Sharif Digital Repository

The classification of biological sequences is an open issue for a variety of data sets, such as viral and metagenomics sequences. Therefore, many studies utilize neural network tools, as the well-known methods in this field, and focus on designing customized network structures. However, a few works focus on more effective factors, such as input encoding method or implementation technology, to address accuracy and efficiency issues in this area. Therefore, in this work, we propose an image-based encoding method, called as WalkIm, whose adoption, even in a simple neural network, provides competitive accuracy and superior efficiency, compared to the existing classification methods (e.g. VGDC,... 

Normal human breathing exhibits complex variability in both respiratory rhythm and volume. Analyzing such nonlinear fluctuations may provide clinically relevant information in patients with complex illnesses such as asthma. We compared the cycle-by-cycle fluctuations of inter-breath interval (IBI) and lung volume (LV) among healthy volunteers and patients with various types of asthma. Continuous respiratory datasets were collected from forty agematched men including 10 healthy volunteers, 10 patients with controlled atopic asthma, 10 patients with uncontrolled atopic asthma, and 10 patients with uncontrolled non-atopic asthma during 60 min spontaneous breathing. Complexity of breathing... 

Recent studies have provided clues for participation of apoptosis related genes in the development of periodontitis. We examined expression of four apoptosome related genes namely CPSF7, AGO2, WDR33 and HUR1 in the blood and tissues of patients with stage III-IV periodontitis compared with control blood/tissue samples. Expression of AGO2 was significantly higher in the blood specimens of individual having periodontitis compared with healthy persons (ratio of mean expression = 6.9, P value = 4.79E−02). However, when categorizing individuals based on their gender, none of comparisons yielded significant results. Expression of AGO2 was not different between tissue samples of patients and... 

Introduction: In recent years, artificial intelligence (AI) has been applied in various ways in medicine and dentistry. Advancements in AI technology show promising results in the practice of orthodontics. This scoping review aimed to investigate the effectiveness of AI-based models employed in orthodontic landmark detection, diagnosis, and treatment planning. Methods: A precise search of electronic databases was conducted, including PubMed, Google Scholar, Scopus, and Embase (English publications from January 2010 to July 2020). Quality Assessment and Diagnostic Accuracy Tool 2 (QUADAS-2) was used to assess the quality of the articles included in this review. Results: After applying... 

Objective: Crohn's disease (CD) is one the important illnesses can affect any part of the gastrointestinal tract. CD is not easily diagnosed using the clinical tests. Thus, the discovery of proper methods would be a major step towards CD diagnosis. The aim of this study was to seek the metabolic biomarkers causes of CD compare to control group. Materials and Methods: In present study, we employed metabolic profiling using proton nuclear magnetic resonance spectroscopy (1HNMR) to find metabolites in serum which are helpful for the diagnosis of CD. Classification of CD and healthy subject was done using classification and regression trees (CART). The metabolites that caused changes in people... 

This paper presents a novel approach for evaluating LBP in various settings. The proposed system uses cost-effective inertial sensors, in conjunction with pattern recognition techniques, for identifying sensitive classifiers towards discriminate identification of LB patients. 24 healthy individuals and 28 low back pain patients performed trunk motion tasks in five different directions for validation. Four combinations of these motions were selected based on literature, and the corresponding kinematic data was collected. Upon filtering (4th order, low pass Butterworth filter) and normalizing the data, Principal Component Analysis was used for feature extraction, while Support Vector Machine... 

Alzheimer’s disease (AD) is currently ranked as the sixth leading cause of death in the United States and recent estimates indicate that the disorder may rank third, just behind heart disease and cancer, as a cause of death for older people. Clearly, predicting this disease in the early stages and preventing it from progressing is of great importance. The diagnosis of Alzheimer’s disease (AD) requires a variety of medical tests, which leads to huge amounts of multivariate heterogeneous data. It can be difficult and exhausting to manually compare, visualize, and analyze this data due to the heterogeneous nature of medical tests, therefore, an efficient approach for accurate prediction of the... 

This paper aims to propose a high-speed and accurate fully-automated method to detect COVID-19 from the patient's chest CT scan images. We introduce a new dataset that contains 48,260 CT scan images from 282 normal persons and 15,589 images from 95 patients with COVID-19 infections. At the first stage, this system runs our proposed image processing algorithm that analyzes the view of the lung to discard those CT images that inside the lung is not properly visible in them. This action helps to reduce the processing time and false detections. At the next stage, we introduce a novel architecture for improving the classification accuracy of convolutional networks on images containing small... 

LncRNAs are involved in the modulation of several signaling pathways which have a crucial effect in the differentiation of periodontal ligament cells and the induction of cementum regeneration. Autophagy and Wnt signaling are two important pathways with a wide range of interrelationships associated with periodontitis. We chose four lncRNAs based on their potential interaction with these two pathways. We examined the expression of FOXD2-AS1, NNT-AS1, GAS8-AS1, and CCAT1 lncRNAs in tissues and blood specimens of patients with periodontitis and unaffected controls using qRT-PCR. Expression amounts of FOXD2-AS1 were lower in blood of cases compared with controls (relative expression (RE) = 0.08,... 

