• Genomics & Informatics
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• v.19 no.1
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• pp.4.1-4.9
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• 2021

Lip and oral cavity cancer, which can occur in any part of the mouth, is the 11th most common type of cancer worldwide. The major obstacles to patients' survival are the poor prognosis, lack of specific biomarkers, and expensive therapeutic alternatives. This study aimed to identify the main genes and pathways associated with lip and oral cavity carcinoma using network analysis and to analyze its molecular mechanism and prognostic significance further. In this study, 472 genes causing lip and oral cavity carcinoma were retrieved from the DisGeNET database. A protein-protein interaction network was developed for network analysis using the STRING database. VEGFA, IL6, MAPK3, INS, TNF, MAPK8, MMP9, CXCL8, EGF, and PTGS2 were recognized as network hub genes using the maximum clique centrality algorithm available in cytoHubba, and nine potential drug candidates (ranibizumab, siltuximab, sulindac, pomalidomide, dexrazoxane, endostatin, pamidronic acid, cetuximab, and apricoxib) for lip and oral cavity cancer were identified from the DGIdb database. Gene enrichment analysis was also performed to identify the gene ontology categorization of cellular components, biological processes, molecular functions, and biological pathways. The genes identified in this study could furnish a new understanding of the underlying molecular mechanisms of carcinogenesis and provide more reliable biomarkers for early diagnosis, prognostication, and treatment of lip and oral cavity cancer.

• Genomics & Informatics
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• v.19 no.4
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• pp.43.1-43.12
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• 2021

Campylobacter jejuni is one of the most prevalent organisms associated with foodborne illness across the globe causing campylobacteriosis and gastritis. Many proteins of C. jejuni are still unidentified. The purpose of this study was to determine the structure and function of a non-annotated hypothetical protein (HP) from C. jejuni. A number of properties like physiochemical characteristics, 3D structure, and functional annotation of the HP (accession No. CAG2129885.1) were predicted using various bioinformatics tools followed by further validation and quality assessment. Moreover, the protein-protein interactions and active site were obtained from the STRING and CASTp server, respectively. The hypothesized protein possesses various characteristics including an acidic pH, thermal stability, water solubility, and cytoplasmic distribution. While alpha-helix and random coil structures are the most prominent structural components of this protein, most of it is formed of helices and coils. Along with expected quality, the 3D model has been found to be novel. This study has identified the potential role of the HP in 2-methylcitric acid cycle and propionate catabolism. Furthermore, protein-protein interactions revealed several significant functional partners. The in-silico characterization of this protein will assist to understand its molecular mechanism of action better. The methodology of this study would also serve as the basis for additional research into proteomic and genomic data for functional potential identification.

• The Journal of Korean Medicine
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• v.45 no.1
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• pp.114-125
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• 2024

Objectives: Network pharmacology is an analysis method that explores drug-centered efficacy and mechanism by constructing a compound-target-disease network based on system biology, and is attracting attention as a methodology for studying herbal medicine that has the characteristics for multi-compound therapeutics. Thus, we investigated the potential functions and pathways of Myrrha on Allergic Rhinitis (AR) via network pharmacology analysis and molecular docking. Methods: Using public databases and PubChem database, compounds of Myrrha and their target genes were collected. The putative target genes of Myrrha and known target genes of AR were compared and found the correlation. Then, the network was constructed using STRING database, and functional enrichment analysis was conducted based on the Gene Ontology (GO) Biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways. Binding-Docking stimulation was performed using CB-Dock. Results: The result showed that total 3 compounds and 55 related genes were gathered from Myrrha. 33 genes were interacted with AR gene set, suggesting that the effects of Myrrha are closely related to AR. Target genes of Myrrha are considerably associated with various pathways including 'Fc epsilon RI signaling pathway' and 'JAK-STAT signaling pathway'. As a result of blinding docking, AKT1, which is involved in both mechanisms, had high binding energies for abietic acid and dehydroabietic acid, which are components of Myrrha. Conclusion: Through a network pharmacological method, Myrrha was predicted to have high relevance with AR by regulating AKT1. This study could be used as a basis for studying therapeutic effects of Myrrha on AR.

