Search results for: Protein Ontology

Authors: Laima Silina, Ilze Gramatina, Lija Dukalska, Liga Skudra, Tatjana Rakcejeva, Dace Klava, Anita Blija

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The objective of the present study was to determine quality parameters changes of red wine marinade marinated venison during storage. Beef as a control was analysed. Protein, fat, moisture and pH content dynamics as well microbiological quality was analyzed. The meat pieces were marinated in red wine marinade at 4±2ºC temperature for 48±1h. Marinated meat was placed in polypropylene trays, hermetically sealed with high barrier polymer film Multibarrier 60 under modified atmosphere (CO₂ 40%+N₂ 60%) without and with oxygen absorber sachets, as a control packaging in air ambiance packed marinated venison and beef was used. Meat samples were analyzed after 0, 4, 7, 11 and 14 days of storage. During the storage of meat, protein and moisture content significantly (p<0.05) decreased, pH and colony forming units significantly (p<0.05) increased, fat content does not change in all treatments irrespective of the packaging method.

Keywords: Marinating, modified atmosphere, quality, venison.

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Authors: Dominykas Broga

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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: Jing Zhang, Lian Wu, Jie-ming Qu, Chun-xue Bai, Mervyn J Merrilees, Peter N Black

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COPD is characterized by loss of elastic fibers from small airways and alveolar walls, with the decrease in elastin increasing with disease severity. It is unclear why there is a lack of repair of elastic fibers. We have examined fibroblasts cultured from lung tissue from normal and COPD subjects to determine if the secretory profile explains lack of tissue repair. In this study, fibroblasts were cultured from lung parenchyma of bronchial carcinoma patients with varying degrees of COPD; controls (non-COPD, n=5), mild COPD (GOLD 1, n=5) and moderate-severe COPD (GOLD 2-3, n=12). Measurements were made of proliferation, senescence-associated beta-galactosidase-1, mRNA expression of IL-6, IL-8, MMP-1, tropoelastin and versican, and protein levels for IL-6, IL-8, PGE2, tropoelastin, insoluble elastin, and versican. It was found that GOLD 2-3 fibroblasts proliferated more slowly (p<0.01) and had higher levels of senescence-associated beta-galactosidase-1 (p<0.001) than controls (non-COPD). GOLD 2-3 fibroblasts showed significant increases in mRNA and/or protein for IL-6, IL-8, MMP-1, PGE2, versican (p<0.01) and tropoelastin (p<0.05). mRNA expression and/or protein levels of tropoelastin (p<0.01), versican (p<0.02), IL-6 (p<0.05) and IL-8 (p<0.05) were negatively correlated with FEV1%. Insoluble elastin was not increased. In summary, fibroblasts from moderate to severe COPD subjects display a secretory phenotype with up-regulation of inflammatory molecules including the matrix proteoglycan versican, and increased soluble, but not insoluble, elastin. Versican inhibits assembly of tropoelastin into insoluble elastin and we conclude that the pro-inflammatory phenotype of COPD fibroblasts it is not compatible with repair elastic fibers.

Keywords: COPD, pulmonary fibroblasts, pro-inflammatory phenotype, versican, elastin

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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: Ngo Thanh Xuan, Mai Thi Hang, Vu Nguyen Thanh

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A. niger XP isolated from Vietnam produces very low amount of acidic phytase with optimal pH at 2.5 and 5.5. The phytase production of this strain was successfully improved through gene cloning and expression. A 1.4 - kb DNA fragment containing the coding region of the phyA gene was amplified by PCR and inserted into the expression vector pPICZαA with a signal peptide α- factor, under the control of AOX1 promoter. The recombined plasmid was transformed into the host strain P. pastoris KM71H and X33 by electroporation. Both host strains could efficiently express and secret phytase. The multicopy strains were screened for over expression of phytase. All the selected multicopy strains of P. pastoris X33 were examined for phytase activity, the maximum phytase yield of 1329 IU/ml was obtained after 4 days of incubation in medium BMM. The recombinant protein with MW of 97.4 KW showed to be the only one protein secreted in the culture broth. Multicopy transformant P. pastoris X33 supposed to be potential candidate for producing the commercial preparation of phytase.

Keywords: Aspergillus niger XP, cloning, over expression, Pichia pastoris, phyA , phytase.

