Search results for: phenotype profiles.

Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

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Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Keywords: Metagenomics, phenotype prediction, deep learning, embeddings, multiple instance learning.

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Authors: Waqas Saleem, Fan Yuqing

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A strategy is implemented to find the improved configuration design of an existing aircraft structure by executing topology and shape optimizations. Structural analysis of the Initial Design Space is performed in ANSYS under the loads pertinent to operating and ground conditions. By using the FEA results and data, an initial optimized layout configuration is attained by exploiting nonparametric topology optimization in TOSCA software. Topological optimized surfaces are then smoothened and imported in ANSYS to develop the geometrical features. Nodes at the critical locations of resulting voids are selected for sketching rough profiles. Rough profiles are further refined and CAD feasible geometric features are generated. The modified model is then analyzed under the same loadings and constraints as defined for topology optimization. Shape at the peak stress concentration areas are further optimized by exploiting the shape optimization in TOSCA.shape module. The harmonized stressed model with the modified surfaces is then imported in CATIA to develop the final design.

Keywords: Structural optimization, Topology optimization, Shape optimization, Tail fin

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Authors: Rafał Adamczak

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State-of-the-art methods for secondary structure (Porter, Psi-PRED, SAM-T99sec, Sable) and solvent accessibility (Sable, ACCpro) predictions use evolutionary profiles represented by the position specific scoring matrix (PSSM). It has been demonstrated that evolutionary profiles are the most important features in the feature space for these predictions. Unfortunately applying PSSM matrix leads to high dimensional feature spaces that may create problems with parameter optimization and generalization. Several recently published suggested that applying feature extraction for the PSSM matrix may result in improvements in secondary structure predictions. However, none of the top performing methods considered here utilizes dimensionality reduction to improve generalization. In the present study, we used simple and fast methods for features selection (t-statistics, information gain) that allow us to decrease the dimensionality of PSSM matrix by 75% and improve generalization in the case of secondary structure prediction compared to the Sable server.

Keywords: Secondary structure prediction, feature selection, position specific scoring matrix.

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Authors: Farzad Khajavi, Farzaneh Jalilfar, Faranak Jafari, Leila Shokrani

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Formulation of gliclazide in the form of extended-release tablet in 30 and 60 mg dosage forms was performed using hypromellose (HPMC K4M) as a retarding agent. Drug-release profiles were investigated in comparison with references Diamicron MR 30 and 60 mg tablets. The effect of size of powder particles, the amount of hypromellose in formulation, hardness of tablets, and also the effect of halving the tablets were investigated on drug release profile. A mathematical model which describes hypromellose behavior in initial times of drug release was proposed for the estimation of hypromellose content in modified-release gliclazide 60 mg tablet. This model is based on erosion of hypromellose in dissolution media. The model is applicable to describe release profiles of insoluble drugs. Therefore, by using dissolved amount of drug in initial times of dissolution and the model, the amount of hypromellose in formulation can be predictable. The model was used to predict the HPMC K4M content in modified-release gliclazide 30 mg and extended-release quetiapine 200 mg tablets.

Keywords: Hypromellose, gliclazide, drug release, modified-release tablet, mathematical model.

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Authors: Asfaw Gezae Daful

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In the present study, two distinctly different approaches are followed for modeling of reactive distillation column, the equilibrium stage model and the nonequilibrium stage model. These models are simulated with a computer code developed in the present study using MATLAB programming. In the equilibrium stage models, the vapor and liquid phases are assumed to be in equilibrium and allowance is made for finite reaction rates, where as in the nonequilibrium stage models simultaneous mass transfer and reaction rates are considered. These simulated model results are validated from the experimental data reported in the literature. The simulated results of equilibrium and nonequilibrium models are compared for concentration, temperature and reaction rate profiles in a reactive distillation column for Methyl Tert Butyle Ether (MTBE) production. Both the models show similar trend for the concentration, temperature and reaction rate profiles but the nonequilibrium model predictions are higher and closer to the experimental values reported in the literature.

