Search results for: genomic data analysis

Authors: Yunus Doğan, Ahmet Durap

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Coastal regions are the one of the most commonly used places by the natural balance and the growing population. In coastal engineering, the most valuable data is wave behaviors. The amount of this data becomes very big because of observations that take place for periods of hours, days and months. In this study, some statistical methods such as the wave spectrum analysis methods and the standard statistical methods have been used. The goal of this study is the discovery profiles of the different coast areas by using these statistical methods, and thus, obtaining an instance based data set from the big data to analysis by using data mining algorithms. In the experimental studies, the six sample data sets about the wave behaviors obtained by 20 minutes of observations from Mersin Bay in Turkey and converted to an instance based form, while different clustering techniques in data mining algorithms were used to discover similar coastal places. Moreover, this study discusses that this summarization approach can be used in other branches collecting big data such as medicine.

Keywords: Clustering algorithms, coastal engineering, data mining, data summarization, statistical methods.

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Authors: Yu Zhang, Pedro Desouza

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Since big data has become substantially more accessible and manageable due to the development of powerful tools for dealing with unstructured data, people are eager to mine information from social media resources that could not be handled in the past. Sentiment analysis, as a novel branch of text mining, has in the last decade become increasingly important in marketing analysis, customer risk prediction and other fields. Scientists and researchers have undertaken significant work in creating and improving their sentiment models. In this paper, we present a concept of selecting appropriate classifiers based on the features and qualities of data sources by comparing the performances of five classifiers with three popular social media data sources: Twitter, Amazon Customer Reviews, and Movie Reviews. We introduced a couple of innovative models that outperform traditional sentiment classifiers for these data sources, and provide insights on how to further improve the predictive power of sentiment analysis. The modeling and testing work was done in R and Greenplum in-database analytic tools.

Keywords: Sentiment Analysis, Social Media, Twitter, Amazon, Data Mining, Machine Learning, Text Mining.

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Authors: Qi Xiu, Hiromu Hota, Yohsuke Ishii, Takuya Oda

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Recently, collectable manufacturing data are rapidly increasing. On the other hand, mega recall is getting serious as a social problem. Under such circumstances, there are increasing needs for preventing mega recalls by defect analysis such as root cause analysis and abnormal detection utilizing manufacturing data. However, the time to classify strings in manufacturing data by traditional method is too long to meet requirement of quick defect analysis. Therefore, we present String Length Distribution Classification method (SLDC) to correctly classify strings in a short time. This method learns character features, especially string length distribution from Product ID, Machine ID in BOM and asset list. By applying the proposal to strings in actual manufacturing data, we verified that the classification time of strings can be reduced by 80%. As a result, it can be estimated that the requirement of quick defect analysis can be fulfilled.

Keywords: Data quality, feature selection, probability distribution, string classification, string length.

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Authors: S. Turkan

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In this paper, the Turkey’s Top 500 Industrial Enterprises data in 2014 were analyzed by data envelopment analysis. Data envelopment analysis is used to detect efficient decision-making units such as universities, hospitals, schools etc. by using inputs and outputs. The decision-making units in this study are enterprises. To detect efficient enterprises, some financial ratios are determined as inputs and outputs. For this reason, financial indicators related to productivity of enterprises are considered. The efficient foreign weighted owned capital enterprises are detected via super efficiency model. According to the results, it is said that Mercedes-Benz is the most efficient foreign weighted owned capital enterprise in Turkey.

Keywords: Data envelopment analysis, super efficiency, financial ratios, BCC model.

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Authors: Benjamin Y. M. Kwan, Jennifer Y. Y. Kwan, Hon Keung Kwan

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In the paper, the relative performances on spectral classification of short exon and intron sequences of the human and eleven model organisms is studied. In the simulations, all combinations of sixteen one-sequence numerical representations, four threshold values, and four window lengths are considered. Sequences of 150-base length are chosen and for each organism, a total of 16,000 sequences are used for training and testing. Results indicate that an appropriate combination of one-sequence numerical representation, threshold value, and window length is essential for arriving at top spectral classification results. For fixed-length sequences, the precisions on exon and intron classification obtained for different organisms are not the same because of their genomic differences. In general, precision increases as sequence length increases.

