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    Learning Interpretable Representation of Drugs based on Microscopy Images

    , M.Sc. Thesis Sharif University of Technology Sanian, Mohammad Vali (Author) ; Rohban, Mohammad Hossein (Supervisor)
    Abstract
    In this study, we aim to learn representations from microscopic cell images that effectively capture the features of drugs affecting the cells, allowing us to identify effective drugs for treating a disease. We employ two parallel learning paths using predictive and generative models. Specifically, we have achieved a predictive model on the RxRx19a dataset that, unlike previous models, is interpretable, optimized, and robust to dras- tic changes in drug properties. Additionally, we have developed the first generative model on this dataset, which not only generates high-quality images but also discovers a meaningful latent space. This latent space divides the representation into relevant... 

    Feasibility and Supply an Optimal Integrated Model of the Energy and Exergy for Producing of Biogas and Ethanol from Solid Waste and wastewaters flows: in Tehran

    , M.Sc. Thesis Sharif University of Technology Vali, Fatemeh (Author) ; Avami, Akram (Supervisor)
    Abstract
    In recent years, access to clean energy sources is the major instruments for sustainable development. Limitation of energy resources and the problems resulting from the use of fossil fuels was caused attention to biomass in different countries as a stable source of renewable energy. Organic waste in municipal solid waste and domestic wastewater are biomasses that can be used as a raw material used in the production of energy. Practical studies show that quality and quantity of municipal solid waste to produce biogas and bioethanol in Iran is very appropriate. In this process, the household solid waste and wastewater are in the anaerobic digestion reactors and fermentation systems without any... 

    Embedded System Vulnerability Analysis Approach Based on Firmware Modification Attacks in Industrial Control Systems

    , M.Sc. Thesis Sharif University of Technology Pour Vali Moghadam, Hamed (Author) ; Jahangir, Amir Hossein (Supervisor)
    Abstract
    A wide range of field devices, including Intelligent Electronic Devices (IEDs) and Remote Terminal Units (RTUs), are used in Industrial Control Systems (ICSs). These devices are embedded systems that are responsible for protecting the power system devices against faults and damage by controlling circuit breakers. Disruptions in command and control can result in accidents and harm. Due to their physical accessibility and the possibility of backdoors, blackout attacks may be designed and implemented on these devices in a manner similar to what has occurred in many countries in recent year.Many vulnerabilities have been reported for Real-Time Operating System (RTOS), firmware, and software of... 

    A molecular dynamics simulation study of nanomechanical properties of asymmetric lipid bilayer

    , Article Journal of Membrane Biology ; Volume 246, Issue 1 , 2013 , Pages 67-73 ; 00222631 (ISSN) Maftouni, N ; Amininasab, M ; Vali, M ; Ejtehadi, M ; Kowsari, F ; Sharif University of Technology
    2013
    Abstract
    A very important part of the living cells of biological systems is the lipid membrane. The mechanical properties of this membrane play an important role in biophysical studies. Investigation as to how the insertion of additional phospholipids in one leaflet of a bilayer affects the physical properties of the obtained asymmetric lipid membrane is of recent practical interest. In this work a coarse-grained molecular dynamics simulation was carried out in order to compute the pressure tensor, the lateral pressure, the surface tension and the first moment of lateral pressure in each leaflet of such a bilayer. Our simulations indicate that adding more phospholipids into one monolayer results in... 

    Niusha, the first persian speech-enabled IVR platform

    , Article 2010 5th International Symposium on Telecommunications, IST 2010, 4 December 2010 through 6 December 2010, Tehran ; 2010 , Pages 591-595 ; 9781424481835 (ISBN) Bokaei, M. H ; Sameti, H ; Eghbal-Zadeh, H ; BabaAli, B ; Hosseinzadeh, K. H ; Bahrani, M ; Veisi, H ; Sanian, A ; Sharif University of Technology
    2010
    Abstract
    This paper introduces Niusha, the first Persian speech-enabled IVR platform. This platform uses Persian recognizer and Persian text-to-speech synthesizer engines in order to interact with users. The platform is designed in a way that it can simply be customized in various domains and its components are adjustable with new words  

    Polarization maintaining optical fiber multi-intruder sensor

    , Article Optics and Laser Technology ; Volume 44, Issue 7 , October , 2012 , Pages 2026-2031 ; 00303992 (ISSN) Bahrampour, A. R ; Bathaee, M ; Tofighi, S ; Bahrampour, A ; Farman, F ; Vali, M ; Sharif University of Technology
    Elsevier  2012
    Abstract
    In this paper, an optical fiber multi-intruder sensor based on polarization maintaining optical fiber (PMF), without any interferometric fiber loop, is introduced. To map the local coordinates of intruders on the beating spectrum of the output modes, radiation from a ramp frequency modulated laser is injected at the input of PMF optical fiber sensor. It is shown that the local coordinates and some characteristics of intruders can be obtained by the measurement of the frequencies and amplitudes of the output mode beating spectrum. Generally the number of beating frequencies is more than the number of intruders. Among the beating frequencies, a group with maximum signal to noise ratio is... 

