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   Table of Contents - Current issue
January-March 2021
Volume 11 | Issue 1
Page Nos. 1-65

Online since Saturday, January 30, 2021

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Contribution of physical methods in decellularization of animal tissues p. 1
Mohsen Rabbani, Nasrin Zakian, Nima Alimoradi
Biologic scaffolds composed of extracellular matrix (ECM) are frequently used for clinical purposes of tissue regeneration. Different methods have been developed for this purpose. All methods of decellularization including chemical and physical approaches leave some damage on the ECM; however, the effects of these methods are different which make some of these procedures more proper to maintain ECM structure than other methods. This review is aimed to introduce and compare new physical methods for the decellularization of different tissues and organs in tissue engineering. All recent reports and research that have used at least one physical method in the procedure of decellularization, were included and evaluated in this paper. The advantages and drawbacks of each method were examined and compared considering the effectiveness. This review tried to highlight the prospective potentials and benefits of applying physical methods for decellularization protocols in tissue engineering instead of the current chemical methods. These chemical methods are harsh in nature and were shown to be destructive and harmful to essential substances of ECM and scaffold structure. Therefore, using physical methods as a partial or even a whole protocol could save time, costs, and quality of the final acellular tissue in complicated decellularization procedures. Moreover, regarding the control factor that could be achieved easily with physical methods, optimization of different decellularization protocols would be quite satisfactory. Combined methods take advantage of both chemical and physical approaches.
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Evaluation of asymmetry in right and left eyes of normal individuals using extracted features from optical coherence tomography and fundus images p. 12
Tahereh Mahmudi, Raheleh Kafieh, Hossein Rabbani, Alireza Mehri, Mohammad-Reza Akhlaghi
Background: Asymmetry analysis of retinal layers in right and left eyes can be a valuable tool for early diagnoses of retinal diseases. To determine the limits of the normal interocular asymmetry in retinal layers around macula, thickness measurements are obtained with optical coherence tomography (OCT). Methods: For this purpose, after segmentation of intraretinal layer in threedimensional OCT data and calculating the midmacular point, the TM of each layer is obtained in 9 sectors in concentric circles around the macula. To compare corresponding sectors in the right and left eyes, the TMs of the left and right images are registered by alignment of retinal raphe (i.e. diskfovea axes). Since the retinal raphe of macular OCTs is not calculable due to limited region size, the TMs are registered by first aligning corresponding retinal raphe of fundus images and then registration of the OCTs to aligned fundus images. To analyze the asymmetry in each retinal layer, the mean and standard deviation of thickness in 9 sectors of 11 layers are calculated in 50 normal individuals. Results: The results demonstrate that some sectors of retinal layers have signifcant asymmetry with P < 0.05 in normal population. In this base, the tolerance limits for normal individuals are calculated. Conclusion: This article shows that normal population does not have identical retinal information in both eyes, and without considering this reality, normal asymmetry in information gathered from both eyes might be interpreted as retinal disorders.
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Bone age assessment of iranian children in an automatic manner p. 24
Farzaneh Dehghani, Alireza Karimian, Mehri Sirous, Javad Rasti, Ali Soleymanpour
Background: Bone age assessment (BAA) is a radiological process with the aim of identifying growth disorders in children. The objective of this study is to assess the bone age of Iranian children in an automatic manner. Methods: In this context, three computer vision techniques including histogram of oriented gradients (HOG), local binary pattern (LBP), and scale-invariant feature transform (SIFT) are applied to extract appropriate features from the carpal and epiphyseal regions of interest. Two different datasets are applied here: the University of Southern California hand atlas for training this computer-aided diagnosis (CAD) system and Iranian radiographs for evaluating the performance of this system for BAA of Iranian children. In this study, the concatenation of HOG, LBP, and dense SIFT feature vectors and background subtraction are applied to improve the performance of this approach. Support vector machine (SVM) and K-nearest neighbor are used here for classification and the better results yielded by SVM. Results: The accuracy of female radiographs is 90% and of male is 71.42%. The mean absolute error is 0.16 and 0.42 years for female and male test radiographs, respectively. Cohen's kappa coefficients are 0.86 and 0.6, P < 0.05, for female and male radiographs, respectively. The results indicate that this proposed approach is in substantial agreement with the bone age reported by the experienced radiologist. Conclusion: This approach is easy to implement and reliable, thus qualified for CAD and automatic BAA of Iranian children.
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Molecular docking analysis of anti-severe acute respiratory syndrome-Coronavirus 2 ligands against spike glycoprotein and the 3-chymotrypsin-like protease p. 31
Ali Hassan Daghir Janabi
Background: The severe acute respiratory syndrome-like disease coronavirus disease 2019 (COVID-19) is a disastrous global pandemic with 16,288,490 infected cases and 649,884 deaths. Until now, no effective treatments are found. Methods: The virus uses the 3-chymotrypsin-like protease for inducing the activity of the viral polyproteins and the spike (S) glycoprotein for human cell entry through the human angiotensin-converting enzyme 2 receptor. Blocking the active binding sites of these molecules might be beneficial for decreasing the activity of the virus and suppressing the viral entry to the human cells. Here, docking methods were used to identify a group of ligands may perform the blocking operations. Results: The results revealed the strongest binding affinities, sorted high to low, for tadalafil (Cialis) (phosphodiesterase type 5 inhibitor, tirofiban (antiplatelet), paraxanthine (central nervous system stimulant), dexamethasone, gentian violet cation (triphenylmethane), salbutamol, and amlodipine (calcium channel blocker). Conclusion: These substances may provide vital help for further clinical investigation in fighting against the current global pandemic of the COVID-19.
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Selection of optimal bioinformatic tools and proper reference for reducing the alignment error in targeted sequencing data p. 37
Hannane Mohammadi Nodehi, Mohammad Amin Tabatabaiefar, Mohammadreza Sehhati
Background: Careful design in the primary steps of a next-generation sequencing study is critical for obtaining successful results in downstream analysis. Methods: In this study, a framework is proposed to evaluate and improve the sequence mapping in targeted regions of the reference genome. In this regard, simulated short reads were produced from the coding regions of the human genome and mapped to a Customized Target-Based Reference (CTBR) by the alignment tools that have been introduced recently. The short reads produced by different sequencing technologies aligned to the standard genome and also CTBR with and without well-defined mutation types where the amount of unmapped and misaligned reads and runtime was measured for comparison. Results: The results showed that the mapping accuracy of the reads generated from Illumina Hiseq2500 using Stampy as the alignment tool whenever the CTBR was used as reference was significantly better than other evaluated pipelines. Using CTBR for alignment significantly decreased the mapping error in comparison to other expanded or more limited references. While intentional mutations were imported in the reads, Stampy showed the minimum error of 1.67% using CTBR. However, the lowest error obtained by stampy too using whole genome and one chromosome as references was 3.78% and 20%, respectively. Maximum and minimum misalignment errors were observed on chromosome Y and 20, respectively. Conclusion: Therefore using the proposed framework in a clinical targeted sequencing study may lead to predict the error and improve the performance of variant calling regarding the genomic regions targeted in a clinical study.
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Investigating the dosimetric characteristics of microbeam radiation treatment p. 45