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Authors: O. Aluko, M. R. Brai, A. O. Adelore

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Healthy snack (cookie) was produced from corn flour and moringa seed flour blends. The samples were mixed in various proportions and analysed for proximate composition and functional characteristics. The healthy snack (cookies) was evaluated for sensory parameters of Colour, Crispness, Taste, Aroma and Overall Acceptability. The proximate analysis of the flour obtained from different proportion showed that proximate composition increased with increase in substitution level of moringa seed flour especially with protein, fat and crude fibre. The protein contents of samples range from 1.75 to 6.58, fat from 0.60 to 6.80, while fibre from 0.85 to 2.06. There was no significance difference in the functional properties of the blend when compared with 100% corn flour. Sensory evaluation results shows a significant difference in Colour, Taste, Crispness, Aroma and Overall Acceptability of healthy snack (cookies) sample from different blends at 5% significance level.

Keywords: Healthy snack, moringa.

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Authors: Hong Ding, Fatiha Benslimane, Isra Marei, Chris R. Triggle

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Hyperglycaemia is a key factor that contributes to the development of diabetes-related microvascular disease and a major risk factor for endothelial dysfunction. In the current study, we have explored glucose-induced abnormal intracellular calcium (Ca2+ i) homeostasis in mouse microvessel endothelial cells (MMECs) in high glucose (HG) (40mmol/L) versus control (low glucose, LG) (11 mmol/L). We demonstrated that the exposure of MMECs to HG for 3 days did not change basal Ca2+ i, however, there was a significant increase of acetylcholine-induced Ca2+ entry. Western blots illustrated that exposure to HG also increased STIM1 (Stromal Interaction Molecule 1), but not Orai1 (the pore forming subunit), protein expression levels. Although the link between HG-induced changes in STIM1 expression, enhanced Ca2+ entry and endothelial dysfunction requires further study, the current data are suggestive that targeting these pathways may reduce the impact of HG on endothelial function.

Keywords: store-operated calcium entry, hyperglycaemia, STIM1, endothelial dysfunction

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Authors: A. E. O. Malau-Aduli, B. W. B. Holman, P. A. Lane

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Our objectives were to evaluate the effects of sire breed, type of protein supplement, level of supplementation and sex on wool spinning fineness (SF), its correlations with other wool characteristics and prediction accuracy in F1 Merino crossbred lambs. Texel, Coopworth, White Suffolk, East Friesian and Dorset rams were mated with 500 purebred Merino dams at a ratio of 1:100 in separate paddocks within a single management system. The F1 progeny were raised on ryegrass pasture until weaning, before forty lambs were randomly allocated to treatments in a 5 x 2 x 2 x 2 factorial experimental design representing 5 sire breeds, 2 supplementary feeds (canola or lupins), 2 levels of supplementation (1% or 2% of liveweight) and sex (wethers or ewes). Lambs were supplemented for six weeks after an initial three weeks of adjustment, wool sampled at the commencement and conclusion of the feeding trial and analyzed for SF, mean fibre diameter (FD), coefficient of variation (CV), standard deviation, comfort factor (CF), fibre curvature (CURV), and clean fleece yield. Data were analyzed using mixed linear model procedures with sire fitted as a random effect, and sire breed, sex, supplementary feed type, level of supplementation and their second-order interactions as fixed effects. Sire breed (P<0.001), sex (P<0.004), sire breed x level of supplementation (P<0.004), and sire breed x sex (P<0.019) interactions significantly influenced SF. SF ranged from 22.7 ± 0.2μm in White Suffolk-sired lambs to 25.1 ± 0.2μm in East Friesian crossbred lambs. Ewes had higher SF than wethers. There were significant (P<0.001) correlations between SF and FD (0.93), CV (0.40), CF (-0.94) and CURV (-0.12). Its strong relationship with other wool quality traits enabled accurate predictions explaining up to about 93% of the observed variation. The interactions between sire breed genetics and nutrition will have an impact on the choices that dual-purpose sheep producers make when selecting sire breeds and protein supplementary feed levels to achieve optimal wool spinning fineness at the farmgate level. This will facilitate selective breeding programs being able to better account for SF and its interactions with other wool characteristics.

