Search results for: differentially expressed genes

Authors: Ju-Chun Chien

Abstract:

The main purpose of this study was to figure out employees’ attitudes toward the new performance appraisal program and to examine whether three different types of appraisal processes differentially affected job satisfaction and employee engagement. The second purpose of this study was to investigate the relationship between performance appraisal reform, job satisfaction, and employee engagement. A large polyester and textile corporation had 2046 non-operational employees in February 2014. The valid participants were 1474 (72.04%) in this study. Data analysis included descriptive statistics, one-way ANOVA, one-way MANOVA, Pearson correlation, Content Validity Index, the exploratory factor analysis, and reliability analysis. The general results showed that employees who received the new performance appraisal program evaluated the program more positively and showed more job satisfaction than those who did not. In particular, the implementation effects of this new performance appraisal program were most highly rated by employees who used the KPI to rate their job performance. Moreover, employees’ attitudes toward the new performance appraisal program were positively related to their job satisfaction and employee engagement. Lastly, most employees regarded themselves as engaged workers. To sum up, the HR department of this company has made an effective contribution to performance appraisal reforms.

Keywords: Change management, Employee engagement, Job satisfaction, Performance appraisal reform.

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Authors: T. Yamaguchi, Y. Fujii, A. Takita, T. Kanai

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To compute dynamic characteristics of nonlinear viscoelastic springs with elastic structures having huge degree-of-freedom, Yamaguchi proposed a new fast numerical method using finite element method [1]-[2]. In this method, restoring forces of the springs are expressed using power series of their elongation. In the expression, nonlinear hysteresis damping is introduced. In this expression, nonlinear complex spring constants are introduced. Finite element for the nonlinear spring having complex coefficients is expressed and is connected to the elastic structures modeled by linear solid finite element. Further, to save computational time, the discrete equations in physical coordinate are transformed into the nonlinear ordinary coupled equations using normal coordinate corresponding to linear natural modes. In this report, the proposed method is applied to simulation for impact responses of a viscoelastic shock absorber with an elastic structure (an S-shaped structure) by colliding with a concentrated mass. The concentrated mass has initial velocities and collides with the shock absorber. Accelerations of the elastic structure and the concentrated mass are measured using Levitation Mass Method proposed by Fujii [3]. The calculated accelerations from the proposed FEM, corresponds to the experimental ones. Moreover, using this method, we also investigate dynamic errors of the S-shaped force transducer due to elastic mode in the S-shaped structure.

Keywords: Transient response, Finite Element analysis, Numerical analysis, Viscoelastic shock absorber, Force transducer.

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Authors: Laith Jaafer Habeeb

Abstract:

The present work is concerned with the free convective two dimensional flow and heat transfer, in isotropic fluid filled porous rectangular enclosure with differentially heated walls for steady state incompressible flow have been investigated for non- Darcy flow model. Effects of Darcy number (0.0001 £Da£ 10), Rayleigh number (10 £Ra£ 5000), and aspect ratio (0.25 £AR£ 4), for a range of porosity (0.4 £e£ 0.9) with and without moving lower wall have been studied. The cavity was insulated at the lower and upper surfaces. The right and left heated surfaces allows convective transport through the porous medium, generating a thermal stratification and flow circulations. It was found that the Darcy number, Rayleigh number, aspect ratio, and porosity considerably influenced characteristics of flow and heat transfer mechanisms. The results obtained are discussed in terms of the Nusselt number, vectors, contours, and isotherms.

Keywords: Numerical study, moving-wall cavity flow, saturated porous medium, different Darcy and Rayleigh numbers.

