Search results for: Tropical Rainfall Measuring Mission
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 868

Search results for: Tropical Rainfall Measuring Mission

598 Climatic Change, Drought and Dust Crisis in Iran

Authors: Akram Keramat, Behrouz Marivani, Mehdi Samsami

Abstract:

Drought is a phenomenon caused by environmental and climatic changes. This phenomenon is affected by shortage of rainfall and temperature. Dust is one of important environmental problems caused by climate change and drought. With recent multi-year drought, many environmental crises caused by dust in Iran and Middle East. Dust in the vast areas of the provinces occurs with high frequency. By dust affecting many problems created in terms of health, social and economic. In this study, we tried to study the most important factors causing dust. In this way we have used the satellite images and meteorological data. Finally, strategies to deal with the dust will be mentioned.

Keywords: Drought, Environment, Dust.

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597 Measuring the Influence of Functional Proximity on Environmental Urban Performance via Integrated Modification Methodology: Four Study Cases in Milan

Authors: M. Tadi, M. Hadi Mohammad Zadeh, Ozge Ogut

Abstract:

Although how cities’ forms are structured is studied, more efforts are needed on systemic comprehensions and evaluations of the urban morphology through quantitative metrics that are able to describe the performance of a city in relation to its formal properties. More research is required in this direction in order to better describe the urban form characteristics and their impact on the environmental performance of cities and to increase their sustainability stewardship. With the aim of developing a better understanding of the built environment’s systemic structure, the intention of this paper is to present a holistic methodology for studying the behavior of the built environment and investigate the methods for measuring the effect of urban structure to the environmental performance. This goal will be pursued through an inquiry into the morphological components of the urban systems and the complex relationships between them. Particularly, this paper focuses on proximity, referring to the proximity of different land-uses, is a concept with which Integrated Modification Methodology (IMM) explains how land-use allocation might affect the choice of mobility in neighborhoods, and especially, encourage or discourage non-motived mobility. This paper uses proximity to demonstrate that the structure attributes can quantifiably relate to the performing behavior in the city. The target is to devise a mathematical pattern from the structural elements and correlate it directly with urban performance indicators concerned with environmental sustainability. The paper presents some results of this rigorous investigation of urban proximity and its correlation with performance indicators in four different areas in the city of Milan, each of them characterized by different morphological features.

Keywords: Built environment, ecology, sustainable indicators, sustainability, urban morphology.

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596 The Building Thermal Performance and Carbon Sequestration Evaluation for Psophocarpus tetrogonobulus on Biofaçade Wall in the Tropical Environment

Authors: Abdul M. A. Rahman , Foong S. Yeok, Atikah F. Amir

Abstract:

Plants are commonly known for its positive correlation in reducing temperature. Since it can benefit buildings by modifying the microclimate, it-s also believed capable of reducing the internal temperature. Various experiments have been done in Universiti Sains Malaysia, Penang to investigate the comparison in thermal benefits between two rooms, one being a typical control room (exposed wall) and the other a biofacade room (plant shaded wall). The investigations were conducted during non-rainy season for approximately a month. Climbing plant Psophocarpus tetrogonobulus from legume species was selected as insulation for the biofacade wall. Conclusions were made on whether the biofacade can be used to tackle the energy efficiency, based on the parameters taken into consideration.

Keywords: biofacade, thermal benefits, carbon sequestration, Psophocarpus tetrogonobulus.

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595 Implementation of an On-Line PD Measurement System Using HFCT

Authors: F. Haghjoo, M. Sarlak, S.M. Shahrtash

Abstract:

In order to perform on-line measuring and detection of PD signals, a total solution composing of an HFCT, A/D converter and a complete software package is proposed. The software package includes compensation of HFCT contribution, filtering and noise reduction using wavelet transform and soft calibration routines. The results have shown good performance and high accuracy.