Keywords: Exons and introns classification, Human genome, Model organism genome, Spectral analysis

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Authors: J. Grira, Y. Bédard, S. Roche

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The aim of this research is to design a collaborative framework that integrates risk analysis activities into the geospatial database design (GDD) process. Risk analysis is rarely undertaken iteratively as part of the present GDD methods in conformance to requirement engineering (RE) guidelines and risk standards. Accordingly, when risk analysis is performed during the GDD, some foreseeable risks may be overlooked and not reach the output specifications especially when user intentions are not systematically collected. This may lead to ill-defined requirements and ultimately in higher risks of geospatial data misuse. The adopted approach consists of 1) reviewing risk analysis process within the scope of RE and GDD, 2) analyzing the challenges of risk analysis within the context of GDD, and 3) presenting the components of a risk-based collaborative framework that improves the collection of the intended/forbidden usages of the data and helps geo-IT experts to discover implicit requirements and risks.

Keywords: Collaborative risk analysis, intention of use, Geospatial database design, Geospatial data misuse.

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Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

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Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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Authors: M. Pollar, M. Jaroensutasinee, K. Jaroensutasinee

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The population structure of the Tor tambroides was investigated with morphometric data (i.e. morphormetric measurement and truss measurement). A morphometric analysis was conducted to compare specimens from three waterfalls: Sunanta, Nan Chong Fa and Wang Muang waterfalls at Khao Nan National Park, Nakhon Si Thammarat, Southern Thailand. The results of stepwise discriminant analysis on seven morphometric variables and 21 truss variables per individual were the same as from a neural network. Fish from three waterfalls were separated into three groups based on their morphometric measurements. The morphometric data shows that the nerual network model performed better than the stepwise discriminant analysis.

Keywords: Morphometric, Tor tambroides, Stepwise Discriminant Analysis , Neural Network Analysis.

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Authors: Younies Mahmoud, Mai Mabrouk, Elsayed Sallam

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Analyzing DNA microarray data sets is a great challenge, which faces the bioinformaticians due to the complication of using statistical and machine learning techniques. The challenge will be doubled if the microarray data sets contain missing data, which happens regularly because these techniques cannot deal with missing data. One of the most important data analysis process on the microarray data set is feature selection. This process finds the most important genes that affect certain disease. In this paper, we introduce a technique for imputing the missing data in microarray data sets while performing feature selection.

Keywords: DNA microarray, feature selection, missing data, bioinformatics.

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Authors: Luminita Dumitriu, Cristina Segal, Marian Craciun, Adina Cocu, Lucian P. Georgescu

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There are several approaches in trying to solve the Quantitative 1Structure-Activity Relationship (QSAR) problem. These approaches are based either on statistical methods or on predictive data mining. Among the statistical methods, one should consider regression analysis, pattern recognition (such as cluster analysis, factor analysis and principal components analysis) or partial least squares. Predictive data mining techniques use either neural networks, or genetic programming, or neuro-fuzzy knowledge. These approaches have a low explanatory capability or non at all. This paper attempts to establish a new approach in solving QSAR problems using descriptive data mining. This way, the relationship between the chemical properties and the activity of a substance would be comprehensibly modeled.

Keywords: association rules, classification, data mining, Quantitative Structure - Activity Relationship.

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Authors: Ritu Vijay, Rekha Govil

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The design of a complete expansion that allows for compact representation of certain relevant classes of signals is a central problem in signal processing applications. Achieving such a representation means knowing the signal features for the purpose of denoising, classification, interpolation and forecasting. Multilayer Neural Networks are relatively a new class of techniques that are mathematically proven to approximate any continuous function arbitrarily well. Radial Basis Function Networks, which make use of Gaussian activation function, are also shown to be a universal approximator. In this age of ever-increasing digitization in the storage, processing, analysis and communication of information, there are numerous examples of applications where one needs to construct a continuously defined function or numerical algorithm to approximate, represent and reconstruct the given discrete data of a signal. Many a times one wishes to manipulate the data in a way that requires information not included explicitly in the data, which is done through interpolation and/or extrapolation. Tidal data are a very perfect example of time series and many statistical techniques have been applied for tidal data analysis and representation. ANN is recent addition to such techniques. In the present paper we describe the time series representation capabilities of a special type of ANN- Radial Basis Function networks and present the results of tidal data representation using RBF. Tidal data analysis & representation is one of the important requirements in marine science for forecasting.

Keywords: ANN, RBF, Tidal Data.

