Sharif Digital Repository

Control problem in a biological system is the problem of finding an interventional policy for changing the state of the biological system from an undesirable state, e.g. disease, into a desirable healthy state. Boolean networks are utilized as a mathematical model for gene regulatory networks. This paper provides an algorithm to solve the control problem in Boolean networks. The proposed algorithm is implemented and applied on two biological systems: T-cell receptor network and Drosophila melanogaster network. Results show that the proposed algorithm works faster in solving the control problem over these networks, while having similar accuracy, in comparison to previous exact methods. Source... 

Given a weighted graph G=(V,E) with weight functions c:E→R+ and π:V→R+, and a subset U⊆V, the normalized cut value for U is defined as the sum of the weights of edges exiting U divided by the weight of vertices in U. The mean isoperimetry problem, ISO1(G,k), for a weighted graph G is a generalization of the classical uniform sparsest cut problem in which, given a parameter k, the objective is to find k disjoint nonempty subsets of V minimizing the average normalized cut value of the parts. The robust version of the problem seeks an optimizer where the number of vertices that fall out of the subpartition is bounded by some given integer 0≤ρ≤|V|. The problem may also be considered as the... 

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... 

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... 

Background: Codon degeneracy and codon usage by organisms is an interesting and challenging problem. Researchers demonstrated the relation between codon usage and various functions or properties of genes and proteins, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Researchers usually represent segments of proteins responsible for specific functions or structures in a family of proteins as sequence patterns or motifs. We asked the question if organisms use the same codons in pattern segments as compared to the rest of the sequence. Methods. We used the likelihood ratio test, Pearson's chi-squared test, and mutual information... 

Background: Basic epidemiological data can provide estimates when discussing disease burden and in the planning and provision of healthcare strategies. There is little quantitative information in the literature regarding prevalence of traumatic injuries from developing countries. Objectives: The aim of the current preliminary study was to reveal the prevalence and age and gender distribution of various traumatic injuries in a tertiary referral orthopedic hospital in Iran. Patients and Methods: In a prospective descriptive study, all traumatic injured patients attending the Orthopedic Trauma Unit of our center in a five year period were included. Demographic details, the cause of injury,... 

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... 

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... 

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... 

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... 

Classification is the most important part of brain-computer interface (BCI) systems. Because the neural activities of different individuals are not identical, using the ordinary methods of subject-dependent classification, does not lead to high accuracy in betweensubject classification problems. As a result, in this study, we propose a novel method for classification that performs well in between-subject classification. In the proposed method, at first, the subject-dependent classifiers obtained from the train subjects are applied to the test trials to obtain a set of scores and labels for the trials. Using these scores and the real labels of the labeled test trials, linear regression is... 

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...