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An ultrasensitive label free human papilloma virus DNA biosensor using gold nanotubes based on nanoporous polycarbonate in electrical alignment
, Article Analytica Chimica Acta ; Volume 1048 , 2019 , Pages 31-41 ; 00032670 (ISSN) ; Ghorbani, M ; Sasanpour, P ; Karimizefreh, A ; Sharif University of Technology
Elsevier B.V
2019
Abstract
An impedimetric human papilloma virus (HPV) DNA biosensor based on gold nanotubes (AuNTs) in label free detection was materialized. The AuNTs decorated nanoporous polycarbonate (AuNTs-PC) template as biosensor electrode was fabricated by electrodeposition method. The single strand DNA (ss-DNA) probe was covalently immobilized onto the AuNTs-PC electrode. The hybridization of target sequences with the ss-DNA probe was observed by the electrochemical impedance spectroscopy (EIS). The biosensor showed high selectivity and could differentiate between the complementary, mismatch and non-complementary DNA sequences. The EIS measurements were matched to Randle's equivalent circuit. The...
The use of ladder particle swarm optimisation for quantitative structure-activity relationship analysis of human immunodeficiency virus-1 integrase inhibitors
, Article Molecular Simulation ; Volume 37, Issue 15 , 2011 , Pages 1221-1233 ; 08927022 (ISSN) ; Ebrahimi-Najafabadi, H ; Sharif University of Technology
2011
Abstract
This contribution focuses on the use of ladder particle swarm optimisation (LPSO) on modelling of oxadiazole- and triazolesubstituted naphthyridines as human immunodeficiency virus-1 integrase inhibitors. Artificial neural network (ANN) and Monte Carlo cross-validation techniques were combined with LPSO to develop a quantitative structure-activity relationship model. The techniques of LPSO, ANN and sample set partitioning based on joint x-y distances were applied as feature selection, mapping and model evaluation, respectively. The variables selected by LPSO were used as inputs of Bayesian regularisation ANN. The statistical parameters of correlation of deterministic, R2, and...
Structure of DNA Confined in Nano-Environment
, M.Sc. Thesis Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor)
Abstract
Ejtehadi, M. R. (Mohammad Reza)All cells store their hereditary information in the same linear chemical code, DNA molecule. These information organize all activities of the cell. Therefore, studying various properties of DNA is a big step toward understanding life. Physicists are interested in elastic properties of DNA molecule. DNA is somehow a chain of successive atoms that have been arranged in a helical ladder shape. DNA is a stiff polymer so one has to use a large amount of energy to bend it. Interestingly, in most of the natural cases, DNA is highly packed into spaces that are much smaller that its total length. Cell’s nucleus and viral capsids are some examples. Virus maybe the...
Discontinuous Galerkin Methods for Simulating Bioreactive Transport of Viruses in Porous Media
, M.Sc. Thesis Sharif University of Technology ; Razvan, Mohammad Reza (Supervisor)
Abstract
Primal discontinuous Galerkin (DG) methods are formulated to solve the transport equations for modeling migration and survival of viruses with kinetic and equilibrium adsorption in porous media. An entropy analysis is conducted to show that DG schemes are numerically stable and that the free energy of a DG approximation decreases with time in a manner similar to the exact solution. Combining results for free and attached virus concentrations, we establish optimal a priori error estimates for the coupled partial and ordinary differential equations of virus transport
Csr Effect on Customer Loyalty during a Pandemic: a Case Study of Mobile-Phone Operator Companies in Iran
, M.Sc. Thesis Sharif University of Technology ; Kiamehr, Mehdi (Supervisor)
Abstract
Customer loyalty plays one of the most vital roles in business profitability. This concept gives special prominence to attaining new customers, which is by far less costly than attracting new ones. Therefore, investigating the impact of factors affecting customer retention is of precise significance. In the respect, corporate social responsibility, as an imperative factor impacting customer loyalty, gained more attention by various companies in the last decades.Over the past few months, the world has encountered the hazard of the Coronavirus pandemic. Most aspects of daily life in different parts of the globe have been affected by this disease. Companies are no exception. The coronavirus has...
