Search results for: making
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 1361

Search results for: making

821 The Development of Decision Support System for Waste Management; a Review

Authors: M. S. Bani, Z. A. Rashid, K. H. K. Hamid, M. E. Harbawi, A.B.Alias, M. J. Aris

Abstract:

Most Decision Support Systems (DSS) for waste management (WM) constructed are not widely marketed and lack practical applications. This is due to the number of variables and complexity of the mathematical models which include the assumptions and constraints required in decision making. The approach made by many researchers in DSS modelling is to isolate a few key factors that have a significant influence to the DSS. This segmented approach does not provide a thorough understanding of the complex relationships of the many elements involved. The various elements in constructing the DSS must be integrated and optimized in order to produce a viable model that is marketable and has practical application. The DSS model used in assisting decision makers should be integrated with GIS, able to give robust prediction despite the inherent uncertainties of waste generation and the plethora of waste characteristics, and gives optimal allocation of waste stream for recycling, incineration, landfill and composting.

Keywords: Review, decision support system, GIS and waste management.

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820 Managing, Sustaining, and Future Proofing the Business of Educational Provision Following Large-Scale Disaster and Disruption

Authors: Judy Yarwood, Lesley Seaton, Philippa Seaton

Abstract:

A catastrophic earthquake measuring 6.3 on the Richter scale struck the Christchurch, New Zealand Central Business District on February 22, 2012, abruptly disrupting the business of teaching and learning at Christchurch Polytechnic Institute of Technology. This paper presents the findings from a study undertaken about the complexity of delivering an educational programme in the face of this traumatic natural event. Nine interconnected themes emerged from this multiple method study: communication, decision making, leader- and follower-ship, balancing personal and professional responsibilities, taking action, preparedness and thinking ahead, all within a disruptive and uncertain context. Sustainable responses that maximise business continuity, and provide solutions to practical challenges, are among the study-s recommendations.

Keywords: Business continuity, earthquake, education, sustainability

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819 Intrapreneurship Discovery: Standard Strategy to Boost Innovation inside Companies

Authors: Chiara Mansanta, Daniela Sani

Abstract:

This paper studies the concept of intrapreneurship discovery for innovation and technology development related to the manufacturing industries set up in the center of Italy, in Marche Region. The study underlined the key drivers of the innovation process and the main factors that influence innovation. Starting from a literature study on open innovation, this paper examines the role of human capital to support company’s development. The empirical part of the study is based on a survey to 151 manufacturing companies that represent the 34% of that universe at the regional level. The survey underlined the main KPI’s that influence companies in their decision processes; then tools for these decision processes are presented.

Keywords: Business model, decision making, intrapreneurship discovery, open innovation, standard methodology.

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818 Observation of the Correlations between Pair Wise Interaction and Functional Organization of the Proteins, in the Protein Interaction Network of Saccaromyces Cerevisiae

Authors: N. Tuncbag, T. Haliloglu, O. Keskin

Abstract:

Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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817 Facebook Spam and Spam Filter Using Artificial Neural Networks

Authors: Fahim A., Mutahira N. Naseem

Abstract:

Spam is any unwanted electronic message or material in any form posted too many people. As the world is growing as global world, social networking sites play an important role in making world global providing people from different parts of the world a platform to meet and express their views. Among different social networking sites Facebook become the leading one. With increase in usage different users start abusive use of Facebook by posting or creating ways to post spam. This paper highlights the potential spam types nowadays Facebook users’ faces. This paper also provide the reason how user become victim to spam attack. A methodology is proposed in the end discusses how to handle different types of spam.

Keywords: Artificial neural networks, Facebook spam, social networking sites, spam filter.

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816 Modeling Erosion Control in Oil Production Wells

Authors: Kenneth I.Eshiet, Yong Sheng

Abstract:

The sand production problem has led researchers into making various attempts to understand the phenomenon. The generally accepted concept is that the occurrence of sanding is due to the in-situ stress conditions and the induced changes in stress that results in the failure of the reservoir sandstone during hydrocarbon production from wellbores. By using a hypothetical cased (perforated) well, an approach to the problem is presented here by using Finite Element numerical modelling techniques. In addition to the examination of the erosion problem, the influence of certain key parameters is studied in order to ascertain their effect on the failure and subsequent erosion process. The major variables investigated include: drawdown, perforation depth, and the erosion criterion. Also included is the determination of the optimal mud pressure for given operational and reservoir conditions. The improved understanding between parameters enables the choice of optimal values to minimize sanding during oil production.

