Search results for: Biological Models

Authors: Erika Ann Schaub, Christian J Darken

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Sociological models (e.g., social network analysis, small-group dynamic and gang models) have historically been used to predict the behavior of terrorist groups. However, they may not be the most appropriate method for understanding the behavior of terrorist organizations because the models were not initially intended to incorporate violent behavior of its subjects. Rather, models that incorporate life and death competition between subjects, i.e., models utilized by scientists to examine the behavior of wildlife populations, may provide a more accurate analysis. This paper suggests the use of biological models to attain a more robust method for understanding the behavior of terrorist organizations as compared to traditional methods. This study also describes how a biological population model incorporating predator-prey behavior factors can predict terrorist organizational recruitment behavior for the purpose of understanding the factors that govern the growth and decline of terrorist organizations. The Lotka-Volterra, a biological model that is based on a predator-prey relationship, is applied to a highly suggestive case study, that of the Irish Republican Army. This case study illuminates how a biological model can be utilized to understand the actions of a terrorist organization.

Keywords: Biological Models, Lotka-Volterra Predator-Prey Model, Terrorist Organizational Behavior, Terrorist Recruitment.

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Authors: Werner Sandmann, Verena Wolf

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Stochastic models of biological networks are well established in systems biology, where the computational treatment of such models is often focused on the solution of the so-called chemical master equation via stochastic simulation algorithms. In contrast to this, the development of storage-efficient model representations that are directly suitable for computer implementation has received significantly less attention. Instead, a model is usually described in terms of a stochastic process or a "higher-level paradigm" with graphical representation such as e.g. a stochastic Petri net. A serious problem then arises due to the exponential growth of the model-s state space which is in fact a main reason for the popularity of stochastic simulation since simulation suffers less from the state space explosion than non-simulative numerical solution techniques. In this paper we present transition class models for the representation of biological network models, a compact mathematical formalism that circumvents state space explosion. Transition class models can also serve as an interface between different higher level modeling paradigms, stochastic processes and the implementation coded in a programming language. Besides, the compact model representation provides the opportunity to apply non-simulative solution techniques thereby preserving the possible use of stochastic simulation. Illustrative examples of transition class representations are given for an enzyme-catalyzed substrate conversion and a part of the bacteriophage λ lysis/lysogeny pathway.

Keywords: Computational Modeling, Biological Networks, Stochastic Models, Markov Chains, Transition Class Models.

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Authors: Micheal Olaolu Arowolo, Muhammad Azam, Fei He, Mihail Popescu, Dong Xu

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As the quantity of biological articles rises, so does the number of biological route figures. Each route figure shows gene names and relationships. Manually annotating pathway diagrams is time-consuming. Advanced image understanding models could speed up curation, but they must be more precise. There is rich information in biological pathway figures. The first step to performing image understanding of these figures is to recognize gene names automatically. Classical optical character recognition methods have been employed for gene name recognition, but they are not optimized for literature mining data. This study devised a method to recognize an image bounding box of gene name as a photo using deep Siamese neural network models to outperform the existing methods using ResNet, DenseNet and Inception architectures, the results obtained about 84% accuracy.

Keywords: Biological pathway, gene identification, object detection, Siamese network, ResNet.

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Authors: Yanqi Yang, Chongshan Liao, Cheuk Hin Ho, Susan Bridges

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Aim: To investigate students’ perceptions of using e-models in an inquiry-based curriculum. Approach: 52 second-year dental students completed a pre- and post-test questionnaire relating to their perceptions of e-models and their use in inquiry-based learning. The pre-test occurred prior to any learning with e-models. The follow-up survey was conducted after one year's experience of using e-models. Results: There was no significant difference between the two sets of questionnaires regarding students’ perceptions of the usefulness of e-models and their willingness to use e-models in future inquiry-based learning. Most students preferred using both plaster models and e-models in tandem. Conclusion: Students did not change their attitude towards e-models and most of them agreed or were neutral that e-models are useful in inquiry-based learning. Whilst recognizing the utility of 3D models for learning, students' preference for combining these with solid models has implications for the development of haptic sensibility in an operative discipline.