Keywords: Reactive Distillation, Equilibrium model, Nonequilibrium model, Methyl Tert-Butyl Ether

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Authors: Jean François Chatelain, Imed Zaghbani, Joseph Monier

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The machining of Carbon Fiber Reinforced Plastics has come to constitute a significant challenge for many fields of industry. The resulting surface finish of machined parts is of primary concern for several reasons, including contact quality and impact on the assembly. Therefore, the characterization and prediction of roughness based on machining parameters are crucial for costeffective operations. In this study, a PCD tool comprised of two straight flutes was used to trim 32-ply carbon fiber laminates in a bid to analyze the effects of the feed rate and the cutting speed on the surface roughness. The results show that while the speed has but a slight impact on the surface finish, the feed rate for its part affects it strongly. A detailed study was also conducted on the effect of fiber orientation on surface roughness, for quasi-isotropic laminates used in aerospace. The resulting roughness profiles for the four-ply orientation lay-up were compared, and it was found that fiber angle is a critical parameter relating to surface roughness. One of the four orientations studied led to very poor surface finishes, and characteristic roughness profiles were identified and found to only relate to the ply orientations of multilayer carbon fiber laminates.

Keywords: Roughness, Detouring, Composites, Aerospace

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Authors: Ming-Lun Chiang, Chieh Wu, Ming-Ju Chen

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Three strains of Vibrio parahaemolyticus (690, BCRC 13023 and BCRC 13025) implicated in food poisoning outbreaks in Taiwan were subjected to acid adaptation at pH 5.5 for 90 min. The growth behaviors of acid-adapted and non-adapted V. parahaemolyticus in the media supplemented with various nitrogen and carbon sources were investigated. The effects of acid adaptation on the thermostable direct hemolysin (TDH) secretion and fatty acid profiles of V. parahaemolyticus were also examined. Results showed that acid-adapted and non-adapted V. parahaemolyticus 690, BCRC 13023 and BCRC 13025 grew similarly in TSB-3% NaCl and basal media supplemented with various carbon and nitrogen sources during incubation period. Higher TDH secretion was noted with V. parahaemolyticus 690 among the three strains. However, acid-adapted strains produced less amounts of TDH than non-adapted strains when they were grown in TSB-3% NaCl. Additionally, acid adaptation increased the ratio of SFA/USFA in cells of V. parahaemolyticus strains.

Keywords: Vibrio parahaemolyticus, acid adaptation, thermostable direct hemolysin, fatty acid profile.

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Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.

Keywords: Metabolic network, gene knockout, flux balance analysis, microarray data, integration.

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Authors: Kasthurirangan Gopalakrishnan, Anshu Manik

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Subgrade moisture content varies with environmental and soil conditions and has significant influence on pavement performance. Therefore, it is important to establish realistic estimates of expected subgrade moisture contents to account for the effects of this variable on predicted pavement performance during the design stage properly. The initial boundary soil suction profile for a given pavement is a critical factor in determining expected moisture variations in the subgrade for given pavement and climatic and soil conditions. Several numerical models have been developed for predicting water and solute transport in saturated and unsaturated subgrade soils. Soil hydraulic properties are required for quantitatively describing water and chemical transport processes in soils by the numerical models. The required hydraulic properties are hydraulic conductivity, water diffusivity, and specific water capacity. The objective of this paper was to determine isothermal moisture profiles in a soil fill and predict the soil moisture movement above the ground water table using a simple one-dimensional finite difference model.

Keywords: Fill, Hydraulic Conductivity, Pavement, Subgrade.

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

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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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Authors: Zhang Tianci, Ding Meng, Zuo Hongfu, Zeng Lina, Sun Zejun

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Automation of airport operations can greatly improve ground movement efficiency. In this paper, we study the speed profile design problem for advanced airport ground movement control and guidance. The problem is constrained by the surface four-dimensional trajectory generated in taxi planning. A decomposed approach of two stages is presented to solve this problem efficiently. In the first stage, speeds are allocated at control points, which ensure smooth speed profiles can be found later. In the second stage, detailed speed profiles of each taxi interval are generated according to the allocated control point speeds with the objective of minimizing the overall fuel consumption. We present a swarm intelligence based algorithm for the first-stage problem and a discrete variable driven enumeration method for the second-stage problem, since it only has a small set of discrete variables. Experimental results demonstrate the presented methodology performs well on real world speed profile design problems.

Keywords: Airport ground movement, fuel consumption, particle swarm optimization, smoothness, speed profile design.

