Search results for: CAZAC sequence.

Authors: Chia-Ta Tsai, Wen-Lin Huang, Shinn-Jang Ho, Li-Sun Shu, Shinn-Ying Ho

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Prediction of bacterial virulent protein sequences can give assistance to identification and characterization of novel virulence-associated factors and discover drug/vaccine targets against proteins indispensable to pathogenicity. Gene Ontology (GO) annotation which describes functions of genes and gene products as a controlled vocabulary of terms has been shown effectively for a variety of tasks such as gene expression study, GO annotation prediction, protein subcellular localization, etc. In this study, we propose a sequence-based method Virulent-GO by mining informative GO terms as features for predicting bacterial virulent proteins. Each protein in the datasets used by the existing method VirulentPred is annotated by using BLAST to obtain its homologies with known accession numbers for retrieving GO terms. After investigating various popular classifiers using the same five-fold cross-validation scheme, Virulent-GO using the single kind of GO term features with an accuracy of 82.5% is slightly better than VirulentPred with 81.8% using five kinds of sequence-based features. For the evaluation of independent test, Virulent-GO also yields better results (82.0%) than VirulentPred (80.7%). When evaluating single kind of feature with SVM, the GO term feature performs much well, compared with each of the five kinds of features.

Keywords: Bacterial virulence factors, GO terms, prediction, protein sequence.

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: Begomovirus, AV1 gene, sequence, cloning, whitefly, okra, cotton, tomato, RAPD, phylogenetic tree and SDS-PAGE.

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Authors: Maha Sharkas, Dahlia ElShafie, Nadder Hamdy

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Image watermarking has become an important tool for intellectual property protection and authentication. In this paper a watermarking technique is suggested that incorporates two watermarks in a host image for improved protection and robustness. A watermark, in form of a PN sequence (will be called the secondary watermark), is embedded in the wavelet domain of a primary watermark before being embedded in the host image. The technique has been tested using Lena image as a host and the camera man as the primary watermark. The embedded PN sequence was detectable through correlation among other five sequences where a PSNR of 44.1065 dB was measured. Furthermore, to test the robustness of the technique, the watermarked image was exposed to four types of attacks, namely compression, low pass filtering, salt and pepper noise and luminance change. In all cases the secondary watermark was easy to detect even when the primary one is severely distorted.

Keywords: DWT, Image watermarking, watermarkingtechniques, wavelets.

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Authors: Nitish Sharma, G. G. Karady

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This paper presents a scheme for the protection of loop system from all type of faults using the direction of fault current. The presence of distributed generation in today’s system increases the complexity of fault detection as the power flow is bidirectional. Hence, protection scheme specific to this purpose needs to be developed. This paper shows a fast protection scheme using communication which can be fiber optic or wireless. In this paper, the possibility of wireless communication for protection is studied to exchange the information between the relays. The negative sequence and positive sequence directional elements are used to determine the direction of fault current. A PSCAD simulation is presented and validated using commercial SEL relays.

Keywords: Smart grid protection, pilot protection, power system simulation, wireless communication.

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Authors: Ruilian Zhao, Ling Lin

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MM-Path, an acronym for Method/Message Path, describes the dynamic interactions between methods in object-oriented systems. This paper discusses the classifications of MM-Path, based on the characteristics of object-oriented software. We categorize it according to the generation reasons, the effect scope and the composition of MM-Path. A formalized representation of MM-Path is also proposed, which has considered the influence of state on response method sequences of messages. .Moreover, an automatic MM-Path generation approach based on UML Statechart diagram has been presented, and the difficulties in identifying and generating MM-Path can be solved. . As a result, it provides a solid foundation for further research on test cases generation based on MM-Path.

Keywords: MM-Path, Message Sequence, Object-Oriented Integration Testing, Response Method Sequence, UML Statechart Diagram.

