Sharif Digital Repository

Feature Extraction is an inseparable part of many machine learning algorithms. The extracted feature from the input data, while preserving the label information as much as possible, should make label inference more feasible than the input data itself. Additionally, in many machine learning, information theory, and privacy problems we have another constraint on eliminating sensitive, confounding, or unwanted information from the feature. That is why the problem of feature extraction with information regularization (preserving desired information and removing unwanted one) becomes an important issue that has been considered from different aspects, inter-connecting various fields.In this... 

Asparagainase is a therapeutic enzyme which has been a subject of research for decades. The enzyme catalyzes the hydrolysis of the amide group in asparagine and similar amides. Altering the substrate specificity and stabilization of this enzyme can increase its therapeutic properties. Moreover, asparaginases may be evolved to catalyze the hydrolysis of other similar compounds. These can be achieved through directed evolution and computational methods.In this study, the gene encoding L-asparaginase II enzyme from E. coli was amplified by polymerase chain reaction (PCR) and was cloned into an expression vector. The recombinant protein was expressed by an appropriate host secreting the... 

Single-cell RNA-sequencing has opened opportunities to unlock the cell transcriptome at cellular-level resolution and investigate cell population structures and cell-type-specific gene expression patterns. Previously, we were only able to perform bulk RNA sequencing regardless of the cell type composition of cell populations. Now, with the advancements in sequencing technologies, it is possible to extract cell-level and cell-type-specific sequences, related to each type of cell separately and in a scalable and high-throughput manner. For such large studies, logistical constraints inevitably dictate that data be generated separately i.e., at different times and with different operators.... 

The reductase enzymes perform an important function in the cell. These enzymes are usually coupled with other enzymes and participate in reactions such as halogenation, reduction of alkene, and carboxylic acids. These reactions are carried out by reproducing cofactors such as FADH2 and NAD+; however, there is no evidence that this enzyme alone can perform an organic reaction. In this work, we aim to examine whether recombinant flavin reductase can carry out organic reactions. In order to amplify the flavin reductase enzyme gene from the E. coli genome by PCR (Polymerase Chain Reaction) method, two synthetic primers were designed; The forward primer of the gene contained a cleavage site for... 

In this thesis, we have shown that unique subgraphs of a graph have a key role in structure of the graph. Using unique subgraph which is called “anchor” here, the reconstruction of graphs is explained. Using anchor, we have shown that almost every n-vertex graph is determined by its 3log(n)-vertex subgraphs. In the second part of the thesis, a novel randomized algorithm is proposed for the graph isomorphism problem which is very simple and fast. It solves this problem with running time O(n^{2.373} \log(n)) for any pair of $n$-vertex graphs whose adjacency matrices are not strongly co-det. Strongly co-det pair of matrices have very special symmetric structure which can be disarranged to be... 

Using automated assistants in medical applications has been increased in recent years. One of the most popular methods are artificial intelligence and deep learning methods which are specifically used in medical images analysis. Using these methods can improve the diagnosis accuracy, while performing in a faster time. So these methods can reduce the economical costs, error rate, and response time. But one important challenge in deep learning methods, is the interpretability of neural networks. In this research we focused on introducing an interpretability method for our pixel-wise segmentation network which is applied to the lung nodules dataset. In this research we first implemented a... 

The highly developed biological data collection methods enable scientists to capture protein-protein interaction (PPI) in the human body, which could be analyzed as biological networks such as protein-protein interaction networks. These networks reveal essential information about the biological process in human cells and can be used to identify genes associated with cancers. Effectively identifying disease-related genes would contribute to improving the treatment and diagnosis of various diseases. Current methods for identifying disease-related genes mainly focus on the hypothesis of guilt-by-association and do not consider the global information in the PPI network. Besides, most methods pay... 

Cancer is the leading cause of death worldwide, and colorectal cancer is the second leading cause of death in women and the third in men. On the other hand, colon polyps can cause colorectal cancer. Therefore, early detection of polyps is of great importance. In recent years, many methods have been proposed for polyp detection using deep learning with high accuracy, but most of them have problems with speed, accuracy, or interpretability. Speed is important because colonoscopy should be performed as quickly and promptly as possible, and in many cases, it is not possible to repeat the colonoscopy. In addition, many of them only address the issue of polyp detection, while from a medical point... 

One of the main sources of genetic variations are structural variations, including the widespread Copy Number Variations (CNVs). CNVs include two types, copy of genetic material (duplication) and loss of part of genetic sequence (deletion) and typically range from one kilobase pairs (Kbp) to several megabase pairs (Mbp) in size. Most of the copy number variations are occured in in healthy people; however, these variants can also contribute to numerous diseases through several genetic mechanisms (e.g. change gene dosage through insertions, duplications or deletions). The CNV study can provide greater insight into the etiology of disease phenotypes. Nowadays, with the huge amount of investment... 

