Search results for: human contact networks

Authors: A. Kawamura, K. Ishida, K. Okada, T. Sato

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Simultaneous measurements of the curves for wear versus distance, wear rate versus distance, and coefficient of friction versus distance were performed in situ to distinguish the transition from severe running-in wear to mild wear. The effects of the initial surface roughness on the severe running-in wear volume were investigated. Disk-on-plate friction and wear tests were carried out with SUS304 austenitic stainless steel in contact with itself under repeated dry sliding conditions at room temperature. The wear volume was dependent on the initial surface roughness. The wear volume when the initial surfaces on the plate and disk had dissimilar roughness was lower than that when these surfaces had similar roughness. For the dissimilar roughness, the wear volume decreased with decreasing initial surface roughness and reached a minimum; it stayed nearly constant as the roughness was less than the mean size of the oxide particles.

Keywords: Austenitic stainless steel, initial surface roughness, running-in, severe wear.

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Authors: Mohammad Ali Baradaran Ghahfarokhi, Parvin Baradaran Ghahfarokhi

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In this paper, first we introduce the stable distribution, stable process and theirs characteristics. The a -stable distribution family has received great interest in the last decade due to its success in modeling data, which are too impulsive to be accommodated by the Gaussian distribution. In the second part, we propose major applications of alpha stable distribution in telecommunication, computer science such as network delays and signal processing and financial markets. At the end, we focus on using stable distribution to estimate measure of risk in stock markets and show simulated data with statistical softwares.

Keywords: stable distribution, SaS, infinite variance, heavy tail networks, VaR.

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Authors: Sung Jun Ban, Hyeonwoo Cho, ChangWoo Lee, Sang Woo Kim

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A packet analyzer is a tool for debugging sensor network systems and is convenient for developers. In this paper, we introduce a new packet analyzer based on an embedded system. The proposed packet analyzer is compatible with IEEE 802.15.4, which is suitable for the wireless communication standard for sensor networks, and is available for remote control by adopting a server-client scheme based on the Ethernet interface. To confirm the operations of the packet analyzer, we have developed two types of sensor nodes based on PIC4620 and ATmega128L microprocessors and tested the functions of the proposed packet analyzer by obtaining the packets from the sensor nodes.

Keywords: Sensor network, embedded system, packet analyzer.

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Authors: Hong Choon Ong

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Naïve Bayes classifiers are simple probabilistic classifiers. Classification extracts patterns by using data file with a set of labeled training examples and is currently one of the most significant areas in data mining. However, Naïve Bayes assumes the independence among the features. Structural learning among the features thus helps in the classification problem. In this study, the use of structural learning in Bayesian Network is proposed to be applied where there are relationships between the features when using the Naïve Bayes. The improvement in the classification using structural learning is shown if there exist relationship between the features or when they are not independent.

Keywords: Bayesian Network, Classification, Naïve Bayes, Structural Learning.

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Authors: Shiau-Feng Lin, Chiuhsiang Joe Lin, Rou-Wen Wang, Wei-Jung Shiang

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The Virtual Reality (VR) is becoming increasingly important for business, education, and entertainment, therefore VR technology have been applied for training purposes in the areas of military, safety training and flying simulators. In particular, the superior and high reliability VR training system is very important in immersion. Manipulation training in immersive virtual environments is difficult partly because users must do without the hap contact with real objects they rely on in the real world to orient themselves and their manipulated. In this paper, we create a convincing questionnaire of immersion and an experiment to assess the influence of immersion on performance in VR training system. The Immersion Questionnaire (IQ) included spatial immersion, Psychological immersion, and Sensory immersion. We show that users with a training system complete visual attention and detection of signals. Twenty subjects were allocated to a factorial design consisting of two different VR systems (Desktop VR and Projector VR). The results indicated that different VR representation methods significantly affected the participants- Immersion dimensions.

