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    StrongestPath: a Cytoscape application for protein-protein interaction analysis

    , Article BMC bioinformatics ; Volume 22, Issue 1 , 2021 , Pages 352- ; 14712105 (ISSN) Mousavian, Z ; Khodabandeh, M ; Sharifi Zarchi, A ; Nadafian, A ; Mahmoudi, A ; Sharif University of Technology
    NLM (Medline)  2021
    BACKGROUND: StrongestPath is a Cytoscape 3 application that enables the analysis of interactions between two proteins or groups of proteins in a collection of protein-protein interaction (PPI) network or signaling network databases. When there are different levels of confidence over the interactions, the application is able to process them and identify the cascade of interactions with the highest total confidence score. Given a set of proteins, StrongestPath can extract a set of possible interactions between the input proteins, and expand the network by adding new proteins that have the most interactions with highest total confidence to the current network of proteins. The application can... 

    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... 

    Influence of heavy nanocrystals on spermatozoa and fertility of mammals

    , Article Materials Science and Engineering C ; Volume 69 , 2016 , Pages 52-59 ; 09284931 (ISSN) Akhavan, O ; Hashemi, E ; Zare, H ; Shamsara, M ; Taghavinia, N ; Heidari, F ; Sharif University of Technology
    Elsevier Ltd 
    In recent years, quantum dots (QDs) have been widely used in upcoming nanotechnology-based solar cells, light-emitting diodes and even bioimaging, due to their tunable optical properties and excellent quantum yields. But, such nanostructures are currently constituted by heavy elements which can threat the human health and living environment. Hence, in this work, the in vivo effects of CdTe nanocrystals (NCs) (as one of the promising QDs) on spermatozoa of male mice and subsequently on fertility of female mice were investigated, for the first time. To do this, CdTe NCs were synthesized through an environment-friendly (aqueous-based solution) method. The sperm cells presented a high potential... 

    Synthesis and cyto-genotoxicity evaluation of graphene on mice spermatogonial stem cells

    , Article Colloids and Surfaces B: Biointerfaces ; Volume 146 , 2016 , Pages 770-776 ; 09277765 (ISSN) Hashemi, E ; Akhavan, O ; Shamsara, M ; Daliri, M ; Dashtizad, M ; Farmany, A ; Sharif University of Technology
    Elsevier  2016
    The present study analyzed the dose-dependent cyto- and genotoxicity of graphene oxide and reduced graphene oxide on spermatogonial stem cells (SSCs) for the first time. The results showed that graphene oxide significantly increased oxidative stress at concentrations of 100 and 400 μg/ml, while low concentrations did not have a significant effect. In addition, according to the MTT assay, the cell number decreased in high-concentration (100 and 400 μg/ml) graphene oxide-treated samples compared to untreated cells. However, a reduced graphene-treated sample demonstrated a significant increase in cell number. Moreover, microscopic analysis found high concentrations of graphene nanosheets in... 

    VirSense: A novel haptic device with fixed-base motors and a gravity compensation system

    , Article Industrial Robot ; Vol. 41, Issue. 1 , 2014 , pp. 37-49 ; ISSN: 0143991X Mashayekhi, A ; Nahvi, A ; Yazdani, M ; Moghadam, M. M ; Arbabtafti, M ; Norouzi, M ; Sharif University of Technology
    Purpose - This paper aims to present the design and implementation of VirSense, a novel six-DOF haptic interface system, with an emphasis on its gravity compensation and fixed-base motors. Design/methodology/approach - In this paper, the design and manufacture of the VirSense robot and its comparison with the existing haptic devices are presented. The kinematic analysis of the robot, design of the components, and manufacturing of the robot are explained as well. Findings - The proposed system is employed to generate a Virtual Sense (VirSense) with fixed-base motors and a spring compensation system for counterbalancing the torques generated by the weight of the links. The fixed bases of the... 

    Functional analyses of recombinant mouse hepcidin-1 in cell culture and animal model

    , Article Biotechnology Letters ; Volume 35, Issue 8 , August , 2013 , Pages 1191-1197 ; 01415492 (ISSN) Yazdani, Y ; Keyhanvar, N ; Kalhor, H. R ; Rezaei, A ; Sharif University of Technology
    Hepcidin is a peptide hormone that plays an important role in iron metabolism. We have produced a recombinant mouse hepcidin-1 by using baculovirus expression system. Its expression yield was 25 μg/ml when cell culture media were supplemented with a protease inhibitor cocktail. The recombinant mouse hepcidin-1 and synthetic human hepcidin-25 had similar effects on reducing ferroportin expression in J774A cell line and in peritoneal macrophages. However, synthetic human hepcidin-25 was more efficient than recombinant mouse hepcidin-1 in reducing iron concentration in blood circulation (p < 0.01)  