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Authors: Monika Chuchro, Maciej Dwornik

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The extraction of meaningful information from image could be an alternative method for time series analysis. In this paper, we propose a graphical analysis of time series grouped into table with adjusted colour scale for numerical values. The advantages of this method are also discussed. The proposed method is easy to understand and is flexible to implement the standard methods of pattern recognition and verification, especially for noisy environmental data.

Keywords: graphical analysis, time series, seasonality, noisy environmental data

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Authors: M.R. Safizadeh, M. Hussein, K. F. Samat, M.S. Che Kob, M.S. Yaacob, M.Z. Md Zain

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The aim of this paper is to present the kinematic analysis and mechanism design of an assistive robotic leg for hemiplegic and hemiparetic patients. In this work, the priority is to design and develop the lightweight, effective and single driver mechanism on the basis of experimental hip and knee angles- data for walking speed of 1 km/h. A mechanism of cam-follower with three links is suggested for this purpose. The kinematic analysis is carried out and analysed using commercialized MATLAB software based on the prototype-s links sizes and kinematic relationships. In order to verify the kinematic analysis of the prototype, kinematic analysis data are compared with the experimental data. A good agreement between them proves that the anthropomorphic design of the lower extremity exoskeleton follows the human walking gait.

Keywords: Kinematic analysis, assistive robotic leg, lower extremity exoskeleton, cam-follower mechanism.

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Authors: Chuen Tse Kuah, Kuan Yew Wong, Farzad Behrouzi

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This paper is aimed to give an illustration on the application of Data Envelopment Analysis (DEA) as a tool to assess Quality Management (QM) efficiency. A variant of DEA, slack based measure (SBM) is used for this purpose. From this study, it is found that DEA is suitable to measure QM efficiency and give improvement suggestions to the inefficient QM.

Keywords: Quality Management, Data Envelopment Analysis, Slack Based Measure, Efficiency Measurement.

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Authors: Shishen Xie, Yingda L. Xie

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Tuberculosis (TB) is a potentially serious infectious disease that remains a health concern. The Interferon Gamma Release Assay (IGRA) is a blood test to find out if an individual is tuberculous positive or negative. This study applies statistical analysis to the clinical data of interferon-gamma levels of seventy-three subjects who diagnosed pulmonary TB in an anti-tuberculous treatment. Data analysis is performed to determine if there is a significant decline in interferon-gamma levels for the subjects during a period of six months, and to infer if the anti-tuberculous treatment is effective.

Keywords: Data analysis, interferon gamma release assay, statistical methods, tuberculosis infection.

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Authors: S. Moghaddaszadeh-Ahrabi, S. Farajnia, Gh. Rahimi-Mianji, A. Nejati-Javaremi

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In recent years, there has been an increasing interest toward the use of bovine genotyped embryos for commercial embryo transfer programs. Biopsy of a few cells in morulla stage is essential for preimplantation genetic diagnosis (PGD). Low amount of DNA have limited performing the several molecular analyses within PGD analyses. Whole genome amplification (WGA) promises to eliminate this problem. We evaluated the possibility and performance of an improved primer extension preamplification (I-PEP) method with a range of starting bovine genomic DNA from 1-8 cells into the WGA reaction. We optimized a short and simple I-PEP (ssI-PEP) procedure (~3h). This optimized WGA method was assessed by 6 loci specific polymerase chain reactions (PCRs), included restriction fragments length polymorphism (RFLP). Optimized WGA procedure possesses enough sensitivity for molecular genetic analyses through the few input cells. This is a new era for generating characterized bovine embryos in preimplantation stage.

Keywords: Whole genome amplification (WGA), Genotyping, Bovine, Preimplantation genetic diagnosis (PGD)

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Authors: S. Sarumathi, N. Shanthi, P. Ranjetha

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Data mining is the procedure of determining interesting patterns from the huge amount of data. With the intention of accessing the data faster the most supporting processes needed is clustering. Clustering is the process of identifying similarity between data according to the individuality present in the data and grouping associated data objects into clusters. Cluster ensemble is the technique to combine various runs of different clustering algorithms to obtain a general partition of the original dataset, aiming for consolidation of outcomes from a collection of individual clustering outcomes. The performances of clustering ensembles are mainly affecting by two principal factors such as diversity and quality. This paper presents the overview about the different cluster ensemble algorithm along with their methods used in cluster ensemble to improve the diversity and quality in the several cluster ensemble related papers and shows the comparative analysis of different cluster ensemble also summarize various cluster ensemble methods. Henceforth this clear analysis will be very useful for the world of clustering experts and also helps in deciding the most appropriate one to determine the problem in hand.

