• Genomics & Informatics
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• v.15 no.4
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• pp.136-141
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• 2017

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.10 no.1
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• pp.136-151
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• 2016

Flexible large-scale WLANs are now widely deployed in crowded and highly mobile places such as campus, airport, shopping mall and company etc. But network management is hard for large-scale WLANs due to highly uneven interference and throughput among links. So the traffic is difficult to predict accurately. In the paper, through analysis of traffic in two real large-scale WLANs, Granger Causality is found in both scenarios. In combination with information entropy, it shows that the traffic prediction of target AP considering Granger Causality can be more predictable than that utilizing target AP alone, or that of considering irrelevant APs. So We develops new method -Granger Causality and Vector Auto-Regression (GCVAR), which takes APs series sharing Granger Causality based on Vector Auto-regression (VAR) into account, to predict the traffic flow in two real scenarios, thus redundant and noise introduced by multivariate time series could be removed. Experiments show that GCVAR is much more effective compared to that of traditional univariate time series (e.g. ARIMA, WARIMA). In particular, GCVAR consumes two orders of magnitude less than that caused by ARIMA/WARIMA.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.11 no.11
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• pp.5282-5300
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• 2017

Multi-hop cellular networks (MCNs) reduce the transmit power and improve the system performance. Recently, several research studies have been conducted on MCNs. The mobile relay selection scheme is a rising issue in the design of MCNs that achieves these advantages. The conventional opportunistic relaying (OR) is performed on the single factor for maximum signal-to-interference-plus-noise ratio (SINR). In this paper, a comprehensive OR scheme based on Bi-Target is proposed to improve the system throughput and reduce the relay handover by constraining the amount of required bandwidth and SINR. Moreover, the proposed algorithm captures the variability and the mobility that makes it more suitable for dynamic real scenarios. Numerical and simulation results show the superiority of the proposed algorithm in both enhancing the overall performance and reducing the handover.

• Journal of Microbiology and Biotechnology
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• v.16 no.9
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• pp.1362-1368
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• 2006

A new constitutive episomal expression vector, pGAPZ-E, was constructed and used for initial screening of eukaryotic target gene expression in Pichia pastoris. Two reporter genes such as beta-galactosidase gene and GFPuv gene were overexpressed in P. pastoris. The expression level of the episomal pGAPZ-E strain was higher than that of the integrated form when the beta-galactosidase gene was used as the reporter gene in P. pastoris X33. The avoiding of both the integration procedure and an induction step simplified the overall screening process for eukaryotic target gene expression in P. pastoris. Nine human protein targets from the Core 50, family of Northeast Structural Genomics Consortium (http://www.nesg.org), which were intractable when expressed in E. coli, were subjected to rapid screening for soluble expression in P. pastoris. HR547, HR919, and HR1697 human proteins, which had previously been found to express poorly or to be insoluble in E. coli, expressed in soluble form in P. pastoris. Therefore, the new episomal GAP promoter vector provides a convenient and alternative system for high-throughput screening of eukaryotic protein expression in P. pastoris.

• Journal of the Society of Cosmetic Scientists of Korea
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• v.31 no.1 s.49
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• pp.13-16
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• 2005

For the high-throughput-screening system (HTS) of depigmenting agents using a protein chip, effects of oligonucleotide-inhibitor sequence on the binding of Mitf protein to E box of MC1R was investigated. The sequence of oligonucletide-inhibitor affected the binding of the target DNA to Mitf, depending on the location of the sequence variation in the inhibitor nucleotide. The oligonucletide-inhibitor that changed the CATGTG sequence didn't show enough inhibition of the target DNA to Mitf, whereas significant inhibition was observed when the sequence outside the CATGTG was changed. This result indicated that CATCTG is crucial sequence for the binding of Mitf to I-box which initiates the transcription of pigmenting genes.

• Animal Bioscience
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• v.34 no.5
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• pp.801-810
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• 2021

