The scientific literature is full of studies that provide evidence highlighting the role of microbiome in type 2 diabetes (T2D) development and progression, still, discrepancies are evident when studying the link between certain taxonomic groupings and T2D, thus, eliminating the discrepancy between such studies is crucial to build on a robust systematic approach to identify the possible linkage between such taxonomic groups and diabetes development and progression, hence developing a potential treatment. Here we aimed to use a publicly available data set of gut and nares microbiome of

Purpose: Heart segmentation in cardiac magnetic resonance images is heavily used during the assessment of left ventricle global function. Automation of the segmentation is crucial to standardize the analysis. This study aims at developing a CNN-based framework to aid the clinical measurements of the left ventricle and right ventricle in cardiac magnetic resonance images. Methods: We propose a fully automated framework for localization and segmentation of the left ventricle and right ventricle in both short- and long-axis views from cardiac magnetic resonance images. The localization module

The prevalence of skin melanoma is rapidly increasing as well as the recorded death cases of its patients. Automatic image segmentation tools play an important role in providing standardized computer-assisted analysis for skin melanoma patients. Current state-of-the-art segmentation methods are based on fully convolutional neural networks, which utilize an encoder-decoder approach. However, these methods produce coarse segmentation masks due to the loss of location information during the encoding layers. Inspired by Pyramid Scene Parsing Network (PSP-Net), we propose an encoder-decoder model

Skin cancer is one of the leading causes of death globally. Early diagnosis of skin lesion significantly increases the prevalence of recovery. Automatic classification of the skin lesion is a challenging task to provide clinicians with the ability to differentiate between different kind of lesion categories and recommend the suitable treatment. Recently, Deep Convolutional Neural Networks have achieved tremendous success in many machine learning applications and have shown an outstanding performance in various computer-assisted diagnosis applications. Our goal is to develop an automated

OBJECTIVES Minimally invasive aortic valve replacement has proven its value over the last decade by its significant advancement and reduction in mortality, morbidity and admission time. However, minimally invasive aortic valve replacement is associated with some on-site difficulties such as limited aortic annulus exposure. Currently, computed tomography scans are used to evaluate the anatomical relationship among the intercostal spaces, ascending aorta and aortic valve prior to surgery. We hypothesized that quantitative measurements of access distance and access angle are associated with

Transforming growth factor beta (TGF-β) acts as a tumor-suppressing cytokine in healthy tissues and non-malignant tumors. Yet, in malignancy, TGF-β can exert the opposite effects that can promote proliferation of cancer cells. C-Kit plays a prominent role in stem cell activation and liver regeneration after injury. However, little is known about the cross-talk between TGF-β and C-Kit and its role in the progression of hepatocellular carcinoma (HCC). Here, we studied the effect of increasing doses of TGF-β1 on CD44+CD90+ liver stem cells (LSCs) and C-Kit gene expression in malignant and

Metagenomics is a rapidly emerging field that is concerned with the study of microbial communities 'microbiomes' on both levels of taxonomic classification and functional annotation. Targeted amplicon (16S rRNA) and whole genome shotgun (WGS) sequencing are the two main sequencing strategies in metagenomics. As amplicon sequencing provides a cheap way to classify the composition of a microbial community, it lacks the ability to identify microbial genes and annotate its corresponding functions. On the other hand, WGS sequencing allows further investigation of the complete genomes with all

Taxonomic assignment is the core of targeted metagenomics approaches that aims to assign sequencing reads to their corresponding taxonomy. Sequence similarity searching and machine learning (ML) are two commonly used approaches for taxonomic assignment based on the 16S rRNA. Similarity based approaches require high computation resources, while ML approaches dont need these resources in prediction. The majority of these ML approaches depend on k-mer frequency rather than direct sequence, which leads to low accuracy on short reads as k-mer frequency doesnt consider k-mer position. Moreover

Detection of pedestrians on embedded devices, such as those on-board of robots and drones, has many applications including road intersection monitoring, security, crowd monitoring and surveillance, to name a few. However, the problem can be challenging due to continuously-changing camera viewpoint and varying object appearances as well as the need for lightweight algorithms suitable for embedded systems. This paper proposes a robust framework for pedestrian detection in many footages. The framework performs fine and coarse detections on different image regions and exploits temporal and spatial

Semantic Segmentation of satellite images is one of the most challenging problems in computer vision as it requires a model capable of capturing both local and global information at each pixel. Current state of the art methods are based on Fully Convolutional Neural Networks (FCNN) with mostly two main components: an encoder which is a pretrained classification model that gradually reduces the input spatial size and a decoder that transforms the encoder's feature map into a predicted mask with the original size. We change this conventional architecture to a model that makes use of full