Search results for: Gene selection

Authors: Yoonsuh Jung

Abstract:

As DNA microarray data contain relatively small sample size compared to the number of genes, high dimensional models are often employed. In high dimensional models, the selection of tuning parameter (or, penalty parameter) is often one of the crucial parts of the modeling. Cross-validation is one of the most common methods for the tuning parameter selection, which selects a parameter value with the smallest cross-validated score. However, selecting a single value as an ‘optimal’ value for the parameter can be very unstable due to the sampling variation since the sample sizes of microarray data are often small. Our approach is to choose multiple candidates of tuning parameter first, then average the candidates with different weights depending on their performance. The additional step of estimating the weights and averaging the candidates rarely increase the computational cost, while it can considerably improve the traditional cross-validation. We show that the selected value from the suggested methods often lead to stable parameter selection as well as improved detection of significant genetic variables compared to the tradition cross-validation via real data and simulated data sets.

Keywords: Cross Validation, Parameter Averaging, Parameter Selection, Regularization Parameter Search.

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Authors: Mohamed A. Mahfouz, M. A. Ismail

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Biclustering is a very useful data mining technique for identifying patterns where different genes are co-related based on a subset of conditions in gene expression analysis. Association rules mining is an efficient approach to achieve biclustering as in BIMODULE algorithm but it is sensitive to the value given to its input parameters and the discretization procedure used in the preprocessing step, also when noise is present, classical association rules miners discover multiple small fragments of the true bicluster, but miss the true bicluster itself. This paper formally presents a generalized noise tolerant bicluster model, termed as μBicluster. An iterative algorithm termed as BIDENS based on the proposed model is introduced that can discover a set of k possibly overlapping biclusters simultaneously. Our model uses a more flexible method to partition the dimensions to preserve meaningful and significant biclusters. The proposed algorithm allows discovering biclusters that hard to be discovered by BIMODULE. Experimental study on yeast, human gene expression data and several artificial datasets shows that our algorithm offers substantial improvements over several previously proposed biclustering algorithms.

Keywords: Machine learning, biclustering, bi-dimensional clustering, gene expression analysis, data mining.

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Authors: H. Merhni, A. Sbiti, I. Ratbi, A. Sefiani

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The proximal spinal muscular atrophy (SMA) is a group of neuromuscular disorders characterized by progressive muscle weakness due to the degeneration and loss of anterior motor neurons of the spinal cord. Depending on the age of onset of symptoms and their evolution, four types of SMA, varying in severity, result in a mutations of the SMN gene (survival of Motor neuron). We have analyzed the DNA of 295 patients referred to our genetic counseling; since January 1996 until October 2014; for suspected SMA. The homozygous deletion of exon 7 of the SMN gene was found in 133 patients; of which, 40.6% were born to consanguineous parents. In countries like Morocco, where the frequency of heterozygotes for SMA is high, genetic testing should be offered as first-line and, after careful clinical assessment, especially in newborns and infants with congenital hypotonia unexplained and prognosis compromise. The molecular diagnosis of SMA allows a quick and certainly diagnosis, provide adequate genetic counseling for families at risk and suggest, for couples who want prenatal diagnosis. The analysis of the SMN gene is a perfect example of genetic testing with an excellent cost/benefit ratio that can be of great interest in public health, especially in low-income countries. We emphasize in this work for the benefit of the generalization of molecular diagnosis of SMA by the technique of PCR-enzymatic digestion in other centers in Morocco.

Keywords: Exon7, PCR-digestion, SMA, SMN gene.

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Authors: R. Ramli, M. I. Ghazali, H. Ibrahim, M. M. Kasim, F. M. Kamal, S.Vikneswari

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Teachers form the backbone of any educational system, hence selecting qualified candidates is very crucial. In Malaysia, the decision making in the selection process involves a few stages: Initial filtering through academic achievement, taking entry examination and going through an interview session. The last stage is the most challenging since it highly depends on human judgment. Therefore, this study sought to identify the selection criteria for teacher candidates that form the basis for an efficient multi-criteria teacher-candidate selection model for that last stage. The relevant criteria were determined from the literature and also based on expert input that is those who were involved in interviewing teacher candidates from a public university offering the formal training program. There are three main competency criteria that were identified which are content of knowledge, communication skills and personality. Further, each main criterion was divided into a few subcriteria. The Analytical Hierarchy Process (AHP) technique was employed to allocate weights for the criteria and later, integrated a Simple Weighted Average (SWA) scoring approach to develop the selection model. Subsequently, a web-based Decision Support System was developed to assist in the process of selecting the qualified teacher candidates. The Teacher-Candidate Selection (TeCaS) system is able to assist the panel of interviewers during the selection process which involves a large amount of complex qualitative judgments.