Keywords: E-models, inquiry-based curriculum, education.

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Authors: Mohamed S. Sasi, Adel M. Mlitan, Abdulfattah M. Alkherraz

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This research project aims to investigate difference in relative rates concerning phosphoryl transfer relevant to biological catalysis of DNA and RNA in the pH-independent reactions. Activated Models of DNA and RNA for alkyl-aryl phosphate diesters (with 4-nitrophenyl as a good leaving group) have successfully been prepared to gather kinetic parameters. Eyring plots for the pH– independent hydrolysis of 1 and 2 were established at different temperatures in the range 100–160 °C. These measurements have been used to provide a better estimate for the difference in relative rates between the reactivity of DNA and RNA cleavage. Eyring plot gave an extrapolated rate of kH2O = 1 × 10-10 s -1 for 1 (RNA model) and 2 (DNA model) at 25°C. Comparing the reactivity of RNA model and DNA model shows that the difference in relative rates in the pH-independent reactions is surprisingly very similar at 25°. This allows us to obtain chemical insights into how biological catalysts such as enzymes may have evolved to perform their current functions.

Keywords: DNA & RNA Models, Relative Rates, Reactivity.

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Authors: Muhammad Azam, Micheal Olaolu Arowolo, Fei He, Mihail Popescu, Dong Xu

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The number of biological papers is growing quickly, which means that the number of biological pathway figures in those papers is also increasing quickly. Each pathway figure shows extensive biological information, like the names of genes and how the genes are related. However, manually annotating pathway figures takes a lot of time and work. Even though using advanced image understanding models could speed up the process of curation, these models still need to be made more accurate. To improve gene name recognition from pathway figures, we applied a Siamese network to map image segments to a library of pictures containing known genes in a similar way to person recognition from photos in many photo applications. We used a triple loss function and a triplet spatial pyramid pooling network by combining the triplet convolution neural network and the spatial pyramid pooling (TSPP-Net). We compared VGG19 and VGG16 as the Siamese network model. VGG16 achieved better performance with an accuracy of 93%, which is much higher than Optical Character Recognition (OCR) results.

Keywords: Biological pathway, image understanding, gene name recognition, object detection, Siamese network, Visual Geometry Group.

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Authors: Yogesh D. Bansod, Jiri Bursa

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The quantitative study of cell mechanics is of paramount interest, since it regulates the behaviour of the living cells in response to the myriad of extracellular and intracellular mechanical stimuli. The novel experimental techniques together with robust computational approaches have given rise to new theories and models, which describe cell mechanics as combination of biomechanical and biochemical processes. This review paper encapsulates the existing continuum-based computational approaches that have been developed for interpreting the mechanical responses of living cells under different loading and boundary conditions. The salient features and drawbacks of each model are discussed from both structural and biological points of view. This discussion can contribute to the development of even more precise and realistic computational models of cell mechanics based on continuum approaches or on their combination with microstructural approaches, which in turn may provide a better understanding of mechanotransduction in living cells.

Keywords: Cell mechanics, computational models, continuum approach, mechanical models.

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Authors: Antonio Di Leva, Roberto Berchi, Gianpiero Pescarmona, Michele Sonnessa

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The aim of a biological model is to understand the integrated structure and behavior of complex biological systems as a function of the underlying molecular networks to achieve simulation and forecast of their operation. Although several approaches have been introduced to take into account structural and environment related features, relatively little attention has been given to represent the behavior of biological systems. The Abstract Biological Process (ABP) model illustrated in this paper is an object-oriented model based on UML (the standard object-oriented language). Its main objective is to bring into focus the functional aspects of the biological system under analysis.

Keywords: Biological processes, system dynamics, systemmodeling, UML.

