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histology
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An Approach for Cancer Diagnosis Based on Graph Modeling
, M.Sc. Thesis Sharif University of Technology ; Habibi, Jafar (Supervisor)
Abstract
Digital image analysis of histological datasets is a currently expanding field of research. Histological images are inherently complex in nature and contain a wide variety of visual information. Graph-based methods have recently gained immense popularity, as these methods can effectively describe tissue architecture and provide adequate numeric information for subsequent computer-based analysis. Graphs have the ability to represent spatial arrangements and neighborhood relationships of different tissue components, which are essential characteristics observed visually by pathologists during the investigation of specimens. In this thesis, we proposed an automatic approach for classification...
Domain Generalization in Deep Learning Models for Histopathology
, M.Sc. Thesis Sharif University of Technology ; Rohban, Mohammad Hossein (Supervisor)
Abstract
Domain shift is an inevitable issue when histopathological images are analyzed in a standard laboratory. This is due to the variations in tissue handling, manual procedures for sample preparation, and differences in scanners. This can result in reduced performance of machine learning algorithms trained on images from one laboratory when applied to another. In this framework, the goal of utilizing domain generalization techniques in machine learning is to develop models that perform well in different domains. This research examines various methods of dealing with the domain shift challenges within the context of detecting mitotic cells, and proposes algorithms to improve domain generalization...
A novel laparoscopic grasper with two parallel jaws capable of extracting the mechanical behaviour of soft tissues
, Article Journal of Medical Engineering and Technology ; Volume 41, Issue 5 , 2017 , Pages 339-345 ; 03091902 (ISSN) ; Farahmand, F ; Mirbagheri, A ; Afshari, E ; Sharif University of Technology
Taylor and Francis Ltd
2017
Abstract
Data related to force-deformation behaviour of soft tissue plays an important role in medical/surgical applications such as realistically modelling mechanical behaviour of soft tissue as well as minimally invasive surgery (MIS) and medical diagnosis. While the mechanical behaviour of soft tissue is very complex due to its different constitutive components, some issues increase its complexity like behavioural changes between the live and dead tissues. Indeed, an adequate quantitative description of mechanical behaviour of soft tissues requires high quality in vivo experimental data to be obtained and analysed. This paper describes a novel laparoscopic grasper with two parallel jaws capable of...
A reliable ensemble-based classification framework for glioma brain tumor segmentation
, Article Signal, Image and Video Processing ; Volume 14, Issue 8 , 2020 , Pages 1591-1599 ; Jamzad, M ; Sharif University of Technology
Springer Science and Business Media Deutschland GmbH
2020
Abstract
Glioma is one of the most frequent primary brain tumors in adults that arise from glial cells. Automatic and accurate segmentation of glioma is critical for detecting all parts of tumor and its surrounding tissues in cancer detection and surgical planning. In this paper, we present a reliable classification framework for detection and segmentation of abnormal tissues including brain glioma tumor portions such as edemas and tumor core. This framework learns weighted features extracted from the 3D cubic neighborhoods regarding to gray-level differences that indicate the spatial relationships among voxels. In addition to intensity values in each slice, we consider sets of three consecutive...
A three-dimensional statistical volume element for histology informed micromechanical modeling of brain white matter
, Article Annals of Biomedical Engineering ; Volume 48, Issue 4 , 2020 , Pages 1337-1353 ; Farahmand, F ; Ahmadian, M. T ; Sharif University of Technology
Springer
2020
Abstract
This study presents a novel statistical volume element (SVE) for micromechanical modeling of the white matter structures, with histology-informed randomized distribution of axonal tracts within the extracellular matrix. The model was constructed based on the probability distribution functions obtained from the results of diffusion tensor imaging as well as the histological observations of scanning electron micrograph, at two structures of white matter susceptible to traumatic brain injury, i.e. corpus callosum and corona radiata. A simplistic representative volume element (RVE) with symmetrical arrangement of fully alligned axonal fibers was also created as a reference for comparison. A...
