Search results for: Protein Oriented immobilization

Authors: Omer Ishag Eldai, Ahmed Hassan M. H. Ali, S. Raviraja

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Web-based systems have become increasingly important due to the fact that the Internet and the World Wide Web have become ubiquitous, surpassing all other technological developments in our history. The Internet and especially companies websites has rapidly evolved in their scope and extent of use, from being a little more than fixed advertising material, i.e. a "web presences", which had no particular influence for the company's business, to being one of the most essential parts of the company's core business. Traditional software engineering approaches with process models such as, for example, CMM and Waterfall models, do not work very well since web system development differs from traditional development. The development differs in several ways, for example, there is a large gap between traditional software engineering designs and concepts and the low-level implementation model, many of the web based system development activities are business oriented (for example web application are sales-oriented, web application and intranets are content-oriented) and not engineering-oriented. This paper aims to introduce Increment Iterative extreme Programming (IIXP) methodology for developing web based systems. In difference to the other existence methodologies, this methodology is combination of different traditional and modern software engineering and web engineering principles.

Keywords: Web based systems, Web engineering.

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Authors: Mahmood Doroodchi, Babak K. Farahani, Mahmoud Moravej

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A fast and efficient model of application development called user interface oriented application development (UIOAD) is proposed. This approach introduces a convenient way for users to develop a platform independent client-server application.

Keywords: Software Development, XML, XForms, XUL, eForm, User Interface.

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Authors: Vernie C. Convicto, Henry P. Aringa, Wilson I. Barredo

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This study presents a conformational model of the helical structures of globular protein particularly ferritin in the framework of white noise path integral formulation by using Associated Legendre functions, Bessel and convolution of Bessel and trigonometric functions as modulating functions. The model incorporates chirality features of proteins and their helix-turn-helix sequence structural motif.

Keywords: Globular protein, modulating function, white noise, winding probability.

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Authors: Thiago M. R. Dias, Gray F. Moita, Paulo E. M. Almeida

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Although the World Wide Web is considered the largest source of information there exists nowadays, due to its inherent dynamic characteristics, the task of finding useful and qualified information can become a very frustrating experience. This study presents a research on the information mining systems in the Web; and proposes an implementation of these systems by means of components that can be built using the technology of Web services. This implies that they can encompass features offered by a services oriented architecture (SOA) and specific components may be used by other tools, independent of platforms or programming languages. Hence, the main objective of this work is to provide an architecture to Web mining systems, divided into stages, where each step is a component that will incorporate the characteristics of SOA. The separation of these steps was designed based upon the existing literature. Interesting results were obtained and are shown here.

Keywords: Web Mining, Service Oriented Architecture, WebServices.

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Authors: Claudia L. Zuñiga, Andres F. Millan, Jose L. Abadia, Monica Lora, Andres Navarro, Juan C. Burguillo, Pedro S. Rodriguez

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The increasing popularity of wireless technologies and mobile computing devices has enabled new application areas and research. One of these new areas is pervasive systems in urban environments, because urban environments are characterized by high concentration of these technologies and devices. In this paper we will show the process of pervasive system design in urban environments, using as use case a local zoo in Cali, Colombia. Based on an ethnographic studio, we present the design of a pervasive system for urban computing based on service oriented architecture to controlled environment of Cali Zoo. In this paper, the reader will find a methodological approach for the design of similar systems, using data collection methods, conceptual frameworks for urban environments and considerations of analysis and design of service oriented systems.

Keywords: Service Oriented Architecture, Urban Computing, Design of pervasive systems for urban environments, PSP Design Framework (Public Social Private), Cali Zoo.

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Authors: Leong Lee, Cyriac Kandoth, Jennifer L. Leopold, Ronald L. Frank

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Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm-s computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2].

Keywords: data mining, protein secondary structure prediction, parallelization.

