Search results for: biological information

Authors: Om Parkash, A. K. Thukral, C. P. Gandhi

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Information theory and Statistics play an important role in Biological Sciences when we use information measures for the study of diversity and equitability. In this communication, we develop the link among the three disciplines and prove that sampling distributions can be used to develop new information measures. Our study will be an interdisciplinary and will find its applications in Biological systems.

Keywords: Entropy, concavity, symmetry, arithmetic mean, diversity, equitability.

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Authors: Efendi Zaenudin, Chien-Hung Huang, Ka-Lok Ng

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Essential genes play an important role in the survival of an organism. It has been shown that cancer-associated essential genes are genes necessary for cancer cell proliferation, where these genes are potential therapeutic targets. Also, it was demonstrated that mutations of the cancer-associated essential genes give rise to the resistance of immunotherapy for patients with tumors. In the present study, we focus on studying the biological effects of the essential genes from a network perspective. We hypothesize that one can analyze a biological molecular network by decomposing it into both three-node and four-node digraphs (subgraphs). These network subgraphs encode the regulatory interaction information among the network’s genetic elements. In this study, the frequency of occurrence of the subgraph-associated essential genes in a molecular network was quantified by using the statistical parameter, odds ratio. Biological effects of subgraph-associated essential genes are discussed. In summary, the subgraph approach provides a systematic method for analyzing molecular networks and it can capture useful biological information for biomedical research.

Keywords: Biological molecular networks, essential genes, graph theory, network subgraphs.

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Authors: Chaimaa Messaoudi, Rachida Fissoune, Hassan Badir

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Technological advances of computer science and data analysis are helping to provide continuously huge volumes of biological data, which are available on the web. Such advances involve and require powerful techniques for data integration to extract pertinent knowledge and information for a specific question. Biomedical exploration of these big data often requires the use of complex queries across multiple autonomous, heterogeneous and distributed data sources. Semantic integration is an active area of research in several disciplines, such as databases, information-integration, and ontology. We provide a survey of some approaches and techniques for integrating biological data, we focus on those developed in the ontology community.

Keywords: Semantic data integration, biological ontology, linked data, semantic web, OWL, RDF.

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Authors: Richard L. Summers

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The advanced computational analysis of biological systems is becoming increasingly dependent upon an understanding of the information-theoretic structure of the materials, energy and interactive processes that comprise those systems. The stability and survival of these living systems is fundamentally contingent upon their ability to acquire and process the meaning of information concerning the physical state of its biological continuum (biocontinuum). The drive for adaptive system reconciliation of a divergence from steady state within this biocontinuum can be described by an information metric-based formulation of the process for actionable knowledge acquisition that incorporates the axiomatic inference of Kullback-Leibler information minimization driven by survival replicator dynamics. If the mathematical expression of this process is the Lagrangian integrand for any change within the biocontinuum then it can also be considered as an action functional for the living system. In the direct method of Lyapunov, such a summarizing mathematical formulation of global system behavior based on the driving forces of energy currents and constraints within the system can serve as a platform for the analysis of stability. As the system evolves in time in response to biocontinuum perturbations, the summarizing function then conveys information about its overall stability. This stability information portends survival and therefore has absolute existential meaning for the living system. The first derivative of the Lyapunov energy information function will have a negative trajectory toward a system steady state if the driving force is dissipating. By contrast, system instability leading to system dissolution will have a positive trajectory. The direction and magnitude of the vector for the trajectory then serves as a quantifiable signature of the meaning associated with the living system’s stability information, homeostasis and survival potential.

Keywords: Semiotic meaning, Shannon information, Lyapunov, living systems.

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Authors: Nazar Zaki, Safaai Deris

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The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.

Keywords: Protein homology detection; support vectormachine; string kernel.

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Authors: Antonio Di Leva, Roberto Berchi, Gianpiero Pescarmona, Michele Sonnessa

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The aim of a biological model is to understand the integrated structure and behavior of complex biological systems as a function of the underlying molecular networks to achieve simulation and forecast of their operation. Although several approaches have been introduced to take into account structural and environment related features, relatively little attention has been given to represent the behavior of biological systems. The Abstract Biological Process (ABP) model illustrated in this paper is an object-oriented model based on UML (the standard object-oriented language). Its main objective is to bring into focus the functional aspects of the biological system under analysis.

Keywords: Biological processes, system dynamics, systemmodeling, UML.

