• Korean Journal of Clinical Laboratory Science
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• v.38 no.2
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• pp.99-104
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• 2006

Human Papilloma viruses (HPVs) are etiological agents for cervical cancer and are classified into low- and high-risk categories. The aim of this study was to determine the frequency of the HPV genotype in the HPV screening test of Korean women using PCR-direct sequencing. Consensus primers of L1 legion were used for the amplification of HPV DNA and the PCR products (450 bps) obtained were analyzed by automatic sequencing. Sequences were compared with those in GenBank by using the BLAST program. Cervical swab samples of 3,978 women (20-73 years) were tested and the average age was 37.6 years. In this study, 1,174 samples were HPV positive out of 3,978 cervical swab samples screened (29.5%) and 136 samples (11.6%) showed a double infection. A total of 1,310 HPV genotypes were analyzed. The HPV positive rate was the lowest in the 20 years group (69.5%) and most of the samples of the > 60 years group were found HPV positive. Among thirty seven different HPV types identified by sequencing, 21 were HPV high risk types and 16 HPV low risk types were 69.8% (914/1,310) and 26.0% (340/1,310), respectively. In HPV high-risk types, 16 (13.21%), was the most frequently found. HPV 53 (9.62%) and 58 (9.24%) were also frequently found. This group was followed by HPV types 70 (5.50%), 33 (4.73%), 66 (4.20%), 18 (4.05%), 52 (4.05%), 31 (3.97%) and 56 (3.51%) in descending order of frequency. Among HPV low-risk types, 62 (4.20%), 6 (3.59%), 81 (3.59%), 84 (3.51%), and 11 (2.6%) were frequently found. In conclusion, PCR-direct sequencing could be used for quick and reliable typing of known and novel HPVs from clinical specimens. This data could be useful for epidemiological study of HPV and it also allows type-specific follow-up of women who have been treated for cervical intraepithelial neoplasia.

• Korean Journal of Environmental Biology
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• v.35 no.4
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• pp.694-705
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• 2017

The aim of this study was to isolate and identify marine bacterium with anti-methicillin-resistant Staphylococcus aureus (MRSA) activity, and to purify the anti-MRSA compound, as well as to determine its activity and synergistic effects. Among the marine bacteria isolated in this study, the YJ-1 isolate had the strongest anti-MRSA activity. The YJ-1 isolate was identified on the basis of its biochemical characteristics and an analysis of 16S rRNA gene sequences. The YJ-1 isolate showed over 99.2% homology with Pseudomonas stutzeri, and was designated as a Pseudomonas sp. YJ-1. The optimal culture conditions were $25^{\circ}C$ and initial pH 7.0. For the purification of the anti-MRSA compounds, the YJ-1 was cultured in Pa PES-II medium, and the culture filtrates were extracted by ethyl acetate, hexane, and 80% MeOH. The 80% MeOH fraction was separated by a $C_{18}$ ODS column, silica gel chromatography and a reverse phase HPLC, to yield three anti-MRSA agents, the MR1, MR2, and MR3 compounds. When the MR1 compound of $250{\mu}g\;mL^{-1}$ concentration was applied to the MRSA cells, over 95% of bacterial cells was killed within 48 hr. Compared with vancomycin and ampicillin, the MR1 compound showed significant anti-MRSA activity. In addition, the anti-MRSA activity was increased by dose and time dependent manners. Furthermore, the combination of an MR1 compound with vancomycin produced a more rapid decrease in the MRSA cells than did the MR1 compound alone. Taken together, our results suggest that the Pseudomonas sp. YJ-1 and its anti-MRSA compounds could be employed as a natural antibacterial agent in MRSA infections.

• Journal of Intelligence and Information Systems
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• v.22 no.2
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• pp.127-142
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• 2016

