• Title/Summary/Keyword: g-frames

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A Commensal Thermophile, Symbiobacterium toebii: Distribution, Characterization, and Genome Analysis

  • Bae Jin-Woo;Kim Kwang;Song Jae Jun;Ha Jae Seok;Kim Joong-Jae;Kang Gwan-Tae;Kim Mi-Hwa;Hong Seung-Pyo;Sung Moon-Hee
    • Proceedings of the Microbiological Society of Korea Conference
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    • 2001.11a
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    • pp.46-53
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    • 2001
  • A commensal thermophile, Symbiobacterium toebii, isolated from hay compost (toebii) in Korea commensally interacted with a thermophilic Geobacillus toebii sp. nov., which was a new species within the genus Geobacillus on the basis of the phenotypic traits and molecular systematic data. S. toebii required the crude extracts and/or culture supernatant of the Geobacillus toebii for axenic growth and could grow on the temperature between 45 and $70^{\circ}C$ (optimum: $60^{\circ}C$; 2.4 h doubling time) and pH 6.0 and 9.0 (optimum: pH 7.5). The G+C content of the genomic DNA was $65 mol\%$, and the major quinones were MK-6 and MK-7. A phylogenetic analysis of its 16S rDNA sequence indicated that Symbiobacterium toebii was closely related with solely reported Symbiobacterium thermophilum. The presence of the commensal thermophile 16S rDNA and accumulation of indole in all the enriched cultures indicate that Symbiobacterium toebii is widely distributed in the various soils. The genome of S. toebii constituted a circular chromosome of 3,280,275 base pairs and there was not an extra-chromosomal element (ECE). It contained about 4,107 predicted coding sequences. Of these protein coding genes, about $45.6\%$ was encoded well-known proteins and annotated the functional assignment of 1,874 open reading frames (ORFs), and the rest predicted to have unknown functions. The genes encoding thermostable tyrosine phenol-lyase and tryptophan indole-lyase were cloned from the genomic DNA of S. toebii and the enzymatic production of L-tyrosine and L-tryptophan was carried out with two thermostable enzymes overexpressed in recombinant E. coli.

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Mutations in the gyrB, parC, and parE Genes of Quinolone-Resistant Isolates and Mutants of Edwardsiella tarda

  • Kim, Myoung-Sug;Jun, Lyu-Jin;Shin, Soon-Bum;Park, Myoung-Ae;Jung, Sung-Hee;Kim, Kwang-Il;Moon, Kyung-Ho;Jeong, Hyun-Do
    • Journal of Microbiology and Biotechnology
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    • v.20 no.12
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    • pp.1735-1743
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    • 2010
  • The full-length genes gyrB (2,415 bp), parC (2,277 bp), and parE (1,896 bp) in Edwardsiella tarda were cloned by PCR with degenerate primers based on the sequence of the respective quinolone resistance-determining region (QRDR), followed by elongation of 5' and 3' ends using cassette ligation-mediated PCR (CLMP). Analysis of the cloned genes revealed open reading frames (ORFs) encoding proteins of 804 (GyrB), 758 (ParC), and 631 (ParE) amino acids with conserved gyrase/topoisomerase features and motifs important for enzymatic function. The ORFs were preceded by putative promoters, ribosome binding sites, and inverted repeats with the potential to form cruciform structures for binding of DNA-binding proteins. When comparing the deduced amino acid sequences of E. tarda GyrB, ParC, and ParE with those of the corresponding proteins in other bacteria, they were found to be most closely related to Escherichia coli GyrB (87.6% identity), Klebsiella pneumoniae ParC (78.8% identity), and Salmonella Typhimurium ParE (89.5% identity), respectively. The two topoisomerase genes, parC and parE, were found to be contiguous on the E. tarda chromosome. All 18 quinolone-resistant isolates obtained from Korea thus far did not contain subunit alternations apart from a substitution in GyrA (Ser83$\rightarrow$Arg). However, an alteration in the QRDR of ParC (Ser84$\rightarrow$Ile) following an amino acid substitution in GyrA (Asp87$\rightarrow$Gly) was detected in E. tarda mutants selected in vitro at $8{\mu}g/ml$ ciprofloxacin (CIP). A mutant with a GyrB (Ser464$\rightarrow$Leu) and GyrA (Asp87$\rightarrow$Gly) substitution did not show a significant increase in the minimum inhibitory concentration (MIC) of CIP. None of the in vitro mutants exhibited mutations in parE. Thus, gyrA and parC should be considered to be the primary and secondary targets, respectively, of quinolones in E. tarda.

