Search results for: genome applications

Authors: Ghada Badr, Manar Hosny, Nuha Bintayyash, Eman Albilali, Souad Larabi Marie-Sainte

Abstract:

The median problem is significantly applied to derive the most reasonable rearrangement phylogenetic tree for many species. More specifically, the problem is concerned with finding a permutation that minimizes the sum of distances between itself and a set of three signed permutations. Genomes with equal number of genes but different order can be represented as permutations. In this paper, an algorithm, namely BeamGA median, is proposed that combines a heuristic search approach (local beam) as an initialization step to generate a number of solutions, and then a Genetic Algorithm (GA) is applied in order to refine the solutions, aiming to achieve a better median with the smallest possible reversal distance from the three original permutations. In this approach, any genome rearrangement distance can be applied. In this paper, we use the reversal distance. To the best of our knowledge, the proposed approach was not applied before for solving the median problem. Our approach considers true biological evolution scenario by applying the concept of common intervals during the GA optimization process. This allows us to imitate a true biological behavior and enhance genetic approach time convergence. We were able to handle permutations with a large number of genes, within an acceptable time performance and with same or better accuracy as compared to existing algorithms.

Keywords: Median problem, phylogenetic tree, permutation, genetic algorithm, beam search, genome rearrangement distance.

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Authors: Pingping Lin, Xudong Luo

Abstract:

Natural language often conveys emotions of speakers. Therefore, sentiment analysis on what people say is prevalent in the field of natural language process and has great application value in many practical problems. Thus, to help people understand its application value, in this paper, we survey various applications of sentiment analysis, including the ones in online business and offline business as well as other types of its applications. In particular, we give some application examples in intelligent customer service systems in China. Besides, we compare the applications of sentiment analysis on Twitter, Weibo, Taobao and Facebook, and discuss some challenges. Finally, we point out the challenges faced in the applications of sentiment analysis and the work that is worth being studied in the future.

Keywords: Natural language processing, sentiment analysis, application, online comments.

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Authors: Yongxian Jin, Jingzhou Huang

Abstract:

In an open real-time system environment, the coexistence of different kinds of real-time and non real-time applications makes the system scheduling mechanism face new requirements and challenges. One two-level scheduling scheme of the open real-time systems is introduced, and points out that hard and soft real-time applications are scheduled non-distinctively as the same type real-time applications, the Quality of Service (QoS) cannot be guaranteed. It has two flaws: The first, it can not differentiate scheduling priorities of hard and soft real-time applications, that is to say, it neglects characteristic differences between hard real-time applications and soft ones, so it does not suit a more complex real-time environment. The second, the worst case execution time of soft real-time applications cannot be predicted exactly, so it is not worth while to cost much spending in order to assure all soft real-time applications not to miss their deadlines, and doing that may cause resource wasting. In order to solve this problem, a novel two-level real-time scheduling mechanism (including scheduling profile and scheduling algorithm) which adds the process of dealing with soft real-time applications is proposed. Finally, we verify real-time scheduling mechanism from two aspects of theory and experiment. The results indicate that our scheduling mechanism can achieve the following objectives. (1) It can reflect the difference of priority when scheduling hard and soft real-time applications. (2) It can ensure schedulability of hard real-time applications, that is, their rate of missing deadline is 0. (3) The overall rate of missing deadline of soft real-time applications can be less than 1. (4) The deadline of a non-real-time application is not set, whereas the scheduling algorithm that server 0 S uses can avoid the “starvation" of jobs and increase QOS. By doing that, our scheduling mechanism is more compatible with different types of applications and it will be applied more widely.

Keywords: Hard real-time, two-level scheduling profile, open real-time system, non-distinctive schedule, soft real-time

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Authors: Karanjeet Singh Kahlon, Gurvinder Singh, Arjan Singh

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In the past few years there is a change in the view of high performance applications and parallel computing. Initially such applications were targeted towards dedicated parallel machines. Recently trend is changing towards building meta-applications composed of several modules that exploit heterogeneous platforms and employ hybrid forms of parallelism. The aim of this paper is to propose a model of virtual parallel computing. Virtual parallel computing system provides a flexible object oriented software framework that makes it easy for programmers to write various parallel applications.

