Search results for: gene clusters

Authors: Shannon Steinmetz, Ellen Gethner

Abstract:

In this paper a theoretical foundation is developed to segment, analyze and associate patterns within audio. We explore this on imagery via sonified audio applied to our segmentation framework. The approach involves a geodesic estimator within the statistical manifold, parameterized by musical centricity. We demonstrate viability by processing a database of random imagery to produce statistically significant clusters of similar imagery content.

Keywords: Sonification, musical information geometry, image content extraction, automated quantification, audio segmentation, pattern recognition.

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Authors: Fereshteh Shacheraghi, Mohammad Reza Shakibaie, Hanieh Noveiri

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Fourty one strains of ESBL producing P.aeruginosa which were previously isolated from burn patients in Kerman University general hospital, Iran were subjected to PCR, RFLP and sequencing in order to determine the type of extended spectrum β- lactamases (ESBL), the restriction digestion pattern and possibility of mutation among detected genes. DNA extraction was carried out by phenol chloroform method. PCR for detection of bla genes was performed using specific primer for each gene. Restriction Fragment Length Polymorphism (RFLP) for ESBL genes was carried out using EcoRI, NheI, PVUII, EcoRV, DdeI, and PstI restriction enzymes. The PCR products were subjected to direct sequencing of both the strands for identification of the ESBL genes.The blaCTX-M, blaVEB-1, blaPER-1, blaGES-1, blaOXA-1, blaOXA-4 and blaOXA-10 genes were detected in the (n=1) 2.43%, (n=41)100%, (n=28) 68.3%, (n=10) 24.4%, (n=29) 70.7%, (n=7)17.1% and (n=38) 92.7% of the ESBL producing isolates respectively. The RFLP analysis showed that each ESBL gene has identical pattern of digestion among the isolated strains. Sequencing of the ESBL genes confirmed the genuinety of PCR products and revealed no mutation in the restriction sites of the above genes. From results of the present investigation it can be concluded that blaVEB-1 and blaCTX-M were the most and the least frequently isolated ESBL genes among the P.aeruginosa strains isolated from burn patients. The RFLP and sequencing analysis revealed that same clone of the bla genes were indeed existed among the antibiotic resistant strains.

Keywords: ESBL genes, PCR, RFLP, Sequencing, P.aeruginosa

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Authors: V. Golubev, A. Dosmakanbetova, A. Brener

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The purpose of this work is to establish the theoretical foundations for calculating and designing the sublimationcondensation processes in chemical apparatuses which are intended for production of ultrafine powders of crystalline and amorphous materials with controlled fractional composition. Theoretic analysis of the primary processes of nucleation and growth kinetics of the clusters according to the degree of super-saturation and the homogeneous or heterogeneous nature of nucleation has been carried out. The engineering design procedures of desublimation processes have been offered and tested for modification of the Claus process.

Keywords: Desublimation, controlled fraction composition, nucleation, ultrafine powders.

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Authors: Toshio Akimitsu, Yoichi Okabe, Akira Hirose

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Many experimental results suggest that more precise spike timing is significant in neural information processing. We construct a self-organization model using the spatiotemporal patterns, where Spike-Timing Dependent Plasticity (STDP) tunes the conduction delays between neurons. We show that the fluctuation of conduction delays causes globally continuous and locally distributed firing patterns through the self-organization.

Keywords: Self-organization, synfire-chain, Spike-Timing Dependent Plasticity, distributed information representation

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Authors: Toshio Akimitsu, Yoichi Okabe, Akira Hirose

Abstract:

Many experimental results suggest that more precise spike timing is significant in neural information processing. We construct a self-organization model using the spatiotemporal pat-terns, where Spike-Timing Dependent Plasticity (STDP) tunes the conduction delays between neurons. We show that, for highly syn-chronized inputs, the fluctuation of conduction delays causes globally continuous and locally distributed firing patterns through the self-organization.

Keywords: Self-organization, synfire-chain, Spike-Timing DependentPlasticity, distributed information representation.

