Search results for: Molecular Interaction
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 1327

Search results for: Molecular Interaction

817 ClassMATE: Enabling Ambient Intelligence in the Classroom

Authors: Asterios Leonidis, George Margetis, Margherita Antona, Constantine Stephanidis

Abstract:

Ambient Intelligence (AmI) environments bring significant potential to exploit sophisticated computer technology in everyday life. In particular, the educational domain could be significantly enhanced through AmI, as personalized and adapted learning could be transformed from paper concepts and prototypes to real-life scenarios. In this paper, an integrated framework is presented, named ClassMATE, supporting ubiquitous computing and communication in a school classroom. The main objective of ClassMATE is to enable pervasive interaction and context aware education in the technologically augmented classroom of the future.

Keywords: Ambient intelligence, smart classroom, pervasivecomputing, education.

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816 Extraction in Two-Phase Systems and Some Properties of Laccase from Lentinus polychrous

Authors: K. Ratanapongleka, J. Phetsom

Abstract:

Extraction of laccase produced by L. polychrous in an aqueous two-phase system, composed of polyethylene glycol and phosphate salt at pH 7.0 and 250C was investigated. The effect of PEG molecular weight, PEG concentration and phosphate concentration was determined. Laccase preferentially partitioned to the top phase. Good extraction of laccase to the top phase was observed with PEG 4000. The optimum system was found in the system containing 12% w/w PEG 4000 and 16% w/w phosphate salt with KE of 88.3, purification factor of 3.0-fold and 99.1% yield. Some properties of the enzyme such as thermal stability, effect of heavy metal ions and kinetic constants were also presented in this work. The thermal stability decreased sharply with high temperature above 60 0C. The enzyme was inhibited by Cd2+, Pb2+, Zn2+ and Cu2+. The Vmax and Km values of the enzyme were 74.70 μmol/min/ml and 9.066 mM respectively.

Keywords: Aqueous Two Phase System, Laccase, Lentinuspolychrous,

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815 Study of Metakaolin-Based Geopolymer with Addition of Polymer Admixtures

Authors: Olesia Mikhailova, Pavel Rovnaník

Abstract:

In the present work, metakaolin-based geopolymer including different polymer admixtures was studied. Different types of commercial polymer admixtures VINNAPAS® and polyethylene glycol of different relative molecular weight were used as polymer admixtures. The main objective of this work is to investigate the influence of different types of admixtures on the properties of metakaolin-based geopolymer mortars considering their different dosage. Mechanical properties, such as flexural and compressive strength were experimentally determined. Also, study of the microstructure of selected specimens by using a scanning electron microscope was performed. The results showed that the specimen with addition of 1.5% of VINNAPAS® 7016 F and 10% of polyethylene glycol 400 achieved maximum mechanical properties.

Keywords: Metakaolin, geopolymer, polymer admixtures, mechanical properties, microstructure.

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814 Impact of Mixing Parameters on Homogenization of Borax Solution and Nucleation Rate in Dual Radial Impeller Crystallizer

Authors: A. Kaćunić, M. Ćosić, N. Kuzmanić

Abstract:

Interaction between mixing and crystallization is often ignored despite the fact that it affects almost every aspect of the operation including nucleation, growth, and maintenance of the crystal slurry. This is especially pronounced in multiple impeller systems where flow complexity is increased. By choosing proper mixing parameters, what closely depends on the knowledge of the hydrodynamics in a mixing vessel, the process of batch cooling crystallization may considerably be improved. The values that render useful information when making this choice are mixing time and power consumption. The predominant motivation for this work was to investigate the extent to which radial dual impeller configuration influences mixing time, power consumption and consequently the values of metastable zone width and nucleation rate. In this research, crystallization of borax was conducted in a 15 dm3 baffled batch cooling crystallizer with an aspect ratio (H/T) of 1.3. Mixing was performed using two straight blade turbines (4-SBT) mounted on the same shaft that generated radial fluid flow. Experiments were conducted at different values of N/NJS ratio (impeller speed/ minimum impeller speed for complete suspension), D/T ratio (impeller diameter/crystallizer diameter), c/D ratio (lower impeller off-bottom clearance/impeller diameter), and s/D ratio (spacing between impellers/impeller diameter). Mother liquor was saturated at 30°C and was cooled at the rate of 6°C/h. Its concentration was monitored in line by Na-ion selective electrode. From the values of supersaturation that was monitored continuously over process time, it was possible to determine the metastable zone width and subsequently the nucleation rate using the Mersmann’s nucleation criterion. For all applied dual impeller configurations, the mixing time was determined by potentiometric method using a pulse technique, while the power consumption was determined using a torque meter produced by Himmelstein & Co. Results obtained in this investigation show that dual impeller configuration significantly influences the values of mixing time, power consumption as well as the metastable zone width and nucleation rate. A special attention should be addressed to the impeller spacing considering the flow interaction that could be more or less pronounced depending on the spacing value.

