• KIISE Transactions on Computing Practices
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• v.20 no.9
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• pp.513-518
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• 2014

It has become possible for small scale laboratories to interpret large scale genomic DNA, thanks to the reduction of the sequencing cost by the development of next generation sequencing (NGS). De novo assembly is a method which creates a putative original sequence by reconstructing reads without using a reference sequence. There have been various study results on de novo assembly, however, it is still difficult to get the desired results even by using the same assembly procedures and the analysis tools which were suggested in the studies reported. This is mainly because there are no specific guidelines for the assembly procedures or know-hows for the use of such analysis tools. In this study, to resolve these problems, we introduce steps to finding whole genome of an unknown DNA via NGS technology and de novo assembly, while providing the pros and cons of the various analysis tools used in each step. We used 350Mbp of Toxocara canis DNA as an application case for the detailed explanations of each stated step. We also extend our works for prediction of protein-coding genes and their functions from the draft genome sequence by comparing its homology with reference sequences of other nematodes.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.21 no.4
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• pp.795-803
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• 2017

This paper describes a dual-standard cryptographic processor that efficiently integrates two block ciphers ARIA and AES into a unified hardware. The ARIA-AES crypto-processor was designed to support 128-b and 256-b key sizes, as well as four modes of operation including ECB, CBC, OFB, and CTR. Based on the common characteristics of ARIA and AES algorithms, our design was optimized by sharing hardware resources in substitution layer and in diffusion layer. It has on-the-fly key scheduler to process consecutive blocks of plaintext/ciphertext without reloading key. The ARIA-AES crypto-processor that was implemented with a $0.18{\mu}m$ CMOS cell library occupies 54,658 gate equivalents (GEs), and it can operate up to 95 MHz clock frequency. The estimated throughputs at 80 MHz clock frequency are 787 Mbps, 602 Mbps for ARIA with key size of 128-b, 256-b, respectively. In AES mode, it has throughputs of 930 Mbps, 682 Mbps for key size of 128-b, 256-b, respectively. The dual-standard crypto-processor was verified by FPGA implementation using Virtex5 device.

• Journal of Korean Society of Forest Science
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• v.105 no.2
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• pp.186-192
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• 2016

This study was conducted to develop microsatellite markers in Quercus variabilis using next generation sequencing. A total of 305,771 reads (384 bp on average) were generated on a Roche GS-FLX system, yielding 117 Mbp of sequences. The de novo assembly resulted in 7,346 contigs. A total of 606 contigs (20.75%) including 911 microsatellite loci were derived from the 2,921 contigs longer than 500 bp. A total of 180 primer sets were designed from the 911 microsatellite loci and screened in eight Q. variabilis individual trees sampled from a natural stand to obtain polymorphic loci. As a result, a total of thirteen polymorphic microsatellite loci were selected and used for estimating population genetic parameters in the 54 individual trees. The mean number of effective alleles was 4.996 ranging from 2.439 to 7.515. The observed heterozygosity and the expected heterozygosity ranged between 0.731 and 1.000 with an average of 0.873 and from 0.590 to 0.867 with an average of 0.766, respectively. Null alleles were not detected in all loci. No significant linkage disequilibrium was detected after Bonferroni correction in all loci. In the near future, these novel polymorphic microsatellite markers will be used to study population and conservation genetics of Q. variabilis of Korea in more detail.

