• BMB Reports
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• v.44 no.2
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• pp.118-122
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• 2011

Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-determined coordinates. Secondary structure assignment algorithms using limited $C{\alpha}$ information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with ~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous $C{\alpha}s$. SABA is capable of identifying $\alpha$-helices, $3_{10}$-helices, and $\beta$-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to $C{\alpha}$-only structures, algorithms using limited $C{\alpha}$ information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison.

• Proceedings of the Computational Structural Engineering Institute Conference
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• 1991.10a
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• pp.63-68
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• 1991

The frequency window method has been extended to include strong coupling and multiple connections between the primary structure and the secondary structures. The rational polynomial expansion of the eigenvalue problem and the analytical methods for its solution are novel and distinguish this work from other eigenvalue analysis methods. The key results are the identification of parameters which quantify the resonance and coupling characteristics; the derivation of analytical dosed-form expressions describing the fundamental modal properties of the frequency windows; and the development of an iterative procedure which yields accurate convergent results for strongly-coupled primary-secondary structures.

• Computational Structural Engineering
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• v.4 no.4
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• pp.97-106
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• 1991

The frequency window method has been extended to include strong coupling and multiple connections between the primary structure and the secondary structures. The rational polynomial expansion of the eigenvalue problem and the analytical methods for its solution are novel and distinguish this work from other eigenvalue analysis methods. The key results are the identification of parameters which quantify the resonance and coupling characteristics; the derivation of analytical closed-form expressions describing the fundamental modal properties in the frequency windows; and the development of an iterative procedure which yields accurate convergent results for strongly-coupled primary-secondary structures.

• Proceedings of the PSK Conference
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• 2003.10a
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• pp.92-92
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• 2003

The drug discovery landscape is changing rapidly in the post-genomic era. Mapping of the human genome has led to an abundance of potential drug targets. Drug discovery times and costs can be significantly reduced by developing methods for high throughput target identification/ validation, multiplexed assay development and high efficient combinatorial chemistry. (omitted)

• Journal of Photoscience
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• v.10 no.1
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• pp.165-173
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• 2003

m-Phenylene-linked biscarbenes, bisnitrenes and carbenonitrenes can be formed photochemically from appropriate nitrogenous precursors. Generation of such reactive intermediates under matrix-isolation conditions allows for their characterization by spectroscopic techniques such as ESR, UV /vis and IR. The latter method is also useful in characterizing secondary products derived from these reactive intermediates. Computational chemistry methods complement experimental IR data, aiding, thus, in identification of such compounds. In addition electronic structure calculations help in developing qualitative and semi-quantitative models, which can be useful in predicting ground-state multiplicities. The parent systems of m-phenylene-linked carbenes and nitrenes have high-spin ground states, but a switching to lower multiplicity can be achieved by chemical substitution. The ground state and various low-lying excited states of m-phenylenecarbenonitrenes can be reasonably approximated by simple valence-bond depictions. Finally, m-phenylenecarbenonitrenes are photoreactive in the inert matrix isomerizing to cyclopropene derivatives.

• Journal of Conservation Science
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• v.2 no.2 s.2
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• pp.15-24
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• 1993

To understand the morphological change of ancient woods, samples classified by cell type, burial environment and species were collected and observed using microscopy. Decay of wood by cell type could classified into two types. First, degraded secondary wall was formed granular residues in $S_2$ layer and was remained $S_3$ layer and compound middle lamella. Second, the cell wall was slightly degraded and cracked in secondary wall. A gradual thinning of cell wall was occured. The compound middle lamella was separated from secondary wall. The resistance of degradation is increased at vessels, parenchyma, and tracheid and wood fiber in the order named. The type of degradation by species could be classified into four types. Overall degradation type; the degradation of cell wall is usually heavy and the extent of degradation Varies by part of the same sample. Partial degradation type ; this type shows severely different decay type by part of the sample. Nondegraded cells were mixed with degraded cells on the same sample. Erose degradation type ; thinning of the cell wall was occoured and the degradation type was different by part. Slight degradation types ; secondary wall was slightly degraded, cracked and separated from compound middle lamella. Considering different type of burial environment, dry wood was similiar to sound wood and slightly decayed. Waterlogged and peat burial wood was heavilydecayed. Between species of under the same environment, decay type and extent were diferentiated from each other.