Refractive index correction in optical coherence tomography images of multilayer tissues
, Article Journal of Biomedical Optics ; Volume 23, Issue 7 , 2018 ; 10833668 (ISSN) ; Fatemizadeh, E ; Xu, Q ; Daveluy, S ; Mehregan, D ; Nasiriavanaki, M ; Sharif University of Technology
SPIE
2018
Abstract
We propose an algorithm to compensate for the refractive index error in the optical coherence tomography (OCT) images of multilayer tissues, such as skin. The performance of the proposed method has been evaluated on one-and two-layer solid phantoms, as well as the skin of rat paw. © 2018 Society of Photo-Optical Instrumentation Engineers (SPIE)
Biomimetic proteoglycan nanoparticles for growth factor immobilization and delivery
, Article Biomaterials Science ; Volume 8, Issue 4 , 2020 , Pages 1127-1136 ; Mostafavi, E ; Shokrgozar, M. A ; Tamjid, E ; Webster, T. J ; Annabi, N ; Simchi, A ; Sharif University of Technology
Royal Society of Chemistry
2020
Abstract
The delivery of growth factors is often challenging due to their short half-life, low stability, and rapid deactivation. In native tissues, the sulfated residual of glycosaminoglycan (GAG) polymer chains of proteoglycans immobilizes growth factors through the proteoglycans'/proteins' complexation with nanoscale organization. These biological assemblies can influence growth factor-cell surface receptor interactions, cell differentiation, cell-cell signaling, and mechanical properties of the tissues. Here, we introduce a facile procedure to prepare novel biomimetic proteoglycan nanocarriers, based on naturally derived polymers, for the immobilization and controlled release of growth factors....
Laser induced breakdown spectroscopy and acoustic response techniques to discriminate healthy and cancerous breast tissues
, Article Applied Optics ; Volume 55, Issue 29 , 2016 , Pages 8227-8235 ; 1559128X (ISSN) ; Parvin, P ; Hosseini Motlagh, N. S ; Amjadi, A ; Abachi, S ; Sharif University of Technology
OSA - The Optical Society
Abstract
Laser induced breakdown spectroscopy and subsequent acoustic response during microplasma formation are employed to identify cancerous human breast tissues. The characteristic optical emissions identify Ca, Na, and Mg rich species in cancerous tissues compared to those of healthy ones. Furthermore, we show that the characteristic parameters of the microplasma, generated on the unhealthy tissues, are elevated. We report higher decibel audio signals emanating from laser induced microplasma and a subsequent audio blueshift for malignant tissues. The higher abundance of trace elements in cancerous tissues as well as higher plasma temperature and electron density in laser induced microplasma...
Three-dimensional bioprinting of functional skeletal muscle tissue using gelatin methacryloyl-alginate bioinks
, Article Micromachines ; Volume 10, Issue 10 , 2019 ; 2072666X (ISSN) ; Çelebi Saltik, B ; Barros, N ; Nasiri, R ; Banton, E ; Shamloo, A ; Ashammakhi, N ; Dokmeci, M. R ; Ahadian, S ; Sharif University of Technology
MDPI AG
2019
Abstract
Skeletal muscle tissue engineering aims to fabricate tissue constructs to replace or restore diseased or injured skeletal muscle tissues in the body. Several biomaterials and microscale technologies have been used in muscle tissue engineering. However, it is still challenging to mimic the function and structure of the native muscle tissues. Three-dimensional (3D) bioprinting is a powerful tool to mimic the hierarchical structure of native tissues. Here, 3D bioprinting was used to fabricate tissue constructs using gelatin methacryloyl (GelMA)-alginate bioinks. Mechanical and rheological properties of GelMA-alginate hydrogels were characterized. C2C12 myoblasts at the density 8 × 106 cells/mL...
Magnetic graphene oxide mesoporous silica hybrid nanoparticles with dendritic pH sensitive moieties coated by PEGylated alginate-co-poly (acrylic acid) for targeted and controlled drug delivery purposes
, Article Journal of Polymer Research ; Volume 22, Issue 8 , 2015 ; 10229760 (ISSN) ; Shakerpoor, A ; Tehrani, Z. M ; Bumajdad, A ; Sharif University of Technology
Kluwer Academic Publishers
2015
Abstract
In this study synthesis of a drug delivery system (DDS) is described which has several merits over its counterparts. In order to synthesize this nano-carrier, graphene oxide nano-sheets are used to accommodate MCM-41 nanoparticles. Furthermore Fe3 O4 nanoparticles are introduced to this nano-material to produce a traceable nanoparticle. Since cancerous tissues have lower pH than healthy tissues, pH-sensitive oligomers are attached to this nano-material. Finally the nano-carrier is wrapped by a biocompatible shell (PEGylated sodium alginate); this polymeric shell makes the DDS capable of a more controllable drug release. By measuring in vitro situation, ‘loading content%’...
