Search results for: solar energy collection

Authors: Gabriela-Andreea Despescu, Mădălina-Elena Mavrodin, Gheorghe Lăzăroiu, Florin Adrian Grădinaru

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The purpose of this paper is to contribute to the enhancement of a hydroelectric plant protection by coordinating protection measures / existing security and introducing new measures under a risk management process. In addition, plan identifies key critical elements of a hydroelectric plant, from its level vulnerabilities and threats it is subjected to in order to achieve the necessary protection measures to reduce the level of risk.

Keywords: Critical infrastructure, risk analysis, critical infrastructure protection, vulnerability, risk management, turbine, Impact analysis.

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Authors: Pricillia Priska Sianita

Abstract:

An aesthetic facial profile is one of the goals in Orthodontics treatment. However, this is not easily achieved, especially in patients with Class II Division 1 malocclusion who have the clinical characteristics of convex profile and significant skeletal discrepancy due to mandibular growth deficiency. Malocclusion with skeletal problems require proper treatment timing for growth stimulation, and it must be done in early age and in need of good cooperation from the patient. If this is not done and the patient has passed the growth period, the ideal treatment is orthognathic surgery which is more complicated and more painful. The growth stimulation of skeletal malocclusion requires a careful cephalometric evaluation ranging from diagnosis to determine the parts that require stimulation to post-treatment evaluation to see the success achieved through changes in the measurement of the skeletal parameters shown in the cephalometric analysis. This case report aims to describe skeletal changes cephalometrically that were achieved through orthodontic treatment in growing period. Material and method: Lateral Cephalograms, pre-treatment, and post-treatment of cases of Class II Division 1 malocclusion is selected from a collection of cephalometric radiographic in a private clinic. The Cephalogram is then traced and measured for the skeletal parameters. The result is noted as skeletal condition data of pre-treatment and post-treatment. Furthermore, superimposition is done to see the changes achieved. The results show that growth stimulation through orthodontic treatment can solve the skeletal problem of Class II Division 1 malocclusion and the skeletal changes that occur can be verified through cephalometric analysis. The skeletal changes have an impact on the improvement of patient's facial profile. To sum up, the treatment timing on a skeletal malocclusion is very important to obtain satisfactory results for the improvement of the aesthetic facial profile, and skeletal changes can be verified through cephalometric evaluation of pre- and post-treatment.

Keywords: Cephalometric evaluation, Class II Division 1 malocclusion, growth stimulation, skeletal changes, skeletal problems.

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Authors: Petre Voicu, Mircea Oaida, Radu Vasiu, Catalin Gheorghiu, Aurel Dumitru

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The present work deals with the way in which food and tobacco waste can be used in agriculture. As a result of the lack of efficient technologies for their recycling, we are currently faced with the appearance of appreciable quantities of residual organic residues that find their use only very rarely and only after long storage in landfills. The main disadvantages of long storage of organic waste are the unpleasant smell, the high content of pathogenic agents, and the high content in the water. The release of these enormous amounts imperatively demands the finding of solutions to ensure the avoidance of environmental pollution. The measure practiced by us and presented in this paper consists of the processing of this waste in special installations, testing in pilot experimental perimeters, and later administration on agricultural lands without harming the quality of the soil, agricultural crops, and the environment. The current crisis of raw materials and energy also raises special problems in the field of organic waste valorization, an activity that takes place with low energy consumption. At the same time, their composition recommends them as useful secondary sources in agriculture. The transformation of food scraps and other residues concentrated organics thus acquires a new orientation, in which these materials are seen as important secondary resources. The utilization of food and tobacco waste in agriculture is also stimulated by the increasing lack of chemical fertilizers and the continuous increase in their price, under the conditions that the soil requires increased amounts of fertilizers in order to obtain high, stable, and profitable production. The need to maintain and increase the humus content of the soil is also taken into account, as an essential factor of its fertility, as a source and reserve of nutrients and microelements, as an important factor in increasing the buffering capacity of the soil, and the more reserved use of chemical fertilizers, improving the structure and permeability for water with positive effects on the quality of agricultural works and preventing the excess and/or deficit of moisture in the soil.

Keywords: Organic residue, food and tannery waste, fertilizer, soil.