Keywords: Merino crossbred sheep, protein supplementation, sire breed, wool quality, wool spinning fineness

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Authors: S. B. Fasoyiro, K. A. Arowora

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Pigeon pea (Cajanus cajan) blanched for 20min was dehulled and milled into flour. The flour was incorporated into dried whole fermented maize (Ogi) at five levels. The resultant products were analyzed for chemical and pasting properties. The fortified Ogi samples were also assessed for sensory attributes: appearance, color, flavor, mouth feel and overall acceptability. The protein content in the whole Ogi fortified samples was in the range of 11.2-16.6% and crude fibre 3.22-3.46%. Fortified whole Ogi with pigeon pea at 30%, 40% and 50% of inclusion with pigeon pea flour has higher protein, crude fibre and ash content. Varying range of pasting quality was recorded for the blends, pasting temperature for fortified Obi was in the range of 45.3-49.50C and peak time 5.05-5.210C. The sensory acceptability of the whole Ogi fortified blends prepared into gruel has higher acceptability for various qualities in comparison with the traditional Ogi gruel.

Keywords: Maize Ogi, pigeon pea, chemical, pasting, sensory properties.

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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: Razvan Bocu, Dr Sabin Tabirca

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The study of proteomics reached unexpected levels of interest, as a direct consequence of its discovered influence over some complex biological phenomena, such as problematic diseases like cancer. This paper presents the latest authors- achievements regarding the analysis of the networks of proteins (interactome networks), by computing more efficiently the betweenness centrality measure. The paper introduces the concept of betweenness centrality, and then describes how betweenness computation can help the interactome net- work analysis. Current sequential implementations for the between- ness computation do not perform satisfactory in terms of execution times. The paper-s main contribution is centered towards introducing a speedup technique for the betweenness computation, based on modified shortest path algorithms for sparse graphs. Three optimized generic algorithms for betweenness computation are described and implemented, and their performance tested against real biological data, which is part of the IntAct dataset.

Keywords: Betweenness centrality, interactome networks, protein-protein interactions, sub-communities, sparse networks, speedup tech-nique, IntAct.

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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: Razvan Bocu, Sabin Tabirca

Abstract:

The study of proteomics reached unexpected levels of interest, as a direct consequence of its discovered influence over some complex biological phenomena, such as problematic diseases like cancer. This paper presents a new technique that allows for an accurate analysis of the human interactome network. It is basically a two-step analysis process that involves, at first, the detection of each protein-s absolute importance through the betweenness centrality computation. Then, the second step determines the functionallyrelated communities of proteins. For this purpose, we use a community detection technique that is based on the edge betweenness calculation. The new technique was thoroughly tested on real biological data and the results prove some interesting properties of those proteins that are involved in the carcinogenesis process. Apart from its experimental usefulness, the novel technique is also computationally effective in terms of execution times. Based on the analysis- results, some topological features of cancer mutated proteins are presented and a possible optimization solution for cancer drugs design is suggested.

Keywords: Betweenness centrality, interactome networks, proteinprotein interactions, protein communities, cancer.

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Authors: Masaki Yamaguchi, Akira Ito, Noriaki Okamoto, Yoshinori Kawabe, Masamichi Kamihira

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Heat-inducible gene expression vectors are useful for hyperthermia-induced cancer gene therapy, because the combination of hyperthermia and gene therapy can considerably improve the therapeutic effects. In the present study, we developed an enhanced heat-inducible transgene expression system in which a heat-shock protein (HSP) promoter and tetracycline-responsive transactivator were combined. When the transactivator plasmid containing the tetracycline-responsive transactivator gene was co-transfected with the reporter gene expression plasmid, a high level of heat-induced gene expression was observed compared with that using the HSP promoter without the transactivator. In vitro evaluation of the therapeutic effect using HeLa cells showed that heat-induced therapeutic gene expression caused cell death in a high percentage of these cells, indicating that this strategy is promising for cancer gene therapy.

Keywords: Inducible gene expression, Gene therapy, Hyperthermia, Heat shock protein, Tetracycline transactivator.

