Search results for: intelligent computational technologies.

Authors: E. Barkanov, E. Skukis, M. Wesolowski, A. Chate

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New nondestructive technique, namely an inverse technique based on vibration tests, to characterize nonlinear mechanical properties of adhesive layers in sandwich composites is developed. An adhesive layer is described as a viscoelastic isotropic material with storage and loss moduli which are both frequency dependent values in wide frequency range. An optimization based on the planning of experiments and response surface technique to minimize the error functional is applied to decrease considerably the computational expenses. The developed identification technique has been tested on aluminum panels and successfully applied to characterize viscoelastic material properties of 3M damping polymer ISD-112 used as a core material in sandwich panels.

Keywords: Adhesive layer, finite element method, inverse technique, sandwich panel, vibration test, viscoelastic material properties.

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Authors: Tomáš Ludík, Jiří Barta, Josef Navrátil

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Natural or human made disasters have a significant negative impact on the environment. At the same time there is an extensive effort to support management and decision making in emergency situations by information technologies. Therefore the purpose of the paper is to propose a design patterns applicable in emergency management, enabling better analysis and design of emergency management processes and therefore easier development and deployment of information systems in the field of emergency management. It will be achieved by detailed analysis of existing emergency management legislation, contingency plans and information systems. The result is a set of design patterns focused at emergency management processes that enable easier design of emergency plans or development of new information system. These results will have a major impact on the development of new information systems as well as to more effective and faster solving of emergencies.

Keywords: Analysis and Design, Business Process Modeling Notation, Contingency Plans, Design Patterns, Emergency Management.

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Authors: Jung-Chuan Chou, Wei-Chuan Chen, Chien-Cheng Chen

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This study is concerned with pH solution detection using 2 × 4 flexible sensor array based on a plastic polyethylene terephthalate (PET) substrate that is coated a conductive layer and a ruthenium dioxide (RuO2) sensitive membrane with the technologies of screen-printing and RF sputtering. For data analysis, we also prepared a dynamic measurement system for acquiring the response voltage and analyzing the characteristics of the working electrodes (WEs), such as sensitivity and linearity. In this condition, an array measurement system was designed to acquire the original signal from sensor array, and it is based on the method of digital signal processing (DSP). The DSP modifies the unstable acquisition data to a direct current (DC) output using the technique of digital filter. Hence, this sensor array can obtain a satisfactory yield, 62.5%, through the design measurement and analysis system in our laboratory.

Keywords: Flexible sensor array, PET, RuO2, dynamic measurement, data analysis.

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Authors: Baharak Khoshkholgh-Sima, Soroush Sardari, Jalal Izadi Mobarakeh, Ramezan Ali Khavari-Nejad

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There is an urgent need to develop novel Mycobacterium tuberculosis (Mtb) drugs that are active against drug resistant bacteria but, more importantly, kill persistent bacteria. Our study structured based on integrated analysis of metabolic pathways, small molecule screening and similarity Search in PubChem Database. Metabolic analysis approaches based on Unified weighted used for potent target selection. Our results suggest that pantothenate synthetase (panC) and and 3-methyl-2-oxobutanoate hydroxymethyl transferase (panB) as a appropriate drug targets. In our study, we used pantothenate synthetase because of existence inhibitors. We have reported the discovery of new antitubercular compounds through ligand based approaches using computational tools.

Keywords: In Silico, Ligand-based Virtual Screening, Metabolic Pathways, Mycobacterium tuberculosis

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Authors: P. P. S. Sifolo, M. J. Maimela M. P. Tladi

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This article investigates technology used by Tshwane residents intended for tourism purposes. The aim is to contribute information for planning and management concerning technology within the tourism sector in the city of Tshwane, South Africa. This study identified the types of tourist related technologies used by the Tshwane residents, be it for business purposes or personal use. The study connected the exploitation of technology for tourism purposes through unpacking the tourism sector as it utilizes technology. Quantitative research methodology was used whereby self-completed questionnaires were chosen as research instruments. The research study carried out a search for knowledge on technology for tourism and the Tshwane residents; however the study revealed that technology has certainly imprinted tourism massively because of its effectiveness and efficiency. Technology has assisted tourism businesses stay abreast of competition with integrated communication technology (ICT) and because of that, SA is on the map as one of the economically performing countries in Africa. Moreover, technology and tourism make a meaningful impact on job creation and Gross Domestic Product (GDP).

Keywords: Information and Communication Technology, Technology for tourism, Tshwane residents.

