Search results for: upper bound analysis.

Authors: Najiba Ouled Omar, Azza Harbaoui, Henda Ben Ghezala

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Current research practices sentiment analysis with a focus on social networks, DEfi Fouille de Texte (DEFT) (Text Mining Challenge) evaluation campaign focuses on opinion mining and sentiment analysis on social networks, especially social network Twitter. It aims to confront the systems produced by several teams from public and private research laboratories. DEFT offers participants the opportunity to work on regularly renewed themes and proposes to work on opinion mining in several editions. The purpose of this article is to scrutinize and analyze the works relating to opinions mining and sentiment analysis in the Twitter social network realized by DEFT. It examines the tasks proposed by the organizers of the challenge and the methods used by the participants.

Keywords: Opinion mining, sentiment analysis, emotion, polarity, annotation, OSEE, figurative language, DEFT, Twitter, Tweet.

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Authors: Takashi Ueda, Shinichi Enoki

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Forging parts is used to automobiles; because, they have high strength and it is possible to press them into complicated shape. When itis possible to manufacture hollow forging parts, it leads to reduce weightof the automobiles. But, hollow forging parts are confined to axisymmetrical shape. Hollowforging parts that were pressed to complicated shape are expected. Therefore, we forge a blank that aluminum alloy was inserted in stainless steel. After that, we can providecomplex forging parts that are reduced weight,ifit is possible to be melted the aluminum alloy away by using different of melting points.It is necessary to establish heat forging analysis methodon blank consist of stainless steel and aluminum alloy. Because,this forging is different from conventional forging and this technology is not confirmed. In this study, we compared forging experiment with numerical analysis on the view point of forming load and shape after forming and establish how to set the material temperaturesof two metals and material property of stainless steel on the analysis method. Consequently, temperature difference of stainless steel and aluminum alloy was obtained by experiment. We got material property of stainless steel on forging experimental by compression tests. We had compared numerical analysis that was used the temperature difference of two metals and the material property of stainless steel on forging experimental with forging experiment. Forging analysis method on blankconsist of two metals was established by result of numerical analysis having agreedwith result of forging experiment.

Keywords: Forging, lightweight, analysis, hollow.

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Authors: Niina M. Nissinen

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This paper introduces an approach to construct a set of criteria for evaluating alternative options. Content analysis was used to collet criterion elements. Then the elements were classified and organized yielding to hierarchic structure. The reliability of the constructed criteria was evaluated in an experiment. Finally the criteria were used to evaluate alternative options indecision-making.

Keywords: Conceptual analysis, Content Analysis, Criteria, Decision-Making, Evaluation of Candidates

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Authors: Dong-Jae Kang, Nam-Woo Kim, Duk-Joo Son, Sung-In Jung

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According to dramatic growth of internet services, an easy and prompt service deployment has been important for internet service providers to successfully maintain time-to-market. Before global service deployment, they have to pay the big cost for service evaluation to make a decision of the proper system location, system scale, service delay and so on. But, intra-Lab evaluation tends to have big gaps in the measured data compared with the realistic situation, because it is very difficult to accurately expect the local service environment, network congestion, service delay, network bandwidth and other factors. Therefore, to resolve or ease the upper problems, we propose multiple cloud based GPES Broker system and use case that helps internet service providers to alleviate the above problems in beta release phase and to make a prompt decision for their service launching. By supporting more realistic and reliable evaluation information, the proposed GPES Broker system saves the service release cost and enables internet service provider to make a prompt decision about their service launching to various remote regions.

Keywords: GPES Broker system, Cloud Service Broker, Multiple Cloud, Global performance evaluation service (GPES), Service provisioning

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Authors: M.A. Hosseini, P. Ebrahimi Naghani

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In this research work, a novel parallel manipulator with high positioning and orienting rate is introduced. This mechanism has two rotational and one translational degree of freedom. Kinematics and Jacobian analysis are investigated. Moreover, workspace analysis and optimization has been performed by using genetic algorithm toolbox in Matlab software. Because of decreasing moving elements, it is expected much more better dynamic performance with respect to other counterpart mechanisms with the same degrees of freedom. In addition, using couple of cylindrical and revolute joints increased mechanism ability to have more extended workspace.

