• Interdisciplinary Bio Central
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• v.4 no.4
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• pp.14.1-14.6
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• 2012

Splice site prediction in DNA sequence is a basic search problem for finding exon/intron and intron/exon boundaries. Removing introns and then joining the exons together forms the mRNA sequence. These sequences are the input of the translation process. It is a necessary step in the central dogma of molecular biology. The main task of splice site prediction is to find out the exact GT and AG ended sequences. Then it identifies the true and false GT and AG ended sequences among those candidate sequences. In this paper, we survey research works on splice site prediction based on support vector machine (SVM). The basic difference between these research works is nucleotide encoding technique and SVM kernel selection. Some methods encode the DNA sequence in a sparse way whereas others encode in a probabilistic manner. The encoded sequences serve as input of SVM. The task of SVM is to classify them using its learning model. The accuracy of classification largely depends on the proper kernel selection for sequence data as well as a selection of kernel parameter. We observe each encoding technique and classify them according to their similarity. Then we discuss about kernel and their parameter selection. Our survey paper provides a basic understanding of encoding approaches and proper kernel selection of SVM for splice site prediction.

• Fisheries and Aquatic Sciences
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• v.12 no.3
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• pp.185-193
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• 2009

A complete cDNA, which encodes for a myostatin-like protein (Es-MSTN), was isolated from the Chinese mitten crab, Eriocheir sinensis. Es-MSTN was composed of 2,397 nucleotides and the open reading frame (ORF) specified a protein containing 468 amino acids. Es-MSTN exhibited 32% amino acid sequence identity and 52% similarity to human myostatin. Multiple sequence alignment analysis indicated that Es-MSTN possessed the conserved proteolytic cleavage site (RXXR) for maturation of the protein and nine cysteine residues for disulfide bridges. Besides the conserved structural features, Es-MSTN also exhibits its unique characters; a longer N-terminal domain which is involved in protein folding and latent form of myostatin and absence of the cleavage site for BMP-1/tolloid family of metalloproteinase to activate mature myostatin. Phylogenetic analysis suggests that Es-MSTN showed the closely related to both vertebrate myostatin and GDF11. Es-MSTN is expressed highly in the claw muscle, leg muscle, thoracic muscle and heart, and moderately in the hindgut suggesting that Es-MSTN may play important roles in the muscle tissues. As homolog of mammalian myostatin and GDF11, Es-MSTN may be involved in development of muscular tissue and further study will help to produce high-quality seafood.

• The Korean Journal of Physiology and Pharmacology
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• v.14 no.6
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• pp.441-447
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• 2010

B13, a ceramide analogue, is a ceramidase inhibitor and induces apoptosis to give potent anticancer activity. A series of thiourea B13 analogues was evaluated for their in vitro cytotoxic activities against human renal cancer Caki-2 and leukemic cancer HL-60 in the MTT assay. Some compounds (12, 15, and 16) showed stronger cytotoxicity than B13 and C6-ceramide against both tumor cell lines, and compound (12) gave the most potent activity with $IC_{50}$ values of 36 and $9\;{\mu}M$, respectively. Molecular modeling of thiourea B13 analogues was carried out by comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). We obtained highly reliable and predictive CoMSIA models with cross-validated $q^2$ values of 0.707 and 0.753 and CoMSIA contour maps to show the structural requirements for potent activity. These data suggest that the amide group of B13 could be replaced by thiourea, that the stereochemistry of 1,3-propandiol may not be essential for activity and that long alkyl chains increase cytotoxicity.

