Search results for: gene identification

Authors: Rahib Hidayat Abiyev

Abstract:

This paper presents the development of recurrent neural network based fuzzy inference system for identification and control of dynamic nonlinear plant. The structure and algorithms of fuzzy system based on recurrent neural network are described. To train unknown parameters of the system the supervised learning algorithm is used. As a result of learning, the rules of neuro-fuzzy system are formed. The neuro-fuzzy system is used for the identification and control of nonlinear dynamic plant. The simulation results of identification and control systems based on recurrent neuro-fuzzy network are compared with the simulation results of other neural systems. It is found that the recurrent neuro-fuzzy based system has better performance than the others.

Keywords: Fuzzy logic, neural network, neuro-fuzzy system, control system.

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Authors: Khin May Win, Nan Sai Moon Kham

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Identification of cancer genes that might anticipate the clinical behaviors from different types of cancer disease is challenging due to the huge number of genes and small number of patients samples. The new method is being proposed based on supervised learning of classification like support vector machines (SVMs).A new solution is described by the introduction of the Maximized Margin (MM) in the subset criterion, which permits to get near the least generalization error rate. In class prediction problem, gene selection is essential to improve the accuracy and to identify genes for cancer disease. The performance of the new method was evaluated with real-world data experiment. It can give the better accuracy for classification.

Keywords: Microarray data, feature selection, recursive featureelimination, support vector machines.

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Authors: Atnaf Tiruneh Mulugeta, Mohammed Ali Hussein, Zelleke Habtamu

Abstract:

Thirty six genotypes (8 parents and 28 F1 diallel crosses) were grown in randomized complete block design during 2006 at Mandura, North western Ethiopia. The experiment was executed to study the inheritance of two primary yield component traits: number of seeds per pod and 1000 seed weight. Statistical significant difference was observed between genotypes, parents, and crosses for these traits. The mean square due to GCA was significant for the two traits. However, SCA mean square was significant only for number of seeds per pod. Thus both additive and non-additive types of gene actions were important in the inheritance of number of seeds per pod. Significant b1 component was obtained for this trait. The b2 and b3 components, however, were not significant, suggesting the absence of gene asymmetry. From Wr/Vr graph, inheritance of seeds per pod was governed by partial dominance with additive gene action.

Keywords: Diallel crosses, General combining ability, Phaseolus vulgaris L., Specific combining ability

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Authors: Mohamed Adnan Landolsi, Ali F. Almutairi

Abstract:

The paper addresses the problem of line-of-sight (LOS) vs. non-line-of-sight (NLOS) propagation link identification in ultra-wideband (UWB) wireless networks, which is necessary for improving the accuracy of radiolocation and positioning applications. A LOS/NLOS likelihood hypothesis testing approach is applied based on exploiting distinctive statistical features of the channel impulse response (CIR) using parameters related to the “skewness” of the CIR and its root mean square (RMS) delay spread. A log-normal fit is presented for the probability densities of the CIR parameters. Simulation results show that different environments (residential, office, outdoor, etc.) have measurable differences in their CIR parameters’ statistics, which is then exploited in determining the nature of the propagation channels. Correct LOS/NLOS channel identification rates exceeding 90% are shown to be achievable for most types of environments. Additional improvement is also obtained by combining both CIR skewness and RMS delay statistics.

Keywords: Ultra-wideband, propagation, line-of-sight, non-line-of-sight, identification.

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Authors: Ran-Zan Wang, Yao-Ting Lee

Abstract:

This paper proposes a visual cryptography by random grids scheme with identifiable shares. The method encodes an image O in two shares that exhibits the following features: (1) each generated share has the same scale as O, (2) any share singly has noise-like appearance that reveals no secret information on O, (3) the secrets can be revealed by superimposing the two shares, (4) folding a share up can disclose some identification patterns, and (5) both of the secret information and the designated identification patterns are recognized by naked eye without any computation. The property to show up identification patterns on folded shares establishes a simple and friendly interface for users to manage the numerous shares created by VC schemes.

Keywords: Image Encryption, Image Sharing, Secret Sharing, Visual Cryptography.