Preparation and Characteristics of Snack Using Conger Eel Frame (붕장어 Frame을 이용한 스낵의 제조 및 특성)

  • Kim, Hye-Suk;Kang, Kyung-Tae;Han, Byung-Wook;Kim, Eun-Jung;Heu, Min-Soo;Kim, Jin-Soo
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.35 no.10
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    • pp.1467-1474
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    • 2006
  • Fish-frames, which are left after obtaining fillets or muscle during fish processing, consists of useful food components, such as muscle, collagen, calcium, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). This study was carried out to prepare snack using conger eel frame (SF) for human consumption and also to elucidate food component characterization of the snack. The results of volatile basic nitrogen suggested that conger eel frame was a suitable material for preparing snack. Based on the results of sensory evaluation and costs, starch syrup was an optimal sweetener for preparing snack using conger eel frame. The starch syrup-treated SF appeared safe because the moisture content and peroxide value were below the safety limits described in the guideline of Korea Food and Drug Administration (KFDA). Starch syrup-treated SF was similar in the pattern of fatty acid composition to soybean oil, whereas EPA and DHA were detected in SF. The total content of amino acid in starch syrup-treated SF was 23.9% based on 100 g of raw material. The maj or amino acids were aspartic acid, glutamic acid, glycine and alanine. The total contents of calcium and phosphorus in starch syrup-treated SF were 4.9% and 2.8%, respectively. The Ca/P of starch syrup-treated SF was 1.9, which is a good ratio for absorption of calcium. The SF made with starch syrup was superior in EPA and DHA compositions, total amino acid, calcium and phosphorus contents to commercial snack using eel frame.

Structural Characteristics of Expression Module of Unidentified Genes from Metagenome (메타게놈 유래 미규명 유전자의 발현에 관련된 특성분석)

  • Park, Seung-Hye;Jeong, Young-Su;Kim, Won-Ho;Kim, Geun-Joong;Hur, Byung-Ki
    • KSBB Journal
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    • v.21 no.2
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    • pp.144-150
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    • 2006
  • The exploitation of metagenome, the access to the natural extant of enormous potential resources, is the way for elucidating the functions of organism in environmental communities, for genomic analyses of uncultured microorganism, and also for the recovery of entirely novel natural products from microbial communities. The major breakthrough in metagenomics is opened by the construction of libraries with total DNAs directly isolated from environmental samples and screening of these libraries by activity and sequence-based approaches. Screening with activity-based approach is presumed as a plausible route for finding new catabolic genes under designed conditions without any prior sequence information. The main limitation of these approaches, however, is the very low positive hits in a single round of screening because transcription, translation and appropriate folding are not always possible in E. coli, a typical surrogate host. Thus, to obtain information about these obstacles, we studied the genetic organization of individual URF's(unidentified open reading frame from metagenome sequenced and deposited in GenBank), especially on the expression factors such as codon usage, promoter region and ribosome binding site(rbs), based on DNA sequence analyses using bioinformatics tools. And then we also investigated the above-mentioned properties for 4100 ORFs(Open Reading Frames) of E. coli K-12 generally used as a host cell for the screening of noble genes from metagenome. Finally, we analyzed the differences between the properties of URFs of metagenome and ORFs of E. coli. Information derived from these comparative metagenomic analyses can provide some specific features or environmental blueprint available to screen a novel biocatalyst efficiently.

