Search results for: temporal pattern of gene expression data.

Authors: Irina Spaka, Rita Birkenfelde, Svetlana Kozireva, Jevgenija Osmjana, Madara Upmane, ElenaKashuba, Irina Kholodnyuk Holodnuka

Abstract:

Epstein-Barr virus (EBV) is implicated in the pathogenesis of the endemic Burkitt-s lymphoma (BL). The EBVpositive BL-derived cell lines initially maintain the original tumor phenotype of EBV infection (latency I, LatI), but most of them drift toward a lymphoblast phenotype of EBV latency III (LatIII) during in vitro culturing. The aim of the present work was to characterize the B-cell subsets in EBV-positive BL cell lines and to verify whether a particular cell subset correlates with the type of EBV infection. The phenotype analysis of two EBV-negative and eleven EBV-positive (three of LatI and eight of LatIII) BL cell lines was performed by polychromatic flow cytomery, based on expression pattern of CD19, CD10, CD38, CD27, and CD5 markers. Two cell subsets, CD19+CD10+ and CD19+CD10-, were defined in LatIII BL cell lines. In both subsets, the CD27 and CD5 cell surface expression was detected in a proportion of the cells.

Keywords: B-cell subsets, Burkitt's lymphoma cell lines, EBV latency, phenotype profiles.

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Authors: Alexander Kaplunovsky, Vladimir Khailenko, Alexander Bolshoy, Shara Atambayeva, AnatoliyIvashchenko

Abstract:

Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from the RNA transcripts before translation into a protein. The exon-intron structures of different eukaryotic species are quite different from each other, and the evolution of such structures raises many questions. We try to address some of these questions using statistical analysis of whole genomes. We go through all the protein-coding genes in a genome and study correlations between the net length of all the exons in a gene, the number of the exons, and the average length of an exon. We also take average values of these features for each chromosome and study correlations between those averages on the chromosomal level. Our data show universal features of exon-intron structures common to animals, plants, and protists (specifically, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Cryptococcus neoformans, Homo sapiens, Mus musculus, Oryza sativa, and Plasmodium falciparum). We have verified linear correlation between the number of exons in a gene and the length of a protein coded by the gene, while the protein length increases in proportion to the number of exons. On the other hand, the average length of an exon always decreases with the number of exons. Finally, chromosome clustering based on average chromosome properties and parameters of linear regression between the number of exons in a gene and the net length of those exons demonstrates that these average chromosome properties are genome-specific features.

Keywords: Comparative genomics, exon-intron structure, eukaryotic clustering, linear regression.

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Authors: V. T. S. Dao, T. G. Etoh, C. Vo Le, H. D. Nguyen, K. Takehara, T. Akino, K. Nishi

Abstract:

We present an explicit expression to estimate driving voltage attenuation through RC networks representation of an ultrahigh- speed image sensor. Elmore delay metric for a fundamental RC chain is employed as the first-order approximation. By application of dimensional analysis to SPICE simulation data, we found a simple expression that significantly improves the accuracy of the approximation. Estimation error of the resultant expression for uniform RC networks is less than 2%. Similarly, another simple closed-form model to estimate 50 % delay through fundamental RC networks is also derived with sufficient accuracy. The framework of this analysis can be extended to address delay or attenuation issues of other VLSI structures.

Keywords: Dimensional Analysis, Elmore model, RC network, Signal Attenuation, Ultra-High-Speed Image Sensor.

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Authors: Deniz T. Sodiri, Venkat V S S Sastry

Abstract:

The paper presents an on-line recognition machine (RM) for continuous/isolated, dynamic and static gestures that arise in Flight Deck Officer (FDO) training. RM is based on generic pattern recognition framework. Gestures are represented as templates using summary statistics. The proposed recognition algorithm exploits temporal and spatial characteristics of gestures via dynamic programming and Markovian process. The algorithm predicts corresponding index of incremental input data in the templates in an on-line mode. Accumulated consistency in the sequence of prediction provides a similarity measurement (Score) between input data and the templates. The algorithm provides an intuitive mechanism for automatic detection of start/end frames of continuous gestures. In the present paper, we consider isolated gestures. The performance of RM is evaluated using four datasets - artificial (W TTest), hand motion (Yang) and FDO (tracker, vision-based ). RM achieves comparable results which are in agreement with other on-line and off-line algorithms such as hidden Markov model (HMM) and dynamic time warping (DTW). The proposed algorithm has the additional advantage of providing timely feedback for training purposes.