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Authors: Paola Lecca

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Modeling and simulation of biochemical reactions is of great interest in the context of system biology. The central dogma of this re-emerging area states that it is system dynamics and organizing principles of complex biological phenomena that give rise to functioning and function of cells. Cell functions, such as growth, division, differentiation and apoptosis are temporal processes, that can be understood if they are treated as dynamic systems. System biology focuses on an understanding of functional activity from a system-wide perspective and, consequently, it is defined by two hey questions: (i) how do the components within a cell interact, so as to bring about its structure and functioning? (ii) How do cells interact, so as to develop and maintain higher levels of organization and functions? In recent years, wet-lab biologists embraced mathematical modeling and simulation as two essential means toward answering the above questions. The credo of dynamics system theory is that the behavior of a biological system is given by the temporal evolution of its state. Our understanding of the time behavior of a biological system can be measured by the extent to which a simulation mimics the real behavior of that system. Deviations of a simulation indicate either limitations or errors in our knowledge. The aim of this paper is to summarize and review the main conceptual frameworks in which models of biochemical networks can be developed. In particular, we review the stochastic molecular modelling approaches, by reporting the principal conceptualizations suggested by A. A. Markov, P. Langevin, A. Fokker, M. Planck, D. T. Gillespie, N. G. van Kampfen, and recently by D. Wilkinson, O. Wolkenhauer, P. S. Jöberg and by the author.

Keywords: Mathematical structure, algorithmic implementation, biochemical network models.

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Authors: Y. Tiamaz, N. Souissi

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The purpose of this paper is to present a classification of Lean models which aims to capture all the concepts related to this approach and thus facilitate its implementation. This classification allows the identification of the most relevant models according to several dimensions. From this perspective, we present a review and an analysis of Lean models literature and we propose dimensions for the classification of the current proposals while respecting among others the axes of the Lean approach, the maturity of the models as well as their application domains. This classification allowed us to conclude that researchers essentially consider the Lean approach as a toolbox also they design their models to solve problems related to a specific environment. Since Lean approach is no longer intended only for the automotive sector where it was invented, but to all fields (IT, Hospital, ...), we consider that this approach requires a generic model that is capable of being implemented in all areas.

Keywords: Lean approach, lean models, classification, dimensions, holistic view.

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Authors: Z. Sadeghi, M. R. Omidkhah, M. E. Masoomi

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The purpose of this paper is to examine gas transport behavior of mixed matrix membranes (MMMs) combined with porous particles. Main existing models are categorized in two main groups; two-phase (ideal contact) and three-phase (non-ideal contact). A new coefficient, J, was obtained to express equations for estimating effect of the particle porosity in two-phase and three-phase models. Modified models evaluates with existing models and experimental data using Matlab software. Comparison of gas permeability of proposed modified models with existing models in different MMMs shows a better prediction of gas permeability in MMMs.

Keywords: Mixed Matrix Membrane, Permeation Models, Porous particles, Porosity.

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Authors: Zhang Xiuping, Yang Guowu, Zheng Desheng

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Embedded hardware simulator is a valuable computeraided tool for embedded application development. This paper focuses on the ARM926EJ-S MMU, builds state transition models and formally verifies critical properties for the models. The state transition models include loading instruction model, reading data model, and writing data model. The properties of the models are described by CTL specification language, and they are verified in VIS. The results obtained in VIS demonstrate that the critical properties of MMU are satisfied in the state transition models. The correct models can be used to implement the MMU component in our simulator. In the end of this paper, the experimental results show that the MMU can successfully accomplish memory access requests from CPU.

Keywords: MMU, State transition, Model, Simulation.

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Authors: Ventura Assuncao

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In automotive systems almost all steps concerning the calibration of several control systems, e.g., low idle governor or boost pressure governor, are made with the vehicle because the timeto- production and cost requirements on the projects do not allow for the vehicle analysis necessary to build reliable models. Here is presented a procedure using parametric and NN (neural network) models that enables the generation of vehicle system models based on normal ECU engine control unit) vehicle measurements. These models are locally valid and permit pre and follow-up calibrations so that, only the final calibrations have to be done with the vehicle.

Keywords: Automotive systems, neuro-hybrid models, demodulator, nonlinear systems, identification, and neural networks.

