Search results for: Structural analysis.

Authors: M. Nabeel Rashin, J. Hemalatha

Abstract:

Novel Coconut oil nanofluids of various concentrations have been prepared through ultrasonically assisted sol-gel method. The structural and morphological properties of the copper oxide nanoparticle have been analyzed with respectively and it revealed the monoclinic end-centered structure of crystallite and shuttle like flake morphology of agglomerates. Ultrasonic studies have been made for the nanofluids at different temperatures. The molecular interactions responsible for the changes in acoustical parameter with respect to concentration and temperature are discussed.

Keywords: Cutting Fluid, Molecular Interaction, Nanofluids, Ultrasonic

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Authors: Sónia Alves

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During the last few decades in the academic field, the debate has increased on the effects of social geography on the opportunities of socioeconomic integration. On one hand, it has been discussed how the contents of the urban structure and social geography affect not only the way people interact, but also their chances of social and economic integration. On the other hand, it has also been discussed how the urban structure is also constrained and transformed by the action of social actors. Without questioning the powerful influence of structural factors, related to the logic of the production system, labor markets, education and training, the research has shown the role played by place of residence in shaping individual outcomes such as unemployment. In the context of this debate the importance of territory of residence with respect to the problem of unemployment has been highlighted. Although statistics of unemployment have already demonstrated the unequal incidence of the phenomenon in social groups, the issue of uneven territorial impact on the phenomenon at intra-urban level remains relatively unknown. The purpose of this article is to show and to interpret the spatial patterns of unemployment in the city of Porto using GIS (Geographic Information System - GIS) technology. Under this analysis the overlap of the spatial patterns of unemployment with the spatial distribution of social housing, allows the discussion of the relationship that occurs between these patterns and the reasons that might explain the relative immutability of socioeconomic problems in some neighborhoods.

Keywords: Unemployment, area effects, urban planning, Porto.

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Authors: Abdelwahed Echchatbi, Adil Rizki, Ali Haddi, Nabil Mrani, Noureddine Elalami

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In this note, the robust static output feedback stabilisation of an induction machine is addressed. The machine is described by a non homogenous bilinear model with structural uncertainties, and the feedback gain is computed via an iterative LMI (ILMI) algorithm.

Keywords: Induction machine, Static output feedback, robust stabilisation.

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Authors: Paramet Nualmuenwai, Chutima Prommak

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This paper presents the IP traffic analysis. The traffic was collected from the network of Suranaree University of Technology using the software based on the Simple Network Management Protocol (SNMP). In particular, we analyze the distribution of the aggregated traffic during the hours of peak load and light load. The traffic profiles including the parameters described the traffic distributions were derived. From the statistical analysis applying three different methods, including the Kolmogorov Smirnov test, Anderson Darling test, and Chi-Squared test, we found that the IP traffic distribution is a non-normal distribution and the distributions during the peak load and the light load are different. The experimental study and analysis show high uncertainty of the IP traffic.

Keywords: IP traffic analysis, IP traffic distribution, Traffic uncertainty

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Authors: Y. Liu, M. K. Bera, L. M. Kyaw, G. Q. Lo, E. F. Chor

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The electrical and structural properties of Hf/Al/Ni/Au (20/100/25/50 nm) ohmic contact to n-GaN are reported in this study. Specific contact resistivities of Hf/Al/Ni/Au based contacts have been investigated as a function of annealing temperature and achieve the lowest value of 1.09´10-6 Ω·cm2 after annealing at 650 oC in vacuum. A detailed mechanism of ohmic contact formation is discussed. By using different chemical analyses, it is anticipated that the formation of Hf-Al-N alloy might be responsible to form low temperature ohmic contacts for the Hf-based scheme to n-GaN.