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Authors: Elaheh Jooybar, Mohammad J. Abdekhodaie, Marcel Karperien, Pieter J. Dijkstra

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In this study, hyaluronic acid (HA) microgels were developed for the goal of protein delivery. First, a hyaluronic acid-tyramine conjugate (HA-TA) was synthesized with a degree of substitution of 13 TA moieties per 100 disaccharide units. Then, HA-TA microdroplets were produced using a water in oil emulsion method and crosslinked in the presence of horseradish peroxidase (HRP) and hydrogen peroxide (H₂O₂). Loading capacity and the release kinetics of lysozyme and BSA, as model proteins, were investigated. It was shown that lysozyme, a cationic protein, can be incorporated efficiently in the HA microgels, while the loading efficiency for BSA, as a negatively charged protein, is low. The release profile of lysozyme showed a sustained release over a period of one month. The results demonstrated that the HA-TA microgels are a good carrier for spatial delivery of cationic proteins for biomedical applications.

Keywords: Microgel, inverse emulsion, protein delivery, hyaluronic acid, crosslinking.

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Authors: Zarmina Gillani, Nuzhat Huma, Aysha Sameen, Mulazim Hussain Bukhari

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Whey is an excellent food ingredient owing to its high nutritive value and its functional properties. However, composition of whey varies depending on composition of milk, processing conditions, processing method, and its whey protein content. The aim of this study was to prepare a whey powder from raw whey and to determine the influence of different processing temperatures (160 and 180 °C) on the physicochemical, functional properties during storage of 180 days and on whey protein denaturation. Results have shown that temperature significantly (P < 0.05) affects the pH, acidity, non-protein nitrogen (NPN), protein total soluble solids, fat and lactose contents. Significantly (p < 0.05) higher foaming capacity (FC), foam stability (FS), whey protein nitrogen index (WPNI), and a lower turbidity and solubility index (SI) were observed in whey powder processed at 160 °C compared to whey powder processed at 180 °C. During storage of 180 days, slow but progressive changes were noticed on the physicochemical and functional properties of whey powder. Reverse phase-HPLC analysis revealed a significant (P < 0.05) effect of temperature on whey protein contents. Denaturation of β-Lactoglobulin is followed by α-lacalbumin, casein glycomacropeptide (CMP/GMP), and bovine serum albumin (BSA).

Keywords: Whey powder, temperature, denaturation, reverse phase – HPLC.

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Authors: Bassam Atieh Rajabi, Sai Peck Lee

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Business Process Modeling (BPM) is the first and most important step in business process management lifecycle. Graph based formalism and rule based formalism are the two most predominant formalisms on which process modeling languages are developed. BPM technology continues to face challenges in coping with dynamic business environments where requirements and goals are constantly changing at the execution time. Graph based formalisms incur problems to react to dynamic changes in Business Process (BP) at the runtime instances. In this research, an adaptive and flexible framework based on the integration between Object Oriented diagramming technique and Petri Net modeling language is proposed in order to support change management techniques for BPM and increase the representation capability for Object Oriented modeling for the dynamic changes in the runtime instances. The proposed framework is applied in a higher education environment to achieve flexible, updatable and dynamic BP.

Keywords: Business Process Modeling, Change Management, Graph Based Modeling, Rule Based Modeling, Object Oriented PetriNet.

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Authors: Jehad Al Dallal

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Attributes and methods are the basic contents of an object-oriented class. The connectivity among these class members and the relationship between the class and other classes play an important role in determining the quality of an object-oriented system. Class cohesion evaluates the degree of relatedness of class attributes and methods, whereas class coupling refers to the degree to which a class is related to other classes. Researchers have proposed several class cohesion and class coupling measures. However, the correlation between class coupling and class cohesion measures has not been thoroughly studied. In this paper, using classes of three open-source Java systems, we empirically investigate the correlation between several measures of connectivity-based class cohesion and coupling. Four connectivity-based cohesion measures and eight coupling measures are considered in the empirical study. The empirical study results show that class connectivity-based cohesion and coupling internal quality attributes are inversely correlated. The strength of the correlation depends highly on the cohesion and coupling measurement approaches.

Keywords: Object-oriented class, software quality, class cohesion measure, class coupling measure.

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Authors: Marios Poulos, Eirini Maliagani, Minas Paschopoulos, George Bokos

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The purpose of my research proposal is to demonstrate that there is a relationship between EEG and endometrial cancer. The above relationship is based on an Aristotelian Syllogism; since it is known that the 14-3-3 protein is related to the electrical activity of the brain via control of the flow of Na+ and K+ ions and since it is also known that many types of cancer are associated with 14-3-3 protein, it is possible that there is a relationship between EEG and cancer. This research will be carried out by well-defined diagnostic indicators, obtained via the EEG, using signal processing procedures and pattern recognition tools such as neural networks in order to recognize the endometrial cancer type. The current research shall compare the findings from EEG and hysteroscopy performed on women of a wide age range. Moreover, this practice could be expanded to other types of cancer. The implementation of this methodology will be completed with the creation of an ontology. This ontology shall define the concepts existing in this research-s domain and the relationships between them. It will represent the types of relationships between hysteroscopy and EEG findings.

