• Title/Summary/Keyword: reverse search strategy

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Metaproteomic analysis of harmful algal bloom in the Daechung reservoir, Korea

  • Choi, Jong-Soon;Park, Yun Hwan;Kim, Soo Hyeon;Park, Ju Seong;Choi, Yoon-E
    • Korean Journal of Environmental Biology
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    • v.38 no.3
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    • pp.424-432
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    • 2020
  • The present study aimed to analyze the metaproteome of the microbial community comprising harmful algal bloom (HAB) in the Daechung reservoir, Korea. HAB samples located at GPS coordinates of 36°29'N latitude and 127°28'E longitude were harvested in October 2013. Microscopic observation of the HAB samples revealed red signals that were presumably caused by the autofluorescence of chlorophyll and phycocyanin in viable cyanobacteria. Metaproteomic analysis was performed by a gelbased shotgun proteomic method. Protein identification was conducted through a two-step analysis including a forward search strategy (FSS) (random search with the National Center for Biotechnology Information (NCBI), Cyanobase, and Phytozome), and a subsequent reverse search strategy (RSS) (additional Cyanobase search with a decoy database). The total number of proteins identified by the two-step analysis (FSS and RSS) was 1.8-fold higher than that by one-step analysis (FSS only). A total of 194 proteins were assigned to 12 cyanobacterial species (99 mol%) and one green algae species (1 mol%). Among the species identified, the toxic microcystin-producing Microcystis aeruginosa NIES-843 (62.3%) species was the most dominant. The largest functional category was proteins belonging to the energy category (39%), followed by metabolism (15%), and translation (12%). This study will be a good reference for monitoring ecological variations at the meta-protein level of aquatic microalgae for understanding HAB.

Evaluating Reverse Logistics Networks with Centralized Centers : Hybrid Genetic Algorithm Approach (집중형센터를 가진 역물류네트워크 평가 : 혼합형 유전알고리즘 접근법)

  • Yun, YoungSu
    • Journal of Intelligence and Information Systems
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    • v.19 no.4
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    • pp.55-79
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    • 2013
  • In this paper, we propose a hybrid genetic algorithm (HGA) approach to effectively solve the reverse logistics network with centralized centers (RLNCC). For the proposed HGA approach, genetic algorithm (GA) is used as a main algorithm. For implementing GA, a new bit-string representation scheme using 0 and 1 values is suggested, which can easily make initial population of GA. As genetic operators, the elitist strategy in enlarged sampling space developed by Gen and Chang (1997), a new two-point crossover operator, and a new random mutation operator are used for selection, crossover and mutation, respectively. For hybrid concept of GA, an iterative hill climbing method (IHCM) developed by Michalewicz (1994) is inserted into HGA search loop. The IHCM is one of local search techniques and precisely explores the space converged by GA search. The RLNCC is composed of collection centers, remanufacturing centers, redistribution centers, and secondary markets in reverse logistics networks. Of the centers and secondary markets, only one collection center, remanufacturing center, redistribution center, and secondary market should be opened in reverse logistics networks. Some assumptions are considered for effectively implementing the RLNCC The RLNCC is represented by a mixed integer programming (MIP) model using indexes, parameters and decision variables. The objective function of the MIP model is to minimize the total cost which is consisted of transportation cost, fixed cost, and handling cost. The transportation cost is obtained by transporting the returned products between each centers and secondary markets. The fixed cost is calculated by opening or closing decision at each center and secondary markets. That is, if there are three collection centers (the opening costs of collection center 1 2, and 3 are 10.5, 12.1, 8.9, respectively), and the collection center 1 is opened and the remainders are all closed, then the fixed cost is 10.5. The handling cost means the cost of treating the products returned from customers at each center and secondary markets which are opened at each RLNCC stage. The RLNCC is solved by the proposed HGA approach. In numerical experiment, the proposed HGA and a conventional competing approach is compared with each other using various measures of performance. For the conventional competing approach, the GA approach by Yun (2013) is used. The GA approach has not any local search technique such as the IHCM proposed the HGA approach. As measures of performance, CPU time, optimal solution, and optimal setting are used. Two types of the RLNCC with different numbers of customers, collection centers, remanufacturing centers, redistribution centers and secondary markets are presented for comparing the performances of the HGA and GA approaches. The MIP models using the two types of the RLNCC are programmed by Visual Basic Version 6.0, and the computer implementing environment is the IBM compatible PC with 3.06Ghz CPU speed and 1GB RAM on Windows XP. The parameters used in the HGA and GA approaches are that the total number of generations is 10,000, population size 20, crossover rate 0.5, mutation rate 0.1, and the search range for the IHCM is 2.0. Total 20 iterations are made for eliminating the randomness of the searches of the HGA and GA approaches. With performance comparisons, network representations by opening/closing decision, and convergence processes using two types of the RLNCCs, the experimental result shows that the HGA has significantly better performance in terms of the optimal solution than the GA, though the GA is slightly quicker than the HGA in terms of the CPU time. Finally, it has been proved that the proposed HGA approach is more efficient than conventional GA approach in two types of the RLNCC since the former has a GA search process as well as a local search process for additional search scheme, while the latter has a GA search process alone. For a future study, much more large-sized RLNCCs will be tested for robustness of our approach.