Displaying publications 61 - 80 of 734 in total

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  1. Salman SD, Kadhum AA, Takriff MS, Mohamad AB
    ScientificWorldJournal, 2013;2013:492762.
    PMID: 24078795 DOI: 10.1155/2013/492762
    Numerical investigation of the heat transfer and friction factor characteristics of a circular fitted with V-cut twisted tape (VCT) insert with twist ratio (y = 2.93) and different cut depths (w = 0.5, 1, and 1.5 cm) were studied for laminar flow using CFD package (FLUENT-6.3.26). The data obtained from plain tube were verified with the literature correlation to ensure the validation of simulation results. Classical twisted tape (CTT) with different twist ratios (y = 2.93, 3.91, 4.89) were also studied for comparison. The results show that the enhancement of heat transfer rate induced by the classical and V-cut twisted tape inserts increases with the Reynolds number and decreases with twist ratio. The results also revealed that the V-cut twisted tape with twist ratio y = 2.93 and cut depth w = 0.5 cm offered higher heat transfer rate with significant increases in friction factor than other tapes. In addition the results of V-cut twist tape compared with experimental and simulated data of right-left helical tape inserts (RLT), it is found that the V-cut twist tape offered better thermal contact between the surface and the fluid which ultimately leads to a high heat transfer coefficient. Consequently, 107% of maximum heat transfer was obtained by using this configuration.
    Matched MeSH terms: Models, Theoretical*
  2. Khan I, Ali F, Shafie S
    PLoS One, 2013;8(5):e61531.
    PMID: 23667442 DOI: 10.1371/journal.pone.0061531
    The present work is concerned with exact solutions of Stokes second problem for magnetohydrodynamics (MHD) flow of a Burgers' fluid. The fluid over a flat plate is assumed to be electrically conducting in the presence of a uniform magnetic field applied in outward transverse direction to the flow. The equations governing the flow are modeled and then solved using the Laplace transform technique. The expressions of velocity field and tangential stress are developed when the relaxation time satisfies the condition γ =  λ²/4 or γ> λ²/4. The obtained closed form solutions are presented in the form of simple or multiple integrals in terms of Bessel functions and terms with only Bessel functions. The numerical integration is performed and the graphical results are displayed for the involved flow parameters. It is found that the velocity decreases whereas the shear stress increases when the Hartmann number is increased. The solutions corresponding to the Stokes' first problem for hydrodynamic Burgers' fluids are obtained as limiting cases of the present solutions. Similar solutions for Stokes' second problem of hydrodynamic Burgers' fluids and those for Newtonian and Oldroyd-B fluids can also be obtained as limiting cases of these solutions.
    Matched MeSH terms: Models, Theoretical*
  3. Liang SN, Lan BL
    PLoS One, 2012;7(5):e36430.
    PMID: 22606259 DOI: 10.1371/journal.pone.0036430
    The newtonian and special-relativistic statistical predictions for the mean, standard deviation and probability density function of the position and momentum are compared for the periodically-delta-kicked particle at low speed. Contrary to expectation, we find that the statistical predictions, which are calculated from the same parameters and initial gaussian ensemble of trajectories, do not always agree if the initial ensemble is sufficiently well-localized in phase space. Moreover, the breakdown of agreement is very fast if the trajectories in the ensemble are chaotic, but very slow if the trajectories in the ensemble are non-chaotic. The breakdown of agreement implies that special-relativistic mechanics must be used, instead of the standard practice of using newtonian mechanics, to correctly calculate the statistical predictions for the dynamics of a low-speed system.
    Matched MeSH terms: Models, Theoretical*
  4. Li J, Kendall G
    PLoS One, 2015;10(8):e0136032.
