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Hybrid multiscale modeling and prediction of cancer cell behavior
, Article PLoS ONE ; Volume 12, Issue 8 , 2017 ; 19326203 (ISSN) ; Habibi, J ; Sharif University of Technology
Public Library of Science
2017
Abstract
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...
Unified model of brain tissue microstructure dynamically binds diffusion and osmosis with extracellular space geometry
, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 94, Issue 3 , 2016 ; 15393755 (ISSN) ; Fotouhi, M ; Vejdani, K ; Kamali Zare, P ; Sharif University of Technology
American Physical Society
2016
Abstract
We present a universal model of brain tissue microstructure that dynamically links osmosis and diffusion with geometrical parameters of brain extracellular space (ECS). Our model robustly describes and predicts the nonlinear time dependency of tortuosity (λ=D/D∗) changes with very high precision in various media with uniform and nonuniform osmolarity distribution, as demonstrated by previously published experimental data (D = free diffusion coefficient, D∗ = effective diffusion coefficient). To construct this model, we first developed a multiscale technique for computationally effective modeling of osmolarity in the brain tissue. Osmolarity differences across cell membranes lead to changes...
An implementation of a CBIR system based on SVM learning scheme
, Article Journal of Medical Engineering and Technology ; Volume 37, Issue 1 , 2013 , Pages 43-47 ; 03091902 (ISSN) ; Fatemizadeh, E ; Badie, K ; Sharif University of Technology
2013
Abstract
Content-based image retrieval (CBIR) has been one of the most active areas of research. The retrieval principle of CBIR systems is based on visual features such as colour, texture and shape or the semantic meaning of the images. A CBIR system can be used to locate medical images in large databases. This paper presents a CBIR system for retrieving digital human brain magnetic resonance images (MRI) based on textural features and the support vector machine (SVM) learning method. This system can retrieve similar images from the database in two groups: normal and tumoural. This research uses the knowledge of the CBIR approach to the application of medical decision support and discrimination...
Role of endurance training in preventing pathological hypertrophy via large tumor suppressor (LATS) changes
, Article Iranian Heart Journal ; Volume 20, Issue 3 , 2019 , Pages 52-59 ; 17357306 (ISSN) ; Soori, R ; Choobineh, S ; Gholipour, M ; Sharif University of Technology
Iranian Heart Association
2019
Abstract
Background: One of the negative effects of cardiac sympathetic hyperactivity is pathologic hypertrophy. Recent studies have indicated that large tumor suppressor (LATS) is one of the molecules which play a critical role in cardiomyocyte apoptosis. Considering the preventive role of exercise training, we evaluated the effects of endurance training on LATS gene expression and its upstream pathway in the present study. Methods: Eighteen male Wistar rats were randomly divided into 2 groups: Endurance and control. Endurance training was performed for 8 weeks, 1 hour per day, and 6 days per week on the treadmill at a 15° inclination. Pathologic hypertrophy was induced with the injection of 3...
Generalizability of trunk muscle EMG and spinal forces
, Article IEEE Engineering in Medicine and Biology Magazine ; Volume 20, Issue 6 , 2001 , Pages 72-81 ; 07395175 (ISSN) ; Parnianpour, M ; Sharif University of Technology
2001
Abstract
The generalizability of trunk muscle EMG and spinal loading estimates obtained from an EMG-assisted biomechanical model was assessed over three occasions and three repetitions. The greatest sources of variability consisted of the intersubject differences and the interaction between subject and occasion. The ID (reliability coefficient) was less for trunk muscle activity compared with estimates of anteroposterior shear force, compression force, and gain computed from the biomechanical model. In order to obtain an ID of 0.8, we recommend five testing occasions for submaximal EMG measurements and three testing occasions for biomechanical estimates. Reproducible estimates of maximal trunk...