Keywords: Analytic Hierarchy Process, Simple Weighted Average, Decision Support System, Multi-criteria decision making problem.

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Authors: S. Aghainajafi Zadeh, M.R. Hemami., F. Heydari

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Asiatic Houbara ( Chlamydotis macqueenii ) is a flagship and vulnerable species. In-situ conservation of this threatened species demands for knowledge of its habitat selection. The aim of this study was to determine habitat variables influencing birds wintering and breeding selection in semi- arid central Iran. Habitat features of the detected nest and pellet sites were compared with paired and random plots by quantifying a number of habitat variables. In wintering habitat use at micro scale houbara selected sites where vegetation cover was significantly lower compard to control sites( p< 0.001). Areas with low number of larger plant species (p=0.03) that were not too close to a vegetation patch(p<0.001) were selected for breeding habitat.

Keywords: Asiatic houbara bustard, Habitat selection, Nest, pellet.

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Authors: M. Sadeghzadeh, M. Teshnehlab

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Feature selection has recently been the subject of intensive research in data mining, specially for datasets with a large number of attributes. Recent work has shown that feature selection can have a positive effect on the performance of machine learning algorithms. The success of many learning algorithms in their attempts to construct models of data, hinges on the reliable identification of a small set of highly predictive attributes. The inclusion of irrelevant, redundant and noisy attributes in the model building process phase can result in poor predictive performance and increased computation. In this paper, a novel feature search procedure that utilizes the Ant Colony Optimization (ACO) is presented. The ACO is a metaheuristic inspired by the behavior of real ants in their search for the shortest paths to food sources. It looks for optimal solutions by considering both local heuristics and previous knowledge. When applied to two different classification problems, the proposed algorithm achieved very promising results.

Keywords: Ant colony optimization, Classification, Datamining, Feature selection.

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Authors: Š. Čemerková, M. Wilczková

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The paper deals with the importance of information flow for providing of defined level of customer service in the firms. Setting of the criteria for the selection and implementation of logistics information system is a prerequisite for ensuring of the flow of information in firms. The decision on the selection and implementation of logistics information system is linked to the investment costs and operating costs, which are included in the total logistics costs. The article also deals with the conclusions of the research focused on the logistics information system selection in companies in the Czech Republic.

Keywords: Customer service, information system, logistics, research.

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Authors: M. Pandi, K. Premalatha

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The DNA microarray technology concurrently monitors the expression levels of thousands of genes during significant biological processes and across the related samples. The better understanding of functional genomics is obtained by extracting the patterns hidden in gene expression data. It is handled by clustering which reveals natural structures and identify interesting patterns in the underlying data. In the proposed work clustering gene expression data is done through an Advanced Nelder Mead (ANM) algorithm. Nelder Mead (NM) method is a method designed for optimization process. In Nelder Mead method, the vertices of a triangle are considered as the solutions. Many operations are performed on this triangle to obtain a better result. In the proposed work, the operations like reflection and expansion is eliminated and a new operation called spread-out is introduced. The spread-out operation will increase the global search area and thus provides a better result on optimization. The spread-out operation will give three points and the best among these three points will be used to replace the worst point. The experiment results are analyzed with optimization benchmark test functions and gene expression benchmark datasets. The results show that ANM outperforms NM in both benchmarks.

Keywords: Spread out, simplex, multi-minima, fitness function, optimization, search area, monocyte, solution, genomes.

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Authors: Chia-Ta Tsai, Wen-Lin Huang, Shinn-Jang Ho, Li-Sun Shu, Shinn-Ying Ho

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Prediction of bacterial virulent protein sequences can give assistance to identification and characterization of novel virulence-associated factors and discover drug/vaccine targets against proteins indispensable to pathogenicity. Gene Ontology (GO) annotation which describes functions of genes and gene products as a controlled vocabulary of terms has been shown effectively for a variety of tasks such as gene expression study, GO annotation prediction, protein subcellular localization, etc. In this study, we propose a sequence-based method Virulent-GO by mining informative GO terms as features for predicting bacterial virulent proteins. Each protein in the datasets used by the existing method VirulentPred is annotated by using BLAST to obtain its homologies with known accession numbers for retrieving GO terms. After investigating various popular classifiers using the same five-fold cross-validation scheme, Virulent-GO using the single kind of GO term features with an accuracy of 82.5% is slightly better than VirulentPred with 81.8% using five kinds of sequence-based features. For the evaluation of independent test, Virulent-GO also yields better results (82.0%) than VirulentPred (80.7%). When evaluating single kind of feature with SVM, the GO term feature performs much well, compared with each of the five kinds of features.

