Comparative Analysis of the Korean Population of Magnaporthe oryzae by Multilocus Microsatellite Typing

Choi, Jaehyuk,Kim, Hyojung,Lee, Yong-Hwan The Korean Society of Plant Pathology 2013 Plant Pathology Journal Vol.29 No.4

Rice blast fungus, Magnaporthe oryzae, inflicts serious damage to global rice production. Due to high variability of this fungal pathogen, resistance of newly-released rice cultivars is easily broken down. To understand the population structure of M. oryzae, we analyzed the genetic diversity of the Korean population using multilocus microsatellite typing. Eleven microsatellite markers were applied to the population of 190 rice isolates which had been collected in Korea for two decades since the 1980's. Average values of gene diversity and allele frequency were 0.412 and 6.5, respectively. Comparative analysis of the digitized allele information revealed that the Korean population exhibited a similar level of allele diversity to the integrated diversity of the world populations, suggesting a particularly high diversity of the Korean population. Therefore, these microsatellite markers and the comprehensive collection of field isolates will be useful genetic resources to identify the genetic diversity of M. oryzae population.

EBA: an enhancement of the IEEE 802.11 DCF via distributed reservation

Choi, Jaehyuk,Yoo, Joon,Choi, Sunghyun,Kim, Chongkwon IEEE 2005 IEEE TRANSACTIONS ON MOBILE COMPUTING Vol.4 No.4

The IEEE 802.11 standard for wireless local area networks (WLANs) employs a medium access control (MAC), called distributed coordination function (DCF), which is based on carrier sense multiple access with collision avoidance (CSMA/CA). The collision avoidance mechanism utilizes the random backoff prior to each frame transmission attempt. The random nature of the backoff reduces the collision probability, but cannot completely eliminate collisions. It is known that the throughput performance of the 802.11 WLAN is significantly compromised as the number of stations increases. In this paper, we propose a novel distributed reservation-based MAC protocol, called early backoff announcement (EBA), which is backward compatible with the legacy DCF. Under EBA, a station announces its future backoff information in terms of the number of backoff slots via the MAC header of its frame being transmitted. All the stations receiving the information avoid collisions by excluding the same backoff duration when selecting their future backoff value. Through extensive simulations, EBA is found to achieve a significant increase in the throughput performance as well as a higher degree of fairness compared to the 802.11 DCF.

Genome-wide analysis of T-DNA integration into the chromosomes of <i>Magnaporthe oryzae</i>

Choi, Jaehyuk,Park, Jongsun,Jeon, Junhyun,Chi, Myoung-Hwan,Goh, Jaeduk,Yoo, Sung-Yong,Park, Jaejin,Jung, Kyongyong,Kim, Hyojeong,Park, Sook-Young,Rho, Hee-Sool,Kim, Soonok,Kim, Byeong Ryun,Han, Seong- Blackwell Publishing Ltd 2007 Molecular microbiology Vol.66 No.2

<P><U>A</U><I>grobacterium <U>t</U>umefaciens-</I><U>m</U>ediated <U>t</U>ransformation (ATMT) has become a prevalent tool for functional genomics of fungi, but our understanding of T-DNA integration into the fungal genome remains limited relative to that in plants. Using a model plant-pathogenic fungus, <I>Magnaporthe oryzae</I>, here we report the most comprehensive analysis of T-DNA integration events in fungi and the development of an informatics infrastructure, termed a <U>T</U>-DNA <U>a</U>nalysis <U>p</U>latform (TAP). We identified a total of 1110 <U>T</U>-DNA-<U>t</U>agged <U>l</U>ocations (TTLs) and processed the resulting data via TAP. Analysis of the TTLs showed that T-DNA integration was biased among chromosomes and preferred the promoter region of genes. In addition, irregular patterns of T-DNA integration, such as chromosomal rearrangement and readthrough of plasmid vectors, were also observed, showing that T-DNA integration patterns into the fungal genome are as diverse as those of their plant counterparts. However, overall the observed junction structures between T-DNA borders and flanking genomic DNA sequences revealed that T-DNA integration into the fungal genome was more canonical than those observed in plants. Our results support the potential of ATMT as a tool for functional genomics of fungi and show that the TAP is an effective informatics platform for handling data from large-scale insertional mutagenesis.</P>

Optimal load balancing scheduler for MPTCP-based bandwidth aggregation in heterogeneous wireless environments

Choi, Kae Won,Cho, Young Su,Aneta, Young Su,Lee, Ji Wun,Cho, Sung Min,Choi, Jaehyuk Elsevier 2017 Journal of Computer Communications Vol.112 No.-

<P><B>Abstract</B></P> <P>In this paper, we investigate a scheduler for a multipath transmission control protocol (MPTCP) for bandwidth aggregation in heterogeneous wireless environments. The performance of the MPTCP can be degraded due to the head-of-line (HOL) blocking caused by path heterogeneity, when a buffer size is limited. This performance degradation can be overcome by a careful design of a scheduler, which has a role of allocating each data segment to one of subflows. We derive the theoretical limit of the achievable aggregate throughput and show that the optimality is achieved when the load is balanced between subflows. Based on the analysis, we propose the optimal load balancing (OLB) scheduler that approximately achieves the theoretical throughput limit. By simulations and experiments, we show that the proposed OLB scheduler outperforms the default scheduler of the Linux MPTCP implementation.</P>