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Authors: Mustafa Yorgancılar, Emine Atalay, Necdet Akgün, Ali Topal

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In this study, polymerase chain reaction based Inter-simple sequence repeat (ISSR) from DNA fingerprinting techniques were used to investigate the genetic relationships among barley crossbreed genotypes in Turkey. It is important that selection based on the genetic base in breeding programs via ISSR, in terms of breeding time. 14 ISSR primers generated a total of 97 bands, of which 81 (83.35%) were polymorphic. The highest total resolution power (RP) value was obtained from the F2 (0.53) and M16 (0.51) primers. According to the ISSR result, the genetic similarity index changed between 0.64–095; Lane 3 with Line 6 genotypes were the closest, while Line 36 were the most distant ones. The ISSR markers were found to be promising for assessing genetic diversity in barley crossbreed genotypes.

Keywords: Barley, crossbreed, genetic similarity, ISSR.

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Authors: Patsaraporn Somboonsak, Mud-Armeen Munlin

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The P-Bigram method is a string comparison methods base on an internal two characters-based similarity measure. The edit distance between two strings is the minimal number of elementary editing operations required to transform one string into the other. The elementary editing operations include deletion, insertion, substitution two characters. In this paper, we address the P-Bigram method to sole the similarity problem in DNA sequence. This method provided an efficient algorithm that locates all minimum operation in a string. We have been implemented algorithm and found that our program calculated that smaller distance than one string. We develop PBigram edit distance and show that edit distance or the similarity and implementation using dynamic programming. The performance of the proposed approach is evaluated using number edit and percentage similarity measures.

Keywords: Edit distance, String Matching, String Similarity

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Authors: Xu LiYun, Briand Florent, Fan GuoLiang

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The loop-layout design problem (LLDP) aims at optimizing the sequence of positioning of the machines around the cyclic production line. Traffic congestion is the usual criteria to minimize in this type of problem, i.e. the number of additional cycles spent by each part in the network until the completion of its required routing sequence of machines. This paper aims at applying several improvements mechanisms such as a positioned-based crossover operator for the Genetic Algorithm (GA) called a Two Points Crossover (TPC) and an offspring selection process. The performance of the improved GA is measured using well-known examples from literature and compared to other evolutionary algorithms. Good results show that GA can still be competitive for this type of problem against more recent evolutionary algorithms.

Keywords: Crossover, genetic algorithm, layout design problem, loop-layout, manufacturing optimization.

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Authors: Salam M. H. Kareem

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Instructional or teaching procedures and their proper sequence are essential for high-quality learning outcomes. These actions are the path that the teacher takes during the learning process after setting the learning objectives. Teachers and specialists in the education field should include teaching procedures with putting in place an effective mechanism for the procedure’s implementation to achieve a logical sequence with the desired output of overall education process. Determining the sequence of these actions may be a strategic process outlined by a strategic educational plan or drawn by teachers with a high level of experience, enabling them to determine those logical procedures. While specific actions may be necessary for a specific form, many Physical Education (PE) teachers can work out on various sports disciplines. This study was conducted to investigate the impact of using the teaching sequence of the teaching pyramid in raising the level of enjoyment in swimming classes. Four months later of teaching swimming skills to the control and experimental groups of the study, we figured that using the tools shown in the teaching pyramid with the experimental group led to statistically significant differences in the positive tendencies of students to participate in the swimming classes by using the traditional procedures of teaching and using of successive procedures in the teaching pyramid, and in favor of the teaching pyramid, The students are influenced by enhancing their tendency to participate in swimming classes when the teaching procedures followed are sensitive to individual differences and are based on the element of pleasure in learning, and less positive levels of the tendency of students when using traditional teaching procedures, by getting the level of skills' requirements higher and more difficult to perform. The level of positive tendencies of students when using successive procedures in the teaching pyramid was increased, by getting the level of skills' requirements higher and more difficult to perform, because of the high level of motivation and the desire to challenge the self-provided by the teaching pyramid.

Keywords: Physical education, swimming classes, teaching process, teaching pyramid.

