Search results for: gene expression analysis

Authors: Sambit Prasad Kar, P.Palanisamy

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In this paper a novel method for multiple one dimensional real valued sinusoidal signal frequency estimation in the presence of additive Gaussian noise is postulated. A computationally simple frequency estimation method with efficient statistical performance is attractive in many array signal processing applications. The prime focus of this paper is to combine the subspace-based technique and a simple peak search approach. This paper presents a variant of the Propagator Method (PM), where a collaborative approach of SUMWE and Propagator method is applied in order to estimate the multiple real valued sine wave frequencies. A new data model is proposed, which gives the dimension of the signal subspace is equal to the number of frequencies present in the observation. But, the signal subspace dimension is twice the number of frequencies in the conventional MUSIC method for estimating frequencies of real-valued sinusoidal signal. The statistical analysis of the proposed method is studied, and the explicit expression of asymptotic (large-sample) mean-squared-error (MSE) or variance of the estimation error is derived. The performance of the method is demonstrated, and the theoretical analysis is substantiated through numerical examples. The proposed method can achieve sustainable high estimation accuracy and frequency resolution at a lower SNR, which is verified by simulation by comparing with conventional MUSIC, ESPRIT and Propagator Method.

Keywords: Frequency estimation, peak search, subspace-based method without eigen decomposition, quadratic convex function.

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Authors: Elif Gencturk, Ekin Yurdakul, Ahmet Y. Celik, Senol Mutlu, Kutlu O. Ulgen

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Yeast cells are generally used as a model system of eukaryotes due to their complex genetic structure, rapid growth ability in optimum conditions, easy replication and well-defined genetic system properties. Thus, yeast cells increased the knowledge of the principal pathways in humans. During fermentation, carbohydrates (hexoses and pentoses) degrade into some toxic by-products such as 5-hydroxymethylfurfural (5-HMF or HMF) and furfural. HMF influences the ethanol yield, and ethanol productivity; it interferes with microbial growth and is considered as a potent inhibitor of bioethanol production. In this study, yeast single cell behavior under HMF application was monitored by using a continuous flow single phase microfluidic platform. Microfluidic device in operation is fabricated by hot embossing and thermo-compression techniques from cyclo-olefin polymer (COP). COP is biocompatible, transparent and rigid material and it is suitable for observing fluorescence of cells considering its low auto-fluorescence characteristic. The response of yeast cells was recorded through Red Fluorescent Protein (RFP) tagged Nop56 gene product, which is an essential evolutionary-conserved nucleolar protein, and also a member of the box C/D snoRNP complexes. With the application of HMF, yeast cell proliferation continued but HMF slowed down the cell growth, and after HMF treatment the cell proliferation stopped. By the addition of fresh nutrient medium, the yeast cells recovered after 6 hours of HMF exposure. Thus, HMF application suppresses normal functioning of cell cycle but it does not cause cells to die. The monitoring of Nop56 expression phases of the individual cells shed light on the protein and ribosome synthesis cycles along with their link to growth. Further computational study revealed that the mechanisms underlying the inhibitory or inductive effects of HMF on growth are enriched in functional categories of protein degradation, protein processing, DNA repair and multidrug resistance. The present microfluidic device can successfully be used for studying the effects of inhibitory agents on growth by single cell tracking, thus capturing cell to cell variations. By metabolic engineering techniques, engineered strains can be developed, and the metabolic network of the microorganism can thus be manipulated such that chemical overproduction of target metabolite is achieved along with the maximum growth/biomass yield.  

Keywords: COP, HMF, ribosome biogenesis, thermoplastic microbioreactor, yeast.