Keywords: Kinematics, Workspace, 3-CRS/PU, Parallel robot

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Authors: Afrooz Moatari Kazerouni

Abstract:

In a competitive production environment, critical decision making are based on data resulted by random sampling of product units. Efficiency of these decisions depends on data quality and also their reliability scale. This point leads to the necessity of a reliable measurement system. Therefore, the conjecture process and analysing the errors contributes to a measurement system known as Measurement System Analysis (MSA). The aim of this research is on determining the necessity and assurance of extensive development in analysing measurement systems, particularly with the use of Repeatability and Reproducibility Gages (GR&R) to improve physical measurements. Nowadays in productive industries, repeatability and reproducibility gages released so well but they are not applicable as well as other measurement system analysis methods. To get familiar with this method and gain a feedback in improving measurement systems, this survey would be on “ANOVA" method as the most widespread way of calculating Repeatability and Reproducibility (R&R).

Keywords: Analysis of Variance (ANOVA), MeasurementSystem Analysis (MSA), Part-Operator interaction effect, Repeatability and Reproducibility.

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Authors: Qasim Kriri, Harsh B. Desai

Abstract:

Water supply and sanitation in Saudi Arabia is portrayed by difficulties and accomplishments. One of the fundamental difficulties is water shortage. With a specific end goal to beat water shortage, significant ventures have been attempted in sea water desalination, water circulation, sewerage, and wastewater treatment. The motivation behind Statistical Process Control (SPC) is to decide whether the execution of a procedure is keeping up an acceptable quality level [AQL]. SPC is an analytical decision-making method. A fundamental apparatus in the SPC is the Control Charts, which follow the inconstancy in the estimations of the item quality attributes. By utilizing the suitable outline, administration can decide whether changes should be made with a specific end goal to keep the procedure in charge. The two most important quality factors in the distilled water which were taken into consideration were pH (Potential of Hydrogen) and TDS (Total Dissolved Solids). There were three stages at which the quality checks were done. The stages were as follows: (1) Water at the source, (2) water after chemical treatment & (3) water which is sent for packing. The upper specification limit, central limit and lower specification limit are taken as per Saudi water standards. The procedure capacity to accomplish the particulars set for the quality attributes of Berain water Factory chose to be focused by the proposed SPC system.

Keywords: Acceptable quality level, statistical quality control, control charts, process charts.

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Authors: Kimia Khoshdel Vajari, Saber Saffar

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Reducing the residual stresses caused by welding is desirable for the industry. The effect of welding sequence, as well as the effect of yield stress on the number of residual stresses generated in Inconel X750 superalloy sheets and beams, have been investigated. The finite element model used in this research is a three-dimensional thermal and mechanical model, and the type of analysis is indirect coupling. This analysis is done in two stages. First, thermal analysis is performed, and then the thermal changes of the first analysis are used as the applied load in the second analysis. ABAQUS has been used for modeling, and the Dflux subroutine has been used in the Fortran programming environment to move the arc and the molten pool. The results of this study show that the amount of tensile residual stress in symmetric, discontinuous, and symmetric-discontinuous welds is reduced to a maximum of 27%, 54%, and 37% compared to direct welding, respectively. The results also show that the amount of residual stresses created by welding increases linearly with increasing yield stress with a slope of 40%.

Keywords: Residual stress, X750 superalloy, finite element, welding, thermal analysis.

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Authors: B. X. Tchomeni, A. A. Alugongo, T. B. Tengen

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In this paper, de Laval rotor system has been characterized by a hinge model and its transient response numerically treated for a dynamic solution. The effect of the ensuing non-linear disturbances namely rub and breathing crack is numerically simulated. Subsequently, three analysis methods: Orbit Analysis, Fast Fourier Transform (FFT), and Wavelet Transform (WT) are employed to extract features of the vibration signal of the faulty system. An analysis of the system response orbits clearly indicates the perturbations due to the rotor-to-stator contact. The sensitivities of WT to the variation in system speed have been investigated by Continuous Wavelet Transform (CWT). The analysis reveals that features of crack, rubs and unbalance in vibration response can be useful for condition monitoring. WT reveals its ability to detect nonlinear signal, and obtained results provide a useful tool method for detecting machinery faults.

Keywords: Continuous wavelet, crack, discrete wavelet, high acceleration, low acceleration, nonlinear, rotor-stator, rub.