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Authors: Qurban A. Memon, Mohammad S. Laghari

Abstract:

Integration of system process information obtained through an image processing system with an evolving knowledge database to improve the accuracy and predictability of wear particle analysis is the main focus of the paper. The objective is to automate intelligently the analysis process of wear particle using classification via self organizing maps. This is achieved using relationship measurements among corresponding attributes of various measurements for wear particle. Finally, visualization technique is proposed that helps the viewer in understanding and utilizing these relationships that enable accurate diagnostics.

Keywords: Neural Network, Relationship Measurement, Selforganizing Clusters, Wear Particle Analysis.

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Authors: Eleftheria Tzamali, Panayiota Poirazi, Ioannis G. Tollis, Martin Reczko

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Stable bacterial polymorphism on a single limiting resource may appear if between the evolved strains metabolic interactions take place that allow the exchange of essential nutrients [8]. Towards an attempt to predict the possible outcome of longrunning evolution experiments, a network based on the metabolic capabilities of homogeneous populations of every single gene knockout strain (nodes) of the bacterium E. coli is reconstructed. Potential metabolic interactions (edges) are allowed only between strains of different metabolic capabilities. Bacterial communities are determined by finding cliques in this network. Growth of the emerged hypothetical bacterial communities is simulated by extending the metabolic flux balance analysis model of Varma et al [2] to embody heterogeneous cell population growth in a mutual environment. Results from aerobic growth on 10 different carbon sources are presented. The upper bounds of the diversity that can emerge from single-cloned populations of E. coli such as the number of strains that appears to metabolically differ from most strains (highly connected nodes), the maximum clique size as well as the number of all the possible communities are determined. Certain single gene deletions are identified to consistently participate in our hypothetical bacterial communities under most environmental conditions implying a pattern of growth-condition- invariant strains with similar metabolic effects. Moreover, evaluation of all the hypothetical bacterial communities under growth on pyruvate reveals heterogeneous populations that can exhibit superior growth performance when compared to the performance of the homogeneous wild-type population.

Keywords: Bacterial polymorphism, clique identification, dynamic FBA, evolution, metabolic interactions.

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Authors: Heinz Stockinger

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Certain sciences such as physics, chemistry or biology, have a strong computational aspect and use computing infrastructures to advance their scientific goals. Often, high performance and/or high throughput computing infrastructures such as clusters and computational Grids are applied to satisfy computational needs. In addition, these sciences are sometimes characterised by scientific collaborations requiring resource sharing which is typically provided by Grid approaches. In this article, I discuss Grid computing approaches in High Energy Physics as well as in bioinformatics and highlight some of my experience in both scientific domains.

Keywords: Grid computing, Web services, physics, bioinformatics

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Authors: Hemanth KumarA.R, Sudhakara G., Satyanarayana B.S.

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The Cluster Dimension of a network is defined as, which is the minimum cardinality of a subset S of the set of nodes having the property that for any two distinct nodes x and y, there exist the node Si, s2 (need not be distinct) in S such that ld(x,s1) — d(y, s1)1 > 1 and d(x,s2) < d(x,$) for all s E S — {s2}. In this paper, strictly non overlap¬ping clusters are constructed. The concept of LandMarks for Unique Addressing and Clustering (LMUAC) routing scheme is developed. With the help of LMUAC routing scheme, It is shown that path length (upper bound)PLN,d < PLD, Maximum memory space requirement for the networkMSLmuAc(Az) < MSEmuAc < MSH3L < MSric and Maximum Link utilization factor MLLMUAC(i=3) < MLLMUAC(z03) < M Lc

Keywords: Metric dimension, Cluster dimension, Cluster.

