Search results for: Cross-validation support vector machine

Authors: Khairul Jauhari, Achmad Widodo, Ismoyo Haryanto

Abstract:

In this article, the radial displacement error correction capability of a high precision spindle grinding caused by unbalance force was investigated. The spindle shaft is considered as a flexible rotor mounted on two sets of angular contact ball bearing. Finite element methods (FEM) have been adopted for obtaining the equation of motion of the spindle. In this paper, firstly, natural frequencies, critical frequencies, and amplitude of the unbalance response caused by residual unbalance are determined in order to investigate the spindle behaviors. Furthermore, an optimization design algorithm is employed to minimize radial displacement of the spindle which considers dimension of the spindle shaft, the dynamic characteristics of the bearings, critical frequencies and amplitude of the unbalance response, and computes optimum spindle diameters and stiffness and damping of the bearings. Numerical simulation results show that by optimizing the spindle diameters, and stiffness and damping in the bearings, radial displacement of the spindle can be reduced. A spindle about 4 μm radial displacement error can be compensated with 2 μm accuracy. This certainly can improve the accuracy of the product of machining.

Keywords: Error correction, High precision grinding, Optimization, Radial displacement, Spindle.

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Authors: R. Pesce Delfino, M. Selvaggi, G. V. Celano, C. Dario

Abstract:

Data on 657 lactation from 163 Maltese goat, collected over a 5-year period were analyzed by a mixed model to estimate the variance components for heritability. The considered lactation traits were: milk yield (MY) and lactation length (LL). Year, parity and type of birth (single or twin) were significant sources of variation for lactation length; on the other hand milk yield was significantly influenced only by the year. The average MY was 352.34 kg and the average LL was 230 days. Estimates of heritability were 0.21 and 0.15 for MY and LL respectively. These values suggest there is low correlation between genotype and phenotype so it may be difficult to evaluate animals directly on phenotype. So, the genetic improvement of this breed may be quite slow without the support of progeny test aimed to select Maltese breeders.

Keywords: Heritability estimate, lactation traits, Maltese goat

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Authors: Maria Eliophotou Menon

Abstract:

School leadership is commonly considered to have a significant influence on school effectiveness and improvement. Effective school leaders are expected to successfully introduce and support change and innovation at the school unit. Despite an abundance of studies on educational leadership, very few studies have provided evidence on the link between leadership models, and specific educational and school outcomes. This is true of a popular contemporary approach to leadership, namely, distributed leadership. The paper provides an overview of research findings on the effect of distributed leadership on educational outcomes. The theoretical basis for this approach to leadership is presented, with reference to methodological and research limitations. The paper discusses research findings and draws their implications for educational research on school leadership.

Keywords: Distributed leadership, educational outcomes, leadership research.

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Authors: A. Maruf Aytekin

Abstract:

We present our approach on using continuous delivery pattern for release management. One of the key practices of agile and lean teams is the continuous delivery of new features to stakeholders. The main benefits of this approach lie in the ability to release new applications rapidly which has real strategic impact on the competitive advantage of an organization. Organizations that successfully implement Continuous Delivery have the ability to evolve rapidly to support innovation, provide stable and reliable software in more efficient ways, decrease the amount of resources need for maintenance, and lower the software delivery time and costs. One of the objectives of this paper is to elaborate a case study where IT division of Central Securities Depository Institution (MKK) of Turkey apply Continuous Delivery pattern to improve release management process.

Keywords: Automation, continuous delivery, deployment, release management.

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Authors: Rosziati Ibrahim, Tiu Kian Yong

Abstract:

Reverse Engineering is a very important process in Software Engineering. It can be performed backwards from system development life cycle (SDLC) in order to get back the source data or representations of a system through analysis of its structure, function and operation. We use reverse engineering to introduce an automatic tool to generate system requirements from its program source codes. The tool is able to accept the Cµ programming source codes, scan the source codes line by line and parse the codes to parser. Then, the engine of the tool will be able to generate system requirements for that specific program to facilitate reuse and enhancement of the program. The purpose of producing the tool is to help recovering the system requirements of any system when the system requirements document (SRD) does not exist due to undocumented support of the system.

Keywords: System Requirements, Reverse Engineering, SourceCodes.

