Search results for: phylogenetic trees

Authors: John Hadden, Ashutosh Tiwari, Rajkumar Roy, Dymitr Ruta

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The aim of this paper is to identify the most suitable model for churn prediction based on three different techniques. The paper identifies the variables that affect churn in reverence of customer complaints data and provides a comparative analysis of neural networks, regression trees and regression in their capabilities of predicting customer churn.

Keywords: Churn, Decision Trees, Neural Networks, Regression.

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Authors: Kasim Terzic, Bernd Neumann

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Scene interpretation systems need to match (often ambiguous) low-level input data to concepts from a high-level ontology. In many domains, these decisions are uncertain and benefit greatly from proper context. This paper demonstrates the use of decision trees for estimating class probabilities for regions described by feature vectors, and shows how context can be introduced in order to improve the matching performance.

Keywords: Classification, Decision Trees, Interpretation, Vision

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Authors: González A. Julio, Ramírez L. Leonardo, Puerta A. Gabriel

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Telemedicine services use a large amount of data, most of which are diagnostic images in Digital Imaging and Communications in Medicine (DICOM) and Health Level Seven (HL7) formats. Metadata is generated from each related image to support their identification. This study presents the use of decision trees for the optimization of information search processes for diagnostic images, hosted on the cloud server. To analyze the performance in the server, the following quality of service (QoS) metrics are evaluated: delay, bandwidth, jitter, latency and throughput in five test scenarios for a total of 26 experiments during the loading and downloading of DICOM images, hosted by the telemedicine group server of the Universidad Militar Nueva Granada, Bogotá, Colombia. By applying decision trees as a data mining technique and comparing it with the sequential search, it was possible to evaluate the search times of diagnostic images in the server. The results show that by using the metadata in decision trees, the search times are substantially improved, the computational resources are optimized and the request management of the telemedicine image service is improved. Based on the experiments carried out, search efficiency increased by 45% in relation to the sequential search, given that, when downloading a diagnostic image, false positives are avoided in management and acquisition processes of said information. It is concluded that, for the diagnostic images services in telemedicine, the technique of decision trees guarantees the accessibility and robustness in the acquisition and manipulation of medical images, in improvement of the diagnoses and medical procedures in patients.

Keywords: Cloud storage, decision trees, diagnostic image, search, telemedicine.

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Authors: Ha T. Pham, Shuichi Miyagawa

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Ongoing landscape transformation is one of the major causes behind disappearance of traditional landscapes, and lead to species and resource loss. Tree in paddy fields in the northeast of Thailand is one of those traditional landscapes. Using three different historical time layers, we acknowledged the severe deforestation and rapid urbanization happened in the region. Despite the general thinking of decline in tree density as consequences, the heterogeneous trend of changes in total tree density in three studied landscapes denied the hypothesis that number of trees in paddy field depend on the length of land use practice. On the other hand, due to selection of planting new trees on levees, existence of trees in paddy field now relies on their values for human use. Besides, changes in land use and landscape structure had a significant impact on decision of which tree density level is considered as suitable for the landscape.

Keywords: Aerial photographs, land use change, traditional landscape, tree in paddy fields.

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Authors: Jeevan Malayan, Aparna Warrier, Padmasani Venkat Ramanan, Sanjeeva Reddy N, Elanchezhiyan Manickan

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MMR vaccine failure had been reported globally and here we report that it occurs now in India. Samples were collected from clinically suspected mumps cases were subjected for anti mumps antibodies, virus isolation, RT-PCR, sequencing and phylogenetic tree analysis. 56 samples collected from men and women belonging to various age groups. 30 had been vaccinated and the status of 26 patients was unknown. 28 out of 30 samples were found to be symptomatic and positive for Mumps IgM, indicating active mumps infection in 93.4% of the vaccinated population. A phylogenetic tree comparison of the clinical isolate is shown to be genotype C which is distinct from vaccine strain. Our study clearly sending warning signs that MMR vaccine is a failure and it needs to be revamped for the human use by increasing its efficacy and efficiency.

Keywords: Genotype C, Mumps virus, MMR vaccine, Sero types.