Keywords: Equivalent Plastic Strain, Erosion, Hydrocarbon Production.

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815 A Study of Relationship between Mountaineering Participation Motivation and Risk Perception

Authors: Yen-Chieh Wen, Ching-Hui Lin

Abstract:

The main purpose of this study is to analyze climbers involved in motivation and risk perception and analysis of the predictive ability of the risk perception "mountaineering" involved in motivation. This study used questionnaires, to have to climb the 3000m high mountain in Taiwan climbers object to carry out an investigation in order to non-random sampling, a total of 231 valid questionnaires were. After statistical analysis, the study found that: 1. Climbers the highest climbers involved in motivation "to enjoy the natural beauty of the fun. 2 climbers for climbers "risk perception" the highest: the natural environment of risk. 3. Climbers “seeking adventure stimulate", “competence achievement" motivation highly predictive of risk perception. Based on these findings, this study not only practices the recommendations of the outdoor leisure industry, and also related research proposals for future researchers.

Keywords: Mountaineering, motivation, risk perception, decision-making.

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814 Ethiopian Opposition Political Parties and Rebel Fronts: Past and Present

Authors: Wondwosen Teshome B.

Abstract:

In a representative democracy political parties promote vital competition on different policy issues and play essential roles by offering ideological alternatives. They also give channels for citizens- participation in government decision-making processes and they are significant conduits and interpreters of information about government. This paper attempts to examine how opposition political parties and rebel fronts emerged in Ethiopia, and examines their present conditions. In this paper, selected case studies of political parties and rebel fronts are included to highlight the status and the role of opposition groups in the country in the three successive administrations: Haile Selassie (1930-1974), Derg (1974- 1991), and EPRDF (1991-Present).

Keywords: Ethiopia, Hybrid regime, Incumbent, Multi-Partyelection, Opposition Party, Political Party, Rebel fronts.

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813 Application of “Multiple Risk Communicator“ to the Personal Information Leakage Problem

Authors: Mitsuhiro Taniyama, Yuu Hidaka, Masato Arai, Satoshi Kai, Hiromi Igawa, Hiroshi Yajima, Ryoichi Sasaki

Abstract:

Along with the progress of our information society, various risks are becoming increasingly common, causing multiple social problems. For this reason, risk communications for establishing consensus among stakeholders who have different priorities have become important. However, it is not always easy for the decision makers to agree on measures to reduce risks based on opposing concepts, such as security, privacy and cost. Therefore, we previously developed and proposed the “Multiple Risk Communicator" (MRC) with the following functions: (1) modeling the support role of the risk specialist, (2) an optimization engine, and (3) displaying the computed results. In this paper, MRC program version 1.0 is applied to the personal information leakage problem. The application process and validation of the results are discussed.

Keywords: Decision Making, Personal Information Leakage Problem, Risk Communication, Risk Management

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812 Decision Support Framework in Managerial Learning Environment for Organization

Authors: M. Mazhar Manzoor, Nasar.A, A. Sattar

Abstract:

In the open space of decision support system the mental impression of a manager-s decision has been the subject of large importance than the ordinary famous one, when helped by decision support system. Much of this study is an attempt to realize the relation of decision support system usage and decision outcomes that governs the system. For example, several researchers have proposed so many different models to analyze the linkage between decision support system processes and results of decision making. This study draws the important relation of manager-s mental approach with the use of decision support system. The findings of this paper are theoretical attempts to provide Decision Support System (DSS) in a way to exhibit and promote the learning in semi structured area. The proposed model shows the points of one-s learning improvements and maintains a theoretical approach in order to explore the DSS contribution in enhancing the decision forming and governing the system.

Keywords: Decision Support System , Learning Organization,

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811 Risk and Uncertainty in Aviation: A Thorough Analysis of System Vulnerabilities

Authors: C. V. Pietreanu, S. E. Zaharia, C. Dinu

Abstract:

Hazard assessment and risks quantification are key components for estimating the impact of existing regulations. But since regulatory compliance cannot cover all risks in aviation, the authors point out that by studying causal factors and eliminating uncertainty, an accurate analysis can be outlined. The research debuts by making delimitations on notions, as confusion on the terms over time has reflected in less rigorous analysis. Throughout this paper, it will be emphasized the fact that the variation in human performance and organizational factors represent the biggest threat from an operational perspective. Therefore, advanced risk assessment methods analyzed by the authors aim to understand vulnerabilities of the system given by a nonlinear behavior. Ultimately, the mathematical modeling of existing hazards and risks by eliminating uncertainty implies establishing an optimal solution (i.e. risk minimization).

