Search results for: systematic errors.

Authors: T. Sanches, K. Bousson

Abstract:

As part of the development of a 4D autopilot system for unmanned aerial vehicles (UAVs), i.e. a time-dependent robust trajectory generation and control algorithm, this work addresses the problem of optimal path control based on the flight sensors data output that may be unreliable due to noise on data acquisition and/or transmission under certain circumstances. Although several filtering methods, such as the Kalman-Bucy filter or the Linear Quadratic Gaussian/Loop Transfer Recover Control (LQG/LTR), are available, the utter complexity of the control system, together with the robustness and reliability required of such a system on a UAV for airworthiness certifiable autonomous flight, required the development of a proper robust filter for a nonlinear system, as a way of further mitigate errors propagation to the control system and improve its ,performance. As such, a nonlinear algorithm based upon the LQG/LTR, is validated through computational simulation testing, is proposed on this paper.

Keywords: Autonomous flight, LQG/LTR, nonlinear state estimator, robust flight control and stability.

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Authors: Kwok Tak Kit

Abstract:

Combating climate change is becoming a hot topic in various sectors. Building construction and infrastructure sectors contributed a significant proportion of waste and greenhouse gas (GHG) emissions in the environment of different countries and cities. However, there is little research on the micro-level of waste management, “building construction material wastage management,” and fewer reviews about regulatory control in the building construction sector. This paper focuses on the potentialities and importance of material wastage management and reviews the deficiencies of the current standard to take into account the reduction of material wastage in a systematic and quantitative approach.

Keywords: Quantitative measurement, material wastage management plan, waste management, uncalculated waste, circular economy.

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Authors: A. A. Hossam-Eldin, E. N. Abdallah, M. S. El-Nozahy

Abstract:

The identification and elimination of bad measurements is one of the basic functions of a robust state estimator as bad data have the effect of corrupting the results of state estimation according to the popular weighted least squares method. However this is a difficult problem to handle especially when dealing with multiple errors from the interactive conforming type. In this paper, a self adaptive genetic based algorithm is proposed. The algorithm utilizes the results of the classical linearized normal residuals approach to tune the genetic operators thus instead of making a randomized search throughout the whole search space it is more likely to be a directed search thus the optimum solution is obtained at very early stages(maximum of 5 generations). The algorithm utilizes the accumulating databases of already computed cases to reduce the computational burden to minimum. Tests are conducted with reference to the standard IEEE test systems. Test results are very promising.

Keywords: Bad Data, Genetic Algorithms, Linearized Normal residuals, Observability, Power System State Estimation.

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Authors: Mehrshad Khalaj, Elham Lashkari

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Majority of researches conducted on Iranian urban development plans indicate that they have been almost unsuccessful in terms of draft, execution and goal achievement. Lack or shortage of essential statistics and information can be listed as an important reason of the failure of these plans. Lack of figures and information has turned into an obvious part of the country-s statistics officials. This problem has made urban planner themselves to embark on physical surveys including real estate and land pricing, population and economic census of the city. Apart from the problems facing urban developers, the possibility of errors is high in such surveys. In the present article, applying the interview technique, it has been mentioned that utilizing multipurpose cadastre system as a land information system is essential for urban development plans in Iran. It can minimize or even remove the failures facing urban development plans.

Keywords: Multipurpose Cadastre, Urban Development Plan(UDP), Land Information System (LIS), Interview Technique

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Authors: Farag Azzedin, Ahmad Ridha

Abstract:

The need for reputation assessment is particularly strong in peer-to-peer (P2P) systems because the peers' personal site autonomy is amplified by the inherent technological decentralization of the environment. However, the decentralization notion makes the problem of designing a peer-to-peer based reputation assessment substantially harder in P2P networks than in centralized settings.Existing reputation systems tackle the reputation assessment process in an ad-hoc manner. There is no systematic and coherent way to derive measures and analyze the current reputation systems. In this paper, we propose a reputation assessment process and use it to classify the existing reputation systems. Simulation experiments are conducted and focused on the different methods in selecting the recommendation sources and retrieving the recommendations. These two phases can contribute significantly to the overall performance due to communication cost and coverage.

Keywords: P2P Systems, Trust, Reputation, Performance.

