Search results for: Gene Ontology

Authors: Wandili S. Awuor, Onyango D. Miruka, Waindi N. Eliud

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Foodborne Salmonella infections have become a major problem world wide. Salmonellosis transmitted from fish are quite common. Established quality control measures exist for export oriented fish, none exists for fish consumed locally. This study aimed at characterization of Salmonella isolated from Nile tilapia . The study was carried out in selected beaches along L. Victoria in Western Kenya between March and June 2007. One hundred and twenty fish specimens were collected. Salmonella isolates were confirmed using serotyping, biochemical testing in addition to malic acid dehydrogenase (mdh) and fliC gene sequencing. Twenty Salmonella isolates were confirmed by mdh gene sequencing. Nine (9) were S. enterica serotype typhimurium, four (4) were S. enterica Serotype, enteritidis and seven (7) were S. enterica serotype typhi. Nile tilapia have a role in transmission of Salmonellosis in the study area, poor sanitation was a major cause of pollution at the beach inshore waters.

Keywords: fliC, mdh, Salmonellosis, Serotype

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Authors: R. Haddad, K. Morris, V. Buchanan-Wollaston

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Biochemical and molecular analysis of some antioxidant enzyme genes revealed different level of gene expression on oilseed (Brassica napus). For molecular and biochemical analysis, leaf tissues were harvested from plants at eight different developmental stages, from young to senescence. The levels of total protein and chlorophyll were increased during maturity stages of plant, while these were decreased during the last stages of plant growth. Structural analysis (nucleotide and deduced amino acid sequence, and phylogenic tree) of a complementary DNA revealed a high level of similarity for a family of Catalase genes. The expression of the gene encoded by different Catalase isoforms was assessed during different plant growth phase. No significant difference between samples was observed, when Catalase activity was statistically analyzed at different developmental stages. EST analysis exhibited different transcripts levels for a number of other relevant antioxidant genes (different isoforms of SOD and glutathione). The high level of transcription of these genes at senescence stages was indicated that these genes are senescenceinduced genes.

Keywords: Biochemical analysis, Oilseed, Expression pattern, Growth phases

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Authors: Victoria Konidari, Yvan Abernot

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This paper seeks to explore the actual classroom setting, to examine its role for students- learning, and attitude in the class. It presents a theoretical approach of the classroom as system to be explored and examines the concrete reality of Greek secondary education students, under the light of the above approach. Based on the findings of a quantitative and qualitative research, authors propose a rather ontological approach of the classroom and underline what the key-elements for such approach should be. The paper explores extensively the theoretical dimensions for the change of paradigm required and addresses the new issues to be considered.

Keywords: Group, class, collective subject, field, temporality, ontology.

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Authors: Mohammad Yasrebi, Mehran Mohsenzadeh, Mashalla Abbasi-Dezfuli

Abstract:

Machine-understandable data when strongly interlinked constitutes the basis for the SemanticWeb. Annotating web documents is one of the major techniques for creating metadata on the Web. Annotating websites defines the containing data in a form which is suitable for interpretation by machines. In this paper, we present a new approach to annotate websites and documents by promoting the abstraction level of the annotation process to a conceptual level. By this means, we hope to solve some of the problems of the current annotation solutions.

Keywords: Knowledge base, ontology, semantic annotation, semantic web.

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Authors: Boroňová I., Bernasovská J., Kľoc J., Tomková Z., Petrejčíková E., Gabriková D., Mačeková S.

