Computing Entropy for Ortholog Detection

Biological sequences from different species are called or-thologs if they evolved from a sequence of a common ancestor species and they have the same biological function. Approximations of Kolmogorov complexity or entropy of biological sequences are already well known to be useful in extracting similarity information between such sequences -in the interest, for example, of ortholog detection. As is well known, the exact Kolmogorov complexity is not algorithmically computable. In prac-tice one can approximate it by computable compression methods. How-ever, such compression methods do not provide a good approximation to Kolmogorov complexity for short sequences. Herein is suggested a new ap-proach to overcome the problem that compression approximations may notwork well on short sequences. This approach is inspired by new, conditional computations of Kolmogorov entropy. A main contribution of the empir-ical work described shows the new set of entropy-based machine learning attributes provides good separation between positive (ortholog) and nega-tive (non-ortholog) data - better than with good, previously known alter-natives (which do not employ some means to handle short sequences well).Also empirically compared are the new entropy based attribute set and a number of other, more standard similarity attributes sets commonly used in genomic analysis. The various similarity attributes are evaluated by cross validation, through boosted decision tree induction C5.0, and by Receiver Operating Characteristic (ROC) analysis. The results point to the conclu-sion: the new, entropy based attribute set by itself is not the one giving the best prediction; however, it is the best attribute set for use in improving the other, standard attribute sets when conjoined with them.

M-ary Chaotic Sequence Based SLM-OFDM System for PAPR Reduction without Side-Information

Selected Mapping (SLM) is a PAPR reduction technique, which converts the OFDM signal into several independent signals by multiplication with the phase sequence set and transmits one of the signals with lowest PAPR. But it requires the index of the selected signal i.e. side information (SI) to be transmitted with each OFDM symbol. The PAPR reduction capability of the SLM scheme depends on the selection of phase sequence set. In this paper, we have proposed a new phase sequence set generation scheme based on M-ary chaotic sequence and a mapping scheme to map quaternary data to concentric circle constellation (CCC) is used. It is shown that this method does not require SI and provides better SER performance with good PAPR reduction capability as compared to existing SLMOFDM methods.

Research and Development of a Biomorphic Robot Driven by Shape Memory Alloys

In this study, we used shape memory alloys as actuators to build a biomorphic robot which can imitate the motion of an earthworm. The robot can be used to explore in a narrow space. Therefore we chose shape memory alloys as actuators. Because of the small deformation of a wire shape memory alloy, spiral shape memory alloys are selected and installed both on the X axis and Y axis (each axis having two shape memory alloys) to enable the biomorphic robot to do reciprocating motion. By the mechanism we designed, the robot can increase the distance as it moves in a duty cycle. In addition, two shape memory alloys are added to the robot head for controlling right and left turns. By sending pulses through the I/O card from the controller, the signals are then amplified by a driver to heat the shape memory alloys in order to make the SMA shrink to pull the mechanism to move.

A Brain Inspired Approach for Multi-View Patterns Identification

Biologically human brain processes information in both unimodal and multimodal approaches. In fact, information is progressively abstracted and seamlessly fused. Subsequently, the fusion of multimodal inputs allows a holistic understanding of a problem. The proliferation of technology has exponentially produced various sources of data, which could be likened to being the state of multimodality in human brain. Therefore, this is an inspiration to develop a methodology for exploring multimodal data and further identifying multi-view patterns. Specifically, we propose a brain inspired conceptual model that allows exploration and identification of patterns at different levels of granularity, different types of hierarchies and different types of modalities. A structurally adaptive neural network is deployed to implement the proposed model. Furthermore, the acquisition of multi-view patterns with the proposed model is demonstrated and discussed with some experimental results.

A New High Speed Neural Model for Fast Character Recognition Using Cross Correlation and Matrix Decomposition

Neural processors have shown good results for detecting a certain character in a given input matrix. In this paper, a new idead to speed up the operation of neural processors for character detection is presented. Such processors are designed based on cross correlation in the frequency domain between the input matrix and the weights of neural networks. This approach is developed to reduce the computation steps required by these faster neural networks for the searching process. The principle of divide and conquer strategy is applied through image decomposition. Each image is divided into small in size sub-images and then each one is tested separately by using a single faster neural processor. Furthermore, faster character detection is obtained by using parallel processing techniques to test the resulting sub-images at the same time using the same number of faster neural networks. In contrast to using only faster neural processors, the speed up ratio is increased with the size of the input image when using faster neural processors and image decomposition. Moreover, the problem of local subimage normalization in the frequency domain is solved. The effect of image normalization on the speed up ratio of character detection is discussed. Simulation results show that local subimage normalization through weight normalization is faster than subimage normalization in the spatial domain. The overall speed up ratio of the detection process is increased as the normalization of weights is done off line.