    Effects of short term and long term Extremely Low Frequency Magnetic Field on depressive disorder in mice: Involvement of nitric oxide pathway

    , Article Life Sciences ; Volume 146 , 2016 , Pages 52-57 ; 00243205 (ISSN) Madjid Ansari, A ; Farzam Pour, S ; Sadr, A ; Shekarchi, B ; Majid Zadeh, A. K ; Sharif University of Technology
    Elsevier Inc 
    Aims Previous reports on the possible effects of Extremely Low Frequency Magnetic Fields (ELF MF) on mood have been paradoxical in different settings while no study has yet been conducted on animal behavior. In addition, it was shown that ELF MF exposure makes an increase in brain nitric oxide level. Therefore, in the current study, we aimed to assess the possible effect(s) of ELF MF exposure on mice Forced Swimming Test (FST) and evaluate the probable role of the increased level of nitric oxide in the observed behavior. Main methods Male adult mice NMRI were recruited to investigate the short term and long term ELF MF exposure (0.5 mT and 50 Hz, single 2 h and 2 weeks 2 h a day). Locomotor... 

    Dynamic characterization of a parallel haptic device for application as an actuator in a surgery simulator

    , Article 5th RSI International Conference on Robotics and Mechatronics, IcRoM 2017, 25 October 2017 through 27 October 2017 ; 2018 , Pages 186-191 ; 9781538657034 (ISBN) Khadivar, F ; Sadeghnejad, S ; Moradi, H ; Vossoughi, G ; Farahmand, F ; Sharif University of Technology
    Tactile sense is a key element in developing virtual reality simulators or surgical training systems. In this regard, haptic interfaces, the generator of a sense of touch, play a significant role in producing a realistic haptic feedback force. Since the majority of practical control theories are model-based, the identification of the robot dynamic model is a process of high importance and application. The main concern, accordingly, is to find a precise dynamic model for the aforementioned user interfaces. In this research, we have implemented the Lion identification method to characterize the dynamics of a parallel haptic device in actuating a surgery simulation. We chose the Novint Falcon... 

    Diatoms with invaluable applications in nanotechnology, biotechnology, and biomedicine: Recent advances

    , Article ACS Biomaterials Science and Engineering ; Volume 7, Issue 7 , 2021 , Pages 3053-3068 ; 23739878 (ISSN) Rabiee, N ; Khatami, M ; Jamalipour Soufi, G ; Fatahi, Y ; Iravani, S ; Varma, R. S ; Sharif University of Technology
    American Chemical Society  2021
    Diatoms are unicellular microalga found in soil and almost every aquatic environment (marine and fresh water). Biogenic silica and diatoms are attractive for biotechnological and industrial applications, especially in the field of biomedicine, industrial/synthetic manufacturing processes, and biomedical/pharmaceutical sciences. Deposition of silica by diatoms allows them to create micro- or nanoscale structures which may be utilized in nanomedicine and especially in drug/gene delivery. Diatoms with their unique architectures, good thermal stability, suitable surface area, simple chemical functionalization/modification procedures, ease of genetic manipulations, optical/photonic... 

    Long-term investigation on the phase stability, magnetic behavior, toxicity, and MRI characteristics of superparamagnetic Fe/Fe-oxide core/shell nanoparticles

    , Article International Journal of Pharmaceutics ; Volume 439, Issue 1-2 , 2012 , Pages 28-40 ; 03785173 (ISSN) Masoudi, A ; Madaah Hosseini, H. R ; Seyed Reyhani, S. M ; Shokrgozar, M. A ; Oghabian, M. A ; Ahmadi, R ; Sharif University of Technology
    To efficiently enhance the contrast obtaining from magnetic resonance imaging (MRI), pharmaceutical grade colloidal dispersions of PEG coated iron-based nanoparticles were prepared and compared to conventional pure iron oxide contrast agent. In this study, we synthesized ∼14 nm iron nanoparticles via NaBH4 reduction of iron(III) chloride in an aqueous medium. The resulting nanoparticles were further oxidized by two different methods via (CH3)3NO oxygen transferring agent and exposure to oxygen flow. XRD and electron microscopy analyses confirmed the formation of a second layer on the surface of α-Fe core. As magnetic measurements and Mössbauer spectra of 4-months post prepared nanoparticles... 

    The effect of poly(ethylene glycol) coating on colloidal stability of superparamagnetic iron oxide nanoparticles as potential MRI contrast agent

    , Article International Journal of Pharmaceutics ; Volume 433, Issue 1-2 , 2012 , Pages 129-141 ; 03785173 (ISSN) Masoudi, A ; Madaah Hosseini, H. R ; Shokrgozar, M. A ; Ahmadi, R ; Oghabian, M. A ; Sharif University of Technology
    Superparamganetic iron oxide-based contrast agents in magnetic resonance imaging (MRI) have offered new possibility for early detection of lymph nodes and their metastases. According to important role of nanoparticle size in biodistribution, magnetite nanoparticles coated with different polyethylene glycol (PEG) concentrations up to 10/1 PEG/iron oxide weight ratio in an ex situ manner. To predict the PEG-coated nanoparticle behavior in biological media, such as blood stream or tissue, colloidal stability evaluation was performed to estimate the coating endurance in different conditions. Accordingly, optical absorbance measurements were conducted in solutions with different values of pH and... 

