The enhanced suffix array is an indexing data structure used for a wide range of applications in Bioinformatics. It is basically the suffix array but enhanced with extra tables that provide extra information to improve the performance in theory and in practice. In this paper, we present a number of improvements to the enhanced suffix array: 1) We show how to find a pattern of length m in O(m) time, i.e., independent of the alphabet size. 2) We present an improved representation of the bucket table. 3) We improve the access time of addressing the LCP (longest common prefix) table when one byte

Background: Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons. Results: Most of the software tools available are tailored for one specific task. In contrast, we have developed a novel system CoCoNUT (Computational Comparative geNomics Utility Toolkit) that allows solving several different tasks in a unified framework: (1) finding regions of high similarity among multiple genomic

Wireless Sensor Networks (WSNs) consist of a collection of cheap, easy to deploy Sensor nodes arranged together to fulfill a specific purpose (monitoring, tracking...etc.). A WSN network is composed of a Base Station (BS) and collection of sensors. There are a lot of approaches for the network construction. Amongst them is the hierarchical structure, where the network is divided into clusters and the node inside this cluster communicates with BS through a chosen leader called Cluster Head (CH). In this paper, we present cluster-Head election algorithms for WSNs. We will discuss the operations

Recently, digital forensics analysis got a great attention in IT security. This is especially after cyber incidents are getting new form of organized crime which introduced Advanced Persistent Threats (APT), and hacking Kill Chain definitions. The threat intense rises when it is affecting the healthcare organization where it will be life-threatening. Handling such incidents is a great challenge for handlers to uncover the attack steps. With various sources of evidential data that require analysis, one analysis technique can be more beneficial than another, comparing to the time and resources

Optic Disc (OD) localization is an important pre-processing step that significantly simplifies subsequent segmentation of the OD and other retinal structures. Current OD localization techniques suffer from impractically-high computation times (few minutes per image). In this work, we present a fast technique that requires less than a second to localize the OD. The technique is based upon obtaining two projections of certain image features that encode the x- and y- coordinates of the OD. The resulting 1-D projections are then searched to determine the location of the OD. This avoids searching

Infection with multiple drug resistant (MDR) Escherichia coli poses a life threat to immunocompromised pediatric cancer patients. Our aim is to genotypically characterize the plasmids harbored in MDR E. coli isolates recovered from bacteremic patients of Children’s Cancer Hospital in Egypt 57357 (CCHE 57357). In this study, 21 carbapenem-resistant E. coli (CRE) isolates were selected that exhibit Quinolones and Aminoglycosides resistance. Plasmid shot-gun sequencing was performed using Illumina next- generation sequencing platform. Isolates demonstrated resistant to all beta-lactams

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Purpose. To develop a method for identifying abnormal myocardial function based on studying the normalized wall motion pattern during the cardiac cycle. Methods. The temporal pattern of the normalized myocardial wall thickness is used as a feature vector to assess the cardiac wall motion abnormality. Principal component analysis is used to reduce the feature dimensionality and the maximum likelihood method is used to differentiate between normal and abnormal features. The proposed method was applied on a dataset of 27 cases from normal subjects and patients. Results. The developed method

Global overpopulation, industrial expansion, and urbanization have generated massive amounts of wastes. This is considered as a significant worldwide challenge that requires an urgent solution. Additionally, remarkable advances in the field of biomedicine have impacted the entire spectrum of healthcare and medicine. This has paved the way for further refining of the outcomes of biomedical strategies toward early detection and treatment of different diseases. Various nanomaterials (NMs) have been dedicated to different biomedical applications including drug delivery, vaccinations, imaging

Membrane computing is a computational framework that depends on the behavior and structure of living cells. P systems are arising from the biological processes which occur in the living cells’ organelles in a non-deterministic and maximally parallel manner. This paper aims to build a powerful computational model that combines the rules of active and mobile membranes, called Mutual Dynamic Membranes (MDM). The proposed model will describe the biological mechanisms of the metabolic regulation of mitochondrial dynamics made by mitochondrial membranes. The behaviors of the proposed model regulate