Search results for: next generation sequencing

Authors: Yazhi Huang, Jing Yang, Dingge Ying, Yan Zhang, Vorasuk Shotelersuk, Nattiya Hirankarn, Pak Chung Sham, Yu Lung Lau, Wanling Yang

Abstract:

Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT.

Keywords: Human leukocyte antigens, next generation sequencing, whole exome sequencing, HLA typing.

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Authors: Chien-Ju Li, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu , Darby Tien-Hao Chang

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De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.

Keywords: Contig graph, NGS, de novo assembly, scaffold.

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Authors: Hossein Ahmadi, Ogholgol Nazari

Abstract:

The necessity of grading and sequencing tasks has led to the development of different criteria in this regard. However, appropriateness of these criteria in different situations is less discussed. This paper attempts to shed more light on the priority of different criteria in relation with different factors including learners, teachers, educational, and cultural factors.

Keywords: Criteria, Grading, Sequencing, Language learning tasks.

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Authors: N. Manavizadeh, A. Dehghani, M. Rabbani

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Mixed model assembly lines (MMAL) are a type of production line where a variety of product models similar in product characteristics are assembled. The effective design of these lines requires that schedule for assembling the different products is determined. In this paper we tried to fit the sequencing problem with the main characteristics of make to order (MTO) environment. The problem solved in this paper is a multiple objective sequencing problem in mixed model assembly lines sequencing using weighted Sum Method (WSM) using GAMS software for small problem and an effective GA for large scale problems because of the nature of NP-hardness of our problem and vast time consume to find the optimum solution in large problems. In this problem three practically important objectives are minimizing: total utility work, keeping a constant production rate variation, and minimizing earliness and tardiness cost which consider the priority of each customer and different due date which is a real situation in mixed model assembly lines and it is the first time we consider different attribute to prioritize the customers which help the company to reduce the cost of earliness and tardiness. This mechanism is a way to apply an advance available to promise (ATP) in mixed model assembly line sequencing which is the main contribution of this paper.

Keywords: Available to promise, Earliness & Tardiness, GA, Mixed-Model assembly line Sequencing.

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Authors: Ali W. Alattabi, Khalid S. Hashim, Hassnen M. Jafer, Ali Alzeyadi

Abstract:

This study was performed to optimise the react time (RT) and study its effects on the removal rates of nitrogen compounds in a sequencing batch reactor (SBR) treating synthetic industrial wastewater. The results showed that increasing the RT from 4 h to 10, 16 and 22 h significantly improved the nitrogen compounds’ removal efficiency, it was increased from 69.5% to 95%, 75.7 to 97% and from 54.2 to 80.1% for NH₃-N, NO₃-N and NO₂-N respectively. The results obtained from this study showed that the RT of 22 h was the optimum for nitrogen compounds removal efficiency.

Keywords: Ammonia-nitrogen, retention time, nitrate, nitrite, sequencing batch reactor, sludge characteristics.

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Authors: Fereshteh Shacheraghi, Mohammad Reza Shakibaie, Hanieh Noveiri

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Fourty one strains of ESBL producing P.aeruginosa which were previously isolated from burn patients in Kerman University general hospital, Iran were subjected to PCR, RFLP and sequencing in order to determine the type of extended spectrum β- lactamases (ESBL), the restriction digestion pattern and possibility of mutation among detected genes. DNA extraction was carried out by phenol chloroform method. PCR for detection of bla genes was performed using specific primer for each gene. Restriction Fragment Length Polymorphism (RFLP) for ESBL genes was carried out using EcoRI, NheI, PVUII, EcoRV, DdeI, and PstI restriction enzymes. The PCR products were subjected to direct sequencing of both the strands for identification of the ESBL genes.The blaCTX-M, blaVEB-1, blaPER-1, blaGES-1, blaOXA-1, blaOXA-4 and blaOXA-10 genes were detected in the (n=1) 2.43%, (n=41)100%, (n=28) 68.3%, (n=10) 24.4%, (n=29) 70.7%, (n=7)17.1% and (n=38) 92.7% of the ESBL producing isolates respectively. The RFLP analysis showed that each ESBL gene has identical pattern of digestion among the isolated strains. Sequencing of the ESBL genes confirmed the genuinety of PCR products and revealed no mutation in the restriction sites of the above genes. From results of the present investigation it can be concluded that blaVEB-1 and blaCTX-M were the most and the least frequently isolated ESBL genes among the P.aeruginosa strains isolated from burn patients. The RFLP and sequencing analysis revealed that same clone of the bla genes were indeed existed among the antibiotic resistant strains.

