Sharif Digital Repository

Automatic cell segmentation has various applications in different parts of science. The development of automated methods for cell segmentation, remains challenging in situations where there are touching cells. In this paper we propose a new method for separating touching cells. As the first step, we use a combination of graph segmentation algorithm and thresholding for segmenting foreground objects and producing a binary image. Next, boundary points of separation zone are selected by using a corner detection algorithm. Finally, the marker controller watershed transform is applied to separate touching cells at selected points. © 2008 IEEE  

We investigate the average frequency of positive slope ν +α, crossing the velocity field in the Burgers equation. The level crossing analysis in the inviscid limit and the total number of positive crossings of the velocity field before the creation of singularities are given. The main goal of this paper is to show that this quantity, ν+α, is a good measure for the fluctuations of velocity fields in the Burgers turbulence. © 2006 IOP Publishing Ltd  

For the design of rubble mound breakwaters on soft soil, it is essential to predict the behavior of soft soil and large deformations phenomena occurring in the course of construction of the rubble mound breakwater. Large deformations in various problems can be well simulated using the coupled Eulerian–Lagrangian (CEL) method. In this study, the CEL method has been used to simulate the rubble mounds construction on soft soil and predict the resulting settlements. To validate the numerical model, the results of three experiments conducted in the physical modeling laboratory at Kharazmi University were used. Also, two case studies of real rubble mound breakwaters constructed on soft seabeds... 

Inferring the structure of molecular networks from time series protein or gene expression data provides valuable information about the complex biological processes of the cell. Causal network structure inference has been approached using different methods in the past. Most causal network inference techniques, such as Dynamic Bayesian Networks and ordinary differential equations, are limited by their computational complexity and thus make large scale inference infeasible. This is specifically true if a Bayesian framework is applied in order to deal with the unavoidable uncertainty about the correct model. We devise a novel Bayesian network reverse engineering approach using ordinary... 

In this work, magnetite nanoparticles (mean particle size about 20 nm) were synthesized via coprecipitation method. In order to investigate the kinetics of nanoparticle formation, variation in the amount of reactants within the process was measured using pH-meter and atomic absorption spectroscopy (AAS) instruments. Results show that nanoparticle formation behavior can be described by Avrami equations. Transmission electron microscopy (TEM) and X-ray diffraction (XRD) were performed to study the chemical and morphological characterization of nanoparticles. Some simplifying assumptions were employed for estimating the nucleation and growth rate of magnetite nanoparticles  

Purpose: Endometriosis is a gynecological disease that causes the uterine lining to appear in other organs outside the uterus. As DNA methylation has an important role in this disorder, its profiling can reveal new information to improve the diagnosis and treatment of endometriosis patients. Methods: We conducted a genome-wide methylation profiling of ectopic and eutopic endometrial tissues from women with and without endometriosis using Infinium Human Methylation 450K BeadChip arrays. DNA methylation samples were collected from nine ectopic and nine eutopic endometrial tissues of endometriosis and six endometrial tissues of healthy controls. Results: Correlation heatmaps and the principal... 

The joint probability distribution function (PDF) of the height and its gradients is derived for a zero tension d + 1-dimensional Kardar-Parisi-Zliang (KPZ) equation. It is proved that the height's PDF of zero tension KPZ equation shows lack of positivity after a finite time tc. The properties of zero tension KPZ equation and its differences with the case that it possess an infinitesimal surface tension is discussed. Also potential relation between the time scale tc and the singularity time scale tc,v→0 of the KPZ equation with an infinitesimal surface tension is investigated. © 2004 Springer Science+Business Media, Inc  

We carry out an exact analysis of the average frequency ν+ αxi in the direction x i of positiveslope crossing of a given level α such that, h(x, t) h = α, of growing surfaces in spatial dimension d. Here, h(x, t) is the surface height at time t, and h is its mean value. We analyze the problem when the surface growth dynamics is governed by the Kardar-Parisi-Zhang (KPZ) equation without surface tension, in the time regime prior to appearance of cusp singularities (sharp valleys), as well as in the random deposition (RD) model. The total number N + of such level-crossings with positive slope in all the directions is then shown to scale with time as t d/2 for both the KPZ equation and the RD... 

Intermittency of height fluctuations in stationary state of the Kardar-Parisi-Zhang (KPZ) equation with infinitesimal surface tension in 1+1 dimensions was discussed. Stochastic differential equations were used for the study. It was found that the probability density function [in 1+1] is independent of the coefficient of the linear term. When the random force with smooth spatial correlation was considered, the problem changed to a more complicated one  

The Kardar-Parisi-Zhang (KPZ) equation with infinitesimal surface tension, dynamically develops sharply connected valley structures within which the height derivative is not continuous. We discuss the intermittency issue in the problem of stationary state forced KPZ equation in [Formula presented] dimensions. It is proved that the moments of height increments [Formula presented] behave as [Formula presented] with [Formula presented] for length scales [Formula presented]. The length scale [Formula presented] is the characteristic length of the forcing term. We have checked the analytical results by direct numerical simulation. © 2004 The American Physical Society  

Superparamganetic iron oxide-based contrast agents in magnetic resonance imaging (MRI) have offered new possibility for early detection of lymph nodes and their metastases. According to important role of nanoparticle size in biodistribution, magnetite nanoparticles coated with different polyethylene glycol (PEG) concentrations up to 10/1 PEG/iron oxide weight ratio in an ex situ manner. To predict the PEG-coated nanoparticle behavior in biological media, such as blood stream or tissue, colloidal stability evaluation was performed to estimate the coating endurance in different conditions. Accordingly, optical absorbance measurements were conducted in solutions with different values of pH and... 