Keywords: Applet, Efficiency, Java, LAN

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Authors: Alexander Kaplunovsky, Vladimir Khailenko, Alexander Bolshoy, Shara Atambayeva, AnatoliyIvashchenko

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Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from the RNA transcripts before translation into a protein. The exon-intron structures of different eukaryotic species are quite different from each other, and the evolution of such structures raises many questions. We try to address some of these questions using statistical analysis of whole genomes. We go through all the protein-coding genes in a genome and study correlations between the net length of all the exons in a gene, the number of the exons, and the average length of an exon. We also take average values of these features for each chromosome and study correlations between those averages on the chromosomal level. Our data show universal features of exon-intron structures common to animals, plants, and protists (specifically, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Cryptococcus neoformans, Homo sapiens, Mus musculus, Oryza sativa, and Plasmodium falciparum). We have verified linear correlation between the number of exons in a gene and the length of a protein coded by the gene, while the protein length increases in proportion to the number of exons. On the other hand, the average length of an exon always decreases with the number of exons. Finally, chromosome clustering based on average chromosome properties and parameters of linear regression between the number of exons in a gene and the net length of those exons demonstrates that these average chromosome properties are genome-specific features.

Keywords: Comparative genomics, exon-intron structure, eukaryotic clustering, linear regression.

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Authors: Xizhi Li

Abstract:

Both software applications and their development environment are becoming more and more distributed. This trend impacts not only the way software computes, but also how it looks. This article proposes a Human Computer Interface (HCI) template from three representative applications we have developed. These applications include a Multi-Agent System based software, a 3D Internet computer game with distributed game world logic, and a programming language environment used in constructing distributed neural network and its visualizations. HCI concepts that are common to these applications are described in abstract terms in the template. These include off-line presentation of global entities, entities inside a hierarchical namespace, communication and languages, reconfiguration of entity references in a graph, impersonation and access right, etc. We believe the metaphor that underlies an HCI concept as well as the relationships between a bunch of HCI concepts are crucial to the design of software systems and vice versa.

Keywords: HCI, MAS, computer game, programming language

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Authors: P.S.Prakash, S.Selvan

Abstract:

Packet switched data network like Internet, which has traditionally supported throughput sensitive applications such as email and file transfer, is increasingly supporting delay-sensitive multimedia applications such as interactive video. These delaysensitive applications would often rather sacrifice some throughput for better delay. Unfortunately, the current packet switched network does not offer choices, but instead provides monolithic best-effort service to all applications. This paper evaluates Class Based Queuing (CBQ), Coordinated Earliest Deadline First (CEDF), Weighted Switch Deficit Round Robin (WSDRR) and RED-Boston scheduling schemes that is sensitive to delay bound expectations for variety of real time applications and an enhancement of WSDRR is proposed.

Keywords: QoS, Delay-sensitive, Queuing delay, Scheduling

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Authors: Carlo Bellettini, Alessandro Marchetto, Andrea Trentini

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Web applications have become very complex and crucial, especially when combined with areas such as CRM (Customer Relationship Management) and BPR (Business Process Reengineering), the scientific community has focused attention to Web applications design, development, analysis, and testing, by studying and proposing methodologies and tools. This paper proposes an approach to automatic multi-dimensional concern mining for Web Applications, based on concepts analysis, impact analysis, and token-based concern identification. This approach lets the user to analyse and traverse Web software relevant to a particular concern (concept, goal, purpose, etc.) via multi-dimensional separation of concerns, to document, understand and test Web applications. This technique was developed in the context of WAAT (Web Applications Analysis and Testing) project. A semi-automatic tool to support this technique is currently under development.

Keywords: Aspect Mining, Concepts Analysis, Concerns Mining, Multi-Dimensional Separation of Concerns, Impact Analysis.

