• Title/Summary/Keyword: Optimal candidate

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Selection of Reference Genes for Real-time Quantitative PCR Normalization in the Process of Gaeumannomyces graminis var. tritici Infecting Wheat

  • Xie, Li-hua;Quan, Xin;Zhang, Jie;Yang, Yan-yan;Sun, Run-hong;Xia, Ming-cong;Xue, Bao-guo;Wu, Chao;Han, Xiao-yun;Xue, Ya-nan;Yang, Li-rong
    • The Plant Pathology Journal
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    • v.35 no.1
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    • pp.11-18
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    • 2019
  • Gaeumannomyces graminis var. tritici is a soil borne pathogenic fungus associated with wheat roots. The accurate quantification of gene expression during the process of infection might be helpful to understand the pathogenic molecular mechanism. However, this method requires suitable reference genes for transcript normalization. In this study, nine candidate reference genes were chosen, and the specificity of the primers were investigated by melting curves of PCR products. The expression stability of these nine candidates was determined with three programs-geNorm, Norm Finder, and Best Keeper. $TUB{\beta}$ was identified as the most stable reference gene. Furthermore, the exopolygalacturonase gene (ExoPG) was selected to verify the reliability of $TUB{\beta}$ expression. The expression profile of ExoPG assessed using $TUB{\beta}$ agreed with the results of digital gene expression analysis by RNA-Seq. This study is the first systematic exploration of the optimal reference genes in the infection process of Gaeumannomyces graminis var. tritici.

Selection of Appropriate Location for Civil Defense Shelters Using Genetic Algorithm and Network Analysis (유전자 알고리즘과 네트워크 분석을 활용한 민방위 대피시설 위치 선정)

  • Yoo, Suhong;Kim, Mi-Kyeong;Bae, Junsu;Sohn, Hong-Gyoo
    • Journal of the Korean Society of Surveying, Geodesy, Photogrammetry and Cartography
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    • v.36 no.6
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    • pp.573-580
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    • 2018
  • Various studies have been conducted to analyze the location appropriateness and capacity of shelters. However, research on how to select new shelters is relatively insufficient. Since the shelter is designated in case of emergency, it is also necessary to efficiently select the location of the shelter. Therefore, this study presented a method for selecting the location of the shelter using network analysis that has been used to analyze the location appropriateness of shelters and genetic algorithm which is a representative heuristic algorithm. First, the network analysis using the existing civil defense evacuation facility data was performed and the result showed that the vulnerability of evacuation has a high deviation by region in the study area. In order to minimize the evacuation vulnerable area, the genetic algorithm was designed then the location of new shelters was determined. The initial solution consisting of candidate locations of new shelters was randomly generated and the optimal solution was found through the process of selection, crossover, and mutation. As a result of the experiment, the area with a high percentage of the evacuation vulnerable areas was prioritized and the effectiveness of the proposed method could be confirmed. The results of this study is expected to contribute to the positioning of new shelters and the establishment of an efficient evacuation plan in the future.

The Role of Acid in the Synthesis of Red-Emitting Carbon Dots (장파장 형광 탄소 양자점 제조에 있어서 산의 역할에 대한 연구)

  • Yun, Sohee;Lee, Jinhee;Choi, Jin-sil
    • Applied Chemistry for Engineering
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    • v.33 no.3
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    • pp.309-314
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    • 2022
  • Carbon dots (CDs) are few nanometer-sized carbon-based nanoparticles and emerging candidate materials in various fields such as biosensors and bioimaging due to their excellent optical properties and high biocompatibility. However, most CDs, emitting blue light, have limited their application in biomedical fields due to the low penetration of short-wavelength lights into the biological system. Therefore, there has been enormous need to develop long-wavelength emitting CDs. In this study, red-emitting CDs were successfully synthesized through the hydrothermal reaction of p-phenylenediamine with hydrochloric acid. In addition, the effect of the amount of hydrochloric acid on the formation of carbon dots, resulting in the variation of the chemical structures of CDs, were investigated, which was confirmed with the intensive structural analyses using infrared and X-ray photoelectron spectroscopy. It was found that the chemical structure of CDs governed their optical properties and quantum yield. Therefore, this study provides an insight into the role of acid in forming red-emitting CDs as the optimal probe for biomedical application.

