Search results for: differentially expressed genes

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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Authors: Seung Pil Pack

Abstract:

Carbonic anhydrases (CAs) has been focused as biological catalysis for CO2 sequestration process because it can catalyze the conversion of CO2 to bicarbonate. Here, codon-optimized sequence of α type-CA cloned from Duneliala species. (DsCAopt) was constructed, expressed, and characterized. The expression level in E. coli BL21(DE3) was better for codon-optimized DsCAopt than intact sequence of DsCAopt. DsCAopt enzyme shows high-stability at pH 7.6/10.0. In final, we demonstrated that in the Ca2+ solution, DsCAopt enzyme can catalyze well the conversion of CO2 to CaCO3, as the calcite form.

Keywords: Carbonic anhydrase, Codon-optimization, Duneliala species, CO2 sequestration

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Authors: Dong Hoon Lim

Abstract:

A series of microarray experiments produces observations of differential expression for thousands of genes across multiple conditions. Principal component analysis(PCA) has been widely used in multivariate data analysis to reduce the dimensionality of the data in order to simplify subsequent analysis and allow for summarization of the data in a parsimonious manner. PCA, which can be implemented via a singular value decomposition(SVD), is useful for analysis of microarray data. For application of PCA using SVD we use the DNA microarray data for the small round blue cell tumors(SRBCT) of childhood by Khan et al.(2001). To decide the number of components which account for sufficient amount of information we draw scree plot. Biplot, a graphic display associated with PCA, reveals important features that exhibit relationship between variables and also the relationship of variables with observations.

Keywords: Principal component analysis, singular value decomposition, microarray data, SRBCT

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Authors: Norsinnira Zainul Azlan, Hiroshi Yamaura

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This study is concerned with a new adaptive impedance control strategy to compensate for unknown time-varying environment stiffness and position. The uncertainties are expressed by Function Approximation Technique (FAT), which allows the update laws to be derived easily using Lyapunov stability theory. Computer simulation results are presented to validate the effectiveness of the proposed strategy.

Keywords: Adaptive Impedance Control, Function Approximation Technique (FAT), unknown time-varying environment position and stiffness.

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Authors: Seo Young Kim, Toshimitsu Hamasaki

Abstract:

Microarrays have become the effective, broadly used tools in biological and medical research to address a wide range of problems, including classification of disease subtypes and tumors. Many statistical methods are available for analyzing and systematizing these complex data into meaningful information, and one of the main goals in analyzing gene expression data is the detection of samples or genes with similar expression patterns. In this paper, we express and compare the performance of several clustering methods based on data preprocessing including strategies of normalization or noise clearness. We also evaluate each of these clustering methods with validation measures for both simulated data and real gene expression data. Consequently, clustering methods which are common used in microarray data analysis are affected by normalization and degree of noise and clearness for datasets.

Keywords: Gene expression, clustering, data preprocessing.

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Authors: Said Laachir, Aziz Laaribi

Abstract:

The Helmholtz equation often arises in the study of physical problems involving partial differential equation. Many researchers have proposed numerous methods to find the analytic or approximate solutions for the proposed problems. In this work, the exact analytical solutions of the Helmholtz equation in spherical polar coordinates are presented using the Nikiforov-Uvarov (NU) method. It is found that the solution of the angular eigenfunction can be expressed by the associated-Legendre polynomial and radial eigenfunctions are obtained in terms of the Laguerre polynomials. The special case for k=0, which corresponds to the Laplace equation is also presented.

Keywords: Helmholtz equation, Nikiforov-Uvarov method, exact solutions, eigenfunctions.

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Authors: A. Thabet, G. B. H. Frej, M. Boutayeb

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This paper presents a design of dynamic feedback control based on observer for a class of large scale Lipschitz nonlinear systems. The use of Differential Mean Value Theorem (DMVT) is to introduce a general condition on the nonlinear functions. To ensure asymptotic stability, sufficient conditions are expressed in terms of linear matrix inequalities (LMIs). High performances are shown through real time implementation with ARDUINO Duemilanove board to the one-link flexible joint robot.

Keywords: Feedback stabilization, DMVT, Lipschitz nonlinear systems, nonlinear observer, real time implementation.

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Authors: Zixin Liu

Abstract:

The problem of robust stability and robust stabilization for a class of discrete-time uncertain systems with time delay is investigated. Based on Tchebychev inequality, by constructing a new augmented Lyapunov function, some improved sufficient conditions ensuring exponential stability and stabilization are established. These conditions are expressed in the forms of linear matrix inequalities (LMIs), whose feasibility can be easily checked by using Matlab LMI Toolbox. Compared with some previous results derived in the literature, the new obtained criteria have less conservatism. Two numerical examples are provided to demonstrate the improvement and effectiveness of the proposed method.