Keywords: Bacterial virulence factors, GO terms, prediction, protein sequence.

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Authors: Ethan Shafer, Timothy Graziano, Jay Fisher

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This research seeks to answer whether first-year courses at institutions of higher learning can impact STEM major selection. Unlike many universities, an entry-level technology course (often referred to as CS0) is required for all United States Military Academy (USMA) students–regardless of major–in their first year of attendance. Students at the Academy choose their major at the end of their first year of studies. Through student responses to a multi-semester survey, this paper identifies a number of factors that potentially influence STEM major selection. Student demographic data, pre-existing exposure and access to technology, perceptions of STEM subjects, and initial desire for a STEM major are captured before and after taking a CS0 course. An analysis of factors that contribute to student perception of STEM and major selection are presented. This work provides recommendations and suggestions for institutions currently providing or looking to provide CS0-like courses to their students.

Keywords: STEM major, STEM, pedagogy, digital literacy.

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Authors: Mohammad Darzi, Ali AsgharLiaei, Mahdi Hosseini, HabibollahAsghari

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This article addresses feature selection for breast cancer diagnosis. The present process contains a wrapper approach based on Genetic Algorithm (GA) and case-based reasoning (CBR). GA is used for searching the problem space to find all of the possible subsets of features and CBR is employed to estimate the evaluation result of each subset. The results of experiment show that the proposed model is comparable to the other models on Wisconsin breast cancer (WDBC) dataset.

Keywords: Case-based reasoning; Breast cancer diagnosis; Genetic algorithm; Wrapper feature selection

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Authors: P.S.Prakash, S.Selvan

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Over the past several years, there has been a considerable amount of research within the field of Quality of Service (QoS) support for distributed multimedia systems. One of the key issues in providing end-to-end QoS guarantees in packet networks is determining a feasible path that satisfies a number of QoS constraints. The problem of finding a feasible path is NPComplete if number of constraints is more than two and cannot be exactly solved in polynomial time. We proposed Feasible Path Selection Algorithm (FPSA) that addresses issues with pertain to finding a feasible path subject to delay and cost constraints and it offers higher success rate in finding feasible paths.

Keywords: feasible path, multiple constraints, path selection, QoS routing

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Authors: Ahmad Ali Shahid, Muhammad Shakil Shaukat, Kamran Shehzad Bajwa, Abdul Qayyum Rao, Tayyab Husnain

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Agriculture is the backbone of economy of Pakistan and cotton is the major agricultural export and supreme source of raw fiber for our textile industry. To combat severe problems of insect and weed, combination of three genes namely Cry1Ac, Cry2A and EPSPS genes was transferred in locally cultivated cotton variety MNH-786 with the use of Agrobacterium mediated genetic transformation. The present study focused on the molecular screening of transgenic cotton plants at T3 generation in order to confirm integration and expression of all three genes (Cry1Ac, Cry2A and EPSP synthase) into the cotton genome. Initially, glyphosate spray assay was used for screening of transgenic cotton plants containing EPSP synthase gene at T3 generation. Transgenic cotton plants which were healthy and showed no damage on leaves were selected after 07 days of spray. For molecular analysis of transgenic cotton plants in the laboratory, the genomic DNA of these transgenic cotton plants were isolated and subjected to amplification of the three genes. Thus, seventeen out of twenty (Cry1Ac gene), ten out of twenty (Cry2A gene) and all twenty (EPSP synthase gene) were produced positive amplification. On the base of PCR amplification, ten transgenic plant samples were subjected to protein expression analysis through ELISA. The results showed that eight out of ten plants were actively expressing the three transgenes. Real-time PCR was also done to quantify the mRNA expression levels of Cry1Ac and EPSP synthase gene. Finally, eight plants were confirmed for the presence and active expression of all three genes at T3 generation.