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Authors: Matthias Dehmer, Frank Emmert Streib, Jürgen Kilian, Andreas Zulauf

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Methods for organizing web data into groups in order to analyze web-based hypertext data and facilitate data availability are very important in terms of the number of documents available online. Thereby, the task of clustering web-based document structures has many applications, e.g., improving information retrieval on the web, better understanding of user navigation behavior, improving web users requests servicing, and increasing web information accessibility. In this paper we investigate a new approach for clustering web-based hypertexts on the basis of their graph structures. The hypertexts will be represented as so called generalized trees which are more general than usual directed rooted trees, e.g., DOM-Trees. As a important preprocessing step we measure the structural similarity between the generalized trees on the basis of a similarity measure d. Then, we apply agglomerative clustering to the obtained similarity matrix in order to create clusters of hypertext graph patterns representing navigation structures. In the present paper we will run our approach on a data set of hypertext structures and obtain good results in Web Structure Mining. Furthermore we outline the application of our approach in Web Usage Mining as future work.

Keywords: Clustering methods, graph-based patterns, graph similarity, hypertext structures, web structure mining

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Authors: O. S. Eludoyin, A. A. Aiyeloja, O. C. Ndife

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The study investigated the spatial analysis of trees composition, diversity and richness in the built up area of University of Port Harcourt, Nigeria. Four quadrats of 25m x 25m size were laid randomly in each of the three parks and inventories of trees ≥10cm girth at breast height were taken and used to calculate the species composition, diversity and richness. Results showed that species composition and diversity in Abuja Park was the highest with 134 species and 0.866 respectively while the species richness was highest in Choba Park with a value of 2.496. The correlation between the size of park (spatial coverage) and species composition was 0.99 while the correlation between the size of the park and species diversity was 0.78. There was direct relationship between species composition and diversity while the relationship between species composition and species richness was inversely proportional. Rational use of these resources is encouraged.

Keywords: Built up area, composition, diversity, richness, spatial analysis, urban tree.

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Authors: Mladen Dragičević, Mirjana Pejić Bach, Vanja Šimičević

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The purpose of this paper is to develop models that would enable predicting student success. These models could improve allocation of students among colleges and optimize the newly introduced model of government subsidies for higher education. For the purpose of collecting data, an anonymous survey was carried out in the last year of undergraduate degree student population using random sampling method. Decision trees were created of which two have been chosen that were most successful in predicting student success based on two criteria: Grade Point Average (GPA) and time that a student needs to finish the undergraduate program (time-to-degree). Decision trees have been shown as a good method of classification student success and they could be even more improved by increasing survey sample and developing specialized decision trees for each type of college. These types of methods have a big potential for use in decision support systems.

Keywords: Data mining, knowledge discovery in databases, prediction models, student success.

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Authors: Khalil el Hindi

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This paper presents a simple and effective method for approximate indexing of instances for instance based learning. The method uses an interval tree to determine a good starting search point for the nearest neighbor. The search stops when an early stopping criterion is met. The method proved to be very effective especially when only the first nearest neighbor is required.

Keywords: Instance based learning, interval trees, the knn algorithm, machine learning.

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Authors: P. Panichnumsin, B. K. Ahring, A. Nopharatana, P. Chaipresert

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In this study, we illustrated the performance and microbial community of single- and two-phase systems anaerobically co-digesting cassava pulp and pig manure. The results showed that the volatile solid reduction and biogas productivity of two-phase CSTR were 66 ± 4% and 2000 ± 210 ml l-1 d-1, while those of singlephase CSTR were 59 ± 1% and 1670 ± 60 ml l-1 d-1, respectively. Codigestion in two-phase CSTR gave higher 12% solid degradation and 25% methane production than single-phase CSTR. Phylogenetic analysis of 16S rDNA clone library revealed that the Bacteroidetes were the most abundant group, followed by the Clostridia in singlephase CSTR. In hydrolysis/acidification reactor of two-phase system, the bacteria within the phylum Firmicutes, especially Clostridium, Eubacteriaceae and Lactobacillus were the dominant phylogenetic groups. Among the Archaea, Methanosaeta sp. was the exclusive predominant in both digesters while the relative abundance of Methanosaeta sp. and Methanospirillum hungatei differed between the two systems.