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Authors: J.R. Quevedo, E. Montañés, J. Ranilla, A. Bahamonde

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The new framework the Higher Education is immersed in involves a complete change in the way lecturers must teach and students must learn. Whereas the lecturer was the main character in traditional education, the essential goal now is to increase the students' participation in the process. Thus, one of the main tasks of lecturers in this new context is to design activities of different nature in order to encourage such participation. Seminars are one of the activities included in this environment. They are active sessions that enable going in depth into specific topics as support of other activities. They are characterized by some features such as favoring interaction between students and lecturers or improving their communication skills. Hence, planning and organizing strategic seminars is indeed a great challenge for lecturers with the aim of acquiring knowledge and abilities. This paper proposes a method using Artificial Intelligence techniques to obtain student profiles from their marks and preferences. The goal of building such profiles is twofold. First, it facilitates the task of splitting the students into different groups, each group with similar preferences and learning difficulties. Second, it makes it easy to select adequate topics to be a candidate for the seminars. The results obtained can be either a guarantee of what the lecturers could observe during the development of the course or a clue to reconsider new methodological strategies in certain topics.

Keywords: artificial intelligence, clustering, organizingseminars, student profile

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Authors: Ali Rashash Alzahrani, Elizabeth Stojanovski

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Data on various aspects of education are collected at the institutional and government level regularly. In Australia, for example, students at various levels of schooling undertake examinations in numeracy and literacy as part of NAPLAN testing, enabling longitudinal assessment of such data as well as comparisons between schools and states within Australia. Another source of educational data collected internationally is via the PISA study which collects data from several countries when students are approximately 15 years of age and enables comparisons in the performance of science, mathematics and English between countries as well as ranking of countries based on performance in these standardised tests. As well as student and school outcomes based on the tests taken as part of the PISA study, there is a wealth of other data collected in the study including parental demographics data and data related to teaching strategies used by educators. Overall, an abundance of educational data is available which has the potential to be used to help improve educational attainment and teaching of content in order to improve learning outcomes. A multivariate assessment of such data enables multiple variables to be considered simultaneously and will be used in the present study to help develop profiles of students based on performance in mathematics using data obtained from the PISA study.

Keywords: Cluster analysis, education, mathematics, profiles.

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Authors: Kung-Jen Tu, Danny Vernatha

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To assist individual departments within universities in their energy management tasks, this study explores the application of Building Information Modeling in establishing the ‘BIM based Energy Management Support System’ (BIM-EMSS). The BIM-EMSS consists of six components: (1) sensors installed for each occupant and each equipment, (2) electricity sub-meters (constantly logging lighting, HVAC, and socket electricity consumptions of each room), (3) BIM models of all rooms within individual departments’ facilities, (4) data warehouse (for storing occupancy status and logged electricity consumption data), (5) building energy management system that provides energy managers with various energy management functions, and (6) energy simulation tool (such as eQuest) that generates real time 'standard energy consumptions' data against which 'actual energy consumptions' data are compared and energy efficiency evaluated. Through the building energy management system, the energy manager is able to (a) have 3D visualization (BIM model) of each room, in which the occupancy and equipment status detected by the sensors and the electricity consumptions data logged are displayed constantly; (b) perform real time energy consumption analysis to compare the actual and standard energy consumption profiles of a space; (c) obtain energy consumption anomaly detection warnings on certain rooms so that energy management corrective actions can be further taken (data mining technique is employed to analyze the relation between space occupancy pattern with current space equipment setting to indicate an anomaly, such as when appliances turn on without occupancy); and (d) perform historical energy consumption analysis to review monthly and annually energy consumption profiles and compare them against historical energy profiles. The BIM-EMSS was further implemented in a research lab in the Department of Architecture of NTUST in Taiwan and implementation results presented to illustrate how it can be used to assist individual departments within universities in their energy management tasks.

Keywords: Sensor, electricity sub-meters, database, energy anomaly detection.

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Authors: J. Salaenoi, A. Thongpan, M. Mingmuang

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The activities of alkaline phosphatase and Ca2+ATPase in mud crab (Scylla serrata) collected from a soft-shell crab farm in Chantaburi Province, Thailand, in several stages of molting cycle were observed. The results showed that the activity of alkaline phosphatase in gill after molting was highly significant (p<0.05) comparing to those at intermolt and premolt stages. The activity profiles of alkaline phosphatase in integument and haemolymph were similar showing a decrease from intermolt to 2- week premolt stage and increased during 2-day premolt to 6-h postmolt stage before dropping at 7-day postmolt stage, while this enzyme in the gill was quite low at intermolt and premolt stages. For Ca2+ATPase, the activity profiles in gill and integument corresponded to the molting variation, especially the activities increased during 5-7 day postmolt stage were at highly significant levels (p<0.05) comparing to those at premolt and early postmolt stages. The highest activity of Ca2+ATPase in haemolymph was found at 2-week premolt stage (p<0.05). Changes in alkaline phosphatase and Ca2+ATPase activities over the molting cycle clearly indicated their active functions on calcification.