Keywords: Dual impeller crystallizer, mixing time, power consumption, metastable zone width, nucleation rate.

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813 Radiation Effects in the PVDF/Graphene Oxide Nanocomposites

Authors: Juliana V. Pereira, Adriana S. M. Batista, Jefferson P. Nascimento, Clascídia A. Furtado, Luiz O. Faria

Abstract:

Exposure to ionizing radiation has been found to induce changes in poly(vinylidene fluoride) (PVDF) homopolymers. The high dose gamma irradiation process induces the formation of C=C and C=O bonds in its [CH2-CF2]n main chain. The irradiation also provokes crosslinking and chain scission. All these radio-induced defects lead to changes in the PVDF crystalline structure. As a consequence, it is common to observe a decrease in the melting temperature (TM) and melting latent heat (LM) and some changes in its ferroelectric features. We have investigated the possibility of preparing nanocomposites of PVDF with graphene oxide (GO) through the radio-induction of molecular bonds. In this work, we discuss how the gamma radiation interacts with the nanocomposite crystalline structure.

Keywords: Gamma irradiation, grapheme oxide, nanocomposites, PVDF.

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812 Models and Metamodels for Computer-Assisted Natural Language Grammar Learning

Authors: Evgeny Pyshkin, Maxim Mozgovoy, Vladislav Volkov

Abstract:

The paper follows a discourse on computer-assisted language learning. We examine problems of foreign language teaching and learning and introduce a metamodel that can be used to define learning models of language grammar structures in order to support teacher/student interaction. Special attention is paid to the concept of a virtual language lab. Our approach to language education assumes to encourage learners to experiment with a language and to learn by discovering patterns of grammatically correct structures created and managed by a language expert.

Keywords: Computer-assisted instruction, Language learning, Natural language grammar models, HCI.

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811 Social Structure, Involuntary Relations, and Urban Poverty

Authors: Mahmood Niroobakhsh

Abstract:

This article deals with special structuralism approaches to explain a certain kind of social problem. Widespread presence of poverty is a reminder of deep-rooted unresolved problems of social relations. The expected role from an individual for the social system recognizes poverty derived from an interrelated social structure. By the time, enabled to act on his role in the course of social interaction, reintegration of the poor in society may take place. Poverty and housing type are reflections of the underlying social structure, primarily structure’s elements, systemic interrelations, and the overall strength or weakness of that structure. Poverty varies based on social structure in that the stronger structures are less likely to produce poverty.

Keywords: Absolute poverty, relative poverty, social structure, urban poverty.

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810 Factors Affecting Media Literacy of Early Teenagers

Authors: Khajornjit Bunnag

Abstract:

The purposes of this research are: 1) to study the media literacy of early teenagers, and 2) to study the interaction between gender and timing of media exposure that affects the media literacy of teenagers. The sample of the study included 400 young people aged between 11 to 17 and who were living in Bangkok. The data was collected using questionnaires. Two-way ANOVA was used in analyzing the collected data. The result revealed that gender and timing of media exposure affected the media literacy of early teenagers with statistical significance at the level of 0.05.

Keywords: Gender, Media Literacy, Teenager, Timing of Media Exposure.

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809 An Approach to Physical Performance Analysis for Judo

Authors: Stefano Frassinelli, Alessandro Niccolai, Riccardo E. Zich

Abstract:

Sport performance analysis is a technique that is becoming every year more important for athletes of every level. Many techniques have been developed to measure and analyse efficiently the performance of athletes in some sports, but in combat sports these techniques found in many times their limits, due to the high interaction between the two opponents during the competition. In this paper the problem will be framed. Moreover the physical performance measurement problem will be analysed and three different techniques to manage it will be presented. All the techniques have been used to analyse the performance of 22 high level Judo athletes.