Keywords: ESBL genes, PCR, RFLP, Sequencing, P.aeruginosa

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Authors: M. Sadeghi, H. Pezeshk, R. Tusserkani, A. Sharifi Zarchi, A. Malekpour, M. Foroughmand, S. Goliaei, M. Totonchi, N. Ansari–Pour

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The role and relative importance of intrinsic and extrinsic factors in the development of complex diseases such as cancer still remains a controversial issue. Determining the amount of variation explained by these factors needs experimental data and statistical models. These models are nevertheless based on the occurrence and accumulation of random mutational events during stem cell division, thus rendering cancer development a stochastic outcome. We demonstrate that not only individual genome sequencing is uninformative in determining cancer risk, but also assigning a unique genome sequence to any given individual (healthy or affected) is not meaningful. Current whole-genome sequencing approaches are therefore unlikely to realize the promise of personalized medicine. In conclusion, since genome sequence differs from cell to cell and changes over time, it seems that determining the risk factor of complex diseases based on genome sequence is somewhat unrealistic, and therefore, the resulting data are likely to be inherently uninformative.

Keywords: Cancer risk, extrinsic factors, genome sequencing, intrinsic factors.

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Authors: Şahin Emrah Amrahov, Fatih Aybar, Serhat Doğan

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In this paper we consider the rule reduct generation problem. Rule Reduct Generation (RG) and Modified Rule Generation (MRG) algorithms, that are used to solve this problem, are well-known. Alternative to these algorithms, we develop Pruning Rule Generation (PRG) algorithm. We compare the PRG algorithm with RG and MRG.

Keywords: Rough sets, Decision rules, Rule induction, Classification.

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Authors: Amin Mojiri, Akiyoshi Ohashi, Tomonori Kindaichi

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Synthetic domestic wastewater was treated via combining treatment methods, including electrochemical oxidation, adsorption, and sequencing batch reactor (SBR). In the upper part of the reactor, an anode and a cathode (Ti/RuO₂-IrO₂) were organized in parallel for the electrochemical oxidation procedure. Sodium sulfate (Na₂SO₄) with a concentration of 2.5 g/L was applied as the electrolyte. The voltage and current were fixed on 7.50 V and 0.40 A, respectively. Then, 15% working value of the reactor was filled by activated sludge, and 85% working value of the reactor was added with synthetic wastewater. Powdered cockleshell, 1.5 g/L, was added in the reactor to do ion-exchange. Response surface methodology was employed for statistical analysis. Reaction time (h) and pH were considered as independent factors. A total of 97.0% biochemical oxygen demand, 99.9% phosphorous and 88.6% cadmium were eliminated at the optimum reaction time (80.0 min) and pH (6.4).

Keywords: Adsorption, electrochemical oxidation, metals, sequencing batch reactor.

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Authors: Joanna Nieżurawska, Hanna Karaszewska, Anna Dziadkiewicz

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Contemporary conditions force companies to constantly implement changes and improvements, which is connected with plasticization of their activity in all spheres. Cafeteria systems are a good example of flexible remuneration systems. Cafeteria systems are well-known and often used in the United States, Great Britain and in Western Europe. In Poland, they are hardly ever used and greater flexibility in remuneration packages refers mainly to senior managers and executives. The main aim of this article is to research the attractiveness of the cafeteria system as viewed by generation Z. The additional aim of the article is to prioritize using the importance index of particular types of cafeteria systems from the generation Z’s perspective, as well as to identify the factors which determine the development of cafeteria systems in Poland. The research was conducted in June 2015 among 185 young employees (generation Z). The paper presents some of the results.

Keywords: Cafeteria, generation X, generation Y, generation Z, flexible remuneration systems, plasticization of remuneration.

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Authors: Hamid Barati, Ali Movaghar, Ali Barati, Arash Azizi Mazreah , Ehsan Shahsavari Gogheri, Faranak Mohsenzadeh

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The communication networks development and advancement during two last decades has been toward a single goal and that is gradual change from circuit-switched networks to packed switched ones. Today a lot of networks operates are trying to transform the public telephone networks to multipurpose packed switch. This new achievement is generally called "next generation networks". In fact, the next generation networks enable the operators to transfer every kind of services (sound, data and video) on a network. First, in this report the definition, characteristics and next generation networks services and then ad-hoc networks role in the next generation networks are studied.

Keywords: NGNs services, Ad-hoc Networks, NGN.

