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    Interplay between competitive and cooperative interactions in a three-player pathogen system

    , Article Royal Society Open Science ; Volume 7, Issue 1 , 2020 Pinotti, F ; Ghanbarnejad, F ; Hövel, P ; Poletto, C ; Sharif University of Technology
    Royal Society Publishing  2020
    Abstract
    In ecological systems, heterogeneous interactions between pathogens take place simultaneously. This occurs, for instance, when two pathogens cooperate, while at the same time, multiple strains of these pathogens co-circulate and compete. Notable examples include the cooperation of human immunodeficiency virus with antibiotic-resistant and susceptible strains of tuberculosis or some respiratory infections with Streptococcus pneumoniae strains. Models focusing on competition or cooperation separately fail to describe how these concurrent interactions shape the epidemiology of such diseases. We studied this problem considering two cooperating pathogens, where one pathogen is further structured... 

    Emergence of synergistic and competitive pathogens in a coevolutionary spreading model

    , Article Physical Review E ; Volume 105, Issue 3 , 2022 ; 24700045 (ISSN) Ghanbarnejad, F ; Seegers, K ; Cardillo, A ; Hövel, P ; Sharif University of Technology
    American Physical Society  2022
    Abstract
    Cooperation and competition between pathogens can alter the amount of individuals affected by a coinfection. Nonetheless, the evolution of the pathogens' behavior has been overlooked. Here, we consider a coevolutionary model where the simultaneous spreading is described by a two-pathogen susceptible-infected-recovered model in an either synergistic or competitive manner. At the end of each epidemic season, the pathogens species reproduce according to their fitness that, in turn, depends on the payoff accumulated during the spreading season in a hawk-and-dove game. This coevolutionary model displays a rich set of features. Specifically, the evolution of the pathogens' strategy induces abrupt... 

    Development of a sensitive diagnostic device based on zeolitic imidazolate frameworks-8 using ferrocene-graphene oxide as electroactive indicator for pseudomonas aeruginosa detection

    , Article ACS Sustainable Chemistry and Engineering ; Volume 7, Issue 15 , 2019 , Pages 12760-12769 ; 21680485 (ISSN) Shahrokhian, S ; Ranjbar, S ; Sharif University of Technology
    American Chemical Society  2019
    Abstract
    Since Gram-negative bacteria have a predominant role in nosocomial infections, there are high demands to develop a fast and sensitive method for diagnosis of bacteria in clinical samples. To address this challenge, we designed a novel electrochemical biosensor based on aptamers immobilized in engineered zeolitic imidazolate Framework-8 (ZIFs-8) via EDC-NHS chemistry. Cyclic voltammetry and electrochemical impedance spectroscopy techniques were conducted to monitor the electrochemical characterization. With respect to unique π-πinteractions between aptamer and graphene oxide (GO), the differential pulse voltammetry technique was applied with ferrocene-graphene oxide (Fc-GO) as an... 

    Markovian approach to tackle the interaction of simultaneous diseases

    , Article Physical Review E ; Volume 100, Issue 6 , 2019 ; 24700045 (ISSN) Soriano Panos, D ; Ghanbarnejad, F ; Meloni, S ; Gomez Gardenes, J ; Sharif University of Technology
    American Physical Society  2019
    Abstract
    The simultaneous emergence of several abrupt disease outbreaks or the extinction of some serotypes of multistrain diseases are fingerprints of the interaction between pathogens spreading within the same population. Here, we propose a general and versatile benchmark to address the unfolding of both cooperative and competitive interacting diseases. We characterize the explosive transitions between the disease-free and the epidemic regimes arising from the cooperation between pathogens and show the critical degree of cooperation needed for the onset of such abrupt transitions. For the competing diseases, we characterize the mutually exclusive case and derive analytically the transition point... 