Keywords: On-line Recognition Algorithm, IsolatedDynamic/Static Gesture Recognition, On-line Markovian/DynamicProgramming, Training in Virtual Environments.

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Authors: Byounghyun Kim, Youngjoon Han, Hernsoo Hahn

Abstract:

The purpose of this study is to find natural gait of biped robot such as human being by analyzing the COG (Center Of Gravity) trajectory of human being's gait. It is discovered that human beings gait naturally maintain the stability and use the minimum energy. This paper intends to find the natural gait pattern of biped robot using the minimum energy as well as maintaining the stability by analyzing the human's gait pattern that is measured from gait image on the sagittal plane and COG trajectory on the frontal plane. It is not possible to apply the torques of human's articulation to those of biped robot's because they have different degrees of freedom. Nonetheless, human and 5-link biped robots are similar in kinematics. For this, we generate gait pattern of the 5-link biped robot by using the GA algorithm of adaptation gait pattern which utilize the human's ZMP (Zero Moment Point) and torque of all articulation that are measured from human's gait pattern. The algorithm proposed creates biped robot's fluent gait pattern as that of human being's and to minimize energy consumption because the gait pattern of the 5-link biped robot model is modeled after consideration about the torque of human's each articulation on the sagittal plane and ZMP trajectory on the frontal plane. This paper demonstrate that the algorithm proposed is superior by evaluating 2 kinds of the 5-link biped robot applied to each gait patterns generated both in the general way using inverse kinematics and in the special way in which by considering visuality and efficiency.

Keywords: 5-link biped robot, gait pattern, COG (Center OfGravity), ZMP (Zero Moment Point).

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Authors: Elnaz Lashgari, Emel Demircan

Abstract:

Electromyography (EMG) is one of the most important interfaces between humans and robots for rehabilitation. Decoding this signal helps to recognize muscle activation and converts it into smooth motion for the robots. Detecting each muscle’s pattern during walking and running is vital for improving the quality of a patient’s life. In this study, EMG data from 10 muscles in 10 subjects at 4 different speeds were analyzed. EMG signals are nonlinear with high dimensionality. To deal with this challenge, we extracted some features in time-frequency domain and used manifold learning and Laplacian Eigenmaps algorithm to find the intrinsic features that represent data in low-dimensional space. We then used the Bayesian classifier to identify various patterns of EMG signals for different muscles across a range of running speeds. The best result for vastus medialis muscle corresponds to 97.87±0.69 for sensitivity and 88.37±0.79 for specificity with 97.07±0.29 accuracy using Bayesian classifier. The results of this study provide important insight into human movement and its application for robotics research.

Keywords: Electrocardiogram, manifold learning, Laplacian Eigenmaps, running pattern.

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Authors: V. Kabeer, N.K.Narayanan

Abstract:

This paper reports a new pattern recognition approach for face recognition. The biological model of light receptors - cones and rods in human eyes and the way they are associated with pattern vision in human vision forms the basis of this approach. The functional model is simulated using CWD and WPD. The paper also discusses the experiments performed for face recognition using the features extracted from images in the AT & T face database. Artificial Neural Network and k- Nearest Neighbour classifier algorithms are employed for the recognition purpose. A feature vector is formed for each of the face images in the database and recognition accuracies are computed and compared using the classifiers. Simulation results show that the proposed method outperforms traditional way of feature extraction methods prevailing for pattern recognition in terms of recognition accuracy for face images with pose and illumination variations.

Keywords: Face recognition, Image analysis, Wavelet feature extraction, Pattern recognition, Classifier algorithms

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Authors: Amitava Chakraborty, Sudip Kumar De, Ranjan Dasgupta

Abstract:

Point quad tree is considered as one of the most common data organizations to deal with spatial data & can be used to increase the efficiency for searching the point features. As the efficiency of the searching technique depends on the height of the tree, arbitrary insertion of the point features may make the tree unbalanced and lead to higher time of searching. This paper attempts to design an algorithm to make a nearly balanced quad tree. Point pattern analysis technique has been applied for this purpose which shows a significant enhancement of the performance and the results are also included in the paper for the sake of completeness.

Keywords: Algorithm, Height balanced tree, Point patternanalysis, Point quad tree.

