Multiple Sequence Alignment Using Optimization Algorithms

Proteins or genes that have similar sequences are likely to perform the same function. One of the most widely used techniques for sequence comparison is sequence alignment. Sequence alignment allows mismatches and insertion/deletion, which represents biological mutations. Sequence alignment is usually performed only on two sequences. Multiple sequence alignment, is a natural extension of two-sequence alignment. In multiple sequence alignment, the emphasis is to find optimal alignment for a group of sequences. Several applicable techniques were observed in this research, from traditional method such as dynamic programming to the extend of widely used stochastic optimization method such as Genetic Algorithms (GAs) and Simulated Annealing. A framework with combination of Genetic Algorithm and Simulated Annealing is presented to solve Multiple Sequence Alignment problem. The Genetic Algorithm phase will try to find new region of solution while Simulated Annealing can be considered as an alignment improver for any near optimal solution produced by GAs.

Optimum Design of an 8x8 Optical Switch with Thermal Compensated Mechanisms

This paper studies the optimum design for reducing optical loss of an 8x8 mechanical type optical switch due to the temperature change. The 8x8 optical switch is composed of a base, 8 input fibers, 8 output fibers, 3 fixed mirrors and 17 movable mirrors. First, an innovative switch configuration is proposed with thermal-compensated design. Most mechanical type optical switches have a disadvantage that their precision and accuracy are influenced by the ambient temperature. Therefore, the thermal-compensated design is to deal with this situation by using materials with different thermal expansion coefficients (α). Second, a parametric modeling program is developed to generate solid models for finite element analysis, and the thermal and structural behaviors of the switch are analyzed. Finally, an integrated optimum design program, combining Autodesk Inventor Professional software, finite element analysis software, and genetic algorithms, is developed for improving the thermal behaviors that the optical loss of the switch is reduced. By changing design parameters of the switch in the integrated design program, the final optimum design that satisfies the design constraints and specifications can be found.

The Concept of Place and Sense of Place In Architectural Studies

Place is a where dimension formed by people-s relationship with physical settings, individual and group activities, and meanings. 'Place Attachment', 'Place Identity'and 'Sense of Place' are some concepts that could describe the quality of people-s relationships with a place. The concept of Sense of place is used in studying human-place bonding, attachment and place meaning. Sense of Place usually is defined as an overarching impression encompassing the general ways in which people feel about places, senses it, and assign concepts and values to it. Sense of place is highlighted in this article as one of the prevailing concepts among place-based researches. Considering dimensions of sense of place has always been beneficial for investigating public place attachment and pro-environmental attitudes towards these places. The creation or preservation of Sense of place is important in maintaining the quality of the environment as well as the integrity of human life within it. While many scholars argued that sense of place is a vague concept, this paper will summarize and analyze the existing seminal literature. Therefore, in this paper first the concept of Sense of place and its characteristics will be examined afterward the scales of Sense of place will be reviewed and the factors that contribute to form Sense of place will be evaluated and finally Place Attachment as an objective dimension for measuring the sense of place will be described.

Knowledge Continuity as a Part of Business Continuity Management

Today the intangible assets are the capital of knowledge and are the most important and the most valuable resource for organizations. All employees have knowledge independently of the kind of jobs they do. Knowledge is thus an asset, which influences business operations. The objective of this article is to identify knowledge continuity as an objective of business continuity management. The article has been prepared based on the analysis of secondary sources and the evaluation of primary sources of data by means of a quantitative survey conducted in the Czech Republic. The conclusion of the article is that organizations that apply business continuity management do not focus on the preservation of the knowledge of key employees. Organizations ensure knowledge continuity only intuitively, on a random basis, non-systematically and discontinuously. The non-ensuring of knowledge continuity represents a threat of loss of key knowledge for organizations and can also negatively affect business continuity.