Quantification of in Vitro Drug Effects on COVID-19 through Analysis of Cellular Morphological Features
, M.Sc. Thesis Sharif University of Technology ; Rohban, Mohammad Hossein (Supervisor) ; Sharifi Zarchi, Ali (Supervisor)
Abstract
The epidemic of Covid 19 has killed millions of people worldwide. Despite the efforts of scientists around the world, there is still no cure for this disease. Approval of newly designed drugs due to clinical trial periods is time-consuming and costly. For this reason, in the current emergency situation, it is important to have a solution for screening available approved drugs in order to find effective substances for this disease.High-throughput assays are a good option for such problems. In this field of research, image-based high-throughput assays are amongst the most effective and cost-effective methods that help quantify the response of treated cells by measuring cell...
A new immunization algorithm based on spectral properties for complex networks
, Article 2015 7th Conference on Information and Knowledge Technology, IKT 2015, 26 May 2015 through 28 May 2015 ; May , 2015 , Page(s): 1 - 5 ; 9781467374859 (ISBN) ; Khansari, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2015
Abstract
Nowadays, we are facing epidemic spreading in many different areas; examples are infection propagation, rumor spreading and computer viruses in computer networks. Finding a strategy to control and mitigate the spread of these epidemics is gaining much interest in recent researches. Due to limitation of immunization resources, it is important to establish a strategy for selecting nodes which has the most effect in mitigating epidemics. In this paper, we propose a new algorithm that minimizes the worst expected growth of an epidemic by reducing the size of the largest connected component of the underlying contact network. The proposed algorithm is applicable to any level of available resources...
Prevalence of hepatitis e infection in the general population of Iran: a systematic review and meta-analysis
, Article Future Virology ; Volume 12, Issue 4 , 2017 , Pages 227-236 ; 17460794 (ISSN) ; Sedighi, M ; Mostafaei, S ; Miri, A ; Amiri, H ; Abiri, R ; Babaei, F ; Kabir, K ; Moghoofei, M ; Sharif University of Technology
Abstract
Aim: Hepatitis E is a form of acute viral hepatitis, which is caused by hepatitis E virus (HEV). The study objective was to evaluate the prevalence of HEV to provide an overall relative frequency in Iran. Methods: In this study, databases such as PubMed and Scopus were searched using the following keywords according to MeSH, "Hepatitis E virus", "Epidemiology", "Enzyme-linked immunosorbent assay (ELISA)" and "Iran". Then studies which had reported prevalence of HEV were selected. Results: We selected 36 researches out of 9246 for our study. From all the samples, the pooled estimated prevalence of HEV positive was 9.7%. It should be noted that HEV infection's relative frequency varied from...
Adaptive control strategy for treatment of hepatitis C infection
, Article Industrial and Engineering Chemistry Research ; Volume 58, Issue 33 , 2019 , Pages 15262-15270 ; 08885885 (ISSN) ; Shahrokhi, M ; Sharif University of Technology
American Chemical Society
2019
Abstract
In this work, an efficient treatment strategy for hepatitis C disease using interferon (IFN) has been proposed on the basis of the back-stepping control technique. The basic model of the hepatitis C virus (HCV) has been considered for controller design. To tackle the problem of model parameter variations, the adaptive version of the back-stepping method has been utilized. For applying the proposed treatment, all states should be available while only the viral load is measured. To solve this problem, a nonlinear Luenberger-like observer has been designed to estimate the unmeasured states. In the proposed treatment, limitation of the drug efficacy has been taken into account. Asymptotical...
Graph traversal edit distance and extensions
, Article Journal of Computational Biology ; Volume 27, Issue 3 , 2020 , Pages 317-329 ; Shrestha, A ; Sharifi Zarchi, A ; Gallagher, S. R ; Sahinalp, S. C ; Chitsaz, H ; Sharif University of Technology
Mary Ann Liebert Inc
2020
Abstract
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 article, 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 GTED is the minimum edit distance between two strings formed by the edge labels of respective Eulerian traversals of the two graphs....
