Search results for: Biological sequence

Authors: Yi-Chun Chang, Jian-Wei Li

Abstract:

Web-based cooperative learning focuses on (1) the interaction and the collaboration of community members, and (2) the sharing and the distribution of knowledge and expertise by network technology to enhance learning performance. Numerous research literatures related to web-based cooperative learning have demonstrated that cooperative scripts have a positive impact to specify, sequence, and assign cooperative learning activities. Besides, literatures have indicated that role-play in web-based cooperative learning environments enhances two or more students to work together toward the completion of a common goal. Since students generally do not know each other and they lack the face-to-face contact that is necessary for the negotiation of assigning group roles in web-based cooperative learning environments, this paper intends to further extend the application of genetic algorithm (GA) and propose a GA-based algorithm to tackle the problem of role assignment in web-based cooperative learning environments, which not only saves communication costs but also reduces conflict between group members in negotiating role assignments.

Keywords: genetic algorithm (GA), role assignment, role-play; web-based cooperative learning.

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Authors: Kong Fah Tee, Lutfor Rahman Khan, Hongshuang Li

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An advanced Monte Carlo simulation method, called Subset Simulation (SS) for the time-dependent reliability prediction for underground pipelines has been presented in this paper. The SS can provide better resolution for low failure probability level with efficient investigating of rare failure events which are commonly encountered in pipeline engineering applications. In SS method, random samples leading to progressive failure are generated efficiently and used for computing probabilistic performance by statistical variables. SS gains its efficiency as small probability event as a product of a sequence of intermediate events with larger conditional probabilities. The efficiency of SS has been demonstrated by numerical studies and attention in this work is devoted to scrutinise the robustness of the SS application in pipe reliability assessment. It is hoped that the development work can promote the use of SS tools for uncertainty propagation in the decision-making process of underground pipelines network reliability prediction.

Keywords: Underground pipelines, Probability of failure, Reliability and Subset Simulation.

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Authors: Abdullah Faqihi, John Hedley

Abstract:

Biosensors play a significant role in the healthcare sectors, scientific and technological progress. Developing electrodes that are easy to manufacture and deliver better electrochemical performance is advantageous for diagnostics and biosensing. They can be implemented extensively in various analytical tasks such as drug discovery, food safety, medical diagnostics, process controls, security and defence, in addition to environmental monitoring. Development of biosensors aims to create high-performance electrochemical electrodes for diagnostics and biosensing. A biosensor is a device that inspects the biological and chemical reactions generated by the biological sample. A biosensor carries out biological detection via a linked transducer and transmits the biological response into an electrical signal; stability, selectivity, and sensitivity are the dynamic and static characteristics that affect and dictate the quality and performance of biosensors. In this research, a developed experimental study for laser scribing technique for graphene oxide inside a vacuum chamber for processing of graphene oxide is presented. The processing of graphene oxide (GO) was achieved using the laser scribing technique. The effect of the laser scribing on the reduction of GO was investigated under two conditions: atmosphere and vacuum. GO solvent was coated onto a LightScribe DVD. The laser scribing technique was applied to reduce GO layers to generate rGO. The micro-details for the morphological structures of rGO and GO were visualised using scanning electron microscopy (SEM) and Raman spectroscopy so that they could be examined. The first electrode was a traditional graphene-based electrode model, made under normal atmospheric conditions, whereas the second model was a developed graphene electrode fabricated under a vacuum state using a vacuum chamber. The purpose was to control the vacuum conditions, such as the air pressure and the temperature during the fabrication process. The parameters to be assessed include the layer thickness and the continuous environment. Results presented show high accuracy and repeatability achieving low cost productivity.

Keywords: Laser scribing, LightScribe DVD, graphene oxide, scanning electron microscopy.