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Authors: Carlo Bellettini, Alessandro Marchetto, Andrea Trentini

Abstract:

Web applications have become very complex and crucial, especially when combined with areas such as CRM (Customer Relationship Management) and BPR (Business Process Reengineering), the scientific community has focused attention to Web applications design, development, analysis, and testing, by studying and proposing methodologies and tools. This paper proposes an approach to automatic multi-dimensional concern mining for Web Applications, based on concepts analysis, impact analysis, and token-based concern identification. This approach lets the user to analyse and traverse Web software relevant to a particular concern (concept, goal, purpose, etc.) via multi-dimensional separation of concerns, to document, understand and test Web applications. This technique was developed in the context of WAAT (Web Applications Analysis and Testing) project. A semi-automatic tool to support this technique is currently under development.

Keywords: Concepts Analysis, Concerns Mining, Multi-Dimensional Separation of Concerns, Impact Analysis.

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Authors: Noha M. Rashad, W. Swelam, M. H. Abd ElAzeem

Abstract:

A simple design of array antenna is presented in this paper, supporting millimeter wave applications which can be used in short range wireless communications such as 5G applications. This design enhances the use of V-band, according to IEEE standards, as the antenna works in the 70 GHz band with bandwidth more than 11 GHz and peak gain more than 13 dBi. The design is simulated using different numerical techniques achieving a very good agreement.

Keywords: 5G Technology, array antenna, microstrip, millimeter wave.

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Authors: I. Gokasar, G. Bakioglu

Abstract:

With the unprecedented rates of technological improvements, people start to solve their problems with the help of technological tools. According to application stores and websites in which people evaluate and comment on the traffic apps, there are more than 100 traffic applications which have different features with respect to their purpose of usage ranging from the features of traffic apps for public transit modes to the features of traffic apps for private cars. This study focuses on the top 30 traffic applications which were chosen with respect to their download counts. All data about the traffic applications were obtained from related websites. The purpose of this study is to analyze traffic applications in terms of their categorical attributes with the help of developing a regression model. The analysis results suggest that negative interpretations (e.g., being deficient) does not lead to lower star ratings of the applications. However, those negative interpretations result in a smaller increase in star rate. In addition, women use higher star rates than men for the evaluation of traffic applications.

Keywords: Traffic App, real–time information, traffic congestion, regression analysis, dummy variables.

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Authors: Ahmad Abbas Al-Ameen Salih, Nur Liyana Afiqah Che Ahmad Zaini, Amzari Zhahir

Abstract:

Navigation is the processes of monitoring and controlling the movement of an object from one place to another. Currently, Global Positioning System (GPS) is the main navigation system used all over the world for navigation applications. GPS receiver receives signals from at least three satellites to locate and display itself. Displayed positioning information is updated continuously. Update rate is the number of times per second that a display is illuminated. The speed of update is governed by receiver update rate. A higher update rate decreases display lag time and improves distance measurements and tracking especially when moving on a curvy route. The majority of GPS receivers used nowadays are updated every second continuously. This period is considered reasonable for some applications while it is long relatively for high speed applications. In this paper, the suitability and feasibility of GPS receiver with different update rates will be evaluated for various applications according to the level of speed and update rate needed for particular applications.

Keywords: Navigation, Global Positioning System (GPS), GPS receiver, Update rate, Refresh rate, Satellite navigation, High speed GPS receiver.

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Authors: Masaharu Isshiki, Kenji Murakami, Shun Ido

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This paper describes a proposed support system which enables applications designers to effectively create VR applications using multiple haptic APIs. When the VR designers create applications, it is often difficult to handle and understand many parameters and functions that have to be set in the application program using documentation manuals only. This complication may disrupt creative imagination and result in inefficient coding. So, we proposed the support application which improved the efficiency of VR applications development and provided the interactive components of confirmation of operations with haptic sense previously. In this paper, we describe improvements of our former proposed support application, which was applicable to multiple APIs and haptic devices, and evaluate the new application by having participants complete VR program. Results from a preliminary experiment suggest that our application facilitates creation of VR applications.

Keywords: VR application, Support system, Haptic devices, Haptic APIs.

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Authors: Pedro Acevedo, Carlos Díaz, Mónica Vázquez, Joel Durán

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This paper describes the design of a pulse generator based on the Programmable System-on-Chip (PSoC) module. In this module, using programmable logic is possible to implement different pulses which are required for ultrasonic applications, either in a single channel or multiple channels. This module can operate with programmable frequencies from 3-74 MHz; its programming may be versatile covering a wide range of ultrasonic applications. It is ideal for low-power ultrasonic applications where PZT or PVDF transducers are used.

