Sharif Digital Repository

Bulk tissue RNA-seq data has been widely used for investigating the transcriptome and analyzing it for different purposes. A single bulk sample of a heterogeneous population includes different cell-types each in different proportions. Bulk tissue RNA-seq measures the average expression level of genes across these cell types and does not account for cross-subject variation in cell-type compositions. Furthermore, biological signals might be masked by taking the average of gene expressions. Because of these reasons, bulk-RNA-seq is not suffcient for studying complex tissues. Knowing these cell-type compositions are important, because studying cell-specific changes in the transcriptome might be... 

Water resources planning and management projects are done in order to accomplish several goals. Moreover, social, environmental, political etc impacts of such projects increase the complexity of the problem of choosing the best alternative among others. The project of diversion of water form Zab Watershed into Lake Urmia Watershed is one of these projects which regarding water demands and problems in Lake Urmia Watershed and also Zab Watershed water resources that exceed its water demands has been considered. Therefore, after conducting research studies, five locations have been determined as potential places to build a dam on the Zab River and transferring its water to Lake Urmia Watershed.... 

The problem of separation of audio sources is one of the oldest issues raised in the field of audio processing, which has been studied for more than half a century. The main focus of recent research in this field has been on improving the sound quality resulting from the separation of sound sources with the help of deep neural networks. This is despite the fact that in most applications of audio source separation, such as the application of meeting transcription, we do not need the separated audio of people. Rather, we need a pipeline of converting overlapping speech to text, which, by receiving the audio in which several people have spoken, outputs the text spoken by the people present in... 

Histopathology images exhibit significant variations across different datasets, which can pose challenges for machine learning models. When a model is trained on a certain domain, its performance may severely deteriorate when applied to unseen domains, magnifying the necessity of out-of-distribution generalization. To address this problem, we present a novel framework that harnesses the strengths of self-supervised training to extract domain-invariant features, and combine it with domain transfer techniques. Our approach is built on the premise that pre-trained vision transformers, highly effective in natural image analysis, can be adapted for histopathology image analysis in a... 

There are six core concepts in the organization theories that theorists rely on. These six concepts are: environment , social structure, technology, culture, physical structure, power and control. the insights of theorists about each of these concepts lead to different theory in case, they argue. The enactment environment theory by carl weik, is one way of conceptualizing the organizational environment within the interpretive paradigm and offer an approach about the organization and its environment. The logic of the enactment environment theory based on the belief that organizational realities parallel to people interact and negotiate and make sense of their experiences are socially... 

Study of hydraulic characteristics of two-phase flow is one of the important issues in hydraulic engineering. Two-phase flows usually accur in hydraulic structures such as pressurized flow tunnels, culverts, sewer pipes, junctions, and similar conduits. Under certain conditions, air may also be introduced into pressurized intake systems, which may form large bubbles in portions of the pipe. The bubbles may, in turn, cause an unstable slug flow, or other flow patterns. Slug flow is one of the most probable patterns in these flows. Prediction of pressure in this situation is a complex subject which despite its great importance is rarely discussed. In this study, the results of a laboratory... 

Datasets extracted from gene expression microarrays contain information about the phenotypic behavior of organisms. Turning this information into knowledge, i.e. finding associative genes with a given phenotype, is a daunting task. This is due to the high dimensionality of the data as the number of features on a gene expression microarray is usually very large. Moreover, a phenotype may change the expression pattern of a set of genes rather than changing each gene’s expression independently. To tackle the second problem, integrating other sources of information such as Protein-Protein Interaction (PPI) networks is required. In this thesis, the PPI network extracted from the String database... 

One of the ways to enhance the safety and economic performance of nuclear power plants, is to choose an appropriate policy for arrange the reactor fuel assembly in the beginning of each cycle. There are variety of ways to optimize the layout of the fuel in the reactor core, but to achieve more than one goal, choosing multi-objective method can be used.One of the intelligent optimization methods is the genetic algorithms that emulate nature of biological processes and can be used to optimize two or more of the target.The goals of this research is to increase the neutron multiplication factor is to make maximum use of the fuel in the reactor and maintain the radial power peaking factor for... 

Genome sequencing is one of the fundamental problems in today’s Biology. It has applications in significant problems such as finding association between an individual’s genome sequence and his phenotypes, discovering new genes, and finding evolutionary relations between organisms. Following the rapid advances in sequencing technologies and generation of a huge amount of short reads, efficient computational tools are needed for processing sequencing data. Shortness of reads is a factor that makes the task of reconstructing repetitive genomic regions complicated. In fact, the main challenge in both sequencing and resequencing problems is reconstruction of repeat regions. Common resequencing... 

Dnase I Hypersensitive Sites (DHSs) are known as comprehensive markers of DNA regulatory elements. The main function of regulatory elements is repressing or enhancing transcription of genes. Hence, the recruitment of the data is prevalent in many studies of genome. One of the applications of this data is to utilize it to predict active regulatory regions (Transcription Factor Binding Sites).There are different means to do this, divided in three major groups: first, the methods only use the number of DNase-seq reads that surround a candidate binding site. While robust, these methods do not reflect the shape of the signal. A second strategy uses a variety of approaches to model and identify... 