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Authors: Junfeng Song, Xianshu Luo, Qing Fang, Lianxi Jia, Xiaoguang Tu, Tsung-Yang Liow, Mingbin Yu, Guo-Qiang Lo

Abstract:

We demonstrate a 1×4 coarse wavelength division-multiplexing (CWDM) planar concave grating multiplexer/demultiplexer and its application in re-configurable optical add/drop multiplexer (ROADM) system in silicon-on-insulator substrate. The wavelengths of the demonstrated concave grating multiplexer align well with the ITU-T standard. We demonstrate a prototype of ROADM comprising two such concave gratings and four wide-band thermo-optical MZI switches. Undercut technology which removes the underneath silicon substrate is adopted in optical switches in order to minimize the operation power. For all the thermal heaters, the operation voltage is smaller than 1.5 V, and the switch power is ~2.4 mW. High throughput pseudorandom binary sequence (PRBS) data transmission with up to 100 Gb/s is demonstrated, showing the high-performance ROADM functionality.

Keywords: ROADM, Optical switch, low power consumption, Integrated devices.

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Authors: Seong-Bae Park, Hee-Geun Yoon

Abstract:

It is an important task in Korean-English machine translation to classify the gender of names correctly. When a sentence is composed of two or more clauses and only one subject is given as a proper noun, it is important to find the gender of the proper noun for correct translation of the sentence. This is because a singular pronoun has a gender in English while it does not in Korean. Thus, in Korean-English machine translation, the gender of a proper noun should be determined. More generally, this task can be expanded into the classification of the general Korean names. This paper proposes a statistical method for this problem. By considering a name as just a sequence of syllables, it is possible to get a statistics for each name from a collection of names. An evaluation of the proposed method yields the improvement in accuracy over the simple looking-up of the collection. While the accuracy of the looking-up method is 64.11%, that of the proposed method is 81.49%. This implies that the proposed method is more plausible for the gender classification of the Korean names.

Keywords: machine translation, natural language processing, gender of proper nouns, statistical method

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Authors: Ahmed Mohsen, Yoshinobu Kitamura, Katsuyuki Shimizu

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The improvement of irrigation systems in the Nile Delta is one of the most important attempts in Egypt to implement more effective irrigation technology by improving the existing irrigation networks. Demand delivery system in the existing irrigation network is using of mechanical gates structures to automatically divert water from one portion of an agricultural field to another in the desired amount and sequence. This paper discusses evaluating main irrigation networks system under the government managed before and after improvement systems in the Nile Delta. The overall results indicate that policy of using the demand delivery concept through irrigation networks is successful by improving water delivery performance among them than the rotation delivery concept that used before. It is provided fair share of water delivery among irrigation districts and available water in the end of irrigation network, although this system located in an end of irrigation networks in the Nile Delta.

Keywords: Automation system, Irrigation district, Rotation system, Water delivery performance

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Authors: Ahmad Manbohi, Seyyed Hamid Ahmadi

Abstract:

A low-cost paper-based microfluidic device (PAD) for the multiplex electrochemical determination of glucose, uric acid, and dopamine in biological fluids was developed. Using wax printing, PAD containing a central zone, six channels, and six detection zones was fabricated, and the electrodes were printed on detection zones using pre-made electrodes template. For each analyte, two detection zones were used. The carbon working electrode was coated with chitosan-BSA (and enzymes for glucose and uric acid). To detect glucose and uric acid, enzymatic reactions were employed. These reactions involve enzyme-catalyzed redox reactions of the analytes and produce free electrons for electrochemical measurement. Calibration curves were linear (R^² > 0.980) in the range of 0-80 mM for glucose, 0.09–0.9 mM for dopamine, and 0–50 mM for uric acid, respectively. Blood samples were successfully analyzed by the proposed method.

Keywords: Multiplex, microfluidic paper-based electrochemical biosensors, biomarkers, biological fluids.