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Authors: Naghmeh Moradpoor Sheykhkanloo

Abstract:

Thousands of organisations store important and confidential information related to them, their customers, and their business partners in databases all across the world. The stored data ranges from less sensitive (e.g. first name, last name, date of birth) to more sensitive data (e.g. password, pin code, and credit card information). Losing data, disclosing confidential information or even changing the value of data are the severe damages that Structured Query Language injection (SQLi) attack can cause on a given database. It is a code injection technique where malicious SQL statements are inserted into a given SQL database by simply using a web browser. In this paper, we propose an effective pattern recognition neural network model for detection and classification of SQLi attacks. The proposed model is built from three main elements of: a Uniform Resource Locator (URL) generator in order to generate thousands of malicious and benign URLs, a URL classifier in order to: 1) classify each generated URL to either a benign URL or a malicious URL and 2) classify the malicious URLs into different SQLi attack categories, and a NN model in order to: 1) detect either a given URL is a malicious URL or a benign URL and 2) identify the type of SQLi attack for each malicious URL. The model is first trained and then evaluated by employing thousands of benign and malicious URLs. The results of the experiments are presented in order to demonstrate the effectiveness of the proposed approach.

Keywords: Neural Networks, pattern recognition, SQL injection attacks, SQL injection attack classification, SQL injection attack detection.

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Authors: Samuel Olajide Babawale, O. O. Ogunkoya

Abstract:

The study mapped selected wells in Inisa town, Osun state, in the guinea savanna region of southwest Nigeria, and determined the water quality considering certain elements. It also assessed the variation in the elevation of the water table surface to depth of the wells in the months of August and November. This is with a view to determine the level of contamination of the water with respect to land use and anthropogenic activities, and also to determine the variation that occurs in the quantity of well water in the rainy season and the start of the dry season. Results show a random pattern of the distribution of the mapped wells and shows that there is a shallow water table in the study area. The temporal changes in the elevation show that there are no significant variations in the depth of the water table surface over the period of study implying that there is a sufficient amount of water available to the town all year round. It also shows a high concentration of sodium in the water sample analyzed compared to other elements that were considered, which include iron, copper, calcium, and lead. This is attributed majorly to anthropogenic activities through the disposal of waste in landfill sites. There is a low concentration of lead which is a good indication of a reduced level of pollution.

Keywords: Water quality, temporal changes, elevation, water table surface, land use, anthropogenic activities.

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Authors: Deniz T. Sodiri, Venkat V S S Sastry

Abstract:

The paper presents an on-line recognition machine (RM) for continuous/isolated, dynamic and static gestures that arise in Flight Deck Officer (FDO) training. RM is based on generic pattern recognition framework. Gestures are represented as templates using summary statistics. The proposed recognition algorithm exploits temporal and spatial characteristics of gestures via dynamic programming and Markovian process. The algorithm predicts corresponding index of incremental input data in the templates in an on-line mode. Accumulated consistency in the sequence of prediction provides a similarity measurement (Score) between input data and the templates. The algorithm provides an intuitive mechanism for automatic detection of start/end frames of continuous gestures. In the present paper, we consider isolated gestures. The performance of RM is evaluated using four datasets - artificial (W TTest), hand motion (Yang) and FDO (tracker, vision-based ). RM achieves comparable results which are in agreement with other on-line and off-line algorithms such as hidden Markov model (HMM) and dynamic time warping (DTW). The proposed algorithm has the additional advantage of providing timely feedback for training purposes.

Keywords: On-line Recognition Algorithm, IsolatedDynamic/Static Gesture Recognition, On-line Markovian/DynamicProgramming, Training in Virtual Environments.

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Authors: Tingke Wu, Man Yuan

Abstract:

“National Territorial Planning (2016-2030)” was issued by the State Council of China in 2017. As an important initiative of putting it into effect, territorial planning at provincial level makes overall arrangement of territorial development, resources and environment protection, comprehensive renovation and security system construction. Hubei province, as the pivot of the “Rise of Central China” national strategy, is now confronted with great opportunities and challenges in territorial development, protection, and renovation. Territorial spatial pattern experiences long time evolution, influenced by multiple internal and external driving forces. It is not clear what are the main causes of its formation and what are effective ways of optimizing it. By analyzing land use data in 2016, this paper reveals present status of territory in Hubei. Combined with economic and social data and construction information, driving forces of territorial spatial pattern are then analyzed. Research demonstrates that the three types of territorial space aggregate distinctively. The four aspects of driving forces include natural background which sets the stage for main functions, population and economic factors which generate agglomeration effect, transportation infrastructure construction which leads to axial expansion and significant provincial strategies which encourage the established path. On this basis, targeted strategies for optimizing territory spatial pattern are then put forward. Hierarchical protection pattern should be established based on development intensity control as respect for nature. By optimizing the layout of population and industry and improving the transportation network, polycentric network-based development pattern could be established. These findings provide basis for Hubei Territorial Planning, and reference for future territorial planning in other provinces.

