• Genomics & Informatics
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• v.5 no.1
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• pp.10-18
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• 2007

Numerous studies have reported that genes with similar expression patterns are co-regulated. From gene expression data, we have assumed that genes having similar expression pattern would share similar transcription factor binding sites (TFBSs). These function as the binding regions for transcription factors (TFs) and thereby regulate gene expression. In this context, various analysis tools have been developed. However, they have shortcomings in the combined analysis of expression patterns and significant TFBSs and in the functional analysis of target genes of significantly overrepresented putative regulators. In this study, we present a web-based A Functional Clustering Analysis Tool for Predicted Transcription Regulatory Elements and Gene Ontology Terms (FCAnalyzer). This system integrates microarray clustering data with similar expression patterns, and TFBS data in each cluster. FCAnalyzer is designed to perform two independent clustering procedures. The first process clusters gene expression profiles using the K-means clustering method, and the second process clusters predicted TFBSs in the upstream region of previously clustered genes using the hierarchical biclustering method for simultaneous grouping of genes and samples. This system offers retrieved information for predicted TFBSs in each cluster using $Match^{TM}$ in the TRANSFAC database. We used gene ontology term analysis for functional annotation of genes in the same cluster. We also provide the user with a combinatorial TFBS analysis of TFBS pairs. The enrichment of TFBS analysis and GO term analysis is statistically by the calculation of P values based on Fisher’s exact test, hypergeometric distribution and Bonferroni correction. FCAnalyzer is a web-based, user-friendly functional clustering analysis system that facilitates the transcriptional regulatory analysis of co-expressed genes. This system presents the analyses of clustered genes, significant TFBSs, significantly enriched TFBS combinations, their target genes and TFBS-TF pairs.

• Journal of the Institute of Electronics Engineers of Korea TC
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• v.46 no.4
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• pp.95-103
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• 2009

In this paper, a generation method of transmit and receive beamforming vectors based on base station cooperation is proposed which maximizes the user SINR in mobile cellular multi-user MIMO systems. There are two main sources of interference which deteriorate the performance of the system, i.e. the inter-user interference caused by the usage of the same radio resource for multiple users in the system, and the inter-cluster interference from neighboring base stations which are not participating in cooperative transmission. The proposed scheme cancels out the inter-user interference by using the block diagonalization(BD) method, and mitigate the inter-cluster interference by using optimal transmit and receive beamforming vectors based on optimal combining(OC) with the statistic information of inter-cluster interference. We perform computer simulations to verify the performance of the proposed scheme, and compare the result to the conventional performance obtained from utilizing the receiver side information only or utilizing the information from neither sides. The performance evaluations are conducted not only over the independent MIMO channels, but over correlated MIMO channels to demonstrate the robustness of the proposed scheme over the channels with correlation among antennas.

• Allergy, Asthma & Immunology Research
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• v.10 no.6
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• pp.614-627
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• 2018

Purpose: Asthma is a heterogeneous disease that responds to medications to varying degrees. Cluster analyses have identified several phenotypes and variables related to fixed airway obstruction; however, few longitudinal studies of lung function have been performed on adult asthmatics. We investigated clinical, demographic, and inflammatory factors related to persistent airflow limitation based on lung function trajectories over 1 year. Methods: Serial post-bronchodilator forced expiratory volume (FEV) 1% values were obtained from 1,679 asthmatics who were followed up every 3 months for 1 year. First, a hierarchical cluster analysis was performed using Ward's method to generate a dendrogram for the optimum number of clusters using the complete post-FEV1 sets from 448 subjects. Then, a trajectory cluster analysis of serial post-FEV1 sets was performed using the k-means clustering for the longitudinal data trajectory method. Next, trajectory clustering for the serial post-FEV1 sets of a total of 1,679 asthmatics was performed after imputation of missing post-FEV1 values using regression methods. Results: Trajectories 1 and 2 were associated with normal lung function during the study period, and trajectory 3 was associated with a reversal to normal of the moderately decreased baseline FEV1 within 3 months. Trajectories 4 and 5 were associated with severe asthma with a marked reduction in baseline FEV1. However, the FEV1 associated with trajectory 4 was increased at 3 months, whereas the FEV1 associated with trajectory 5 was persistently disturbed over 1 year. Compared with trajectory 4, trajectory 5 was associated with older asthmatics with less atopy, a lower immunoglobulin E (IgE) level, sputum neutrophilia and higher dosages of oral steroids. In contrast, trajectory 4 was associated with higher sputum and blood eosinophil counts and more frequent exacerbations. Conclusions: Trajectory clustering analysis of FEV1 identified 5 distinct types, representing well-preserved to severely decreased FEV1. Persistent airflow obstruction may be related to non-atopy, a low IgE level, and older age accompanied by neutrophilic inflammation and low baseline FEV1 levels.

