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    Semi-supervised Breast Cancer Subtype Clustering Using Microarray Datasets

    , M.Sc. Thesis Sharif University of Technology Vasei, Hamed (Author) ; Motahhari, Abolfazl (Supervisor)
    Abstract
    Gene expression microarrays can be used for precision medicine and targeted therapies. The data generated by microarrays are high-dimensional causing statistical inference of any parameter a daunting task. In this thesis, it is shown that regardless of high-dimensional datasets produced by microarrays, the inference can be robust in the sense that random selection of features results in the same conclusion as far as the number of selected features are chosen appropriately. Stratifying patients with breast cancer based on their gene expression levels shows that patient subtypes are almost independent of the feature selection strategy. Moreover, using less noisy datasets coming from RNAseq... 

    A Simulation for Better Understanding of Integrin Clustering and Activation

    , M.Sc. Thesis Sharif University of Technology Shams, Shahab (Author) ; Motahhari, Abolfazl (Supervisor)
    Abstract
    Today, computer simulations are employed prevalently by researchers to understand biological processes. The tendency to use computational methods has been increased recently due to the high costs and errors of experimental methods. Integrins are membrane proteins that mechanically attach cells to the extra cellular matrix (ECM) and derive some behaviors such as cell migration. Moreover, integrins have biochemical functions. They transduce environment signals and trigger chemical pathways. As a result, integrins regulate cell shape, motility, etc. The investigation of integrin behavior in a real environment is very difficult due to the presence of many other proteins that interfere with the... 

    A Thesis Submitted in Partial Fulfillment of the Requirement for the Degree of Master of Science in Electrical Engineering

    , M.Sc. Thesis Sharif University of Technology Mohammadi, Mahsa (Author) ; Jahed, Mehran (Supervisor) ; Motahhari, Abolfazl (Co-Advisor)
    Abstract
    Dnase I Hypersensitive Sites (DHSs) are known as comprehensive markers of DNA regulatory elements. The main function of regulatory elements is repressing or enhancing transcription of genes. Hence, the recruitment of the data is prevalent in many studies of genome. One of the applications of this data is to utilize it to predict active regulatory regions (Transcription Factor Binding Sites).There are different means to do this, divided in three major groups: first, the methods only use the number of DNase-seq reads that surround a candidate binding site. While robust, these methods do not reflect the shape of the signal. A second strategy uses a variety of approaches to model and identify... 

    Evaluation of Base Calling Methods in Next Generation Sequencing

    , M.Sc. Thesis Sharif University of Technology Gharibi, Hadi (Author) ; Hossein Khalaj, Babak (Supervisor) ; Motahhari, Abolfazl (Supervisor)
    Abstract
    In the mid twentieth century by discovering the existence of genetic strands and understanding their role in diseases and phenotypes of species, research initiated to decipher their content. Sequencing of the first human genome at early twenty-first century paved the way to study and even cure complex human deseases having genetic origin. Next Generation Sequencing (NGS) Technologies have significantly reduced the expenses and the timing complexity of DNA Sequencing and this has an improving trend. In this thesis, we evaluate Base Calling methods, a critical step in analyzing next generation sequencing information and deals with massive sequencing data. Base Calling tries to optimally detect... 

    Design and Analysis of DNA Sequencing Methods

    , Ph.D. Dissertation Sharif University of Technology Nashtaali, Damoun (Author) ; Hossein Khalaj, Babak (Supervisor) ; Abolfazl, Motahhari (Co-Advisor)
    Abstract
    A DNA sequence is the information source of living kinds. Information of this sequence is at its constructing bases which has four different kinds. Sequencing DNA is necessary to resolve this information. At 1977, Sanger reported the first sequence of a DNA string. Recently, a human DNA string can be sequenced with 1000 in ~2 hours. Knowing DNA sequence helps to find function of each organism, predict and cure diseases (especially in cancer). Next Generation Sequencing (NGS) methods are based on shot-gun sequencing which fragmentize DNA strings and sequence each fragment. After sequencing, processing information of DNA is performed by the processing machine in two different types: alignment... 