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Authors: N. Rugthaicharoencheep, S. Auchariyamet

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Distributed Generation (DG) in the form of renewable power generation systems is currently preferred for clean power generation. It has a significant impact on the distribution systems. This impact may be either positively or negatively depending on the distribution system, distributed generator and load characteristics. In this works, an overview of DG is briefly introduced. The technology of DG is also listed while the technical impacts and economic impacts are explained.

Keywords: Distributed Generation, Technical Impacts, Economic Impacts.

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Authors: Abdulrahman A. Bahaddad, Mohammed Beshir

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The objective of this paper is to demonstrate and describe eight different types of power generation technologies and to understand the history and future trends of each technology. In addition, a comparative analysis between these technologies will be presented with respect to their cost analysis and associated performance.

Keywords: Conventional power generation, economic analysis, environmental impact, renewable energy power generation.

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Authors: Ali Mchirgui, Nejib Hidouri, Mourad Magherbi, Ammar Ben Brahim

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The paper provides a numerical investigation of the entropy generation analysis due to natural convection in an inclined square porous cavity. The coupled equations of mass, momentum, energy and species conservation are solved using the Control Volume Finite-Element Method. Effect of medium permeability and inclination angle on entropy generation is analysed. It was found that according to the Darcy number and the porous thermal Raleigh number values, the entropy generation could be mainly due to heat transfer or to fluid friction irreversibility and that entropy generation reaches extremum values for specific inclination angles.

Keywords: Porous media, entropy generation, convection, numerical method.

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Authors: V. Phupha, T. Lantharthong, N. Rugthaicharoencheep

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The problem of generation expansion planning (GEP) has been extensively studied for many years. This paper presents three topics in GEP as follow: statistical model, models for generation expansion, and expansion problem. In the topic of statistical model, the main stages of the statistical modeling are briefly explained. Some works on models for GEP are reviewed in the topic of models for generation expansion. Finally for the topic of expansion problem, the major issues in the development of a longterm expansion plan are summarized.

Keywords: Generation expansion planning, strategies, power system

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Authors: Osamah A. Alsayegh, Fatma A. Fairouz

Abstract:

This paper compares planning results of the electricity and water generation inventory up to year 2030 in the State of Kuwait. Currently, the generation inventory consists of oil and gas fired technologies only. The planning study considers two main cases. The first case, Reference case, examines a generation inventory based on oil and gas fired generation technologies only. The second case examines the inclusion of renewables as part of the generation inventory under two scenarios. In the first scenario, Ref-RE, renewable build-out is based on optimum economic performance of overall generation system. Result shows that the optimum installed renewable capacity with electric energy generation of 11% . In the second scenario, Ref-RE20, the renewable capacity build-out is forced to provide 20% of electric energy by 2030. The respective energy systems costs of Reference, Ref-RE and Ref-RE20 case scenarios reach US dollar 24, 10 and 14 billion annually in 2030.

Keywords: Generation inventory, solar, planning, TIMES, wind.

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Authors: Hiroaki Sumi, Kiichiro Hayashi

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Now, the use of renewable energy power generation has been advanced. In this paper, we compared the usable amount of resource for photovoltaic power generation which was estimated using the NEDO formula and the expansion support policy of photovoltaic power generation which was researched using Internet in the municipality level in Hokkaido and Aichi Prefecture, Japan. This paper will contribute to grasp the current situation especially about the policy. As a result, there were municipalities which seemed to be no consideration of fitting the amount of resources. We think it would need to consider the suitability between the resources and policies.

Keywords: Photovoltaic power generation, expansion support policy, amount of resources, Japan.

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Authors: Abdulrahim Shamayleh

Abstract:

In this work, the surgical theater of a local hospital in KSA was analyzed using simulation. The focus was on attempting to answer questions related to how many Operating Rooms (ORs) to open and to analyze the performance of the surgical theater in general and mainly the Post Anesthesia Care Unit (PACU) to assist making decisions regarding PACU staffing. The surgical theater consists of ten operating rooms and the PACU unit which has a maximum capacity of fifteen beds. Different sequencing rules to sequence the surgical cases were tested and the Longest Case First (LCF) were superior to others. The results of the different alternatives developed and tested can be used by the manager as a tool to plan and manage the OR and PACU

Keywords: Operating room, post anesthesia care unit, PACUstaffing, sequencing, healthcare

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Authors: S. H. Oudjana, A. Hellal, I. Hadj Mahammed

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Photovoltaic power generation forecasting is an important task in renewable energy power system planning and operating. This paper explores the application of neural networks (NN) to study the design of photovoltaic power generation forecasting systems for one week ahead using weather databases include the global irradiance, and temperature of Ghardaia city (south of Algeria) using a data acquisition system. Simulations were run and the results are discussed showing that neural networks Technique is capable to decrease the photovoltaic power generation forecasting error.

