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    Inferring Signaling Pathways from RNAi Data Using Machine Learning

    , M.Sc. Thesis Sharif University of Technology Mazloomian, Alborz (Author) ; Beigy, Hamid (Supervisor)
    One of the standing problems in Molecular Biology and Bioinformatics is uncovering signaling pathways. Discovering the causes of many cancer-like diseases and developing better treatments for them, requires a better understanding of the behavior of cellular processes. Understanding signaling pathways can help to realize cellular processes. Due to the fast increase of possible signaling pathways when the number of components increases, the problem seems to have an inherent complexity. One of the recent methods for generating data relating to such networks is RNA interference technique. In this thesis we use data which are provided by this method. We propose two methods to infer signaling... 

    The effect of nanoparticles on spontaneous imbibition of brine into initially oil-wet sandstones

    , Article Energy Sources, Part A: Recovery, Utilization and Environmental Effects ; Volume 41, Issue 22 , 2019 , Pages 2746-2756 ; 15567036 (ISSN) Sobhani, A ; Ghasemi Dehkordi, M ; Sharif University of Technology
    Taylor and Francis Inc  2019
    In this paper, the effect of silica nanoparticles on oil production due to the spontaneous imbibition of brine into oil-wet sandstones has been studied. The imbibed fluids were NaCl 3 wt. % solutions containing various concentrations of nanoparticles and the recovered oil for each solution was compared. The results revealed that nanoparticles yielded more oil recovery. Nanofluid was used after brine imbibition, and the oil recovery increased from 17.8% to 40% while in the case of using the same nanofluid as the first imbibed fluid the oil recovery was 53%. Also, the results indicated that the oil recovery depends on nanoparticle concentrations. © 2019, © 2019 Taylor & Francis Group, LLC  

    Performance assessment of thermophotovoltaic application in steel industry

    , Article Solar Energy Materials and Solar Cells ; Volume 157 , 2016 , Pages 55-64 ; 09270248 (ISSN) Shoaei, E ; Sharif University of Technology
    Elsevier  2016
    The potential for using Thermophotovoltaic (1TPV) generators as an alternative for recovering energy losses in steel production industry is assessed. A mathematical model for the assessment of the performance of TPV application in the iron and steel industry has been developed. In order to support the mathematical model, a sample TPV apparatus in laboratory scale based on an IR emitter has been designed and assembled. The key modeling parameters of TPV generator include: the open circuit voltage, the short circuit current density and fill factor of the TPV cell. These parameters have been considered in the model as functions of several variables such as: the emitter (hot steel slab)... 

    Atorvastatin treatment softens human red blood cells: an optical tweezers study

    , Article Biomedical Optics Express ; Volume 9, Issue 3 , 2018 ; 21567085 (ISSN) Sheikh Hasani, V ; Babaei, M ; Azadbakht, A ; Pazoki Toroudi, H ; Mashaghi, A ; Moosavi Movahedi, A. A ; Seyed Reihani, .N ; Sharif University of Technology
    OSA - The Optical Society  2018
    Optical tweezers are proven indispensable single-cell micro-manipulation and mechanical phenotyping tools. In this study, we have used optical tweezers for measuring the viscoelastic properties of human red blood cells (RBCs). Comparison of the viscoelastic features of the healthy fresh and atorvastatin treated cells revealed that the drug softens the cells. Using a simple modeling approach, we proposed a molecular model that explains the drug-induced softening of the RBC membrane. Our results suggest that direct interactions between the drug and cytoskeletal components underlie the drug-induced softening of the cells. © 2018 Optical Society of America  

    Integrative Utilization of Microenvironments, Biomaterials and Computational Techniques for Advanced Tissue Engineering

    , Article Journal of Biotechnology ; Volume 212 , 2015 , Pages 71-89 ; 01681656 (ISSN) Shamloo, A ; Mohammadaliha, N ; Mohseni, M ; Sharif University of Technology
    Elsevier  2015
    This review aims to propose the integrative implementation of microfluidic devices, biomaterials, and computational methods that can lead to a significant progress in tissue engineering and regenerative medicine researches. Simultaneous implementation of multiple techniques can be very helpful in addressing biological processes. Providing controllable biochemical and biomechanical cues within artificial extracellular matrix similar to in vivo conditions is crucial in tissue engineering and regenerative medicine researches. Microfluidic devices provide precise spatial and temporal control over cell microenvironment. Moreover, generation of accurate and controllable spatial and temporal... 