Prioritizing the target watersheds for permeable pavement to reduce flood damage in urban watersheds considering future climate scenarios (미래 기후 시나리오를 고려한 도시 유역 홍수 피해 저감을 위한 투수성 포장 시설 대상 유역 우선순위 선정)

  • Chae, Seung Taek;Song, Young Hoon;Lee, Joowon;Chung, Eun-Sung
    • Journal of Korea Water Resources Association
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    • v.55 no.2
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    • pp.159-170
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    • 2022
  • As the severity of water-related disasters increases in urban watersheds due to climate change, reducing flood damage in urban watersheds is one of the important issues. This study focuses on prioritizing the optimal site for permeable pavement to maximize the efficiency of reducing flood damage in urban watersheds in the future climate environment using multi-criteria decision making techniques. The Mokgamcheon watershed which is considerably urbanized than in the past was selected for the study area and its 27 sub-watersheds were considered as candidate sites. Six General Circulation Model (GCM) of Coupled Model Intercomparison Project 6(CMIP6) according to two Shared Socioeconomic Pathway (SSP) scenarios were used to estimate future monthly precipitation for the study area. The Driving force-Pressure-State-Impact-Response (DPSIR) framework was used to select the water quantity evaluation criteria for prioritizing permeable pavement, and the study area was modeled using ArcGIS and Storm Water Management Model (SWMM). For the values corresponding to the evaluation criteria based on the DPSIR framework, data from national statistics and long-term runoff simulation value of SWMM according to future monthly precipitation were used. Finally, the priority for permeable pavement was determined using the Fuzzy TOPSIS and Minimax regret method. The high priorities were concentrated in the downstream sub-watersheds where urbanization was more progressed and densely populated than the upstream watersheds.

Exploring the role and characterization of Burkholderia cepacia CD2: a promising eco-friendly microbial fertilizer isolated from long-term chemical fertilizer-free soil

  • HyunWoo Son;Justina Klingaite;Sihyun Park;Jae-Ho Shin
    • Journal of Applied Biological Chemistry
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    • v.66
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    • pp.394-403
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    • 2023
  • In the pursuit of sustainable and environmentally-friendly agricultural practices, we conducted an extensive study on the rhizosphere bacteria inhabiting soils that have been devoid of chemical fertilizers for an extended period exceeding 40 years. Through this investigation, we isolated a total of 80 species of plant growth-promoting rhizosphere bacteria and assessed their potential to enhance plant growth. Among these isolates, Burkholderia cepacia CD2 displayed remarkable plant growth-promoting activity, making it an optimal candidate for further analysis. Burkholderia cepacia CD2 exhibited a range of beneficial characteristics conducive to plant growth, including phosphate solubilization, siderophore production, denitrification, nitrate utilization, and urease activity. These attributes are well-known to positively influence the growth and development of plants. To validate the taxonomic classification of the strain, 16S rRNA gene sequencing confirmed its placement within the Burkholderia genus, providing further insights into its phylogenetic relationship. To delve deeper into the potential mechanisms underlying its plant growth-promoting properties, we sought to confirm the presence of specific genes associated with plant growth promotion in CD2. To achieve this, whole genome sequencing (WGS) was performed by Plasmidsaurus Inc. (USA) utilizing Oxford Nanopore technology (Abingdon, UK). The WGS analysis of the genome of CD2 revealed the existence of a subsystem function, which is thought to be a pivotal factor contributing to improved plant growth. Based on these findings, it can be concluded that Burkholderia cepacia CD2 has the potential to serve as a microbial fertilizer, offering a sustainable alternative to chemical fertilizers.

