Search results for: DNA computing
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 849

Search results for: DNA computing

849 A Simulation Software for DNA Computing Algorithms Implementation

Authors: M. S. Muhammad, S. M. W. Masra, K. Kipli, N. Zamhari

Abstract:

The capturing of gel electrophoresis image represents the output of a DNA computing algorithm. Before this image is being captured, DNA computing involves parallel overlap assembly (POA) and polymerase chain reaction (PCR) that is the main of this computing algorithm. However, the design of the DNA oligonucleotides to represent a problem is quite complicated and is prone to errors. In order to reduce these errors during the design stage before the actual in-vitro experiment is carried out; a simulation software capable of simulating the POA and PCR processes is developed. This simulation software capability is unlimited where problem of any size and complexity can be simulated, thus saving cost due to possible errors during the design process. Information regarding the DNA sequence during the computing process as well as the computing output can be extracted at the same time using the simulation software.

Keywords: DNA computing, PCR, POA, simulation software

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848 Faster FPGA Routing Solution using DNA Computing

Authors: Manpreet Singh, Parvinder Singh Sandhu, Manjinder Singh Kahlon

Abstract:

There are many classical algorithms for finding routing in FPGA. But Using DNA computing we can solve the routes efficiently and fast. The run time complexity of DNA algorithms is much less than other classical algorithms which are used for solving routing in FPGA. The research in DNA computing is in a primary level. High information density of DNA molecules and massive parallelism involved in the DNA reactions make DNA computing a powerful tool. It has been proved by many research accomplishments that any procedure that can be programmed in a silicon computer can be realized as a DNA computing procedure. In this paper we have proposed two tier approaches for the FPGA routing solution. First, geometric FPGA detailed routing task is solved by transforming it into a Boolean satisfiability equation with the property that any assignment of input variables that satisfies the equation specifies a valid routing. Satisfying assignment for particular route will result in a valid routing and absence of a satisfying assignment implies that the layout is un-routable. In second step, DNA search algorithm is applied on this Boolean equation for solving routing alternatives utilizing the properties of DNA computation. The simulated results are satisfactory and give the indication of applicability of DNA computing for solving the FPGA Routing problem.

Keywords: FPGA, Routing, DNA Computing.

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847 DNA Computing for an Absolute 1-Center Problem: An Evolutionary Approach

Authors: Zuwairie Ibrahim, Yusei Tsuboi, Osamu Ono, Marzuki Khalid

Abstract:

Deoxyribonucleic Acid or DNA computing has emerged as an interdisciplinary field that draws together chemistry, molecular biology, computer science and mathematics. Thus, in this paper, the possibility of DNA-based computing to solve an absolute 1-center problem by molecular manipulations is presented. This is truly the first attempt to solve such a problem by DNA-based computing approach. Since, part of the procedures involve with shortest path computation, research works on DNA computing for shortest path Traveling Salesman Problem, in short, TSP are reviewed. These approaches are studied and only the appropriate one is adapted in designing the computation procedures. This DNA-based computation is designed in such a way that every path is encoded by oligonucleotides and the path-s length is directly proportional to the length of oligonucleotides. Using these properties, gel electrophoresis is performed in order to separate the respective DNA molecules according to their length. One expectation arise from this paper is that it is possible to verify the instance absolute 1-center problem using DNA computing by laboratory experiments.

Keywords: DNA computing, operation research, 1-center problem.

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846 Cognitive Radio Networks (CRN): Resource Allocation Techniques Based On DNA-inspired Computing

Authors: Santosh Kumar Singh, Krishna Chandra Roy, Vibhakar Pathak

Abstract:

Spectrum is a scarce commodity, and considering the spectrum scarcity faced by the wireless-based service providers led to high congestion levels. Technical inefficiencies from pooled, since all networks share a common pool of channels, exhausting the available channels will force networks to block the services. Researchers found that cognitive radio (CR) technology may resolve the spectrum scarcity. A CR is a self-configuring entity in a wireless networking that senses its environment, tracks changes, and frequently exchanges information with their networks. However, CRN facing challenges and condition become worst while tracks changes i.e. reallocation of another under-utilized channels while primary network user arrives. In this paper, channels or resource reallocation technique based on DNA-inspired computing algorithm for CRN has been proposed.