Implementation of Video-Forensic System for Extraction of Violent Scene in Elevator (엘리베이터 내의 폭행 추출을 위한 영상포렌식 시스템 구현)

  • Shin, Kwang-Seong;Shin, Seong-Yoon
    • Journal of the Korea Institute of Information and Communication Engineering
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    • v.18 no.10
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    • pp.2427-2432
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    • 2014
  • Color-$X^2$ is used as a method for scene change detection. It extracts a violent scene in an elevator and then could be used for real-time surveillance of criminal acts. The scene could be also used to secure after-discovered evidences and to prove analysis processes. Video Forensic is defined as a research on various methods to efficiently analyze evidences upon crime-related visual images in the field of digital forensic. The method to use differences of color-histogram detects the difference values of histogram for RGB color from two frames respectively. Our paper uses Color-$X^2$ histogram that is composed of merits of color histogram and ones of $X^2$ histogram, in order to efficiently extract violent scenes in elevator. Also, we use a threshold so as to find out key frame, by use of existing Color-$X^2$ histogram. To increase the probability that discerns whether a real violent scene or not, we take advantage of statistical judgments with 20 sample visual images.

Optimizing a Multimedia File System for Streaming Severs (스트리밍 서버를 위한 멀티미디어 파일 시스템 최적화)

  • 박진연;김두한;원유집;류연승
    • Journal of KIISE:Computer Systems and Theory
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    • v.31 no.5_6
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    • pp.268-278
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    • 2004
  • In this paper, we describe our experience in the design and implementation of the SMART file system to handle multimedia workload. Our work has three design objectives: (ⅰ) efficient support for sequential workload, (ⅱ) avoiding disk fragmentation, (ⅲ) logical unit based file access. To achieve these three objectives, we develop a file system where a file consists of linked list of Data Unit Group. Instead of tree like structure of the legacy Unix file system, we use single level file structure. Our file system can also access the file based upon the logical unit which can be video frame or audio samples. Data Unit Group is a group of logical data units which is allocated continuous disk blocks. At the beginning of each Data Unit Group, there exists an index array. Each index points to the beginning of logical data units, e.g. frames in the Data Unit Group. This index array enables the random access and sequencial access of semantic data units. SMART file system is elaborately tailored to effectively support multimedia workload. We perform physical experiments and compare the performance of SMART file system with EXT2 file system and SGI XFS file system. In this experiment, SMART file system exhibits superior performance under streaming workload.

Metaphor and Archives (상징아카이빙 대통령기록을 중심으로)

  • Lee, Young-Nam
    • The Korean Journal of Archival Studies
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    • no.38
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    • pp.125-187
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    • 2013
  • This essay would focus on a kinds of new archival strategy. The main frame has been the kinds of activities regulated by laws, or formal activities since 1999. In the case of presidential archives has no another frame. There had never kinds of presidential archives system until President Noh, if anything. It means that the frame has some important points. Although it is, we have to say about the limits of the frame. This essay show 'metaphor frame' for archival system. I think that we have to guess there are methodologies below the two frames. One is quantitative study methodology, and another is qualitative research methodology. The later focuses on the experiences for making narratives. We have to know that this methodology is out of fashioned in the field of history department and cultural anthropology department for the purpose of alternative studies. This essay says about 'archival field description' and 'narrative records' for the new records in archival field. I have to say about that we needs to discuss about kinds of new archival discours. And to conclude, we should manage the records in culture.

Content and Meaning of Royal Garden Sightseeing Event in Pyoam's 「Hogayugeumwongi」 (표암(豹菴)의 「호가유금원기(扈駕遊禁苑記)」에 나타난 궁원 유람행사의 내용과 의미)