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Authors: Yi Hong, Zhao Yang Dong

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This paper presents the performance analysis of space-time trellis codes in orthogonal frequency division multiplexing systems (STTC-OFDMs) over quasi-static frequency selective fading channels. In particular, the effect of channel delay distributions on the code performance is discussed. For a STTCOFDM over multiple-tap channels, two extreme conditions that produce the largest minimum determinant are highlighted. The analysis also proves that the corresponding coding gain increases with the maximum tap delay. The performance of STTC-OFDM, under various channel conditions, is evaluated by simulation. It is shown that the simulation results agree with the performance analysis.

Keywords: Space-time trellis code, OFDM, delay profile.

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Authors: Phang Chang, Phang Piau

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Wavelet transform or wavelet analysis is a recently developed mathematical tool in applied mathematics. In numerical analysis, wavelets also serve as a Galerkin basis to solve partial differential equations. Haar transform or Haar wavelet transform has been used as a simplest and earliest example for orthonormal wavelet transform. Since its popularity in wavelet analysis, there are several definitions and various generalizations or algorithms for calculating Haar transform. Fast Haar transform, FHT, is one of the algorithms which can reduce the tedious calculation works in Haar transform. In this paper, we present a modified fast and exact algorithm for FHT, namely Modified Fast Haar Transform, MFHT. The algorithm or procedure proposed allows certain calculation in the process decomposition be ignored without affecting the results.

Keywords: Fast Haar Transform, Haar transform, Wavelet analysis.

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Authors: Saleem Z. Ramadan

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In this paper, a model is proposed to determine the life distribution parameters of the useful life region for the PV system utilizing a combination of non-parametric and linear regression analysis for the failure data of these systems. Results showed that this method is dependable for analyzing failure time data for such reliable systems when the data is scarce.

Keywords: Masking, Bathtub model, reliability, non-parametric analysis, useful life.

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Authors: Sungnam Hong, Sun-Kyu Park, Dooyong Cho, Jinwoong Choi

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In this paper, a strategy for long-span bridge disaster response was developed, divided into risk analysis, business impact analysis, and emergency response plan. At the risk analysis stage, the critical risk was estimated. The critical risk was “car accident."The critical process by critical-risk classification was assessed at the business impact analysis stage. The critical process was the task related to the road conditions and traffic safety. Based on the results of the precedent analysis, an emergency response plan was established. By making the order of the standard operating procedures clear, an effective plan for dealing with disaster was formulated. Finally, a prototype software was developed based on the research findings. This study laid the foundation of an information-technology-based disaster response guideline and is significant in that it computerized the disaster response plan to improve the plan-s accessibility.

Keywords: Emergency response; Long-span bridge; Disaster management; Standard operating procedure; Ubiquitous.

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Authors: Omid A. Zargar

Abstract:

Material damages dynamic analysis is difficult to deal with different material geometry and mechanism. In addition, it is difficult to measure the dynamic behavior of cracks, debond and delamination inside the material. Different simulation methods are developed in recent years for different physical features of mechanical systems like vibration and acoustic. Nonlinear fractures are analyzed and identified for different locations in this paper. The main idea of this work is to perform dynamic analysis on different types of materials (from normal homogeneous material to complex composite laminates). Technical factors like cracks, voids, interfaces and the damages’ locations are evaluated. In this project the modal analysis is performed on different types of materials. The results could be helpful in finding modal frequencies, natural frequencies, Time domain and fast Fourier transform (FFT) in industrial applications.

Keywords: Finite element method, dynamic analysis, vibration and acoustic, composite, crack, delamination.

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Authors: Chiang-Ho Cheng, An-Shik Yang, Hong-Yih Cheng, Ming-Yu Lai

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This paper presents the design and fabrication of a novel piezoelectric actuator for a gas micro pump with check valve having the advantages of miniature size, light weight and low power consumption. The micro pump is designed to have eight major components, namely a stainless steel upper cover layer, a piezoelectric actuator, a stainless steel diaphragm, a PDMS chamber layer, two stainless steel channel layers with two valve seats, a PDMS check valve layer with two cantilever-type check valves and an acrylic substrate. A prototype of the gas micro pump, with a size of 52 mm × 50 mm × 5.0 mm, is fabricated by precise manufacturing. This device is designed to pump gases with the capability of performing the self-priming and bubble-tolerant work mode by maximizing the stroke volume of the membrane as well as the compression ratio via minimization of the dead volume of the micro pump chamber and channel. By experiment apparatus setup, we can get the real-time values of the flow rate of micro pump and the displacement of the piezoelectric actuator, simultaneously. The gas micro pump obtained higher output performance under the sinusoidal waveform of 250 Vpp. The micro pump achieved the maximum pumping rates of 1185 ml/min and back pressure of 7.14 kPa at the corresponding frequency of 120 and 50 Hz.

