Search results for: Factor analysis model

Authors: Huynh Quyet Thang, Le Hai Quan

Abstract:

Interaction Model plays an important role in Modelbased Intelligent Interface Agent Architecture for developing Intelligent User Interface. In this paper we are presenting some improvements in the algorithms for development interaction model of interface agent including: the action segmentation algorithm, the action pair selection algorithm, the final action pair selection algorithm, the interaction graph construction algorithm and the probability calculation algorithm. The analysis of the algorithms also presented. At the end of this paper, we introduce an experimental program called “Personal Transfer System".

Keywords: interface agent, interaction model, user model.

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Authors: N. Hamzah, M.A. Khoiry, I. Arshad, W.H.W. Badaruzzaman, N. M. Tawil

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Construction delay is unavoidable in developing countries including Malaysia. It is defined as time overrun or extension of time for completion of a project. The purpose of the study is to determine the causes of delay in Malaysian construction industries based on previous worldwide research. The field survey conducted includes the experienced developers, consultants and contractors in Malaysia. 34 causes of the construction delay have been determined and 24 have been selected using the Rasch model analysis. The analysis result will be used as the baseline for the next research to find the causes of delay in the Malaysian construction industry taking place in Malaysian higher learning institutions.

Keywords: Causes of construction delay, construction projects, Malaysian construction industry, Rasch model analysis.

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Authors: Bhim Singh

Abstract:

Due to increased pressure from global competitors, manufacturing organizations are switching over to lean philosophies from traditional mass production. Lean manufacturing is a manufacturing philosophy which focuses on elimination of various types of wastes and creates maximum value for the end customers. Lean thinking aims to produce high quality products and services at the lowest possible cost with maximum customer responsiveness. Indian Industry is facing lot of problems in this transformation from traditional mass production to lean production. Through this paper an attempt has been made to identify various lean implementation hurdles in Indian industries with the help of a structured survey. Identified hurdles are grouped with the help of factor analysis and rated by calculating descriptive statistics. To show the effect of lean implementation hurdles a hypothesis “Organizations having higher level of lean implementation hurdles will have poor (negative) performance” has been postulated and tested using correlation matrix between performance parameters of the organizations and identified hurdles. The findings of the paper will be helpful to prepare road map to identify and eradicate the lean implementation hurdles.

Keywords: Factor analysis, global competition, lean implementation and lean hurdles.

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Authors: Aleš Florian, Lenka Ševelová, Rudolf Hela

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Complex statistical analysis of stresses in concrete slab of the real type of rigid pavement is performed. The computational model of the pavement is designed as a spatial (3D) model, is based on a nonlinear variant of the finite element method that respects the structural nonlinearity, enables to model different arrangement of joints, and the entire model can be loaded by the thermal load. Interaction of adjacent slabs in joints and contact of the slab and the subsequent layer are modeled with help of special contact elements. Four concrete slabs separated by transverse and longitudinal joints and the additional subgrade layers and soil to the depth of about 3m are modeled. The thickness of individual layers, physical and mechanical properties of materials, characteristics of joints, and the temperature of the upper and lower surface of slabs are supposed to be random variables. The modern simulation technique Updated Latin Hypercube Sampling with 20 simulations is used for statistical analysis. As results, the estimates of basic statistics of the principal stresses s1 and s3 in 53 points on the upper and lower surface of the slabs are obtained.

Keywords: concrete, FEM, pavement, simulation.

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Authors: Qian-Ping Guo, Hou-Biao Li

Abstract:

The generalized Higham matrix is a complex symmetric matrix A = B + iC, where both B ∈ Cn×n and C ∈ Cn×n are Hermitian positive definite, and i = √−1 is the imaginary unit. The growth factor in Gaussian elimination is less than 3√2 for this kind of matrices. In this paper, we give a new brief proof on this result by different techniques, which can be understood very easily, and obtain some new findings.

Keywords: CSPD matrix, positive definite, Schur complement, Higham matrix, Gaussian elimination, Growth factor.