Keywords: Virtual Reality, Training, Immersion, Visual Attention, Visual Detection

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Authors: Dong-Woo Lim, Chang-Jae Chun, Hyung-Myung Kim

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We consider a two-way relay network where two sources exchange information. A relay helps the two sources exchange information using the decode-and-XOR-forward protocol. We investigate the power minimization problem with minimum rate constraints. The system needs two time slots and in each time slot the required rate pair should be achievable. The power consumption is minimized in each time slot and we obtained the closed form solution. The simulation results confirm that the proposed power allocation scheme consumes lower total power than the conventional schemes.

Keywords: Decode-and-XOR-forward, power minimization, two-way relay

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Authors: Bharat B. Gulyani, Anuj Jain, Shalendra Kumar

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Customarily, the LMTD correction factor, FT, is used to screen alternative designs for a heat exchanger. Designs with unacceptably low FT values are discarded. In this paper, authors have proposed a more fundamental criterion, based on feasibility of a multipass exchanger as the only criteria, followed by economic optimization. This criterion, coupled with asymptotic energy targets, provide the complete optimization space in a heat exchanger network (HEN), where cost-optimization of HEN can be performed with only Heat Recovery Approach temperature (HRAT) and number-of-shells as variables.

Keywords: heat exchanger, heat exchanger networks, LMTD correction factor, shell targeting.

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Authors: Oktay Nusratov, Ramin Rzaev, Aydin Goyushov

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Fuzzy inference method based approach to the forming of modular intellectual system of assessment the quality of communication services is proposed. Developed under this approach the basic fuzzy estimation model takes into account the recommendations of the International Telecommunication Union in respect of the operation of packet switching networks based on IPprotocol. To implement the main features and functions of the fuzzy control system of quality telecommunication services it is used multilayer feedforward neural network.

Keywords: Quality of communication, IP-telephony, Fuzzy set, Fuzzy implication, Neural network.

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Authors: Zhalmagambetov Yerlanbek, Assymova Dariya, Tashieva Saltanat, and Aliya Bolatkhan

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The relevance of the study of everyday life in Almaty and Kyzylorda are associated with the emergence of the modern trends in historiography and socializing areas of government reform. The relevance is due to the fact that in the early twentieth century Kyzylorda and Almaty began to develop as a city and this period has a special place in the life of the state. An interesting aspect of the everyday life of the inhabitants of the new city, which was built in the era of Stalin's Five-Year Plans, can be examined through the eyes of the Soviet people living in a specific environment, reflecting the life of the citizens. The study of industrialization of the Soviet Union and the attention paid to new developments in the first five years of everyday aspects as the impact of the modernization of the 1930s was one of the decisive factors in the lives of residents. Among these factors, we would like to highlight the medical field, which is the basis of all human life, specifically focusing on the state of medicine in Alma-Ata in the first 20-30-years of the twentieth century, and analyze the different aspects of human life, determining the quality of medical care to the population during this period.

Keywords: Alma Ata, capital, epidemic diseases, health care, Kyzylorda, the USSR, Vernyj.

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Authors: Srinivasa Reddy Mallampati, Chi-Hyeon Lee, Nguyen Thi Thanh Truc, Byeong-Kyu Lee

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In the present study, feasibility of the selective surface hydrophilization of polyvinyl chloride (PVC) by microwave treatment was evaluated to facilitate the separation from automotive shredder residue (ASR), by the froth flotation. The combination of 60 sec microwave treatment with PAC, a sharp and significant decrease about 16.5° contact angle of PVC was observed in ASR plastic compared with other plastics. The microwave treatment with the addition of PAC resulted in a synergetic effect for the froth flotation, which may be a result of the 90% selective separation of PVC from ASR plastics, with 82% purity. While, simple mixing with a nanometallic Ca/CaO/PO4 dispersion mixture immobilized 95-100% of heavy metals in ASR soil/residues. The quantity of heavy metals leached from thermal residues after treatment by nanometallic Ca/CaO/PO4 was lower than the Korean standard regulatory limit for hazardous waste landfills. Microwave treatment can be a simple and effective method for PVC separation from ASR plastics.