Keywords: pulse generator, PVDF, Programmable System-on-Chip (PSoC), ultrasonic transducer

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Authors: Melek Oktay, Ayşe Betül Gülbağcı, Mustafa Sarıöz

Abstract:

Enterprise applications are complex systems that are hard to develop and deploy in organizations. Although software application development tools, frameworks, methodologies and patterns are rapidly developing; many projects fail by causing big costs. There are challenging issues that programmers and designers face with while working on enterprise applications. In this paper, we present the three of the significant issues: Architectural, technological and performance. The important subjects in each issue are pointed out and recommendations are given. In architectural issues the lifecycle, meta-architecture, guidelines are pointed out. .NET and Java EE platforms are presented in technological issues. The importance of performance, measuring performance and profilers are explained in performance issues.

Keywords: Enterprise Applications, Architecture, Technology, Performance.

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Authors: R. Eslami Farsani, R. Fazaeli

Abstract:

Carbon fibers have specific characteristics in comparison with industrial and structural materials used in different applications. Special properties of carbon fibers make them attractive for reinforcing and fabrication of composites. These fibers have been utilized for composites of metals, ceramics and plastics. However, it-s mainly used in different forms to reinforce lightweight polymer materials such as epoxy resin, polyesters or polyamides. The composites of carbon fiber are stronger than steel, stiffer than titanium, and lighter than aluminum and nowadays they are used in a variety of applications. This study explains applications of carbon fibers in different fields such as space, aviation, transportation, medical, construction, energy, sporting goods, electronics, and the other commercial/industrial applications. The last findings of composites with polymer, metal and ceramic matrices containing carbon fibers and their applications in the world investigated. Researches show that carbon fibers-reinforced composites due to unique properties (including high specific strength and specific modulus, low thermal expansion coefficient, high fatigue strength, and high thermal stability) can be replaced with common industrial and structural materials.

Keywords: Polyacrylonitrile Fibers, Carbon Fibers, Application

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Authors: Jaouadi Imen, Ben Djemaa Raoudha, Ben Abdallah Hanene

Abstract:

The access to relevant information that is adapted to user’s needs, preferences and environment is a challenge in many applications running. That causes an appearance of context-aware systems. To facilitate the development of this class of applications, it is necessary that these applications share a common context metamodel. In this article, we will present our context metamodel that is defined using the OMG Meta Object facility (MOF).This metamodel is based on the analysis and synthesis of context concepts proposed in literature.

Keywords: Context, metamodel, Meta Object Facility (MOF), awareness system.

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Authors: Asaad Moosa

Abstract:

In recent years with the rapid development of Internet and the Web, more and more web applications have been deployed in many fields and organizations such as finance, military, and government. Together with that, hackers have found more subtle ways to attack web applications. According to international statistics, SQL Injection is one of the most popular vulnerabilities of web applications. The consequences of this type of attacks are quite dangerous, such as sensitive information could be stolen or authentication systems might be by-passed. To mitigate the situation, several techniques have been adopted. In this research, a security solution is proposed using Artificial Neural Network to protect web applications against this type of attacks. The solution has been experimented on sample datasets and has given promising result. The solution has also been developed in a prototypic web application firewall called ANNbWAF.

Keywords: Artificial Neural Networks ANN, SQL Injection, Web Application Firewall WAF, Web Application Scanner WAS.

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Authors: Neven Vrček, Goran Bubaš, Neven Bosilj

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Location-based services (LBS) exploit the known location of a user to provide services dependent on their geographic context and personalized needs [1]. The development and arrival of broadband mobile data networks supported with mobile terminals equipped with new location technologies like GPS have finally created opportunities for implementation of LBS applications. But, from the other side, collecting location information data in general raises privacy concerns. This paper presents results from two surveys of LBS acceptance in Croatia. The first survey was administered on 181 students, and the second extended survey involved pattern of 180 Croatian citizens. We developed questionnaire which consists of descriptions of 15 different applications with scale which measures perceptions and attitudes of users towards these applications. We report the results to identify potential commercial applications for LBS in B2C segment. Our findings suggest that some types of applications like emergency&safety services and navigation have significantly higher rate of acceptance than other types.

