• Journal of Life Science
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• v.14 no.6 s.67
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• pp.906-912
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• 2004

Helicobacter pylori infection is highly prevalent, as high as 2/3 of whole population infected, in Korea. H. pylori infection initiates inflammation by induction of interleukin-8 through type IV secretion of CagA. It was recently suggested that induction failure of IL-8 is not associated with defect in cag PAI but associated with cagE locus diversity. This study was designed to investigate ability of 11-8 in-duction according to sequence variation within the cagE gene, cagA TP motifs and vacA m-types in vitro study using AGS cell-line, and to evaluate its association with different clinical outcome. Seventy-four H. pylori stains were isolated from 23 patients with gastric cancer (Ca), 24 subjects with gastritis (G) and 27 patients with duodenal ulcer (Du) in Kangnam St. Mary's Hospital, Seoul, Korea. cagE gene diversity was confirmed by the PCR-RFLP methods with MboI/NlaIII and tyrosine phosphate motifs (TPMs) of cagA was determined TPM-A and C by using DdeI/Tsp5091 restriction enzyme and TPM-B was determend by Real time PCR the method of Owen et al. and IL-8 was measured by ELISA assay. IL-8 activity was positively detected in 59 among 74 strains $(79.7\%)$. IL-8 secretion was significantly increased in MboI A and MboI B type compared to MboI C type and in MboI/NlaIII A-C and B-C type than C-C type. 1L-8 activity was not associated with either the number or composition of cagA tyrosine phosphorylation motifs and vacA m-type. There was no significant difference in IL-8 activity among patient groups. cagE gene diversity is thought to be mainly associated with the induction of IL-8 in H. pylori infection.

• Journal of the Korean Society for Marine Environment & Energy
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• v.17 no.4
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• pp.283-296
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• 2014

The distribution of heavy metals in the stormwater runoffs from industrial sites around Shihwa Lake that implements the total pollutant load management system (TPLMS) was studied to characterize the temporal changes of metal concentrations and to assess the ecological risk in dissolved and particulate phases of the selected metals. The dissolved Co and Ni concentration demonstrated first flush and tended to decrease with increasing of the duration of rainfall. The intensity of precipitation was found to be the main controlling factor of particulate metals in the stromwater runoffs. The particulate concentration of Pb accounted for 97.2% so the particulate phase was its main form. Other metals followed the sequence: Pb>Cu>Cd>Co>Zn>Ni. The particulate-dissolved partitioning coefficient ($K_d$) indicated that the $K_d$ of Pb were bigger than that of other metals because the metal Pb in the stormwater runoffs is quickly removed into the particulate phase. In a single day rainfall event, total runoff fluxes for total metals as the sum of dissolved and particulate forms through only two sewer outlets were 2.21 kg for Co, 30.5 kg for Ni, 278.3 kg for Cu, 398.3 kg for Zn, 0.39 kg for Cd and 40.0 kg for Pb, respectively. Given the annual rainfall, the number of rain days and the basin area for total pollutant load management system (TPLMS) of Shihwa area, enormous amount of non-point metal pollutants were entered into Lake with any treatment. The dissolved metals (e.g., Ni, Cu and Zn) in the stormwater runoffs exceeded the acute water quality criteria. Additionally, all metals were significantly enriched in the particulate phase and exceeded the PEL criteria of sediment quality guidelines (SQGs). These results indicated that the heavy metals in the stormwater runoffs may pose a very high ecological risk to the coastal environments and ecosystem.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.6 no.2
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• pp.81-92
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• 2001

According to analyses of high-resolution seismic profiles (air gun, sparker, and SBP) and a deep-drill core(YSDP 105) in the mid-eastern Yellow Sea, stratigraphic and geoacoustic models have been established and seismo-acoustic modeling has been fulfilled using ray tracing of finite element method. Stratigraphic model reflects seismo-, litho-, and chrono-stratigraphic sequences formed under a significant influence of Quaternary glacio-eustatic sea-level fluctuations. Each sequence consists of terrestrial to very-shallow-marine coarse-grained lowstand systems tract and tidal fine-grained transgressive to highstand systems tract. Based on mean grain-size data (121 samples) of the drill core, bulk density and P-wave velocity of depositional units have been inferred and extrapolated down to a depth of the recovery using the Hamilton's regression equations. As goo-acoustic parameters, the 121 pairs of bulk density and P-wave velocity have been averaged on each unit of the stratigraphic model. As a result of computer ray-tracing simulation of the subsurface strata, we have found that there are complex ray paths and many acoustic-shadow zones owing to the presence of irregular layer boundaries and low-velocity layers.