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Authors: George N. Prodromidis, Frank A. Coutelieris

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Biogas can be currently considered as an alternative option for electricity production, mainly due to its high energy content (hydrocarbon-rich source), its renewable status and its relatively low utilization cost. Solid Oxide Fuel Cell (SOFC) stacks convert fuel’s chemical energy to electricity with high efficiencies and reveal significant advantages on fuel flexibility combined with lower emissions rate, especially when utilize biogas. Electricity production by biogas constitutes a composite problem which incorporates an extensive parametric analysis on numerous dynamic variables. The main scope of the presented study is to propose a detailed thermodynamic model on the optimization of SOFC-based power plants’ operation based on fundamental thermodynamics, energy and exergy balances. This model named THERMAS (THERmodynamic MAthematical Simulation model) incorporates each individual process, during electricity production, mathematically simulated for different case studies that represent real life operational conditions. Also, THERMAS offers the opportunity to choose a great variety of different values for each operational parameter individually, thus allowing for studies within unexplored and experimentally impossible operational ranges. Finally, THERMAS innovatively incorporates a specific criterion concluded by the extensive energy analysis to identify the most optimal scenario per simulated system in exergy terms. Therefore, several dynamical parameters as well as several biogas mixture compositions have been taken into account, to cover all the possible incidents. Towards the optimization process in terms of an innovative OPF (OPtimization Factor), presented here, this research study reveals that systems supplied by low methane fuels can be comparable to these supplied by pure methane. To conclude, such an innovative simulation model indicates a perspective on the optimal design of a SOFC stack based system, in the direction of the commercialization of systems utilizing biogas.

Keywords: Biogas, Exergy, Optimization, SOFC.

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Authors: Turgay Temel, John Hallam

Abstract:

An improved processing description to be employed in biosonar signal processing in a cochlea model is proposed and examined. It is compared to conventional models using a modified discrimination analysis and both are tested. Their performances are evaluated with echo data captured from natural targets (trees).Results indicate that the phase characteristics of low-pass filters employed in the echo processing have a significant effect on class separability for this data.

Keywords: Cochlea model, discriminant analysis, neurospikecoding, classification.

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Authors: C. E. Madubueze, S. C. Madubueze, S. Ajama

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Cholera is a disease that is predominately common in developing countries due to poor sanitation and overcrowding population. In this paper, a deterministic model for the dynamics of cholera is developed and control measures such as health educational message, therapeutic treatment, and vaccination are incorporated in the model. The effective reproduction number is computed in terms of the model parameters. The existence and stability of the equilibrium states, disease free and endemic equilibrium states are established and showed to be locally and globally asymptotically stable when R0 < 1 and R0 > 1 respectively. The existence of backward bifurcation of the model is investigated. Furthermore, numerical simulation of the model developed is carried out to show the impact of the control measures and the result indicates that combined control measures will help to reduce the spread of cholera in the population.

Keywords: Backward bifurcation, cholera, equilibrium, dynamics, stability.

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Authors: Cecilia Perri, Vincenzo Corvello

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The aim of the present study is to investigate consumers' determinants of intention toward the adoption of Smart Grid solutions and technologies. Ajzen's Theory of Planned Behaviour (TPB) model is applied and tested to explain the formation of such adoption intention. An exogenous variable, taking into account the resistance to change of individuals, was added to the basic model. The elicitation study allowed obtaining salient modal beliefs, which were used, with the support of literature, to design the questionnaire. After the screening phase, data collected from the main survey were analysed for evaluating measurement model's reliability and validity. Consistent with the theory, the results of structural equation analysis revealed that attitude, subjective norm, and perceived behavioural control positively, which affected the adoption intention. Specifically, the variable with the highest estimate loading factor was found to be the perceived behavioural control, and, the most important belief related to each construct was determined (e.g., energy saving was observed to be the most significant belief linked with attitude). Further investigation indicated that the added exogenous variable has a negative influence on intention; this finding confirmed partially the hypothesis, since this influence was indirect: such relationship was mediated by attitude. Implications and suggestions for future research are discussed.

Keywords: Adoption of innovation, consumers behaviour, energy management, smart grid, theory of planned behaviour.

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Authors: P. Bhramara, V. D. Rao, K. V. Sharma , T. K. K. Reddy

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In designing of condensers, the prediction of pressure drop is as important as the prediction of heat transfer coefficient. Modeling of two phase flow, particularly liquid – vapor flow under diabatic conditions inside a horizontal tube using CFD analysis is difficult with the available two phase models in FLUENT due to continuously changing flow patterns. In the present analysis, CFD analysis of two phase flow of refrigerants inside a horizontal tube of inner diameter, 0.0085 m and 1.2 m length is carried out using homogeneous model under adiabatic conditions. The refrigerants considered are R22, R134a and R407C. The analysis is performed at different saturation temperatures and at different flow rates to evaluate the local frictional pressure drop. Using Homogeneous model, average properties are obtained for each of the refrigerants that is considered as single phase pseudo fluid. The so obtained pressure drop data is compared with the separated flow models available in literature.