Environmental Impact Assessment of Gotv and Hydro-Electric Dam on the Karoon River Using ICOLD Technique

Today Environmental Impact Assessment (EIA) is known as one of the most important tools for decision makers in the construction of civil and industrial projects towards sustainable development. In the past, projects were evaluated based on cost and benefit analysis regardless of the physical and biological environmental effects and its socio-economical impacts. According to the Department of Environment (DOE) of Iran's regulations, the construction of hydroelectric dams is an activity that requires an EIA report. In this paper the environmental impact assessment of the Gotvand hydro-electrical dam has been evaluated in the three environment elements, biological, Physical-chemical and cultural units. This dam is one of the largest dams in Iran with a volume of 4500 MCM and is going to be the last dam on the Karoon River in the south of Iran. In this paper the ICOLD (International Commission on Large Dams) technique was employed for the environmental impact assessment of the dam. The research includes all socio economical and environmental effects of the dam during the construction and operation of the hydro electric dam and Environmental management, monitoring and mitigation of negative impacts were analyzed. In this project the results led to using some techniques to protect the destructive impacts on biological aspects beside the effective long time period impacts on the biological aspects. The impacts on physical aspects are temporary and negative commonly that could be restored and rehabilitated in natural process in the long time in operation period.

Virtual E-Medic: A Cloud Based Medical Aid

This paper discusses about an intelligent system to be installed in ambulances providing professional support to the paramedics on board. A video conferencing device over mobile 4G services enables specialists virtually attending the patient being transferred to the hospital. The data centre holds detailed databases on the patients past medical history and hospitals with the specialists. It also hosts various software modules that compute the shortest traffic –less path to the closest hospital with the required facilities, on inputting the symptoms of the patient, on a real time basis.

Complexity of Mathematical Expressions in Adaptive Multimodal Multimedia System Ensuring Access to Mathematics for Visually Impaired Users

Our adaptive multimodal system aims at correctly presenting a mathematical expression to visually impaired users. Given an interaction context (i.e. combination of user, environment and system resources) as well as the complexity of the expression itself and the user-s preferences, the suitability scores of different presentation format are calculated. Unlike the current state-of-the art solutions, our approach takes into account the user-s situation and not imposes a solution that is not suitable to his context and capacity. In this wok, we present our methodology for calculating the mathematical expression complexity and the results of our experiment. Finally, this paper discusses the concepts and principles applied on our system as well as their validation through cases studies. This work is our original contribution to an ongoing research to make informatics more accessible to handicapped users.

Application of Generalized Stochastic Petri Nets(GSPN) in Modeling and Evaluating a Resource Sharing Flexible Manufacturing System

In most study fields, a phenomenon may not be studied directly but it will be examined indirectly by phenomenon model. Making an accurate model of system, there is attained new information from modeled phenomenon without any charge, danger, etc... there have been developed more solutions for describing and analyzing the recent complicated systems but few of them have analyzed the performance in the range of system description. Petri nets are of limited solutions which may make such union. Petri nets are being applied in problems related to modeling and designing the systems. Theory of Petri nets allow a system to model mathematically by a Petri net and analyzing the Petri net can then determine main information of modeled system-s structure and dynamic. This information can be used for assessing the performance of systems and suggesting corrections in the system. In this paper, beside the introduction of Petri nets, a real case study will be studied in order to show the application of generalized stochastic Petri nets in modeling a resource sharing production system and evaluating the efficiency of its machines and robots. The modeling tool used here is SHARP software which calculates specific indicators helping to make decision.

Reactive Neural Control for Phototaxis and Obstacle Avoidance Behavior of Walking Machines

This paper describes reactive neural control used to generate phototaxis and obstacle avoidance behavior of walking machines. It utilizes discrete-time neurodynamics and consists of two main neural modules: neural preprocessing and modular neural control. The neural preprocessing network acts as a sensory fusion unit. It filters sensory noise and shapes sensory data to drive the corresponding reactive behavior. On the other hand, modular neural control based on a central pattern generator is applied for locomotion of walking machines. It coordinates leg movements and can generate omnidirectional walking. As a result, through a sensorimotor loop this reactive neural controller enables the machines to explore a dynamic environment by avoiding obstacles, turn toward a light source, and then stop near to it.