Keywords: Robust stabilization, robust stability, discrete-time system, time delay.

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Authors: Weng Ian Ho, Seng Fat Wong

Abstract:

In recent years, Radio Frequency Identification (RFID) is followed with interest by many researches, especially for the purpose of indoor positioning as the innate properties of RFID are profitable for achieving it. A lot of algorithms or schemes are proposed to be used in the RFID-based positioning system, but most of them are lack of environmental consideration and it induces inaccuracy of application. In this research, a lot of algorithms and schemes of RFID indoor positioning are discussed to see whether effective or not on application, and some rules are summarized for achieving accurate positioning. On the other hand, a new term “Noise Factor" is involved to describe the signal loss between the target and the obstacle. As a result, experimental data can be obtained but not only simulation; and the performance of the positioning system can be expressed substantially.

Keywords: Indoor positioning, LANDMARC, noise factors, RFID.

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Authors: Sara Bragança, Eric Costa

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The work presented in this paper was performed for a workstation of an assembly section in a company that manufactures radio modules and air conditioning for cars. After performing a workstation analysis and a questionnaire to the operators it was possible to understand the need to investigate the risk of musculoskeletal disorders originated from both the handling of loads as the incorrect dimensioning of the workstation. Regarding the handling of loads the NIOSH Equation was used and it was verified that there was no risk of musculoskeletal disorders. As the operators expressed their lack of satisfaction regarding back pains due to posture adopted they were established the appropriate dimensions (to satisfy 97.5% of the population and using the table of anthropometric data of the Portuguese population) for the workstation and it was proposed the availability of a chair for the workers.

Keywords: Anthropometry, Musculoskeletal disorders, NIOSH Equation.

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Authors: Z. M. Biyasheva, M. Zh. Tleubergenova, Y. A. Zaripova, A. L. Shakirov, V. V. Dyachkov

Abstract:

In recent years, interest in ecogenetic and biomedical problems related to the effects on the population of radon and its daughter decay products has increased significantly. Of particular interest is the assessment of the consequence of irradiation at hazardous radon areas, which includes the Almaty region due to the large number of tectonic faults that enhance radon emanation. In connection with the foregoing, the purpose of this work was to study the genetic effects of exposure to supernormal radon doses on the alpha-radiation model. Irradiation does not affect the growth of the cell, but rather its ability to differentiate. In addition, irradiation can lead to somatic mutations, morphoses and modifications. These damages most likely occur from changes in the composition of the substances of the cell. Such changes are epigenetic since they affect the regulatory processes of ontogenesis. Variability in the expression of regulatory genes refers to conditional mutations that modify the formation of signs of intraspecific similarity. Characteristic features of these conditional mutations are the dominant type of their manifestation, phenotypic asymmetry and their instability in the generations. Currently, the terms “morphosis” and “modification” are used to describe epigenetic variability, which are maintained in Drosophila melanogaster cultures using linkaged X- chromosomes, and the mutant X-chromosome is transmitted along the paternal line. In this paper, we investigated the epigenetic effects of alpha particles, whose source in nature is mainly radon and its daughter decay products. In the experiment, an isotope of plutonium-238 (Pu²³⁸), generating radiation with an energy of about 5500 eV, was used as a source of alpha particles. In an experiment in the first generation (F₁), deformities or morphoses were found, which can be called "radiation syndromes" or mutations, the manifestation of which is similar to the pleiotropic action of genes. The proportion of morphoses in the experiment was 1.8%, and in control 0.4%. In this experiment, the morphoses in the flies of the first and second generation looked like black spots, or melanomas on different parts of the imago body; "generalized" melanomas; curled, curved wings; shortened wing; bubble on one wing; absence of one wing, deformation of thorax, interruption and violation of tergite patterns, disruption of distribution of ocular facets and bristles; absence of pigmentation of the second and third legs. Statistical analysis by the Chi-square method showed the reliability of the difference in experiment and control at P ≤ 0.01. On the basis of this, it can be considered that alpha particles, which in the environment are mainly generated by radon and its isotopes, have a mutagenic effect that manifests itself, mainly in the formation of morphoses or deformities.

Keywords: Alpha-radiation, genotoxicity, morphoses, radioecology, radon.

