Search results for: expression analysis

Authors: Mohammed A. Hajeeh

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This paper examines the behavior of a system, which upon failure is either replaced with certain probability p or imperfectly repaired with probability q. The system is analyzed using Kolmogorov's forward equations method; the analytical expression for the steady state availability is derived as an indicator of the system’s performance. It is found that the analysis becomes more complex as the number of imperfect repairs increases. It is also observed that the availability increases as the number of states and replacement probability increases. Using such an approach in more complex configurations and in dynamic systems is cumbersome; therefore, it is advisable to resort to simulation or heuristics. In this paper, an example is provided for demonstration.

Keywords: Repairable models, imperfect, availability, exponential distribution.

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Authors: Maysam Mard-Soltani, Mohamad Javad Rasaee, Saeed Khalili, Abdol Karim Sheikhi, Mehdi Hedayati

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Production of specific antibody responses against hTSH is a cumbersome process due to the high identity between the hTSH and the other members of the glycoprotein hormone family (FSH, LH and HCG) and the high identity between the human hTSH and host animals for antibody production. Therefore, two polyclonal antibodies were purified against two recombinant proteins. Four possible ELISA tests were designed based on these antibodies. These ELISA tests were checked against hTSH and other glycoprotein hormones, and their sensitivity and specificity were assessed. Bioinformatics tools were used to analyze the immunological properties. After the immunogen region selection from hTSH protein, c terminal of B hTSH was selected and applied. Two recombinant genes, with these cut pieces (first: two repeats of C terminal of B hTSH, second: tetanous toxin+B hTSH C terminal), were designed and sub-cloned into the pET32a expression vector. Standard methods were used for protein expression, purification, and verification. Thereafter, immunizations of the white New Zealand rabbits were performed and the serums of them were used for antibody titration, purification and characterization. Then, four ELISA tests based on two antibodies were employed to assess the hTSH and other glycoprotein hormones. The results of these assessments were compared with standard amounts. The obtained results indicated that the desired antigens were successfully designed, sub-cloned, expressed, confirmed and used for in vivo immunization. The raised antibodies were capable of specific and sensitive hTSH detection, while the cross reactivity with the other members of the glycoprotein hormone family was minimum. Among the four designed tests, the test in which the antibody against first protein was used as capture antibody, and the antibody against second protein was used as detector antibody did not show any hook effect up to 50 miu/l. Both proteins have the ability to induce highly sensitive and specific antibody responses against the hTSH. One of the antibody combinations of these antibodies has the highest sensitivity and specificity in hTSH detection.

Keywords: hTSH, bioinformatics, protein expression, cross reactivity.

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Authors: Alan S. Hoback

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Most people see human faces in car front and back ends because of the process of pareidolia. 96 people were surveyed to see how many of them saw a face in the vehicle styling. Participants were aged 18 to 72 years. 94% of the participants saw faces in the front-end design of production models. All participants that recognized faces indicated that most styles showed some degree of an angry expression. It was found that women were more likely to see faces in inanimate objects. However, with respect to whether women were more likely to perceive anger in the vehicle design, the results need further clarification. Survey responses were correlated to the design features of vehicles to determine what cues the respondents were likely looking at when responding. Whether the features looked anthropomorphic was key to anger perception. Features such as the headlights which could represent eyes and the air intake that could represent a mouth had high correlations to trends in scores. Results are compared among models, makers, by groupings of body styles classifications for the top 12 brands sold in the US, and by year for the top 20 models sold in the US in 2016. All of the top models sold increased in perception of an angry expression over the last 20 years or since the model was introduced, but the relative change varied by body style grouping.

Keywords: Aggressive driving, face recognition, road rage, vehicle styling.