Keywords: Driving forces, Hubei, optimizing strategies, spatial pattern, territory.

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Authors: Rima Hleiss, Elie Bitar, Mahmoud Hassan, Mohamad Khalil

Abstract:

A comprehensive study of object recognition in the human brain requires combining both spatial and temporal analysis of brain activity. Here, we are mainly interested in three issues: the time perception of visual objects, the ability of discrimination between two particular categories (objects vs. animals), and the possibility to identify a particular spatial representation of visual objects. Our experiment consisted of acquiring dense electroencephalographic (EEG) signals during a picture-naming task comprising a set of objects and animals’ images. These EEG responses were recorded from nine participants. In order to determine the time perception of the presented visual stimulus, we analyzed the Event Related Potentials (ERPs) derived from the recorded EEG signals. The analysis of these signals showed that the brain perceives animals and objects with different time instants. Concerning the discrimination of the two categories, the support vector machine (SVM) was applied on the instantaneous EEG (excellent temporal resolution: on the order of millisecond) to categorize the visual stimuli into two different classes. The spatial differences between the evoked responses of the two categories were also investigated. The results showed a variation of the neural activity with the properties of the visual input. Results showed also the existence of a spatial pattern of electrodes over particular regions of the scalp in correspondence to their responses to the visual inputs.

Keywords: Brain activity, dense EEG, evoked responses, spatiotemporal analysis, SVM, perception.

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Authors: Shyue-Ran Li, Kuohsiang Chen

Abstract:

The study explored varied types of human smiles and extracted most of the key factors affecting the smiles. These key factors then were converted into a set of control points which could serve to satisfy the needs for creation of facial expression for 3D animators and be further applied to the face simulation for robots in the future. First, hundreds of human smile pictures were collected and analyzed to identify the key factors for face expression. Then, the factors were converted into a set of control points and sizing parameters calculated proportionally. Finally, two different faces were constructed for validating the parameters via the process of simulating smiles of the same type as the original one.

Keywords: 3D animation, facial expression, numerical, robot, smile parameter.

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Authors: Parvaneh Shabanzadeh, Malik Hj Abu Hassan, Leong Wah June, Maryam Mohagheghtabar

Abstract:

Clustering is one of an interesting data mining topics that can be applied in many fields. Recently, the problem of cluster analysis is formulated as a problem of nonsmooth, nonconvex optimization, and an algorithm for solving the cluster analysis problem based on nonsmooth optimization techniques is developed. This optimization problem has a number of characteristics that make it challenging: it has many local minimum, the optimization variables can be either continuous or categorical, and there are no exact analytical derivatives. In this study we show how to apply a particular class of optimization methods known as pattern search methods to address these challenges. These methods do not explicitly use derivatives, an important feature that has not been addressed in previous studies. Results of numerical experiments are presented which demonstrate the effectiveness of the proposed method.

Keywords: Clustering functions, Non-smooth Optimization, Nonconvex Optimization, Pattern Search Method.

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Authors: Sanjay Kumar Srivastava, Anu Rani Sharma, Kamna Sachdeva

Abstract:

The aim of the paper is to analyze the characteristics of winter fog in terms of its trend and spatial-temporal variability over Indo-Gangetic plains. The study reveals that during last four and half decades (1971-2015), an alarming increasing trend in fog frequency has been observed during the winter months of December and January over the study area. The frequency of fog has increased by 118.4% during the peak winter months of December and January. It has also been observed that on an average central part of IGP has 66.29% fog days followed by west IGP with 41.94% fog days. Further, Empirical Orthogonal Function (EOF) decomposition and Mann-Kendall variation analysis are used to analyze the spatial and temporal patterns of winter fog. The findings have significant implications for the further research of fog over IGP and formulate robust strategies to adapt the fog variability and mitigate its effects. The decision by Delhi Government to implement odd-even scheme to restrict the use of private vehicles in order to reduce pollution and improve quality of air may result in increasing the alarming increasing trend of fog over Delhi and its surrounding areas regions of IGP.

