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    IMOS: improved meta-aligner and minimap2 on spark

    , Article BMC Bioinformatics ; Volume 20, Issue 1 , 2019 ; 14712105 (ISSN) Hadadian Nejad Yousefi, M ; Goudarzi, M ; Motahari, A ; Sharif University of Technology
    BioMed Central Ltd  2019
    Abstract
    Background: Long reads provide valuable information regarding the sequence composition of genomes. Long reads are usually very noisy which renders their alignments on the reference genome a daunting task. It may take days to process datasets enough to sequence a human genome on a single node. Hence, it is of primary importance to have an aligner which can operate on distributed clusters of computers with high performance in accuracy and speed. Results: In this paper, we presented IMOS, an aligner for mapping noisy long reads to the reference genome. It can be used on a single node as well as on distributed nodes. In its single-node mode, IMOS is an Improved version of Meta-aligner (IM)... 

    Distributed Processing of Next Generation Sequencing Data Set

    , M.Sc. Thesis Sharif University of Technology Hadadian Nejad Yousefi, Mostafa (Author) ; Goudarzi, Maziar (Supervisor) ; Motahari, Abolfazl (Supervisor)
    Abstract
    DNA analysis plays a significant role in fields such as pharmacy, agriculture, genealogy, and forensics. Next generation sequencing datasets cover a gene several times due to a large number of readings. Therefore, the initial data volume is several times the amount of memory required to store the DNA strand. First, the DNA sequence of a sample should be made using the primary data, and then the difference should be found by comparing the sample DNA sequence with the reference DNA sequence. By finding these differences, one can extract the characteristics of the tested species. The extracted properties are precious for genetics researchers. For example, they can produce drugs that are... 

    Detection and Mitigation of Application-Layer Denial of Service Attacks

    , M.Sc. Thesis Sharif University of Technology Hadadian Neghad Yousefi, Mohammad (Author) ; Kharrazi, Mehdi (Supervisor)
    Abstract
    With increasing the internet in sociality, lots of researches have been done about web security in three main principles: confidentiality, integrity, and availability. Attacks on availability have been there for lots of time and high-rate denial of service attacks ran against servers. These years lots of web applications have been developed with various and complex technologies and so we are facing another type of low-cost DoS attack on the application layer where attackers can crash down services by exploiting flaws in implementations by just a single carefully crafted request. Although works on finding vulnerabilities are worthy, as there are always some flaws in applications, we need... 

    SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks

    , Article BMC Bioinformatics ; Volume 22, Issue 1 , 2021 ; 14712105 (ISSN) Akbarinejad, S ; Hadadian Nejad Yousefi, M ; Goudarzi, M ; Sharif University of Technology
    BioMed Central Ltd  2021
    Abstract
    Background: Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from precise in low-coverage cases. To be accurate, they need to use high-coverage data, which in turn, results in an extremely time-consuming pipeline, especially in the alignment phase. Therefore, it is of utmost importance to have a structural variation calling pipeline which is both fast and precise for low-coverage data. Results: In this paper, we present SVNN, a fast yet accurate, structural variation calling pipeline for PacBio long-reads... 

    SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks

    , Article BMC Bioinformatics ; Volume 22, Issue 1 , 2021 ; 14712105 (ISSN) Akbarinejad, S ; Hadadian Nejad Yousefi, M ; Goudarzi, M ; Sharif University of Technology
    BioMed Central Ltd  2021
    Abstract
    Background: Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variation detection methods are far from precise in low-coverage cases. To be accurate, they need to use high-coverage data, which in turn, results in an extremely time-consuming pipeline, especially in the alignment phase. Therefore, it is of utmost importance to have a structural variation calling pipeline which is both fast and precise for low-coverage data. Results: In this paper, we present SVNN, a fast yet accurate, structural variation calling pipeline for PacBio long-reads... 

