Search results for: systems biology

Authors: Jayson G. Balansag

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An integrated biology and chemistry (iBC) course for freshmen college students was developed in University of Delaware. This course will prepare students to (1) become interdisciplinary thinkers in the field of biology and (2) collaboratively work with others from multiple disciplines in the future. This paper documents and describes the implementation of the course. The information gathered from reading literature, classroom observations, and interviews were used to carry out the purpose of this paper. The major goal of the iBC course is to align the concepts between Biology and Chemistry, so that students can draw science concepts from both disciplines which they can apply in their interdisciplinary researches. This course is offered every fall and spring semesters of each school year. Students enrolled in Biology are also enrolled in Chemistry during the same semester. The iBC is composed of lectures, laboratories, studio sessions, and workshops and is taught by the faculty from the biology and chemistry departments. In addition, the preceptors, graduate teaching assistants, and studio fellows facilitate the laboratory and studio sessions. These roles are interdependent with each other. The iBC can be used as a model for higher education institutions who wish to implement an integrated biology course.

Keywords: Integrated biology and chemistry, integration, interdisciplinary research, new biology, undergraduate science education.

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Authors: George Eleftherakis, Petros Kefalas, Anna Sotiriadou, Evangelos Kehris

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Recent advances in both the testing and verification of software based on formal specifications of the system to be built have reached a point where the ideas can be applied in a powerful way in the design of agent-based systems. The software engineering research has highlighted a number of important issues: the importance of the type of modeling technique used; the careful design of the model to enable powerful testing techniques to be used; the automated verification of the behavioural properties of the system; the need to provide a mechanism for translating the formal models into executable software in a simple and transparent way. This paper introduces the use of the X-machine formalism as a tool for modeling biology inspired agents proposing the use of the techniques built around X-machine models for the construction of effective, and reliable agent-based software systems.

Keywords: Biology inspired agent, formal methods, x-machines.

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Authors: N. Nor Azman, M. F. Kamarudin, S. I. Ong, N. Maaulot

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PERMATApintar^® National Gifted Center is, to the author’s best of knowledge, the first center in Malaysia that provides a platform for Malaysian talented students with high ability in thinking. This center has built a teaching and learning biology curriculum that suits the ability of these gifted students. The level of PERMATApintar^® biology curriculum is basically higher than the national biology curriculum. Here, the foundation students are exposed to the PERMATApintar^® biology curriculum at the age of as early as 11 years old. This center practices a 4-time-a-year examination system to monitor the academic performances of the students. Generally, most of the time, male students show no or low interest towards biology subject compared to female students. This study is to investigate the association of students’ gender and their academic performances in biology examination. A total of 39 students’ scores in twelve sets of biology examinations in 3 years have been collected and analyzed by using the statistical analysis. Based on the analysis, there are no significant differences between male and female students against the biology academic performances with a significant level of p = 0.05. This indicates that gender is not associated with the scores of biology examinations among the students. Another result showed that the average score for male studenta was higher than the female students. Future research can be done by comparing the biology academic achievement in Malaysian National Examination (Sijil Pelajaran Malaysia, SPM) between the Foundation 3 students (Grade 9) and Level 2 students (Grade 11) with similar PERMATApintar^® biology curriculum.

Keywords: Academic performances, biology, gender differences, gifted students.

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Authors: Murniza Muhamad, Halimah Badioze Zaman, Azlina Ahmad

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This study aims to conduct a preliminary investigation to determine the topic to be focused in developing Virtual Laboratory For Biology (VLab-Bio). Samples involved in answering the questionnaire are form five students (equivalent to A-Level) and biology teachers. Time and economical resources for the setting up and construction of scientific laboratories can be solved with the adaptation of virtual laboratories as an educational tool. Thus, it is hoped that the proposed virtual laboratory will help students to learn the abstract concepts in biology. Findings show that the difficult topic chosen is Cell Division and the learning objective to be focused in developing the virtual lab is “Describe the application of knowledge on mitosis in cloning".

Keywords: biology education, computer simulation, virtual laboratory, virtual reality

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Authors: E. Tazabekova, B. Amirasheva, L. Amirasheva

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This article examines the nature and structure of ecological education of biology specialists in Kazakhstan. Also characterizes the ecological education in high school and specific features in training of biology specialists.