• Journal of Physiology & Pathology in Korean Medicine
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• v.25 no.6
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• pp.945-960
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• 2011

The BianMaiFa chapter, which is the first chapter of SongBon ShangHanLun, is the scholarly description(專論) of the pulse and pathological mechanism but has not been studied and published yet. This study is about article 1-10 which is the first part of The BianMaiFa chapter. We compared the original texts within the editions, comparing and analyzing the annotations of successive dynastic medical group. The articles of The SongBon ShangHanLun BianMaiFa chapter 1-10 is consisted as is shown: article 1 discriminates pulse by yin-yang and states about the prognosis of disease according to pulse, article 2 states about binding in yin and binding in yang which is from abnormal exuberance of yin and yang, article 3 states about the pulse and pathological mechanism of chills with fever, article 4 states about pathological mechanism and symptom of nutrient and defense through pulse, article 5 distinguishes within binding in yang(陽結), binding in yin(陰結), yang faintness(陽微), yang debilitation(陽衰), blood collapse(亡血) by the pulse which was in article 2 3 4, article 6 7 8 9 10 states states about the shape or pathological mechanism of bound pulse(結脈) skipping pulse(促脈) stirred pulse(動脈) moderate pulse(緩脈) string-like pulse(弦脈) tight pulse(緊脈) drumskin pulse(革脈). Article 4 could be understood that inch pulse is floating and deficient shape and cubit pulse is sunken and weak shape(寸脈浮虛, 尺脈沈弱) related to article 3, article 5 could be understood as binding in yin and yang is aggregation shape related to article 2, yang-qi faintness is floating and debilitation shape, yang-qi debilitation is sunken and faint shape, blood collapse is deficient and stasis shape related to article 3 4.

• Journal of KIISE:Computer Systems and Theory
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• v.32 no.1
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• pp.9-20
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• 2005

Recently, the MPEG-7 standard a multimedia content description standard is wide]y used for content based image/video retrieval systems. However, since the descriptors standardized in MPEG-7 are usually multidimensional and the problem called 'Curse of dimensionality', previously proposed indexing methods(for example, multidimensional indexing methods, dimensionality reduction methods, filtering methods, and so on) could not be used to effectively index the multimedia database represented in MPEG-7. This paper proposes an efficient multimedia data indexing mechanism reflecting the characteristics of MPEG-7 visual descriptors. In the proposed indexing mechanism, the descriptor is transformed into a histogram of some attributes. By representing the value of each bin as a binary number, the histogram itself that is a visual descriptor for the object in multimedia database could be represented as a bit string. Bit strings for all objects in multimedia database are collected to form an index file, bitmap index, in the proposed indexing mechanism. By XORing them with the descriptors for query object, the candidate solutions for similarity search could be computed easily and they are checked again with query object to precisely compute the similarity with exact metric such as Ll-norm. These indexing and searching mechanisms are efficient because the filtering process is performed by simple bit-operation and it reduces the search space dramatically. Upon experimental results with more than 100,000 real images, the proposed indexing and searching mechanisms are about IS times faster than the sequential searching with more than 90% accuracy.

• Journal of KIISE:Databases
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• v.32 no.4
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• pp.383-393
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• 2005

Retrieval of images from image databases by spatial relationship can be effectively performed through visual interface systems. In these systems, the representation of image with 2D strings, which are derived from symbolic projections, provides an efficient and natural way to construct image index and is also an ideal representation for the visual query. With this approach, retrieval is reduced to matching two symbolic strings. However, using 2D-string representations, spatial relationships between the objects in the image might not be exactly specified. Ambiguities arise for the retrieval of images of 3D scenes. In order to remove ambiguous description of object spatial relationships, in this paper, images are referred by considering spatial relationships using the spatial location algebra for the 3D image scene. Also, we remove the repetitive spatial relationships using the several reduction rules. A reduction mechanism using these rules can be used in query processing systems that retrieve images by content. This could give better precision and flexibility in image retrieval.

