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... 

Introduction: The application of doxorubicin (DOX) in cancer therapy has been limited due to its drug resistance and poor internalization. Graphene oxide (GO) nanostructures have the capacity for DOX delivery while promoting its cytotoxicity in cancer. Areas covered: The favorable characteristics of GO nanocomposites, preparation method, and application in cancer therapy are described. Then, DOX resistance in cancer, GO-mediated photothermal therapy, and DOX delivery for cancer suppression are described. Preparation of stimuli-responsive GO nanocomposites, surface functionalization, hybrid nanoparticles, and theranostic applications are emphasized in DOX chemotherapy. Expert opinion: GO... 

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... 

Tumor microenvironment (TME) is a multi-scale biological environment that can control tumor dynamics with many biomechanical and biochemical factors. Investigating the physiology of TME with a heterogeneous structure and abnormal functions not only can achieve a deeper understanding of tumor behavior but also can help develop more efficient anti-cancer strategies. In this work, we develop a hybrid multi-scale mathematical model of TME to simulate the progression of a three-dimensional tumor and elucidate its response to different chemotherapy approaches. The chemotherapy approaches include multiple low dose (MLD) of anti-cancer drug, maximum tolerated dose (MTD) of anti-cancer drug,... 

In the present study, first, Fe3O4nanoparticles were functionalized using glutaric acid and then composited with CQDs. Doxorubicin (DOX) drug was loaded to evaluate the performance of the nanocomposite for targeted drug delivery applications. The XRD pattern confirmed the presence of characteristic peaks of CQDs and Fe3O4. In the FTIR spectrum, the presence of carboxyl functional groups on Fe3O4/CQDs was observed; DOX (positive charge) is loaded onto Fe3O4/CQDs (negative charge) by electrostatic absorption. FESEM and AFM images showed that the particle sizes of Fe3O4and CQDs were 23-75 and 1-3 nm, respectively. The hysteresis curves showed superparamagnetic properties for Fe3O4and Fe3O4/CQDs... 

Polysaccharides (PSA) have taken specific position among biomaterials for advanced applications in medicine. Nevertheless, poor mechanical properties are known as the main drawback of PSA, which highlights the need for PSA modification. Nanocomposites PSA (NPSA) are a class of biomaterials widely used as biomedical platforms, but despite their importance and worldwide use, they have not been reviewed. Herein, we critically reviewed the application of NPSA by categorizing them into generic and advanced application realms. First, the application of NPSA as drug and gene delivery systems, along with their role in the field as an antibacterial platform and hemostasis agent is discussed. Then,... 

Background: The advent of high throughput sequencing has enabled researchers to systematically evaluate the genetic variations in cancer, identifying many cancer-associated genes. Although cancers in the same tissue are widely categorized in the same group, they demonstrate many differences concerning their mutational profiles. Hence, there is no definitive treatment for most cancer types. This reveals the importance of developing new pipelines to identify cancer-associated genes accurately and re-classify patients with similar mutational profiles. Classification of cancer patients with similar mutational profiles may help discover subtypes of cancer patients who might benefit from specific... 

Central Nervous System (CNS) malignant tumors are a leading cause of death worldwide with a high mortality rate. While numerous strategies have been proposed to treat CNS tumors, the treatment efficacy is still low mainly due to the existence of the Blood–Brain Barrier (BBB). BBB is a natural cellular layer between the circulatory system and brain extracellular fluid, limiting the transfer of drug particles and confining the routine treatment strategies in which drugs are released in the blood. Consequently, direct drug delivery methods have been devised to bypass the BBB. However, the efficiency of these methods is not enough to treat deep and large brain tumors. In the study at hand, the... 

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...