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Authors: P. Bárta

Abstract:

Increasing demand on the performance of Subsea Production Systems (SPS) suggests a need for more detailed investigation of fluid behavior taking place in subsea equipment. Complete CFD cool down analyses of subsea equipment are very time demanding. The objective of this paper is to investigate a Locked CFD approach, which enables significant reduction of the computational time and at the same time maintains sufficient accuracy during thermal cool down simulations. The result comparison of a dead leg simulation using the Full CFD and the three LCFD-methods confirms the validity of the locked flow field assumption for the selected case. For the tested case the LCFD simulation speed up by factor of 200 results in the absolute thermal error of 0.5 °C (3% relative error), speed up by factor of 10 keeps the LCFD results within 0.1 °C (0.5 % relative error) comparing to the Full CFD.

Keywords: CFD, Locked Flow Field, Speed up of CFD simulation time, Subsea

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Authors: Ding Guo-hao, Li Hua, Wang Wen-long

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A parallel computational fluid dynamics code has been developed for the study of aerodynamic heating problem in hypersonic flows. The code employs the 3D Navier-Stokes equations as the basic governing equations to simulate the laminar hypersonic flow. The cell centered finite volume method based on structured grid is applied for spatial discretization. The AUSMPW+ scheme is used for the inviscid fluxes, and the MUSCL approach is used for higher order spatial accuracy. The implicit LU-SGS scheme is applied for time integration to accelerate the convergence of computations in steady flows. A parallel programming method based on MPI is employed to shorten the computing time. The validity of the code is demonstrated by comparing the numerical calculation result with the experimental data of a hypersonic flow field around a blunt body.

Keywords: Aerodynamic Heating, AUSMPW+, MPI, ParallelComputation

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Authors: Min Goo Choi, Jung Hoon Jung, Jae Wook Jeon

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Assessment for image quality traditionally needs its original image as a reference. The conventional method for assessment like Mean Square Error (MSE) or Peak Signal to Noise Ratio (PSNR) is invalid when there is no reference. In this paper, we present a new No-Reference (NR) assessment of image quality using blur and noise. The recent camera applications provide high quality images by help of digital Image Signal Processor (ISP). Since the images taken by the high performance of digital camera have few blocking and ringing artifacts, we only focus on the blur and noise for predicting the objective image quality. The experimental results show that the proposed assessment method gives high correlation with subjective Difference Mean Opinion Score (DMOS). Furthermore, the proposed method provides very low computational load in spatial domain and similar extraction of characteristics to human perceptional assessment.

Keywords: No Reference, Image Quality Assessment, blur, noise.

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Authors: Sadia Afroza, Rakiba Rouf

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Road safety and associated behaviors have received significant attention in recent years, reflecting general public concern. This paper portrays a statistical scenario of the young drivers in UAE with emphasis on various concern points of young driver’s behavior and license issuance. Although there are many factors contributing to road accidents, statistically it is evident that age plays a major role in road accidents. Despite ensuring strict road safety laws enforced by the UAE government, there is a staggering correlation among road accidents and young driver’s at UAE. However, private organizations like BMW and RoadSafetyUAE have extended its support on conducting surveys on driver’s behavior with an aim to ensure road safety. Various strategies such as road safety law enforcement, license issuance, adapting new technologies like safety cameras and raising awareness can be implemented to improve the road safety concerns among young drivers.

Keywords: Driving behavior, GLDS, road safety, UAE drivers, young drivers.

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Authors: Isaias Ramirez, Jose Luis Silva, Carlos Gonzalez, Gustavo Candelaria, Jose Pepe Rasgado, Carlos Carrillo

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This paper presents the experience in an eLearning training project that is being implemented for electrical planning engineers from the national Mexican utility Comision Federal de Electricidad (CFE) Distribution. This modality is implemented and will be used in the utility for training purposes to help personnel in their daily technical activities. One important advantage of this training project is that once it is implemented and applied, financial resources will be saved by CFE Distribution Company because online training will be used in all the country; the infrastructure for the eLearning training will be uploaded in computational servers installed in the National CFE Distribution Training Department, in Ciudad de Mexico, and can be used in workplaces of 16 Distribution Divisions and 150 Zones of CFE Distribution. In this way, workers will not need to travel to the National Training Department, saving enormous efforts, financial, and human resources.

Keywords: Moodle, eLearning, corporate training, electrical planning engineer.