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Authors: Nai-Chieh Wei, I-Ming Chao, Chin-Jung Liuand, Hong Long Chen

Abstract:

This paper combines the branch-and-bound method and the petri net to solve the two-sided assembly line balancing problem, thus facilitating effective branching and pruning of tasks. By integrating features of the petri net, such as reachability graph and incidence matrix, the propose method can support the branch-and-bound to effectively reduce poor branches with systematic graphs. Test results suggest that using petri net in the branching process can effectively guide the system trigger process, and thus, lead to consistent results.

 

Keywords: Branch-and-Bound Method, Petri Net, Two-Sided Assembly Line Balancing Problem.

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Authors: Lokesh Varshney, R. K. Saket

Abstract:

This paper presents reliability indices evaluation of the rotor core magnetization of the induction motor operated as a self excited induction generator by using probability distribution approach and Monte Carlo simulation. Parallel capacitors with calculated minimum capacitive value across the terminals of the induction motor operated as a SEIG with unregulated shaft speed have been connected during the experimental study. A three phase, 4 poles, 50Hz, 5.5 hp, 12.3A, 230V induction motor coupled with DC Shunt Motor was tested in the electrical machine laboratory with variable reactive loads. Based on this experimental study, it is possible to choose a reliable induction machines operated as a SEIG for unregulated renewable energy application in remote area or where grid is not available. Failure density function, cumulative failure distribution function, survivor function, hazard model, probability of success and probability of failure for reliability evaluation of the three phase induction motor operating as a SEIG have been presented graphically in this paper.

Keywords: Residual magnetism, magnetization curve, induction motor, self excited induction generator, probability distribution, Monte Carlo simulation.

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Authors: Sidhartha Panda, Narayana Prasad Padhy

Abstract:

This paper presents a systematic procedure for modelling and simulation of a power system installed with a power system stabilizer (PSS) and a flexible ac transmission system (FACTS)-based controller. For the design purpose, the model of example power system which is a single-machine infinite-bus power system installed with the proposed controllers is developed in MATLAB/SIMULINK. In the developed model synchronous generator is represented by model 1.1. which includes both the generator main field winding and the damper winding in q-axis so as to evaluate the impact of PSS and FACTS-based controller on power system stability. The model can be can be used for teaching the power system stability phenomena, and also for research works especially to develop generator controllers using advanced technologies. Further, to avoid adverse interactions, PSS and FACTS-based controller are simultaneously designed employing genetic algorithm (GA). The non-linear simulation results are presented for the example power system under various disturbance conditions to validate the effectiveness of the proposed modelling and simultaneous design approach.

Keywords: Genetic algorithm, modelling and simulation, MATLAB/SIMULINK, power system stabilizer, thyristor controlledseries compensator, simultaneous design, power system stability.

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Authors: Patrick Maier, Marcus Tönnis, Gudrun Klinker

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Spatial understanding and the understanding of dynamic change in the spatial structure of molecules during a reaction is essential for designing new molecules. Knowing the physical processes in the reactions helps to speed up the designing process. To support the designer with the correct representation of the designed molecule as well as showing the dynamic behavior of the whole reacting system is the goal of our application. Our system shows the spatial deformation of the molecules at every time interval by minimizing the energy level of the molecules. The position and orientation of the molecules can be intuitively controlled by manipulating objects of the real world using Augmented Reality techniques. Our approach has the potential to speed up the design of new molecules and help students to understand the chemical processes better.

Keywords: Augmented Augmented Chemical Reactions, Augmented Reality, chemistry, education.

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Authors: Haeng A. Seo, Changseok Oh, Seung Jun Yoo

Abstract:

This study attempts to examine the disparities in S&T innovation capacity from 14 developing countries to discuss how to support specific features in national innovation systems. It includes East-Asian, Middle-Asian, Central American and African countries. Here, we particularly focus on five dimensions- resources, activities, network, environment and performance- with 37 indicators. They were derived as structuring components of the relevant diagnostic model, which encompasses the whole process of S&T innovation from the input of resources to the output of economically valuable results. For many developing nations, economic industries remain weaker than actual S&T capabilities, and relevant regulatory authorities may not exist. This paper will be helpful to provide basic evidence and to set directions for better national S&T Innovation capacities and toward national competitiveness.

Keywords: Developing countries, measurement, NIS, S&T innovation capacity.