Keywords: Ad hoc networks, channels reallocation, cognitive radio, DNA local sequence alignment.

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845 Analysis of DNA from Fired Cartridge Casings

Authors: S. Mawlood, L. Dennany, N. Watson, B. Pickard

Abstract:

DNA analysis has been widely accepted as providing valuable evidence concerning the identity of the source of biological traces. Our work has showed that DNA samples can survive on cartridges even after firing. The study also raised the possibility of determining other information such as the age of the donor. Such information may be invaluable in certain cases where spent cartridges from automatic weapons are left behind at the scene of a crime. In spite of the nature of touch evidence and exposure to high chamber temperatures during shooting, we were still capable to retrieve enough DNA for profile typing. In order to estimate age of contributor, DNA methylation levels were analyzed using EpiTect system for retrieved DNA. However, results were not conclusive, due to low amount of input DNA.

Keywords: Age prediction, Fired cartridge, Trace DNA sample.

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844 Some Relationships between Classes of Reverse Watson-Crick Finite Automata

Authors: Kazuki Murakami, Takashige Nakamura, Noriko Sakamoto, Kunio Aizawa

Abstract:

A Watson-Crick automaton is recently introduced as a computational model of DNA computing framework. It works on tapes consisting of double stranded sequences of symbols. Symbols placed on the corresponding cells of the double-stranded sequences are related by a complimentary relation. In this paper, we investigate a variation of Watson-Crick automata in which both heads read the tape in reverse directions. They are called reverse Watson-Crick finite automata (RWKFA). We show that all of following four classes, i.e., simple, 1-limited, all-final, all-final and simple, are equal to non-restricted version of RWKFA.

Keywords: automaton, DNA computing, formal languages, Watson-Crick automaton

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843 Identification of Disease Causing DNA Motifs in Human DNA Using Clustering Approach

Authors: G. Tamilpavai, C. Vishnuppriya

Abstract:

Studying DNA (deoxyribonucleic acid) sequence is useful in biological processes and it is applied in the fields such as diagnostic and forensic research. DNA is the hereditary information in human and almost all other organisms. It is passed to their generations. Earlier stage detection of defective DNA sequence may lead to many developments in the field of Bioinformatics. Nowadays various tedious techniques are used to identify defective DNA. The proposed work is to analyze and identify the cancer-causing DNA motif in a given sequence. Initially the human DNA sequence is separated as k-mers using k-mer separation rule. The separated k-mers are clustered using Self Organizing Map (SOM). Using Levenshtein distance measure, cancer associated DNA motif is identified from the k-mer clusters. Experimental results of this work indicate the presence or absence of cancer causing DNA motif. If the cancer associated DNA motif is found in DNA, it is declared as the cancer disease causing DNA sequence. Otherwise the input human DNA is declared as normal sequence. Finally, elapsed time is calculated for finding the presence of cancer causing DNA motif using clustering formation. It is compared with normal process of finding cancer causing DNA motif. Locating cancer associated motif is easier in cluster formation process than the other one. The proposed work will be an initiative aid for finding genetic disease related research.

Keywords: Bioinformatics, cancer motif, DNA, k-mers, Levenshtein distance, SOM.

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842 Analysis of DNA-Recognizing Enzyme Interaction using Deaminated Lesions

Authors: Seung Pil Pack

Abstract:

Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.