Keywords: Fog, climatology, spatial variability, temporal variability, empirical orthogonal function, visibility, Mann-Kendall test, variation point.

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Authors: Mohamed El Aroussi, Mohammed El Hassouni, Sanaa Ghouzali, Mohammed Rziza, Driss Aboutajdine

Abstract:

In this paper the problem of face recognition under variable illumination conditions is considered. Most of the works in the literature exhibit good performance under strictly controlled acquisition conditions, but the performance drastically drop when changes in pose and illumination occur, so that recently number of approaches have been proposed to deal with such variability. The aim of this work is to introduce an efficient local appearance feature extraction method based steerable pyramid (SP) for face recognition. Local information is extracted from SP sub-bands using LBP(Local binary Pattern). The underlying statistics allow us to reduce the required amount of data to be stored. The experiments carried out on different face databases confirm the effectiveness of the proposed approach.

Keywords: Face recognition (FR), Steerable pyramid (SP), localBinary Pattern (LBP).

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Authors: Patrick Nwabueze Okechukwu, Ima Nirwana Soelaiman, Gabriele Anisah Ruth Froemming, Mohd Yusri Idorus, Norazlina Mohamed

Abstract:

Supplementation of palm vitamin E has been reported to prevent loss of bone density in ovariectomised female rats. The mechanism by which palm vitamin E exerts these effects is still unknown. We hypothesized that palm vitamin E may act by preventing the protein expression changes. Two dimensional poly acyrilamide gel electrophoresis (2-D PAGE) and PD Quest software genomic solutions Investigator (proteomics) was used to analyze the differential protein expression profile in femoral and humeri bones harvested from three groups of rats; sham-operated rats (SO), ovariectomised rats (Ovx) and ovariectomised rats supplemented for 2 months with palm vitamin E. The results showed that there were over 300 valued spot on each of the groups PVE and OVX as compared to about 200 in SO. Comparison between the differential protein expression between OVX and PVE groups showed that ten spots were down –regulated in OVX but up-regulated in PVE. The ten differential spots were separately named P1-P10. The identification and understanding of the pathway of the differential protein expression among the groups is ongoing and may account for the molecular mechanism through which palm vitamin E exert its anti-osteoporotic effect.

Keywords: Palm vitamin E, ovariectomised, osteoporosis protein expression, 2-d-page.

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Authors: Fuad M. Alkoot

Abstract:

DNA data have been used in forensics for decades. However, current research looks at using the DNA as a biometric identity verification modality. The goal is to improve the speed of identification. We aim at using gene data that was initially used for autism detection to find if and how accurate is this data for identification applications. Mainly our goal is to find if our data preprocessing technique yields data useful as a biometric identification tool. We experiment with using the nearest neighbor classifier to identify subjects. Results show that optimal classification rate is achieved when the test set is corrupted by normally distributed noise with zero mean and standard deviation of 1. The classification rate is close to optimal at higher noise standard deviation reaching 3. This shows that the data can be used for identity verification with high accuracy using a simple classifier such as the k-nearest neighbor (k-NN). 

Keywords: Biometrics, identity verification, genetic data, k-nearest neighbor.

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Authors: Youngji Yoo, Seung Hwan Park, Daewoong An, Sung-Shick Kim, Jun-Geol Baek

Abstract:

The yield management system is very important to produce high-quality semiconductor chips in the semiconductor manufacturing process. In order to improve quality of semiconductors, various tests are conducted in the post fabrication (FAB) process. During the test process, large amount of data are collected and the data includes a lot of information about defect. In general, the defect on the wafer is the main causes of yield loss. Therefore, analyzing the defect data is necessary to improve performance of yield prediction. The wafer bin map (WBM) is one of the data collected in the test process and includes defect information such as the fail bit patterns. The fail bit has characteristics of spatial point patterns. Therefore, this paper proposes the feature extraction method using the spatial point pattern analysis. Actual data obtained from the semiconductor process is used for experiments and the experimental result shows that the proposed method is more accurately recognize the fail bit patterns.

Keywords: Semiconductor, wafer bin map (WBM), feature extraction, spatial point patterns, contour map.