Keywords: PDMS, Check valve, Micro pump, Piezoelectric.

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Authors: Sanga Monthatipkul, Pio Iovenitti, Igor Sbarski

Abstract:

Bicycle usage for exercise, recreation, and commuting to work in Australia shows that pedal cycling is the fourth most popular activity with 10.6% increase in participants between 2001 and 2007. As with other means of transport, accident and injury becomes common although mandatory bicycle helmet wearing has been introduced. The research aims to develop a face surrogate made of sandwich of rigid foam and rubber sheets to represent human facial bone under blunt impact. The facial surrogate will serve as an important test device for further development of facial-impact protection for cyclist. A test procedure was developed to simulate the energy of impact and record data to evaluate the effect of impact on facial bones. Drop tests were performed to establish a suitable combination of materials. It was found that the sandwich structure of rigid extruded-polystyrene foam (density of 40 kg/m3 with a pattern of 6-mm-holes), Neoprene rubber sponge, and Abrasaflex rubber backing, had impact characteristics comparable to that of human facial bone. In particular, the foam thickness of 30 mm and 25 mm was found suitable to represent human zygoma (cheekbone) and maxilla (upper-jaw bone), respectively.

Keywords: Facial impact protection, face surrogate, cyclist, accident prevention

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Authors: Zare Aliabad, H., Mirzaei, S.

Abstract:

This work presents a theoretical investigation of the simultaneous absorption of CO2 and H2S into aqueous solutions of MDEA and DEA. In this process the acid components react with the basic alkanolamine solution via an exothermic, reversible reaction in a gas/liquid absorber. The use of amine solvents for gas sweetening has been investigated using process simulation programs called HYSYS and ASPEN. We use Electrolyte NRTL and Amine Package and Amines (experimental) equation of state. The effects of temperature and circulation rate and amine concentration and packed column and murphree efficiency on the rate of absorption were studied. When lean amine flow and concentration increase, CO2 and H2S absorption increase too. With the improvement of inlet amine temperature in absorber, CO2 and H2S penetrate to upper stages of absorber and absorption of acid gases in absorber decreases. The CO2 concentration in the clean gas can be greatly influenced by the packing height, whereas for the H2S concentration in the clean gas the packing height plays a minor role. HYSYS software can not estimate murphree efficiency correctly and it applies the same contributions in all diagrams for HYSYS software. By improvement in murphree efficiency, maximum temperature of absorber decrease and the location of reaction transfer to the stages of bottoms absorber and the absorption of acid gases increase.

Keywords: Absorber, DEA, MDEA, Simulation.

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Authors: Po-Jen Su, Huann-Ming Chou

Abstract:

In this article, we used the residual correction method to deal with transient thermoelastic problems with a hollow spherical region when the continuum medium possesses spherically isotropic thermoelastic properties. Based on linear thermoelastic theory, the equations of hyperbolic heat conduction and thermoelastic motion were combined to establish the thermoelastic dynamic model with consideration of the deformation acceleration effect and non-Fourier effect under the condition of transient thermal shock. The approximate solutions of temperature and displacement distributions are obtained using the residual correction method based on the maximum principle in combination with the finite difference method, making it easier and faster to obtain upper and lower approximations of exact solutions. The proposed method is found to be an effective numerical method with satisfactory accuracy. Moreover, the result shows that the effect of transient thermal shock induced by deformation acceleration is enhanced by non-Fourier heat conduction with increased peak stress. The influence on the stress increases with the thermal relaxation time.

Keywords: Maximum principle, non-Fourier heat conduction, residual correction method, thermo-elastic response.

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Authors: Hei-Chia Wang, Wei-Pin Chiu

Abstract:

As research performance in academia is treated as one of indices for national competency, many countries devote much attention and resources to increasing their research performance. Understand the research trend is the basic step to improve the research performance. The goal of this research is to design an analysis system to evaluate research trends from analyzing data from different countries. In this paper, information system researches in Taiwan and other countries, including Asian countries and prominent countries represented by the Group of Eight (G8) is used as example. Our research found the trends are varied in different countries. Our research suggested that Taiwan-s scholars can pay more attention to interdisciplinary applications and try to increase their collaboration with other countries, in order to increase Taiwan's competency in the area of information science.