    Cytotoxicity and cell cycle effects of bare and poly(vinyl alcohol)-coated iron oxide nanoparticles in mouse fibroblasts

    , Article Advanced Engineering Materials ; Volume 11, Issue 12 , 2009 , Pages B243-B250 ; 14381656 (ISSN) Mahmoudi, M ; Simchi, A ; Vali, H ; Imani, M ; Shokrgozar, M. A ; Azadmanesh, K ; Azari, F ; Sharif University of Technology
    2009
    Abstract
    Super-paramagnetic iron oxide nanoparticles (SPIONs) are recognized as powerful biocompatible materials for use in various biomedical applications, such as drug delivery, magnetic-resonance imaging, cell/protein separation, hyperthermia and transfection. This study investigates the impact of high concentrations of SPIONs on cytotoxicity and cell-cycle effects. The interactions of surfacesaturated (via interactions with cell medium) bare SPIONs and those coated with poly(vinyl alcohol) (PVA) with adhesive mouse fibroblast cells (L929) are investigated using an MTT assay. The two SPION formulations are synthesized using a co-precipitation method. The bare and coated magnetic nanoparticles with... 

    The efficient synthesis of carbon–carbon double bonds via Knoevenagel condensation using red mud packed in a column

    , Article Green Chemistry Letters and Reviews ; Volume 1, Issue 1 , 2007 , Pages 61-64 ; 17518253 (ISSN) Khezri, S. H ; Mohammad Vali, M ; Eftekhari Sis, B ; Mahmoodi Hashemi, M ; Baniasadi, M. H ; Sharif University of Technology
    2007
    Abstract
    Red mud (RM) is generated as a by-product during the production of alumina from bauxite ore. In this study, RM packing in a column is used as a catalyst for carbon–carbon double bond formation via Knoevenagel condensation. The reactants are added to the top of the column and then eluted with solvent. The products are collected in high yields and short time. RM packed in a column eliminates a catalyst separation step from the reaction mixture in this work. © 2007 Taylor & Francis Group, LLC  

    Red mud catalyzed one-pot synthesis of nitriles from aldehydes and hydroxylamine hydrochloride under microwave irradiation

    , Article Arkivoc ; Volume 2007, Issue 15 , 2007 , Pages 162-170 ; 1551-7012 (ISSN) Hadi Khezri, S ; Azimi, N ; Mohammed Vali, M ; Eftekhari Sis, B ; Hashemi, M. M ; Baniasadi, M. H ; Teimouri, F ; Sharif University of Technology
    Arkat  2007
    Abstract
    Red mud (RM) which emerges as a by-product from the alumina producing process has been used as an efficient catalyst for one-pot direct synthesis of nitrile compounds from aldehydes and hydroxylamine hydrochloride under microwave irradiation. ©ARKAT USA, Inc  

    Structural characterization of a rhamnolipid-type biosurfactant produced by Pseudomonas aeruginosa MR01: Enhancement of di-rhamnolipid proportion using gamma irradiation

    , Article Colloids and Surfaces B: Biointerfaces ; Volume 81, Issue 2 , 2010 , Pages 397-405 ; 09277765 (ISSN) Lotfabad, T. B ; Abassi, H ; Ahmadkhaniha, R ; Roostaazad, R ; Masoomi, F ; Zahiri, H. S ; Ahmadian, G ; Vali, H ; Noghabi, K. A ; Sharif University of Technology
    2010
    Abstract
    We previously reported that MR01, an indigenous strain of Pseudomonas aeruginosa, was able to produce a rhamnolipid-type biosurfactant. Here, we attempted to define the structural properties of this natural product. The analysis of the extracted biosurfactant by thin-layer chromatography (TLC) revealed the presence of two compounds corresponding to those of authentic mono- and di-rhamnolipid. The identity of two structurally distinguished rhamnolipids was confirmed by 1H and 13C nuclear magnetic resonance (NMR) spectroscopy. Liquid chromatography/mass spectrometry (LC/MS) of extracted biosurfactant revealed up to seventeen different rhamnolipid congeners. Further quantification showed... 