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Osteoporosis is a complex health disease characterized by low bone mineral density, which is determined by an interaction of genetics with metabolic and environmental factors. Current research in genetics of osteoporosis is focused on identification of responsible genes and polymorphisms. TNFRSF11B gene plays a key role in bone remodeling. The aim of this study was to investigate the genotype and allele distribution of A163G (rs3102735) osteoprotegerin gene promoter and G1181C (rs2073618) osteoprotegerin first exon polymorphisms in the group of 180 unrelated postmenopausal women with diagnosed osteoporosis and 180 normal controls. Genomic DNA was isolated from peripheral blood leukocytes using standard methodology. Genotyping for presence of different polymorphisms was performed using the Custom Taqman®SNP Genotyping assays. Hardy-Weinberg equilibrium was tested for each SNP in the groups of participants using the chi-square (χ²) test. The distribution of investigated genotypes in the group of patients with osteoporosis were as follows: AA (66.7%), AG (32.2%), GG (1.1%) for A163G polymorphism; GG (19.4%), CG (44.4%), CC (36.1%) for G1181C polymorphism. The distribution of genotypes in normal controls were follows: AA (71.1%), AG (26.1%), GG (2.8%) for A163G polymorphism; GG (22.2%), CG (48.9%), CC (28.9%) for G1181C polymorphism. In A163G polymorphism the variant G allele was more common among patients with osteoporosis: 17.2% versus 15.8% in normal controls. Also, in G1181C polymorphism the phenomenon of more frequent occurrence of C allele in the group of patients with osteoporosis was observed (58.3% versus 53.3%). Genotype and allele distributions showed no significant differences (A163G: χ²=0.270, p=0.605; χ²=0.250, p=0.616; G1181C: χ²= 1.730, p=0.188; χ²=1.820, p=0.177). Our results represents an initial study, further studies of more numerous file and associations studies will be carried out. Knowing the distribution of genotypes is important for assessing the impact of these polymorphisms on various parameters associated with osteoporosis. Screening for identification of “at-risk” women likely to develop osteoporosis and initiating subsequent early intervention appears to be most effective strategy to substantially reduce the risks of osteoporosis.

Keywords: Osteoporosis, Real-time PCR method, SNP polymorphisms.

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Authors: Mohammad Yasrebi, Mehran Mohsenzadeh

Abstract:

The third phase of web means semantic web requires many web pages which are annotated with metadata. Thus, a crucial question is where to acquire these metadata. In this paper we propose our approach, a semi-automatic method to annotate the texts of documents and web pages and employs with a quite comprehensive knowledge base to categorize instances with regard to ontology. The approach is evaluated against the manual annotations and one of the most popular annotation tools which works the same as our tool. The approach is implemented in .net framework and uses the WordNet for knowledge base, an annotation tool for the Semantic Web.

Keywords: Semantic Annotation, Metadata, Information Extraction, Semantic Web, knowledge base.

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Authors: Adama Sow, Abdoulaye Guiss´e, Oumar Niang

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To assist medical diagnosis, we propose a federation of several existing and open medical ontologies and terminologies. The goal is to merge the strengths of all these resources to provide clinicians the access to a variety of shared knowledges that can facilitate identification and association of human diseases and all of their available characteristic signs such as symptoms and clinical signs. This work results to an integration model loaded from target known ontologies of the bioportal platform such as DOID, MESH, and SNOMED for diseases selection, SYMP, and CSSO for all existing signs.

Keywords: Medical decision, medical ontologies, ontologies integration, linked data, knowledge ingeneering, e-health system.

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Authors: N. Hoosain, S. Nene, B. Pearce, C. Jacobs, M. Du Plessis, M. Benjeddou

Abstract:

Organic cation transporter (OCT) 1could influence an individual’s response to various treatments and increase their susceptibility to diseases.Genotypic and allelic frequencies of nineteen non-synonymous and one intronic Single Nucleotide Polymorphism (SNP) from the OCT1 gene were determined in 101 unrelated healthy Zulu participants, using a SNaPshot^® multiplex assay. Minor allele frequencies (MAF)were compared to representative populations of Africa, Asia and Europe, from Ensembl. MAFs for S14F, V519F, rs622342 and P341L were 2.0%, 6.0%, 6.0% and 1.0%, respectively. Sixteen of nineteen investigated non-synonymous SNPs were monomorphic. No study participant harbored variant alleles for S189L, G220V, P283L, G401S, M420V, M440I, G465R, I542V, R61C, R287G, C88S, A306T, A413V, I421F, C436F and V501E. Haplotype, CGTCGCCGCGCAAGAGGTGA, was most frequently observed (81.23%).Further investigations are encouraged to evaluate potential roles these SNPs could play in the therapeutic efficacy of clinically important drugs and in the development of various diseases in the Zulu population.

