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Conifer: clonal tree inference for tumor heterogeneity with single-cell and bulk sequencing data
, Article BMC Bioinformatics ; Volume 22, Issue 1 , 2021 ; 14712105 (ISSN) ; Goliaei, S ; Foroughmand Araabi, M. H ; Shariatpanahi, P ; Goliaei, B ; Sharif University of Technology
BioMed Central Ltd
2021
Abstract
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...
Conceptual design of a social robot for pediatric hospitals
, Article 4th RSI International Conference on Robotics and Mechatronics, ICRoM 2016, 26 October 2016 through 28 October 2016 ; 2017 , Pages 566-571 ; 9781509032228 (ISBN) ; Alemi, M ; Khamooshi, M ; Amoozandeh, A ; Shariati, A ; Mozafari, B ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2017
Abstract
No-one likes being confined to a hospital bed. Children particularly can feel lonely, bored or frightened in these conditions. Hours feel like days, and they may not be able to fully comprehend why they are there. Among kids hospitalized because of distinct diseases, children with cancer have incomparable status and needs. They experience physical and mental problems caused by cancer and medications. Cancer treatment may cause distress which can lessen the effectiveness of the treatment. Utilizing social robots to interact with children in clinical environments has been verified to both diminish their distress level and enhance the effectiveness of the treatment process. To improve the...
Computer modeling of drug distribution after intravitreal administration
, Article World Academy of Science, Engineering and Technology ; Volume 77 , 2011 , Pages 706-716 ; 2010376X (ISSN) ; Abdekhodaie, M. J ; Cheng, Y. L ; Saadatmand, M ; Sharif University of Technology
2011
Abstract
Intravitreal injection (IVI) is the most common treatment for eye posterior segment diseases such as endopthalmitis, retinitis, age-related macular degeneration, diabetic retinopathy, uveitis, and retinal detachment. Most of the drugs used to treat vitreoretinal diseases, have a narrow concentration range in which they are effective, and may be toxic at higher concentrations. Therefore, it is critical to know the drug distribution within the eye following intravitreal injection. Having knowledge of drug distribution, ophthalmologists can decide on drug injection frequency while minimizing damage to tissues. The goal of this study was to develop a computer model to predict intraocular...
Computer aided decision making for heart disease detection using hybrid neural network-Genetic algorithm
, Article Computer Methods and Programs in Biomedicine ; Volume 141 , 2017 , Pages 19-26 ; 01692607 (ISSN) ; Alizadehsani, R ; Roshanzamir, M ; Moosaei, H ; Yarifard, A. A ; Sharif University of Technology
Elsevier Ireland Ltd
2017
Abstract
Cardiovascular disease is one of the most rampant causes of death around the world and was deemed as a major illness in Middle and Old ages. Coronary artery disease, in particular, is a widespread cardiovascular malady entailing high mortality rates. Angiography is, more often than not, regarded as the best method for the diagnosis of coronary artery disease; on the other hand, it is associated with high costs and major side effects. Much research has, therefore, been conducted using machine learning and data mining so as to seek alternative modalities. Accordingly, we herein propose a highly accurate hybrid method for the diagnosis of coronary artery disease. As a matter of fact, the...
Computational simulation of non-Newtonian blood flow in carotid bifurcation for investigation the various rheological blood models
, Article ASME 2007 International Mechanical Engineering Congress and Exposition, IMECE 2007, 11 November 2007 through 15 November 2007 ; Volume 2 , 2007 , Pages 263-270 ; 0791842967 (ISBN) ; Firoozabadi, B ; Goodarzvand Chegini, A ; ASME ; Sharif University of Technology
American Society of Mechanical Engineers (ASME)
2007
Abstract
One of the leading causes for death after heart diseases and cancer in all over the world is still stroke. Most strokes happen because an artery carrying blood from the heart to the brain is clogged. Most of the time, as with heart attacks, the problem is atherosclerosis, hardening of the arteries, calcified build up of fatty deposits on the vessel wall. The primary troublemaker is the carotid artery, one on each side of the neck, the main thoroughfare for blood to the brain. In this study, the fluid dynamic simulations were done in the carotid bifurcation artery for studying the formation of atherosclerosis, and shear thinning behavior of blood as well as Newtonian comportment was studied....
