Search results for: 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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Authors: Mubarak Saif Mohsen, Zurinahni Zainol, Rosalina Abdul Salam, Wahidah Husain

Abstract:

One of the major problems in genomic field is to perform sequence comparison on DNA and protein sequences. Executing sequence comparison on the DNA and protein data is a computationally intensive task. Sequence comparison is the basic step for all algorithms in protein sequences similarity. Parallel computing is an attractive solution to provide the computational power needed to speedup the lengthy process of the sequence comparison. Our main research is to enhance the protein sequence algorithm using dynamic programming method. In our approach, we parallelize the dynamic programming algorithm using multithreaded program to perform the sequence comparison and also developed a distributed protein database among many PCs using Remote Method Interface (RMI). As a result, we showed how different sizes of protein sequences data and computation of scoring matrix of these protein sequence on different number of processors affected the processing time and speed, as oppose to sequential processing.

Keywords: Protein sequence algorithm, dynamic programming algorithm, multithread

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Authors: Zurinahni Zainol, Rosalina Abdul Salam, Rosni Abdullah, Nur'Aini, Wahidah Husain

Abstract:

The size, complexity and number of databases used for protein information have caused bioinformatics to lag behind in adapting to the need to handle this distributed information. Integrating all the information from different databases into one database is a challenging problem. Our main research is to develop a tool which can be used to access and manipulate protein information from difference databases. In our approach, we have integrated difference databases such as Swiss-prot, PDB, Interpro, and EMBL and transformed these databases in flat file format into relational form using XML and Bioperl. As a result, we showed this tool can search different sizes of protein information stored in relational database and the result can be retrieved faster compared to flat file database. A web based user interface is provided to allow user to access or search for protein information in the local database.

Keywords: Protein sequence database, relational database, integrated database.

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Authors: Jehad A. H. Hammad, Nur'Aini binti Abdul Rashid

Abstract:

With the rapid development in the field of life sciences and the flooding of genomic information, the need for faster and scalable searching methods has become urgent. One of the approaches that were investigated is indexing. The indexing methods have been categorized into three categories which are the lengthbased index algorithms, transformation-based algorithms and mixed techniques-based algorithms. In this research, we focused on the transformation based methods. We embedded the N-gram method into the transformation-based method to build an inverted index table. We then applied the parallel methods to speed up the index building time and to reduce the overall retrieval time when querying the genomic database. Our experiments show that the use of N-Gram transformation algorithm is an economical solution; it saves time and space too. The result shows that the size of the index is smaller than the size of the dataset when the size of N-Gram is 5 and 6. The parallel N-Gram transformation algorithm-s results indicate that the uses of parallel programming with large dataset are promising which can be improved further.

Keywords: Biological sequence, Database index, N-gram indexing, Parallel computing, Sequence retrieval.

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Authors: Dhany Saputra, Dayang R. A. Rambli, Oi Mean Foong

Abstract:

In this paper, we propose an improvement of pattern growth-based PrefixSpan algorithm, called I-PrefixSpan. The general idea of I-PrefixSpan is to use sufficient data structure for Seq-Tree framework and separator database to reduce the execution time and memory usage. Thus, with I-PrefixSpan there is no in-memory database stored after index set is constructed. The experimental result shows that using Java 2, this method improves the speed of PrefixSpan up to almost two orders of magnitude as well as the memory usage to more than one order of magnitude.

Keywords: ArrayList, ArrayIntList, minimum support, sequence database, sequential patterns.