Keywords: Cluster Ensemble, Consensus Function, CSPA, Diversity, HGPA, MCLA.

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Authors: Paula Simões, Isabel Natário

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This paper reviews a number of theoretical aspects for implementing an explicit spatial perspective in econometrics for modelling non-continuous data, in general, and count data, in particular. It provides an overview of the several spatial econometric approaches that are available to model data that are collected with reference to location in space, from the classical spatial econometrics approaches to the recent developments on spatial econometrics to model count data, in a Bayesian hierarchical setting. Considerable attention is paid to the inferential framework, necessary for structural consistent spatial econometric count models, incorporating spatial lag autocorrelation, to the corresponding estimation and testing procedures for different assumptions, to the constrains and implications embedded in the various specifications in the literature. This review combines insights from the classical spatial econometrics literature as well as from hierarchical modeling and analysis of spatial data, in order to look for new possible directions on the processing of count data, in a spatial hierarchical Bayesian econometric context.

Keywords: Spatial data analysis, spatial econometrics, Bayesian hierarchical models, count data.

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Authors: M. A. Hasan, M. R. Islam, R. A. Tarefder

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Currently, there are few user friendly Weigh-in- Motion (WIM) data analysis softwares available which can produce traffic input data for the recently developed AASHTOWare pavement Mechanistic-Empirical (ME) design software. However, these softwares have only rudimentary Quality Control (QC) processes. Therefore, they cannot properly deal with erroneous WIM data. As the pavement performance is highly sensible to the quality of WIM data, it is highly recommended to use more refined QC process on raw WIM data to get a good result. This study develops a userfriendly software, which can produce traffic input for the ME design software. This software takes the raw data (Class and Weight data) collected from the WIM station and processes it with a sophisticated QC procedure. Traffic data such as traffic volume, traffic distribution, axle load spectra, etc. can be obtained from this software; which can directly be used in the ME design software.

Keywords: Weigh-in-motion, software, axle load spectra, traffic distribution, AASHTOWare.

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Authors: Maria E. Manioudaki, Panayiota Poirazi

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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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Authors: Mohammad Shoyaib, M. Abdullah-Al-Wadud, Oksam Chae

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Proteomics is one of the largest areas of research for bioinformatics and medical science. An ambitious goal of proteomics is to elucidate the structure, interactions and functions of all proteins within cells and organisms. Predicting Protein-Protein Interaction (PPI) is one of the crucial and decisive problems in current research. Genomic data offer a great opportunity and at the same time a lot of challenges for the identification of these interactions. Many methods have already been proposed in this regard. In case of in-silico identification, most of the methods require both positive and negative examples of protein interaction and the perfection of these examples are very much crucial for the final prediction accuracy. Positive examples are relatively easy to obtain from well known databases. But the generation of negative examples is not a trivial task. Current PPI identification methods generate negative examples based on some assumptions, which are likely to affect their prediction accuracy. Hence, if more reliable negative examples are used, the PPI prediction methods may achieve even more accuracy. Focusing on this issue, a graph based negative example generation method is proposed, which is simple and more accurate than the existing approaches. An interaction graph of the protein sequences is created. The basic assumption is that the longer the shortest path between two protein-sequences in the interaction graph, the less is the possibility of their interaction. A well established PPI detection algorithm is employed with our negative examples and in most cases it increases the accuracy more than 10% in comparison with the negative pair selection method in that paper.

Keywords: Interaction graph, Negative training data, Protein-Protein interaction, Support vector machine.

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Authors: Sannikumar Patel, Brian Nolan, Markus Hofmann, Philip Owende, Kunjan Patel

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Sentiment analysis and opinion mining have become emerging topics of research in recent years but most of the work is focused on data in the English language. A comprehensive research and analysis are essential which considers multiple languages, machine translation techniques, and different classifiers. This paper presents, a comparative analysis of different approaches for multilingual sentiment analysis. These approaches are divided into two parts: one using classification of text without language translation and second using the translation of testing data to a target language, such as English, before classification. The presented research and results are useful for understanding whether machine translation should be used for multilingual sentiment analysis or building language specific sentiment classification systems is a better approach. The effects of language translation techniques, features, and accuracy of various classifiers for multilingual sentiment analysis is also discussed in this study.