Keywords: Automotive shredder residue, microwave treatment, chlorinated plastics, separation, heavy metals, Immobilization, separation.

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Authors: Vishnu Pratap Singh Kirar

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Wireless sensor network (WSN) is a network of many interconnected networked systems, they equipped with energy resources and they are used to detect other physical characteristics. On WSN, there are many researches are performed in past decades. WSN applicable in many security systems govern by military and in many civilian related applications. Thus, the security of WSN gets attention of researchers and gives an opportunity for many future aspects. Still, there are many other issues are related to deployment and overall coverage, scalability, size, energy efficiency, quality of service (QoS), computational power and many more. In this paper we discus about various applications and security related issue and requirements of WSN.

Keywords: Wireless Sensor Network (WSN), Wireless Network Attacks, Wireless Network Security.

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Authors: Sergey N. Sayapin, Anatoly P. Karpenko, Suan H. Dang

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Comparative analysis of robotic vehicles for pipe inspection is presented in this paper. The promising concept of self-propelled intelligent robotic vehicle (SPIRV) based on octahedral dodekapod for inspection and operation in active branched pipelines with variable cross-sections is reasoned. SPIRV is able to move in pipeline, regardless of its spatial orientation. SPIRV can also be used to move along the outside of the pipelines as well as in space between surfaces of annular tubes. Every one of faces of the octahedral dodekapod can clamp/unclamp a thing with a closed loop surface of various forms as well as put pressure on environmental surface of contact. These properties open new possibilities for its applications in SPIRV. We examine design principles of octahedral dodekapod as future intelligent building blocks for various robotic vehicles that can self-move and self-reconfigure.

Keywords: Modular robot, octahedral dodekapod, pipe inspection robot, spatial parallel structure.

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Authors: Maziar Ramezani, Zaidi Mohd Ripin

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In a metal forming process, the friction between the material and the tools influences the process by modifying the stress distribution of the workpiece. This frictional behaviour is often taken into account by using a constant coefficient of friction in the finite element simulations of sheet metal forming processes. However, friction coefficient varies in time and space with many parameters. The Stribeck friction model is investigated in this study to predict springback behaviour of AA6061-T4 sheets during V-bending process. The coefficient of friction in Stribeck curve depends on sliding velocity and contact pressure. The plane-strain bending process is simulated in ABAQUS/Standard. We compared the computed punch load-stroke curves and springback related to the constant coefficient of friction with the defined friction model. The results clearly showed that the new friction model provides better agreement between experiments and results of numerical simulations. The influence of friction models on stress distribution in the workpiece is also studied numerically

Keywords: Friction model, Stress distribution, V-bending.

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Authors: S. Barabas, F. Sarbu, B. Barabas, A. Fota

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Main objective of this paper is to establish a link between inertial forces of the bearings used in construction of wind power plant and its behavior. Using bearings with lower inertial forces has the immediate effect of decreasing inertia rotor system, with significant results in increased energy efficiency, due to decreased friction forces between rollers and raceways. The F.E.M. analysis shows the appearance of uniform contact stress at the ends of the rollers, demonstrated the necessity of production of low mass bearings. Favorable results are expected in the economic field, by reducing material consumption and by increasing the durability of bearings. Using low mass bearings with hollow rollers instead of solid rollers has an impact on working temperature, on vibrations and noise which decrease. Implementation of types of hollow rollers of cylindrical tubular type, instead of expensive rollers with logarithmic profile, will bring significant inertial forces decrease with large benefits in behavior of wind power plant.

Keywords: Inertial forces, Von Mises stress, hollow rollers.