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Authors: M. Yousaf, S. Usman

Abstract:

Numerical studies were conducted using Lattice Boltzmann Method (LBM) to study the natural convection in a square cavity in the presence of roughness. An algorithm based on a single relaxation time Bhatnagar-Gross-Krook (BGK) model of Lattice Boltzmann Method (LBM) was developed. Roughness was introduced on both the hot and cold walls in the form of sinusoidal roughness elements. The study was conducted for a Newtonian fluid of Prandtl number (Pr) 1.0. The range of Ra number was explored from 10^3 to 10^6 in a laminar region. Thermal and hydrodynamic behavior of fluid was analyzed using a differentially heated square cavity with roughness elements present on both the hot and cold wall. Neumann boundary conditions were introduced on horizontal walls with vertical walls as isothermal. The roughness elements were at the same boundary condition as corresponding walls. Computational algorithm was validated against previous benchmark studies performed with different numerical methods, and a good agreement was found to exist. Results indicate that the maximum reduction in the average heat transfer was 16.66 percent at Ra number 10^5.

Keywords: Lattice Boltzmann Method Natural convection, Nusselt Number Rayleigh number, Roughness.

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Authors: Assel S. Issabekova, Olga A. Berillo, Vladimir A. Khailenko, Shara A. Atambayeva, Mireille Regnier, Anatoly T. Ivachshenko

Abstract:

Regulatory relationships of 686 intronic miRNA and 784 intergenic miRNAs with mRNAs of 51 intronic miRNA coding genes were established. Interaction features of studied miRNAs with 5'UTR, CDS and 3'UTR of mRNA of each gene were revealed. Functional regions of mRNA were shown to be significantly heterogenous according to the number of binding sites of miRNA and to the location density of these sites.

Keywords: 5'UTR, 3'UTR, CDS, miRNA, target mRNA

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Authors: S. Banerjee, A. Apte Deshpande, N. Mandi, S. Padmanabhan

Abstract:

We report a novel fusion tag for expressing recombinant proteins in E. coli. The fusion tag is the C-terminus part of the human GMCSF gene comprising 45 amino acids, which aid in over expression of otherwise non expressible genes. Expression of hIFN a2b with this fusion tag also escapes the requirement of rare codons for expression. This is also a first report of a small fusion tag of human origin having affinity to heparin sepharose column facilitating the purification of fusion protein.

Keywords: fusion tag, bacterial expression, rare codons, human GMCSF

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Authors: Valentina Koliskina

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Change in impedance of an encircling coil is obtained in the present paper for the case where the electric conductivity and magnetic permeability of a metal cylindrical tube depend on the radial coordinate. The system of equations for the vector potential is solved by means of the Fourier cosine transform. The solution is expressed in terms of improper integral containing modified Bessel functions of complex order.

Keywords: Eddy currents, magnetic permeability, Besselfunctions

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Authors: C.-C. Lin, S.-C. Kan, C.-W. Yeh, C.-I Chen, C.-J. Shieh, Y.-C. Liu

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In this study, lipid-deprived residuals of microalgae were hydrolyzed for the production of reducing sugars by using the recombinant Bacillus cellulosome, carrying eight genes from the Clostridium thermocellum ATCC27405. The obtained cellulosome was found to exist mostly in the broth supernatant with a cellulosome activity of 2.4 U/mL. Furthermore, the Michaelis-Menten constant (Km) and Vmax of cellulosome were found to be 14.832 g/L and 3.522 U/mL. The activation energy of the cellulosome to hydrolyze microalgae LDRs was calculated as 32.804 kJ/mol.

Keywords: Lipid-deprived residuals of microalgae, cellulosome, cellulose, reducing sugars, kinetics.

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Authors: Jienny Lee, In-Soo Cho, Sang-Ho Cha