    Overcoming drug resistance by co-targeting

    , Article Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010, 18 December 2010 through 21 December 2010 ; December , 2010 , Pages 198-202 ; 9781424483075 (ISBN) Ayati, M ; Taheri, G ; Arab, S ; Wong, L ; Eslahchi, C ; Sharif University of Technology
    2010
    Abstract
    Removal or suppression of key proteins in an essential pathway of a pathogen is expected to disrupt the pathway and prohibit the pathogen from performing a vital function. Thus disconnecting multiple essential pathways should disrupt the survival of a pathogen even when it has multiple pathways to drug resistance. We consider a scenario where the drug-resistance pathways are unknown. To disrupt these pathways, we consider a cut set S of G, where G is a connected simple graph representing the protein interaction network of the pathogen, so that G-S splits to two partitions such that the endpoints of each pathway are in different partitions. If the difference between the sizes of the two... 

    Smart chip for visual detection of bacteria using the electrochromic properties of polyaniline

    , Article Analytical Chemistry ; Volume 91, Issue 23 , 2019 , Pages 14960-14966 ; 00032700 (ISSN) Ranjbar, S ; Farahmand Nejad, M. A ; Parolo, C ; Shahrokhian, S ; Merkoci, A ; Sharif University of Technology
    American Chemical Society  2019
    Abstract
    Finding fast and reliable ways to detect pathogenic bacteria is crucial for addressing serious public health issues in clinical, environmental, and food settings. Here, we present a novel assay based on the conversion of an electrochemical signal into a more convenient optical readout for the visual detection of Escherichia coli. Electropolymerizing polyaniline (PANI) on an indium tin oxide screen-printed electrode (ITO SPE), we achieved not only the desired electrochromic behavior but also a convenient way to modify the electrode surface with antibodies (taking advantage of the many amine groups of PANI). Applying a constant potential to the PANI-modified ITO SPE induces a change in their... 

    Machine Learning Approaches for the Prediction of Pathogenicity in Genome Variations

    , M.Sc. Thesis Sharif University of Technology Sahebi, Alireza (Author) ; Sharifi Zarchi, Ali (Supervisor) ; Asgari, Ehsannedin (Supervisor)
    Abstract
    Genome mutations whose effects are not specified pose one of the challenges in identifying genetic diseases. Utilizing wet lab tests to detect the pathogenicity of variants can be time-consuming and fiscally expensive. A rapid and cost-effective solution to this problem is the use of machine learning-based variant effect predictors, which have the ability to determine whether a mutation is pathogenic or not. The objective of this research is to predict the pathogenicity of genome variations. The proposed model exclusively utilizes the protein sequence as its input feature and does not have access to other protein features. The data used to construct the model comprises mutations with... 

    Molecular machinery responsible for graphene oxide's distinct inhibitory effects toward pseudomonas aeruginosa and staphylococcus aureus pathogens

    , Article ACS Applied Bio Materials ; Volume 4, Issue 1 , 2021 , Pages 660-668 ; 25766422 (ISSN) Ashari Astani, N ; Najafi, F ; Maghsoumi, A ; Huma, K ; Azimi, L ; Karimi, A ; Ejtehadi, M. R ; Gumbart, J. C ; Naseri, N ; Sharif University of Technology
    American Chemical Society  2021
    Abstract
    Graphene oxide flakes are considered as potential inhibitors for different pathogenic bacteria. However, the efficacy of inhibition changes for different types and strains of bacteria. In this work, we examine Pseudomonas aeruginosa and Staphylococcus aureus, two common hospital-acquired infections, which react quite differently to graphene oxide flakes. The minimum inhibitory tests yield two distinct outcomes: stopped proliferation for S. aureus versus almost no effect for P. aeruginosa. Integrating our experimental evidence with molecular dynamics simulations, we elucidate the molecular machinery involved, explaining the behavior we see in scanning electron microscopy images. According to... 

    Design, Construction and Application of Nanostructured Electrochemical Biosensor Based on Aptamers for Diagnosis Some of the Pathogenic Bacteria

    , Ph.D. Dissertation Sharif University of Technology Ranjbar, Saba (Author) ; Shahrokhian, Saeed (Supervisor)
    Abstract
    Since that pathogenic bacteria have a predominant role in different aspects of human life such as clinical analysis and spread of contagious disease, food quality control and monitoring of environmental microbial infections, the aim of these studies is design and construction of electrochemical and electro-optical biosensors based on nanomaterials employing specific aptamer and antibody for detection of different bacteria in various real samples. An impedimetric biosensor based on nanoporous gold (NPG) was presented in the first part of the thesis for detection of Salmonella typhimurium as one of the main food- borne pathogenic bacterium. Three-dimensional structure of NPG was synthesized... 