Keywords: Agriculture, Cotton, Transformation, Cry Genes, ELISA and PCR.

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Authors: Amir-Massoud Bidgoli, Mehdi Naseri Parsa

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In this paper a combined feature selection method is proposed which takes advantages of sample domain filtering, resampling and feature subset evaluation methods to reduce dimensions of huge datasets and select reliable features. This method utilizes both feature space and sample domain to improve the process of feature selection and uses a combination of Chi squared with Consistency attribute evaluation methods to seek reliable features. This method consists of two phases. The first phase filters and resamples the sample domain and the second phase adopts a hybrid procedure to find the optimal feature space by applying Chi squared, Consistency subset evaluation methods and genetic search. Experiments on various sized datasets from UCI Repository of Machine Learning databases show that the performance of five classifiers (Naïve Bayes, Logistic, Multilayer Perceptron, Best First Decision Tree and JRIP) improves simultaneously and the classification error for these classifiers decreases considerably. The experiments also show that this method outperforms other feature selection methods.

Keywords: feature selection, resampling, reliable features, Consistency Subset Evaluation.

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Authors: A. Perolini

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Feature and model selection are in the center of attention of many researches because of their impact on classifiers- performance. Both selections are usually performed separately but recent developments suggest using a combined GA-SVM approach to perform them simultaneously. This approach improves the performance of the classifier identifying the best subset of variables and the optimal parameters- values. Although GA-SVM is an effective method it is computationally expensive, thus a rough method can be considered. The paper investigates a joined approach of Genetic Algorithm and kernel matrix criteria to perform simultaneously feature and model selection for SVM classification problem. The purpose of this research is to improve the classification performance of SVM through an efficient approach, the Kernel Matrix Genetic Algorithm method (KMGA).

Keywords: Feature and model selection, Genetic Algorithms, Support Vector Machines, kernel matrix.

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Authors: Chintanu K. Sarmah, Sandhya Samarasinghe, Don Kulasiri, Daniel Catchpoole

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Gene expression profiling is rapidly evolving into a powerful technique for investigating tumor malignancies. The researchers are overwhelmed with the microarray-based platforms and methods that confer them the freedom to conduct large-scale gene expression profiling measurements. Simultaneously, investigations into cross-platform integration methods have started gaining momentum due to their underlying potential to help comprehend a myriad of broad biological issues in tumor diagnosis, prognosis, and therapy. However, comparing results from different platforms remains to be a challenging task as various inherent technical differences exist between the microarray platforms. In this paper, we explain a simple ratio-transformation method, which can provide some common ground for cDNA and Affymetrix platform towards cross-platform integration. The method is based on the characteristic data attributes of Affymetrix- and cDNA- platform. In the work, we considered seven childhood leukemia patients and their gene expression levels in either platform. With a dataset of 822 differentially expressed genes from both these platforms, we carried out a specific ratio-treatment to Affymetrix data, which subsequently showed an improvement in the relationship with the cDNA data.

Keywords: Gene expression profiling, microarray, cDNA, Affymetrix, childhood leukaemia.

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Authors: Houshmand E. Masoumi

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Residential self-selection has gained increasing attention in the Western travel behavior research during the past decade. Many studies in the US, UK, and Germany conclude that the role of individuals’ residential location choice on commute travel behavior is more important than that of the built environment or at least it has considerable effects. However the effectiveness of location choice in many countries and cultures like Iran is unclear. This study examines the self-selections in two neighborhoods in Tehran. As a part of a research about the influences of land use on travel behavior information about people’s location preferences was collected by direct questioning. The findings show that the main reasons for selecting the location of residential units are related to socio-economic factors such as rise of house price and affordability of house prices. Transportation has little impacts on location decisions. Moreover, residential self-selection accounts for only 3 to 7.5 percent of the pedestrian, PT, and car trips.

Keywords: Residential self-selection, Tehran, travel behavior, urban transportation.

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Authors: Onder Turkmen, Musa Seymen, Sali Fidan, Mustafa Paksoy

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There is a requirement for registered edible seed pumpkin suitable for eating in Turkey. A total of 81 genotypes collected from the researchers in 2005 originated from Eskisehir, Konya, Nevsehir, Tekirdag, Sakarya, Kayseri and Kirsehir provinces were utilized. The used genetic materials were brought to S5 generation by the research groups among 2006 and 2010 years. In this research, S5 stage reached in the genotype given some of the morphological features, and selection of promising genotypes generated scale were made. Results showed that the A-1 (420), A-7 (410), A-8 (420), A-32 (420), B-17 (410), B-24 (410), B-25 (420), B-33 (400), C-24 (420), C-25 (410), C-26 (410) and C-30 (420) genotypes are expected to be promising varieties.