Fullerene C60 nanoparticle attenuates pain and tumor necrosis factor-α protein expression in the hippocampus following diabetic neuropathy in rats
, Article Physiology and Pharmacology (Iran) ; Volume 26, Issue 4 , 2022 , Pages 451-458 ; 24765236 (ISSN) ; Bahrami, F ; Bahari, Z ; Ghanbari, B ; Shahyad, S ; Mohammadi, M. T ; Sharif University of Technology
Iranian Society of Physiology and Pharmacology
2022
Abstract
Introduction: Diabetic neuropathy is a common complication of diabetes mellitus. It is associated with nerve damage due to oxidative stress and high levels of pro-inflammatory mediators. In the present study, we examined the anti-nociceptive effects of Fullerene nanoparticle, as a potent anti-oxidant, during diabetic neuropathy. Methods: Diabetes mellitus induced through injection of streptozotocin (STZ) (40 mg/kg). Four groups were used in the study as follows: the control, control+fullerene, diabetes, and diabetes +fullerene groups. All four groups received sesame oil. Treatment rats received fullerene C60 (1mg/kg/day) for 9 weeks by intra-gastric gavage. Then, cold allodynia, histology,...
Tool-tissue force estimation in laparoscopic surgery using geometric features
, Article Studies in Health Technology and Informatics ; Volume 184 , 2013 , Pages 225-229 ; 09269630 (ISSN) ; Behzadipour, S ; Farahmand, F ; Sharif University of Technology
IOS Press
2013
Abstract
This paper introduces three geometric features, from deformed shape of a soft tissue, which demonstrate good correlation with probing force and maximum local stress. Using FEM simulation, 2D and 3D model of an in vivo porcine liver was built for different probing tasks. Maximum deformation angle, maximum deformation depth and width of displacement constraint of the reconstructed shape of the deformed body were calculated. Two neural networks were trained from these features and the calculated interaction forces. The features are shown to have high potential to provide force estimation either for haptic devices or to assess the damage to the tissue in large deformations of up to 40%
A non-linear mass-spring model for more realistic and efficient simulation of soft tissues surgery
, Article Medicine Meets Virtual Reality 16 - Parallel, Combinatorial, Convergent: NextMed by Design, MMVR 2008, Long Beach, CA, 30 January 2008 through 1 February 2008 ; Volume 132 , 2008 , Pages 23-25 ; 09269630 (ISSN); 9781586038229 (ISBN) ; Farahmand, F ; Vossoughi, G ; Sharif University of Technology
IOS Press
2008
Abstract
An extension to the classical mass-spring model for more realistic simulation of soft tissues for surgery simulation was proposed. The conventional equations of mass-spring model were generalized for non-linear springs, and model parameters were tuned using experimental data. Results show that the proposed model is fast and interactive, and also demonstrate the typical nonlinear and visco-elastic behaviors of soft tissues well. © 2008 The authors. All rights reserved
Fabrication and characterization of an injectable reinforced composite scaffold for cartilage tissue engineering: An in vitro study
, Article Biomedical Materials (Bristol) ; Volume 16, Issue 4 , 2021 ; 17486041 (ISSN) ; Mashayekhan, S ; Zarei, F ; Sayyahpour, F. A ; Taghiyar, L ; Eslaminejad, M. B ; Sharif University of Technology
IOP Publishing Ltd
2021
Abstract
There are limitations in current medications of articular cartilage injuries. Although injectable bioactive hydrogels are promising options, they have decreased biomechanical performance. Researchers should consider many factors when providing solutions to overcome these challenges. In this study, we created an injectable composite hydrogel from chitosan and human acellular cartilage extracellular matrix (ECM) particles. In order to enhance its mechanical properties, we reinforced this hydrogel with microporous microspheres composed of the same materials as the structural building blocks of the scaffold. Articular cartilage from human donors was decellularized by a combination of physical,...
Intensity estimation of spontaneous facial action units based on their sparsity properties
, Article IEEE Transactions on Cybernetics ; Volume 46, Issue 3 , 2016 , Pages 817-826 ; 21682267 (ISSN) ; Fatemizadeh, E ; Mahoor, M. H ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2016
Abstract
Automatic measurement of spontaneous facial action units (AUs) defined by the facial action coding system (FACS) is a challenging problem. The recent FACS user manual defines 33 AUs to describe different facial activities and expressions. In spontaneous facial expressions, a subset of AUs are often occurred or activated at a time. Given this fact that AUs occurred sparsely over time, we propose a novel method to detect the absence and presence of AUs and estimate their intensity levels via sparse representation (SR). We use the robust principal component analysis to decompose expression from facial identity and then estimate the intensity of multiple AUs jointly using a regression model...