Keywords: Anaerobic co-digestion, Cassava pulp, Microbialdiversity, Pig manure.

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Authors: R. AliMohammadzadeh, M. Haghir Chehreghani, A. Zarnani, M. Rahgozar

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Mining frequent tree patterns have many useful applications in XML mining, bioinformatics, network routing, etc. Most of the frequent subtree mining algorithms (i.e. FREQT, TreeMiner and CMTreeMiner) use anti-monotone property in the phase of candidate subtree generation. However, none of these algorithms have verified the correctness of this property in tree structured data. In this research it is shown that anti-monotonicity does not generally hold, when using weighed support in tree pattern discovery. As a result, tree mining algorithms that are based on this property would probably miss some of the valid frequent subtree patterns in a collection of trees. In this paper, we investigate the correctness of anti-monotone property for the problem of weighted frequent subtree mining. In addition we propose W3-Miner, a new algorithm for full extraction of frequent subtrees. The experimental results confirm that W3-Miner finds some frequent subtrees that the previously proposed algorithms are not able to discover.

Keywords: Semi-Structured Data Mining, Anti-Monotone Property, Trees.

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Authors: Doru Anastasiu Popescu, Dan Rădulescu

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In this paper, we determine the similarity of two HTML web applications. We are going to use a genetic algorithm in order to determine the most significant web pages of each application (we are not going to use every web page of a site). Using these significant web pages, we will find the similarity value between the two applications. The algorithm is going to be efficient because we are going to use a reduced number of web pages for comparisons but it will return an approximate value of the similarity. The binary trees are used to keep the tags from the significant pages. The algorithm was implemented in Java language.

Keywords: Tag, HTML, web page, genetic algorithm, similarity value, binary tree.

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Authors: Tessy Badriyah, Jim S. Briggs, Dave R. Prytherch

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It is well known that Logistic Regression is the gold standard method for predicting clinical outcome, especially predicting risk of mortality. In this paper, the Decision Tree method has been proposed to solve specific problems that commonly use Logistic Regression as a solution. The Biochemistry and Haematology Outcome Model (BHOM) dataset obtained from Portsmouth NHS Hospital from 1 January to 31 December 2001 was divided into four subsets. One subset of training data was used to generate a model, and the model obtained was then applied to three testing datasets. The performance of each model from both methods was then compared using calibration (the χ2 test or chi-test) and discrimination (area under ROC curve or c-index). The experiment presented that both methods have reasonable results in the case of the c-index. However, in some cases the calibration value (χ2) obtained quite a high result. After conducting experiments and investigating the advantages and disadvantages of each method, we can conclude that Decision Trees can be seen as a worthy alternative to Logistic Regression in the area of Data Mining.

Keywords: Decision Trees, Logistic Regression, clinical outcome, risk of mortality.

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Authors: Djamila Benhaddouche, Abdelkader Benyettou

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In this paper, we used data mining to extract biomedical knowledge. In general, complex biomedical data collected in studies of populations are treated by statistical methods, although they are robust, they are not sufficient in themselves to harness the potential wealth of data. For that you used in step two learning algorithms: the Decision Trees and Support Vector Machine (SVM). These supervised classification methods are used to make the diagnosis of thyroid disease. In this context, we propose to promote the study and use of symbolic data mining techniques.

Keywords: A classifier, Algorithms decision tree, knowledge extraction, Support Vector Machine.