Keywords: Sport performance, physical performance, judo, performance coefficients.

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808 Force on a High Voltage Capacitor with Asymmetrical Electrodes

Authors: Jiří Primas, Michal Malík, Darina Jašíková, Václav Kopecký

Abstract:

When a high DC voltage is applied to a capacitor with strongly asymmetrical electrodes, it generates a mechanical force that affects the whole capacitor. This phenomenon is most likely to be caused by the motion of ions generated around the smaller of the two electrodes and their subsequent interaction with the surrounding medium. A method to measure this force has been devised and used. A formula describing the force has also been derived. After comparing the data gained through experiments with those acquired using the theoretical formula, a difference was found above a certain value of current. This paper also gives reasons for this difference.

Keywords: Capacitor with asymmetrical electrodes, Electricalfield, Mechanical force, Motion of ions.

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807 Making Businesses Work Smarter with Mobile Business Intelligence

Authors: Zeljko Panian

Abstract:

Through the course of this paper we outline how mobile Business Intelligence (m-BI) can help businesses to work smarter and to improve their agility. When we analyze the industry from the usage perspective or how interaction with the enterprise BI system happens via mobile devices, we may easily understand that there are two major types of mobile BI: passive and active. Active mobile BI gives provisions for users to interact with the BI systems on-the-fly. Active mobile business intelligence often works as a combination of both “push and pull" techniques. Some mistakes were done in the up-to-day progress of mobile technologies and mobile BI, as well as some problems that still have to be resolved. We discussed in the paper rather broadly.

Keywords: Business intelligence, mobile business intelligence, business agility, mobile technologies, optimization

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806 Relating Interface Properties with Crack Propagation in Composite Laminates

Authors: Tao Qu, Chandra Prakash, Vikas Tomar

Abstract:

The interfaces between organic and inorganic phases in natural materials have been shown to be a key factor contributing to their high performance. This work analyzes crack propagation in a 2-ply laminate subjected to uniaxial tensile mode-I crack propagation loading that has laminate properties derived based on biological material constituents (marine exoskeleton- chitin and calcite). Interfaces in such laminates are explicitly modeled based on earlier molecular simulations performed by authors. Extended finite element method and cohesive zone modeling based simulations coupled with theoretical analysis are used to analyze crack propagation. Analyses explicitly quantify the effect that interface mechanical property variation has on the delamination as well as the transverse crack propagation in examined 2-ply laminates.

Keywords: Chitin, composites, interfaces, fracture.

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805 Social Media as a ‘Service’ for Value Co-Creation by Integrating Sponsoring Companies, Sports Entities and Fans

Authors: Harri Jalonen

Abstract:

Social media has changed the ways we communicate, collaborate and connect with each other. It has also influenced our habits of consuming sports. Social media has allowed direct interaction between sponsoring companies, athletes/players and fans. Drawing on the service dominant logic of value co-creation, the conceptual paper identifies three operant resources which are beneficial for value co-creation: i) social identity and sense of community, ii) congruence and brand personality, and iii) participatory culture and fan activation. The paper contributes to the theoretical discussion on how social can be media used for value co-creation purposes in the sports industry.

Keywords: Sport, value co-creation, social media, service.

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804 Promoting Reflection through Action Learning in a 3D Virtual World

Authors: R.L. Sanders, L. McKeown

Abstract:

An international cooperation between educators in Australia and the US has led to a reconceptualization of the teaching of a library science course at Appalachian State University. The pedagogy of Action Learning coupled with a 3D virtual learning environment immerses students in a social constructivist learning space that incorporates and supports interaction and reflection. The intent of this study was to build a bridge between theory and practice by providing students with a tool set that promoted personal and social reflection, and created and scaffolded a community of practice. Besides, action learning is an educational process whereby the fifty graduate students experienced their own actions and experience to improve performance.

Keywords: action learning, action research, reflection, metacognition, virtual worlds

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803 The Influence of Electrode Heating On the Force Generated On a High Voltage Capacitor with Asymmetrical Electrodes

Authors: Jiří Primas, Michal Malík, Darina Jašíková, Václav Kopecký

Abstract:

When a high DC voltage is applied to a capacitor with strongly asymmetrical electrodes, it generates a mechanical force that affects the whole capacitor. This is caused by the motion of ions generated around the smaller of the two electrodes and their subsequent interaction with the surrounding medium. If one of the electrodes is heated, it changes the conditions around the capacitor and influences the process of ionisation, thus changing the value of the generated force. This paper describes these changes and gives reasons behind them. Further the experimental results are given as proof of the ionic mechanism of the phenomenon.

