• Title/Summary/Keyword: Sequencing Strategy

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A Symbiotic Evolutionary Algorithm for Balancing and Sequencing Mixed Model Assembly Lines with Multiple Objectives (다목적을 갖는 혼합모델 조립라인의 밸런싱과 투입순서를 위한 공생 진화알고리즘)

  • Kim, Yeo-Keun;Lee, Sang-Seon
    • Journal of the Korean Operations Research and Management Science Society
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    • v.35 no.3
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    • pp.25-43
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    • 2010
  • We consider a multi-objective balancing and sequencing problem in mixed model assembly lines, which is important for an efficient use of the assembly lines. In this paper, we present a neighborhood symbiotic evolutionary algorithm to simultaneously solve the two problems of balancing and model sequencing under multiple objectives. We aim to find a set of well-distributed solutions close to the true Pareto optimal solutions for decision makers. The proposed algorithm has a two-leveled structure. At Level 1, two populations are operated : One consists of individuals each of which represents a partial solution to the balancing problem and the other consists of individuals for the sequencing problem. Level 2, which is an upper level, works one population whose individuals represent the combined entire solutions to the two problems. The process of Level 1 imitates a neighborhood symbiotic evolution and that of Level 2 simulates an endosymbiotic evolution together with an elitist strategy to promote the capability of solution search. The performance of the proposed algorithm is compared with those of the existing algorithms in convergence, diversity and computation time of nondominated solutions. The experimental results show that the proposed algorithm is superior to the compared algorithms in all the three performance measures.

FASIM: Fragments Assembly Simulation using Biased-Sampling Model and Assembly Simulation for Microbial Genome Shotgun Sequencing

  • Hur Cheol-Goo;Kim Sunny;Kim Chang-Hoon;Yoon Sung-Ho;In Yong-Ho;Kim Cheol-Min;Cho Hwan-Gue
    • Journal of Microbiology and Biotechnology
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    • v.16 no.5
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    • pp.683-688
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    • 2006
  • We have developed a program for generating shotgun data sets from known genome sequences. Generation of synthetic data sets by computer program is a useful alternative to real data to which students and researchers have limited access. Uniformly-distributed-sampling clones that were adopted by previous programs cannot account for the real situation where sampled reads tend to come from particular regions of the target genome. To reflect such situation, a probabilistic model for biased sampling distribution was developed by using an experimental data set derived from a microbial genome project. Among the experimental parameters tested (varied fragment or read lengths, chimerism, and sequencing error), the extent of sequencing error was the most critical factor that hampered sequence assembly. We propose that an optimum sequencing strategy employing different insert lengths and redundancy can be established by performing a variety of simulations.

Developing e-Learning Contents Based on SCORM 2004 (SCORM 2004 기반 e-러닝 콘텐츠 설계 및 구현)

  • Choi, Yong-Suk;Ko, Bo-Young;Lee, Ka-Young
    • Journal of Digital Contents Society
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    • v.10 no.1
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    • pp.107-113
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    • 2009
  • Recently, a number of research efforts have been taken to enhance interoperability and reusability of e-learning contents by developing ADL SCORM 2004 compliant contents. For useful and effective learning contents, content devlopers have to build the strategy of content sequencing in the phase of instructional design. However, many developers have difficulties in understanding the complicated specification of SCORM 2004 S&N(Sequencing&Navigation) and implementing SCORM sequencing. In this paper, we develop SCORM 2004 based best-practice sample contents utilizing SCORM sequencing and thus present a reference guide to the design and implementation of SCORM 2004 contents. It is expected that our sample contents illustrate an effective and useful application of SCORM 2004 as a de-facto e-learning standard, domestically and also internationally.

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An Optimized Strategy for Genome Assembly of Sanger/pyrosequencing Hybrid Data using Available Software

  • Jeong, Hae-Young;Kim, Ji-Hyun F.
    • Genomics & Informatics
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    • v.6 no.2
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    • pp.87-90
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    • 2008
  • During the last four years, the pyrosequencing-based 454 platform has rapidly displaced the traditional Sanger sequencing method due to its high throughput and cost effectiveness. Meanwhile, the Sanger sequencing methodology still provides the longest reads, and paired-end sequencing that is based on that chemistry offers an opportunity to ensure accurate assembly results. In this report, we describe an optimized approach for hybrid de novo genome assembly using pyrosequencing data and varying amounts of Sanger-type reads. 454 platform-derived contigs can be used as single non-breakable virtual reads or converted to simpler contigs that consist of editable, overlapping pseudoreads. These modified contigs maintain their integrity at the first jumpstarting assembly stage and are edited by fragmenting and rejoining. Pre-existing assembly software then can be applied for mixed assembly with 454-derived data and Sanger reads. An effective method for identifying genomic differences between reference and sample sequences in whole-genome resequencing procedures also is suggested.