Keywords: Candidate cultivar, edible seed pumpkin, morphologic parameters, selection.

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Authors: M. Maimunah, G.A. Froemming, H. Nawawi, M.I. Nafeeza, O. Effat, M.R. Rohayu Izanwati, M.S. Mohamed Saifulaman

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Attachment of the circulating monocytes to the endothelium is the earliest detectable events during formation of atherosclerosis. The adhesion molecules, chemokines and matrix proteases genes were identified to be expressed in atherogenesis. Expressions of these genes may influence structural integrity of the luminal endothelium. The aim of this study is to relate changes in the ultrastructural morphology of the aortic luminal surface and gene expressions of the endothelial surface, chemokine and MMP-12 in normal and hypercholesterolemic rabbits. Luminal endothelial surface from rabbit aortic tissue was examined by scanning electron microscopy (SEM) using low vacuum mode to ascertain ultrastructural changes in development of atherosclerotic lesion. Gene expression of adhesion molecules, MCP-1 and MMP-12 were studied by Real-time PCR. Ultrastructural observations of the aortic luminal surface exhibited changes from normal regular smooth intact endothelium to irregular luminal surface including marked globular appearance and ruptures of the membrane layer. Real-time PCR demonstrated differentially expressed of studied genes in atherosclerotic tissues. The appearance of ultrastructural changes in aortic tissue of hypercholesterolemic rabbits is suggested to have relation with underlying changes of endothelial surface molecules, chemokine and MMP-12 gene expressions.

Keywords: Ultrastructure of luminal endothelial surface, Macrophage metalloelastase (MMP-12), Real-time PCR.

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Authors: C. Ardil

Abstract:

This paper presents preference programming technique based multiple criteria decision making analysis for selecting a facility location for a new organization or expansion of an existing facility which is of vital importance for a decision support system and strategic planning process. The implementation of decision support systems is considered crucial to sustain competitive advantage and profitability persistence in turbulent environment. As an effective strategic management and decision making is necessary, multiple criteria decision making analysis supports the decision makers to formulate and implement the right strategy. The investment cost associated with acquiring the property and facility construction makes the facility location selection problem a long-term strategic investment decision, which rationalize the best location selection which results in higher economic benefits through increased productivity and optimal distribution network. Selecting the proper facility location from a given set of alternatives is a difficult task, as many potential qualitative and quantitative multiple conflicting criteria are to be considered. This paper solves a facility location selection problem using preference programming, which is an effective multiple criteria decision making analysis tool applied to deal with complex decision problems in the operational research environment. The ranking results of preference programming are compared with WSM, TOPSIS and VIKOR methods.

Keywords: Facility Location Selection, Multiple Criteria Decision Making, Multiple Criteria Decision Making Analysis, Preference Programming, Location Selection, WSM, TOPSIS, VIKOR

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Authors: C. Ardil

Abstract:

This article presents a multiple criteria evaluation approach to uncertainty, vagueness, and imprecision analysis for ranking alternatives with fuzzy data for decision making using the Technique for Order Preference by Similarity to Ideal Solution (TOPSIS). The fighter aircraft evaluation and selection decision making problem is modeled in a fuzzy environment with triangular fuzzy numbers. The fuzzy decision information related to the fighter aircraft selection problem is taken into account in ordering the alternatives and selecting the best candidate. The basic fuzzy TOPSIS procedure steps transform fuzzy decision matrices into matrices of alternatives evaluated according to all decision criteria. A practical numerical example illustrates the proposed approach to the fighter aircraft selection problem.