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Authors: Dewi Liesnoor Setyowati, Puji Hardati, Tri Marhaeni Puji Astuti, Muhammad Amin

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Universitas Negeri Semarang (UNNES) is a university with a vision of conservation. The impact of the UNNES conservation is the existence of a positive response from the community for the effort of greening the campus and the planting of conservation value in the academic community. But in reality,  energy consumption in UNNES campus tends to increase. The objectives of the study were to analyze the energy consumption in the campus area, to analyze the absorption of emissions by trees and the awareness of UNNES citizens in reducing emissions. Research focuses on energy consumption, carbon emissions, and awareness of citizens in reducing emissions. Research subjects in this study are UNNES citizens (lecturers, students and employees). The research area covers 6 faculties and one administrative center building. Data collection is done by observation, interview and documentation. The research used a quantitative descriptive method to analyze the data. The number of trees in UNNES is 10,264. Total emission on campus UNNES is 7.862.281.56 kg/year, the tree absorption is 6,289,250.38 kg/year. In UNNES campus area there are still 1,575,031.18 kg/year of emissions, not yet absorbed by trees. There are only two areas of the faculty whose trees are capable of absorbing emissions. The awareness of UNNES citizens in reducing energy consumption is seen in change the habit of: using energy-saving equipment (65%); reduce energy consumption per unit (68%); do energy literacy for UNNES citizens (74%). UNNES leaders always provide motivation to the citizens of UNNES, to reduce and change patterns of energy consumption.

Keywords: Energy consumption, carbon emission absorption, emission reduction, energy literation.

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Authors: Salsabil Trabelsi, Zied Elouedi, Khaled Mellouli

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The belief decision tree (BDT) approach is a decision tree in an uncertain environment where the uncertainty is represented through the Transferable Belief Model (TBM), one interpretation of the belief function theory. The uncertainty can appear either in the actual class of training objects or attribute values of objects to classify. In this paper, we develop a post-pruning method of belief decision trees in order to reduce size and improve classification accuracy on unseen cases. The pruning of decision tree has a considerable intention in the areas of machine learning.

Keywords: machine learning, uncertainty, belief function theory, belief decision tree, pruning.

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Authors: Adedokun D. A., Ndambuki J. M., Salim R. W.

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Due to urbanization, trees and plants which covered a great land mass of the earth and are an excellent carbon dioxide (CO2) absorber through photosynthesis are being replaced by several concrete based structures. It is therefore important to have these cement based structures absorb the large volume of carbon dioxide which the trees would have removed from the atmosphere during their useful lifespan. Hence the need for these cement based structures to be designed to serve other useful purposes in addition to shelter. This paper reviews the properties of Sodium carbonate and sugar as admixtures in concrete with respect to improving carbon sequestration in concrete.

Keywords: Carbon sequestration, Sodium carbonate, Sugar, concrete, Carbon dioxide.

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Authors: Ali Shojaei-Fard

Abstract:

In this paper we consider quantum motion integrals depended on the algebraic reconstruction of BPHZ method for perturbative renormalization in two different procedures. Then based on Bogoliubov character and Baker-Campbell-Hausdorff (BCH) formula, we show that how motion integral condition on components of Birkhoff factorization of a Feynman rules character on Connes- Kreimer Hopf algebra of rooted trees can determine a family of fixed point equations.

Keywords: Birkhoff Factorization, Connes-Kreimer Hopf Algebra of Rooted Trees, Integral Renormalization, Lax Pair Equation, Rota- Baxter Algebras.

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Authors: Amr A. El Hanafy, Muhammad Qureshi, Jamal Sabir, Mohamed Mutawakil, Mohamed M. Ahmed, Hassan El Ashmaoui, Hassan Ramadan, Mohamed Abou-Alsoud, Mahmoud Abdel Sadek

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Domestic goats (Capra hircus) are extremely diverse species and principal animal genetic resource of the developing world. These facilitate a persistent supply of meat, milk, fibre, and skin and are considered as important revenue generators in small pastoral environments. This study aimed to fingerprint β-LG gene at PCR-RFLP level in native Saudi goat breeds (Ardi, Habsi and Harri) in an attempt to have a preliminary image of β-LG genotypic patterns in Saudi breeds as compared to other foreign breeds such as Indian and Egyptian. Also, the Phylogenetic analysis was done to investigate evolutionary trends and similarities among the caprine β-LG gene with that of the other domestic specie, viz. cow, buffalo and sheep. Blood samples were collected from 300 animals (100 for each breed) and genomic DNA was extracted. A fragment of the β-LG gene (427bp) was amplified using specific primers. Subsequent digestion with Sac II restriction endonuclease revealed two alleles (A and B) and three different banding patterns or genotypes i.e. AA, AB and BB. The statistical analysis showed a general trend that β-LG AA genotype had higher milk yield than β-LG AB and β-LG BB genotypes. Nucleotide sequencing of the selected β-LG fragments was done and submitted to GenBank NCBI (Accession No. KJ544248, KJ588275, KJ588276, KJ783455, KJ783456 and KJ874959). Phylogenetic analysis on the basis of nucleotide sequences of native Saudi goats indicated evolutional similarity with the GenBank reference sequences of goat, Bubalus bubalis and Bos taurus. However, the origin of sheep which is the most closely related from the evolutionary point of view, was located some distance away.