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Authors: Md. Ashikur Rahman Khan, M. M. Rahman

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In electrical discharge machining (EDM), a complete and clear theory has not yet been established. The developed theory (physical models) yields results far from reality due to the complexity of the physics. It is difficult to select proper parameter settings in order to achieve better EDM performance. However, modelling can solve this critical problem concerning the parameter settings. Therefore, the purpose of the present work is to develop mathematical model to predict performance characteristics of EDM on Ti-5Al-2.5Sn titanium alloy. Response surface method (RSM) and artificial neural network (ANN) are employed to develop the mathematical models. The developed models are verified through analysis of variance (ANOVA). The ANN models are trained, tested, and validated utilizing a set of data. It is found that the developed ANN and mathematical model can predict performance of EDM effectively. Thus, the model has found a precise tool that turns EDM process cost-effective and more efficient.

Keywords: Analysis of variance, artificial neural network, material removal rate, modelling, response surface method, surface finish.

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Authors: Fiona Browne, Huiru Zheng, Haiying Wang, Francisco Azuaje

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Recent years have seen a growing trend towards the integration of multiple information sources to support large-scale prediction of protein-protein interaction (PPI) networks in model organisms. Despite advances in computational approaches, the combination of multiple “omic" datasets representing the same type of data, e.g. different gene expression datasets, has not been rigorously studied. Furthermore, there is a need to further investigate the inference capability of powerful approaches, such as fullyconnected Bayesian networks, in the context of the prediction of PPI networks. This paper addresses these limitations by proposing a Bayesian approach to integrate multiple datasets, some of which encode the same type of “omic" data to support the identification of PPI networks. The case study reported involved the combination of three gene expression datasets relevant to human heart failure (HF). In comparison with two traditional methods, Naive Bayesian and maximum likelihood ratio approaches, the proposed technique can accurately identify known PPI and can be applied to infer potentially novel interactions.

Keywords: Bayesian network, Classification, Data integration, Protein interaction networks.

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Authors: Olatinwo M. O., Oyeleke Olaosebikan, David Henry O.

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Rain attenuation plays a lot of roles in the design of satellite and terrestrial microwave radio links, hence a good knowledge of its effect is of great interest to Engineers and scientists in that it is often required to give a high level of accuracy of the rainrate distribution that expresses rainrate from the lowest value to the highest. This study proposes a model to express rainrate parameters alpha (α) and beta (β) as a function of geographical location at 0.01% of the time. The tropical locations used in the development of the effect were Ilorin, Ile-Ife, Douala, Dar-es-Selam, Nairobi, Lusaka, and Brazilia.

This expression clearly confirms the variability of rainfall from place to place. When consistency test was carried out using the expression to generate rainrate for each location examined, the result obtained was reliable for rain intensities between 5mm/h and 200mm/h. The variability of α and β with latitude also shows that different latitudes have different cumulative rain distribution. The model proposed in this study would be one of the useful tools to Radio Engineers since the precipitation effect in the design of satellite and terrestrial microwave radio links is among the factors to consider when designing communication systems.

Keywords: Rain rate, attenuation, geographical location.

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Authors: Maged Ahmed, Ahmed El-Mahdy

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In this paper, Selective Adaptive Parallel Interference Cancellation (SA-PIC) technique is presented for Multicarrier Direct Sequence Code Division Multiple Access (MC DS-CDMA) scheme. The motivation of using SA-PIC is that it gives high performance and at the same time, reduces the computational complexity required to perform interference cancellation. An upper bound expression of the bit error rate (BER) for the SA-PIC under Rayleigh fading channel condition is derived. Moreover, the implementation complexities for SA-PIC and Adaptive Parallel Interference Cancellation (APIC) are discussed and compared. The performance of SA-PIC is investigated analytically and validated via computer simulations.