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Authors: Mohammadi K., Ghalavand A., Aghaalikhani M

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In order to evaluation the effects of natural, biological and chemical fertilizers on grain yield and chickpea quality, field experiments were carried out in 2007 and 2008 growing seasons. In this research the effects of different organic, chemical and biological fertilizers were investigated on grain yield and quality of chickpea. Experimental units were arranged in split-split plots based on randomized complete blocks with three replications. The highest amounts of yield and yield components were obtained in G1×N5 interaction. Significant increasing of N, P, K, Fe and Mg content in leaves and grains emphasized on superiority of mentioned treatment because each one of these nutrients has an approved role in chlorophyll synthesis and photosynthesis ability of the crop. The combined application of compost, farmyard manure and chemical phosphorus (N5) had the best grain quality due to high protein, starch and total sugar contents, low crude fiber and reduced cooking time.

Keywords: soil fertility, grain yield, chickpea, natural resources.

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Authors: Monika Jain, Shikhar Puri, Shivali Unishree

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This paper presents the ‘Eye Ball Motion Controlled Wheelchair using IR Sensors’ for the elderly and differently abled people. In this eye tracking based technology, three Proximity Infrared (IR) sensor modules are mounted on an eye frame to trace the movement of the iris. Since, IR sensors detect only white objects; a unique sequence of digital bits is generated corresponding to each eye movement. These signals are then processed via a micro controller IC (PIC18F452) to control the motors of the wheelchair. The potential and efficiency of previously developed rehabilitation systems that use head motion, chin control, sip-n-puff control, voice recognition, and EEG signals variedly have also been explored in detail. They were found to be inconvenient as they served either limited usability or non-affordability. After multiple regression analyses, the proposed design was developed as a cost-effective, flexible and stream-lined alternative for people who have trouble adopting conventional assistive technologies.

Keywords: Eye tracking technology, Intelligent wheelchair, IR module, rehabilitation technology.

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Authors: M. Jändel

Abstract:

A new conceptual architecture for low-level neural pattern recognition is presented. The key ideas are that the brain implements support vector machines and that support vectors are represented as memory patterns in competitive queuing memories. A binary classifier is built from two competitive queuing memories holding positive and negative valence training examples respectively. The support vector machine classification function is calculated in synchronized evaluation cycles. The kernel is computed by bisymmetric feed-forward networks feed by sensory input and by competitive queuing memories traversing the complete sequence of support vectors. Temporary summation generates the output classification. It is speculated that perception apparatus in the brain reuses structures that have evolved for enabling fluent execution of prepared action sequences so that pattern recognition is built on internalized motor programmes.

Keywords: Competitive queuing model, Olfactory system, Pattern recognition, Support vector machine, Thalamus

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Authors: Pablo Enrique Sartor Del Giudice

Abstract:

Penalty shootouts often decide the outcome of important soccer matches. Although usually referred to as ”lotteries”, there is evidence that some national teams and clubs consistently perform better than others. The outcomes are therefore not explained just by mere luck, and therefore there are ways to improve the average performance of players, naturally at the expense of some sort of effort. In this article we study the payoff of player performance improvements in terms of the performance of the team as a whole. To do so we develop an analytical model with static individual performances, as well as Monte Carlo models that take into account the known influence of partial score and round number on individual performances. We find that within a range of usual values, the team performance improves above 70% faster than individual performances do. Using these models, we also estimate that the new ABBA penalty shootout ordering under test reduces almost all the known bias in favor of the first-shooting team under the current ABAB system.

Keywords: Football, penalty shootouts, Montecarlo simulation, ABBA.

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Authors: R. Santhosh, T. Ravichandran

Abstract:

This paper evaluates the accrual based scheduling for cloud in single and multi-resource system. Numerous organizations benefit from Cloud computing by hosting their applications. The cloud model provides needed access to computing with potentially unlimited resources. Scheduling is tasks and resources mapping to a certain optimal goal principle. Scheduling, schedules tasks to virtual machines in accordance with adaptable time, in sequence under transaction logic constraints. A good scheduling algorithm improves CPU use, turnaround time, and throughput. In this paper, three realtime cloud services scheduling algorithm for single resources and multiple resources are investigated. Experimental results show Resource matching algorithm performance to be superior for both single and multi-resource scheduling when compared to benefit first scheduling, Migration, Checkpoint algorithms.

Keywords: Cloud computing, Scheduling, Migration, Checkpoint, Resource Matching.

