• 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.

• The Journal of Korean Orthopaedic Ultrasound Society
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• v.4 no.1
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• pp.1-6
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• 2011

Purpose: To evaluate the usefulness of ultrasonography in diagnosis of the medial meniscus tear as a screening tool before performing magnetic resonance imaging. Materials and Methods: From April 2009 to September 2010, magnetic resonance imaging (MRI) was taken in 147 knees out of 341 knees examined with ultrasonography (US) under the suspicion of medial meniscus tear. The sonographic findings were 16 without abnormality, 12 inhomogeneity, 4 cluster, 60 cleavage and 55 more than 5mm medial extrusion of medial meniscus. In Statistical analysis, sensitivity and specificity, positive predictive value and negative predictive values were calculated. Results: The MRI showed abnormality in 104 knees. Sensitivity and specificity of ultrasonography for MRI was 94.2% and 23.3%, respectively. Positive predictive value was 74.8%, negative predictive value was 62.5%. The positive predictive value of ultrasonography were 58.3% in heterogeneity, 100% in showing cluster, 75% in visible cleft and 80% in medial extrusion. Conclusion: The US is a useful tool in prediction of medial meniscus tear before confirming it in high-cost MRI.

• Proceedings of the Korean Vacuum Society Conference
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• 2012.02a
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• pp.96-97
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• 2012

In nitride and oxide film deposition, sputtered metals react with nitrogen or oxygen gas in a vacuum chamber to form metal nitride or oxide films on a substrate. The physical properties of sputtered films (metals, oxides, and nitrides) are strongly influenced by magnetron plasma density during the deposition process. Typical target power densities on the magnetron during the deposition process are ~ (5-30) W/cm2, which gives a relatively low plasma density. The main challenge in reactive sputtering is the ability to generate a stable, arc free discharge at high plasma densities. Arcs occur due to formation of an insulating layer on the target surface caused by the re-deposition effect. One current method of generating an arc free discharge is to use the commercially available Pinnacle Plus+ Pulsed DC plasma generator manufactured by Advanced Energy Inc. This plasma generator uses a positive voltage pulse between negative pulses to attract electrons and discharge the target surface, thus preventing arc formation. However, this method can only generate low density plasma and therefore cannot allow full control of film properties. Also, after long runs ~ (1-3) hours, depends on duty cycle the stability of the reactive process is reduced due to increased probability of arc formation. Between 1995 and 1999, a new way of magnetron sputtering called HIPIMS (highly ionized pulse impulse magnetron sputtering) was developed. The main idea of this approach is to apply short ${\sim}(50-100){\mu}s$ high power pulses with a target power densities during the pulse between ~ (1-3) kW/cm2. These high power pulses generate high-density magnetron plasma that can significantly improve and control film properties. From the beginning, HIPIMS method has been applied to reactive sputtering processes for deposition of conductive and nonconductive films. However, commercially available HIPIMS plasma generators have not been able to create a stable, arc-free discharge in most reactive magnetron sputtering processes. HIPIMS plasma generators have been successfully used in reactive sputtering of nitrides for hard coating applications and for Al2O3 films. But until now there has been no HIPIMS data presented on reactive sputtering in cluster tools for semiconductors and MEMs applications. In this presentation, a new method of generating an arc free discharge for reactive HIPIMS using the new Cyprium plasma generator from Zpulser LLC will be introduced. Data (or evidence) will be presented showing that arc formation in reactive HIPIMS can be controlled without applying a positive voltage pulse between high power pulses. Arc-free reactive HIPIMS processes for sputtering AlN, TiO2, TiN and Si3N4 on the Applied Materials ENDURA 200 mm cluster tool will be presented. A direct comparison of the properties of films sputtered with the Advanced Energy Pinnacle Plus + plasma generator and the Zpulser Cyprium plasma generator will be presented.

• The Korean Journal of Mycology
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• v.27 no.2 s.89
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• pp.124-131
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• 1999