Keywords: Adiabatic conditions, CFD analysis, Homogeneousmodel and Liquid – Vapor flow.

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Authors: Makram Ben Jeddou

Abstract:

ABC classification is widely used by managers for inventory control. The classical ABC classification is based on Pareto principle and according to the criterion of the annual use value only. Single criterion classification is often insufficient for a closely inventory control. Multi-criteria inventory classification models have been proposed by researchers in order to consider other important criteria. From these models, we will consider a specific model in order to make a sensitive analysis on the composite score calculated for each item. In fact, this score, based on a normalized average between a good and a bad optimized index, can affect the ABC-item classification. We will focus on items differently assigned to classes and then propose a classification compromise.

Keywords: ABC classification, Multi criteria inventory classification models, ZF-model.

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Authors: P. Pongsumpun

Abstract:

Malaria is transmitted to the human by biting of infected Anopheles mosquitoes. This disease is a serious, acute and chronic relapsing infection to humans. Fever, nausea, vomiting, back pain, increased sweating anemia and splenomegaly (enlargement of the spleen) are the symptoms of the patients who infected with this disease. It is caused by the multiplication of protozoa parasite of the genus Plasmodium. Plasmodium falciparum, Plasmodium vivax, Plasmodium malariae and Plasmodium ovale are the four types of Plasmodium malaria. A mathematical model for the transmission of Plasmodium Malaria is developed in which the human and vector population are divided into two classes, the susceptible and the infectious classes. In this paper, we formulate the dynamical model of Plasmodium falciparum and Plasmodium vivax malaria. The standard dynamical analysis is used for analyzing the behavior for the transmission of this disease. The Threshold condition is found and numerical results are shown to confirm the analytical results.

Keywords: Dynamical analysis, Malaria, mathematical model, threshold condition.

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Authors: Musthaya Patchanee

Abstract:

The study of Sanitary landfill in Bang Nok-khwaek municipality consists of two procedures. First, to survey and create the spatial database by using physical factor, environmental factor, economical factor and social factor to follow the method of Geographic information system: GIS, second, to analyze the proper spatial for allocating the sanitary landfill in Bang Nok-khwaek municipality by using Overlay techniques to calculate the weighting linear total in Arc GIS program. The study found that there are 2.49 sq.km. proper spatial for the sanitary landfill in Bang Nok-khwaek municipals city which is 66.76% of the whole area. The highest proper spatial is 0.02 sq.km. which is 0.54%, The high proper spatial is 0.3 sq.km. which is 8.04%, the moderate spatial is 1.62 sq.km. which is 43.43% and the low proper spatial is 0.55 sq.km. which is 14.75%. These results will be used as the guideline to select the sanitary landfill area in accordance with sanitation standard for Subdistrict Administrative Organization and Subbdistrict Municipality in Samut Songkhram provice.

Keywords: An application of Geographic Information System, select areas for sanitary landfill and Bang Nok-khwaek municipality.

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Authors: Nabila Charkaoui

Abstract:

Interest in Human Consciousness has been revived in the late 20th century from different scientific disciplines. Consciousness studies involve both its understanding and its application. In this paper, a computational model of the minimum consciousness functions necessary in my point of view for Artificial Intelligence applications is presented with the aim of improving the way computations will be made in the future. In section I, human consciousness is briefly described according to the scope of this paper. In section II, a minimum set of consciousness functions is defined - based on the literature reviewed - to be modelled, and then a computational model of these functions is presented in section III. In section IV, an analysis of the model is carried out to describe its functioning in detail.

Keywords: Consciousness, perception, attention.

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Authors: B. Marungsri, S. Boonpoke, A. Rawangpai, A. Oonsivilai, C. Kritayakornupong

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This study describes analysis of tower grounding resistance effected the back flashover voltage across insulator string in a transmission system. This paper studies the 500 kV transmission lines from Mae Moh, Lampang to Nong Chok, Bangkok, Thailand, which is double circuit in the same steel tower with two overhead ground wires. The factor of this study includes magnitude of lightning stroke, and front time of lightning stroke. Steel tower uses multistory tower model. The assumption of studies based on the return stroke current ranged 1-200 kA, front time of lightning stroke between 1 μs to 3 μs. The simulations study the effect of varying tower grounding resistance that affect the lightning current. Simulation results are analyzed lightning over voltage that causes back flashover at insulator strings. This study helps to know causes of problems of back flashover the transmission line system, and also be as a guideline solving the problem for 500 kV transmission line systems, as well.