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Authors: S. M. M. Syairah, M. H. Rajikin, A-R. Sharaniza

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Several embryonic cellular mechanism including cell cycle, growth and apoptosis are regulated by phosphatidylinositol-3- kinase (PI3K)/Akt signaling pathway. The goal of present study is to determine the effects of annatto (Bixa orellana)-derived δ-tocotrienol (δ-TCT) on the regulations of PI3K/Akt genes in murine morula. Twenty four 6-8 week old (23-25g) female balb/c mice were randomly divided into four groups (G1-G4; n=6). Those groups were subjected to the following treatments for 7 consecutive days: G1 (control) received tocopherol stripped corn oil, G2 was given 60 mg/kg/day of δ-TCT mixture (contains 90% delta & 10% gamma isomers), G3 was given 60 mg/kg/day of pure δ-TCT (>98% purity) and G4 received 60 mg/kg/day α-TOC. On Day 8, females were superovulated with 5 IU Pregnant Mare’s Serum Gonadotropin (PMSG) for 48 hours followed with 5 IU human Chorionic Gonadotropin (hCG) before mated with males at the ratio of 1:1. Females were sacrificed by cervical dislocation for embryo collection 48 hours post-coitum. About fifty morulas from each group were used in the gene expression analyses using Affymetrix QuantiGene Plex 2.0 Assay. Present data showed a significant increase (p<0.05) in the average number (mean + SEM) of morula produced in G2 (27.32 + 0.23), G3 (25.42 + 0.21) and G4 (27.21 + 0.34) compared to control group (G1 – 14.61 + 0.25). This is parallel with the high expression of PDK1 gene with increase of 2.75-fold (G2), 3.07-fold (G3) and 3.59-fold (G4) compared to G1. From the present data, it can be concluded that supplementation with δ-TCT(s) and α-TOC induced high expression of PDK1 in G2-G4 which enhanced the PI3K/Akt signaling activity, resulting in the increased number of morula.

Keywords: Embryonic development, morula, nicotine, vitamin E.

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Authors: W. Chattinnawat

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Consider a mass production of HDD arms where hundreds of CNC machines are used to manufacturer the HDD arms. According to an overwhelming number of machines and models of arm, construction of separate control chart for monitoring each HDD arm model by each machine is not feasible. This research proposed a strategy to optimize the SPC management on shop floor. The procedure started from identifying the clusters of the machine with similar manufacturing performance using clustering technique. The three way control chart ( I - MR - R ) is then applied to each clustered group of machine. This proposed research has advantageous to the manufacturer in terms of not only better performance of the SPC but also the quality management paradigm.

Keywords: Three way control chart. I - MR - R , between/within variation, HDD arm.

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Authors: Qurban A Memon, Mohammad S. Laghari

Abstract:

Integration of system process information obtained through an image processing system with an evolving knowledge database to improve the accuracy and predictability of wear debris analysis is the main focus of the paper. The objective is to automate intelligently the analysis process of wear particle using classification via self-organizing maps. This is achieved using relationship measurements among corresponding attributes of various measurements for wear debris. Finally, visualization technique is proposed that helps the viewer in understanding and utilizing these relationships that enable accurate diagnostics.

Keywords: Relationship Network, Relationship Measurement, Self-organizing Clusters, Wear Debris Analysis, Kohonen Network

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Authors: S.Aranganayagi, K.Thangavel

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K-Modes is an extension of K-Means clustering algorithm, developed to cluster the categorical data, where the mean is replaced by the mode. The similarity measure proposed by Huang is the simple matching or mismatching measure. Weight of attribute values contribute much in clustering; thus in this paper we propose a new weighted dissimilarity measure for K-Modes, based on the ratio of frequency of attribute values in the cluster and in the data set. The new weighted measure is experimented with the data sets obtained from the UCI data repository. The results are compared with K-Modes and K-representative, which show that the new measure generates clusters with high purity.

Keywords: Clustering, categorical data, K-Modes, weighted dissimilarity measure

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Authors: M. Margarida Costa, Jorge Simão

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The minimal condition for symmetry breaking in morphogenesis of cellular population was investigated using cellular automata based on reaction-diffusion dynamics. In particular, the study looked for the possibility of the emergence of branching structures due to mechanical interactions. The model used two types of cells an external gradient. The results showed that the external gradient influenced movement of cell type-I, also revealed that clusters formed by cells type-II worked as barrier to movement of cells type-I.

Keywords: Morphogenesis, branching structures, symmetrybreaking.