Keywords: Bibliometric analysis, research trend, scientometric analysis.

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Authors: Shruti Taksali

Abstract:

This paper focuses on the analysis of Nanoptenna for extreme fast communication. The Nanoptenna is basically a nano antenna designed for communication at optical range of frequencies. Since, this range of frequencies includes the visible spectrum of the light, so there is a high possibility of the data transfer at high rates and extreme fast communication (XFC). The shape chosen for the analysis is a bow tie structure due to its various characteristics of electric field enhancement.

Keywords: Nanoptenna, communication, optical range, XFC.

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Authors: Maria Istvanova

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The acquisition of the correct pronunciation in Chinese is closely linked to the initial phase of the study. Based on the contrastive analysis, we determine the differences in the pronunciation of stop consonants in Chinese and Slovak taking into consideration the place and manner of articulation to gain a better understanding of the students' main difficulties in the process of acquiring correct pronunciation of Chinese stop consonants. We employ the software Praat for the analysis of the recorded samples with an emphasis on the pronunciation of the students with a varying command of Chinese. The comparison of the voice onset time (VOT) length for the individual consonants in the students' pronunciation and the pronunciation of the native speaker exposes the differences between the correct pronunciation and the deviant pronunciation of the students.

Keywords: Chinese, contrastive analysis, Praat, pronunciation, Slovak.

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Authors: H. Ahmed, A. Schlenkhoff, R. Rousta, R. Abdelaziz

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Vertical slotted walls can be used as permeable breakwaters to provide economical and environmental protection from undesirable waves and currents inside the port. The permeable breakwaters are partially protection and have been suggested to overcome the environmental disadvantages of fully protection breakwaters. For regular waves a semi-analytical model is based on an eigenfunction expansion method and utilizes a boundary condition at the surface of each wall are developed to detect the energy dissipation through the slots. Extensive laboratory tests are carried out to validate the semi-analytic models. The structure of the physical model contains two walls and it consists of impermeable upper and lower part, where the draft is based a decimal multiple of the total depth. The middle part is permeable with a porosity of 50%. The second barrier is located at a distant of 0.5, 1, 1.5 and 2 times of the water depth from the first one. A comparison of the theoretical results with previous studies and experimental measurements of the present study show a good agreement and that, the semi-analytical model is able to adequately reproduce most the important features of the experiment.

Keywords: Permeable breakwater, double vertical slotted walls, semi-analytical model, transmission coefficient, reflection coefficient, energy dissipation coefficient.

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Authors: Yongyoon Suh, Yongtae Park

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The interaction among information and communication technology (ICT) industries is a recently ubiquitous phenomenon through fixed-mobile integration. To monitor the impact of interaction, previous research has mainly focused on measuring spillover effect among ICT industries using various methods. Among others, inter-industry analysis is one of the useful methods for examining spillover effect between industries. However, more complex ICT industries become, more important the impact within an industry is. Inter-industry analysis is limited in mirroring intra-relationships within an industry. Thus, this study applies the analytic network process (ANP) to measure the spillover effect, capturing all of the intra and inter-relationships. Using ANP-based intra and inter-industry analysis, the spillover effect is effectively measured, mirroring the complex structure of ICT industries. A main ICT industry and its linkages are also explored to show the current structure of ICT industries. The proposed approach is expected to allow policy makers to understand interactions of ICT industries and their impact.

Keywords: ANP, intra and inter-industry analysis, spillover effect

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Authors: Itgel Bayarsaikhan, Jimin Lee, Sejong Oh

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Classification is one of the primary themes in computational biology. The accuracy of classification strongly depends on quality of a dataset, and we need some method to evaluate this quality. In this paper, we propose a new graphical analysis method using 'Membership-Deviation Graph (MDG)' for analyzing quality of a dataset. MDG represents degree of membership and deviations for instances of a class in the dataset. The result of MDG analysis is used for understanding specific feature and for selecting best feature for classification.

Keywords: feature, classification, machine learning algorithm.