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Authors: B. Chouhan, A. Denesyuk, J. Heino, M. S. Johnson, K. Denessiouk

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Integrins are a large family of multidomain α/β cell signaling receptors. Some integrins contain an additional inserted I domain, whose earliest expression appears to be with the chordates, since they are observed in the urochordates Ciona intestinalis (vase tunicate) and Halocynthia roretzi (sea pineapple), but not in integrins of earlier diverging species. The domain-s presence is viewed as a hallmark of integrins of higher metazoans, however in vertebrates, there are clearly three structurally-different classes: integrins without I domains, and two groups of integrins with I domains but separable by the presence or absence of an additional αC helix. For example, the αI domains in collagen-binding integrins from Osteichthyes (bony fish) and all higher vertebrates contain the specific αC helix, whereas the αI domains in non-collagen binding integrins from vertebrates and the αI domains from earlier diverging urochordate integrins, i.e. tunicates, do not. Unfortunately, within the early chordates, there is an evolutionary gap due to extinctions between the tunicates and cartilaginous fish. This, coupled with a knowledge gap due to the lack of complete genomic data from surviving species, means that the origin of collagen-binding αC-containing αI domains remains unknown. Here, we analyzed two available genomes from Callorhinchus milii (ghost shark/elephant shark; Chondrichthyes – cartilaginous fish) and Petromyzon marinus (sea lamprey; Agnathostomata), and several available Expression Sequence Tags from two Chondrichthyes species: Raja erinacea (little skate) and Squalus acanthias (dogfish shark); and Eptatretus burgeri (inshore hagfish; Agnathostomata), which evolutionary reside between the urochordates and osteichthyes. In P. marinus, we observed several fragments coding for the αC-containing αI domain, allowing us to shed more light on the evolution of the collagen-binding integrins.

Keywords: Integrin αI domain, integrin evolution, collagen binding, structure, αC helix

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Authors: Abdallah S. Abdallah, Mohamad A bou El-Nasr, A. Lynn Abbott

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This paper presents a new color face image database for benchmarking of automatic face detection algorithms and human skin segmentation techniques. It is named the VT-AAST image database, and is divided into four parts. Part one is a set of 286 color photographs that include a total of 1027 faces in the original format given by our digital cameras, offering a wide range of difference in orientation, pose, environment, illumination, facial expression and race. Part two contains the same set in a different file format. The third part is a set of corresponding image files that contain human colored skin regions resulting from a manual segmentation procedure. The fourth part of the database has the same regions converted into grayscale. The database is available on-line for noncommercial use. In this paper, descriptions of the database development, organization, format as well as information needed for benchmarking of algorithms are depicted in detail.

Keywords: Image database, color image analysis, facedetection, skin segmentation.

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Authors: P. Varzakas

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In this paper, the problem of estimating the optimal radio capacity of a single-cell spread spectrum (SS) multiple-inputmultiple- output (MIMO) system operating in a Rayleigh fading environment is examined. The optimisation between the radio capacity and the theoretically achievable average channel capacity (in the sense of information theory) per user of a MIMO single-cell SS system operating in a Rayleigh fading environment is presented. Then, the spectral efficiency is estimated in terms of the achievable average channel capacity per user, during the operation over a broadcast time-varying link, and leads to a simple novel-closed form expression for the optimal radio capacity value based on the maximization of the achieved spectral efficiency. Numerical results are presented to illustrate the proposed analysis.

Keywords: Channel capacity, MIMO systems, Radio capacity, Rayleigh fading, Spectral efficiency.

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Authors: Dwitya Elvira, Eryati Darwin