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Authors: G.Durai, N.Rajamohan, C.Karthikeyan, M.Rajasimman

Abstract:

In this study, aerobic digestion of tannery industry wastewater was carried out using mixed culture obtained from common effluent treatment plant treating tannery wastewater. The effect of pH, temperature, inoculum concentration, agitation speed and initial substrate concentration on the reduction of organic matters were found. The optimum conditions for COD reduction was found to be pH - 7 (60%), temperature - 30ÔùªC (61%), inoculum concentration - 2% (61%), agitation speed - 150rpm (65%) and initial substrate concentration - 1560 mg COD/L (74%). Kinetics studies were carried by using Monod model, First order, Diffusional model and Singh model. From the results it was found that the Monod model suits well for the degradation of tannery wastewater using mixed microbial consortium.

Keywords: Tannery, Wastewater, Biological treatment, Aerobic, Mixed culture, Kinetics.

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Authors: Ahmed A. Hussain, Abbas A. Mohammed, Heba. H. Ibrahim, Amir H. Abbas

Abstract:

In this study the extracts of the Iraqi herb Tribulus terrestris (Al-Hassage or Al-Kutub) was done by using of polar and non polar solvents, then the biological activity of these extractants was studied in three fields, First, the antibacterial activity (in vitro) on gram positive bacteria (Staphylococcus aureus), and gram negative bacteria (E. coli, Proteus vulgaris, Pseudomonas aerugiuosa, and Klebsiella), all extracts showed considerable activity against all bacteria. Second, the effect of extracts on free serum testosterone level in male mice (in vivo), the alcoholic, and acetonitrilic extracts showed significant (P < 0.05) increase in free serum testosterone level, and we found that the extracts contained compounds with less genotoxic effects in mice germ cells. 3rd, was to study the effect of methanolic extract of T. terrestris in diabetes management.

Keywords: Genotoxic, germ cells, tribulus terrestris, testosterone.

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Authors: M. Naresh Kumar, Abhijit Mitra, C. Ardil

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A fast adaptive Tomlinson Harashima (T-H) precoder structure is presented for indoor wireless communications, where the channel may vary due to rotation and small movement of the mobile terminal. A frequency-selective slow fading channel which is time-invariant over a frame is assumed. In this adaptive T-H precoder, feedback coefficients are updated at the end of every uplink frame by using system identification technique for channel estimation in contrary with the conventional T-H precoding concept where the channel is estimated during the starting of the uplink frame via Wiener solution. In conventional T-H precoder it is assumed the channel is time-invariant in both uplink and downlink frames. However assuming the channel is time-invariant over only one frame instead of two, the proposed adaptive T-H precoder yields better performance than conventional T-H precoder if the channel is varied in uplink after receiving the training sequence.

Keywords: Tomlinson-Harashima precoder, Adaptive channel estimation, Indoor wireless communication, Bit error rate.

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Authors: Nermin A. Mohamed, Mohamed F. Madkour

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We address the problem of joint beamforming and multipath channel parameters estimation in Wideband Code Division Multiple Access (WCDMA) communication systems that employ Multiple-Access Interference (MAI) suppression techniques in the uplink (from mobile to base station). Most of the existing schemes rely on time multiplex a training sequence with the user data. In WCDMA, the channel parameters can also be estimated from a code multiplexed common pilot channel (CPICH) that could be corrupted by strong interference resulting in a bad estimate. In this paper, we present new methods to combine interference suppression together with channel estimation when using multiple receiving antennas by using adaptive signal processing techniques. Computer simulation is used to compare between the proposed methods and the existing conventional estimation techniques.

Keywords: Adaptive arrays, channel estimation, interferencecancellation, wideband code division multiple access (WCDMA).