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Authors: G. Candel, D. Naccache

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t-SNE is an embedding method that the data science community has widely used. It helps two main tasks: to display results by coloring items according to the item class or feature value; and for forensic, giving a first overview of the dataset distribution. Two interesting characteristics of t-SNE are the structure preservation property and the answer to the crowding problem, where all neighbors in high dimensional space cannot be represented correctly in low dimensional space. t-SNE preserves the local neighborhood, and similar items are nicely spaced by adjusting to the local density. These two characteristics produce a meaningful representation, where the cluster area is proportional to its size in number, and relationships between clusters are materialized by closeness on the embedding. This algorithm is non-parametric. The transformation from a high to low dimensional space is described but not learned. Two initializations of the algorithm would lead to two different embedding. In a forensic approach, analysts would like to compare two or more datasets using their embedding. A naive approach would be to embed all datasets together. However, this process is costly as the complexity of t-SNE is quadratic, and would be infeasible for too many datasets. Another approach would be to learn a parametric model over an embedding built with a subset of data. While this approach is highly scalable, points could be mapped at the same exact position, making them indistinguishable. This type of model would be unable to adapt to new outliers nor concept drift. This paper presents a methodology to reuse an embedding to create a new one, where cluster positions are preserved. The optimization process minimizes two costs, one relative to the embedding shape and the second relative to the support embedding’ match. The embedding with the support process can be repeated more than once, with the newly obtained embedding. The successive embedding can be used to study the impact of one variable over the dataset distribution or monitor changes over time. This method has the same complexity as t-SNE per embedding, and memory requirements are only doubled. For a dataset of n elements sorted and split into k subsets, the total embedding complexity would be reduced from O(n2) to O(n2/k), and the memory requirement from n2 to 2(n/k)2 which enables computation on recent laptops. The method showed promising results on a real-world dataset, allowing to observe the birth, evolution and death of clusters. The proposed approach facilitates identifying significant trends and changes, which empowers the monitoring high dimensional datasets’ dynamics.

Keywords: Concept drift, data visualization, dimension reduction, embedding, monitoring, reusability, t-SNE, unsupervised learning.

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Authors: K. D. Mroczek

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In the study presented institutional context is discussed in terms of companies’ entry mode choice. In contrary to many previous analyses, instead of using one or two aggregated variables, a set of eleven determinants is used to establish equity and non-equity internationalization friendly conditions. Based on secondary data, 140 countries are analyzed and grouped into clusters revealing similar framework. The range of the economies explored is wide as it covers all regions distinguished by The World Bank. The results can prove a useful alternative for operationalization of institutional variables in further research concerning entry modes or strategic management in international markets.

Keywords: Clustering, entry mode choice, institutional environment, transaction costs.

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Authors: K. Nikovics, D. Riccobono, M. Oger, H. Morin, L. Barbier, T. Poyot, X. Holy, A. Bendahmane, M. Drouet, A. L. Favier

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Muscle regeneration after injury (as irradiation) is of great importance. However, the molecular and cellular mechanisms are still unclear. Cytokines are believed to play fundamental role in the different stages of muscle regeneration. They are secreted by many cell populations, but the predominant producers are macrophages and helper T cells. On the other hand, it has been shown that adipose tissue derived stromal/stem cell (ASC) injection could improve muscle regeneration. Stem cells probably induce the coordinated modulations of gene expression in different macrophage cells. Therefore, we investigated the patterns and timing of changes in gene expression of different cytokines occurring upon stem cells loading. Muscle regeneration was studied in an irradiated muscle of minipig animal model in presence or absence of ASC treatment (irradiated and treated with ASCs, IRR+ASC; irradiated not-treated with ASCs, IRR; and non-irradiated no-IRR). We characterized macrophage populations by immunolabeling in the different conditions. In our study, we found mostly M2 and a few M1 macrophages in the IRR+ASC samples. However, only few M2b macrophages were noticed in the IRR muscles. In addition, we found intensive fibrosis in the IRR samples. With in situ hybridization and immunolabeling, we analyzed the cytokine expression of the different macrophages and we showed that M2d macrophage are the most abundant in the IRR+ASC samples. By in situ hybridization, strong expression of the transforming growth factor β (TGF-β) was observed in the IRR+ASC but very week in the IRR samples. But when we analyzed TGF-β level with immunolabeling the expression was very different: many M2 macrophages showed week expression in IRR+ASC and few cells expressing stronger level in IRR muscles. Therefore, we investigated the MMP expressions in the different muscles. Our data showed that the M2 macrophages of the IRR+ASC muscle expressed MMP2 proteins. Our working hypothesis is that MMP2 expression of the M2 macrophages can decrease fibrosis in the IRR+ASC muscle by capturing TGF-β.

