• Title/Summary/Keyword: STRING database

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Basic network pharmacological analysis of Salvia miltiorrhiza root for further application to an animal stroke model (단삼(丹參)을 뇌졸중 동물모델에 적용하기 위한 기초적인 네트워크 약리학 분석)

  • Choi, Myeongjin;Yang, Wonjin;Lee, Byoungho;Cho, Suin
    • Herbal Formula Science
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    • v.29 no.1
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    • pp.19-31
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    • 2021
  • Objectives : The root of Salvia miltiorrhiza, known as 'Dansam (DS, 丹參)', is used for and treating cardiovascular diseases based on its efficacy of promoting blood circulation and breaking through a blood stasis. In this study, we would like to see if DS could be effectively used for stroke from the perspective of network pharmacology. Methods : The analysis was conducted using Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database to derive the main active compounds of DS and identify the mechanism of each compound acting on the human body. The networks between compounds, target protein and disease were expressed through Cytoscape. Protein-protein interaction (PPI) analysis was performed using STRING database. Results : Fifty two active compounds of DS were identified by screening the ingredients of DS through TCMSP. Based on the networks of these compounds with target protein and disease, it can be said that DS might be effective for preventing and treating stroke. PPI result showed that adrenergic receptor has many interactions among proteins, indicating its significance in stroke pathway. Conclusion : In this study, we derived target proteins and target diseases of DS that could be used in study of stroke. However, since it is uncertain if these targets can be controlled by DS extracts or not, we would like to confirm the results with further animal experiments.

Analysis of the Active Compounds and Therapeutic Mechanisms of Yijin-tang on Meniere's Disease Using Network Pharmacology(I) (네트워크 약리학을 활용한 메니에르병에 대한 이진탕(二陳湯)의 활성 성분과 치료 기전 연구(I))

  • SunKyung Jin;Hae-Jeong Nam
    • The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
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    • v.36 no.1
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    • pp.50-63
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    • 2023
  • Objectives : This study used a network pharmacology approach to explore the active compounds and therapeutic mechanisms of Yijin-tang on Meniere's disease. Methods : The active compounds of Yijin-tang were screened via the TCMSP database and their target proteins were screened via the STITCH database. The GeneCard was used to establish the Meniere's disease-related genes. The intersection targets were obtained through Venny 2.1.0. The related protein interaction network was constructed with the STRING database, and topology analysis was performed through CytoNCA. GO biological function analysis and KEGG enrichment analysis for core targets were performed through the ClueGO. Results : Network analysis identified 126 compounds in five herbal medicines of Yijin-tang. Among them, 15 compounds(naringenin, beta-sitosterol, stigmasterol, baicalein, baicalin, calycosin, dihydrocapsaicin, formononetin, glabridin, isorhamnetin, kaempferol, mairin, quercetin, sitosterol, nobiletin) were the key chemicals. The target proteins were 119, and 7 proteins(TNF, CASP9, PARP1, CCL2, CFTR, NOS2, NOS1) were linked to Meniere's disease-related genes. Core genes in this network were TNF, CASP9, and NOS2. GO/KEGG pathway analysis results indicate that these targets are primarily involved in regulating biological processes, such as excitotoxicity, oxidative stress, and apoptosis. Conclusion : Pharmacological network analysis can help to explain the applicability of Yijin-tang on Meniere's disease.

A Study on A Biometric Bits Extraction Method of A Cancelable face Template based on A Helper Data (보조정보에 기반한 가변 얼굴템플릿의 이진화 방법의 연구)