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Authors: Gnanaprakash K, Madhusudhana Chetty C, Ramkanth S, Alagusundaram M, Tiruvengadarajan VS, Angala Parameswari S, Mohamed Saleem TS

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Carbon tetrachloride (CCl4) is a well-known hepatotoxin and exposure to this chemical is known to induce oxidative stress and causes liver injury by the formation of free radicals. Flacourtia indica commonly known as 'Baichi' has been reported as an effective remedy for the treatment of a variety of diseases. The objective of this study was to investigate the hepatoprotective activity of aqueous extract of leaves of Flacourtia indica against CCl4 induced hepatotoxicity. Animals were pretreated with the aqueous extract of Flacourtia indica (250 & 500 mg/kg body weight) for one week and then challenged with CCl4 (1.5 ml/kg bw) in olive oil (1:1, v/v) on 7th day. Serum marker enzymes (ALP, AST, ALT, Total Protein & Total Bilirubin) and TBARS level (Marker for oxidative stress) were estimated in all the study groups. Alteration in the levels of biochemical markers of hepatic damage like AST, ALT, ALP, Total Protein, Total Bilirubin and lipid peroxides (TBARS) were tested in both CCl4 treated and extract treated groups. CCl4 has enhanced the AST, ALT, ALP and the Lipid peroxides (TBARS) in liver. Treatment of aqueous extract of Flacourtia indica leaves (250 & 500 mg/kg) exhibited a significant protective effect by altering the serum levels of AST, ALT, ALP, Total Protein, Total Bilirubin and liver TBARS. These biochemical observations were supported by histopathological study of liver sections. From this preliminary study it has been concluded that the aqueous extract of the leaves of Flacourtia indica protects liver against oxidative damages and could be used as an effective protector against CCl4 induced hepatic damage. Our findings suggested that Flacourtia indica possessed good hepatoprotective activity

Keywords: Carbon Tetrachloride, Flacourtia indica, Hepatoprotective activity, Oxidative stress

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Authors: V. Viliene, V. Sasyte, A. Raceviciute-Stupeliene, R. Gruzauskas

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In horse nutrition, the most suitable cereal for their rations composition could be defined as oats and barley. Oats have high nutritive value because it provides more protein, fiber, iron and zinc than other whole grains, has good taste, and an activity of stimulating metabolic changes in the body. Another cereal – barley is very similar to oats as a feed except for some characteristics that affect how it is used; however, barley is lower in fiber than oats and is classified as a "heavy" feed. The value of oats and barley grain, first of all is dependent on its composition. Near-infrared spectroscopy (NIRS) has long been considered and used as a significant method in component and quality analysis and as an emerging technology for authenticity applications for cereal quality control. This paper presents the chemical and amino acid composition of different varieties of barley and oats, also digestible energy of different cereals for horses. Ten different spring barley (n = 5) and oats (n = 5) varieties, grown in one location in Lithuania, were assayed for their chemical composition (dry matter, crude protein, crude fat, crude ash, crude fiber, starch) and amino acids content, digestible amino acids and amino acids digestibility. Also, the grains digestible energy for horses was calculated. The oats and barley samples reflectance spectra were measured by means of NIRS using Foss-Tecator DS2500 equipment. The chemical components: fat, crude protein, starch and fiber differed statistically (P<0.05) between the oats and barley varieties. The highest total amino acid content between oats was determined in variety Flamingsprofi (4.56 g/kg) and the lowest – variety Circle (3.57 g/kg), and between barley - respectively in varieties Publican (3.50 g/kg) and Sebastian (3.11 g/kg). The different varieties of oats digestible amino acid content varied from 3.11 g/kg to 4.07 g/kg; barley different varieties varied from 2.59 g/kg to 2.94 g/kg. The average amino acids digestibility of oats varied from 74.4% (Liz) to 95.6% (Fen) and in barley - from 75.8 % (Tre) to 89.6% (Fen). The amount of digestible energy in the analyzed varieties of oats and barley was an average compound 13.74 MJ/kg DM and 14.85 MJ/kg DM, respectively. An analysis of the results showed that different varieties of oats compared with barley are preferable for horse nutrition according to the crude fat, crude fiber, ash and separate amino acids content, but the analyzed barley varieties dominated the higher amounts of crude protein, the digestible Liz amount and higher DE content, and thus, could be recommended for making feed formulation for horses combining oats and barley, taking into account the chemical composition of using cereal varieties.

Keywords: Barley, digestive energy, horses, nutritional value, oats.