    PMID: 26288088 DOI: 10.1371/journal.pone.0136032
    In evolutionary game theory, evolutionarily stable states are characterised by the folk theorem because exact solutions to the replicator equation are difficult to obtain. It is generally assumed that the folk theorem, which is the fundamental theory for non-cooperative games, defines all Nash equilibria in infinitely repeated games. Here, we prove that Nash equilibria that are not characterised by the folk theorem do exist. By adopting specific reactive strategies, a group of players can be better off by coordinating their actions in repeated games. We call it a type-k equilibrium when a group of k players coordinate their actions and they have no incentive to deviate from their strategies simultaneously. The existence and stability of the type-k equilibrium in general games is discussed. This study shows that the sets of Nash equilibria and evolutionarily stable states have greater cardinality than classic game theory has predicted in many repeated games.
    Matched MeSH terms: Models, Theoretical*
  5. Jesudason CG
    PLoS One, 2016;11(1):e0145026.
    PMID: 26760507 DOI: 10.1371/journal.pone.0145026
    The Carnot cycle and its deduction of maximum conversion efficiency of heat inputted and outputted isothermally at different temperatures necessitated the construction of isothermal and adiabatic pathways within the cycle that were mechanically "reversible", leading eventually to the Kelvin-Clausius development of the entropy function S with differential dS = dq/T such that [symbol: see text]C dS = 0 where the heat absorption occurs at the isothermal paths of the elementary Carnot cycle. Another required condition is that the heat transfer processes take place infinitely slowly and "reversibly", implying that rates of transfer are not explicitly featured in the theory. The definition of 'heat' as that form of energy that is transferred as a result of a temperature difference suggests that the local mode of transfer of "heat" in the isothermal segments of the pathway implies a Fourier-like heat conduction mechanism which is apparently irreversible, leading to an increase in entropy of the combined reservoirs at either end of the conducting material, and which is deemed reversible mechanically. These paradoxes are circumvented here by first clarifying the terms used before modeling heat transfer as a thermodynamically reversible but mechanically irreversible process and applied to a one dimensional atomic lattice chain of interacting particles subjected to a temperature difference exemplifying Fourier heat conduction. The basis of a "recoverable trajectory" i.e. that which follows a zero entropy trajectory is identified. The Second Law is strictly maintained in this development. A corollary to this zero entropy trajectory is the generalization of the Zeroth law for steady state non-equilibrium systems with varying temperature, and thus to a statement about "equilibrium" in steady state non-thermostatic conditions. An energy transfer rate term is explicitly identified for each particle and agrees quantitatively (and independently) with the rate of heat absorbed at the reservoirs held at different temperatures and located at the two ends of the lattice chain in MD simulations, where all energy terms in the simulation refer to a single particle interacting with its neighbors. These results validate the theoretical model and provides the necessary boundary conditions (for instance with regard to temperature differentials and force fields) that thermodynamical variables must comply with to satisfy the conditions for a recoverable trajectory, and thus determines the solution of the differential and integral equations that are used to model these processes. These developments and results, if fully pursued would imply that not only can the Carnot cycle be viewed as describing a local process of energy-work conversion by a single interacting particle which feature rates of energy transfer and conversion not possible in the classical Carnot development, but that even irreversible local processes might be brought within the scope of this cycle, implying a unified treatment of thermodynamically (i) irreversible (ii) reversible (iii) isothermal and (iv) adiabatic processes by conflating the classically distinct concept of work and heat energy into a single particle interactional process. A resolution to the fundamental and long-standing conjecture of Benofy and Quay concerning the Fourier principle is one consequence of the analysis.
    Matched MeSH terms: Models, Theoretical*
  6. See HH, Mamat NA, Hauser PC
    Molecules, 2018 Apr 24;23(5).