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Authors: Cafer Görkem Pınar, İlker Coşar, Serkan Uzun, Atahan Çelebi, Mehmet Ali Ersoy, Ali Pınarbaşı

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In this study, it was numerically investigated that a 1:1 scale model of the Renault Clio MK4 SW brand vehicle aerodynamic analysis was performed in the commercial computational fluid dynamics (CFD) package program of ANSYS CFX 2021 R1 under steady, subsonic, and 3-D conditions. The model of vehicle used for the analysis was made independent of the number of mesh elements and the k-epsilon turbulence model was applied during the analysis. Results were interpreted as streamlines, pressure gradient, and turbulent kinetic energy contours around the vehicle at 50 km/h and 100 km/h speeds. In addition, the validity of the analysis was decided by comparing the drag coefficient of the vehicle with the values in the literature. As a result, the pressure gradient contours of the taillight of the Renault Clio MK4 SW vehicle were examined and the behavior of the total force at speeds of 50 km/h and 100 km/h was interpreted.

Keywords: CFD, k-epsilon, aerodynamics, drag coefficient, taillight.

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Authors: Lei Wang, Jiahao Zhou

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The development of heterogeneous computing clusters provides robust computational support for large-scale workflows, commonly seen in domains such as scientific computing and artificial intelligence. However, the tasks within these large-scale workflows are increasingly heterogeneous, exhibiting varying demands on computing resources. This shift necessitates the integration of resource-constrained considerations into the workflow scheduling problem on heterogeneous computing platforms. In this study, we propose a scheduling algorithm designed to minimize the makespan under heterogeneous constraints, employing a greedy strategy to effectively address the scheduling challenges posed by heterogeneous workflows. We evaluate the performance of the proposed algorithm using randomly generated heterogeneous workflows and a corresponding heterogeneous computing platform. The experimental results demonstrate a 15.2% improvement in performance compared to existing state-of-the-art methods.

Keywords: Heterogeneous Computing, Workflow Scheduling, Constrained Resources, Minimal Makespan.

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Authors: E. Sok, Y. Zhuo, S. Wang

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A hybrid Photovoltaic/Thermal (PV/T) solar system integrates photovoltaic and solar thermal technologies into one single solar energy device, with dual generation of electricity and heat energy. The aim of the present study is to evaluate the potential for introduction of the PV/T technology into Northern China. For this purpose, outdoor experiments were conducted on a prototype of a PV/T water-heating system. The annual thermal and electrical performances were investigated under the climatic conditions of Beijing. An economic analysis of the system was then carried out, followed by a sensitivity study. The analysis revealed that the hybrid system is not economically attractive with the current market and energy prices. However, considering the continuous commitment of the Chinese government towards policy development in the renewable energy sector, and technological improvements like the increasing cost-effectiveness of PV cells, PV/Thermal technology may become economically viable in the near future.

Keywords: Hybrid Photovoltaic/Thermal (PV/T), Solar energy, Economic analysis

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Authors: Achraf El Allali, John R. Rose

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A number of competing methodologies have been developed to identify genes and classify DNA sequences into coding and non-coding sequences. This classification process is fundamental in gene finding and gene annotation tools and is one of the most challenging tasks in bioinformatics and computational biology. An information theory measure based on mutual information has shown good accuracy in classifying DNA sequences into coding and noncoding. In this paper we describe a species independent iterative approach that distinguishes coding from non-coding sequences using the mutual information measure (MIM). A set of sixty prokaryotes is used to extract universal training data. To facilitate comparisons with the published results of other researchers, a test set of 51 bacterial and archaeal genomes was used to evaluate MIM. These results demonstrate that MIM produces superior results while remaining species independent.

Keywords: Coding Non-coding Classification, Entropy, GeneRecognition, Mutual Information.

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Authors: Igor Nedelkovski, Ilios Vilos, Tale Geramitcioski

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Computational simulation of steam flow and heat transfer in power plant condensers on the basis of the threedimensional mathematical model for the flow through porous media is presented. In order to solve the mathematical model of steam flow and heat transfer in power plant condensers, the Streamline Upwind Petrov-Galerkin finite element method is applied. By comparison of the results of simulation with experimental results about an experimental condenser, it is confirmed that SUPG finite element method can be successfully applied for solving the three-dimensional mathematical model of steam flow and heat transfer in power plant condensers.

Keywords: Navier-Stokes, FEM, condensers, steam.