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Authors: L. Godinho, N. Teixeira

Abstract:

Nowadays, massification of Internet access represents one of the major challenges to the traditional powers of the State, among which the power to control its external image. The virtual world has also sparked the interest of social sciences which consider it a new field of study, an immense open text where sense is expressed. In this paper, that immense text has been accessed to so as to understand the perception Internet users from all over the world have of Portugal. Ours is a quantitative and qualitative approach, as we have resorted to buzz, thematic and category analysis. The results confirm the predominance of sea stereotype in others' vision of the Portuguese people, and evidence that national image has adapted to network communication through processes of individuation and paganization.

Keywords: Internet, national image, perception, web analytics.

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Authors: Rita Riekstina-Dolge, Zanda Kruma, Daina Karklina

Abstract:

Aroma forming volatiles are important components of fermented beverages. The aim of current research is to evaluate the volatile compounds and phenolic compounds of commercial ciders. Volatile aroma compounds and TPC of seven commercial ciders were determined. Extraction of aroma compounds was performed using solid phase microextraction (DVB/Car/PDMS fibre). Analysis of volatile aroma compounds was made using a Perkin Elmer Clarus 500 GC/MS. Total phenol content (TPC) was determined according to the Folin-Ciocalteu spectrophotometric method and results were expressed as gallic acid equivalents. The highest volatile compounds were in apple ciders with pear flavor. The highest TPC and lower content of volatile compounds were detected in French ciders.

Keywords: cider, TPC, volatile compounds

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Authors: Junseok Ham, Chansun Jung, Junhyung Park, Jihye Ryeo, Ilju Ko

Abstract:

It is hard to express emotion through only speech when we watch a character in a movie or a play because we cannot estimate the size, kind, and quantity of emotion. So this paper proposes an artificial emotion model for visualizing current emotion with color and location in emotion model. The artificial emotion model is designed considering causality of generated emotion, difference of personality, difference of continual emotional stimulus, and co-relation of various emotions. This paper supposed the Emotion Field for visualizing current emotion with location, and current emotion is expressed by location and color in the Emotion Field. For visualizing changes within current emotion, the artificial emotion model is adjusted to characters in Hamlet.

Keywords: Emotion, Artificial Emotion, Visualizing, EmotionModel.

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Authors: Anjali Verma, Ram Jiwari, Jitender Kumar

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This paper presents a new function expansion method for finding traveling wave solution of a non-linear equation and calls it the (G'/G)-expansion method. The shallow water wave equation is reduced to a non linear ordinary differential equation by using a simple transformation. As a result the traveling wave solutions of shallow water wave equation are expressed in three forms: hyperbolic solutions, trigonometric solutions and rational solutions.

Keywords: Shallow water wave equation, Exact solutions, (G'/G) expansion method.

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Authors: Sing-Wu Liou, Yin-Fu Huang

Abstract:

For identifying the discriminative sequence features between exons and introns, a new paradigm, rescaled-range frameshift analysis (RRFA), was proposed. By RRFA, two new sequence features, the frameshift sensitivity (FS) and the accumulative penta-mer complexity (APC), were discovered which were further integrated into a new feature of larger scale, the persistency in anti-mutation (PAM). The feature-validation experiments were performed on six model organisms to test the power of discrimination. All the experimental results highly support that FS, APC and PAM were all distinguishing features between exons and introns. These identified new sequence features provide new insights into the sequence composition of genes and they have great potentials of forming a new basis for recognizing the exonintron boundaries in gene sequences.

Keywords: Exon-Intron Discrimination, Rescaled-Range Frameshift Analysis, Frameshift Sensitivity, Accumulative Sequence Complexity

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Authors: Anupma Bansal, R. K. Gupta

Abstract:

In this paper, we study a new modified Novikov equation for its classical and nonclassical symmetries and use the symmetries to reduce it to a nonlinear ordinary differential equation (ODE). With the aid of solutions of the nonlinear ODE by using the modified (G/G)-expansion method proposed recently, multiple exact traveling wave solutions are obtained and the traveling wave solutions are expressed by the hyperbolic functions, trigonometric functions and rational functions.

Keywords: New Modified Novikov Equation, Lie Classical Method, Nonclassical Method, Modified (G'/G)-Expansion Method, Traveling Wave Solutions.

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Authors: Sunita Verma , Divya Tiwari, Ajay Verma

Abstract:

Water samples were collected from river Pandu at six stations where human and animal activities were high. Composite samples were analyzed for dissolved oxygen (DO), biochemical oxygen demand (BOD), chemical oxygen demand (COD) , pH values during dry and wet seasons as well as the harmattan period. The total data points were used to establish relationships between the parameters and data were also subjected to statistical analysis and expressed as mean ± standard error of mean (SEM) at a level of significance of p<0.05. Regression analysis was carried out to establish relationships if any between studied parameters and relationships in form of scatter plots were obtained between DO/BOD, COD/DO, BOD/COD, COD/pH, BOD/pH and DO/pH. The high to moderate correlation coefficient observed, R2 ranged from 0.68 to 0.15 between these parameters.