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Authors: Ahmad Atieh, Masoud Kalantari, Roozbeh Ahmadi, Javad Dargahi, Muthukumaran Packirisamy, Mehrdad Hosseini Zadeh

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The present paper presents a finite element model and analysis for the interaction between a piezoresistive tactile sensor and biological tissues. The tactile sensor is proposed for use in minimally invasive surgery to deliver tactile information of biological tissues to surgeons. The proposed sensor measures the relative hardness of soft contact objects as well as the contact force. Silicone rubbers were used as the phantom of biological tissues. Finite element analysis of the silicone rubbers and the mechanical structure of the sensor were performed using COMSOL Multiphysics (v3.4) environment. The simulation results verify the capability of the sensor to be used to differentiate between different kinds of silicone rubber materials.

Keywords: finite element analysis, minimally invasive surgery, Neo-Hookean hyperelastic materials, tactile sensor.

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Authors: Micheal Olaolu Arowolo, Muhammad Azam, Fei He, Mihail Popescu, Dong Xu

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As the quantity of biological articles rises, so does the number of biological route figures. Each route figure shows gene names and relationships. Manually annotating pathway diagrams is time-consuming. Advanced image understanding models could speed up curation, but they must be more precise. There is rich information in biological pathway figures. The first step to performing image understanding of these figures is to recognize gene names automatically. Classical optical character recognition methods have been employed for gene name recognition, but they are not optimized for literature mining data. This study devised a method to recognize an image bounding box of gene name as a photo using deep Siamese neural network models to outperform the existing methods using ResNet, DenseNet and Inception architectures, the results obtained about 84% accuracy.

Keywords: Biological pathway, gene identification, object detection, Siamese network, ResNet.

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Authors: Jung-Hyun Kim, Kew-Cheol Shim, Shin-Cheol Song, Kyoungho Kim, Nam-Il Kim, Jinho Bae, Keum-Hyun So

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The purpose of present paper was to investigate perceptions of Korean secondary school students about social issues related to biological sciences. Twenty issues were selected based on topics of articles in the newspaper from 2005 to 2010. The issues were categorized into biotechnology, health-disease and environment domains. Subjects were 541 high school students (male 253 and female 288). On the survey, students were asked to answer on 5-point Lickert scales how they thought of the effect of biological phenomena or events related to biological issues on the individual life and the society. They perceived that the biological issues would be more effectible on the society than on the individual life. Female students had a little more perceptions than males.

Keywords: biological issue, biological sciences, perception, secondary school

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Authors: E. Kritzinger, E. Smith

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Human-related information security breaches within organizations are primarily caused by employees who have not been made aware of the importance of protecting the information they work with. Information security awareness is accordingly attracting more attention from industry, because stakeholders are held accountable for the information with which they work. The authors developed an Information Security Retrieval and Awareness model – entitled “ISRA" – that is tailored specifically towards enhancing information security awareness in industry amongst all users of information, to address shortcomings in existing information security awareness models. This paper is principally aimed at expounding a prototype for the ISRA model to highlight the advantages of utilizing the model. The prototype will focus on the non-technical, humanrelated information security issues in industry. The prototype will ensure that all stakeholders in an organization are part of an information security awareness process, and that these stakeholders are able to retrieve specific information related to information security issues relevant to their job category, preventing them from being overburdened with redundant information.

Keywords: Information security, information security awareness, information security awareness programs

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Authors: S. H. Mirhossaini, H. Godini, A. Jafari

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Biological Ammonia removal (nitrification), the oxidation of ammonia to nitrate catalyzed by bacteria, is a key part of global nitrogen cycling. In the first step of nitrification, chemolithoautotrophic ammonia oxidizer transform ammonia to nitrite, this subsequently oxidized to nitrate by nitrite oxidizing bacteria. This process can be affected by several factors. In this study the effect of influent COD on biological ammonia removal in a bench-scale biological reactor was investigated. Experiments were carried out using synthetic wastewater. The initial ammonium concentration was 25mgNH4 +-N L-1. The effect of COD between 247.55±1.8 and 601.08±3.24mgL-1 on biological ammonia removal was investigated by varying the COD loading supplied to reactor. From the results obtained in this study it could be concluded in the range of 247.55±1.8 to 351.35±2.05mgL-1, there is a direct relationship between amount of COD and ammonia removal. However more than 351.35±2.05 up to 601.08±3.24mgL-1 were found an indirect relationship between them.

Keywords: Ammonia biological removal, Nitrification, InfluentCOD.

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Authors: Shattyk Aliyev, Zhakypbek Altayev, Zuchra Ismagambetova, Yerkin Massanov

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Information society is an absolutely new public formation at which the infrastructure and the social relations correspond to the socialized essence of «information genotype» mankind. Information society is a natural social environment which allows the person to open completely the information nature, to use intelligence for joint creation with other people of new information on the basis of knowledge earlier saved up by previous generations.