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Authors: P. M. Arun Kumar, S. Chandramathi

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The proliferation of multimedia technology and services in today’s world provide ample research scope in the frontiers of visual signal processing. Wide spread usage of video based applications in heterogeneous environment needs viable methods of Video Quality Assessment (VQA). The evaluation of video quality not only depends on high QoS requirements but also emphasis the need of novel term ‘QoE’ (Quality of Experience) that perceive video quality as user centric. This paper discusses two vital video quality assessment methods namely, subjective and objective assessment methods. The evolution of various video quality metrics, their classification models and applications are reviewed in this work. The Mean Opinion Score (MOS) based subjective measurements and algorithm based objective metrics are discussed and their challenges are outlined. Further, this paper explores the recent progress of VQA in emerging technologies such as mobile video and 3D video.

Keywords: 3D-Video, no reference metric, quality of experience, video quality assessment, video quality metrics.

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Authors: Ch. Surawut, D. Sukawat

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In order to utilize results from global climate models, dynamical and statistical downscaling techniques have been developed. For dynamical downscaling, usually a limited area numerical model is used, with associated high computational cost. This research proposes dynamic equation for specific space-time regional climate downscaling from the Educational Global Climate Model (EdGCM) for Southeast Asia. The equation is for surface air temperature. This equation provides downscaling values of surface air temperature at any specific location and time without running a regional climate model. In the proposed equations, surface air temperature is approximated from ground temperature, sensible heat flux and 2m wind speed. Results from the application of the equation show that the errors from the proposed equations are less than the errors for direct interpolation from EdGCM.

Keywords: Dynamic Equation, Downscaling, Inverse distance weight interpolation.

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Authors: Ying-Wen Bai, Ju-Maw Chen

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To successfully provide a fast FIR filter with FTT algorithms, overlapped-save algorithms can be used to lower the computational complexity and achieve the desired real-time processing. As the length of the input block increases in order to improve the efficiency, a larger volume of zero padding will greatly increase the computation length of the FFT. In this paper, we use the overlapped block digital filtering to construct a parallel structure. As long as the down-sampling (or up-sampling) factor is an exact multiple lengths of the impulse response of a FIR filter, we can process the input block by using a parallel structure and thus achieve a low-complex fast FIR filter with overlapped-save algorithms. With a long filter length, the performance and the throughput of the digital filtering system will also be greatly enhanced.

Keywords: FIR Filter, Overlapped-save Algorithm, ParallelStructure

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Authors: Jianyin Lu, Masayoshi Seike, Wei Liu, Peihong Wu, Lihua Wang, Yihua Wu, Yasuhiro Naito, Hiromu Nakajima, Yasuhiro Kouchi

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To extract the important physiological factors related to diabetes from an oral glucose tolerance test (OGTT) by mathematical modeling, highly informative but convenient protocols are required. Current models require a large number of samples and extended period of testing, which is not practical for daily use. The purpose of this study is to make model assessments possible even from a reduced number of samples taken over a relatively short period. For this purpose, test values were extrapolated using a support vector machine. A good correlation was found between reference and extrapolated values in evaluated 741 OGTTs. This result indicates that a reduction in the number of clinical test is possible through a computational approach.

Keywords: SVM regression, OGTT, diabetes, mathematical model

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Authors: Ion Smeureanu, Adriana Reveiu, Marian Dardala, Titus Felix Furtuna, Roman Kanala

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This paper proposes a linear model for optimizing domestic energy consumption in Romania. The particularity of the model is that it is putting in competition both tangible technologies and thermal insulation projects with different financing modes. The model is optimizing the energy system by minimizing the global discounted cost in household sector, by integrating residential lighting, space heating, hot water, combined space heating – hot water, as well as space cooling, in a monolithic model. Another demand sector included is the passenger transport. This paper focuses on space heating part, analyzing technical and economic issues related to investment decisions to envelope and insulate buildings, in order to minimize energy consumption.

Keywords: Consumer behavior, energy modelling, Open Source Energy Modeling System (OSeMOSYS), MARKAL/TIMES Romanian energy model.