    PMID: 29695126 DOI: 10.3390/molecules23051000
    A method for on-line matrix elimination to enable selective quantification of ultraviolet absorbing analytes by a flow-injection analysis procedure is described. Selectivity is achieved by electric field driven extraction across a polymer inclusion membrane. The method was demonstrated on the example of the determination of naproxen from spiked human urine. Membranes of 10 μm thickness were employed which consisted of 7.5 mg cellulose triacetate as base polymer, 5 mg of o-nitrophenyl octyl ether as plasticizer and 7.5 mg of Aliquat 336 as cationic carrier. Ten μL of sample was introduced into a continuous stream of background solution consisting of 100 µM aqueous NaClO₄ with a flow rate of 2 μL/min while applying a voltage of 150 V to the extraction cell. The target ion was electrokinetically transported across the membrane and enriched in 1.5 μL of a stagnant acceptor solution. This was subsequently pumped past a flow-through UV detector for quantification. The method showed a linear range from 5 to 200 µM with a correlation coefficient of 0.9978 and a reproducibility of typically 7% (n = 8). The detection limit of the method for naproxen was 2 µM.
    Matched MeSH terms: Models, Theoretical*
  7. Azizan A, Sieben M, Wandrey G, Büchs J
    Biotechnol Bioeng, 2019 11;116(11):2983-2995.
    PMID: 31350917 DOI: 10.1002/bit.27132
    Shake flasks are still the most relevant experimental tool in the development of viscous fermentation processes. The phase number, which defines the onset of the unfavorable out-of-phase (OP) phenomenon in shake flasks, was previously defined via specific power input measurements. In the OP state, the bulk liquid no longer follows the orbital movement of the imposed centrifugal force, which is for example, detrimental to oxygen transfer. In this study, an optical fluorescence technique was used to measure the three-dimensional liquid distribution in shake flasks. Four new optically derived evaluation criteria for the phase transition between the in-phase and OP condition were established: (a) thickness of the liquid film left on the glass wall by the rotating bulk liquid, (b) relative slope of the leading edge of bulk liquid (LB) lines, (c) trend of the angular position of LB, and (d) very high angular position of the leading edge. In contrast to the previously applied power input measurements, the new optical evaluation criteria describe the phase transition in greater detailed. Instead of Ph = 1.26, a less conservative value of Ph = 0.91 is now suggested for the phase transfer, which implies a broader operating window for shake flask cultivations with higher viscosities.
    Matched MeSH terms: Models, Theoretical*
  8. Tahmasbi F, Maleki S, Shariati M, Ramli Sulong NH, Tahir MM
    PLoS One, 2016;11(8):e0156989.
    PMID: 27478894 DOI: 10.1371/journal.pone.0156989
    This paper investigates the behaviour of C-shaped and L-shaped angle shear connectors embedded in solid concrete slabs. An effective finite element model is proposed to simulate the push out tests of these shear connectors that encompass nonlinear material behaviour, large displacement and damage plasticity. The finite element models are validated against test results. Parametric studies using this nonlinear model are performed to investigate the variations in concrete strength and connector dimensions. The finite element analyses also confirm the test results that increasing the length of shear connector increases their shear strength proportionately. It is observed that the maximum stress in L-shaped angle connectors takes place in the weld attachment to the beam, whereas in the C-shaped angle connectors, it is in the attached leg. The location of maximum concrete compressive damage is rendered in each case. Finally, a new equation for prediction of the shear capacity of C-shaped angle connectors is proposed.
    Matched MeSH terms: Models, Theoretical*
  9. Roy S, Ramiah H, Reza AW, Lim CC, Ferrer EM
    PLoS One, 2016;11(7):e0158954.
    PMID: 27391136 DOI: 10.1371/journal.pone.0158954
    Micro-electro mechanical system (MEMS) based oscillators are revolutionizing the timing industry as a cost effective solution, enhanced with more features, superior performance and better reliability. The design of a sustaining amplifier was triggered primarily to replenish MEMS resonator's high motion losses due to the possibility of their 'system-on-chip' integrated circuit solution. The design of a sustaining amplifier observing high gain and adequate phase shift for an electrostatic clamp-clamp (C-C) beam MEMS resonator, involves the use of an 180nm CMOS process with an unloaded Q of 1000 in realizing a fixed frequency oscillator. A net 122dBΩ transimpedance gain with adequate phase shift has ensured 17.22MHz resonant frequency oscillation with a layout area consumption of 0.121 mm2 in the integrated chip solution, the sustaining amplifier draws 6.3mW with a respective phase noise of -84dBc/Hz at 1kHz offset is achieved within a noise floor of -103dBC/Hz. In this work, a comparison is drawn among similar design studies on the basis of a defined figure of merit (FOM). A low phase noise of 1kHz, high figure of merit and the smaller size of the chip has accredited to the design's applicability towards in the implementation of a clock generative integrated circuit. In addition to that, this complete silicon based MEMS oscillator in a monolithic solution has offered a cost effective solution for industrial or biomedical electronic applications.
