• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4469-4475
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• 2012

Background: The potential use of hypomethylation of Long INterspersed Element 1 (LINE-1) and Alu elements (Alu) as a biomarker has been comprehensively assessed in several cancers, including head and neck squamous cell carcinoma (HNSCC). Failure to detect occult metastatic head and neck tumors on radical neck lymph node dissection can affect the therapeutic measures taken. Objective: The aim of this study was to investigate the LINE-1 and Alu methylation status and determine whether it can be applied for detection of occult metastatic tumors in HNSCC cases. Methods: We used the Combine Bisulfite Restriction Analysis (COBRA) technique to analyse LINE-1 and Alu methylation status. In addition to the methylation level, LINE-1 and Alu loci were classified based on the methylation statuses of two CpG dinucleotides in each allele as follows: hypermethylation ($^mC^mC$), hypomethylation ($^uC^uC$), and 2 forms of partial methylation ($^mC^uC$ and $^uC^mC$). Sixty-one lymph nodes were divided into 3 groups: 1) non-metastatic head and neck cancer (NM), 2) histologically negative for tumor cells of cases with metastatic head and neck cancer (LN), and 3) histologically positive for tumor cells (LP). Results: Alu methylation change was not significant. However, LINE-1 methylation of both LN and LP was altered, as demonstrated by the lower LINE-1 methylation levels (p<0.001), higher percentage of $^mC^uC$ (p<0.01), lower percentage of $^uC^mC$ (p<0.001) and higher percentage of $^uC^uC$ (p<0.001). Using receiver operating characteristic (ROC) curve analysis, $%^uC^mC$ and $%^mC^uC$ values revealed a high level of AUC at 0.806 and 0.716, respectively, in distinguishing LN from NM. Conclusion: The LINE-1 methylation changes in LN have the same pattern as that in LP. This epigenomic change may be due to the presence of occult metastatic tumor in LN cases.

• Proceedings of the Korean Institute of Communication Sciences Conference
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• 2006.07a
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• pp.423-423
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• 2006

• Journal of Embryo Transfer
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• v.28 no.4
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• pp.355-360
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• 2013

Precise, rapid and simple methods for species identification in animals are among the most important techniques in the livestock industry and research fields including meat classification. In this study, polymerase chain reaction (PCR) based molecular identification using inter species polymorphisms were examined by PCR-restriction fragment length polymorphism (RFLP) analysis for mitochondrial DNA (mtDNA) cytochrome b (CYTB) gene sequences among four mammalian livestock animals (cattle, horse, goat and pig). The results from PCR-RFLP analysis using the AluI restriction enzyme were also provided for the species-specific band patterns among CYTB gene sequences in these four species. The AluI-digestion for CYTB genes provided interesting migration patterns differentially displayed according to each species. Cattle and horse had one AluI-recognition site at different nucleotide positions and their AluI-digested fragments showed different band patterns on the gels. Pig had two AluI-recognition sites within the amplified CYTB sequences and produced three bands on the gels. Goat had no AluI-recognition site and was located at the same position as the uncut PCR product. The results showed the species-specific band patterns on a single gel among the four livestock animal species by AluI-RFLP. In addition, the results from blind tests for the meat samples collected from providers without any records showed the identical information on the species recorded by observing their phenotypes before slaughter. The application of this PCR-RFLP method can be useful and provide rapid, simple, and clear information regarding species identification for various tissue samples originating from tested livestock species.

• Journal of the Korean Institute of Telematics and Electronics C
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• v.36C no.3
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• pp.8-16
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• 1999

This paper describes a VLSI design of Reed-Solomon(RS) decoder using the modified Euclid algorithm, with the main theme focused on the $\textit{GF}(2^8)$. To get area-efficient design, a number of new architectures have been devised with maximal register and Euclidean ALU unit sharing. One ALU is shared to replace 18 ALUs which computes an error locator polynomial and an error evaluation polynomial. Also, 18 registers are shared to replace 24 registers which stores coefficients of those polynomials. The validity and efficiency of the proposed architecture have been verified by simulation and by FLEX$^TM$ FPGA implementation in hardware description language VHDL. The proposed Reed-Solomon decoder, which has the capability of decoding RS(208,192,17) and RS(182,172,11) for Digital Versatile Disc(DVD), has been designed by using O.6$\mu\textrm{m}$ CMOS TLM Compass$^TM$ technology library, which contains totally 17k gates with a core area of 2.299$\times$2.284 (5.25$\textrm{mm}^2$). The chip can run at 20MHz while the DVD requirement is 3.74MHz.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.3
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• pp.939-944
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• 2016

Background: Cell-free DNA circulating in blood is a candidate biomarker for malignant tumors. Unlike uniformly truncated DNA released from apoptotic non diseased cells, DNA released from necrotic cancer cells varies in size. Objectives: To measure the DNA integrity index in serum and the absolute DNA concentration to assess their clinical utility as potential serum biomarkers for colorectal carcinoma (CRC) compared to CEA and CA19-9. Materials and Methods: Fifty patients with CRC, 10 with benign colonic polyps and 20 healthy sex and age matched volunteers, were investigated by real time PCR of ALU repeats (ALU q-PCR) using two sets of primers (115 and 247 bp) amplifying different lengths of DNA fragments. The DNA integrity index was calculated as the ratio of q-PCR results of ALU 247/ALU 115bp. Results: Serum DNA integrity was statistically significantly higher in CRC patients compared to the benign and control groups (p<0.001). ROC curves for differentiating CRC patients from normal controls and benign groups had areas under curves of 0.90 and 0.85 respectively. Conclusions: The DNA integrity index is superior to the absolute DNA concentration as a potential serum biomarker for screening and diagnosis of CRC. It may also serve as an indicator for monitoring the progression of CRC patients. Combining CEA and CA19-9 with either of the genetic markers studied is better than either of them alone.