    Designing and modeling a centrifugal microfluidic device to separate target blood cells

    , Article Journal of Micromechanics and Microengineering ; Volume 26, Issue 3 , 2016 ; 09601317 (ISSN) Shamloo, A ; Selahi, Aa ; Madadelahi, M ; Sharif University of Technology
    Institute of Physics Publishing  2016
    The objective of this study is to design a novel and efficient portable lab-on-a-CD (LOCD) microfluidic device for separation of specific cells (target cells) using magnetic beads. In this study the results are shown for neutrophils as target cells. However, other kinds of target cells can be separated in a similar approach. The designed microfluidics can be utilized as a point of care system for neutrophil detection. This microfluidic system employs centrifugal and magnetic forces for separation. After model validation by the experimental data in the literature (that may be used as a design tool for developing centrifugo-magnetophoretic devices), two models are presented for separation of... 

    Protein corona impact on nanoparticle-cell interactions: Toward an energy-based model of endocytosis

    , Article Journal of Physics Condensed Matter ; Volume 32, Issue 11 , 2020 Shadmani, P ; Mehrafrooz, B ; Montazeri, A ; Naghdabadi, R ; Sharif University of Technology
    Institute of Physics Publishing  2020
    Upon incubation of nanoparticles in biological fluids, a new layer called the protein corona is formed on their surface affecting the interactions between nanoparticles and targeted cells during the endocytosis process. In the present study, a mathematical model based on the diffusion of membrane mobile receptors is proposed. Opposing the endocytosis proceeding, membrane bending and tension energies are named as resistant energy. Also, the binding energy and free-energy associated with the configurational entropy are collectively termed promoter energy. Utilizing this model, endocytosis of gold nanoparticle (GNP) is simulated to explore the biological media effect. The results reveal that... 

    Simulation of softening kinetics and microstructural events in aluminum alloy subjected to single and multi-pass rolling operations

    , Article Applied Mathematical Modelling ; Volume 40, Issue 17-18 , 2016 , Pages 7571-7582 ; 0307904X (ISSN) Shabaniverki, S ; Serajzadeh, S ; Sharif University of Technology
    Elsevier Inc 
    In this study, a multi-scale model is proposed to assess softening kinetics and microstructural changes during isothermal annealing within an aluminum alloy. In the first stage, an elastic-plastic finite element analysis is performed for computing the distributions of effective plastic strain and stress while the stored energy after cold rolling is defined based on the predicted data and then utilized for generation of the initial conditions in the microstructural analysis. In the next stage, an algorithm based on cellular automata coupled with a first order rate equation is used to determine the progress of softening behavior at elevated temperatures while both recrystallization and... 

    Application of a new spherical super element in predicting the deformation of biological cells in microinjection

    , Article Proceedings of the ASME Design Engineering Technical Conference, 28 August 2011 through 31 August 2011 ; Volume 7 , August , 2011 , Pages 41-49 ; 9780791854846 (ISBN) Sarvi, M. N ; Ahmadian, M. T ; Sharif University of Technology
    Biological cell injection is a sensitive and important work which is implemented in injection of foreign materials into individual cells. Microinjection is significantly developed in the field of drug discovery and genetics so predicting the behavior of cell in microinjection is remarkably important because a tiny excessive manipulation force can destroy the tissue of the biological cell. There are a few analytical methods available to simulate the cell injection, hence the numerical methods such as FEM are suitable to be used to model the microinjection. In this study, a new spherical super element is presented to model the biological cells and deformation of a specific cell under an... 

    Comparison of deformation analysis of a biological cell under an injection force using analytical, experimental and finite element methods and Artificial Neural Network

    , Article ASME 2011 International Mechanical Engineering Congress and Exposition, IMECE 2011 ; Volume 2 , 2011 , Pages 499-507 ; 9780791854884 (ISBN) Sarvi, M. N ; Ahmadian, M. T ; ASME ; Sharif University of Technology
    Biological cell injection is a sensitive and important work which is implemented in injection of foreign materials into individual cells. Microinjection is significantly developed in the field of drug discovery and genetics so predicting the behavior of cell in microinjection is remarkably important because a tiny excessive manipulation force can destroy the tissue of the biological cell. There are a few analytical methods available to simulate the cell injection, hence the numerical methods such as FEM are suitable to be used to model the microinjection. In this study, a new spherical super element is presented to model the biological cells and deformation of a specific cell under an... 

    Toward chemical perfection of graphene-based gene carrier via ugi multicomponent assembly process

    , Article Biomacromolecules ; Volume 17, Issue 9 , 2016 , Pages 2963-2971 ; 15257797 (ISSN) Rezaei, A ; Akhavan, O ; Hashemi, E ; Shamsara, M ; Sharif University of Technology
    American Chemical Society 
    The graphene-based materials with unique, versatile, and tunable properties have brought new opportunities for the leading edge of advanced nanobiotechnology. In this regard, the use of graphene in gene delivery applications is still at early stages. In this study, we successfully designed a new complex of carboxylated-graphene (G-COOH) with ethidium bromide (EtBr) and used it as a nanovector for efficient gene delivery into the AGS cells. G-COOH, with carboxyl functions on its surface, in the presence of EtBr, formaldehyde, and cyclohexylisocyanide were participated in Ugi four component reaction to fabricate a stable amphiphilic graphene-EtBr (AG-EtBr) composite. The coupling reaction was... 