Deep learning model is a kind of neural networks that allows multiple hidden layers. There are various deep learning architectures such as convolutional neural networks, deep belief networks and recurrent neural networks. Those have been applied to fields like computer vision, automatic speech recognition, natural language processing, audio recognition and bioinformatics where they have been shown to produce state-of-the-art results on various tasks. Among those architectures, convolutional neural networks and recurrent neural networks are classified as the supervised learning model. And in recent years, those supervised learning models have gained more popularity than unsupervised learning models such as deep belief networks, because supervised learning models have shown fashionable applications in such fields mentioned above. Deep learning models can be trained with backpropagation algorithm. Backpropagation is an abbreviation for "backward propagation of errors" and a common method of training artificial neural networks used in conjunction with an optimization method such as gradient descent. The method calculates the gradient of an error function with respect to all the weights in the network. The gradient is fed to the optimization method which in turn uses it to update the weights, in an attempt to minimize the error function. Convolutional neural networks use a special architecture which is particularly well-adapted to classify images. Using this architecture makes convolutional networks fast to train. This, in turn, helps us train deep, muti-layer networks, which are very good at classifying images. These days, deep convolutional networks are used in most neural networks for image recognition. Convolutional neural networks use three basic ideas: local receptive fields, shared weights, and pooling. By local receptive fields, we mean that each neuron in the first(or any) hidden layer will be connected to a small region of the input(or previous layer's) neurons. Shared weights mean that we're going to use the same weights and bias for each of the local receptive field. This means that all the neurons in the hidden layer detect exactly the same feature, just at different locations in the input image. In addition to the convolutional layers just described, convolutional neural networks also contain pooling layers. Pooling layers are usually used immediately after convolutional layers. What the pooling layers do is to simplify the information in the output from the convolutional layer. Recent convolutional network architectures have 10 to 20 hidden layers and billions of connections between units. Training deep learning networks has taken weeks several years ago, but thanks to progress in GPU and algorithm enhancement, training time has reduced to several hours. Neural networks with time-varying behavior are known as recurrent neural networks or RNNs. A recurrent neural network is a class of artificial neural network where connections between units form a directed cycle. This creates an internal state of the network which allows it to exhibit dynamic temporal behavior. Unlike feedforward neural networks, RNNs can use their internal memory to process arbitrary sequences of inputs. Early RNN models turned out to be very difficult to train, harder even than deep feedforward networks. The reason is the unstable gradient problem such as vanishing gradient and exploding gradient. The gradient can get smaller and smaller as it is propagated back through layers. This makes learning in early layers extremely slow. The problem actually gets worse in RNNs, since gradients aren't just propagated backward through layers, they're propagated backward through time. If the network runs for a long time, that can make the gradient extremely unstable and hard to learn from. It has been possible to incorporate an idea known as long short-term memory units (LSTMs) into RNNs. LSTMs make it much easier to get good results when training RNNs, and many recent papers make use of LSTMs or related ideas.

• Journal of the Geological Society of Korea
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• v.54 no.5
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• pp.477-488
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• 2018

Fluid muds commonly occur in estuarine environments, but their ancient examples have rarely been studied in terms of depositional characteristics and processes. Cores of estuarine channel deposits of the Early Cretaceous McMurray Formation, Alberta, Canada show various mudstone layers that possess depositional characteristics of high clay-concentration flows. These mudstone layers are examined in detail through microscopic observation of thin sections and classified into three microfacies (<1 to 25 mm thick) on the basis of sedimentary texture and structures. Structureless mudstone (Microfacies 1) consists mainly of clay particles and contains randomly dispersed coarser grains (coarse silt to fine sand). This microfacies is interpreted as being deposited by cohesive mud flows, i.e., fluid muds, which possessed sufficient strength to support suspended coarser grains (quasi-laminar plug flow). Silt-streaked mudstone (Microfacies 2) mainly comprises mudstone with dispersed coarse grains and includes very thin, discontinuous silt streaks of coarse-silt to very-fine-sand grains. The texture similar to Microfacies 1 indicates that Microfacies 2 was also deposited by cohesive fluid muds. The silt streaks are, however, suggestive of the presence of intermittent weak turbulence under the plug (upper transitional plug flow). Heterolithic laminated mudstone (Microfacies 3) is characterized by alternation of relatively thick silt laminae and much thinner clay laminae. It is either parallel-laminated or low-angle cross-laminated, occasionally showing low-amplitude ripple forms. The heterolithic laminae are interpreted as the results of shear sorting in the basal turbulent zone under a cohesive plug. They may represent low-amplitude bed-waves formed under lower transitional plug flows. These three microfacies reflect a range of flow phases of fluid muds, which change with flow velocities and suspended mud concentrations. The results of this study provide important knowledge to recognize fluid-mud deposits in ancient sequences and to better understand depositional processes of mudstones.

• The Journal of the Petrological Society of Korea
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• v.23 no.3
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• pp.167-185
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• 2014