Keywords: Ecological education, environment.

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Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur

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Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions, and the modeling of evolution. Various global rearrangements of permutations, such as reversals and transpositions,have recently become of interest because of their applications in computational molecular biology. A reversal is an operation that reverses the order of a substring of a permutation. A transposition is an operation that swaps two adjacent substrings of a permutation. The problem of determining the smallest number of reversals required to transform a given permutation into the identity permutation is called sorting by reversals. Similar problems can be defined for transpositions and other global rearrangements. In this work we perform a study about some genome rearrangement primitives. We show how a genome is modelled by a permutation, introduce some of the existing primitives and the lower and upper bounds on them. We then provide a comparison of the introduced primitives.

Keywords: Sorting Primitives, Genome Rearrangements, Transpositions, Block Interchanges, Strip Exchanges.

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Authors: M. F. Miah, H. Ali, E. Zannath, T. M. Shuvra, M. N. Naser, M. K. Ahmed

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In this study, breeding biology and induced breeding of freshwater mud eel, Monopterus cuchia was observed during the experimental period from February to June, 2013. Breeding biology of freshwater mud eel, Monopterus cuchia was considered in terms of gonadosomatic index, length-weight relationship of gonad, ova diameter and fecundity. The ova diameter was recorded from 0.3 mm to 4.30 mm and the individual fecundity was recorded from 155 to 1495 while relative fecundity was found from 2.64 to 12.45. The fecundity related to body weight and length of fish was also discussed. A peak of GSI was observed 2.14±0.2 in male and 5.1 ±1.09 in female. Induced breeding of freshwater mud eel, Monopterus cuchia was also practiced with different doses of different inducing agents like pituitary gland (PG), human chorionic gonadotropin (HCG), Gonadotropin releasing hormone (GnRH) and Ovuline-a synthetic hormone in different environmental conditions. However, it was observed that the artificial breeding of freshwater mud eel, Monopterus cuchia was not yet succeeded through inducing agents in captive conditions, rather the inducing agent showed negative impacts on fecundity and ovarian tissues. It was seen that mature eggs in the oviduct were reduced, absorbed and some eggs were found in spoiled condition.

Keywords: Breeding biology, induced breeding, Monopterus cuchia.

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Authors: Georgi Yordanov Georgiev, Michael Daly, Erin Gombos, Amrit Vinod, Gajinder Hoonjan

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Measures of complexity and entropy have not converged to a single quantitative description of levels of organization of complex systems. The need for such a measure is increasingly necessary in all disciplines studying complex systems. To address this problem, starting from the most fundamental principle in Physics, here a new measure for quantity of organization and rate of self-organization in complex systems based on the principle of least (stationary) action is applied to a model system - the central processing unit (CPU) of computers. The quantity of organization for several generations of CPUs shows a double exponential rate of change of organization with time. The exact functional dependence has a fine, S-shaped structure, revealing some of the mechanisms of self-organization. The principle of least action helps to explain the mechanism of increase of organization through quantity accumulation and constraint and curvature minimization with an attractor, the least average sum of actions of all elements and for all motions. This approach can help describe, quantify, measure, manage, design and predict future behavior of complex systems to achieve the highest rates of self organization to improve their quality. It can be applied to other complex systems from Physics, Chemistry, Biology, Ecology, Economics, Cities, network theory and others where complex systems are present.

Keywords: Organization, self-organization, complex system, complexification, quantitative measure, principle of least action, principle of stationary action, attractor, progressive development, acceleration, stochastic.

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Authors: Tom Snir, Eitan Rubin

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Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.

Keywords: Systems Biology, Protein Length

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Authors: Arne Koschel, Irina Astrova, Elena Deutschkämer, Jacob Ester, Johannes Feldmann

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In this paper various techniques in relation to large-scale systems are presented. At first, explanation of large-scale systems and differences from traditional systems are given. Next, possible specifications and requirements on hardware and software are listed. Finally, examples of large-scale systems are presented.

Keywords: Distributed file systems, cashing, large scale systems, MapReduce algorithm, NoSQL databases.