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Background: Graves’ disease (GD) is an autoimmune thyroid disease. Imbalance of Th1/Th2 cells and T-regulatory (Treg)/Th17 cells was thought to play pivotal role in the pathogenesis of GD. Treg FoxP3 produced TGF-β to maintain regulatory function, and Th17 cells produced IL-17 as cytokines that were thought in mediating several autoimmune diseases. The aim of this study is to assess the role of IL-17 and TGF-β in the pathogenesis of GD and to investigate its correlation with Thyroid Stimulating Hormone Receptor Antibody (TRAb) and Treg FoxP3 expression. Method: 30 GD patients and 27 age and sex-matched controls were enrolled in this study. Diagnosis of GD was based on clinical and biochemical of GD. Serum IL-17, TGF-β, TRAb, and FoxP3 were measured by enzyme-linked immunosorbent assay (ELISA). Data were analyzed by using SPSS 21.0 (SPSS Inc.). Spearman rank correlation test was used for assessment of correlation. The statistical significance was accepted as P<0.05. Result: There was no significant correlation between IL-17 and TGF-β serum with expression of FoxP3 level in GD, but there was significant correlation between TGF-β and TRAb serum level (P<0.05). Serum levels of IL-17 and TGF-β were found to be elevated in patient group compared to control, where mean values of IL-17 were 14.43±2.15 pg/mL and TGF-β were 10.44±3.19 pg/mL in patients group; and in control group, level of IL-17 were 7.1±1.45 pg/mL and TGF-β were 4.95±1.35 pg/mL. Conclusion: Serum Il-17 and TGF-β were elevated in GD patients that reflect the role of inflammatory and regulatory cytokines activation in pathogenesis of GD. There was significant correlation between TGF-β and TRAb, revealing that Treg cytokines may play a role in pathogenesis of GD.

Keywords: IL-17, TGF-β, FoxP3, Graves’ disease.

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Authors: Patsaraporn Somboonsak, Mud-Armeen Munlin

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

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

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Authors: Nichole Haag, Kimberly Velk, Tyler McCune, Chun Wu

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Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Keywords: Dihydroxyacetone kinase, essential genes, Methicillin-resistant Staphylococcus aureus, drug target.

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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: Kristyanto B.

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Plenty of analyses based on Biomechanics were carried out on many jobs in manufactures or services. Now Biomechanics analysis is being applied on mothers who are giving birth. The analysis conducted in terms of normal condition of the birth process without Gyn Bed (Obstetric Bed). The aim of analysis is to study whether it is risky or not when choosing the position of mother’s postures when delivering the baby. This investigation was applied on two positions that generally appear in common birth process. Results will show the analysis of both positions to support the birth process based on the Biomechanics analysis (Ergonomic approaches). 

Keywords: Biomechanics analysis, Birth process, Position of postures analysis, Ergonomic approaches.

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Authors: Razagh Hafezi, Ahmad Keshavarz, Vida Moshfegh

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This paper presents a novel algorithm of stereo correspondence with rank transform. In this algorithm we used the genetic algorithm to achieve the accurate disparity map. Genetic algorithms are efficient search methods based on principles of population genetic, i.e. mating, chromosome crossover, gene mutation, and natural selection. Finally morphology is employed to remove the errors and discontinuities.

Keywords: genetic algorithm, morphology, rank transform, stereo correspondence

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Authors: Ada Yurman

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Using the case of Israeli Atomic Spy Mordechai Vanunu as an example, this study sought to examine social response to political deviance whereby social response can be mobilized in order to achieve social control. Mordechai Vanunu, a junior technician in the Dimona Atomic Research Center, played a normative role in the militaristic discourse while working in the “holy shrine” of the Israeli defense system for many years. At a certain stage, however, Vanunu decided to detach himself from this collective and launched an assault on this top-secret circle. Israeli society in general and the security establishment in particular found this attack intolerable and unforgivable. They presented Vanunu as a ticking time bomb, delegitimized him and portrayed him as “other”. In addition, Israeli enforcement authorities imposed myriad prohibitions and sanctions on Vanunu even after his release from prison – “as will be done to he who desecrates holiness.” Social response to Vanunu at the time of his capture and trial was studied by conducting a content analysis of six contemporary daily newspapers. The analysis focused on use of language and forms of expression. In contrast with traditional content analysis methodology, this study did not just look at frequency of expressions of ideas and terms in the text and covert content; rather, the text was analyzed as a structural whole, and included examination of style, tone and unusual use of imagery, and more, in order to uncover hidden messages within the text. The social response to this case was extraordinarily intense, not only because in this case of political deviance, involving espionage and treason, Vanunu’s actions comprised a real potential threat to the country, but also because of the threat his behavior posed to the symbolic universe of society. Therefore, the response to this instance of political deviance can be seen as being part of a mechanism of social control aiming to protect world view of society as a whole, as well as to punish the criminal.