• Journal of the Korean Society of Earth Science Education
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• v.15 no.2
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• pp.285-298
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• 2022

This study is to investigate the effects and characteristics of science and engineering integrated lessons on elementary students' creative engineering problem solving propensity (CEPSP). The science and engineering integrated lessons used in this study was a 10 lesson-hours STEM program, co-developed by University of Minnesota and Purdue University. The program was implemented in the 6th grade science class of H Elementary School located in P Metropolitan city. The main data of this study are the pre-post CEPSP result and interview with 5 students collected before and after the research. The CEPSP result was analyzed by a paired-sample t-test and hierarchical cluster analysis. As a result of the t-test, it was found that overall, the program has a positive effect on the students' CEPSP score. As a result of cluster analysis, it was confirmed that studnets' CEPSP could be classified into two groups (lower and higher score cluster). Five students whose, CEPSP score has significantly improved after the lessons were interviewed to find out what the characteristics of the program that contribute the significant change are. As a result of conducting centroid analysis of the interview transcription and the hybrid analysis method, it was found that the meaningful experiences that the five students commonly shared were 'problem solving through collaboration' and 'through repeated experiments (redesign)', problem solving' and 'utilization of scientific knowledge'. As minor reactions, 'choice of the best experimental method' and 'difference between science and engineering' appeared.

• Journal of the Korean Crystal Growth and Crystal Technology
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• v.33 no.2
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• pp.45-53
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• 2023

The growth of Si on 4H-SiC substrate has a wide range of applications as a very useful material in power semiconductors, bipolar junction transistors and optoelectronics. However, it is considerably difficult to grow very fine crystalline Si on 4H-SiC owing to the lattice mismatch of approximately 20 % between Si and 4H-SiC. In this paper, we report the growth of a Si epilayer by an Al-related nanostructure cluster grown on a 4H-SiC substrate using a mixed-source hydride vapor phase epitaxy (HVPE) method. In order to grow hexagonal Si on the 4H-SIC substrate, we observed the process in which an Al-related nanostructure cluster was first formed and an epitaxial layer was formed by absorbing Si atoms. From the FE-SEM and Raman spectrum results of the Al-related nanostructure cluster and the hexagonal Si epitaxial layer, it was considered that the hexagonal Si epitaxial layer had different characteristics from the general cubic Si structure.

• Journal of Korea Multimedia Society
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• v.20 no.6
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• pp.845-852
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• 2017

In this paper, we propose a binarization algorithm using LVQ-Merge clustering method for fast and accurate extraction of cells from cell images. The proposed method clusters pixel data of a given image by using LVQ to remove noise and divides the result into two clusters by applying a hierarchical clustering algorithm to improve the accuracy of binarization. As a result, the execution speed is somewhat slower than that of the conventional LVQ or Otsu algorithm. However, the results of the binarization have very good quality and are almost identical to those judged by the human eye. Especially, the bigger and the more complex the image, the better the binarization quality. This suggests that the proposed method is a useful method for medical image processing field where high-resolution and huge medical images must be processed in real time. In addition, this method is possible to have many clusters instead of two cluster, so it can be used as a method to complement a hierarchical clustering algorithm.

• Spatial Information Research
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• v.13 no.4 s.35
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• pp.355-364
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• 2005

Vector data sets (e.g. maps) are currently major sources of displaying, querying, and identifying locations of spatial features in a variety of applications. Especially in mobile environment, the needs for using spatial data is increasing, and the relative large size of vector maps need to be smaller. Recently, there have been several studies about vector map compression. There was clustering-based compression method with novel encoding/decoding scheme. However, precedent studies did not consider that spatial data have to be updated periodically. This paper explores the problem of existing clustering-based compression method. We propose an adaptive approximation method that is capable of handling data updates as well as reducing error levels. Experimental evaluation showed that when an updated event occurred the proposed adaptive approximation method showed enhanced positional accuracy compared with simple cluster based compression method.