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Authors: Ko-Shao Chen, Yun Tsao, Chia-Hsuan Tsen, Chien-Chung Chen, Shu-Chuan Liao

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Electrospun microtube array membranes (MTAMs) made of PLLA (poly-L-lactic acid) have wide potential applications in tissue engineering. However, their surface hydrophobicity and poor biocompatability have limited their further usage. In this study, the surface of PLLA MTAMs were made hydrophilic by introducing extra functional groups, such as peroxide, via an acetic acid plasma (AAP). UV-graft polymerization of acrylic acid (G-AAc) was then used to produce carboxyl group on MTAMs surface, which bonded covalently with chitosan through EDC / NHS crosslinking agents. To evaluate the effects of the surface modification on PLLA MTAMs, water contact angle (WCA) measurement and cell compatibility tests were carried out. We found that AAP treated electrospun PLLA MTAMs grafted with AAc and, finally, with chitosan immobilized via crosslinking agent, exhibited improved hydrophilic and cell compatibility.

Keywords: Plasma, EDC/NHS, UV grafting, chitosan, microtube array membrane.

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Authors: Toshitaka Higashino, Naoki Wakamiya

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Human beings perform a task by perceiving information from outside, recognizing them, and responding them. There have been various attempts to analyze and understand internal processes behind the reaction to a given stimulus by conducting psychological experiments and analysis from multiple perspectives. Among these, we focused on Model Human Processor (MHP). However, it was built based on psychological experiments and thus the relation with brain activity was unclear so far. To verify the validity of the MHP and propose our model from a viewpoint of neuroscience, EEG (Electroencephalography) measurements are performed during experiments in this study. More specifically, first, experiments were conducted where Latin alphabet characters were used as visual stimuli. In addition to response time, ERPs (event-related potentials) such as N100 and P300 were measured by using EEG. By comparing cycle time predicted by the MHP and latency of ERPs, it was found that N100, related to perception of stimuli, appeared at the end of the perceptual processor. Furthermore, by conducting an additional experiment, it was revealed that P300, related to decision making, appeared during the response decision process, not at the end. Second, by experiments using Japanese Hiragana characters, i.e. Japan's own phonetic symbols, those findings were confirmed. Finally, Japanese Kanji characters were used as more complicated visual stimuli. A Kanji character usually has several readings and several meanings. Despite the difference, a reading-related task and a meaning-related task exhibited similar results, meaning that they involved similar information processing processes of the brain. Based on those results, our model was proposed which reflects response time and ERP latency. It consists of three processors: the perception processor from an input of a stimulus to appearance of N100, the cognitive processor from N100 to P300, and the decision-action processor from P300 to response. Using our model, an application system which reflects brain activity can be established.

Keywords: Brain activity, EEG, information processing model, model human processor.

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Authors: Ren-Jieh Kuo, Chun-Shou Huang

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The research of juice flavor forecasting has become more important in China. Due to the fast economic growth in China, many different kinds of juices have been introduced to the market. If a beverage company can understand their customers’ preference well, the juice can be served more attractive. Thus, this study intends to introducing the basic theory and computing process of grapes juice flavor forecasting based on support vector regression (SVR). Applying SVR, BPN, and LR to forecast the flavor of grapes juice in real data shows that SVR is more suitable and effective at predicting performance.

Keywords: Flavor forecasting, artificial neural networks, support vector regression, grape juice flavor.

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Authors: Muhammad Ijaz Khan, Samina Jalali, Beenish Shahid, S. A. Shami, Muhammad Ikramullah

