Search results for: O-antigen gene cluster

Authors: M. A. I Perera, C. R. Wijesinghe, A. R. Weerasinghe

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his study was conducted to review and identify the unsupervised techniques that can be employed to analyze gene expression data in order to identify better subtypes of tumors. Identifying subtypes of cancer help in improving the efficacy and reducing the toxicity of the treatments by identifying clues to find target therapeutics. Process of gene expression data analysis described under three steps as preprocessing, clustering, and cluster validation. Feature selection is important since the genomic data are high dimensional with a large number of features compared to samples. Hierarchical clustering and K Means are often used in the analysis of gene expression data. There are several cluster validation techniques used in validating the clusters. Heatmaps are an effective external validation method that allows comparing the identified classes with clinical variables and visual analysis of the classes.

Keywords: cancer subtypes, gene expression data analysis, clustering, cluster validation

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Authors: Peng Hou

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Natural products produced from marine bacteria serve as an immense reservoir for anti-infective drugs and therapeutic agents. Nowadays, heterologous expression of gene clusters of interests has been widely adopted as an effective strategy for natural product discovery. Briefly, the heterologous expression flowchart would be: biosynthetic gene cluster identification, pathway construction and expression, and product detection. However, gene cluster capture using traditional Transformation-associated recombination (TAR) protocol is low-efficient (0.5% positive colony rate). To make things worse, most of these putative new natural products are only predicted by bioinformatics analysis such as antiSMASH, and their corresponding natural products biosynthetic pathways are either not expressed or expressed at very low levels under laboratory conditions. Those setbacks have inspired us to focus on seeking new technologies to efficiently edit and refractor of biosynthetic gene clusters. Recently, two cutting-edge techniques have attracted our attention - the CRISPR-Cas9 and Gibson Assembly. By now, we have tried to pretreat Brevibacillus laterosporus strain genomic DNA with CRISPR-Cas9 nucleases that specifically generated breaks near the gene cluster of interest. This trial resulted in an increase in the efficiency of gene cluster capture (9%). Moreover, using Gibson Assembly by adding/deleting certain operon and tailoring enzymes regardless of end compatibility, the silent construct (~80kb) has been successfully refactored into an active one, yielded a series of analogs expected. With the appearances of the novel molecular tools, we are confident to believe that development of a high throughput mature pipeline for DNA assembly, transformation, product isolation and identification would no longer be a daydream for marine natural product discovery.

Keywords: biosynthesis, CRISPR-Cas9, DNA assembly, refactor, TAR cloning

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Authors: Abu Salim Mustafa

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Brucellosis is a zoonotic disease endemic in Kuwait. Human brucellosis can be caused by several Brucella species with Brucella melitensis causing the most severe and Brucella abortus the least severe disease. Furthermore, relapses are common after successful chemotherapy of patients. The classical biochemical methods of culture and serology for identification of Brucellae provide information about the species and serotypes only. However, to differentiate between relapse and reinfection/epidemiological investigations, the identification of genotypes using molecular methods is essential. In this study, four molecular methods [16S rRNA gene sequencing, real-time PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR and multilocus variable-number tandem-repeat analysis (MLVA)-16] were evaluated for the identification and typing of 75 strains of Brucella isolated in Kuwait. The 16S rRNA gene sequencing suggested that all the strains were B. melitensis and real-time PCR confirmed their species identity as B. melitensis. The ERIC-PCR band profiles produced a dendrogram of 75 branches suggesting each strain to be of a unique type. The cluster classification, based on ~ 80% similarity, divided all the ERIC genotypes into two clusters, A and B. Cluster A consisted of 9 ERIC genotypes (A1-A9) corresponding to 9 individual strains. Cluster B comprised of 13 ERIC genotypes (B1-B13) with B5 forming the largest cluster of 51 strains. MLVA-16 identified all isolates as B. melitensis and divided them into 71 MLVA-types. The cluster analysis of MLVA-16-types suggested that most of the strains in Kuwait originated from the East Mediterranean Region, a few from the African group and one new genotype closely matched with the West Mediterranean region. In conclusion, this work demonstrates that B. melitensis, the most pathogenic species of Brucella, is prevalent in Kuwait. Furthermore, MLVA-16 is the best molecular method, which can identify the Brucella species and genotypes as well as determine their origin in the global context. Supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: Brucella, ERIC-PCR, MLVA-16, RT-PCR, 16S rRNA gene sequencing