Site Selection for Geologic Records of Extreme Climate Events based on Environmental Change and Topographic Analyses using Paleo Map for Myeongsanimni Coast, South Korea (고지도 기반 환경변화연구 및 지형분석을 통한 명사십리 해안의 제4기 연안지대 이상기후 퇴적기록 적지선정)

  • Kim, Jieun;Yu, Jaehyung;Yang, Dongyoon
    • Economic and Environmental Geology
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    • v.47 no.6
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    • pp.589-599
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    • 2014
  • This study selected optimal sites in Myeongsasimni located in west coast of Korea for stratigraphic research containing extreme climate event during quaternary period by spatio-temporal analyses of changes in sedimentary environment and land use employing 1918 topographic map, 2000 digital terrain map, 1976 and 2012 air photographies. The study area shows no significant changes in topographic characteristics that hilly areas with relatively large variations in elevation are distributed over north and south part of the study area, and sand dues are developed along the coast line. Moreover, flat low lying areas are located at the back side of the sand dues. The movement of surface run off and sediment loads shows two major trends of inland direction flow from back sides of sand dunes and outland direction flow from high terrains inland, and the two flows merge into the stream located in the center of the study area. Two sink with individual area of $0.2km^2$ are observed in Yongjeong-ri and Jaryong-ri which are located in south central part and south part of the study area, respectively. In addition, sea level change simulation reveals that $3.4km^2$ and $3.64km^2$ are inundated with 3 m of sea level rise in 1918 and 2000, respectively, and it would contribute to chase sea level change records preserved in stratigraphy. The inundated areas overlaps well with sink areas where it indicates the low lying areas located in south cental and south part of the study area are identical for sediment accumulation. The areas with minimal human impact on sediment records over last 100 years are $3.51km^2$ distributed over central and south part of the study area with the land use changes of mud and rice field in 1918 to rice field in 2012. The candidate sites of $0.15km^2$ in central part and $0.09km^2$ in south part are identified for preferable locations of geologic record of extreme climate events during quaternary period based on the overlay analysis of optimal sedimentary environment and land use changes.

The Performance Bottleneck of Subsequence Matching in Time-Series Databases: Observation, Solution, and Performance Evaluation (시계열 데이타베이스에서 서브시퀀스 매칭의 성능 병목 : 관찰, 해결 방안, 성능 평가)

  • 김상욱
    • Journal of KIISE:Databases
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    • v.30 no.4
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    • pp.381-396
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    • 2003
  • Subsequence matching is an operation that finds subsequences whose changing patterns are similar to a given query sequence from time-series databases. This paper points out the performance bottleneck in subsequence matching, and then proposes an effective method that improves the performance of entire subsequence matching significantly by resolving the performance bottleneck. First, we analyze the disk access and CPU processing times required during the index searching and post processing steps through preliminary experiments. Based on their results, we show that the post processing step is the main performance bottleneck in subsequence matching, and them claim that its optimization is a crucial issue overlooked in previous approaches. In order to resolve the performance bottleneck, we propose a simple but quite effective method that processes the post processing step in the optimal way. By rearranging the order of candidate subsequences to be compared with a query sequence, our method completely eliminates the redundancy of disk accesses and CPU processing occurred in the post processing step. We formally prove that our method is optimal and also does not incur any false dismissal. We show the effectiveness of our method by extensive experiments. The results show that our method achieves significant speed-up in the post processing step 3.91 to 9.42 times when using a data set of real-world stock sequences and 4.97 to 5.61 times when using data sets of a large volume of synthetic sequences. Also, the results show that our method reduces the weight of the post processing step in entire subsequence matching from about 90% to less than 70%. This implies that our method successfully resolves th performance bottleneck in subsequence matching. As a result, our method provides excellent performance in entire subsequence matching. The experimental results reveal that it is 3.05 to 5.60 times faster when using a data set of real-world stock sequences and 3.68 to 4.21 times faster when using data sets of a large volume of synthetic sequences compared with the previous one.