Synergy between hemagglutinin 2 (HA2) subunit of influenza fusogenic membrane glycoprotein and oncolytic Newcastle disease virus suppressed tumor growth and further enhanced by Immune checkpoint PD-1 blockade
, Article Cancer Cell International ; Volume 20, Issue 1 , August , 2020 ; Ebrahimzadeh, M. S ; Abdolalipour, E ; Yazdi, M ; Hosseini Ravandi, H ; Ghaemi, A ; Sharif University of Technology
BioMed Central Ltd
2020
Abstract
Background: Newcastle disease virus (NDV) has shown noticeable oncolytic properties, especially against cervical cancer. However, in order to improve the spread rate and oncotoxicity of the virus, employment of other therapeutic reagents would be helpful. It has been shown that some viral fusogenic membrane glycoproteins (FMGs) could facilitate viral propagation and increase the infection rate of tumor cells by oncolytic viruses. Additionally, immune checkpoint blockade has widely been investigated for its anti-tumor effects against several types of cancers. Here, we investigated for the first time whether the incorporation of influenza hemagglutinin-2 (HA2) FMG could improve the oncolytic...
Carbosilane dendrimers: Drug and gene delivery applications
, Article Journal of Drug Delivery Science and Technology ; Volume 59 , 2020 ; Ahmadvand, S ; Ahmadi, S ; Fatahi, Y ; Dinarvand, R ; Bagherzadeh, M ; Rabiee, M ; Tahriri, M ; Tayebi, L ; Hamblin, M. R ; Sharif University of Technology
Editions de Sante
2020
Abstract
Carbosilane dendrimers are a particular type of dendrimer structure that has been used as delivery vehicles for drugs and nucleic acids. They have a defined structure according to their generation number, and their terminal groups can be rendered cationic or anionic. The cationic charges can address the limitation of electrostatic repulsion between the negatively charged phosphate groups of nucleic acids and negatively charged cell membranes. Specific drugs can be loaded into the central part of the dendrimer or attached at the exterior, and the overall positive charge may improve the efficacy of anti-inflammatory drugs. One promising feature of dendrimers is their non-toxicity both in vitro...
Capturing an intruder in the pyramid
, Article 1st International Computer Science Symposium in Russia, CSR 2006, St. Petersburg, 8 June 2006 through 12 June 2006 ; Volume 3967 LNCS , 2006 , Pages 580-590 ; 03029743 (ISSN) ; Imani, N ; Sarbazi Azad, H ; Sharif University of Technology
Springer Verlag
2006
Abstract
In this paper, we envision a solution for the problem of capturing an intruder in one of the most popular interconnection topologies, namely the pyramid. A set of agents collaborate to capture a hostile intruder in the network. While the agents can move in the network one hop at a time, the intruder is assumed to be arbitrarily fast, i.e. it can traverse any number of nodes contiguously as far as there are no agents in those nodes. Here we consider a new version of the problem where each agent can replicate new agents when needed, i.e. the algorithm starts with a single agent and new agents are created on demand. In particular, we propose two different algorithms on the pyramid network and...
Mathematical Models of the Interrelated Dynamics of Hepatitis D and B
, M.Sc. Thesis Sharif University of Technology ; Hesaraki, Mahmoud (Supervisor)
Abstract
The hepatitis delta virus (HDV) is a rarest form of viral hepatitis, but has the worst outcomes for patients.It is a subviral satellite dependent on coinfection with hepatitis B (HBV) to replicate within the host liver.To date, there has been little to no modeling effort for HDV. Deriving and analyzing such a mathematicalmodel poses difficulty as it requires the inclusion of (HBV). Here we begin with a well-studied HBV modelfrom the literature and expand it to incorporate HDV. We investigate two models, one with and one withoutinfected hepatocyte replication. Additionally, we consider treatment by the drug lamivudine. Comparison of model simulations with experimental results of lamivudine...
Multiway investigation of interaction between fluorescence labeled DNA strands and unmodified gold nanoparticles
, Article Analytical Chemistry ; Volume 84, Issue 15 , July , 2012 , Pages 6603-6610 ; 00032700 (ISSN) ; Kompany Zareh, M ; Hormozi Nezhad, M. R ; Sharif University of Technology
ACS
2012
Abstract
The single stranded DNA can be adsorbed on the negatively charged surface of gold nanoparticles (AuNPs), but the rigid structure of double stranded DNA prevents it from adsorption. Signal of a tagged single stranded DNA will be quenched by the plasmon effect of the AuNP surface after its adsorption. This phenomenon has been used to study the DNA hybridization and interactions of two complementary 21mer oligonucleotides each tagged with a different fluorescent dye in the presence of 13 nm gold nanoparticles. The DNA strands used in this study belong to the genome of HIV. The obtained rank deficient three-way fluorescence data sets were resolved by both PARAFAC and restricted Tucker3 models....