Keywords: Cross-language analysis, machine learning, machine translation, sentiment analysis.

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Authors: Karan Vishavjit, Aakash Lakra, Shafaq Khan

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The COVID-19 pandemic has pushed healthcare professionals to use big data analytics as a vital tool for tracking and evaluating the effects of contagious viruses. To effectively analyse huge datasets, efficient NoSQL databases are needed. The analysis of post-COVID-19 health and well-being outcomes and the evaluation of the effectiveness of government efforts during the pandemic is made possible by this research’s integration of several datasets, which cuts down on query processing time and creates predictive visual artifacts. We recommend applying sharding and indexing technologies to improve query effectiveness and scalability as the dataset expands. Effective data retrieval and analysis are made possible by spreading the datasets into a sharded database and doing indexing on individual shards. Analysis of connections between governmental activities, poverty levels, and post-pandemic wellbeing is the key goal. We want to evaluate the effectiveness of governmental initiatives to improve health and lower poverty levels. We will do this by utilising advanced data analysis and visualisations. The findings provide relevant data that support the advancement of UN sustainable objectives, future pandemic preparation, and evidence-based decision-making. This study shows how Big Data and NoSQL databases may be used to address problems with global health.

Keywords: COVID-19, big data, data analysis, indexing, NoSQL, sharding, scalability, poverty.

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Authors: Woong Hee Kim, Ilhwan Park

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Steganography is the art of hiding and transmitting data through apparently innocuous carriers in an effort to conceal the existence of the data. A lot of steganography algorithms have been proposed recently. Many of them use the digital image data as a carrier. In data hiding scheme of halftoning and coordinate projection, still image data is used as a carrier, and the data of carrier image are modified for data embedding. In this paper, we present three features for analysis of data hiding via halftoning and coordinate projection. Also, we present a classifier using the proposed three features.

Keywords: Steganography, steganalysis, digital halftoning, data hiding.

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Authors: Minsoo Lee, Yun-mi Kim, Yearn Jeong Kim, Yoon-kyung Lee, Hyejung Yoon

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Biological data has several characteristics that strongly differentiate it from typical business data. It is much more complex, usually large in size, and continuously changes. Until recently business data has been the main target for discovering trends, patterns or future expectations. However, with the recent rise in biotechnology, the powerful technology that was used for analyzing business data is now being applied to biological data. With the advanced technology at hand, the main trend in biological research is rapidly changing from structural DNA analysis to understanding cellular functions of the DNA sequences. DNA chips are now being used to perform experiments and DNA analysis processes are being used by researchers. Clustering is one of the important processes used for grouping together similar entities. There are many clustering algorithms such as hierarchical clustering, self-organizing maps, K-means clustering and so on. In this paper, we propose a clustering algorithm that imitates the ecosystem taking into account the features of biological data. We implemented the system using an Ant-Colony clustering algorithm. The system decides the number of clusters automatically. The system processes the input biological data, runs the Ant-Colony algorithm, draws the Topic Map, assigns clusters to the genes and displays the output. We tested the algorithm with a test data of 100 to1000 genes and 24 samples and show promising results for applying this algorithm to clustering DNA chip data.

Keywords: Ant colony system, biological data, clustering, DNA chip.

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Authors: Ana Cázares

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Aims for this study: first, to compare the expertise level in data analysis, communication and information technologies in undergraduate psychology students. Second, to verify the factor structure of E-ETICA (Escala de Experticia en Tecnologias de la Informacion, la Comunicacion y el Análisis or Data Analysis, Communication and Information'Expertise Scale) which had shown an excellent internal consistency (α= 0.92) as well as a simple factor structure. Three factors, Complex, Basic Information and Communications Technologies and E-Searching and Download Abilities, explains 63% of variance. In the present study, 260 students (119 juniors and 141 seniors) were asked to respond to ETICA (16 items Likert scale of five points 1: null domain to 5: total domain). The results show that both junior and senior students report having very similar expertise level; however, E-ETICA presents a different factor structure for juniors and four factors explained also 63% of variance: Information E-Searching, Download and Process; Data analysis; Organization; and Communication technologies.

Keywords: Data analysis, Information, Communications Technologies, Expertise'Levels.