Keywords: Deaminated lesion, DNA-protein interaction, DNA-recognizing enzymes

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841 Open Cloud Computing with Fault Tolerance

Authors: K. Zuva, T. Zuva, K. O. M. Mapoka

Abstract:

Cloud Computing (CC) has become one of the most talked about emerging technologies that provides powerful computing and large storage environments through the use of the Internet. Cloud computing provides different dynamically scalable computing resources as a service. It brings economic benefits to individuals and businesses that adopt the technology. In theory adoption of cloud computing reduces capital and operational expenditure on information technology. For this to be a reality there is need to solve some challenges and at the same time addressing concerns that consumers have about cloud computing. This paper looks at Cloud Computing in general then highlights the challenges of Cloud Computing and finally suggests solutions to some of the challenges.

Keywords: Cloud Computing, SaaS, PaaS, IaaS, Internet.

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840 An Automatic Gridding and Contour Based Segmentation Approach Applied to DNA Microarray Image Analysis

Authors: Alexandra Oliveros, Miguel Sotaquirá

Abstract:

DNA microarray technology is widely used by geneticists to diagnose or treat diseases through gene expression. This technology is based on the hybridization of a tissue-s DNA sequence into a substrate and the further analysis of the image formed by the thousands of genes in the DNA as green, red or yellow spots. The process of DNA microarray image analysis involves finding the location of the spots and the quantification of the expression level of these. In this paper, a tool to perform DNA microarray image analysis is presented, including a spot addressing method based on the image projections, the spot segmentation through contour based segmentation and the extraction of relevant information due to gene expression.

Keywords: Contour segmentation, DNA microarrays, edge detection, image processing, segmentation, spot addressing.

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839 Cloud Computing: Changing Cogitation about Computing

Authors: Mehrdad Mahdavi Boroujerdi, Soheil Nazem

Abstract:

Cloud Computing is a new technology that helps us to use the Cloud for compliance our computation needs. Cloud refers to a scalable network of computers that work together like Internet. An important element in Cloud Computing is that we shift processing, managing, storing and implementing our data from, locality into the Cloud; So it helps us to improve the efficiency. Because of it is new technology, it has both advantages and disadvantages that are scrutinized in this article. Then some vanguards of this technology are studied. Afterwards we find out that Cloud Computing will have important roles in our tomorrow life!

Keywords: Cloud Computing, Grid Computing, Internet as a Platform, On-demand Computing, Software as a Service.

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838 A New Method for Rapid DNA Extraction from Artemia (Branchiopoda, Crustacea)

Authors: R. Manaffar, R. Maleki, S. Zare, N. Agh, S. Soltanian, B. Sehatnia, P. Sorgeloos, P. Bossier, G. Van Stappen

Abstract:

Artemia is one of the most conspicuous invertebrates associated with aquaculture. It can be considered as a model organism, offering numerous advantages for comprehensive and multidisciplinary studies using morphologic or molecular methods. Since DNA extraction is an important step of any molecular experiment, a new and a rapid method of DNA extraction from adult Artemia was described in this study. Besides, the efficiency of this technique was compared with two widely used alternative techniques, namely Chelex® 100 resin and SDS-chloroform methods. Data analysis revealed that the new method is the easiest and the most cost effective method among the other methods which allows a quick and efficient extraction of DNA from the adult animal.

Keywords: APD, Artemia, DNA extraction, Molecularexperiments

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837 Green Computing: From Current to Future Trends

Authors: Tariq Rahim Soomro, Muhammad Sarwar

Abstract:

During recent years, attention in 'Green Computing' has moved research into energy-saving techniques for home computers to enterprise systems' Client and Server machines. Saving energy or reduction of carbon footprints is one of the aspects of Green Computing. The research in the direction of Green Computing is more than just saving energy and reducing carbon foot prints. This study provides a brief account of Green Computing. The emphasis of this study is on current trends in Green Computing; challenges in the field of Green Computing and the future trends of Green Computing.

