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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
    Abstract
    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... 

    Melt electrowriting of PLA, PCL, and composite PLA/PCL scaffolds for tissue engineering application

    , Article Scientific Reports ; Volume 12, Issue 1 , 2022 ; 20452322 (ISSN) Shahverdi, M ; Seifi, S ; Akbari, A ; Mohammadi, K ; Shamloo, A ; Movahhedy, M. R ; Sharif University of Technology
    Nature Research  2022
    Abstract
    Fabrication of well-ordered and bio-mimetic scaffolds is one of the most important research lines in tissue engineering. Different techniques have been utilized to achieve this goal, however, each method has its own disadvantages. Recently, melt electrowriting (MEW) as a technique for fabrication of well-organized scaffolds has attracted the researchers’ attention due to simultaneous use of principles of additive manufacturing and electrohydrodynamic phenomena. In previous research studies, polycaprolactone (PCL) has been mostly used in MEW process. PCL is a biocompatible polymer with characteristics that make it easy to fabricate well-arranged structures using MEW device. However, 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
    2013
    Abstract
    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)  

    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
    Abstract
    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... 

    Image Flow and INS Sensor Fusion for the Accurate Localization of Planner Micro Robots

    , M.Sc. Thesis Sharif University of Technology khomejani, Shabnaz (Author) ; Vossoughi, Gholamreza (Supervisor)
    Abstract
    This research focuses on the robust mobile robot localization exploiting motion information acquired from an optical mouse operating based on optical flow technology. Most techniques of visual motion measurement are based on the well research discipline called “optical flow”. Theoretically, optical flow as a method of localization can be highly accurate, but it is sensitive to the noise and surface texture/optical characteristics and distance variations between the CCD detector and surface. As one could not achieve acceptable results in practical situations, to handle these problems, we propose to attach an acceleration – gyro (INS) sensor on the CCD detector (optical mouse) to improve the... 

    Electrospinning of nanodiamond-modified polysaccharide nanofibers with physico-mechanical properties close to natural skins

    , Article Marine Drugs ; Volume 14, Issue 7 , 2016 ; 16603397 (ISSN) Mahdavi, M ; Mahmoudi, N ; Rezaie Anaran, F ; Simchi, A ; Sharif University of Technology
    MDPI AG 
    Abstract
    Electrospinning of biopolymers has gained significant interest for the fabrication of fibrous mats for potential applications in tissue engineering, particularly for wound dressing and skin regeneration. In this study, for the first time, we report successful electrospinning of chitosan-based biopolymers containing bacterial cellulous (33 wt %) and medical grade nanodiamonds (MND) (3 nm; up to 3 wt %). Morphological studies by scanning electron microscopy showed that long and uniform fibers with controllable diameters from 80 to 170 nm were prepared. Introducing diamond nanoparticles facilitated the electrospinning process with a decrease in the size of fibers. Fourier transform infrared... 

    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
    Abstract
    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... 

    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
    Abstract
    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... 

    Graphene/cobalt nanocarrier for hyperthermia therapy and MRI diagnosis

    , Article Colloids and Surfaces B: Biointerfaces ; Volume 146 , 2016 , Pages 271-279 ; 09277765 (ISSN) Hatamie, S ; Ahadian, M. M ; Ghiass, M. A ; Iraji zad, A ; Saber, R ; Parseh, B ; Oghabian, M. A ; Shanehsazzadeh, S ; Sharif University of Technology
    Elsevier 
    Abstract
    Graphene/cobalt nanocomposites are promising materials for theranostic nanomedicine applications, which are defined as the ability to diagnose, provide targeted therapy and monitor the response to the therapy. In this study, the composites were synthesized via chemical method, using graphene oxide as the source material and assembling cobalt nanoparticles of 15 nm over the surface of graphene sheets. Various characterization techniques were then employed to reveal the morphology, size and structure of the nanocomposites, such as X-ray diffraction analysis, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, high resolution transmission electron microscopy and... 

    Graphene oxide negatively regulates cell cycle in embryonic fibroblast cells

    , Article International Journal of Nanomedicine ; Volume 15 , 2020 , Pages 6201-6209 Hashemi, E ; Akhavan, O ; Shamsara, M ; Ansari Majd, S ; Sanati, M. H ; Daliri Joupari, M ; Farmany, A ; Sharif University of Technology
    Dove Medical Press Ltd  2020
    Abstract
    Background: Unique properties of graphene and its derivatives make them attractive in the field of nanomedicine. However, the mass application of graphene might lead to side effects, which has not been properly addressed in previous studies, especially with regard to its effect on the cell cycle. Methods: The effect of two concentrations (100 and 200 μg/mL) of nano-and microsized graphene oxide (nGO and mGO) on apoptosis, cell cycle, and ROS generation was studied. The effect of both sizes on viability and genotoxicity of the embryonic fibroblast cell cycle was evaluated. MTT and flow cytometry were applied to evaluate the effects of graphene oxide (GO) nanosheets on viability of cells.... 