    Inferring Relation between World and Iranian Populations from Microarray Data

    , M.Sc. Thesis Sharif University of Technology Saberi, Sasan (Author) ; Hossein Khalaj, Babak (Supervisor) ; Motahhari, Abolfazl (Supervisor)
    Abstract
    One of the branches of genetic studies is population genetics. Each population has its own characteristics due to its evolutionary history, cultural characteristics and geography, which distinguish it from other populations. Scientific and technological advances in recent decades have led to the production of new generation sequencing machines and the creation of large genetic data. These data contain important genetic information and answers to many questions about the origin of humans, the history of populations and their evolutionary process. More and better understanding of the human genome and the distance between populations can help to better understand biological mechanisms and deal... 

    Prediction of Protein Ligand Binding Affinity Using Deep Networks

    , M.Sc. Thesis Sharif University of Technology Gholamzadeh Lanjavi, Atena (Author) ; Kalhor, Hamid Reza (Supervisor) ; Motahhari, Abolfazl (Co-Supervisor)
    Abstract
    Protein-ligand binding affinity is extremely important for finding new candidates in drug discovery and computational biochemistry. One of the physical characteristics for protein ligand interactions has been dissociation constant (KD) which can be obtain experimentally. However, there have been tremendous efforts to predict KD using modeling and computational approaches for protein-ligand interactions. In this project, we have exploited Convolutional Neural Network (CNN) model based on KDeep design, PDBBind version 2016 refined set training data, and examining it with KDeep core set test data. In order to modify KDeep,instead of 24 rotations (0, 90, 180 and 270 degrees in selection of two... 

    On Improving Scalability of Blockchain Systems Using Coding and Redundancy Methods

    , M.Sc. Thesis Sharif University of Technology Badihi, Ahmad Reza (Author) ; Motahhari, Abolfazl (Supervisor) ; Maddah Ali, Mohammad Ali (Supervisor)
    Abstract
    Blockchains are not scalable by design, and it is known to be the most important barrier in the way of development of these systems. One of the main approaches to this problem is sharding, that is under development in industry and academia. Sharding scales the system up by reducing redundancy, that makes blockchains vulnerable in terms of security. In this paper, we will study the effect of sharding on availability of these systems, and will show that sharding can magnify the unavailability of the service, and introduce an adversary threat model that takes real concerns of availability in today’s Internet like DoS attacks into account. We also introduce a basic unavailability-resistant... 

    An innovative workflow for selecting appraisal area in low permeability greenfield development under uncertainties

    , Article Journal of Petroleum Science and Engineering ; Volume 206 , 2021 ; 09204105 (ISSN) Motahhari, S. M ; Rafizadeh, M ; Pishvaie, M. R ; Ahmadi, M ; Sharif University of Technology
    Elsevier B.V  2021
    Abstract
    There are uncertainties in both inherent geological properties and IOR/EOR performance parameters of low permeability greenfield reservoirs. Therefore, efforts to reduce uncertainties in the appraisal phase are necessary for the development and production phases. An adequate selection of the appraisal area in the hydrocarbon field is an imperative factor since the results of the appraisal well drilling and IOR/EOR pilot tests will be utilized for the development of the entire field. The major challenge in selecting an appraisal area is the lack of an integrated and systematic approach. In this study, we present a novel systematic and quantitative approach consisting of a better... 

    Application of Gis & Fuzzy Technique for Order-Preference by Similarity to Ideal Solution (Topsis) in Siting Water Reservoires

    , M.Sc. Thesis Sharif University of Technology Jozaghi, ali (Author) ; Shamsai, Abolfazl (Supervisor)
    Abstract
    Sustainable agricultural development in the country without regard to water supply problems in terms of time and place is not possible. Construction of water storage tanks filled with water and seasonal use in dry seasons in the effective action in the optimal use of water in the climate of (low and irregular rainfall) is. The most important step in the construction of water storage tanks to choose the best point for the construction of the reservoir basin in order to reduce costs and increase efficiency. Chndmyarh different methods to decide the best option for finding a few options from there. Among these methods can be Tapsys two methods (TOPSIS) and hierarchical analysis (AHP) pointed... 