  • Lee, Hyung-Gu;Kim, Jai-Hie
    • Journal of the Institute of Electronics Engineers of Korea SP
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    • v.47 no.1
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    • pp.83-90
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    • 2010
  • Cancelable biometrics is a robust and secure biometric recognition method using revocable biometric template in order to prevent possible compromisation of the original biometric data. In this paper, we present a new cancelable bits extraction method for the facial data. We use our previous cancelable feature template for the bits extraction. The adopted cancelable template is generated from two different original face feature vectors extracted from two different appearance-based approaches. Each element of feature vectors is re-ordered, and the scrambled features are added. With the added feature, biometric bits string is extracted using helper data based method. In this technique, helper data is generated using statistical property of the added feature vector, which can be easily replaced with straightforward revocation. Because, the helper data only utilizes partial information of the added feature, our proposed method is a more secure method than our previous one. The proposed method utilizes the helper data to reduce feature variance within the same individual and increase the distinctiveness of bit strings of different individuals for good recognition performance. For a security evaluation of our proposed method, a scenario in which the system is compromised by an adversary is also considered. In our experiments, we analyze the proposed method with respect to performance and security using the extended YALEB face database

A Passport Recognition and face Verification Using Enhanced fuzzy ART Based RBF Network and PCA Algorithm (개선된 퍼지 ART 기반 RBF 네트워크와 PCA 알고리즘을 이용한 여권 인식 및 얼굴 인증)

  • Kim Kwang-Baek
    • Journal of Intelligence and Information Systems
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    • v.12 no.1
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    • pp.17-31
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    • 2006
  • In this paper, passport recognition and face verification methods which can automatically recognize passport codes and discriminate forgery passports to improve efficiency and systematic control of immigration management are proposed. Adjusting the slant is very important for recognition of characters and face verification since slanted passport images can bring various unwanted effects to the recognition of individual codes and faces. Therefore, after smearing the passport image, the longest extracted string of characters is selected. The angle adjustment can be conducted by using the slant of the straight and horizontal line that connects the center of thickness between left and right parts of the string. Extracting passport codes is done by Sobel operator, horizontal smearing, and 8-neighborhood contour tracking algorithm. The string of codes can be transformed into binary format by applying repeating binary method to the area of the extracted passport code strings. The string codes are restored by applying CDM mask to the binary string area and individual codes are extracted by 8-neighborhood contour tracking algerian. The proposed RBF network is applied to the middle layer of RBF network by using the fuzzy logic connection operator and proposing the enhanced fuzzy ART algorithm that dynamically controls the vigilance parameter. The face is authenticated by measuring the similarity between the feature vector of the facial image from the passport and feature vector of the facial image from the database that is constructed with PCA algorithm. After several tests using a forged passport and the passport with slanted images, the proposed method was proven to be effective in recognizing passport codes and verifying facial images.

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Efficient Image Retrieval using Minimal Spatial Relationships (최소 공간관계를 이용한 효율적인 이미지 검색)

  • Lee, Soo-Cheol;Hwang, Een-Jun;Byeon, Kwang-Jun
    • 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.

Video Index Generation and Search using Trie Structure (Trie 구조를 이용한 비디오 인덱스 생성 및 검색)

  • 현기호;김정엽;박상현
    • Journal of KIISE:Software and Applications
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    • v.30 no.7_8
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    • pp.610-617
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    • 2003
  • Similarity matching in video database is of growing importance in many new applications such as video clustering and digital video libraries. In order to provide efficient access to relevant data in large databases, there have been many research efforts in video indexing with diverse spatial and temporal features. however, most of the previous works relied on sequential matching methods or memory-based inverted file techniques, thus making them unsuitable for a large volume of video databases. In order to resolve this problem, this paper proposes an effective and scalable indexing technique using a trie, originally proposed for string matching, as an index structure. For building an index, we convert each frame into a symbol sequence using a window order heuristic and build a disk-resident trie from a set of symbol sequences. For query processing, we perform a depth-first search on the trie and execute a temporal segmentation. To verify the superiority of our approach, we perform several experiments with real and synthetic data sets. The results reveal that our approach consistently outperforms the sequential scan method, and the performance gain is maintained even with a large volume of video databases.