SHRIMP zircon U-Pb ages and major element and Sr-Nd isotopic compositions were determined for drill cores (374-3390 m in depth) recovered from three boreholes in the Pohonag basin, southeastern Korea. Shallow-seated volcanic rocks and underlain plutonic rocks were geochemically classified as rhyolite and gabbro-granite, respectively. They showed high-K calc-alkaline trends on the $K_2O-SiO_2$ and AFM diagrams. Zircons from volcanic rocks of borehole PB-1 yielded concordia ages of $66.84{\pm}0.66Ma$ (n=12, MSWD=0.02) and $66.52{\pm}0.55Ma$ (n=12, MSWD=0.46). Zircons from volcanic rocks of borehole PB-2 gave a concordia age of $71.34{\pm}0.85Ma$ (n=11, MSWD=0.79) and a weighted mean $^{206}Pb/^{238}U$ ages of $49.40{\pm}0.37Ma$ (n=11, MSWD=1.9). On the other hand, zircons from plutonic rocks of borehole PB-3 yielded weighted mean $^{206}Pb/^{238}U$ ages of $262.4{\pm}3.6Ma$ (n=21, MSWD=4.5), $252.4{\pm}3.6Ma$ (n=8, MSWD=1.9) and $261.8{\pm}1.5Ma$ (n=31, MSWD=1.3). Detrital zircons from the sedimentary strata overlain the volcanic rocks showed a wide age span from Neoproterozoic to Cenozoic, with the youngest population corresponding to $21.89{\pm}1.1Ma$ (n=15, MSWD=0.04) and $21.68{\pm}1.2Ma$ (n=10, MSWD=19). These dating results indicate that the basement of the Pohang basin is composed of Late Permian plutonic rocks and overlain Late Cretaceous to Eocene volcanic sequences. Miocene sediments were deposited in the uppermost part of the basin, possibly associated with the opening of the East Sea. The Sr-Nd isotopic compositions of the Permian plutonic rocks were comparable with those reported from Permian-Triassic granitoids in the Yeongdeok area, northern Gyeongsang basin. They may have been recycled into parts of the Cretaceous-Paleogene magmatic rocks within the Gyeongsang basin.

• Korean Journal of Soil Science and Fertilizer
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• v.40 no.6
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• pp.447-453
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• 2007

With a broad objective for the development of microbial based fertilizers, a total of 373 strains were isolated from rhizoplane and rhizosphere of pepper, tomato, lettuce, pasture, and grass. The efficacy of the isolates to augument overall plant growth was evaluated. After screening for their plant growth promotion and antagonistic properties in vitro efficient strains were further selected. The most efficient strains was characterized by 16S rRNA gene sequences and biochemical techniques and was designated as Bacillus subtilis S37-2. The strains facilitated plant growth and inhibited the plant phathogenic fungi such as Fusarium oxysporum (KACC 40037, Rhizoctonia solani (KACC 40140), and Sclerotinia sclerotiorum (KACC 40457). Pot based bioassay using lettuce as test plant was conducted by inoculating suspension ($10^5$ to $10^8cells\;mL^{-1}$) of B. subtilis S37-2 to the rhizosphere of lettuce cultivated in soil pots. Compared with non-inoculated pots, marked increase in leaf (42.3%) and root mass (48.7%) was observed in the inoculation group where the 50ml of cell mixture ($8.7{\times}10^8cells\;ml^{-1}$) was applied to the rhizosphere of letuce either once or twice. Antagonistic effects of B. subtilis S37-2 strain on S. sclerotiorum (KACC 40457) were tested. All the tested lettuce plants perished after 9 days in treatment containing only S. sclerotiorum, but only 17% of lettuce was perished in the inoculation plot. B. subtilis grew well in the TSB culture medium. The isolates grew better in yeast extracts than peptone and tryptone as nitrogen source. The growth rate was 2~4 times greater at $37^{\circ}C$ as compared with $30^{\circ}C$ incubation temperature. B. subitlis S37-2 produced $0.1{\mu}g\;ml^{-1}$ of IAA (indole 3-acetic acid) in the TSB medium containing L-tryptophan($20mg\;L^{-1}$) in 24 hours.

• Korean Journal of Breeding Science
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• v.42 no.4
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• pp.397-406
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• 2010

Field screening method has been commonly used for purity test of $F_1$ hybrid seeds in melon and oriental melon. However, as this method takes a lot of time and cost, molecular marker-based purity test is necessary. To develop molecular markers for purity test, thirty pairs of SNP (single nucleotide polymorphism) primers were obtained from melon EST sequences, and 10 polymorphic markers showing HRM (high resolution melting) polymorphisms between parents of two melon cultivars and one oriental melon cultivar were selected. Blind tests were performed to validate usefulness of the selected markers for purity test. Blind test results showed that HRM genotypes were matched with the expected identity of individual sample, $F_1$ hybrid, male or female parents. Three HRM-based SNP markers were converted to CAPS markers for general use which is favor to breeders. We expect that SNP markers developed in this study will be useful for purity test of $F_1$ hybrid seeds in melon and oriental melon.