Keywords: Scylla serrata, molting cycle, alkaline phosphatase, Ca2+ATPase

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Authors: Shyam Kumar, Nannuri Srinivasulu, Ashok Khanna

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Bubble columns have a variety of applications in absorption, bio-reactions, catalytic slurry reactions, and coal liquefaction; because they are simple to operate, provide good heat and mass transfer, having less operational cost. The use of Computational Fluid Dynamics (CFD) for bubble column becomes important, since it can describe the fluid hydrodynamics on both local and global scale. Euler- Euler two-phase fluid model has been used to simulate two-phase (air and water) transient up-flow in bubble column (15cm diameter) using FLUENT6.3. These simulations and experiments were operated over a range of superficial gas velocities in the bubbly flow and churn turbulent regime (1 to16 cm/s) at ambient conditions. Liquid velocity was varied from 0 to 16cm/s. The turbulence in the liquid phase is described using the standard k-ε model. The interactions between the two phases are described through drag coefficient formulations (Schiller Neumann). The objectives are to validate CFD simulations with experimental data, and to obtain grid-independent numerical solutions. Quantitatively good agreements are obtained between experimental data for hold-up and simulation values. Axial liquid velocity profiles and gas holdup profiles were also obtained for the simulation.

Keywords: Bubble column, Computational fluid dynamics, Gas holdup profile, k-ε model.

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Authors: S. M. Ali, A. Salam Khan, A. U. Khan, M. Tariq, M. S. Hussain, B. A. Abbasi, I. Hussain, U. Farid

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Environment and surrounding plays a pivotal rule in structuring life-style of the consumers. Living standards intern effect the energy consumption of the consumers. In smart grid paradigm, climate drifts, weather parameter and green environmental directly relates to the energy profiles of the various consumers, such as residential, commercial and industrial. Considering above factors helps policy in shaping utility load curves and optimal management of demand and supply. Thus, there is a pressing need to develop correlation models of load and weather parameters and critical analysis of the factors effecting energy profiles of smart grid consumers. In this paper, we elaborated various environment and weather parameter factors effecting demand of consumers. Moreover, we developed correlation models, such as Pearson, Spearman, and Kendall, an inter-relation between dependent (load) parameter and independent (weather) parameters. Furthermore, we validated our discussion with real-time data of Texas State. The numerical simulations proved the effective relation of climatic drifts with energy consumption of smart grid consumers.

Keywords: Climatic drifts, correlation analysis, energy consumption, smart grid, weather parameter.

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Authors: N. Siva Shanmugam, G. Buvanashekaran, K. Sankaranarayanasamy

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In this research work, investigations are carried out on Continuous Wave (CW) Nd:YAG laser welding system after preliminary experimentation to understand the influencing parameters associated with laser welding of AISI 304. The experimental procedure involves a series of laser welding trials on AISI 304 stainless steel sheets with various combinations of process parameters like beam power, beam incident angle and beam incident angle. An industrial 2 kW CW Nd:YAG laser system, available at Welding Research Institute (WRI), BHEL Tiruchirappalli, is used for conducting the welding trials for this research. After proper tuning of laser beam, laser welding experiments are conducted on AISI 304 grade sheets to evaluate the influence of various input parameters on weld bead geometry i.e. bead width (BW) and depth of penetration (DOP). From the laser welding results, it is noticed that the beam power and welding speed are the two influencing parameters on depth and width of the bead. Three dimensional finite element simulation of high density heat source have been performed for laser welding technique using finite element code ANSYS for predicting the temperature profile of laser beam heat source on AISI 304 stainless steel sheets. The temperature dependent material properties for AISI 304 stainless steel are taken into account in the simulation, which has a great influence in computing the temperature profiles. The latent heat of fusion is considered by the thermal enthalpy of material for calculation of phase transition problem. A Gaussian distribution of heat flux using a moving heat source with a conical shape is used for analyzing the temperature profiles. Experimental and simulated values for weld bead profiles are analyzed for stainless steel material for different beam power, welding speed and beam incident angle. The results obtained from the simulation are compared with those from the experimental data and it is observed that the results of numerical analysis (FEM) are in good agreement with experimental results, with an overall percentage of error estimated to be within ±6%.