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Authors: C. K. Chear, S. S. Dol

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For a bluff body, dimples behave like roughness elements in stimulating a turbulent boundary layer, leading to delayed flow separation, a smaller wake and lower form drag. This is very different in principle from the application of dimples to streamlined body, where any reduction in drag would be predominantly due to a reduction in skin friction. In the present work, a car model with different dimple geometry is simulated using k-ε turbulence modeling to determine its effect to the aerodynamics performance. Overall, the results show that the application of dimples manages to reduce the drag coefficient of the car model.

Keywords: Aerodynamics, Boundary Layer, Dimple, Drag, Kinetic Energy, Turbulence.

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Authors: Zakir Husain, Neem Sagar, Neeraj Gupta

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Due to the increased penetration of renewable energy resources in the distribution system, the system is no longer passive in nature. In this paper, a steady state analysis of the distribution system has been done with the inclusion of wind generation. The modeling of wind turbine generator system and wind generator has been made to obtain the average active and the reactive power injection into the system. The study has been conducted on a IEEE-33 bus system with two wind generators. The present research work is useful not only to utilities but also to customers.

Keywords: Distributed generation, distribution network, radial network, wind turbine generating system.

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Authors: Sui Yan Wong, Keat Ping Yeoh, Chi Wai Hui

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In this study, supercritical steam is introduced to Combined Cycle Power Plant (CCPP) in an attempt to further optimize energy recovery. Subcritical steam is commonly used in the CCPP, operating at maximum pressures around 150-160 bar. Supercritical steam is an alternative to increase heat recovery during vaporization period of water. The idea of improvement using supercritical steam is further examined with the use of exergy, pinch analysis and Aspen Plus simulation.

Keywords: Exergy, pinch, combined cycle power plant, CCPP, supercritical steam.

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Authors: Tshimangadzo Oscar Magadze

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For successful re-integration, the individual offender must adapt and transform, which requires that the offender should adopt and internalise socially approved norms, attitudes, values, and beliefs. However, the offender’s labelling and community stigmatisation decide the destination of the offender. Community involvement in ex-offenders’ re-integration is an important issue in efforts to reduce recidivism and to control overcrowding in our correctional facilities. Crime is a social problem that requires society to come together to fight against it. This study was conducted in the Limpopo Province in Vhembe District Municipality within four local municipalities, namely Musina, Makhado, Mutale, and Thulamela. A total number of 30 participants were interviewed, and all were members of the Community Corrections Forums. This was necessitated by the fact that Musina is a very small area, which compelled the Department of Correctional Services to combine the two (Musina and Makhado) into one social re-integration entity. This is a qualitative research study where participants were selected through the use of purposive sampling. Participants were selected based on the value they would add to this study in order to achieve the objectives. The data collection method of this study was the focus group, which comprised of three groups of 10 participants each. Thulamela and Mutale local municipalities formed a group with (10) participants each, whereas Musina (2) and Makhado (8) formed another. Results indicate that the current situation is not conducive for re-integration to be successful. Participants raised many factors that need serious redress, namely offenders’ discrimination, lack of forgiveness by members of the community, which is fuelled by lack of community awareness due to the failure of the Department of Correctional Services in educating communities on ex-offenders’ re-integration.

Keywords: Ex-offender, labelling, re-integration, stigmatisation.

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Authors: Xiangbin Zhu, Wenjuan Zhang

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In wireless sensor networks,the mobile agent technology is used in data fusion. According to the node residual energy and the results of partial integration,we design the node clustering algorithm. Optimization of mobile agent in the routing within the cluster strategy for wireless sensor networks to further reduce the amount of data transfer. Through the experiments, using mobile agents in the integration process within the cluster can be reduced the path loss in some extent.

Keywords: wireless sensor networks, data fusion, mobile agent

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Authors: M.A. Mohammadi, H.Alinejad, A.Piri

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The current sheath dynamics in plasma focus facilities is the most important factors. In this paper the current sheath velocity at three dimensional with Sahand plasma focus facility is investigated. For this purpose the discharge is produced in argon gas with deposited energy lying in the range of 20-37kJ. The current sheath is monitored using two tridimensional magnetic probes. These probes installed near the surface of the interior electrode (anode) at 125mm from the anode axis (pinch place). The effect of gas pressure on the current sheath velocity also is investigated.