Keywords: Capacitor with asymmetrical electrodes, Generated force, Heated electrode, High voltage.

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802 Modular Workflow System for HPC Applications

Authors: Y. Yudin, T. Krasikova, Y. Dorozhko, N. Currle-Linde

Abstract:

Nowadays, HPC, Grid and Cloud systems are evolving very rapidly. However, the development of infrastructure solutions related to HPC is lagging behind. While the existing infrastructure is sufficient for simple cases, many computational problems have more complex requirements.Such computational experiments use different resources simultaneously to start a large number of computational jobs.These resources are heterogeneous. They have different purposes, architectures, performance and used software.Users need a convenient tool that allows to describe and to run complex computational experiments under conditions of HPC environment. This paper introduces a modularworkflow system called SEGL which makes it possible to run complex computational experiments under conditions of a real HPC organization. The system can be used in a great number of organizations, which provide HPC power. Significant requirements to this system are high efficiency and interoperability with the existing HPC infrastructure of the organization without any changes.

Keywords: HPC, Molecular Dynamics, Workflow Languages, Workflow Management.

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801 Nonlinear Modelling of Sloshing Waves and Solitary Waves in Shallow Basins

Authors: Mohammad R. Jalali, Mohammad M. Jalali

Abstract:

The earliest theories of sloshing waves and solitary waves based on potential theory idealisations and irrotational flow have been extended to be applicable to more realistic domains. To this end, the computational fluid dynamics (CFD) methods are widely used. Three-dimensional CFD methods such as Navier-Stokes solvers with volume of fluid treatment of the free surface and Navier-Stokes solvers with mappings of the free surface inherently impose high computational expense; therefore, considerable effort has gone into developing depth-averaged approaches. Examples of such approaches include Green–Naghdi (GN) equations. In Cartesian system, GN velocity profile depends on horizontal directions, x-direction and y-direction. The effect of vertical direction (z-direction) is also taken into consideration by applying weighting function in approximation. GN theory considers the effect of vertical acceleration and the consequent non-hydrostatic pressure. Moreover, in GN theory, the flow is rotational. The present study illustrates the application of GN equations to propagation of sloshing waves and solitary waves. For this purpose, GN equations solver is verified for the benchmark tests of Gaussian hump sloshing and solitary wave propagation in shallow basins. Analysis of the free surface sloshing of even harmonic components of an initial Gaussian hump demonstrates that the GN model gives predictions in satisfactory agreement with the linear analytical solutions. Discrepancies between the GN predictions and the linear analytical solutions arise from the effect of wave nonlinearities arising from the wave amplitude itself and wave-wave interactions. Numerically predicted solitary wave propagation indicates that the GN model produces simulations in good agreement with the analytical solution of the linearised wave theory. Comparison between the GN model numerical prediction and the result from perturbation analysis confirms that nonlinear interaction between solitary wave and a solid wall is satisfactorilly modelled. Moreover, solitary wave propagation at an angle to the x-axis and the interaction of solitary waves with each other are conducted to validate the developed model.

Keywords: Even harmonic components of sloshing waves, Green–Naghdi equations, nonlinearity, solitary waves.

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800 On Constructing Approximate Convex Hull

Authors: M. Zahid Hossain, M. Ashraful Amin

Abstract:

The algorithms of convex hull have been extensively studied in literature, principally because of their wide range of applications in different areas. This article presents an efficient algorithm to construct approximate convex hull from a set of n points in the plane in O(n + k) time, where k is the approximation error control parameter. The proposed algorithm is suitable for applications preferred to reduce the computation time in exchange of accuracy level such as animation and interaction in computer graphics where rapid and real-time graphics rendering is indispensable.

Keywords: Convex hull, Approximation algorithm, Computational geometry, Linear time.