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Authors: Malaw Ndiaye, Karim Konate

Abstract:

Smart contracts are computer protocols that facilitate, verify, and execute the negotiation or execution of a contract, or that render a contractual term unnecessary. Blockchain and smart contracts can be used to facilitate almost any financial transaction. Thanks to these smart contracts, the settlement of dividends and coupons could be automated. Smart contracts have become lucrative and profitable targets for attackers because they can hold a great amount of money. Smart contracts, although widely used in blockchain technology, are far from perfect due to security concerns. Although a series of attacks are listed, there is a lack of discussions and proposals on improving security. This survey takes stock of smart contract security from a more comprehensive perspective by correlating the level of vulnerability and systematic review of security levels in smart contracts.

Keywords: Blockchain, bitcoin, smart Contract, criminal smart contract, security.

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Authors: Hyoup-Sang Yoon

Abstract:

The quality of video transmitted by mobile ad hoc networks (MANETs) can be influenced by several factors, including protocol layers; parameter settings of each protocol. In this paper, we are concerned with understanding the functional relationship between these influential factors and objective video quality in MANETs. We illustrate a systematic statistical design of experiments (DOE) strategy can be used to analyze MANET parameters and performance. Using a 2^k factorial design, we quantify the main and interactive effects of 7 factors on a response metric (i.e., mean opinion score (MOS) calculated by PSNR with Evalvid package) we then develop a first-order linear regression model between the influential factors and the performance metric.

Keywords: Evalvid, full factorial design, mobile ad hoc networks, ns-2.

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Authors: S. Pullteap

Abstract:

In this paper, a fiber based Fabry-Perot interferometer is proposed and demonstrated for a non-contact displacement measurement. A piece of micro-prism which attached to the mechanical vibrator is served as the target reflector. Interference signal is generated from the superposition between the sensing beam and the reference beam within the sensing arm of the fiber sensor. This signal is then converted to the displacement value by using a developed program written in visual Cµ programming with a resolution of λ/8. A classical function generator is operated for controlling the vibrator. By fixing an excitation frequency of 100 Hz and varying the excitation amplitude range of 0.1 – 3 Volts, the output displacements measured by the fiber sensor are obtained from 1.55 μm to 30.225 μm. A reference displacement sensor with a sensitivity of ~0.4 μm is also employed for comparing the displacement errors between both sensors. We found that over the entire displacement range, a maximum and average measurement error are obtained of 0.977% and 0.44% respectively.

Keywords: Non-contact displacement measurement, extrinsicfiber based Fabry-Perot interferometer, interference signal, zerocrossingfringe counting technique.

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Authors: Gilberto Gonzalez-A, Ignacio Rodríguez- A., Dunia Nuñez-P

Abstract:

A bond graph model of a two degrees of freedom PUMA is described. System inversion gives the system input required to generate a given system output. In order to get the system inversion of the PUMA manipulator, a linearization of the nonlinear bond graph is obtained. Hence, the bicausality of the linearized bond graph of the PUMA manipulator is applied. Thus, the bicausal bond graph provides a systematic way of generating the equations of the system inversion. Simulation results to verify the calculated input for a given output are shown.

Keywords: Bond graph, system inversion, bicausality, PUMA manipulator

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Authors: Dr. N.H. Mvungi

Abstract:

The control of commutation of switched reluctance (SR) motor has nominally depended on a physical position detector. The physical rotor position sensor limits robustness and increases size and inertia of the SR drive system. The paper describes a method to overcome these limitations by using magnetization characteristics of the motor to indicate rotor and stator teeth overlap status. The method is using active current probing pulses of same magnitude that is used to simulate flux linkage in the winding being probed. A microprocessor is used for processing magnetization data to deduce rotor-stator teeth overlap status and hence rotor position. However, the back-of-core saturation and mutual coupling introduces overlap detection errors, hence that of commutation control. This paper presents the concept of the detection scheme and the effects of backof core saturation.

Keywords: Microprocessor control, rotor position, sensorless, switched reluctance.

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Authors: Mashitah Mohd Hussain, Salleh Serwan, Zuhaina Hj Zakaria

Abstract:

This paper presents a method to estimate load profile in a multiple power flow solutions for every minutes in 24 hours per day. A method to calculate multiple solutions of non linear profile is introduced. The Power System Simulation/Engineering (PSS®E) and python has been used to solve the load power flow. The result of this power flow solutions has been used to estimate the load profiles for each load at buses using Independent Component Analysis (ICA) without any knowledge of parameter and network topology of the systems. The proposed algorithm is tested with IEEE 69 test bus system represents for distribution part and the method of ICA has been programmed in MATLAB R2012b version. Simulation results and errors of estimations are discussed in this paper.