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Authors: Mohamed A. Khlifi, Badr M. Alshammari

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This paper discusses the general methods to saturation in the steady-state, two axis (d & q) frame models of synchronous machines. In particular, the important role of the magnetic coupling between the d-q axes (cross-magnetizing phenomenon), is demonstrated. For that purpose, distinct methods of saturation modeling of dumper synchronous machine with cross-saturation are identified, and detailed models synthesis in d-q axes. A number of models are given in the final developed form. The procedure and the novel models are verified by a critical application to prove the validity of the method and the equivalence between all developed models is reported. Advantages of some of the models over the existing ones and their applicability are discussed.

Keywords: Cross-magnetizing, models synthesis, synchronous machine, saturated modeling, state-space vectors.

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Authors: Mária Stachová, Lukáš Sobíšek

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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: Entisar A. Elgmati

Abstract:

Recurrent event data is a special type of multivariate survival data. Dynamic and frailty models are one of the approaches that dealt with this kind of data. A comparison between these two models is studied using the empirical standard deviation of the standardized martingale residual processes as a way of assessing the fit of the two models based on the Aalen additive regression model. Here we found both approaches took heterogeneity into account and produce residual standard deviations close to each other both in the simulation study and in the real data set.

Keywords: Dynamic, frailty, misspecification, recurrent events.

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Authors: Iliana Marinova, Valentin Mateev

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For investigations of electromagnetic field distributions in biological structures by Finite Element Method (FEM), a method for automatic 3D model building of human anatomical objects is developed. Models are made by meshed structures and specific electromagnetic material properties for each tissue type. Mesh is built according to specific FEM criteria for achieving good solution accuracy. Several FEM models of anatomical objects are built. Formulation using magnetic vector potential and scalar electric potential (A-V, A) is used for modeling of electromagnetic fields in human tissue objects. The developed models are suitable for investigations of electromagnetic field distributions in human tissues exposed in external fields during magnetic stimulation, defibrillation, impedance tomography etc.

Keywords: electromagnetic field, finite element method, humantissue.

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Authors: Kaziyev G. Z., Nabiyeva G. S., Kalizhanova A.U.

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We consider herein a concise view of discreet programming models and methods. There has been conducted the models and methods analysis. On the basis of discreet programming models there has been elaborated and offered a new class of problems, i.e. block-symmetry models and methods of applied tasks statements and solutions.

Keywords: Discreet programming, block-symmetry, analysis methods, information systems development.

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Authors: Omer F. Cansiz, Said M. Easa

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The purpose of this study is mainly to predict collision frequency on the horizontal tangents combined with vertical curves using artificial neural network methods. The proposed ANN models are compared with existing regression models. First, the variables that affect collision frequency were investigated. It was found that only the annual average daily traffic, section length, access density, the rate of vertical curvature, smaller curve radius before and after the tangent were statistically significant according to related combinations. Second, three statistical models (negative binomial, zero inflated Poisson and zero inflated negative binomial) were developed using the significant variables for three alignment combinations. Third, ANN models are developed by applying the same variables for each combination. The results clearly show that the ANN models have the lowest mean square error value than those of the statistical models. Similarly, the AIC values of the ANN models are smaller to those of the regression models for all the combinations. Consequently, the ANN models have better statistical performances than statistical models for estimating collision frequency. The ANN models presented in this paper are recommended for evaluating the safety impacts 3D alignment elements on horizontal tangents.

Keywords: Collision frequency, horizontal tangent, 3D two-lane highway, negative binomial, zero inflated Poisson, artificial neural network.

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Authors: Y. N. Phang, E. F. Loh

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The zero inflated models are usually used in modeling count data with excess zeros where the existence of the excess zeros could be structural zeros or zeros which occur by chance. These type of data are commonly found in various disciplines such as finance, insurance, biomedical, econometrical, ecology, and health sciences which involve sex and health dental epidemiology. The most popular zero inflated models used by many researchers are zero inflated Poisson and zero inflated negative binomial models. In addition, zero inflated generalized Poisson and zero inflated double Poisson models are also discussed and found in some literature. Recently zero inflated inverse trinomial model and zero inflated strict arcsine models are advocated and proven to serve as alternative models in modeling overdispersed count data caused by excessive zeros and unobserved heterogeneity. The purpose of this paper is to review some related literature and provide a variety of examples from different disciplines in the application of zero inflated models. Different model selection methods used in model comparison are discussed.