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799 Effects of Irradiation to Morphological, Physicochemical and Biocompatibility Properties of Carrageenan

Authors: Jhalique Jane R. Fojas, Rizalinda L. De Leon, Lucille V. Abad

Abstract:

The characterization of κ-carrageenan could provide a better understanding of its functions in biological, medical and industrial applications. Chemical and physical analyses of carrageenan from seaweeds, Euchema cottonii L., were done to offer information on its properties and the effects of Co-60 γ-irradiation on its thermochemical characteristics. The structural and morphological characteristics of κ-carrageenan were determined using scanning electron microscopy (SEM) while the composition, molecular weight and thermal properties were determined using attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), gel permeation chromatography (GPC), thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC). Further chemical analysis was done using hydrogen-1 nuclear magnetic resonance (1H NMR) and functional characteristics in terms of biocompatibility were evaluated using cytotoxicity test.

Keywords: Biocompatibility, carrageenan, DSC, FTIR, GPC, irradiation, NMR, physicochemical, SEM, TGA.

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798 The Image as an Initial Element of the Cognitive Understanding of Words

Authors: S. Pesina, T. Solonchak

Abstract:

An analysis of word semantics focusing on the invariance of advanced imagery in several pressing problems. Interest in the language of imagery is caused by the introduction, in the linguistics sphere, of a new paradigm, the center of which is the personality of the speaker (the subject of the language). Particularly noteworthy is the question of the place of the image when discussing the lexical, phraseological values ​​and the relationship of imagery and metaphors. In part, the formation of a metaphor, as an interaction between two intellective entities, occurs at a cognitive level, and it is the category of the image, having cognitive roots, which aides in the correct interpretation of the results of this process on the lexical-semantic level.

Keywords: Image, metaphor, concept, creation of a metaphor, cognitive linguistics, erased image, vivid image.

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797 Enhancing Seamless Communication Through a user Co-designed Wearable Device

Authors: A. Marcengo, A. Rapp, E. Guercio

Abstract:

This work aims to describe the process of developing services and applications of seamless communication within a Telecom Italia long-term research project, which takes as central aim the design of a wearable communication device. In particular, the objective was to design a wrist phone integrated into everyday life of people in full transparency. The methodology used to design the wristwatch was developed through several subsequent steps also involving the Personas Layering Framework. The data collected in this phases have been very useful for designing an improved version of the first two concepts of wrist phone going to change aspects related to the four critical points expressed by the users.

Keywords: Design, Interaction, User Centred Design, Wristphone.

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796 Users’ Preferences for Map Navigation Gestures

Authors: Y. Y. Pang, N. A. Ismail

Abstract:

Map is a powerful and convenient tool in helping us to navigate to different places, but the use of indirect devices often makes its usage cumbersome. This study intends to propose a new map navigation dialogue that uses hand gesture. A set of dialogue was developed from users’ perspective to provide users complete freedom for panning, zooming, rotate, tilt and find direction operations. A participatory design experiment was involved here where one hand gesture and two hand gesture dialogues had been analysed in the forms of hand gestures to develop a set of usable dialogues. The major finding was that users prefer one-hand gesture compared to two-hand gesture in map navigation.

Keywords: Hand gesture, map navigation, participatory design, intuitive interaction.

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795 Study on the Design of Supermarket Store Layouts: The Principle of “Sales Magnet“

Authors: Masao Ohta, Yoshiyuki Higuchi

Abstract:

This study analyses store layout among the many factors that underlie supermarket store design, this; in terms of what to display in a shop and where to place the items. This report examines newly-opened stores and evaluates their interior shop floor layouts, which we then attempt to categorize by various styles. We then consider the interaction between shop floor layout and customer behavior from the perspective of the supermarket as the seller. At this point, we focus on the “store magnets"–the main sections within the shop likely to attract customers into the store.

Keywords: Supermarket Store Layout, Sales magnet, Customer Circulation Rate, Section Drop-by Rates.

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794 Genetic Comparison of Two Different Arabian Oryx Populations in UAE Based on Microsatellite Analysis

Authors: Mohammed A. Khidhir, K. Praveen Kumar, Marwa Al-Aseer

Abstract:

This is a genetic comparison study of Arabian Oryx (Oryx leucoryx) population at two different locations (A &B) based on nuclear microsatellite DNA markers. Arabian Oryx is listed as vulnerable and endanger by the World Conservation Union (IUCN). Thirty microsatellite markers from bovine family were applied to investigate the genetic diversity of the Arabian Oryx and to set up a molecular inventory. Among 30 microsatellite markers used, 13 markers were moderately polymorphic. Arabian Oryx at location A has shown better gene diversity over location B. However, mean number of alleles were less than location B. Data of within population inbreeding coefficient indicates inbreeding at both locations (A&B). Based on the analysis of polymorphic microsatellite markers, the study revealed that Arabian Oryx need a genetically designed breeding program.