Continuous Monitoring System for Invasive Alien Plant Pests

Jaehyuk Choi,Yang-Sup Bae,Heechan Kang 한국응용곤충학회 2018 한국응용곤충학회 학술대회논문집 Vol.2018 No.04

In recent decades, introduction of the alien plant pests into Korea was dramatically increased and the role of plant quarantine became more important than ever. At the same time, early detection of the introduced population of the alien pests is critical for protection of their spread. However, continuous monitoring for their distribution or spread has not been performed yet in Korea. Present monitoring systems in Korea is not unified but sectored according to three institutes. There are some limitations in managing human resources, executing budgets, and collecting information among them, resuling in delayed responses to the introduced alien pests. Our study focused on 1) constructing nation-wide continuous monitoring system, 2) developing a decision flow chart for evaluating risks, 3) performing the benefits and costs analysis. Continuous monitoring will clarify overall distribution of alien pests, support government’s quarantine negotiation, and enable early detection of alien pests. Furthermore, the system will provide scientific data management and early responses to invasion of alien pests.

Fast swaption pricing in Gaussian term structure model

Jaehyuk Choi,Sungchan Shin 한국재무학회 2013 한국재무학회 학술대회 Vol.2013 No.05

We propose a fast and accurate numerical method to price European swaptions in a multi-factor Gaussian term structure model that can speed up the calibration to the volatility surface. Pricing an interest rate option in such a multi-factor term structure model involves evaluating a multi-dimensional integration of the underlying claim's payo on a domain where the payo is positive. In our method, we approximate the exercise boundary of the state variables as a hyperplane tangent to the maximum probability point on the boundary and simplify the multi-dimensional integration into an analytic form. The maximum probability point can be found using the gradient descent method. We show that the quality of our method is superior to the result of previous studies by directly comparing them to the exact price obtained from the numerical integration.

A novel performance analysis model for an IEEE 802.11 wireless LAN

Choi, Jaehyuk,Yoo, Joon,Kim, Chong-kwon IEEE 2006 IEEE communications letters Vol.10 No.5

This letter presents a novel analytic model that accurately evaluates the performance of a single-hop IEEE 802.11 wireless LAN (WLAN). By using a closed queuing network, we model an IEEE 802.11 WLAN system that consists of a fixed number of stations and derive the saturated throughput of the IEEE 802.11 distributed coordination function (DCF). The ns-2 simulation results show that our new analysis model is very accurate in evaluating the performance of the IEEE 802.11 DCF.

Improved iterative methods for solving risk parity portfolio

( Jaehyuk Choi ),( Rong Chen ) 한국파생상품학회 2022 선물연구 Vol.30 No.2

Risk parity, also known as equal risk contribution, has recently gained increasing attention as a portfolio allocation method. However, solving portfolio weights must resort to numerical methods as the analytic solution is not available. This study improves two existing iterative methods: the cyclical coordinate descent (CCD) and Newton methods. The authors enhance the CCD method by simplifying the formulation using a correlation matrix and imposing an additional rescaling step. The authors also suggest an improved initial guess inspired by the CCD method for the Newton method. Numerical experiments show that the improved CCD method performs the best and is approximately three times faster than the original CCD method, saving more than 40% of the iterations.

Analysis of Cross-Layer Interaction in Multirate 802.11 WLANs

Jaehyuk Choi,Kihong Park,Chong-kwon Kim IEEE 2009 IEEE TRANSACTIONS ON MOBILE COMPUTING Vol.8 No.5

<P>Recent works in empirical 802.11 wireless LAN performance evaluation have shown that cross-layer interactions in WLANs can be subtle, sometimes leading to unexpected results. Two such instances are: (i) significant throughput degradation resulting from automatic rate fallback (ARF) having difficulty distinguishing collision from channel noise, and (ii) scalable TCP over DCF performance that is able to mitigate the negative performance effect of ARF by curbing multiple access contention even when the number of stations is large. In this paper, we present a framework for analyzing complex cross-layer interactions in 802.11 WLANs, with the aim of providing effective tools for understanding and improving WLAN performance. We focus on cross-layer interactions between ARF, DCF, and TCP, where ARF adjusts coding at the physical layer, DCF mediates link layer multiple access control, and TCP performs end-to-end transport. We advance station-centric Markov chain models of ARF, ARF-DCF with and without RTS/CTS, and TCP over DCF that may be viewed as multi-protocol extensions of Bianchi's IEEE 802.11 model. We show that despite significant increase in complexity the analysis framework leads to tractable and accurate performance predictions. Our results complement empirical and simulation-based findings, demonstrating the versatility and efficacy of station-centric Markov chain analysis for capturing cross-layer WLAN dynamics.</P>

온톨로지를 이용한 웹 페이지 분류 시스템 구현

최재혁(Jaehyuk Choi),서혜성(Haesung Seo),노상욱(Sanguk Noh),최경희(Kyunghee Choi),정기현(Gihyun Jung) 한국통신학회 2003 한국통신학회 학술대회논문집 Vol.2003 No.11