Comparison of transplantation of bone marrow stromal cells (BMSC) and stem cell mobilization by granulocyte colony stimulating factor after traumatic brain injury in rat
, Article Iranian Biomedical Journal ; Volume 14, Issue 4 , Oct , 2010 , Pages 142-149 ; 1028852X (ISSN) ; Marzban, M ; Mehdizadeh, M ; Joghataei, M. T ; Khoei, S ; Pirhajati Mahabadi, V ; Laribi, B ; Tondar, M ; Moshkforoush, A ; Sharif University of Technology
2010
Abstract
Background: Recent clinical studies of treating traumatic brain injury (TBI) with autologous adult stem cells led us to compare effect of intravenous injection of bone marrow mesenchymal stem cells (BMSC) and bone marrow hematopoietic stem cell mobilization, induced by granulocyte colony stimulating factor (G-CSF), in rats with a cortical compact device. Methods: Forty adult male Wistar rats were injured with controlled cortical impact device and divided randomly into four groups. The treatment groups were injected with 2 × 106 intravenous bone marrow stromal stem cell (n = 10) and also with subcutaneous G-CSF (n = 10) and sham-operation group (n = 10) received PBS and "bromodeoxyuridine...
Comparison of logarithmic, elliptic, and conical helical spiral for isolation of circulating tumor cells based on inertial method
, Article Physics of Fluids ; Volume 34, Issue 9 , 2022 ; 10706631 (ISSN) ; Mozhdehbakhsh Mofrad, Y ; Safari, M ; Naseri, T ; Sharif University of Technology
American Institute of Physics Inc
2022
Abstract
Cancer is one of the most significant causes of death in the world. It has been shown that the role of circulating tumor cells (CTCs) in the early detection of cancer is crucial. Since the number of these cancerous cells in blood is very rare, the inertial microfluidic devices are one of the best candidates for the isolation of CTCs because they result in a high throughput process. Consequently, they can process a large volume of blood in a short time. Despite extensive computational and experimental studies on inertial microfluidic platforms, the impact of the curvature has not been thoroughly investigated during separation. In this paper, the feasibility of isolation of CTCs for...
Comparison of ECG fiducial point extraction methods based on dynamic bayesian network
, Article 2017 25th Iranian Conference on Electrical Engineering, ICEE 2017, 2 May 2017 through 4 May 2017 ; 2017 , Pages 95-100 ; 9781509059638 (ISBN) ; Shamsollahi, M. B ; Jutten, C ; Sharif University of Technology
Abstract
Cardiovascular diseases are one of the major causes of mortality in humans. One way to diagnose heart diseases and abnormalities is processing of cardiac signals such as electrocardiogram (ECG) signal. In many ECG analysis, location of peak, onset and offset of ECG waves must be extracted as a preprocessing step. These points are called ECG fiducial points (FPs) and convey clinically useful information. In this paper, we compare some FP extraction methods including three methods proposed recently by our research team. These methods are based on extended Kalman filter (EKF), hidden Markov model (HMM) and switching Kalman filter (SKF). Results are given for ECG signals of QT database. For all...
Comparison of acidity and metal ion affinity of D-Glucosamine and N-acetyl-D-glucosamine, a DFT study
, Article Journal of Molecular Graphics and Modelling ; Volume 98 , April , 2020 ; Fattahi, A ; Sharif University of Technology
Elsevier Inc
2020
Abstract
The derivatives of glucose such as glucosamine (β-D-GlcN) and N-acetyl-D-β-glucosamine (GlcNAc) are significant in several biological systems. D-GlcN has been used widely to treat osteoarthritis in humans and animal models as well as GlcNAc has been proposed as a treatment for autoimmune diseases. The DFT/B3LYP/6–311++G (d,p) method as well as QTAIM and NBO analyses were used to the acidity values of D-GlcN and GlcNAc sugars and their complexes with alkali ions in the gas phase. The Li+, Na+ and K+ prefer bi-dentate chelate in these complexes. The computed results indicate that metal ion affinity (MIA) in GlcNAc is higher than that in D-GlcN. There are direct correlations between the MIA...
Comments regarding: Pereira SA, Lopez M, Lavado N, Abreu JM, Silva H. A clinical risk prediction model of orthodontic-induced external apical root resorption. Revista Portuguesa de Estomatologia, Medicina Dentária e Cirurgia Maxilofacial 2014;55(2):66-72
, Article Revista Portuguesa de Estomatologia, Medicina Dentaria e Cirurgia Maxilofacial ; Volume 56, Issue 3 , 2015 , Pages 141-142 ; 16462890 (ISSN) ; Sharif University of Technology
Elsevier Doyma
2015
Clinical validation of a smartphone-based handheld ECG device: A validation study
, Article Critical Pathways in Cardiology ; Volume 21, Issue 4 , 2022 , Pages 165-171 ; 1535282X (ISSN) ; Gharebaghi, M ; Kamalian, E ; Hajghassem, H ; Ghanbari, A ; Karimi, A ; Mansoury, B ; Dayari, M. S ; Khatmi Nemati, M ; Karimi, A ; Zarghami, M. H ; Vasheghani Farahani, A ; Sharif University of Technology
Lippincott Williams and Wilkins
2022
Abstract
Background: Remote cardiac monitoring and screening have already become an integral telemedicine component. The wide usage of several different wireless electrocardiography (ECG) devices warrants a validation study on their accuracy and reliability. Methods: Totally, 300 inpatients with the Nabz Hooshmand-1 handheld ECG device and the GE MAC 1200 ECG system (as the reference) were studied to check the accuracy of the devices in 1 and 6-limb lead performance. Simultaneous 10-second resting ECGs were assessed for the most common ECG parameters in lead I. Afterward, 6-lead ECGs (limb leads), were performed immediately and studied for their morphologies. Results: Of the 300 patients, 297 had...