Keywords: OCT1, PCR, SNaPshot assay, Zulu population.

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Authors: Erin Lynne Plettenberg, Jeremy Vickery

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In an access-control situation, the role of a user determines whether a data request is appropriate. This paper combines vetted web mining and logic modeling to build a lightweight system for determining the role of a health care provider based only on their prior authorized requests. The model identifies provider roles with 100% recall from very little data. This shows the value of vetted web mining in AI systems, and suggests the impact of the ICD classification on medical practice.

Keywords: Ontology, logic modeling, electronic medical records, information extraction, vetted web mining.

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Authors: Hadi Khosravi Farsani, Mohammadali Nematbakhsh

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To overcome the product overload of Internet shoppers, we introduce a semantic recommendation procedure which is more efficient when applied to Internet shopping malls. The suggested procedure recommends the semantic products to the customers and is originally based on Web usage mining, product classification, association rule mining, and frequently purchasing. We applied the procedure to the data set of MovieLens Company for performance evaluation, and some experimental results are provided. The experimental results have shown superior performance in terms of coverage and precision.

Keywords: Personalization, Recommendation, OWL Ontology, Electronic Catalogs, Classification.

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Authors: A. Doosti, P. Ghasemi Dehkordi, M. Zamani, S. Taheri, M. Banitalebi, M. Mahmoudzadeh

Abstract:

The p53 tumor suppressor gene plays two important roles in genomic stability: blocking cell proliferation after DNA damage until it has been repaired, and starting apoptosis if the damage is too critical. Codon 72 exon4 polymorphism (Arg72Pro) of the P53 gene has been implicated in cancer risk. Various studies have been done to investigate the status of p53 at codon 72 for arginine (Arg) and proline (Pro) alleles in different populations and also the association of this codon 72 polymorphism with various tumors. Our objective was to investigate the possible association between P53 Arg72Pro polymorphism and susceptibility to colorectal cancer among Isfahan and Chaharmahal Va Bakhtiari (a part of south west of Iran) population. We investigated the status of p53 at codon 72 for Arg/Arg, Arg/Pro and Pro/Pro allele polymorphisms in blood samples from 145 colorectal cancer patients and 140 controls by Nested-PCR of p53 exon 4 and digestion with BstUI restriction enzyme and the DNA fragments were then resolved by electrophoresis in 2% agarose gel. The Pro allele was 279 bp, while the Arg allele was restricted into two fragments of 160 and 119 bp. Among the 145 colorectal cancer cases 49 cases (33.79%) were homozygous for the Arg72 allele (Arg/Arg), 18 cases (12.41%) were homozygous for the Pro72 allele (Pro/Pro) and 78 cases (53.8%) found in heterozygous (Arg/Pro). In conclusion, it can be said that p53Arg/Arg genotype may be correlated with possible increased risk of this kind of cancers in south west of Iran.

Keywords: TP53, Polymorphism, Colorectal Cancer, Iran

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Authors: B.A.Gobin, R.K.Subramanian

Abstract:

This paper gives an overview of the mapping mechanism of SEAM-a methodology for the automatic generation of knowledge models and its mapping onto Java codes. It discusses the rules that will be used to map the different components in the knowledge model automatically onto Java classes, properties and methods. The aim of developing this mechanism is to help in the creation of a prototype which will be used to validate the knowledge model which has been generated automatically. It will also help to link the modeling phase with the implementation phase as existing knowledge engineering methodologies do not provide for proper guidelines for the transition from the knowledge modeling phase to development phase. This will decrease the development overheads associated to the development of Knowledge Based Systems.