Keywords: Bioinformatics, Protein 14-3-3, EEG, Endometrial cancer, Ontology.

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Authors: Sahba Paktinat, Afshin Salajeghe, Mir Ali Seyyedi, Yousef Rastegari

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Service Oriented Architecture (SOA) allows modeling of dynamic interaction between incongruous providers, which enables governing the development of complex applications. However, implementation of SOA comes with some challenges, including its adaptability and robustness. Dynamism is inherent to the nature of service based applications and of their running environment. These factors lead to necessity for dynamic adaptation. In this paper we try to describe basics and main structure of SOA adaptation process with a conceptual view to this issue. In this survey we will review the relevant adaptation approaches. This paper allows studying how different approaches deal with service oriented architecture adaptation life-cycle and provides basic guidelines for their analysis, evaluation and comparison.

Keywords: Context-aware, Dynamic Adaptation, Quality of Services, Service Oriented Architecture, Service Based Application.

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Authors: S. Ashrafpour, T. Tohidi Moghadam, B. Ranjbar

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Identifying the nature of protein-nanoparticle interactions and favored binding sites is an important issue in functional characterization of biomolecules and their physiological responses. Herein, interaction of silver nanoparticles with lysozyme as a model protein has been monitored via fluorescence spectroscopy. Formation of complex between the biomolecule and silver nanoparticles (AgNPs) induced a steady state reduction in the fluorescence intensity of protein at different concentrations of nanoparticles. Tryptophan fluorescence quenching spectra suggested that silver nanoparticles act as a foreign quencher, approaching the protein via this residue. Analysis of the Stern-Volmer plot showed quenching constant of 3.73 μM−1. Moreover, a single binding site in lysozyme is suggested to play role during interaction with AgNPs, having low affinity of binding compared to gold nanoparticles. Unfolding studies of lysozyme showed that complex of lysozyme- AgNPs has not undergone structural perturbations compared to the bare protein. Results of this effort will pave the way for utilization of sensitive spectroscopic techniques for rational design of nanobiomaterials in biomedical applications.

Keywords: Nanocarrier, Nanoparticles, Surface Plasmon Resonance, Quenching Fluorescence.

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Authors: Rossi A. Hassad

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There is widespread emphasis on reform in the teaching of introductory statistics at the college level. Underpinning this reform is a consensus among educators and practitioners that traditional curricular materials and pedagogical strategies have not been effective in promoting statistical literacy, a competency that is becoming increasingly necessary for effective decision-making and evidence-based practice. This paper explains the historical context of, and rationale for reform-oriented teaching of introductory statistics (at the college level) in the health, social and behavioral sciences (evidence-based disciplines). A firm understanding and appreciation of the basis for change in pedagogical approach is important, in order to facilitate commitment to reform, consensus building on appropriate strategies, and adoption and maintenance of best practices. In essence, reform-oriented pedagogy, in this context, is a function of the interaction among content, pedagogy, technology, and assessment. The challenge is to create an appropriate balance among these domains.

Keywords: Reform-oriented, reform, introductory statistics, health, behavioral sciences, evidence-based, psychology, teaching, learning.

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Authors: Patrick Nwabueze Okechukwu, Ima Nirwana Soelaiman, Gabriele Anisah Ruth Froemming, Mohd Yusri Idorus, Norazlina Mohamed

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Supplementation of palm vitamin E has been reported to prevent loss of bone density in ovariectomised female rats. The mechanism by which palm vitamin E exerts these effects is still unknown. We hypothesized that palm vitamin E may act by preventing the protein expression changes. Two dimensional poly acyrilamide gel electrophoresis (2-D PAGE) and PD Quest software genomic solutions Investigator (proteomics) was used to analyze the differential protein expression profile in femoral and humeri bones harvested from three groups of rats; sham-operated rats (SO), ovariectomised rats (Ovx) and ovariectomised rats supplemented for 2 months with palm vitamin E. The results showed that there were over 300 valued spot on each of the groups PVE and OVX as compared to about 200 in SO. Comparison between the differential protein expression between OVX and PVE groups showed that ten spots were down –regulated in OVX but up-regulated in PVE. The ten differential spots were separately named P1-P10. The identification and understanding of the pathway of the differential protein expression among the groups is ongoing and may account for the molecular mechanism through which palm vitamin E exert its anti-osteoporotic effect.