A foreign body response-on-a-chip platform
, Article Advanced Healthcare Materials ; Volume 8, Issue 4 , 2019 ; 21922640 (ISSN) ; Htwe, S. S ; Righi, M ; Liu, H ; Pietralunga, A ; Yesil Celiktas, O ; Maharjan, S ; Cha, B. H ; Shin, S. R ; Dokmeci, M. R ; Vrana, N. E ; Ghaemmaghami, A. M ; Khademhosseini, A ; Zhang, Y. S ; Sharif University of Technology
Wiley-VCH Verlag
2019
Abstract
Understanding the foreign body response (FBR) and desiging strategies to modulate such a response represent a grand challenge for implant devices and biomaterials. Here, the development of a microfluidic platform is reported, i.e., the FBR-on-a-chip (FBROC) for modeling the cascade of events during immune cell response to implants. The platform models the native implant microenvironment where the implants are interfaced directly with surrounding tissues, as well as vasculature with circulating immune cells. The study demonstrates that the release of cytokines such as monocyte chemoattractant protein 1 (MCP-1) from the extracellular matrix (ECM)-like hydrogels in the bottom tissue chamber...
Personalised deposition maps for micro- and nanoparticles targeting an atherosclerotic plaque: attributions to the receptor-mediated adsorption on the inflamed endothelial cells
, Article Biomechanics and Modeling in Mechanobiology ; Volume 18, Issue 3 , 2019 , Pages 813-828 ; 16177959 (ISSN) ; Forouzandehmehr, M ; Sharif University of Technology
Springer Verlag
2019
Abstract
Endothelial inflammation as a prominent precursor to atherosclerosis elicits a distinct pathological surface expression of particular vascular proteins. To exhibit a site-specific behaviour, micro- and nanoparticles, as carriers of therapeutics or imaging agents, can distinguish and use these proteins as targeted docking sites. Here, a computational patient-specific model capturing the exclusive luminal qualities has been developed to study the transport and adsorption of particles decorated with proper antibodies over an atherosclerotic plaque located in the LAD artery of the patient. Particles, in nano- and micron sizes, have been decorated with Sialyl Lewisx (sLex), P-selectin aptamer...
Cancer cell enrichment on a centrifugal microfluidic platform using hydrodynamic and magnetophoretic techniques
, Article Scientific Reports ; Volume 11, Issue 1 , 2021 ; 20452322 (ISSN) ; Naghdloo, A ; Besanjideh, M ; Sharif University of Technology
Nature Research
2021
Abstract
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...
Fabrication of chitosan/poly(lactic acid)/graphene oxide/TiO2 composite nanofibrous scaffolds for sustained delivery of doxorubicin and treatment of lung cancer
, Article International Journal of Biological Macromolecules ; Volume 110 , 2018 , Pages 416-424 ; 01418130 (ISSN) ; Moradkhani, M ; Beheshti, H ; Irani, M ; Aliabadi, M ; Sharif University of Technology
Elsevier B.V
2018
Abstract
In this work, the synthesized graphene oxide/TiO2/doxorubicin (GO/TiO2/DOX) composites were loaded into the chitosan/poly(lactic acid) (PLA) solutions to fabricate the electrospun chitosan/PLA/GO/TiO2/DOX nanofibrous scaffolds via electrospinning process. The synthesized composites and nanofibers were characterized using X-ray powder diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analysis. Three-factor three-level central composite design was used to determine the influence of PLA to chitosan ratio, TiO2/DOX content and GO/TiO2/DOX content on the release of DOX from nanofibrous scaffolds. Drug loading efficiency and drug release behavior from...
Distinct dynamics of migratory response to pd-1 and ctla-4 blockade reveals new mechanistic insights for potential t-cell reinvigoration following immune checkpoint blockade
, Article Cells ; Volume 11, Issue 22 , 2022 ; 20734409 (ISSN) ; Goliaei, B ; Aref, A. R ; Foroughmand-Araabi, M. H ; Goliaei, S ; Lorch, J ; Jenkins, R. W ; Barbie, D. A ; Shariatpanahi, S. P ; Rüegg, C ; Sharif University of Technology
MDPI
2022
Abstract
Cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1), two clinically relevant targets for the immunotherapy of cancer, are negative regulators of T-cell activation and migration. Optimizing the therapeutic response to CTLA-4 and PD-1 blockade calls for a more comprehensive insight into the coordinated function of these immune regulators. Mathematical modeling can be used to elucidate nonlinear tumor–immune interactions and highlight the underlying mechanisms to tackle the problem. Here, we investigated and statistically characterized the dynamics of T-cell migration as a measure of the functional response to these pathways. We used a previously...