Keywords: KBS, OWL, ontology, knowledge models

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Authors: Mohamed Kholif, Suaad Awad Mohamed

Abstract:

In this paper we present semantic assistant agent (SAA), an open source digital library agent which takes user query for finding information in the digital library and takes resources- metadata and stores it semantically. SAA uses Semantic Web to improve browsing and searching for resources in digital library. All metadata stored in the library are available in RDF format for querying and processing by SemanSreach which is a part of SAA architecture. The architecture includes a generic RDF-based model that represents relationships among objects and their components. Queries against these relationships are supported by an RDF triple store.

Keywords: Digital Library, Dublin Core, Ontology, Semantic web.

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Authors: Fiona Browne, Huiru Zheng, Haiying Wang, Francisco Azuaje

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Recent years have seen a growing trend towards the integration of multiple information sources to support large-scale prediction of protein-protein interaction (PPI) networks in model organisms. Despite advances in computational approaches, the combination of multiple “omic" datasets representing the same type of data, e.g. different gene expression datasets, has not been rigorously studied. Furthermore, there is a need to further investigate the inference capability of powerful approaches, such as fullyconnected Bayesian networks, in the context of the prediction of PPI networks. This paper addresses these limitations by proposing a Bayesian approach to integrate multiple datasets, some of which encode the same type of “omic" data to support the identification of PPI networks. The case study reported involved the combination of three gene expression datasets relevant to human heart failure (HF). In comparison with two traditional methods, Naive Bayesian and maximum likelihood ratio approaches, the proposed technique can accurately identify known PPI and can be applied to infer potentially novel interactions.

Keywords: Bayesian network, Classification, Data integration, Protein interaction networks.

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Authors: Miquel Colobran, Josep M. Basart

Abstract:

One of the most ancient humankind concerns is knowledge formalization i.e. what a concept is. Concept Analysis, a branch of analytical philosophy, relies on the purpose of decompose the elements, relations and meanings of a concept. This paper aims at presenting a method to make a concept analysis obtaining a knowledge representation suitable to be processed by a computer system using either object-oriented or ontology technologies. Security notion is, usually, known as a set of different concepts related to “some kind of protection". Our method concludes that a more general framework for the concept, despite it is dynamic, is possible and any particular definition (instantiation) depends on the elements used by its construction instead of the concept itself.

Keywords: Concept analysis, Knowledge representation, Security, UML.

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Authors: Abdulwahab Kammon, Tan Sheau Wei, Abdul Rahman Omar, Abdunaser Dayhum, Ibrahim Eldghayes, Monier Sharif

Abstract:

Infectious bronchitis virus (IBV) is a very dynamic and evolving virus, causing major economic losses to the global poultry industry. Recently, the Libyan poultry industry faced severe outbreak of respiratory distress associated with high mortality and dramatic drop in egg production. Tracheal and cloacal swabs were analyzed for several poultry viruses. IBV was detected using SYBR Green I real-time PCR detection based on the nucleocapsid (N) gene. Sequence analysis of the partial N gene indicated high similarity (~ 94%) to IBV strain 3382/06 that was isolated from Taiwan. Even though the IBV strain 3382/06 is more similar to that of the Mass type H120, the isolate has been implicated associated with intertypic recombinant of 3 putative parental IBV strains namely H120, Taiwan strain 1171/92 and China strain CK/CH/LDL/97I. Complete sequencing and antigenicity studies of the Libya IBV strains are currently underway to determine the evolution of the virus and its importance in vaccine induced immunity. In this paper we documented for the first time the presence of possibly variant IBV strain from Libya which required dramatic change in vaccination program.

Keywords: Libya, Infectious bronchitis, Molecular characterization.