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Adult mesenchymal stem cells (MSCs) have been investigated using preclinical approaches for tissue regeneration. Porcine MSCs (pMSCs) are capable of growing and attaching to plastic with a fibroblast-like morphology and then differentiating into bone, adipose, and cartilage tissues in vitro. This study was conducted to investigate the proliferating abilities, differentiation potentials, and multipotency of miniature pig adipose tissue-derived MSCs (mpAD-MSCs) with or without long-term cryopreservation, considering that cryostorage has the potential for use in clinical applications. After confirming the characteristics of the mpAD-MSCs, we examined the effect of long-term cryopreservation (> 2 years) on expression of cell surface markers (CD34, CD90 and CD105), proliferating abilities (cumulative population doubling level, doubling time, colony-forming unit, and MTT assay) and differentiation potentials into mesodermal cell lineages. As a result, the expression of cell surface markers is similar between thawed and fresh mpAD-MSCs. However, long-term cryopreservation significantly lowered the differentiation potentials (adipogenic, chondrogenic, and osteogenic) of mpAD-MSCs. When compared with fresh mpAD-MSCs, thawed mpAD-MSCs exhibited lower expression of mesodermal cell lineage-related genes such as peroxisome proliferator-activated receptor-g2, lipoprotein lipase, collagen Type II alpha 1, osteonectin, and osteocalcin. Interestingly, long-term cryostoraged mpAD-MSCs exhibited significantly higher cell viability than the fresh mpAD-MSCs. Long-term cryopreservation induced a 30% increase in the cell viability of mpAD-MSCs when compared with the fresh mpAD-MSCs at 5 days after thawing. However, long-term cryopreservation significantly lowered expression of stemness markers such as Oct3/4, Sox2, and Nanog. Furthermore, long-term cryopreservation negatively affected expression of senescence-associated genes such as telomerase reverse transcriptase and heat shock protein 90 of mpAD-MSCs when compared with the fresh mpAD-MSCs. The results from this study might be important for the successful application of MSCs in clinical trials after long-term cryopreservation.

Keywords: Mesenchymal stem cells, Cryopreservation, Stemness, Senescence.

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Authors: Ayse Okvuran

Abstract:

Creative drama which interconnects with the concepts of play, theatre, animation and role playing is a field which can only be learnt and expressed through experiencing. This study about assessment of the drama teaching in preschools by children was conducted in 3 preschools in Ankara with participation of 12 children of 6 ages who had taken drama learning courses. Qualitative research approach and semi-structured interviewing technique were employed. The results of the study indicated that all of 12 children defined drama as a game and entertainment.

Keywords: Creative drama, preschoolers, drama courses

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Authors: H. Y. Jung, Ju H. Park, S. M. Lee

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Sampled-data controller is presented for solid oxide fuel cell systems which is expressed by a sector bounded nonlinear model. The proposed control law is obtained by solving a convex problem satisfying several linear matrix inequalities. Simulation results are given to show the effectiveness of the proposed design method.

Keywords: Sampled-data control, Sector bound, Solid oxide fuel cell, Time-delay.

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Authors: E. Al Daoud

Abstract:

The purpose of computing the similarity and the diversity in the species is to trace the process of evolution and to find the relationship between the species and discover the unique, the special, the common and the universal proteins. The proteins of the whole genome of 40 species are compared with the cronobacter genome which is used as reference genome. More than 3 billion pairwise alignments are performed using blastp. Several findings are introduced in this study, for example, we found 172 proteins in cronobacter genome which have insignificant hits in other species, 116 significant proteins in the all tested species with very high score value and 129 common proteins in the plants but have insignificant hits in mammals, birds, fishes, and insects.

Keywords: Genome, species, blastp, conserved genes, cronobacter.

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Authors: Darby Tien-Hao Chang, Guan-Yu Shiu, You-Jie Sun

Abstract:

Various cis-regulatory module (CRM) predictors have been proposed in the last decade. Several well-established CRM predictors adopted different categories of prediction strategies, including window clustering, probabilistic modeling and phylogenetic footprinting. Appropriate integration of them has a potential to achieve high quality CRM prediction. This study analyzed four existing CRM predictors (ClusterBuster, MSCAN, CisModule and MultiModule) to seek a predictor combination that delivers a higher accuracy than individual CRM predictors. 465 CRMs across 140 Drosophila melanogaster genes from the RED fly database were used to evaluate the integrated CRM predictor proposed in this study. The results show that four predictor combinations achieved superior performance than the best individual CRM predictor.

