Sharif Digital Repository

Single nucleotide polymorphism (SNP) in human genomes is considered to be highly associated with complex genetic diseases. As a consequence, obtaining all SNPs from human populations is one of the primary goals of recent studies on human genomics. The two sequences of SNPs in diploid human organisms are called haplotypes. In this paper, the problem of haplotype reconstruction from SNP fragments with and without genotype information is studied. Minimum error correction (MEC) is an important model for this problem but only effective when the error rate of the fragments is low. MEC/GI, as an extension to MEC model, employs the related genotype information besides the SNP fragments and,... 

A Timetabling problem is usually defined as assigning a set of events to a number of rooms and timeslots such that they satisfy a number of constraints. Particle swarm optimization (PSO) is a stochastic, population-based computer problem-solving algorithm; it is a kind of swarm intelligence that is based on social-psychological principles and provides insights into social behavior, as well as contributing to engineering applications. This paper applies the Particle Swarm Optimization algorithm to the classic Timetabling problem. This is inspired by similar attempts belonging to the evolutionary paradigm in which the metaheuristic involved is tweaked to suit the grouping nature of problems... 

Recently, there has been great interest in Bio informatics among researches from various disciplines such as computer science, mathematics, statistics and artificial intelligence. Bioinformatics mainly deals with solving biological problems at molecular levels. One of the classic problems of bioinformatics which has gain a lot attention lately is Haplotyping, the goal of which is categorizing SNP-fragments into two clusters and deducing a haplotype for each. Since the problem is proved to be NP-hard, several computational and heuristic methods have addressed the problem seeking feasible answers. In this work it is shown that using PCM to solve Haplotyping problem in DALY dataset yields... 

Reconstructing haplotype in MEC (Minimum Error Correction) model is an important clustering problem which focuses on inferring two haplotypes from SNP fragments (Single Nucleotide Polymorphism) containing gaps and errors. Mutated form of human genome is responsible for genetic diseases which mostly occur in SNP sites. In this paper, a fuzzy clustering approach is performed for haplotype reconstruction or haplotype assembly from a given sample Single Nucleotide Polymorphism (SNP). In the best previous approach based on reconstruction rate (Wang 2007[2]), all SNP-fragments are considered with equal values. In our proposed method the value of the fragments are based on the degree of membership... 

Most positions of the human genome are typically invariant (99%) and only some positions (1%) are commonly variant which are associated with complex genetic diseases. Haplotype reconstruction is to divide aligned SNP fragments, which is the most frequent form of difference to address genetic diseases, into two classes, and thus inferring a pair of haplotypes from them. Minimum error correction (MEC) is an important model for this problem but only effective when the error rate of the fragments is low. MEC/GI as an extension to MEC employs the related genotype information besides the SNP fragments and so results in a more accurate inference. The haplotyping problem, due to its NP-hardness, may... 

Breast cancer is one of the most lethal cancers, especially in women. Despite many efforts, side effects of anti-cancer drugs and metastasis are still the main challenges in breast cancer treatment. Recently, advanced technologies such as 3D-printing and nanotechnology have created new horizons in cancer treatment. In this work, we report an advanced drug delivery system based on 3D-printed gelatin-alginate scaffolds containing paclitaxel-loaded niosomes (Nio-PTX@GT-AL). The morphology, drug release, degradation, cellular uptake, flow cytometry, cell cytotoxicity, migration, gene expression, and caspase activity of scaffolds, and control samples (Nio-PTX, and Free-PTX) were investigated.... 

An appropriate pre-processing algorithm in classification is not only of great importance with respect to classifier choice, but also would be more crucial. In this paper, a pre-processing step is proposed in order to increase accuracy of classification. The aim of this approach is finding a transformation matrix causes classes to be more discriminable by transforming data into the new space and consequently, increases the classification accuracy. This transformation matrix is computed through two methods based on linear discrimination. In the first method, we use class independent LDA to increase classification accuracy by finding a transformation that maximizes the between-class scatter... 

Four 5-, 10-, 20- and 30-story moment frames, representing low-, mid-, and two high-rise structures, were subjected to a great number of idealized directivity pulses. The amplitudes and periods of pulses vary from 0.02 g to 1.0 g and 0.5 to 12 sec, respectively. Over 1400 nonlinear dynamic analyses of low- to high-rise moment frames were performed which were feasible through using modified fish-bone model. The distribution of interstory drift along the height was studied and two applied contours were proposed: (i) the maximum interstory drift contour, and (ii) the critical story contour. These contours were demonstrated versus the ratio of natural period of the structure to the pulse period... 

In this article singular points of a parallel manipulator are obtained based on a novel geometrical method. Here we introduce the constrained plain method (CPM) and some of its application in parallel mechanism. Given the definition of constraint plane (CP) and infinite constraint plane (ICP) the dependency conditions of constraints is achieved with the use of a new theorem based on the Ceva geometrical theorem. The direction of angular velocity of a body is achieved by having three ICPs with the use of another theorem. Finally, with the use of the above two novel theorems singularities of the 3UPF_PU mechanism are obtained. It should be emphasized that this method is completely geometrical,... 