Keywords: Gallium nitride, ohmic contact, Hafnium

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Authors: M. H. Hairi, H. Zainuddin, M.H.N. Talib, A. Khamis, J. Y. Lichun

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Short circuit currents plays a vital role in influencing the design and operation of equipment and power system and could not be avoided despite careful planning and design, good maintenance and thorough operation of the system. This paper discusses the short circuit analysis conducted in KSO briefly comprising of its significances, methods and results. A result sample of the analysis based on a single transformer is detailed in this paper. Furthermore, the results of the analysis and its significances were also discussed and commented.

Keywords: Short circuit currents, Transformer fault current

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Authors: Mohammadreza Salek Faramarzi, Touraj Taghikhany

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In this paper, seismic fragility assessment of a recently developed hybrid structural system, known as the strongback system (SBS) is investigated. In this system, to mitigate the occurrence of the soft-story mechanism and improve the distribution of story drifts over the height of the structure, an elastic vertical truss is formed. The strengthened members of the braced span are designed to remain substantially elastic during levels of excitation where soft-story mechanisms are likely to occur and impose a nearly uniform story drift distribution. Due to the distinctive characteristics of near-field ground motions, it seems to be necessary to study the effect of these records on seismic performance of the SBS. To this end, a set of 56 near-field ground motion records suggested by FEMA P695 methodology is used. For fragility assessment, nonlinear dynamic analyses are carried out in OpenSEES based on the recommended procedure in HAZUS technical manual. Four damage states including slight, moderate, extensive, and complete damage (collapse) are considered. To evaluate each damage state, inter-story drift ratio and floor acceleration are implemented as engineering demand parameters. Further, to extend the evaluation of the collapse state of the system, a different collapse criterion suggested in FEMA P695 is applied. It is concluded that SBS can significantly increase the collapse capacity and consequently decrease the collapse risk of the structure during its life time. Comparing the observing mean annual frequency (MAF) of exceedance of each damage state against the allowable values presented in performance-based design methods, it is found that using the elastic vertical truss, improves the structural response effectively.

Keywords: Strongback System, Near-fault, Seismic fragility, Uncertainty, IDA, Probabilistic performance assessment.

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Authors: Majid A. AlSayari

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The study reported here investigated social cognitive theory (SCT) in the context of Vocational Rehab (VR) for people with disabilities. The prime purpose was to increase knowledge of VR phenomena and make recommendations for improving VR services. The sample consisted of 242 persons with Spinal Cord Injuries (SCI) who completed questionnaires. A further 32 participants were Trainers. Analysis of questionnaire data was carried out using factor analysis, multiple regression analysis, and thematic analysis. The analysis suggested that, in motivational terms, and consistent with research carried out in other academic contexts, self-efficacy was the best predictor of VR performance. The author concludes that that VR self-efficacy predicted VR training performance.

Keywords: Social cognitive theory, vocational rehab, self-efficacy, proxy efficacy, people with disabilities.

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Authors: Mohammed Mahmood, Walid Tizani, Carlo Sansour

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In this paper, experimental testing and numerical analysis were used to investigate the effect of tube thickness on the face bending for concrete filled hollow sections connected to other structural members using Extended Hollobolts. Six samples were tested experimentally by applying pull-out load on the bolts. These samples were designed to fail by column face bending. The main variable in all tests is the column face thickness. Finite element analyses were also performed using ABAQUS 6.11 to extend the experimental results and to quantify the effect of column face thickness. Results show that, the column face thickness has a clear impact on the connection strength and stiffness. However, the amount of improvement in the connection stiffness by changing the column face thickness from 5mm to 6.3mm seems to be higher than that when increasing it from 6.3mm to 8mm. The displacement at which the bolts start pulling-out from their holes increased with the use of thinner column face due to the high flexibility of the section. At the ultimate strength, the yielding of the column face propagated to the column corner and there was no yielding in its walls. After the ultimate resistance is reached, the propagation of the yielding was mainly in the column face with a miner yielding in the walls.

Keywords: Anchored bolted connection, Extended Hollobolt, Column faces bending and concrete filled hollow sections.