Keywords: Militarism, political deviance, social construction, social control.

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Authors: Seyedfateh Moradi, Abas Ali Rahbar

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The present study focuses on investigating group psychoanalysis in the Middle East. The study uses a descriptive-analytic method and library resources have been used to collect the data. Additionally, the researcher’s observations of people’s everyday behavior have played an important role in the production and analysis of the study. Group psychoanalysis in the Middle East can be conducted through people’s daily behaviors, proverbs, poetry, mythology, etc., and some of the general characteristics of people in the Middle East include: xenophobia, revivalism, fatalism, nostalgic, wills and so on. Members of the group have often failed to achieve Libido wills and it is very important in unifying and reproduction violence. Therefore, if libidinal wills are irrationally fixed, it will be important in forming fundamentalist and racist groups, a situation that is dominant among many groups in the Middle East. Adversities, from early childhood and afterwards, in the subjects have always been influential in the political behavior of group members, and it manifests itself as counter-projections. Consequently, it affects the foreign policy of the governments. On the other hand, two kinds of subjects are identifiable in the Middle East, one; classical subject that is related to nostalgia and mythology and, two; modern subjects which is self-alienated. As a result, both subjects are seeking identity and self-expression in public in relation to forming groups. Therefore, collective unconscious in the Middle East shows itself as extreme boundaries and leads to forming groups characterized with violence. Psychoanalysis shows important aspects to identify many developments in the Middle East; totally analysis of Freud, Carl Jung and Reich about groups can be applied in the present Middle East.

Keywords: Politics, political psychoanalysis, group, Middle East.

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Authors: Richard L. Summers

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The advanced computational analysis of biological systems is becoming increasingly dependent upon an understanding of the information-theoretic structure of the materials, energy and interactive processes that comprise those systems. The stability and survival of these living systems is fundamentally contingent upon their ability to acquire and process the meaning of information concerning the physical state of its biological continuum (biocontinuum). The drive for adaptive system reconciliation of a divergence from steady state within this biocontinuum can be described by an information metric-based formulation of the process for actionable knowledge acquisition that incorporates the axiomatic inference of Kullback-Leibler information minimization driven by survival replicator dynamics. If the mathematical expression of this process is the Lagrangian integrand for any change within the biocontinuum then it can also be considered as an action functional for the living system. In the direct method of Lyapunov, such a summarizing mathematical formulation of global system behavior based on the driving forces of energy currents and constraints within the system can serve as a platform for the analysis of stability. As the system evolves in time in response to biocontinuum perturbations, the summarizing function then conveys information about its overall stability. This stability information portends survival and therefore has absolute existential meaning for the living system. The first derivative of the Lyapunov energy information function will have a negative trajectory toward a system steady state if the driving force is dissipating. By contrast, system instability leading to system dissolution will have a positive trajectory. The direction and magnitude of the vector for the trajectory then serves as a quantifiable signature of the meaning associated with the living system’s stability information, homeostasis and survival potential.

Keywords: Semiotic meaning, Shannon information, Lyapunov, living systems.