Keywords: Partial Discharge, Measurement, On-line, HFCT

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594 Characteristics of Different Solar PV Modules under Partial Shading

Authors: Hla Hla Khaing, Yit Jian Liang, Nant Nyein Moe Htay, Jiang Fan

Abstract:

Partial shadowing is one of the problems that are always faced in terrestrial applications of solar photovoltaic (PV). The effects of partial shadow on the energy yield of conventional mono-crystalline and multi-crystalline PV modules have been researched for a long time. With deployment of new thin-film solar PV modules in the market, it is important to understand the performance of new PV modules operating under the partial shadow in the tropical zone. This paper addresses the impacts of different partial shadowing on the operating characteristics of four different types of solar PV modules that include multi-crystalline, amorphous thin-film, CdTe thin-film and CIGS thin-film PV modules.

Keywords: Partial shade, CdTe, CIGS, multi-crystalline (mc-Si), amorphous silicon (a-Si), bypass diode.

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593 Genetic Algorithm Based Optimal Control for a 6-DOF Non Redundant Stewart Manipulator

Authors: A. Omran, G. El-Bayiumi, M. Bayoumi, A. Kassem

Abstract:

Applicability of tuning the controller gains for Stewart manipulator using genetic algorithm as an efficient search technique is investigated. Kinematics and dynamics models were introduced in detail for simulation purpose. A PD task space control scheme was used. For demonstrating technique feasibility, a Stewart manipulator numerical-model was built. A genetic algorithm was then employed to search for optimal controller gains. The controller was tested onsite a generic circular mission. The simulation results show that the technique is highly convergent with superior performance operating for different payloads.

Keywords: Stewart kinematics, Stewart dynamics, task space control, genetic algorithm.

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592 Advanced Deployable/Retractable Solar Panel System for Satellite Applications

Authors: Zane Brough, Claudio Paoloni

Abstract:

Modern low earth orbit (LEO) satellites that require multi-mission flexibility are highly likely to be repositioned between different operational orbits. While executing this process the satellite may experience high levels of vibration and environmental hazards, exposing the deployed solar panel to dangerous stress levels, fatigue and space debris, hence it is desirable to retract the solar array before satellite repositioning to avoid damage or failure.

A novel concept of deployable/retractable hybrid solar array systemcomposed of both rigid and flexible solar panels arranged within a petal formation, aimed to provide a greater power to volume ratio while dramatically reducing mass and cost is proposed.

Keywords: Deployable Solar Panel, Satellite, Retractable Solar Panel, Hybrid Solar Panel.

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591 Conceptual Design of an Aircraft with Maglev Landing System

Authors: Nishanth Murugan, Mohammed Niyasdeen Nejaamtheen, S. Sounder Rajan

Abstract:

The accelerated growth in aircraft industries desire effectual schemes, programs, innovative designs of advanced systems to accomplishing the augmenting need for home-free air transportation. In this paper, a contemporary conceptual design of an airplane has been proposed without landing gear systems in order to reducing accidents, time consumption, and to eliminating drawbacks by using superconducting levitation phenomenon. This invention of an airplane with superconductive material coating, on the solar plexus region assist to reduce weight by approximately 4% of the total takeoff weight, and cost effective. Moreover, we conjectured that superconductor landing system reduces ground friction, mission fuel, total drag, take-off and landing distance.

Keywords: Aircraft landing system, Magnetic levitation, Superconductors, Take-off and landing.

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590 Climatic Factors Affecting on Influenza Casesin Nakhon Si Thammarat

Authors: S. Chumkiew, W. Srisang, M. Jaroensutasinee, K. Jaroensutasinee

Abstract:

This study investigated the climatic factors associated with Influenza incidence in Nakhon Si Thammarat, Southern Thailand. Climatic factors comprised of the amount of rainfall, percent of rainy days, relative humidity, wind speed, maximum, minimum temperatures and temperature difference. A multiple stepwise regression technique was used to fit the statistical model. The result showed that the temperature difference and percent of rainy days were positively associated with Influenza incidence in Nakhon Si Thammarat.