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Authors: M. F. Omar, R. A. Salam, R. Abdullah, N. A. Rashid

Abstract:

Proteins or genes that have similar sequences are likely to perform the same function. One of the most widely used techniques for sequence comparison is sequence alignment. Sequence alignment allows mismatches and insertion/deletion, which represents biological mutations. Sequence alignment is usually performed only on two sequences. Multiple sequence alignment, is a natural extension of two-sequence alignment. In multiple sequence alignment, the emphasis is to find optimal alignment for a group of sequences. Several applicable techniques were observed in this research, from traditional method such as dynamic programming to the extend of widely used stochastic optimization method such as Genetic Algorithms (GAs) and Simulated Annealing. A framework with combination of Genetic Algorithm and Simulated Annealing is presented to solve Multiple Sequence Alignment problem. The Genetic Algorithm phase will try to find new region of solution while Simulated Annealing can be considered as an alignment improver for any near optimal solution produced by GAs.

Keywords: Simulated annealing, genetic algorithm, sequence alignment, multiple sequence alignment.

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Authors: A. F. Ali, D. M. Shawky

Abstract:

Discovering new biological knowledge from the highthroughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a new approach for protein classification. Proteins that are evolutionarily- and thereby functionally- related are said to belong to the same classification. Identifying protein classification is of fundamental importance to document the diversity of the known protein universe. It also provides a means to determine the functional roles of newly discovered protein sequences. Our goal is to predict the functional classification of novel protein sequences based on a set of features extracted from each protein sequence. The proposed technique used datasets extracted from the Structural Classification of Proteins (SCOP) database. A set of spectral domain features based on Fast Fourier Transform (FFT) is used. The proposed classifier uses multilayer back propagation (MLBP) neural network for protein classification. The maximum classification accuracy is about 91% when applying the classifier to the full four levels of the SCOP database. However, it reaches a maximum of 96% when limiting the classification to the family level. The classification results reveal that spectral domain contains information that can be used for classification with high accuracy. In addition, the results emphasize that sequence similarity measures are of great importance especially at the family level.

Keywords: Bioinformatics, Artificial Neural Networks, Protein Sequence Analysis, Feature Extraction.

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Authors: Bogdan Walek, Cyril Klimes

Abstract:

This paper focuses on testing database of existing information system. At the beginning we describe the basic problems of implemented databases, such as data redundancy, poor design of database logical structure or inappropriate data types in columns of database tables. These problems are often the result of incorrect understanding of the primary requirements for a database of an information system. Then we propose an algorithm to compare the conceptual model created from vague requirements for a database with a conceptual model reconstructed from implemented database. An algorithm also suggests steps leading to optimization of implemented database. The proposed algorithm is verified by an implemented prototype. The paper also describes a fuzzy system which works with the vague requirements for a database of an information system, procedure for creating conceptual from vague requirements and an algorithm for reconstructing a conceptual model from implemented database.

Keywords: testing, database, relational database, information system, conceptual model, fuzzy, uncertain information, database testing, reconstruction, requirements, optimization

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Authors: Norjihan Abdul Ghani, Zailani Mohd Sidek

Abstract:

Nowadays, organizations and business has several motivating factors to protect an individual-s privacy. Confidentiality refers to type of sharing information to third parties. This is always referring to private information, especially for personal information that usually needs to keep as a private. Because of the important of privacy concerns today, we need to design a database system that suits with privacy. Agrawal et. al. has introduced Hippocratic Database also we refer here as a privacy-aware database. This paper will explain how HD can be a future trend for web-based application to enhance their privacy level of trustworthiness among internet users.

Keywords: Hippocratic database, privacy, privacy-aware.

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Authors: Yun Bai

Abstract:

This paper is to investigate the impplementation of security mechanism in object oriented database system. Formal methods plays an essential role in computer security due to its powerful expressiveness and concise syntax and semantics. In this paper, both issues of specification and implementation in database security environment will be considered; and the database security is achieved through the development of an efficient implementation of the specification without compromising its originality and expressiveness.

