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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  

    GTED: Graph traversal edit distance

    , Article 22nd International Conference on Research in Computational Molecular Biology, RECOMB 2018, 21 April 2018 through 24 April 2018 ; Volume 10812 LNBI , 2018 , Pages 37-53 ; 03029743 (ISSN); 9783319899282 (ISBN) Ebrahimpour Boroojeny, A ; Shrestha, A ; Sharifi Zarchi, A ; Gallagher, S. R ; Sahinalp, S. C ; Chitsaz, H ; Sharif University of Technology
    Springer Verlag  2018
    Many problems in applied machine learning deal with graphs (also called networks), including social networks, security, web data mining, protein function prediction, and genome informatics. The kernel paradigm beautifully decouples the learning algorithm from the underlying geometric space, which renders graph kernels important for the aforementioned applications. In this paper, we give a new graph kernel which we call graph traversal edit distance (GTED). We introduce the GTED problem and give the first polynomial time algorithm for it. Informally, the graph traversal edit distance is the minimum edit distance between two strings formed by the edge labels of respective Eulerian traversals... 

    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)... 

    Application of hyperelastic models in mechanical properties prediction of mouse oocyte and embryo cells at large deformations

    , Article Scientia Iranica ; Volume 25, Issue 2B , March , 2018 , Pages 700-710 ; 10263098 (ISSN) Abbasi, A. A ; Ahmadian, M. T ; Alizadeh, A ; Tarighi, S ; Sharif University of Technology
    Sharif University of Technology  2018
    Biological cell studies have many applications in biology, cell manipulation, and diagnosis of diseases such as cancer and malaria. In this study, Inverse Finite Element Method (IFEM) combined with Levenberg-Marquardt optimization algorithm has been used to extract and characterize material properties of mouse oocyte and embryo cells at large deformations. Then, the simulation results have been validated using data from experimental works. In this study, it is assumed that cell material is hyperelastic, isotropic, homogenous, and axisymmetric. For inverse analysis, FEM model of cell injection experiment implemented in Abaqus software has been coupled with Levenberg-Marquardt optimization... 

    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... 

    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  

    Inferring causal molecular networks: Empirical assessment through a community-based effort

    , Article Nature Methods ; Volume 13, Issue 4 , 2016 , Pages 310-322 ; 15487091 (ISSN) Hill, S. M ; Heiser, L.M ; Cokelaer, T ; Linger, M ; Nesser, N. K ; Carlin, D. E ; Zhang, Y ; Sokolov, A ; Paull, E. O ; Wong, C. K ; Graim, K ; Bivol, A ; Wang, H ; Zhu, F ; Afsari, B ; Danilova, L. V ; Favorov, A. V ; Lee, W. S ; Taylor, D ; Hu, C. W ; Long, B. L ; Noren, D. P ; Bisberg, A. J ; Mills, G. B ; Gray, J. W ; Kellen, M ; Norman, T ; Friend, S ; Qutub, A. A ; Fertig, E. J ; Guan, Y ; Song, M ; Stuart, J. M ; Spellman, P. T ; Koeppl, H ; Stolovitzky, G ; Saez Rodriguez, J ; Mukherjee, S ; Afsari, B ; Al-Ouran, R ; Anton, B ; Arodz, T ; Askari Sichani, O ; Bagheri, N ; Berlow, N ; Bisberg, A. J ; Bivol, A ; Bohler, A ; Bonet, J ; Bonneau, R ; Budak, G ; Bunescu, R ; Caglar, M ; Cai, B ; Cai, C ; Carlin, D. E ; Carlon, A ; Chen, L ; Ciaccio, M. F ; Cokelaer, T ; Cooper, G ; Coort, S ; Creighton, C. J ; Daneshmand, S. M. H ; De La Fuente, A ; Di Camillo, B ; Danilova, L. V ; Dutta-Moscato, J ; Emmett, K ; Evelo, C ; Fassia, M. K. H ; Favorov, A. V ; Fertig, E. J ; Finkle, J. D ; Finotello, F ; Friend, S ; Gao, X ; Gao, J ; Garcia Garcia, J ; Ghosh, S ; Giaretta, A ; Graim, K ; Gray, J. W ; Großeholz, R ; Guan, Y ; Guinney, J ; Hafemeister, C ; Hahn, O ; Haider, S ; Hase, T ; Heiser, L. M ; Hill, S. M ; Hodgson, J ; Hoff, B ; Hsu, C. H ; Hu, C. W ; Hu, Y ; Huang, X ; Jalili, M ; Jiang, X ; Kacprowski, T ; Kaderali, L ; Kang, M ; Kannan, V ; Kellen, M ; Kikuchi, K ; Kim, D. C ; Kitano, H ; Knapp, B ; Komatsoulis, G ; Koeppl, H ; Krämer, A ; Kursa, M. B ; Kutmon, M ; Lee, W. S ; Li, Y ; Liang, X ; Liu, Z ; Liu, Y ; Long, B. L ; Lu, S ; Lu, X ; Manfrini, M ; Matos, M. R. A ; Meerzaman, D ; Mills, G. B ; Min, W ; Mukherjee, S ; Müller, C. L ; Neapolitan, R. E ; Nesser, N. K ; Noren, D. P ; Norman, T ; Oliva, B ; Opiyo, S. O ; Pal, R ; Palinkas, A ; Paull, E. O ; Planas Iglesias, J ; Poglayen, D ; Qutub, A. A ; Saez Rodriguez, J ; Sambo, F ; Sanavia, T ; Sharifi-Zarchi, A ; Slawek, J ; Sokolov, A ; Song, M ; Spellman, P. T ; Streck, A ; Stolovitzky, G ; Strunz, S ; Stuart, J. M ; Taylor, D ; Tegnér, J ; Thobe, K ; Toffolo, G. M ; Trifoglio, E ; Unger, M ; Wan, Q ; Wang, H ; Welch, L ; Wong, C. K ; Wu, J. J ; Xue, A. Y ; Yamanaka, R ; Yan, C ; Zairis, S ; Zengerling, M ; Zenil, H ; Zhang, S ; Zhang, Y ; Zhu, F ; Zi, Z ; Sharif University of Technology
    Nature Publishing Group  2016
    It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was... 