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Authors: Sawangjit Sopid

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Atrazine, a herbicide widely used in sugarcane and corn production, is a frequently detected groundwater contaminant. An atrazine-degrading bacterium, strain KB02, was obtained from long-term atrazine-treated sugarcane field soils in Kanchanaburi province of Thailand. Strain KB02 had a rod-to-coccus morphological cycle during growth. Sequence analysis of the PCR product indicated that the 16S rRNA gene in strain KB02 was ranging from 97-98% identical to the same region in Klebsiella sp. Based on biochemical, physiological analysis and 16S rDNA sequence analysis of one representative isolate, strain KB02, the isolates belong to the genus Klebsiella in the family Enterobacteriaceae. Interestingly that the various primers for atzA, B and C failed to amplify genomic DNA of strain KB02. Whereas the expected PCR product of atzA, B and C were obtained from the reference strain, Arthrobacter sp. strain KU001.

Keywords: Atrazine, atz gene, Biodegradation, bioremediation, Klebsiella

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Authors: D. Ouahdi, R. Ladjeroud, I. Habi

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The distance protection mainly the impedance relay which is considered as the main protection for transmission lines can be subjected to impedance measurement error which is, mainly, due to the fault resistance and to the power fluctuation. Thus, the impedance relay may not operate for a short circuit at the far end of the protected line (case of the under reach) or operates for a fault beyond its protected zone (case of overreach). In this paper, an approach to fault detection by a distance protection, which distinguishes between the faulty conditions and the effect of overload operation mode, has been developed. This approach is based on the symmetrical components; mainly the negative sequence, and it is taking into account both the effect of fault resistance and the overload situation which both have an effect upon the reliability of the protection in terms of dependability for the former and security for the latter.

Keywords: Distance Protection, Fault Detection, negative sequence, overload, Transmission line.

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Authors: Yunbin Yang, Liangli He, Fengjun Wang

Abstract:

The essentiality of maintenance assessment and maintenance optimization in design stage is analyzed, and the existent problems of conventional maintenance design method are illuminated. MDMVM (Maintenance Design Method based Virtual Maintenance) is illuminated, and the process of MDMVM established, and the MDMVM architecture is given out. The key techniques of MDMVM are analyzed, and include maintenance design based KBE (Knowledge Based Engineering) and virtual maintenance based physically attribute. According to physical property, physically based modeling, visual object movement control, the simulation of operation force and maintenance sequence planning method are emphatically illuminated. Maintenance design system based virtual maintenance is established in foundation of maintenance design method.

Keywords: Digital mock-up, virtual maintenance, knowledge engineering, maintenance sequence planning.

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Authors: Mussarat Abdullah, Fazal Wahab

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Data hiding into text documents itself involves pretty complexities due to the nature of text documents. A robust text watermarking scheme targeting an object based environment is presented in this research. The heart of the proposed solution describes the concept of watermarking an object based text document where each and every text string is entertained as a separate object having its own set of properties. Taking advantage of the z-ordering of objects watermark is applied with the z-axis letting zero fidelity disturbances to the text. Watermark sequence of bits generated against user key is hashed with selected properties of given document, to determine the bit sequence to embed. Bits are embedded along z-axis and the document has no fidelity issues when printed, scanned or photocopied.

Keywords: Digital Watermarking, Object Based Environment, Watermark, z-ordering.

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Authors: V. Anil Kumar, Abhijit Mitra, S. R. Mahadeva Prasanna

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We analyze the effectivity of different pseudo noise (PN) and orthogonal sequences for encrypting speech signals in terms of perceptual intelligence. Speech signal can be viewed as sequence of correlated samples and each sample as sequence of bits. The residual intelligibility of the speech signal can be reduced by removing the correlation among the speech samples. PN sequences have random like properties that help in reducing the correlation among speech samples. The mean square aperiodic auto-correlation (MSAAC) and the mean square aperiodic cross-correlation (MSACC) measures are used to test the randomness of the PN sequences. Results of the investigation show the effectivity of large Kasami sequences for this purpose among many PN sequences.

Keywords: Speech encryption, pseudo-noise codes, maximallength, Gold, Barker, Kasami, Walsh-Hadamard, autocorrelation, crosscorrelation, figure of merit.