Keywords: Energy consumption, e-waste recycling, Green Computing, Green IT

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836 Parallel Double Splicing on Iso-Arrays

Authors: V. Masilamani, D.K. Sheena Christy, D.G. Thomas

Abstract:

Image synthesis is an important area in image processing. To synthesize images various systems are proposed in the literature. In this paper, we propose a bio-inspired system to synthesize image and to study the generating power of the system, we define the class of languages generated by our system. We call image as array in this paper. We use a primitive called iso-array to synthesize image/array. The operation is double splicing on iso-arrays. The double splicing operation is used in DNA computing and we use this to synthesize image. A comparison of the family of languages generated by the proposed self restricted double splicing systems on iso-arrays with the existing family of local iso-picture languages is made. Certain closure properties such as union, concatenation and rotation are studied for the family of languages generated by the proposed model.

Keywords: DNA computing, splicing system, iso-picture languages, iso-array double splicing system, iso-array self splicing.

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835 In silico Simulations for DNA Shuffling Experiments

Authors: Luciana Montera

Abstract:

DNA shuffling is a powerful method used for in vitro evolute molecules with specific functions and has application in areas such as, for example, pharmaceutical, medical and agricultural research. The success of such experiments is dependent on a variety of parameters and conditions that, sometimes, can not be properly pre-established. Here, two computational models predicting DNA shuffling results is presented and their use and results are evaluated against an empirical experiment. The in silico and in vitro results show agreement indicating the importance of these two models and motivating the study and development of new models.

Keywords: Computer simulation, DNA shuffling, in silico andin vitro comparison.

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834 Applying Autonomic Computing Concepts to Parallel Computing using Intelligent Agents

Authors: Blesson Varghese, Gerard T. McKee

Abstract:

The work reported in this paper is motivated by the fact that there is a need to apply autonomic computing concepts to parallel computing systems. Advancing on prior work based on intelligent cores [36], a swarm-array computing approach, this paper focuses on 'Intelligent agents' another swarm-array computing approach in which the task to be executed on a parallel computing core is considered as a swarm of autonomous agents. A task is carried to a computing core by carrier agents and is seamlessly transferred between cores in the event of a predicted failure, thereby achieving self-ware objectives of autonomic computing. The feasibility of the proposed swarm-array computing approach is validated on a multi-agent simulator.

Keywords: Autonomic computing, intelligent agents, swarm-array computing.

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833 DNA Nanowires: A Charge Transfer Approach

Authors: S. Behnia, S. Fathizadeh

Abstract:

Conductivity properties of DNA molecule is investigated in a simple, but chemically specific approach that is intimately related to the Su-Schrieffer-Heeger (SSH) model. This model is a tight-binding linear nanoscale chain. We have tried to study the electrical current flowing in DNA and investigated the characteristic I-V diagram. As a result, It is shown that there are the (quasi-) ohmic areas in I-V diagram. On the other hand, the regions with a negative differential resistance (NDR) are detectable in diagram.

Keywords: Charge transfer in DNA, Chaos theory, Molecular electronics, Negative Differential resistance.

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832 An Improved Fast Search Method Using Histogram Features for DNA Sequence Database

Authors: Qiu Chen, Feifei Lee, Koji Kotani, Tadahiro Ohmi

Abstract:

In this paper, we propose an efficient hierarchical DNA sequence search method to improve the search speed while the accuracy is being kept constant. For a given query DNA sequence, firstly, a fast local search method using histogram features is used as a filtering mechanism before scanning the sequences in the database. An overlapping processing is newly added to improve the robustness of the algorithm. A large number of DNA sequences with low similarity will be excluded for latter searching. The Smith-Waterman algorithm is then applied to each remainder sequences. Experimental results using GenBank sequence data show the proposed method combining histogram information and Smith-Waterman algorithm is more efficient for DNA sequence search.

Keywords: Fast search, DNA sequence, Histogram feature, Smith-Waterman algorithm, Local search

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831 Using Cloud Computing for E-Government: Challenges and Benefits

Authors: Sajjad Hashemi, Khalil Monfaredi, Mohammad Masdari

Abstract:

Cloud computing is a style of computing which is formed from the aggregation and development of technologies such as grid computing distributed computing, parallel computing and service-oriented architecture. And its aim is to provide computing, communication and storage resources in a safe environment based on service, as fast as possible, which is virtually provided via Internet platform. Considering that the provided Services in e-government are available via the Internet, thus cloud computing can be used in the implementation of e-government architecture and provide better service with the lowest economic cost using its benefits. In this paper, the Methods of using cloud computing in e-government has been studied and it's been attempted to identify the challenges and benefits of the cloud to get used in the e-government and proposals have been offered to overcome its shortcomings, encourage and partnership of governments and people to use this economical and new technology.