    Development and Evaluation of Improved Structures for EVs Integrated Battery Chargers Based on Various Types of Propulsion Motors in V2G and G2V Applications

    , M.Sc. Thesis Sharif University of Technology Sadeghi Nejad, Emad (Author) ; Parniani, Mostafa (Supervisor) ; Askarian Abyaneh, Iman (Co-Supervisor)
    Abstract
    The integrated battery charger (IBC), made from the combination of a battery charger and the traction propulsion system of EVs is an emerging concept that can save the volume and final cost of battery chargers. As a type of on-board EV battery charger, IBC topology must work with expected performance in two modes of operation separately, charging mode and propulsion mode. In this thesis, to propose new topologies of IBCs, firstly the previous studies relevant to EV battery chargers and their different types have been reviewed. By analysis and investigation of IBC topologies, the principles of integrating battery chargers have been inferred and presented. These principles help us to evaluate... 

    A bi-objective robust optimization model for a blood collection and testing problem: an accelerated stochastic benders decomposition

    , Article Annals of Operations Research ; 2018 ; 02545330 (ISSN) Yousefi Nejad Attari, M ; Pasandideh, S. H. R ; Aghaie, A ; Akhavan Niaki, S. T ; Sharif University of Technology
    2018
    Abstract
    Blood transfusion services are vital components of healthcare systems all over the world. In this paper, a generalized network optimization model is developed for a complex blood supply chain in accordance with Iranian blood transfusion organization (IBTO) structure. This structure consist of four types facilities. Blood collection centers, blood collection and processing centers, mobile teams and blood transfusion center have various duties in IBTO structure. The major contribution is to develop a novel hybrid approach based on stochastic programming, ε-constraint and robust optimization (HSERO) to simultaneously model two types of uncertainties by including stochastic scenarios for total... 

    Improving self-care and health literacy in hemodialysis patients: Using software engineering

    , Article Proceedings - 2012 7th International Conference on Computing and Convergence Technology (ICCIT, ICEI and ICACT), ICCCT 2012, 3 December 2012 through 5 December 2012 ; December , 2012 , Pages 317-320 ; 9788994364216 (ISBN) Shahbazi, B ; Edalat-Nejad, M ; Edalat-Nejad, N ; Sharif University of Technology
    2012
    Abstract
    The use of Computer Science in order to categorize and store information, improve diagnostic and therapeutic procedures, patient education and the training of a skilled labor force, has taken important steps and there are constantly new developments in this area  

    Introduction of clinical, simulation-based software for medical sciences teachings

    , Article Procedia Engineering ; Volume 29 , 2012 , Pages 43-47 ; 18777058 (ISSN) Shahbazi, B ; Edalat-Nejad, M ; Edalat Nejad, N ; Edalatnejad, M ; Sharif University of Technology
    2012
    Abstract
    Simulation is the gold standard for training in aviation and trauma medicine. Now it is available for diseases diagnosis and treatment. With simulation, clinicians can practice their art in a realistic, consequence free environment, combining both theory and practice in a comprehensive program. Method and materials - In the virtual clinical environment of "VPsoft mentor" software, the practitioner reviews a patient's history, orders laboratory tests and procedures, interprets findings, renders diagnoses, and prescribes medication. Every diagnostic or treatment decision the clinician makes for the patient is analyzed by E-mentor, providing instant feedback.Results - This software have been... 

    Electrodepositon of Platinum Nanotubes

    , M.Sc. Thesis Sharif University of Technology Yousefi, Elahe (Author) ; Dolati, Abolghasem (Supervisor)
    Abstract
    Platinum nanotubes were deposited inside the pores of polycarbonate template with the pore size of 200 nm by electrochemical methods. In this regard a solution containing of 0.05 M H2PtCl6 and 0. 1 M H2SO4 in doubly distilled water was utilized. The electrodeposition process was studied by electrochemical techniques such as voltammetry and chronoamperometry methods. It was observed that the process was conducted in several stages including; nucleation and growth in steady state regime. Furthermore, it was concluded that electrodeposition was affected by mass transport restriction and was controlled by a diffusion process. In this regard, all the voltammograms were shifted to more negative... 