Keywords: Information society, Philosophy, Education, Globalization and innovation.

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Authors: Sang Keun Rhee, Hyojeong Jin, Jihye Lee, Misoo Kwon, Myon-Woong Park, Sungdo Ha

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Extensive information is required within a R&D environment, and a considerable amount of time and efforts are being spent on finding the necessary information. An adaptive information providing system would be beneficial to the environment, and a conceptual model of the resources, people and context is mandatory for developing such applications. In this paper, an information model on various contexts and resources is proposed which provides the possibility of effective applications for use in adaptive information systems within a R&D project and meeting environment.

Keywords: Adaptive Hypermedia, Adaptive System, ContextAwareness, Information Model, Information System, Personalisation.

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Authors: Muhammad Azam, Micheal Olaolu Arowolo, Fei He, Mihail Popescu, Dong Xu

Abstract:

The number of biological papers is growing quickly, which means that the number of biological pathway figures in those papers is also increasing quickly. Each pathway figure shows extensive biological information, like the names of genes and how the genes are related. However, manually annotating pathway figures takes a lot of time and work. Even though using advanced image understanding models could speed up the process of curation, these models still need to be made more accurate. To improve gene name recognition from pathway figures, we applied a Siamese network to map image segments to a library of pictures containing known genes in a similar way to person recognition from photos in many photo applications. We used a triple loss function and a triplet spatial pyramid pooling network by combining the triplet convolution neural network and the spatial pyramid pooling (TSPP-Net). We compared VGG19 and VGG16 as the Siamese network model. VGG16 achieved better performance with an accuracy of 93%, which is much higher than Optical Character Recognition (OCR) results.

Keywords: Biological pathway, image understanding, gene name recognition, object detection, Siamese network, Visual Geometry Group.

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Authors: Sh. Ladan, A. Yari, H. Khodabandeh

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The need for Information Security in organizations, regardless of their type and size, is being addressed by emerging standards and recommended best practices. The various standards and practices which evolved in recent years and are still being developed and constantly revised, address the issue of Information Security from different angles. This paper attempts to provide an overview of Information Security Standards and Practices by briefly discussing some of the most popular ones. Through a comparative study of their similarities and differences, some insight can be obtained on how their combination may lead to an increased level of Information Security.

Keywords: Information security management, information security standard, BS7799, ISO 17799, COBIT.

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Authors: Batel Noureddine, Mehenni Mohamed, Kouadik Smain

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In a transcutanious inductive coupling of a biomedical implant, a new formula is given for the study of the Radio Frequency power attenuation by the biological tissue. The loss of the signal power is related to its interaction with the biological tissue and the composition of this one. A confrontation with the practical measurements done with a synthetic muscle into a Faraday cage, allowed a checking of the obtained theoretical results. The supply/data transfer systems used in the case of biomedical implants, can be well dimensioned by taking in account this type of power attenuation.

Keywords: Biological tissue, coupled coils, implanted device, power attenuation.

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Authors: Sedigheh Mirzaei S., Debasis Sengupta

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Parametric models have been quite popular for studying human growth, particularly in relation to biological parameters such as peak size velocity and age at peak size velocity. Longitudinal data are generally considered to be vital for fittinga parametric model to individual-specific data, and for studying the distribution of these biological parameters in a human population. However, cross-sectional data are easier to obtain than longitudinal data. In this paper, we present a method of combining longitudinal and cross-sectional data for the purpose of estimating the distribution of the biological parameters. We demonstrate, through simulations in the special case ofthePreece Baines model, how estimates based on longitudinal data can be improved upon by harnessing the information contained in cross-sectional data.We study the extent of improvement for different mixes of the two types of data, and finally illustrate the use of the method through data collected by the Indian Statistical Institute.

Keywords: Preece-Baines growth model, MCMC method, Mixed effect model

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Authors: Yu-Chi Shiue, Jyong Lin, Shih-Chang Chen

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With the increase of economic behavior and the upgrade of living standar, the ratio for people in Taiwan who own automobiles and motorcycles have recently increased with multiples. Therefore, parking issues will be a big challenge to facilitate traffic network and ensure urban life quality. The Parking Guidance and Information System is one of important systems for Advanced Traveler Information Services (ATIS). This research proposes a parking guidance and information system which integrates GPS and 3G network for a map on the Geographic Information System to solution inadequate of roadside information kanban. The system proposed in this study mainly includes Parking Host, Parking Guidance and Information Server, Geographic Map and Information System as well as Parking Guidance and Information Browser. The study results show this system can increase driver-s efficiency to find parking space and efficiently enhance parking convenience in comparison with roadside kanban system.