The ruby lattice is a four-valent lattice interpolating between honeycomb and triangular lattices. In this work we investigate the topological spin-liquid phases of a spin Hamiltonian with Kitaev interactions on the ruby lattice using exact diagonalization and perturbative methods. The latter interactions combined with the structure of the lattice yield a model with Z2×Z2 gauge symmetry. We mapped out the phase diagram of the model and found gapped and gapless spin-liquid phases. While the low-energy sector of the gapped phase corresponds to the well-known topological color code model on a honeycomb lattice, the low-energy sector of the gapless phases is described by an effective spin model... 

The stochastic φ4-theory in d dimensions dynamically develops domain wall structures within which the order parameter is not continuous. We develop a statistical theory for the φ4-theory driven with a random forcing which is white in time and Gaussian-correlated in space. A master equation is derived for the probability density function (PDF) of the order parameter, when the forcing correlation length is much smaller than the system size, but much larger than the typical width of the domain walls. Moreover, exact expressions for the one-point PDF and all the moments 〈 φn 〉 are given. We then investigate the intermittency issue in the strong coupling limit, and derive the tail of the PDF of... 

In order to evaluate the long-term viability, the iron content stability, and the labeling efficiency of mammalian cells using magnetic cell labeling; dextran-coated ultrasmall superparamagnetic iron oxide (USPIOs) nanoparticles with plain surfaces having a hydrodynamic size of 25 nm were used for this study. Tests were carried out in four groups each containing 5 flasks of 5.5 × 10 6 AD-293 embryonic kidney cells. The cell lines were incubated for 24 h using four different iron concentrations with and without protamine sulfate (Pro), washed with phosphate-buffered saline (PBS) and centrifuged three times to remove the unbounded USPIOs. Cell viability was also verified using USPIOs. There... 

Foliar characteristics, especially the overall leaf shape, are useful features for the taxonomic identification of plants. Computer-aided plant species identification systems make it possible to investigate a large number of leaves in a short period of time. In this study, a fully automatic system was developed to accurately classify eight species of maples (Acer L.) in Iran using the leaf shape characteristics of harvested leaves. Maples show a broad range of leaf morphology, and the provided dataset is a diverse collection of simple leaves which can be a good representative of woody plant leaves with any overall shape and margin pattern. The applied method consisted of preprocessing,... 

The Kardar-Parisi-Zhang (KPZ) equation in (1 + 1) dimensions dynamically develops sharply connected valley structures within which the height derivative is not continuous. We develop a statistical theory for the KPZ equation in (1 + 1) dimensions driven with a random forcing that is white in time and Gaussian-correlated in space. A master equation is derived for the joint probability density function of height difference and height gradient P(h-h̄,∂xh,t) when the forcing correlation length is much smaller than the system size and much larger than the typical sharp valley width. In the time scales before the creation of the sharp valleys, we find the exact generating function of h-h̄ and ∂xh.... 

The Kardar-Parisi-Zhang (KPZ) equation in [formula presented] dimensions dynamically develops sharply connected valley structures within which the height derivative is not continuous. We develop a statistical theory for the KPZ equation in [formula presented] dimensions driven with a random forcing that is white in time and Gaussian-correlated in space. A master equation is derived for the joint probability density function of height difference and height gradient [formula presented] when the forcing correlation length is much smaller than the system size and much larger than the typical sharp valley width. In the time scales before the creation of the sharp valleys, we find the exact... 

The incidence of apnea-bradycardia episodes in preterm infants may lead to neurological disorders. Prediction and detection of these episodes are an important task in healthcare systems. In this paper, a coupled hidden Markov model (CHMM) based method is applied to detect apnea-bradycardia episodes. This model is evaluated and compared with two other methods based on hidden Markov model (HMM) and hidden semi-Markov model (HSMM). Evaluation and comparison are performed on a dataset of 233 apnea-bradycardia episodes which have been manually annotated. Observations are composed of RR-interval time series and QRS duration time series. The performance of each method was evaluated in terms of... 

Magnetite nanoparticles (mean particle size ranging from 10 to 20 nm) were prepared by a biomoleculeassisted solution-phase approach under ultrasonic irradiation. Cysteine was used as the capping agent in the solution. The results show that cysteine could be an efficient biocapping agent in producing Fe3O4 nanoparticles. The crystal structure and magnetic properties of the nanoparticles were characterized by XRD and VSM techniques, respectively. FT-IR was used to investigate the presence of cysteine on the nanoparticles surface. The influence of pH value of the solution on the size distribution and hydrodynamic size of nanoparticles were studied by TEM and DLS methods, respectively. The MTT... 

By detailed analytical treatment of the shock dynamics in the Burgers turbulence with large scale forcing we calculate the velocity structure functions between pairs of points displaced both in time and space. Our analytical treatment verifies the so-called Taylor's frozen-flow hypothesis without relying on any closure and under very general assumptions. We discuss the limitation of the hypothesis and show that it is valid up to time scales smaller than the correlation time scale of temporal velocity correlation function. We support the analytical calculation by performing numerical simulation of the periodically kicked Burgers equation. © 2008 The American Physical Society