Keywords: Electrical Distribution System, Power Flow Solution, Distribution Network, Independent Component Analysis, Newton Raphson, Power System Simulation for Engineering.

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Authors: Taegyoo Woo, Jong Kang Park, Jong Tae Kim

Abstract:

Visible Light Communication (VLC) provides wireless communication features in illumination systems. One of the key applications is to recognize the user location by indoor illuminators such as light emitting diodes. For localization of individual receivers in these systems, we usually assume that receivers and transmitters are placed in parallel. However, it is difficult to satisfy this assumption because the receivers move randomly in real case. It is necessary to analyze the case when transmitter is not placed perfectly parallel to receiver. It is also important to identify changes on optical gain by the tilted angles and distances of them against the illuminators. In this paper, we simulate optical gain for various cases where the tilt of the receiver and the distance change. Then, we identified changing patterns of optical gains according to tilted angles of a receiver and distance. These results can help many VLC applications understand the extent of the location errors with regard to optical gains of the receivers and identify the root cause.

Keywords: Visible light communication, optical channel, indoor positioning, Lambertian radiation.

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Authors: Ali Gholami

Abstract:

In this research the Preparation of Land use map of scanner LISS III satellite data, belonging to the IRS in the Aghche region in Isfahan province, is studied carefully. For this purpose, the IRS satellite images of August 2008 and various land preparation uses in region including rangelands, irrigation farming, dry farming, gardens and urban areas were separated and identified. Therefore, the GPS and Erdas Imaging software were used and three methods of Maximum Likelihood, Mahalanobis Distance and Minimum Distance were analyzed. In each of these methods, matrix error and Kappa index were calculated and accuracy of each method, based on percentages: 53.13, 56.64 and 48.44, were obtained respectively. Considering the low accuracy of these methods in separation of land preparation use, the visual interpretation of the map was used. Finally, regional visits of 150 points were noted at random and no error was observed. It shows that the map prepared by visual interpretation is in high accuracy. Although the probable errors due to visual interpretation and geometric correction might happen but the desired accuracy of the map which is more than 85 percent is reliable.

Keywords: Land use map, Aghche Region, Erdas Imagine, satellite images

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Authors: Shih-Ching Lo

Abstract:

Discrete choice model is the most used methodology for studying traveler-s mode choice and demand. However, to calibrate the discrete choice model needs to have plenty of questionnaire survey. In this study, an aggregative model is proposed. The historical data of passenger volumes for high speed rail and domestic civil aviation are employed to calibrate and validate the model. In this study, different models are compared so as to propose the best one. From the results, systematic equations forecast better than single equation do. Models with the external variable, which is oil price, are better than models based on closed system assumption.

Keywords: forecasting, passenger volume, dynamic competition model, external variable, oil price

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Authors: E. Grochowska-Niedworok, K. Brukalo, B. Całyniuk, J. Piekorz, M. Kardas

Abstract:

The aim of the study was to assess diets of residents of nursing homes. Provided by social welfare home, 10 day menus were introduced into the computer program Diet 5 and analyzed in respect of protein, fats, carbohydrates, energy, vitamin D and calcium. The resulting mean values of 10-day menus were compared with the existing Nutrition Standards for Polish population. The analysis menus showed that the average amount of energy supplied from food is not sufficient. Carbohydrates in food supply are too high and represent 257% of normal. The average value of fats and proteins supplied with food is adequate 85.2 g/day and 75.2 g/day. The calcium content of the diet is 513.9 mg/day. The amount of vitamin D supplied in the age group 51-65 years is 2.3 µg/day. Dietary errors that have been shown are due to the lack of detailed nutritional guidelines for nursing homes, as well as state-owned care facilities in general.

Keywords: Assessment of diet, essential nutrients, social welfare home, nutrition.