Keywords: Plasma focus, Current sheath, magnetic probe

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Authors: Frederike Ohrem, Lukas Sikorski, Bastian Haarmann

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Often the users of a semantic search application are facing the problem that they do not find appropriate terms for their search. This holds especially if the data to be searched is from a technical field in which the user does not have expertise. In order to support the user finding the results he seeks, we developed a domain-specific ontology and implemented it into a search application. The ontology serves as a knowledge base, suggesting technical terms to the user which he can add to his query. In this paper, we present the search application and the underlying ontology as well as the project EnArgus in which the application was developed.

Keywords: Information system, knowledge representation, ontology, semantic search.

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Authors: Joon Ho Kim, Duck Su Kim, Tae Kwon Ha

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Aluminum/Copper clad sheet has been fabricated using asymmetric extrusion method, which caused severe shear deformation between Al and Cu plate to easily bond to each other. Interfacial microstructure and mechanical properties of Al/Cu clad were studied by scanning electron microscope equipped with energy dispersive X-ray detector, micro-hardness, and tension tests. The asymmetric extrusion bonding was very effective to provide a good interface for atoms diffusion during subsequent annealing. The strength of bonding was higher with the increasing extrusion ratio.

Keywords: Aluminum/Copper clad sheet, Asymmetric extrusion, Interfacial microstructure, Annealing, Tensile test.

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Authors: Mahmoud Beshr, Ivan Andonovic, Moustafa H. Aly

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Visible Light Communication (VLC) offers advantages of low energy consumption, licence free and RF interference free operation. One application area for VLC is in the provision of health centred services circumventing issues of interference with any biomedical device within the environment. VLC performamce is affected by natural light restricting systems avilability and relibility. The paper presents an analysis of the performance of VLC systems under different meteorological conditions. The evaluation considered the impact of natural light as a function of different reflection surfaces in different room sizes.

Keywords: Visible light communication, impulse reponse , performance analysis , natural light.

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Authors: N. Bahiyah Baba, W. Waugh, A.M. Davidson

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The paper discusses optimising work on a method of processing ceramic / metal composite coatings for various applications and is based on preliminary work on processing anodes for solid oxide fuel cells (SOFCs). The composite coating is manufactured by the electroless co-deposition of nickel and yttria stabilised zirconia (YSZ) simultaneously on to a ceramic substrate. The effect on coating characteristics of substrate surface treatments and electroless nickel bath parameters such as pH and agitation methods are also investigated. Characterisation of the resulting deposit by scanning electron microscopy (SEM) and energy dispersive X-ray analysis (EDXA) is also discussed.

Keywords: Electroless deposition, nickel, YSZ, composite

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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: Sh. Hamada, N. Burtebayev, N. Amangeldi, A. Amar

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An experiment was performed with a 24.5 MeV 14N beam on a 12C target in the cyclotron DC-60 located in Astana, Kazakhstan, to study the elastic scattering of 14N on 12C; the scattering was also analyzed at different energies for tracking the phenomenon of remarkable structure at large angles. Its aims were to extend the measurements to very large angles, and attempt to uniquely identify the elastic scattering potential. Good agreement between the theoretical and experimental data has been obtained with suitable optical potential parameters. Optical model calculations with l -dependent imaginary potentials were also applied to the data and relatively good agreement was found.

Keywords: Optical Potential Codes, Elastic Scattering, SPIVALCode.

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Authors: Derya Burcu Ozkan, Onur Kiziler, Duriye Bilge

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Cogeneration may be defined as a system which contains electricity production and regain of the thermo value of exhaust gases simultaneously. The examination is based on the data-s of an active cogeneration plant. This study, it is aimed to determine which component of the system should be revised first to raise the efficiency and decrease the loss of exergy. For this purpose, second law analysis of thermodynamics is applied to each component due to consider the effects of environmental conditions and take the quality of energy into consideration as well as the quantity of it. The exergy balance equations are produced and exergy loss is calculated for each component. 44,44 % loss of exergy in heat exchanger, 29,59 % in combustion chamber, 18,68 % in steam boiler, 5,25 % in gas turbine and 2,03 % in compressor is calculated.