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Authors: Niousha Bagheri Khulenjani, Mohammad Saniee Abadeh

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Learning from very big datasets is a significant problem for most present data mining and machine learning algorithms. MicroRNA (miRNA) is one of the important big genomic and non-coding datasets presenting the genome sequences. In this paper, a hybrid method for the classification of the miRNA data is proposed. Due to the variety of cancers and high number of genes, analyzing the miRNA dataset has been a challenging problem for researchers. The number of features corresponding to the number of samples is high and the data suffer from being imbalanced. The feature selection method has been used to select features having more ability to distinguish classes and eliminating obscures features. Afterward, a Convolutional Neural Network (CNN) classifier for classification of cancer types is utilized, which employs a Genetic Algorithm to highlight optimized hyper-parameters of CNN. In order to make the process of classification by CNN faster, Graphics Processing Unit (GPU) is recommended for calculating the mathematic equation in a parallel way. The proposed method is tested on a real-world dataset with 8,129 patients, 29 different types of tumors, and 1,046 miRNA biomarkers, taken from The Cancer Genome Atlas (TCGA) database.

Keywords: Cancer classification, feature selection, deep learning, genetic algorithm.

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Authors: Nittaya Kerdprasop, Narin Muenrat, Kittisak Kerdprasop

Abstract:

A learning content management system (LCMS) is an environment to support web-based learning content development. Primary function of the system is to manage the learning process as well as to generate content customized to meet a unique requirement of each learner. Among the available supporting tools offered by several vendors, we propose to enhance the LCMS functionality to individualize the presented content with the induction ability. Our induction technique is based on rough set theory. The induced rules are intended to be the supportive knowledge for guiding the content flow planning. They can also be used as decision rules to help content developers on managing content delivered to individual learner.

Keywords: Decision rules, Knowledge induction, Learning content management system, Rough set.

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Authors: Kanika Sood, Sijie Shang

Abstract:

A fundamental goal of education includes preparing students to become a part of the global workforce by making beneficial contributions to society. In this paper, we analyze student performance for multiple courses that involve different teaching pedagogies: a cooperative learning technique and an inquiry-based learning strategy. Student performance includes student engagement, grades, and attendance records. We perform this study in the Computer Science department for online and in-person courses for 450 students. We will perform correlation analysis to study the relationship between student scores and other parameters such as gender, mode of learning. We use natural language processing and machine learning to analyze student feedback data and performance data. We assess the learning outcomes of two teaching pedagogies for undergraduate and graduate courses to showcase the impact of pedagogical adoption and learning outcome as determinants of academic achievement. Early findings suggest that when using the specified pedagogies, students become experts on their topics and illustrate enhanced engagement with peers.

Keywords: Bag-of-words, cooperative learning, education, inquiry-based learning, in-person learning, Natural Language Processing, online learning, sentiment analysis, teaching pedagogy.

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Authors: Zhou Xiong, Kang Shao Bo, Yang Bo

Abstract:

To date, high-performance structural steel has been widely used for columns in construction practices due to its significant advantages over conventional steel. However, the same design approach with conventional steel columns is still adopted in the design of high-performance steel columns. As a result, its superior properties cannot be fully considered in design. This paper conducts a test and finite element analysis on the overall stability behaviour of welded Q460GJ steel box columns. In the test, four steel columns with different slenderness and width-to-thickness ratio were compressed under an axial compression testing machine. And finite element models were established in which material nonlinearity and residual stress distributions of test columns were included. Then, comparisons were made between test results and finite element result, it showed that finite element analysis results are agree well with the test result. It means that the test and finite element model are reliable. Then, we compared the test result with the design value calculated by current code, the result showed that Q460GJ steel box columns have the higher overall buckling capacity than the design value. It is necessary to update the design curves for Q460GJ steel columns so that the overall stability capacity of Q460GJ box columns can be designed appropriately.

Keywords: Axial compression, Finite element analysis, Overall stability, Q460GJ steel, Welded box columns.

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Authors: Manish Jain, Dinesh Gopalani

Abstract:

Growing dependency of mankind on software technology increases the need for thorough testing of the software applications and automated testing techniques that support testing activities. We have outlined our testing strategy for performing various types of automated testing of Java applications using AspectJ which has become the de-facto standard for Aspect Oriented Programming (AOP). Likewise JUnit, a unit testing framework is the most popular Java testing tool. In this paper, we have evaluated our proposed AOP approach for automated testing and JUnit on various parameters. First we have provided the similarity between the two approaches and then we have done a detailed comparison of the two testing techniques on factors like lines of testing code, learning curve, testing of private members etc. We established that our AOP testing approach using AspectJ has got several advantages and is thus particularly more effective than JUnit.