Keywords: Laser welding, Butt weld, 304 SS, FEM.

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Authors: Yessine Hadj Kacem, Adel Mahfoudhi, Hedi Tmar, Mohamed Abid

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Unified Modeling Language (UML) extensions for real time embedded systems (RTES) co-design, are taking a growing interest by a great number of industrial and research communities. The extension mechanism is provided by UML profiles for RTES. It aims at improving an easily-understood method of system design for non-experts. On the other hand, one of the key items of the co- design methods is the Hardware/Software partitioning and scheduling tasks. Indeed, it is mandatory to define where and when tasks are implemented and run. Unfortunately the main goals of co-design are not included in the usual practice of UML profiles. So, there exists a need for mapping used models to an execution platform for both schedulability test and HW/SW partitioning. In the present work, test schedulability and design space exploration are performed at an early stage. The proposed approach adopts Model Driven Engineering MDE. It starts from UML specification annotated with the recent profile for the Modeling and Analysis of Real Time Embedded systems MARTE. Following refinement strategy, transformation rules allow to find a feasible schedule that satisfies timing constraints and to define where tasks will be implemented. The overall approach is experimented for the design of a football player robot application.

Keywords: MDE, UML profile, scheduling analysis, HW/SW partitioning.

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Authors: S. Chiali, Z.Eberrichi, M.Malki

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The number of framework conceived for e-learning constantly increase, unfortunately the creators of learning materials and educational institutions engaged in e-formation adopt a “proprietor" approach, where the developed products (courses, activities, exercises, etc.) can be exploited only in the framework where they were conceived, their uses in the other learning environments requires a greedy adaptation in terms of time and effort. Each one proposes courses whose organization, contents, modes of interaction and presentations are unique for all learners, unfortunately the latter are heterogeneous and are not interested by the same information, but only by services or documents adapted to their needs. Currently the new tendency for the framework conceived for e-learning, is the interoperability of learning materials, several standards exist (DCMI (Dublin Core Metadata Initiative)[2], LOM (Learning Objects Meta data)[1], SCORM (Shareable Content Object Reference Model)[6][7][8], ARIADNE (Alliance of Remote Instructional Authoring and Distribution Networks for Europe)[9], CANCORE (Canadian Core Learning Resource Metadata Application Profiles)[3]), they converge all to the idea of learning objects. They are also interested in the adaptation of the learning materials according to the learners- profile. This article proposes an approach for the composition of courses adapted to the various profiles (knowledge, preferences, objectives) of learners, based on two ontologies (domain to teach and educational) and the learning objects.

Keywords: Adaptive educational hypermedia systems (AEHS), E-learning, Learner's model, Learning objects, Metadata, Ontology.

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Authors: Valentina L. Kouznetsova, Jonathan W. Wang, Igor F. Tsigelny

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Metabolomics has become a rising field of research for various diseases, particularly cancer. Increases or decreases in metabolite concentrations in the human body are indicative of various cancers. Further elucidation of metabolic pathways and their significance in cancer research may greatly spur medicinal discovery. We analyzed the metabolomics profiles of lung cancer. Thirty-three metabolites were selected as significant. These metabolites are involved in 37 metabolic pathways delivered by MetaboAnalyst software. The top pathways are glyoxylate and dicarboxylate pathway (its hubs are formic acid and glyoxylic acid) along with Citrate cycle pathway followed by Taurine and hypotaurine pathway (the hubs in the latter are taurine and sulfoacetaldehyde) and Glycine, serine, and threonine pathway (the hubs are glycine and L-serine). We studied interactions of the metabolites with the proteins involved in cancer-related signaling networks, and developed an approach to metabolomics biomarker use in cancer diagnostics. Our analysis showed that a significant part of lung-cancer-related metabolites interacts with main cancer-related signaling pathways present in this network: PI3K–mTOR–AKT pathway, RAS–RAF–ERK1/2 pathway, and NFKB pathway. These results can be employed for use of metabolomics profiles in elucidation of the related cancer proteins signaling networks.