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Authors: V. Piscopo

Abstract:

In the traditional buckling analysis of rectangular plates the classical thin plate theory is generally applied, so neglecting the plating shear deformation. It seems quite clear that this method is not totally appropriate for the analysis of thick plates, so that in the following the two variable refined plate theory proposed by Shimpi (2006), that permits to take into account the transverse shear effects, is applied for the buckling analysis of simply supported isotropic rectangular plates, compressed in one and two orthogonal directions. The relevant results are compared with the classical ones and, for rectangular plates under uniaxial compression, a new direct expression, similar to the classical Bryan-s formula, is proposed for the Euler buckling stress. As the buckling analysis is a widely diffused topic for a variety of structures, such as ship ones, some applications for plates uniformly compressed in one and two orthogonal directions are presented and the relevant theoretical results are compared with those ones obtained by a FEM analysis, carried out by ANSYS, to show the feasibility of the presented method.

Keywords: Buckling analysis, Thick plates, Biaxial stresses

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Authors: Myung Jin Kim, Hyun Bae Jin, Wui Jun Chung

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In this study, to accurately predict cavitation of a centrifugal pump, numerical analysis was compared with experimental results modeled on a small industrial centrifugal pump. In this study, numerical analysis was compared with experimental results modeled on a small industrial centrifugal pump for reliable prediction on cavitation of a centrifugal pump. To improve validity of the numerical analysis, transient analysis was conducted on the calculated domain of full-type geometry, such as an experimental apparatus. The numerical analysis from the results was considered to be a reliable prediction of cavitaion.

Keywords: Centrifugal Pump, Cavitation, NPSH, CFD.

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Authors: Assad Maalouf, Lunjin Lu, James Lynott

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We design and implement a precise model of string operations using finite state machine transformers and state transformers to approximate the values string variables can take throughout the execution of the program.We use our model to analyze Android program string variables. Our experimental results show that our string analysis is very efficient at detecting the contextual effect of string operations on the string variables. Our model proved to be very useful when it came to verifying statements about the string variables of the program.

Keywords: Abstract interpretation, android, static analysis, string analysis.

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Authors: Marek Halenár, Eva Tvrdá, Tomáš Slanina, Ľubomír Ondruška, Eduard Kolesár, Peter Massányi, Adriana Kolesárová

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The present in vitro study was designed to reveal whether amygdalin (AMG) is able to cause changes to the motility, viability and mitochondrial activity of rabbit spermatozoa. New Zealand White rabbits (n = 10) aged four months were used in the study. Semen samples were collected from each animal and used for the in vitro incubation. The samples were divided into five equal parts and diluted with saline supplemented with 0, 0.5, 1, 2.5 and 5 mg/mL AMG. At times 0h, 3h and 5h spermatozoa motion parameters were assessed using the SpermVision™ computer-aided sperm analysis (CASA) system, cell viability was examined with the metabolic activity (MTT) assay, and the eosin-nigrosin staining technique was used to evaluate the viability of rabbit spermatozoa. All AMG concentrations exhibited stimulating effects on the spermatozoa activity, as shown by a significant preservation of the motility (P<0.05 with respect to 0.5 mg/mL and 1 mg/mL AMG; Time 5 h) and mitochondrial activity (P< 0.05 in case of 0.5 mg/mL AMG; P< 0.01 in case of 1 mg/mL AMG; P < 0.001 with respect to 2.5 mg/mL and 5 mg/mL AMG; Time 5 h). None of the AMG doses supplemented had any significant impact of the spermatozoa viability. In conclusion, the data revealed that short-term co-incubation of spermatozoa with AMG may result in a higher preservation of the sperm structural integrity and functional activity.

Keywords: Amygdalin, CASA, mitochondrial activity, motility, rabbits, spermatozoa, viability.