Keywords: Benefits, Cloud computing, Committee, Challenges, E-Government, Participation.

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830 Novel Inhibitor of E. coli DNA Adenine Methyltransferase (Ecodam)

Authors: H. Elsawy, A. Jeltsch

Abstract:

EcoDam is an adenine-N6 DNA methyltransferase that methylates the GATC sites in the Escherichia coli genome. DNA-adenine methylation is not present in higher eukaryotes including humans. These observations raise the possibility that dam inhibitors may be used as anti-microbial agents. Polyphosphate (Poly(P)) is an important metabolite and signaling molecule in prokaryotes and eukaryotes. Here, by using gel retardation experiments to investigate the competition of DNA binding by EcoDam in the presence of polyphosphate, we found that Poly (P) strongly interferes with DNA binding by EcoDam, while same concentration of monophosphate does not. In addition, we demonstrated that Poly (P) binding inhibits the activity of EcoDam and our results suggest that Poly (P) led to strong inhibition of the EcoDam catalytic activity, while monophosphate had only moderate effect.

Keywords: Antibacterial drugs, EcoDam inhibitors, Polyphosphate.

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829 Comparing Spontaneous Hydrolysis Rates of Activated Models of DNA and RNA

Authors: Mohamed S. Sasi, Adel M. Mlitan, Abdulfattah M. Alkherraz

Abstract:

This research project aims to investigate difference in relative rates concerning phosphoryl transfer relevant to biological catalysis of DNA and RNA in the pH-independent reactions. Activated Models of DNA and RNA for alkyl-aryl phosphate diesters (with 4-nitrophenyl as a good leaving group) have successfully been prepared to gather kinetic parameters. Eyring plots for the pH– independent hydrolysis of 1 and 2 were established at different temperatures in the range 100–160 °C. These measurements have been used to provide a better estimate for the difference in relative rates between the reactivity of DNA and RNA cleavage. Eyring plot gave an extrapolated rate of kH2O = 1 × 10-10 s -1 for 1 (RNA model) and 2 (DNA model) at 25°C. Comparing the reactivity of RNA model and DNA model shows that the difference in relative rates in the pH-independent reactions is surprisingly very similar at 25°. This allows us to obtain chemical insights into how biological catalysts such as enzymes may have evolved to perform their current functions.

Keywords: DNA & RNA Models, Relative Rates, Reactivity.

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828 Towards Self-ware via Swarm-Array Computing

Authors: Blesson Varghese, Gerard McKee

Abstract:

The work reported in this paper proposes Swarm-Array computing, a novel technique inspired by swarm robotics, and built on the foundations of autonomic and parallel computing. The approach aims to apply autonomic computing constructs to parallel computing systems and in effect achieve the self-ware objectives that describe self-managing systems. The constitution of swarm-array computing comprising four constituents, namely the computing system, the problem/task, the swarm and the landscape is considered. Approaches that bind these constituents together are proposed. Space applications employing FPGAs are identified as a potential area for applying swarm-array computing for building reliable systems. The feasibility of a proposed approach is validated on the SeSAm multi-agent simulator and landscapes are generated using the MATLAB toolkit.

Keywords: Swarm-Array computing, Autonomic computing, landscapes.