• Journal of Microbiology and Biotechnology
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• v.21 no.8
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• pp.838-845
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• 2011

The present work describes the identification, purification, and characterization of bile salt hydrolase (BSH) from Bifidobacterium animalis subsp. lactis. The enzyme was purified to electrophoretic homogeneity by hydrophobic chromatography, ion-exchange chromatography and ultrafiltration. SDS-PAGE analysis of putative BSH and gel filtration revealed that the analyzed protein is presumably a tetramer composed of four monomers each of about 35 kDa. The purified enzyme was analyzed by liquid chromatography coupled to LTQ FT ICR mass spectrometry and unambiguously identified as a bile salt hydrolase from B. animalis. The isoelectric point of the studied protein was estimated to be around pH 4.9. The pH optimum of the purified BSH is between 4.7 to 6.5, and the temperature optimum is around 50oC. The BSH of B. animalis could deconjugate all tested bile salts, with clear preference for glycine-conjugated bile salts over taurine-conjugated forms. Genetic analysis of the bsh showed high similarity to the previously sequenced bsh gene from B. animalis and confirmed the usefulness of bile salt hydrolase as a genetic marker for B. animalis identification.

• The Korean Journal of Physiology and Pharmacology
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• v.15 no.6
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• pp.423-429
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• 2011

B13 analogues are being considered as therapeutic agents for cancer cells, since B13 is a ceramide analogue and inhibits ceramidase to promote apoptosis in cancer cells. B13 sulfonamides are assumed to have biological activity similar to B13, since they are made by bioisosterically substituting the carboxyl moiety of B13 with sulfone group. Twenty B13 sulfonamides were evaluated for their in vitro cytotoxicities against human colon cancer HT-29 and lung cancer A549 cell lines using MTT assays. Replacement of the amide group with a sulfonamide group increased cytotoxicity in both cancer cell lines. The sulfonamides with long alkyl chains exhibited activities two to three times more potent than that of B13 and compound (15) had the most potent activity with $IC_{50}$ values of 27 and $28.7{\mu}M$ for HT-29 and A549, respectively. The comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to carry out QSAR molecular modeling of these compounds. The predictive CoMSIA models for HT-29 and A549 gave cross-validated q2 values of 0.703 and 0.830, respectively. From graphical analysis of these models, we suppose that the stereochemistry of 1,3-propandiol is not important for activity and that introduction of a sulfonamide group and long alkyl chains into B13 can increase cytotoxicity.

• Animal Systematics, Evolution and Diversity
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• v.32 no.1
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• pp.1-8
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• 2016

Vermamoeba vermiformis is a very important free-living amoeba for human health in association with Legionnaires' disease and keratitis. This interesting amoeba was firstly isolated from a freshwater of Dokdo (island), which was historically used for drinking water. Trophozoites and cyst forms of V. vermiformis strain MG1 are very similar to previous reported species. Trophozoites of V. vermiformis strain MG1 showed cylindrical shape with prominent anterior hyaline region. The average ratio of length and width was about 6.5. Typically, cysts of the strain MG1 showed a spherical or slightly ovoidal shape with smooth wall, and lacked cyst pores. Some cysts had crenulate-walled ectocyst, which was separated from endocyst wall. Further, 18S rRNA gene sequence of V. vermiformis strain MG1 showed very high similarity to other V. vermiformis species (99.4%-99.9% identity). Molecular phylogenetic analysis based on 18S rRNA gene sequences clearly confirmed that the isolate was one strain of V. vermiformis with maximum bootstrap value (maximum likelihood: 100%) and Bayesian posterior probability of 1. Thus, the freshwater of Dokdo in Korea could harbor potentially pathogenic amoeba that may cause diseases in humans.

• Journal of architectural history
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• v.7 no.4 s.17
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• pp.49-60
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• 1998

The first aim of this paper is to investigate and analyze Alan Colquhoun's architectural hermeneutics of tradition, 'conceptual displacement of the past.' The second aim is to overcome the limit of it, and to suggest new architectural hermeneutics of tradition, 'the reactivation of the past.' The architectural work is reduced by Colquhoun to typology or arbitrary language because he believes that without arbitrary language natural language is not able to work effectively. However, he ignores that two languages cannot be separable. When they are separated the key to natural language is understood to be an unverifiable similarity between a sense perception and its correspondence in the architectural object, while the key to arbitrary language becomes mere artificial agreement on the value and function of the linguistic sign. Therefore, natural language is appropriate only when it permits spontaneous combinations of sensory data within complex structures which emerge from, and support, complex human interaction and communication(the shining of the world and of the possibility of creative being in each individual thing). Only when architecture is translated into this kind of language, can it reactivate the world's past, and become poetic.