    Fabrication and Enhancement of an Antibacterial Chitosancoated Allantoin-Loaded Skin Wound Dressing for Clinic Use

    , M.Sc. Thesis Sharif University of Technology Haki Zahi Margouk, Mohamamd (Author) ; Shamloo, Amir (Supervisor) ; Akbari, Javad (Supervisor)
    Abstract
    Skin as the largest organ of the body is constructed of three distinctive layers referred to as epidermis, dermis, and hypodermis. Epidermis is the outermost layer of the skin and acts as body’s first barrier against infectious agents and contains mostly sweat glands. Dermis is the mid-layer of the skin which makes up to 70% of the skin and plays a significant role in maintaining body’s metabolism and is home to a huge part of skin’s vascular network, nerve cells and hair follicles. Hypodermis on other hand, is the deepest layer of the skin and mainly acts as a bonding layer between upper skin layers and the soft tissue underneath. Although skin is proved to have a profound ability to... 

    Bacterial components as naturally inspired nano-carriers for drug/gene delivery and immunization: set the bugs to work?

    , Article Biotechnology Advances ; Volume 36, Issue 4 , 2018 , Pages 968-985 ; 07349750 (ISSN) Farjadian, F ; Moghoofei, M ; Mirkiani, S ; Ghasemi, A ; Rabiee, N ; Hadifar, S ; Beyzavi, A ; Karimi, M ; Hamblin, M. R ; Sharif University of Technology
    Elsevier Inc  2018
    Abstract
    Drug delivery is a rapidly growing area of research motivated by the nanotechnology revolution, the ideal of personalized medicine, and the desire to reduce the side effects of toxic anti-cancer drugs. Amongst a bewildering array of different nanostructures and nanocarriers, those examples that are fundamentally bio-inspired and derived from natural sources are particularly preferred. Delivery of vaccines is also an active area of research in this field. Bacterial cells and their components that have been used for drug delivery, include the crystalline cell-surface layer known as “S-layer” bacterial ghosts, bacterial outer membrane vesicles, and bacterial products or derivatives (e.g.... 

    Improving the performance of a photonic PCR system using TiO2 nanoparticles

    , Article Journal of Industrial and Engineering Chemistry ; 2020 Amadeh, A ; Ghazimirsaeed, E ; Shamloo, A ; Dizani, M ; Sharif University of Technology
    Korean Society of Industrial Engineering Chemistry  2020
    Abstract
    Nucleic acid amplification using polymerase chain reaction (PCR) method has been widely used in different fields such as agricultural science, medicine, pathogen identification, and forensics to name a few. Today, it seems inevitable to have a robust, simple PCR system for diagnostics at the point-of-care (POC) level. Many photonic PCR systems have been proposed in the literature that benefit from plasmonic photothermal heating to achieve the common PCR thermal cycling. However, non-homogeneous temperature distribution is a challenge in some of them. In the present work, to achieve more efficient gene amplification, the effect of adding TiO2 nanoparticles has been investigated in a photonic... 

    Optimization and characterization of tannic acid loaded niosomes for enhanced antibacterial and anti-biofilm activities

    , Article Advanced Powder Technology ; 2020 Heidari, F ; Akbarzadeh, I ; Nourouzian, D ; Mirzaie, A ; Bakhshandeh, H ; Sharif University of Technology
    Elsevier B.V  2020
    Abstract
    The purpose of this study was to prepare and characterize an optimized system of tannic acid-loaded niosomes as a potential carrier for antibacterial and anti-biofilm delivery. The niosomal formulation was optimized using response surface methodology (RSM). The effects of the molar ratio of surfactant to cholesterol, drug concentration, and molar ratio of Span 60 to Tween 60 on particle size and drug entrapment efficiency of the niosomal nanocarrier were studied. The optimized nanoparticles were characterized in terms of the morphology, in vitro release profile, and antibacterial properties. Moreover, Fourier-transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC)... 