Keywords: β-Lactoglobulin, Saudi goats, PCR-RFLP, Phylogenetic analysis.

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Authors: Abdullah H. Özcan, Dilara Hisar, Yetkin Sayar, Cem Ünsalan

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In this study, an automated building and tree detection method is proposed using DSM data and true orthophoto image. A multiscale matched filtering is used on DSM data. Therefore, first watershed transform is applied. Then, Otsu’s thresholding method is used as an adaptive threshold to segment each watershed region. Detected objects are masked with NDVI to separate buildings and trees. The proposed method is able to detect buildings and trees without entering any elevation threshold. We tested our method on ISPRS semantic labeling dataset and obtained promising results.

Keywords: Building detection, tree detection, matched filtering, multiscale, local maximum filtering, watershed segmentation.

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Authors: Riad S. Jabri

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Pattern matching based on regular tree grammars have been widely used in many areas of computer science. In this paper, we propose a pattern matcher within the framework of code generation, based on a generic and a formalized approach. According to this approach, parsers for regular tree grammars are adapted to a general pattern matching solution, rather than adapting the pattern matching according to their parsing behavior. Hence, we first formalize the construction of the pattern matches respective to input trees drawn from a regular tree grammar in a form of the so-called match trees. Then, we adopt a recently developed generic parser and tightly couple its parsing behavior with such construction. In addition to its generality, the resulting pattern matcher is characterized by its soundness and efficient implementation. This is demonstrated by the proposed theory and by the derived algorithms for its implementation. A comparison with similar and well-known approaches, such as the ones based on tree automata and LR parsers, has shown that our pattern matcher can be applied to a broader class of grammars, and achieves better approximation of pattern matches in one pass. Furthermore, its use as a machine code selector is characterized by a minimized overhead, due to the balanced distribution of the cost computations into static ones, during parser generation time, and into dynamic ones, during parsing time.

Keywords: Bottom-up automata, Code selection, Pattern matching, Regular tree grammars, Match trees.

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Authors: Matthias Dehmer, Frank Emmert Streib, Alexander Mehler, Jürgen Kilian, Max Mühlhauser

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Due to the tremendous amount of information provided by the World Wide Web (WWW) developing methods for mining the structure of web-based documents is of considerable interest. In this paper we present a similarity measure for graphs representing web-based hypertext structures. Our similarity measure is mainly based on a novel representation of a graph as linear integer strings, whose components represent structural properties of the graph. The similarity of two graphs is then defined as the optimal alignment of the underlying property strings. In this paper we apply the well known technique of sequence alignments for solving a novel and challenging problem: Measuring the structural similarity of generalized trees. In other words: We first transform our graphs considered as high dimensional objects in linear structures. Then we derive similarity values from the alignments of the property strings in order to measure the structural similarity of generalized trees. Hence, we transform a graph similarity problem to a string similarity problem for developing a efficient graph similarity measure. We demonstrate that our similarity measure captures important structural information by applying it to two different test sets consisting of graphs representing web-based document structures.

Keywords: Graph similarity, hierarchical and directed graphs, hypertext, generalized trees, web structure mining.