    Matched MeSH terms: Models, Theoretical*
  10. Rahman Z, Hashim F, Rasid MFA, Othman M
    PLoS One, 2018;13(6):e0197087.
    PMID: 29874237 DOI: 10.1371/journal.pone.0197087
    Underwater Wireless Sensor Network (UWSN) has emerged as promising networking techniques to monitor and explore oceans. Research on acoustic communication has been conducted for decades, but had focused mostly on issues related to physical layer such as high latency, low bandwidth, and high bit error. However, data gathering process is still severely limited in UWSN due to channel impairment. One way to improve data collection in UWSN is the design of routing protocol. Opportunistic Routing (OR) is an emerging technique that has the ability to improve the performance of wireless network, notably acoustic network. In this paper, we propose an anycast, geographical and totally opportunistic routing algorithm for UWSN, called TORA. Our proposed scheme is designed to avoid horizontal transmission, reduce end to end delay, overcome the problem of void nodes and maximize throughput and energy efficiency. We use TOA (Time of Arrival) and range based equation to localize nodes recursively within a network. Once nodes are localized, their location coordinates and residual energy are used as a matrix to select the best available forwarder. All data packets may or may not be acknowledged based on the status of sender and receiver. Thus, the number of acknowledgments for a particular data packet may vary from zero to 2-hop. Extensive simulations were performed to evaluate the performance of the proposed scheme for high network traffic load under very sparse and very dense network scenarios. Simulation results show that TORA significantly improves the network performance when compared to some relevant existing routing protocols, such as VBF, HHVBF, VAPR, and H2DAB, for energy consumption, packet delivery ratio, average end-to-end delay, average hop-count and propagation deviation factor. TORA reduces energy consumption by an average of 35% of VBF, 40% of HH-VBF, 15% of VAPR, and 29% of H2DAB, whereas the packet delivery ratio has been improved by an average of 43% of VBF, 26% of HH-VBF, 15% of VAPR, and 25% of H2DAB. Moreover, the average end-to-end delay has been reduced by 70% of VBF, 69% of HH-VBF, 46% of VAPR, and 73% of H2DAB. Furthermore, average hope-count has been improved by 57%, 53%, 16% and 31% as compared to VBF, HHVBF, VAPR, and H2DAB, respectively. Also, propagation delay has been reduced by 34%, 30%, 15% and 23% as compared to VBF, HHVBF, VAPR, and H2DAB, respectively.
    Matched MeSH terms: Models, Theoretical*
  11. Al-Mayouf YR, Ismail M, Abdullah NF, Wahab AW, Mahdi OA, Khan S, et al.
    PLoS One, 2016;11(11):e0165966.