Keywords: database security, authorization policy, logic basedspecification

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Authors: M. K. Bhuyan

Abstract:

The use of human hand as a natural interface for humancomputer interaction (HCI) serves as the motivation for research in hand gesture recognition. Vision-based hand gesture recognition involves visual analysis of hand shape, position and/or movement. In this paper, we use the concept of object-based video abstraction for segmenting the frames into video object planes (VOPs), as used in MPEG-4, with each VOP corresponding to one semantically meaningful hand position. Next, the key VOPs are selected on the basis of the amount of change in hand shape – for a given key frame in the sequence the next key frame is the one in which the hand changes its shape significantly. Thus, an entire video clip is transformed into a small number of representative frames that are sufficient to represent a gesture sequence. Subsequently, we model a particular gesture as a sequence of key frames each bearing information about its duration. These constitute a finite state machine. For recognition, the states of the incoming gesture sequence are matched with the states of all different FSMs contained in the database of gesture vocabulary. The core idea of our proposed representation is that redundant frames of the gesture video sequence bear only the temporal information of a gesture and hence discarded for computational efficiency. Experimental results obtained demonstrate the effectiveness of our proposed scheme for key frame extraction, subsequent gesture summarization and finally gesture recognition.

Keywords: Hand gesture, MPEG-4, Hausdorff distance, finite state machine.

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Authors: Dalanya Asaad Mohammed, Dara Abdul Razaq

Abstract:

A total of twenty tensile biopsies were collected from children undergoing tonsillectomy from teaching hospital ENT department and Kurdistan private hospital in sulaimani city. All biopsies were homogenized and cultured; the obtained bacterial isolates were purified and identified by biochemical tests and VITEK 2 compact system. Among the twenty studied samples, only one Pseudomonas putida with probability of 99% was isolated. Antimicrobial susceptibility was carried out by disk diffusion method, Pseudomonas putida showed resistance to all antibiotics used except vancomycin. The isolate further subjected to PCR and DNA sequence analysis of blaVIM gene using different set of primers for different regions of VIM gene. The results were found to be PCR positive for the blaVIM gene. To determine the sequence of blaVIM gene, DNA sequencing performed. Sequence alignment of blaVIM gene with previously recorded blaVIM gene in NCBI- database showed that P. putida isolate have different blaVIM gene.

Keywords: Clinical isolates, Putida, Sulaimani, Vim gene.

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Authors: Zine-Eddine Bouras, Abdelouaheb Talai

Abstract:

The need to merge software artifacts seems inherent to modern software development. Distribution of development over several teams and breaking tasks into smaller, more manageable pieces are an effective means to deal with the kind of complexity. In each case, the separately developed artifacts need to be assembled as efficiently as possible into a consistent whole in which the parts still function as described. In addition, earlier changes are introduced into the life cycle and easier is their management by designers. Interaction-based specifications such as UML sequence diagrams have been found effective in this regard. As a result, sequence diagrams can be used not only for capturing system behaviors but also for merging changes in order to create a new version. The objective of this paper is to suggest a new approach to deal with the problem of software merging at the level of sequence diagrams by using the concept of dependence analysis that captures, formally, all mapping, and differences between elements of sequence diagrams and serves as a key concept to create a new version of sequence diagram.

Keywords: System behaviors, sequence diagram merging, dependence analysis, sequence diagram slicing.

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Authors: Bogdan Walek, Cyril Klimes

Abstract:

In present days the area of data migration is very topical. Current tools for data migration in the area of relational database have several disadvantages that are presented in this paper. We propose a methodology for data migration of the database tables and their data between various types of relational database systems (RDBMS). The proposed methodology contains an expert system. The expert system contains a knowledge base that is composed of IFTHEN rules and based on the input data suggests appropriate data types of columns of database tables. The proposed tool, which contains an expert system, also includes the possibility of optimizing the data types in the target RDBMS database tables based on processed data of the source RDBMS database tables. The proposed expert system is shown on data migration of selected database of the source RDBMS to the target RDBMS.

Keywords: Expert system, fuzzy, data migration, database, relational database, data type, relational database management system.