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Authors: Raniya Alsharif

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The color theory of good and evil is the association of colors to the omnipresent concept of good and evil, where human behavior and perception can be highly influenced by seeing black and white, making these connotations almost dangerously distinctive where they can be very hard to distinguish. This theory is a human construct that dates back to ancient Egypt and has been used since then in almost all forms of communication and expression, such as art, fashion, literature, and religious manuscripts, helping the implantation of preconceived ideas that influence behavior and society. This is a mixed-methods research that uses both surveys to collect quantitative data related to the theory and a vignette to collect qualitative data by using a scenario where participants aged between 18-25 will style two characters of good and bad characteristics with color contrasting clothes, both yielding results about the nature of the preconceived perceptions associated with ‘black and white’ and ‘good and evil’, illustrating the important role of media and communications in human behavior and subconscious, and also uncover how far this theory goes in the age of social media enlightenment.

Keywords: Color perception, interpretivism, thematic analysis, vignettes.

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Authors: Reza Nadimi, Fariborz Jolai

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This article combines two techniques: data envelopment analysis (DEA) and Factor analysis (FA) to data reduction in decision making units (DMU). Data envelopment analysis (DEA), a popular linear programming technique is useful to rate comparatively operational efficiency of decision making units (DMU) based on their deterministic (not necessarily stochastic) input–output data and factor analysis techniques, have been proposed as data reduction and classification technique, which can be applied in data envelopment analysis (DEA) technique for reduction input – output data. Numerical results reveal that the new approach shows a good consistency in ranking with DEA.

Keywords: Effectiveness, Decision Making, Data EnvelopmentAnalysis, Factor Analysis

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Authors: Jörg Linde, Ekaterina Buyko, Robert Altwasser, Udo Hahn, Reinhard Guthke

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Reverse engineering of full-genomic interaction networks based on compendia of expression data has been successfully applied for a number of model organisms. This study adapts these approaches for an important non-model organism: The major human fungal pathogen Candida albicans. During the infection process, the pathogen can adapt to a wide range of environmental niches and reversibly changes its growth form. Given the importance of these processes, it is important to know how they are regulated. This study presents a reverse engineering strategy able to infer fullgenomic interaction networks for C. albicans based on a linear regression, utilizing the sparseness criterion (LASSO). To overcome the limited amount of expression data and small number of known interactions, we utilize different prior-knowledge sources guiding the network inference to a knowledge driven solution. Since, no database of known interactions for C. albicans exists, we use a textmining system which utilizes full-text research papers to identify known regulatory interactions. By comparing with these known regulatory interactions, we find an optimal value for global modelling parameters weighting the influence of the sparseness criterion and the prior-knowledge. Furthermore, we show that soft integration of prior-knowledge additionally improves the performance. Finally, we compare the performance of our approach to state of the art network inference approaches.

Keywords: Pathogen, network inference, text-mining, Candida albicans, LASSO, mutual information, reverse engineering, linear regression, modelling.

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Authors: Meriem Bahij, Ahmed Nafidi, Boujemâa Achchab, Sílvio M. A. Gama, José A. O. Matos

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Stochastic modeling concerns the use of probability to model real-world situations in which uncertainty is present. Therefore, the purpose of stochastic modeling is to estimate the probability of outcomes within a forecast, i.e. to be able to predict what conditions or decisions might happen under different situations. In the present study, we present a model of a stochastic diffusion process based on the bi-Weibull distribution function (its trend is proportional to the bi-Weibull probability density function). In general, the Weibull distribution has the ability to assume the characteristics of many different types of distributions. This has made it very popular among engineers and quality practitioners, who have considered it the most commonly used distribution for studying problems such as modeling reliability data, accelerated life testing, and maintainability modeling and analysis. In this work, we start by obtaining the probabilistic characteristics of this model, as the explicit expression of the process, its trends, and its distribution by transforming the diffusion process in a Wiener process as shown in the Ricciaardi theorem. Then, we develop the statistical inference of this model using the maximum likelihood methodology. Finally, we analyse with simulated data the computational problems associated with the parameters, an issue of great importance in its application to real data with the use of the convergence analysis methods. Overall, the use of a stochastic model reflects only a pragmatic decision on the part of the modeler. According to the data that is available and the universe of models known to the modeler, this model represents the best currently available description of the phenomenon under consideration.