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Authors: Mei-Hsiu Chi, Jyh-Yang Wu, Sheng-Gwo Chen

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The diffusion-reaction equations are important Partial Differential Equations in mathematical biology, material science, physics, and so on. However, finding efficient numerical methods for diffusion-reaction systems on curved surfaces is still an important and difficult problem. The purpose of this paper is to present a convergent geometric method for solving the reaction-diffusion equations on closed surfaces by an O(r)-LTL configuration method. The O(r)-LTL configuration method combining the local tangential lifting technique and configuration equations is an effective method to estimate differential quantities on curved surfaces. Since estimating the Laplace-Beltrami operator is an important task for solving the reaction-diffusion equations on surfaces, we use the local tangential lifting method and a generalized finite difference method to approximate the Laplace-Beltrami operators and we solve this reaction-diffusion system on closed surfaces. Our method is not only conceptually simple, but also easy to implement.

Keywords: Close surfaces, high-order approach, numerical solutions, reaction-diffusion systems.

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Authors: Panchalee Sukjit, Herwig Unger

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IT infrastructures are becoming more and more difficult. Therefore, in the first industrial IT systems, the P2P paradigm has replaced the traditional client server and methods of self-organization are gaining more and more importance. From the past it is known that especially regular structures like grids may significantly improve the system behavior and performance. This contribution introduces a new algorithm based on a biologic analogue, which may provide the growth of several regular structures on top of anarchic grown P2P- or social network structures.

Keywords: P2P, Pattern generation, Grid, Social network, Inheritance, Reproduction

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Authors: K. P. Csányi, L. T. Kóczy, D. Tikk

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This paper indicate the importance of telecommunications supervision systems (TSS), integrating heterogeneous TSS into single system thru umbrella systems, introduces the structure, features, requirements of TSS and TSS related intelligent solutions.

Keywords: Telecommunication, telecommunication supervisionsystems, umbrella systems

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Authors: Ikbal Zammouri, Béchir Ayeb

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In this paper, we propose a new method to describe fractal shapes using parametric l-systems. First we introduce scaling factors in the production rules of the parametric l-systems grammars. Then we decorticate these grammars with scaling factors using turtle algebra to show the mathematical relation between l-systems and iterated function systems (IFS). We demonstrate that with specific values of the scaling factors, we find the exact relationship established by Prusinkiewicz and Hammel between l-systems and IFS.

Keywords: Fractal shapes, IFS, parametric l-systems, turtlealgebra.

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Authors: Nidhi Gadura

Abstract:

Given the increase in the number of students and administrators asking for online courses the author developed two partially online courses. One was a biology majors at genetics course while the other was a non-majors at biology course. The student body at Queensborough Community College is generally underprepared and has work and family obligations. As an educator, one has to be mindful about changing the pedagogical approach, therefore, special care was taken when designing the course material. Despite the initial concerns, both of these partially online courses were received really well by students. Lessons learnt were that student engagement is the key to success in an online course. Good practices to run a successful online course for underprepared students are discussed in this paper. Also discussed are the lessons learnt for making the eLearning environment better for all the students in the class, overachievers and underachievers alike.

Keywords: Partially online course, pedagogy, student engagement, community college.

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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: H. Mahboubi, B. Moshiri, A. Khaki Seddigh

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In the past decade, because of wide applications of hybrid systems, many researchers have considered modeling and control of these systems. Since switching systems constitute an important class of hybrid systems, in this paper a method for optimal control of linear switching systems is described. The method is also applied on the two-tank system which is a much appropriate system to analyze different modeling and control techniques of hybrid systems. Simulation results show that, in this method, the goals of control and also problem constraints can be satisfied by an appropriate selection of cost function.

Keywords: Hybrid systems, optimal control, switched systems, two-tank system

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Authors: Albertus G. Joubert, Roelien Goede

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This paper explores how Critical Systems Thinking and Action Research can be used to improve student performance in Networking. When describing a system from a systems thinking perspective, the following aspects can be identified: the total system performance, the systems environment, the resources, the components and the management of the system. Following the history of system thinking we observe three emerged methodologies namely, hard systems, soft systems, and critical systems. This paper uses Critical Systems Thinking (CST) which describes systems in terms of contradictions and conflict. It demonstrates how CST can be used in an Action Research (AR) project to improve the performance of students. Intervention in terms of student assessment is discussed and the impact of the intervention is discussed.