    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... 

    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... 

    BLESS: A simple and efficient scheme for prolonging PCM lifetime

    , Article 53rd Annual ACM IEEE Design Automation Conference, DAC 2016, 5 June 2016 through 9 June 2016 ; Volume 05-09 , June-2016 , 2016 ; 0738100X (ISSN); 9781450342360 (ISBN) Asadinia, M ; Jalili, M ; Sarbazi Azad, H ; Sharif University of Technology
    Institute of Electrical and Electronics Engineers Inc  2016
    Limited endurance problem and low cell reliability are main challenges of phase change memory (PCM) as an alternative to DRAM. To further prolong the lifetime of a PCM device, there exist a number of techniques that can be grouped in two categories: 1) reducing the write rate to PCM cells, and 2) handling cell failures when faults occur. Our experiments confirm that during write operations, an extensive non-uniformity in bit ips is exhibited. To reduce this non-uniformity, we present byte-level shifting scheme (BLESS) which reduces write pressure over hot cells of blocks. Additionally, this shifting mechanism can be used for error recovery purpose by using the MLC capability of PCM and... 

    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... 

    Produced Water Treatment with Simultaneous Bioenergy Production Using Novel Bioelectrochemical Systems

    , Article Electrochimica Acta ; Volume 180 , 2015 , Pages 535-544 ; 00134686 (ISSN) Ghasemi Naraghi, Z ; Yaghmaei, S ; Mardanpour, M. M ; Hasany, M ; Sharif University of Technology
    Elsevier Ltd  2015
    The present study investigated the biological treatment of produced water in a microbial electrochemical cell (MXC). The main objectives were to develop a novel spiral microbial electrochemical cell (SMXC) and test its performance for produced water treatment under highly saline conditions (salinity > 200000 ppm). The bioelectrochemical performance of the system was also evaluated in terms of power and hydrogen production over time. The comparatively inexpensive material and ease of application increased the feasibility of the SMXC configuration for produced water treatment. Optimal SMXC performance as a microbial fuel cell was achieved at a maximum open circuit potential of 330 mV, maximum... 

    On spatial filtering of flow variables in high-order finite volume methods

    , Article Computers and Fluids ; Volume 132 , 2016 , Pages 19-31 ; 00457930 (ISSN) Ghadimi, M ; Farshchi, M ; Hejranfar, K ; Sharif University of Technology
    Elsevier Ltd  2016
    A new method of spatial filtering in high-order finite volume methods is presented and assessed. The base of this method is to filter face-averaged variables (fluxes) and then the recovery of cell-averaged ones. Two kinds of filtering method are proposed. The first kind is highly dissipative and appropriate for the numerical regions that need high dissipation, e.g. sponge zones. The second kind, on the other hand, is a precise method and hence is suitable for applying the high-order finite difference filters to the finite volume methods. Applying high-order finite difference filters directly to the high-order finite volume methods without using the proposed method causes stability problems... 