Keywords: Diffusion process, discrete sampling, likelihood estimation method, simulation, stochastic diffusion equation, trends functions, bi-parameters Weibull density function.

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Authors: Antonella Bandiera

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A new sythetic gene coding for a Human Elastin-Like Polypeptide was constructed and expressed. The recombinant product was tested as coating agent to realize a surface suitable for cell growth. Coatings showed peculiar features and different human cell lines were seeded and cultured. All cell lines tested showed to adhere and proliferate on this substrate that has been shown also to exert a specific effect on cells, depending on cell type.

Keywords: elastin, recombinant protein, coating, cell adhesion.

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Authors: Dib Djalel, Haddouche Ali, Chellali Benachiba

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When a lightning strike falls near an overhead power line, the intense electromagnetic field radiated by the current of the lightning return stroke coupled with power lines and there induced transient overvoltages, which can cause a back-flashover in electrical network. The indirect lightning represents a major danger owing to the fact that it is more frequent than that which results from the direct strikes. In this paper we present an analysis of the electromagnetic coupling between an external electromagnetic field generated by the lightning and an electrical overhead lines, so we give an important and original contribution: We are based on our experimental measurements which we carried in the high voltage laboratories of EPFL in Switzerland during the last trimester of 2005, on the recent works of other authors and with our mathematical improvement a new particular analytical expression of the electromagnetic field generated by the lightning return stroke was developed and presented in this paper. The results obtained by this new electromagnetic field formulation were compared with experimental results and give a reasonable approach.

Keywords: Lightning, overhead lines, electromagneticcoupling, return stroke, models, induced overvoltages.

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Authors: Seyed Ali Mir Heydari, Mohsen Sayadiharikandeh

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Static analysis of source code is used for auditing web applications to detect the vulnerabilities. In this paper, we propose a new algorithm to analyze the PHP source code for detecting LFI and RFI potential vulnerabilities. In our approach, we first define some patterns for finding some functions which have potential to be abused because of unhandled user inputs. More precisely, we use regular expression as a fast and simple method to define some patterns for detection of vulnerabilities. As inclusion functions could be also used in a safe way, there could occur many false positives (FP). The first cause of these FP-s could be that the function does not use a usersupplied variable as an argument. So, we extract a list of usersupplied variables to be used for detecting vulnerable lines of code. On the other side, as vulnerability could spread among the variables like by multi-level assignment, we also try to extract the hidden usersupplied variables. We use the resulted list to decrease the false positives of our method. Finally, as there exist some ways to prevent the vulnerability of inclusion functions, we define also some patterns to detect them and decrease our false positives.

Keywords: User-supplied Variables, hidden user-supplied variables, PHP vulnerabilities.

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Authors: Helyane B. Borges, Julio Cesar Nievola

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Hierarchical classification is a problem with applications in many areas as protein function prediction where the dates are hierarchically structured. Therefore, it is necessary the development of algorithms able to induce hierarchical classification models. This paper presents experimenters using the algorithm for hierarchical classification called Multi-label Hierarchical Classification using a Competitive Neural Network (MHC-CNN). It was tested in ten datasets the Gene Ontology (GO) Cellular Component Domain. The results are compared with the Clus-HMC and Clus-HSC using the hF-Measure.

Keywords: Hierarchical Classification, Competitive Neural Network, Global Classifier.

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Authors: Serkawt Khola

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A feature weighting and selection method is proposed which uses the structure of a weightless neuron and exploits the principles that govern the operation of Genetic Algorithms and Evolution. Features are coded onto chromosomes in a novel way which allows weighting information regarding the features to be directly inferred from the gene values. The proposed method is significant in that it addresses several problems concerned with algorithms for feature selection and weighting as well as providing significant advantages such as speed, simplicity and suitability for real-time systems.