Keywords: Adipose tissue derived stromal/stem cell, cytokine, macrophage, muscle regeneration.

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Authors: Surajit Debnath, Soma Addya

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Human genome is not only the evolutionary summation of all advantageous events, but also houses lesions of deleterious foot prints. A single gene mutation sometimes may express multiple consequences in numerous tissues and a linear relationship of the genotype and the phenotype may often be obscure. ß Thalassemia minor, a transfusion independent mild anaemia, coupled with environment among other factors may articulate into phenotypic pleotropy with Hypocholesterolemia, Vitamin D deficiency, Tissue hypoxia, Hyper-parathyroidism and Psychological alterations. Occurrence of Pancreatic insufficiency, resultant steatorrhoea, Vitamin-D (25-OH) deficiency (13.86 ngm/ml) with Hypocholesterolemia (85mg/dl) in a 30 years old male ß Thal-minor patient (Hemoglobin 11mg/dl with Fetal Hemoglobin 2.10%, Hb A2 4.60% and Hb Adult 84.80% and altered Hemogram) with increased Para thyroid hormone (62 pg/ml) & moderate Serum Ca+2 (9.5mg/ml) indicate towards a cascade of phenotypic pleotropy where the ß Thalassemia mutation ,be it in the 5’ cap site of the mRNA , differential splicing etc in heterozygous state is effecting several metabolic pathways. Compensatory extramedulary hematopoiesis may not coped up well with the stressful life style of the young individual and increased erythropoietic stress with high demand for cholesterol for RBC membrane synthesis may have resulted in Hypocholesterolemia.Oxidative stress and tissue hypoxia may have caused the pancreatic insufficiency, leading to Vitamin D deficiency. This may in turn have caused the secondary hyperparathyroidism to sustain serum Calcium level. Irritability and stress intolerance of the patient was a cumulative effect of the vicious cycle of metabolic compromises. From these findings we propose that the metabolic deficiencies in the ß Thalassemia mutations may be considered as the phenotypic display of the pleotropy to explain the genetic epidemiology. According to the recommendations from the NIH Workshop on Gene-Environment Interplay in Common Complex Diseases: Forging an Integrative Model, study design of observations should be informed by gene-environment hypotheses and results of a study (genetic diseases) should be published to inform future hypotheses. Variety of approaches is needed to capture data on all possible aspects, each of which is likely to contribute to the etiology of disease. Speakers also agreed that there is a need for development of new statistical methods and measurement tools to appraise information that may be missed out by conventional method where large sample size is needed to segregate considerable effect. A meta analytic cohort study in future may bring about significant insight on to the title comment.

Keywords: Genetic disease, Genetic epidemiology, Heterozygous, Phenotype, Pleotropy, ß Thalassemia minor, Metabolic compromises.

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Authors: Elaine C. Barboza, Antonio J. Machado

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This paper discusses micrometeorological aspects of the urban climate in three cities in Western São Paulo State: Presidente Prudente, Assis and Iepê. Particular attention is paid to the method used to estimate the components of the energy balance at the surface. Estimates of convective fluxes showed that the Bowen ratio was an indicator of the local climate and that its magnitude varied between 0.3 and 0.7. Maximum values for the Bowen ratio occurred earlier in Iepê (11:00 am) than in Presidente Prudente (4:00 pm). The results indicate that the Bowen ratio is modulated by the radiation balance at the surface and by different clusters of vegetation.

Keywords: Bowen ratio, medium-sized cities, surface energy balance, urban climate.