An analytical model is proposed to study the effect of particle size on melting enthalpy and entropy of metallic nanoparticles (NPs). The Mott's and Regel's equations for melting entropy in the combination of core average coordination number (CAC) and surface average coordination number (SAC) of freestanding NPs are considered. Clusters of icosahedral (IC), body centered cubic (BCC), and body centered tetragonal (BCT) structure without any vacancies and defects are modeled. Using the variable coordination number made this model to be in good agreement with experimental and molecular dynamic (MD) results of different crystal structures. The model predicts melting entropy and enthalpy of... 

Grinding is widely used for manufacturing of components that require fine surface finish and good dimensional accuracy. In this study a thermo-mechanical finite element analysis is conducted to find out how grinding parameters can affect temperature and residual stress distribution in the workpiece. Results of parametric study presented in this work indicate, by carefully selecting the grinding parameters, minimum thermal and mechanical damage can be achieved. Higher workpiece velocities produce higher surface residual stress. By increasing depths of cut, depth of tensile residual stresses increases. Convection heat coefficient does not have any considerable effect on surface residual stress... 

Adaptive Noise Cancellation (ANC) is a well-known technique for background noise reduction in automobile and vehicular environments. The noise fields in automobile and other vehicle interior obey the diffuse noise field model closely. On the other hand, the ANC does not provide sufficient noise reduction in the diffuse noise fields. In this paper, a new multistage post-filter is designed for ANC as a solution to diffuse noise conditions. The designed post-filter is a single channel Linear Prediction (LP) based speech enhancement system. The LP is performed by an adaptive lattice filter and attempts to extract speech components by using intermediate ANC signals. The post-filter has no... 

Shot peening is widely used to improve the fretting fatigue strength of critical surfaces. Fretting fatigue occurs in contacting parts that are subjected to fluctuating loads and sliding movements at the same time. This paper presents a sequential finite element simulation to investigate the shot peening effects on normal stress, shear stress, bulk stress and slip amplitude, which are considered to be the controlling parameters of fretting damage. The results demonstrated that among the modifications related to shot peening, compressive residual stress has a dominant effect on the fretting parameters  

One-dimensional (1D) MgO structures were successfully synthesized via carbothermic reduction of mechanically activated mixture of MgO and graphite. Mechanical activation of source materials before carbothermic reduction can substantially enhance the formation of MgO products at a temperature (1000 °C) relatively lower than that required in previous approaches (≥1200 °C). However, the morphology of MgO formed is dependent on the degree of mechanical activation and the condition of the subsequent carbothermic reduction. Two distinctive morphologies were found for MgO products synthesized using our method: single crystalline nanorods with rectangular cross-sections whose diameters range from 50... 

Attitude and vibration control of a general form of flexible satellites is addressed in this paper. Partial differential dynamic equations are derived considering new details such as multi sectioned solar panels and elastic connections between main hub and solar panels. Boundary control approach is adopted to eliminate simplification errors of discrete models, using just one actuator in the hub. Asymptotic stability of attitude dynamics is proved for a group of boundary controllers and necessary conditions for asymptotic stability of vibrations are discussed. Being independent of modeling accuracy and using easily measurable feedbacks are among advantages of the proposed class of... 

Characterization and calcination behavior of a low-grade manganese ore, as a part of Mn ferroalloys production, was studied by XRF, ex-situ XRD, in-situ XRD, and SEM-EDS techniques. Calcination experiments were carried out at and up to 900 °C (1173 K) in air and argon atmospheres. The samples were in particles and powder forms. The results indicated that both quartz and calcite phases in the ore exhibit a bimodal spatial distribution; as relatively large regions and finely distributed in the Mn- and Fe-containing phases. By Rietveld analysis of the in-situ XRD data, the reactions occurring upon heating during the calcination process were deduced. Thermal decomposition and reactive diffusion... 

Estimating the position of a mobile set is of great importance in new mobile services. However, in most cases, the accuracy should be less than 100 meters. This accuracy is hard to reach especially in urban areas. The main problem is that there are a lot of obstacles like buildings between the BTS and the mobile set. Thus the time measured between BTS and the mobile set is somehow greater than the time it takes the wave to travel directly between two points. This paper introduces an optimized solution for TDOA as one of the most efficient ways for finding the location of a mobile phone. Considering the standards and limitations of both GSM and UMTS, the Authors present a solution for... 

Weighting elements to achieve radiation patterns with desired characteristics is a classical work in phased array antennas. These characteristics can be low sidelobe level, narrow beamwidth, high directivity, pattern nulling in special angle and etc. For each of these characteristics, different methods have been introduced. Most of methods have been presented for uniform arrays, however there are lots of methods to obtain a desired pattern for antennas with non-uniform element distances. The problem with these methods is complexity or not very good results. In this paper, fast and easy methods based on Least Square Error that leads to good results are presented. In addition, weighting of... 

The elastic behavior of an edge dislocation, which is positioned outside of a nanoscale elliptical inhomogeneity, is studied within the interface elasticity approach incorporating the elastic moduli and surface tension of the interface. The complex potential function method is used. The dislocation stress field and the image force acting on the dislocation are found and analyzed in detail. The difference between the solutions obtained within the classical-elasticity and interface-elasticity approaches is discussed. It is shown that for the stress field, this difference can be significant in those points of the inhomogeneity-matrix interface, where the radius of curvature is smaller and which...