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Authors: M. Kaomek, J. R. Ketudat-Cairns

Abstract:

The cDNA encoding the 326 amino acids of a Class I basic chitinase gene from Leucaena leucocephala de Wit (KB3, Genbank accession: AAM49597) was cloned under the control of CaMV35S promoter in pCAMBIA 1300 and transferred to Koshihikari. Calli of Koshihikari rice was transformed with agrobacterium with this construct expressing the chitinase and β- glucouronidase (GUS). The frequencies of calli 90 % has been obtained from rice seedlings cultured on NB medium. The high regeneration frequencies, 74% was obtained from calli cultured on regeneration medium containing 4 mg/l BAP, and 7 g/l phytagel at 25°C. Various factors were studied in order to establish a procedure for the transformation of Koshihikari Agrobacterium tumefaciens. Supplementation of 50 mM acetosyringone to the medium during coculivation was important to enhance the frequency to transient transformation. The 4 week-old scutellum-derived calli were excellent starting materials. Selection medium based on NB medium supplement with 40 mg/l hygromycin and 400 mg/l cefotaxime were an optimized medium for selection of transformed rice calli. The percentage of transformation 70 was obtained. Recombinant calli and regenerated rice plants were checked the expression of chitinase and gus by PCR, northern blot gel, southern blot gel, and gus assay. Chitinase and gus were expressed in all parts of recombinant rice. The rice line expressing the KB3 chiitnase was more resistant to the blast fungus Fusarium monoliforme than control line.

Keywords: chitinase, Leucaena leucocephala de Wit, Koshihikari, transgenic rice.

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Authors: R.Goudarzizadeh, N.Hedayat, S.H.Mousavi Jahromi

Abstract:

Channel junctions can be analyzed in two ways of division (lateral intake) and combined flows (confluence). The present paper investigates 3D flow pattern at lateral intake using Navier-Stokes equation and κ -ε (RNG) turbulent model. The equations are solved by Finite-Volume Method (FVM) and results are compared with the experimental data of (Barkdoll, B.D., 1997) to test the validity of the findings. Comparison of the results with the experimental data indicated a close proximity between the two sets of data which suggest a very close simulation. Results further indicated an inverse relation between the effects of discharge ratio ( r Q ) on the length and width of the separation zone. In other words, as the discharge ration increases, the length and width of separation zone decreases.

Keywords: 900 junction, flow division, turbulent flow, numerical modeling, flow separation zone.

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Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur

Abstract:

Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions, and the modeling of evolution. Various global rearrangements of permutations, such as reversals and transpositions,have recently become of interest because of their applications in computational molecular biology. A reversal is an operation that reverses the order of a substring of a permutation. A transposition is an operation that swaps two adjacent substrings of a permutation. The problem of determining the smallest number of reversals required to transform a given permutation into the identity permutation is called sorting by reversals. Similar problems can be defined for transpositions and other global rearrangements. In this work we perform a study about some genome rearrangement primitives. We show how a genome is modelled by a permutation, introduce some of the existing primitives and the lower and upper bounds on them. We then provide a comparison of the introduced primitives.

Keywords: Sorting Primitives, Genome Rearrangements, Transpositions, Block Interchanges, Strip Exchanges.

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Authors: Hong Ding, Fatiha Benslimane, Isra Marei, Chris R. Triggle

Abstract:

Hyperglycaemia is a key factor that contributes to the development of diabetes-related microvascular disease and a major risk factor for endothelial dysfunction. In the current study, we have explored glucose-induced abnormal intracellular calcium (Ca2+ i) homeostasis in mouse microvessel endothelial cells (MMECs) in high glucose (HG) (40mmol/L) versus control (low glucose, LG) (11 mmol/L). We demonstrated that the exposure of MMECs to HG for 3 days did not change basal Ca2+ i, however, there was a significant increase of acetylcholine-induced Ca2+ entry. Western blots illustrated that exposure to HG also increased STIM1 (Stromal Interaction Molecule 1), but not Orai1 (the pore forming subunit), protein expression levels. Although the link between HG-induced changes in STIM1 expression, enhanced Ca2+ entry and endothelial dysfunction requires further study, the current data are suggestive that targeting these pathways may reduce the impact of HG on endothelial function.