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Authors: Chih-Wei Hsieh, Chau-Yi Chou, Sheng-HsiuKuo, Tsung-Che Tsai, I-Chen Wu

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This paper presents the benchmarking results and performance evaluation of differentclustersbuilt atthe National Center for High-Performance Computingin Taiwan. Performance of processor, memory subsystem andinterconnect is a critical factor in the overall performance of high performance computing platforms. The evaluation compares different system architecture and software platforms. Most supercomputer used HPL to benchmark their system performance, in accordance with the requirement of the TOP500 List. In this paper we consider system memory access factors that affect benchmark performance, such as processor and memory performance.We hope these works will provide useful information for future development and construct cluster system.

Keywords: Performance Evaluation, Benchmarking and High-Performance Computing

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Authors: Fayez Mostafa Alhamoui, Adnan Hadi Mahdi Al- Helali

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The main issue in designing a wireless sensor network (WSN) is the finding of a proper routing protocol that complies with the several requirements of high reliability, short latency, scalability, low power consumption, and many others. This paper proposes a novel routing algorithm that complies with these design requirements. The new routing protocol divides the WSN into several subnetworks and each sub-network is divided into several clusters. This division is designed to reduce the number of radio transmission and hence decreases the power consumption. The network division may be changed dynamically to adapt with the network changes and allows the realization of the design requirements.

Keywords: Wireless sensor networks, routing protocols, ad hoc topology, cluster, sub-network, WSN design requirements.

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Authors: M. Vivodík, Ž. Balážová, Z. Gálová

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The aim of this work was to detect genetic variability among the set of 40 castor genotypes using 8 RAPD markers. Amplification of genomic DNA of 40 genotypes, using RAPD analysis, yielded in 66 fragments, with an average of 8.25 polymorphic fragments per primer. Number of amplified fragments ranged from 3 to 13, with the size of amplicons ranging from 100 to 1200 bp. Values of the polymorphic information content (PIC) value ranged from 0.556 to 0.895 with an average of 0.784 and diversity index (DI) value ranged from 0.621 to 0.896 with an average of 0.798. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared and analyzed genotypes were grouped into two main clusters and only two genotypes could not be distinguished. Knowledge on the genetic diversity of castor can be used for future breeding programs for increased oil production for industrial uses.

Keywords: Dendrogram, polymorphism, RAPD technique, Ricinus communis L.

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Authors: S.Aranganayagi, K.Thangavel

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Clustering categorical data is more complicated than the numerical clustering because of its special properties. Scalability and memory constraint is the challenging problem in clustering large data set. This paper presents an incremental algorithm to cluster the categorical data. Frequencies of attribute values contribute much in clustering similar categorical objects. In this paper we propose new similarity measures based on the frequencies of attribute values and its cardinalities. The proposed measures and the algorithm are experimented with the data sets from UCI data repository. Results prove that the proposed method generates better clusters than the existing one.

Keywords: Clustering, Categorical, Incremental, Frequency, Domain

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Authors: Soumya Banerjee, Indrajit Mukherjee, P.K. Mahanti

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Scheduling of diversified service requests in distributed computing is a critical design issue. Cloud is a type of parallel and distributed system consisting of a collection of interconnected and virtual computers. It is not only the clusters and grid but also it comprises of next generation data centers. The paper proposes an initial heuristic algorithm to apply modified ant colony optimization approach for the diversified service allocation and scheduling mechanism in cloud paradigm. The proposed optimization method is aimed to minimize the scheduling throughput to service all the diversified requests according to the different resource allocator available under cloud computing environment.

Keywords: Ant Colony, Cloud Computing, Grid, Resource allocator, Service Request.

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Authors: S.Aksoy, Y.Caglar

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n-CdO/p-Si heterojunction diode was fabricated using sol-gel spin coating technique which is a low cost and easily scalable method for preparing of semiconductor films. The structural and morphological properties of CdO film were investigated. The X-ray diffraction (XRD) spectra indicated that the film was of polycrystalline nature. The scanning electron microscopy (SEM) images indicate that the surface morphology CdO film consists of the clusters formed with the coming together of the nanoparticles. The electrical characterization of Au/n-CdO/p–Si/Al heterojunction diode was investigated by current-voltage. The ideality factor of the diode was found to be 3.02 for room temperature. The reverse current of the diode strongly increased with illumination intensity of 100 mWcm-2 and the diode gave a maximum open circuit voltage Voc of 0.04 V and short-circuits current Isc of 9.92×10-9 A.

