• Genomics & Informatics
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• v.16 no.4
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• pp.23.1-23.5
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• 2018

Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current International Committee on Taxonomy of Viruses taxonomy using an in silico approach, aiming to identify the specific sequence for each virus. We applied this approach to norovirus in Caliciviridae, which causes 90% of gastroenteritis cases worldwide. First, based on the dogma "protein structure determines its function," we hypothesized that the specific sequence can be identified by the specific structure. Firstly, we extracted the coding region (CDS). Secondly, the CDS protein sequences of each genus were annotated by the conserved domain database (CDD) search. Finally, the conserved domains of each genus in Caliciviridae are classified by RPS-BLAST with CDD. The analysis result is that Caliciviridae has sequences including RNA helicase in common. In case of Norovirus, Calicivirus coat protein C terminal and viral polyprotein N-terminal appears as a specific domain in Caliciviridae. It does not include in the other genera in Caliciviridae. If this method is utilized to detect specific conserved domains, it can be used as classification keywords based on protein functional structure. After determining the specific protein domains, the specific protein domain sequences would be converted to gene sequences. This sequences would be re-used one of viral bio-marks.

• Journal of Broadcast Engineering
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• v.21 no.4
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• pp.578-591
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• 2016

In this paper, the fast encoding algorithm in High Efficiency Video Coding (HEVC) encoder was studied. For the encoding efficiency, the current HEVC reference software is divided the input image into Coding Tree Unit (CTU). then, it should be re-divided into CU up to maximum depth in form of quad-tree for RDO (Rate-Distortion Optimization) in encoding precess. But, it is one of the reason why complexity is high in the encoding precess. In this paper, to reduce the high complexity in the encoding process, it proposed the method by determining the maximum depth of the CU using a hierarchical clustering at the pre-processing. The hierarchical clustering results represented an average combination of motion vectors (MV) on neighboring blocks. Experimental results showed that the proposed method could achieve an average of 16% time saving with minimal BD-rate loss at 1080p video resolution. When combined the previous fast algorithm, the proposed method could achieve an average 45.13% time saving with 1.84% BD-rate loss.

• Molecules and Cells
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• v.39 no.12
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• pp.888-897
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• 2016

Stable expression of Foxp3 is ensured by demethylation of CpG motifs in the Foxp3 intronic element, the conserved non-coding sequence 2 (CNS2), which persists throughout the lifespan of regulatory T cells (Tregs). However, little is known about the mechanisms on how CNS2 demethylation is sustained. In this study, we found that Ten-Eleven-Translocation (Tet) DNA dioxygenase protects the CpG motifs of CNS2 from re-methylation by DNA methyltransferases (Dnmts) and prevents Tregs from losing Foxp3 expression under inflammatory conditions. Upon stimulation of Tregs by interleukin-6 (IL6), Dnmt1 was recruited to CNS2 and induced methylation, which was inhibited by Tet2 recruited by IL2. Tet2 prevented CNS2 re-methylation by not only the occupancy of the CNS2 locus but also by its enzymatic activity. These results show that the CNS2 methylation status is dynamically regulated by a balance between Tets and Dnmts which influences the expression of Foxp3 in Tregs.

• The Journal of the Acoustical Society of Korea
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• v.26 no.3
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• pp.109-114
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• 2007

In this paper, we Propose a pyramid VQ to quantize the transform coefficients of TCX module for the audio improvement of AMR-WB+ codec. The Proposed pyramid VQ is compared to the $RE_8$ Lattice VQ used in the AMR-WB+ standard codec. demonstrating improvement 4% and 5.7%. respectively, in Mean Squared Error (MSE) and 3.3% and 4.7%. respectively, in Perceptual Evaluation of Audio Quality (PEAQ) by 8-dimensional and 16-dimensional Pyramid VQ.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.31 no.4C
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• pp.391-399
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• 2006

We propose a novel low complexity video encoder, at the expense of a complex decoder, where video frames are intra-coded periodically and frames in between successive intra-coded frames are coded efficiently using a proposed irregular binning technique. We investigate a method of forming an irregular binning which is capable of quantizing any value effectively with only small number of bins, by exploiting the correlation between successive frames. This correlation is additionally exploited at the decoder, where the quality of reconstructed frames is enhanced gradually by applying POCS(projection on the convex sets). After an image frame is reconstructed with the irregular binning information at the proposed decoder, we can further improve the resulting quality by modifying the reconstructed image with motion-compensated image components from the neighboring frames which are considered to contain image details. In the proposed decoder, several iterations of these modification and re-projection steps can be invoked. Experimental results show that the performance of the proposed coding scheme is comparable to that of H.264/AVC coding in m mode. Since the proposed video coding does not require motion estimation at the encoder, it can be considered as an alternative for some versions of H.264/AVC in applications requiring a simple encoder.