Keywords: Cogeneration, Exergy loss, Second law analysis

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Authors: Esther T. Akinlabi, Stephen A. Akinlabi

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Friction Stir Welding (FSW) is a solid state welding process invented and patented by The Welding Institute (TWI) in the United Kingdom in 1991 for butt and lap welding of metals and plastics. This paper highlights the benefits of friction stir welding process as an energy efficient and a green technology process in the field of welding. Compared to the other conventional welding processes, its benefits, typical applications and its use in joining similar and dissimilar materials are also presented.

Keywords: Dissimilar materials, Friction Stir Welding, Green technology, similar materials.

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Authors: M. Momeni Feyli

Abstract:

Many recent high energy physics calculations involving charm and beauty invoke wave function at the origin (WFO) for the meson bound state. Uncertainties of charm and beauty quark masses and different models for potentials governing these bound states require a simple numerical algorithm for evaluation of the WFO's for these bound states. We present a simple algorithm for this propose which provides WFO's with high precision compared with similar ones already obtained in the literature.

Keywords: Mesons, Bound states, Schrodinger equation, Nonrelativistic quark model.

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Authors: R. M. Kashim

Abstract:

The study investigated primary school teachers’ conceptual and procedural knowledge of rational numbers and its effects on pupil’s achievement in rational numbers. Specifically, primary school teachers’ level of conceptual knowledge about rational numbers, primary school teachers’ level of procedural knowledge about rational numbers, and the effects of teachers conceptual and procedural knowledge on their pupils understanding of rational numbers in primary schools is investigated. The study was carried out in Bauchi metropolis in the Bauchi state of Nigeria. The design of the study was a multi-stage design. The first stage was a descriptive design. The second stage involves a pre-test, post-test only quasi-experimental design. Two instruments were used for the data collection in the study. These were Conceptual and Procedural knowledge test (CPKT) and Rational number achievement test (RAT), the population of the study comprises of three (3) mathematics teachers’ holders of Nigerian Certificate in Education (NCE) teaching primary six and 210 pupils in their intact classes were used for the study. The data collected were analyzed using mean, standard deviation, analysis of variance, analysis of covariance and t- test. The findings indicated that the pupils taught rational number by a teacher that has high conceptual and procedural knowledge understand and perform better than the pupil taught by a teacher who has low conceptual and procedural knowledge of rational number. It is, therefore, recommended that teachers in primary schools should be encouraged to enrich their conceptual knowledge of rational numbers. Also, the superiority performance of teachers in procedural knowledge in rational number should not become an obstruction of understanding. Teachers Conceptual and procedural knowledge of rational numbers should be balanced so that primary school pupils will have a view of better teaching and learning of rational number in our contemporary schools.

Keywords: Achievement, conceptual knowledge, procedural knowledge, rational numbers.

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Authors: Leila Batmany

Abstract:

This research studies the relationship between the feeling of distributive justice and national identity of the youth. The present analysis intends to experimentally investigate the various dimensions of the justice feeling and its effect on the national identity components. The study has taken justice into consideration from four different points of view on the basis of availability of valuable social sources such as power, wealth, knowledge and status in the political, economic, and cultural and status justice respectively. Furthermore, the national identity has been considered as the feeling of honour, attachment and commitment towards national society and its seven components i.e. history, language, culture, political system, religion, geographical territory and society. The 'field study' has been used as the method for the research with the individual as unit, taking 368 young between the age of 18 and 29 living in Tehran, chosen randomly according to Cochran formula. The individual samples have been randomly chosen among five districts in north, south, west, east, and centre of Tehran, based on the multistage cluster sampling. The data collection has been performed with the use of questionnaire and interview. The most important results are as follows: i) The feeling of economic justice is the weakest one among the youth. ii) The strongest and the weakest dimensions of the national identity are, respectively, the historical and the social dimension. iii) There is a positive and meaningful relationship between the feeling political and statues justice and then national identity, whereas no meaningful relationship exists between the economic and cultural justice and the national identity. iv) There is a positive and meaningful relationship between the feeling of justice in all dimensions and legitimacy of the political system. There is also such a relationship between the legitimacy of the political system and national identity. v) Generally, there is a positive and meaningful relationship between the feeling of distributive justice and national identity among the youth. vi) It is through the legitimacy of the political system that justice feeling can have an influence on the national identity.