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Authors: Mohammad Ahangari

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Schizophrenia is a psychiatric disorder with symptoms that include cognitive deficits and nicotine has been suggested to have an effect on cognition. In recent years, the advents of Genome-Wide Association Studies(GWAS) has evolved our understanding about the genetic causes of complex disorders such as schizophrenia and studying the role of genome-wide significant genes could potentially lead to the development of new therapeutic agents for treatment of cognitive deficits in schizophrenia. The current study identified six Single Nucleotide Polymorphisms (SNP) from schizophrenia and smoking GWAS that are located on or in close proximity to the nicotinic receptor gene cluster (CHRN) and studied their association with cognition in an Irish sample of 1297 cases and controls using linear regression analysis. Further on, the interaction between CHRN gene cluster and Dopamine receptor D2 gene (DRD2) during working memory was investigated. The effect of these polymorphisms on nicotinic and dopaminergic neurotransmission, which is disrupted in schizophrenia, have been characterized in terms of their effects on memory, attention, social cognition and IQ as measured by a neuropsychological test battery and significant effects in two polymorphisms were found across global IQ domain of the test battery.

Keywords: cognition, dopamine, GWAS, nicotine, schizophrenia, SNPs

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Authors: Yu-Chen Hu

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Gene editing by CRISPR and gene regulation by microRNA or CRISPR activation have dramatically changed the way to manipulate cellular gene expression and cell fate. In recent years, various gene editing and gene manipulation technologies have been applied to control stem cell differentiation to enhance tissue regeneration. This research will focus on how to develop CRISPR, CRISPR activation (CRISPRa), CRISPR inhibition (CRISPRi), as well as bi-directional CRISPR-AI gene regulation technologies to control cell differentiation and bone regeneration. Moreover, in this study, CRISPR/Cas13d-mediated RNA editng for miRNA editing and bone regeneration will be discussed.

Keywords: gene therapy, bone regeneration, stem cell, CRISPR, gene regulation

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Authors: Prittesh Patel, Ramar Krishnamurthy

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In the present study, nine strains of C. falcatum obtained from different places and cultivars were characterized for sporulation, growth rate, and 18S rRNA gene sequence. All isolates had characteristic fast-growing sparse and fleecy aerial mycelia on potato dextrose agar with sickle shape conidia (length x width: varied from 20.0 X 3.89 to 25.52 X 5.34 μm) and blackish to orange acervuli with setae (length x width: varied from 112.37X 2.78 to 167.66 X 6.73 μm). They could be divided into two groups on the base of morphology; P1, dense mycelia with concentric growth and P2, sparse mycelia with uneven growth. Genomic DNA isolation followed by PCR amplification with ITS1 and ITS4 primer produced ~550bp amplicons for all isolates. Phylogeny generated by 18S rRNA gene sequence confirmed the variation in isolates and mainly grouped into two clusters; cluster 1 contained CoC671 isolates (cfNAV and cfPAR) and Co86002 isolate (cfTIM). Other isolates cfMAD, cfKAM, and cfMAR were grouped into cluster 2. Remaining isolates did not fall into any cluster. Isolate cfGAN, collected from Co86032 was found highly diverse of all the nine isolates. In a nutshell, we found considerable genetic divergence and morphological variation within C. falcatum accessions collected from different areas of south Gujarat, India and these can be used for the breeding program.

Keywords: Colletotrichum falcatum, ITS, morphology, red rot, sugarcane

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Authors: Abdelsabour G. A. Khaled, Ahmed W. A. Abdalla And Sabry Y. M. Mahmoud

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Banana plants showing typical mosaic and yellow stripes on leaves as symptoms were collected from Assiut Governorate in Egypt. The causal agent was identified as Cucumber mosaic virus (CMV) on the basis of symptoms, transmission, serology, transmission electron microscopy and reverse transcription polymerase chain reaction (RT-PCR). Coat protein (CP) gene was amplified using gene specific primers for coat protein (CP), followed by cloning into desired cloning vector for sequencing. In this study the CMV was transmitted into propagation host either by aphid or mechanically. The transmission was confirmed through Direct Antigen Coating Enzyme Linked Immuno Sorbent Assay (DAC-ELISA). Analysis of the 120 deduced amino acid sequence of the coat protein gene revealed that the EG-A strain of CMV shared from 97.50 to 98.33% with those strains belonging to subgroup IA. The cluster analysis grouped the Egyptian isolate with strains Fny and Ri8 belonging sub-group IA. It appears that there occurs a high incidence of CMV infecting banana belonging to IA subgroup in most parts of Egypt.