Keywords: Influenza, Climatic Factor, Relative Humidity, Rainy day, Wind Speed.

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589 Harvesting of Kinetic Energy of the Raindrops

Authors: K. C. R. Perera, B. G. Sampath, V. P. C. Dassanayake, B. M. Hapuwatte.

Abstract:

This paper presents a methodology to harvest the kinetic energy of the raindrops using piezoelectric devices. In the study 1m×1m PVDF (Polyvinylidene fluoride) piezoelectric membrane, which is fixed by the four edges, is considered for the numerical simulation on deformation of the membrane due to the impact of the raindrops. Then according to the drop size of the rain, the simulation is performed classifying the rainfall types into three categories as light stratiform rain, moderate stratiform rain and heavy thundershower. The impact force of the raindrop is dependent on the terminal velocity of the raindrop, which is a function of raindrop diameter. The results were then analyzed to calculate the harvestable energy from the deformation of the piezoelectric membrane.

Keywords: Raindrop, piezoelectricity, deformation, terminal velocity.

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588 Heritage Tree Expert Assessment and Classification: Malaysian Perspective

Authors: B.-Y.-S. Lau, Y.-C.-T. Jonathan, M.-S. Alias

Abstract:

Heritage trees are natural large, individual trees with exceptionally value due to association with age or event or distinguished people. In Malaysia, there is an abundance of tropical heritage trees throughout the country. It is essential to set up a repository of heritage trees to prevent valuable trees from being cut down. In this cross domain study, a web-based online expert system namely the Heritage Tree Expert Assessment and Classification (HTEAC) is developed and deployed for public to nominate potential heritage trees. Based on the nomination, tree care experts or arborists would evaluate and verify the nominated trees as heritage trees. The expert system automatically rates the approved heritage trees according to pre-defined grades via Delphi technique. Features and usability test of the expert system are presented. Preliminary result is promising for the system to be used as a full scale public system.

Keywords: Arboriculture, Delphi, expert system, heritage tree, urban forestry.

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587 Internal Surface Measurement of Nanoparticle with Polarization-interferometric Nonlinear Confocal Microscope

Authors: Chikara Egami, Kazuhiro Kuwahara

Abstract:

Polarization-interferometric nonlinear confocal microscopy is proposed for measuring a nano-sized particle with optical anisotropy. The anisotropy in the particle was spectroscopically imaged through a three-dimensional distribution of third-order nonlinear dielectric polarization photoinduced.

Keywords: nanoparticle, optical storage, microscope

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586 Energy Management Techniques in Mobile Robots

Authors: G. Gurguze, I. Turkoglu

Abstract:

Today, the developing features of technological tools with limited energy resources have made it necessary to use energy efficiently. Energy management techniques have emerged for this purpose. As with every field, energy management is vital for robots that are being used in many areas from industry to daily life and that are thought to take up more spaces in the future. Particularly, effective power management in autonomous and multi robots, which are getting more complicated and increasing day by day, will improve the performance and success. In this study, robot management algorithms, usage of renewable and hybrid energy sources, robot motion patterns, robot designs, sharing strategies of workloads in multiple robots, road and mission planning algorithms are discussed for efficient use of energy resources by mobile robots. These techniques have been evaluated in terms of efficient use of existing energy resources and energy management in robots.

Keywords: Energy management, mobile robot, robot administration, robot management, robot planning.

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585 God in Jesus, a Daimonion in Socrates and Their Respective Divine Communication

Authors: Yip-Mei Loh

Abstract:

Jesus and Socrates shared a remarkable gift; a channel of inner spiritual communication, to afford them truthful guidance in their respective religious discourse. Jesus is part of the Trinity; he is the Son, the Son of God. In mortal life he is the son of a carpenter. He called on all peoples to repent of their sins but fell foul of the authorities and was crucified. Socrates was an ancient Greek philosopher and the son of an artisan. His mission is to drive the Athenians to investigate truth, but he too incurs the displeasure of fellow citizens, to the extent of execution. The accusations made against them centre around, in Jesus’ case, proclaiming himself the Son of God, with the means to pardon, and in Socrates’, that a daimonion, an inner voice, speaks to him in his heart. Jesus talks with God directly through prayer, as the pneuma of God, i.e. to pneuma to hagion, or Holy Spirit, is with him. Socrates seems to enter what we would now think of as a trance-like condition, wherein he communicates with his inner daimonion, who directs him to take courage on the righteous path.

