Sharif Digital Repository

Analysis of cancer mutational signatures have been instrumental in identification of responsible endogenous and exogenous molecular processes in cancer. The quantitative approach used to deconvolute mutational signatures is becoming an integral part of cancer research. Therefore, development of a stand-alone tool with a user-friendly interface for analysis of cancer mutational signatures is necessary. In this manuscript we introduce CANCERSIGN, which enables users to identify 3-mer and 5-mer mutational signatures within whole genome, whole exome or pooled samples. Additionally, this tool enables users to perform clustering on tumor samples based on the proportion of mutational signatures in... 

The main goal of this study is to lay out the map of the soil radionuclide activity concentrations and the terrestrial outdoor gamma dose rates in the western Mazandaran Province of Iran, and to present an evaluation scheme. Mazandaran Province was selected due to its special geographical characteristics, high population density and the long terrestrial and aquatic borders with the neighbouring countries possessing nuclear facilities. A total of 54 topsoil samples were collected, ranging from the Nour to Ramsar regions, and were based on geological conditions, vegetation coverage and the sampling standards outlined by the International Atomic Energy Agency. The excess lifetime cancer risks... 

Despite the great potential of carbon nanotubes (CNTs) in various areas of biomedicine, concerns regarding their carcinogenicity, inefficient dispersion in aqueous solutions and biological activity in vivo still remain. One important and feasible route to overcome these barriers is modification of CNTs with polymers, which are widely studied and play a vital role in biological and biomedical fields, especially in drug delivery. This comprehensive review focuses on the achievements of our and other groups in currently used methods to functionalize the surface of CNTs with polymers to produce anticancer drug delivery systems. We have intensively studied covalent and noncovalent interactions... 

Various methods, such as those developed by the Medical Internal Radiation Dosimetry (MIRD) Committee of the Society of Nuclear Medicine or employing dose point kernels, have been applied to the radiation dosimetry of 131I radionuclide therapy. However, studies have not shown a strong relationship between tumour absorbed dose and its overall therapeutic response, probably due in part to inaccuracies in activity and dose estimation. In the current study, the GATE Monte Carlo computer code was used to facilitate voxel-level radiation dosimetry for organ activities measured in an . 131I-treated thyroid cancer patient. This approach allows incorporation of the size, shape and composition of... 

Nanoparticles of high-Z elements exhibit stronger photoelectric effects than soft tissues under gamma irradiation. Hence, they can be used as effective radiosensitizers for increasing the efficiency of current radiotherapy. In this work, superparamagnetic zinc ferrite spinel (ZnFe2O4) nanoparticles were synthesized by a hydrothermal reaction method and used as radiosensitizers in cancer therapy. The magnetic nanoparticles showed fast separation from solutions (e.g., ~ 1 min for 2 mg mL- 1 of the nanoparticles in ethanol) by applying an external magnetic field (~ 1 T). The ZnFe2O4 nanoparticles were applied in an in vitro radiotherapy of lymph node carcinoma of prostate cells (as high... 

Carbon-based quantum dots (CQDs) are a newly developed class of carbon nano-materials that have attracted much interest and attention as promising competitors to already available semiconductor quantum dots owing to their un-comparable and unique properties. In addition, controllability of CQDs unique physiochemical properties is as a result of their surface passivation and functionalization. This is an update article (between 2013 and 2016) on the recent progress, characteristics and synthesis methods of CQDs and different advantages in varieties of applications. © 2017 Elsevier Masson SAS  

This article presents the thorough design procedure, specifications, and performance of a mobile social robot friend Arash for educational and therapeutic involvement of children with cancer based on their interests and needs. Our research focuses on employing Arash in a pediatric hospital environment to entertain, assist, and educate children with cancer who suffer from physical pain caused by both the disease and its treatment process. Since cancer treatment causes emotional distress, which can reduce the efficiency of medications, using social robots to interact with children with cancer in a hospital environment could decrease this distress, thereby improving the effectiveness of their... 

In this paper, we propose using mobile nanosensors (MNSs) for early stage anomaly detection. For concreteness, we focus on the detection of cancer cells located in a particular region of a blood vessel. These cancer cells produce and emit special molecules, so-called biomarkers, which are symptomatic for the presence of anomaly, into the cardiovascular system. Detection of cancer biomarkers with conventional blood tests is difficult in the early stages of a cancer due to the very low concentration of the biomarkers in the samples taken. However, close to the cancer cells, the concentration of the cancer biomarkers is high. Hence, detection is possible if a sensor with the ability to detect... 

The search for efficient chemotherapy drugs and other anti-cancer treatments would benefit from a deeper understanding of the tumor microenvironment (TME) and its role in tumor progression. Because in vivo experimental methods are unable to isolate or control individual factors of the TME and in vitro models often do not include all the contributing factors, some questions are best addressed with systems biology mathematical models. In this work, we present a new fully-coupled, agent-based, multi-scale mathematical model of tumor growth, angiogenesis and metabolism that includes important aspects of the TME spanning subcellular-, cellular- and tissue-level scales. The mathematical model is... 

Background: Genetic heterogeneity of a cancer tumor that develops during clonal evolution is one of the reasons for cancer treatment failure, by increasing the chance of drug resistance. Clones are cell populations with different genotypes, resulting from differences in somatic mutations that occur and accumulate during cancer development. An appropriate approach for identifying clones is determining the variant allele frequency of mutations that occurred in the tumor. Although bulk sequencing data can be used to provide that information, the frequencies are not informative enough for identifying different clones with the same prevalence and their evolutionary relationships. On the other... 