    Multiphysics flow modeling and in vitro toxicity of iron oxide nanoparticles coated with poly(vinyl alcohol)

    , Article Journal of Physical Chemistry C ; Volume 113, Issue 6 , 2009 , Pages 2322-2331 ; 19327447 (ISSN) Mahmoudi, M ; Shokrgozar, M. A ; Simchi, A ; Imani, M ; Milani, A. S ; Stroeve, P ; Vali, H ; Häfeli, U. O ; Bonakdar, S ; Sharif University of Technology
    2009
    Abstract
    This study investigated the behavior of ferrofluids containing superparamagnetic iron oxide nanoparticles (SPION) of various compositions for potential applications in drug delivery and imaging. To ensure biocompatibility, the interaction of these SPION with two cell lines (adhesive and suspended) was also investigated using an MTT (3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyltetrazolium bromide) assay. The cell lines studied were primary mouse connective tissue cells (adhesive) and human leukemia cells (suspended). SPION were synthesized with a co-precipitation method under different stirring rates and NaOH molarities. The SPION demonstrated a range of magnetic saturations due to their... 

    Nanoscale characterization of the biomolecular corona by cryo-electron microscopy, cryo-electron tomography, and image simulation

    , Article Nature Communications ; Volume 12, Issue 1 , 2021 ; 20411723 (ISSN) Sheibani, S ; Basu, K ; Farnudi, A ; Ashkarran, A ; Ichikawa, M ; Presley, J. F ; Bui, K. H ; Ejtehadi, M. R ; Vali, H ; Mahmoudi, M ; Sharif University of Technology
    Nature Research  2021
    Abstract
    The biological identity of nanoparticles (NPs) is established by their interactions with a wide range of biomolecules around their surfaces after exposure to biological media. Understanding the true nature of the biomolecular corona (BC) in its native state is, therefore, essential for its safe and efficient application in clinical settings. The fundamental challenge is to visualize the biomolecules within the corona and their relationship/association to the surface of the NPs. Using a synergistic application of cryo-electron microscopy, cryo-electron tomography, and three-dimensional reconstruction, we revealed the unique morphological details of the biomolecules and their... 

    Construction of an Experimental Device for Foaming Agent and an Experimental Study of the Properties of Foaming Agent

    , M.Sc. Thesis Sharif University of Technology Mohammad Karami (Author) ; Bazargan, Mohammad (Supervisor)
    Abstract
    The primary purpose of acidizing operations in the oil and gas industry is to enhance hydrocarbon production. Acidizing has been a common and conventional method for years, especially when production engineers face issues like declining reservoir pressure leading to reduced production rates. Initially, the treatment solution is referred to as matrix acidizing. In acidizing operations, different additives are combined with the acid to control its behavior in the reservoir. These additives may include iron control agents, corrosion inhibitors, friction reducers, and more. Incompatibility among these additives, the acid, and reservoir fluids can lead to severe damage to the reservoir.... 

    Cell "vision": Complementary factor of protein corona in nanotoxicology

    , Article Nanoscale ; Volume 4, Issue 17 , 2012 , Pages 5461-5468 ; 20403364 (ISSN) Mahmoudi, M ; Saeedi-Eslami, S. N ; Shokrgozar, M. A ; Azadmanesh, K ; Hassanlou, M ; Kalhor, H. R ; Burtea, C ; Rothen Rutishauser, B ; Laurent, S ; Sheibani, S ; Vali, H ; Sharif University of Technology
    RSC  2012
    Abstract
    Engineered nanoparticles are increasingly being considered for use as biosensors, imaging agents and drug delivery vehicles. Their versatility in design and applications make them an attractive proposition for new biological and biomedical approaches. Despite the remarkable speed of development in nanoscience, relatively little is known about the interaction of nanoscale objects with living systems. In a biological fluid, proteins associate with nanoparticles, and the amount and the presentation of the proteins on their surface could lead to a different in vivo response than an uncoated particle. Here, in addition to protein adsorption, we are going to introduce concept of cell "vision",... 

