Sharif Digital Repository

Development of DNA sequencing technologies in the recent years magnifies the need for computational tools in genomic data processing, and thus has attracted inten- sive research interest to this area. Among them, Genome-Wide Association Study (GWAS) refers to discovering of causal relationships among genetic sequences of living organisms and the macroscopic phenotypes present in their physiological structure. Chosen phenotypes for genomic association studies are mostly vulnerability or im- munity to common genetic diseases. Conventional methods in GWAS consists of statistical hypothesis testing algorithms in case/control approaches; Most of which are based upon single-locus analysis and... 

Using statistical tools in machine learning and artificial intelligence to infer knowledge from high-dimensional data, namely data science, has attracted a siginificant research interest over the past two decades. The number of real databases around the world continues to grow with an increasing pace, which are used to store huge amounts of high-dimensional data points of various types. However, applying machine learning tools to high-dimensional data has also raised potential concerns, specially with respect to the fundamental capability of such tools to be useful in practical situations. In fact, the large dimension of a data could eventually damage the outcome of any statistical... 

“Sustainable development” is a frequently used phrase, but the idiom has been experienced little since it was coined by the Brundtland, due to its intrinsic complications. The issue is going to compromise two key components; economy and ecology. One of the solutions based on concept of sustainable development that has been proposed for maintaining water quality at acceptable levels is to cap pollutant emissions at a sustainable level, then establish an economic market in which the right to discharge pollutants is traded according to market supply and demand mechanisms. Water quality trading or pollution trading is one such kind of market-based program that has also been described using names... 

One of the main challenges of Water Resources Planning and Management (WRPM) is to balance water allocation between different uses. Usually, due to political and economic power of other uses, ecosystem receives less attention. Environmental flow is the allocated flow to ecosystem. Ecosystem provides a wide range of services to humanity. Therefore, environmental flow is not exclusively a matter of sustaining ecosystem but also a matter of providing humans with better life. Several methods have been developed to determine the environmental flow but only a few consider its socio-economic aspects. Consideration of these aspects could assist decision-makers with determining the optimum flow and... 

Sustainable agricultural development in the country without regard to water supply problems in terms of time and place is not possible. Construction of water storage tanks filled with water and seasonal use in dry seasons in the effective action in the optimal use of water in the climate of (low and irregular rainfall) is. The most important step in the construction of water storage tanks to choose the best point for the construction of the reservoir basin in order to reduce costs and increase efficiency. Chndmyarh different methods to decide the best option for finding a few options from there. Among these methods can be Tapsys two methods (TOPSIS) and hierarchical analysis (AHP) pointed... 

Nowadays, applications of the synthetic materials are developing in civil engineering projects and widely used in these projects. Therefore, during previous years; use of the Geotextiles as one of the Geosynthetic materials in order to filtration, drainage, separation, soil protection, etc have developed ever-increasing. The goal of this research is modeling and studies of the Geotextiles application in the downstream filter zone of embankment dams in combination with granular materials using FLAC2D software. Gordeh Bin embankment dam situated in West Azerbaijan province has been chosen as case study. In this matter, different models have been made with changes in thickness of the inclined... 

Groundwater quality protection has a significant importance due to abundant applications of these resources in various fields such as agriculture, industry and drinking water. Removal of groundwater pollution is a time and money consuming process and often pollution is detected when improving the quality of groundwater is nearly impossible. For this vulnerability assessment there are three methods: Processing, Overlap-Index and Statistical Methods. Overlap-Index is composed of variety of maps such as Geology, Soil, Groundwater Depth and etc which uses in determining of vulnerability Index. In the present study for underground pollution potential determining, four indexes such as AVI، GOD،... 

Entrance of air to close water conduits occurs in many ways. This phenomenon makes displeasing effects on water transport structures. Two-phase flows in closed conduits are studied experimentally, numerically and theoretically. Even after decades, due to the complexity of the subject, these studies still require development and reformation. Numerical and theoretical two-phase models are often limited to a special regime of flow."Volume Of Fluid"(VOF) is a model for non-mixing two-phase flows. "Fluent" software uses this model in this field of flows. Volume of fluid is used successfully in some problems like dam break or rising bubbles. Main disadvantage of this model is distribution of the... 

Today, computer simulations are employed prevalently by researchers to understand biological processes. The tendency to use computational methods has been increased recently due to the high costs and errors of experimental methods. Integrins are membrane proteins that mechanically attach cells to the extra cellular matrix (ECM) and derive some behaviors such as cell migration. Moreover, integrins have biochemical functions. They transduce environment signals and trigger chemical pathways. As a result, integrins regulate cell shape, motility, etc. The investigation of integrin behavior in a real environment is very difficult due to the presence of many other proteins that interfere with the... 

Gene expression microarrays can be used for precision medicine and targeted therapies. The data generated by microarrays are high-dimensional causing statistical inference of any parameter a daunting task. In this thesis, it is shown that regardless of high-dimensional datasets produced by microarrays, the inference can be robust in the sense that random selection of features results in the same conclusion as far as the number of selected features are chosen appropriately. Stratifying patients with breast cancer based on their gene expression levels shows that patient subtypes are almost independent of the feature selection strategy. Moreover, using less noisy datasets coming from RNAseq... 