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Authors: Abhijit Mitra

Abstract:

Different pseudo-random or pseudo-noise (PN) as well as orthogonal sequences that can be used as spreading codes for code division multiple access (CDMA) cellular networks or can be used for encrypting speech signals to reduce the residual intelligence are investigated. We briefly review the theoretical background for direct sequence CDMA systems and describe the main characteristics of the maximal length, Gold, Barker, and Kasami sequences. We also discuss about variable- and fixed-length orthogonal codes like Walsh- Hadamard codes. The equivalence of PN and orthogonal codes are also derived. Finally, a new PN sequence is proposed which is shown to have certain better properties than the existing codes.

Keywords: Code division multiple access, pseudo-noise codes, maximal length, Gold, Barker, Kasami, Walsh-Hadamard, autocorrelation, crosscorrelation, figure of merit.

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Authors: Safyeh Soufian, Hoosein Naderi-Manesh, Abdoali Alizadeh, Mohammad Nabi Sarbolouki

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Aurein 1.2 is a 13-residue amphipathic peptide with antibacterial and anticancer activity. Aurein1.2 and its retro analog were synthesized to study the activity of the peptides in relation to their structure. The antibacterial test result showed the retro-analog is inactive. The secondary structural analysis by CD spectra indicated that both of the peptides at TFE/Water adopt alpha-helical conformation. MD simulation was performed on aurein 1.2 and retro-analog in water and TFE in order to analyse the factors that are involved in the activity difference between retro and the native peptide. The simulation results are discussed and validated in the light of experimental data from the CD experiment. Both of the peptides showed a relatively similar pattern for their hydrophobicity, hydrophilicity, solvent accessible surfaces, and solvent accessible hydrophobic surfaces. However, they showed different in directions of dipole moment of peptides. Also, Our results further indicate that the reversion of the amino acid sequence affects flexibility .The data also showed that factors causing structural rigidity may decrease the activity. Consequently, our finding suggests that in the case of sequence-reversed peptide strategy, one has to pay attention to the role of amino acid sequence order in making flexibility and role of dipole moment direction in peptide activity. KeywordsAntimicrobial peptides, retro, molecular dynamic, circular dichroism.

Keywords: Antimicrobial peptides, retro, molecular dynamic, circular dichroism.

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Authors: Gurjit Kaur, Neena Gupta

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In this paper, we have analyzed and compared the performance of various coding schemes. The basic ID prime sequence codes are unique in only dimension, i.e. time slots, whereas 2D coding techniques are not unique by their time slots but with their wavelengths also. In this research, we have evaluated and compared the performance of 1D and 2D coding techniques constructed using prime sequence coding pattern for Optical Code Division Multiple Access (OCDMA) system on a single platform. Analysis shows that 2D prime code supports lesser number of active users than 1D codes, but they are having large code family and are the most secure codes compared to other codes. The performance of all these codes is analyzed on basis of number of active users supported at a Bit Error Rate (BER) of 10-9.

Keywords: CDMA, OCDMA, BER, OOC, PC, EPC, MPC, 2-D PC/PC, λc, λa.

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Authors: Mohammad N. Alanazi, David A. Gustafson

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In this article, we introduce a new approach for analyzing UML designs to detect the inconsistencies between multiple state diagrams and sequence diagrams. The Super State Analysis (SSA) identifies the inconsistencies in super states, single step transitions, and sequences. Because SSA considers multiple UML state diagrams, it discovers inconsistencies that cannot be discovered when considering only a single UML state diagram. We have introduced a transition set that captures relationship information that is not specifiable in UML diagrams. The SSA model uses the transition set to link transitions of multiple state diagrams together. The analysis generates three different sets automatically. These sets are compared to the provided sets to detect the inconsistencies. SSA identifies five types of inconsistencies: impossible super states, unreachable super states, illegal transitions, missing transitions, and illegal sequences.

Keywords: Modeling Languages, Object-Oriented Analysis, Sequence Diagrams, Software Models, State Diagrams, UML.