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Authors: Somayeh Abedian, Pirhossein Kolivand, Hamid Reza Lornejad, Amin Karampour, Ebrahim Keshavarz Safari

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For emergency and relief service providers such as pre-hospital emergencies, quick arrival at the scene of an accident or any EMS mission is one of the most important requirements of effective service delivery. EMS Response time (the interval between the time of the call and the time of arrival on scene) is a critical factor in determining the quality of pre-hospital Emergency Medical Services (EMS). This is especially important for heart attack, stroke, or accident patients that seconds are vital in saving their lives. Location-based e-services can be broadly defined as any service that provides information pertinent to the current location of an active mobile handset or precise address of landline phone call at a specific time window, regardless of the underlying delivery technology used to convey the information. According to research, one of the effective methods of meeting this goal is determining the location of the caller via the cooperation of landline and mobile phone operators in the country. The follow-up of the Communications Regulatory Authority (CRA) organization has resulted in the receipt of two separate secured electronic web services. Thus, to ensure human privacy, a secure technical architecture was required for launching the services in the pre-hospital EMS information management system. In addition, to quicken medics’ arrival at the patient's bedside, rescue vehicles should make use of an intelligent transportation system to estimate road traffic using a GPS-based mobile navigation system independent of the Internet. This paper seeks to illustrate the architecture of the practical national model used by the Iranian EMS organization.

Keywords: response time, geographic location inquiry service, location-based services, emergency medical services information system

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Authors: I. Herraiz-Cardona, C. González-Buch, E. Ortega, V. Pérez-Herranz, J. García-Antón

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Hydrogen is considered to be the most promising candidate as a future energy carrier. One of the most used technologies for the electrolytic hydrogen production is alkaline water electrolysis. However, due to the high energy requirements, the cost of hydrogen produced in such a way is high. In continuous search to improve this process using advanced electrocatalytic materials for the hydrogen evolution reaction (HER), Ni type Raney and macro-porous Ni-Co electrodes were prepared on AISI 304 stainless steel substrates by electrodeposition. The developed electrodes were characterized by SEM and confocal laser scanning microscopy. HER on these electrodes was evaluated in 30 wt.% KOH solution by means of hydrogen discharge curves and galvanostatic tests. Results show that the developed electrodes present a most efficient behaviour for HER when comparing with the smooth Ni cathode. It has been reported a reduction in the energy consumption of the electrolysis cell of about 25% by using the developed coatings as cathodes.

Keywords: Alkaline water electrolysis, energy efficiency, porous nickel electrodes

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Authors: Anant Oonsivilai, Kenedy A. Greyson

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The growth and interconnection of power networks in many regions has invited complicated techniques for energy management services (EMS). State estimation techniques become a powerful tool in power system control centers, and that more information is required to achieve the objective of EMS. For the online state estimator, assuming the continuous time is equidistantly sampled with period Δt, processing events must be finished within this period. Advantage of Kalman Filtering (KF) algorithm in using system information to improve the estimation precision is utilized. Computational power is a major issue responsible for the achievement of the objective, i.e. estimators- solution at a small sampled period. This paper presents the optimum utilization of processors in a state estimator based on KF. The model used is presented using Petri net (PN) theory.

Keywords: Kalman filters, model, Petri Net, power system, sequential State estimator.

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Authors: J. Carlos Frutos Dordelly, M. Coillot, M. El Mankibi, R. Enríquez Miranda, M. José Jimenez, J. Arce Landa

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Natural ventilation systems have increasingly been the subject of research due to rising energetic consumption within the building sector and increased environmental awareness. In the last two decades, the mounting concern of greenhouse gas emissions and the need for an efficient passive ventilation system have driven the development of new alternative passive technologies such as ventilated facades, trombe walls or solar chimneys. The objective of the study is the assessment of PCM panels in an in situ solar chimney for the establishment of a numerical model. The PCM integrated solar chimney shows slight performance improvement in terms of mass flow rate and external temperature and outlet temperature difference. An increase of 11.3659 m³/h can be observed during low wind speed periods. Additionally, the surface temperature across the chimney goes beyond 45 °C and allows the activation of PCM panels.

Keywords: Energy storage, passive ventilation, phase changing materials, solar chimney, solar energy.

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Authors: A. Badarudin, C. S. Oon, S. N. Kazi, N. Nik-Ghazali, Y. J. Lee, W. T. Chong

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An experimental and simulation flight test has been carried out to evaluate the longitudinal gliding characteristics of a lifting body with blunted half-cone geometry. The novelty here is the lifting body's pitch control mechanism, which consists of a pair of leading-edge rotating cylinders. Flight simulation uses aerodynamic data from computational fluid dynamics supported by wind-tunnel test. Flight test consists of releasing an aluminum lifting body model from a moving vehicle at the appropriate wind speed while measuring the lifting body's variation of altitude against time of flight. Results show that leading-edge rotating cylinder is able to give small amounts of improvement to the longitudinal stability and pitch control to the lifting body.