Objective: microRNAs (miRNAs) can play a role in a variety of physiological and pathological processes, and their role is achieved by regulating the expression of target genes. Our previous high-throughput sequencing found that ssc-miR-185 plays an important regulatory role in piglet diarrhea, but its specific target genes and functions in intestinal porcine epithelial cell (IPEC-J2) are still unclear. We intended to verify the target relationship between porcine miR-185 and cell division cycle 42 (CDC42) gene in IPEC-J2 and to explore the effect of miR-185 on the proliferation of IPEC-J2 cells. Methods: The TargetScan, miRDB, and miRanda software were used to predict the target genes of porcine miR-185, and CDC42 was selected as a candidate target gene. The CDC42-3' UTR-wild type (WT) and CDC42-3'UTR-mutant type (MUT) segments were successfully cloned into pmirGLO luciferase vector, and the luciferase activity was detected after co-transfection with miR-185 mimics and pmirGLO-CDC42-3'UTR. The expression level of CDC42 was analyzed using quantitative polymerase chain reaction and Western blot. The proliferation of IPEC-J2 was detected using cell counting kit-8 (CCK-8), methylthiazolyldiphenyl-tetrazolium bromide (MTT), and 5-ethynyl-2'-deoxyuridine (EdU) assays. Results: Double enzyme digestion and sequencing confirmed that CDC42-3'UTR-WT and CDC42-3'UTR-MUT were successfully cloned into pmirGLO luciferase reporter vector, and the luciferase activity was significantly reduced after co-transfection with miR-185 mimics and CDC42-3'UTR-WT. Further we found that the mRNA and protein expression level of CDC42 were down-regulated after transfection with miR-185 mimics, while the opposite trend was observed after transfection with miR-185 inhibitor (p<0.01). In addition, the CCK-8, MTT, and EdU results demonstrated that miR-185 promotes IPEC-J2 cells proliferation by targeting CDC42. Conclusion: These findings indicate that porcine miR-185 can directly target CDC42 and promote the proliferation of IPEC-J2 cells. However, the detailed regulatory mechanism of miR-185/CDC42 axis in piglets' resistance to diarrhea is yet to be elucidated in further investigation.

• Journal of the Institute of Electronics Engineers of Korea SD
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• v.42 no.5 s.335
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• pp.55-62
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• 2005

In this paper, we propose an efficient symbol detection algorithm for space-frequency OFDM (SF-OFDM) transmit diversity scheme and present the implementation results of the SF-OFDM WLAN baseband processor with the proposed algorithm. When the number of sub-carriers in SF-OFDM scheme is small, the interference between adjacent sub-carriers may be generated. The proposed algorithm eliminates this interference in a parallel manner and obtains a considerable performance improvement over the conventional detection algorithm. The bit error rate (BER) performance of the proposed detection algorithm is evaluated by the simulation. In the case of 2 transmit and 2 receive antennas, at $BER=10^{-4}$ the proposed algorithm obtains about 3 dB gain over the conventional detection algorithm. The packet error rate (PER), link throughput, and coverage performance of the SF-OFDM WLAN with the proposed detection algorithm are also estimated. For the target throughput at $80\%$ of the peak data rate, the SF-OFDM WLAN achieves the average SNR gain of about 5.95 dB and the average coverage gain of 3.98 meter. The SF-OFDM WLAN baseband processor with the proposed algorithm was designed in a hardware description language and synthesized to gate-level circuits using 0.18um 1.8V CMOS standard cell library. With the division-free architecture, the total logic gate count for the processor is 945K. The real-time operation is verified and evaluated using a FPGA test system.

• Journal of the Institute of Electronics Engineers of Korea TC
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• v.43 no.11 s.353
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• pp.85-94
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• 2006

Simple-relay aided resource allocation (SRARA) schemes are incorporated with throughput guarantee scheduling (TGS) in IEEE 802.16 type TDD-OFDMA downlink to enhance service coverage, where the amount of resources at each relay is limited due to either its available power which is much smaller than base station (BS) power or the required overhead The performance of SRARA schemes is evaluated with both proportional fair (PF) and TGS schedulers at 64 kbps and 128 kbps user throughput requirements. For SRARA with RSs of relatively lower power, a scheme putting total power into only one subchannel shows larger coverage than when both subchnnels are used in a manner of equal power allocation, while the RS with evenly power-allocated two subchannels could provide larger coverage gain for a relatively higher power. In a lower target (64kbps), more improvement comes from relay scheme rather than scheduler design. For a relatively higher level (128 kbps), it comes from scheduler design rather than relay.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.29 no.6A
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• pp.667-667
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• 2004

We must design the buffer algorithm that protects traffic congestion and decreasing throughput at satellite communication network. It is important that buffer algorithm is satisfied with the good performance of transmission packet, responsibility of many connecting traffic and the QOS for connecting character. Old buffer algorithms are not the suitable algorithms when we have the satellite communication network environment. RED buffer algorithm is proposed by Floyd. It has a better performance than old buffer algorithm. But this algorithm is not well adapted a number of connecting TCP packet and changing network, so this algorithm has a bad performance on satellite communication network that is many of connecting user at same time. This paper propose the TARED(Target Adaptive RED). It has a good performance, adaptation and stability on satellite communication network and has not overflow and underflow of the buffer level.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.29 no.6A
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• pp.666-676
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• 2004

We must design the buffer algorithm that protects traffic congestion and decreasing throughput at satellite communication network. It is important that buffer algorithm is satisfied with the good performance of transmission packet, responsibility of many connecting traffic and the 005 for connecting character. Old buffer algorithms are not the suitable algorithms when we have the satellite communication network environment. RED buffer algorithm is proposed by Floyd. It has a better performance than old buffer algorithm. But this algorithm is not well adapted a number of connecting TCP packet and changing network, so this algorithm has a bad Performance on satellite communication network that is many of connecting user at same time. This paper Propose the TARED(Target Adaptive RED). It has a good performance, adaptation and stability on satellite communication network and has not overflow and underflow of the buffer level.