Sharif Digital Repository

Karyotype is a genetic test that is used for detection of chromosomal defects. In a karyotype test, an image is captured from chromosomes during the cell division. The captured images are then analyzed by cytogeneticists in order to detect possible chromosomal defects. In this paper, we have proposed an automated pipeline for analysis of karyotype images. There are three main steps for karyotype image analysis: image enhancement, image segmentation and chromosome classification. In this paper, we have proposed a novel chromosome segmentation algorithm to decompose overlapped chromosomes. We have also proposed a CNN-based classifier which outperforms all the existing classifiers. Our... 

Human infertility is a multifactorial disease that affects 8%–12% of reproductive-aged couples worldwide. However, the genetic causes of human infertility are still poorly understood. Synaptonemal complex (SC) is a conserved tripartite structure that holds homologous chromosomes together and plays an indispensable role in the meiotic progression. Here, we identified three homozygous mutations in the SC coding gene C14orf39/SIX6OS1 in infertile individuals from different ethnic populations by whole-exome sequencing (WES). These mutations include a frameshift mutation (c.204_205del [p.His68Glnfs∗2]) from a consanguineous Pakistani family with two males suffering from non-obstructive... 

Supercoiled DNA, crumpled interphase chromosomes, and topologically constrained ring polymers often adopt treelike, double-folded, randomly branching configurations. Here we study an elastic lattice model for tightly double-folded ring polymers, which allows for the spontaneous creation and deletion of side branches coupled to a diffusive mass transport, which is local both in space and on the connectivity graph of the tree. We use Monte Carlo simulations to study systems falling into three different universality classes: ideal double-folded rings without excluded volume interactions, self-avoiding double-folded rings, and double-folded rings in the melt state. The observed static properties... 

Local three-stranded DNA/RNA hybrid regions of genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for mouse and human telomeres, clearly suggested by the identification of the complementary RNA Telomeric repeat-containing RNA “TERRA”. However, the tremendous disparity in the information obtained with antibody-based technology drove us to investigate a new strategy. Based on the observation that DNA/RNA hybrids in a triplex complex genome co-purify with the double-stranded chromosomal DNA fraction, we developed a direct preparative approach from total protein-free cellular... 

Alzheimer’s disease (AD) is an irreversible neurological disorder that progresses gradually and can cause severe cognitive and behavioral impairments. This disease is currently considered a social and economic incurable issue due to its complicated and multifactorial characteristics. Despite decades of extensive research, we still lack definitive AD diagnostic and effective therapeutic tools. Consequently, one of the most challenging subjects in modern medicine is the need for the development of new strategies for the treatment of AD. A large body of evidence indicates that amyloid-β (Aβ) peptide fibrillation plays a key role in the onset and progression of AD. Recent studies have reported... 

Background: Long reads provide valuable information regarding the sequence composition of genomes. Long reads are usually very noisy which renders their alignments on the reference genome a daunting task. It may take days to process datasets enough to sequence a human genome on a single node. Hence, it is of primary importance to have an aligner which can operate on distributed clusters of computers with high performance in accuracy and speed. Results: In this paper, we presented IMOS, an aligner for mapping noisy long reads to the reference genome. It can be used on a single node as well as on distributed nodes. In its single-node mode, IMOS is an Improved version of Meta-aligner (IM)... 

In vivo dose-dependent effects of nanoscale graphene oxide (NGO) sheets on reproduction capability of Balb/C mice were investigated. Biodistribution study of the NGO sheets (intravenously injected into male mice at dose of ∼2000 μg/mL or 4 mg/kg of body weight) showed a high graphene uptake in testis. Hence, in vivo effects of the NGO sheets on important characteristics of spermatozoa (including their viability, morphology, kinetics, DNA damage and chromosomal aberration) were evaluated. Significant in vivo effects was found at the injected concentrations ≥200 μg/mL after (e.g., ∼45% reduction in sperm viability and motility at 2000 μg/mL). Observation of remarkable DNA fragmentations and... 

Single-layer reduced graphene oxide nanoribbons (rGONRs) were obtained through an oxidative unzipping of multi-walled carbon nanotubes and a subsequent deoxygenation by hydrazine and bovine serum albumin. Human mesenchymal stem cells (hMSCs) were isolated from umbilical cord blood and used for checking the concentration- and time-dependent cyto- and geno-toxic effects of the rGONRs and reduced graphene oxide sheets (rGOSs). The cell viability assay indicated significant cytotoxic effects of 10 μg/mL rGONRs after 1 h exposure time, while the rGOSs exhibited the same cytotoxicity at concentration of 100 μg/mL after 96 h. The oxidative stress was found as the main mechanism involved in the... 

Analyzing the features of the chromosomes can be very useful for diagnosis of many genetic disorders or prediction of the possible abnormalities that may occur in the future generations. For this purpose, karyotype is often used which to make it, there is necessary to identify each one of the 24 chromosomes from the microscopic images. Definition and extraction of the morphological and band pattern based features for each chromosome is the first step to identify them. An important class of the morphological features is the location of the chromosome's centromere. Thus, centromere localization is an initial step in designing an automatic karyotyping system. In this paper, a novel algorithm... 

Reduced graphene oxide nanoplatelets (rGONPs) were synthesized by sonication of covalently PEGylated GO sheets followed by a chemical reduction using hydrazine and bovine serum albumin. Human mesenchymal stem cells (hMSCs), as a fundamental factor in tissue engineering, were isolated from umbilical cord blood (as a recently proposed source for extracting fresh hMSCs) to investigate, for the first time, the size-dependent cyto- and geno-toxic effects of the rGONPs on the cells. The cell viability test showed significant cell destructions by 1.0 μg/mL rGONPs with average lateral dimensions (ALDs) of 11±4 nm, while the rGO sheets with ALDs of 3.8±0.4 μm could exhibit a significant cytotoxic... 