Keywords: BOD, DO, COD, pH, Regression analysis.

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Authors: Süha Yılmaz, Emin Özyılmaz, Melih Turgut, Şuur Nizamoğlu

Abstract:

In this paper, position vector of a partially null unit speed curve with respect to standard frame of Minkowski space-time is studied. First, it is proven that position vector of every partially null unit speed curve satisfies a vector differential equation of fourth order. In terms of solution of the differential equation, position vector of a partially null unit speed curve is expressed.

Keywords: Frenet Equations, Partially Null Curves, Minkowski Space-time, Vector Differential Equation.

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Authors: V. Kahya, A. Birinci, R. Erdol

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A frictionless contact problem for a two-layer orthotropic elastic medium loaded through a rigid flat stamp is considered. It is assumed that tensile tractions are not allowed and only compressive tractions can be transmitted across the interface. In the solution, effect of gravity is taken into consideration. If the external load on the rigid stamp is less than or equal to a critical value, continuous contact between the layers is maintained. The problem is expressed in terms of a singular integral equation by using the theory of elasticity and the Fourier transforms. Numerical results for initial separation point, critical separation load and contact stress distribution are presented.

Keywords: Frictionless contact, Initial separation, Orthotropicmaterial, Singular integral equation.

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Authors: Jana Kisková, Dana Gabriková

Abstract:

Monoamine oxidase A gene (MAOA) is suggested to be a candidate gene implicated in many neuropsychiatric disorders, including autism spectrum disorder (ASD). This meta-analytic review evaluates the relationship between ASD and MAOA markers such as 30 bp variable number tandem repeats in the promoter region (uVNTR) and single nucleotide polymorphisms (SNPs) by using findings from recently published studies. It seems that in Caucasian males, the risk of developing ASD increase with the presence of 4- repeat allele in the promoter region of MAOA gene whereas no differences were found between autistic patients and controls in Egyptian, West Bengal and Korean population. Some studies point to the importance of specific haplotype groups of SNPs and interaction of MAOA with others genes (e. g. FOXP2 or SRY). The results of existing studies are insufficient and further research is needed.

Keywords: Autism spectrum disorder, MAOA, uVNTR, single nucleotide polymorphism.

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Authors: Achraf El Allali, John R. Rose

Abstract:

A number of competing methodologies have been developed to identify genes and classify DNA sequences into coding and non-coding sequences. This classification process is fundamental in gene finding and gene annotation tools and is one of the most challenging tasks in bioinformatics and computational biology. An information theory measure based on mutual information has shown good accuracy in classifying DNA sequences into coding and noncoding. In this paper we describe a species independent iterative approach that distinguishes coding from non-coding sequences using the mutual information measure (MIM). A set of sixty prokaryotes is used to extract universal training data. To facilitate comparisons with the published results of other researchers, a test set of 51 bacterial and archaeal genomes was used to evaluate MIM. These results demonstrate that MIM produces superior results while remaining species independent.

Keywords: Coding Non-coding Classification, Entropy, GeneRecognition, Mutual Information.

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Authors: Sandeep Chandana, Rene V. Mayorga, Christine W. Chan

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This article outlines conceptualization and implementation of an intelligent system capable of extracting knowledge from databases. Use of hybridized features of both the Rough and Fuzzy Set theory render the developed system flexibility in dealing with discreet as well as continuous datasets. A raw data set provided to the system, is initially transformed in a computer legible format followed by pruning of the data set. The refined data set is then processed through various Rough Set operators which enable discovery of parameter relationships and interdependencies. The discovered knowledge is automatically transformed into a rule base expressed in Fuzzy terms. Two exemplary cancer repository datasets (for Breast and Lung Cancer) have been used to test and implement the proposed framework.

Keywords: Knowledge Extraction, Fuzzy Sets, Rough Sets, Neuro–Fuzzy Systems, Databases

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Authors: Ozlem Faydasicok, Sabri Arik

Abstract:

This paper derives some new sufficient conditions for the stability of a class of neutral-type neural networks with discrete time delays by employing a suitable Lyapunov functional. The obtained conditions can be easily verified as they can be expressed in terms of the network parameters only. It is shown that the results presented in this paper for neutral-type delayed neural networks establish a new set of stability criteria, and therefore can be considered as the alternative results to the previously published literature results. A numerical example is also given to demonstrate the applicability of our proposed stability criterion.