Keywords: Adaptive interference cancellation, communicationsystems, multicarrier signal processing, spread spectrum

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Authors: Ali Anaissi, Paul J. Kennedy, Madhu Goyal

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Analysis and visualization of microarraydata is veryassistantfor biologists and clinicians in the field of diagnosis and treatment of patients. It allows Clinicians to better understand the structure of microarray and facilitates understanding gene expression in cells. However, microarray dataset is a complex data set and has thousands of features and a very small number of observations. This very high dimensional data set often contains some noise, non-useful information and a small number of relevant features for disease or genotype. This paper proposes a non-linear dimensionality reduction algorithm Local Principal Component (LPC) which aims to maps high dimensional data to a lower dimensional space. The reduced data represents the most important variables underlying the original data. Experimental results and comparisons are presented to show the quality of the proposed algorithm. Moreover, experiments also show how this algorithm reduces high dimensional data whilst preserving the neighbourhoods of the points in the low dimensional space as in the high dimensional space.

Keywords: Linear Dimension Reduction, Non-Linear Dimension Reduction, Principal Component Analysis, Biologists.

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Authors: Yeskendirov N.R., Karjaubaeva S.K., Ahmet A. K.

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A number of theoretical and methodological problems connected with substantiation of a new approach and searches of a new research paradigm and the analysis of features of formation and development of the Kazakh stage are considered in the article. The wide spectrum of questions connected with genesis of the Kazakh stage art has caused necessity of consideration of world outlook and social cultural aspects which have affected formation of the given phenomenon in the Kazakh culture. But how can we define the form of expression and aesthetics of the national theatre? Probably, the answer to this question we will find if we apply to deep world view sources, and, as a consequence, it is necessary to study deeply the plot dramaturgy, which is based on myths, rites and eposes, mastering of symbolic gestures and mimics, allegory of a word, etc.

Keywords: Tradition, theater, art, culture, nomadic Kazakhs.

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Authors: Hui-Chuan Chu, Min-Ju Liao, Wei-Kai Cheng, William Wei-Jen Tsai, Yuh-Min Chen

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Avoiding learning failures in mathematics e-learning environments caused by emotional problems in students with autism has become an important topic for combining of special education with information and communications technology. This study presents an adaptive emotional adjustment model in mathematics e-learning for students with autism, emphasizing the lack of emotional perception in mathematics e-learning systems. In addition, an emotion classification for students with autism was developed by inducing emotions in mathematical learning environments to record changes in the physiological signals and facial expressions of students. Using these methods, 58 emotional features were obtained. These features were then processed using one-way ANOVA and information gain (IG). After reducing the feature dimension, methods of support vector machines (SVM), k-nearest neighbors (KNN), and classification and regression trees (CART) were used to classify four emotional categories: baseline, happy, angry, and anxious. After testing and comparisons, in a situation without feature selection, the accuracy rate of the SVM classification can reach as high as 79.3-%. After using IG to reduce the feature dimension, with only 28 features remaining, SVM still has a classification accuracy of 78.2-%. The results of this research could enhance the effectiveness of eLearning in special education.

Keywords: Emotion classification, Physiological and facial Expression measures, Students with autism, Mathematics e-learning.

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Authors: M. Kaomek, J. R. Ketudat-Cairns

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The cDNA encoding the 326 amino acids of a Class I basic chitinase gene from Leucaena leucocephala de Wit (KB3, Genbank accession: AAM49597) was cloned under the control of CaMV35S promoter in pCAMBIA 1300 and transferred to Koshihikari. Calli of Koshihikari rice was transformed with agrobacterium with this construct expressing the chitinase and β- glucouronidase (GUS). The frequencies of calli 90 % has been obtained from rice seedlings cultured on NB medium. The high regeneration frequencies, 74% was obtained from calli cultured on regeneration medium containing 4 mg/l BAP, and 7 g/l phytagel at 25°C. Various factors were studied in order to establish a procedure for the transformation of Koshihikari Agrobacterium tumefaciens. Supplementation of 50 mM acetosyringone to the medium during coculivation was important to enhance the frequency to transient transformation. The 4 week-old scutellum-derived calli were excellent starting materials. Selection medium based on NB medium supplement with 40 mg/l hygromycin and 400 mg/l cefotaxime were an optimized medium for selection of transformed rice calli. The percentage of transformation 70 was obtained. Recombinant calli and regenerated rice plants were checked the expression of chitinase and gus by PCR, northern blot gel, southern blot gel, and gus assay. Chitinase and gus were expressed in all parts of recombinant rice. The rice line expressing the KB3 chiitnase was more resistant to the blast fungus Fusarium monoliforme than control line.