• ALGAE
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• v.28 no.4
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• pp.307-330
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• 2013

The genus Cryptomonas is easily recognized by having two flagella, green brownish color, and a swaying behavior. They have relatively simple morphology, and limited diagnostic characters, which present a major difficulty in differentiating between species of the genus. To understand species delineation and phylogenetic relationships among Cryptomonas species, the nuclear-encoded internal transcribed spacer 2 (ITS2), partial large subunit (LSU) and small subunit ribosomal DNA (rDNA), and chloroplast-encoded psbA and LSU rDNA sequences were determined and used for phylogenetic analyses, using Bayesian and maximum likelihood methods. In addition, nuclear-encoded ITS2 sequences were predicted to secondary structures, and were used to determine nine species and four unidentified species from 47 strains. Sequences of helix I, II, and IIIb in ITS2 secondary structure were very useful for the identification of Cryptomonas species. However, the helix IV was the most variable region across species in alignment. The phylogenetic tree showed that fourteen species were monophyletic. However, some strains of C. obovata had chloroplasts with pyrenoid while others were without pyrenoid, which used as a key character in few species. Therefore, classification systems depending solely on morphological characters are inadequate, and require the use of molecular data.

• Journal of Nuclear Fuel Cycle and Waste Technology(JNFCWT)
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• v.20 no.1
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• pp.99-110
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• 2022

In decommissioning a nuclear power plant, numerous concrete structures need to be demolished and decontaminated. Although concrete decontamination technologies have been developed globally, concrete cutting remains problematic due to the secondary waste production and dispersion risk from concrete scabbling. To minimize workers' radiation exposure and secondary waste in dismantling and decontaminating concrete structures, the following conceptual designs were developed. A micro-blast type scabbling technology using explosive materials and a multi-dimensional contamination measurement and artificial intelligence (AI) mapping technology capable of identifying the contamination status of concrete surfaces. Trials revealed that this technology has several merits, including nuclide identification of more than 5 nuclides, radioactivity measurement capability of 0.1-10⁷ Bq·g^-1, 1.5 kg robot weight for easy handling, 10 cm robot self-running capability, 100% detonator performance, decontamination factor (DF) of 100 and 8,000 cm²·hr^-1 decontamination speed, better than that of TWI (7,500 cm²·hr^-1). Hence, the micro-blast type scabbling technology is a suitable method for concrete decontamination. As the Korean explosives industry is well developed and robot and mapping systems are supported by government research and development, this scabbling technology can efficiently aid the Korean decommissioning industry.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.1-8
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• 2019

Due to the major role played by several species of Streptococcus in the etiology of periodontitis, it is important to assess the pattern of Streptococcus pathogenic pathways within the infected subgingival pockets using a bacterial specific 16S rRNA fragment. From the total of 50 patients with periodontitis included in the study, only 23 Streptococcal isolates were considered for further analyses, in which their 16S rRNA fragments were amplified and sequenced. Then, a comprehensive phylogenetic tree was constructed and in silico prediction was performed for the observed Streptococcal species. The phylogenetic analysis of the subgingival Streptococcal species revealed a high discrimination power of the 16S rRNA fragment to accurately identify three groups of Streptococcus on the species level, including S. salivarius (14 isolates), S. anginosus (5 isolates), and S. gordonii (4 isolates). The employment of state-of-art in silico tools indicated that each Streptococcal species group was characterized with particular transcription factors that bound exclusively with a different 16S rRNA-based secondary structure. In conclusion, the observed data of the present study provided in-depth insights into the mechanism of each Streptococcal species in its pathogenesis, which differ in each observed group, according to the differences in the 16S rRNA secondary structure it takes, and the consequent binding with its corresponding transcription factors. This study paves the way for further interventions of the in silico prediction, with the main conventional in vitro microbiota identification to present an interesting insight in terms of the gene expression pattern and the signaling pathway that each pathogenic species follows in the infected subgingival site.

• Proceedings of the Korea Society for Industrial Systems Conference
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• 2000.05a
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• pp.59-64
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• 2000

Active radar reflector may be less familiar, since their uses have been limited to military applications, especially the enhancement of the effective radar cross-sections of missile test range in the drone aircraft and missiles. Perhaps the most widely-blown applications of radar transponders are Identification Friend or Foe(IFF) and its civilian counterpart, secondary surveilliance radar for Air Traffic Control(ATC), and most recently, as Search And Rescue Transponder(SART) in the Global Maritime Distress and Safety System(GMDSS). Since it happens frequently accidents on the sea, the problems of the contamination more seriously considered. The conventional navigation buoy and utilities are not sufficient to maintain the safety of the sea and thus new structured concept must be considered. Therefore, this paper propose and implement the active radar reflector with a enhanced structure. The results are shown that the performance of the system is significantly improved comparing with the conventional utilities.