Hierarchical Enhancement of Optical Coherence Tomography Images
, Article 24th Iranian Conference on Biomedical Engineering and 2017 2nd International Iranian Conference on Biomedical Engineering, ICBME 2017, 30 November 2017 through 1 December 2017 ; 2018 ; 9781538636091 (ISBN) ; Fatemizadeh, E ; Nasiri Avanaki, M ; Sharif University of Technology
Institute of Electrical and Electronics Engineers Inc
2018
Abstract
Optical coherence tomography (OCT) is a noninvasive imaging modality that provides cross-sectional images from microstructures of tissues. This optical imaging system works based on Michelson interferometry principle and has intermediate resolution and penetration depth which makes it appropriate for imaging thin tissues such as skin and eye. OCT images suffer from three main artifacts that make images difficult to be analyzed. The first one is small grainy structures called speckle which degrade image quality and decreases axial and lateral resolution. The second one is light intensity attenuation which is a function of depth. It happens because of absorbing and scattering nature of tissue...
Chitosan-gelatin sheets as scaffolds for muscle tissue engineering
, Article Artificial Cells, Nanomedicine and Biotechnology ; Volume 43, Issue 2 , Nov , 2015 , Pages 124-132 ; 21691401 (ISSN) ; Mashayekhan, S ; Nazaripouya, A ; Naji, M ; Hunkeler, D ; Rajabi Zeleti, S ; Sharifiaghdas, F ; Sharif University of Technology
Informa Healthcare
2015
Abstract
Hydrogels made of natural polymers [chitosan (CS) and gelatin (G)] have been prepared having mechanical properties similar to those of muscle tissues. In this study, the effect of polymer concentration and scaffold stiffness on the behavior of seeded muscle-derived cells (MDCs) on the CS-G hydrogel sheets has been evaluated. Both variables were found to be important in cell viability. Viability was assessed by observation of the cell morphology after 1 day as well as a 14-day MTT assay. The CS-G hydrogels were characterized using Fourier transform infrared (FTIR) analysis, which revealed evidences of strong intermolecular interactions between CS and G. Hydrogel samples with intermediate...
Apoptotic and anti-apoptotic genes transcripts patterns of graphene in mice
, Article Materials Science and Engineering C ; Volume 71 , 2017 , Pages 460-464 ; 09284931 (ISSN) ; Hashemi, E ; Akhavan, O ; Shamsara, M ; Hashemi, M ; Farmany, A ; Daliri Joupari, M ; Sharif University of Technology
Elsevier Ltd
2017
Abstract
Recent studies showed that a large amount of graphene oxide accumulated in kidney and liver when it injected intravenously. Evaluation of lethal and apoptosis gene expression in these tissues, which are under stress is very important. In this paper the in vivo dose-dependent effects of graphene oxide and reduced graphene oxide nanoplatelets on kidney and liver of mice were studied. Balb/C mice were treated by 20 mg/kg body weight of nanoplatelets. Molecular biology analysis showed that graphene nanoplatelets injected intravenously lead to overexpression of BAX gene in both kidney and liver tissues (P ≥ 0.01). In addition these nanoparticles significantly increase BCL2 gene expression in both...
A three-dimensional micromechanical model of brain white matter with histology-informed probabilistic distribution of axonal fibers
, Article Journal of the Mechanical Behavior of Biomedical Materials ; Volume 88 , 2018 , Pages 288-295 ; 17516161 (ISSN) ; Farahmand, F ; Shamloo, A ; Sharif University of Technology
Elsevier Ltd
2018
Abstract
This paper presents a three-dimensional micromechanical model of brain white matter tissue as a transversely isotropic soft composite described by the generalized Ogden hyperelastic model. The embedded element technique, with corrected stiffness redundancy in large deformations, was used for the embedment of a histology-informed probabilistic distribution of the axonal fibers in the extracellular matrix. The model was linked to a multi-objective, multi-parametric optimization algorithm, using the response surface methodology, for characterization of material properties of the axonal fibers and extracellular matrix in an inverse finite element analysis. The optimum hyperelastic...
The role of oxygen defects in magnetic properties of gamma-irradiated reduced graphene oxide
, Article Journal of Alloys and Compounds ; Volume 784 , 2019 , Pages 134-148 ; 09258388 (ISSN) ; Nemati, A ; Zarrabi, A ; Shokrgozar, M. A ; Sharif University of Technology
Elsevier Ltd
2019
Abstract
Recently, graphene oxide and its unconventional magnetism have attracted much interest due to their novel applications in spintronics, memory chips and theranostics. Owing to the excellent biocompatibility, cellular uptake, bio-conjugation possibilities, flexible chemical modification and characteristic broad-wavelength absorbance, graphene oxide and its derivatives have been utilized as contrast agents for various imaging modalities such as photoluminescence, photoacoustic or ultrasound. Despite their suitable applications in bioimaging and due to lack of magnetic moment, graphene oxide cannot confer magnetic resonance imaging contrast without incorporating the magnetic component. Such...