Keywords: Arabian oryx, Microsatellites

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793 The Shanghai Cooperation Organization: China's Grand Strategy in Central Asia

Authors: Mara Gubaidullina, Aigerim Yelibayeva

Abstract:

The Shanghai Cooperation Organization is one of the successful outcomes of China's foreign policy since the end of the Cold war. The expansion of multilateral ties all over the world by dint of pursuing institutional strategies as SCO, identify China as a more constructive power. SCO became a new model of cooperation that was formed on remains of collapsed Soviet system, and predetermined China's geopolitical role in the region. As the fast developing effective regional mechanism, SCO today has more of external impact on the international system and forms a new type of interaction for promoting China's grand strategy of 'peaceful rise'.

Keywords: Central Asia, China's grand strategy, Shanghai Cooperation Organization.

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792 Ginzburg-Landau Model for Curved Two-Phase Shallow Mixing Layers

Authors: Irina Eglite, Andrei A. Kolyshkin

Abstract:

Method of multiple scales is used in the paper in order to derive an amplitude evolution equation for the most unstable mode from two-dimensional shallow water equations under the rigid-lid assumption. It is assumed that shallow mixing layer is slightly curved in the longitudinal direction and contains small particles. Dynamic interaction between carrier fluid and particles is neglected. It is shown that the evolution equation is the complex Ginzburg-Landau equation. Explicit formulas for the computation of the coefficients of the equation are obtained.

Keywords: Shallow water equations, mixing layer, weakly nonlinear analysis, Ginzburg-Landau equation

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791 The Conditioning Effect on Celebrity Multiple Endorsements

Authors: Chia-Ching Tsai

Abstract:

This research adapts experimental design to investigate the effect of conditioning or not and pre-exposure or not on brand attitude, so it is a 2×2=4 factorial design. The results show that the brand attitude of conditioning group is significantly higher than that of unconditioning group. The brand attitude with pre-exposure is significantly higher than that without pre-exposure. Conditioning or not and pre-exposure or not have significant interaction. No matter the celebrity is pre-exposure or not, the brand attitude is higher under conditioning process.

Keywords: Celebrity, Multiple endorsements, Pre-exposure, Classical condition, Second-order conditioning

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790 Investigation of Some Flotation Parameters and the Role of Dispersants in the Flotation of Chalcopyrite

Authors: H. A. Taner, V. Önen

Abstract:

A suitable choice of flotation parameters and reagents have a strong effect on the effectiveness of flotation process. The objective of this paper is to give an overview of the flotation of chalcopyrite with the different conditions and dispersants. Flotation parameters such as grinding time, pH, type, and dosage of dispersant were investigated. In order to understand the interaction of some dispersants, sodium silicate, sodium hexametaphosphate and sodium polyphosphate were used. The optimum results were obtained at a pH of 11.5 and a grinding time of 10 minutes. A copper concentrate was produced assaying 29.85% CuFeS2 and 65.97% flotation recovery under optimum rougher flotation conditions with sodium silicate.

Keywords: Chalcopyrite, dispersant, flotation, copper.

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789 CMOS Solid-State Nanopore DNA System-Level Sequencing Techniques Enhancement

Authors: Syed Islam, Yiyun Huang, Sebastian Magierowski, Ebrahim Ghafar-Zadeh

Abstract:

This paper presents system level CMOS solid-state nanopore techniques enhancement for speedup next generation molecular recording and high throughput channels. This discussion also considers optimum number of base-pair (bp) measurements through channel as an important role to enhance potential read accuracy. Effective power consumption estimation offered suitable range of multi-channel configuration. Nanopore bp extraction model in statistical method could contribute higher read accuracy with longer read-length (200 < read-length). Nanopore ionic current switching with Time Multiplexing (TM) based multichannel readout system contributed hardware savings.

Keywords: DNA, Nanopore, Amplifier, ADC, Multichannel.

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788 From Primer Generation to Chromosome Identification: A Primer Generation Genotyping Method for Bacterial Identification and Typing

Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

Abstract:

A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: Bacteria chromosome, bacterial identification, sequence, primer generation.

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