Keywords: Daimonion, God, Holy Spirit, life, truth.

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584 Adaptive Thermal Comfort Model for Air-Conditioned Lecture Halls in Malaysia

Authors: B. T. Chew, S. N. Kazi, A. Amiri

Abstract:

This paper presents an adaptive thermal comfort model study in the tropical country of Malaysia. A number of researchers have been interested in applying the adaptive thermal comfort model to different climates throughout the world, but so far no study has been performed in Malaysia. For the use as a thermal comfort model, which better applies to hot and humid climates, the adaptive thermal comfort model was developed as part of this research by using the collected results from a large field study in six lecture halls with 178 students. The relationship between the operative temperature and behavioral adaptations was determined. In the developed adaptive model, the acceptable indoor neutral temperatures lay within the range of 23.9-26.0C, with outdoor temperatures ranging between 27.0-34.6C. The most comfortable temperature for students in lecture hall was 25.7C.

Keywords: Hot and humid, Lecture halls, Neutral temperature, Adaptive thermal comfort model.

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583 A Mathematical Framework for Expanding a Railway’s Theoretical Capacity

Authors: Robert L. Burdett, Bayan Bevrani

Abstract:

Analytical techniques for measuring and planning railway capacity expansion activities have been considered in this article. A preliminary mathematical framework involving track duplication and section sub divisions is proposed for this task. In railways, these features have a great effect on network performance and for this reason they have been considered. Additional motivations have also arisen from the limitations of prior models that have not included them.

Keywords: Capacity analysis, capacity expansion, railways.

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582 Data Oriented Model of Image: as a Framework for Image Processing

Authors: A. Habibizad Navin, A. Sadighi, M. Naghian Fesharaki, M. Mirnia, M. Teshnelab, R. Keshmiri

Abstract:

This paper presents a new data oriented model of image. Then a representation of it, ADBT, is introduced. The ability of ADBT is clustering, segmentation, measuring similarity of images etc, with desired precision and corresponding speed.

Keywords: Data oriented modelling, image, clustering, segmentation, classification, ADBT and image processing.

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581 MIOM: A Mixed-Initiative Operational Model for Robots in Urban Search and Rescue

Authors: Mario Gianni, Federico Nardi, Federico Ferri, Filippo Cantucci, Manuel A. Ruiz Garcia, Karthik Pushparaj, Fiora Pirri

Abstract:

In this paper, we describe a Mixed-Initiative Operational Model (MIOM) which directly intervenes on the state of the functionalities embedded into a robot for Urban Search&Rescue (USAR) domain applications. MIOM extends the reasoning capabilities of the vehicle, i.e. mapping, path planning, visual perception and trajectory tracking, with operator knowledge. Especially in USAR scenarios, this coupled initiative has the main advantage of enhancing the overall performance of a rescue mission. In-field experiments with rescue responders have been carried out to evaluate the effectiveness of this operational model.

Keywords: Actively articulated tracked vehicles, mixed-initiative planning interfeces, robot planning, urban search and rescue.

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580 Multidisciplinary and Multilevel Design Methodology of Unmanned Aerial Vehicles Using Enhanced Collaborative Optimization

Authors: Pedro F. Albuquerque, Pedro V. Gamboa, Miguel A. Silvestre

Abstract:

The present work describes the implementation of the Enhanced Collaborative Optimization (ECO) multilevel architecture with a gradient-based optimization algorithm with the aim of performing a multidisciplinary design optimization of a generic unmanned aerial vehicle with morphing technologies. The concepts of weighting coefficient and dynamic compatibility parameter are presented for the ECO architecture. A routine that calculates the aircraft performance for the user defined mission profile and vehicle’s performance requirements has been implemented using low fidelity models for the aerodynamics, stability, propulsion, weight, balance and flight performance. A benchmarking case study for evaluating the advantage of using a variable span wing within the optimization methodology developed is presented.