Keywords: banana, CMV, transmission, CP gene, RT-PCR

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Authors: Fadhl Alakwaa

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One of the sustainable goals of the system biology is understanding gene-gene interactions. Hence, gene regulatory networks (GRN) need to be constructed for understanding the disease ontology and to reduce the cost of drug development. To construct gene regulatory from gene expression we need to overcome many challenges such as data denoising and dimensionality. In this paper, we develop an integrated system to reduce data dimension and remove the noise. The generated network from our system was validated via available interaction databases and was compared to previous methods. The result revealed the performance of our proposed method.

Keywords: gene regulatory network, biclustering, denoising, system biology

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Authors: Restu Misrianti

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The amino acid variation of Asn (allele A) at position 631 in Mx gene was specific to positive antiviral to avian viral desease. This research was aimed at identifying polymorphism of Mx gene in duck using molecular technique. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) technique was used to select the genotype of AA, AG and GG. There were thirteen duck from Indragiri Hulu regency (Riau Province) used in this experiment. DNA amplification results showed that the Mx gene in duck is found in a 73 bp fragment. Mx gene in duck did not show any polymorphism. The frequency of the resistant allele (AA) was 0%, while the frequency of the susceptible allele (GG) was 100%.

Keywords: duck, Mx gene, PCR, RFLP

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Authors: Saeid Doaei

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The various studies have examined the relationship between FTO gene expression and macronutrients levels. In order to obtain better viewpoint from this interactions, all of the existing studies were reviewed systematically. All published papers have been obtained and reviewed using standard and sensitive keywords from databases such as CINAHL, Embase, PubMed, PsycInfo, and the Cochrane, from 1990 to 2016. The results indicated that all of 6 studies that met the inclusion criteria (from a total of 428 published article) found FTO gene expression changes at short-term follow-ups. Four of six studies found an increased FTO gene expression after calorie restriction, while two of them indicated decreased FTO gene expression. The effect of protein, carbohydrate and fat were separately assessed and suggested by all of six studies. In conclusion, the level of FTO gene expression in hypothalamus is related to macronutrients levels. Future research should evaluate the long-term impact of dietary interventions.

Keywords: obesity, gene expression, FTO, macronutrients

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Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.

Keywords: metabolic network, gene knockout, flux balance analysis, microarray data, integration

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Authors: Pragya Bhawsar, Utpal Chattopadhyay

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Small and Medium Enterprises play crucial role in contributing to economic objectives of an emerging nation. To support SMEs, the idea of creation of clusters has been prevalent since past two decades. In this paper, an attempt has been done to explore the impact of being in the cluster on the competitiveness of SMEs. To meet the objective, Nasik Cluster (India) has been selected. The information was collected by means of two focus group discussions and survey of thirty SMEs. The finding generates interest revealing the fact that under the concept ‘Cluster’ a lot of ambiguity flourish. Besides the problems and opportunities of the firms in the cluster the results bring to notice that the benefits of clusterization can only reach to SMEs when the whole location can be considered/understood as a cluster, rather than many subsets (various forms of clusters) prevailing under it. Fostering such an understanding calls for harmony among the various stakeholders of the clusters. The dynamics of interaction among government, local industry associations, relevant institutions, large firms and finally SMEs which makes the most of the location based cluster, are significant in shaping the host cluster’s competitiveness and vice versa.