    PMID: 27855165 DOI: 10.1371/journal.pone.0165966
    Vehicular ad hoc networks (VANETs) are considered an emerging technology in the industrial and educational fields. This technology is essential in the deployment of the intelligent transportation system, which is targeted to improve safety and efficiency of traffic. The implementation of VANETs can be effectively executed by transmitting data among vehicles with the use of multiple hops. However, the intrinsic characteristics of VANETs, such as its dynamic network topology and intermittent connectivity, limit data delivery. One particular challenge of this network is the possibility that the contributing node may only remain in the network for a limited time. Hence, to prevent data loss from that node, the information must reach the destination node via multi-hop routing techniques. An appropriate, efficient, and stable routing algorithm must be developed for various VANET applications to address the issues of dynamic topology and intermittent connectivity. Therefore, this paper proposes a novel routing algorithm called efficient and stable routing algorithm based on user mobility and node density (ESRA-MD). The proposed algorithm can adapt to significant changes that may occur in the urban vehicular environment. This algorithm works by selecting an optimal route on the basis of hop count and link duration for delivering data from source to destination, thereby satisfying various quality of service considerations. The validity of the proposed algorithm is investigated by its comparison with ARP-QD protocol, which works on the mechanism of optimal route finding in VANETs in urban environments. Simulation results reveal that the proposed ESRA-MD algorithm shows remarkable improvement in terms of delivery ratio, delivery delay, and communication overhead.
    Matched MeSH terms: Models, Theoretical*
  12. Ullah I, Bhattacharyya K, Shafie S, Khan I
    PLoS One, 2016;11(10):e0165348.
    PMID: 27776174 DOI: 10.1371/journal.pone.0165348
    Numerical results are presented for the effect of first order chemical reaction and thermal radiation on mixed convection flow of Casson fluid in the presence of magnetic field. The flow is generated due to unsteady nonlinearly stretching sheet placed inside a porous medium. Convective conditions on wall temperature and wall concentration are also employed in the investigation. The governing partial differential equations are converted to ordinary differential equations using suitable transformations and then solved numerically via Keller-box method. It is noticed that fluid velocity rises with increase in radiation parameter in the case of assisting flow and is opposite in the case of opposing fluid while radiation parameter has no effect on fluid velocity in the forced convection. It is also seen that fluid velocity and concentration enhances in the case of generative chemical reaction whereas both profiles reduces in the case of destructive chemical reaction. Further, increase in local unsteadiness parameter reduces fluid velocity, temperature and concentration. Over all the effects of physical parameters on fluid velocity, temperature and concentration distribution as well as on the wall shear stress, heat and mass transfer rates are discussed in detail.
    Matched MeSH terms: Models, Theoretical*
  13. Zomorodian M, Lai SH, Homayounfar M, Ibrahim S, Fatemi SE, El-Shafie A
    J Environ Manage, 2018 Dec 01;227:294-304.
    PMID: 30199725 DOI: 10.1016/j.jenvman.2018.08.097
    In recent years, water resources management has become more complicated and controversial due to the impacts of various factors affecting hydrological systems. System Dynamics (SD) has in turn become increasingly popular due to its advantages as a tool for dealing with such complex systems. However, SD also has some limitations. This review contains a comprehensive survey of the existing literature on SD as a potential method to deal with the complexity of system integrated modeling, with a particular focus on the application of SD to the integrated modeling of water resources systems. It discusses the limitations of SD in these contexts, and highlights a number of studies which have applied a combination of SD and other methods to overcome these limitations. Finally, our study makes a number of recommendations for future modifications in the application of SD methods in order to enhance their performance.
    Matched MeSH terms: Models, Theoretical*
  14. Wong YF, Ng HT, Leung KY, Chan KY, Chan SY, Loy CC
    J Biomed Inform, 2017 Oct;74:130-136.
    PMID: 28923366 DOI: 10.1016/j.jbi.2017.09.005
    OBJECTIVE: Oral pills, including tablets and capsules, are one of the most popular pharmaceutical dosage forms available. Compared to other dosage forms, such as liquid and injections, oral pills are very stable and are easy to be administered. However, it is not uncommon for pills to be misidentified, be it within the healthcare institutes or after the pills were dispensed to the patients. Our objective is to develop groundwork for automatic pill identification and verification using Deep Convolutional Network (DCN) that surpasses the existing methods.

    MATERIALS AND METHODS: A DCN model was developed using pill images captured with mobile phones under unconstraint environments. The performance of the DCN model was compared to two baseline methods of hand-crafted features.