• KIPS Transactions on Software and Data Engineering
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• v.3 no.6
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• pp.215-218
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• 2014

In hashing-based methods for approximate nearest neighbors(ANN) search, by mapping data points to k-bit binary codes, nearest neighbors are searched in a binary embedding space. In this paper, we present a hashing method using a PCA-based clustering method, Principal Direction Divisive Partitioning(PDDP). PDDP is a clustering method which repeatedly partitions the cluster with the largest variance into two clusters by using the first principal direction. The proposed hashing method utilizes the first principal direction as a projective direction for binary coding. Experimental results demonstrate that the proposed method is competitive compared with other hashing methods.

• Journal of Technology Innovation
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• v.10 no.1
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• pp.22-37
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• 2002

The importance of selecting the strategic research field is increasingly emphasized by research manager and technology policy-maker in perspective of the strategic allocation of R&D resources, employing the R&D personnel, and formulating technology policy. Among various methods for selecting the strategic research field, it is, however, very difficult to find the method that involves the path-dependant trend, and interdisciplinary nature of technology development. This study suggests modified technology cluster analysis (TCA) as a method for selecting strategic research field in order to include the recent technology trend in quantitative approach. TCA is the method that groups the near technologies of which the innovation pattern is similar. TCA model can be a very necessary method for multidisciplinary government research institutes (GRIs) which conduct multi research field with forward oriented positioning. It is more difficult for them to select the strategic research field mainly due to their diversity and intangibility of research scope. In this study, we applied this method to Korea Institute of Science and Technology (KIST) which represents the most adequate research institute in terms of research diversity and forwardness. As a result of the application, we found that seven main technology groups come from TCA analysis, coincide with the technology topics of KIST's recent R&D planning. Even though this method designed for multidisciplinary research institutes, but it also can be used for establishing the research strategy of other (private or public) Research Institute which have the similar mission and scope of research.

• Journal of Yeungnam Medical Science
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• v.12 no.2
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• pp.366-385
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• 1995

Epidemiological studies are important in both the prevention and treatment of mycobacterial infections. This study was initiated to establish the pulsed-field gel electrophoresis (PFGE) method, which are not yet extensively studied. The most apprpriate restriction endonucleases included DraI, AsnI, and XbaI. The optimal PFGE condition was different according to the enzymes used. Two stage PFGE was performed, in case of DraI first stage was performed with 10 seconds of initial pulse and 15 seconds of final pulse, while the second stage was performed with 60 seconds of initial pulse and 70 seconds of final pulse. The electrophoresis time for DraI-PFGE was 14 hours for each stage. Electrophoresis was performed for 22 hours, in case of XbaI, with 3 seconds of initial pulse and 12 seconds of final pulse. Electrophoresis was performed for 22 hours, in case of AsnI, with 5 seconds of initial pulse and 25 seconds of final pulse. In all cases the voltage of the electrophoresis was maintained constantly at 200 voltage. Standard mycobacterial strains, which included Mycobacterium bovis BCG, M. tuberculosis, and M. fortuitum, could not be differentiated by PFGE analysis. PFGE analysis was performed to differentiate 9 clinically isolated M. fortuitum strains using AsnI. All M. fortuitum strains showed different genotypes except 2 strains. Cluster analysis divided M. fortuitum strains into 2 large groups. PFGE analysis was performed to further differentiate M. fortuitum isolates using XbaI. The undifferentiated 2 M. fortuitum strains showed different PFGE patterns with Xba I. Cluster analysis of the XbaI-PFGE patterns showed more complex grouping than AsnI-PFGE patterns, which showed that XbaI-PFGE analysis was better than AsnI-PFGE in M. fortuitum genotyping. The top dissimilarity values of AsnI-PFGE and XbaI-PFGE were 0.74 and 0.75, respectively. This value was higher than that of arbitrarily primed polymerase chain reaction (AP-PCR) analysis and lower than that of restriction fragment length polymorphism (RFLP) analysis. This suggested that PFGE can be used as a supportive or alternative genotyping method to RFLP analysis.