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Authors: M. J. Norashirene, Y. Zakiah, S. Nurdiana, I. Nur Hilwani, M. H. Siti Khairiyah, M. J. Muhamad Arif

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In this study, six bacterial isolates of a slightly thermophilic organism from the Sg. Klah hot spring, Malaysia were successfully isolated and designated as M7T55D1, M7T55D2, M7T55D3, M7T53D1, M7T53D2 and M7T53D3 respectively. The bacterial isolates were screened for their cellulose hydrolytic ability on Carboxymethlycellulose agar medium. The isolated bacterial strains were identified morphologically, biochemically and molecularly with the aid of 16S rDNA sequencing. All of the bacteria showed their optimum growth at a slightly alkaline pH of 7.5 with a temperature of 55°C. All strains were Gram-negative, non-spore forming type, strictly aerobic, catalase-positive and oxidase-positive with the ability to produce thermostable cellulase. Based on BLASTn results, bacterial isolates of M7T55D2 and M7T53D1 gave the highest homology (97%) with similarity to Tepidimonas ignava while isolates M7T55D1, M7T55D3, M7T53D2 and M7T53D3 showed their closest homology (97%-98%) with Tepidimonas thermarum. These cellulolytic thermophiles might have a commercial potential to produce valuable thermostable cellulase.

Keywords: Cellulase, Cellulolytic, Thermophiles, 16S rDNA Gene.

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Authors: Yahia I. Mohamed, Ahmed I. Marzouk, Mohamed A. Yacout

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Aim of this work was to study the genetic basis for oil accumulation in olive fruit via tracking DGAT2 (Diacylglycerol acyltransferase type-2) gene in three Egyptian Origen Olive cultivars namely Toffahi, Hamed and Maraki using molecular marker techniques and bioinformatics tools. Results illustrate that, firstly: specific genomic band of Maraki cultivars was identified as DGAT2 (Diacylglycerol acyltransferase type-2) and identical for this gene in Olea europaea with 100% of similarity. Secondly, differential genomic band of Maraki cultivars which produced from RAPD fingerprinting technique reflected predicted distinguished sequence which identified as DGAT2 (Diacylglycerol acyltransferase type-2) in Fragaria vesca subsp. Vesca with 76% of sequential similarity. Third and finally, specific genomic specific band of Hamed cultivars was identified as two fragments, 1- Olea europaea cultivar Koroneiki diacylglycerol acyltransferase type 2 mRNA, complete cds with two matches regions with 99% or 2- Predicted: Fragaria vesca subsp. vesca diacylglycerol O-acyltransferase 2-like (LOC101313050), mRNA with 86 % of similarity.

Keywords: Olea europaea, fingerprinting, Diacylglycerol acyltransferase type- 2 (DGAT2).

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Authors: Hendry Muljadi, Hideaki Takeda, Koichi Ando

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A manufacturing feature can be defined simply as a geometric shape and its manufacturing information to create the shape. In a feature-based process planning system, feature library plays an important role in the extraction of manufacturing features with their proper manufacturing information. However, to manage the manufacturing information flexibly, it is important to build a feature library that is easy to modify. In this paper, a Wiki-based feature library is proposed.

Keywords: Manufacturing feature, feature library, feature ontology, process planning, Wiki, MediaWiki.

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Authors: Permphan Dharmasaroja

Abstract:

Mutations of the telomeric copy of the survival motor neuron 1 (SMN1) gene cause spinal muscular atrophy. A deletion of the Eef1a2 gene leads to lower motor neuron degeneration in wasted mice. Indirect evidences have been shown that the eEF1A protein family may interact with SMN, and our previous study showed that abnormalities of neuromuscular junctions in wasted mice were similar to those of Smn mutant mice. To determine potential colocalization between SMN and tissue-specific translation elongation factor 1A2 (eEF1A2), an immunochemical analysis of HeLa cells transfected with the plasmid pcDNA3.1(+)C-hEEF1A2- myc and a new quantitative test of colocalization by intensity correlation analysis (ICA) was used to explore the association of SMN and eEF1A2. Here the results showed that eEF1A2 redistributed from the cytoplasm to the nucleus in response to serum and epidermal growth factor. In the cytoplasm, compelling evidence showed that staining for myc-tagged eEF1A2 varied in synchrony with that for SMN, consistent with the formation of a SMN-eEF1A2 complex in the cytoplasm of HeLa cells. These findings suggest that eEF1A2 may colocalize with SMN in the cytoplasm and may be a component of the SMN complex. However, the limitation of the ICA method is an inability to resolve colocalization in components of small organelles such as the nucleus.