• Journal of the Korean Society of Costume
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• v.59 no.10
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• pp.38-50
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• 2009

Since Homeros in Greece, Mimesis was thought to be an art to imitate the nature, and it means an imitation of the nature classically. Mimetic theories were set to be a kind of art work in the era of Renaissance, and the terminology of mimesis was widely used to replace it with an originality in the 15th century. The purpose of this study is to understand the aesthetics of mimesis expressed in 2000s fashion. For this purpose, I investigated the theories of the mimesis, categorized the definition, then applied those categories for 2000s fashion. Documentary studies were conducted through aesthetics, fashion books and demonstrative studies were processed by analyzing photos from collection fashion magazines and fashion site of internet. In the history of aesthetics, the mimesis could be defined into three categories; the similarity and the representation mimesis, the symbol mimesis and the abstraction mimesis. In fashion, the representation mimesis included a natural and a folk, a period that of 1900s and ancient representation mimesis. The symbol mimesis included psychology and fear symbol mimesis. The abstraction mimesis included hard color, a geometric simplification and distortion mimesis. Analysis on the mimesis expressed in 2000s modern fashion may provide an excellent method for understanding human aesthetic in costume.

• Journal of the Korean Society of Costume
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• v.57 no.1 s.110
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• pp.176-186
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• 2007

The purpose of this study is to reconstruct upper class women's costume of 'Mongol-pung' and 'Goryeo-yang' in a civilization-exchanged period between Mongolia and Korea, for making movie or soap opera costume and historical animation. 'Mongol-pung' was a cultural influence from Mogolia to Korea. For example, sleeveless bi-gap(比甲) and half-sleeved dap-ho(搭忽) were put on by many women at that time. On the basis of old literature, I suggest a 'Mongol-pung' costume as a set of seeran-chulrik(膝欄 terlig), em-broidered bigap, dapho of meat-red color for women. 'Goryeo-yang' was a cultural influence from Korea to Mongolia. Due to old poem of Yuan, 'Short outer Jacket with square neckline, half sleeves, and clear color(方領過腰半臂)' was a representative of 'Goryeo-yang' in Mongolian royal women's costumes. Many women were dressed in it with short inner jacket and wide skirt. In the case of making soap opera costume, the budget of broadcasting station, appearence of nowaday's actor and actress, similarity between old fabric and modern fabric must be considered altogether.

• Fashion & Textile Research Journal
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• v.17 no.3
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• pp.421-428
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• 2015

This research is to understand customer satisfaction with virtual fitting based on a 3D body scanner and avatars as well as differences between avatars and the 'real me'. To this end, this research examined Korean college students to facilitate 3D body scanning, avatar generation and surveys. The author used 3D body scan data with direct measurements to identify differences between the 3D body scan data-based 'my avatar' and 'real me' in the virtual dress fitting system. The survey results on 'the level of customer awareness on 3D body scanner' found that the majority of both genders did not know about it and indicated a lower usability to incorporate IT technology into the fashion industry. The question in the 3D body scanning and avatar found an affirmative attitude. Satisfaction levels on the 3D avatars' similarity with 'own body' and garment fitting were positive and indicated a need for further technological improvements to express the avatars identical to customers' own body. More research is necessary for the accuracy of sizes for 3D body scanning that measure body sizes while wearing clothes. Avatars based on such datamay be less similar to 'own body' and cause customer dissatisfaction. Thus, further technology development is required to narrow gaps using data to make avatars that provide more accurate virtual fitting simulation services to customers.