Keywords: Cancer, metabolites, metabolic pathway, signaling pathway.

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Authors: Maha ALjohani, James Blustein

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Communicating users' needs, goals and problems help designers and developers overcome challenges faced by end users. Personas are used to represent end users’ needs. In our research, creating personas allowed the following questions to be answered: Who are the potential user groups? What do they want to achieve by using the service? What are the problems that users face? What should the service provide to them? To develop realistic personas, we conducted a focus group discussion with undergraduate and graduate students and also interviewed a university librarian. The personas were created to help evaluating the Institutional Repository that is based on the DSpace system. The profiles helped to communicate users' needs, abilities, tasks, and problems, and the task scenarios used in the heuristic evaluation were based on these personas. Four personas resulted of a focus group discussion with undergraduate and graduate students and from interviewing a university librarian. We then used these personas to create focused task-scenarios for a heuristic evaluation on the system interface to ensure that it met users' needs, goals, problems and desires. In this paper, we present the process that we used to create the personas that led to devise the task scenarios used in the heuristic evaluation as a follow up study of the DSpace university repository.

Keywords: Heuristic Evaluation, Institutional Repositories, User Experience, Human Computer Interaction, User Profiles, Personas, Task Scenarios, Heuristics.

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Authors: Pramote Paengkoum, Y. Han , S. Traiyakun, J. Khotsakdee, S. Paengkoum

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This experiment was performed with the purpose of investigating effect of additional blend of probiotics Saccharomyces cerevisiae and Lactobacillus acidophilus on plasma fatty acid profiles particularly conjugated linoleic acid (CLA) in growing goats fed corn silage, and selected the optimal levels of the probiotics for further study. Twenty-four growing crossbred (Thai native x Anglo-Nubian) goats that weighed (14.2 ± 2.3) kg, aged about 6 months, were purchased and allocated to 4 treatments according to Randomized Complete Block Design (RCBD) with 6 goats in each treatment. The blocks were made by weight into heavy, medium, and light goats and each of the treatments contained two goats from each of the blocks. In the mean time, ruminal average pH unaffected, but the NH3-N and also plasma urea nitrogen (p<0.05), total volatile fatty acid (p>0.05) were raised, but propionic proportion (p<0.05) and butyric proportion (p>0.05) were reduced in concurrent with raise of acetic proportion and resultantly C2:C3 ratio (p>0.05). On plasma fatty acid profiles, total saturated fatty acids (p>0.05) was increased, and contrasted with decrease of C15:0 (p<0.01), C16:0 (p>0.05), and C18-C22 polyunsaturated fatty acids (p<0.05 or p<0.01). In addition, the experiment proved that the supplemented probiotics was in force for heightening CLA (p<0.01); for raising desirable fatty acids (p<0.05); for reducing ratio of PUFA: SFA (p>0.05) and for raising ratio of n6:n3 (p<0.05).

Keywords: Probiotic, conjugated linoleic acid, plasma fattyacid, goats

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Authors: Taposh Roy, Dipankar Choudhury, Belinda Pingguan-Murphy

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The tribological outcomes of micro dent are found to be outstanding in many engineering and natural surfaces. Ceramic (Al₂O₃) is considered one of the most potential material to bearing surfaces particularly, artificial hip or knee implant. A well-defined micro dent on alumina oxide interface could further decrease friction and wear rate, thus increase their stability and durability. In this study we fabricated circular micro dent surface profiles (Dia: 400µm, Depth 20µm, P: 1.5mm; Dia: 400µm, Depth 20µm, P: 2mm) on pure Al₂O₃ (99.6%) substrate by using a micro tool machines. A preliminary tribological experiment was carried out to compare friction coefficient of these fabricated dent surfaces with that of non-textured surfaces. The experiment was carried on well know pin-on-disk specimens while other experimental parameters such as hertz pressure, speed, lubrication, and temperature were maintained to standard of simulated hip joints condition. The experiment results revealed that micro dent surface texture reduced 15%, 8% and 4% friction coefficient under 0.132,0.162, 0.187 GPa contact pressure respectively. Since this is a preliminary tribological study, we will pursue further experiments considering higher ranges of dent profiles and longer run experiments. However, the preliminary results confirmed the suitability of fabricating dent profile to ceramic surfaces by using micro tooling, and also their improved tribological performance in simulated hip joints.