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Authors: K. -H. Yang

Abstract:

In the past, the quay crane operations have been well studied. There were a certain number of scheduling algorithms for quay crane operations, but without considering some nuisance factors that might disrupt the quay crane operations. For example, bad grapples make a crane unable to load or unload containers or a sudden strong breeze stops operations temporarily. Although these disruptive conditions randomly occur, they influence the efficiency of quay crane operations. The disruption is not considered in the operational procedures nor is evaluated in advance for its impacts. This study applies simulation and optimization approaches to develop structures of pre-analysis and post-analysis for the Quay Crane Scheduling Problem to deal with disruptive scenarios for quay crane operation. Numerical experiments are used for demonstrations for the validity of the developed approaches.

Keywords: Disruptive Quay Crane Scheduling, pre-analysis, post-analysis, disruption.

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Authors: Saule Mussabekova, Samal Abzhanova

Abstract:

The Kazakh Language Fluency Test, based on the IELTS exam, was implemented in 2012 at Nazarbayev University in Astana, Kazakhstan. We would like to share our experience in developing this exam and some exam results with other language instructors. In this paper, we will cover all these peculiarities and their related issues. The Kazakh Language Fluency Test is a young exam. During its development, we faced many difficulties. One of the goals of the university and the country is to encourage fluency in the Kazakh language for all citizens of the Republic. Nazarbayev University has introduced a Kazakh language program to assist in achieving this goal. This policy is one-step in ensuring that NU students have a thorough understanding of the Kazakh language through a fluency test based on the International English Language Testing System (IELTS). The Kazakh Language Fluency Test exam aims to determine student’s knowledge of Kazakh language. The fact is that there are three types of students at Nazarbayev University: Kazakh-speaking heritage learners, Russian-speaking and English-speaking students. Unfortunately, we have Kazakh students who do not speak Kazakh. All students who finished school with Russian language instruction are given Kazakh Language Fluency Test in order to determine their Kazakh level. After the test exam, all students can choose appropriate Kazakh course: Basic Kazakh, Intermediate Kazakh and Upper-Intermediate Kazakh. The Kazakh Language Fluency Test consists of four parts: Listening, Reading, Writing and Speaking. They are taken on the same day in the abovementioned order.

Keywords: Diagnostic language test, Kazakh language, placement test, test result.

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Authors: Hari Mohan Kushwaha, Santosh K. Sahu

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In the present study, analysis of heat transfer is carried out in the slip flow region for the fluid flowing between two parallel plates by employing the asymmetric heat fluxes at surface of the plates. The flow is assumed to be hydrodynamically and thermally fully developed for the analysis. The second order velocity slip and viscous dissipation effects are considered for the analysis. Closed form expressions are obtained for the Nusselt number as a function of Knudsen number and modified Brinkman number. The limiting condition of the present prediction for Kn = 0, Kn2 = 0, and Brq1 = 0 is considered and found to agree well with other analytical results.

Keywords: Knudsen Number, Modified Brinkman Number, Slip Flow, Velocity Slip.

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Authors: A. Hossein Sahoolizadeh, B. Zargham Heidari, C. Hamid Dehghani

Abstract:

In this paper, a new face recognition method based on PCA (principal Component Analysis), LDA (Linear Discriminant Analysis) and neural networks is proposed. This method consists of four steps: i) Preprocessing, ii) Dimension reduction using PCA, iii) feature extraction using LDA and iv) classification using neural network. Combination of PCA and LDA is used for improving the capability of LDA when a few samples of images are available and neural classifier is used to reduce number misclassification caused by not-linearly separable classes. The proposed method was tested on Yale face database. Experimental results on this database demonstrated the effectiveness of the proposed method for face recognition with less misclassification in comparison with previous methods.

Keywords: Face recognition Principal component analysis, Linear discriminant analysis, Neural networks.

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Authors: Dhananjay C. Joshi, Jung-Hsin Lin

Abstract:

Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.

Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations

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Authors: Alexandra Oliveros, Miguel Sotaquirá

Abstract:

DNA microarray technology is widely used by geneticists to diagnose or treat diseases through gene expression. This technology is based on the hybridization of a tissue-s DNA sequence into a substrate and the further analysis of the image formed by the thousands of genes in the DNA as green, red or yellow spots. The process of DNA microarray image analysis involves finding the location of the spots and the quantification of the expression level of these. In this paper, a tool to perform DNA microarray image analysis is presented, including a spot addressing method based on the image projections, the spot segmentation through contour based segmentation and the extraction of relevant information due to gene expression.

Keywords: Contour segmentation, DNA microarrays, edge detection, image processing, segmentation, spot addressing.

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