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Authors: Sa’ed Abed, Mohammad H. Al Shayeji, Ovais Ahmed, Sahel Alouneh

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Session Initiation Protocol (SIP) is a signaling layer protocol for building, adjusting and ending sessions among participants including Internet conferences, telephone calls and multimedia distribution. SIP facilitates user movement by proxying and forwarding requests to the present location of the user. In this paper, we provide a formal Specification and Description Language (SDL) and Message Sequence Chart (MSC) to model and define the Internet Engineering Task Force (IETF) SIP protocol and its sample services resulted from informal SIP specification. We create an “Abstract User Interface” using case analysis so that can be applied to identify SIP services more explicitly. The issued sample SIP features are then used as case scenarios; they are revised in MSCs format and validated to their corresponding SDL models.

Keywords: Modeling, MSC, SDL, SIP, validating.

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Authors: Natarajan Vijayarangan, Prasanna S. Bidare

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Cryptography, Image watermarking and E-banking are filled with apparent oxymora and paradoxes. Random sequences are used as keys to encrypt information to be used as watermark during embedding the watermark and also to extract the watermark during detection. Also, the keys are very much utilized for 24x7x365 banking operations. Therefore a deterministic random sequence is very much useful for online applications. In order to obtain the same random sequence, we need to supply the same seed to the generator. Many researchers have used Deterministic Random Number Generators (DRNGs) for cryptographic applications and Pseudo Noise Random sequences (PNs) for watermarking. Even though, there are some weaknesses in PN due to attacks, the research community used it mostly in digital watermarking. On the other hand, DRNGs have not been widely used in online watermarking due to its computational complexity and non-robustness. Therefore, we have invented a new design of generating DRNG using Pi-series to make it useful for online Cryptographic, Digital watermarking and Banking applications.

Keywords: E-tokens, LFSR, non-linear, Pi series, pseudo random number.

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Authors: Sh. A. Yousif, M. Bhave

Abstract:

There is strong evidence that water channel proteins 'aquaporins (AQPs)' are central components in plant-water relations as well as a number of other physiological parameters. We had previously reported the isolation of 24 plasma membrane intrinsic protein (PIP) type AQPs. However, the gene numbers in rice and the polyploid nature of bread wheat indicated a high probability of further genes in the latter. The present work focused on identification of further AQP isoforms in bread wheat. With the use of altered primer design, we identified five genes homologous, designated PIP1;5b, PIP2;9b, TaPIP2;2, TaPIP2;2a, TaPIP2;2b. Sequence alignments indicate PIP1;5b, PIP2;9b are likely to be homeologues of two previously reported genes while the other three are new genes and could be homeologs of each other. The results indicate further AQP diversity in wheat and the sequence data will enable physical mapping of these genes to identify their genomes as well as genetic to determine their association with any quantitative trait loci (QTLs) associated with plant-water relation such as salinity or drought tolerance.

Keywords: Aquaporins, homeologues, PIP, wheat

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Authors: Musammat F. Nahar, Anna Roujeinikova

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Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.

Keywords: Helicobacter pylori, molecular chaperone DnaK, pyrrhocoricin, structural biology.

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Authors: Elena Carcano, Mirzi Betasolo

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This study helps Public Water Bureaus in giving reliable answers to water concession requests. Rapidly increasing water requests can be supported provided that further uses of a river course are not totally compromised, and environmental features are protected as well. Strictly speaking, a water concession can be considered a continuous drawing from the source and causes a mean annual streamflow reduction. Therefore, deciding if a water concession is appropriate or inappropriate seems to be easily solved by comparing the generic demand to the mean annual streamflow value at disposal. Still, the immediate shortcoming for such a comparison is that streamflow data are information available only for few catchments and, most often, limited to specific sites. Subsequently, comparing the generic water demand to mean daily discharge is indeed far from being completely satisfactory since the mean daily streamflow is greater than the water withdrawal for a long period of a year. Consequently, such a comparison appears to be of little significance in order to preserve the quality and the quantity of the river. In order to overcome such a limit, this study aims to complete the information provided by flow duration curves introducing a link between Flow Duration Curves (FDCs) and recession curves and aims to show the chronological sequence of flows with a particular focus on low flow data. The analysis is carried out on 25 catchments located in North-Eastern Italy for which daily data are provided. The results identify groups of catchments as hydrologically homogeneous, having the lower part of the FDCs (corresponding streamflow interval is streamflow Q between 300 and 335, namely: Q(300), Q(335)) smoothly reproduced by a common recession curve. In conclusion, the results are useful to provide more reliable answers to water request, especially for those catchments which show similar hydrological response and can be used for a focused regionalization approach on low flow data. A mathematical link between streamflow duration curves and recession curves is herein provided, thus furnishing streamflow duration curves information upon a temporal sequence of data. In such a way, by introducing assumptions on recession curves, the chronological sequence upon low flow data can also be attributed to FDCs, which are known to lack this information by nature.