    Design of Power Amplifier in Ku Band in the Process of GaAs-pHEMT

    , M.Sc. Thesis Sharif University of Technology Yousefi, Alireza (Author) ; Medi, Ali (Supervisor)
    Abstract
    Power amplifiers are used as the last block of transmitters. This block can be categorized as the one of most important part in communication systems. However, in transmitter systems which require high power to create stable link with the receivers, fabrication process like CMOS are unable to provide such level of power. Thus, designers employ another group of integrated circuits which names MMIC that offers this capability to designers. MMIC is the abbreviation of Microwave Integrated Circuit which is implemented in compound substrates like GaAs. Monolithic microwave integrated circuits enable the implementation of amplifiers in small size, large number, with high precision and appropriate... 

    Wide-band high-efficiency Ku-band power amplifier

    , Article IET Circuits, Devices and Systems ; Vol. 8, issue. 6 , December , 2014 , p. 583-592 ; 1751858X Yousefi, A ; Medi, A ; Sharif University of Technology
    2014
    Abstract
    A 37 dBm power amplifier (PA) is designed on a 0.25 μm optical T-gate pseudomorphic high electron mobility transistor (pHEMT) technology. The design of this two-stage PA along with a step-by-step design procedure is presented in this paper. This methodology can be used for design of PA in different technologies and frequencies. The PA delivers 5 W output power over the frequency band of 13-19 GHz. It shows average power-added efficiency of 37% and large signal gain of 15 dB in measurements which is consistent with simulation results. The output power and efficiency of the realised amplifier reach maximums of 37.6 dBm and 45%, respectively. Considering output power, bandwidth, chip area and... 

    A Comparison between Virtual Private LAN Service (VPLS)and P2MP IP-only LAN Service (IPLS)

    , M.Sc. Thesis Sharif University of Technology Yousefi, Dariush (Author) ; Ajorloo, Hossein (Supervisor)
    Abstract
    Today Ethernet is the predominant technology for implementing Local Area Networks. Its privileges encourage service providers to extend Ethernet from Local Area Networks to Metropolitan Area Networks or even Wide Area Networks. Ethernet benefits such as low operational costs, well interoperability, plug-n-paly characteristic and rapid provisioning on demand make Ethernet ideal for Metropolitan Area Networks.But Ethernet by itself has some weakness like flat structure that makes it unfit for use in Metropolitan Area Networks. A suitable solution for taking advantages of Ethernet benefits in service provider network is using Ethernet in access network and applying multi-point to multi-point... 

    Effects of free quartz on mechanical behaviour of kaolinite based geopolymers

    , Article Materials Technology ; Volume 26, Issue 2 , Jul , 2011 , Pages 96-99 ; 10667857 (ISSN) Yousefi, E ; Majidi, B ; Sharif University of Technology
    2011
    Abstract
    Quartz is usually detected as an impurity of kaolinite clays. The present work attempts to evaluate the role and behaviour of quartz particles in geopolymerisation and its probable effects on mechanical behaviour of geopolymeric products. Two kaolinite clays with different free quartz contents were used as raw materials to produce geopolymers. Results showed that using high content quartz kaolin causes higher compressive strength. Scanning electron microscopy studies confirmed that quartz does not participate in geopolymerisation and completely remains in the structure as fine particles. High hardness quartz particles by retarding crack growth in the geopolymer matrix enhance mechanical... 

    investigation of the Effect of Piezo-Electric Patch on the Modal Properties and Flutter Speed of Turbomachine Blade

    , M.Sc. Thesis Sharif University of Technology Yousefi, Masoud (Author) ; Haddadpour, Hassan (Supervisor)
    Abstract
    In order to investigaton of dynamics behavior and determination of the aeroelastic stability of the turbomachine blade. the turbomachine blade is modeled by using the beam model, taking into account all degrees of freedom, the effect of warping, rotation and seting angle. For aerodynamic modeling, the Smith and Whitehead models are used which are valid in subsonic flow. The validity of the derived formulation is confirmed through comparison with those obtained from the finite element software and the available results in the literature. Then, by using the state feedback controller, the effect of sensor and piezoelectric actuator on the vibrations reduction of the structure and increasing the... 