Stable regions in the parameter space of delays for LTI fractional-order systems with two delays
, Article Signal Processing ; Volume 107 , February , 2015 , Pages 415-424 ; 01651684 (ISSN) ; Haeri, M ; Sharif University of Technology
Elsevier
2015
Abstract
This paper studies fractional-order systems of retarded type with two independent delays, and determines the stability regions in spaces of delays. In this approach, an auxiliary polynomial is employed to calculate all purely imaginary roots of the characteristic equation of the system on the imaginary axis. Since roots of the characteristic equation are continuous with respect to delays, these purely imaginary roots determine the stability regions in delay space. Also, the necessary and sufficient condition for stability independent of delays is developed for the systems. Furthermore, a simple inequality constraint is established to obtain pure imaginary poles of the scalar systems....
The immunomodulatory effects of probiotics on respiratory viral infections: A hint for COVID-19 treatment?
, Article Microbial Pathogenesis ; Volume 148 , November , 2020 ; Miri, S. M ; Abdolalipour, E ; Ghaemi, A ; Sharif University of Technology
Academic Press
2020
Abstract
Respiratory virus infections are among the most prevalent diseases in humans and contribute to morbidity and mortality in all age groups. Moreover, since they can evolve fast and cross the species barrier, some of these viruses, such as influenza A and coronaviruses, have sometimes caused epidemics or pandemics and were associated with more serious clinical diseases and even mortality. The recently identified Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a Public Health Emergency of International concern and has been associated with rapidly progressive pneumonia. To ensure protection against emerging respiratory tract...
Neural networks in analytical chemistry
, Article Methods in Molecular Biology ; Volume 458 , 2008 , Pages 81-121 ; 10643745 (ISSN); 9781588297181 (ISBN) ; Sharif University of Technology
2008
Abstract
This chapter covers a part of the spectrum of neural-network uses in analytical chemistry. Different architectures of neural networks are described briefly. The chapter focuses on the development of three-layer artificial neural network for modeling the anti-HIV activity of the HETP derivatives and activity parameters (pIC 50) of heparanase inhibitors. The use of a genetic algorithm-kernel partial least squares algorithm combined with an artificial neural network (GA-KPLS-ANN) is described for predicting the activities of a series of aromatic sulfonamides. The retention behavior of terpenes and volatile organic compounds and predicting the response surface of different detection systems are...
Serological assays and host antibody detection in coronavirus-related disease diagnosis
, Article Archives of Virology ; Volume 166, Issue 3 , 2021 , Pages 715-731 ; 03048608 (ISSN) ; Shabani, E ; Abdekhodaie, M. J ; Sharif University of Technology
Springer
2021
Abstract
Coronaviruses (CoV) are a family of viral pathogens that infect both birds and mammals, including humans. Seven human coronaviruses (HCoV) have been recognized so far. HCoV-229E, -OC43, -NL63, and -HKU1 account for one-third of common colds with mild symptoms. The other three members are severe acute respiratory syndrome (SARS)-CoV, Middle East respiratory syndrome (MERS)-CoV, and SARS-CoV-2. These viruses are responsible for SARS, MERS, and CoV disease 2019 (COVID-19), respectively. A variety of diagnostic techniques, including chest X-rays, computer tomography (CT) scans, analysis of viral nucleic acids, proteins, or whole virions, and host antibody detection using serological assays have...
Continuous submicron particle separation Via Vortex-Enhanced ionic concentration polarization: a numerical investigation
, Article Micromachines ; Volume 13, Issue 12 , 2022 ; 2072666X (ISSN) ; Amiri, H.A ; Collins, D.J ; Miansari, M ; Sharif University of Technology
MDPI
2022
Abstract
Separation and isolation of suspended submicron particles is fundamental to a wide range of applications, including desalination, chemical processing, and medical diagnostics. Ion concentration polarization (ICP), an electrokinetic phenomenon in micro-nano interfaces, has gained attention due to its unique ability to manipulate molecules or particles in suspension and solution. Less well understood, though, is the ability of this phenomenon to generate circulatory fluid flow, and how this enables and enhances continuous particle capture. Here, we perform a comprehensive study of a low-voltage ICP, demonstrating a new electrokinetic method for extracting submicron particles via flow-enhanced...