Estimation of Substring Selectivity in Biological Sequence Database (생물학 서열 데이타베이스에서 부분 문자열의 선적도 추정)

  • 배진욱;이석호
    • Journal of KIISE:Databases
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    • v.30 no.2
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    • pp.168-175
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    • 2003
  • Until now, substring selectivities have been estimated by two steps. First step is to build up a count-suffix tree, which has statistical information about substrings, and second step is to estimate substring selectivity using it. However, it's actually impossible to build up a count-suffix tree from biological sequences because their lengths are too long. So, this paper proposes a novel data structure, count q-gram tree, consisting of fixed length substrings. The Count q-gram tree retains the exact counts of all substrings whose lengths are equal to or less than q and this tree is generated in 0(N) time and in site not subject to total length of all sequences, N. This paper also presents an estimation technique, k-MO. k-MO can choose overlapping length of splitted substrings from a query string, and this choice will affect accuracy of selectivity and query processing time. Experiments show k-MO can estimate very accurately.

Weighted Disassemble-based Correction Method to Improve Recognition Rates of Korean Text in Signboard Images (간판영상에서 한글 인식 성능향상을 위한 가중치 기반 음소 단위 분할 교정)

  • Lee, Myung-Hun;Yang, Hyung-Jeong;Kim, Soo-Hyung;Lee, Guee-Sang;Kim, Sun-Hee
    • The Journal of the Korea Contents Association
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    • v.12 no.2
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    • pp.105-115
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    • 2012
  • In this paper, we propose a correction method using phoneme unit segmentation to solve misrecognition of Korean Texts in signboard images using weighted Disassemble Levenshtein Distance. The proposed method calculates distances of recognized texts which are segmented into phoneme units and detects the best matched texts from signboard text database. For verifying the efficiency of the proposed method, a database dictionary is built using 1.3 million words of nationwide signboard through removing duplicated words. We compared the proposed method to Levenshtein Distance and Disassemble Levenshtein Distance which are common representative text string comparison algorithms. As a result, the proposed method based on weighted Disassemble Levenshtein Distance represents an improvement in recognition rates 29.85% and 6% on average compared to that of conventional methods, respectively.

Network pharmacology-based prediction of efficacy and mechanism of Myrrha acting on Allergic Rhinitis (네트워크 약리학을 활용한 알레르기 비염에서의 몰약의 치료 효능 및 기전 예측)

  • Yebin Lim;Bitna Kweon;Dong-Uk Kim;Gi-Sang Bae
    • 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.

A Case Study of Dan-Ryung Construction in Early 16th Century -Based on the Shrouds from Excavated Tomb of Kim, Heum Jo- (16세기 전기 단령의 구성법 일례 -김흠보(1461-1528) 분묘 출토의 단령을 중심으로-)

  • 이은주
    • The Research Journal of the Costume Culture
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    • v.6 no.2
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    • pp.127-140
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    • 1998
  • A study on the construction of Dan-Ryung in the early 16th century based on the shrouds from excavated tomb of Kim, Heum-Jo(1461-1528) is reported in this paper. This study is aimed at establishing database for a traditional Korean costume construction and emphasizing the necessity for development of methodology in writing report from excavated costume including measuring, construction methods and materials. This paper includes examples of measured length for each part of 'Dan-Ryung', reconstructured drawings, pictures, and construction methods. The followings on the construction of Dan-Ryung in the early 16th century are found in this study: 1) Dan-Ryung robes were made of less expensive hemp, cotton, silk & cotton, and ramie & silk. 2) As a whole, Dan-Ryung was lengthy and spacious and it had straighter and narrower sleeves when compared to the ones from the late Chosun. 3) There existed Moo which was large rectangular guest with double pleats at Dan-Ryung's side seam. Its round collar was constructed with a 3 cm width bias. Ball buttons on the outer collar and loops on the right shoulder are attached. 4) There existed a pair of indirectly attached slim and short strings. Inside string is directly attached. 5) Inside of the shoulder, a U-shaped shoulder pad made of the same cloth as the inner cloth was attached. hand sewing methods used include delicate flat-felled seam stitch, back-stitch and sew-up stitch.

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