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In the present study, the response of Nili Ravi buffalo oocytes to recombinant human follicle stimulating hormone (rhFSH) (Organon) on meiotic maturation in vitro was examined. Oocytes were matured in vitro in medium containing either 0 or 0.05 IU/ ml rhFSH and the stage of nuclear maturation recorded after 24 hours. The percentage of oocytes in the control group undergoing germinal vesicle breakdown (GVBD) observed after 24 hours of culture was 29 % whereas as in rhFSH group the percentage was 10 % were at this stage (P< 0.001).Thus in the presence of rhFSH, a significantly greater number of oocytes had progressed to the more advanced stages of nuclear maturation. Indeed, the maturation of GV (Germinal Vesicle) stage oocytes to the metaphase II (M II) stage after 24 hours was significantly (P< 0.0001) increased by the addition of rhFSH (82 % VS 47 %). The percentage of degenerated oocytes after 24 hours of culture was 24 % in control group, whereas in rhFSH group the percentage was 8 % after 24 hours. Degeneration of the oocytes after 24 hours was not significantly (P = 0. 9361) decreased.

Keywords: Buffalo, in vitro, oocytes, recombinant FSH.

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Authors: M. Hassani, Y. Hassani, N. Ajudanioskooei, N. N. Benvid

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Laser Forming process as a non-contact thermal forming process is widely used to forming and bending of metallic and non-metallic sheets. In this process, according to laser irradiation along a specific path, sheet is bent. One of the most important output parameters in laser forming is bending angle that depends on process parameters such as physical and mechanical properties of materials, laser power, laser travel speed and the number of scan passes. In this paper, Artificial Neural Network and Fuzzy Logic System were used to predict of bending angle in laser forming process. Inputs to these models were laser travel speed and laser power. The comparison between artificial neural network and fuzzy logic models with experimental results has been shown both of these models have high ability to prediction of bending angles with minimum errors.

Keywords: Artificial neural network, bending angle, fuzzy logic, laser forming.

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Authors: Raeesa Moolla, Ryan S. Johnson

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Air travel, and the use of airports, has experienced proliferative growth in the past few decades, resulting in the concomitant release of air pollutants. Air pollution needs to be monitored because of the known relationship between exposure to air pollutants and increased adverse effects on human health. This study monitored a group of volatile organic compounds (VOCs); specifically BTEX (viz. benzene, toluene, ethyl-benzene and xylenes), as many are detrimental to human health. Through the use of passive sampling methods, the spatial variability of BTEX within an international airport was investigated, in order to determine ‘hotspots’ where occupational exposure to BTEX may be intensified. The passive sampling campaign revealed BTEX_total concentrations ranged between 12.95–124.04 µg m^-3. Furthermore, BTEX concentrations were dispersed heterogeneously within the airport. Due to the slow wind speeds recorded (1.13 m.s^-1); the hotspots were located close to their main BTEX sources. The main hotspot was located over the main apron of the airport. Employees working in this area may be chronically exposed to these emissions, which could be potentially detrimental to their health.

Keywords: Air pollution, air quality, hotspot monitoring, volatile organic compounds.

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Authors: Eszter Tóth, Ervin Welker

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Shadoo protein (Sho) was described in 2003 as the newest member of Prion protein superfamily [1]. Sho has similar structural motifs like prion protein (PrP) that is known for its central role in transmissible spongiform enchephalopathies. Although a great number of functions have been proposed, the exact physiological function of PrP is not known yet. Investigation of the function and localization of Sho may help us to understand the function of the Prion protein superfamily. Analyzing the subcellular localization of YFP-tagged forms of Sho, we detected the protein in the plasma membrane and in the nucleus of various cell lines. To reveal the localization of the endogenous protein we generated antibodies against Shadoo as well as employed commercially available anti-Shadoo antibodies: i) EG62 anti-mouse Shadoo antibody generated by Eurogentec Ltd.; ii) S-12 anti-human Shadoo antibody by Santa Cruz Biotechnology Inc.; iii) R-12 anti-mouse Shadoo antibody by Santa Cruz Biotechnology Inc.; iv) SPRN antibody against human Shadoo by Abgent Inc. We carried out immunocytochemistry on non-transfected HeLa, Zpl 2-1, Zw 3-5, GT1-1, GT1-7 and SHSY5Y cells as well as on YFP-Sho, Sho-YFP, and YFP-GPI transfected HeLa cells. Their specificity (in antibody-peptide competition assay) and co-localization (with the YFP signal) were assessed.