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Authors: Hongzhi Wang, Jianzhong Li, Hong Gao

Abstract:

XML is an important standard of data exchange and representation. As a mature database system, using relational database to support XML data may bring some advantages. But storing XML in relational database has obvious redundancy that wastes disk space, bandwidth and disk I/O when querying XML data. For the efficiency of storage and query XML, it is necessary to use compressed XML data in relational database. In this paper, a compressed relational database technology supporting XML data is presented. Original relational storage structure is adaptive to XPath query process. The compression method keeps this feature. Besides traditional relational database techniques, additional query process technologies on compressed relations and for special structure for XML are presented. In this paper, technologies for XQuery process in compressed relational database are presented..

Keywords: XML, compression, query processing

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Authors: M. Michael Gromiha, Y. Yabuki, K. Imai, P. Horton, K. Fukui

Abstract:

We have developed a database for membrane protein functions, which has more than 3000 experimental data on functionally important amino acid residues in membrane proteins along with sequence, structure and literature information. Further, we have proposed different methods for identifying membrane proteins based on their functions: (i) discrimination of membrane transport proteins from other globular and membrane proteins and classifying them into channels/pores, electrochemical and active transporters, and (ii) β-signal for the insertion of mitochondrial β-barrel outer membrane proteins and potential targets. Our method showed an accuracy of 82% in discriminating transport proteins and 68% to classify them into three different transporters. In addition, we have identified a motif for targeting β-signal and potential candidates for mitochondrial β-barrel membrane proteins. Our methods can be used as effective tools for genome-wide annotations.

Keywords: Membrane proteins, database, transporters, discrimination, β-signal.

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Authors: N. Subramanian, C. Murugesan

Abstract:

The double difference sequence space I2 (M, of fuzzy numbers for both 1 < p < oo and 0 < p < 1, is introduced. Some general properties of this sequence space are studied. Some inclusion relations involving this sequence space are obtained.

Keywords: Orlicz function, solid space, metric space, completeness

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Authors: Omid Sharifi, Member, ACM, Zeki Bayram, Member, ACM

Abstract:

We demonstrate through a sample application, Ebanking, that the Web Service Modelling Language Ontology component can be used as a very powerful object-oriented database design language with logic capabilities. Its conceptual syntax allows the definition of class hierarchies, and logic syntax allows the definition of constraints in the database. Relations, which are available for modelling relations of three or more concepts, can be connected to logical expressions, allowing the implicit specification of database content. Using a reasoning tool, logic queries can also be made against the database in simulation mode.

Keywords: Semantic web, ontology, E-banking, database, WSML, WSMO, E-R diagram.

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Authors: Bogdan Walek, Cyril Klimes

Abstract:

Current tools for data migration between documentoriented and relational databases have several disadvantages. We propose a new approach for data migration between documentoriented and relational databases. During data migration the relational schema of the target (relational database) is automatically created from collection of XML documents. Proposed approach is verified on data migration between document-oriented database IBM Lotus/ Notes Domino and relational database implemented in relational database management system (RDBMS) MySQL.

Keywords: data migration, database, document-oriented database, XML, relational schema

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Authors: JiEun Jeong, Se-Won Kang, Hee-Ju Hwang, Sung-Hwa Chae, Sang-Haeng Choi, Hong-SeogPark, YeonSoo Han, Bok-Reul Lee, Dae-Hyun Seog, Yong Seok Lee

Abstract:

Tofurther advance research on immune-related genes from T. molitor, we constructed acDNA library and analyzed expressed sequence taq (EST) sequences from 1,056 clones. After removing vector sequence and quality checkingthrough thePhred program (trim_alt 0.05 (P-score>20), 1039 sequences were generated. The average length of insert was 792 bp. In addition, we identified 162 clusters, 167 contigs and 391 contigs after clustering and assembling process using a TGICL package. EST sequences were searchedagainst NCBI nr database by local BLAST (blastx, EKeywords: EST, Innate immunity, Tenebriomolitor

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Authors: Sing-Wu Liou, Yin-Fu Huang

Abstract:

For identifying the discriminative sequence features between exons and introns, a new paradigm, rescaled-range frameshift analysis (RRFA), was proposed. By RRFA, two new sequence features, the frameshift sensitivity (FS) and the accumulative penta-mer complexity (APC), were discovered which were further integrated into a new feature of larger scale, the persistency in anti-mutation (PAM). The feature-validation experiments were performed on six model organisms to test the power of discrimination. All the experimental results highly support that FS, APC and PAM were all distinguishing features between exons and introns. These identified new sequence features provide new insights into the sequence composition of genes and they have great potentials of forming a new basis for recognizing the exonintron boundaries in gene sequences.

Keywords: Exon-Intron Discrimination, Rescaled-Range Frameshift Analysis, Frameshift Sensitivity, Accumulative Sequence Complexity

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Authors: Shuzhen Yao, Fengjing Zhao, Jianwei He

Abstract:

The UML modeling of complex distributed systems often is a great challenge due to the large amount of parallel real-time operating components. In this paper the problems of verification of such systems are discussed. ECPN, an Extended Colored Petri Net is defined to formally describe state transitions of components and interactions among components. The relationship between sequence diagrams and Free Choice Petri Nets is investigated. Free Choice Petri Net theory helps verifying the liveness of sequence diagrams. By converting sequence diagrams to ECPNs and then comparing behaviors of sequence diagram ECPNs and statecharts, the consistency among models is analyzed. Finally, a verification process for an example model is demonstrated.

Keywords: Consistency, liveness, Petri Net, sequence diagram.

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Authors: Kolar Jan, Dvorak Vaclav

Abstract:

In this study, an optimization of supersonic air-to-air ejector is carried out by a recently developed single-objective genetic algorithm based on adaption of sequence of individuals. Adaptation of sequence is based on Shape-based distance of individuals and embedded micro-genetic algorithm. The optimal sequence found defines the succession of CFD-aimed objective calculation within each generation of regular micro-genetic algorithm. A spring-based deformation mutates the computational grid starting the initial individualvia adapted population in the optimized sequence. Selection of a generation initial individual is knowledge-based. A direct comparison of the newly defined and standard micro-genetic algorithm is carried out for supersonic air-to-air ejector. The only objective is to minimize the loose of total stagnation pressure in the ejector. The result is that sequence-adopted micro-genetic algorithm can provide comparative results to standard algorithm but in significantly lower number of overall CFD iteration steps.

Keywords: Grid deformation, Micro-genetic algorithm, shapebased sequence, supersonic ejector.

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Authors: Patsaraporn Somboonsak, Mud-Armeen Munlin

Abstract:

In April 2009, a new variant of Influenza A virus subtype H1N1 emerged in Mexico and spread all over the world. The influenza has three subtypes in human (H1N1, H1N2 and H3N2) Types B and C influenza tend to be associated with local or regional epidemics. Preliminary genetic characterization of the influenza viruses has identified them as swine influenza A (H1N1) viruses. Nucleotide sequence analysis of the Haemagglutinin (HA) and Neuraminidase (NA) are similar to each other and the majority of their genes of swine influenza viruses, two genes coding for the neuraminidase (NA) and matrix (M) proteins are similar to corresponding genes of swine influenza. Sequence similarity between the 2009 A (H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Nucleic acid sequence Maximum Likelihood (MCL) and DNA Empirical base frequencies, Phylogenetic relationship amongst the HA genes of H1N1 virus isolated in Genbank having high nucleotide sequence homology. In this paper we used 16 HA nucleotide sequences from NCBI for computing sequence relationships similarity of swine influenza A virus using the following method MCL the result is 28%, 36.64% for Optimal tree with the sum of branch length, 35.62% for Interior branch phylogeny Neighber – Join Tree, 1.85% for the overall transition/transversion, and 8.28% for Overall mean distance.