Keywords: Cis-regulatory module, transcription factor binding site.

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Authors: Younies Mahmoud, Mai Mabrouk, Elsayed Sallam

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Analyzing DNA microarray data sets is a great challenge, which faces the bioinformaticians due to the complication of using statistical and machine learning techniques. The challenge will be doubled if the microarray data sets contain missing data, which happens regularly because these techniques cannot deal with missing data. One of the most important data analysis process on the microarray data set is feature selection. This process finds the most important genes that affect certain disease. In this paper, we introduce a technique for imputing the missing data in microarray data sets while performing feature selection.

Keywords: DNA microarray, feature selection, missing data, bioinformatics.

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Authors: Essam Al Daoud

Abstract:

This study solves a phylogeny problem by using modified wild dog pack optimization. The least squares error is considered as a cost function that needs to be minimized. Therefore, in each iteration, new distance matrices based on the constructed trees are calculated and used to select the alpha dog. To test the suggested algorithm, ten homologous genes are selected and collected from National Center for Biotechnology Information (NCBI) databanks (i.e., 16S, 18S, 28S, Cox 1, ITS1, ITS2, ETS, ATPB, Hsp90, and STN). The data are divided into three categories: 50 taxa, 100 taxa and 500 taxa. The empirical results show that the proposed algorithm is more reliable and accurate than other implemented methods.

Keywords: Least squares, neighbor joining, phylogenetic tree, wild dogpack.

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Authors: Antonella Bandiera

Abstract:

A new sythetic gene coding for a Human Elastin-Like Polypeptide was constructed and expressed. The recombinant product was tested as coating agent to realize a surface suitable for cell growth. Coatings showed peculiar features and different human cell lines were seeded and cultured. All cell lines tested showed to adhere and proliferate on this substrate that has been shown also to exert a specific effect on cells, depending on cell type.

Keywords: elastin, recombinant protein, coating, cell adhesion.

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Authors: Diako Azizi, Hosein Heydari, Ahmad Gholami

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Today with the rapid growth of telecommunications equipment, electronic and developing more and more networks of power, influence of electromagnetic waves on one another has become hot topic discussions. So in this article, this issue and appropriate mechanisms for EMC operations have been presented. First, impact of high voltage lines on the surrounding environment especially on the control room has been investigated, then to reduce electromagnetic radiation, various methods of shielding are provided and shielding effectiveness of them has been compared. It should be expressed that simulations have been done by the finite element method (FEM).

Keywords: Electrical field, EMC, field distribution, finite element method

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Authors: Nang Thwe Thwe Oo

Abstract:

Traditional object segmentation methods are time consuming and computationally difficult. In this paper, onedimensional object detection along the secant lines is applied. Statistical features of texture images are computed for the recognition process. Example matrices of these features and formulae for calculation of similarities between two feature patterns are expressed. And experiments are also carried out using these features.

Keywords: 1-D object segmentation, secant lines, objectoccurrence(frequency) matrix, contiguity matrix, statistical features.

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Authors: Carole Salis, Marie F. Wilson, Fabrizio Murgia, Cristian Lai, Franco Atzori, Giulia M. Orrù

Abstract:

ANDASA is a knowledge management platform for the capitalization of knowledge and cultural assets for the artistic and cultural sectors. It was built based on the priorities expressed by the participating artists. Through mapping artistic activities and specificities, it enables to highlight various aspects of the artistic research and production. Such instrument will contribute to create networks and partnerships, as it enables to evidentiate who does what, in what field, using which methodology. The platform is accessible to network participants and to the general public.

Keywords: Cultural promotion, knowledge representation, cultural mapping, ICT.

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Authors: Seo Young Kim, Jae Won Lee, Jong Sung Bae

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Microarray experiments are information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. For biologists, a key aim when analyzing microarray data is to group genes based on the temporal patterns of their expression levels. In this paper, we used an iterative clustering method to find temporal patterns of gene expression. We evaluated the performance of this method by applying it to real sporulation data and simulated data. The patterns obtained using the iterative clustering were found to be superior to those obtained using existing clustering algorithms.