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Authors: J. H. Lv, W. Z. Wang, S.W. Liu

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The major concern in the aviation industry is the flight safety. Although great effort has been put onto the development of material and system reliability, the failure cases of fatal accidents still occur nowadays. Due to the complexity of the aviation system, and the interaction among the failure components, the failure analysis of the related equipment is a little difficult. This study focuses on surveying the failure cases in aviation, which are extracted from failure analysis journals, including Engineering Failure Analysis and Case studies in Engineering Failure Analysis, in order to obtain the failure sensitive factors or failure sensitive parts. The analytical results show that, among the failure cases, fatigue failure is the largest in number of occurrence. The most failed components are the disk, blade, landing gear, bearing, and fastener. The frequently failed materials consist of steel, aluminum alloy, superalloy, and titanium alloy. Therefore, in order to assure the safety in aviation, more attention should be paid to the fatigue failures.

Keywords: Aviation industry, failure analysis, failure component, fatigue.

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Authors: Mario Gómez, Won Ho Kim, Ángel Licona, José Carlos Rodríguez

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This article analyzes innovation activity in Mexico and South Korea. It develops an econometric model to test for structural breaks in the number of patent applications filed by residents and nonresidents in these countries during the period of 1965 to 2012. These changes may suggest that firms’ innovative capabilities have changed because of implementing different science, technology and innovation (STI) policies in Mexico and South Korea. Two important features characterize this research from others already developed by these authors. First, the theoretical research framework in this research is the debate between the assimilation view of growth and the accumulation view of growth. This characteristic suggests that trade liberalization should be accompanied by an adequate STI policy to boost competitiveness among indigenous firms. Second, the analysis in this research stresses the importance of key actors (e.g. governments) to successfully develop innovation capabilities among indigenous firms. Therefore, the question conducting this research is how STI policies in Mexico and South Korea contributed to develop firms’ innovation capabilities in these countries during last decades? The results from this research suggests that STI policy in South Korea was more suitable to boost innovation firms to compete in markets. Data to develop this research was released by the World Intellectual Property Organization (WIPO).

Keywords: Econometric methods, innovation, Mexico, South Korea, STI Policy.

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Authors: Lamia Hammadi, Abdellah Ait Ouhman, Aomar Ibourk

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It is widely assumed that the case of Customs Supply Chain is classified as a complex system, due to not only the variety and large number of actors, but also their complex structural links, and the interactions between these actors, that’s why this system is subject to various types of Risks. The economic, political and social impacts of those risks are highly detrimental to countries, businesses and the public, for this reason, Risk management in the customs supply chain is becoming a crucial issue to ensure the sustainability, security and safety. The main characteristic of customs risk management approach is determining which goods and means of transport should be examined? To what extend? And where future compliance resources should be directed? The purposes of this article are, firstly to deal with the concept of customs supply chain, secondly present our risk management approach based on Cross Activity Based Costing (ABC) Method as an interactive tool to support decision making in customs risk management. Finally, analysis of case study of Moroccan customs to putting theory into practice and will thus draw together the various elements of a structured and efficient risk management approach.

Keywords: Cross ABC Method, Customs Supply Chain, Risk, Risk Management.

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Authors: P. Řehoř, D. Holátová, V. Doležalová

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Paper deals with analysis of strategic management methods in non-profit making organization in the Czech Republic. Strategic management represents an aggregate of methods and approaches that can be applied for managing organizations - in this article the organizations which associate owners and keepers of nonstate forest properties. Authors use these methods of strategic management: analysis of stakeholders, SWOT analysis and questionnaire inquiries. The questionnaire was distributed electronically via e-mail. In October 2013 we obtained data from a total of 84 questionnaires. Based on the results the authors recommend the using of confrontation strategy which improves the competitiveness of non-profit making organizations.

Keywords: Strategic management, non-profit making organization, strategy analysis, SWOT analysis, strategy, competitiveness.