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Authors: Abu Salim Mustafa

Abstract:

Rv3873 is a relatively large size protein (371 amino acids in length) and its gene is located in the immunodominant genomic region of difference (RD)1 that is present in the genome of Mycobacterium tuberculosis but deleted from the genomes of all the vaccine strains of Bacillus Calmette Guerin (BCG) and most other mycobacteria. However, when tested for cellular immune responses using peripheral blood mononuclear cells from tuberculosis patients and BCG-vaccinated healthy subjects, this protein was found to be a major stimulator of cell mediated immune responses in both groups of subjects. In order to further identify the sequence of immunodominant epitopes and explore their Human Leukocyte Antigen (HLA)-restriction for epitope recognition, 24 peptides (25-mers overlapping with the neighboring peptides by 10 residues) covering the sequence of Rv3873 were synthesized chemically using fluorenylmethyloxycarbonyl chemistry and tested in cell mediated immune responses. The results of these experiments helped in the identification of an immunodominant peptide P9 that was recognized by people expressing varying HLA-DR types. Furthermore, it was also predicted to be a promiscuous binder with multiple epitopes for binding to HLA-DR, HLA-DP and HLA-DQ alleles of HLA-class II molecules that present antigens to T helper cells, and to HLA-class I molecules that present antigens to T cytotoxic cells. In addition, the evaluation of peptide P9 using an immunogenicity predictor server yielded a high score (0.94), which indicated a greater probability of this peptide to elicit a protective cellular immune response. In conclusion, P9, a peptide with multiple epitopes and ability to bind several HLA class I and class II molecules for presentation to cells of the cellular immune response, may be useful as a peptide-based vaccine against tuberculosis.

Keywords: Mycobacterium tuberculosis, Rv3873, peptides, vaccine

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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: 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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Authors: Alicia Y. C. Tang, Rukaini Hj. Abdullah, Sharifuddin M. Zain

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This paper discusses the development of a qualitative simulator (abbreviated QRiOM) for predicting the behaviour of organic chemical reactions. The simulation technique is based on the qualitative process theory (QPT) ontology. The modelling constructs of QPT embody notions of causality which can be used to explain the behaviour of a chemical system. The major theme of this work is that, in a qualitative simulation environment, students are able to articulate his/her knowledge through the inspection of explanations generated by software. The implementation languages are Java and Prolog. The software produces explanation in various forms that stresses on the causal theories in the chemical system which can be effectively used to support learning.

Keywords: Chemical reactions, explanation, qualitative processtheory, simulation

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Authors: Rabia Göçmen, Gülşah Kanbur, Sinan Sefa Parlat

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This study was conducted to determine that carrot powder obtain by different drying methods (oven and vacuum-freeze dryer) of carrot unfit for human consumption that whether feed additives in animal nutrition or not. Carrots randomly divided 2 groups. First group was dried by using oven, second group was by using vacuum freeze dryer methods. Dried carrot prepared from fresh carrot was analysed nutrient matter (energy, crude protein, crude oil, crude ash, beta carotene, mineral concentration and colour). The differences between groups in terms of energy, crude protein, ash, Ca and Mg was not significant (P>0,05). Crude oil, P, beta carotene content and colour values (L, a, b) with vacuum-freeze dryer group was greater than oven group (P<0,05). Consequently, carrot powder obtained by drying the vacuum-freeze dryer method can be used as a source of carotene. 

Keywords: Carrot, vacuum freeze dryer, oven, beta carotene.

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Authors: John R. Rose, James P. Cleveland, Alvin Fox

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Tandem mass spectrometry (MS/MS) is the engine driving high-throughput protein identification. Protein mixtures possibly representing thousands of proteins from multiple species are treated with proteolytic enzymes, cutting the proteins into smaller peptides that are then analyzed generating MS/MS spectra. The task of determining the identity of the peptide from its spectrum is currently the weak point in the process. Current approaches to de novo sequencing are able to compute candidate peptides efficiently. The problem lies in the limitations of current scoring functions. In this paper we introduce the concept of proteome signature. By examining proteins and compiling proteome signatures (amino acid usage) it is possible to characterize likely combinations of amino acids and better distinguish between candidate peptides. Our results strongly support the hypothesis that a scoring function that considers amino acid usage patterns is better able to distinguish between candidate peptides. This in turn leads to higher accuracy in peptide prediction.