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Authors: Brandon Foggo, Nanpeng Yu

Abstract:

Power distribution circuits undergo frequent network topology changes that are often left undocumented. As a result, the documentation of a circuit’s connectivity becomes inaccurate with time. The lack of reliable circuit connectivity information is one of the biggest obstacles to model, monitor, and control modern distribution systems. To enhance the reliability and efficiency of electric power distribution systems, the circuit’s connectivity information must be updated periodically. This paper focuses on one critical component of a distribution circuit’s topology - the secondary transformer to phase association. This topology component describes the set of phase lines that feed power to a given secondary transformer (and therefore a given group of power consumers). Finding the documentation of this component is call Phase Identification, and is typically performed with physical measurements. These measurements can take time lengths on the order of several months, but with supervised learning, the time length can be reduced significantly. This paper compares several such methods applied to Phase Identification for a large range of real distribution circuits, describes a method of training data selection, describes preprocessing steps unique to the Phase Identification problem, and ultimately describes a method which obtains high accuracy (> 96% in most cases, > 92% in the worst case) using only 5% of the measurements typically used for Phase Identification.

Keywords: Distribution network, machine learning, network topology, phase identification, smart grid.

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Authors: R. Majidzadeh Heravi, M. Sankian, H. Kermanshahi, M. R. Nassiri, A. Heravi Moussavi, S. A. Lari, A. R. Varasteh

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The use of probiotics engineered to express specific enzymes has been the subject of considerable attention in poultry industry because of increased nutrient availability and reduced cost of enzyme supplementation. Phytase enzyme is commonly added to poultry feed to improve digestibility and availability of phosphorus from plant sources. To construct a probiotic with potential of phytate degradation, phytase gene (appA) from E. coli was cloned and transformed into two probiotic bacteria Lactobacillus salivarius and Lactococcus lactis. L. salivarous showed plasmid instability, unable to express the gene. The expression of appA gene in L. lactis was analyzed by detecting specific RNA and zymography assay. Phytase enzyme was isolated from cellular extracts of recombinant L. lactis, showing a 46 kDa band upon the SDS-PAGE analysis. Zymogram also confirmed the phytase activity of the 46 kDa band corresponding to the enzyme. An enzyme activity of 4.9U/ml was obtained in cell extracts of L. lactis. The growth of native and recombinant L. lactis was similar in the presence of two concentrations of ox bile.

Keywords: Lactobacillus salivarus, Lactococcus lactis, recombinant, phytase, poultry.

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Authors: Abduladheem A. Ali, Easa A. Abd

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The robot is a repeated task plant. The control of such a plant under parameter variations and load disturbances is one of the important problems. The aim of this work is to design Geno-Fuzzy controller suitable for online applications to control single link rigid robot arm plant. The genetic-fuzzy online controller (indirect controller) has two genetic-fuzzy blocks, the first as controller, the second as identifier. The identification method is based on inverse identification technique. The proposed controller it tested in normal and load disturbance conditions.

Keywords: Fuzzy network, genetic algorithm, robot control, online genetic control, parameter identification.

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

Abstract:

Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence, and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, Brassinosteroids, Phylogenetic analysis, Transcription factor.

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Authors: Mohammed Zidane, Said Safi, Mohamed Sabri, Ahmed Boumezzough

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In this paper we propose an algorithm based on higher order cumulants, for blind impulse response identification of frequency radio channels and downlink (MC−CDMA) system Equalization. In order to test its efficiency, we have compared with another algorithm proposed in the literature, for that we considered on theoretical channel as the Proakis’s ‘B’ channel and practical frequency selective fading channel, called Broadband Radio Access Network (BRAN C), normalized for (MC−CDMA) systems, excited by non-Gaussian sequences. In the part of (MC−CDMA), we use the Minimum Mean Square Error (MMSE) equalizer after the channel identification to correct the channel’s distortion. The simulation results, in noisy environment and for different signal to noise ratio (SNR), are presented to illustrate the accuracy of the proposed algorithm.

Keywords: Blind identification and equalization, Higher Order Cumulants, (MC−CDMA) system, MMSE equalizer.