    RESULTS: The DCN model outperforms the baseline methods. The mean accuracy rate of DCN at Top-1 return was 95.35%, whereas the mean accuracy rates of the two baseline methods were 89.00% and 70.65%, respectively. The mean accuracy rates of DCN for Top-5 and Top-10 returns, i.e., 98.75% and 99.55%, were also consistently higher than those of the baseline methods.

    DISCUSSION: The images used in this study were captured at various angles and under different level of illumination. DCN model achieved high accuracy despite the suboptimal image quality.

    CONCLUSION: The superior performance of DCN underscores the potential of Deep Learning model in the application of pill identification and verification.

    Matched MeSH terms: Models, Theoretical*
  15. Al-Dhaqm A, Razak S, Othman SH, Ngadi A, Ahmed MN, Ali Mohammed A
    PLoS One, 2017;12(2):e0170793.
    PMID: 28146585 DOI: 10.1371/journal.pone.0170793
    Database Forensics (DBF) is a widespread area of knowledge. It has many complex features and is well known amongst database investigators and practitioners. Several models and frameworks have been created specifically to allow knowledge-sharing and effective DBF activities. However, these are often narrow in focus and address specified database incident types. We have analysed 60 such models in an attempt to uncover how numerous DBF activities are really public even when the actions vary. We then generate a unified abstract view of DBF in the form of a metamodel. We identified, extracted, and proposed a common concept and reconciled concept definitions to propose a metamodel. We have applied a metamodelling process to guarantee that this metamodel is comprehensive and consistent.
    Matched MeSH terms: Models, Theoretical*
  16. Yeoh KL, Puay HT, Abdullah R, Abd Manan TS
    Water Sci Technol, 2023 Jul;88(1):75-91.
    PMID: 37452535 DOI: 10.2166/wst.2023.193
    Short-term streamflow prediction is essential for managing flood early warning and water resources systems. Although numerical models are widely used for this purpose, they require various types of data and experience to operate the model and often tedious calibration processes. Under the digital revolution, the application of data-driven approaches to predict streamflow has increased in recent decades. In this work, multiple linear regression (MLR) and random forest (RF) models with three different input combinations are developed and assessed for multi-step ahead short-term streamflow predictions, using 14 years of hydrological datasets from the Kulim River catchment, Malaysia. Introducing more precedent streamflow events as predictor improves the performance of these data-driven models, especially in predicting peak streamflow during the high-flow event. The RF model (Nash-Sutcliffe efficiency (NSE): 0.599-0.962) outperforms the MLR model (NSE: 0.584-0.963) in terms of overall prediction accuracy. However, with the increasing lead-time length, the models' overall prediction accuracy on the arrival time and magnitude of peak streamflow decrease. These findings demonstrate the potential of decision tree-based models, such as RF, for short-term streamflow prediction and offer insights into enhancing the accuracy of these data-driven models.
    Matched MeSH terms: Models, Theoretical*
  17. Kishore DJK, Mohamed MR, Sudhakar K, Peddakapu K
    Environ Sci Pollut Res Int, 2023 Jul;30(35):84167-84182.
    PMID: 37358770 DOI: 10.1007/s11356-023-28248-8
    At present, a photovoltaic (PV) system takes responsibility to reduce the risk of global warming and generate electricity. However, the PV system faces numerous problems to track global maximum peak power (GMPP) owing to the nonlinear nature of the environment especially due to partial shading conditions (PSC). To solve these difficulties, previous researchers have utilized various conventional methods for investigations. Nevertheless, these methods have oscillations around the GMPP. Hence, a new metaheuristic method such as an opposition-based equilibrium optimizer (OBEO) algorithm is used in this work for mitigating the oscillations around GMPP. To find the effectiveness of the proposed method, it can be evaluated with other methods such as SSA, GWO, and P&O. As per the simulation outcome, the proposed OBEO method provides maximum efficiency against all other methods. The efficiency for the proposed method under dynamic PSC is 95.09% in 0.16 s, similarly, 96.17% for uniform PSC and 86.25% for complex PSC.