• Molecules and Cells
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• v.37 no.6
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• pp.467-472
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• 2014

Obesity is known to be strongly associated with cardiovascular disease and cancer, the leading causes of mortality worldwide, and develops owing to interactions between genes and the environment. DNA methylation can act as a downstream effector of environmental signals, and analysis of this process therefore holds substantial promise for identifying mechanisms through which genetic and environmental factors jointly contribute to disease risk. Global DNA methylation of peripheral blood cells has recently been proposed as a potential biomarker for disease risk. Repetitive element DNA methylation has been shown to be associated with prominent obesity-related chronic diseases, but little is known about its relationship with weight status. In this study, we quantified the methylation of Alu elements in the peripheral blood DNA of 244 healthy women with a range of body mass indexes (BMIs) using pyrosequencing technology. Among the study participants, certain clinical laboratory parameters, including hemoglobin, serum glutamic oxaloacetic transaminase, serum glutamic- pyruvic transaminase, total cholesterol, and triglyceride levels were found to be strongly associated with BMI. Moreover, a U-shaped association between BMI and Alu methylation was observed, with the lowest methylation levels occurring at BMIs of between 23 and $30kg/m^2$. However, there was no significant association between Alu methylation and age, smoking status, or alcohol consumption. Overall, we identified a differential influence of BMI on global DNA methylation in healthy Korean women, indicating that BMI-related changes in Alu methylation might play a complex role in the etiology and pathogenesis of obesity. Further studies are required to elucidate the mechanisms underlying this relationship.

• Microbiology and Biotechnology Letters
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• v.38 no.4
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• pp.455-460
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• 2010

A polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis was applied to detect and identify ten Weissella spp. frequently found in kimchi. The previously reported genus-specific primers designed from 16S rDNA sequences of Weissella spp. were adopted but PCR was performed at the increased annealing temperature by $4^{\circ}C$. The sizes of amplified PCR products and restricted fragments produced by AluI, MseI, and BceAI endonucleases were well correspond with the expected sizes. W. kandleri, W. koreensis, W. confusa, W. minor, W. viridescens, W. cibaria, and W. soli were distinguished by AluI and MseI and W. hellenica and W. paramesenteroides were identified by BceAI. W. thailandensis was distinguished when restriction pattern of other species was compared but identified by the single use of MspI.

• Journal of the Korean Institute of Telematics and Electronics A
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• v.28A no.11
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• pp.915-922
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• 1991

This research paper presents an ALU unit using 1.0$\mu$m CMOS technology capable of doing IEEE standard single and double precision floating poing calculation within 32ns (2 clock) at 60 MHz clock speed. This 32ns speed was achieved by using 9ns 1's complement arithmetic 54 bit carry select adder instead of previous 2's complement adders. On the first cycle, this adder is used for addition or subtraction and the second cycle uses this adder for rounding. This reduces the number of required adders from two to one. Speed improvement is 2 to 5 times compared with previous 40MHz design. Design goal was 60MHz, however, this unit is functioning at 80 MHz at room temperature.

• Genomics & Informatics
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• v.10 no.4
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• pp.226-233
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• 2012

Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mechanisms, including de novo TE insertions, TE insertion-mediated deletions, and recombination events, they manipulate their host genomes. In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem repeats/Alu (SVA) elements and discuss how they have affected primate genomes, especially the human and chimpanzee genomes, since their divergence.

• Progress in Superconductivity
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• v.9 no.2
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• pp.157-161
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• 2008

Due to high speed operations and ultra low power consumptions RSFQ logic circuit is a very good candidate for future electronic device. The focus of the RSFQ circuit development has been on the advancement of analog-to-digital converters and microprocessors. Recent works on RSFQ ALU development showed the successful operation of an 1-bit block of ALU at 40 GHz. Recently, the study of an RSFQ analog-to-digital converter has been extended to the development of a single chip RF digital receiver. Compared to the voltage logic circuits, RSFQ circuits operate based on the pulse logic. This naturally leads the circuit structure of RSFQ circuit to be pipelined. Delay time on each pipelined stage determines the ultimate operating speed of the circuit. In simulations, a two junction Josephson transmission line's delay time was about 10 ps, a splitter's 14.5 ps, a switch's 13 ps, a half adder's 67 ps. Optimization of the 4-bit ALU circuit has been made with delay time consideration to operate comfortably at 10 GHz or above.