Sharif Digital Repository

In this paper, a Kalman filter technique which is operated in time is introduced for noise reduction on CT set of projections to reconstruct medical images. The experiments were done on medical image of kidneys and the simulated projections are captured by CT scanner. Evaluation results indicated that as the number of projections increase in the collected ray sums corrupted by noise the quality of reconstructed image becomes better in terms of contrast and transparency. However, for the comparison issue, the same conditions are applied for reconstruction of medical image in frequency domain using filter back projection technique. It observes that filter back projection technique does not... 

Based on previous studies, empirical distribution of the bacterial burst size varies even in a population of isogenic bacteria. Since bacteriophage progenies increase linearly with time, it is the lysis time variation that results in the bacterial burst size variations. Here, the burst size variation is computationally modeled by considering the lysis time decisions as a game. Each player in the game is a bacteriophage that has initially infected and lysed its host bacterium. Also, the payoff of each burst size strategy is the average number of bacteria that are solely infected by the bacteriophage progenies after lysis. For calculating the payoffs, a new version of ball and bin model with... 

Medical images contain information about vital organic tissues inside of human body and are widely used for diagnoses of disease or for surgical purposes. Image reconstruction is essential for medical images for some applications such as suppression of noise or de-blurring the image to provide images with better quality and contrast. In this paper Kalman filter technique is introduced for medical image reconstruction. This technique is operated in time domain unlike the filtered back projection which operates in frequency domain. Results indicated that as the number of projection increases in both the collected ray sum corrupted by noise and by blurring the quality of reconstructed image... 

Patterns on proteins and genomic sequences are vastly analyzed, extracted and collected in databases. Although protein patterns originate from genomic coding regions, very few works have directly or indirectly dealt with coding region patterns induced from protein patterns. Results: In this paper, we have defined a new genomic pattern structure suitable for representing induced patterns from proteins. The provided pattern structure, which is called "Consecutive Positions Scoring Matrix (CPSSM)", is a replacement for protein patterns and profiles in the genomic context. CPSSMs can be identified, discovered, and searched in genomes. Then, we have presented a novel pattern matching algorithm... 

Medical images contain information about vital organic tissues inside of human body and are widely used for diagnoses of disease or for surgical purposes. Due to vital rule of image reconstruction in medical sciences the corresponding algorithms with better efficiency and higher speed is desirable. Most algorithms in image reconstruction are operated on frequency domain such as filtered back projection. In this paper, a Kalman filter technique which is operated in time domain is introduced for reconstruction of CT medical images. Results indicated that as the number of projection increases in both normal collected ray sum and the collected ray sum corrupted by noise the quality of... 

In recent years, analyzing genome-wide expression profiles to find genetic markers has received much attention as a challenging field of research aiming at unveiling biological mechanisms behind complex disorders. The identification of reliable and reproducible markers has lately been achieved by integrating genome-scale functional relationships and transcriptome datasets, and a number of algorithms have been developed to support this strategy. In this paper, we present a promising and easily applicable tool to accomplish this goal, namely CytoGTA, which is a Cytoscape plug-in that relies on an optimistic game theoretic approach (GTA) for identifying subnetwork markers. Given transcriptomic... 

Although it is known that synonymous codons are not chosen randomly, the role of the codon usage in gene regulation is not clearly understood, yet. Researchers have investigated the relation between the codon usage and various properties, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Recently, a universal codon usage based mechanism for gene regulation is proposed. We studied the role of protein sequence patterns on the codons usage by related genes. Considering a subsequence of a protein that matches to a pattern or motif, we showed that, parts of the genes, which are translated to this subsequence, use specific ratios of... 

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... 

The wavelength-based machine is a computational model working with light and optical devices. Wavelength-Based machine assumes that it can breakdown light to several very small pieces and act on them simultaneously to achieve efficiency in computation. In this paper, first we introduce the wavelength-based machine. Then, we define two new operations: concentration and double concentration operations, which give the wavelength-based machine the ability to check the emptiness of one and two light rays. Both of the concentration and double concentration operations are implemented by white-black imaging systems. In this paper, we compare the computational power of P-uniform wavelength-based... 

Signal machines form an abstract and idealized model of collision computing. Based on dimensionless signals moving on the real line, they model particle/signal dynamics in Cellular Automata. Each particle, or signal, moves at constant speed in continuous time and space. When signals meet, they get replaced by other signals. A signal machine defines the types of available signals, their speeds, and the rules for replacement in collision. A signal machine A simulates another one B if all the space-time diagrams of B can be generated from space-time diagrams of A by removing some signals and renaming other signals according to local information. Given any finite set of speeds S we construct a... 

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... 

Learning a foreign language encompasses a process of trial and error that can lead to the progression of the learner's interlanguage, meaning that the learners make use of their language knowledge that receives feedback and brings about progress through diagnosis of the problems and being corrected by the teacher. Therefore, there exists a need to analyze the underlying reasons causing the students to remain taciturn with a low willingness to communicate (WTC) during a language class. There has been much work done investigating the role of the learner's stable personal characteristics (traits) along with their situational changes at a specific time (states) that influence the student's... 

Using 3-D scanned data to analyze and extract pore network plays a vital role in investigation of porous media's characteristics. In this paper, a new simple method is developed to detect pores and throats for analyzing the connectivity and permeability of the network. This automated method utilizes some of the common and well-known image processing functions which are widely accessible by researchers and this has led to an easy algorithm implementation. In this method, after polishing and quality control of images, using city-block distance function and watershed segmentation algorithm, pores and throats are detected and 3-D network is produced. This method can also be applied on 2-D images... 

In this paper, we try to recognize and distinguish different groups of arrhythmia using novel features which have been obtained from the heart rate's phase space in recent years. For this purpose, we used Triangular Phase Space Mapping (TPSM) and Parabolic Phase Space Mapping (PPSM). For recognition, we used three groups of 15 subjects using the Physionet database (Arrhythmia, Congestive Heart Failure (CHF), and Atrial Fibrillation (AF)) with Normal Sinus Rhythm (NSR). The obtained features discriminate arrhythmia from NSR by p