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827 Proposition of a Knowledge Management Approach Based on the Cloud Computing

Authors: Imane Chikhi, Hafida Abed

Abstract:

The significant growth in the use of technologies in all life domains created numerous hurdles that derailed many knowledge management projects. Cloud computing choices are commencement to untangle these obstacles. Linking Cloud computing with knowledge management (KM) is a challenging task. Small amount of researches have been done regarding cloud computing and KM. In this paper, we consider Cloud-based KM as a new KM approach, and study the contribution of Cloud Computing to organizational KM. In fact, KM and cloud computing have many things in common, this similarity allows deriving very interesting features. Our approach is based on these features and focuses on the advantages of Cloud computing in the context of organizational KM. Finally, we highlight some challenges that have to be addressed when adopting a Cloud Computing approach to KM.

Keywords: Knowledge management, cloud computing, knowledge management approaches, cloud-based knowledge management.

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826 A DNA-Based Nanobiosensor for the Rapid Detection of the Dengue Virus in Mosquito

Authors: Lilia M. Fernando, Matthew K. Vasher, Evangelyn C. Alocilja

Abstract:

This paper describes the development of a DNA-based nanobiosensor to detect the dengue virus in mosquito using electrically active magnetic (EAM) nanoparticles as concentrator and electrochemical transducer. The biosensor detection encompasses two sets of oligonucleotide probes that are specific to the dengue virus: the detector probe labeled with the EAM nanoparticles and the biotinylated capture probe. The DNA targets are double hybridized to the detector and the capture probes and concentrated from nonspecific DNA fragments by applying a magnetic field. Subsequently, the DNA sandwiched targets (EAM-detector probe– DNA target–capture probe-biotin) are captured on streptavidin modified screen printed carbon electrodes through the biotinylated capture probes. Detection is achieved electrochemically by measuring the oxidation–reduction signal of the EAM nanoparticles. Results indicate that the biosensor is able to detect the redox signal of the EAM nanoparticles at dengue DNA concentrations as low as 10 ng/μl.

Keywords: Dengue, magnetic nanoparticles, mosquito, nanobiosensor.

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825 DNA Methylation Changes Caused by Lawsone

Authors: Zuzana Poborilova, Anna B. Ohlsson, Torkel Berglund, Anna Vildova, Petr Babula

Abstract:

Lawsone is a pigment that occurs naturally in plants. It has been used as a skin and hair dye for a long time. Moreover, its different biological activities have been reported. The present study focused on the effect of lawsone on a plant cell model represented by tobacco BY-2 cell suspension culture, which is used as a model comparable with the HeLa cells. It has been shown that lawsone inhibits the cell growth in the concentration-dependent manner. In addition, changes in DNA methylation level have been determined. We observed decreasing level of DNA methylation in the presence of increasing concentrations of lawsone. These results were accompanied with overproduction of reactive oxygen species (ROS). Since epigenetic modifications can be caused by different stress factors, there could be a connection between the changes in the level of DNA methylation and ROS production caused by lawsone.

Keywords: DNA methylation, Lawsone, Naphthoquinone, Reactive Oxygen Species.

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824 Exploring the Combinatorics of Motif Alignments Foraccurately Computing E-values from P-values

Authors: T. Kjosmoen, T. Ryen, T. Eftestøl

Abstract:

In biological and biomedical research motif finding tools are important in locating regulatory elements in DNA sequences. There are many such motif finding tools available, which often yield position weight matrices and significance indicators. These indicators, p-values and E-values, describe the likelihood that a motif alignment is generated by the background process, and the expected number of occurrences of the motif in the data set, respectively. The various tools often estimate these indicators differently, making them not directly comparable. One approach for comparing motifs from different tools, is computing the E-value as the product of the p-value and the number of possible alignments in the data set. In this paper we explore the combinatorics of the motif alignment models OOPS, ZOOPS, and ANR, and propose a generic algorithm for computing the number of possible combinations accurately. We also show that using the wrong alignment model can give E-values that significantly diverge from their true values.

Keywords: Motif alignment, combinatorics, p-value, E-value, OOPS, ZOOPS, ANR.