Keywords: SMEs, industry clusters, common facility centres, co-creation, policy

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Authors: Naomi Seidu, Edward Poluyi, Chibuikem Ikwuegbuenyi, Eghosa Morgan

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The current poor prognosis of glioblastoma has called for the need for an improvement in treatment methods in order to improve its survival rate. Despite the different interventions currently available for this tumor, the average survival is still only a few months. (12-15). The aim is to create a more favorable prognosis and have a reduction in the resistance to treatment currently being experienced, even with surgical interventions and chemotherapy. From the available literature, there is a relationship between the presence of HOX genes (Homeobox genes) and glioblastoma, which could be attributable to the increasing treatment resistance. Hence silencing these genes can be a key to improving survival rates of glioblastoma. A series of studies have highlighted the role that HOX genes play in glioblastoma prognosis. Promotion of human glioblastoma initiation, aggressiveness, and resistance to Temozolomide has been associated with HOXA9. The role of HOX gene expression in cancer stem cells should be studied as it could provide a means of designing CSC-targeted therapies, as CSCs play a part in the initiation and progression of solid tumors.

Keywords: GBM- glioblastoma, HOXA gene- homeobox genes cluster, signaling pathways, temozolomide

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Authors: Manverpreet Kaur, Amarpreet Singh

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The demand of Vehicular ad hoc networks is increasing day by day, due to offering the various applications and marvelous benefits to VANET users. Clustering in VANETs is most important to overcome the connectivity problems of VANETs. In this paper, we proposed a new clustering technique Enhanced cluster based connectivity maintenance in vehicular ad hoc network. Our objective is to form long living clusters. The proposed approach is grouping the vehicles, on the basis of the longest list of neighbors to form clusters. The cluster formation and cluster head selection process done by the RSU that may results it reduces the chances of overhead on to the network. The cluster head selection procedure is the vehicle which has closest speed to average speed will elect as a cluster Head by the RSU and if two vehicles have same speed which is closest to average speed then they will be calculate by one of the new parameter i.e. distance to their respective destination. The vehicle which has largest distance to their destination will be choosing as a cluster Head by the RSU. Our simulation outcomes show that our technique performs better than the existing technique.

Keywords: VANETs, clustering, connectivity, cluster head, intelligent transportation system (ITS)

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Authors: Mohammad Reza Shojaei, Mahdeih Mirzaeinia

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We have studied the cluster structure of even-even stable isotopes of Ge and Sr. The Schrodinger equation has been solved using the generalized parametric Nikiforov-Uvarov method with a phenomenological potential. This potential is the sum of the attractive Yukawa-like potential, a Manning-Rosen-type potential, and the repulsive Yukawa potential for interaction between the cluster and the core. We have shown that the available experimental data of the first rotational band energies can be well described by assuming a binary system of the α cluster and the core and using an analytical solution. Our results were consistent with experimental values. Hence, this model can be applied to study the other even-even isotopes

Keywords: cluser model, NU method, ge and Sr, potential central

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Authors: Lillian Musila, Valerie Oundo, Daniel Erwin, Willie Sang

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Staphylococcus aureus infections are a major cause of nosocomial infections in Kenya. Methicillin resistant S. aureus (MRSA) infections are a significant burden to public health and are associated with considerable morbidity and mortality. At a hospital in Western Kenya two clusters of MRSA cases emerged within short periods of time. In this study we explored whether these clusters represented a nosocomial outbreak by characterizing the isolates using phenotypic and molecular assays and examining epidemiological data to identify possible transmission patterns. Specimens from the site of infection of the subjects were collected, cultured and S. aureus isolates identified phenotypically and confirmed by APIStaph™. MRSA were identified by cefoxitin disk screening per CLSI guidelines. MRSA were further characterized based on their antibiotic susceptibility patterns and spa gene typing. Characteristics of cases with MRSA isolates were compared with those with MSSA isolated around the same time period. Two cases of MRSA infection were identified in the two week period between 21 April and 4 May 2015. A further 2 MRSA isolates were identified on the same day on 7 September 2015. The antibiotic resistance patterns of the two MRSA isolates in the 1st cluster of cases were different suggesting that these were distinct isolates. One isolate had spa type t2029 and the other had a novel spa type. The 2 isolates were obtained from urine and an open skin wound. In the 2nd cluster of MRSA isolates, the antibiotic susceptibility patterns were similar but isolates had different spa types: one was t037 and the other a novel spa type different from the novel MRSA spa type in the first cluster. Both cases in the second cluster were admitted into the hospital but one infection was community- and the other hospital-acquired. Only one of the four MRSA cases was classified as an HAI from an infection acquired post-operatively. When compared to other S. aureus strains isolated within the same time period from the same hospital only one spa type t2029 was found in both MRSA and non-MRSA strains. None of the cases infected with MRSA in the two clusters shared any common epidemiological characteristic such as age, sex or known risk factors for MRSA such as prolonged hospitalization or institutionalization. These data suggest that the observed MRSA clusters were multi strain clusters and not an outbreak of a single strain. There was no clear relationship between the isolates by spa type suggesting that no transmission was occurring within the hospital between these cluster cases but rather that the majority of the MRSA strains were circulating in the community. There was high diversity of spa types among the MRSA strains with none of the isolates sharing spa types. Identification of disease clusters in space and time is critical for immediate infection control action and patient management. Spa gene typing is a rapid way of confirming or ruling out MRSA outbreaks so that costly interventions are applied only when necessary.