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Authors: Young-Seok Choi

Abstract:

This paper presents a subband adaptive filter (SAF) for a system identification where an impulse response is sparse and disturbed with an impulsive noise. Benefiting from the uses of l1-norm optimization and l0-norm penalty of the weight vector in the cost function, the proposed l0-norm sign SAF (l0-SSAF) achieves both robustness against impulsive noise and much improved convergence behavior than the classical adaptive filters. Simulation results in the system identification scenario confirm that the proposed l0-norm SSAF is not only more robust but also faster and more accurate than its counterparts in the sparse system identification in the presence of impulsive noise.

Keywords: Subband adaptive filter, l0-norm, sparse system, robustness, impulsive interference.

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Authors: Chad Goldsworthy, B. Rajeswari Matam

Abstract:

The use of deep learning for species identification in camera trap images has revolutionised our ability to study, conserve and monitor species in a highly efficient and unobtrusive manner, with state-of-the-art models achieving accuracies surpassing the accuracy of manual human classification. The high imbalance of camera trap datasets, however, results in poor accuracies for minority (rare or endangered) species due to their relative insignificance to the overall model accuracy. This paper investigates the use of Focal Loss, in comparison to the traditional Cross Entropy Loss function, to improve the identification of minority species in the “255 Bird Species” dataset from Kaggle. The results show that, although Focal Loss slightly decreased the accuracy of the majority species, it was able to increase the F1-score by 0.06 and improve the identification of the bottom two, five and ten (minority) species by 37.5%, 15.7% and 10.8%, respectively, as well as resulting in an improved overall accuracy of 2.96%.

Keywords: Convolutional neural networks, data imbalance, deep learning, focal loss, species classification, wildlife conservation.

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Authors: Dana Gabriková, Martin Mistrík, Jarmila Bernasovská, Iveta Tóthová, Jana Kisková

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The Roma (Gypsies) is a transnational minority with a high degree of consanguineous marriages. Similar to other genetically isolated founder populations, the Roma harbor a number of unique or rare genetic disorders. This paper discusses about a rare form of Charcot-Marie-Tooth disease – type 4G (CMT4G), also called Hereditary Motor and Sensory Neuropathy type Russe, an autosomal recessive disease caused by mutation private to Roma characterized by abnormally increased density of non-myelinated axons. CMT4G was originally found in Bulgarian Roma and in 2009 two putative causative mutations in the HK1 gene were identified. Since then, several cases were reported in Roma families mainly from Bulgaria and Spain. Here we present a Slovak Roma family in which CMT4G was diagnosed on the basis of clinical examination and genetic testing. This case is a further proof of the role of the HK1 gene in pathogenesis of the disease. It confirms that mutation in the HK1 gene is a common cause of autosomal recessive CMT disease in Roma and should be considered as a common part of a diagnostic procedure.

Keywords: Gypsies, HK1, HSMN-Russe, rare disease.

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Authors: Wajdi Ghezaiel, Amel Ben Slimane Rahmouni, Ezzedine Ben Braiek

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Many applications of speech communication and speaker identification suffer from the problem of co-channel speech. This paper deals with a multi-resolution dyadic wavelet transform method for usable segments of co-channel speech detection that could be processed by a speaker identification system. Evaluation of this method is performed on TIMIT database referring to the Target to Interferer Ratio measure. Co-channel speech is constructed by mixing all possible gender speakers. Results do not show much difference for different mixtures. For the overall mixtures 95.76% of usable speech is correctly detected with false alarms of 29.65%.

Keywords: Co-channel speech, usable speech, multi-resolutionanalysis, speaker identification

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Authors: Sana Bouzaida, Anis Sakly, Faouzi M'Sahli

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In this paper, a TSK-type Neuro-fuzzy Inference System that combines the features of fuzzy sets and neural networks has been applied for the identification of MIMO systems. The procedure of adapting parameters in TSK model employs a Shuffled Frog Leaping Algorithm (SFLA) which is inspired from the memetic evolution of a group of frogs when seeking for food. To demonstrate the accuracy and effectiveness of the proposed controller, two nonlinear systems have been considered as the MIMO plant, and results have been compared with other learning methods based on Particle Swarm Optimization algorithm (PSO) and Genetic Algorithm (GA).

Keywords: Identification, Shuffled frog Leaping Algorithm (SFLA), TSK-type neuro-fuzzy model.