Keywords: Multidisciplinary, Multilevel, Morphing, Enhanced Collaborative Optimization (ECO).

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579 Validation on 3D Surface Roughness Algorithm for Measuring Roughness of Psoriasis Lesion

Authors: M.H. Ahmad Fadzil, Esa Prakasa, Hurriyatul Fitriyah, Hermawan Nugroho, Azura Mohd Affandi, S.H. Hussein

Abstract:

Psoriasis is a widespread skin disease affecting up to 2% population with plaque psoriasis accounting to about 80%. It can be identified as a red lesion and for the higher severity the lesion is usually covered with rough scale. Psoriasis Area Severity Index (PASI) scoring is the gold standard method for measuring psoriasis severity. Scaliness is one of PASI parameter that needs to be quantified in PASI scoring. Surface roughness of lesion can be used as a scaliness feature, since existing scale on lesion surface makes the lesion rougher. The dermatologist usually assesses the severity through their tactile sense, therefore direct contact between doctor and patient is required. The problem is the doctor may not assess the lesion objectively. In this paper, a digital image analysis technique is developed to objectively determine the scaliness of the psoriasis lesion and provide the PASI scaliness score. Psoriasis lesion is modelled by a rough surface. The rough surface is created by superimposing a smooth average (curve) surface with a triangular waveform. For roughness determination, a polynomial surface fitting is used to estimate average surface followed by a subtraction between rough and average surface to give elevation surface (surface deviations). Roughness index is calculated by using average roughness equation to the height map matrix. The roughness algorithm has been tested to 444 lesion models. From roughness validation result, only 6 models can not be accepted (percentage error is greater than 10%). These errors occur due the scanned image quality. Roughness algorithm is validated for roughness measurement on abrasive papers at flat surface. The Pearson-s correlation coefficient of grade value (G) of abrasive paper and Ra is -0.9488, its shows there is a strong relation between G and Ra. The algorithm needs to be improved by surface filtering, especially to overcome a problem with noisy data.

Keywords: psoriasis, roughness algorithm, polynomial surfacefitting.

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578 Making a ‘Once-upon-a-Time’ Mythology in Kazuo Ishiguro’s The Buried Giant

Authors: Masami Usui

Abstract:

Kazuo Ishiguro’s challenging novel, The Buried Giant, embodies how contemporary writers and readers have to discover the voices buried in our history. By avoiding setting or connecting the modern and contemporary historical incidents such as World War II this time, Ishiguro ventures into retelling myth, transfiguring historical facts, and revealing what has been forgotten in a process of establishing history and creating mythology. As generally known, modernist writers in the twentieth century employed materials from authorized classical mythologies, especially Greek mythology. As an heir of this tradition, Ishiguro imposes his mission of criticizing the repeatedly occurring yet easily-forgotten history of dictatorship and a slaughter on mythology based on King Arthur and its related heroes and myths in Britain. On an open ground, Ishiguro can start his own mythical story and space.

Keywords: English literature, fantasy, global literature, mythology.

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577 An Analysis of Learners’ Reports for Measuring Co-Creational Education

Authors: Takatoshi Ishii, Koji Kimita, Keiichi Muramatsu, Yoshiki Shimomura

Abstract:

To increase the quality of learning, teacher and learner need mutual effort for realization of educational value. For this purpose, we need to manage the co-creational education among teacher and learners. In this research, we try to find a feature of co-creational education. To be more precise, we analyzed learners’ reports by natural language processing, and extract some features that describe the state of the co-creational education.

Keywords: Co-creational education, e-portfolios, ICT integration, labeled Latent Dirichlet allocation.