    Oncolytic newcastle disease virus delivered by mesenchymal stem cells-engineered system enhances the therapeutic effects altering tumor microenvironment

    , Article Virology Journal ; Volume 17, Issue 1 , 2020 Keshavarz, M ; Ebrahimzadeh, M. S ; Miri, S. M ; Dianat Moghadam, H ; Ghorbanhosseini, S. S ; Mohebbi, S. R ; Keyvani, H ; Ghaemi, A ; Sharif University of Technology
    BioMed Central Ltd  2020
    Abstract
    Background: Human papillomavirus (HPV)-associated malignancy remain a main cause of cancer in men and women. Cancer immunotherapy has represented great potential as a new promising cancer therapeutic approach. Here, we report Mesenchymal stem cells (MSCs) as a carrier for the delivery of oncolytic Newcastle disease virus (NDV) for the treatment of HPV-associated tumor. Methods: For this purpose, MSCs obtained from the bone marrow of C57BL mice, then cultured and characterized subsequently by the flow cytometry analysis for the presence of cell surface markers. In this study, we sought out to determine the impacts of MSCs loaded with oncolytic NDV on splenic T cell and cytokine immune... 

    Homozygous mutations in C14orf39/SIX6OS1 cause non-obstructive azoospermia and premature ovarian insufficiency in humans

    , Article American Journal of Human Genetics ; Volume 108, Issue 2 , 2021 , Pages 324-336 ; 00029297 (ISSN) Fan, S ; Jiao, Y ; Khan, R ; Jiang, X ; Javed, A. R ; Ali, A ; Zhang, H ; Zhou, J ; Naeem, M ; Murtaza, G ; Li, Y ; Yang, G ; Zaman, Q ; Zubair, M ; Guan, H ; Zhang, X ; Ma, H ; Jiang, H ; Ali, H ; Dil, S ; Shah, W ; Ahmad, N ; Zhang, Y ; Shi, Q ; Sharif University of Technology
    Cell Press  2021
    Abstract
    Human infertility is a multifactorial disease that affects 8%–12% of reproductive-aged couples worldwide. However, the genetic causes of human infertility are still poorly understood. Synaptonemal complex (SC) is a conserved tripartite structure that holds homologous chromosomes together and plays an indispensable role in the meiotic progression. Here, we identified three homozygous mutations in the SC coding gene C14orf39/SIX6OS1 in infertile individuals from different ethnic populations by whole-exome sequencing (WES). These mutations include a frameshift mutation (c.204_205del [p.His68Glnfs∗2]) from a consanguineous Pakistani family with two males suffering from non-obstructive... 

    Preparation and evaluation of bioactive and compatible starch based superabsorbent for oral drug delivery systems

    , Article Journal of Drug Delivery Science and Technology ; Volume 23, Issue 5 , 2013 , Pages 511-517 ; 17732247 (ISSN) Pourjavadi, A ; Ebrahimi, A. A ; Barzegar, S ; Sharif University of Technology
    2013
    Abstract
    Novel types of highly swelling hydrogels (superabsorbent) were prepared by grafting crosslinked poly acrylic acid-co-2-hydroxyethylmetacrylate (PAA-co-HEMA) chains onto starch through a free radical polymerization method. The effect of grafting variables (i.e., concentration of methylenebisacrylamide (MBA), acrylic acid/2-hydroxy methymetacrylate (AA/HEMA) weight ratio, ammonium persulfate (APS), starch, neutralization percent, were systematically optimized to achieve a hydrogel with a maximum swelling capacity. The superabsorbent (SAP) formation was confirmed by Fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). The controlled-release behavior of... 