Keywords: triangular fuzzy number (TFN), multiple criteria decision making analysis, decision making, aircraft selection, MCDMA, fuzzy TOPSIS

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Authors: Ouadoudi Zytoune, Youssef Fakhri, Driss Aboutajdine

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This paper focuses on reducing the power consumption of wireless sensor networks. Therefore, a communication protocol named LEACH (Low-Energy Adaptive Clustering Hierarchy) is modified. We extend LEACHs stochastic cluster-head selection algorithm by a modifying the probability of each node to become cluster-head based on its required energy to transmit to the sink. We present an efficient energy aware routing algorithm for the wireless sensor networks. Our contribution consists in rotation selection of clusterheads considering the remoteness of the nodes to the sink, and then, the network nodes residual energy. This choice allows a best distribution of the transmission energy in the network. The cluster-heads selection algorithm is completely decentralized. Simulation results show that the energy is significantly reduced compared with the previous clustering based routing algorithm for the sensor networks.

Keywords: Wireless Sensor Networks, Energy efficiency, WirelessCommunications, Clustering-based algorithm.

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Authors: B. Vahdani, S. M. Mousavi, R. Tavakkoli-Moghaddam

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Nowadays, the plant location selection has a critical impact on the performance of numerous companies. In this paper, a methodology is presented to solve this problem. The three decision making methods, namely Delphi, AHP and improved VIKOR, are hybridized in order to make the best use of information available based on the decision makers or experts. In this respect, the aim of using Delphi is to select the most influential criteria by a few decision makers. The AHP is utilized to give weights of the selected criteria. Finally, the improved VIKOR method is applied to rank alternatives. At the end of paper, an application example demonstrates the applicability of the proposed methodology.

Keywords: Decision making, Plant location selection, Delphi, AHP, Improved VIKOR.

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Authors: A. Jrade, N. Markiz, N. Albelwi

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Optimizing equipment selection in heavy earthwork operations is a critical key in the success of any construction project. The objective of this research incentive was geared towards developing a computer model to assist contractors and construction managers in estimating the cost of heavy earthwork operations. Economical operation analysis was conducted for an equipment fleet taking into consideration the owning and operating costs involved in earthwork operations. The model is being developed in a Microsoft environment and is capable of being integrated with other estimating and optimization models. In this study, Caterpillar® Performance Handbook [5] was the main resource used to obtain specifications of selected equipment. The implementation of the model shall give optimum selection of equipment fleet not only based on cost effectiveness but also in terms of versatility. To validate the model, a case study of an actual dam construction project was selected to quantify its degree of accuracy.

Keywords: Operation analysis, optimization model, equipment economics, equipment selection.

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Authors: Bharatendra Rai

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Predictive data analysis and modeling involving machine learning techniques become challenging in presence of too many explanatory variables or features. Presence of too many features in machine learning is known to not only cause algorithms to slow down, but they can also lead to decrease in model prediction accuracy. This study involves housing dataset with 79 quantitative and qualitative features that describe various aspects people consider while buying a new house. Boruta algorithm that supports feature selection using a wrapper approach build around random forest is used in this study. This feature selection process leads to 49 confirmed features which are then used for developing predictive random forest models. The study also explores five different data partitioning ratios and their impact on model accuracy are captured using coefficient of determination (r-square) and root mean square error (rsme).

Keywords: Housing data, feature selection, random forest, Boruta algorithm, root mean square error.

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Authors: Mehrdad Hashemi, Mitra Behrooz Aghdam, Reza Mahdian, Ahmad Reza Kamyab

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Cytogenetic analysis still remains the gold standard method for prenatal diagnosis of trisomy 21 (Down syndrome, DS). Nevertheless, the conventional cytogenetic analysis needs live cultured cells and is too time-consuming for clinical application. In contrast, molecular methods such as FISH, QF-PCR, MLPA and quantitative Real-time PCR are rapid assays with results available in 24h. In the present study, we have successfully used a novel MGB TaqMan probe-based real time PCR assay for rapid diagnosis of trisomy 21 status in Down syndrome samples. We have also compared the results of this molecular method with corresponding results obtained by the cytogenetic analysis. Blood samples obtained from DS patients (n=25) and normal controls (n=20) were tested by quantitative Real-time PCR in parallel to standard G-banding analysis. Genomic DNA was extracted from peripheral blood lymphocytes. A high precision TaqMan probe quantitative Real-time PCR assay was developed to determine the gene dosage of DSCAM (target gene on 21q22.2) relative to PMP22 (reference gene on 17p11.2). The DSCAM/PMP22 ratio was calculated according to the formula; ratio=2 -ΔΔCT. The quantitative Real-time PCR was able to distinguish between trisomy 21 samples and normal controls with the gene ratios of 1.49±0.13 and 1.03±0.04 respectively (p value <0.001). These results represent the presence of 3 copies of target gene in DS samples Vs 2 copies in normal controls. The results of quantitative Real-time PCR were in complete agreement with results of cytogenetic analysis. This study confirms previous reports regarding successful implementation of quantitative Real-time PCR for detection of trisomy 21. However, the assay has been improved by using MGB probes and more accurate data analysis. This assay, in particular, when performed in combination with another molecular assay such as QF-PCR or MLPA, can be used as a reliable technique for rapid prenatal diagnosis of trisomy 21.