• The Journal of the Petrological Society of Korea
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• v.28 no.2
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• pp.111-128
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• 2019

Ulleung Island is the top of an intraplate alkalic volcano rising 3200 m from sea floor in the East Sea (or Sea of Japan). The emergent 984.6 m consist of eruptive products of basaltic, trachytic and phonolitic magmas, which are divided into Dodong Basaltic Rocks, and Ulleung, Seonginbong and Nari groups. The Maljandeung Tuff in the Nari Group consists of thick pyroclastic sequences which are subdivided into 4 members (N-5, U-4, 3, 2), generating from explosive eruptions during past 18.8~5.6 ka B.P. From chemical data, the Member N-5, phonolitic in composition, is considerably enriched in incompatible elements and REE patterns with significant negative Eu anomalies. The members 4, 3 and 2 are phonolitic to tephriphonolitic in composition, and their REE patterns do not have significant Eu anomalies. In variation trend diagrams, many elements show abrupt compositional gaps between members, and gradual upward-mafic variations from phonolite to tephriphonolite within each member. It suggests a downward-mafic zonation that were evolved into phonolitic zone in the lower part to tephriphonolitic zone in upper part of magma chamber. It is supposed that the chemical stratification generated from multiple mechanisms of thermal gravidiffusion, crystal fractionation, and gradual melting and sequential emplacement. The stratified magmas were explosively erupted to generate a small caldera during short period (11 ka B.P.). Especially both members (U-3, 2) were accumulated by gradually erupting from the upper phonoltic zone to the lower tephriphonoltic zone of the stratified chamber in 8.4 ka B.P. and 5.6 ka B.P. time, respectively.

• Journal of Life Science
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• v.28 no.11
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• pp.1301-1315
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• 2018

We purified an antimicrobial peptide from the acidified hemocyte extract of Mytilus coruscus by $C_{18}$ reversed-phase high-performance liquid chromatography (RP-HPLC). The peptide was 4041.866 Da based on matrix-assisted laser desorption ionization time-of-flight mass spectrophotometer (MALDI-TOF/MS) and the 25 amino acids of the N-terminus sequence were identified. Comparison of this sequence of the purified peptide with the N-terminus sequences of other antimicrobial peptides revealed 100% identity with the mytilin B precursor of Mytilus coruscus. We also identified a 312 bp open-reading frame (ORF) encoding 103 amino acids based on the obtained amino acid residues. The nucleotide sequence of this ORF and the amino acid sequence also revealed 100% identity with the mytilin B precursor of Mytilus coruscus. We synthesized two antimicrobial peptides with an alanine residue in the C-terminus, and designated them mytilin B1 and B2. These two antimicrobial peptides showed antimicrobial activity against gram-positive bacteria, including Bacillus cereus and Streptococcus parauberis (minimal effective concentration, MECs $41.6-89.7{\mu}g/ml$), gram-negative bacteria, including Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Providencia stuartii, Pseudomonas aeruginosa, and Vibrio ichthyoenteri (MECs $7.4-39.5{\mu}g/ml$), and the fungus Candida albicans (MECs $26.0-31.8{\mu}g/ml$). This antimicrobial activity was stable under heat and salt conditions. Furthermore, the peptides did not exhibit significant hemolytic activity or cytotoxic effects. These results suggest that mytilin B could be applied as alternative antibiotic agent, and they add to the understanding of the innate immunity of hard-shelled mussels.

• Korean Journal of Heritage: History & Science
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• v.52 no.3
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• pp.74-93
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• 2019

The Bird Track Site in the Haman Formation in Yongsanri (Natural Monument No. 222) was reported on the named Koreanaornis hamanensis and Jindongornipes kimi sauropod footprint Brontopodus and ichnospecies Ochlichnus formed by Nematoda. This site has outstanding academic value because it is where the second-highest number of bird tracks have been reported in the world. However, only 25% of the site remains after being designated a natural monument in 1969. This is due to artificial damage caused by worldwide fame and quarrying for flat stone used in Korean floor heating systems. The Haman Formation, including this fossil site, has lithofacies showing reddish-grey siltstone and black shale, alternately. The boundary of the two rocks is progressive, and sedimentary structures like ripple marks and sun cracks can clearly be found. This site was divided into seven formations according to sedimentary sequences and structures. The results of a nondestructive deterioration evaluation showed that chemical and biological damage rates were very low for all formations. Also, physical damage displayed low rates with 0.49% on exfoliation, 0.04% on blistering, 0.28% on break-out; however, the joint crack index was high, 6.20. Additionally, efflorescence was observed on outcrops at the backside and the northwestern side. Physical properties measured by an indirect ultrasonic analysis were found to be moderately weathered (MW). Above all, the southeastern side was much fresher, though some areas around the column of protection facility appeared more weathered. Furthermore, five kinds of discontinuity surface can be found at this site, with the bedding plane showing the higher share. There is the possibility of toppling failure occurring at this site but stable on plane and wedge failure by means of stereographic projection. We concluded that the overall level of deterioration and stability were relatively fine. However, continuous monitoring and conservation treatment and management should be performed as situations such as the physicochemical weathering of the fossil layer, and the efflorescence of the mortar adjoining the protection facility's column appear to be challenging to control.