Analysis and Preservation of Lime-Kilns in Corsica

The aim of this paper is the analysis and preservation of lime kilns, focusing on the structure, construction, and functionality of vertical shaft lime kilns of the Cap Corse in Corsica. Plans and sections of two lime kilns are presented in detail, providing an overall picture of this specific industrial heritage. The potential damage areas are identified performing structural analysis of a lime kiln using the finite element method. A restoration and strengthening technique that satisfies the directions of the Charter of Venice is presented using post-tensioning tendons. Recommendations are given to preserve and promote these important historical structures integrating them into the custom footpath.

A New Fast Intra Prediction Mode Decision Algorithm for H.264/AVC Encoders

The H.264/AVC video coding standard contains a number of advanced features. Ones of the new features introduced in this standard is the multiple intramode prediction. Its function exploits directional spatial correlation with adjacent block for intra prediction. With this new features, intra coding of H.264/AVC offers a considerably higher improvement in coding efficiency compared to other compression standard, but computational complexity is increased significantly when brut force rate distortion optimization (RDO) algorithm is used. In this paper, we propose a new fast intra prediction mode decision method for the complexity reduction of H.264 video coding. for luma intra prediction, the proposed method consists of two step: in the first step, we make the RDO for four mode of intra 4x4 block, based the distribution of RDO cost of those modes and the idea that the fort correlation with adjacent mode, we select the best mode of intra 4x4 block. In the second step, we based the fact that the dominating direction of a smaller block is similar to that of bigger block, the candidate modes of 8x8 blocks and 16x16 macroblocks are determined. So, in case of chroma intra prediction, the variance of the chroma pixel values is much smaller than that of luma ones, since our proposed uses only the mode DC. Experimental results show that the new fast intra mode decision algorithm increases the speed of intra coding significantly with negligible loss of PSNR.

Challenges of Implementing Urban Master Plans: The Lahore Experience

Master plan is a tool to guide and manage the growth of cities in a planned manner. The soul of a master plan lies in its implementation framework. If not implemented, people are trapped in a mess of urban problems and laissez-faire development having serious long term repercussions. Unfortunately, Master Plans prepared for several major cities of Pakistan could not be fully implemented due to host of reasons and Lahore is no exception. Being the second largest city of Pakistan with a population of over 7 million people, Lahore holds the distinction that the first ever Master Plan in the country was prepared for this city in 1966. Recently in 2004, a new plan titled `Integrated Master Plan for Lahore-2021- has been approved for implementation. This paper provides a comprehensive account of the weaknesses and constraints in the plan preparation process and implementation strategies of Master Plans prepared for Lahore. It also critically reviews the new Master Plan particularly with respect to the proposed implementation framework. The paper discusses the prospects and pre-conditions for successful implementation of the new Plan in the light of historic analysis, interviews with stakeholders and the new institutional context under the devolution plan.

Analysis of Blind Decision Feedback Equalizer Convergence: Interest of a Soft Decision

In this paper the behavior of the decision feedback equalizers (DFEs) adapted by the decision-directed or the constant modulus blind algorithms is presented. An analysis of the error surface of the corresponding criterion cost functions is first developed. With the intention of avoiding the ill-convergence of the algorithm, the paper proposes to modify the shape of the cost function error surface by using a soft decision instead of the hard one. This was shown to reduce the influence of false decisions and to smooth the undesirable minima. Modified algorithms using the soft decision during a pseudo-training phase with an automatic switch to the properly tracking phase are then derived. Computer simulations show that these modified algorithms present better ability to avoid local minima than conventional ones.

Effect of Acid Rain on Vigna radiata

The acid rain causes change in pH level of soil it is directly influence on root and leaf growth. Yield of the crop was reduced if acidity of soil is more. Acid rain seeps into the earth and poisons plants and trees by dissolving toxic substances in the soil, such as aluminum, which get absorbed by the roots. In present investigation, effect of acid rain on crop Vigna radiata was studied. The effect of acid rain on change in soil fertility was detected in which pH of control sample was 6.5 and pH of 1% H2SO4 and 1% HNO3 were 3.5. Nitrogen nitrate in soil was high in 1% HNO3 treated soil & Control sample. Ammonium nitrogen in soil was low in 1% HNO3 & H2SO4 treated soil. Ammonium nitrogen was medium in control and other samples. The effect of acid rain on seed germination on 3rd day of germination control sample growth was 6.1cm with plumule 0.001% HNO3 & 0.001% H2SO4 was 5.5cm with plumule and 8cm with plumule. On 10th day fungal growth was observed in 1% and 0.1% H2SO4 concentrations when all plants were dead. The effect of acid rain on crop productivity was investigated on 3rd day roots were developed in plants. On 12th day Vigna radiata showed more growth in 0.1% HNO3 and 0.1% H2SO4 treated plants as compare to control plants. On 20th day development of discoloration of plant pigments were observed on acid treated plants leaves. On 34th day Vigna radiata showed flower in 0.1% HNO3, 0.01% HNO3 and 0.01% H2SO4treated plants and no flowers were observed on control plants. On 42th day 0.1% HNO3, 0.01% HNO and 0.01% H2SO4 treated Vigna radiata variety and control plants were showed seeds on plants. In Vigna radiate variety 0.1%, 0.01% HNO3, 0.01% H2SO4treated plants were dead on 46th day and fungal growth was observed. The toxicological study was carried out on Vigna radiata plants exposed to 1% HNO3 cells were damaged more than 1% H2SO4. Leaf sections exposed to 0.001% HNO3 & H2SO4 showed less damaged of cells and pigmentation observed in entire slide when compare with control plant.