    An integrated analysis to predict micro-RNAs targeting both stemness and metastasis in breast cancer stem cells

    , Article Journal of Cellular and Molecular Medicine ; Volume 23, Issue 4 , 2019 , Pages 2442-2456 ; 15821838 (ISSN) Rahimi, M ; Sharifi Zarchi, A ; Firouzi, J ; Azimi, M ; Zarghami, N ; Alizadeh, E ; Ebrahimi, M ; Sharif University of Technology
    Blackwell Publishing Inc  2019
    Several evidences support the idea that a small population of tumour cells representing self-renewal potential are involved in initiation, maintenance, metastasis, and outcomes of cancer therapy. Elucidation of microRNAs/genes regulatory networks activated in cancer stem cells (CSCs) is necessary for the identification of new targets for cancer therapy. The aim of the present study was to predict the miRNAs pattern, which can target both metastasis and self-renewal pathways using integration of literature and data mining. For this purpose, mammospheres derived from MCF-7, MDA-MB231, and MDA-MB468 were used as breast CSCs model. They had higher migration, invasion, and colony formation... 

    Polymer-Coated NH2-UiO-66 for the codelivery of DOX/pCRISPR

    , Article ACS Applied Materials and Interfaces ; Volume 13, Issue 9 , 2021 , Pages 10796-10811 ; 19448244 (ISSN) Rabiee, N ; Bagherzadeh, M ; Heidarian Haris, M ; Ghadiri, A. M ; Matloubi Moghaddam, F ; Fatahi, Y ; Dinarvand, R ; Jarahiyan, A ; Ahmadi, S ; Shokouhimehr, M ; Sharif University of Technology
    American Chemical Society  2021
    Herein, the NH2-UiO-66 metal organic framework (MOF) has been green synthesized with the assistance of high gravity to provide a suitable and safe platform for drug loading. The NH2-UiO-66 MOF was characterized using a field-emission scanning electron microscope, transmission electron microscope (TEM), X-ray diffraction, and zeta potential analysis. Doxorubicin was then encapsulated physically on the porosity of the green MOF. Two different stimulus polymers, p(HEMA) and p(NIPAM), were used as the coating agents of the MOFs. Doxorubicin was loaded onto the polymer-coated MOFs as well, and a drug payload of more than 51% was obtained, which is a record by itself. In the next step, pCRISPR was... 

    The performances of the chi-square test and complexity measures for signal recognition in biological sequences

    , Article Journal of Theoretical Biology ; Volume 251, Issue 2 , 2008 , Pages 380-387 ; 00225193 (ISSN) Pirhaji, L ; Kargar, M ; Sheari, A ; Poormohammadi, H ; Sadeghi, M ; Pezeshk, H ; Eslahchi, C ; Sharif University of Technology
    With large amounts of experimental data, modern molecular biology needs appropriate methods to deal with biological sequences. In this work, we apply a statistical method (Pearson's chi-square test) to recognize the signals appear in the whole genome of the Escherichia coli. To show the effectiveness of the method, we compare the Pearson's chi-square test with linguistic complexity on the complete genome of E. coli. The results suggest that Pearson's chi-square test is an efficient method for distinguishing genes (coding regions) form pseudogenes (noncoding regions). On the other hand, the performance of the linguistic complexity is much lower than the chi-square test method. We also use the... 

    Design of two Inertial-based microfluidic devices for cancer cell separation from Blood: A serpentine inertial device and an integrated inertial and magnetophoretic device

    , Article Chemical Engineering Science ; 2021 ; 00092509 (ISSN) Nasiri, R ; Shamloo, A ; Akbari, J ; Sharif University of Technology
    Elsevier Ltd  2021
    The separation of cancer cells from a heterogeneous biological sample such as blood plays a vital role in cancer study and future treatments. In this paper, we designed and investigated two microfluidic devices for cancer cell separation, including a serpentine inertial device and an integrated inertial-magnetophoretic device. Firstly, numerical modeling was carried out to study the fluid flow, particles’ trajectories in the inertial device. Then the device was fabricated using soft photolithography and suspension of two types of microparticles with the size of 10 and 15 µm were injected into the microchannel separately to investigate the particles’ trajectories and focusing behavior at... 