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Authors: Tarunjit S. Butalia, William E. Wolfe

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This study demonstrates the use of Class F fly ash in combination with lime or lime kiln dust in the full depth reclamation (FDR) of asphalt pavements. FDR, in the context of this paper, is a process of pulverizing a predetermined amount of flexible pavement that is structurally deficient, blending it with chemical additives and water, and compacting it in place to construct a new stabilized base course. Test sections of two structurally deficient asphalt pavements were reclaimed using Class F fly ash in combination with lime and lime kiln dust. In addition, control sections were constructed using cement, cement and emulsion, lime kiln dust and emulsion, and mill and fill. The service performance and structural behavior of the FDR pavement test sections were monitored to determine how the fly ash sections compared to other more traditional pavement rehabilitation techniques. Service performance and structural behavior were determined with the use of sensors embedded in the road and Falling Weight Deflectometer (FWD) tests. Monitoring results of the FWD tests conducted up to 2 years after reclamation show that the cement, fly ash+LKD, and fly ash+lime sections exhibited two year resilient modulus values comparable to open graded cement stabilized aggregates (more than 750 ksi). The cement treatment resulted in a significant increase in resilient modulus within 3 weeks of construction and beyond this curing time, the stiffness increase was slow. On the other hand, the fly ash+LKD and fly ash+lime test sections indicated slower shorter-term increase in stiffness. The fly ash+LKD and fly ash+lime section average resilient modulus values at two years after construction were in excess of 800 ksi. Additional longer-term testing data will be available from ongoing pavement performance and environmental condition data collection at the two pavement sites.

Keywords: Coal fly ash, full depth reclamation, FWD, pavement rehabilitation

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Authors: J. R. Wang, H. T. Lin, H. C. Chen, C. Shih, S. W. Chen, S. C. Chiang, C. C. Liu

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In this research, TRACE model of Chinshan BWR/4 nuclear power plant (NPP) has been developed for the simulation and analysis of ultimate response guideline (URG).The main actions of URG are the depressurization and low pressure water injection of reactor and containment venting. This research focuses to verify the URG efficiency under Fukushima-like conditions. TRACE analysis results show that the URG can keep the PCT below the criteria 1088.7 K under Fukushima-like conditions. It indicated that Chinshan NPP was safe.

Keywords: BWR, TRACE, safety analysis, URG.

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Authors: Lo Kar Yin

Abstract:

In view of the increasing speed and quantity of the housing supply, building, and civil engineering infrastructure works triggered by the pandemic across the globe, contractors, professional services providers (PSP), including consultants (e.g., architect, project manager, civil/geotechnical/structural engineer, building services engineer, quantity surveyor/cost manager, etc.) and suppliers have faced tremendous challenges of the fierce market, limited manpower, and resources under contract prices fluctuation and competitive fee and price. With qualitative analysis, this paper is to identify the available information from the industry stakeholders with a view to finding solutions for enhancing efficiency, safety, and quality of construction value chain services for public and private organisations/companies’ sustainable growth, not limited to checking the deliverables and data transfer from multi-disciplinary parties. Technology, contracts, and people are the key requirements for shaping the construction industry. With the integration of a modern engineering contract (e.g., NEC) collaborative approach, practical workflows are designed to address loopholes together with different levels of people employment/retention and technology adoption to achieve the best value for money.

Keywords: Sustainable Development, Sustainable solutions, contract, construction value chain, Building Information Modelling, BIM integration.

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Authors: Ewa Dostatni, Jacek Diakun, Damian Grajewski, Radosław Wichniarek, Anna Karwasz

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In the paper the method of product analysis from recycling point of view has been described. The analysis bases on set of measures that assess a product from the point of view of final stages of its lifecycle. It was assumed that such analysis will be performed at the design phase – in order to conduct such analysis the computer system that aids the designer during the design process has been developed. The structure of the computer tool, based on agent technology, and example results has been also included in the paper.

Keywords: Agent technology, PLM, design for environment, ecodesign.