FSM-based Recognition of Dynamic Hand Gestures via Gesture Summarization Using Key Video Object Planes

The use of human hand as a natural interface for humancomputer interaction (HCI) serves as the motivation for research in hand gesture recognition. Vision-based hand gesture recognition involves visual analysis of hand shape, position and/or movement. In this paper, we use the concept of object-based video abstraction for segmenting the frames into video object planes (VOPs), as used in MPEG-4, with each VOP corresponding to one semantically meaningful hand position. Next, the key VOPs are selected on the basis of the amount of change in hand shape – for a given key frame in the sequence the next key frame is the one in which the hand changes its shape significantly. Thus, an entire video clip is transformed into a small number of representative frames that are sufficient to represent a gesture sequence. Subsequently, we model a particular gesture as a sequence of key frames each bearing information about its duration. These constitute a finite state machine. For recognition, the states of the incoming gesture sequence are matched with the states of all different FSMs contained in the database of gesture vocabulary. The core idea of our proposed representation is that redundant frames of the gesture video sequence bear only the temporal information of a gesture and hence discarded for computational efficiency. Experimental results obtained demonstrate the effectiveness of our proposed scheme for key frame extraction, subsequent gesture summarization and finally gesture recognition.

Model Transformation with a Visual Control Flow Language

Graph rewriting-based visual model processing is a widely used technique for model transformation. Visual model transformations often need to follow an algorithm that requires a strict control over the execution sequence of the transformation steps. Therefore, in Visual Model Processors (VMPs) the execution order of the transformation steps is crucial. This paper presents the visual control flow support of Visual Modeling and Transformation System (VMTS), which facilitates composing complex model transformations of simple transformation steps and executing them. The VMTS Visual Control Flow Language (VCFL) uses stereotyped activity diagrams to specify control flow structures and OCL constraints to choose between different control flow branches. This paper introduces VCFL, discusses its termination properties and provides an algorithm to support the termination analysis of VCFL transformations.

The Overall Aspects of E-Leaning Issues, Developments, Opportunities and Challenges

Rapid steps made in the field of Information and Communication Technology (ICT) has facilitated the development of teaching and learning methods and prepared them to serve the needs of an assorted educational institution. In other words, the information age has redefined the fundamentals and transformed the institutions and method of services delivery forever. The vision is the articulation of a desire to transform the method of teaching and learning could proceed through e-learning. E-learning is commonly deliberated to use of networked information and communications technology in teaching and learning practice. This paper deals the general aspects of the e-leaning with its issues, developments, opportunities and challenges, which can the higher institutions own.

Applying GQM Approach towards Development of Criterion-Referenced Assessment Model for OO Programming Courses

The most influential programming paradigm today is object oriented (OO) programming and it is widely used in education and industry. Recognizing the importance of equipping students with OO knowledge and skills, it is not surprising that most Computer Science degree programs offer OO-related courses. How do we assess whether the students have acquired the right objectoriented skills after they have completed their OO courses? What are object oriented skills? Currently none of the current assessment techniques would be able to provide this answer. Traditional forms of OO programming assessment provide a ways for assigning numerical scores to determine letter grades. But this rarely reveals information about how students actually understand OO concept. It appears reasonable that a better understanding of how to define and assess OO skills is needed by developing a criterion referenced model. It is even critical in the context of Malaysia where there is currently a growing concern over the level of competency of Malaysian IT graduates in object oriented programming. This paper discussed the approach used to develop the criterion-referenced assessment model. The model can serve as a guideline when conducting OO programming assessment as mentioned. The proposed model is derived by using Goal Questions Metrics methodology, which helps formulate the metrics of interest. It concluded with a few suggestions for further study.