Keywords: Control, human factor, optimization, risk management, uncertainty.

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810 Aquatic Modeling: An Interplay between Scales

Authors: Christina G. Siontorou

Abstract:

This paper presents an integrated knowledge-based approach to multi-scale modeling of aquatic systems, with a view to enhancing predictive power and aiding environmental management and policy-making. The basic phases of this approach have been exemplified in the case of a bay in Saronicos Gulf (Attiki, Greece). The results showed a significant problem with rising phytoplankton blooms linked to excessive microbial growth, arisen mostly due to increased nitrogen inflows; therefore, the nitrification/denitrification processes of the benthic and water column sub-systems have provided the quality variables to be monitored for assessing environmental status. It is thereby demonstrated that the proposed approach facilitates modeling choices and implementation option decisions, while it provides substantial support for knowledge and experience capitalization in long-term water management.

Keywords: Aquatic ecosystem, integrated modeling, multi-scale modeling, ontological platform.

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809 A New History Based Method to Handle the Recurring Concept Shifts in Data Streams

Authors: Hossein Morshedlou, Ahmad Abdollahzade Barforoush

Abstract:

Recent developments in storage technology and networking architectures have made it possible for broad areas of applications to rely on data streams for quick response and accurate decision making. Data streams are generated from events of real world so existence of associations, which are among the occurrence of these events in real world, among concepts of data streams is logical. Extraction of these hidden associations can be useful for prediction of subsequent concepts in concept shifting data streams. In this paper we present a new method for learning association among concepts of data stream and prediction of what the next concept will be. Knowing the next concept, an informed update of data model will be possible. The results of conducted experiments show that the proposed method is proper for classification of concept shifting data streams.

Keywords: Data Stream, Classification, Concept Shift, History.

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808 Using Degree of Adaptive (DOA) Model for Partner Selection in Supply Chain

Authors: Habibollah Javanmard

Abstract:

In order to reduce cost, increase quality, and for timely supplying production systems has considerably taken the advantages of supply chain management and these advantages are also competitive. Selection of appropriate supplier has an important role in improvement and efficiency of systems. The models of supplier selection which have already been used by researchers have considered selection one or more suppliers from potential suppliers but in this paper selecting one supplier as partner from one supplier that have minimum one period supplying to buyer is considered. This paper presents a conceptual model for partner selection and application of Degree of Adoptive (DOA) model for final selection. The attributes weight in this model is prepared through AHP model. After making the descriptive model, determining the attributes and measuring the parameters of the adaptive is examined in an auto industry of Iran(Zagross Khodro co.) and results are presented.

Keywords: Partnership, Degree of Adaptive, AHP, SupplyChain.

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807 Flexibility in Modular Furniture Systems in Open Offices, Famagusta, North Cyprus

Authors: E. Farjami, La. Mohammadzadeh Afshar, Li. Mohammadzade Afshar, A. Taran

Abstract:

Nowadays, flexibility introduced as a modern technology in furniture systems especially in interior planning design. According to results, the most important impact of these systems can be seen on open plan design that makes workspaces comfortable and increases the productivity of employees besides making good relationship between them. Briefly, there are some factors along with new systems in furniture design help create inappropriate space to make working better and easier while it has modular planning organization. It brings about some approaches to have a successful space for open offices with modular design and flexible furniture systems. These approaches have been investigated in open and close offices at Eastern Mediterranean University (EMU) in Famagusta, Cyprus, using information extracted from questionnaires.

Keywords: Flexibility, Flexible Furniture, Modular design, Open offices, Modular furniture systems.

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806 A Performance Model for Designing Network in Reverse Logistic

Authors: S. Dhib, S. A. Addouche, T. Loukil, A. Elmhamedi

Abstract:

In this paper, a reverse supply chain network is investigated for a decision making. This decision is surrounded by complex flows of returned products, due to the increasing quantity, the type of returned products and the variety of recovery option products (reuse, recycling, and refurbishment). The most important problem in the reverse logistic network (RLN) is to orient returned products to the suitable type of recovery option. However, returned products orientations from collect sources to the recovery disposition have not well considered in performance model. In this study, we propose a performance model for designing a network configuration on reverse logistics. Conceptual and analytical models are developed with taking into account operational, economic and environmental factors on designing network.