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Authors: Samson Henry Dogo, Allan Clark, Elena Kulinskaya

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The objective of meta-analysis is to combine results from several independent studies in order to create generalization and provide evidence base for decision making. But recent studies show that the magnitude of effect size estimates reported in many areas of research significantly changed over time and this can impair the results and conclusions of meta-analysis. A number of sequential methods have been proposed for monitoring the effect size estimates in meta-analysis. However they are based on statistical theory applicable only to fixed effect model (FEM) of meta-analysis. For random-effects model (REM), the analysis incorporates the heterogeneity variance, τ 2 and its estimation create complications. In this paper we study the use of a truncated CUSUM-type test with asymptotically valid critical values for sequential monitoring in REM. Simulation results show that the test does not control the Type I error well, and is not recommended. Further work required to derive an appropriate test in this important area of applications.

Keywords: Meta-analysis, random-effects model, sequential testing, temporal changes in effect sizes.

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Authors: G.Ramana Murthy, C.Senthilpari, P.Velrajkumar, Lim Tien Sze

Abstract:

The proposed multiplexer-based novel 1-bit full adder cell is schematized by using DSCH2 and its layout is generated by using microwind VLSI CAD tool. The adder cell layout interconnect analysis is performed by using BSIM4 layout analyzer. The adder circuit is compared with other six existing adder circuits for parametric analysis. The proposed adder cell gives better performance than the other existing six adder circuits in terms of power, propagation delay and PDP. The proposed adder circuit is further analyzed for interconnect analysis, which gives better performance than other adder circuits in terms of layout thickness, width and height.

Keywords: Full Adder, Interconnect Analysis, Low-Power, Multiplexer, Propagation Delay, Parametric Analysis.

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Authors: Norazah Mohd Suki, Norbayah Mohd Suki

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This research aims to examine the influence of mediating effect of corporate social responsibility on the relationship between consumer awareness of green marketing and purchase intentions in the retail setting. Data from 200 valid questionnaires was analyzed using the partial least squares (PLS) approach for the analysis of structural equation models with SmartPLS computer program version 2.0 as research data does not necessarily have a multivariate normal distribution and is less sensitive to sample size than other covariance approaches. PLS results revealed that corporate social responsibility partially mediated the link between consumer awareness of green marketing and purchase intentions of the product in the retail setting. Marketing managers should allocate a sufficient portion of their budget to appropriate corporate social responsibility activities by engaging in voluntary programs for positive return on investment leading to increased business profitability and long run business sustainability. The outcomes of the mediating effects of corporate social responsibility add a new impetus to the growing literature and preceding discoveries on consumer green marketing awareness, which is inadequately researched in the Malaysian setting. Direction for future research is also presented.

Keywords: Green marketing awareness, corporate social responsibility, partial least squares, purchase intention.

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Authors: Hromada Martin

Abstract:

Risk analysis is considered as a fundamental aspect relevant for ensuring the level of critical infrastructure protection, where the critical infrastructure is seen as system, asset or its part which is important for maintaining the vital societal functions. Article actually discusses and analyzes the potential application of selected tools of information support for the implementation and within the framework of risk analysis and critical infrastructure protection. Use of the information in relation to their risk analysis can be viewed as a form of simplifying the analytical process. It is clear that these instruments (information support) for these purposes are countless, so they were selected representatives who have already been applied in the selected area of critical infrastructure, or they can be used. All presented fact were the basis for critical infrastructure resilience evaluation methodology development.

Keywords: Critical infrastructure, Protection, Resilience, Risk Analysis.

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Authors: Kee-Young Kwahk, Xi Ge, Jun-Hyung Park

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This study aims to examine the determinants of purchase intention in C2C e-commerce. Specifically the role of instant messaging in the C2C e-commerce contextis investigated. In addition to instant messaging, we brought in two antecedents of purchase intention - trust and customer satisfaction - to establish a theoretical research model. Structural equation modeling using LISREL was used to analyze the data.We discussed the research findings and suggested some implications for researchers and practitioners.