Keywords: Feature weighting, genetic algorithm, pattern recognition, weightless neuron.

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Authors: Seongmin Yim, Hyun-Kyu Kang

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As a part of evaluation system for R&D program, the Korean government has applied feasibility analysis since 2008. Various professionals put forth a great effort in order to catch up the high degree of freedom of R&D programs, and make contributions to evolving the feasibility analysis. We analyze diverse R&D programs from various viewpoints, such as technology, policy, and Economics, integrate the separate analysis, and finally arrive at a definite result; whether a program is feasible or unfeasible. This paper describes the concept and method of the feasibility analysis as a decision making tool. The analysis unit and content of each criterion, which are key elements in a comprehensive decision making structure, are examined

Keywords: Decision Making of New Government R&D Program, Feasibility Analysis Study

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Authors: Saruhan Kartal, Ilker Kalkan

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The present paper reports the cracking moment estimates of a set of steel-reinforced, Fiber Reinforced Polymer (FRP)-reinforced and hybrid steel-FRP reinforced concrete beams, calculated from different analytical formulations in the codes, together with the experimental cracking load values. A total of three steel-reinforced, four FRP-reinforced, 12 hybrid FRP-steel over-reinforced and five hybrid FRP-steel under-reinforced concrete beam tests were analyzed within the scope of the study. Glass FRP (GFRP) and Basalt FRP (BFRP) bars were used in the beams as FRP bars. In under-reinforced hybrid beams, rupture of the FRP bars preceded crushing of concrete, while concrete crushing preceded FRP rupture in over-reinforced beams. In both types, steel yielding took place long before the FRP rupture and concrete crushing. The cracking moment mainly depends on two quantities, namely the moment of inertia of the section at the initiation of cracking and the flexural tensile strength of concrete, i.e. the modulus of rupture. In the present study, two different definitions of uncracked moment of inertia, i.e. the gross and the uncracked transformed moments of inertia, were adopted. Two analytical equations for the modulus of rupture (ACI 318M and Eurocode 2) were utilized in the calculations as well as the experimental tensile strength of concrete from prismatic specimen tests. The ACI 318M modulus of rupture expression produced cracking moment estimates closer to the experimental cracking moments of FRP-reinforced and hybrid FRP-steel reinforced concrete beams when used in combination with the uncracked transformed moment of inertia, yet the Eurocode 2 modulus of rupture expression gave more accurate cracking moment estimates in steel-reinforced concrete beams. All of the analytical definitions produced analytical values considerably different from the experimental cracking load values of the solely FRP-reinforced concrete beam specimens.

Keywords: Cracking moment, four-point bending, hybrid use of reinforcement, polymer reinforcement.

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Authors: Jamal Abdi

Abstract:

This paper is largely a response/critique of Samuel P. Huntington´s Clash of Civilizations thesis. The overriding argument is that Huntington´s thesis is characterized by failure to distinguish between ´groups´ and ´categories´. Multinational civilizations overcoming their internal collective action problems, which would enable them to pursue a unified strategy vis-à-vis the West, is a rather foundational assumption in his theory. Without assigning sufficient intellectual attention to the processes through which multinational civilizations may gain capacity for concerted action i.e. become a group, he contended that the post-cold-war world would be shaped in large measure by interactions among seven or eight major civilizations. Thus, failure in providing a convincing analysis of multi-national civilizations´ transition from categories to groups is a significant weakness in Huntington´s clash theory. It is also suggested that so-called Islamic terrorism and the war on terror is not to be taken as an expression of presence of clash between a Western and an Islamic civilization, as terrorist organizations would be superfluous in a world characterized by clash of civilizations. Consequences of multinational civilizations becoming a group are discussed in relation to contemporary Western superiority.

Keywords: Clash of civilizations, groups, categories, groupism.