Keywords: chitinase, Leucaena leucocephala de Wit, Koshihikari, transgenic rice.

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Authors: Jose William Porras Ferreira

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This paper presents two solutions to the Fermat’s Last Theorem (FLT). The first one using some algebraic basis related to the Pythagorean theorem, expression of equations, an analysis of their behavior, when compared with power  and power  and using " the “Well Ordering Principle” of natural numbers it is demonstrated that in Fermat equation . The second one solution is using the connection between  and power  through the Pascal’s triangle or  Newton’s binomial coefficients, where de Fermat equation do not fulfill the first coefficient, then it is impossible that:

zⁿ=xⁿ+yⁿ for n>2 and (x, y, z) E Z⁺ - {0}

 

Keywords: Fermat’s Last Theorem, Pythagorean Theorem, Newton Binomial Coefficients, Pascal’s Triangle, Well Ordering Principle.

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Authors: Chiung-Tsun Kuoa, Tzu-Hao Liu, Fang-Yi Lin, Tai-Hao Hsu, Hui-Yin Chen

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Hyperglycemia-mediated accumulation of advanced glycation end-products (AGEs) play a pivotal role in the development of diabetic complications by inducing inflammation. In the present study, we evaluated the possible effects of water/ethanol (1/1, v/v) extracts (WEE) and its fractions from Canarium album Raeusch. (Chinese olive) which is a fruit used on AGEs-stimulated oxidative stress and inflammation in monocytes and vascular endothelial cells. Co-incubation of EA.hy926 endothelial cells with WEE and its fractions for 24h resulted in a significant decrease of monocyte–endothelial cell adhesion, the expression of ICAM-1, generation of intracellular ROS and depletion of GSH induced by AGEs. Chinese olive fruit extracts also reduced the expression of pro-inflammatory mediates, such as TNF-α, IL-1β and IL-6 in THP-1 cells. These findings suggested that Chinese olive fruit was able to protect vascular endothelium from dysfunction induced by AGEs. 

Keywords: Advanced glycation end-products (AGEs), Canarium album Raeusch, endothelial dysfunction, inflammation.

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Authors: Georgi Bebrov, Rozalina Dimova

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In the field of quantum secure communication, there is no evaluation that characterizes quantum secure communication (QSC) protocols in a complete, general manner. The current paper addresses the problem concerning the lack of such an evaluation for QSC protocols by introducing an optimality evaluation, which is expressed as the average over the three main parameters of QSC protocols: efficiency, security, and practicality. For the efficiency evaluation, the common expression of this parameter is used, which incorporates all the classical and quantum resources (bits and qubits) utilized for transferring a certain amount of information (bits) in a secure manner. By using criteria approach whether or not certain criteria are met, an expression for the practicality evaluation is presented, which accounts for the complexity of the QSC practical realization. Based on the error rates that the common quantum attacks (Measurement and resend, Intercept and resend, probe attack, and entanglement swapping attack) induce, the security evaluation for a QSC protocol is proposed as the minimum function taken over the error rates of the mentioned quantum attacks. For the sake of clarity, an example is presented in order to show how the optimality is calculated.

Keywords: Quantum cryptography, quantum secure communcation, quantum secure direct communcation security, quantum secure direct communcation efficiency, quantum secure direct communcation practicality.