    Deformation prediction of mouse embryos in cell injection experiment by a feedforward artificial neural network

    , Article Proceedings of the ASME Design Engineering Technical Conference, 28 August 2011 through 31 August 2011 ; Volume 2, Issue PARTS A AND B , August , 2011 , Pages 543-550 ; 9780791854792 (ISBN) Abbasi, A. A ; Ahmadian, M. T ; Vossoughi, G. R ; Sharif University of Technology
    2011
    Abstract
    In this study, neural network models have been used to predict the mechanical behaviors of mouse embryos. In addition, sensitivity analysis has been carried out to investigate the influence of the significance of input parameters on the mechanical behavior of mouse embryos. In order to reach these purposes two neural network models have been implemented. Experimental data earlier deduced-by [Flückiger, M. (2004). Cell Membrane Mechanical Modeling for Microrobotic Cell Manipulation. Diploma Thesis, ETHZ Swiss Federal Institute of Technology, Zurich, WS03/04]-were collected to obtain training and test data for the neural network. The results of these investigations show that the correlation... 

    Polyrotaxane capped quantum dots as new candidates for cancer diagnosis and therapy

    , Article Journal of Nanostructured Polymers and Nanocomposites ; Volume 7, Issue 1 , 2011 , Pages 18-31 ; 17904439 (ISSN) Sarabi, R. S ; Sadeghi, E ; Hosseinkhani, H ; Mahmoudi, M ; Kalantari, M ; Adeli, M ; Sharif University of Technology
    2011
    Abstract
    Molecular self-assembly of cadmium selenide quantum dots-end-capped polyrotaxane hybrid nanostructures (PRCdSe QDs) was led to a new type of core-shell hybrid nanomaterials consisting of cadmium selenide quantum dot (CdSe QDs) core and polyrotaxane shell (PR@QDs). Structure of PR@QDs was characterized using various techniques. It has been observed that the size of PR@QDs was between 20-25 nm in which diameter of core and thickness of shell were between 15-20 and 2-3 nm, respectively. Short-term in vitro cytotoxicity tests, using MTT (3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, were conducted on mouse tissue connective fibroblast adhesive cell line (L929) in order to... 

    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 
    Abstract
    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... 

    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
    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... 

    DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism

    , Article BMC Genomics ; 2017 , Volume 18, Issue 1 ; 14712164 (ISSN) Sharifi Zarchi, A ; Gerovska, D ; Adachi, K ; Totonchi, M ; Pezeshk, H ; Taft, R. J ; Schöler, H. R ; Chitsaz, H ; Sadeghi, M ; Baharvand, H ; Araúzo Bravo, M. J ; Sharif University of Technology
    Abstract
    Background: DNA methylation at promoters is largely correlated with inhibition of gene expression. However, the role of DNA methylation at enhancers is not fully understood, although a crosstalk with chromatin marks is expected. Actually, there exist contradictory reports about positive and negative correlations between DNA methylation and H3K4me1, a chromatin hallmark of enhancers. Results: We investigated the relationship between DNA methylation and active chromatin marks through genome-wide correlations, and found anti-correlation between H3K4me1 and H3K4me3 enrichment at low and intermediate DNA methylation loci. We hypothesized "seesaw" dynamics between H3K4me1 and H3K4me3 in the low... 

    Developmental barcoding of whole mouse via homing CRISPR

    , Article Science ; Volume 361, Issue 6405 , 2018 ; 00368075 (ISSN) Kalhor, R ; Kalhor, K ; Mejia, L ; Leeper, K ; Graveline, A ; Mali, P ; Church, G. M ; Sharif University of Technology

    Temporal activation of LRH-1 and RAR-γ in human pluripotent stem cells induces a functional naïve-like state

    , Article EMBO Reports ; Volume 21, Issue 10 , 2020 Taei, A ; Kiani, T ; Taghizadeh, Z ; Moradi, S ; Samadian, A ; Mollamohammadi, S ; Sharifi Zarchi, A ; Guenther, S ; Akhlaghpour, A ; Asgari Abibeiglou, B ; Najar Asl, M ; Karamzadeh, R ; Khalooghi, K ; Braun, T ; Hassani, S. N ; Baharvand, H ; Sharif University of Technology
    Wiley-VCH Verlag  2020
    Abstract
    Naïve pluripotency can be established in human pluripotent stem cells (hPSCs) by manipulation of transcription factors, signaling pathways, or a combination thereof. However, differences exist in the molecular and functional properties of naïve hPSCs generated by different protocols, which include varying similarities with pre-implantation human embryos, differentiation potential, and maintenance of genomic integrity. We show here that short treatment with two chemical agonists (2a) of nuclear receptors, liver receptor homologue-1 (LRH-1) and retinoic acid receptor gamma (RAR-γ), along with 2i/LIF (2a2iL) induces naïve-like pluripotency in human cells during reprogramming of fibroblasts,...