Keywords: cluster, Kenya, MRSA, spa typing

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Authors: Christopher Lama, Alix Rieser, Aleksandra Molchanova, Charles Thangaraj

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New technologies like Tesla’s Dojo have made high-performance embedded computing more available. Although automobile computing has developed and benefited enormously from these more recent technologies, the costs are still high, prohibitively high in some cases for broader adaptation, particularly for the after-market and enthusiast markets. This project aims to implement a Raspberry Pi-based low-power (under one hundred Watts) highly mobile computing cluster for a neural network. The computing cluster built from off-the-shelf components is more affordable and, therefore, makes wider adoption possible. The paper describes the design of the neural network, Raspberry Pi-based cluster, and applications the cluster will run. The neural network will use input data from sensors and cameras to project a live view of the road state as the user drives. The neural network will be trained to predict traffic behavior and generate warnings when potentially dangerous situations are predicted. The significant outcomes of this study will be two folds, firstly, to implement and test the low-cost cluster, and secondly, to ascertain the effectiveness of the predictive AI implemented on the cluster.

Keywords: CS pedagogy, student research, cluster computing, machine learning

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Authors: Alhadi Bustaman, Soeganda Formalidin, Titin Siswantining

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DNA microarray technology is used to analyze thousand gene expression data simultaneously and a very important task for drug development and test, function annotation, and cancer diagnosis. Various clustering methods have been used for analyzing gene expression data. However, when analyzing very large and heterogeneous collections of gene expression data, conventional clustering methods often cannot produce a satisfactory solution. Biclustering algorithm has been used as an alternative approach to identifying structures from gene expression data. In this paper, we introduce a transform technique based on singular value decomposition to identify normalized matrix of gene expression data followed by Mixed-Clustering algorithm and the Lift algorithm, inspired in the node-deletion and node-addition phases proposed by Cheng and Church based on Agglomerative Hierarchical Clustering (AHC). Experimental study on standard datasets demonstrated the effectiveness of the algorithm in gene expression data.

Keywords: agglomerative hierarchical clustering (AHC), biclustering, gene expression data, lymphoma, singular value decomposition (SVD)

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Authors: Purevdolgor Luvsantseren, Ajnai Luvsan-Ish, Oyuntsetseg Sandag, Javzmaa Tsend, Akhit Tileubai, Baasandorj Chilhaasuren, Jargalbat Puntsagdash, Galbadrakh Chuluunbaatar