Keywords: Tower grounding resistance, back flashover, multistory tower model, lightning stroke current.

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Authors: Cor M. Rops, Giaco C. Oosterbaan, Cees W.M. v/d Geld

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Equipment miniaturisation offers several opportunities such as an increased surface-to-volume ratio and higher heat transfer coefficients. However, moving towards small-diameter channels demands extra attention to fouling, reliability and stable operation of the system. The present investigation explores possibilities to enhance the stability of the once-through micro evaporator by reducing its flow boiling induced pressure fluctuations. Experimental comparison shows that the measured reduction factor approaches a theoretically derived value. Pressure fluctuations are reduced by a factor of ten in the solid conical channel and a factor of 15 in the porous conical channel. This presumably leads to less backflow and therefore to a better flow control.

Keywords: Flow boiling, Operation stability, Microfluidics, Microchannels.

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Authors: Iveta Řepková

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The aim of this paper is to estimate the efficiency of the Slovak commercial banks employing the Data Envelopment Analysis (DEA) window analysis approach during the period 2003-2012. The research is based on unbalanced panel data of the Slovak commercial banks. Undesirable output was included into analysis of banking efficiency. It was found that most efficient banks were Postovabanka, UniCredit Bank and Istrobanka in CCR model and the most efficient banks were Slovenskasporitelna, Istrobanka and UniCredit Bank in BCC model. On contrary, the lowest efficient banks were found Privatbanka and CitiBank. We found that the largest banks in the Slovak banking market were lower efficient than medium-size and small banks. Results of the paper is that during the period 2003-2008 the average efficiency was increasing and then during the period 2010-2011 the average efficiency decreased as a result of financial crisis.

Keywords: Data Envelopment Analysis, efficiency, Slovak banking sector, window analysis.

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Authors: Abdelhalim Kessal

Abstract:

This paper treats a design of combined control of a single phase power factor correction (PFC). The strategy of the proposed control is based on two parts, the first, for the outer loop (DC output regulated voltage), and the second govern the input current of the converter in order to achieve a sinusoidal form in phase with the grid voltage. Two kinds of regulators are used, Fuzzy controller for the outer loop and predictive controller for the inner loop. The controllers are verified and discussed through simulation under MATLAB/Simulink platform. Also an experimental confirmation is applied. Results present a high dynamic performance under various parameters changes.

Keywords: Boost converter, harmonic distortion, Fuzzy, prediction, unity power factor.

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Authors: Sana Bembli, Nahla Khraief Haddad, Safya Belghith

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This paper deals with a robust model free terminal sliding mode with gravity compensation approach used to control an exoskeleton-upper limb system. The considered system is a 2-DoF robot in interaction with an upper limb used for rehabilitation. The aim of this paper is to control the flexion/extension movement of the shoulder and the elbow joints in presence of matched disturbances. In the first part, we present the exoskeleton-upper limb system modeling. Then, we controlled the considered system by the model free terminal sliding mode with gravity compensation. A stability study is realized. To prove the controller performance, a robustness analysis was needed. Simulation results are provided to confirm the robustness of the gravity compensation combined with to the Model free terminal sliding mode in presence of uncertainties.

Keywords: Exoskeleton-upper limb system, gravity compensation, model free terminal sliding mode, robustness analysis, Monte Carlo, H∞ methods.

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Authors: S.A. Alqallaf, S.A. Al-Mawsawi, A. Haider

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In order to evaluate the performance of a unified power flow controller (UPFC), mathematical models for steady state and dynamic analysis are to be developed. The steady state model is mainly concerned with the incorporation of the UPFC in load flow studies. Several load flow models for UPFC have been introduced in literature, and one of the most reliable models is the decoupled UPFC model. In spite of UPFC decoupled load flow model simplicity, it is more robust compared to other UPFC load flow models and it contains unique capabilities. Some shortcoming such as additional set of nonlinear equations are to be solved separately after the load flow solution is obtained. The aim of this study is to investigate the different control strategies that can be realized in the decoupled load flow model (individual control and combined control), and the impact of the location of the UPFC in the network on its control parameters.