    A new genetic algorithm for multiple sequence alignment

    , Article International Journal of Computational Intelligence and Applications ; Volume 11, Issue 4 , December , 2012 ; 14690268 (ISSN) Narimani, Z ; Beigy, H ; Abolhassani, H ; Sharif University of Technology
    Multiple sequence alignment (MSA) is one of the basic and important problems in molecular biology. MSA can be used for different purposes including finding the conserved motifs and structurally important regions in protein sequences and determine evolutionary distance between sequences. Aligning several sequences cannot be done in polynomial time and therefore heuristic methods such as genetic algorithms can be used to find approximate solutions of MSA problems. Several algorithms based on genetic algorithms have been developed for this problem in recent years. Most of these algorithms use very complicated, problem specific and time consuming mutation operators. In this paper, we propose a... 

    Development of an aqueous TiO2 paste in terms of morphological manipulation of nanostructured photoanode electrode of dye-sensitized solar cells

    , Article Journal of Sol-Gel Science and Technology ; Volume 75, Issue 2 , August , 2015 , Pages 447-459 ; 09280707 (ISSN) Moradzaman, M ; Mohammadi, M. R ; Sharif University of Technology
    Kluwer Academic Publishers  2015
    Abstract: A novel simple synthetic procedure for improving cell efficiency and reducing the production cost of TiO2 dye-sensitized solar cells (DSSCs) by modification and optimization of homemade formulated paste is reported. This is achieved in terms of morphological manipulation of deposited monolayer TiO2 films by controlling three processing parameters of paste formulation. These parameters are tailored to obtain a paste with proper viscosity suitable for spin-coating technique and to achieve uniform, homogeneous, and crack-free films with good connections between TiO2 grains and porous structure. Photovoltaic measurements show that TiO2... 

    A new modeling and control scheme for cascaded split-source converter cells

    , Article IEEE Transactions on Industrial Electronics ; 2021 ; 02780046 (ISSN) Montazeri, S. H ; Milimonfared, J ; Zolghadri, M. R ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2021
    Cascaded split-source inverter (CSSI) is a new single-stage modular multilevel topology. Each cell of this converter converts DC to AC power in the buck or boost operation mode without any additional power switch. This paper develops a design method based on a detailed model for CSSI. This model shows that energy storage elements experience double-fundamental frequency ripples besides high-frequency ones. It accurately calculates voltage gains and capacitor voltage and inductor current ripples. On the other hand, common carrier-based multilevel modulations have been modified in terms of both reference and carrier signals to control the inverter under symmetric and asymmetric conditions. With... 

    3D distributed modeling of trolling-mode AFM during 2D manipulation of a spherical cell

    , Article Journal of Nanoparticle Research ; Volume 23, Issue 4 , 2021 ; 13880764 (ISSN) Mohammadi, S.Z ; Nejat Pishkenari, H ; Mohammadi Moghaddam, M ; Sharif University of Technology
    Springer Science and Business Media B.V  2021
    In this study, a general 3D distributed modeling of Trolling-Mode AFM (TR-AFM) as a nanorobot is presented to analyze the 2D manipulation process of a spherical cell. To this aim, the analysis is categorized into 3 sections. In the first section, 6 deformations of TR-AFM are taken into account, and the standard model of the system is obtained. Moreover, the system is simulated in ANSYS Workbench. The results of modal and transient analyses of the system from both analytical and software methods reveal high agreement, which confirms the accuracy of the presented analytical model. In the second section, by utilizing the 3D derived model, displacement of a spherical yeast single cell (W303)... 

    Protein corona composition of gold nanoparticles/nanorods affects amyloid beta fibrillation process

    , Article Nanoscale ; Volume 7, Issue 11 , Feb , 2015 , Pages 5004-5013 ; 20403364 (ISSN) Mirsadeghi, S ; Dinarvand, R ; Ghahremani, M. H ; Hormozi-Nezhad, M. R ; Mahmoudi, Z ; Hajipour, M. J ; Atyabi, F ; Ghavami, M ; Mahmoudi, M ; Sharif University of Technology
    Royal Society of Chemistry  2015
    Protein fibrillation process (e.g., from amyloid beta (Aβ) and α-synuclein) is the main cause of several catastrophic neurodegenerative diseases such as Alzheimer's and Parkinson diseases. During the past few decades, nanoparticles (NPs) were recognized as one of the most promising tools for inhibiting the progress of the disease by controlling the fibrillation kinetic process; for instance, gold NPs have a strong capability to inhibit Aβ fibrillations. It is now well understood that a layer of biomolecules would cover the surface of NPs (so called "protein corona") upon the interaction of NPs with protein sources. Due to the fact that the biological species (e.g., cells and amyloidal...