Keywords: Photovoltaic Power Forecasting, Regression, Neural Networks.

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Authors: Norfifah Bachok, Norihan Md. Arifin

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In this paper we use classical linear stability theory to investigate the effects of uniform internal heat generation on the onset of Marangoni convection in a horizontal layer of fluid heated from below. We use a analytical technique to obtain the close form analytical expression for the onset of Marangoni convection when the lower boundary is conducting with free-slip condition. We show that the effect of increasing the internal heat generation is always to destabilize the layer.

Keywords: Marangoni convection, heat generation, free-slip

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Authors: Gayadhar Panda, Sidhartha Panda, C. Ardil

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The design of Automatic Generation Control (AGC) system plays a vital role in automation of power system. This paper proposes Hybrid Neuro Fuzzy (HNF) approach for AGC of two-area interconnected reheat thermal power system with the consideration of Generation Rate Constraint (GRC). The advantage of proposed controller is that it can handle the system non-linearities and at the same time the proposed approach is faster than conventional controllers. The performance of HNF controller has been compared with that of both conventional Proportional Integral (PI) controller as well as Fuzzy Logic Controller (FLC) both in the absence and presence of Generation Rate Constraint (GRC). System performance is examined considering disturbance in each area of interconnected power system.

Keywords: Automatic Generation Control (AGC), Dynamic Response, Generation Rate Constraint (GRC), Proportional Integral(PI) Controller, Fuzzy Logic Controller (FLC), Hybrid Neuro-Fuzzy(HNF) Control, MATLAB/SIMULINK.

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Authors: Raju Kaduru, Narsaiah Srinivas Gondlala

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This paper presents an analytical approach for evaluating distribution system reliability indices in the presence of distributed generation. Modeling distributed generation and evaluation of distribution system reliability indices using the frequency duration technique. Using model implements and case studies are discussed. Results showed that location of DG and its effect in distribution reliability indices. In this respect, impact of DG on distribution system is investigated using the IEEE Roy Billinton test system (RBTS2) included feeder 1. Therefore, it will help to the distribution system planners in the DG resource placement.

Keywords: Distributed Generation, DG Location, Distribution System, Reliability Indices.

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Authors: Tung-Sheng Zhan, Chih-Cheng Kao, Chin-Der Yang, Jong-Ian Tsai

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Fossil fuel-firing power plants dominate electric power generation in Taiwan, which are also the major contributor to Green House gases (GHG). CO2 is the most important greenhouse gas that cause global warming. This paper penetrates the relationship between carbon trading for GHG reduction and power generation expansion planning (GEP) problem for the electrical utility. The Particle Swarm Optimization (PSO) Algorithm is presented to deal with the generation expansion planning strategy of the utility with independent power providers (IPPs). The utility has to take both the IPPs- participation and environment impact into account when a new generation unit is considering expanded from view of supply side.

Keywords: Carbon Trading, CO2 Emission, GenerationExpansion Planning (GEP), Green House gases (GHG), ParticleSwarm Optimization (PSO).

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Authors: Amir Lotfi, Seyed Hamid Hosseini

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During the recent past, due to the increase of electrical energy demand and governmental resources constraints in creating additional capacity in the generation, transmission, and distribution, privatization, and restructuring in electrical industry have been considered. So, in most of the countries, different parts of electrical industry like generation, transmission, and distribution have been separated in order to create competition. Considering these changes, environmental issues, energy growth, investment of private equity in energy generation units and difficulties of transmission lines expansion, distributed generation (DG) units have been used in power systems. Moreover, reduction in the need for transmission and distribution, the increase of reliability, improvement of power quality, and reduction of power loss have caused DG to be placed in power systems. On the other hand, considering low liquidity need, private investors tend to spend their money for DGs. In this project, the main goal is to offer an algorithm for planning and placing DGs in order to reduce the need for transmission and distribution network.

Keywords: Planning, transmission, distributed generation, power security, power systems.