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576 Suitability of Black Box Approaches for the Reliability Assessment of Component-Based Software

Authors: Anjushi Verma, Tirthankar Gayen

Abstract:

Although, reliability is an important attribute of quality, especially for mission critical systems, yet, there does not exist any versatile model even today for the reliability assessment of component-based software. The existing Black Box models are found to make various assumptions which may not always be realistic and may be quite contrary to the actual behaviour of software. They focus on observing the manner in which the system behaves without considering the structure of the system, the components composing the system, their interconnections, dependencies, usage frequencies, etc.As a result, the entropy (uncertainty) in assessment using these models is much high.Though, there are some models based on operation profile yet sometimes it becomes extremely difficult to obtain the exact operation profile concerned with a given operation. This paper discusses the drawbacks, deficiencies and limitations of Black Box approaches from the perspective of various authors and finally proposes a conceptual model for the reliability assessment of software.

Keywords: Black Box, faults, failure, software reliability.

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575 Soil Mass Loss Reduction during Rainfalls by Reinforcing the Slopes with the Surficial Confinement

Authors: Ramli Nazir, Hossein Moayedi

Abstract:

Soil confinement systems serve as effective solutions to any erosion control project. Various confinements systems, namely triangular, circular and rectangular with the size of 50, 100, and 150 mm, and with a depth of 10 mm, were embedded in soil samples at slope angle of 60°. The observed soil mass losses for the confined soil systems were much smaller than those from unconfined system. As a result, the size of confinement and rainfall intensity have a direct effect on the soil mass loss. The triangular and rectangular confinement systems showed the lowest and highest soil loss masses, respectively. The slopes also failed much faster in the unconfined system than in the confined slope.

Keywords: Erosion control, Soil confinement, Soil erosion, Slope stability.

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574 Dynamics of Functional Composition of a Brazilian Tropical Forest in Response to Drought Stress

Authors: Theodore N.S. Karfakis, Anna Andrade

Abstract:

The aim of this study was to examine the dynamics of functional composition of a non flooded Amazonian forest in response to drought stress in terms of diameter growth, recruitment and mortality. The survey was carried out in the continuous forest of the Biological dynamics of forest fragments project 90 km outside the city of Manaus, state of Amazonas Brazil. All stems >10 cm dbh where identified to species level and monitored in 18 one hectare permanent sample plots from 1981 to 2004.For statistical analysis all species where aggregated in three ecological guilds. Two distinct drought events occurred in 1983 and 1997. Results showed that more early successional species performed better than later successional ones. Response was significant for both events but for the 1997 event this was more pronounced possibly because of the fact that the event was in the middle of the dry rather than the wet period as was the 1983 one.

Keywords: Brazil, functional composition, drought, Amazonian non flooded forest.

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573 Using High Performance Computing for Online Flood Monitoring and Prediction

Authors: Stepan Kuchar, Martin Golasowski, Radim Vavrik, Michal Podhoranyi, Boris Sir, Jan Martinovic

Abstract:

The main goal of this article is to describe the online flood monitoring and prediction system Floreon+ primarily developed for the Moravian-Silesian region in the Czech Republic and the basic process it uses for running automatic rainfall-runoff and hydrodynamic simulations along with their calibration and uncertainty modeling. It takes a long time to execute such process sequentially, which is not acceptable in the online scenario, so the use of a high performance computing environment is proposed for all parts of the process to shorten their duration. Finally, a case study on the Ostravice River catchment is presented that shows actual durations and their gain from the parallel implementation.

Keywords: Flood prediction process, High performance computing, Online flood prediction system, Parallelization.

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572 A Mark-Up Approach to Add Value

Authors: Ivaylo I. Atanasov, Evelina N.Pencheva

Abstract:

This paper presents a mark-up approach to service creation in Next Generation Networks. The approach allows deriving added value from network functions exposed by Parlay/OSA (Open Service Access) interfaces. With OSA interfaces service logic scripts might be executed both on callrelated and call-unrelated events. To illustrate the approach XMLbased language constructions for data and method definitions, flow control, time measuring and supervision and database access are given and an example of OSA application is considered.