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Authors: M. Anidha, K. Premalatha

Abstract:

Feature Selection is significant in order to perform constructive classification in the area of cancer diagnosis. However, a large number of features compared to the number of samples makes the task of classification computationally very hard and prone to errors in microarray gene expression datasets. In this paper, we present an innovative method for selecting highly informative gene subsets of gene expression data that effectively classifies the cancer data into tumorous and non-tumorous. The hybrid gene selection technique comprises of combined Mutual Information and Fisher score to select informative genes. The gene selection is validated by classification using Support Vector Machine (SVM) which is a supervised learning algorithm capable of solving complex classification problems. The results obtained from improved Mutual Information and F-Score with SVM as a classifier has produced efficient results.

Keywords: Gene selection, mutual information, Fisher score, classification, SVM.

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Authors: Seok Hong Min, Tae Kwon Ha

Abstract:

In this study, thermal fatigue properties of 400 series ferritic stainless steels have been evaluated in the temperature ranges of 200-800oC and 200-900oC. Systematic methods for control of temperatures within the predetermined range and measurement of load applied to specimens as a function of temperature during thermal cycles have been established. Thermal fatigue tests were conducted under fully constrained condition, where both ends of specimens were completely fixed. It has been revealed that load relaxation behavior at the temperatures of thermal cycle was closely related with the thermal fatigue property. Thermal fatigue resistance of 430J1L stainless steel is found to be superior to the other steels.

Keywords: Ferritic stainless steel, automotive exhaust, thermal fatigue, microstructure, load relaxation.

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Authors: M.R. Osman, F. Abas, M.S. Noh, A. Mohamad Suffian, O. Ilhamah, H.Z. Zarir, A.B. Wahida, P. Noor Faradila, M.F. Siti Atiqah

Abstract:

Safety Health and Environment Code of Practice (SHE COP) was developed to help road transportation operators to manage its operation in a systematic and safe manner. A study was conducted to determine the effectiveness of SHE COP implementation during non-OPS period. The objective of the study is to evaluate the implementations of SHE COP among bus operators during wee hour operations. The data was collected by completing a set of checklist after observing the activities during pre departure, during the trip, and upon arrival. The results show that there are seven widely practiced SHE COP elements. 22% of the buses have average speed exceeding the maximum permissible speed on the highways (90 km/h), with 13% of the buses were travelling at the speed of more than 100 km/h. The statistical analysis shows that there is only one significant association which relates speeding with prior presence of enforcement officers.

Keywords: Safety practices, speeding, wee hour.

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Authors: Ahd Aljarf, Saad Amin

Abstract:

Images are important source of information used as evidence during any investigation process. Their clarity and accuracy is essential and of the utmost importance for any investigation. Images are vulnerable to losing blocks and having noise added to them either after alteration or when the image was taken initially, therefore, having a high performance image processing system and it is implementation is very important in a forensic point of view. This paper focuses on improving the quality of the forensic images. For different reasons packets that store data can be affected, harmed or even lost because of noise. For example, sending the image through a wireless channel can cause loss of bits. These types of errors might give difficulties generally for the visual display quality of the forensic images. Two of the images problems: noise and losing blocks are covered. However, information which gets transmitted through any way of communication may suffer alteration from its original state or even lose important data due to the channel noise. Therefore, a developed system is introduced to improve the quality and clarity of the forensic images.

Keywords: Image Filtering, Image Reconstruction, Image Processing, Forensic Images.

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Authors: R. Bremananth, Andy W. H. Khong, A. Chitra

Abstract:

Visualizing sound and noise often help us to determine an appropriate control over the source localization. Near-field acoustic holography (NAH) is a powerful tool for the ill-posed problem. However, in practice, due to the small finite aperture size, the discrete Fourier transform, FFT based NAH couldn-t predict the activeregion- of-interest (AROI) over the edges of the plane. Theoretically few approaches were proposed for solving finite aperture problem. However most of these methods are not quite compatible for the practical implementation, especially near the edge of the source. In this paper, a zip-stuffing extrapolation approach has suggested with 2D Kaiser window. It is operated on wavenumber complex space to localize the predicted sources. We numerically form a practice environment with touch impact databases to test the localization of sound source. It is observed that zip-stuffing aperture extrapolation and 2D window with evanescent components provide more accuracy especially in the small aperture and its derivatives.

Keywords: Acoustic source localization, Near-field acoustic holography (NAH), FFT, Extrapolation, k-space wavenumber errors.