Keywords: UPFC, Decoupled model, Load flow.

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Authors: Ching-I Chen

Abstract:

The continued rise of e-commerce is the main driver of the rapid growth of global online purchase. Consumers can nearly buy everything they want at one occasion through online shopping. The purchase behavior models which focus on single product category are insufficient to describe online shopping behavior. Therefore, analysis of multi-category purchase gets more and more popular. For example, market basket analysis explores customers’ buying tendency of the association between product categories. The information derived from market basket analysis facilitates to make cross-selling strategies and product recommendation system.

To detect the association between different product categories, we use the market basket analysis with the multidimensional scaling technique to build an associated map which describes how likely multiple product categories are bought at the same time. Besides, we also build an inter-purchase time model for associated products to describe how likely a product will be bought after its associated product is bought. We classify inter-purchase time behaviors of multi-category products into nine types, and use a mixture regression model to integrate those behaviors under our assumptions of purchase sequences. Our sample data is from comScore which provides a panelist-label database that captures detailed browsing and buying behavior of internet users across the United States. Finding the inter-purchase time from books to movie is shorter than the inter-purchase time from movies to books. According to the model analysis and empirical results, this research finally proposes the applications and recommendations in the management.

Keywords: Multiple-category purchase behavior, inter-purchase time, market basket analysis.

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Authors: Ekrem Erdem, Can Tansel Tugcu

Abstract:

Improved resource efficiency of production is a key requirement for sustainable growth, worldwide. In this regards, by considering the energy and tourism as the extra inputs to the classical Coub-Douglas production function, this study aims at investigating the efficiency changes in the North African countries. To this end, the study uses panel data for the period 1995-2010 and adopts the Malmquist index based on the data envelopment analysis. Results show that tourism increases technical and scale efficiencies, while it decreases technological and total factor productivity changes. On the other hand, when the production function is augmented by the energy input; technical efficiency change decreases, while the technological change, scale efficiency change and total factor productivity change increase. Thus, in order to satisfy the needs for sustainable growth, North African governments should take some measures for increasing the contribution that the tourism makes to economic growth and some others for efficient use of resources in the energy sector.

Keywords: Data envelopment analysis, Economic efficiency, North African countries, Sustainable growth.

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Authors: Se Kyung Oh, Ary Bachtiar Krishna Putra, Soo Whan Ahn

Abstract:

A numerical study on the turbulent flow and heat transfer characteristics in the rectangular channel with different types of baffles is carried out. The inclined baffles have the width of 19.8 cm, the square diamond type hole having one side length of 2.55 cm, and the inclination angle of 5o. Reynolds number is varied between 23,000 and 57,000. The SST turbulence model is applied in the calculation. The validity of the numerical results is examined by the experimental data. The numerical results of the flow field depict that the flow patterns around the different baffle type are entirely different and these significantly affect the local heat transfer characteristics. The heat transfer and friction factor characteristics are significantly affected by the perforation density of the baffle plate. It is found that the heat transfer enhancement of baffle type II (3 hole baffle) has the best values.

Keywords: Turbulent flow, rectangular channel, inclined baffle, heat transfer, friction factor.

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Authors: M. Saravani, M. Azizi,

Abstract:

The V-notches are most possible case for initiation of cracks in parts. The specifications of cracks on the tip of the notch will be influenced via opening angle, tip radius and depth of V-notch. In this study, the effects of V-notch-s opening angle on stress intensity factor and T-stress of crack on the notch has been investigated. The experiment has been done in different opening angles and various crack length in mode (I) loading using Photoelasticity method. The results illustrate that while angle increases in constant crack-s length, SIF and T-stress will decrease. Beside, the effect of V-notch angle in short crack is more than long crack. These V-notch affects are negligible by increasing the length of crack, and the crack-s behavior can be considered as a single-edge crack specimen. Finally, the results have been evaluated with numerical finite element analysis and good agreement was obvious.

Keywords: Photoelasticity, Stress intensity factor, T-stress, V-notch.