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One of the indicators of the quality of university services is student satisfaction. Aim: We aimed to study the level of satisfaction of students in the first year of premedical courses in the course of Medical Physics using the cluster method. Materials and Methods: In the framework of this goal, a questionnaire was collected from a total of 324 students who studied the medical physics course of the 1st course of the premedical course at the Mongolian National University of Medical Sciences. When determining the level of satisfaction, the answers were obtained on five levels of satisfaction: "excellent", "good", "medium", "bad" and "very bad". A total of 39 questionnaires were collected from students: 8 for course evaluation, 19 for teacher evaluation, and 12 for student evaluation. From the research, a database with 39 fields and 324 records was created. Results: In this database, cluster analysis was performed in MATLAB and R programs using the k-means method of data mining. Calculated the Hopkins statistic in the created database, the values are 0.88, 0.87, and 0.97. This shows that cluster analysis methods can be used. The course evaluation sub-fund is divided into three clusters. Among them, cluster I has 150 objects with a "good" rating of 46.2%, cluster II has 119 objects with a "medium" rating of 36.7%, and Cluster III has 54 objects with a "good" rating of 16.6%. The teacher evaluation sub-base into three clusters, there are 179 objects with a "good" rating of 55.2% in cluster II, 108 objects with an "average" rating of 33.3% in cluster III, and 36 objects with an "excellent" rating in cluster I of 11.1%. The sub-base of student evaluations is divided into two clusters: cluster II has 215 objects with an "excellent" rating of 66.3%, and cluster I has 108 objects with an "excellent" rating of 33.3%. Evaluating the resulting clusters with the Silhouette coefficient, 0.32 for the course evaluation cluster, 0.31 for the teacher evaluation cluster, and 0.30 for student evaluation show statistical significance. Conclusion: Finally, to conclude, cluster analysis in the model of the medical physics lesson “good” - 46.2%, “middle” - 36.7%, “bad” - 16.6%; 55.2% - “good”, 33.3% - “middle”, 11.1% - “bad” in the teacher evaluation model; 66.3% - “good” and 33.3% of “bad” in the student evaluation model.

Keywords: questionnaire, data mining, k-means method, silhouette coefficient

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Authors: Wen-Hsiang Lai

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Except for the internal aspects of entrepreneurship (i.e. motivation, opportunity perspective and alertness), there are external aspects that affecting entrepreneurship (i.e. the industrial cluster). By comparing the machinery companies located inside and outside the industrial district, this study aims to explore the cluster effects on the entrepreneurship of companies in Taiwan machinery clusters (TMC). In this study, three factors affecting the entrepreneurship in TMC are conducted as “competition”, “embedded-ness” and “specialized knowledge”. The “competition” in the industrial cluster is defined as the competitive advantages that companies gain in form of demand effects and diversified strategies; the “embedded-ness” refers to the quality of company relations (relational embedded-ness) and ranges (structural embedded-ness) with the industry components (universities, customers and complementary) that affecting knowledge transfer and knowledge generations; the “specialized knowledge” shares the internal knowledge within industrial clusters. This study finds that when comparing to the companies which are outside the cluster, the industrial cluster has positive influence on the entrepreneurship. Additionally, the factor of “relational embedded-ness” has significant impact on the entrepreneurship and affects the adaptation ability of companies in TMC. Finally, the factor of “competition” reveals partial influence on the entrepreneurship.

Keywords: entrepreneurship, industrial cluster, industrial district, economies of agglomerations, Taiwan Machinery Cluster (TMC)

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Authors: Hazha Hidayat, Shayma Ibrahim

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Folate metabolism plays a crucial role in the normal development of the neonatal central nervous system. It is regulated by MTHFR gene polymorphism. Any factors, which will affect this metabolism either by hereditary or gene mutation will lead to many mental disorders. The purpose of this study was to investigate whether MTHFR gene mutation contributes to the development of mental retardation and CP combined with mental retardation in Erbil city. DNA was isolated from the peripheral blood samples of 40 cases suffering from mental retardation (MR) and CP combined with MR were recruited, sequence the 4, 6, 7, 8 exons of the MTHFR gene were done to identify the variants. Exons were amplified by PCR technique and then sequenced according to Sanger method to show the differences with MTHFR reference sequences. We observed (14) mutations in 4, 6, 7, 8 exons in the MTHFR gene associated with Cerebral Palsy combined with mental retardation included deletion, insertion, Substitution. The current study provides additional evidence that multiple variations in the MTHFR gene are associated with mental retardation and Cerebral Palsy.