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Authors: Wiriya Loongyai, Kiettisak Promphet, Nilubol Kangsukul, Ratchawat Noppha

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Polymerase chain reaction (PCR) assay and conventional microbiological methods were used to detect bacterial contamination of egg shells and egg content in different commercial housing systems, open house system and evaporative cooling system. A PCR assay was developed for direct detection using a set of primers specific for the invasion by A gene (invA) of Salmonella spp. PCR detected the presence of Salmonella in 2 samples of shell egg from the evaporative cooling system, while conventional cultural methods detected no Salmonella from the same samples.

Keywords: egg content, egg shell, invA gene, PCR, Salmonellaspp.

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Authors: Chih-Neng Liang, Huang-Bin Huang, Bo-Chiuan Chen

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Nowadays, keyless entry systems are widely adopted for vehicle immobilizer systems due to both advantages of security and convenience. Keyless entry systems could overcome brute-force key guessing attack, statistics attack and masquerade attack, however, they can't prevent from thieves stealing behavior. In this paper, we proposed a new architecture try to improve the existent flaws. The integration of the keyless entry system and the fingerprint identification technology is more suitable to implement on the portable transponder to achieve higher security needs. We also adopt and modify AES security protocol for life expectancy and security of the portable transponder. In addition, the identification of a driver's fingerprint makes the service of automatic reinstatement of a driver's preferences become possible. Our design can satisfy not only the three kinds of previous illegal attacks, but also the stealing situation. Furthermore, many practical factors, such as costs, life expectancy and performance, have been well considered in the design of portable transponder.

Keywords: Keyless entry-system, fingerprint identification, AES security protocol, vehicle immobilizer system.

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Authors: Eleonora Tudora, Adriana Alexandru

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The radio frequency identification (RFID) is a technology for automatic identification of items, particularly in supply chain, but it is becoming increasingly important for industrial applications. Unlike barcode technology that detects the optical signals reflected from barcode labels, RFID uses radio waves to transmit the information from an RFID tag affixed to the physical object. In contrast to today most often use of this technology in warehouse inventory and supply chain, the focus of this paper is an overview of the structure of RFID systems used by RFID technology and it also presents a solution based on the application of RFID for brand authentication, traceability and tracking, by implementing a production management system and extending its use to traders.

Keywords: RFID, RFID Tag, Electronic Product Code (EPC), EPC network, Object Naming Service (ONS), Authentication, Traceability.

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Authors: Yen-Po Wang, Ming-Chih Huang, Ming-Lian Chang

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A scheme integrated with deterministic–stochastic subspace system identification and the method of damage localization vector is proposed in this study for damage detection of structures based on seismic response data. A series of shaking table tests using a five-storey steel frame has been conducted in National Center for Research on Earthquake Engineering (NCREE), Taiwan. Damage condition is simulated by reducing the cross-sectional area of some of the columns at the bottom. Both single and combinations of multiple damage conditions at various locations have been considered. In the system identification analysis, either full or partial observation conditions have been taken into account. It has been shown that the damaged stories can be identified from global responses of the structure to earthquakes if sufficiently observed. In addition to detecting damage(s) with respect to the intact structure, identification of new or extended damages of the as-damaged (ill-conditioned) counterpart has also been studied. The proposed scheme proves to be effective.

Keywords: Damage locating vectors, deterministic-stochastic subspace system, shaking table tests, system identification.

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Authors: S. Kherchaoui, A. Houacine

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This paper presents a facial expression recognition system. It performs identification and classification of the seven basic expressions; happy, surprise, fear, disgust, sadness, anger, and neutral states. It consists of three main parts. The first one is the detection of a face and the corresponding facial features to extract the most expressive portion of the face, followed by a normalization of the region of interest. Then calculus of curvelet coefficients is performed with dimensionality reduction through principal component analysis. The resulting coefficients are combined with two ratios; mouth ratio and face edge ratio to constitute the whole feature vector. The third step is the classification of the emotional state using the SVM method in the feature space.

Keywords: Facial expression identification, curvelet coefficients, support vector machine (SVM).