Keywords: Stability Analysis, Neutral-Type Neural Networks, Time Delay Systems, Lyapunov Functionals.

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Authors: Ahmet Çay, Savvas Vassiliadis, Maria Rangoussi, Işık Tarakçıoğlu

Abstract:

This paper presents a novel approach to assessing textile porosity by the application of the image analysis techniques. The images of different types of sample fabrics, taken through a microscope when the fabric is placed over a constant light source,transfer the problem into the image analysis domain. Indeed, porosity can thus be expressed in terms of a brightness percentage index calculated on the digital microscope image. Furthermore, it is meaningful to compare the brightness percentage index with the air permeability and the tightness indices of each fabric type. We have experimentally shown that there exists an approximately linear relation between brightness percentage and air permeability indices.

Keywords: Textile fabrics, porosity, air permeability, image analysis, light transmission.

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Authors: M. A. Koroma, Z. Chuangyi, A. F., Kamara, A. M. H. Conteh

Abstract:

In this work, we apply the Modified Laplace decomposition algorithm in finding a numerical solution of Blasius’ boundary layer equation for the flat plate in a uniform stream. The series solution is found by first applying the Laplace transform to the differential equation and then decomposing the nonlinear term by the use of Adomian polynomials. The resulting series, which is exactly the same as that obtained by Weyl 1942a, was expressed as a rational function by the use of diagonal padé approximant.

Keywords: Modified Laplace decomposition algorithm, Boundary layer equation, Padé approximant, Numerical solution.

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Authors: Yomna Amr Ahmed Lotfi Koraim, Dalia Moati Rasmi Elkhateeb

Abstract:

Vertical landscape is introduced in this study as an alternative innovative technology for urban sustainable developments for its diverse environmental, economic, and psycho-social advantages. The main aim is to investigate the social acceptance of vertical landscape in Cairo, Egypt. The study objectives were to explore the perceptions of residents concerning this certain phenomenon and their opinions about its implementation. Survey questionnaires were administrated to 60 male and female residents from the Greater Cairo area. Despite the various concerns expressed about the application of vertical landscape, there was a clear majority of approval about its suitability. This is quite encouraging for the prospect of vertical landscape implementation in Cairo, Egypt.

Keywords: Vertical landscape, green facades, social acceptance, sustainable urban development.

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Authors: Serifenur Cebesoy, Yelda Aygar, Elgiz Bairamov

Abstract:

In this study, we examine some spectral properties of non-selfadjoint matrix-valued difference equations consisting of a polynomial-type Jost solution. The aim of this study is to investigate the eigenvalues and spectral singularities of the difference operator L which is expressed by the above-mentioned difference equation. Firstly, thanks to the representation of polynomial type Jost solution of this equation, we obtain asymptotics and some analytical properties. Then, using the uniqueness theorems of analytic functions, we guarantee that the operator L has a finite number of eigenvalues and spectral singularities.

Keywords: Difference Equations, Jost Functions, Asymptotics, Eigenvalues, Continuous Spectrum, Spectral Singularities.

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Authors: Amin Almasi

Abstract:

Reliability assessment and risk analysis of rotating machine rotors in various overload and malfunction situations present challenge to engineers and operators. In this paper a new analytical method for evaluation of rotor under large deformation is addressed. Model is presented in general form to include also composite rotors. Presented simulation procedure is based on variational work method and has capability to account for geometric nonlinearity, large displacement, nonlinear support effect and rotor contacting other machine components. New shape functions are presented which capable to predict accurate nonlinear profile of rotor. The closed form solutions for various operating and malfunction situations are expressed. Analytical simulation results are discussed

Keywords: Large Deformation, Nonlinear, Rotor.

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Authors: S. Dorbani, M. Badaoui, D. Benouar

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The goal of the paper is to highlight the effect of the building design and epicentral distance on the storey lateral displacements, for several reinforced concrete buildings (6, 9 and 12 stories). These structures are subjected to seismic accelerations from the Boumerdes earthquake (Algeria, May 21st, Mw = 6.8). Using the response spectrum method (modal spectral approach), the analysis is performed in both longitudinal and transverse directions. The building design is expressed through the fundamental period and epicentral distance is used to represent the earthquake effect variation on storey lateral displacements and interstory drift for the considered buildings.

Keywords: Epicentral distance, interstory drift, lateral displacement, natural period, reinforced concrete buildings.

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