Keywords: Palm vitamin E, ovariectomised, osteoporosis protein expression, 2-d-page.

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Authors: Norlin Pauzi, Ahmad R.M. Yahya, Zairossani Nor, Amirul A. Abdullah

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Strain M was isolated from the latex of Hevea brasiliensis that grow in the rubber farm area of Malaysia Rubber Board. Strain M was tentatively identified as Bacillus sp. Strain M demonstrated high protease production at pH 9, and this was suitable to be applied in rubber processing that was in alkaline conditions. The right and suitable proportion to be used in applying supernatant into the latex was two parts of latex and one part of enzyme. In this proportion, the latex was stable throughout the 72 hours of treatment. The potential of strain M to degrade protein in the natural rubber latex was proven with the reduction of 79.3% nitrogen in 24 hours treatment. Centrifugation process of the latex before undergoing the treatment had increased the protein degradation in latex. Although the centrifugation process did not achieve zero nitrogen content, it had improved the performance of protein denaturing in the natural rubber.

Keywords: Hevea brasiliensis, Bacillus sp., protease, latex.

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Authors: Jehad Al Dallal

Abstract:

An application framework provides a reusable design and implementation for a family of software systems. If the framework contains defects, the defects will be passed on to the applications developed from the framework. Framework defects are hard to discover at the time the framework is instantiated. Therefore, it is important to remove all defects before instantiating the framework. In this paper, two measures for the adequacy of an object-oriented system-based testing technique are introduced. The measures assess the usefulness and uniqueness of the testing technique. The two measures are applied to experimentally compare the adequacy of two testing techniques introduced to test objectoriented frameworks at the system level. The two considered testing techniques are the New Framework Test Approach and Testing Frameworks Through Hooks (TFTH). The techniques are also compared analytically in terms of their coverage power of objectoriented aspects. The comparison study results show that the TFTH technique is better than the New Framework Test Approach in terms of usefulness degree, uniqueness degree, and coverage power.

Keywords: Object-oriented framework, object-oriented framework testing, test case generation, testing adequacy.

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Authors: M. Al-Jepoori, D. Bennett

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Teaching Object-Oriented Programming (OOP) as part of a Computing-related university degree is a very difficult task; the road to ensuring that students are actually learning object oriented concepts is unclear, as students often find it difficult to understand the concept of objects and their behavior. This problem is especially obvious in advanced programming modules where Design Pattern and advanced programming features such as Multi-threading and animated GUI are introduced. Looking at the students’ performance at their final year on a university course, it was obvious that the level of students’ understanding of OOP varies to a high degree from one student to another. Students who aim at the production of Games do very well in the advanced programming module. However, the students’ assessment results of the last few years were relatively low; for example, in 2016-2017, the first quartile of marks were as low as 24.5 and the third quartile was 63.5. It is obvious that many students were not confident or competent enough in their programming skills. In this paper, the reasons behind poor performance in Advanced OOP modules are investigated, and a suggested practice for teaching OOP based on a complex case study is described and evaluated.

Keywords: Complex programming case study, design pattern, learning advanced programming, object oriented programming.

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Authors: Vita Strazdina, Aleksandrs Jemeljanovs, Vita Sterna

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Not all proteins have the same nutritional value, since protein quality strongly depends on its amino acid composition and digestibility. The meat of game animals could be a high protein source because of its well-balanced essential amino acids composition. Investigations about biochemical composition of game meat such as wild boar (Sus scrofa scrofa), roe deer (Capreolus capreolus) and beaver (Castor fiber) are not very much. Therefore, the aim of the investigation was evaluate protein composition of game meat hunted in Latvia. The biochemical analysis, evaluation of connective tissue and essential amino acids in meat samples were done, the amino acids score were calculate. Results of analysis showed that protein content 20.88-22.05% of all types of meat samples is not different statistically. The content of connective tissue from 1.3% in roe deer till 1.5% in beaver meat allowed classified game animal as high quality meat. The sum of essential amino acids in game meat samples were determined 7.05–8.26g100g-1. Roe deer meat has highest protein content and lowest content of connective tissues among game meat hunted in Latvia. Concluded that amino acid score for limiting amino acids phenylalanine and tyrosine is high and shows high biological value of game meat.