• The KIPS Transactions:PartB
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• v.11B no.4
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• pp.509-516
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• 2004

Semantic interpretation of image is incomplete without some mechanism for understanding semantic content that is not directly visible. For this reason, human assisted content-annotation through natural language is an attachment of textual description to image. However, keyword-based retrieval is in the level of syntactic pattern matching. In other words, dissimilarity computation among terms is usually done by using string matching not concept matching. In this paper, we propose a method for computerized semantic similarity calculation In WordNet space. We consider the edge, depth, link type and density as well as existence of common ancestors. Also, we have introduced method that applied similarity measurement on semantic image retrieval. To combine wi#h the low level features, we use the spatial color distribution model. When tested on a image set of Microsoft's 'Design Gallery Line', proposed method outperforms other approach.

• Wind and Structures
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• v.23 no.6
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• pp.615-639
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• 2016

Although the underlying mechanism of rain-wind induced vibrations (RWIVs) of stay cables has not been fully understood, some countermeasures have been successfully applied to mitigating this kind of vibration. Among these, installing dampers near the bridge deck was widely adopted, and several field observations have shown its effectiveness. In this study, the effectiveness of dampers to RWIVs of stay cables is numerically investigated comprehensively by means of finite difference method (FDM). Based on the free vibration analysis of a taut string, it is found that the 3-points triangle scheme, which can be easily implemented in FDM, can offer an excellent approximation of the concentrated damping coefficient (expressed as a Dirac delta function) at the location where the damper is installed. Then, free vibration analysis of a 3-D continuous stay cable attached with two dampers is carried out to study the relationship of modal damping ratio and damping coefficient of the dampers. The effects of orientation of the dampers and cable sag on the modal damping ratio are investigated in detail. Finally, the RWIV response of a 3-D continuous stay cable attached with two dampers is examined. The results indicate that 0.5% of damping ratio is sufficient to reduce the RWIV vibration of the Cable A20 on the No.2 Nanjing Bridge over Yangtze River.

• Proceedings of the IEEK Conference
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• 1999.06a
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• pp.942-945
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• 1999

In this work, we proposed Proper etching algorithm for ultra-large scale integrated circuit device and simulated etching process using the proposed algorithm in the case of ICP (inductive coupled plasma) 〔1〕source. Until now, many algorithms for etching process simulation have been proposed such as Cell remove algorithm, String algorithm and Ray algorithm. These algorithms have several drawbacks due to analytic function; these algorithms are not appropriate for sub 0.1 ${\mu}{\textrm}{m}$ device technologies which should deal with each ion. These algorithms could not present exactly straggle and interaction between Projectile ions and could not consider reflection effects due to interactions among next projectile ions, reflected ions and sputtering ions, simultaneously In order to apply ULSI process simulation, algorithm considering above mentioned interactions at the same time is needed. Proposed algorithm calculates interactions both in plasma source region and in target material region, and uses BCA (binary collision approximation4〕method when ion impact on target material surface. Proposed algorithm considers the interaction between source ions in sheath region (from Quartz region to substrate region). After the collision between target and ion, reflected ion collides next projectile ion or sputtered atoms. In ICP etching, because the main mechanism is sputtering, both SiO$_2$ and Si can be etched. Therefore, to obtain etching profiles, mask thickness and mask composition must be considered. Since we consider both SiO$_2$ etching and Si etching, it is possible to predict the thickness of SiO$_2$ for etching of ULSI.

• Journal of KIISE:Databases
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• v.31 no.2
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• pp.183-194
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• 2004

As XML is a do facto standard for a data exchange language, there have been several researches on efficient processing XML queries. The most important thing to consider when processing XML queries is how efficiently we can process path expressions in queries. Some previous works make results by performing a sequence of join operations on all records corresponding to labels in the path expression. Others works check the existence of paths in the query using an RDBMS's string comparison operator and make results by extracting the records corresponding to the paths. In this paper we suggested a new query planning algorithm based on path containment relationships and two join operators supporting the planning algorithm. The join operators use only the records related to the paths in a query as input data, scan them only once, and generate result data using a pipelining mechanism. By analysis and experiments, we confirmed that our techniques(a new query planning algorithm and two join operators) achieved significantly higher performance than other previous works.