Background: High-radiation therapeutic gain could be achieved by the modern technique of microbeam radiation treatment (MRT). The aim of this study was to investigate the dosimetric properties of MRT. Methods: The EGSnrc Monte Carlo (MC) code system was used to transport photons and electrons in MRT. The mono-energetic beams (1 cm × 1 cm array) of 50, 100, and 150 keV and the spectrum photon beam (European Synchrotron Radiation Facility [ESRF]) were modeled to transport through multislit collimators with the aperture's widths of 25 and 50 μm and the center-to-center (c-t-c) distance between two adjacent microbeams (MBs) of 200 μm. The calculated phase spaces at the upper surface of water phantom (1 cm × 1 cm) were implemented in DOSXYZnrc code to calculate the percentage depth dose (PDD), the dose profile curves (in depths of 0–1, 1–2, and 3–4 cm), and the peak-to-valley dose ratios (PVDRs). Results: The PDD, dose profile curves, and PVDRs were calculated for different effective parameters. The more flatness of lateral dose profile was obtained for the ESRF spectrum MB. With constant c-t-c distance, an increase in the MB size increased the peak and valley dose; simultaneously, the PVDR was larger for the 25 μm MB (33.5) compared to 50 μm MB (21.9) beam, due to the decreased scattering photons followed to the lower overlapping of the adjacent MBs. An increase in the depth decreased the PVDRs (i.e., 54.9 in depth of 0–1 cm). Conclusion: Our MC model of MRT successfully calculated the effect of dosimetric parameters including photon's energy, beam width, and depth to estimate the dose distribution.
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Real-time fast fourier transform-based notch filter for single-frequency noise cancellation: Application to electrocardiogram signal denoising p. 52
Anis Ben Slimane, Azza Ouled Zaid
Despite the considerable improvement of the common-mode rejection ratio of digital filtering techniques, the electrocardiogram (ECG) traces recorded by commercialized devices are still contaminated by residual power line interference (PLI). In this study, we address this issue by proposing a novel real-time filter adapted to single-frequency noise cancellation and automatic power line frequency detection. The filtering process is principally based on a point-by-point fast Fourier transform and a judicious choice of the analysis window length. Intensive experiments conducted on real and synthetic signals have shown that our filtering method offers very clean ECGs, due to the suppression of spikes corresponding to the PLI and the preservation of spikes outside the filter band. In addition, this method is characterized by its low computational complexity which makes it suitable for real-time cleaning of ECG signals and thus can serve for more accurate diagnosis in computer-based automated cardiac system.
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An analysis on top commented posts in reddit social network about COVID-19 p. 62
Khalil Kimiafar, Mehdi Dadkhah, Masoumeh Sarbaz, Mohammad Mehraeen
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