Keywords: Shadoo, prion protein, immunocytochemistry, antibody-peptide competition assay, antibody.

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Authors: Hamoud Al-Hadrami, Hossein Emadi, Athar Hussain

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Green hydrogen is quickly emerging as a new source of the renewable energy for the world. Hydrogen production using water electrolysis is deemed as an environmentally friendly and safe source of energy for transportation and other industries. However, storing high volumes of hydrogen seems to be a significant challenge. Abandoned hydrocarbon reservoirs are considered as viable hydrogen storage options because of the availability of the required infrastructure such as wells and surface facilities. However, long-term wellbore integrity in these wells could be a serious challenge. The aim of this research is to investigate the effect of stored hydrogen on the wellbore integrity such as casing cement. The methodology is to experimentally expose hydrogen to wet and dry cement and measure the impact on cement rheological and mechanical properties. Hydrogen reduces the compressive strength of a set cement if it gets in contact with the cement slurry. Also, mixing hydrogen with cement slurry slightly increases its density and rheological properties which need to be considered to have a successful primary cementing operation.

Keywords: Green hydrogen, underground storage, wellbore integrity, cement, compressive strength.

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Authors: Nan-Chyuan Tsai, Jiun-Sheng Liou, Chih-Che Lin, Tuan Li

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For micro-gyroscopes, the angular rate detection components have to oscillate forwards and backwards alternatively. An innovative design of micro-electromagnetic drive module is proposed to make a Π-type disc reciprocally and efficiently rotate within a certain of angular interval. Twelve Electromagnetic poles enclosing the thin disc are designed to provide the magnetic drive power. Isotropic etching technique is employed to fabricate the high-aspect-ratio trench, so that the contact angle of wire against trench can be increased and the potential defect of cavities and pores within the wire can be prevented. On the other hand, a Π-type thin disc is designed to conduct the pitch motion as an angular excitation, in addition to spinning, is exerted on the gyroscope. The efficacy of the micro-magnetic drive module is verified by the commercial software, Ansoft Maxewll. In comparison with the conventional planar windings in micro-scale systems, the magnetic drive force is increased by 150%.

Keywords: Micro-gyroscope, micro-electromagnetic, micro actuator.

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Authors: Rodrigo Chandia, Mauricio Papa

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Efforts to secure supervisory control and data acquisition (SCADA) systems must be supported under the guidance of sound security policies and mechanisms to enforce them. Critical elements of the policy must be systematically translated into a format that can be used by policy enforcement components. Ideally, the goal is to ensure that the enforced policy is a close reflection of the specified policy. However, security controls commonly used to enforce policies in the IT environment were not designed to satisfy the specific needs of the SCADA environment. This paper presents a language, based on the well-known XACML framework, for the expression of authorization policies for SCADA systems.

Keywords: Access policy specification, process control systems, network security.

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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: M. Schukat, M.P. Cullen, D. O'Beirne

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This paper describes a UDP over IP based, server-oriented redundant host configuration protocol (RHCP) that can be used by collaborating embedded systems in an ad-hoc network to acquire a dynamic IP address. The service is provided by a single network device at a time and will be dynamically reassigned to one of the other network clients if the primary provider fails. The protocol also allows all participating clients to monitor the dynamic makeup of the network over time. So far the algorithm has been implemented and tested on an 8-bit embedded system architecture with a 10Mbit Ethernet interface.

Keywords: Ad-Hoc Networks, Collaborating Embedded Systems, Dynamic Host Configuration, Redundancy.