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Authors: Sa-aat Niwitpong, Rada Somkhuean, Suparat Niwitpong

Abstract:

This paper presents the generalized p-values for testing the Behrens-Fisher problem when one variance is unknown. We also derive a closed form expression of the upper bound of the proposed generalized p-value.

Keywords: Generalized p-value, hypothesis testing, upper bound.

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Authors: Ramesh K. Sunkaria

Abstract:

The linear methods of heart rate variability analysis such as non-parametric (e.g. fast Fourier transform analysis) and parametric methods (e.g. autoregressive modeling) has become an established non-invasive tool for marking the cardiac health, but their sensitivity and specificity were found to be lower than expected with positive predictive value <30%. This may be due to considering the RR-interval series as stationary and re-sampling them prior to their use for analysis, whereas actually it is not. This paper reviews the non-linear methods of HRV analysis such as correlation dimension, largest Lyupnov exponent, power law slope, fractal analysis, detrended fluctuation analysis, complexity measure etc. which are currently becoming popular as these uses the actual RR-interval series. These methods are expected to highly accurate cardiac health prognosis.

Keywords: chaos, nonlinear dynamics, sample entropy, approximate entropy, detrended fluctuation analysis.

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Authors: A. Felimban, A. Prieto, U. Knaack, T. Klein

Abstract:

This study aims to present an overview of recent research in building energy-retrofitting strategy applications and analyzing them within the context of hot arid climate regions which is in this case study represented by the Kingdom of Saudi Arabia. The main goal of this research is to do an analytical study of recent research approaches to show where the primary gap in knowledge exists and outline which possible strategies are available that can be applied in future research. Also, the paper focuses on energy retrofitting strategies at a building envelop level. The study is limited to specific measures within the hot arid climate region. Scientific articles were carefully chosen as they met the expression criteria, such as retrofitting, energy-retrofitting, hot-arid, energy efficiency, residential buildings, which helped narrow the research scope. Then the papers were explored through descriptive analysis and justified results within the Saudi context in order to draw an overview of future opportunities from the field of study for the last two decades. The conclusions of the analysis of the recent research confirmed that the field of study had a research shortage on investigating actual applications and testing of newly introduced energy efficiency applications, lack of energy cost feasibility studies and there was also a lack of public awareness. In terms of research methods, it was found that simulation software was a major instrument used in energy retrofitting application research. The main knowledge gaps that were identified included the need for certain research regarding actual application testing; energy retrofitting strategies application feasibility; the lack of research on the importance of how strategies apply first followed by the user acceptance of developed scenarios.

Keywords: Energy efficiency, energy retrofitting, hot arid climate, Saudi Arabia.

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Authors: Yan Ren, Fei Guo, Jun Qiao, Shengwei Hu, Hui Zhang, Yuanzhi Wang, Pengyan Wang, Jinliang Sheng, Xinli Gu, Xiaojun Liu, Chuangfu Chen

Abstract:

Bovine viral diarrhea virus (BVDV) can cause lifelong persistent infection. One reason for the phenomena is attributed to BVDV infection to placenta tissue. However the mechanisms that BVDV invades into placenta tissue remain unclear. To clarify the molecular mechanisms, we investigated the possible means that BVDV entered into bovine trophoblast cells (TPC). Yeast two-hybrid system was used to identify proteins extracted from TPC, which interact with BVDV envelope glycoprotein E2. A PGbkt7-E2 yeast expression vector and TPC cDNA library were constructed. Through two rounds of screening, three positive clones were identified. Sequencing analysis indicated that all the three positive clones encoded the same protein clathrin. Physical interaction between clathrin and BVDV E2 protein was further confirmed by coimmunoprecipitation experiments. This result suggested that the clathrin might play a critical role in the process of BVDV entry into placenta tissue and might be a novel antiviral target for preventing BVDV infection.

Keywords: Bovine viral diarrhea virus, clathrin, glycoprotein E2, yeast two-hybrid system.

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