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823 Towards Cloud Computing Anatomy

Authors: Maria Salama, Mohamed Kouta

Abstract:

Cloud Computing has recently emerged as a compelling paradigm for managing and delivering services over the internet. The rise of Cloud Computing is rapidly changing the landscape of information technology, and ultimately turning the longheld promise of utility computing into a reality. As the development of Cloud Computing paradigm is speedily progressing, concepts, and terminologies are becoming imprecise and ambiguous, as well as different technologies are interfering. Thus, it becomes crucial to clarify the key concepts and definitions. In this paper, we present the anatomy of Cloud Computing, covering its essential concepts, prominent characteristics, its affects, architectural design and key technologies. We differentiate various service and deployment models. Also, significant challenges and risks need are tackled in order to guarantee the long-term success of Cloud Computing. The aim of this paper is to provide a better understanding of the anatomy of Cloud Computing and pave the way for further research in this area.

Keywords: Anatomy, Aspects, Cloud Computing, Challenges.

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822 An Index based Forward Backward Multiple Pattern Matching Algorithm

Authors: Raju Bhukya, DVLN Somayajulu

Abstract:

Pattern matching is one of the fundamental applications in molecular biology. Searching DNA related data is a common activity for molecular biologists. In this paper we explore the applicability of a new pattern matching technique called Index based Forward Backward Multiple Pattern Matching algorithm(IFBMPM), for DNA Sequences. Our approach avoids unnecessary comparisons in the DNA Sequence due to this; the number of comparisons of the proposed algorithm is very less compared to other existing popular methods. The number of comparisons rapidly decreases and execution time decreases accordingly and shows better performance.

Keywords: Comparisons, DNA Sequence, Index.

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821 The Prevalence of Transfusion-Transmitted Virus (TTV) Infection inIranian Patients with Chronic Hepatitis B

Authors: P. Ghasemi Dehkordi, A. Doosti, M. R. Hajimirzaei

Abstract:

TTV is an unenveloped circular single-stranded DNA virus with a diameter of 30-32 nm that first was described in 1997 in Japan. TTV was detected in various populations without proven pathology, including blood donors and in patients with chronic HBV and HCV hepatitis. The aim of this study was to determine the prevalence of TTV DNA in Iranian patients with chronic hepatitis B and C. Viral TTV-DNA was studied in 442 samples (202 with HBV, 138 with HCV and 102 controls) collected from west south of Iran. All extracted serum DNA was amplified by TTV ORF1 gene specific primers using the semi nested PCR technique. TTV DNA was detected in the serum of 8.9% and 10.8% patients with chronic hepatitis B and C, respectively. Prevalence of TTV-DNA in the serum of 102 controls was 2.9%. Results showed significant relation of TTV with HBV and HCV in patients by using T test examination (P<0.01). The prevalence of TTV-DNA in Iranian hepatitis B and C patients is rather high, and compare with other countries. To control and prevention of the distribution of TT-virus, examination of the blood and blood products it seems to be necessary.

Keywords: Transfusion-transmitted virus (TTV), Hepatitis Cvirus (HCV), Hepatitis B virus (HBV), ORF1 gene, Semi nested PCR, Iran.

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820 Use of Cloud Computing and Smart Devices in Healthcare

Authors: Nikunj Agarwal, M. P. Sebastian

Abstract:

Cloud computing can reduce the start-up expenses of implementing EHR (Electronic Health Records). However, many of the healthcare institutions are yet to implement cloud computing due to the associated privacy and security issues. In this paper, we analyze the challenges and opportunities of implementing cloud computing in healthcare. We also analyze data of over 5000 US hospitals that use Telemedicine applications. This analysis helps to understand the importance of smart phones over the desktop systems in different departments of the healthcare institutions. The wide usage of smartphones and cloud computing allows ubiquitous and affordable access to the health data by authorized persons, including patients and doctors. Cloud computing will prove to be beneficial to a majority of the departments in healthcare. Through this analysis, we attempt to understand the different healthcare departments that may benefit significantly from the implementation of cloud computing.

Keywords: Cloud computing, smart devices, healthcare, telemedicine.

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