    Pyrolytic carbon coating for cytocompatibility of titanium oxide nanoparticles: A promising candidate for medical applications

    , Article Nanotechnology ; Volume 23, Issue 4 , 2012 ; 09574484 (ISSN) Behzadi, S ; Imani, M ; Yousefi, M ; Galinetto, P ; Simchi, A ; Amiri, H ; Stroeve, P ; Mahmoudi, M ; Sharif University of Technology
    Nanoparticles for biomedical use must be cytocompatible with the biological environment that they are exposed to. Current research has focused on the surface functionalization of nanoparticles by using proteins, polymers, thiols and other organic compounds. Here we show that inorganic nanoparticles such as titanium oxide can be coated by pyrolytic carbon (PyC) and that the coating has cytocompatible properties. Pyrolization and condensation of methane formed a thin layer of pyrolytic carbon on the titanium oxide core. The formation of the PyC shell retards coalescence and sintering of the ceramic phase. Our MTT assay shows that the PyC-coated particles are cytocompatible at employed doses  

    Design and Synthesis of Novel Polyglycerol Hybrid Nanomaterials for Potential Applications in Drug Delivery Systems

    , Article Macromolecular Bioscience ; Volume 11, Issue 3 , NOV , 2011 , Pages 383-390 ; 16165187 (ISSN) Zarrabi, A ; Adeli, M ; Vossoughi, M ; Shokrgozar, M. A ; Sharif University of Technology
    The synthesis of a new drug delivery system based on hybrid nanomaterials containing a β-CD core and hyperbranched PG is described. Conjugating PG branches onto β-CD not only increases its water solubility but also affects its host/guest properties deeply. It can form molecular inclusion complexes with small hydrophobic guest molecules such as ferrocene or FITC with reasonable release. In addition, the achievable payloads are significantly higher as for carriers such as hyperbranched PGs. Short-term in vitro cytotoxicity and hemocompatibility tests on L929 cell lines show that the hybrid nanomaterial is highly biocompatible. Due to their outstanding properties, β-CD-g-PG hybrid nanomaterials... 

    Fabrication of new magnetite-graphene nanocomposite and comparison of its laser-hyperthermia properties with conventionally prepared magnetite-graphene hybrid

    , Article Materials Science and Engineering C ; Volume 75 , 2017 , Pages 572-581 ; 09284931 (ISSN) Tayyebi, A ; Moradi, S ; Azizi, F ; Outokesh, M ; Shadanfar, K ; Mousavi, S. S ; Sharif University of Technology
    A single step supercritical method was introduced for synthesis of “magnetite - reduced graphene oxide (M-rGO)” composite in supercritical methanol. Modified surface, smaller size, lesser cytotoxicity, and homogenous dispersion of Fe3O4 nanoparticles on the graphene surface were advantages of this new M-rGO composite in comparison to the materials synthesized by conventional wet chemical method (M-GO). Nanocomposites were injected in tissue equivalent phantoms of agarose gel in 10 mg/g dosage, and were irradiated by a 1600 mW laser beam at wavelength of 800–810 nm. The M-rGO and M-GO were found to be the most and the least efficient samples for increasing the temperature of the phantom. As... 

    Plant protein-based hydrophobic fine and ultrafine carrier particles in drug delivery systems

    , Article Critical Reviews in Biotechnology ; Volume 38, Issue 1 , 2018 , Pages 47-67 ; 07388551 (ISSN) Malekzad, H ; Mirshekari, H ; Sahandi Zangabad, P ; Moosavi Basri, S. M ; Baniasadi, F ; Sharifi Aghdam, M ; Karimi, M ; Hamblin, M. R ; Sharif University of Technology
    Taylor and Francis Ltd  2018
    For thousands of years, plants and their products have been used as the mainstay of medicinal therapy. In recent years, besides attempts to isolate the active ingredients of medicinal plants, other new applications of plant products, such as their use to prepare drug delivery vehicles, have been discovered. Nanobiotechnology is a branch of pharmacology that can provide new approaches for drug delivery by the preparation of biocompatible carrier nanoparticles (NPs). In this article, we review recent studies with four important plant proteins that have been used as carriers for targeted delivery of drugs and genes. Zein is a water-insoluble protein from maize; Gliadin is a 70% alcohol-soluble... 