Keywords: Chronological sequence of discharges, recession curves, streamflow duration curves, water concession.

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Authors: Renáta Iváncsy, István Vajk

Abstract:

The various types of frequent pattern discovery problem, namely, the frequent itemset, sequence and graph mining problems are solved in different ways which are, however, in certain aspects similar. The main approach of discovering such patterns can be classified into two main classes, namely, in the class of the levelwise methods and in that of the database projection-based methods. The level-wise algorithms use in general clever indexing structures for discovering the patterns. In this paper a new approach is proposed for discovering frequent sequences and tree-like patterns efficiently that is based on the level-wise issue. Because the level-wise algorithms spend a lot of time for the subpattern testing problem, the new approach introduces the idea of using automaton theory to solve this problem.

Keywords: Frequent pattern discovery, graph mining, pushdownautomaton, sequence mining, state machine, tree mining.

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Authors: M. Sivakumar, S. Saravanan

Abstract:

The main function of Medium Access Control (MAC) is to share the channel efficiently between all nodes. In the real-time scenario, there will be certain amount of wastage in bandwidth due to back-off periods. More bandwidth will be wasted in idle state if the back-off period is very high and collision may occur if the back-off period is small. So, an optimization is needed for this problem. The main objective of the work is to reduce delay due to back-off period thereby reducing collision and increasing throughput. Here a method, called the virtual back-off algorithm (VBA) is used to optimize the back-off period and thereby it increases throughput and reduces collisions. The main idea is to optimize the number of transmission for every node. A counter is introduced at each node to implement this idea. Here counter value represents the sequence number. VBA is classified into two types VBA with counter sharing (VBA-CS) and VBA with no counter sharing (VBA-NCS). These two classifications of VBA are compared for various parameters. Simulation is done in NS-2 environment. The results obtained are found to be promising. 

Keywords: VBA, sequence number, counter, back-off period.

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Authors: Oi Mean Foong, Tan Jung Low, Satrio Wibowo

Abstract:

Hand gesture is one of the typical methods used in sign language for non-verbal communication. It is most commonly used by people who have hearing or speech problems to communicate among themselves or with normal people. Various sign language systems have been developed by manufacturers around the globe but they are neither flexible nor cost-effective for the end users. This paper presents a system prototype that is able to automatically recognize sign language to help normal people to communicate more effectively with the hearing or speech impaired people. The Sign to Voice system prototype, S2V, was developed using Feed Forward Neural Network for two-sequence signs detection. Different sets of universal hand gestures were captured from video camera and utilized to train the neural network for classification purpose. The experimental results have shown that neural network has achieved satisfactory result for sign-to-voice translation.

Keywords: Hand gesture detection, neural network, signlanguage, sequence detection.

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Authors: Wanatchapong Kongkaew

Abstract:

This paper proposes an application of probabilistic technique, namely Gaussian process regression, for estimating an optimal sequence of the single machine with total weighted tardiness (SMTWT) scheduling problem. In this work, the Gaussian process regression (GPR) model is utilized to predict an optimal sequence of the SMTWT problem, and its solution is improved by using an iterated local search based on simulated annealing scheme, called GPRISA algorithm. The results show that the proposed GPRISA method achieves a very good performance and a reasonable trade-off between solution quality and time consumption. Moreover, in the comparison of deviation from the best-known solution, the proposed mechanism noticeably outperforms the recently existing approaches.