Keywords: methylenetetrahydrofolate reductase (MTHFR) gene, SNPs, homocysteine, sequencing

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Authors: P. Sindhumole, K. Soumya, R. Renjimol

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Rice (Oryza sativa L.) is the major staple food crop over the world. It is prone to a number of biotic and abiotic stresses, out of which Bacterial Leaf Blight (BLB), caused by Xanthomonas oryzae pv. oryzae, is the most rampant. Management of this disease through chemicals or any other means is very difficult. The best way to control BLB is by the development of Host Plant Resistance. BLB resistance is not an activity of a single gene but it involves a cluster of more than thirty genes reported. Among these, Xa5 and Xa13 genes are two important ones, which can be diagnosed through marker assisted selection using closely linked molecular markers. During 2014, the first phase of field screening using forty traditional rice genotypes was carried out and twenty resistant symptomless genotypes were identified. Molecular characterisation of these genotypes using RM 122 SSR marker revealed the presence of Xa5 gene in thirteen genotypes. Forty-two traditional rice genotypes were used for the second phase of field screening for BLB resistance. Among these, sixteen resistant genotypes were identified. These genotypes, along with two susceptible check genotypes, were subjected to marker assisted selection for Xa13 gene, using the linked STS marker RG-136. During this process, presence of Xa13 gene could be detected in ten resistant genotypes. In future, these selected genotypes can be directly utilised as donors in Marker assisted breeding programmes for BLB resistance in rice.

Keywords: oryza sativa, SSR, STS, marker, disease, breeding

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Authors: A. Akın, H. Çoban

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This study was carried out to determine the effects of Control (C), 1/3 Cluster Tip Reduction (1/3 CTR), 1/6 Cluster Tip Reduction (1/6 CTR), 1/9 Cluster Tip Reduction (1/9 CTR), 1/3 CTR + Boric Acid (BA), 1/6 CTR + BA, 1/9 CTR + BA applications on yield and yield components of four years old Alphonse Lavallee grape variety (Vitis vinifera L.) grown on grafted 110 Paulsen rootstock in Konya province in Turkey in the vegetation period in 2015. According to the results, the highest maturity index 21.46 with 1/9 CTR application; the highest grape juice yields 736.67 ml with 1/3 CTR + BA application; the highest L* color value 32.07 with 1/9 CTR application; the highest a* color value 1.74 with 1/9 CTR application; the highest b* color value 3.72 with 1/9 CTR application were obtained. The effects of applications on grape fresh yield, cluster weight and berry weight were not found statistically significant.

Keywords: alphonse lavallee grape cultivar, different cluster tip reduction (1/3, 1/6, 1/9), foliar boric acid application, yield, quality

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Authors: Insiya Kapasi, Roshni Udyavar Yehuda

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Cluster Redevelopment is a new concept in the city of Mumbai. Its regulations were laid down by the government in 2009. The concept of cluster redevelopment encompasses a group of buildings defined by a boundary as specified by the municipal authority (in this case, Mumbai), which may be dilapidated or approved for redevelopment. The study analyses the effect of cluster redevelopment in the form of renewal of old group of buildings as compared to refurbishment or restoration - on energy consumption. The methodology includes methods of assessment to determine increase or decrease in energy consumption in cluster redevelopment based on different criteria such as carpet area of the units, building envelope and its architectural elements. Results show that as the area and number of units increase the Energy consumption increases and the EPI (energy performance index) decreases as compared to the base case. The energy consumption per unit area declines by 29% in the proposed cluster redevelopment as compared to the original settlement. It is recommended that although the development is spacious and provides more light and ventilation, aspects such as glass type, traditional architectural features and consumer behavior are critical in the reduction of energy consumption.

Keywords: Cluster Redevelopment, Energy Consumption, Energy Efficiency, Typologies

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Authors: Hala Alshamlan, Ghada Badr, Yousef Alohali

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Cancer is one of the dreadful diseases, which causes considerable death rate in humans. DNA microarray-based gene expression profiling has been emerged as an efficient technique for cancer classification, as well as for diagnosis, prognosis, and treatment purposes. In recent years, a DNA microarray technique has gained more attraction in both scientific and in industrial fields. It is important to determine the informative genes that cause cancer to improve early cancer diagnosis and to give effective chemotherapy treatment. In order to gain deep insight into the cancer classification problem, it is necessary to take a closer look at the proposed gene selection methods. We believe that they should be an integral preprocessing step for cancer classification. Furthermore, finding an accurate gene selection method is a very significant issue in a cancer classification area because it reduces the dimensionality of microarray dataset and selects informative genes. In this paper, we classify and review the state-of-art gene selection methods. We proceed by evaluating the performance of each gene selection approach based on their classification accuracy and number of informative genes. In our evaluation, we will use four benchmark microarray datasets for the cancer diagnosis (leukemia, colon, lung, and prostate). In addition, we compare the performance of gene selection method to investigate the effective gene selection method that has the ability to identify a small set of marker genes, and ensure high cancer classification accuracy. To the best of our knowledge, this is the first attempt to compare gene selection approaches for cancer classification using microarray gene expression profile.