• Neonatal Medicine
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• v.18 no.1
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• pp.124-129
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• 2011

Purpose: To evaluate the effect of oral sildenafil therapy in neonates with persistent pulmonary hypertension of the newborn (PPHN) Methods: We conducted a retrospective review of 32 neonates ${\geq}$35 weeks' gestation and fraction of inspired oxygen ($FiO_2$) 1.0 with PPHN. The first dose (0.5 mg/kg) of oral sildenafil was started and 1 mg/kg was given every 6 hour thereafter. Mean airway pressure (MAP), $FiO_2$, oxygenation index (OI), mean arterial blood pressure (MBP) were documented before and 6, 12, 24, and 48 hours after sildenafil. For adverse effects, gastrointestinal symptoms, brain ultrasound, funduscopy and auditory brainstem response results were evaluated. Results: The underlying diseases of PPHN (n=32) were meconium aspiration syndrome (n=9), respiratory distress syndrome (n=8), pneumonia (n=3), and idiopathic (n=12). Thirty-one neonates survived; 3 neonates were transferred for inhaled nitric oxide (iNO) and all of them survived. In 28 infants, $FiO_2$ and OI improved significantly by 6 hours and MAP improved significantly by 48 hours after initiation of sildenafil. There were no clinically significant adverse effects of sildenafil. Conclusion: Sildenafil may be an effective and safe agent for near-term and term neonates with PPHN, providing significant improvement in oxygenation, and thus may be especially useful in the treatment of PPHN in hospitals without iNO.

• Journal of KIISE:Computer Systems and Theory
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• v.33 no.7
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• pp.413-420
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• 2006

The speed of present-day network technology exceeds a gigabit and is developing rapidly. When using TCP/IP in these high-speed networks, a high load is incurred in processing TCP/IP protocol in a host CPU. To solve this problem, research has been carried out into TCP/IP Offload Engine (TOE). The TOE processes TCP/IP on a network adapter instead of using a host CPU; this reduces the processing burden on the host CPU. In this paper, we developed two software-based TOEs. One is the TOE implementation using an embedded Linux. The other is the TOE implementation using Lightweight TCP/IP (lwIP). The TOE using an embedded Linux did not have the bandwidth more than 62Mbps. To overcome the poor performance of the TOE using an embedded Linux, we ported the lwIP to the embedded system and enhanced the lwIP for the high performance. We eliminated the memory copy overhead of the lwIP. We added a delayed ACK and a TCP Segmentation Offload (TSO) features to the lwIP and modified the default parameters of the lwIP for large data transfer. With the aid of these modifications, the TOE using the modified lwIP shows a bandwidth of 194 Mbps.

• Journal of Plant Biotechnology
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• v.29 no.2
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• pp.93-98
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• 2002

A VP6 fragments was subcloned with BamHI in the binary pMBP-1 vector under Califlower Mosaic Virus (CaMV) 355 promoter and neomycin phosphotransferase II (npt II) gene. The recombinant binary vector was mobilized into Agrobacterium-tumefaciens LBA4404 by the freeze-thaw method and potato (Solanum tubensum L. cv Desiree) was transformed by modified leaf-disc cocultivation. Shoots were induced on MS medium with 0.01 mg/L NAA, 0.1 mg/L GA$_3$, 2.0 mg/L Zeatin, 100.0 mg/L kanamycin, 500.0 mg/L carbenicillin. In order to identify the copy number of VP6 into potato plant, total genomic DNA was isolated from transgenic potato and analysed by Southern blotting. Genomic DNA and total mRNA analysis demonstrated the incorporation of the foreign gene into the potato genome, as well as their transcription.

• Journal of Internet Computing and Services
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• v.8 no.4
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• pp.61-70
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• 2007

In this paper, we propose and observe the Adaptive Modulation system with optimal Turbo Coded V-BLAST(Vertical-Bell-lab Layered Space-Time) technique that is applied the extrinsic information from MAP Decoder in decoding Algorithm of V-BLAST: ordering and slicing. And comparing the proposed system with the Adaptive Modulation system using conventional Turbo Coded V-BLAST technique that is simply combined V-BLAST with Turbo Coding scheme, we observe how much throughput performance and SNR has been improved. In addition, we show that the proposed system using STD(Selection Transmit Diversity) scheme results in on improved result, By using simulation and comparing to conventional Turbo Coded V-BLAST technique with the Adaptive Modulation systems, the optimal Turbo Coded V-BLAST technique with the Adaptive Modulation systems has SNR gain over all SNR range and better throughput gain that is about 350Kbps in 11dB SNR range. Also, comparing with the conventional Turbo Coded V-BLAST technique using 2 transmit and 2 receive antennas, the proposed system with STD scheme show that the improvement of maximum throughput is about 1.77Mbps in the same SNR range and the SNR gain is about 5.88dB to satisfy 4Mbps throughput performance.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.58 no.3
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• pp.283-291
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• 2013