Diabetes mellitus is a group of disorders where the level of blood sugar remains high for a long period of time. This increase may be due to either reduced insulin secretion from the pancreatic gland, or insulin resistance, or both. Another key reason is the destruction of beta cells due to functional defect in the body’s immune system. Current treatments include controlling diet, insulin injection and pancreatic transplantation, all of which are temporary. For this reason, finding genetic factors participating in the progression of the disease and adapting treatments to these factors are under intensive studies.In this thesis, available information resources including genomic, biological... 

Distributed learning has been a popular area of machine learning for researchers according to having access to an unprecedented amount of data distributed over many clients in a network. Moreover, high dimensional learning, when the dimensions of data are high but the effective features are low, has great usage in learning especially in medical science. In this paper, we attempted to develop a method for learning high-dimensional sparse problems in a distributed manner, whit a star shape network. Our main focus in this research is on optimizing the communication flow in the network. The prominent idea of our proposed method is to extract the main feature in the first step, then continuing... 

The increasing advancement of computed tomography (CT) systems has led to the recognition of this type of imaging as an accurate and reliable method in diagnosing and assessing damage to humans and materials. Adding dual energy imaging to these systems can increase the material's ability to differentiate in this system and provide higher contrast than usual. Recently, a medical imaging technique has been introduced that uses an X-ray tube and two detector layers on top of each other, each layer absorbing a different energy spectrum.dual layer computed tomography system has been introduced today as a suitable tool for evaluating and diagnosing many diseases, due to the reliability and... 

Over the past few decades, brachytherapy has been used as one of the leading methods in the treatment of a wide range of cancers, including breast cancer. Due to the high dose gradient of brachytherapy radiation sources, this method is used to treat such tumors that are grown at the vicinity of sensitive points or tissues of the body. Therefore, as irradiation get started by implanting radiation sources in the desired position, at the same time healthy tissue are also receiving the same dose as tumor tissues do Reducing healthy tissue dose along with increasing the dose of tumor tissue is one of the challenging topics that researchers are always looking for a solution. In the left breast... 

Prediction of groundwater level fluctuations is absolutely necessary for the proper manag ement of these precious resources. There are different methods to predict hydrological time series such as groundwater level. Linear models inefficiency in predicting nonlinear and n on-stationary time series cause researchers widely use artificial intelligence techniques such as Artificial Neural Networks (ANN), Fuzzy Inference System (FIS), Genetic Algorithm (GA) and their hybrid models such as Artificial Neural – Fuzzy Inference System (ANFIS). These smart models are capable to simulate nonlinear and non-stationary time series in suitable accu-racy using by a few time and data. By emersion of Wavelet... 

Numerical simulations and large eddy simulations (LES) of turbulent flow downstream of diversion dam , pool-riffle bedform in different geometrical ratios (different lengths of riffle and pool) with flow Reynolds number of 3.0 E+04 to 3.3E+04, downstream of special case study "Mill and Moghan diversion dam" with Froude number of 0.5 are presented The calculations are performed using a computational fluid dynamics model, FLOW-3D, which solves the Navier-Stokes equations in three dimensions with finite volume method. Numerical simulations are validated by comparing the numerical results of time-averaged flow patterns downstream of pool-riffle sequence with that of the experimental... 

Coinciding with the worldwide environmental issues and increasing demand for clean energy sources, hydropower plants have highly attracted decision- makers attention. Low manufacturing costs and pollutions which are made by these plants in comparison with another types of powerhouses, could be reason of that. And so on, hydropower locating and evaluating studies have been highly increased recently, specifically in developing countries. From the point of operation procedure, hydropower plants are generally divided in two types, run-of-he-river and storage projects. This study has concentrated on run-of-he-river projects and due to spotting plant location, Sefidbarg river basin... 

In this thesis, we determine the optimal capacity of the power plants considering site specifications and Flow Duration Curve and evaluating economic parameters. Finally a design with more sufficient economical and hydrualical performance would be selected. The optimization algorithm used in this thesis is called "Charged System search" that is one of the newest meta-heuristic algorithms. This algorithm is inspired by the coulomb and gauss's laws of electrostatics in physics and utilizes a number of charged particles which influence each other based on their fitness values and their separation distances considering the governing law of coulomb.The proposed method in this thesis can be... 

Prostate cancer is the second most common cancer in men and the fourth most common cancer in all cancers. Cancer treatment is done according to the type of cancer and its diagnosis stage with different treatment methods and plans. Brachytherapy is one of the most common methods of cancer treatment along with teletherapy, surgery and chemotherapy. In this method, the source of radiation is located near or inside the tumor, and its advantage is to achieve a lower dose ratio of healthy tissue to the tumor is lower compared to teletherapy. One of the challenges in brachytherapy is to prescribe the appropriate treatment plan for the patient, so that the maximum dose of sources reaches the...