    Matched MeSH terms: Models, Theoretical*
  18. Aldhaibani JA, Yahya A, Ahmad RB
    ScientificWorldJournal, 2014;2014:815720.
    PMID: 24672378 DOI: 10.1155/2014/815720
    The poor capacity at cell boundaries is not enough to meet the growing demand and stringent design which required high capacity and throughput irrespective of user's location in the cellular network. In this paper, we propose new schemes for an optimum fixed relay node (RN) placement in LTE-A cellular network to enhance throughput and coverage extension at cell edge region. The proposed approach mitigates interferences between all nodes and ensures optimum utilization with the optimization of transmitted power. Moreover, we proposed a new algorithm to balance the transmitted power of moving relay node (MR) over cell size and providing required SNR and throughput at the users inside vehicle along with reducing the transmitted power consumption by MR. The numerical analysis along with the simulation results indicates that an improvement in capacity for users is 40% increment at downlink transmission from cell capacity. Furthermore, the results revealed that there is saving nearly 75% from transmitted power in MR after using proposed balancing algorithm. ATDI simulator was used to verify the numerical results, which deals with real digital cartographic and standard formats for terrain.
    Matched MeSH terms: Models, Theoretical
  19. Lim KS, Buyamin S, Ahmad A, Shapiai MI, Naim F, Mubin M, et al.
    ScientificWorldJournal, 2014;2014:364179.
    PMID: 24883386 DOI: 10.1155/2014/364179
    The vector evaluated particle swarm optimisation (VEPSO) algorithm was previously improved by incorporating nondominated solutions for solving multiobjective optimisation problems. However, the obtained solutions did not converge close to the Pareto front and also did not distribute evenly over the Pareto front. Therefore, in this study, the concept of multiple nondominated leaders is incorporated to further improve the VEPSO algorithm. Hence, multiple nondominated solutions that are best at a respective objective function are used to guide particles in finding optimal solutions. The improved VEPSO is measured by the number of nondominated solutions found, generational distance, spread, and hypervolume. The results from the conducted experiments show that the proposed VEPSO significantly improved the existing VEPSO algorithms.
    Matched MeSH terms: Models, Theoretical
  20. Kalsum HU, Shah ZA, Othman RM, Hassan R, Rahim SM, Asmuni H, et al.
    Comput Biol Med, 2009 Nov;39(11):1013-9.
    PMID: 19720371 DOI: 10.1016/j.compbiomed.2009.08.002
    Protein domains contain information about the prediction of protein structure, function, evolution and design since the protein sequence may contain several domains with different or the same copies of the protein domain. In this study, we proposed an algorithm named SplitSSI-SVM that works with the following steps. First, the training and testing datasets are generated to test the SplitSSI-SVM. Second, the protein sequence is split into subsequence based on order and disorder regions. The protein sequence that is more than 600 residues is split into subsequences to investigate the effectiveness of the protein domain prediction based on subsequence. Third, multiple sequence alignment is performed to predict the secondary structure using bidirectional recurrent neural networks (BRNN) where BRNN considers the interaction between amino acids. The information of about protein secondary structure is used to increase the protein domain boundaries signal. Lastly, support vector machines (SVM) are used to classify the protein domain into single-domain, two-domain and multiple-domain. The SplitSSI-SVM is developed to reduce misleading signal, lower protein domain signal caused by primary structure of protein sequence and to provide accurate classification of the protein domain. The performance of SplitSSI-SVM is evaluated using sensitivity and specificity on single-domain, two-domain and multiple-domain. The evaluation shows that the SplitSSI-SVM achieved better results compared with other protein domain predictors such as DOMpro, GlobPlot, Dompred-DPS, Mateo, Biozon, Armadillo, KemaDom, SBASE, HMMPfam and HMMSMART especially in two-domain and multiple-domain.
    Matched MeSH terms: Models, Theoretical
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