Keywords: Intensity correlation analysis, intensity correlation quotient.

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Authors: Dominykas Broga

Abstract:

Until recently it would have been unusual to consider classifying population movements and refugees as security problem. However, efforts at shaping our world to make ourselves secure have paradoxically led to ever greater insecurity. The feeling of uncertainty, pertinent throughout all discourses of security, has led to the creation of security production into seemingly benign routines of everyday life. Yet, the paper argues, neither of security discourses accounted for, disclosed and challenged the fundamental aporias embedded in Western security narratives. In turn, the paper aims to unpick the conventional security wisdom, which is haunted with strong ontologies, embedded in the politics of Orientalism, and (in)security nexus. The paper concludes that current security affair conceals the integral impossibility of fulfilling its very own promise of assured security. The paper also provides suggestions about alternative security discourse based on mutual dialogue.

Keywords: Identity, (in)security, migration, ontology

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Authors: L. K. Davis

Abstract:

The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time based DNA codes, writing DNA code from scratch.

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Authors: Qurban A Memon, Shakeel A. Khoja

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Generally, administrative systems in an academic environment are disjoint and support independent queries. The objective in this work is to semantically connect these independent systems to provide support to queries run on the integrated platform. The proposed framework, by enriching educational material in the legacy systems, provides a value-added semantics layer where activities such as annotation, query and reasoning can be carried out to support management requirements. We discuss the development of this ontology framework with a case study of UAE University program administration to show how semantic web technologies can be used by administration to develop student profiles for better academic program management.

Keywords: Academic Program Administration, Semantic Web, Web Technology

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Authors: Amani Ashari, Julia Omar, Arif Hashim, Shahrul Hamid

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Apolipoprotein E (APOE) gene polymorphism has influence on serum lipids which relates to cardiovascular risk. The purpose of this study was to determine the frequency distribution of APOE alleles among Malaysian Type 2 Diabetes Mellitus (DM) patients with and without coronary artery disease (CAD) and their association with serum lipid profiles. A total of 115 patients were recruited in which 78 patients had Type 2 DM without CAD and 37 patients had Type 2 DM with CAD. The APOE polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The APOE ɛ3 allele was the most common one in both groups. There was no significant association between the APOE genotypes and the CAD status in Type 2 DM using Pearson χ² test. Further analysis indicated there were no significant differences in all lipid parameters between E2, E3 and E4 subgroups in both groups. The study showed that the E4 allele carriers of Type 2 DM with CAD patients had higher LDL-C level and lower HDL-C level compared to the other allele carriers. However, analyses showed these levels were not statistically different. The study also showed that the Type 2 DM with CAD group with E2 allele had higher triglyceride (TG). In conclusion, further study with larger sample size is needed to confirm role of E4 as a marker of CAD among Type 2 DM patients in Malaysian population.

Keywords: Apolipoprotein E, diabetes mellitus, cardiovascular disease, lipids.

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Authors: Zundong Zhang, Limin Jia, Yuanyuan Chai

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Control of complex systems is one of important files in complex systems, that not only relies on the essence of complex systems which is denoted by the core concept – emergence, but also embodies the elementary concept in control theory. Aiming at giving a clear and self-contained description of emergence, the paper introduces a formal way to completely describe the formation and dynamics of emergence in complex systems. Consequently, this paper indicates the Emergence-Oriented Control methodology that contains three kinds of basic control schemes: the direct control, the system re-structuring and the system calibration. As a universal ontology, the Emergence-Oriented Control provides a powerful tool for identifying and resolving control problems in specific systems.

Keywords: Complex System Control, Emergence, Emergence- Oriented Control Methodology.