Keywords: Distributive justice, national identity, legitimacy of political system, Cochran formula, multistage cluster sampling.

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Authors: M. Douak, Z. Aouachria

Abstract:

The aim of our study is to project an optimized wind turbine of Darrieus type. This type of wind turbine is characterized by a low starting torque in comparison with the Savonius rotor allowing them to operate for a period greater than wind speed. This led us to reconsider the Darrieus rotor to optimize a design which will increase its starting torque. The study of a system of monitoring and control of the angle of attack of blade profile, which allows an auto start to wind speeds as low as possible is presented for the straight blade of Darrieus turbine. The study continues to extend to other configurations namely those of parabolic type.

Keywords: Darrieus turbine, pitch angle, self-stating, wind energy.

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Authors: Aneta Oblouková, Eva Vítková

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The article deals with the issue of water and sewerage charge rate prices in the Czech Republic. The research is specifically focused on the analysis of the development of the average prices of water and sewerage charge rate in the Czech Republic in 1994-2021 and on the validation of the chosen methodology relevant for the prediction of the development of the average prices of water and sewerage charge rate in the Czech Republic. The research is based on data collection. The data for this research were obtained from the Czech Statistical Office. The aim of the paper is to validate the relevance of the mathematical linear trend estimate technique for the calculation of the predicted average prices of water and sewerage charge rates. The real values of the average prices of water and sewerage charge rates in the Czech Republic in 1994-2018 were obtained from the Czech Statistical Office and were converted into a mathematical equation. The same type of real data was obtained from the Czech Statistical Office for 2019-2021. Prediction of the average prices of water and sewerage charge rates in the Czech Republic in 2019-2021 was also calculated using a chosen method – a linear trend estimation technique. The values obtained from the Czech Statistical Office and the values calculated using the chosen methodology were subsequently compared. The research result is a validation of the chosen mathematical technique to be a suitable technique for this research.

Keywords: Czech Republic, linear trend estimation, price prediction, water and sewerage charge rate.

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Authors: Tim Byrnes

Abstract:

Quantum computation using qubits made of two component Bose-Einstein condensates (BECs) is analyzed. We construct a general framework for quantum algorithms to be executed using the collective states of the BECs. The use of BECs allows for an increase of energy scales via bosonic enhancement, resulting in two qubit gate operations that can be performed at a time reduced by a factor of N, where N is the number of bosons per qubit. We illustrate the scheme by an application to Deutsch-s and Grover-s algorithms, and discuss possible experimental implementations. Decoherence effects are analyzed under both general conditions and for the experimental implementation proposed.

Keywords: Quantum, computing, information, Bose-Einstein condensates, macroscopic.

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Authors: Abiodun M. Lawal, Benjamin O. Olley

Abstract:

Long Distance Truck Drivers (LDTDs) have been found to be a high risk group in the spread of HIV/AIDS globally; perhaps, due to their high Sexual Risk Behaviours (SRBs). Interventions for reducing SRBs in trucking population have not been fully exploited. A quasi-experimental control group pretest-posttest design was used to assess the efficacy of psycho-education and behavioural skills training in reducing SRBs among LDTDs. Sixteen drivers rivers were randomly assigned into either experimental or control groups using balloting technique. Questionnaire was used as an instrument for data collection. Repeated measures t-test and independent t-test were used to test hypotheses. Intervention had significant effect on the SRBs among LDTDs at post-test (t{7}= 6.01, p<.01) and at follow up (t{7} = 6.42, p<.01). No significant difference in sexual risk behaviour of LDTDs at post-test and at follow-up stage. Similarly, intervention had significant effects on sexual risk behaviour at post-test (t {14} = - 4.69, p<.05) and at follow-up (t {14} = -9.56, p<.05) respectively. At post-test and follow-up stages, drivers in experimental group reported reduced SRBs than those in control group. Drivers in experimental group reported lower sexual risk behaviour a week after intervention as well as at three months follow-up than those in control group. It is concluded that HIV/AIDS preventive intervention that provides the necessary informational and behavioural skills content can significantly impact long distance truck drivers’ sexual risk behaviours.