An Innovation Capability Maturity Model – Development and Initial Application

The seemingly ambiguous title of this paper – use of the terms maturity and innovation in concord – signifies the imperative of every organisation within the competitive domain. Where organisational maturity and innovativeness were traditionally considered antonymous, the assimilation of these two seemingly contradictory notions is fundamental to the assurance of long-term organisational prosperity. Organisations are required, now more than ever, to grow and mature their innovation capability – rending consistent innovative outputs. This paper describes research conducted to consolidate the principles of innovation and identify the fundamental components that constitute organisational innovation capability. The process of developing an Innovation Capability Maturity Model is presented. A brief description is provided of the basic components of the model, followed by a description of the case studies that were conducted to evaluate the model. The paper concludes with a summary of the findings and potential future research.

Real E-Government, Real Convenience

In this paper we have suggested a new system for egovernment. In this method a government can design a precise and perfect system to control people and organizations by using five major documents. These documents contain the important information of each member of a society and help all organizations to do their informatics tasks through them. This information would be available by only a national code and a secure program would support it. The suggested system can give a good awareness to the society and help it be managed correctly.

Trust Building Mechanisms for Electronic Business Networks and Their Relation to eSkills

Globalization, supported by information and communication technologies, changes the rules of competitiveness and increases the significance of information, knowledge and network cooperation. In line with this trend, the need for efficient trust-building tools has emerged. The absence of trust building mechanisms and strategies was identified within several studies. Through trust development, participation on e-business network and usage of network services will increase and provide to SMEs new economic benefits. This work is focused on effective trust building strategies development for electronic business network platforms. Based on trust building mechanism identification, the questionnairebased analysis of its significance and minimum level of requirements was conducted. In the paper, we are confirming the trust dependency on e-Skills which play crucial role in higher level of trust into the more sophisticated and complex trust building ICT solutions.

Study of Remote Sensing and Satellite Images Ability in Preparing Agricultural Land Use Map (ALUM)

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.

Evaluation of Chlorophyll Content and Chlorophyll Fluorescence Parameters and Relationships between Chlorophyll a, b and Chlorophyll Content Index under Water Stress in Olea europaea cv. Dezful

This study was conducted to determine effect of water stress on chlorophyll content and chlorophyll fluorescence parameter in young `Dezful- olive trees. Three irrigation regimes (40% ETcrop, 65% ETcrop and 100% ETcrop) were used. After irrigation treatments were applied, some of biochemical parameters including chlorophyll a, b, total chlorophyll, chlorophyll fluorescence and also chlorophyll content index (C.C.I) were measured. Results of Analysis of variance showed that irrigation treatments had significant effect on chlorophylla, total chlorophyll (chl a+b), C.C.I and Fv/Fm ratio. The amount of decreased chlorophyll a and total chlorophyll in plants were received 40% ETcrop were 51.55% and 46.86%, respectively, compared with 100% ETcrop.

Detecting Abnormal ECG Signals Utilising Wavelet Transform and Standard Deviation

ECG contains very important clinical information about the cardiac activities of the heart. Often the ECG signal needs to be captured for a long period of time in order to identify abnormalities in certain situations. Such signal apart of a large volume often is characterised by low quality due to the noise and other influences. In order to extract features in the ECG signal with time-varying characteristics at first need to be preprocessed with the best parameters. Also, it is useful to identify specific parts of the long lasting signal which have certain abnormalities and to direct the practitioner to those parts of the signal. In this work we present a method based on wavelet transform, standard deviation and variable threshold which achieves 100% accuracy in identifying the ECG signal peaks and heartbeat as well as identifying the standard deviation, providing a quick reference to abnormalities.