Keywords: CdO, heterojunction semiconductor devices, ideality factor, current-voltage characteristics

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Authors: I. Erins, J. Erina

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The aim of this article is to assess the existing business models used by the banks operating in the CEE countries in the time period from 2006 till 2011. In order to obtain research results, the authors performed qualitative analysis of the scientific literature on bank business models, which have been grouped into clusters that consist of such components as: 1) capital and reserves; 2) assets; 3) deposits, and 4) loans. In their turn, bank business models have been developed based on the types of core activities of the banks, and have been divided into four groups: Wholesale, Investment, Retail and Universal Banks. Descriptive statistics have been used to analyse the models, determining mean, minimal and maximal values of constituent cluster components, as well as standard deviation. The analysis of the data is based on such bank variable indices as Return on Assets (ROA) and Return on Equity (ROE).

Keywords: Banks, Business model, CEE, ROA, ROE.

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Authors: Assel S. Issabekova, Olga A. Berillo, Vladimir A. Khailenko, Shara A. Atambayeva, Mireille Regnier, Anatoly T. Ivachshenko

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Regulatory relationships of 686 intronic miRNA and 784 intergenic miRNAs with mRNAs of 51 intronic miRNA coding genes were established. Interaction features of studied miRNAs with 5'UTR, CDS and 3'UTR of mRNA of each gene were revealed. Functional regions of mRNA were shown to be significantly heterogenous according to the number of binding sites of miRNA and to the location density of these sites.

Keywords: 5'UTR, 3'UTR, CDS, miRNA, target mRNA

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Authors: Shuhua Lai, Kairui Chen

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In this paper, we present a fast and efficient mesh coarsening algorithm for 3D triangular meshes. Theis approach can be applied to very complex 3D meshes of arbitrary topology and with millions of vertices. The algorithm is based on the clustering of the input mesh elements, which divides the faces of an input mesh into a given number of clusters for clustering purpose by approximating the Centroidal Voronoi Tessellation of the input mesh. Once a clustering is achieved, it provides us an efficient way to construct uniform tessellations, and therefore leads to good coarsening of polygonal meshes. With proliferation of 3D scanners, this coarsening algorithm is particularly useful for reverse engineering applications of 3D models, which in many cases are dense, non-uniform, irregular and arbitrary topology. Examples demonstrating effectiveness of the new algorithm are also included in the paper.

Keywords: Coarsening, mesh clustering, shape approximation, mesh simplification.

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Authors: George E. Tsekouras, Dimitris Papageorgiou, Sotiris Kotsiantis, Christos Kalloniatis, Panagiotis Pintelas

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We develop a three-step fuzzy logic-based algorithm for clustering categorical attributes, and we apply it to analyze cultural data. In the first step the algorithm employs an entropy-based clustering scheme, which initializes the cluster centers. In the second step we apply the fuzzy c-modes algorithm to obtain a fuzzy partition of the data set, and the third step introduces a novel cluster validity index, which decides the final number of clusters.

Keywords: Categorical data, cultural data, fuzzy logic clustering, fuzzy c-modes, cluster validity index.

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Authors: L. Petrovičová, Ž. Balážová, Z. Gálová, M. Wójcik-Jagła, M. Rapacz

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In the present study, RAPD-PCR was used to assess genetic diversity of the rye including landrances and new rye cultivars coming from Central Europe and the Union of Soviet Socialist Republics (SUN). Five arbitrary random primers were used to determine RAPD polymorphism in the set of 38 rye genotypes. These primers amplified altogether 43 different DNA fragments with an average number of 8.6 fragments per genotypes. The number of fragments ranged from 7 (RLZ 8, RLZ 9 and RLZ 10) to 12 (RLZ 6). DI and PIC values of all RAPD markers were higher than 0.8 that generally means high level of polymorphism detected between rye genotypes. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared. The cultivars were grouped into two main clusters. In this experiment, RAPD proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars.

Keywords: Genetic diversity, polymorphism, RAPD markers, Secalecereale L.

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