3D calculation of absorbed dose for 131I-targeted radiotherapy: A monte carlo study
, Article Radiation Protection Dosimetry ; Volume 150, Issue 3 , October , 2012 , Pages 298-305 ; 01448420 (ISSN) ; Sarkar, S ; Abbaspour Tehrani Fard, A ; Ay, M. R ; Khosravi, H. R ; Loudos, G ; Sharif University of Technology
2012
Abstract
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...
Over-Expression of immune-related lncrnas in inflammatory demyelinating polyradiculoneuropathies
, Article Journal of Molecular Neuroscience ; Volume 71, Issue 5 , 2021 , Pages 991-998 ; 08958696 (ISSN) ; Ghafouri-Fard, S ; Mazdeh, M ; Nicknafs, F ; Nazer, N ; Sayad, A ; Taheri, M ; Sharif University of Technology
Humana Press Inc
2021
Abstract
Long non-coding RNAs (lncRNAs) have crucial roles in the pathogenesis of immune-related disorders. However, their role in the pathobiology of inflammatory demyelinating polyradiculoneuropathies remains unclear. In the current study, we measured peripheral expression of four lncRNAs, namely TUG1, FAS-AS1, NEAT1, and GAS5, in patients with acute/chronic inflammatory demyelinating polyradiculoneuropathies (AIDP/CIDP) compared with healthy subjects. Notably, all lncRNAs were over-expressed in patients compared with controls (P < 0.0001 for all lncRNAs). When assessing their expressions in AIDP and CIDP groups separately, TUG1 and NEAT1 were up-regulated in both patient groups compared with...
Parallel nonlinear analysis of weighted brain's gray and white matter images for Alzheimer's dementia diagnosis
, Article Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference ; 2010 , Pages 5573-5576 ; 1557170X (ISSN) ; Torabi, M ; Kim, K ; Sharif University of Technology
2010
Abstract
In this study, we are proposing a novel nonlinear classification approach to discriminate between Alzheimer's Disease (AD) and a control group using T1-weighted and T2-weighted Magnetic Resonance Images (MRI's) of brain. Since T1-weighted images and T2-weighted images have inherent physical differences, obviously each of them has its own particular medical data and hence, we extracted some specific features from each. Then the variations of the relevant eigenvalues of the extracted features were tracked to pick up the most informative ones. The final features were assigned to two parallel systems to be nonlinearly categorized. Considering the fact that AD defects the white and gray regions...
Polymeric nanoparticles for nasal drug delivery to the brain: relevance to alzheimer's disease
, Article Advanced Therapeutics ; Volume 4, Issue 3 , 2021 ; 23663987 (ISSN) ; Ahmadi, S ; Afshari, R ; Khalaji, S ; Rabiee, M ; Bagherzadeh, M ; Fatahi, Y ; Dinarvand, R ; Tahriri, M ; Tayebi, L ; Hamblin, M. R ; Webster, T. J ; Sharif University of Technology
Blackwell Publishing Ltd
2021
Abstract
Currently, Alzheimer's disease (AD) accounts for more than half of all dementia cases. Although genetics, age, and environmental factors affect the disease, the cause of AD is not yet fully known. Various drugs have been proposed for the prevention and treatment of AD, but the delivery of these therapeutic agents to the brain is difficult. The blood–brain barrier prevents systemic drugs from accessing the central nervous system and designing a suitable system to overcome this barrier has attracted much attention. The intranasal pathway, given its proximity to the brain, provides a great opportunity for drug delivery. Understanding the physiological characteristics of the nose can be useful...
Significant pathological voice discrimination by computing posterior distribution of balanced accuracy
, Article Biomedical Signal Processing and Control ; Volume 73 , 2022 ; 17468094 (ISSN) ; Jahed, M ; Sharif University of Technology
Elsevier Ltd
2022
Abstract
The ability to speak lucidly plays a key role in social relations. Consequently, the role of the larynx is quite important, and timely diagnosis of laryngeal diseases has proved to be crucial. In this study, a simple computational model for inverse of speech production model is employed to extract the glottal waveform using speech signal. This waveform has useful information about vocal folds performance in terms of providing evidence for distinguishing pathological disorders. Furthermore, obtaining the significance of classification results is important, because it leads to reliable inferences. This study utilizes the sustained vowel sound /a/ and a well-referenced database, namely MEEI. In...