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Authors: Hanh Huu Hoang, Tho Manh Nguyen

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Ever increasing capacities of contemporary storage devices inspire the vision to accumulate (personal) information without the need of deleting old data over a long time-span. Hence the target of SemanticLIFE project is to create a Personal Information Management system for a human lifetime data. One of the most important characteristics of the system is its dedication to retrieve information in a very efficient way. By adopting user demands regarding the reduction of ambiguities, our approach aims at a user-oriented and yet powerful enough system with a satisfactory query performance. We introduce the query system of SemanticLIFE, the Virtual Query System, which uses emerging Semantic Web technologies to fulfill users- requirements.

Keywords: Ontology-based Information Retrieval, Digital Memories, SemanticLIFE.

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Authors: Natalia Koltovaya, Nadezhda Zhuchkina, Ksenia Lyubimova

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We study the biological effects induced by ionizing radiation in view of therapeutic exposure and the idea of space flights beyond Earth's magnetosphere. In particular, we examine the differences between base pair substitution induction by ionizing radiation in model haploid and diploid yeast Saccharomyces cerevisiae cells. Such mutations are difficult to study in higher eukaryotic systems. In our research, we have used a collection of six isogenic trp5-strains and 14 isogenic haploid and diploid cyc1-strains that are specific markers of all possible base-pair substitutions. These strains differ from each other only in single base substitutions within codon-50 of the trp5 gene or codon-22 of the cyc1 gene. Different mutation spectra for two different haploid genetic trp5- and cyc1-assays and different mutation spectra for the same genetic cyc1-system in cells with different ploidy — haploid and diploid — have been obtained. It was linear function for dose-dependence in haploid and exponential in diploid cells. We suggest that the differences between haploid yeast strains reflect the dependence on the sequence context, while the differences between haploid and diploid strains reflect the different molecular mechanisms of mutations.

Keywords: Base pair substitutions, γ-rays, haploid and diploid cells, yeast Saccharomyces cerevisiae.

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Authors: Mohib ur Rehman, Imran Ihsan, Mobin Uddin Ahmed, Nadeem Iftikhar, Muhammad Abdul Qadir

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Multimedia, as it stands now is perhaps the most diverse and rich culture around the globe. One of the major needs of Multimedia is to have a single system that enables people to efficiently search through their multimedia catalogues. Many Domain Specific Systems and architectures have been proposed but up till now no generic and complete architecture is proposed. In this paper, we have suggested a generic architecture for Multimedia Database. The main strengths of our architecture besides being generic are Semantic Libraries to reduce semantic gap, levels of feature extraction for more specific and detailed feature extraction according to classes defined by prior level, and merging of two types of queries i.e. text and QBE (Query by Example) for more accurate yet detailed results.

Keywords: Multimedia Database Architecture, Semantics, Feature Extraction, Ontology.

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Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur

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Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions, and the modeling of evolution. Various global rearrangements of permutations, such as reversals and transpositions,have recently become of interest because of their applications in computational molecular biology. A reversal is an operation that reverses the order of a substring of a permutation. A transposition is an operation that swaps two adjacent substrings of a permutation. The problem of determining the smallest number of reversals required to transform a given permutation into the identity permutation is called sorting by reversals. Similar problems can be defined for transpositions and other global rearrangements. In this work we perform a study about some genome rearrangement primitives. We show how a genome is modelled by a permutation, introduce some of the existing primitives and the lower and upper bounds on them. We then provide a comparison of the introduced primitives.

Keywords: Sorting Primitives, Genome Rearrangements, Transpositions, Block Interchanges, Strip Exchanges.

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Authors: Antonio Di Leva, Carla Reyneri, Michele Sonnessa

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PARADIGMA (PARticipative Approach to DIsease Global Management) is a pilot project which aims to develop and demonstrate an Internet based reference framework to share scientific resources and findings in the treatment of major diseases. PARADIGMA defines and disseminates a common methodology and optimised protocols (Clinical Pathways) to support service functions directed to patients and individuals on matters like prevention, posthospitalisation support and awareness. PARADIGMA will provide a platform of information services - user oriented and optimised against social, cultural and technological constraints - supporting the Health Care Global System of the Euro-Mediterranean Community in a continuous improvement process.

Keywords: Decision Support Systems, Ontology, Healt Care, Clinical Pathway

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