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Authors: R. Sammoura

Abstract:

In Lebanon, public construction projects are awarded to the contractor submitting the lowest bid price based on a competitive bidding process. The contractor has to make a strategic decision in choosing the appropriate bid price that will offer a satisfactory profit with a greater probability to win. A simulation model for bid price decision making based on the lowest bid price evaluation is developed. The model, built using Crystal Ball decisionengineering software, considers two main factors affecting the bidding process: the number of qualified bidders and the size of the project. The validity of the model is tested on twelve separate projects. The study also shows how to use the model to conduct risk analysis and help any specific contractor to decide on his bid price with associated certainty level in a scientific method.

Keywords: Bid price, Competition, Decision making, Simulation.

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Authors: Mária Stachová, Lukáš Sobíšek

Abstract:

Data mining incorporates a group of statistical methods used to analyze a set of information, or a data set. It operates with models and algorithms, which are powerful tools with the great potential. They can help people to understand the patterns in certain chunk of information so it is obvious that the data mining tools have a wide area of applications. For example in the theoretical chemistry data mining tools can be used to predict moleculeproperties or improve computer-assisted drug design. Classification analysis is one of the major data mining methodologies. The aim of thecontribution is to create a classification model, which would be able to deal with a huge data set with high accuracy. For this purpose logistic regression, Bayesian logistic regression and random forest models were built using R software. TheBayesian logistic regression in Latent GOLD software was created as well. These classification methods belong to supervised learning methods. It was necessary to reduce data matrix dimension before construct models and thus the factor analysis (FA) was used. Those models were applied to predict the biological activity of molecules, potential new drug candidates.

Keywords: data mining, classification, drug design, QSAR

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Authors: García López

Abstract:

The Government Departments of Health have the task of informing and educating citizens about public health issues. For this, they use channels like Twitter, key in the search for health information and the propagation of content. The tweets, important in the virality of the content, may contain emotions that influence the contagion and exchange of knowledge. The goal of this study is to perform an analysis of the emotional projection of health information shared on Twitter by official American accounts: the disease control account CDCgov, National Institutes of Health, NIH, the government agency HHSGov, and the professional organization PublicHealth. For this, we used Tone Analyzer, an International Business Machines Corporation (IBM) tool specialized in emotion detection in text, corresponding to the categorical model of emotion representation. For 15 days, all tweets from these accounts were analyzed with the emotional analysis tool in text. The results showed that their tweets contain an important emotional load, a determining factor in the success of their communications. This exposes that official accounts also use subjective language and contain emotions. The predominance of emotion joy over sadness and the strong presence of emotions in their tweets stimulate the virality of content, a key in the work of informing that government health departments have.

Keywords: Emotions in tweets emotion detection in text, health information on Twitter, American health official accounts, emotions on Twitter, emotions and content.

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Authors: J. Kala, P. Hradil, V. Salajka

Abstract:

Reinforced concrete crash barriers used in road traffic must meet a number of criteria. Crash barriers are laid lengthwise, one behind another, and joined using specially designed steel locks. While developing BSV reinforced concrete crash barriers (type ŽPSV), experiments and calculations aimed to optimize the shape of a newly designed lock and the reinforcement quantity and distribution in a crash barrier were carried out. The tension carrying capacity of two parallelly joined locks was solved experimentally. Based on the performed experiments, adjustments of nonlinear properties of steel were performed in the calculations. The obtained results served as a basis to optimize the lock design using a computational model that takes into account the plastic behaviour of steel and the influence of the surrounding concrete [6]. The response to the vehicle impact has been analyzed using a specially elaborated complex computational model, comprising both the nonlinear model of the damping wall or crash barrier and the detailed model of the vehicle [7].

Keywords: Crash Barrier, impact, static analysis, concrete nonlinear model.

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Authors: José Antonio Esparza Isasa, Finn Overgaard Hansen, Peter Gorm Larsen

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This paper presents a new methodology to study power and energy consumption in mechatronic systems early in the development process. This new approach makes use of two modeling languages to represent and simulate embedded control software and electromechanical subsystems in the discrete event and continuous time domain respectively within a single co-model. This co-model enables an accurate representation of power and energy consumption and facilitates the analysis and development of both software and electro-mechanical subsystems in parallel. This makes the engineers aware of energy-wise implications of different design alternatives and enables early trade-off analysis from the beginning of the analysis and design activities.

Keywords: Energy consumption, embedded systems, modeldriven engineering, power awareness.

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Authors: Alan Luo, Hunter N. B. Moseley

Abstract:

Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for X-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across X-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: Biomacromolecular structure, coenzyme, electron density discrepancy analysis, X-ray crystallography.

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