Transplantation of autologous epidermal melanocyte–keratinocyte cells suspension for cell therapy of vitiligo: A clinical evaluation and biometric assessment
, Article Journal of Cosmetic Dermatology ; Volume 21, Issue 12 , 2022 , Pages 7147-7152 ; 14732130 (ISSN) ; Farshi, S ; Nouri, M ; Alavi, S ; Bayat Tork, B ; Jaffary, F ; Zare, S ; Sharif University of Technology
John Wiley and Sons Inc
2022
Abstract
Introduction: Among several surgical treatments, the use of transplantation of epidermal cultured melanocytes or melanocytes–keratinocytes cell suspension has gained many researchers and dermatologists' attention as a new technique for the treatment of vitiligo. The present study aimed to transplant autologous epidermal melanocytes–keratinocytes cell suspension for the treatment of vitiligo. Methods: In this study, 15 volunteer patients aged between 18 and 45 years old were studied. The autologous melanocytes–keratinocytes cell suspension was then transplanted to the region after dermabrasion. The included patients were evaluated by VisioFace, MPA9, and Skin Scanner-DUB once before and 1, 2,...
A multi-scale model for determining the effects of pathophysiology and metabolic disorders on tumor growth
, Article Scientific Reports ; Volume 10, Issue 1 , 20 February , 2020 ; Firoozabadi, B ; Mozafari, A ; Munn, L. L ; Sharif University of Technology
Nature Research
2020
Abstract
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...
Investigation of cancer response to chemotherapy: a hybrid multi-scale mathematical and computational model of the tumor microenvironment
, Article Biomechanics and Modeling in Mechanobiology ; Volume 21, Issue 4 , 2022 , Pages 1233-1249 ; 16177959 (ISSN) ; Firoozabadi, B ; Sharif University of Technology
Springer Science and Business Media Deutschland GmbH
2022
Abstract
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,...
Defining microRNA signatures of hair follicular stem and progenitor cells in healthy and androgenic alopecia patients
, Article Journal of Dermatological Science ; Volume 101, Issue 1 , 2021 , Pages 49-57 ; 09231811 (ISSN) ; Nilforoushzadeh, M. A ; Youssef, K. K ; Sharifi Zarchi, A ; Moradi, S ; Khosravani, P ; Aghdami, R ; Taheri, P ; Hosseini Salekdeh, G ; Baharvand, H ; Aghdami, N ; Sharif University of Technology
Elsevier Ireland Ltd
2021
Abstract
Background: The exact pathogenic mechanism causes hair miniaturization during androgenic alopecia (AGA) has not been delineated. Recent evidence has shown a role for non-coding regulatory RNAs, such as microRNAs (miRNAs), in skin and hair disease. There is no reported information about the role of miRNAs in hair epithelial cells of AGA. Objectives: To investigate the roles of miRNAs affecting AGA in normal and patient's epithelial hair cells. Methods: Normal follicular stem and progenitor cells, as well as follicular patient's stem cells, were sorted from hair follicles, and a miRNA q-PCR profiling to compare the expression of 748 miRNA (miRs) in sorted cells were performed. Further, we...
Analysis of P300 classifiers in brain computer interface speller
, Article 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS'06, New York, NY, 30 August 2006 through 3 September 2006 ; 2006 , Pages 6205-6208 ; 05891019 (ISSN); 1424400325 (ISBN); 9781424400324 (ISBN) ; Fazel Rezai, R ; Shamsollahi, M. B ; Sharif University of Technology
2006
Abstract
In this paper, the performance of five classifiers in P300 speller paradigm are compared. Theses classifiers are Linear Support Vector Machine (LSVM), Gaussian Support Vector Machine (RSVM), Neural Network (NN), Fisher Linear Discriminant (FLD), and Kernel Fisher Discriminant (KFD). In classification of P300 waves, there has been a trend to use SVM classifiers. Although they have shown a good performance, in this paper, it is shown that the FLD classifiers outperform the SVM classifiers. FLD classifier uses only ten channels of the recorded electroencephalogram (EEG) signals. This makes them a very good candidate for real-time applications. In addition, FLD approach does not need any...