    In vitro co-culture of human skin keratinocytes and fibroblasts on a biocompatible and biodegradable scaffold

    , Article Iranian Biomedical Journal ; Volume 13, Issue 3 , 2009 , Pages 169-177 ; 1028852X (ISSN) Shariati, S. R. P ; Shokrgozar, M. A ; Vossoughi, M ; Eslamifar, A ; Sharif University of Technology
    Background: Extensive full-thickness burns require replacement of both epidermis and dermis. In designing skin replacements, the goal has been to re-create this model and make a product which has both essential components. Methods: In the present study, we developed procedures for establishing confluent, stratified layers of cultured human keratinocytes on the surface of modified collagen-chitosan scaffold that contains fibroblasts. The culture methods for propagation of keratinocytes and fibroblasts isolated from human neonatal foreskin were developed. The growth and proliferation of normal human keratinocytes were evaluated in serum-free (keratinocyte growth medium) and our modified... 

    Dynamic characterization and control of a parallel haptic interaction with an admittance type virtual environment

    , Article Meccanica ; Volume 55, Issue 3 , 2020 , Pages 435-452 Khadivar, F ; Sadeghnejad, S ; Moradi, H ; Vossoughi, G ; Sharif University of Technology
    Springer  2020
    Haptic interfaces, a kinesthetic link between a virtual environment and a human operator play a pivotal role in the reproduction of realistic haptic force feedback of the virtual reality-based simulators. Since most of the practical control theories are model-based, the identification of the robot’s dynamics, for precise modeling of the system dynamics, is a process of high significance and usage. This research addresses dynamic characterization, performance issues, and structural stability, associated with a parallel haptic device interaction with an admittance type virtual environment. In this regard, considering the Lion identification scheme, we characterized the dynamics of a robot... 

    Fabrication and characterization of scaffolds containing different amounts of allantoin for skin tissue engineering

    , Article Scientific Reports ; Volume 11, Issue 1 , 2021 ; 20452322 (ISSN) Dorri Nokoorani, Y ; Shamloo, A ; Bahadoran, M ; Moravvej, H ; Sharif University of Technology
    Nature Research  2021
    Using the skin tissue engineering approach is a way to help the body to recover its lost skin in cases that the spontaneous healing process is either impossible or inadequate, such as severe wounds or burns. In the present study, chitosan/gelatin-based scaffolds containing 0.25, 0.5, 0.75, and 1% allantoin were created to improve the wounds’ healing process. EDC and NHS were used to cross-link the samples, which were further freeze-dried. Different in-vitro methods were utilized to characterize the specimens, including SEM imaging, PBS absorption and degradation tests, mechanical experiments, allantoin release profile assessment, antibacterial assay, and cell viability and adhesion tests.... 

    Evaluation of radiogallium-labeled, folate-embedded superparamagnetic nanoparticles in fibrosarcoma-bearing mice

    , Article Journal of Cancer Research and Therapeutics ; Volume 8, Issue 2 , 2012 , Pages 204-208 ; 09731482 (ISSN) Hosseini Salekdeh, S. L ; Jalilian, A.R ; Yousefnia, H ; Shafaii, K ; Pouladian, M ; Mahmoudi, M ; Sharif University of Technology
    Context: Elevated expression of the folate receptor (FR) occurs in many human malignancies. Thus, folate targeting is widely utilized in drug delivery purposes specially using nano-radioactive agents. Aims: In this work, we report production and biological evaluation of gallium-67 labeled superparamagnetic iron oxide nanoparticles, embedded by folic acid (67 Ga-SPION-folate) complex especially in tumor-bearing mice for tumor imaging studies. Settings and Design: The structure of SPION-folate was confirmed by X-ray diffraction (XRD), transmission electron microscopy (TEM) and foureir transform infrared spectroscopy (FT-IR) analyses. The radiolabeled SPION-folate formation was confirmed by... 

    A new approach for the in vitro identification of the cytotoxicity of superparamagnetic iron oxide nanoparticles

    , Article Colloids and Surfaces B: Biointerfaces ; Volume 75, Issue 1 , 2010 , Pages 300-309 ; 09277765 (ISSN) Mahmoudi, M ; Simchi, A ; Imani, M ; Shokrgozar, M. A ; Milani, A. S ; Häfeli, U. O ; Stroeve, P ; Sharif University of Technology
    Superparamagnetic iron oxide nanoparticles (SPIONs) are increasingly used in medical applications, such as targeting delivery and imaging. In the future, patients are more likely to be exposed to pharmaceutical products containing such particles. The study of toxicity of SPIONs has become of great importance in recent years, although the published data in this arena is limited. The aim of the present work is to investigate the cytotoxicity of SPIONs and the effect of the particles on the cell medium components. For this purpose, uncoated and polyvinyl alcohol (PVA) coated SPIONs with narrow size distribution were synthesized via a well-known coprecipitation method. The mouse fibroblast cell...