Keywords: Acceptance, location-based services, m-application.

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Authors: Ilias Spais, George Bafas

Abstract:

Natural Language Understanding Systems (NLU) will not be widely deployed unless they are technically mature and cost effective to develop. Cost effective development hinges on the availability of tools and techniques enabling the rapid production of NLU applications through minimal human resources. Further, these tools and techniques should allow quick development of applications in a user friendly way and should be easy to upgrade in order to continuously follow the evolving technologies and standards. This paper presents a visual tool for the structuring and editing of dialog forms, the key element of driving conversation in NLU applications based on IBM technology. The main focus is given on the basic component used to describe Human – Machine interactions of that kind, the Dialogue Manager. In essence, the description of a tool that enables the visual representation of the Dialogue Manager mainly during the implementation phase is illustrated.

Keywords: Conversational Applications, Forms Dialogue Manager (FDM), Natural Language Processing, Natural Language Understanding.

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Authors: Ayush Chugh, Gaurav Gupta

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Today’s technology is heavily dependent on web applications. Web applications are being accepted by users at a very rapid pace. These have made our work efficient. These include webmail, online retail sale, online gaming, wikis, departure and arrival of trains and flights and list is very long. These are developed in different languages like PHP, Python, C#, ASP.NET and many more by using scripts such as HTML and JavaScript. Attackers develop tools and techniques to exploit web applications and legitimate websites. This has led to rise of web application security; which can be broadly classified into Declarative Security and Program Security. The most common attacks on the applications are by SQL Injection and XSS which give access to unauthorized users who totally damage or destroy the system. This paper presents a detailed literature description and analysis on Web Application Security, examples of attacks and steps to mitigate the vulnerabilities.

Keywords: Attacks, Injection, JavaScript, SQL, Vulnerability, XSS.

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Authors: Abdulmohsen A. AlBesher, Richard T. Stone

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Star rating for mobile applications is a very useful way to differentiate between the best and worst rated applications. However, the question is whether the rating reflects the level of usability or not. The aim of this paper is to find out if the user’ star ratings on mobile apps correlate with the usability of those apps. Thus, we tested three mobile apps, which have different star ratings: low, medium, and high. Participating in the study, 15 mobile phone users were asked to do one single task for each of the three tested apps. After each task, the participant evaluated the app by answering a survey based on the System Usability Scale (SUS). The results found that there is no major correlation between the star rating and the usability. However, it was found that the task completion time and the numbers of errors that may happen while completing the task were significantly correlated to the usability.

Keywords: Mobile applications, SUS, Star rating, Usability.

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Authors: Vijay Janyani, Neetu Joshi, Jigyasa Pagaria, Parul Pathak

Abstract:

Photonic Crystal (PhC) based devices are being increasingly used in multifunctional, compact devices in integrated optical communication systems. They provide excellent controllability of light, yet maintaining the small size required for miniaturization. In this paper, the band gap properties of PhCs and their typical applications in optical waveguiding are considered. Novel PhC based applications such as nonlinear switching and tapers are considered and simulation results are shown using the accurate time-domain numerical method based on Finite Difference Time Domain (FDTD) scheme. The suitability of these devices for novel applications is discussed and evaluated.

Keywords: Band gap engineering, Nonlinear switching, Photonic crystals, PhC tapers, waveguides.

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Authors: Dawit Mengistu, Lars Lundberg, Paul Davidsson

Abstract:

A major requirement for Grid application developers is ensuring performance and scalability of their applications. Predicting the performance of an application demands understanding its specific features. This paper discusses performance modeling and prediction of multi-agent based simulation (MABS) applications on the Grid. An experiment conducted using a synthetic MABS workload explains the key features to be included in the performance model. The results obtained from the experiment show that the prediction model developed for the synthetic workload can be used as a guideline to understand to estimate the performance characteristics of real world simulation applications.

Keywords: Grid computing, Performance modeling, Performance prediction, Multi-agent simulation.