    Numerical Analysis of An Annular Gas Turbine Combustor

    , M.Sc. Thesis Sharif University of Technology Gandomi, Mohammad Hossein (Author) ; Farshchi, Mohammad (Supervisor)
    Abstract
    The goal of this research is the simulation of the annular combustion chamber of the turbine engine utilized by liquid fuel. The achievement to this goal will lead to create numerical tools for parametric study, analysis and combustion chamber designing.For this reason simple geometry has been considered. This simplicity of geometry causes to facilitate in parametric study and decrease in saving time for modeling and meshing. This combustion chamber is a simplified model of engine CF6. In recent study, the k – ε realizable model has been used for turbulence modeling. For non-adiabatic condition, chemical reaction is dissolved by utilizing probability density function along with laminar... 

    Simulation of thermal profile in a single pellet during drying process with CFD method

    , Article Proceedings of the 24th International Mining Congress of Turkey, IMCET 2015, 14 April 2015 through 17 April 2015 ; 2015 , Pages 797-803 ; 9786050107050 (ISBN) Gitiara, A ; Namehi, A ; Vali, H ; Shahrokhshahi, H. R ; Soltani, H ; Alamdari, E. K ; Cheraghi, A ; Karadeniz, M ; Gulsun Kilic, M ; Torun Bilgic, E ; Basarir, H ; Onel, O ; Sharif University of Technology
    TMMOB Maden Muhendisleri Odasi  2015
    Abstract
    Green iron oxide pellets are indurated with thermal treatment in pelletizing plant to achieve sufficient mechanical properties and to be used in iron-steel industry. In the first stage, the pellets are dried with hot air coming from the firing unit. High heat transfer makes the evaporation rate exceeding the outgoing steam rate from the pellets and as a result, increasing the inner pressure of the pellets and fragment. On the other hand, low heat transfer causes low production rate. Using the related equations and considering the pellets' moisture and porosity and applying the pellets' condition on parameters such as specific heat capacity and heat conductivity, an acceptable standard is... 

    A misbehavior‐tolerant multipath routing protocol for wireless Ad hoc networks [electronic resource]

    , Article International Journal of Research in Wireless Systems (IJRWS) ; Vol. 2, Issue 9, pp. , Sep. 2013 Sedghi, H. (Haniyeh) ; Pakravan, Mohammad Reza ; Aref, Mohammad Reza ; Sharif University of Technology
    Abstract
    Secure routing is a major key to service maintenance in ad hoc networks. Ad hoc nature exposes the network to several types of node misbehavior or attacks. As a result of the resource limitations in such networks nodes may have a tendency to behave selfishly. Selfish behavior can have drastic impacts on network performance. We have proposed a Misbehavior-Tolerant Multipath Routing protocol (MTMR) which detects and punishes all types of misbehavior such as selfish behavior, wormhole, sinkhole and grey-hole attacks. The protocol utilizes a proactive approach to enforce cooperation. In addition, it uses a novel data redirection method to mitigate the impact of node misbehavior on network... 

    Theoretical and Experimental Study to Conversion of AUC to UO2 by Microwave Heating

    , Ph.D. Dissertation Sharif University of Technology Labbaf, Mohammad Hossein (Author) ; Otukesh, Mohammad (Supervisor) ; Ghannadi Maragheh, Mohammad (Co-Advisor) ; Ghasemi, Mohammad Reza (Co-Advisor)

    Estimating Possible Effects of Subsidies in Competition and Development of Fixed Broadband Internet

    , M.Sc. Thesis Sharif University of Technology Mohammadi, Mohammad Ali (Author) ; Vesal, Mohammad (Supervisor) ; Rahmati, Mohammad Hossein (Supervisor)
    Abstract
    In this work, the dynamic competition between firms providing internet services is studied. The framework is Markov equilibrium whereby structural parameters are obtained using two-step estimations, allowing for analyzing the situation in case of subsidies for service upgrade. The results show that such subsidy has little effect on the number of firms while increasing the number of fast firms  

    SAR Imaging Using the TomoSAR Technique to Resolve Multiple Scatterers

    , M.Sc. Thesis Sharif University of Technology Omati, Mohammad Mahdi (Author) ; Bastani, Mohammad Hassan (Supervisor) ; Karbasi, Mohammad (Co-Supervisor)
    Abstract
    During the last few years, the study of urban environment structures is considered as a research field of interest in remote sensing. In satellite observations of the earth's surface, continuous imaging in terms of time and space has caused the remote sensing technique to be proposed as a useful and efficient tool for the analysis of urban areas. Obtaining quantitative spatial information from the urban environment in fields such as determining the height of buildings plays an essential role in urban planning, monitoring damage to buildings, establishing communication bases and digital cities. During the last two decades, the use of Tomosar approach in order to reconstruct the structures of...