    Efficient Management of River Water Quality Based on Pollution Trading Approach

    , Ph.D. Dissertation Sharif University of Technology Sarang , Amin (Author) ; Shamsai, Abolfazl (Supervisor)
    Abstract
    “Sustainable development” is a frequently used phrase, but the idiom has been experienced little since it was coined by the Brundtland, due to its intrinsic complications. The issue is going to compromise two key components; economy and ecology. One of the solutions based on concept of sustainable development that has been proposed for maintaining water quality at acceptable levels is to cap pollutant emissions at a sustainable level, then establish an economic market in which the right to discharge pollutants is traded according to market supply and demand mechanisms. Water quality trading or pollution trading is one such kind of market-based program that has also been described using names... 

    Assessment of Optimum Environmental Flows Using Economic Evaluation Methods

    , M.Sc. Thesis Sharif University of Technology Mazdarani, Sohrab (Author) ; Shamsai, Abolfazl (Supervisor)
    Abstract
    One of the main challenges of Water Resources Planning and Management (WRPM) is to balance water allocation between different uses. Usually, due to political and economic power of other uses, ecosystem receives less attention. Environmental flow is the allocated flow to ecosystem. Ecosystem provides a wide range of services to humanity. Therefore, environmental flow is not exclusively a matter of sustaining ecosystem but also a matter of providing humans with better life. Several methods have been developed to determine the environmental flow but only a few consider its socio-economic aspects. Consideration of these aspects could assist decision-makers with determining the optimum flow and... 

    Numerical Study of Geotextile Application in Downstream Filter Zone of an Embankment Dam with Clay Core

    , M.Sc. Thesis Sharif University of Technology Maghsoodian, Maedeh (Author) ; Shamsaie, Abolfazl (Supervisor)
    Abstract
    Nowadays, applications of the synthetic materials are developing in civil engineering projects and widely used in these projects. Therefore, during previous years; use of the Geotextiles as one of the Geosynthetic materials in order to filtration, drainage, separation, soil protection, etc have developed ever-increasing. The goal of this research is modeling and studies of the Geotextiles application in the downstream filter zone of embankment dams in combination with granular materials using FLAC2D software. Gordeh Bin embankment dam situated in West Azerbaijan province has been chosen as case study. In this matter, different models have been made with changes in thickness of the inclined... 

    , M.Sc. Thesis Sharif University of Technology Nazari, Fatemeh (Author) ; Shamsaei, Abolfazl (Supervisor)
    Abstract
    Entrance of air to close water conduits occurs in many ways. This phenomenon makes displeasing effects on water transport structures. Two-phase flows in closed conduits are studied experimentally, numerically and theoretically. Even after decades, due to the complexity of the subject, these studies still require development and reformation. Numerical and theoretical two-phase models are often limited to a special regime of flow."Volume Of Fluid"(VOF) is a model for non-mixing two-phase flows. "Fluent" software uses this model in this field of flows. Volume of fluid is used successfully in some problems like dam break or rising bubbles. Main disadvantage of this model is distribution of the... 

    Assessment of waterlogging and provide risk maps by using RS, GIS and field data (case study: Qazvin plain)

    , M.Sc. Thesis Sharif University of Technology Mansourian, Hamid (Author) ; Shamsaei, Abolfazl (Supervisor)
    Abstract
    Groundwater quality protection has a significant importance due to abundant applications of these resources in various fields such as agriculture, industry and drinking water. Removal of groundwater pollution is a time and money consuming process and often pollution is detected when improving the quality of groundwater is nearly impossible. For this vulnerability assessment there are three methods: Processing, Overlap-Index and Statistical Methods. Overlap-Index is composed of variety of maps such as Geology, Soil, Groundwater Depth and etc which uses in determining of vulnerability Index. In the present study for underground pollution potential determining, four indexes such as AVI، GOD،... 

    groundwater level fluctuations forecasting using conjunction models of Wavelet - Neural-Fuzzy Network (WNF) and Wavelet-Neural Network (WNN) and linear model of ARIMA (case study: Qom plain