Keywords: Micro dent, tribology, ceramic on ceramic hipjoints.

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Authors: Muhibul Haque Bhuyan, Farseem Mannan Mohammedy, Quazi Deen Mohd Khosru

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This paper presents the doping profile measurement and characterization technique for the pocket implanted nano scale n-MOSFET. Scanning capacitance microscopy and atomic force microscopy have been used to image the extent of lateral dopant diffusion in MOS structures. The data are capacitance vs. voltage measurements made on a nano scale device. The technique is nondestructive when imaging uncleaved samples. Experimental data from the published literature are presented here on actual, cleaved device structures which clearly indicate the two-dimensional dopant profile in terms of a spatially varying modulated capacitance signal. Firstorder deconvolution indicates the technique has much promise for the quantitative characterization of lateral dopant profiles. The pocket profile is modeled assuming the linear pocket profiles at the source and drain edges. From the model, the effective doping concentration is found to use in modeling and simulation results of the various parameters of the pocket implanted nano scale n-MOSFET. The potential of the technique to characterize important device related phenomena on a local scale is also discussed.

Keywords: Linear Pocket Profile, Pocket Implanted n-MOSFET, Scanning Capacitance Microscope, Atomic Force Microscope.

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Authors: Seyeon Park, Mi Jang

Abstract:

Tumor cells have an invasive and metastatic phenotype that is the main cause of death for cancer patients. Tumor establishment and penetration consists of a series of complex processes involving multiple changes in gene expression. In this study, intraperitoneal administration of a high concentration of ascorbic acid inhibited tumor establishment and decreased tumor mass in BALB/C mice implanted with S-180 sarcoma cancer cells. To identify proteins involved in the ascorbic acid-mediated inhibition of tumor progression, changes in the tumor proteome associated with ascorbic acid treatment of BALB/C mice implanted with S-180 were investigated using two-dimensional gel electrophoresis and mass spectrometry. Twenty protein spots were identified whose expression was different between control and ascorbic acid treatment groups.

Keywords: Ascorbic acid, Proteomic analysis, S-180 implantedBALB/C mouse

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Authors: Rubén Bãnos, José Arcos, Oscar Bautista, Federico Méndez

Abstract:

The Oscillatory electroosmotic flow (OEOF) in power law fluids through a microchannel is studied numerically. A time-dependent external electric field (AC) is suddenly imposed at the ends of the microchannel which induces the fluid motion. The continuity and momentum equations in the x and y direction for the flow field were simplified in the limit of the lubrication approximation theory (LAT), and then solved using a numerical scheme. The solution of the electric potential is based on the Debye-H¨uckel approximation which suggest that the surface potential is small,say, smaller than 0.025V and for a symmetric (z : z) electrolyte. Our results suggest that the velocity profiles across the channel-width are controlled by the following dimensionless parameters: the angular Reynolds number, Reω, the electrokinetic parameter, ¯κ, defined as the ratio of the characteristic length scale to the Debye length, the parameter λ which represents the ratio of the Helmholtz-Smoluchowski velocity to the characteristic length scale and the flow behavior index, n. Also, the results reveal that the velocity profiles become more and more non-uniform across the channel-width as the Reω and ¯κ are increased, so oscillatory OEOF can be really useful in micro-fluidic devices such as micro-mixers.

Keywords: Oscillatory electroosmotic flow, Non-Newtonian fluids, power-law model, low zeta potentials.

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Authors: Surajit Debnath, Soma Addya

Abstract:

Human genome is not only the evolutionary summation of all advantageous events, but also houses lesions of deleterious foot prints. A single gene mutation sometimes may express multiple consequences in numerous tissues and a linear relationship of the genotype and the phenotype may often be obscure. ß Thalassemia minor, a transfusion independent mild anaemia, coupled with environment among other factors may articulate into phenotypic pleotropy with Hypocholesterolemia, Vitamin D deficiency, Tissue hypoxia, Hyper-parathyroidism and Psychological alterations. Occurrence of Pancreatic insufficiency, resultant steatorrhoea, Vitamin-D (25-OH) deficiency (13.86 ngm/ml) with Hypocholesterolemia (85mg/dl) in a 30 years old male ß Thal-minor patient (Hemoglobin 11mg/dl with Fetal Hemoglobin 2.10%, Hb A2 4.60% and Hb Adult 84.80% and altered Hemogram) with increased Para thyroid hormone (62 pg/ml) & moderate Serum Ca+2 (9.5mg/ml) indicate towards a cascade of phenotypic pleotropy where the ß Thalassemia mutation ,be it in the 5’ cap site of the mRNA , differential splicing etc in heterozygous state is effecting several metabolic pathways. Compensatory extramedulary hematopoiesis may not coped up well with the stressful life style of the young individual and increased erythropoietic stress with high demand for cholesterol for RBC membrane synthesis may have resulted in Hypocholesterolemia.Oxidative stress and tissue hypoxia may have caused the pancreatic insufficiency, leading to Vitamin D deficiency. This may in turn have caused the secondary hyperparathyroidism to sustain serum Calcium level. Irritability and stress intolerance of the patient was a cumulative effect of the vicious cycle of metabolic compromises. From these findings we propose that the metabolic deficiencies in the ß Thalassemia mutations may be considered as the phenotypic display of the pleotropy to explain the genetic epidemiology. According to the recommendations from the NIH Workshop on Gene-Environment Interplay in Common Complex Diseases: Forging an Integrative Model, study design of observations should be informed by gene-environment hypotheses and results of a study (genetic diseases) should be published to inform future hypotheses. Variety of approaches is needed to capture data on all possible aspects, each of which is likely to contribute to the etiology of disease. Speakers also agreed that there is a need for development of new statistical methods and measurement tools to appraise information that may be missed out by conventional method where large sample size is needed to segregate considerable effect. A meta analytic cohort study in future may bring about significant insight on to the title comment.

Keywords: Genetic disease, Genetic epidemiology, Heterozygous, Phenotype, Pleotropy, ß Thalassemia minor, Metabolic compromises.

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Authors: Ibrahim Yakubu Seini, Oluwole Daniel Makinde

Abstract:

MHD chemically reacting viscous fluid flow towards a vertical surface with slip and convective boundary conditions has been conducted. The temperature and the chemical species concentration of the surface and the velocity of the external flow are assumed to vary linearly with the distance from the vertical surface. The governing differential equations are modeled and transformed into systems of ordinary differential equations, which are then solved numerically by a shooting method. The effects of various parameters on the heat and mass transfer characteristics are discussed. Graphical results are presented for the velocity, temperature, and concentration profiles whilst the skin-friction coefficient and the rate of heat and mass transfers near the surface are presented in tables and discussed. The results revealed that increasing the strength of the magnetic field increases the skin-friction coefficient and the rate of heat and mass transfers toward the surface. The velocity profiles are increased towards the surface due to the presence of the Lorenz force, which attracts the fluid particles near the surface. The rate of chemical reaction is seen to decrease the concentration boundary layer near the surface due to the destructive chemical reaction occurring near the surface.

Keywords: Boundary layer, surface slip, MHD flow, chemical reaction, heat transfer, mass transfer.

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Authors: Kasthurirangan Gopalakrishnan, Marshall R. Thompson, Anshu Manik

Abstract:

This paper describes the use of artificial neural networks (ANN) for predicting non-linear layer moduli of flexible airfield pavements subjected to new generation aircraft (NGA) loading, based on the deflection profiles obtained from Heavy Weight Deflectometer (HWD) test data. The HWD test is one of the most widely used tests for routinely assessing the structural integrity of airport pavements in a non-destructive manner. The elastic moduli of the individual pavement layers backcalculated from the HWD deflection profiles are effective indicators of layer condition and are used for estimating the pavement remaining life. HWD tests were periodically conducted at the Federal Aviation Administration-s (FAA-s) National Airport Pavement Test Facility (NAPTF) to monitor the effect of Boeing 777 (B777) and Beoing 747 (B747) test gear trafficking on the structural condition of flexible pavement sections. In this study, a multi-layer, feed-forward network which uses an error-backpropagation algorithm was trained to approximate the HWD backcalculation function. The synthetic database generated using an advanced non-linear pavement finite-element program was used to train the ANN to overcome the limitations associated with conventional pavement moduli backcalculation. The changes in ANN-based backcalculated pavement moduli with trafficking were used to compare the relative severity effects of the aircraft landing gears on the NAPTF test pavements.

Keywords: Airfield pavements, ANN, backcalculation, newgeneration aircraft

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