Sharif Digital Repository

In this paper, we have proposed, designed, implemented, and characterized a low-cost camera-based microarray scanner which is capable of imaging fluorescently-labeled DNA or Protein microarrays. The proposed system is designed to simultaneously measure two different fluorescent dyes using two parallel channels which increase the overall scan speed. We have shown that the wide dynamic range of system makes it able to detect fluorophore densities from 100-106 molecule/μm2. In each capture, a 5.6 mm × 3.7 mm field is imaged on a 22.3 mm × 14.9 mm (18 megapixels) CMOS sensor. Therefore, the microarray can be scanned with ∼ 1μm2 spatial resolution which is high enough to distinguish borders of... 

We study the sample complexity of learning a high-dimensional simplex from a set of points uniformly sampled from its interior. Learning of simplices is a long studied problem in computer science and has applications in computational biology and remote sensing, mostly under the name of “spectral unmixing.” We theoretically show that a sufficient sample complexity for reliable learning of a K-dimensional simplex up to a total-variation error of ε is O(Kε2 log Kε ), which yields a substantial improvement over existing bounds. Based on our new theoretical framework, we also propose a heuristic approach for the inference of simplices. Experimental results on synthetic and real-world datasets... 

Genome-Wide Association Study (GWAS) addresses the problem of associating subsequences of individuals' genomes to the observable characteristics called phenotypes. In a genome of length G, it is observed that each characteristic is only related to a specific subsequence of it with length L, called the causal subsequence. The objective is to recover the causal subsequence, using a dataset of N individuals' genomes and their observed characteristics. Recently, the problem has been investigated from an information theoretic point of view in [1]. It has been shown that there is a threshold effect for reliable learning of the causal subsequence at Gh ( N L/G ) by characterizing the capacity of... 

Background: Nutrigenomic has revolutionized our understanding of nutrition. As plants make up a noticeable part of our diet, in the present study we chose microRNAs of edible plants and investigated if they can perfectly match human genes, indicating potential regulatory functionalities. Methods: miRNAs were obtained using the PNRD database. Edible plants were separated and microRNAs in common in at least four of them entered our analysis. Using vmatchPattern, these 64 miRNAs went through four steps of refinement to improve target prediction: Alignment with the whole genome (2581 results), filtered for those in gene regions (1371 results), filtered for exon regions (66 results) and finally... 

A central machine is interested in estimating the underlying structure of a sparse Gaussian Graphical Model (GGM) from a dataset distributed across multiple local machines. The local machines can communicate with the central machine through a wireless multiple access channel. In this paper, we are interested in designing effective strategies where reliable learning is feasible under power and bandwidth limitations. Two approaches are proposed: Signs and Uncoded methods. In the Signs method, the local machines quantize their data into binary vectors and an optimal channel coding scheme is used to reliably send the vectors to the central machine where the structure is learned from the received... 

In this paper, we develop the machinery of real interference alignment. This machinery is extremely powerful in achieving the sum degrees of freedom (DoF) of single antenna systems. The scheme of real interference alignment is based on designing single-layer and multilayer constellations used for modulating information messages at the transmitters. We show that constellations can be aligned in a similar fashion as that of vectors in multiple antenna systems and space can be broken up into fractional dimensions. The performance analysis of the signaling scheme makes use of a recent result in the field of Diophantine approximation, which states that the convergence part of the... 

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... 

ABSTRACT: Pyrolysis, so-called devolatilization, is one of the first steps of all thermochemical processes occurring in an inert atmosphere. The authors discuss the main kinetic features of heavy oil pyrolysis, on the basis of the data derived m from a TGA analysis and by using a kinetic model. The samples were heated over a range of temperature from 400 K to 430°C at various heating rates between 10 and 80°C/min. Experimental results showed that the effect of time is considerable in the case of tar conversion, compared to char and gases  

In this paper, we introduce new unblind and blind multiuser detectors for an optical code-division multiple-access system. The detectors have two soft and hard stages. In the soft stage, a soft estimation of the interference is obtained by solving an unconstrained maximum-likelihood problem via the iterative expectation-maximization (EM) algorithm. Then, the hard stage detects the user information bit by solving a one-dimensional Boolean constrained problem conditioned on knowing the interference. Our results reveal that the proposed detectors have very low complexity, and are robust against changes in parameters. Moreover, the numerical results illustrate that despite of their simplicities,... 

In this article, experimental and numerical investigations are performed to study a thermogravitational column (TGC) for the separation of toluene/n-heptane mixture. This research has tried to determine the main significant parameters and their effects on the performance of the process. In experimental examinations, the influence of the main parameters such as feed flow rate, cut and temperature gradient on the performance of the TGC efficiency is studied. In addition, computational fluid dynamics is used to simulate the separation process in this review. The response surface methodology (RSM) was also applied to minimize the number of runs and investigate the optimum operating conditions.... 

In this article, numerical simulations are performed to investigate the performance of the thermal diffusion column for the separation of n-heptane/benzene mixture. The present work tried to optimize column by analyzing significant parameters such as feed flow rate, temperature and cut. In order to obtain the hydrodynamic and temperature and mass distribution inside thermal diffusion column, computational fluid dynamic (CFD) method is applied to solve the Navier–Stocks equations. Numerical simulations are conducted to study the main parameters in both stationary and time-dependent conditions. By using the separation work unit as a function of cut, the optimal cut for maximum SWU occurs... 

The study of salt tolerance mechanisms in halophyte plants can provide valuable information for crop breeding and plant engineering programs. The aim of the present study was to investigate whole transcriptome analysis of Aeluropus littoralis in response to salinity stress (200 and 400 mM NaCl) by de novo RNA-sequencing. To assemble the transcriptome, Trinity v2.4.0 and Bridger tools, were comparatively used with two k-mer sizes (25 and 32 bp). The de novo assembled transcriptome by Bridger (k-mer 32) was chosen as final assembly for subsequent analysis. In general, 103290 transcripts were obtained. The differential expression analysis (log2 FC > 1 and FDR < 0.01) showed that 1861... 

In this paper, a new method is proposed for solving the obstacle avoidance problem of discretely actuated hyper-redundant manipulators. In each step of the solution, the closest collision to the base is removed and then the configuration of the next part of the manipulator is modified without considering the obstacles. This process is performed repeatedly until no collision is found. The Suthakorn method is applied to solve the inverse kinematics problem. Two new ideas are proposed to reduce the errors of this method: the two-by-two searching method, and iterations. To verify the proposed method, some problems are solved numerically for 2D and 3D manipulators, each in two different obstacle...