    Apoptotic and anti-apoptotic genes transcripts patterns of graphene in mice

    , Article Materials Science and Engineering C ; Volume 71 , 2017 , Pages 460-464 ; 09284931 (ISSN) Ahmadian, H ; Hashemi, E ; Akhavan, O ; Shamsara, M ; Hashemi, M ; Farmany, A ; Daliri Joupari, M ; Sharif University of Technology
    Elsevier Ltd  2017
    Recent studies showed that a large amount of graphene oxide accumulated in kidney and liver when it injected intravenously. Evaluation of lethal and apoptosis gene expression in these tissues, which are under stress is very important. In this paper the in vivo dose-dependent effects of graphene oxide and reduced graphene oxide nanoplatelets on kidney and liver of mice were studied. Balb/C mice were treated by 20 mg/kg body weight of nanoplatelets. Molecular biology analysis showed that graphene nanoplatelets injected intravenously lead to overexpression of BAX gene in both kidney and liver tissues (P ≥ 0.01). In addition these nanoparticles significantly increase BCL2 gene expression in both... 

    Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation

    , Article Heliyon ; Volume 6, Issue 12 , December , 2020 Kordzadeh, A ; Ramazani Saadatabadi, A ; Hadi, A ; Sharif University of Technology
    Elsevier Ltd  2020
    A coronavirus identified as COVID-19 is the reason for an infection outbreak which is started in December 2019. NO completely effective drugs and treatments are not recognized for this virus. Recently, saffron and its compounds were used to treat different viral diseases. Saffron extract and its major ingredients have shown antiviral effects. In this study, the steered molecular dynamics simulation was used for investigating the effect of four main components of saffron that include: crocin, crocetin, safranal, and picrocrocin as candidate for drug molecules, on COVID-19. The binding energies between drug molecules and spike protein and the main protease of the virus were evaluated. 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... 

    Multifunctional core-shell nanoplatforms (gold@graphene oxide) with mediated NIR thermal therapy to promote miRNA delivery

    , Article Nanomedicine: Nanotechnology, Biology, and Medicine ; Volume 14, Issue 6 , 2018 , Pages 1891-1903 ; 15499634 (ISSN) Assali, A ; Akhavan, O ; Adeli, M ; Razzazan, S ; Dinarvand, R ; Zanganeh, S ; Soleimani, M ; Dinarvand, M ; Atyabi, F ; Sharif University of Technology
    Elsevier Inc  2018
    Recent insights into the nanomedicine have revealed that nanoplatforms enhance the efficacy of carrier in therapeutic applications. Here, multifunctional nanoplatforms were utilized in miRNA-101 delivery and NIR thermal therapy to induce apoptosis in breast cancer cells. Au nanorods (NRs) or nanospheres (NSs) covered with graphene oxide (GO) were prepared and functionalized with polyethylene glycol as a stabilizer and poly-L-arginine (P-L-Arg) as a targeting agent. In nanoplatforms, coupling Au@GO prepared stable structures with higher NIR reactivity. P-L-Arg substantially enhanced the cellular uptake and gene retardation of stuffs coated by them. However, rod-shape nanoplatforms indicated... 

    Producing functional recombinant human keratinocyte growth factor in Pichia pastoris and investigating its protective role against irradiation

    , Article Enzyme and Microbial Technology ; Volume 111 , April , 2018 , Pages 12-20 ; 01410229 (ISSN) Bahadori, Z ; Kalhor, H. R ; Mowla, S. J ; Sharif University of Technology
    Elsevier Inc  2018
    Keratinocyte Growth Factor (KGF) is a paracrine-acting, epithelial mitogen that plays a prominent role in the regeneration of damaged epithelial tissues. In spite of different attempts to produce recombinant human KGF in many organisms, including bacteria, mammalian cells, plant cells and insect cells; production of recombinant form suffers from lower yields and recovery relative to other recombinant proteins of similar size and properties. Due to many advantages of Pichia pastoris expression systems for producing industrial enzymes and pharmaceutical proteins, in this study P. pastoris was chosen as a host for KGF expression. For preparing human KGF coding sequence, MCF-7 cell line was...