Sharif Digital Repository

Nanostructured copper-doped uorapatite (Cux.Ca(10X).(PO4)6.F2) having crystallite sizes of 19, 29, and 34 nm at x = 0:9, 0.4, and 0.0, respectively, was synthesized by planetary ball milling of CaO, P2O5, CaF2, and CuO powders. Specifications of the products were determined by Fourier-transform infrared spectroscopy, eld emission scanning electron microscopy, transmission electron microscopy, and X-ray di raction analyses. In-vitro studies and Mossman's Tetrazole Test (MTT) assays were also conducted by incubating Cux.Ca(10X).(PO6).F2 powder into Kokubo's Simulated Body Fluid (SBF) and against BT-20 cell, respectively, to determine bioactivity and biocompatibility of the materials.... 

We determined the mechanism of mechanochemical synthesis of fluorapatite from CaO, CaF2 and P2O5 by characterisation of the intermediate compounds. We used atomic absorption spectroscopy, X-ray diffraction, field emission scanning electron microscopy, FTIR spectroscopy and transmission electron microscopy to find the transitional compounds. Investigation of the binary and ternary powder mixtures revealed the appearance of H3PO4, Ca(OH)2, Ca2P2O7 and CaCO3 as the intermediate compounds. At early stages of the milling, conversions of P2O5 to H3PO4 and CaO to Ca(OH)2 occurred in the wet atmosphere. Later, a combination of Ca(OH)2 and H3PO4 formed Ca2P2O7 while the unreacted CaO was converted to... 

von Willebrand factor (VWF) is a naturally collapsed protein that participates in primary haemostasis and coagulation events. The clotting process is triggered by the adsorption and conformational changes of the plasma VWFs localized to the collagen fibres found near the site of injury. We develop coarse-grained models to simulate the adsorption dynamics of VWF flowing near the adhesive collagen fibres at different shear rates and investigate the effect of factors such as interaction and cooperativity of VWFs on the success of adsorption events. The adsorption probability of a flowing VWF confined to the receptor field is enhanced when it encounters an adhered VWF in proximity to the... 

Harnessing neural stem cells to repair neuronal damage is a promising potential treatment for neuronal diseases. To enable future therapeutic efficacy, the survival, proliferation, migration and differentiation of neural stem/progenitor cells (NPCs) should be accurately studied and optimized in in vitro platforms before transplanting these cells into the body for treatment purposes. Such studies can determine the appropriate quantities of the biochemical and biomechanical factors needed to control and optimize NPC behavior in vivo. In this study, NPCs were cultured within a microfluidic device while being encapsulated within the collagen matrix. The migration and differentiation of NPCs were... 

Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological mechanisms. However, in-laboratory techniques for protein function prediction are not as efficient as methods developed and processed for protein sequencing. While more than 70 million protein sequences are available today, only the functionality of around one percent of them are known. These facts have encouraged researchers to develop computational methods to infer protein functionalities from their sequences. Gene Ontology is the most well-known database for protein functions which has a hierarchical structure, where deeper terms are... 

Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditions has increased considerably in recent years. The practical utility of these aptamers depends on the detailed knowledge about the putative interactions with their target proteins. Therefore, understanding the aptamer-protein interactions at the atomic scale can offer significant insights into the optimal apta-biosensor design. In this study, we consider one RNA and one DNA aptamer that were previously used as apta-biosensors for detecting the infection biomarker protein TNF-α, as an example of a novel computational workflow for... 

Pretrained representations have recently gained attention in various machine learning applications. Nonetheless, the high computational costs associated with training these models have motivated alternative approaches for representation learning. Herein we introduce TripletProt, a new approach for protein representation learning based on the Siamese neural networks. Representation learning of biological entities which capture essential features can alleviate many of the challenges associated with supervised learning in bioinformatics. The most important distinction of our proposed method is relying on the protein-protein interaction (PPI) network. The computational cost of the generated... 

The use of external fields such as magnet and ultrasound to enhance the targeted drug delivery (TDD) by nano-microcarriers could be a potential method. In this research, the drug delivery of magnetic nanoparticles (NPs) coated nanoliposomes and microbubbles (MBs) to the atherosclerosis plaque was investigated under magnetic and ultrasound fields in terms of their adhesion to the plaque through ligand–receptor binding. The Halbach arrangement enhanced the surface density of nanoliposomes and MBs adhered to the plaque by ∼ (Formula presented.) and ∼ (Formula presented.), respectively. A focused transducer at the power of (Formula presented.) led to better drug delivery performance and caused ∼... 

The use of external fields such as magnet and ultrasound to enhance the targeted drug delivery (TDD) by nano-microcarriers could be a potential method. In this research, the drug delivery of magnetic nanoparticles (NPs) coated nanoliposomes and microbubbles (MBs) to the atherosclerosis plaque was investigated under magnetic and ultrasound fields in terms of their adhesion to the plaque through ligand–receptor binding. The Halbach arrangement enhanced the surface density of nanoliposomes and MBs adhered to the plaque by ∼ (Formula presented.) and ∼ (Formula presented.), respectively. A focused transducer at the power of (Formula presented.) led to better drug delivery performance and caused ∼... 

The exothermic reactions in Al+Ni system were used as a power source for welding of Al1100 alloy so that the obtained joint was reinforced with in situ produced Al3Ni intermetallic compound, simultaneously. Due to the combustion heat, the surfaces of the plates were melted down which, in turn, eventuated in formation of a strong surficial bond. The cross sections of joints were analyzed using optical microscopy, EDS-equipped scanning electron microscopy (SEM), and X-ray diffraction experiments. XRD and EDS results represented the Al3Ni intermetallic compound as the reaction product. The compressive shear strength of the joint was 20 MPa  

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,... 

Several methods have been proposed to construct Statistical Shape Model (SSM) to aim image analysis using computer in field Computer Aided Diagnosis (CAD), Computer Assisted Surgery (CAS), and other medical applications by providing a prior knowledge. The major challenge for liver shape model is a high variation in geometry such as size, shape and volume between livers. In this paper, we have presented a new technique for the automatic Multi-Scale Statistical Shape Model (MS-SSM) of three-dimensional (3-D) liver from volumetric segmented images data. The procedure included both building of Spherical Harmonics shape description and the Wavelet transform. Principal Component Analysis (PCA) was... 

This study proposes a mathematical model to evaluate the impact of oxygen carriers and scaffold geometry on oxygen distribution and cell growth in a 3D cardiac construct using computational fluid dynamics (CFD). Flow equations, oxygen balance equation and cell balance equation were solved using special initial and boundary conditions. The modeling results revealed that 55% increase in cardiac cell density occurred by using 6.4% perfluorocarbon oxygen carrier (PFC) compared to pure culture medium without PFC supplementation. Moreover, the effects of the scaffold geometry on cell density were examined by changing the channel numbers and the construct length. A 30% increase in the average cells... 

Background: In nuclear medicine application often it is required to use computational methods for evaluation of organ absorbed dose. Monte Carlo simulation and phantoms have been used in many works before. The shape, size and volume in organs are varied, and this variation will produce error in dose calculation if no correction is applied. Materials and Methods: A computational framework for constructing individual phantom for dosimetry was performed on five liver CT scan data sets of Japanese normal individuals. The Zubal phantom was used as an original phantom to be adjusted by each individual data set. This registration was done by Spherical Harmonics (SH) and Thin-Plate Spline methods.... 

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...