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Authors: Erika Pigliapoco, Valerio Freschi, Alessandro Bogliolo

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This work presents a new phonetic transcription system based on a tree of hierarchical pronunciation rules expressed as context-specific grapheme-phoneme correspondences. The tree is automatically inferred from a phonetic dictionary by incrementally analyzing deeper context levels, eventually representing a minimum set of exhaustive rules that pronounce without errors all the words in the training dictionary and that can be applied to out-of-vocabulary words. The proposed approach improves upon existing rule-tree-based techniques in that it makes use of graphemes, rather than letters, as elementary orthographic units. A new linear algorithm for the segmentation of a word in graphemes is introduced to enable outof- vocabulary grapheme-based phonetic transcription. Exhaustive rule trees provide a canonical representation of the pronunciation rules of a language that can be used not only to pronounce out-of-vocabulary words, but also to analyze and compare the pronunciation rules inferred from different dictionaries. The proposed approach has been implemented in C and tested on Oxford British English and Basic English. Experimental results show that grapheme-based rule trees represent phonetically sound rules and provide better performance than letter-based rule trees.

Keywords: Automatic phonetic transcription, pronunciation rules, hierarchical tree inference.

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Authors: Yan Ren, Jun Qiao, Xianxia Liu, Pengyan Wang, Qiang Fu, Huijun Shi, Fei Guo, Yuanzhi Wang, Hui Zhang, Jinliang Sheng, Xinli Gu, Xiao-Jun Liu, Chuangfu Chen

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As part of national epidemiological survey on bovine viral diarrhea virus (BVDV), a total of 274 dejecta samples were collected from 14 cattle farms in 8 areas of Xinjiang Uygur Autonomous Region in northwestern China. Total RNA was extracted from each sample, and 5--untranslated region (UTR) of BVDV genome was amplified by using two-step reverse transcriptase-polymerase chain reaction (RT-PCR). The PCR products were subsequently sequenced to study the genetic variations of BVDV in these areas. Among the 274 samples, 33 samples were found virus-positive. According to sequence analysis of the PCR products, the 33 samples could be arranged into 16 groups. All the sequences, however, were highly conserved with BVDV Osloss strains. The virus possessed theses sequences belonged to BVDV-1b subtype by phylogenetic analysis. Based on these data, we established a typing tree for BVDV in these areas. Our results suggested that BVDV-1b was a predominant subgenotype in northwestern China and no correlation between the genetic and geographical distances could be observed above the farm level.

Keywords: bovine viral diarrhea virus, molecular epidemiology, phylogenetic analysis.

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Authors: Luay A. Fraiwan, Natheer Y. Khaswaneh, Khaldon Y. Lweesy

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Sleep stage scoring is the process of classifying the stage of the sleep in which the subject is in. Sleep is classified into two states based on the constellation of physiological parameters. The two states are the non-rapid eye movement (NREM) and the rapid eye movement (REM). The NREM sleep is also classified into four stages (1-4). These states and the state wakefulness are distinguished from each other based on the brain activity. In this work, a classification method for automated sleep stage scoring based on a single EEG recording using wavelet packet decomposition was implemented. Thirty two ploysomnographic recording from the MIT-BIH database were used for training and validation of the proposed method. A single EEG recording was extracted and smoothed using Savitzky-Golay filter. Wavelet packets decomposition up to the fourth level based on 20th order Daubechies filter was used to extract features from the EEG signal. A features vector of 54 features was formed. It was reduced to a size of 25 using the gain ratio method and fed into a classifier of regression trees. The regression trees were trained using 67% of the records available. The records for training were selected based on cross validation of the records. The remaining of the records was used for testing the classifier. The overall correct rate of the proposed method was found to be around 75%, which is acceptable compared to the techniques in the literature.

Keywords: Features selection, regression trees, sleep stagescoring, wavelet packets.