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Authors: Liping Jing, Michael K. Ng, Tieyong Zeng

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Microarray data profiles gene expression on a whole genome scale, therefore, it provides a good way to study associations between gene expression and occurrence or progression of cancer. More and more researchers realized that microarray data is helpful to predict cancer sample. However, the high dimension of gene expressions is much larger than the sample size, which makes this task very difficult. Therefore, how to identify the significant genes causing cancer becomes emergency and also a hot and hard research topic. Many feature selection algorithms have been proposed in the past focusing on improving cancer predictive accuracy at the expense of ignoring the correlations between the features. In this work, a novel framework (named by SGS) is presented for stable gene selection and efficient cancer prediction . The proposed framework first performs clustering algorithm to find the gene groups where genes in each group have higher correlation coefficient, and then selects the significant genes in each group with Bayesian Lasso and important gene groups with group Lasso, and finally builds prediction model based on the shrinkage gene space with efficient classification algorithm (such as, SVM, 1NN, Regression and etc.). Experiment results on real world data show that the proposed framework often outperforms the existing feature selection and prediction methods, say SAM, IG and Lasso-type prediction model.

Keywords: Gene Selection, Cancer Prediction, Lasso, Clustering, Classification.

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Authors: Hechmi Saidi, Noureddine Hamdi

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The performance of hybrid amplify and forward - decode and forward (AF-DF) hybrid radio frequency/free space optical (RF/FSO) communication system, that adopts M-ary pulse position modulation (MPPM) techniques, is analyzed. Both exact and approximate symbol-error rates (SERs) are derived. The random variations of the received optical irradiance, produced by the atmospheric turbulence, is modeled by the gamma-gamma (GG) statistical distribution. A closed-form expression for the probability density function (PDF) is derived for the whole above system is obtained. Thanks to the use of hybrid AF-DF hybrid RF/FSO configuration and MPPM, the effects of atmospheric turbulence is mitigated; hence the capacity of combating atmospheric turbulence and the transmissitted signal quality are improved.

Keywords: FSO, RF, hybrid, AF, DF, SER, SNR, GG channel.

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Authors: Marlene Weber, Joseph Giacomin, Alessio Malizia, Lee Skrypchuk, Voula Gkatzidou

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Technological and sociological developments in the automotive sector are shifting the focus of design towards developing a better understanding of driver needs, desires and emotions. Human centred design methods are being more frequently applied to automotive research, including the use of systems to detect human emotions in real-time. One method for a non-contact measurement of emotion with low intrusiveness is Facial-Expression Analysis (FEA). This paper describes a research study investigating emotional responses of 22 participants in a naturalistic driving environment by applying a multi-method approach. The research explored the possibility to investigate emotional responses and their frequencies during naturalistic driving through real-time FEA. Observational analysis was conducted to assign causes to the collected emotional responses. In total, 730 emotional responses were measured in the collective study time of 440 minutes. Causes were assigned to 92% of the measured emotional responses. This research establishes and validates a methodology for the study of emotions and their causes in the driving environment through which systems and factors causing positive and negative emotional effects can be identified.

Keywords: Affective computing, case study, emotion recognition, human computer interaction.

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Authors: V. T. S. Dao, T. G. Etoh, C. Vo Le, H. D. Nguyen, K. Takehara, T. Akino, K. Nishi

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Since 2004, we have been developing an in-situ storage image sensor (ISIS) that captures more than 100 consecutive images at a frame rate of 10 Mfps with ultra-high sensitivity as well as the video camera for use with this ISIS. Currently, basic research is continuing in an attempt to increase the frame rate up to 100 Mfps and above. In order to suppress electro-magnetic noise at such high frequency, a digital-noiseless imaging transfer scheme has been developed utilizing solely sinusoidal driving voltages. This paper presents highly efficient-yet-accurate expressions to estimate attenuation as well as phase delay of driving voltages through RC networks of an ultra-high-speed image sensor. Elmore metric for a fundamental RC chain is employed as the first-order approximation. By application of dimensional analysis to SPICE data, we found a simple expression that significantly improves the accuracy of the approximation. Similarly, another simple closed-form model to estimate phase delay through fundamental RC networks is also obtained. Estimation error of both expressions is much less than previous works, only less 2% for most of the cases . The framework of this analysis can be extended to address similar issues of other VLSI structures.