    Improving the performance of a photonic PCR system using TiO2 nanoparticles

    , Article Journal of Industrial and Engineering Chemistry ; Volume 94 , 2021 , Pages 195-204 ; 1226086X (ISSN) Amadeh, A ; Ghazimirsaeed, E ; Shamloo, A ; Dizani, M ; Sharif University of Technology
    Korean Society of Industrial Engineering Chemistry  2021
    Abstract
    Nucleic acid amplification using polymerase chain reaction (PCR) method has been widely used in different fields such as agricultural science, medicine, pathogen identification, and forensics to name a few. Today, it seems inevitable to have a robust, simple PCR system for diagnostics at the point-of-care (POC) level. Many photonic PCR systems have been proposed in the literature that benefit from plasmonic photothermal heating to achieve the common PCR thermal cycling. However, non-homogeneous temperature distribution is a challenge in some of them. In the present work, to achieve more efficient gene amplification, the effect of adding TiO2 nanoparticles has been investigated in a photonic... 

    Metal-organic frameworks (MOF) based heat transfer: A comprehensive review

    , Article Chemical Engineering Journal ; Volume 449 , 2022 ; 13858947 (ISSN) Moayed Mohseni, M ; Jouyandeh, M ; Mohammad Sajadi, S ; Hejna, A ; Habibzadeh, S ; Mohaddespour, A ; Rabiee, N ; Daneshgar, H ; Akhavan, O ; Asadnia, M ; Rabiee, M ; Ramakrishna, S ; Luque, R ; Reza Saeb, M ; Sharif University of Technology
    Elsevier B.V  2022
    Abstract
    Higher than a standard level, the humidity provides a suitable environment for the pathogenic microorganisms to grow and increases energy consumption for cooling, increasing greenhouse gas emissions. Desiccant air-conditioning (DAC) is an effective method to reduce humidity and energy simultaneously. Conventional desiccants are not suitable for use as a desiccant in building air conditioners, mainly because of high regeneration temperature and other issues such as limited equilibrium capacity and hydrothermal and cyclic instability. Metal-organic frameworks (MOFs) are a novel class of porous crystalline materials without the disadvantages of traditional desiccants. They benefit from a huge... 

    Detection and a possible link between parvovirus B19 and thyroid cancer

    , Article Tumor Biology ; Volume 39, Issue 6 , 2017 ; 10104283 (ISSN) Etemadi, A ; Mostafaei, S ; Yari, K ; Ghasemi, A ; Chenar, H. M ; Moghoofei, M ; Sharif University of Technology
    Abstract
    Human parvovirus B19 (B19) is a small, non-enveloped virus and belongs to Parvoviridae family. B19 persists in many tissues such as thyroid tissue and even thyroid cancer. The main aim of this study was to determine the presence of B19, its association with increased inflammation in thyroid tissue, and thus its possible role in thyroid cancer progression. Studies have shown that virus replication in non-permissive tissue leads to overexpression of non-structural protein and results in upregulation of proinflammatory cytokines such as interleukin 6 and tumor necrosis factor alpha. A total of 36 paraffin-embedded thyroid specimens and serum were collected from patients and 12 samples were used... 

    Design of an effective piezoelectric microcantilever biosensor for rapid detection of COVID-19

    , Article Journal of Medical Engineering and Technology ; Volume 45, Issue 6 , 2021 , Pages 423-433 ; 03091902 (ISSN) Kabir, H ; Merati, M ; Abdekhodaie, M. J ; Sharif University of Technology
    Taylor and Francis Ltd  2021
    Abstract
    Acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also called COVID-19, is one of the most contagious viruses resulting in a progressive pandemic. Since specific antiviral treatments have not been developed yet and its fatal rate is almost high, early and fast detection is critical for controlling the outbreak. In this study, a piezoelectric microcantilever biosensor has been designed for detecting COVID-19 samples directly without requiring preparation steps. The biosensor acts as a transducer and is coated with the related antibody. When the SARS-CoV-2 antigens adsorbed on the microcantilever top surface through their spike proteins, a surface stress due to the mass change would be...