Increase of Heat Index over Bangladesh: Impact of Climate Change

Heat Index describes the combined effect of temperature and humidity on human body. This combined effect is causing a serious threat to the health of people because of the changing climate. With climate change, climate variability and thus the occurrence of heat waves is likely to increase. Evidence is emerging from the analysis of long-term climate records of an increase in the frequency and duration of extreme temperature events in all over Bangladesh particularly during summer. Summer season has prolonged while winters have become short in Bangladesh. Summers have become hotter and thus affecting the lives of the people engaged in outdoor activities during scorching sun hours. In 2003 around 62 people died due to heat wave across the country. In this paper Bangladesh is divided in four regions and heat index has been calculated from 1960 to 2010 in these regions of the country. The aim of this paper is to identify the spots most vulnerable to heat strokes and heat waves due to high heat index. The results show upward trend of heat index in almost all the regions of Bangladesh. The highest increase in heat index value has been observed in areas of South-west region and North-west Region. The highest change in average heat index has been found in Jessore by almost 5.50C.

Vertical Silicon Nanowire MOSFET With A Fully-Silicided (FUSI) NiSi2 Gate

This paper presents a vertical silicon nanowire n- MOSFET integrated with a CMOS-compatible fully-silicided (FUSI) NiSi2 gate. Devices with nanowire diameter of 50nm show good electrical performance (SS < 70mV/dec, DIBL < 30mV/V, Ion/Ioff > 107). Most significantly, threshold voltage tunability of about 0.2V is shown. Although threshold voltage remains low for the 50nm diameter device, it is expected to become more positive as nanowire diameter reduces.

Project Management in Student Satellite Projects: A University – Industry Collaboration View

This research contribution propels the idea of collaborating environment for the execution of student satellite projects in the backdrop of project management principles. The recent past has witnessed a technological shift in the aerospace industry from the big satellite projects to the small spacecrafts especially for the earth observation and communication purposes. This vibrant shift has vitalized the academia and industry to share their resources and to create a win-win paradigm of mutual success and technological development along with the human resource development in the field of aerospace. Small student satellites are the latest jargon of academia and more than 100 CUBESAT projects have been executed successfully all over the globe and many new student satellite projects are in the development phase. The small satellite project management requires the application of specific knowledge, skills, tools and techniques to achieve the defined mission requirements. The Authors have presented the detailed outline for the project management of student satellites and presented the role of industry to collaborate with the academia to get the optimized results in academic environment.

Operational Risk – Scenario Analysis

This paper focuses on operational risk measurement techniques and on economic capital estimation methods. A data sample of operational losses provided by an anonymous Central European bank is analyzed using several approaches. Loss Distribution Approach and scenario analysis method are considered. Custom plausible loss events defined in a particular scenario are merged with the original data sample and their impact on capital estimates and on the financial institution is evaluated. Two main questions are assessed – What is the most appropriate statistical method to measure and model operational loss data distribution? and What is the impact of hypothetical plausible events on the financial institution? The g&h distribution was evaluated to be the most suitable one for operational risk modeling. The method based on the combination of historical loss events modeling and scenario analysis provides reasonable capital estimates and allows for the measurement of the impact of extreme events on banking operations.

Noise Performance Optimization of a Fast Wavelength Calibration Algorithm for OSAs

A new fast correlation algorithm for calibrating the wavelength of Optical Spectrum Analyzers (OSAs) was introduced in [1]. The minima of acetylene gas spectra were measured and correlated with saved theoretical data [2]. So it is possible to find the correct wavelength calibration data using a noisy reference spectrum. First tests showed good algorithmic performance for gas line spectra with high noise. In this article extensive performance tests were made to validate the noise resistance of this algorithm. The filter and correlation parameters of the algorithm were optimized for improved noise performance. With these parameters the performance of this wavelength calibration was simulated to predict the resulting wavelength error in real OSA systems. Long term simulations were made to evaluate the performance of the algorithm over the lifetime of a real OSA.

High Performance Liquid Chromatographic Method for Determination of Colistin Sulfate and its Application in Medicated Premixand Animal Feed

The aim of the present study was to develop and validate an inexpensive and simple high performance liquid chromatographic (HPLC) method for the determination of colistin sulfate. Separation of colistin sulfate was achieved on a ZORBAX Eclipse XDB-C18 column using UV detection at λ=215 nm. The mobile phase was 30 mM sulfate buffer (pH 2.5):acetonitrile(76:24). An excellent linearity (r2=0.998) was found in the concentration range of 25 - 400 μg/mL. Intra- day and inter-day precisions of method (%RSD, n=3) were less than 7.9%.The developed and validated method was applied to determination of the content of colistin sulfate in medicated premix and animal feed sample.The recovery of colistin from animal feed was satisfactorily ranged from 90.92 to 93.77%. The results demonstrated that the HPLC method developed in this work is appropriate for direct determination of colistin sulfate in commercial medicated premixes and animal feed.