Keywords: Dimensional Analysis, ISIS, Digital-noiseless, RC network, Attenuation, Phase Delay, Elmore model

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Authors: Mouse, cardiac myocytes, computer simulation, action potential.

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Heterogeneous repolarization causes dispersion of the T-wave and has been linked to arrhythmogenesis. Such heterogeneities appear due to differential expression of ionic currents in different regions of the heart, both in healthy and diseased animals and humans. Mice are important animals for the study of heart diseases because of the ability to create transgenic animals. We used our previously reported model of mouse ventricular myocytes to develop 2D mouse ventricular tissue model consisting of 14,000 cells (apical or septal ventricular myocytes) and to study the stability of action potential propagation and Ca2+ dynamics. The 2D tissue model was implemented as a FORTRAN program code for highperformance multiprocessor computers that runs on 36 processors. Our tissue model is able to simulate heterogeneities not only in action potential repolarization, but also heterogeneities in intracellular Ca2+ transients. The multicellular model reproduced experimentally observed velocities of action potential propagation and demonstrated the importance of incorporation of realistic Ca2+ dynamics for action potential propagation. The simulations show that relatively sharp gradients of repolarization are predicted to exist in 2D mouse tissue models, and they are primarily determined by the cellular properties of ventricular myocytes. Abrupt local gradients of channel expression can cause alternans at longer pacing basic cycle lengths than gradual changes, and development of alternans depends on the site of stimulation.

Keywords: Mouse, cardiac myocytes, computer simulation, action potential

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Authors: Kiyoko Yoshimura, Yasunobu Kino

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Focusing on professional call centers where workers with expertise perform services, this study aims to clarify the relationships between emotional labor and job satisfaction and the effects of recognition of customer feedback. Since the professional call center operators consist of professional license holders (qualification holders) and those who do not (non-holders), the following three points are analyzed in the two groups by using covariance structure analysis and simultaneous multi-population analysis: 1) The relationship between emotional labor and job satisfaction, 2) customer feedback and job satisfaction, and 3) the intermediation effect between the emotional labor of customer feedback and job satisfaction. The following results are obtained: i) No direct effect is found between job satisfaction and emotional labor for qualification holders and non-holders, ii) for qualification holders and non-holders, recognition of positive feedback and recognition of negative feedback had positive and negative effects on job satisfaction, respectively, iii) for qualification and non-holders, “consideration for colleagues” influences job satisfaction by recognizing positive feedback, and iv) only for qualification holders, the factors “customer-oriented emotional expression” and “emotional disharmony” have a positive and negative effect on job satisfaction, respectively, through recognition of positive feedback and recognition of negative feedback.

Keywords: Call center, emotional labor, professional service, job satisfaction, customer feedback.

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Authors: Muñoz-Sanchez, Victor Manuel, Perez-Flores, Antonio Manuel

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The main objective of this paper is to establish the relationship between models of state organization and the various types of collective identity expressed by the Spanish. The question of nationalism and identity ascription in Spain has always been a topic of special importance due to the presence in that country of territories where the population emits very different opinions of nationalist sentiment than the rest of Spain. The current situation of sovereignty challenge of Catalonia to the central government exemplifies the importance of the subject matter. In order to analyze this process of interrelation, we use a secondary data mining by applying the multiple correspondence analysis technique (MCA). As a main result a typology of four types of expression of collective identity based on models of State organization are shown, which are connected with the party position on this issue.

Keywords: Models of organization of the state, nationalism, collective identity, Spain, political parties.

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Authors: Amr A. Fouad, Hamed A. Alwadaani, Iyad Jresat

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The present study investigated the protective effect of thymoquinone (TQ), against cadmium-induced kidney injury in rats. Cadmium chloride (1.2 mg Cd/kg/day, s.c.), was given for nine weeks. TQ treatment (40 mg/kg/day, p.o.) started on the same day of cadmium administration and continued for nine weeks. TQ significantly decreased serum creatinine, renal malondialdehyde and nitric oxide, and significantly increased renal reduced glutathione in rats received cadmium. Histopathological examination showed that TQ markedly minimized renal tissue damage induced by cadmium. Immunohistochemical analysis revealed that TQ markedly decreased the cadmium-induced expression of inducible nitric oxide synthase, tumor necrosis factor-α, cyclooxygenase-2, and caspase-3 in renal tissue. It was concluded that TQ significantly protected against cadmium nephrotoxicity in rats, through its antioxidant, antiinflammatory, and antiapoptotic actions.