Keywords: Overdispersed count data, model selection methods, likelihood ratio, AIC, BIC.

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Authors: Alfred L. Guiffrida

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A review of the literature on supply chain delivery models which use delivery windows to measure delivery performance is presented. The review herein serves to meet the following objectives: (i) provide a synthesis of previously published literature on supply chain delivery performance models, (ii) provide in one paper a consolidation of research that can serve as a single source to keep researchers up to date with the research developments in supply chain delivery models, and (iii) identify gaps in the modeling of supply chain delivery performance which could stimulate new research agendas.

Keywords: Delivery performance, Delivery window, Supply chain delivery models, Supply chain performance.

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Authors: Abdelghafour Galadi

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In this paper, accurate power MOSFET models including quasi-saturation effect are presented. These models have no internal node voltages determined by the circuit simulator and use one JFET or one depletion mode MOSFET transistors controlled by an “effective” gate voltage taking into account the quasi-saturation effect. The proposed models achieve accurate simulation results with an average error percentage less than 9%, which is an improvement of 21 percentage points compared to the commonly used standard power MOSFET model. In addition, the models can be integrated in any available commercial circuit simulators by using their analytical equations. A description of the models will be provided along with the parameter extraction procedure.

Keywords: Power MOSFET, drift layer, quasi-saturation effect, SPICE model, circuit simulation.

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Authors: Ali Mamizadeh, Ires Iskender

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The most important parameter in transformers life expectancy is the hot-spot temperature level which accelerates the rate of aging of the insulation. The aim of this paper is to present thermal models for transformers loaded at prefabricated MV/LV transformer substations and outdoor situations. The hot-spot temperature of transformers is studied using their top-oil temperature rise models. The thermal models proposed for hot-spot and top-oil temperatures of different operating situations are compared. Since the thermal transfer is different for indoor and outdoor transformers considering their operating conditions, their hot-spot thermal models differ from each other. The proposed thermal models are verified by the results obtained from the experiments carried out on a typical 1600 kVA, 30 /0.4 kV, ONAN transformer for both indoor and outdoor situations.

Keywords: Hot-spot Temperature, Dynamic Thermal Model, MV/LV Prefabricated, Oil Immersed Transformers

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Authors: M. A. Basunia

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Thirty three re-wetting tests were conducted at different combinations of temperatures (5.7- 46.30C) and relative humidites (48.2-88.6%) with barley. Two most commonly used thinlayer drying and rewetting models i.e. Page and Diffusion were compared for their ability to the fit the experimental re-wetting data based on the standard error of estimate (SEE) of the measured and simulated moisture contents. The comparison shows both the Page and Diffusion models fit the re-wetting experimental data of barley well. The average SEE values for the Page and Diffusion models were 0.176 % d.b. and 0.199 % d.b., respectively. The Page and Diffusion models were found to be most suitable equations, to describe the thin-layer re-wetting characteristics of barley over a typically five day re-wetting. These two models can be used for the simulation of deep-bed re-wetting of barley occurring during ventilated storage and deep bed drying.

Keywords: Thin-layer, barley, re-wetting parameters, temperature, relative humidity.

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Authors: João Paulo Teixeira, Paula Odete Fernandes

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The authors have been developing several models based on artificial neural networks, linear regression models, Box- Jenkins methodology and ARIMA models to predict the time series of tourism. The time series consist in the “Monthly Number of Guest Nights in the Hotels" of one region. Several comparisons between the different type models have been experimented as well as the features used at the entrance of the models. The Artificial Neural Network (ANN) models have always had their performance at the top of the best models. Usually the feed-forward architecture was used due to their huge application and results. In this paper the author made a comparison between different architectures of the ANNs using simply the same input. Therefore, the traditional feed-forward architecture, the cascade forwards, a recurrent Elman architecture and a radial based architecture were discussed and compared based on the task of predicting the mentioned time series.