Keywords: gene selection, feature selection, cancer classification, microarray, gene expression profile

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Authors: Somyung Oh, Jeonghyeon Ha, Kyungwon Lee, Sejong Oh

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Microarray is a general scheme to find differentially expressed genes for target concept. The output is expressed by heat map, and biologists analyze related terms of gene ontology to find some characteristics of differentially expressed genes. In this paper, we propose integrated visualization tool for heat map and gene ontology graph. Previous two methods are used by static manner and separated way. Proposed visualization tool integrates them and users can interactively manage it. Users may easily find and confirm related terms of gene ontology for given differentially expressed genes. Proposed tool also visualize connections between genes on heat map and gene ontology graph. We expect biologists to find new meaningful topics by proposed tool.

Keywords: heat map, gene ontology, microarray, differentially expressed gene

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Authors: Pil Seong Park

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Homemade HPC clusters are widely used in many small labs, because they are easy to build and cost-effective. Even though incremental growth is an advantage of clusters, it results in heterogeneous systems anyhow. Instead of adding new nodes to the cluster, we can extend clusters to include some other Internet servers working independently on the same LAN, so that we can make use of their idle times, especially during the night. However extension across a firewall raises some security problems with NFS. In this paper, we propose a method to solve such a problem using SSH tunneling, and suggest a modified structure of the cluster that implements it.

Keywords: extension of HPC clusters, security, NFS, SSH tunneling

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Authors: Ritu Vashistha, Jitender Kumar

Abstract:

Clustering using the K-means algorithm is a very common way to understand and analyze the obtained output data. When a similar object is grouped, this is called the basis of Clustering. There is K number of objects and C number of cluster in to single cluster in which k is always supposed to be less than C having each cluster to be its own centroid but the major problem is how is identify the cluster is correct based on the data. Formulation of the cluster is not a regular task for every tuple of row record or entity but it is done by an iterative process. Each and every record, tuple, entity is checked and examined and similarity dissimilarity is examined. So this iterative process seems to be very lengthy and unable to give optimal output for the cluster and time taken to find the cluster. To overcome the drawback challenge, we are proposing a formula to find the clusters at the run time, so this approach can give us optimal results. The proposed approach uses the Euclidian distance formula as well melanosis to find the minimum distance between slots as technically we called clusters and the same approach we have also applied to Ant Colony Optimization(ACO) algorithm, which results in the production of two and multi-dimensional matrix.

Keywords: ant colony optimization, data clustering, centroids, data mining, k-means

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Authors: Shahed Vahedi, Mohd Salmi Md Noorani

Abstract:

This paper investigates cluster synchronization phenomena between community networks. We focus on the situation where a variety of dynamics occur in the clusters. In particular, we show that different synchronization states simultaneously occur between the networks. The controller is designed having an adaptive control gain, and theoretical results are derived via Lyapunov stability. Simulations on well-known dynamical systems are provided to elucidate our results.

Keywords: cluster synchronization, adaptive control, community network, simulation

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Authors: Ishtiaq Wahid, Masood Ahmad, Nighat Ayub, Sajad Ali

Abstract:

Lifetime of a wireless sensor network (WSN) is directly proportional to the energy consumption of its constituent nodes. Routing in wireless sensor network is very challenging due its inherit characteristics. In hierarchal routing the sensor filed is divided into clusters. The cluster-heads are selected from each cluster, which forms a hierarchy of nodes. The cluster-heads are used to transmit the data to the base station while other nodes perform the sensing task. In this way the lifetime of the network is increased. In this paper a comparative study of hierarchal routing protocols are conducted. The simulation is done in NS-2 for validation.

Keywords: WSN, cluster, routing, sensor networks

Procedia PDF Downloads 445