Nowadays, many progresses in biology and medicine such as diagnosis of diseases and drug discoveries depend heavily on analyzing biological datasets collected from advanced machines. DNA Microarrays are amongst such machines applicable in measuring the expressions levels of thousand of genes and genotyping of a set of single nucleotide polymorphic sites to name a few. Compared to the more advanced Next Generation Sequencing (NGS) technology, the microarray platform produces lower quality of datasets. However, there has been tones of efforts to produce, process, and curate datasets from microarrays based on well designed protocols for sample preparation, hybridization, image processing, and... 

Conventional MRI has been used to diagnose different types of brain injuries. However these methods have generally failed to diagnose mild types of injury. We are working on the specification of mild traumatic brain injury, using diffusion MRI data, based on a multi compartment simulation of white matter tissue. This effort is essential for better understanding of underlying tissue micro-structure changes in patients with trauma. Some studies have been used in similar data fitting approaches in order to estimate axon diameter distribution. Specifically, a comparative study between different Compartment Models has shown that “ActiveAx” model has the best agreement with underlying tissue... 

The present M.Sc. thesis consists of two sections including the static calculation and neutron noise calculation in rectangular and hexagonal geometries. The multi-group, two dimensional neutron diffusion equations and corresponding adjoint equations are solved in the static calculation. The spatial discretization of equations is based on Average Current Nodal Expansion Method (ACNEM). Size of nodes is the same size of the fuel assemblies in modeling both of rectangular and hexagonal geometries. The results are benchmarked against the valid results for BIBLIS-2D and IAEA-2D benchmark problems. In the second section, neutron noise calculations are performed for two types of noise sources,... 

Since direct measurement of neutron energy, unlike measuring the energy of ionizing radiation, is difficult, and the use of indirect methods for detecting and measuring neutron energy with high resolution and acceptable efficiency are not possible, the neutron time of flight method is the only direct neutron energy spectroscopy method. This issue is considered and evaluated in two methods: direct and scattering neutron time of flight. For this purpose, we have considered the 241Am-9Be source. In this method, neutron velocity can be determined by measuring time. is the time for the neutron that travels at distance of . The next method is the dispersed neutron time of flight method, in... 

The Electron Paramagnetic Resonance(EPR) is a retrospective and accurate dosimetry method to measure irradiated-induced radical population in the matter for determination the induced dose in the matter. The dose uncertainties will be about 1 percent. in the first stage of the present research, the response of EPR system to a reference sample has been measured. Then, responses due to the other samples has been compared with it and the secondary sample dose has been calculated. The reference sample usually is alanine. Unlike the perturbation theory forecast,the EPR signal intensity response to dose for alanine is not linear. In this thesis, first, the alanine samples (with pellet form) have... 

Isoforms are mRNAs that are produced from a same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of multiexon genes in humans have undergone Alternative Splicing. Although there are few changes in mRNA sequence, They may have a systematic effect on cell function and regulation. It is widely reported that isoforms of a gene have distinct or even contrasting functions. Most studies have shown that alternative splicing plays a significant role in human health and disease. Despite the wide range of gene function studies, there is little information about isoforms’ functionalities. Recently, some computational methods based on Multiple Instance... 

Validation of dosimetry accuracy in the context of advanced methods for radiotherapy, including proton therapy for ensure the accuracy of treatment plan is nessecory. One of the reasons for using MC code is the modeling of PT systems and the support of more accurate computation of dose distribution in clinical tarin. The purpose of this project is to validate the modeling of a spot scanning proton therapy system using a GATE MC code. In this study, the dose distribution calculated in the calibration process of the device and syno TPS is used as a criterion and the dose distribution obtained from the GATE MC code is calculated and validated with it. For this purpose, a water phantom was used... 

Neutron Radiography is one of the non-destructive testing methods of materials and due to its special application compared to gamma or X-ray imaging, it is highly regarded and developed in the world. A special application of neutron imaging is the imaging of materials with a low atomic number, even when coated with a material with a high atomic number. Neutron Radiography has different methods for capturing and recording images by neutrons. Among these methods, the following 7 methods can be mentioned: Neutron radiography (film), Track Etch, Digital neutron imaging, Neutron camera (DR System), Image plates (CR System), Flat panel silicon detectors (DR system) and Micro channel plates (DR... 

Dams are constructed for various purposes, including flood control, drinking water supply, agriculture irrigation, electricity generation, etc. The dam converts the river's natural and dynamic flow into a stagnant artificial lake where humans control the outflow of water, reducing the velocity of water movement and increasing residence time, followed by the entry and accumulation of nutrients in the reservoir, resulting in phenomena such as thermal stratification and eutrophication. Due to the changing climatic conditions of Iran and sudden droughts and wet periods, the need to monitor the water level of dam reservoirs and their water quality to keep them in the best operational condition... 

Following dramatic changes after using deep learning method as a solution for Natural Language Processing tasks, Transformer architecture get popular. Based on that, then BERT Language model presented and get state-of-the-art as a solution for a lot of language processing tasks. It was a turning point in Natural Language Processing field. Also, in cross-lingual methods research line motivated by developing a common space for representation of language units, e.g. words, sentences, in more that one language, get some remarkable improvements. However, for languages distant from English such as Persian or Arabic the methods' performance was not clear. In this work, we performed some innovative...