Keywords: Reverse logistics, Network design, Performance model, Open loop configuration.

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805 Balancing Neural Trees to Improve Classification Performance

Authors: Asha Rani, Christian Micheloni, Gian Luca Foresti

Abstract:

In this paper, a neural tree (NT) classifier having a simple perceptron at each node is considered. A new concept for making a balanced tree is applied in the learning algorithm of the tree. At each node, if the perceptron classification is not accurate and unbalanced, then it is replaced by a new perceptron. This separates the training set in such a way that almost the equal number of patterns fall into each of the classes. Moreover, each perceptron is trained only for the classes which are present at respective node and ignore other classes. Splitting nodes are employed into the neural tree architecture to divide the training set when the current perceptron node repeats the same classification of the parent node. A new error function based on the depth of the tree is introduced to reduce the computational time for the training of a perceptron. Experiments are performed to check the efficiency and encouraging results are obtained in terms of accuracy and computational costs.

Keywords: Neural Tree, Pattern Classification, Perceptron, Splitting Nodes.

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804 Two-Phase Optimization for Selecting Materialized Views in a Data Warehouse

Authors: Jiratta Phuboon-ob, Raweewan Auepanwiriyakul

Abstract:

A data warehouse (DW) is a system which has value and role for decision-making by querying. Queries to DW are critical regarding to their complexity and length. They often access millions of tuples, and involve joins between relations and aggregations. Materialized views are able to provide the better performance for DW queries. However, these views have maintenance cost, so materialization of all views is not possible. An important challenge of DW environment is materialized view selection because we have to realize the trade-off between performance and view maintenance. Therefore, in this paper, we introduce a new approach aimed to solve this challenge based on Two-Phase Optimization (2PO), which is a combination of Simulated Annealing (SA) and Iterative Improvement (II), with the use of Multiple View Processing Plan (MVPP). Our experiments show that 2PO outperform the original algorithms in terms of query processing cost and view maintenance cost.

Keywords: Data warehouse, materialized views, view selectionproblem, two-phase optimization.

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803 Concurrency without Locking in Parallel Hash Structures used for Data Processing

Authors: Ákos Dudás, Sándor Juhász

Abstract:

Various mechanisms providing mutual exclusion and thread synchronization can be used to support parallel processing within a single computer. Instead of using locks, semaphores, barriers or other traditional approaches in this paper we focus on alternative ways for making better use of modern multithreaded architectures and preparing hash tables for concurrent accesses. Hash structures will be used to demonstrate and compare two entirely different approaches (rule based cooperation and hardware synchronization support) to an efficient parallel implementation using traditional locks. Comparison includes implementation details, performance ranking and scalability issues. We aim at understanding the effects the parallelization schemes have on the execution environment with special focus on the memory system and memory access characteristics.

Keywords: Lock-free synchronization, mutual exclusion, parallel hash tables, parallel performance

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802 Easy-Interactive Ordering of the Pareto Optimal Set with Imprecise Weights

Authors: Maria Kalinina, Aron Larsson, Leif Olsson

Abstract:

In the multi objective optimization, in the case when generated set of Pareto optimal solutions is large, occurs the problem to select of the best solution from this set. In this paper, is suggested a method to order of Pareto set. Ordering the Pareto optimal set carried out in conformity with the introduced distance function between each solution and selected reference point, where the reference point may be adjusted to represent the preferences of a decision making agent. Preference information about objective weights from a decision maker may be expressed imprecisely. The developed elicitation procedure provides an opportunity to obtain surrogate numerical weights for the objectives, and thus, to manage impreciseness of preference. The proposed method is a scalable to many objectives and can be used independently or as complementary to the various visualization techniques in the multidimensional case.

Keywords: Imprecise weights, Multiple objectives, Pareto optimality, Visualization.