Keywords: Aspect oriented programming, AspectJ, Aspects, JUnit, software testing.

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Authors: Madiajagan Muthaiyan, Neha Goel, Deepti Sunder Prakash

Abstract:

This paper discusses about an intelligent system to be installed in ambulances providing professional support to the paramedics on board. A video conferencing device over mobile 4G services enables specialists virtually attending the patient being transferred to the hospital. The data centre holds detailed databases on the patients past medical history and hospitals with the specialists. It also hosts various software modules that compute the shortest traffic –less path to the closest hospital with the required facilities, on inputting the symptoms of the patient, on a real time basis.

Keywords: 4G mobile services, cloud computing, data centre, intelligent system, optimization, real time traffic reporting, SaaS, video conferencing.

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Authors: E. Rak

Abstract:

The aim of the paper is to identify some of the specific characteristics of employee development, as observed in the practice of small enterprises in Poland. Results suggest that a sizeable percentage of employers are not interested in improving the development of their employee base. This aspect is often perceived as insignificant. In addition, many employers have no theoretical or practical knowledge of employee development methods. Lack of sufficient financial support is reported as third on the list of the most important barriers to employee development. Employees, on the other hand, typically offload the responsibility of initiating this type of activities onto the employer. Employee development plans are typically flexible and accommodating. The original value offered by this research comes in the form of a detailed characteristics of employee development in small enterprises, accompanied by identification of specificity of human resource development in Polish companies.

Keywords: Employee development specificity, human resources development, small businesses, trainings.

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Authors: Masoud Hekmatpanah, Mohammad Sadroddin, Saeid Shahbaz, Farhad Mokhtari, Farahnaz Fadavinia

Abstract:

The six sigma method is a project-driven management approach to improve the organization-s products, services, and processes by continually reducing defects in the organization. Understanding the key features, obstacles, and shortcomings of the six sigma method allows organizations to better support their strategic directions, and increasing needs for coaching, mentoring, and training. It also provides opportunities to better implement six sigma projects. The purpose of this paper is the survey of six sigma process and its impact on the organizational productivity. So I have studied key concepts , problem solving process of six sigmaas well as the survey of important fields such as: DMAIC, six sigma and productivity applied programme, and other advantages of six sigma. In the end of this paper, present research conclusions. (direct and positive relation between six sigma and productivity)

Keywords: Six sigma, project management, quality, theory, productivity.

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Authors: Fereshteh Mahdavi, Maizatul Akmar Ismail, Noorhidawati Abdullah

Abstract:

Currently WWW is the first solution for scholars in finding information. But, analyzing and interpreting this volume of information will lead to researchers overload in pursuing their research. Trend detection in scientific publication retrieval systems helps scholars to find relevant, new and popular special areas by visualizing the trend of input topic. However, there are few researches on trend detection in scientific corpora while their proposed models do not appear to be suitable. Previous works lack of an appropriate representation scheme for research topics. This paper describes a method that combines Semantic Web and ontology to support advance search functions such as trend detection in the context of scholarly Semantic Web system (SSWeb).

Keywords: Trend, Semi-Automatic Trend Detection, Ontology, Semantic Trend Detection.

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Authors: Sanghoon Park, Ki-Jin Kim, Kwang-Ho Ahn, Hyeon-Woo Lee

Abstract:

It is very effective way to utilize a very wide tunable filter in co-existing multi-standards wireless communications environment. Especially, as the long term evolution (LTE) communication era has come, the multi-band coverage is one of the important features required for the RF components. In this paper, we present the frequency conversion technique, and so generate two types of RF filters which are specially designed for the superb tunable ability to support multiple wireless communication standards. With the help of a complex mixing structure, the inherent image signal is suppressed. The RF band-pass filter (BPF) and notch filter achieve 1.8dB and 1.6dB insertion losses and 18 dB and 17 dB attenuations, respectively. The quality factor show greater than 30.

Keywords: RF filters, interference, wideband, tunable, channel selection, complex mixing, balanced mixer.