Classification of vascular function in upper limb using bilateral photoplethysmographic signals
, Article Physiological Measurement ; Volume 29, Issue 3 , 2008 , Pages 365-374 ; 09673334 (ISSN) ; Zahedi, E ; Jajai, H. M ; Sharif University of Technology
2008
Abstract
Bilateral PPG signals have been used for comparative study of two groups of healthy (free from any cardiovascular risk factors) and diabetic (as cardiovascular disease risk group) subjects in the age-matched range 40-50 years. The peripheral blood pulsations were recorded simultaneously from right and left index fingers for 90 s. Pulses have been modeled with the ARX440 model in the interval of 300 sample points with 100 sample points overlap between segments. Model parameters of three segments based on the highest fitness (higher than 80%) of modeled segments were retained for each subject. Subsequently, principal component analysis (PCA) was applied to the parameters of retained segments...
Classification of normal and diseased liver shapes based on spherical harmonics coefficients
, Article Journal of Medical Systems ; Vol. 38, issue. 5 , April , 2014 ; ISSN: 01485598 ; Zoroofi, R. A ; Tehrani-Fard, A. A ; Akhlaghpoor, S ; Sato, Y ; Sharif University of Technology
Abstract
Liver-shape analysis and quantification is still an open research subject. Quantitative assessment of the liver is of clinical importance in various procedures such as diagnosis, treatment planning, and monitoring. Liver-shape classification is of clinical importance for corresponding intra-subject and inter-subject studies. In this research, we propose a novel technique for the liver-shape classification based on Spherical Harmonics (SH) coefficients. The proposed liver-shape classification algorithm consists of the following steps: (a) Preprocessing, including mesh generation and simplification, point-set matching, and surface to template alignment; (b) Liver-shape parameterization,...
Classification of asthma based on nonlinear analysis of breathing pattern
, Article PLoS ONE ; Volume 11, Issue 1 , 2016 ; 19326203 (ISSN) ; Ghafari, T ; Darooei, R ; Nazari, M ; Mahdaviani, S. A ; Eslaminejad, A. R ; Almasnia, M ; Gharibzadeh, S ; Mani, A. R ; Hajizadeh, S ; Sharif University of Technology
Public Library of Science
2016
Abstract
Normal human breathing exhibits complex variability in both respiratory rhythm and volume. Analyzing such nonlinear fluctuations may provide clinically relevant information in patients with complex illnesses such as asthma. We compared the cycle-by-cycle fluctuations of inter-breath interval (IBI) and lung volume (LV) among healthy volunteers and patients with various types of asthma. Continuous respiratory datasets were collected from forty agematched men including 10 healthy volunteers, 10 patients with controlled atopic asthma, 10 patients with uncontrolled atopic asthma, and 10 patients with uncontrolled non-atopic asthma during 60 min spontaneous breathing. Complexity of breathing...
Classification of abnormalities in mammograms by new asymmetric fractal features
, Article Biocybernetics and Biomedical Engineering ; Volume 36, Issue 1 , 2016 , Pages 56-65 ; 02085216 (ISSN) ; Ahmadi Noubari, H ; Fatemizadeh, E ; Khalili, M ; Sharif University of Technology
PWN-Polish Scientific Publishers
2016
Abstract
In this paper we use fractal method for detection and diagnosis of abnormalities in mammograms. We have used 168 images that were carefully selected by a radiologist and their abnormalities were also confirmed by biopsy. These images included asymmetric lesions, architectural distortion, normal tissue and mass lesion where in case of mass lesion they included circumscribed benign, ill-defined and spiculated malignant masses. At first, by using wavelet transform and piecewise linear coefficient mapping, image enhancement were done. Secondly detection of lesions was done by fractal method as a ROI. Since in investigation of breast cancer, it is important that fibroglandular tissues in both...