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Authors: Shuangquan Liu, Jinwen Wang, Dada Wang

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A case study of the generation scheduling optimization of the multi-hydroplants on the Yuan River Basin in China is reported in this paper. Concerning the uncertainty of the inflows, the long/mid-term generation scheduling (LMTGS) problem is solved by a stochastic model in which the inflows are considered as stochastic variables. For the short-term generation scheduling (STGS) problem, a constraint violation priority is defined in case not all constraints are satisfied. Provided the stage-wise separable condition and low dimensions, the hydroplant-based operational region schedules (HBORS) problem is solved by dynamic programming (DP). The coordination of LMTGS and STGS is presented as well. The feasibility and the effectiveness of the models and solution methods are verified by the numerical results.

Keywords: generation scheduling, multi-hydroplants, optimization.

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Authors: Donna M. G. Comissiong, Tyrone D. Dass, Harold Ramkissoon, Alana R. Sankar

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The B'enard-Marangoni thermal instability problem for a viscoelastic Jeffreys- fluid layer with internal heat generation is investigated. The fluid layer is bounded above by a realistic free deformable surface and by a plane surface below. Our analysis shows that while the internal heat generation and the relaxation time both destabilize the fluid layer, its stability may be enhanced by an increased retardation time.

Keywords: Viscoelastic fluid, Jeffreys' model, Maxwell model, internal heat generation, retardation time, relaxation time.

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Authors: N. Rugthaicharoencheep, T. Langtharthong

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This paper presents the optimal placement and sizing of distributed generation (DG) in a distribution system. The problem is to reliability improvement of distribution system with distributed generations. The technique employed to solve the minimization problem is based on a developed Tabu search algorithm and reliability worth analysis. The developed methodology is tested with a distribution system of Roy Billinton Test System (RBTS) bus 2. It can be seen from the case study that distributed generation can reduce the customer interruption cost and therefore improve the reliability of the system. It is expected that our proposed method will be utilized effectively for distribution system operator.

Keywords: Distributed generation Optimization technique Reliability improvement, Distribution system.

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Authors: Sheng-An Yang, Ren-Yi Hung, Ying-Yi Ho

Abstract:

This paper aims to perform the second law analysis of thermodynamics on the laminar film condensation of pure saturated vapor flowing in the direction of gravity on an ellipsoid with variable wall temperature. The analysis provides us understanding how the geometric parameter- ellipticity and non-isothermal wall temperature variation amplitude “A." affect entropy generation during film-wise condensation heat transfer process. To understand of which irreversibility involved in this condensation process, we derived an expression for the entropy generation number in terms of ellipticity and A. The result indicates that entropy generation increases with ellipticity. Furthermore, the irreversibility due to finite temperature difference heat transfer dominates over that due to condensate film flow friction and the local entropy generation rate decreases with increasing A in the upper half of ellipsoid. Meanwhile, the local entropy generation rate enhances with A around the rear lower half of ellipsoid.

Keywords: Free convection; Non-isothermal; Thermodynamic second law; Entropy, Ellipsoid.

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Authors: Ahmed S. Al-Abdulwahab

Abstract:

Generation system reliability assessment is an important task which can be performed using deterministic or probabilistic techniques. The probabilistic approaches have significant advantages over the deterministic methods. However, more complicated modeling is required by the probabilistic approaches. Power generation model is a basic requirement for this assessment. One form of the generation models is the well known capacity outage probability table (COPT). Different analytical techniques have been used to construct the COPT. These approaches require considerable mathematical modeling of the generating units. The unit-s models are combined to build the COPT which will add more burdens on the process of creating the COPT. Decimal to Binary Conversion (DBC) technique is widely and commonly applied in electronic systems and computing This paper proposes a novel utilization of the DBC to create the COPT without engaging in analytical modeling or time consuming simulations. The simple binary representation , “0 " and “1 " is used to model the states o f generating units. The proposed technique is proven to be an effective approach to build the generation model.

Keywords: Decimal to Binary, generation, reliability.

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Authors: Lei Lei, Hongbo Zhang, Donald J. Bergstrom, Bing Zhang, K. Y. Song, W. J. Zhang

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This paper presents a model for a modified T-junction device for microspheres generation. The numerical model is developed using a commercial software package: COMSOL Multiphysics. In order to test the accuracy of the numerical model, multiple variables, such as the flow rate of cross-flow, fluid properties, structure, and geometry of the microdevice are applied. The results from the model are compared with the experimental results in the diameter of the microsphere generated. The comparison shows a good agreement. Therefore the model is useful in further optimization of the device and feedback control of microsphere generation if any.

Keywords: CFD modeling, validation, microsphere generation, modified T-junction.

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