Sharif Digital Repository

The most important factor in protein's function and its 3D structure is folding. Misfolding or native folding perturbation in some peptides and proteins force them get into amyloid fibril aggregation. It has been observed that these aggregations are the cause of some debilitative diseases especially ones that are related to aging like Alzheimer disease, Hantington's disease, typeII diabets etc. Recently it has been shown that specific regions in human catalase protein interact with some amyloid fibrils, such as Aß, IAPP, PrP etc. Inteins are self-splicing protein enzymes, which excise themselves from the mature protein and join the two flanking adjacent sequences by a new peptide bond in a... 

In recent years, machine learning has been widely used to solve various computational problems. One of the most fundamental and integral type of these issues is the problem of classification, in which the data samples of different types such as image, voice, or video are classified into different categories. Since these data types are inherently sequential, the problem of classifying sequential data, is of great importance. This problem has a wide range of applications, including but not restricted to, handwriting recognition, voice recognition, malware detection, and fraud detection in financial transactions. Regarding the fact that in many cases, the length of the sequence (which could be... 

Online social services and stores has become more popular in recent years . With the growing number of products and services available in these online stores and websites , recommendation systems play an important role in predicting which products and services are good for each user so that they can buy the product they need or use the online services they want without wasting their time to find the right ones . We propose a method called Temporal Socio-Content Poisson Factorization (TSCPF) which aims to recommend the most probable document to be read by each user at any given time . We model users’ behaviors and interests by using temporal point processes to capture temporal dynamics of... 

We consider a manifold M equipped with 1-forms eta(1)...eta(s) which satisfy certain contact like properties. We prove a generalization of the classical Darboux theorem for such manifolds  

In this thesis, we review the proof to standardness of Einstein solvamanifolds which is based on some results from Geometric Invariant Theory and stratification of topological spaces. Standardness is a very simple and yet powerful algebraic condition on the lie algebra of a solvmanifold which yields to remarkable existence and uniqueness and obstruction results  

Expansion of using social networks for reading and sharing news on the one hand, allows for quick and easy access to the news, but on the other hand, increases the spread of fake news and misleads many users. Therefore, identifying the fake news and attempting to mitigate its spreading on social networks is one of the major research areas in recent years. An important issue in this regard is reducing the time gap between news release time and identifying it as fake and starting to take action. Many researches has been done on detection of fake news, but since there is a trade-off between minimizing the time gap and maximizing accuracy, work on these models continues. There are also different... 

Quorum Sensing is a cell-to-cell communication pr°Cess depending on cell concentration. Communication among bacterial cells °Ccurs through small molecular signals called autoinducers. The consequences of quorum sensing include the activation of pathogenic properties and activation of the gene for biofilm formation. Biofilms are aggregations of bacteria that adhere to surfaces through extracellular polymeric substances. Bacteria in the biofilm phase are much more resistant to antimicrobial agents than their free-swimming counterparts (i.e. the bacteria in planktonic form). In this study, first a series of coumarin derivatives were synthesized; but due to low solubility of the synthesized... 

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...