Isolation of rare cancer cells is one of the important and valuable stages of cancer research. Regarding the rarity of cancer cells in blood samples, it is important to invent an efficient separation device for cell enrichment. In this study, two centrifugal microfluidic devices were designed and fabricated for the isolation of rare cancer cells. The first design (passive plan) employs a contraction–expansion array (CEA) microchannel which is connected to a bifurcation region. This device is able to isolate the target cells through inertial effects and bifurcation law. The second design (hybrid plan) also utilizes a CEA microchannel, but instead of using the bifurcation region, it is... 

A series of metal-organic frameworks (MOFs) based on aluminum-benzene dicarboxylates (MIL-53, NH2-MIL-53, and NH2-MIL-101) at different ratios have been synthesized, and their adsorption performances for methotrexate (MTX), an anti-cancer drug, have been investigated in terms of adsorption kinetics, isotherms, solution pH, thermodynamics, mechanism, and recyclability. Maximum adsorption values of 374.97, 387.82, and 457.69 mg/g were observed for MIL-53, NH2-MIL-53, and NH2-MIL-101, respectively. Our study shows that adsorption capacity of MTX depends not only on surface area and pore volume but also on the zeta potential and the presence of suitable functional groups. Higher adsorption of... 

A series of metal-organic frameworks (MOFs) based on aluminum-benzene dicarboxylates (MIL-53, NH2-MIL-53, and NH2-MIL-101) at different ratios have been synthesized, and their adsorption performances for methotrexate (MTX), an anti-cancer drug, have been investigated in terms of adsorption kinetics, isotherms, solution pH, thermodynamics, mechanism, and recyclability. Maximum adsorption values of 374.97, 387.82, and 457.69 mg/g were observed for MIL-53, NH2-MIL-53, and NH2-MIL-101, respectively. Our study shows that adsorption capacity of MTX depends not only on surface area and pore volume but also on the zeta potential and the presence of suitable functional groups. Higher adsorption of... 

Background: The abundance of gene expression microarray data has led to the development of machine learning algorithms applicable for tackling disease diagnosis, disease prognosis, and treatment selection problems. However, these algorithms often produce classifiers with weaknesses in terms of accuracy, robustness, and interpretability. This paper introduces fuzzy support vector machine which is a learning algorithm based on combination of fuzzy classifiers and kernel machines for microarray classification.Results: Experimental results on public leukemia, prostate, and colon cancer datasets show that fuzzy support vector machine applied in combination with filter or wrapper feature selection... 

Green tea-reduced graphene oxide (GT-rGO) sheets have been exploited for high efficiency near infrared (NIR) photothermal therapy of HT29 and SW48 colon cancer cells. The biocompatibility of GT-rGO sheets was investigated by means of MTT assays. The polyphenol constituents of GT-rGO act as effective targeting ligands for the attachment of rGO to the surface of cancer cells, as confirmed by the cell granularity test in flow cytometry assays and also by scanning electron microscopy. The photo-thermal destruction of higher metastatic cancer cells (SW48) is found to be more than 20% higher than that of the lower metastatic one (HT29). The photo-destruction efficiency factor of the GT-rGO is... 

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... 

Background: Understanding cancer development crossing several spatial-temporal scales is of great practical significance to better understand and treat cancers. It is difficult to tackle this challenge with pure biological means. Moreover, hybrid modeling techniques have been proposed that combine the advantages of the continuum and the discrete methods to model multiscale problems. Methods: In light of these problems, we have proposed a new hybrid vascular model to facilitate the multiscale modeling and simulation of cancer development with respect to the agent-based, cellular automata and machine learning methods. The purpose of this simulation is to create a dataset that can be used for... 

Reduced graphene oxide nanomesh (rGONM), as one of the recent structures of graphene with a surprisingly strong near-infrared (NIR) absorption, is used for achieving ultraefficient photothermal therapy. First, by using TiO2 nanoparticles, graphene oxide nanoplatelets (GONPs) are transformed into GONMs through photocatalytic degradation. Then rGONMs functionalized by polyethylene glycol (PEG), arginine-glycine-aspartic acid (RGD)-based peptide, and cyanine 7 (Cy7) are utilized for in vivo tumor targeting and fluorescence imaging of human glioblastoma U87MG tumors having ανβ3 integrin receptors, in mouse models. The rGONM-PEG suspension (1 μg mL -1) exhibits about 4.2- and 22.4-fold higher NIR... 

During the drug delivery process in chemotherapy, both of the cancer cells and normal healthy cells may be killed. In this paper, three mathematical cell-kill models including log-kill hypothesis, Norton-Simon hypothesis and Emax hypothesis are considered. Three control approaches including optimal linear regulation, nonlinear optimal control based on variation of extremals and H∞-robust control based on μ-synthesis are developed. An appropriate cost function is defined such that the amount of required drug is minimized while the tumor volume is reduced. For the first time, performance of the system is investigated and compared for three control strategies; applied on three nonlinear models... 

A detailed 3D Monte Carlo simulation of the grid geometrical parameters in screen-film mammography (SFM) and digital mammography (DM) systems has been performed. A combination of IEC 60627:2013 international standard conditions and other more clinically relevant parameters were used for this simulation. Accuracy of our results has been benchmarked with previously published data and good agreement has been obtained. Calculations in a wide range of linear anti-scatter grid geometries have been carried out. The evaluated parameters for the SFM system were the Bucky factor (BF) and contrast improvement factor (CIF) and for the DM system it was signal differenceto- noise ratio improvement factor...