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,... 

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... 

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... 

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... 

In a MIMO (Multiple Input Multiple Output) radar system, proper design of transmit signal and receive filter is an advantageous tool to improve the detection performance. Thus, in this paper, we consider the problem of transmit code and receive filter design, in order to maximize the Signal to Noise Ratio (SNR) at the receiver while enforcing a similarity constraint between the transmit space-time code (STC) and a reference STC which has a desirable ambiguity function. We will show that by solving such constrained optimization problem through successive iterations, our proposed method leads to satisfactory results  

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... 

Distributed generation connected with AC, DC, or hybrid loads and energy storage systems is known as a microgrid. Campus microgrids are an important load type. A university campus microgrids, usually, contains distributed generation resources, energy storage, and electric vehicles. The main aim of the microgrid is to provide sustainable, economical energy, and a reliable system. The advanced energy management system (AEMS) provides a smooth energy flow to the microgrid. Over the last few years, many studies were carried out to review various aspects such as energy sustainability, demand response strategies, control systems, energy management systems with different types of optimization... 

This paper resolve the salinity-dependent interactions of polar components of crude oil at calcite-brine interface in atomic resolution. Molecular dynamics simulations carried out on the present study showed that ordered water monolayers develop immediate to a calcite substrate in contact with a saline solution. Carboxylic compounds, herein represented by benzoic acid (BA), penetrate into those hydration layers and directly linking to the calcite surface. Through a mechanism termed screening effect, development of hydrogen bonding between –COOH functional groups of BA and carbonate groups is inhibited by formation of a positively-charged Na+ layer over CaCO3 surface. Contrary to the common... 

An important tool for assessing a radar's performance is the ambiguity function. On the other hand, many different schemes have been designed for the transmit waveforms of a MIMO radar. For each one, a criterion has been chosen to improve the performace, e.g. achieving better missed detection. In this paper, considering the ambiguity function as the benchmark, we propose a waveform design scheme, which optimizes the ambiguity function of the MIMO radar system  

Flow hydrodynamics of laminar falling film of aqueous Li Br solution (Li Br - H2O) on a horizontal elliptical tube has been investigated in this research. The film velocity distribution and film thickness, namely, the flow characteristics are determined by solving analytically simultaneous simplified Navier - Stokes equations and continuity equation in polar and Cartesian coordinates. The analysis is based on steady state laminar flow of falling liquid film of Li Br - H2O on a horizontal elliptical tube in polar model and Cartesian model (CM), for cases in which traction on the film surface is considered negligible. Models are compared with each other in three cases of aspect ratios (Ar),... 

Velocity distributions in (r,θ) directions are evaluated by solving simultaneous simplified Navier-Stokes equations (NSE) and continuity equation (CE) in polar coordinate. The analysis is based on steady state laminar flow of thin falling liquid film on a horizontal circular tube, for cases in which traction on the film surface is considered negligible. It is a common geometry for part of engineering problems such as evaporator, condenser, absorber, generator of absorption chillers and other similar units in mechanical and chemical engineering. Knowledge of the velocity profiles is usually needed for: 1 - solving governing energy and species equations 2- estimating the average and film... 

Velocity distributions in (r,θ) directions are evaluated by solving simultaneous simplified Navier-Stokes equations (NSE) and continuity equation (CE) in polar coordinate. The analysis is based on steady state laminar flow of thin falling liquid film on a horizontal circular tube, for cases in which traction on the film surface is considered negligible. It is a common geometry for part of engineering problems such as evaporator, condenser, absorber, generator of absorption chillers and other similar units in mechanical and chemical engineering. Knowledge of the velocity profiles is usually needed for: 1- solving governing energy and species equations 2- estimating the average and film... 

This work concerns the experimental investigation of surfactant alternating CO 2 injection in carbonate rocks. The core samples provided from a low-temperature fractured light oil reservoir, located in southwest Iran. The experiments were designed to observe the effect of CO 2-foam injection on gas mobility and oil recovery at different surfactant concentrations. The core samples were initially saturated with synthetic/field brine, 5,000 ppm, and then flooded with live oil to reach connate water saturation at reservoir condition, 115F and 1,700 psia. The commercial surfactant used was sodium lauryl sulfate as an anionic surfactant. The results of this work, along with field-scale simulation... 

Knowledge of Air-water two phase flows is significant to different engineering systems such as chemical reactors and power plant and petrochemical and petroleum industry. One of the most industrial cases of two phase flow is two phase flow in vertical large pipes. In this paper in order to find two phase flow behavior along vertical large diameter pipes we simulate air inlets with different number of holes and different hole diameters in the same flow rate of air. In addition, flow characteristics such as cross-sectional void fraction and velocity and pressure were considered. To achieve this aim, main equations of flow have been developed for investigation of flow behavior in air-water two... 

The present work investigates the thermal performance of a five turn Open Loop Pulsating Heat Pipe (OLPHP). The effects of working fluid namely water and ferrofluid, heat input, ferrofluid concentration, charging ratio, and orientation will be considered. Experimental results show that using ferrofluids can enhance the thermal performance in comparison with the case of distilled water. In addition, applying a magnetic field on the OLPHP charged with ferrofluid reduces its thermal resistance. Variation of the ferrofluid concentration results in different thermal performance of the OLPHP. Best charging ratio for the distilled water and ferrofluid without magnetic field is 60 % in most of the... 

Accurate estimation of the capacity curve of offshore jacket structures to achieve performance levels and ductility is of great importance. Proper modeling of compressive members to correctly investigate global and local buckling is crucial in estimation of the capacity curve. Buckling modes and deformations due to local buckling can be considered, if the compressive braces are modeled by shell or solid elements. The purpose of this paper is to achieve the correct compressive behavior of braces with solid type elements and investigate the effects of five different parameters such as D/t, L/D, mesh size, mesh size ratio, and imperfections. ABAQUS FE software is used for this purpose. The...