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Authors: Rumena D. Stancheva, Ilona I. Iatcheva

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In working mode some unexpected changes could be arise in inner structure of electromagnetic device. They influence modification in electromagnetic field propagation map. The field values at an observed boundary are also changed. The development of the process has to be watched because the arising structural changes would provoke the device to be gone out later. The probabilistic assessment of the state is possible to be made. The numerical assessment points if the resulting changes have only accidental character or they are due to the essential inner structural disturbances. The presented application example is referring to the 200MW turbine-generator. A part of the stator core end teeth zone is simulated broken. Quasi three-dimensional electromagnetic and temperature field are solved applying FEM. The stator core state diagnosis is proposed to be solved as an identification problem on the basis of a statistical criterion.

Keywords: Identification, structural disturbance, statistical criterion.

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Authors: Ardhendu Behera, Denis Lalanne, Rolf Ingold

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This paper proposes a method, combining color and layout features, for identifying documents captured from low-resolution handheld devices. On one hand, the document image color density surface is estimated and represented with an equivalent ellipse and on the other hand, the document shallow layout structure is computed and hierarchically represented. Our identification method first uses the color information in the documents in order to focus the search space on documents having a similar color distribution, and finally selects the document having the most similar layout structure in the remaining of the search space.

Keywords: Document color modeling, document visualsignature, kernel density estimation, document identification.

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Authors: Yu-Ting Tsai, Yu-da Lee, Jin H. Huang

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The nonlinear damping behavior is usually ignored in the design of a miniature moving-coil loudspeaker. But when the loudspeaker operated in air, the damping parameter varies with the voice-coil displacement corresponding due to viscous air flow. The present paper presents an identification model as inverse problem to identify the nonlinear damping parameter in the lumped parameter model for the loudspeaker. Theoretical results for the nonlinear damping are verified by using laser displacement measurement scanner. These results indicate that the damping parameter has the greatly different nonlinearity between in air and vacuum. It is believed that the results of the present work can be applied in diagnosis and sound quality improvement of a miniature loudspeaker.

Keywords: Miniature loudspeaker, non-linear damping, system identification, Lumped parameter model.

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Authors: Fabian Horn, Reinhard Guthke

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In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus.

Keywords: bottom-up approach, gene clusters, melting temperature, metabolic pathway, microarray probe design, probe selection

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Authors: Rosarin Rujananon, Poonsuk Prasertsan, Amornrat Phongdara, Tanate Panrat, Jibin Sun, Sugima Rappert, An-Ping Zeng

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In this study, a synthetic pathway was created by assembling genes from Clostridium butyricum and Escherichia coli in different combinations. Among the genes were dhaB1 and dhaB2 from C. butyricum VPI1718 coding for glycerol dehydratase (GDHt) and its activator (GDHtAc), respectively, involved in the conversion of glycerol to 3-hydroxypropionaldehyde (3-HPA). The yqhD gene from E.coli BL21 was also included which codes for an NADPHdependent 1,3-propanediol oxidoreductase isoenzyme (PDORI) reducing 3-HPA to 1,3-propanediol (1,3-PD). Molecular modeling analysis indicated that the conformation of fusion protein of YQHD and DHAB1 was favorable for direct molecular channeling of the intermediate 3-HPA. According to the simulation results, the yqhD and dhaB1 gene were assembled in the upstream of dhaB2 to express a fusion protein, yielding the recombinant strain E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP41Y3). Strain BP41Y3 gave 10-fold higher 1,3-PD concentration than E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP31Y2) expressing the recombinant enzymes simultaneously but in a non-fusion mode. This is the first report using a gene fusion approach to enhance the biological conversion of glycerol to the value added compound 1,3- PD.

Keywords: Recombinant E.coli, 1, 3-propanediol, glycerol, fusion protein.

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Authors: Javad Khazaei, Rick S. Blum

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Distributed control is an efficient and flexible approach for coordination of multi-agent systems. One of the main challenges in designing a distributed controller is identifying the governing dynamics of the dynamical systems. Data-driven system identification is currently undergoing a revolution. With the availability of high-fidelity measurements and historical data, model-free identification of dynamical systems can facilitate the control design without tedious modeling of high-dimensional and/or nonlinear systems. This paper develops a distributed control design using consensus theory for linear and nonlinear dynamical systems using sparse identification of system dynamics. Compared with existing consensus designs that heavily rely on knowing the detailed system dynamics, the proposed model-free design can accurately capture the dynamics of the system with available measurements and input data and provide guaranteed performance in consensus and tracking problems. Heterogeneous damped oscillators are chosen as examples of dynamical system for validation purposes.

