D space by using the multidimensional scaling(MDS). To see how effective this system is, we had users control facial expressions of 3D avatar by using the system. As a result of that, users estimate that system is very useful to control facial expression of 3D avatar in real-time.

• Journal of the Korea Computer Industry Society
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• v.4 no.4
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• pp.569-578
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• 2003

This paper presents a method in which the user produces a real-time facial animation by navigating in the space of facial expressions created from a great number of captured facial expressions. The core of the method is define the distance between each facial expressions and how to distribute into suitable intuitive space using it and user interface to generate realtime facial expression animation in this space. We created the search space from about 2,400 raptured facial expression frames. And, when the user free travels through the space, facial expressions located on the path are displayed in sequence. To visually distribute about 2,400 captured racial expressions in the space, we need to calculate distance between each frames. And we use Floyd's algorithm to get all-pairs shortest path between each frames, then get the manifold distance using it. The distribution of frames in intuitive space apply a multi-dimensional scaling using manifold distance of facial expression frames, and distributed in 2D space. We distributed into intuitive space with keep distance between facial expression frames in the original form. So, The method presented at this paper has large advantage that free navigate and not limited into intuitive space to generate facial expression animation because of always existing the facial expression frames to navigate by user. Also, It is very efficient that confirm and regenerate nth realtime generation using user interface easy to use for facial expression animation user want.