This study was carried out to identify the phylogenetic relationship among Phellinus species by comparing the DNA sequences of the 5.8S ribosomal DNA (rDNA) and the internal transcribed spacers (ITSs), ITS1 and ITS2 regions. Two primers from the 3' end of 18S rDNA and the 5' end of 28S rDNA sequences were chosen to amplify the specific ITS regions of Phellinus spp. Phellinus strains used in the study were divided into four clusters by the phylogenetic tree based on the amplified regions of ITS and 5.8S rDNA sequences. The first cluster consist of Phellinus hartigii IMSNU 32041 and Phellinus robustus IMSNU 32068, and the second cluster consists of Phellinus linteus strains and Phellinus weirianus IMSNU 32021. Phellinus laevigatus KCTC 6229, KCTC 6230 and Phellinus igniarius KCTC 6227, KCTC 6228 belong to the third cluster. Finally, Phellinus chrysoloma KCTC 6225 and Phellinus chrysoloma KCTC 6226 are the fourth cluster. In the second cluster the differentiation between Phellinus linteus strains and Phellinus weirianus species were not possible by the comparison of the ITS sequences. These results revealed that Phellinus linteus and Phellinus weirianus cannot be established the concept of species level only by the ITS sequences. Therefore, both physiological and molecular biological methods as well as the sequences of type strains are necessary to classify the strains of these two species accurately. The comparison of the ITS sequences of four Phellinus species indicated that the sequences of the ITS1 generally are more divergent than those of the ITS2. Although the ITS sequences are varied in some species, the conserved regions in both ITS1 and ITS2 are useful tool to differentiate the species. Phellinus linteus and related species have their specific sequences in the ITS1 compared to the other species.

• Journal of the Korean Home Economics Association
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• v.43 no.5 s.207
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• pp.93-105
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• 2005

This study focused on the development of scales measuring the characteristics related to appearance management behaviors of businessmen for on-line image consulting. The purposes of this study were, 1) to develop a tool which can measure the ideal image, 2) to develop a tool which can measure personality, and 3) to develop a scale measuring the physical characteristics and body cathexis. The data were collected from 380 businessmen in Seoul, Korea and were analyzed by frequency, factor analysis, reliability test, cluster analysis, correlation analysis, one-wav ANOVA and Duncan test. The results from this study were as follows .1)Five factors of the ideal image were identified: stylish, able, active, neat/confident and easy. The total variance was 74.29$\%$ and Cronbach's alpha of the 5 factors ranged from .74-.90. One item was selected to represent each factor. 2) Five factors of personality were identified: preference of social function, sociable, dynamic, achievement-motivated, and success-oriented. The totai variance was 60.63$\%$ and Cronbach's alpha ranged from .56-.83. One item was selected to represent each factor. 3) Five factors of body cathexis were identified: satisfaction with girth, length, physique, nose and eyes. The total variance was 73_46$\%$ and Cronbach's alpha ranged from .68-.85.

• Tuberculosis and Respiratory Diseases
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• v.60 no.3
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• pp.290-296
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• 2006

Background : IS6110 DNA fingerprint is a very useful tool for investigating the transmission of tuberculosis. The aim of this study was to identify the epidemiological situations within a given area (one province). Methods : The 681 Mycbobacterium tuberculosis isolates from patients, who were registered at health centers in Gyeonggi Province from May to December in 2004, were subjected to IS6110 DNA fingerprinting. Patients belonging to clusters were interviewed by health-workers to determine their previous contacts or household TB history. Results : The number of IS6110 copies of the 681 isolates showed diverse fingerprint patterns from 0 to 21 of which the most prevalent copy number was 10 from 120 isolates (17.6%). Thirty-three isolates (4.8%) belonged to the K strain, and 128 isolates (18.8%) belonged to the K family. There were 180 (26.4%) isolates belonged belonging to fifty clusters, of which two clusters were within household transmission. Forty-three (23.9%) out of 180 patients resided in an area under the same health center control. The rate of clusters in those aged 60-70 was higher than in any other age group ( 95% CI of RR : 1.072 ~ 1.988). Conclusion : This is the first report of an epidemiological survey based on a whole province using a DNA fingerprinting technique for M. tuberculosis. These results will be helpful in developing a program or policies to prevent the transmission of TB.

• Health Policy and Management
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• v.3 no.2
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• pp.100-129
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• 1993