Keywords: Action research, computer networks, critical systems thinking, higher education.

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Authors: Raman Paranjape

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We present a new approach to evaluation of Cyber Security in Power Systems using the method of modeling the power systems Infrastructure using software agents. Interfaces between module and the home smart meter are recognized as the primary points of intrusion.

Keywords: Power Systems, Modeling and Simulation, Agent systems.

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Authors: Roelien Goede

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Data warehousing success is not high enough. User dissatisfaction and failure to adhere to time frames and budgets are too common. Most traditional information systems practices are rooted in hard systems thinking. Today, the great systems thinkers are forgotten by information systems developers. A data warehouse is still a system and it is worth investigating whether systems thinkers such as Churchman can enhance our practices today. This paper investigates data warehouse development practices from a systems thinking perspective. An empirical investigation is done in order to understand the everyday practices of data warehousing professionals from a systems perspective. The paper presents a model for the application of Churchman-s systems approach in data warehouse development.

Keywords: Data warehouse development, Information systemsdevelopment, Interpretive case study, Systems thinking

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Authors: Kholoud A. Al-Shammery , Badr El-Sabah A. Fetoh, Ahmed M. Alshammari

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Protein and Esterase electrophoresis were used to genetically identify two Saudi tick species. Engorged females of the camel tick Hyalomma dromedarii (Koch) (Acari: Ixodidae) and the cattle tick Boophilus annulatus (Say) (Acari: Ixodidae) ticks collected from infested camels and cattle in the animals resting house at Hail region in KSA were used. The results showed that there are a variation in both of protein and esterase activity levels and a high polymorphism within and between the genera and species of Hyalomma and Boophilus . In conclusion, the protein and esterase electrophoretic analysis used in the present study could successfully distinguish among tick species, commonly found in Saudi Arabia.

Keywords: Molecular biology, The camel tick Hyalomma dromedarii, The cattle tick Boophilus annulatus , Ticks.

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Authors: Åsa Smedberg

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There are different kinds of online systems on the Internet for people who need support and develop new knowledge. Online communities and Ask the Expert systems are two such systems. In the health care area, the number of users of these systems has increased at a rapid pace. Interactions with medical trained experts take place online, and people with concerns about similar health problems come together to share experiences and advice. The systems are also used as storages and browsed for health information. Over the years, studies have been conducted of the usage of the different systems. However, in what ways the systems can be used together to enhance learning has not been explored. This paper presents results from a study of online health-communities and an Ask the Expert system for people who suffer from overweight. Differences and similarities in regards to posted issues and replies are discussed, and suggestions for a new holistic design of the two systems are presented.

Keywords: Learning, Ask the Expert, online community, healthcare, holistic, overweight.

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Authors: Mitchell J. McHugh, John J. Case

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Systems engineering is a holistic discipline that seeks to organize and optimize complex, interdisciplinary systems. With the growth of artificial intelligence, systems engineers must face the challenge of leveraging artificial intelligence systems to solve complex problems. This paper analyzes the integration of systems engineering and artificial intelligence and discusses how artificial intelligence systems embody the systems decision process (SDP). The SDP is a four-stage problem-solving framework that outlines how systems engineers can design and implement solutions using value-focused thinking. This paper argues that artificial intelligence models can replicate the SDP, thus validating its flexible, value-focused foundation. The authors demonstrate this by developing a machine vision mobile application that can classify weapons to augment the decision-making role of an Army subject matter expert. This practical application was an end-to-end design challenge that highlights how artificial intelligence systems embody systems engineering principles. The impact of this research demonstrates that the SDP is a dynamic tool that systems engineers should leverage when incorporating artificial intelligence within the systems that they develop.

Keywords: Computer vision, machine learning, mobile application, systems engineering, systems decision process.