Keywords: Geographic Information System, 3G, GPS, parkinginformation

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Authors: Mingaleva Zhanna, Kapuskina Tatiana

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The article touches upon questions of information security in Russian Economy. It covers theoretical bases of information security and causes of its development. The theory is proved by the analysis of business activities and the main tendencies of information security development. Perm region has been chosen as the bases for the analysis, being the fastestdeveloping region that uses methods of information security in managing it economy. As a result of the study the authors of the given article have formulated their own vision of the problem of information security in various branches of economy and stated prospects of information security development and its growing role in Russian economy

Keywords: security of business, management of information security, institutional analyses.

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Authors: Siriporn Poolsuwan

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This research aims to explore the information needs, information usages, and problems of information usage of the older people club’s members in Dusit district, Bangkok. There are 12 clubs and 746 club’s members in this district. The research results use for older person service in this district. Data is gathered from 252 club’s members by using questionnaires. The quantitative approach uses in research by percentage, means and standard deviation. The results are as follows (1) The older people need Information for entertainment, occupation and academic in the field of short story, computer work, and religion and morality. (2) The participants use Information from various sources. (3) The Problem of information usage is their language skills because of the older people’s literacy problem.

Keywords: Information Behavior, Older Person, Information Seeking.

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Authors: Altynbek Moshkalov

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Along with the basic features of students\' culture information, with its widely usage oriented on implementation of the new information technologies in educational process that determines the search for ways of pointing to the similarity of interdisciplinary connections content, aims and objectives of the study. In this regard, the article questions about students\' information culture, and also presented information about the aims and objectives of the information culture process among students. In the formation of a professional interest in relevant information, which is an opportunity to assist in informing the professional activities of the essence of effective use of interactive methods and innovative technologies in the learning process. The result of the experiment proves the effectiveness of the information culture process of students in training the system of higher education based on the credit technology. The main purpose of this paper is a comprehensive review of students\' information culture.

Keywords: Information culture, methods of information culture of students, educational system of the credit technology, distance learning, information of interest, information and communication technologies and tools.

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Authors: H. Buluthan Cetintas

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Corporate identity, which has several advantages such that the employees become integrated with their corporations, corporation is distinguished from its competitors and it is recognized by the masses, is the total of the distinctive corporate features that and corporation has. That the information takes part in production as a more important component than labor and capital has required that the corporations are reorganized as information-based. Therefore, information and its management have reached a basic and prevalent position in having sustainable competitive advantage. Thanks to the information management which regulates the information and makes it reachable and available, information will be produced in line with a specific purpose in the corporations and be used in all the corporate processes. As an auxiliary power for increase in the economic potential, efficiency and productivity of the corporation, corporate identity consists of four components. These are corporate philosophy, corporate design, corporate behavior and corporate communication. In this study, the effects of the information management on corporate identity are discussed from the point of these four elements.

Keywords: Corporate identity, information management.

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Authors: S. Mawlood, L. Dennany, N. Watson, B. Pickard

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DNA analysis has been widely accepted as providing valuable evidence concerning the identity of the source of biological traces. Our work has showed that DNA samples can survive on cartridges even after firing. The study also raised the possibility of determining other information such as the age of the donor. Such information may be invaluable in certain cases where spent cartridges from automatic weapons are left behind at the scene of a crime. In spite of the nature of touch evidence and exposure to high chamber temperatures during shooting, we were still capable to retrieve enough DNA for profile typing. In order to estimate age of contributor, DNA methylation levels were analyzed using EpiTect system for retrieved DNA. However, results were not conclusive, due to low amount of input DNA.

Keywords: Age prediction, Fired cartridge, Trace DNA sample.

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Authors: Jaehun Joo, Mie-jung Kim, Ismatilla Normatov, Lyunhwa Kim

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The purpose of this paper is to analyze determinants of information security affecting adoption of the Web-based integrated information systems (IIS). We introduced Web-based information systems which are designed to formulate strategic plans for Peruvian government. Theoretical model is proposed to test impact of organizational factors (deterrent efforts and severity; preventive efforts) and individual factors (information security threat; security awareness) on intentions to proactively use the Web-based IIS .Our empirical study results highlight that deterrent efforts and deterrent severity have no significant influence on the proactive use intentions of IIS, whereas, preventive efforts play an important role in proactive use intentions of IIS. Thus, we suggest that organizations need to do preventive efforts by introducing various information security solutions, and try to improve information security awareness while reducing the perceived information security threats.