Keywords: Tandem mass spectrometry, proteomics, scoring, peptide, de novo, mutual information

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Authors: Ricardo Avila, Gabriel Lopes, Vania Vidal, Jose Macedo

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This proposal aims for semantic enrichment between glossaries using the Simple Knowledge Organization System (SKOS) vocabulary to discover synonyms, hyponyms and hyperonyms semiautomatically, in Brazilian Portuguese, generating new semantic relationships based on WordNet. To evaluate the quality of this proposed model, experiments were performed by the use of two sets containing new relations, being one generated automatically and the other manually mapped by the domain expert. The applied evaluation metrics were precision, recall, f-score, and confidence interval. The results obtained demonstrate that the applied method in the field of Oil Production and Extraction (E&P) is effective, which suggests that it can be used to improve the quality of terminological mappings. The procedure, although adding complexity in its elaboration, can be reproduced in others domains.

Keywords: Ontology matching, mapping enrichment, semantic web, linked data, SKOS.

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Authors: Ivan Stanev, Maria Koleva

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Common Platform for Automated Programming (CPAP) is defined in details. Two versions of CPAP are described: Cloud based (including set of components for classic programming, and set of components for combined programming); and Knowledge Based Automated Software Engineering (KBASE) based (including set of components for automated programming, and set of components for ontology programming). Four KBASE products (Module for Automated Programming of Robots, Intelligent Product Manual, Intelligent Document Display, and Intelligent Form Generator) are analyzed and CPAP contributions to automated programming are presented.

Keywords: Automated Programming, Cloud Computing, Knowledge Based Software Engineering, Service Oriented Architecture.

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Authors: Mohammadsadegh Zanganehfar

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Through the emergence of modern architecture, an aggressive desire for new design theories appeared through the works of architects and critics. The discourse of complexity and volumetric composition happened to be an important and controversial issue in the discipline of architecture which was discussed through a general point of view in Robert Venturi and Denise Scott Brown's book “Complexity and contradiction in architecture” in 1966, this paper attempts to identify chaos theory as a scientific model of complexity and its relation to architecture design theory by conducting a qualitative analysis and multidisciplinary critical approach through architecture and basic sciences resources. Accordingly, we identify chaotic architecture as the correlation between chaos theory and the discipline of architecture, and as an independent nonlinear design theory with specific characteristics and properties.

Keywords: Architecture complexity, chaos theory, fractals, nonlinear dynamic systems, nonlinear ontology.

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Authors: Raza Hussain, Claire Gaiani, Joël Scher

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Dispersions of casein micelles (CM) were studied at a constant protein concentration of 5 wt % in high NaCl environment ranging from 0% to 12% by Dynamic light scattering (DLS) and Fourier Transform Infrared (FTIR). The rehydration profiles obtained were interpreted in term of wetting, swelling and dispersion stages by using a turbidity method. Two behaviours were observed depending on the salt concentration. The first behaviour (low salt concentration) presents a typical rehydration profile with a significant change between 3 and 6% NaCl indicating quick wetting, swelling and long dispersion stage. On the opposite, the dispersion stage of the second behaviour (high salt concentration) was significantly shortened indicating a strong modification of the protein backbone. A salt increase result to a destabilization of the micelle and the formation of mini-micelles more or less aggregated indicating an average micelles size ranging from 100 to 200 nm. For the first time, the estimations of secondary structural elements (irregular, ß-sheet, α-helix and turn) by the Amide III assignments were correlated with results from Amide I.

Keywords: Casein, DLS, FTIR, Ionic environment.

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Authors: Manolo Dulva Hina, Clement Thierry, Assia Soukane, Amar Ramdane-Cherif

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In this paper, we presented our innovative way of determining the driving context for a driving assistance system. We invoke the fusion of all parameters that describe the context of the environment, the vehicle and the driver to obtain the driving context. We created a training set that stores driving situation patterns and from which the system consults to determine the driving situation. A machine-learning algorithm predicts the driving situation. The driving situation is an input to the fission process that yields the action that must be implemented when the driver needs to be informed or assisted from the given the driving situation. The action may be directed towards the driver, the vehicle or both. This is an ongoing work whose goal is to offer an alternative driving assistance system for safe driving, green driving and comfortable driving. Here, ontologies are used for knowledge representation.

Keywords: Cognitive driving, intelligent transportation system, multimodal system, ontology, machine learning.