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Authors: Chao Qi, Fuyang Peng, Bo Deng, Xiaoyan Su

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In the upgrade process of enterprise information systems, whether new systems will be success and their development will be efficient, depends on how to deal with and utilize those legacy systems. We propose an evaluation system, which comprehensively describes the capacity of legacy information systems in five aspects. Then a practical legacy systems evaluation method is scripted. Base on the evaluation result, we put forward 4 kinds of migration strategy: eliminated, maintenance, modification, encapsulating. The methods and strategies play important roles in practice.

Keywords: Legacy Systems, Evaluation Method, Migration Strategy.

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Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.

Keywords: Metabolic network, gene knockout, flux balance analysis, microarray data, integration.

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Authors: Federico Cabitza, Bernardo Dal Seno

Abstract:

In this paper DJess is presented, a novel distributed production system that provides an infrastructure for factual and procedural knowledge sharing. DJess is a Java package that provides programmers with a lightweight middleware by which inference systems implemented in Jess and running on different nodes of a network can communicate. Communication and coordination among inference systems (agents) is achieved through the ability of each agent to transparently and asynchronously reason on inferred knowledge (facts) that might be collected and asserted by other agents on the basis of inference code (rules) that might be either local or transmitted by any node to any other node.

Keywords: Knowledge-Based Systems, Expert Systems, Distributed Inference Systems, Parallel Production Systems, Ambient Intelligence, Mobile Agents.

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Authors: Michael Torggler

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Modern information and communication technologies offer a variety of support options for the efficient handling of customer relationships. CRM systems have been developed, which are designed to support the processes in the areas of marketing, sales and service. Along with technological progress, CRM systems are constantly changing, i.e. the systems are continually enhanced by new functions. However, not all functions are suitable for every company because of different frameworks and business processes. In this context the question arises whether or not CRM systems are widely used in Austrian companies and which business processes are most frequently supported by CRM systems. This paper aims to shed light on the popularity of CRM systems in Austrian companies in general and the use of different functions to support their daily business. First of all, the paper provides a theoretical overview of the structure of modern CRM systems and proposes a categorization of currently available software functionality for collaborative, operational and analytical CRM processes, which provides the theoretical background for the empirical study. Apart from these theoretical considerations, the paper presents the empirical results of a field survey on the use of CRM systems in Austrian companies and analyzes its findings.

Keywords: CRM systems, CRM system adoption, CRM system diffusion, CRM functionality, Market study.

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Authors: Rihab Gam, Anis Sakly, Faouzi M'sahli

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A new strategy of control is formulated for chaos synchronization of non-identical chaotic systems with different orders using the Borne and Gentina practical criterion associated with the Benrejeb canonical arrow form matrix, to drift the stability property of dynamic complex systems. The designed controller ensures that the state variables of controlled chaotic slave systems globally synchronize with the state variables of the master systems, respectively. Numerical simulations are performed to illustrate the efficiency of the proposed method.

Keywords: Synchronization, Non-identical chaotic systems, Different orders, Arrow form matrix.

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Authors: K. Liagkouras, K. Metaxiotis

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Customer relationship management (CRM) systems in business are a reality of the contemporary business world for the last decade or so. Still, there are grey areas regarding the successful implementation and operation of CRM systems in business. This paper, through the systematic study of the CRM implementation paradigm, attempts to identify the most important challenges and opportunities that the CRM systems face in a rapidly changing business world.

Keywords: Customer Relationship Management, CRM, Business, Information Systems.

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Authors: Nidhi Gadura

Abstract:

To ensure student success in a non-majors biology course, a flipped classroom pedagogical approach was developed and implemented. All students were assigned online lectures to listen to before they come to class. A three hour lecture was split into one hour of online component, one hour of in class lecture and one hour of worksheets done by students in the classroom. This deviation from a traditional 3 hour in class lecture has resulted in increased student interest in science as well as better understanding of difficult scientific concepts. A pre and post survey was given to measure the interest in the subject and grades were used to measure the success rates. While the overall grade average did not change dramatically, students reported a much better appreciation of biology. Also, students overwhelmingly like the use of worksheets in class to help them understand the concepts. They liked the fact that they could listen to lectures at their own pace on line and even repeat if needed. The flipped classroom approach turned out to work really well our non-science majors and the author is ready to implement this in other classrooms.

Keywords: Flipped classroom, non-science majors, pedagogy, technological pedagogical model.

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