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Authors: Mohamed A. Mahfouz, M. A. Ismail

Abstract:

Biclustering is a very useful data mining technique for identifying patterns where different genes are co-related based on a subset of conditions in gene expression analysis. Association rules mining is an efficient approach to achieve biclustering as in BIMODULE algorithm but it is sensitive to the value given to its input parameters and the discretization procedure used in the preprocessing step, also when noise is present, classical association rules miners discover multiple small fragments of the true bicluster, but miss the true bicluster itself. This paper formally presents a generalized noise tolerant bicluster model, termed as μBicluster. An iterative algorithm termed as BIDENS based on the proposed model is introduced that can discover a set of k possibly overlapping biclusters simultaneously. Our model uses a more flexible method to partition the dimensions to preserve meaningful and significant biclusters. The proposed algorithm allows discovering biclusters that hard to be discovered by BIMODULE. Experimental study on yeast, human gene expression data and several artificial datasets shows that our algorithm offers substantial improvements over several previously proposed biclustering algorithms.

Keywords: Machine learning, biclustering, bi-dimensional clustering, gene expression analysis, data mining.

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Authors: Dimitrios J. Dimitriou

Abstract:

The decades after the end of the second War provide evidence that infrastructures investments contibute to economic development, on terms of productivity and income growth. In order to force productivity and increase competitiveness the financing of large transport infrastructure projects are on the top of the agenda in strategic planning process. Such a decision may take form some days to some decades and stakeholders as well as decision makers need tools in order to estimate the economic impact on natioanl economy of such an investment. The key question in such decisions is if the effects caused by the new infrastructure could be able to boost economic development on one hand, and create new jobs and activities on the other. This paper deals with the review of estimation of the mega transport infrastructure projects economic effects in economy.

Keywords: Economic impact, transport infrastructure, strategic planning.

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Authors: Carol Shepherd, Madelon Alpert, Marilyn Koeller

Abstract:

In order to provide and maintain effective pedagogy for the burgeoning virtual reality community, it is vital to have trained faculty in the institutions of higher education who will teach these courses and be able to make full use of their academic knowledge and expertise. As the number of online courses continues to grow, there is a need for these institutions to establish mentoring programs that will support the novice online instructor. The environment in which this takes place and the factors that ensure its success are critical to the adoption of the new instructional delivery format taught by both seasoned educators and adjunct instructors. Effective one-on-one mentoring promotes a professional, compassionate and collegial faculty who will provide a consistent and rigorous academic program for students online.

Keywords: Mentoring seasoned faculty, staff development, online pedagogy, online andragogy.

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Authors: Eva Kotlánová

Abstract:

After recession that began in 2007 in the United States and subsequently spilled over the Europe we could expect recovery of economic growth. According to the last estimation of economic progress of European countries, this recovery is not strong enough. Among others, it will depend on economic policy, where and in which way, the economic indicators will proceed. Economic theories postulate that the economic subjects prefer stably, continual economic policy without repeated and strong fluctuations. This policy is perceived as support of economic growth. Mostly in crises period, when the government must cope with consequences of recession, the economic policy becomes unpredictable for many subjects and economic policy uncertainty grows, which have negative influence on economic growth. The aim of this paper is to use panel regression to prove or disprove this hypothesis on the example of five largest European economies in the period 2008–2012.

Keywords: Economic Crises in Europe, Economic Policy, Uncertainty, Panel Analysis Regression.

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Authors: Najwa Alsayed Omar

Abstract:

With the increasing popularity of the Internet, online reading has become an essential source for EFL readers. Using strategies to comprehend information on online reading texts play a crucial role in students’ academic success. Metacognitive reading strategies are effective factors that enhance EFL learners reading comprehension. This study aimed at exploring the use of online metacognitive reading strategies by postgraduate Libyan EFL students. Quantitative data was collected using the Survey of Online Reading Strategies (OSORS). The findings revealed that the participants were moderate users of metacognitive online reading strategies. Problem solving strategies were the most frequently reported used strategies, while support reading strategies were the least. The five most and least frequently reported strategies were identified. Based on the findings, some future research recommendations were presented.

Keywords: Metacognitive strategies, Online reading, Online reading strategies, Postgraduate students.

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Authors: Eiad Yafi, M. A. Alam, Ranjit Biswas

Abstract:

Knowledge Discovery of Databases (KDD) is the process of extracting previously unknown but useful and significant information from large massive volume of databases. Data Mining is a stage in the entire process of KDD which applies an algorithm to extract interesting patterns. Usually, such algorithms generate huge volume of patterns. These patterns have to be evaluated by using interestingness measures to reflect the user requirements. Interestingness is defined in different ways, (i) Objective measures (ii) Subjective measures. Objective measures such as support and confidence extract meaningful patterns based on the structure of the patterns, while subjective measures such as unexpectedness and novelty reflect the user perspective. In this report, we try to brief the more widely spread and successful subjective measures and propose a new subjective measure of interestingness, i.e. shocking.