This study is designed to find out some intra-clinic factors affecting the content of practice provided by primary care physicians in Korea, and proposed factors in this study are characteristcs of each private clinc --- physician-related variables(age, sex, specialty), bfed-related variables for inpatient care, laboratory-related variables for precise diagnosis. We have tried to estimate the difference of disease entities cared by each primary care physician according to above factors by analyzin gdisease data claimed during one month(April, 1992) to National Federation of Medical Insurance. The diagnosis codes by ICD-9 in the research disease data were reclassified to 'diagnosis clusters' by virtue of clinical similarities for effective analyses. We have converted frequent-tsing ICD-9 codes to 86 diagnosis clusters, which incorporated 97.4 percents of all ambulatory visits to private clinics. This result means proposed diagnosis-cluster method is effective tool for analysis of the content of ambulatory medical care carried out by primary care physicians. Comparisons and analyses of multiple diagnosis-clusters made on the basis of presented factors were done and the results were as follows; - Major factors affecting the difference between diagnosis-cluster pattern by each variables were phyusician's age, sex, specialty and bed counts of each private clinic for inpatient care and the size of laboratories of each clinic. - Middle aged(30th to 40th) group physicians are providing more comprehensive care than 20th or above 50th aged groups. Male physicians are more adequate for comprehensive care than female physicians, because woman-doctors are providing narrow-spectrum care. The content of practice of obstetricians and gynecologists shows much difference from primary medical practice, and they cannot be included in primary care physician, this study suggested. Pediatricians are also providing short-spectum acre, and nearly all visits to pediatricians were incorporated only 2-3 diagnosis-clusters. General surgeons' practices are very similar to general practioners' or family physicians' practices, the means they are providing primary care rather than special surgical care. And small number of beds(under 5 beds) and only basic(2-3 sorts of)diagnostic apparatuses are sufficient for primary physicians' clinic to carry out primary care. In conclusion, to reinforce primary care department in Korea, there must be support with health policy to expand office-based primary care practice-- with small number of beds for inpatient care and only basic laboratories-- provided by general practitioner of family physician.

• Journal of the Korean earth science society
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• v.28 no.1
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• pp.87-104
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• 2007

As part of the SPVS (Short-Period Variability Survey) which is a wide-field $(90'{\times}60')$ photometric monitering program at Bohyunsan Optical Astronomy (BOAO), we performed V band time-series CCD photometric observations ofthe young open cluster NGC 129 for 11 nights between October 12, 2004 and November 3, 2005 using the 155mm refractor equipped with $3K{\times}2K$ CCD camera. From the observation we obtained 2400 V band CCD frames and color-magnitude diagram of the cluster. To transform instrumental magnitude to standard magnitude, we applied ensemble normalization technique to all observed time-series data. After the photometric reduction process, we examined variations of 9537 stars. As a result, sixty six of the new variable stars were discovered. To determine the periods of the sevariables, we used DFT(Discrete Fourier Transform) and phase-matching technique. According to light curve shape, period, amplitude and the position on a C-M diagram, we classified these variables as 9 SPB type, 9 ${\delta}$ Scuti type, 29 eclipsing, 17 long term variables. However, two of them were not classified. From this study, we learned that small telescopes could be a very useful tool to observe variable stars in the open cluster in survey program.

• Journal of KIISE
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• v.43 no.10
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• pp.1115-1123
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• 2016

Assumption-based truth maintenance system (ATMS) is a tool that maintains the reasoning process of inference engine. It also supports non-monotonic reasoning based on dependency-directed backtracking. Bookkeeping all the reasoning processes allows it to quickly check and retract beliefs and efficiently provide solutions for problems with large search space. However, the amount of data has been exponentially grown recently, making it impossible to use a single machine for solving large-scale problems. The maintaining process for solving such problems can lead to high computation cost due to large memory overhead. To overcome this drawback, this paper presents an approach towards incrementally maintaining the reasoning process of inference engine on cluster using Spark. It maintains data dependencies such as assumption, label, environment and justification on a cluster of machines in parallel and efficiently updates changes in a large amount of inferred datasets. We deployed the proposed ATMS on a cluster with 5 machines, conducted OWL/RDFS reasoning over University benchmark data (LUBM) and evaluated our system in terms of its performance and functionalities such as assertion, explanation and retraction. In our experiments, the proposed system performed the operations in a reasonably short period of time for over 80GB inferred LUBM2000 dataset.

• Microbiology and Biotechnology Letters
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• v.41 no.1
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• pp.96-104
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• 2013

Staphylococcus aureus is a major human pathogen that produces a wide array of toxins, leading to a number of adverse symptoms. We examined 275 strains of Staphylococcus aureus isolated from various foods between 2006 and 2008 for antimicrobial susceptibility. At least 259 (94.2%) of the tested strains showed antibiotic resistant properties, and 106 (40.7%) of them showed multiple antibiotic resistance. Eleven of the tested strains were resistant to oxacillin and mec A-positive. Moreover, oxacillin-resistant strains were significantly more likely to be multi-drug resistant (p < 0.01). Of the 275 isolates tested, 24.4% were noted as being positive for slime production and 30.5% were positive for biofilm assay. Antibiotic resistance was not associated with a significantly higher prevalence of biofilm formation. Twenty strains were classified using the DiversiLab system. Most of the strains could be classified into 2 clusters and 4 unique types. All 10 mec A-positive strains (cluster I) were grouped together into the same sub-cluster. Cluster II (6 strains) was not found to be resistant to oxacillin in this study. Although the prevalence of methicillin-resistant S. aureus in food is currently low, the risk of its transmission through the food chain cannot be disregarded.