Keywords: Clustering, microarray experiment, temporal pattern of gene expression data.

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Authors: Hiba Hasan, Khalid Raza

Abstract:

Reverse engineering of genetic regulatory network involves the modeling of the given gene expression data into a form of the network. Computationally it is possible to have the relationships between genes, so called gene regulatory networks (GRNs), that can help to find the genomics and proteomics based diagnostic approach for any disease. In this paper, clustering based method has been used to reconstruct genetic regulatory network from time series gene expression data. Supercoiled data set from Escherichia coli has been taken to demonstrate the proposed method.

Keywords: Gene expression, gene regulatory networks (GRNs), clustering, data preprocessing, network visualization.

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Authors: Jaroslav Krutil, František Pochylý, Simona Fialová

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The article presents two mathematical models of the interaction between a rotating shaft and an incompressible fluid. The mathematical model includes both the journal bearings and the axially traversed hydrodynamic sealing gaps of hydraulic machines. A method is shown for the identification of additional effects of the fluid acting on the rotor of the machine, both for a linear and a nonlinear model. The interaction is expressed by matrices of mass, stiffness and damping.

Keywords: CFD modeling, hydrodynamic gap, matrices of mass, stiffness and damping, nonlinear mathematical model.

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Authors: Belma Turker, Cigdem Alkas, Ebru Aylar, Ramazan Gurel, Oylum Akkus Ispir

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This study has been prepared with the purpose to get the views of senior class Elementary Education Mathematics preservice teachers on proving. Data have been obtained via surveys and interviews carried out with 104 preservice teachers. According to the findings, although preservice teachers have positive views about using proving in mathematics teaching, it is seen that their experiences related to proving is limited to courses and they think proving is a work done only for the exams. Furthermore, they have expressed in the interviews that proving is difficult for them, and because of this reason they prefer memorizing instead of learning.

Keywords: Belief on Proving, Mathematics Education, Proof.

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Authors: Zixin Liu, Shu Lü, Shouming Zhong, Mao Ye

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The discrete-time uncertain system with time delay is investigated for bounded input bounded output (BIBO). By constructing an augmented Lyapunov function, three different sufficient conditions are established for BIBO stabilization. These conditions are expressed in the form of linear matrix inequalities (LMIs), whose feasibility can be easily checked by using Matlab LMI Toolbox. Two numerical examples are provided to demonstrate the effectiveness of the derived results.

Keywords: Robust BIBO stabilization, delay-dependent stabilization, discrete-time system, time delay.

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Authors: I. Nassiri, B. Goliaei, M. Tavassoli

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The ability to distinguish missense nucleotide substitutions that contribute to harmful effect from those that do not is a difficult problem usually accomplished through functional in vivo analyses. In this study, instead current biochemical methods, the effects of missense mutations upon protein structure and function were assayed by means of computational methods and information from the databases. For this order, the effects of new missense mutations in exon 5 of PTEN gene upon protein structure and function were examined. The gene coding for PTEN was identified and localized on chromosome region 10q23.3 as the tumor suppressor gene. The utilization of these methods were shown that c.319G>A and c.341T>G missense mutations that were recognized in patients with breast cancer and Cowden disease, could be pathogenic. This method could be use for analysis of missense mutation in others genes.

Keywords: Bioinformatics, missense mutations, PTEN tumorsuppressor gene.

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Authors: Aníbal Rodríguez Fuentes, Juan V. Lorenzo Ginori, Ricardo Grau Ábalo

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Identifying protein coding regions in DNA sequences is a basic step in the location of genes. Several approaches based on signal processing tools have been applied to solve this problem, trying to achieve more accurate predictions. This paper presents a new predictor that improves the efficacy of three techniques that use the Fourier Transform to predict coding regions, and that could be computed using an algorithm that reduces the computation load. Some ideas about the combination of the predictor with other methods are discussed. ROC curves are used to demonstrate the efficacy of the proposed predictor, based on the computation of 25 DNA sequences from three different organisms.