Keywords: Thymoquinone, cadmium, kidney, rats.

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Authors: D. R. Ambika, K. R. Radhika, D. Seshachalam

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Unconstrained authentication is an important component for personal automated systems and human-computer interfaces. Existing solutions mostly use face as the primary object of analysis. The performance of face-based systems is largely determined by the extent of deformation caused in the facial region and amount of useful information available in occluded face images. Periocular region is a useful portion of face with discriminative ability coupled with resistance to deformation. A reliable portion of periocular area is available for occluded images. The present work demonstrates that joint representation of periocular texture and periocular structure provides an effective expression and poses invariant representation. The proposed methodology provides an effective and compact description of periocular texture and shape. The method is tested over four benchmark datasets exhibiting varied acquisition conditions.

Keywords: Periocular authentication, Zernike moments, LBPV, shape and texture fusion.

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Authors: S. Hariharan, P. Muthuchidambaranathan

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In this paper, we consider a multi user multiple input multiple output (MU-MIMO) based cooperative reporting system for cognitive radio network. In the reporting network, the secondary users forward the primary user data to the common fusion center (FC). The FC is equipped with linear equalizers and an energy detector to make the decision about the spectrum. The primary user data are considered to be a digital video broadcasting - terrestrial (DVB-T) signal. The sensing channel and the reporting channel are assumed to be an additive white Gaussian noise and an independent identically distributed Raleigh fading respectively. We analyzed the detection probability of MU-MIMO system with linear equalizers and arrived at the closed form expression for average detection probability. Also the system performance is investigated under various MIMO scenarios through Monte Carlo simulations.

Keywords: Cooperative MU-MIMO, DVB-T, Linear Equalizers.

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Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

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Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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Authors: Hung-Ming Lai, Andreas Albrecht, Kathleen Steinhöfel

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Cancers could normally be marked by a number of differentially expressed genes which show enormous potential as biomarkers for a certain disease. Recent years, cancer classification based on the investigation of gene expression profiles derived by high-throughput microarrays has widely been used. The selection of discriminative genes is, therefore, an essential preprocess step in carcinogenesis studies. In this paper, we have proposed a novel gene selector using information-theoretic measures for biological discovery. This multivariate filter is a four-stage framework through the analyses of feature relevance, feature interdependence, feature redundancy-dependence and subset rankings, and having been examined on the colon cancer data set. Our experimental result show that the proposed method outperformed other information theorem based filters in all aspect of classification errors and classification performance.

Keywords: Colon cancer, feature interdependence, feature subset selection, gene selection, microarray data analysis.

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Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

Abstract:

Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p>0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: Kidney cancer, molecular biomarker, expression analysis, mutation screening.

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Authors: B. Chouhan, A. Denesyuk, J. Heino, M. S. Johnson, K. Denessiouk

Abstract:

Integrins are a large family of multidomain α/β cell signaling receptors. Some integrins contain an additional inserted I domain, whose earliest expression appears to be with the chordates, since they are observed in the urochordates Ciona intestinalis (vase tunicate) and Halocynthia roretzi (sea pineapple), but not in integrins of earlier diverging species. The domain-s presence is viewed as a hallmark of integrins of higher metazoans, however in vertebrates, there are clearly three structurally-different classes: integrins without I domains, and two groups of integrins with I domains but separable by the presence or absence of an additional αC helix. For example, the αI domains in collagen-binding integrins from Osteichthyes (bony fish) and all higher vertebrates contain the specific αC helix, whereas the αI domains in non-collagen binding integrins from vertebrates and the αI domains from earlier diverging urochordate integrins, i.e. tunicates, do not. Unfortunately, within the early chordates, there is an evolutionary gap due to extinctions between the tunicates and cartilaginous fish. This, coupled with a knowledge gap due to the lack of complete genomic data from surviving species, means that the origin of collagen-binding αC-containing αI domains remains unknown. Here, we analyzed two available genomes from Callorhinchus milii (ghost shark/elephant shark; Chondrichthyes – cartilaginous fish) and Petromyzon marinus (sea lamprey; Agnathostomata), and several available Expression Sequence Tags from two Chondrichthyes species: Raja erinacea (little skate) and Squalus acanthias (dogfish shark); and Eptatretus burgeri (inshore hagfish; Agnathostomata), which evolutionary reside between the urochordates and osteichthyes. In P. marinus, we observed several fragments coding for the αC-containing αI domain, allowing us to shed more light on the evolution of the collagen-binding integrins.

Keywords: Integrin αI domain, integrin evolution, collagen binding, structure, αC helix

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Authors: Dwitya Elvira, Eryati Darwin

Abstract:

Background: Graves’ disease (GD) is an autoimmune thyroid disease. Imbalance of Th1/Th2 cells and T-regulatory (Treg)/Th17 cells was thought to play pivotal role in the pathogenesis of GD. Treg FoxP3 produced TGF-β to maintain regulatory function, and Th17 cells produced IL-17 as cytokines that were thought in mediating several autoimmune diseases. The aim of this study is to assess the role of IL-17 and TGF-β in the pathogenesis of GD and to investigate its correlation with Thyroid Stimulating Hormone Receptor Antibody (TRAb) and Treg FoxP3 expression. Method: 30 GD patients and 27 age and sex-matched controls were enrolled in this study. Diagnosis of GD was based on clinical and biochemical of GD. Serum IL-17, TGF-β, TRAb, and FoxP3 were measured by enzyme-linked immunosorbent assay (ELISA). Data were analyzed by using SPSS 21.0 (SPSS Inc.). Spearman rank correlation test was used for assessment of correlation. The statistical significance was accepted as P<0.05. Result: There was no significant correlation between IL-17 and TGF-β serum with expression of FoxP3 level in GD, but there was significant correlation between TGF-β and TRAb serum level (P<0.05). Serum levels of IL-17 and TGF-β were found to be elevated in patient group compared to control, where mean values of IL-17 were 14.43±2.15 pg/mL and TGF-β were 10.44±3.19 pg/mL in patients group; and in control group, level of IL-17 were 7.1±1.45 pg/mL and TGF-β were 4.95±1.35 pg/mL. Conclusion: Serum Il-17 and TGF-β were elevated in GD patients that reflect the role of inflammatory and regulatory cytokines activation in pathogenesis of GD. There was significant correlation between TGF-β and TRAb, revealing that Treg cytokines may play a role in pathogenesis of GD.

Keywords: IL-17, TGF-β, FoxP3, Graves’ disease.

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Authors: Ghulam Rasool, Ilka Philippow

Abstract:

Modernizing legacy applications is the key issue facing IT managers today because there's enormous pressure on organizations to change the way they run their business to meet the new requirements. The importance of software maintenance and reengineering is forever increasing. Understanding the architecture of existing legacy applications is the most critical issue for maintenance and reengineering. The artifacts recovery can be facilitated with different recovery approaches, methods and tools. The existing methods provide static and dynamic set of techniques for extracting architectural information, but are not suitable for all users in different domains. This paper presents a simple and lightweight pattern extraction technique to extract different artifacts from legacy systems using regular expression pattern specifications with multiple language support. We used our custom-built tool DRT to recover artifacts from existing system at different levels of abstractions. In order to evaluate our approach a case study is conducted.

Keywords: Artifacts recovery, Pattern matching, Reverseengineering, Program understanding, Regular expressions, Sourcecode analysis.

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