Keywords: Dietic product, game meat, amino acids, scores.

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Authors: Jehad Al Dallal

Abstract:

A class in an Object-Oriented (OO) system is the basic unit of design, and it encapsulates a set of attributes and methods. In OO systems, instead of redefining the attributes and methods that are included in other classes, a class can inherit these attributes and methods and only implement its unique attributes and methods, which results in reducing code redundancy and improving code testability and maintainability. Such mechanism is called Class Inheritance. However, some software engineering applications may require accounting for all the inherited class members (i.e., attributes and methods). This paper explains how to account for inherited class members and discusses the software engineering applications that require such consideration.

Keywords: Object-oriented design, inheritance, internal quality attribute, external quality attribute, class flattening.

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Authors: Anna Trusek-Holownia, Andrzej Noworyta

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Using an enzyme of known specificity the hydrolysis of protein was carried out in a controlled manner. The aim was to obtain oligopeptides being the so-called active peptides or their direct precursors. An original way of expression of the protein hydrolysis kinetics was introduced. Peptide bonds contained in the protein were recognized as a diverse-quality substrate for hydrolysis by the applied protease. This assumption was positively verified taking as an example the hydrolysis of albumin by thermolysin. Peptide linkages for this system should be divided into at least four groups. One of them is a group of bonds non-hydrolyzable by this enzyme. These that are broken are hydrolyzed at a rate that differs even by tens of thousands of times. Designated kinetic constants were k'_F = 10991.4 L/g^.h, k'_M = 14.83L/g^.h, k'_S about 10^-1 L/g^.h for fast, medium and slow bonds, respectively. Moreover, a procedure for unfolding of the protein, conducive to the improved susceptibility to enzymatic hydrolysis (approximately three-fold increase in the rate) was proposed.

Keywords: Peptide bond hydrolysis, kinetics, enzyme specificity, biologically active peptides.

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Authors: Xiaoli Shen, Yuehui Chen

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Interactions among proteins are the basis of various life events. So, it is important to recognize and research protein interaction sites. A control set that contains 149 protein molecules were used here. Then 10 features were extracted and 4 sample sets that contained 9 sliding windows were made according to features. These 4 sample sets were calculated by Radial Basis Functional neutral networks which were optimized by Particle Swarm Optimization respectively. Then 4 groups of results were obtained. Finally, these 4 groups of results were integrated by decision fusion (DF) and Genetic Algorithm based Selected Ensemble (GASEN). A better accuracy was got by DF and GASEN. So, the integrated methods were proved to be effective.

Keywords: protein interaction sites, features, sliding windows, radial basis functional neutral networks, genetic algorithm basedselected ensemble.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

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Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

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Authors: Amel Grissa-Touzi, Habib Ounally, Aissa Boulila

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The utility of expert system generators has been widely recognized in many applications. Several generators based on concept of the paradigm object, have been recently proposed. The generator of oriented object expert system (GSEOO) offers languages that are often complex and difficult to use. We propose in this paper an extension of the expert system generator, JESS, which permits a friendly use of this expert system. The new tool, called VISUAL JESS, bring two main improvements to JESS. The first improvement concerns the easiness of its utilization while giving back transparency to the syntax and semantic aspects of the JESS programming language. The second improvement permits an easy access and modification of the JESS knowledge basis. The implementation of VISUAL JESS is made so that it is extensible and portable.

Keywords: Generator of Systems Expert, Programming oriented object classifies, object, inheritance, polymorphism.