Keywords: Information security, Deterrent efforts, deterrentseverity, preventive efforts, information security awareness, information security threats, integrated information systems

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Authors: Noura Meshaan Al-Otaibi, Amin Yousef Noaman

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Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. This research suggests the use of Service Oriented Architecture (SOA) to integrate biological data from different data sources. This work shows SOA will solve the problems that facing integration process and if the biologist scientists can access the biological data in easier way. There are several methods to implement SOA but web service is the most popular method. The Microsoft .Net Framework used to implement proposed architecture.

Keywords: Bioinformatics, Biological data, Data Integration, SOA and Web Services.

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Authors: Manouchehr Amiri

Abstract:

This article presents a general notion of physical bit information that is compatible with the basics of quantum mechanics and incorporates the Shannon entropy as a special case. This notion of physical information leads to the Binary Data Matrix model (BDM), which predicts the basic results of quantum mechanics, general relativity, and black hole thermodynamics. The compatibility of the model with holographic, information conservation, and Landauer’s principle is investigated. After deriving the “Bit Information principle” as a consequence of BDM, the fundamental equations of Planck, De Broglie, Bekenstein, and mass-energy equivalence are derived.

Keywords: Physical theory of information, binary data matrix model, Shannon information theory, bit information principle.

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Authors: Kevser Simsek, Rahime Gunay

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In this paper, we focused primarily on Istanbul data that is gathered by using intelligent transportation systems (ITS), and considered the developments in traffic information delivery and future applications that are being planned for implementation. Since traffic congestion is increasing and travel times are becoming less consistent and less predictable, traffic information delivery has become a critical issue. Considering the fuel consumption and wasted time in traffic, advanced traffic information systems are becoming increasingly valuable which enables travelers to plan their trips more accurately and easily.

Keywords: Data Fusion, Istanbul, ITS, Real Time Information, Traffic Information, Travel Time, Urban Mobility

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Authors: Toshihiko Takemura, Atsushi Umino

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In this paper, the authors examine whether or not there Institute for Information and Communications Policy shows are differences of Japanese Internet users awareness to information security based on individual attributes by using analysis of variance based on non-parametric method. As a result, generally speaking, it is found that Japanese Internet users' awareness to information security is different by individual attributes. Especially, the authors verify that the users who received the information security education would have rather higher recognition concerning countermeasures than other users including self-educated users. It is suggested that the information security education should be enhanced so that the users may appropriately take the information security countermeasures. In addition, the information security policy such as carrying out "e- net caravan" and "information security seminars" are effective in improving the users' awareness on the information security in Japan.

Keywords: Information security education, variance of analysis, Internet users, information security policy, Web-based survey.

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Authors: Yayun Hsu, Henry Horng-Shing Lu

Abstract:

This paper proposes a data-driven, biology-inspired neural segmentation method of 3D drosophila Brainbow images. We use Bayesian Sequential Partitioning algorithm for probabilistic modeling, which can be used to detect somas and to eliminate crosstalk effects. This work attempts to develop an automatic methodology for neuron image segmentation, which nowadays still lacks a complete solution due to the complexity of the image. The proposed method does not need any predetermined, risk-prone thresholds, since biological information is inherently included inside the image processing procedure. Therefore, it is less sensitive to variations in neuron morphology; meanwhile, its flexibility would be beneficial for tracing the intertwining structure of neurons.

Keywords: Brainbow, 3D imaging, image segmentation, neuron morphology, biological data mining, non-parametric learning.

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Authors: Supriyo Goswami, Debabrata Mazumder

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Chrome tannery wastewater causes serious environmental hazard due to its high pollution potential. As a result, rigorous treatment is necessary for abatement of pollution from this type of wastewater. There are many research studies on chrome tannery wastewater treatment in the field of physical, chemical, and biological methods. In general, biological treatment process is found ineffective for direct application because of adverse effects by toxic chromium, sulphide, chloride etc. However, biological methods were employed mainly for a few sub processes generating significant amount of organic matter and without chromium, chlorides etc. In this context the present paper reviews the characteristics feature and pollution potential of wastewater generated from chrome tannery units and treatment of the same. The different biological processes used earlier and their chronological development for treatment of the chrome tannery wastewater are thoroughly reviewed in this paper. In this regard, the scope of hybrid bioreactor - an advanced technology option has also been explored, as this kind of treatment is well suited for the wastewater having inhibitory substances. 

Keywords: Composite tannery wastewater, biological treatment, Hybrid bioreactor, Organic removal

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