• Journal of the Korean Institute of Telematics and Electronics C
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• v.36C no.9
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• pp.76-84
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• 1999

EZW proposed by Shapiro is based on a zerotree constructed in a way that a parent coefficient in a subband is related to four child coefficients in the next finer subband of similar orientation. This fixed treeing based on 1-to-4 parent-child is suitable to exploti hierachical correlations among subbands but not to exploit spatial correlations within a subband. A new treeing by Joo, et al. is suggested to simulatneously exploit those two correlatins by extending parent-child relationship in a flexible way. The flexible treeing leads to increasing the number of symbols and lowering entorpy comparing to the fixed treeing, and therefore a better compression can be resulted. In this paper, we suggest two techniques to suppress the increasing of symbols. First, a probing bit is generated to avoid redundant scan for insignivicant coefficients. Second, since all subbands do not always require the same kind of symbol-set, produced symbols are re-symbolized into binary codes according to a pre-defined procedure. Owing to those techniques, all symbols are generated as binary codes. The binary symbols can be entropy-coded by an adaptive arithmetic coding. Moerover, the binary symbol stream can give comparatively good performances without help of additional entropy coding. Our proposed coding scheme is suggested in two modes: binary coding mode and arithmetic coding mode. We evaluate the effectivenessof our modifications by comparing with the original EZW.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.32 no.2C
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• pp.132-140
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• 2007

In this paper, we proposed a new technique to encode and decode the digital hologram. Since the digital hologram (or fringe pattern) is generated by interference of light, it has much different property from natural 2D (2 dimensional) images. First, we acquisite optical-sensed or computer-generated hologram by digital type, and then extract a chrominance component. The extracted digital hologram for coding is separated into segments to use multi-view properties. The segmented hologram shows the similar characteristics with picturing an object with 2D cameras in various point of view. Since fringe pattern is visually observed like as noise, we expect that the fringe pattern has poor coding efficiency. To obtain high efficiency, the segment is transformed with DCT (Discrete Cosine Transform) which resembles hologram generation process with high performance. Each transformed segment passes the 3D scanning process according to time and spatial correlation, and is organized into a video stream. Since the segment which correspond to frame of a video stream consists of the transformed coefficients with wide range of value, it is classified and re-normalized. Finally it is compressed with coding tools. The proposed algorithm illustrated that it has better properties for reconstruction of 16 times higher compression rate than the previous researches.

• The Journal of Korean Institute of Electromagnetic Engineering and Science
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• v.22 no.10
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• pp.941-950
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• 2011

In this paper, we analysis the end-to-end performance of the incremental cooperative communication with relay selection. In the conventional cooperative scheme, the source(S) broadcasts the signal to the relay(R) and the destination(D) at 1st phase, and the R forwards the signal to the D at 2nd phase. Although this scheme can improve performance and provide diversity gain, it suffers from decreasing spectrum efficiency. In order to overcome this problem, the incremental cooperative model can be used. In this paper, we study two incremental cooperative method : the first uses ARQ with threshold SNR and the second uses HARQ with channel coding. we also evaluated performance of the incremental cooperative communication based on the R arrangement by using both methods.

• Molecules and Cells
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• v.37 no.2
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• pp.149-160
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• 2014

Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 $F_7$ recombinant inbred lines (RILs) from a cross of japonica rice line 'SNU-SG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.1
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• pp.13-18
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• 2018

Objective: Meat quality including muscle color in chickens is an important trait and continuous selective pressures for fast growth and high yield have negatively impacted this trait. This study was conducted to investigate genetic variations responsible for regulating muscle color. Methods: Whole genome re-sequencing analysis using Illumina HiSeq paired end read method was performed with pooled DNA samples isolated from two broiler chicken lines divergently selected for muscle color (high muscle color [HMC] and low muscle color [LMC]) along with their random bred control line (RAN). Sequencing read data was aligned to the chicken reference genome sequence for Red Jungle Fowl (Galgal4) using reference based genome alignment with NGen program of the Lasergene software package. The potential causal single nucleotide polymorphisms (SNPs) showing non-synonymous changes in coding DNA sequence regions were chosen in each line. Bioinformatic analyses to interpret functions of genes retaining SNPs were performed using the ingenuity pathways analysis (IPA). Results: Millions of SNPs were identified and totally 2,884 SNPs (1,307 for HMC and 1,577 for LMC) showing >75% SNP rates could induce non-synonymous mutations in amino acid sequences. Of those, SNPs showing over 10 read depths yielded 15 more reliable SNPs including 1 for HMC and 14 for LMC. The IPA analyses suggested that meat color in chickens appeared to be associated with chromosomal DNA stability, the functions of ubiquitylation (UBC) and quality and quantity of various subtypes of collagens. Conclusion: In this study, various potential genetic markers showing amino acid changes were identified in differential meat color lines, that can be used for further animal selection strategy.