    A Task-Based Greedy Scheduling Algorithm for Minimizing Energy of MapReduce Jobs

    , Article Journal of Grid Computing ; Volume 16, Issue 4 , 2018 , Pages 535-551 ; 15707873 (ISSN) Yousefi, M.H.N ; Goudarzi, M ; Sharif University of Technology
    Springer Netherlands  2018
    Abstract
    MapReduce and its open source implementation, Hadoop, have gained widespread adoption for parallel processing of big data jobs. Since the number of such big data jobs is also rapidly rising, reducing their energy consumption is increasingly more important to reduce environmental impact as well as operational costs. Prior work by Mashayekhy et al. (IEEE Trans. Parallel Distributed Syst. 26, 2720–2733, 2016), has tackled the problem of energy-aware scheduling of a single MapReduce job but we provide a far more efficient heuristic in this paper. We first model the problem as an Integer Linear Program to find the optimal solution using ILP solvers. Then we present a task-based greedy scheduling... 

    A Framework for Formal Analysis of Warning Message Dissemination Schemes in VANETs Using an Extension of Rebeca

    , M.Sc. Thesis Sharif University of Technology Yousefi, Farnaz (Author) ; Movaghar, Ali (Supervisor)
    Abstract
    Vehicular ad-hoc networks have attracted the attention of many researchers during the last years due to the emergence of autonomous vehicles and the safety concerns regarding their use in near future. One of the major applications in this domain is the usage of vehicle to vehicle communication for warning message dissemination in dangerous situations to prevent more damage. A number of schemes have been proposed regarding the selection of forwarding nodes in this application and there is a need for developing frameworks for analysis and comparison of the schemes in fair situation. Most of the proposed frameworks make use of simulation techniques for the analysis of schemes. However, due to... 

    Optimal Model of Industrial Waste Heat Application in Desalination System: A Case Study of Hormozgan Province

    , M.Sc. Thesis Sharif University of Technology Yousefi, Paria (Author) ; Avami, Akram (Supervisor)
    Abstract
    Increasing population growth and scarcity of fresh water resources have created the challenge of water supply, especially in the Mena region. Thus, many countries in the region have turned to innovation in the development of high-energy seawater desalination technologies. Utilizing the waste heat of refineries in the desalination industry can reduce costs and preserve the environment. In this article, effective ways to use the waste heat of other flue recovery steam of Bandar Abbas oil refinery are investigated. The integration of the heat recovery system consisting of recuperative heat exchangers and heat pipes with thermal desalination plants is investigated by multi-stage flash and... 

    Optimization of the Pulp and Paper Mill Wastewater Treatment System from Recycling with the Aim of Reducing COD by Conducting a Laboratory Pilot Plant

    , M.Sc. Thesis Sharif University of Technology Yousefi, Farid (Author) ; Raie, Mohammad (Supervisor)
    Abstract
    Paper and cardboard waste pulping consume large volumes of water, so the discharge of this effluent without proper treatment can have far-reaching environmental consequences. The color and variable COD concentration of wastewater in this industry make treating this wastewater complicated. Therefore, this study aims to reduce the COD of the wastewater treatment plant of a pulp and paper mill under different laboratory conditions to achieve environmental standards in Iran.In this study, coagulation-flocculation and the Fenton process on the wastewater entering the treatment plant were investigated first. It was found that coagulation and flocculation by 750-1250 ppm of alum coagulant and ten... 

    Using three-dimensional finite element analysis for simulation of residual stresses in railway wheels

    , Article Engineering Failure Analysis ; Vol. 45, issue , October , 2014 , p. 449-455 Masoudi Nejad, R ; Sharif University of Technology
    2014
    Abstract
    One of the most important issues in railway wheels is residual stresses. It is desirable to produce less residual stresses when possible and to decrease the remaining residual stresses in the wheels. The objective of this paper is to provide an estimation of the residual stresses in the rail wheel caused by the stress field from heat treatment process of a railway wheel. A three-dimensional nonlinear stress analysis model has been applied to estimate stress fields of the railway mono-block wheel in heat treatment process. After forging or casting, railway wheels are heat-treated to induce the desirable circumferential compressive residual stress in the upper rim. Finite element analysis...