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning
, Article BMC Bioinformatics ; Volume 23, Issue 1 , 2022 ; 14712105 (ISSN) ; Kashaninia, E ; Mardani, B ; Rabiee, H. R ; Sharif University of Technology
BioMed Central Ltd
2022
Abstract
Background: Several types of RNA in the cell are usually involved in biological processes with multiple functions. Coding RNAs code for proteins while non-coding RNAs regulate gene expression. Some single-strand RNAs can create a circular shape via the back splicing process and convert into a new type called circular RNA (circRNA). circRNAs are among the essential non-coding RNAs in the cell that involve multiple disorders. One of the critical functions of circRNAs is to regulate the expression of other genes through sponging micro RNAs (miRNAs) in diseases. This mechanism, known as the competing endogenous RNA (ceRNA) hypothesis, and additional information obtained from biological datasets...
Chronic subdural hematoma outcome prediction using logistic regression and an artificial neural network
, Article Neurosurgical Review ; Volume 32, Issue 4 , 2009 , Pages 479-484 ; 03445607 (ISSN) ; Rashidi, A ; Zandi Toghani, M ; Behzadi, M ; Asadollahi, M ; Sharif University of Technology
2009
Abstract
Artificial neural networks (ANN) have not been used in chronic subdural hematoma (CSDH) outcome prediction following surgery. We used two methods, namely logistic regression and ANN, to predict using eight variables CSDH outcome as assessed by the Glasgow outcome score (GOS) at discharge. We had 300 patients (213 men and 87 women) and potential predictors were age, sex, midline shift, intracranial air, hematoma density, hematoma thickness, brain atrophy, and Glasgow coma score (GCS). The dataset was randomly divided to three subsets: (1) training set (150 cases), (2) validation set (75 cases), and (3) test set (75 cases). The training and validation sets were combined for regression...
Chemotherapeutic effects of Apigenin in breast cancer: Preclinical evidence and molecular mechanisms; enhanced bioavailability by nanoparticles
, Article Biotechnology Reports ; Volume 34 , 2022 ; 2215017X (ISSN) ; Zahmatkeshan, M ; Akbarzadeh, A ; Rabiee, N ; Ahmadi, S ; Keyhanvar, P ; Rezayat, S. M ; Seifalian, A. M ; Sharif University of Technology
Elsevier B.V
2022
Abstract
This review highlights using nanotechnology in increasing the bioavailability of AP (Apigenin) to enhance its therapeutic efficacy in breast cancer treatment. Breast cancer is one of the most leading causes of cancer death in women both in developed and developing countries. According to several epidemiological and clinical trial studies that indicate progestin-stimulated breast cancer in post-menopausal women; it is necessary to determine compounds to suppress or attenuate the tumor-promoting effects of progestins in breast cells. For this purpose, using the natural anti-progestins, including AP compared with the chemical ones could be significantly effective due to the lack of toxicities...
Chemo-mechanistic multi-scale model of a three-dimensional tumor microenvironment to quantify the chemotherapy response of cancer
, Article Biotechnology and Bioengineering ; Volume 118, Issue 10 , 2021 , Pages 3871-3887 ; 00063592 (ISSN) ; Firoozabadi, B ; Mozafari, A ; Sharif University of Technology
John Wiley and Sons Inc
2021
Abstract
Exploring efficient chemotherapy would benefit from a deeper understanding of the tumor microenvironment (TME) and its role in tumor progression. As in vivo experimental methods are unable to isolate or control individual factors of the TME, and in vitro models often cannot include all the contributing factors, some questions are best addressed with mathematical models of systems biology. In this study, we establish a multi-scale mathematical model of the TME to simulate three-dimensional tumor growth and angiogenesis and then implement the model for an array of chemotherapy approaches to elucidate the effect of TME conditions and drug scheduling on controlling tumor progression. The...
Channelopathy-related SCN10A gene variants predict cerebellar dysfunction in multiple sclerosis
, Article Neurology ; Volume 86, Issue 5 , 2016 , Pages 410-417 ; 00283878 (ISSN) ; Sadaghiani, S ; Park, M. T. M ; Mashhadi, R ; Nazeri, A ; Noshad, S ; Salehi, M. J ; Naghibzadeh, M ; Moghadasi, A. N ; Owji, M ; Doosti, R ; Hashemi Taheri, A. P ; Rad, A. S ; Azimi, A ; Chakravarty, M. M ; Voineskos, A. N ; Nazeri, A ; Sahraian, M. A ; Sharif University of Technology
Lippincott Williams and Wilkins
Abstract
Objective: To determine the motor-behavioral and neural correlates of putative functional common variants in the sodium-channel NaV1.8 encoding gene (SCN10A) in vivo in patients with multiple sclerosis (MS). Methods: We recruited 161 patients with relapsing-onset MS and 94 demographically comparable healthy participants. All patients with MS underwent structural MRI and clinical examinations (Expanded Disability Status Scale [EDSS] and Multiple Sclerosis Functional Composite [MSFC]). Whole-brain voxel-wise and cerebellar volumetry were performed to assess differences in regional brain volumes between genotype groups. Resting-state fMRI was acquired from 62 patients with MS to evaluate...