Keywords: Bioinformatics, Coding region prediction, Computational load reduction, Digital Signal Processing, Fourier Transform.

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Authors: Jeffrey L. Duffany

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An optimal solution for a large number of constraint satisfaction problems can be found using the technique of substitution and elimination of variables analogous to the technique that is used to solve systems of equations. A decision function f(A)=max(A2) is used to determine which variables to eliminate. The algorithm can be expressed in six lines and is remarkable in both its simplicity and its ability to find an optimal solution. However it is inefficient in that it needs to square the updated A matrix after each variable elimination. To overcome this inefficiency the algorithm is analyzed and it is shown that the A matrix only needs to be squared once at the first step of the algorithm and then incrementally updated for subsequent steps, resulting in significant improvement and an algorithm complexity of O(n3).

Keywords: Algorithm, complexity, constraint, np-complete.

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Authors: Houda Jalali, Hassan Abbassi

Abstract:

In this numerical work, natural convection and entropy generation of Al₂O₃–water nanofluid in square cavity have been studied. A two-dimensional steady laminar natural convection in a differentially heated square cavity of length L, filled with a nanofluid is investigated numerically. The horizontal walls are considered adiabatic. Vertical walls corresponding to x=0 and x=L are respectively maintained at hot temperature, T_h and cold temperature, T_c. The resolution is performed by the CFD code "FLUENT" in combination with GAMBIT as mesh generator. These simulations are performed by maintaining the Rayleigh numbers varied as 10³ ≤ Ra ≤ 10⁶, while the solid volume fraction varied from 1% to 5%, the particle size is fixed at dp=33 nm and a range of the temperature from 20 to 70 °C. We used models of thermophysical nanofluids properties based on experimental measurements for studying the effect of adding solid particle into water in natural convection heat transfer and entropy generation of nanofluid. Such as models of thermal conductivity and dynamic viscosity which are dependent on solid volume fraction, particle size and temperature. The average Nusselt number is calculated at the hot wall of the cavity in a different solid volume fraction. The most important results is that at low temperatures (less than 40 °C), the addition of nanosolids Al₂O₃ into water leads to a decrease in heat transfer and entropy generation instead of the expected increase, whereas at high temperature, heat transfer and entropy generation increase with the addition of nanosolids. This behavior is due to the contradictory effects of viscosity and thermal conductivity of the nanofluid. These effects are discussed in this work.

Keywords: Entropy generation, heat transfer, nanofluid, natural convection.

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Authors: L. Ludovic, R. Daniel, S-E Tbahriti

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Database management systems that integrate user preferences promise better solution for personalization, greater flexibility and higher quality of query responses. This paper presents a tentative work that studies and investigates approaches to express user preferences in queries. We sketch an extend capabilities of SQLf language that uses the fuzzy set theory in order to define the user preferences. For that, two essential points are considered: the first concerns the expression of user preferences in SQLf by so-called fuzzy commensurable predicates set. The second concerns the bipolar way in which these user preferences are expressed on mandatory and/or optional preferences.

Keywords: Flexible query language, relational database, userpreference.

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Authors: Alexandra Oliveros, Miguel Sotaquirá

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DNA microarray technology is widely used by geneticists to diagnose or treat diseases through gene expression. This technology is based on the hybridization of a tissue-s DNA sequence into a substrate and the further analysis of the image formed by the thousands of genes in the DNA as green, red or yellow spots. The process of DNA microarray image analysis involves finding the location of the spots and the quantification of the expression level of these. In this paper, a tool to perform DNA microarray image analysis is presented, including a spot addressing method based on the image projections, the spot segmentation through contour based segmentation and the extraction of relevant information due to gene expression.

Keywords: Contour segmentation, DNA microarrays, edge detection, image processing, segmentation, spot addressing.

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