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801 A Centroid Ranking Approach Based Fuzzy MCDM Model

Authors: T. C. Chu, S.H. Wu

Abstract:

This paper suggests ranking alternatives under fuzzy MCDM (multiple criteria decision making) via an centroid based ranking approach, where criteria are classified to benefit qualitative, benefit quantitative and cost quantitative ones. The ratings of alternatives versus qualitative criteria and the importance weights of all criteria are assessed in linguistic values represented by fuzzy numbers. The membership function for the final fuzzy evaluation value of each alternative can be developed through α-cuts and interval arithmetic of fuzzy numbers. The distance between the original point and the relative centroid is applied to defuzzify the final fuzzy evaluation values in order to rank alternatives. Finally a numerical example demonstrates the computation procedure of the proposed model.

Keywords: Fuzzy MCDM, Criteria, Fuzzy number, Ranking, Relative centroid.

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800 Study on Scheduling of the Planning Method Using the Web-based Visualization System in a Shipbuilding Block Assembly Shop

Authors: A. Eui Koog Ahn, B. Gi-Nam Wang, C. Sang C. Park

Abstract:

Higher productivity and less cost in the ship manufacturing process are required to maintain the international competitiveness of morden manufacturing industries. In shipbuilding, however, the Engineering To Order (ETO) production method and production process is very difficult. Thus, designs change frequently. In accordance with production, planning should be set up according to scene changes. Therefore, fixed production planning is very difficult. Thus, a scheduler must first make sketchy plans, then change the plans based on the work progress and modifications. Thus, data sharing in a shipbuilding block assembly shop is very important. In this paper, we proposed to scheduling method applicable to the shipbuilding industry and decision making support system through web based visualization system.

Keywords: Shipbuilding, Monitoring, Block assembly shop, Visualization

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799 Sustainable Development in Disaster Affected Rural Areas: The Case of Dinar Villages

Authors: Nese Dikmen

Abstract:

Post-disaster reconstruction projects offer opportunities to facilitate physical, social and economic development and to reduce future hazard vulnerability long after the disasters. Sustainability of post-disaster reconstruction project conducted in the villages of Dinar following the 1995 earthquake was investigated in this paper. Officials of the Government who were involved in the project were interviewed. Besides, two field surveys were done in 12 villages of Dinar in winter months of 2008. Beneficiaries were interviewed and physical, socio-cultural and economic impacts of the reconstruction were examined. The research revealed that the postdisaster reconstruction project has negative aspects from the point view of sustainability. The physical, socio-cultural and economic factors were not considered during decision making process of the project.

Keywords: Dinar, Post-disaster reconstruction, Sustainable development, Turkey.

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798 A Case-Based Reasoning-Decision Tree Hybrid System for Stock Selection

Authors: Yaojun Wang, Yaoqing Wang

Abstract:

Stock selection is an important decision-making problem. Many machine learning and data mining technologies are employed to build automatic stock-selection system. A profitable stock-selection system should consider the stock’s investment value and the market timing. In this paper, we present a hybrid system including both engage for stock selection. This system uses a case-based reasoning (CBR) model to execute the stock classification, uses a decision-tree model to help with market timing and stock selection. The experiments show that the performance of this hybrid system is better than that of other techniques regarding to the classification accuracy, the average return and the Sharpe ratio.

Keywords: Case-based reasoning, decision tree, stock selection, machine learning.

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797 Performance Analysis of Artificial Neural Network with Decision Tree in Prediction of Diabetes Mellitus

Authors: J. K. Alhassan, B. Attah, S. Misra

Abstract:

Human beings have the ability to make logical decisions. Although human decision - making is often optimal, it is insufficient when huge amount of data is to be classified. Medical dataset is a vital ingredient used in predicting patient’s health condition. In other to have the best prediction, there calls for most suitable machine learning algorithms. This work compared the performance of Artificial Neural Network (ANN) and Decision Tree Algorithms (DTA) as regards to some performance metrics using diabetes data. WEKA software was used for the implementation of the algorithms. Multilayer Perceptron (MLP) and Radial Basis Function (RBF) were the two algorithms used for ANN, while RegTree and LADTree algorithms were the DTA models used. From the results obtained, DTA performed better than ANN. The Root Mean Squared Error (RMSE) of MLP is 0.3913 that of RBF is 0.3625, that of RepTree is 0.3174 and that of LADTree is 0.3206 respectively.

Keywords: Artificial neural network, classification, decision tree, diabetes mellitus.