Keywords: Service creation, mark-up approach.

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571 Hydrological Method to Evaluate Environmental Flow (Case Study: Gharasou River, Ardabil)

Authors: Mehdi Fuladipanah, Mehdi Jorabloo

Abstract:

Water flow management is one of the most important parts of river engineering. Non-uniformity distribution of rainfall and various flow demand with unreasonable flow management will be caused destroyed of river ecosystem. Then, it is very serious to determine ecosystem flow requirement. In this paper, Flow duration curve indices method which has hydrological based was used to evaluate environmental flow in Gharasou River, Ardabil, Iran. Using flow duration curve, Q90 and Q95 for different return periods were calculated. Their magnitude were determined as 1-day, 3-day, 7-day and 30 day. According the second method, hydraulic alteration indices often had low and medium range. In order to maintain river at an acceptable ecological condition, minimum daily discharge of index Q95 is 0.7 m3.s-1.

Keywords: Ardabil, Environmental flow, Flow Duration Curve, Gharasou River.

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570 Rule Insertion Technique for Dynamic Cell Structure Neural Network

Authors: Osama Elsarrar, Marjorie Darrah, Richard Devin

Abstract:

This paper discusses the idea of capturing an expert’s knowledge in the form of human understandable rules and then inserting these rules into a dynamic cell structure (DCS) neural network. The DCS is a form of self-organizing map that can be used for many purposes, including classification and prediction. This particular neural network is considered to be a topology preserving network that starts with no pre-structure, but assumes a structure once trained. The DCS has been used in mission and safety-critical applications, including adaptive flight control and health-monitoring in aerial vehicles. The approach is to insert expert knowledge into the DCS before training. Rules are translated into a pre-structure and then training data are presented. This idea has been demonstrated using the well-known Iris data set and it has been shown that inserting the pre-structure results in better accuracy with the same training.

Keywords: Neural network, rule extraction, rule insertion, self-organizing map.

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569 SAF: A Substitution and Alignment Free Similarity Measure for Protein Sequences

Authors: Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski

Abstract:

The literature reports a large number of approaches for measuring the similarity between protein sequences. Most of these approaches estimate this similarity using alignment-based techniques that do not necessarily yield biologically plausible results, for two reasons. First, for the case of non-alignable (i.e., not yet definitively aligned and biologically approved) sequences such as multi-domain, circular permutation and tandem repeat protein sequences, alignment-based approaches do not succeed in producing biologically plausible results. This is due to the nature of the alignment, which is based on the matching of subsequences in equivalent positions, while non-alignable proteins often have similar and conserved domains in non-equivalent positions. Second, the alignment-based approaches lead to similarity measures that depend heavily on the parameters set by the user for the alignment (e.g., gap penalties and substitution matrices). For easily alignable protein sequences, it's possible to supply a suitable combination of input parameters that allows such an approach to yield biologically plausible results. However, for difficult-to-align protein sequences, supplying different combinations of input parameters yields different results. Such variable results create ambiguities and complicate the similarity measurement task. To overcome these drawbacks, this paper describes a novel and effective approach for measuring the similarity between protein sequences, called SAF for Substitution and Alignment Free. Without resorting either to the alignment of protein sequences or to substitution relations between amino acids, SAF is able to efficiently detect the significant subsequences that best represent the intrinsic properties of protein sequences, those underlying the chronological dependencies of structural features and biochemical activities of protein sequences. Moreover, by using a new efficient subsequence matching scheme, SAF more efficiently handles protein sequences that contain similar structural features with significant meaning in chronologically non-equivalent positions. To show the effectiveness of SAF, extensive experiments were performed on protein datasets from different databases, and the results were compared with those obtained by several mainstream algorithms.

Keywords: Protein, Similarity, Substitution, Alignment.

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