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Authors: Faisal Kalota

Abstract:

Big Data and analytics have gained a huge momentum in recent years. Big Data feeds into the field of Learning Analytics (LA) that may allow academic institutions to better understand the learners’ needs and proactively address them. Hence, it is important to have an understanding of Big Data and its applications. The purpose of this descriptive paper is to provide an overview of Big Data, the technologies used in Big Data, and some of the applications of Big Data in education. Additionally, it discusses some of the concerns related to Big Data and current research trends. While Big Data can provide big benefits, it is important that institutions understand their own needs, infrastructure, resources, and limitation before jumping on the Big Data bandwagon.

Keywords: Analytics, Big Data in Education, Hadoop, Learning Analytics.

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Authors: S. Bokka

Abstract:

Fiber filter membranes have a high surface area-to-volume ratio and high porosity making them ideal for various filtration and separation applications. Using the conventional filter membrane, a filtration efficiency of > 95% can be achieved. Specific applications such as air and fuel filtration require nearly 100% filtration efficiency, which is harder to achieve using conventional filter membranes. To achieve high filtration efficiencies additional costs are incurred due to increasing the cost of membrane and operating cost. Due to the simultaneous electrostatic attraction and mechanical capture, the electret filters have shown nearly 100% filtration efficiency. This article presents an overview of the charged filter membrane, its applications, and a discussion on factors contributing to increasing charge.

Keywords: Charged fiber membrane, piezoelectric materials, filtration, polymeric materials.

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Authors: A.Khaja Kamaluddin, B.Muhammed Yousoof

Abstract:

Routing places an important role in determining the quality of service in wireless networks. The routing methods adopted in wireless networks have many drawbacks. This paper aims to review the current routing methods used in wireless networks. This paper proposes an innovative solution to overcome the problems in routing. This solution is aimed at improving the Quality of Service. This solution is different from others as it involves the resuage of the part of the virtual circuits. This improvement in quality of service is important especially in propagation of multimedia applications like video, animations etc. So it is the dire need to propose a new solution to improve the quality of service in ATM wireless networks for multimedia applications especially during this era of multimedia based applications.

Keywords: Packet buffering, Routing Table, Virtual Circuits (VC)

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Authors: Norah Almubairik, Wadha Almattar, Amani Alqarni

Abstract:

Social media applications are increasingly being used in our everyday communications. These applications utilise end-to-end encryption mechanisms which make them suitable tools for criminals to exchange messages. These messages are preserved in the volatile memory until the device is restarted. Therefore, volatile forensics has become an important branch of digital forensics. In this study, the WormHex tool was developed to inspect the memory dump files for Windows and Mac based workstations. The tool supports digital investigators by enabling them to extract valuable data written in Arabic and English through web-based WhatsApp and Twitter applications. The results confirm that social media applications write their data into the memory, regardless of the operating system running the application, with there being no major differences between Windows and Mac.

Keywords: Volatile memory, REGEX, digital forensics, memory acquisition

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Authors: Swapnoneel Roy, Ashok Kumar Thakur, Minhazur Rahman

Abstract:

The Block Sorting problem is to sort a given permutation moving blocks. A block is defined as a substring of the given permutation, which is also a substring of the identity permutation. Block Sorting has been proved to be NP-Hard. Until now two different 2-Approximation algorithms have been presented for block sorting. These are the best known algorithms for Block Sorting till date. In this work we present a different characterization of Block Sorting in terms of a transposition cycle graph. Then we suggest a heuristic, which we show to exhibit a 2-approximation performance guarantee for most permutations.

Keywords: Block Sorting, Optical Character Recognition, Genome Rearrangements, Sorting Primitives, ApproximationAlgorithms

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Authors: Y. Cifuentes, L. Beltrán, L. Ramírez

Abstract:

The availability to deploy mobile applications for health care is increasing daily thru different mobile app stores. But within these capabilities the number of hacking attacks has also increased, in particular into medical mobile applications. The security vulnerabilities in medical mobile apps can be triggered by errors in code, incorrect logic, poor design, among other parameters. This is usually used by malicious attackers to steal or modify the users’ information. The aim of this research is to analyze the vulnerabilities detected in mobile medical apps according to risk factor standards defined by OWASP in 2014.

Keywords: mHealth apps, OWASP, protocols, security vulnerabilities, risk factors.

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