Splenocyte-mediated immune enhancing activity of Sargassum horneri extracts (괭생이 모자반 추출물의 비장세포 면역활성 증강 효과)

  • Kim, Dong-Sub;Sung, Nak-Yun;Han, In-Jun;Lee, Byung-Soo;Park, Sang-Yun;Nho, Eun Young;Eom, Ji;Kim, Geon;Kim, Kyung-Ah
    • Journal of Nutrition and Health
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    • v.52 no.6
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    • pp.515-528
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    • 2019
  • Purpose: This study examined the immunological activity and optimized the mixture conditions of Sargassum horneri (S. horneri) extracts in vitro and in vivo models. Methods: S. horneri was extracted using three different methods: hot water extraction (HWE), 50% ethanol extraction (EE), and supercritical fluid extraction (SFE). Splenocyte proliferation and cytokine production (Interleukin-2 and Interferon-γ) were measured using a WST-1 assay and enzyme-linked immunosorbent assay, respectively. The levels of nitric oxide and T cell activation production were measured using a Griess assay and flow cytometry, respectively. The natural killer (NK) cell activity was determined using an EZ-LDH kit. Results: Among the three different types of extracts, HWE showed the highest levels of splenocyte proliferation and cytokine production in vitro. In the animal model, three different types of extracts were administrated for 14 days (once/day) at 50 and 100 mg/kg body weight. HWE and SFE showed a high level of splenocyte proliferation and cytokine production in the with and without mitogen-treated groups, whereas EE administration did not induce the splenocyte activation. When RAW264.7 macrophage cells were treated with different mixtures (HWE with 5, 10, 15, 20% of SFE) to determine the optimal mixture ratio of HWE and SFE, the levels of nitric oxide and cytokine production increased strongly in the HWE with 5% and 10% of SFE containing group. In the animal model, HWE with 5% and 10% of SFE mixture administration increased the levels of splenocyte proliferation, cytokine production, and activated CD4+ cell population significantly, with the highest level observed in the HWE with 5% of SFE group. Moreover, the NK cell activity was increased significantly in the HWE with 5% of SFE mixture-treated group compared to the control group. Conclusion: The optimal mixture condition of S. horneri with immune-enhancing activity is the HWE with 5% of SFE mixture. These results confirmed that the extracts of S. horneri and its mixtures are potential candidate materials for immune enhancement.

Optimization of Multiclass Support Vector Machine using Genetic Algorithm: Application to the Prediction of Corporate Credit Rating (유전자 알고리즘을 이용한 다분류 SVM의 최적화: 기업신용등급 예측에의 응용)