Keywords: Artificial Neural Network Architectures, time series forecast, tourism.

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Authors: Mikel Alonso López

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In order to begin the process of studying the task of making consumer decisions, the main decision models must be analyzed. The objective of this task is to see if there is a presence of emotions in those models, and analyze how authors that have created them consider their impact in consumer choices. In this paper, the most important models of consumer behavior are analysed. This review is useful to consider an unproblematic background knowledge in the literature. The order that has been established for this study is chronological.

Keywords: Consumer behaviour, emotions, decision making, consumer psychology.

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Authors: Rafayel A. Azizyan, Aram E. Gevorgyan, Valeri B. Arakelyan, Emil S. Gevorgyan

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Currently, mathematical and computer modeling are widely used in different biological studies to predict or assess behavior of such a complex systems as a biological are. This study deals with mathematical and computer modeling of bi-substrate enzymatic reactions, which play an important role in different biochemical pathways. The main objective of this study is to represent the results from in silico investigation of bi-substrate enzymatic reactions in the presence of uncompetitive inhibitors, as well as to describe in details the inhibition effects. Four models of uncompetitive inhibition were designed using different software packages. Particularly, uncompetitive inhibitor to the first [ES₁] and the second ([ES₁S₂]; [FS₂]) enzyme-substrate complexes have been studied. The simulation, using the same kinetic parameters for all models allowed investigating the behavior of reactions as well as determined some interesting aspects concerning influence of different cases of uncompetitive inhibition. Besides, it has been shown that uncompetitive inhibitors exhibit specific selectivity depending on mechanism of bi-substrate enzymatic reaction. 

Keywords: Mathematical modeling, bi-substrate enzymatic reactions, sequential mechanism, ping-pong mechanism, uncompetitive inhibition.

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Authors: Jaroslav Masek, Juraj Camaj, Eva Nedeliakova

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The paper is focused on the operational model for transport the single wagon consignments on railway network by using two different models of train formation. The paper gives an overview of possibilities of improving the quality of transport services. Paper deals with two models used in problematic of train formatting - time continuously and time discrete. By applying these models in practice, the transport company can guarantee a higher quality of service and expect increasing of transport performance. The models are also applicable into others transport networks. The models supplement a theoretical problem of train formation by new ways of looking to affecting the organization of wagon flows.

Keywords: Train formation, wagon flows, marshalling yard, railway technology.

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Authors: Neerja Bhatnagar, Benjoe A. Juliano, Renee S. Renner

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This paper presents data annotation models at five levels of granularity (database, relation, column, tuple, and cell) of relational data to address the problem of unsuitability of most relational databases to express annotations. These models do not require any structural and schematic changes to the underlying database. These models are also flexible, extensible, customizable, database-neutral, and platform-independent. This paper also presents an SQL-like query language, named Annotation Query Language (AnQL), to query annotation documents. AnQL is simple to understand and exploits the already-existent wide knowledge and skill set of SQL.

Keywords: annotation query language, data annotations, data annotation models, semantic data annotations

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Authors: Siham G. Farag

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The main objective of this paper is to provide a new methodology for road safety assessment in Oman through the development of suitable accident prediction models. GLM technique with Poisson or NBR using SAS package was carried out to develop these models. The paper utilized the accidents data of 31 un-signalized T-intersections during three years. Five goodness-of-fit measures were used to assess the overall quality of the developed models. Two types of models were developed separately; the flow-based models including only traffic exposure functions, and the full models containing both exposure functions and other significant geometry and traffic variables. The results show that, traffic exposure functions produced much better fit to the accident data. The most effective geometric variables were major-road mean speed, minor-road 85th percentile speed, major-road lane width, distance to the nearest junction, and right-turn curb radius. The developed models can be used for intersection treatment or upgrading and specify the appropriate design parameters of T-intersections. Finally, the models presented in this thesis reflect the intersection conditions in Oman and could represent the typical conditions in several countries in the middle east area, especially gulf countries.

Keywords: Accidents Prediction Models (APMs), Generalized Linear Model (GLM), T-intersections, Oman.

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