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Authors: Manuel A. Alonso-Tarajano, Roberto Mosca, Patrick Aloy

Abstract:

Protein kinases participate in a myriad of cellular processes of major biomedical interest. The in vivo substrate specificity of these enzymes is a process determined by several factors, and despite several years of research on the topic, is still far from being totally understood. In the present work, we have quantified the contributions to the kinase substrate specificity of i) the phosphorylation sites and their surrounding residues in the sequence and of ii) the association of kinases to adaptor or scaffold proteins. We have used position-specific scoring matrices (PSSMs), to represent the stretches of sequences phosphorylated by 93 families of kinases. We have found negative correlations between the number of sequences from which a PSSM is generated and the statistical significance and the performance of that PSSM. Using a subset of 22 statistically significant PSSMs, we have identified specificity determinant residues (SDRs) for 86% of the corresponding kinase families. Our results suggest that different SDRs can function as positive or negative elements of substrate recognition by the different families of kinases. Additionally, we have found that human proteins with known function as adaptors or scaffolds (kAS) tend to interact with a significantly large fraction of the substrates of the kinases to which they associate. Based on this characteristic we have identified a set of 279 potential adaptors/scaffolds (pAS) for human kinases, which is enriched in Pfam domains and functional terms tightly related to the proposed function. Moreover, our results show that for 74.6% of the kinase–pAS association found, the pAS colocalize with the substrates of the kinases they are associated to. Finally, we have found evidence suggesting that the association of kinases to adaptors and scaffolds, may contribute significantly to diminish the in vivo substrate crossed-specificity of protein kinases. In general, our results indicate the relevance of several SDRs for both the positive and negative selection of phosphorylation sites by kinase families and also suggest that the association of kinases to pAS proteins may be an important factor for the localization of the enzymes with their set of substrates.

Keywords: Kinase, phosphorylation, substrate specificity, adaptors, scaffolds, cellular colocalization.

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Authors: Huynh Quyet Thang, Vo Sy Nam

Abstract:

Schema matching plays a key role in many different applications, such as schema integration, data integration, data warehousing, data transformation, E-commerce, peer-to-peer data management, ontology matching and integration, semantic Web, semantic query processing, etc. Manual matching is expensive and error-prone, so it is therefore important to develop techniques to automate the schema matching process. In this paper, we present a solution for XML schema automated matching problem which produces semantic mappings between corresponding schema elements of given source and target schemas. This solution contributed in solving more comprehensively and efficiently XML schema automated matching problem. Our solution based on combining linguistic similarity, data type compatibility and structural similarity of XML schema elements. After describing our solution, we present experimental results that demonstrate the effectiveness of this approach.

Keywords: XML Schema, Schema Matching, SemanticMatching, Automatic XML Schema Matching.

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Authors: Maria E. Manioudaki, Panayiota Poirazi

Abstract:

Yeast cells live in a constantly changing environment that requires the continuous adaptation of their genomic program in order to sustain their homeostasis, survive and proliferate. Due to the advancement of high throughput technologies, there is currently a large amount of data such as gene expression, gene deletion and protein-protein interactions for S. Cerevisiae under various environmental conditions. Mining these datasets requires efficient computational methods capable of integrating different types of data, identifying inter-relations between different components and inferring functional groups or 'modules' that shape intracellular processes. This study uses computational methods to delineate some of the mechanisms used by yeast cells to respond to environmental changes. The GRAM algorithm is first used to integrate gene expression data and ChIP-chip data in order to find modules of coexpressed and co-regulated genes as well as the transcription factors (TFs) that regulate these modules. Since transcription factors are themselves transcriptionally regulated, a three-layer regulatory cascade consisting of the TF-regulators, the TFs and the regulated modules is subsequently considered. This three-layer cascade is then modeled quantitatively using artificial neural networks (ANNs) where the input layer corresponds to the expression of the up-stream transcription factors (TF-regulators) and the output layer corresponds to the expression of genes within each module. This work shows that (a) the expression of at least 33 genes over time and for different stress conditions is well predicted by the expression of the top layer transcription factors, including cases in which the effect of up-stream regulators is shifted in time and (b) identifies at least 6 novel regulatory interactions that were not previously associated with stress-induced changes in gene expression. These findings suggest that the combination of gene expression and protein-DNA interaction data with artificial neural networks can successfully model biological pathways and capture quantitative dependencies between distant regulators and downstream genes.

Keywords: gene modules, artificial neural networks, yeast, stress

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