Introduction: Cardiac contraction significantly degrades quality and quantitative accuracy of gated myocardial perfusion SPECT (MPS) images. In this study, we aimed to explore different techniques in motion-compensated temporal processing of MPS images and their impact on image quality and quantitative accuracy. Material and method: 50 patients without known heart condition underwent gated MPS. 3D motion compensation methods using Motion Freezing by Cedars Sinai (MF), Log-domain Diffeomorphic Demons (LDD) and Free-Form Deformation (FFD) were applied to warp all image phases to fit the end-diastolic (ED) phase. Afterwards, myocardial wall thickness, myocardial to blood pool contrast, and... 

Autism spectrum disorder (ASD) includes different neurodevelopmental disorders characterized by deficits in social communication, and restricted, repetitive patterns of behavior, interests or activities. Based on the importance of early diagnosis for effective therapeutic intervention, several strategies have been employed for detection of the disorder. The artificial neural network (ANN) as a type of machine learning method is a common strategy. In the current study, we extracted genomic data for 487 ASD patients and 455 healthy individuals. All individuals were genotyped in certain single-nucleotide polymorphisms within retinoic acid-related orphan receptor alpha (RORA), gamma-aminobutyric... 

In this work, high-performance thin-layer chromatography (HPTLC) coupled with multivariate image analysis (MIA) is proposed as a fast and reliable tool for authentication and adulteration detection of Iranian saffron samples based on their HPTLC fingerprints. At first, the secondary metabolites of saffron were extracted using ultrasonic-assisted solvent extraction (UASE) which was optimized using central composite design (CCD). Next, the RGB coordinates of HPTLC images were used for estimation of saffron origin based on principal component analysis (PCA). The PCA scores plot showed that saffron samples were clustered into two clear-cut groups which was 92% matched with the geographical... 

Protein inhibitors of activated STAT (PIAS) are involved in the regulation of the JAK/STAT signaling pathway and have interactions with NF-κB, p73 and p53. These proteins regulate immune responses; therefore dysregulation in their expression leads to several immune-mediated disorders. In the present study, we examined expression of PIAS1-4 in peripheral blood of patients with acute/chronic inflammatory demyelinating polyradiculoneuropathy (AIDP/CIDP) compared with healthy subjects. We demonstrated down-regulation of all PIAS genes in both AIDP and CIDP cases compared with controls. Similarly, comparisons in gender-based groups revealed down-regulation of these gene0s in patients of each... 

Background: Remote cardiac monitoring and screening have already become an integral telemedicine component. The wide usage of several different wireless electrocardiography (ECG) devices warrants a validation study on their accuracy and reliability. Methods: Totally, 300 inpatients with the Nabz Hooshmand-1 handheld ECG device and the GE MAC 1200 ECG system (as the reference) were studied to check the accuracy of the devices in 1 and 6-limb lead performance. Simultaneous 10-second resting ECGs were assessed for the most common ECG parameters in lead I. Afterward, 6-lead ECGs (limb leads), were performed immediately and studied for their morphologies. Results: Of the 300 patients, 297 had... 

The ability to speak lucidly plays a key role in social relations. Consequently, the role of the larynx is quite important, and timely diagnosis of laryngeal diseases has proved to be crucial. In this study, a simple computational model for inverse of speech production model is employed to extract the glottal waveform using speech signal. This waveform has useful information about vocal folds performance in terms of providing evidence for distinguishing pathological disorders. Furthermore, obtaining the significance of classification results is important, because it leads to reliable inferences. This study utilizes the sustained vowel sound /a/ and a well-referenced database, namely MEEI. In... 

Background: Colorectal cancer (CRC) is one of the most common malignancies in the world and has a high mortality rate. It is believed that dysfunction in the expression of mucins and aberrant expression of some lncRNAs are associated with the occurrence and development of CRC. Therefore, the aim of the present study was to investigate the expression of MUC15, MUC16, MUC20, PCAT1, CCAT1 and HOTAIR genes in colorectal cancer and its relationship with clinicopathological variables. Materials and methods: This research was prospective case-control study. Tumors from CRC patients were collected from the Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran. RNA... 

Growth arrest-specific gene 6 (GAS6) is a growth factor-like cytokine whose function is related with vitamin K. This protein interacts with receptor tyrosine kinase proteins such as Tyro3, Axl, and TAM Receptor family, therefore affecting the tumorigenic processes via different mechanisms. GAS6-antisense 1 (GAS6-AS1) is a long non-coding RNAs (lncRNAs) that is transcribed from a genomic regions nearby GAS6. This lncRNA is also implicated in the pathobiology of cancer. We intended to judge the role of GAS6 and GAS6-AS1 in the pathogenesis of breast cancer through appraisal of their expression levels in breast cancer tissues and their paired neighboring non-cancerous samples. Expression of...