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Authors: Sidi Yang, Haiyi Zhang

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Twitter is a microblogging platform, where millions of users daily share their attitudes, views, and opinions. Using a probabilistic Latent Dirichlet Allocation (LDA) topic model to discern the most popular topics in the Twitter data is an effective way to analyze a large set of tweets to find a set of topics in a computationally efficient manner. Sentiment analysis provides an effective method to show the emotions and sentiments found in each tweet and an efficient way to summarize the results in a manner that is clearly understood. The primary goal of this paper is to explore text mining, extract and analyze useful information from unstructured text using two approaches: LDA topic modelling and sentiment analysis by examining Twitter plain text data in English. These two methods allow people to dig data more effectively and efficiently. LDA topic model and sentiment analysis can also be applied to provide insight views in business and scientific fields.

Keywords: Text mining, Twitter, topic model, sentiment analysis.

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Authors: W. Katsarapong, W. Srisang, K. Jaroensutasinee, M. Jaroensutasinee

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National Biodiversity Database System (NBIDS) has been developed for collecting Thai biodiversity data. The goal of this project is to provide advanced tools for querying, analyzing, modeling, and visualizing patterns of species distribution for researchers and scientists. NBIDS data record two types of datasets: biodiversity data and environmental data. Biodiversity data are specie presence data and species status. The attributes of biodiversity data can be further classified into two groups: universal and projectspecific attributes. Universal attributes are attributes that are common to all of the records, e.g. X/Y coordinates, year, and collector name. Project-specific attributes are attributes that are unique to one or a few projects, e.g., flowering stage. Environmental data include atmospheric data, hydrology data, soil data, and land cover data collecting by using GLOBE protocols. We have developed webbased tools for data entry. Google Earth KML and ArcGIS were used as tools for map visualization. webMathematica was used for simple data visualization and also for advanced data analysis and visualization, e.g., spatial interpolation, and statistical analysis. NBIDS will be used by park rangers at Khao Nan National Park, and researchers.

Keywords: GLOBE protocol, Biodiversity, Database System, ArcGIS, Google Earth and webMathematica.

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Authors: M. Omer Faruk, A. M. A. M. Zonaed Siddiki, M. Fazal Karim, Md. Masuduzzaman, S. Chowdhury, Md. Shafiqul Islam, M. Alamgir Hossain

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The dog tapeworms Echinococcus granulosus develop hydatid cysts in various organs in human and domestic animals worldwide including Bangladesh. The aim of this study was to identify and characterize the genotype of E. granulosus isolated from cattle using 12S rRNA and Cytochrome oxidase 1 (COX 1) genes. A total of 43 hydatid cyst samples were collected from 390 examined cattle samples derived from slaughterhouses. Among them, three cysts were fertile. Genomic DNA was extracted from germinal membrane and/or protoscoleces followed by PCR amplification of mitochondrial 12S rRNA and Cytochrome oxidase 1 gene fragments. The sequence data revealed existence of G1 (64.28%) and possible G3 (21.43%) genotypes for the first time in Bangladesh. The study indicates that common sheep strain G1 is the dominant subtype of E. granulosus in Chittagong region of Bangladesh. This will increase our understanding of the epidemiology of hydatidosis in the southern part of the country and will be useful to plan suitable control measures in the long run.

Keywords: Echinococcus granulosus, molecular characterization, cattle, Bangladesh.

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Authors: Takahiro Nishigaki, Takashi Onoda

Abstract:

In recent years, the number of document data has been increasing since the spread of the Internet. Many methods have been studied for extracting topics from large document data. We proposed Independent Topic Analysis (ITA) to extract topics independent of each other from large document data such as newspaper data. ITA is a method for extracting the independent topics from the document data by using the Independent Component Analysis. The topic represented by ITA is represented by a set of words. However, the set of words is quite different from the topics the user imagines. For example, the top five words with high independence of a topic are as follows. Topic1 = {"scor", "game", "lead", "quarter", "rebound"}. This Topic 1 is considered to represent the topic of "SPORTS". This topic name "SPORTS" has to be attached by the user. ITA cannot name topics. Therefore, in this research, we propose a method to obtain topics easy for people to understand by using the web search engine, topics given by the set of words given by independent topic analysis. In particular, we search a set of topical words, and the title of the homepage of the search result is taken as the topic name. And we also use the proposed method for some data and verify its effectiveness.

Keywords: Independent topic analysis, topic extraction, topic naming, web search engine.

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