Keywords: Lifting body, pitch control, aerodynamic, rotating cylinder.

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Authors: Tim Wollert, Fabian Behrendt

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Value Stream Management (VSM) is a widely used methodology in the context of Lean Management for improving end-to-end material and information flows from a supplier to a customer from a company’s perspective. Whereas the design principles, e.g. Pull, value-adding, customer-orientation and further ones are still valid against the background of an increasing digitalized and dynamic environment, the methodology itself for mapping a value stream is characterized as time- and resource-intensive due to the high degree of manual activities. The digitalization of processes in the context of Industry 4.0 enables new opportunities to reduce these manual efforts and make the VSM approach more agile. The paper at hand aims at providing a modular data and calculation framework, utilizing the available business data, provided by information and communication technologies for automizing the value stream mapping process with focus on the manufacturing process.

Keywords: Industry 4.0, lean management 4.0, value stream management 4.0, value stream mapping.

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Authors: Walid Cherif

Abstract:

Data mining has, over recent years, seen big advances because of the spread of internet, which generates everyday a tremendous volume of data, and also the immense advances in technologies which facilitate the analysis of these data. In particular, classification techniques are a subdomain of Data Mining which determines in which group each data instance is related within a given dataset. It is used to classify data into different classes according to desired criteria. Generally, a classification technique is either statistical or machine learning. Each type of these techniques has its own limits. Nowadays, current data are becoming increasingly heterogeneous; consequently, current classification techniques are encountering many difficulties. This paper defines new measure functions to quantify the resemblance between instances and then combines them in a new approach which is different from actual algorithms by its reliability computations. Results of the proposed approach exceeded most common classification techniques with an f-measure exceeding 97% on the IRIS Dataset.

Keywords: Data mining, knowledge discovery, machine learning, similarity measurement, supervised classification.

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Authors: Jeong-Hwan Choi, Hyo-Sang Park, Tae-Hyung Lee

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The transmission tower is one of the crucial lifeline structures in a modern society, and it needs to be protected against extreme loading conditions. However, the transmission tower is a very complex structure and, therefore, it is very difficult to simulate the actual damage and the collapse behavior of the tower structure. In this study, the actual collapse behavior of the transmission tower due to lateral loading conditions such as wind load is evaluated through the computational simulation. For that, a progressive collapse procedure is applied to the simulation. In this procedure, after running the simulation, if a member of the tower structure fails, the failed member is removed and the simulation run again. The 154kV transmission tower is selected for this study. The simulation is performed by nonlinear static analysis procedure, namely pushover analysis, using OpenSEES, an earthquake simulation platform. Three-dimensional finite element models of those towers are developed.

Keywords: Transmission tower, OpenSEES, pushover analysis, progressive collapse.

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Authors: B. Salmasian, A. Rabiee, T. Yousefzadeh

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In this research, the risk assessment of radiation hazard for the Research Nuclear Reactor has been studied. In the current study, the MCNPx computational code has been used and coupled with a developed program using MATLAB software to evaluate Total Effective Dose Equivalent (TEDE) and cancer risk according to the BEIR equations for various human organs. In this study, the risk assessment of cancer has been calculated for ten years after exposure, in each of body organs of different ages and sexes. Also, the risk assessment of cancer has been calculated in each of body organs of different ages and sexes due to exposure after the retirement of the reactor staff. According to obtained results, a conservative whole-body dose rate, during a year, is 0.261 Sv and the probability the cancer risk for women is more than men and for children is more than adults. It has been shown that thyroid cancer was more possible than others.

Keywords: MCNPx code, BEIR equation, equivalent dose, risk analysis.

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Authors: Fan Gao, Lior Pachter

Abstract:

The primary tool currently used to pre-process 10X chromium single-cell ATAC-seq data is Cell Ranger, which can take very long to run on standard datasets. To facilitate rapid pre-processing that enables reproducible workflows, we present a suite of tools called scATAK for pre-processing single-cell ATAC-seq data that is 15 to 18 times faster than Cell Ranger on mouse and human samples. Our tool can also calculate chromatin interaction potential matrices and generate open chromatin signal and interaction traces for cell groups. We use scATAK tool to explore the chromatin regulatory landscape of a healthy adult human brain and unveil cell-type specific features, and show that it provides a convenient and computational efficient approach for pre-processing single-cell ATAC-seq data.

Keywords: single-cell, ATAC-seq, bioinformatics, open chromatin landscape, chromatin interactome

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