Rice varieties with suitable flour-making quality are required to promote rice processed-food industry and boost rice consumption in Korea. 'Namil (SA)-flo1' is an advanced mutant line with floury endosperm which shows good flour-making quality under dry-milling process. Genetic analysis was carried out to localize the chromosomal region responsible for the floury endosperm of 'Namil (SA)- flo1'. By using 94 F2 progenies, which were derived from 'Namil (SA)-flo1' ${\times}$ 'Milyang 23', floury grains percentage was investigated as phenotypic data, and genotyping was conducted with 54 SSR markers. Association analysis showed that the target genetic region for floury endosperm is on middle-low region of chromosome 5. Through further association analysis with increased number of SSR markers on chromosome 5, we found that genotypic variation in RM164 explains 79.7% of the variation in floury grains percentage of F2:3 seeds. The floury endosperm locus was localized on 17.7-20.7 Mbp region of chromosome 5 and will be further analyzed for fine mapping and gene identification.

• Journal of Internet Computing and Services
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• v.16 no.1
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• pp.1-8
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• 2015

Ultra-wide-angle wireless endoscopes are demonstrated in this paper. The endoscope is composed of an ultra-wide-angle camera module and wireless transmission module. A lens unit with the ultra-wide FOV of 162 degrees is designed and manufactured. The lens, image sensor, and camera processor unit are packaged together in a $3{\times}3{\times}9-cm3$ case. The wireless transmission modules are implemented based on UWB- and WiFi-based platform, respectively. The UWB-based module can transmit HD video to a computer in resolution of $2048{\times}1536$ (QXGA) and the frame rate of 15 fps in MJPEG compression mode. The maximum data transfer rate reaches 41.2 Mbps. The FOV and the resolution of the endoscope is comparable to a medical-grade endoscope. The FOV and resolution is ~3X and 16X higher than that of a commercial high-performance WiFi endoscope, respectively. The WiFi-based module streams out video to a smart device with th maximum date transfer rate of 1.5 Mbps at the resolution of $640{\times}480$ (VGA) and the frame rate of 30 fps in MJPEG compression mode. The implemented components show the feasibility of cheap medical-grade wireless electronic endoscopes, which can be effectively used in u-healthcare, emergency treatment, home-healthcare, remote diagnosis, etc.

• Journal of Life Science
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• v.25 no.2
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• pp.136-150
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• 2015

Pseudomonas syringae pathovar tabaci is a plant pathogenic bacterium that causes wildfire disease in tobacco plants. In P. syringae pv. tabaci, PsyI, a LuxI-type protein, acts as an AHL synthase, while primary and secondary sequence analysis of PsyR has revealed that it is a homolog of the LuxR-type transcriptional regulator that responds to AHL molecules. In this study, using phenotypic and genetic analyses in P. syringae pv. tabaci, we show the effect of PsyR protein as a quorum-sensing (QS) transcriptional regulator. Regulatory effects of PsyR on swarming motility and production of siderophores, tabtoxin, and N-acyl homoserine lactones were examined via phenotypic assays, and confirmed by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). Further qRT-PCR showed that PsyR regulates expression of these virulence genes in response to environmental signals. However, an upstream region of the gene was not bound with purified MBP-PsyR protein; rather, PsyR was only able to shift the upstream region of psyI. These results suggested that PsyR may be indirectly controlled via intermediate-regulatory systems and that auto-regulation by PsyR does not occur.