Keywords: E-commerce, Online marketing, C2C, Purchase Intention

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Authors: M. Klimavicius

Abstract:

This paper proposes a modeling methodology for the development of data analysis solution. The Author introduce the approach to address data warehousing issues at the at enterprise level. The methodology covers the process of the requirements eliciting and analysis stage as well as initial design of data warehouse. The paper reviews extended business process model, which satisfy the needs of data warehouse development. The Author considers that the use of business process models is necessary, as it reflects both enterprise information systems and business functions, which are important for data analysis. The Described approach divides development into three steps with different detailed elaboration of models. The Described approach gives possibility to gather requirements and display them to business users in easy manner.

Keywords: Data warehouse, data analysis, business processmanagement.

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Authors: Carlo Bellettini, Alessandro Marchetto, Andrea Trentini

Abstract:

Web applications have become very complex and crucial, especially when combined with areas such as CRM (Customer Relationship Management) and BPR (Business Process Reengineering), the scientific community has focused attention to Web applications design, development, analysis, and testing, by studying and proposing methodologies and tools. This paper proposes an approach to automatic multi-dimensional concern mining for Web Applications, based on concepts analysis, impact analysis, and token-based concern identification. This approach lets the user to analyse and traverse Web software relevant to a particular concern (concept, goal, purpose, etc.) via multi-dimensional separation of concerns, to document, understand and test Web applications. This technique was developed in the context of WAAT (Web Applications Analysis and Testing) project. A semi-automatic tool to support this technique is currently under development.

Keywords: Aspect Mining, Concepts Analysis, Concerns Mining, Multi-Dimensional Separation of Concerns, Impact Analysis.

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Authors: Sayali Vyas, Atharva Desai, Shreyas Badave, Apurv Kulkarni, B. Rajiv

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The Failure Modes and Effect Analysis (FMEA) is an efficient evaluation technique to identify potential failures in products, processes, and services. FMEA is designed to identify and prioritize failure modes. It proves to be a useful method for identifying and correcting possible failures at its earliest possible level so that one can avoid consequences of poor performance. In this paper, FMEA tool is used in detection of failures of various components of heat exchanger cycle and to identify critical failures of the components which may hamper the system’s performance. Further, a detailed Pareto analysis is done to find out the most critical components of the cycle, the causes of its failures, and possible recommended actions. This paper can be used as a checklist which will help in maintainability of the system.

Keywords: FMEA, heat exchanger cycle, Ishikawa diagram, Pareto analysis, risk priority number.

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Authors: Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski

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The literature reports a large number of approaches for measuring the similarity between protein sequences. Most of these approaches estimate this similarity using alignment-based techniques that do not necessarily yield biologically plausible results, for two reasons. First, for the case of non-alignable (i.e., not yet definitively aligned and biologically approved) sequences such as multi-domain, circular permutation and tandem repeat protein sequences, alignment-based approaches do not succeed in producing biologically plausible results. This is due to the nature of the alignment, which is based on the matching of subsequences in equivalent positions, while non-alignable proteins often have similar and conserved domains in non-equivalent positions. Second, the alignment-based approaches lead to similarity measures that depend heavily on the parameters set by the user for the alignment (e.g., gap penalties and substitution matrices). For easily alignable protein sequences, it's possible to supply a suitable combination of input parameters that allows such an approach to yield biologically plausible results. However, for difficult-to-align protein sequences, supplying different combinations of input parameters yields different results. Such variable results create ambiguities and complicate the similarity measurement task. To overcome these drawbacks, this paper describes a novel and effective approach for measuring the similarity between protein sequences, called SAF for Substitution and Alignment Free. Without resorting either to the alignment of protein sequences or to substitution relations between amino acids, SAF is able to efficiently detect the significant subsequences that best represent the intrinsic properties of protein sequences, those underlying the chronological dependencies of structural features and biochemical activities of protein sequences. Moreover, by using a new efficient subsequence matching scheme, SAF more efficiently handles protein sequences that contain similar structural features with significant meaning in chronologically non-equivalent positions. To show the effectiveness of SAF, extensive experiments were performed on protein datasets from different databases, and the results were compared with those obtained by several mainstream algorithms.

Keywords: Protein, Similarity, Substitution, Alignment.

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