Keywords: Shocking rules (SHR).

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Authors: K. Piórkowska

Abstract:

The overarching aim of the paper is to incorporate the micro-foundations perspective in strategic management and offering possibilities to bridge the macro–micro divide, to review the concept of habits, as well as to propose research findings and directions in terms of further exploring the habit construct and its impact on higher epistemological level phenomena (for instance organizational routines, which is a domain inherently multilevel in nature). To realize this aim, the following sections have been developed: (1) habits’ origins, (2) habits – cognitive constellations, (3) interrelationships between habits and mental representations, intentions, (4) habits and organizational routines, and (5) habits and routines linkages with adaptation. The conclusions that have been made support recent and current studies linking the level of individual heterogeneous agents with the level of macro (organizational) outcomes.

Keywords: Behaviorism, habits, micro-foundations, routines.

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Authors: S. Manaseer, F. A. Masooud, A. A. Sharieh

Abstract:

Fault tolerance is critical in many of today's large computer systems. This paper focuses on improving fault tolerance through testing. Moreover, it concentrates on the memory faults: how to access the editable part of a process memory space and how this part is affected. A special Software Fault Injection Technique (SFIT) is proposed for this purpose. This is done by sequentially scanning the memory of the target process, and trying to edit maximum number of bytes inside that memory. The technique was implemented and tested on a group of programs in software packages such as jet-audio, Notepad, Microsoft Word, Microsoft Excel, and Microsoft Outlook. The results from the test sample process indicate that the size of the scanned area depends on several factors. These factors are: process size, process type, and virtual memory size of the machine under test. The results show that increasing the process size will increase the scanned memory space. They also show that input-output processes have more scanned area size than other processes. Increasing the virtual memory size will also affect the size of the scanned area but to a certain limit.

Keywords: Complex software systems, Error detection, Fault tolerance, Injection and testing methodology, Memory faults, Process and virtual memory.

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Authors: Norihiro Nishio, Yuki Deguchi, Takahiro Sugiyama, Yoichi Takebayashi

Abstract:

We developed a multi-camera control system that a (one) cameraman can operate several cameras at a compact studio. we analyzed a workflow of a cameraman of some program shootings with two cameras and clarified their heavy tasks. The system based on a dynamic workflow which adapts a program progressing and recommends of cameraman. we perform the automation of multicamera controls by modeling of studio environment and perform automatic camera adjustment for suitable angle of view with face detection. Our experiment at a real program shooting showed that one cameraman can carry out the task of shooting sufficiently.

Keywords: Camera work, compact studio, dynamic workflow, shooting support.

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Authors: Paola Lecca, Lorenzo Dematte

Abstract:

Reactiondiffusion systems are mathematical models that describe how the concentration of one or more substances distributed in space changes under the influence of local chemical reactions in which the substances are converted into each other, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear parabolic partial differential equations, whose general form is ÔêétX(x, t) = DΔX(x, t), where X(x, t) is the state vector, D is the matrix of the diffusion coefficients and Δ is the Laplace operator. If the solute move in an homogeneous system in thermal equilibrium, the diffusion coefficients are constants that do not depend on the local concentration of solvent and of solutes and on local temperature of the medium. In this paper a new stochastic reaction-diffusion model in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces of solvent and solute is presented. Such a model provides a more realistic description of the molecular kinetics in non-homogenoeus and highly structured media as the intra- and inter-cellular spaces. The movement of a molecule A from a region i to a region j of the space is described as a first order reaction Ai k- → Aj , where the rate constant k depends on the diffusion coefficient. Representing the diffusional motion as a chemical reaction allows to assimilate a reaction-diffusion system to a pure reaction system and to simulate it with Gillespie-inspired stochastic simulation algorithms. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the specific speed of reaction and diffusion events. Redi is the software tool, developed to implement the model of reaction-diffusion kinetics and dynamics. It is a free software, that can be downloaded from http://www.cosbi.eu. To demonstrate the validity of the new reaction-diffusion model, the simulation results of the chaperone-assisted protein folding in cytoplasm obtained with Redi are reported. This case study is redrawing the attention of the scientific community due to current interests on protein aggregation as a potential cause for neurodegenerative diseases.

Keywords: Reaction-diffusion systems, Fick's law, stochastic simulation algorithm.

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