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Authors: Maria Toader, Gheorghe Valentin Roman

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The importance of fruit trees and bushes growing for Romania is due the concordance that exists between the different ecological conditions in natural basins, and the requirements of different species and varieties. There are, in Romania, natural areas dedicated to the main trees species: plum, apple, pear, cherry, sour cherry, finding optimal conditions for harnessing the potential of fruitfulness, making fruit quality both in terms of ratio commercial, and content in active principles. The share of fruits crops in the world economy of agricultural production is due primarily to the role of fruits in nourishment for human, and in the prevention and combating of diseases, in increasing the national income of cultivator countries and to improve comfort for human life. For Romania, the perspectives of the sector are positive, and are due to European funding opportunities, which provide farmers a specialized program that meets the needs of development and modernization of fruit growing industry, cultivation technology and equipment, organization and grouping of producers, creating storage facilities, conditioning, marketing and the joint use of fresh fruit. This paper shows the evolution of fruit growing, in Romania compared to other states. The document presents the current situation of the main tree species both in terms of surface but also of the productions and the role that this activity may have for the development of rural communities.

Keywords: Fruit growing, fruits trees, productivity, rural development.

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: Begomovirus, AV1 gene, sequence, cloning, whitefly, okra, cotton, tomato, RAPD, phylogenetic tree and SDS-PAGE.

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Authors: Frank Emmert-Streib, Matthias Dehmer, Jing Liu, Max Muhlhauser

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The major objective of this paper is to introduce a new method to select genes from DNA microarray data. As criterion to select genes we suggest to measure the local changes in the correlation graph of each gene and to select those genes whose local changes are largest. More precisely, we calculate the correlation networks from DNA microarray data of cervical cancer whereas each network represents a tissue of a certain tumor stage and each node in the network represents a gene. From these networks we extract one tree for each gene by a local decomposition of the correlation network. The interpretation of a tree is that it represents the n-nearest neighbor genes on the n-th level of a tree, measured by the Dijkstra distance, and, hence, gives the local embedding of a gene within the correlation network. For the obtained trees we measure the pairwise similarity between trees rooted by the same gene from normal to cancerous tissues. This evaluates the modification of the tree topology due to tumor progression. Finally, we rank the obtained similarity values from all tissue comparisons and select the top ranked genes. For these genes the local neighborhood in the correlation networks changes most between normal and cancerous tissues. As a result we find that the top ranked genes are candidates suspected to be involved in tumor growth. This indicates that our method captures essential information from the underlying DNA microarray data of cervical cancer.

Keywords: Graph similarity, generalized trees, graph alignment, DNA microarray data, cervical cancer.

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Authors: Langa Hendrick Musawenkosi, Twala Bhekisipho

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The success or failure of students is a concern for every academic institution, college, university, governments and students themselves. Several approaches have been researched to address this concern. In this paper, a view is held that when a student enters a university or college or an academic institution, he or she enters an academic environment. The academic environment is unique concept used to develop the solution for making predictions effectively. This paper presents a model to determine the propensity of a student to succeed or fail in the French South African Schneider Electric Education Center (FSASEC) at the Vaal University of Technology (VUT). The Decision Tree algorithm is used to implement the model at FSASEC.

Keywords: Academic environment model, decision trees, FSASEC, K-nearest neighbor, machine learning, popularity index, support vector machine.

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Authors: Ghada Badr, Manar Hosny, Nuha Bintayyash, Eman Albilali, Souad Larabi Marie-Sainte

Abstract:

The median problem is significantly applied to derive the most reasonable rearrangement phylogenetic tree for many species. More specifically, the problem is concerned with finding a permutation that minimizes the sum of distances between itself and a set of three signed permutations. Genomes with equal number of genes but different order can be represented as permutations. In this paper, an algorithm, namely BeamGA median, is proposed that combines a heuristic search approach (local beam) as an initialization step to generate a number of solutions, and then a Genetic Algorithm (GA) is applied in order to refine the solutions, aiming to achieve a better median with the smallest possible reversal distance from the three original permutations. In this approach, any genome rearrangement distance can be applied. In this paper, we use the reversal distance. To the best of our knowledge, the proposed approach was not applied before for solving the median problem. Our approach considers true biological evolution scenario by applying the concept of common intervals during the GA optimization process. This allows us to imitate a true biological behavior and enhance genetic approach time convergence. We were able to handle permutations with a large number of genes, within an acceptable time performance and with same or better accuracy as compared to existing algorithms.

Keywords: Median problem, phylogenetic tree, permutation, genetic algorithm, beam search, genome rearrangement distance.

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