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Authors: Jianjun Yuan, Changjun Jiang

Abstract:

Pairwise testing, which requires that every combination of valid values of each pair of system factors be covered by at lease one test case, plays an important role in software testing since many faults are caused by unexpected 2-way interactions among system factors. Although meta-heuristic strategies like simulated annealing can generally discover smaller pairwise test suite, they may cost more time to perform search, compared with greedy algorithms. We propose a new method, improved Extremal Optimization (EO) based on the Bak-Sneppen (BS) model of biological evolution, for constructing pairwise test suites and define fitness function according to the requirement of improved EO. Experimental results show that improved EO gives similar size of resulting pairwise test suite and yields an 85% reduction in solution time over SA.

Keywords: Covering Arrays, Extremal Optimization, Simulated Annealing, Software Testing.

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Authors: K. Kasiri, M. J. Dehghani

Abstract:

In this paper we propose a blind algorithm for peakto- average power ratio (PAPR) reduction in OFDM systems, based on selected mapping (SLM) algorithm as a distortionless method. The main drawback of the conventional SLM technique is the need for transmission of several side information bits, for each data block, which results in loss in data rate transmission. In the proposed method some special number of carriers in the OFDM frame is reserved to be rotated with one of the possible phases according to the number of phase sequence blocks in SLM algorithm. Reserving some limited number of carriers wont effect the reduction in PAPR of OFDM signal. Simulation results show using ML criteria at the receiver will lead to the same system-performance as the conventional SLM algorithm, while there is no need to send any side information to the receiver.

Keywords: Orthogonal Frequency Division Multiplexing(OFDM), Peak-to-Average Power Ratio (PAPR), Selected Mapping(SLM), Blind SLM (BSLM).

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Authors: Michal Mardiak, Jaroslav Polec

Abstract:

In this paper we proposed comparison of four content based objective metrics with results of subjective tests from 80 video sequences. We also include two objective metrics VQM and SSIM to our comparison to serve as “reference” objective metrics because their pros and cons have already been published. Each of the video sequence was preprocessed by the region recognition algorithm and then the particular objective video quality metric were calculated i.e. mutual information, angular distance, moment of angle and normalized cross-correlation measure. The Pearson coefficient was calculated to express metrics relationship to accuracy of the model and the Spearman rank order correlation coefficient to represent the metrics relationship to monotonicity. The results show that model with the mutual information as objective metric provides best result and it is suitable for evaluating quality of video sequences.

Keywords: Objective quality metrics, mutual information, region recognition, content based metrics

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Authors: Richard L. Summers

Abstract:

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: László Lengyel, Tihamér Levendovszky, Gergely Mezei, Hassan Charaf

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Graph rewriting-based visual model processing is a widely used technique for model transformation. Visual model transformations often need to follow an algorithm that requires a strict control over the execution sequence of the transformation steps. Therefore, in Visual Model Processors (VMPs) the execution order of the transformation steps is crucial. This paper presents the visual control flow support of Visual Modeling and Transformation System (VMTS), which facilitates composing complex model transformations of simple transformation steps and executing them. The VMTS Visual Control Flow Language (VCFL) uses stereotyped activity diagrams to specify control flow structures and OCL constraints to choose between different control flow branches. This paper introduces VCFL, discusses its termination properties and provides an algorithm to support the termination analysis of VCFL transformations.

Keywords: Control Flow, Metamodel-Based Visual ModelTransformation, OCL, Termination Properties, UML.

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Authors: Ratanaporn Leesing, Ratanaporn Baojungharn

Abstract:

Microbial oil was produced by soil isolated oleaginous yeast YU5/2 in flask-batch fermentation. The yeast was identified by molecular genetics technique based on sequence analysis of the variable D1/D2 domain of the large subunit (26S) ribosomal DNA and it was identified as Torulaspora globosa. T. globosa YU5/2 supported maximum values of 0.520 g/L/d, 0.472 g lipid/g cells, 4.16 g/L, and 0.156 g/L/d for volumetric lipid production rate, and specific yield of lipid, lipid concentration, and specific rate of lipid production respectively, when culture was performed in nitrogen-limiting medium supplemented with 80g/L glucose. Among the carbon sources tested, maximum cell yield coefficient (YX/S, g/L), maximum specific yield of lipid (YP/X, g lipid/g cells) and volumetric lipid production rate (QP, g/L/d) were found of 0.728, 0.237, and 0.619, respectively, using sweet potato tubers hydrolysates as carbon source.