  • Ahn, Hyunchul
    • Information Systems Review
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    • v.16 no.3
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    • pp.161-177
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    • 2014
  • Corporate credit rating assessment consists of complicated processes in which various factors describing a company are taken into consideration. Such assessment is known to be very expensive since domain experts should be employed to assess the ratings. As a result, the data-driven corporate credit rating prediction using statistical and artificial intelligence (AI) techniques has received considerable attention from researchers and practitioners. In particular, statistical methods such as multiple discriminant analysis (MDA) and multinomial logistic regression analysis (MLOGIT), and AI methods including case-based reasoning (CBR), artificial neural network (ANN), and multiclass support vector machine (MSVM) have been applied to corporate credit rating.2) Among them, MSVM has recently become popular because of its robustness and high prediction accuracy. In this study, we propose a novel optimized MSVM model, and appy it to corporate credit rating prediction in order to enhance the accuracy. Our model, named 'GAMSVM (Genetic Algorithm-optimized Multiclass Support Vector Machine),' is designed to simultaneously optimize the kernel parameters and the feature subset selection. Prior studies like Lorena and de Carvalho (2008), and Chatterjee (2013) show that proper kernel parameters may improve the performance of MSVMs. Also, the results from the studies such as Shieh and Yang (2008) and Chatterjee (2013) imply that appropriate feature selection may lead to higher prediction accuracy. Based on these prior studies, we propose to apply GAMSVM to corporate credit rating prediction. As a tool for optimizing the kernel parameters and the feature subset selection, we suggest genetic algorithm (GA). GA is known as an efficient and effective search method that attempts to simulate the biological evolution phenomenon. By applying genetic operations such as selection, crossover, and mutation, it is designed to gradually improve the search results. Especially, mutation operator prevents GA from falling into the local optima, thus we can find the globally optimal or near-optimal solution using it. GA has popularly been applied to search optimal parameters or feature subset selections of AI techniques including MSVM. With these reasons, we also adopt GA as an optimization tool. To empirically validate the usefulness of GAMSVM, we applied it to a real-world case of credit rating in Korea. Our application is in bond rating, which is the most frequently studied area of credit rating for specific debt issues or other financial obligations. The experimental dataset was collected from a large credit rating company in South Korea. It contained 39 financial ratios of 1,295 companies in the manufacturing industry, and their credit ratings. Using various statistical methods including the one-way ANOVA and the stepwise MDA, we selected 14 financial ratios as the candidate independent variables. The dependent variable, i.e. credit rating, was labeled as four classes: 1(A1); 2(A2); 3(A3); 4(B and C). 80 percent of total data for each class was used for training, and remaining 20 percent was used for validation. And, to overcome small sample size, we applied five-fold cross validation to our dataset. In order to examine the competitiveness of the proposed model, we also experimented several comparative models including MDA, MLOGIT, CBR, ANN and MSVM. In case of MSVM, we adopted One-Against-One (OAO) and DAGSVM (Directed Acyclic Graph SVM) approaches because they are known to be the most accurate approaches among various MSVM approaches. GAMSVM was implemented using LIBSVM-an open-source software, and Evolver 5.5-a commercial software enables GA. Other comparative models were experimented using various statistical and AI packages such as SPSS for Windows, Neuroshell, and Microsoft Excel VBA (Visual Basic for Applications). Experimental results showed that the proposed model-GAMSVM-outperformed all the competitive models. In addition, the model was found to use less independent variables, but to show higher accuracy. In our experiments, five variables such as X7 (total debt), X9 (sales per employee), X13 (years after founded), X15 (accumulated earning to total asset), and X39 (the index related to the cash flows from operating activity) were found to be the most important factors in predicting the corporate credit ratings. However, the values of the finally selected kernel parameters were found to be almost same among the data subsets. To examine whether the predictive performance of GAMSVM was significantly greater than those of other models, we used the McNemar test. As a result, we found that GAMSVM was better than MDA, MLOGIT, CBR, and ANN at the 1% significance level, and better than OAO and DAGSVM at the 5% significance level.

An Application-Specific and Adaptive Power Management Technique for Portable Systems (휴대장치를 위한 응용프로그램 특성에 따른 적응형 전력관리 기법)

  • Egger, Bernhard;Lee, Jae-Jin;Shin, Heon-Shik
    • Journal of KIISE:Computer Systems and Theory
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    • v.34 no.8
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    • pp.367-376
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    • 2007
  • In this paper, we introduce an application-specific and adaptive power management technique for portable systems that support dynamic voltage scaling (DVS). We exploit both the idle time of multitasking systems running soft real-time tasks as well as memory- or CPU-bound code regions. Detailed power and execution time profiles guide an adaptive power manager (APM) that is linked to the operating system. A post-pass optimizer marks candidate regions for DVS by inserting calls to the APM. At runtime, the APM monitors the CPU's performance counters to dynamically determine the affinity of the each marked region. for each region, the APM computes the optimal voltage and frequency setting in terms of energy consumption and switches the CPU to that setting during the execution of the region. Idle time is exploited by monitoring system idle time and switching to the energy-wise most economical setting without prolonging execution. We show that our method is most effective for periodic workloads such as video or audio decoding. We have implemented our method in a multitasking operating system (Microsoft Windows CE) running on an Intel XScale-processor. We achieved up to 9% of total system power savings over the standard power management policy that puts the CPU in a low Power mode during idle periods.