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Authors: Aliyu Isah Agaie, Masrah Azrifah Azmi Murad, Nurfadhlina Mohd Sharef, Aida Mustapha

Abstract:

Natural Language Interfaces typically support a restricted language and also have scopes and limitations that naïve users are unaware of, resulting in errors when the users attempt to retrieve information from ontologies. To overcome this challenge, an auto-suggest feature is introduced into the querying process where users are guided through the querying process using interactive query construction system. Guiding users to formulate their queries, while providing them with an unconstrained (or almost unconstrained) way to query the ontology results in better interpretation of the query and ultimately lead to an effective search. The approach described in this paper is unobtrusive and subtly guides the users, so that they have a choice of either selecting from the suggestion list or typing in full. The user is not coerced into accepting system suggestions and can express himself using fragments or full sentences.

Keywords: Auto-suggest, expressiveness, habitability, natural language interface, query interpretation, user guidance.

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Authors: Aleksandra Aleksandrovna Filimonova, Lev Sergeevich Kazarinov, Tatyana Aleksandrovna Barbasova

Abstract:

A method of effective planning and control of industrial facility energy consumption is offered. The method allows optimally arranging the management and full control of complex production facilities in accordance with the criteria of minimal technical and economic losses at the forecasting control. The method is based on the optimal construction of the power efficiency characteristics with the prescribed accuracy. The problem of optimal designing of the forecasting model is solved on the basis of three criteria: maximizing the weighted sum of the points of forecasting with the prescribed accuracy; the solving of the problem by the standard principles at the incomplete statistic data on the basis of minimization of the regularized function; minimizing the technical and economic losses due to the forecasting errors.

Keywords: Energy consumption, energy efficiency, energy management system, forecasting model, power efficiency characteristics.

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Authors: Asem M. Othman

Abstract:

The expansion of the hospitality industry is distinctive in the 21st century. Services, by nature, are intangible. Hence, service quality, in general, is a complicated process to be measured and evaluated. Hotels, as a service sector and part of the hospitality industry, are growing rapidly. This research paper was carried out to identify the quality determinants that may affect hotel guests’ service quality perception. In this research paper, each quality determinant will be discussed, illustrated, and justified thoroughly via a systematic literature review. This paper sets the stage to measure the significant influence of the service quality determinants on guest satisfaction. The knowledge contribution from this study proposes to practitioners and/or hotel service providers, fundamental elements to adopt the implications into their policies.

Keywords: Hotel service, service quality, quality determinants, quality management.

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Authors: Mohammed A. Almomani, Dina W. Al-Qudah

Abstract:

Product performance depends on the type and quality of its building material. Successful product must be made using high quality material, and using the right methods. Many foot problems took place as a result of using poor insole material. Therefore, selecting a proper insole material is crucial to eliminate these problems. In this study, the analytical hierarchy process (AHP) is used to provide a systematic procedure for choosing the best material adequate for this application among three material alternatives (polyurethane, poron, and plastzote). Several comparison criteria are used to build the AHP model including: density, stiffness, durability, energy absorption, and ease of fabrication. Poron was selected as the best choice. Inconsistency testing indicates that the model is reasonable, and the materials alternative ranking is effective.

Keywords: Materials selection, biomedical insole, footwear insole, AHP.

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Authors: Salwa Aftab, Sehrish Riaz

Abstract:

The objective of this study was to check the impact of grade sensitivity on learning motivation and academic performance of students and to remove the degree of difference that exists among students regarding the cause of their learning motivation and also to gain knowledge about this matter since it has not been adequately researched. Data collection was primarily done through the academic sector of Pakistan and was depended upon the responses given by students solely. A sample size of 208 university students was selected. Both paper and online surveys were used to collect data from respondents. The results of the study revealed that grade sensitivity has a positive relationship with the learning motivation of students and their academic performance. These findings were carried out through systematic correlation and regression analysis.

Keywords: Academic performance, correlation, grade sensitivity, learning motivation, regression.

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Authors: L. Zehtaban, D. Roller

Abstract:

Apart from geometry, functionality is one of the most significant hallmarks of a product. The functionality of a product can be considered as the fundamental justification for a product existence. Therefore a functional analysis including a complete and reliable descriptor has a high potential to improve product development process in various fields especially in knowledge-based design. One of the important applications of the functional analysis and indexing is in retrieval and design reuse concept. More than 75% of design activity for a new product development contains reusing earlier and existing design know-how. Thus, analysis and categorization of product functions concluded by functional indexing, influences directly in design optimization. This paper elucidates and evaluates major classes for functional analysis by discussing their major methods. Moreover it is finalized by presenting a noble hybrid approach for functional analysis.