Vivid banding pattern of the chromosome image is a crucial part for diagnosis in karyotype medical test. Furthermore, thriving computer aided segmentation and classification depend on the initial image quality. In this paper, we propose an adaptive and iterative histogram matching algorithm for chromosome contrast enhancement especially in banding patterns which is one of the most important information laid in chromosome image. Objective histogram, with which the initial image needs to be matched, is created based on processes on the initial image histogram. Calculation of statistical moments of image histogram and determination of parameters in each step of iteration based on these moments... 

In this paper the setup assembly line balancing and scheduling problem (SUALBSP) is considered. Since this problem is NP-hard, a hybrid genetic algorithm (GA) is proposed to solve the problem. This problem involves assigning the tasks to the stations and scheduling them inside each station. A simple permutation is used to determine the sequence of tasks. To determine the assignment of tasks to stations, the algorithm is hybridized using a dynamic programming procedure. Using dynamic programming, at any time a chromosome can be converted to an optimal solution (subject to the chromosome sequence). Since population diversity is very important to prevent from being trapped in local optimum... 

Karyotyping, is the process of classification of human chromosomes within the microscopic images. This is a common task for diagnosing many genetic disorders and abnormalities. Automatic Karyotyping algorithms usually suffer the poor quality of the images due to the non rigid nature of the chromosomes which makes them to have unpredictable shapes and sizes in various images. One of the main problems that usually need operator's interaction is the identification and separation of the overlapping/touching chromosomes. This paper presents an effective algorithm for identification of any cluster of the overlapping/touching chromosomes together with the number of chromosomes in the cluster, which... 

Vivid banding patterns in medical images of chromosomes are a vital feature for karyotyping and chromosome classification. The chromosome image quality may be degraded by many phenomenon such as staining, sample defectness and imaging conditions. Thus, an image enhancement processing algorithm is needed before classification of chromosomes. In this paper, we propose an adaptive and iterative histogram matching (AIHM) algorithm for chromosome contrast enhancement especially in banding patterns. The reference histogram, with which the initial image needs to be matched, is created based on some processes on the initial image histogram. Usage of raw information in the histogram of initial image... 

Evolutionary Algorithms are vastly used in development of rule based classifier systems in data mining where the rule base is usually a set of If-Then rules and an evolutionary trait develops and optimizes these rules. Genetic Algorithm is usually a favorite solution for such tasks as it globally searches for good rule-sets without any prior bias or greedy force, but it is usually slow. Also, designing a good genetic algorithm for rule base evolution requires the design of a recombination operator that merges two rule bases without disrupting the functionalities of each of them. To overcome the speed problem and the need to design recombination operator, this paper presents a novel algorithm... 

Recombination in Genetic Algorithms (GA) is supposed to extract the component characteristics from two parents and reassemble them in different combinations, hopefully producing an offspring that has the good characteristics of both parents, and this requires explicit chromosome and recombination, operator by design. This paper presents a novel evolutionary approach based on symbiogenesis which uses symbiotic combination instead of sexual recombination, and by using this operator, it requires no domain knowledge for chromosome or combination operator design. The algorithm is benchmarked on three problem sets: combinatorial optimization category, deceptive problems, and fully deceptive... 

Single Nucleotide Polymorphisms (SNPs), a single DNA base varying from one individual to another, are believed to be the most frequent form responsible for genetic differences. Genotype is the conflated information of a pair of haplotypes on homologous chromosomes. Although haplotypes have more information for disease associating than individual SNPs and genotype, it is substantially more difficult to determine haplotypes through experiments. Hence, computational methods which can reduce the cost of determining haplotypes become attractive alternatives. MEC, as a standard model for haplotype reconstruction, is fed by fragments as input to infer the best pair of haplotypes with minimum error... 

Recombination in the Genetic Algorithm (GA) is supposed to extract the component characteristics from two parents and reassemble them in different combinations hopefully producing an offspring that has the good characteristics of both parents and this requires explicit chromosome and recombination operator design. This paper presents a novel evolutionary approach based on symbiogenesis which uses symbiotic combination instead of sexual recombination and using this operator, it requires no domain knowledge for chromosome or combination operator design. The algorithm is benchmarked on three problem sets, combinatorial optimization, deceptive, and fully deceptive, and is compared with standard... 

Fuzzy rule-based classifiers are one of the famous forms of the classification systems particularly in the data mining field. Genetic algorithm is a useful technique for discovering this kind of classifiers and it has been used for this purpose in some studies. In this paper, we propose a new symbiotic evolutionary approach to find desired fuzzy rulebased classifiers. For this purpose, a symbiotic combination operator has been designed as an alternative to the recombination operator (crossover) in the genetic algorithms. In the proposed approach, the evolution starts from simple chromosomes and the structure of chromosomes gets complex gradually during the evolutionary process. Experimental... 

In this paper, a genetic algorithm for solving a class of project scheduling problems, called Resource Investment Problems, is presented. Tardiness of the project is permitted with a defined penalty. The decision variables are the level of resources and the start times of the activities. The objective is to minimize the sum of resources and delay penalty costs, subject to the activities' precedence relations and some other constraints. A revised form of the Akpan heuristic method for this problem is used to find better chromosomes. Elements of the algorithm, such as chromosome structure, unfitness function, crossover, mutation, immigration and local search operations, are explained. The...