Keywords: HIV/AIDS interventions, Long distance truck drivers, Nigeria, Sexual risk behaviours.

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Authors: Radek Fisera, Petr Stluka

Abstract:

This paper describes a methodology for remote performance monitoring of retail refrigeration systems. The proposed framework starts with monitoring of the whole refrigeration circuit which allows detecting deviations from expected behavior caused by various faults and degradations. The subsequent diagnostics methods drill down deeper in the equipment hierarchy to more specifically determine root causes. An important feature of the proposed concept is that it does not require any additional sensors, and thus, the performance monitoring solution can be deployed at a low installation cost. Moreover only a minimum of contextual information is required, which also substantially reduces time and cost of the deployment process.

Keywords: Condition monitoring, energy baselining, fault detection and diagnostics, commercial refrigeration.

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Authors: Narcis C. Ostahie, Tudor Sajin

Abstract:

In this paper a numerical simulation of electric and hydrodynamic fields distribution in an electrofilter for dielectric liquids cell is made. The simulation is made with the purpose to determine the trajectory of particles that moves under the action of external force in an electric and hydrodynamic field created inside of an electrofilter for dielectric liquids. Particle trajectory is analyzed for a dielectric liquid-solid particles suspension.

Keywords: Dielectric liquids, electrohydrodynamics, energy, high voltage, particles

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Authors: M. Faraji, F. Berroug

Abstract:

A one-dimensional mathematical model was developed in order to analyze and optimize the latent heat storage wall. The governing equations for energy transport were developed by using the enthalpy method and discretized with volume control scheme. The resulting algebraic equations were next solved iteratively by using TDMA algorithm. A series of numerical investigations were conducted in order to examine the effects of the thickness of the PCM layer on the thermal behavior of the proposed heating system. Results are obtained for thermal gain and temperature fluctuation. The charging discharging process was also presented and analyzed.

Keywords: Phase change material, Building, Concrete, Latent heat, Thermal control.

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Authors: Mehran Nasiri, Ardeshir Poornemat

Abstract:

The aim of this study was to investigate the current and ideal situations of the process of talent identification in Iranian football from the point of view of Iranian instructors of the Asian Football Confederation (AFC). This research was a descriptive-analytical study; in data collection phase a questionnaire was used, whose face validity was confirmed by experts of Physical Education and Sports Science. The reliability of questionnaire was estimated through the use of Cronbach's alpha method (0.91). This study involved 122 participants of Iranian instructors of the AFC who were selected based on stratified random sampling method. Descriptive statistics were used to describe the variables and inferential statistics (Chi-square) were used to test the hypotheses of the study at significant level (p ≤ 0.05). The results of Chi-square test related to the point of view of Iranian instructors of the AFC showed that the grass-roots scientific method was the best way to identify football players (0.001), less than 10 years old were the best ages for talent identification (0.001), the Football Federation was revealed to be the most important organization in talent identification (0.002), clubs were shown to be the most important institution in developing talents (0.001), trained scouts of Football Federation were demonstrated to be the best and most appropriate group for talent identification (0.001), and being referred by the football academy coaches was shown to be the best way to attract talented football players in Iran (0.001). It was also found that there was a huge difference between the current and ideal situation of the process of talent identification in Iranian football from the point of view of Iranian instructors of the AFC. Hence, it is recommended that the policy makers of talent identification for Iranian football provide a comprehensive, clear and systematic model of talent identification and development processes for the clubs and football teams, so that the talent identification process helps to nurture football talents more efficiently.

Keywords: Current situation, talent finding, ideal situation, instructors.

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Authors: Talib Hashim Hasan

Abstract:

This paper describes simple implementation of homotopy (also called continuation) algorithm for determining the proper resistance of the resistor to dissipate energy at a specified rate of an electric circuit. Homotopy algorithm can be considered as a developing of the classical methods in numerical computing such as Newton-Raphson and fixed point methods. In homoptopy methods, an embedding parameter is used to control the convergence. The method purposed in this work utilizes a special homotopy called Newton homotopy. Numerical example solved in MATLAB is given to show the effectiveness of the purposed method

Keywords: electrical circuit homotopy, methods, MATLAB, Newton homotopy

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Authors: Alan Luo, Hunter N. B. Moseley

Abstract:

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

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

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