Adaptive Control of Denitrification by the Extended Kalman Filter in a Sequencing Batch Reactor (확장형칼만필터에 의한 연속회분식반응조의 탈질 적응제어)

  • Kim, Dong Han
    • Journal of Korean Society of Water and Wastewater
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    • v.20 no.6
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    • pp.829-836
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    • 2006
  • The reaction rate of denitrification is primarily affected by the utilization of organics that are usually limited in the anoxic period in a sequencing batch reactor. It is necessary to add an extemal carbon source for sufficient denitrification. An adaptive model of state-space based on the extended Kalman filter is applied to manipulate the dosage rate of extemal carbon automatically. Control strategies for denitrification have been studied to improve control performance through simulations. The normal control strategy of the constant set-point results in the overdosage of external carbon and deterioration of water quality. To prevent the overdosage of external carbon, improved control strategies such as the constrained control action, variable set-point, and variable set-point after dissolved oxygen depletion are required. More stable control is obtained through the application of the variable set-point after dissolved oxygen depletion. The converging value of the estimated denitrification coefficient reflects conditions in the reactor.

The effectiveness of step feeding strategies in sequencing batch reactor for a single-stage deammonification of high strength ammonia wastewater

  • Choi, Wonyoung;Yu, Jaecheul;Kim, Jeongmi;Jeong, Soyeon;Direstiyani, Lucky Caesar;Lee, Taeho
    • Membrane and Water Treatment
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    • v.11 no.1
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    • pp.79-85
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    • 2020
  • A single-stage deammonification with a sequencing batch reactor (SBR) that simultaneous nitritation, anaerobic ammonia oxidation (anammox), and denitrification (SNAD) occur in one reactor has been widely applied for sidestream of wastewater treatment plant. For the stable and well-balanced SNAD, a feeding strategy of influent wastewater is one of the most important operating factors in the single-stage deammonification SBR. In this study, single-stage deammonification SBR (working volume 30L) was operated to treat a high-strength ammonium wastewater (1200 mg NH4+-N/L) with different feeding strategies (single feeding and nine-step feeding) under the condition without COD. Each cycle of the step feeding involved 6 sub-cycles consisted of aerobic and anoxic periods for partial nitritation (PN) and anammox, respectively. Contrary to unstable performance in the single feeding, the step feeding showed better deammonification performance (0.565 kg-N/m3/day). Under the condition with COD, however, the nitrogen removal rate (NRR) decreased to 0.403 kg-N/m3/day when the Nine-step feeding strategies had an additional denitrification period before sub-cycles for PN and anammox. The NRR was recovered to 0.518 kg-N/m3/day by introducing an enhanced multiple-step feeding strategy. The strategy had 50 cycles consisted of feed, denitrification, PN, and anammox, instead of repeated sub-cycles for PN and anammox. The multiple-step feeding strategy without sub-cycle showed the most stable and excellent deammonification performance: high nitrogen removal efficiency (98.6%), COD removal rate (0.131 kg-COD/m3/day), and COD removal efficiency (78.8%). This seemed to be caused by that the elimination of the sub-cycles might reduce COD oxidation during aerobic condition but increase the COD utilization for denitrification period. In addition, among various sensor values, the ORP pattern appeared to be applicable to monitor and control each reaction step for deammonification in the multiple-step feeding strategy without sub-cycle. Further study to optimize the number of multiple-step feeding is still needed but these results show that the multiple-step feeding strategy can contribute to a well-balanced SNAD for deammonification when treating high-strength ammonium wastewater with COD in the single-stage deammonification SBR.

Strategy of Patient-Specific Therapeutics in Cardiovascular Disease Through Single-Cell RNA Sequencing

  • Yunseo Jung;Juyeong Kim;Howon Jang;Gwanhyeon Kim;Yoo-Wook Kwon
    • Korean Circulation Journal
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    • v.53 no.1
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    • pp.1-16
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    • 2023
  • Recently, single cell RNA sequencing (scRNA-seq) technology has enabled the discovery of novel or rare subtypes of cells and their characteristics. This technique has advanced unprecedented biomedical research by enabling the profiling and analysis of the transcriptomes of single cells at high resolution and throughput. Thus, scRNA-seq has contributed to recent advances in cardiovascular research by the generation of cell atlases of heart and blood vessels and the elucidation of mechanisms involved in cardiovascular development and diseases. This review summarizes the overall workflow of the scRNA-seq technique itself and key findings in the cardiovascular development and diseases based on the previous studies. In particular, we focused on how the single-cell sequencing technology can be utilized in clinical field and precision medicine to treat specific diseases.