 

Keywords: Gaussian process regression, iterated local search, simulated annealing, single machine total weighted tardiness.

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Authors: Hany Alashwal, Safaai Deris, Razib M. Othman

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The protein domain structure has been widely used as the most informative sequence feature to computationally predict protein-protein interactions. However, in a recent study, a research group has reported a very high accuracy of 94% using hydrophobicity feature. Therefore, in this study we compare and verify the usefulness of protein domain structure and hydrophobicity properties as the sequence features. Using the Support Vector Machines (SVM) as the learning system, our results indicate that both features achieved accuracy of nearly 80%. Furthermore, domains structure had receiver operating characteristic (ROC) score of 0.8480 with running time of 34 seconds, while hydrophobicity had ROC score of 0.8159 with running time of 20,571 seconds (5.7 hours). These results indicate that protein-protein interaction can be predicted from domain structure with reliable accuracy and acceptable running time.

Keywords: Bioinformatics, protein-protein interactions, support vector machines, protein features.

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Authors: First G.M. Karthik, Second Ramachandra.V.Pujeri, Dr.

Abstract:

Generalized Center String (GCS) problem are generalized from Common Approximate Substring problem and Common substring problems. GCS are known to be NP-hard allowing the problems lies in the explosion of potential candidates. Finding longest center string without concerning the sequence that may not contain any motifs is not known in advance in any particular biological gene process. GCS solved by frequent pattern-mining techniques and known to be fixed parameter tractable based on the fixed input sequence length and symbol set size. Efficient method known as Bpriori algorithms can solve GCS with reasonable time/space complexities. Bpriori 2 and Bpriori 3-2 algorithm are been proposed of any length and any positions of all their instances in input sequences. In this paper, we reduced the time/space complexity of Bpriori algorithm by Constrained Based Frequent Pattern mining (CBFP) technique which integrates the idea of Constraint Based Mining and FP-tree mining. CBFP mining technique solves the GCS problem works for all center string of any length, but also for the positions of all their mutated copies of input sequence. CBFP mining technique construct TRIE like with FP tree to represent the mutated copies of center string of any length, along with constraints to restraint growth of the consensus tree. The complexity analysis for Constrained Based FP mining technique and Bpriori algorithm is done based on the worst case and average case approach. Algorithm's correctness compared with the Bpriori algorithm using artificial data is shown.

Keywords: Constraint Based Mining, FP tree, Data mining, GCS problem, CBFP mining technique.

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Authors: V. H. Mankar, T. S. Das, S. K. Sarkar

Abstract:

In this paper, we have proposed a novel blind watermarking architecture towards its hardware implementation in VLSI. In order to facilitate this hardware realization, cellular automata (CA) concept is introduced. The CA has been already accepted as an attractive structure for VLSI implementation because of its modularity, parallelism, high performance and reliability. The hardware realizable multiresolution spread spectrum watermarking techniques are very few in numbers in spite of their best ever resiliency against signal impairments. This is because of the computational cost and complexity associated with their different filter banks and lifting techniques. The concept of cellular automata theory in order to form a new transform domain technique i.e. Cellular Automata Transform (CAT) have been incorporated. Since CA provides spreading sequences having very low cross-correlation properties, the CA based pseudorandom sequence generator is considered in the present work. Considering the watermarking technique as a digital communication process, an error control coding (ECC) must be incorporated in the data hiding schemes. Besides the hardware implementation of entire CA based data hiding technique, the individual blocks of the algorithm using CA provide the best result than that of some other methods irrespective of the hardware and software technique. The Cellular Automata Transform, CA based PN sequence generator, and CA ECC are the requisite blocks that are developed not only to meet the reliable hardware requirements but also for the basic spread spectrum watermarking features. The proposed algorithm shows statistical invisibility and resiliency against various common signal-processing operations. This algorithmic design utilizes the existing allocated bandwidth in the data transmission channel in a more efficient manner.

Keywords: Cellular automata, watermarking, error control coding, PN sequence, VLSI.

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