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Authors: M. Sumida

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The flow of suspensions of wood pulp fibers in circular pipes has been investigated experimentally. The flow characteristics of pulp suspensions are discussed with regard to five flow regimes designated by the author. In particular, the effects of the shear stress at the pipe wall on the disruption and dispersion of networks of pulp fibers are examined. The values of the disruptive and dispersive shear stresses are formulated as simple expressions depending on only the fiber concentration. Furthermore, the flow properties of the suspensions are described using the yield shear stress.

Keywords: Fiber Concentration, Flow Properties, Pulp Suspension, Yield Shear Stress.

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Authors: Marios N. Moschakis

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This paper deals with the assessment of faulted area around an industrial customer connected to a particular electric grid that will cause a certain sag magnitude on this customer. The faulted (critical or exposed) area’s length is calculated by adding all line lengths in the neighborhood of the critical node (customer). The applied method is the so-called Method of Critical Distances. By using advanced short-circuit analysis, the Critical Area can be accurately calculated for radial and meshed power networks due to all symmetrical and asymmetrical faults. For the demonstration of the effectiveness of the proposed methodology, a study case is used.

Keywords: Critical area, fault-induced voltage sags, industrial customers, power quality.

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Authors: Nhon Do, Hien Nguyen

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Nowadays there are many methods for representing knowledge such as semantic network, neural network, and conceptual graphs. Nonetheless, these methods are not sufficiently efficient when applied to perform and deduce on knowledge domains about supporting in general education such as algebra, analysis or plane geometry. This leads to the introduction of computational network which is a useful tool for representation knowledge base, especially for computational knowledge, especially knowledge domain about general education. However, when dealing with a practical problem, we often do not immediately find a new solution, but we search related problems which have been solved before and then proposing an appropriate solution for the problem. Besides that, when finding related problems, we have to determine whether the result of them can be used to solve the practical problem or not. In this paper, the extension model of computational network has been presented. In this model, Sample Problems, which are related problems, will be used like the experience of human about practical problem, simulate the way of human thinking, and give the good solution for the practical problem faster and more effectively. This extension model is applied to construct an automatic system for solving algebraic problems in middle school.

Keywords: educational software, artificial intelligence, knowledge base system, knowledge representation.

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Authors: Manuel A. Alonso-Tarajano, Roberto Mosca, Patrick Aloy

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Protein kinases participate in a myriad of cellular processes of major biomedical interest. The in vivo substrate specificity of these enzymes is a process determined by several factors, and despite several years of research on the topic, is still far from being totally understood. In the present work, we have quantified the contributions to the kinase substrate specificity of i) the phosphorylation sites and their surrounding residues in the sequence and of ii) the association of kinases to adaptor or scaffold proteins. We have used position-specific scoring matrices (PSSMs), to represent the stretches of sequences phosphorylated by 93 families of kinases. We have found negative correlations between the number of sequences from which a PSSM is generated and the statistical significance and the performance of that PSSM. Using a subset of 22 statistically significant PSSMs, we have identified specificity determinant residues (SDRs) for 86% of the corresponding kinase families. Our results suggest that different SDRs can function as positive or negative elements of substrate recognition by the different families of kinases. Additionally, we have found that human proteins with known function as adaptors or scaffolds (kAS) tend to interact with a significantly large fraction of the substrates of the kinases to which they associate. Based on this characteristic we have identified a set of 279 potential adaptors/scaffolds (pAS) for human kinases, which is enriched in Pfam domains and functional terms tightly related to the proposed function. Moreover, our results show that for 74.6% of the kinase–pAS association found, the pAS colocalize with the substrates of the kinases they are associated to. Finally, we have found evidence suggesting that the association of kinases to adaptors and scaffolds, may contribute significantly to diminish the in vivo substrate crossed-specificity of protein kinases. In general, our results indicate the relevance of several SDRs for both the positive and negative selection of phosphorylation sites by kinase families and also suggest that the association of kinases to pAS proteins may be an important factor for the localization of the enzymes with their set of substrates.

Keywords: Kinase, phosphorylation, substrate specificity, adaptors, scaffolds, cellular colocalization.

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