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Authors: E. Neidhardt

Abstract:

Mobility, for many people, is an important factor in the satisfaction of daily needs and many people are dependent on public transport. In rural areas with a low population density, it is difficult to provide public transportation with sufficient coverage and frequency. Therefore, the available public transport is unattractive. As a result, people use their own car, which is not desirable from a sustainable point of view and not possible for children and elderly people. Sometimes people organize themselves and volunteer transport services are created. These services are similar to demand-oriented taxis. However, these transport services are usually independent from each other and from the available line-based public transport, limiting both their usability and sustainability. We have developed a platform to improve usability and sustainability by connecting the different demand-oriented transport offerings with the line-based public transport. The system was implemented and tested in a rural area in Germany, but the SARS-CoV-2 pandemic limited real live operation.

Keywords: demand-oriented, HubChain, living lab, public transport

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Authors: G. Lavanya Devi, Allam Appa Rao, A. Damodaram, GR Sridhar, G. Jaya Suma

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Cluster analysis divides data into groups that are meaningful, useful, or both. Analysis of biological data is creating a new generation of epidemiologic, prognostic, diagnostic and treatment modalities. Clustering of protein sequences is one of the current research topics in the field of computer science. Linear relation is valuable in rule discovery for a given data, such as if value X goes up 1, value Y will go down 3", etc. The classical linear regression models the linear relation of two sequences perfectly. However, if we need to cluster a large repository of protein sequences into groups where sequences have strong linear relationship with each other, it is prohibitively expensive to compare sequences one by one. In this paper, we propose a new technique named General Regression Model Technique Clustering Algorithm (GRMTCA) to benignly handle the problem of linear sequences clustering. GRMT gives a measure, GR*, to tell the degree of linearity of multiple sequences without having to compare each pair of them.

Keywords: Clustering, General Regression Model, Protein Sequences, Similarity Measure.

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Authors: Pham Thi Quynh, Huynh Quyet Thang

Abstract:

Service-oriented systems have become popular and presented many advantages in develop and maintain process. The coupling is the most important attribute of services when they are integrated into a system. In this paper, we propose a suite of metrics to evaluate service-s quality according to its ability of coupling. We use the coupling metrics to measure the maintainability, reliability, testability, and reusability of services. Our proposed metrics are operated in run-time which bring more exact results.

Keywords: Dynamic coupling metric, SOA, web service, SOAP Extension.

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Authors: Dyah Titisari Widyastuti

Abstract:

Rail-station area development that is based on the concept of TOD (Transit Oriented Development) is principally oriented to pedestrian accessibility for daily mobility. The aim of this research is elaborating how far the existing physical elements of a rail-station district could facilitate pedestrian mobility and establish a pedestrian friendly district toward implementation of a TOD concept. This research was conducted through some steps: (i) mapping the rail-station area pedestrian sidewalk and pedestrian network as well as activity nodes and transit nodes, (ii) assessing the level of pedestrian sidewalk connectivity joining trip origin and destination. The research area coverage in this case is limited to walking distance of the rail station (around 500 meters or 10-15 minutes walking). The findings of this research on the current condition of the street and pedestrian sidewalk network and connectivity, show good preference for the foot modal share (more than 50%) is achieved. Nevertheless, it depends on the distance from the trip origin to destination.

Keywords: Accessibility of daily mobility, pedestrian friendly district, rail-station district, Transit Oriented Development.

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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: Gry M, Bergström J, Lengquist J, Lindberg J, Drobin K, Schwenk J, Nilsson P, Schuppe-Koistinen I.

Abstract:

Sensitive and predictive DILI (Drug Induced Liver Injury) biomarkers are needed in drug R&D to improve early detection of hepatotoxicity. The discovery of DILI biomarkers that demonstrate the predictive power to identify individuals at risk to DILI would represent a major advance in the development of personalized healthcare approaches. In this healthy volunteer acetaminophen study (4g/day for 7 days, with 3 monitored nontreatment days before and 4 after), 450 serum samples from 32 subjects were analyzed using protein profiling by antibody suspension bead arrays. Multiparallel protein profiles were generated using a DILI target protein array with 300 antibodies, where the antibodies were selected based on previous literature findings of putative DILI biomarkers and a screening process using pre dose samples from the same cohort. Of the 32 subjects, 16 were found to develop an elevated ALT value (2Xbaseline, responders). Using the plasma profiling approach together with multivariate statistical analysis some novel findings linked to lipid metabolism were found and more important, endogenous protein profiles in baseline samples (prior to treatment) with predictive power for ALT elevations were identified.

Keywords: DILI, Plasma profiling, PLSDA, Randomforest.

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