Keywords: Trisomy 21, Real-time PCR, MGB-TaqMan Probes, Gene Dosage.

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Authors: Tom Snir, Eitan Rubin

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Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.

Keywords: Systems Biology, Protein Length

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Authors: C. Ardil

Abstract:

Being effective in every organizational activity has become necessary due to the escalating level of competition in all areas of corporate life. In the context of supply chain management, aircraft supplier selection is currently one of the most crucial activities. It is possible to choose the best aircraft supplier and deliver efficiency in terms of cost, quality, delivery time, economic status, and institutionalization if a systematic supplier selection approach is used. In this study, an effective multiple criteria decision-making methodology, proximity measure method (PMM), is used within a fuzzy environment based on the vague structure of the real working environment. The best appropriate aircraft suppliers are identified and ranked after the proposed multiple criteria decision making technique is used in a real-life scenario.

Keywords: Aircraft supplier selection, multiple criteria decision making, fuzzy sets, proximity measure method, Minkowski distance family function, Hausdorff distance function, PMM, MCDM

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Authors: Ngo Thanh Xuan, Mai Thi Hang, Vu Nguyen Thanh

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A. niger XP isolated from Vietnam produces very low amount of acidic phytase with optimal pH at 2.5 and 5.5. The phytase production of this strain was successfully improved through gene cloning and expression. A 1.4 - kb DNA fragment containing the coding region of the phyA gene was amplified by PCR and inserted into the expression vector pPICZαA with a signal peptide α- factor, under the control of AOX1 promoter. The recombined plasmid was transformed into the host strain P. pastoris KM71H and X33 by electroporation. Both host strains could efficiently express and secret phytase. The multicopy strains were screened for over expression of phytase. All the selected multicopy strains of P. pastoris X33 were examined for phytase activity, the maximum phytase yield of 1329 IU/ml was obtained after 4 days of incubation in medium BMM. The recombinant protein with MW of 97.4 KW showed to be the only one protein secreted in the culture broth. Multicopy transformant P. pastoris X33 supposed to be potential candidate for producing the commercial preparation of phytase.

Keywords: Aspergillus niger XP, cloning, over expression, Pichia pastoris, phyA , phytase.

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Authors: Maria E. Manioudaki, Panayiota Poirazi

Abstract:

Yeast cells live in a constantly changing environment that requires the continuous adaptation of their genomic program in order to sustain their homeostasis, survive and proliferate. Due to the advancement of high throughput technologies, there is currently a large amount of data such as gene expression, gene deletion and protein-protein interactions for S. Cerevisiae under various environmental conditions. Mining these datasets requires efficient computational methods capable of integrating different types of data, identifying inter-relations between different components and inferring functional groups or 'modules' that shape intracellular processes. This study uses computational methods to delineate some of the mechanisms used by yeast cells to respond to environmental changes. The GRAM algorithm is first used to integrate gene expression data and ChIP-chip data in order to find modules of coexpressed and co-regulated genes as well as the transcription factors (TFs) that regulate these modules. Since transcription factors are themselves transcriptionally regulated, a three-layer regulatory cascade consisting of the TF-regulators, the TFs and the regulated modules is subsequently considered. This three-layer cascade is then modeled quantitatively using artificial neural networks (ANNs) where the input layer corresponds to the expression of the up-stream transcription factors (TF-regulators) and the output layer corresponds to the expression of genes within each module. This work shows that (a) the expression of at least 33 genes over time and for different stress conditions is well predicted by the expression of the top layer transcription factors, including cases in which the effect of up-stream regulators is shifted in time and (b) identifies at least 6 novel regulatory interactions that were not previously associated with stress-induced changes in gene expression. These findings suggest that the combination of gene expression and protein-DNA interaction data with artificial neural networks can successfully model biological pathways and capture quantitative dependencies between distant regulators and downstream genes.

Keywords: gene modules, artificial neural networks, yeast, stress

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