Advanced Stochastic Models for Partially Developed Speckle

Speckled images arise when coherent microwave, optical, and acoustic imaging techniques are used to image an object, surface or scene. Examples of coherent imaging systems include synthetic aperture radar, laser imaging systems, imaging sonar systems, and medical ultrasound systems. Speckle noise is a form of object or target induced noise that results when the surface of the object is Rayleigh rough compared to the wavelength of the illuminating radiation. Detection and estimation in images corrupted by speckle noise is complicated by the nature of the noise and is not as straightforward as detection and estimation in additive noise. In this work, we derive stochastic models for speckle noise, with an emphasis on speckle as it arises in medical ultrasound images. The motivation for this work is the problem of segmentation and tissue classification using ultrasound imaging. Modeling of speckle in this context involves partially developed speckle model where an underlying Poisson point process modulates a Gram-Charlier series of Laguerre weighted exponential functions, resulting in a doubly stochastic filtered Poisson point process. The statistical distribution of partially developed speckle is derived in a closed canonical form. It is observed that as the mean number of scatterers in a resolution cell is increased, the probability density function approaches an exponential distribution. This is consistent with fully developed speckle noise as demonstrated by the Central Limit theorem.

Increasing Fishery Economic Added Value through Post Fishing Program: Cold Storage Program

The purpose of this paper is to guide the effort in improving the economic added value of Indonesian fisheries product through post fishing program, which is cold storage program. Indonesia's fisheries potential has been acknowledged by the world. FAO (2009) stated that Indonesia is one of the tenth highest producers of fishery products in the world. Based on BPS (Statistics Indonesia data), the national fisheries production in 2011 reached 5.714 million tons, which 93.55% came from marine fisheries and 6.45% from open waters. Indonesian territory consist of 2/3 of Indonesian waters, has given enormous benefits for Indonesia, especially fishermen. To improve the economic level of fishermen requires efforts to develop fisheries business unit. On of the efforts is by improving the quality of products which are marketed in the regional and international levels. It is certainly need the support of the existence of various fishery facilities (infrastructure to superstructure), one of which is cold storage. Given the many benefits of cold storage as a means of processing of fishery resources, Indonesia Maritime Security Coordinating Board (IMSCB) as one of the maritime institutions for maritime security and safety, has a program to empower the coastal community through encourages the development of cold storage in the middle and lower fishery business unit. The development of cold storage facilities which able to run its maximum role requires synergistic efforts of various parties.

A New Protocol for Concealed Data Aggregation in Wireless Sensor Networks

Wireless sensor networks (WSN) consists of many sensor nodes that are placed on unattended environments such as military sites in order to collect important information. Implementing a secure protocol that can prevent forwarding forged data and modifying content of aggregated data and has low delay and overhead of communication, computing and storage is very important. This paper presents a new protocol for concealed data aggregation (CDA). In this protocol, the network is divided to virtual cells, nodes within each cell produce a shared key to send and receive of concealed data with each other. Considering to data aggregation in each cell is locally and implementing a secure authentication mechanism, data aggregation delay is very low and producing false data in the network by malicious nodes is not possible. To evaluate the performance of our proposed protocol, we have presented computational models that show the performance and low overhead in our protocol.

Application of He-s Amplitude Frequency Formulation for a Nonlinear Oscillator with Fractional Potential

In this paper, He-s amplitude frequency formulation is used to obtain a periodic solution for a nonlinear oscillator with fractional potential. By calculation and computer simulations, compared with the exact solution shows that the result obtained is of high accuracy.