Nitrification and Denitrification by Using a Sequencing Batch Reactor System (Sequencing Batch Reactor (SBR)를 이용한 질산화와 탈질산화)

  • PARK Jong-Ho;LEE Won-Ho;CHO Kyu-Seok;HWANG Gyu-Deok
    • Korean Journal of Fisheries and Aquatic Sciences
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    • v.36 no.3
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    • pp.247-253
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    • 2003
  • Sequencing Batch Reactor (SBR) was operated under various experimental conditions to improve the efficiency of biological filters used for the treatment of recycled wastewater from aquaculture. This SBR system was operated for removing COD, ammonia and suspended solid that were the major pollutants in aquaculture wastewater. Aerobic and anoxic conditions after FILL mode were applied intermittently for effective removal of nitrogen. SETTLE and DRAW modes were followed by the complete aerobic and anoxic REACT mode. The total volume of the SBR was 75 liter, while the working volume in a cycle was 35 liters. When the final operating strategy of the SBR was FILL/REACT/SETTLE/DRAW of 0.5/10/1/0.5 hr. the removal efficiencies of TCODcr, $NH_{4}^{+}-N,$ and T-N were 94, 98, and $89\%,$ respectively.

Speculation on the Identity of Bacteria Named TFOs Occurring in the Inefficient P-Removal Phase of a Biological Phosphorus Removal System

  • Lee, Young-Ok;Ahn, Chang-Hoon;Park, Jae-Kwang
    • Environmental Engineering Research
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    • v.15 no.1
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    • pp.3-7
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    • 2010
  • To better understand the ecology of tetrade forming organisms (TFOs) floating in a large amount of dairy wastewater treatment plant (WWTP) effluent (sequencing batch reactor [SBR]) during the inefficient phosphorus (P) removal process of an enhanced biological P removal system, the TFOs from the effluent of a full scale WWTP were separated and attempts made to culture the TFOs in presence/absence of oxygen. The intact TFOs only grew aerobically in the form of unicellular short-rods. Furthermore, to identify the intact TFOs and unicellular short-rods the DNAs of both were extracted, analyzed using their denaturing gradient gel electrophoresis (DGGE)-profiles and then sequenced. The TFOs and unicellular short-rods exhibited the same banding pattern in their DGGE-profiles, and those sequencing data resulted in their identification as Acinetobacter sp. The intact TFOs appeared in clumps and packages of tetrade cells, and were identified as Acinetobacter sp., which are known as strict aerobes and efficient P-removers. The thick layer of extracellular polymeric substance surrounding Acinetobacter sp. may inhibit phosphate uptake, and the cell morphology of TFOs might subsequently be connected with their survival strategy under the anaerobic regime of the SBR system.

Genomic epidemiology and surveillance of zoonotic viruses using targeted next-generation sequencing (표적화 차세대염기서열분석법을 이용한 인수공통 바이러스의 유전체 역학과 예찰)

  • Seonghyeon Lee;Seung-Hwan Baek;Shivani Rajoriya;Sara Puspareni;Won-Keun Kim
    • Korean Journal of Veterinary Service
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    • v.46 no.1
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    • pp.93-106
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    • 2023
  • Emerging and re-emerging zoonotic viruses become critical public health, economic, societal, and cultural burdens. The Coronavirus disease-19 (COVID-19) pandemic reveals needs for effective preparedness and responsiveness against the emergence of variants and the next virus outbreak. The targeted next-generation sequencing (NGS) significantly contributes to the acquisition of viral genome sequences directly from clinical specimens. Using this advanced NGS technology, the genomic epidemiology and surveillance play a critical role in identifying of infectious source and origin, tracking of transmission chains and virus evolution, and characterizing the virulence and developing of vaccines during the outbreak. In this review, we highlight the platforms and preparation of targeted NGS for the viral genomics. We also demonstrate the application of this strategy to take advantage of the responsiveness and prevention of emerging zoonotic viruses. This article provides broad and deep insights into the preparedness and responsiveness for the next zoonotic virus outbreak.