Keywords: Consensus tracking, distributed control, model-free control, sparse identification of dynamical systems.

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Authors: Yu-Xiang Zhao, Chien-Hsing Chou, Mu-Chun Su, Yi-Zeng Hsieh

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The purpose of this study is to design a portable virtual piano. By utilizing optical fiber gloves and the virtual piano software designed by this study, the user can play the piano anywhere at any time. This virtual piano consists of three major parts: finger tapping identification, hand movement and positioning identification, and MIDI software sound effect simulation. To play the virtual piano, the user wears optical fiber gloves and simulates piano key tapping motions. The finger bending information detected by the optical fiber gloves can tell when piano key tapping motions are made. Images captured by a video camera are analyzed, hand locations and moving directions are positioned, and the corresponding scales are found. The system integrates finger tapping identification with information about hand placement in relation to corresponding piano key positions, and generates MIDI piano sound effects based on this data. This experiment shows that the proposed method achieves an accuracy rate of 95% for determining when a piano key is tapped.

Keywords: virtual piano, portable, identification, optical fibergloves.

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Authors: A. Bumbová, M. Čáslavský, F. Božek, J. Dvořák, E. Bakoš

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The paper presents the case study of hazard identification and sensitivity of potential resource of emergency water supply as part of the application of methodology classifying the resources of drinking water for emergency supply of population. The case study has been carried out on a selected resource of emergency water supply in one region of the Czech Republic. The hazard identification and sensitivity of potential resource of emergency water supply is based on a unique procedure and developed general registers of selected types of hazards and sensitivities. The registers have been developed with the help of the “Fault Tree Analysis” method in combination with the “What if method”. The identified hazards for the assessed resource include hailstorms and torrential rains, drought, soil erosion, accidents of farm machinery, and agricultural production. The developed registers of hazards and vulnerabilities and a semi-quantitative assessment of hazards for individual parts of hydrological structure and technological elements of presented drilled wells are the basis for a semi-quantitative risk assessment of potential resource of emergency supply of population and the subsequent classification of such resource within the system of crisis planning.

Keywords: Hazard identification, register of hazards, sensitivity identification, register of sensitivity, emergency water supply, state of crisis, resource of emergency water supply, ground water.

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Authors: T. Holden, G. Tremberger, Jr, E. Cheung, R. Subramaniam, R. Sullivan, N. Gadura, P. Schneider, P. Marchese, A. Flamholz, T. Cheung, D. Lieberman

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A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles were archaeoglobus fulgidus, methanothermobacter thermautotrophicus, methanocaldococcus jannaschii, pyrococcus horikoshii, and thermoplasma acidophilum. The studied five archaea-euryarchaeota thermophiles have fractal dimension values ranging from 1.93 to 1.97. Computer simulation shows that random sequences would have an average of about 2 with a standard deviation about 0.015. The fractal dimension was found to correlate (negative correlation) with the thermophile-s optimal growth temperature with R2 value of 0.90 (N =5). The inclusion of two aracheae-crenarchaeota thermophiles reduces the R2 value to 0.66 (N = 7). Further inclusion of two bacterial thermophiles reduces the R2 value to 0.50 (N =9). The fractal dimension is correlated (positive) to the sequence GC content with an R2 value of 0.89 for the five archaea-euryarchaeota thermophiles (and 0.74 for the entire set of N = 9), although computer simulation shows little correlation. The highest correlation (positive) was found to be between the fractal dimension and di-nucleotide Shannon entropy. However Shannon entropy and sequence GC content were observed to correlate with optimal growth temperature having an R2 of 0.8 (negative), and 0.88 (positive), respectively, for the entire set of 9 thermophiles; thus the correlation lacks species specificity. Together with another correlation study of bacterial radiation dosage with RecA repair gene sequence fractal dimension, it is postulated that fractal dimension analysis is a sensitive tool for studying the relationship between genotype and phenotype among closely related sequences.

Keywords: Fractal dimension, archaea thermophiles, Shannon entropy, GC content

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Authors: Abu Salim Mustafa

Abstract:

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

Keywords: Mycobacterium tuberculosis, Rv3873, peptides, vaccine

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