Keywords: Functional analysis, design reuse, functionalindexing and representation.

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Authors: Nai-Chieh Wei, I-Ming Chao, Chin-Jung Liuand, Hong Long Chen

Abstract:

This paper combines the branch-and-bound method and the petri net to solve the two-sided assembly line balancing problem, thus facilitating effective branching and pruning of tasks. By integrating features of the petri net, such as reachability graph and incidence matrix, the propose method can support the branch-and-bound to effectively reduce poor branches with systematic graphs. Test results suggest that using petri net in the branching process can effectively guide the system trigger process, and thus, lead to consistent results.

 

Keywords: Branch-and-Bound Method, Petri Net, Two-Sided Assembly Line Balancing Problem.

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Authors: Ceren Ince, Berkay Z. Erdem, Shahram Derogar, Nabi Yuzer

Abstract:

Fibre cement plates, often used in construction, generally are made using quartz as an inert material, cement as a binder and cellulose as a fibre. This paper, first of all, investigates the mechanical properties and durability of fibre cement plates when quartz is both partly and fully replaced with diatomite. Diatomite does not only have lower density compared to quartz but also has high pozzolanic activity. The main objective of this paper is the investigation of the effects of supplementary cementing materials (SCMs) on the short and long term mechanical properties and durability characteristics of fibre cement plates prepared using diatomite. Supplementary cementing materials such as ground granulated blast furnace slug (GGBS) and fly ash (FA) are used in this study. Volume proportions of 10, 20, 30 and 40% of GGBS and FA are used as partial replacement materials to cement. Short and long term mechanical properties such as compressive and flexural strengths as well as sorptivity characteristics and mass were investigated. Consistency and setting time at each replacement levels of SCMs were also recorded. The effects of using supplementary cementing materials on the carbonation and sulphate resistance of fibre cement plates were then experimented. The results, first of all, show that the use of diatomite as a full or partial replacement to quartz resulted in a systematic decrease in total mass of the fibre cement plates. The reduction of mass was largely due to the lower density and finer particle size of diatomite compared to quartz. The use of diatomite did not only reduce the mass of these plates but also increased the compressive strength significantly as a result of its high pozzolanic activity. The replacement levels of both GGBS and FA resulted in a systematic decrease in short term compressive strength with increasing replacement levels. This was essentially expected as the total rate of hydration is much lower in GGBS and FA than that of cement. Long term results however, indicated that the compressive strength of fibre cement plates prepared using both GGBS and FA increases with time and hence the compressive strength of plates prepared using SCMs is either equivalent or more than the compressive strength of plates prepared using cement alone. Durability characteristics of fibre cement plates prepared using SCMs were enhanced significantly. Measurements of sopritivty characteristics were also indicated that the plates prepared using SCMs has much lower water absorption capacities compared to plates prepared cement alone. Much higher resistance to carbonation and sulphate attach were observed with plates prepared using SCMs. The results presented in this paper show that the use of SCMs does not only support the production of more sustainable construction materials but also enhances the mechanical properties and durability characteristics of fibre cement plates.

Keywords: Diatomite, fibre, strength, supplementary cementing materials.

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Authors: R. Sadykova

Abstract:

This article analyses the peculiarities of Japan’s policy toward the countries of Central Asia. The increasing role of Central Asia in the system of international relations engendered an objective need for understanding of the policy of leading states, including Japan, in the region in the twenty-first century. The purpose of the study is to investigate the peculiarities of the formation and development of Japan policy in Central Asia and to identify the problems and prospects of Japan’s policy toward the countries of the region on the basis of experts’ opinions. In this article, the method of analysis of the situation and a systematic method were used. Prognostic methods, the collective expert assessment and scenarios were used in the study to determine the prospects of Japan’s policy toward the countries of Central Asia.

Keywords: Japan, Central Asia, the Eurasian concept, ‘Central Asia plus Japan’ Dialogue.

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Authors: Chien-Ju Li, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu , Darby Tien-Hao Chang

Abstract:

De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.

Keywords: Contig graph, NGS, de novo assembly, scaffold.

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