Keywords: Sequence DNA, Relationship of swine, Swineinfluenza, Sequence Similarity

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Authors: T. Balasubramanian, A. Pandiarani

Abstract:

In this paper we introduce some subspaces of fuzzy entire sequence space. Some general properties of these sequence spaces are discussed. Also some inclusion relation involving the spaces are obtained. Mathematics Subject Classification: 40A05, 40D25.

Keywords: Fuzzy Numbers, Entire sequences, completeness, Fuzzy entire sequences

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Authors: M. Heydari, S. A. Torabi

Abstract:

The problem of lot sizing, sequencing and scheduling multiple products in flow line production systems has been studied by several authors. Almost all of the researches in this area assumed that setup times and costs are sequence –independent even though sequence dependent setups are common in practice. In this paper we present a new mixed integer non linear program (MINLP) and a heuristic method to solve the problem in sequence dependent case. Furthermore, a genetic algorithm has been developed which applies this constructive heuristic to generate initial population. These two proposed solution methods are compared on randomly generated problems. Computational results show a clear superiority of our proposed GA for majority of the test problems.

Keywords: Economic lot scheduling problem, finite horizon, genetic algorithm, mixed zero-one nonlinear programming, sequence-dependent.

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Authors: Yuka Kawakami, Tomoyuki Yokogawa, Hisashi Miyazaki, Sousuke Amasaki, Yoichiro Sato, Michiyoshi Hayase

Abstract:

In this paper, we proposed a method for detecting consistency violation between state machine diagrams and a sequence diagram defined in UML 2.0 using SMV. We extended a method expressing these diagrams defined in UML 1.0 with boolean formulas so that it can express a sequence diagram with combined fragments introduced in UML 2.0. This extension made it possible to represent three types of combined fragment: alternative, option and parallel. As a result of experiment, we confirmed that the proposed method could detect consistency violation correctly with SMV.

Keywords: UML, model checking, SMV, sequence diagram.

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Authors: Mohammad H. Abu-Arqoub, Ihab S. Serhed, Waheeb A. Abu-Dawwas, Rashid M. Al-Azzeh

Abstract:

This paper aims at improving web server performance by establishing a middleware layer between web and database servers, which minimizes the overload on the database server. A middleware system has been developed as a service mainly to improve the performance. This system manages connection accesses in a way that would result in reducing the overload on the database server. In addition to the connection management, this system acts as an object-oriented model for best utilization of operating system resources. A web developer can use this Service Broker to improve web server performance.

Keywords: Database server, Improve performance, Middleware, Web server.

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Authors: M. Moosavi, H. Khatibzadeh

Abstract:

In this article, we study demiclosed and strongly quasi-nonexpansive of a sequence generated by the proximal point algorithm for a finite family of quasi-nonexpansive mappings in Hadamard spaces. Δ-convergence of iterations for the sequence of strongly quasi-nonexpansive mappings as well as the strong convergence of the Halpern type regularization of them to a common fixed point of sequence are also established. Our results generalize and improve several previously known results of the existing literature.

Keywords: Fixed point, Hadamard space, proximal point algorithm, quasi-nonexpansive sequence of mappings, resolvent.

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Authors: Chapman Eze Nnadozie

Abstract:

Relational databases constitute a very vital tool for the effective management and administration of both personal and organizational data. Data access ranges from a single user database management software to a more complex distributed server system. This paper intends to appraise the use a programming language extension like structured query language (SQL) to establish links to a relational database (Microsoft Access 2013) using Visual C++ 9 programming language environment. The methodology used involves the creation of tables to form a database using Microsoft Access 2013, which is Object Linking and Embedding (OLE) database compliant. The SQL command is used to query the tables in the database for easy extraction of expected records inside the visual C++ environment. The findings of this paper reveal that records can easily be accessed and manipulated to filter exactly what the user wants, such as retrieval of records with specified criteria, updating of records, and deletion of part or the whole records in a table.

Keywords: Data access, database, database management system, OLE, programming language, records, relational database, software, SQL, table.

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