Keywords: Microbial oil, oleaginous yeast, Torulasporaglobosa YU5/2, sweet potato tubers, kinetic parameters.

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Authors: Mohamed M. Mousa, Aidarkhan Kaltayev Shahwar F. Ragab

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In this paper, a new dependable algorithm based on an adaptation of the standard variational iteration method (VIM) is used for analyzing the transition from steady convection to chaos for lowto-intermediate Rayleigh numbers convection in porous media. The solution trajectories show the transition from steady convection to chaos that occurs at a slightly subcritical value of Rayleigh number, the critical value being associated with the loss of linear stability of the steady convection solution. The VIM is treated as an algorithm in a sequence of intervals for finding accurate approximate solutions to the considered model and other dynamical systems. We shall call this technique as the piecewise VIM. Numerical comparisons between the piecewise VIM and the classical fourth-order Runge–Kutta (RK4) numerical solutions reveal that the proposed technique is a promising tool for the nonlinear chaotic and nonchaotic systems.

Keywords: Variational iteration method, free convection, Chaos, Lorenz equations.

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Authors: Ismail, N., Sarijan, S

Abstract:

The phylogenetic analysis using the most conservative portions of 18S rRNA gene revealed the phylogenetic relationship among the two populations where DNA divergence showed that the nucleotides diversity value were -0.00838 for the Tanjung Dawai, Kedah and -0.00708 for the Cherating, Pahang populations respectively. The net nucleotide divergence among populations (Da) was -0.0073 indicating a low polymorphism among the populations studied. Total number of mutations in the Tanjung Dawai, Kedah samples was higher than Cherating, Pahang samples, which are 73 and 59 respectively while shared mutations across the populations were 8, and reveal the evolutionary in the genome of Malaysian T. gigas. The tree topology of both populations inferred using Neigbour-joining method by comparing 1791 bp of partial 18S rRNA sequence revealed that T. gigas haplotypes were clustered into seven clades, suggesting that they are genetically diverse among populations which derived from a common ancestor.

Keywords: Horseshoe crabs, Tachypleus gigas, 18S rRNA genesequences, phylogenetic analysis

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Authors: M. E. Khalifa, A. A. Gobouri

Abstract:

Potential synthesis of a series of 3-amino-4-arylazothiophene derivatives from reaction of 2-cyano-2-phenylthiocarbamoyl acetamide and the appropriate α-halogenated reagents, followed by coupling with different aryl diazonium salts (Japp-Klingemann reaction), and another series of 5-arylazo-thiazol-2-ylcarbamoyl-thiophene derivatives from base-catalyzed intramolecular condensation of 5-arylazo-2-(N-chloroacetyl)amino-thiazole with selected b-keto compounds (Thorpe-Ziegler reaction) was performed. The biological activity of the two series was studied in vitro. Their versatility for pharmaceutical purposes was reported, where they displayed remarkable activities against selected pathogenic microorganisms; Bacillus subtilis, Staphylococcus aureus (Gram positive bacteria), Escherichia coli, Pseudomonas aeruginosa (Gram negative bacteria), and Aspergillus flavus, Candida albicans (fungi) with various degrees related to their chemical structures.

Keywords: 2-Aminothiazole, antimicrobial, monoazo compounds, thiophene, pathogenic microorganisms.

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Authors: M. D. Kokate, T. R. Sontakke, P. W. Wani

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This paper deals with an adaptive multiuser detector for direct sequence code division multiple-access (DS-CDMA) systems. A modified receiver, precombinig LMMSE is considered under time varying channel environment. Detector updating is performed with two criterions, mean square estimation (MSE) and MOE optimization technique. The adaptive implementation issues of these two schemes are quite different. MSE criterion updates the filter weights by minimizing error between data vector and adaptive vector. MOE criterion together with canonical representation of the detector results in a constrained optimization problem. Even though the canonical representation is very complicated under time varying channels, it is analyzed with assumption of average power profile of multipath replicas of user of interest. The performance of both schemes is studied for practical SNR conditions. Results show that for poor SNR, MSE precombining LMMSE is better than the blind precombining LMMSE but for greater SNR, MOE scheme outperforms with better result.