Keywords: store-operated calcium entry, hyperglycaemia, STIM1, endothelial dysfunction

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Authors: Harleen Kaur

Abstract:

Knowledge Discovery in Databases (KDD) is the process of extracting previously unknown, hidden and interesting patterns from a huge amount of data stored in databases. Data mining is a stage of the KDD process that aims at selecting and applying a particular data mining algorithm to extract an interesting and useful knowledge. It is highly expected that data mining methods will find interesting patterns according to some measures, from databases. It is of vital importance to define good measures of interestingness that would allow the system to discover only the useful patterns. Measures of interestingness are divided into objective and subjective measures. Objective measures are those that depend only on the structure of a pattern and which can be quantified by using statistical methods. While, subjective measures depend only on the subjectivity and understandability of the user who examine the patterns. These subjective measures are further divided into actionable, unexpected and novel. The key issues that faces data mining community is how to make actions on the basis of discovered knowledge. For a pattern to be actionable, the user subjectivity is captured by providing his/her background knowledge about domain. Here, we consider the actionability of the discovered knowledge as a measure of interestingness and raise important issues which need to be addressed to discover actionable knowledge.

Keywords: Data Mining Community, Knowledge Discovery inDatabases (KDD), Interestingness, Subjective Measures, Actionability.

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Authors: Mohamed Hafez, Georg Hausner

Abstract:

The full length mitochondrial small subunit ribosomal (mt-rns) gene has been characterized for Ophiostoma novo-ulmi subspecies americana. The gene was also characterized for Ophiostoma ulmi and a group II intron was noted in the mt-rns gene of O. ulmi. The insertion in the mt-rns gene is at position S952 and it is a group IIB1 intron that encodes a double motif LAGLIDADG homing endonuclease from an open reading frame located within a loop of domain III. Secondary structure models for the mt-rns RNA of O. novo-ulmi subsp. americana and O. ulmi were generated to place the intron within the context of the ribosomal RNA. The in vivo splicing of the O.ul-mS952 group II intron was confirmed with reverse transcription-PCR. A survey of 182 strains of Dutch Elm Diseases causing agents showed that the mS952 intron was absent in what is considered to be the more aggressive species O. novo-ulmi but present in strains of the less aggressive O. ulmi. This observation suggests that the O.ul-mS952 intron can be used as a PCR-based molecular marker to discriminate between O. ulmi and O. novo-ulmi subsp. americana.

Keywords: Dutch Elm Disease, group II introns, mtDNA, species identification

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Authors: Gyumin Hwang, Jihong Lee

Abstract:

This paper studied the CSS-based indoor localization system which is easy to implement, inexpensive to compose the systems, additionally CSS-based indoor localization system covers larger area than other system. However, this system has problem which is affected by reflected distance data. This problem in localization is caused by the multi-path effect. Error caused by multi-path is difficult to be corrected because the indoor environment cannot be described. In this paper, in order to solve the problem by multi-path, we have supplemented the localization system by using pattern matching method based on extended database. Thereby, this method improves precision of estimated. Also this method is verified by experiments in gymnasium. Database was constructed by 1m intervals, and 16 sample data were collected from random position inside the region of DB points. As a result, this paper shows higher accuracy than existing method through graph and table.

Keywords: Chirp Spread Spectrum (CSS), Indoor Localization, Pattern-Matching, Time of Arrival (ToA), Multi-Path, Mahalanobis Distance, Reception Rate, Simultaneous Localization and Mapping (SLAM), Laser Range Finder (LRF).

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Authors: Dima Stopel, Zvi Boger, Robert Moskovitch, Yuval Shahar, Yuval Elovici

Abstract:

Computer worm detection is commonly performed by antivirus software tools that rely on prior explicit knowledge of the worm-s code (detection based on code signatures). We present an approach for detection of the presence of computer worms based on Artificial Neural Networks (ANN) using the computer's behavioral measures. Identification of significant features, which describe the activity of a worm within a host, is commonly acquired from security experts. We suggest acquiring these features by applying feature selection methods. We compare three different feature selection techniques for the dimensionality reduction and identification of the most prominent features to capture efficiently the computer behavior in the context of worm activity. Additionally, we explore three different temporal representation techniques for the most prominent features. In order to evaluate the different techniques, several computers were infected with five different worms and 323 different features of the infected computers were measured. We evaluated each technique by preprocessing the dataset according to each one and training the ANN model with the preprocessed data. We then evaluated the ability of the model to detect the presence of a new computer worm, in particular, during heavy user activity on the infected computers.

Keywords: Artificial Neural Networks, Feature Selection, Temporal Analysis, Worm Detection.

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

Abstract:

Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence, and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, Brassinosteroids, Phylogenetic analysis, Transcription factor.

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Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

Abstract:

Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p>0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: Kidney cancer, molecular biomarker, expression analysis, mutation screening.

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