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796 Evaluating New Service Development Performance Based on Multigranular Linguistic Assessment

Authors: Wen-Pai Wang, Mei-Ching Tang

Abstract:

The service sector continues to grow and the percentage of GDP accounted for by service industries keeps increasing. The growth and importance of service to an economy is not just a phenomenon of advanced economies, service is now a majority of the world gross domestic products. However, the performance evaluation process of new service development problems generally involves uncertain and imprecise data. This paper presents a 2-tuple fuzzy linguistic computing approach to dealing with heterogeneous information and information loss problems while the processes of subjective evaluation integration. The proposed method based on group decision-making scenario to assist business managers in measuring performance of new service development manipulates the heterogeneity integration processes and avoids the information loss effectively.

Keywords: Heterogeneity, Multigranular linguistic computing, New service development, Performance evaluation.

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795 Necessity of using an Optimum Business Model in High-Tech Firms, Nanotechnology Case Study

Authors: Reza Davoodi, Jahangir Yadollahi Farsi, Roya Naseri

Abstract:

In the way of growing and developing firms especially high-tech firms, on many occasions manager of firm is mainly involved in solving problems of his business and decision making about executive activities of the firm, while besides executive measures, attention to planning of firm's success and growth way and application of long experience and sagacity in designing business model are vital and necessary success in a business is achieved as a result of different factors, one of the most important of them is designing and performing an optimal business model at the beginning of the firm's work. This model is determining the limit of profitability achieved by innovation and gained value added. Therefore, business model is the process of connecting innovation environment and technology with economic environment and business and is important for succeeding modern businesses considering their traits.

Keywords: Business Model (BM), Nanotechnology, High- TechFirms.

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794 Making a ‘Once-upon-a-Time’ Mythology in Kazuo Ishiguro’s The Buried Giant

Authors: Masami Usui

Abstract:

Kazuo Ishiguro’s challenging novel, The Buried Giant, embodies how contemporary writers and readers have to discover the voices buried in our history. By avoiding setting or connecting the modern and contemporary historical incidents such as World War II this time, Ishiguro ventures into retelling myth, transfiguring historical facts, and revealing what has been forgotten in a process of establishing history and creating mythology. As generally known, modernist writers in the twentieth century employed materials from authorized classical mythologies, especially Greek mythology. As an heir of this tradition, Ishiguro imposes his mission of criticizing the repeatedly occurring yet easily-forgotten history of dictatorship and a slaughter on mythology based on King Arthur and its related heroes and myths in Britain. On an open ground, Ishiguro can start his own mythical story and space.

Keywords: English literature, fantasy, global literature, mythology.

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793 Hospital Facility Location Selection Using Permanent Analytics Process

Authors: C. Ardil

Abstract:

In this paper, a new MCDMA approach, the permanent analytics process is proposed to assess the immovable valuation criteria and their significance in the placement of the healthcare facility. Five decision factors are considered for the value and selection of immovables. In the multiple factor selection problems, the priority vector of the criteria used to compare several immovables is first determined using the permanent analytics method, a mathematical model for the multiple criteria decisionmaking process. Then, to demonstrate the viability and efficacy of the suggested approach, twenty potential candidate locations were evaluated using the hospital site selection problem's decision criteria. The ranking accuracy of estimation was evaluated using composite programming, which took into account both the permanent analytics process and the weighted multiplicative model. 

Keywords: Hospital Facility Location Selection, Permanent Analytics Process, Multiple Criteria Decision Making (MCDM)

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792 Exploring the Combinatorics of Motif Alignments Foraccurately Computing E-values from P-values

Authors: T. Kjosmoen, T. Ryen, T. Eftestøl

Abstract:

In biological and biomedical research motif finding tools are important in locating regulatory elements in DNA sequences. There are many such motif finding tools available, which often yield position weight matrices and significance indicators. These indicators, p-values and E-values, describe the likelihood that a motif alignment is generated by the background process, and the expected number of occurrences of the motif in the data set, respectively. The various tools often estimate these indicators differently, making them not directly comparable. One approach for comparing motifs from different tools, is computing the E-value as the product of the p-value and the number of possible alignments in the data set. In this paper we explore the combinatorics of the motif alignment models OOPS, ZOOPS, and ANR, and propose a generic algorithm for computing the number of possible combinations accurately. We also show that using the wrong alignment model can give E-values that significantly diverge from their true values.

Keywords: Motif alignment, combinatorics, p-value, E-value, OOPS, ZOOPS, ANR.

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