    , M.Sc. Thesis Sharif University of Technology Fathi, Bahman (Author) ; Shamsaei, Abolfazl (Supervisor)
    Abstract
    Prediction of groundwater level fluctuations is absolutely necessary for the proper manag ement of these precious resources. There are different methods to predict hydrological time series such as groundwater level. Linear models inefficiency in predicting nonlinear and n on-stationary time series cause researchers widely use artificial intelligence techniques such as Artificial Neural Networks (ANN), Fuzzy Inference System (FIS), Genetic Algorithm (GA) and their hybrid models such as Artificial Neural – Fuzzy Inference System (ANFIS). These smart models are capable to simulate nonlinear and non-stationary time series in suitable accu-racy using by a few time and data. By emersion of Wavelet... 

    GIS Based Procedure to Determine Location of Cascade Small Hydropower Plants Case Study, Nokhan Area

    , M.Sc. Thesis Sharif University of Technology Serpoush, Behrad (Author) ; Shamsai, Abolfazl (Supervisor)
    Abstract
    Coinciding with the worldwide environmental issues and increasing demand for clean energy sources, hydropower plants have highly attracted decision- makers attention. Low manufacturing costs and pollutions which are made by these plants in comparison with another types of powerhouses, could be reason of that. And so on, hydropower locating and evaluating studies have been highly increased recently, specifically in developing countries. From the point of operation procedure, hydropower plants are generally divided in two types, run-of-he-river and storage projects. This study has concentrated on run-of-he-river projects and due to spotting plant location, Sefidbarg river basin... 

    Investigation of bed Stability in Downstream for the Diversion dam under Scour (Mill & Moghan case study)

    , M.Sc. Thesis Sharif University of Technology Gorji, Faeze (Author) ; Shamsai, Abolfazl (Supervisor)
    Abstract
    Numerical simulations and large eddy simulations (LES) of turbulent flow downstream of diversion dam , pool-riffle bedform in different geometrical ratios (different lengths of riffle and pool) with flow Reynolds number of 3.0 E+04 to 3.3E+04, downstream of special case study "Mill and Moghan diversion dam" with Froude number of 0.5 are presented The calculations are performed using a computational fluid dynamics model, FLOW-3D, which solves the Navier-Stokes equations in three dimensions with finite volume method. Numerical simulations are validated by comparing the numerical results of time-averaged flow patterns downstream of pool-riffle sequence with that of the experimental... 

    Hydro-economical Method for the Optimal Capacity Design of Small Hydropower Plant (Case Study: Kohneh Lahijan Hydropower Plant)

    , M.Sc. Thesis Sharif University of Technology Mehrvand, Shahryar (Author) ; Shamsai, Abolfazl (Supervisor)
    Abstract
    In this thesis, we determine the optimal capacity of the power plants considering site specifications and Flow Duration Curve and evaluating economic parameters. Finally a design with more sufficient economical and hydrualical performance would be selected. The optimization algorithm used in this thesis is called "Charged System search" that is one of the newest meta-heuristic algorithms. This algorithm is inspired by the coulomb and gauss's laws of electrostatics in physics and utilizes a number of charged particles which influence each other based on their fitness values and their separation distances considering the governing law of coulomb.The proposed method in this thesis can be... 

    Analysis of Genes Regulating Beta Cells Cell Cycle

    , M.Sc. Thesis Sharif University of Technology Saraei, Tannaz (Author) ; Motahari, Abolfazl (Supervisor)
    Abstract
    Diabetes mellitus is a group of disorders where the level of blood sugar remains high for a long period of time. This increase may be due to either reduced insulin secretion from the pancreatic gland, or insulin resistance, or both. Another key reason is the destruction of beta cells due to functional defect in the body’s immune system. Current treatments include controlling diet, insulin injection and pancreatic transplantation, all of which are temporary. For this reason, finding genetic factors participating in the progression of the disease and adapting treatments to these factors are under intensive studies.In this thesis, available information resources including genomic, biological...