Keywords: LMMSE, MOE, MUD.

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Authors: Urska Cvek, Marjan Trutschl, Randolph Stone II, Zanobia Syed, John L. Clifford, Anita L. Sabichi

Abstract:

Expression data analysis is based mostly on the statistical approaches that are indispensable for the study of biological systems. Large amounts of multidimensional data resulting from the high-throughput technologies are not completely served by biostatistical techniques and are usually complemented with visual, knowledge discovery and other computational tools. In many cases, in biological systems we only speculate on the processes that are causing the changes, and it is the visual explorative analysis of data during which a hypothesis is formed. We would like to show the usability of multidimensional visualization tools and promote their use in life sciences. We survey and show some of the multidimensional visualization tools in the process of data exploration, such as parallel coordinates and radviz and we extend them by combining them with the self-organizing map algorithm. We use a time course data set of transitional cell carcinoma of the bladder in our examples. Analysis of data with these tools has the potential to uncover additional relationships and non-trivial structures.

Keywords: microarrays, visualization, parallel coordinates, radviz, self-organizing maps.

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Authors: Alessandro Bevilacqua, Alessandro Gherardi, Ludovico Carozza, Filippo Piccinini

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The last years have seen an increasing use of image analysis techniques in the field of biomedical imaging, in particular in microscopic imaging. The basic step for most of the image analysis techniques relies on a background image free of objects of interest, whether they are cells or histological samples, to perform further analysis, such as segmentation or mosaicing. Commonly, this image consists of an empty field acquired in advance. However, many times achieving an empty field could not be feasible. Or else, this could be different from the background region of the sample really being studied, because of the interaction with the organic matter. At last, it could be expensive, for instance in case of live cell analyses. We propose a non parametric and general purpose approach where the background is built automatically stemming from a sequence of images containing even objects of interest. The amount of area, in each image, free of objects just affects the overall speed to obtain the background. Experiments with different kinds of microscopic images prove the effectiveness of our approach.

Keywords: Microscopy, flat field correction, background estimation, image segmentation.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Zalmiyah Zakaria, Saberi M. Mohamad

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Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm.

Keywords: Automatic clustering, cohesion-and-coupling metric, gene ontology; genetic algorithm, split-and-merge algorithm.

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Authors: Vedansh Gupta, Allyson Lutz, Ameen Razavi, Fatemeh Shirazi

Abstract:

The agriculture industry is especially vulnerable to forecasted water shortages. In the fresh and fresh-cut produce sector, conventional flume-based washing with recirculation exhibits high water demand. This leads to a large water footprint and possible cross-contamination of pathogens. These can be alleviated through advanced water reuse processes, such as membrane technologies including reverse osmosis (RO). Water reuse technologies effectively remove dissolved constituents but can easily foul without pre-treatment. Biological treatment is effective for the removal of organic compounds responsible for fouling, but not at the low temperatures encountered at most produce processing facilities. This study showed that the Microvi MicroNiche Engineering (MNE) technology effectively removes organic compounds (> 80%) at low temperatures (6-8 °C) from wash water. The MNE technology uses synthetic microorganism-material composites with negligible solids production, making it advantageously situated as an effective bio-pretreatment for RO. A preliminary technoeconomic analysis showed 60-80% savings in operation and maintenance costs (OPEX) when using the Microvi MNE technology for organics removal. This study and the accompanying economic analysis indicated that the proposed technology process will substantially reduce the cost barrier for adopting water reuse practices, thereby contributing to increased food safety and furthering sustainable water reuse processes across the agricultural industry.

Keywords: Biological pre-treatment, innovative technology, vegetable processing, water reuse, agriculture, reverse osmosis, MNE biocatalysts.

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