  • Hong, Hyoung-Soon
    • Journal of the Korean Institute of Traditional Landscape Architecture
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    • v.32 no.2
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    • pp.1-11
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    • 2014
  • This study aimed at investigating the content and meaning of royal garden(宮苑) sightseeing event in Pyoam Gang, sehwang's "Hogayugeumwongi" As the research method, descriptive research method was used, which is to consider and interpret the content and meaning in the historical records. Research results are summarized as follows. 1. "Hogayugeumwongi", which recorded the event that the King personally guided and explained the palace to the vassals, is a very precious historical records in Korean landscape gardening cultural history. Such thing is unprecedented in Joseon Dynasty as well as China. 2. The person who recorded this event was famous for shi seo hwa samjeol in the time, and the point that he was Pyoam, who was appreciated as 'the head(總帥) of artistic and literary circles(藝苑)', adds more value to the future generations. 3. The characteristic of this sightseeing event was to praise the vassals' labor, who contributed to the completion of Kyujanggak, to establish King Jongjo's direct rule in the early period of seizure of power, and eojin(御眞) dosa(圖寫), etc., which expressed the King's dignity. Jongjo utilized Geumwon, a forbidden place in the palace, to give a special privilege to the vassals' effort, who took a great part in realizing his political ideal. 4. One of sightseeing lines toward the backyard of Changdeok Palace could be identified. Though the sightseeing lines toward the backyard were not fixed, however this might be the best sightseeing line which Jongjo intentionally chose to enjoy that day's flavor of autumn. 5. The characteristic of this event was informal and somewhat extemporary 'sightseeing'. Therefore, it is considered, that day's event was relatively private and free 'play(遊)', while 'sanghwaeojoyeon(賞花漁釣宴)', which Jongjo gave to the vassals middle after his reign, was a royal 'banquet', which prepared frames, such as event holding time and form, qualification for participation, e.g. flower viewing, fishing, writing poems, etc. This research has a significance that it considered the content and meaning in historical records including the front and the rear context that "Hogayugeumwongi" was written through the consideration of related historical materials. "Hogayugeumwongi" can be utilized as a material for storytelling with regard to royal garden sightseeing in future as a valuable cultural content, also, follow-up study on this is necessary.

Story-based Information Retrieval (스토리 기반의 정보 검색 연구)

  • You, Eun-Soon;Park, Seung-Bo
    • Journal of Intelligence and Information Systems
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    • v.19 no.4
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    • pp.81-96
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    • 2013
  • Video information retrieval has become a very important issue because of the explosive increase in video data from Web content development. Meanwhile, content-based video analysis using visual features has been the main source for video information retrieval and browsing. Content in video can be represented with content-based analysis techniques, which can extract various features from audio-visual data such as frames, shots, colors, texture, or shape. Moreover, similarity between videos can be measured through content-based analysis. However, a movie that is one of typical types of video data is organized by story as well as audio-visual data. This causes a semantic gap between significant information recognized by people and information resulting from content-based analysis, when content-based video analysis using only audio-visual data of low level is applied to information retrieval of movie. The reason for this semantic gap is that the story line for a movie is high level information, with relationships in the content that changes as the movie progresses. Information retrieval related to the story line of a movie cannot be executed by only content-based analysis techniques. A formal model is needed, which can determine relationships among movie contents, or track meaning changes, in order to accurately retrieve the story information. Recently, story-based video analysis techniques have emerged using a social network concept for story information retrieval. These approaches represent a story by using the relationships between characters in a movie, but these approaches have problems. First, they do not express dynamic changes in relationships between characters according to story development. Second, they miss profound information, such as emotions indicating the identities and psychological states of the characters. Emotion is essential to understanding a character's motivation, conflict, and resolution. Third, they do not take account of events and background that contribute to the story. As a result, this paper reviews the importance and weaknesses of previous video analysis methods ranging from content-based approaches to story analysis based on social network. Also, we suggest necessary elements, such as character, background, and events, based on narrative structures introduced in the literature. We extract characters' emotional words from the script of the movie Pretty Woman by using the hierarchical attribute of WordNet, which is an extensive English thesaurus. WordNet offers relationships between words (e.g., synonyms, hypernyms, hyponyms, antonyms). We present a method to visualize the emotional pattern of a character over time. Second, a character's inner nature must be predetermined in order to model a character arc that can depict the character's growth and development. To this end, we analyze the amount of the character's dialogue in the script and track the character's inner nature using social network concepts, such as in-degree (incoming links) and out-degree (outgoing links). Additionally, we propose a method that can track a character's inner nature by tracing indices such as degree, in-degree, and out-degree of the character network in a movie through its progression. Finally, the spatial background where characters meet and where events take place is an important element in the story. We take advantage of the movie script to extracting significant spatial background and suggest a scene map describing spatial arrangements and distances in the movie. Important places where main characters first meet or where they stay during long periods of time can be extracted through this scene map. In view of the aforementioned three elements (character, event, background), we extract a variety of information related to the story and evaluate the performance of the proposed method. We can track story information extracted over time and detect a change in the character's emotion or inner nature, spatial movement, and conflicts and resolutions in the story.