The main goal of this thesis is to classify minimal translation surfaces of three-dimensional Euclidean space. In pursuing that, a method will be introduced that constructs explicit examples. A translation surface is the sum of two regular curves α and β. A minimal surface is a surface, with zero mean curvature. Will be shown that besides the know examples (plane and surfaces of Scherk type) any minimal translation surfaces can be described Ψ(s, t) = α(s)+α(t) , where α is the unit speed curve and its curvature κα is a positive solution of (y ′ ) 2 + y 4 + c3y 2 + c 2 1 y −2 + c1c2 = 0 and its torsion is τ (s) = c1/κ(s) 2 . the above coefficients and their relations will be described  

A decade after discovery of graphene, the unique properties and characteristics of two-dimensional materials, particularly an emerging family of carbides and nitrides (MXenes), have attracted the attention of researchers. MXenes are two-dimensional structures of two or more layers of transition metals, with interstitial carbon and/or nitrogen atoms, with exceptional properties such as high specific surface area, excellent elastic modulus, metallic conductivity, and various termination groups. These properties can be altered by various factors, including chemical composition and synthesis processes, and any changes in these factors significantly affect the properties of MXene sheets. In this... 

Transglutaminase 2 enzyme is expressed in various parts of the human body and is present in almost all tissue cells. The function of this enzyme is multiple and it catalyzes different reactions depending on where it is located in the cell. The most important activities of this enzyme are: isopeptide bond formation between the side chains of two proteins (transamidation reaction), diamidation reaction (hydrolysis of amide bond), esterification, kinase activity. The hen egg white lysozyme protein is another natural antimicrobial protein that has been extensively studied. The muramidase activity of egg white lysozyme against highly gram-positive bacteria is well known, and this property has... 

Multiple object tracking refers to the detection and following of target object classes in video sequences. In this task, all objects belonging to the target classes in the video are detected simultaneously in each frame, and a unique ID is assigned to each of them throughout the video. In recent years, the use of graph neural networks for solving this problem has received significant attention because these models are suitable tools for discovering and improving the relationships between objects in the scene, which can greatly assist in better object pairing. However, there are various challenges to using graph neural networks, the most important of which is the limitation of input graph... 

With the advancement of technologies related to electroencephalography signals, brain and computer interfaces, the program has received much attention. This report deals with one of the new and important issues in this field, i.e. converting thought into text. In this research, the letters, words, and sentences that a person thinks or utters in his mind are decoded and converted into text based on electroencephalography signals. There is still no credible and credible information in neuroscience about whether the same patterns of neuronal activity occur in the brain when thinking about similar letters or words. However, the remarkable growth and development of deep neural networks has made... 

Age-related macular degeneration (AMD) is the most common cause of vision loss in those aged over 50. There are two main types of AMD, Wet and Dry form. Wet AMD is more severe though more treatable. There are three conventional treatments for AMD including laser therapy, surgery and intravitreal injection of anti-VEGF into the eye. Delivery of drugs to the posterior segment of the eye is still challenging and several implants and devices are currently under investigation for their ability to stimulate the retina, producing visual percepts. The application of intravitreal bevacizumab (Avastin) has expanded tremendously from the time of its introduction into ophthalmic care since 3 years ago.... 

In analyzing the structural organization of many real-world networks, identifying important nodes has been a fundamental problem. The network centrality concept deals with the assessment of the relative importance of network nodes based on specific criteria. Central nodes can play significant roles on the spread of influence and idea in social networks, the user activity in mobile phone networks, the contagion process in biological networks, and the bottlenecks in communication networks. High computational cost and the requirement of full knowledge about the network topology are the most significant obstacles for applying the general concept of network centrality to large real-world social... 

Controlled release is a crucial factor in tissue engineering and cancer-therapy applications. The main purpose of current research is to synthesis smart magnetic nanocarriers for hydrophobic drug and embedding them in a fibrous platform for anti-cancer/ tissue engineering applications. In this regard, three different drug delivery systems of magnetic nanocolloid, magnetic fibers and hydrogels were studied. In the first phase, superparamagnetic iron oxide nanoparticles (SPIONs) were synthesized and then were modified using oleic acid and thermo-sensitive polymer of pluronic F127/F68. After characterization of this composite, Response Surface Methodology (RSM) was applied to model the lower... 

Delivering multimedia over wireless Networks is a very challenging task. Multimedia delivery inherently has strict quality-of-service (QoS) requirement on bandwidth, delay, and delay jitter.. The advent of wireless networks further exacerbates the variance of network conditions and brings greater challenges for multimedia delivery. Network coding is realized to have great potential for improving throughput limitation of current multi-hop wireless networks. The most significant characteristic of network coding is to send more information in each transmission by combining information from different sources leading to increased bandwidth and network throughput, decreased energy consumption and... 

In this thesis, a novel method for the design of adaptive wavelet transforms based on the lifting scheme structure is presented. We have compared the proposed adaptive wavelet design method with the exisiting algorithms by providing a brief survey of the recent adaptive lifting scheme techniques. In addition, object detection is selected as the target application and two novel template matching algorithms based on the proposed adaptive lifting scheme transform, called LAPT and RASIM, are presented. As the main building block of the proposed algorithms, given an object as a template, we first select a set of coefficients as object features in the wavelet transform domain and then build an... 

In this study, biodiesel production using enzymatic method for transestrification of castor oil was investigated. It was found that the yield of biodiesel production is affected by methanol to oil molar ratio, temperature, enzyme amount, water content and reaction time. Effective factors were determined first, using two-factorial design method. Methanol to oil molar ratio was found as the most effective factor. Response surface methodology coupled with central composite design was utilized for statistical modeling of enzymatic biodiesel production and the reaction time was found as a non-significant factor. In another attempt, three factors including methanol to oil molar ratio, temperature,...