• Journal of Plant Biotechnology
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• v.39 no.1
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• pp.33-48
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• 2012

As a scientific curiosity to understand the structure and the function of crops and experimental efforts to apply it to plant breeding, genetic maps have been constructed in various crops. Especially, in the case of Brassica crop, genetic mapping has been accelerated since genetic information of model plant $Arabidopsis$ was available. As a result, the whole $B.$ $rapa$ genome (A genome) sequencing has recently been done. The genome sequences offer opportunities to develop molecular markers for genetic analysis in $Brassica$ crops. RFLP markers are widely used as the basis for genetic map construction, but detection system is inefficiency. The technical efficiency and analysis speed of the PCR-based markers become more preferable for many form of $Brassica$ genome study. The massive sequence informative markers such as SSR, SNP and InDels are also available to increase the density of markers for high-resolution genetic analysis. The high density maps are invaluable resources for QTLs analysis, marker assisted selection (MAS), map-based cloning and comparative analysis within $Brassica$ as well as related crop species. Additionally, the advents of new technology, next-generation technique, have served as a momentum for molecular breeding. Here we summarize genetic and genomic resources and suggest their applications for the molecular breeding in $Brassica$ crop.

• Korean Journal of Microbiology
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• v.46 no.1
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• pp.21-26
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• 2010

As the causative agent of Anthrax, Bacillus anthracis causes an acute fatal disease in herbivores such as cattle, sheep, and horses as well as humans. The therapeutics and prevention of anthrax currently available are based on antibiotics and the live attenuated vaccine strains, which may be problematic due to the emergency of antibiotic resistant strains or residual virulence in those vaccine strains. Therefore, it has been required to develop novel therapeutics and vaccines which are safer and applicable to humans. Recently, the development of the multivalent vaccine targeting both spores and vegetative cells of B. anthracis along with anthrax toxin has been reported. In our attempts to screen potential candidates for those multivalent vaccines, the whole genomic expression library of B. anthracis was constructed in this study. To the end, the partial digests of the genomic DNA from B. anthracis (ATCC 14578) with Sau3AI were ligated with the inducible pET30abc expression vectors, resulting in approximately $1{\times}10^5$ clones in E. coli BL21(DE3). The redundancy test by DNA nucleotide sequencing was performed for the randomly selected 111 clones and found 56 (50.5%) B. anthracis genes, 17 (15.3%) vector sequences, and 38 (34.2%) unknown genes with no sequence homology by BLAST. An inducible expression of the recombinant proteins was confirmed by Western blot. Interestingly, some clones could react with the antiserum against B. anthracis. These results imply that the whole genomic library constructed in this study can be applied for analyzing the immunomes of B. anthracis.

• Journal of fish pathology
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• v.6 no.2
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• pp.111-122
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• 1993

The mechanism by which $V_H$ region gene segments is selected in B lymphocyte is not known. Moreover, evidence for both random and nonrandom expression of $V_H$ genes in matured B cells has been presented previously. In this report, the technique of in situ hybridization allowed us to analyze expressed $V_H$ gene families in normal B lymphocyte at the single cell level. The analysis of normal B cells in this study eliminated any posssible bias resulting from transformation protocols used previously and minimized limitation associated with sampling size. Therefore, an accurate measure of the functional and expressed $V_H$ gene repertoire in B lymphocyte could be made. One of the most important controls for the optimization of in situ hybridization is to establish probe concentration and washing stringency due to the degree of nucleotide sequence similarlity between different families which in some cases can be as high as 70%. When the radioactive $C{\mu}$ and $V_{H}J558$ RNA probes are tested on LPS-stimulated adult spleen cells, $2{\sim}4{\times}106cpm$/slide shows low background and reasonable frequency of specific positive cells. For the washing condition. 40~50% formamide at $54^{\circ}C$ is found to be optimum for the $C{\mu}$. $V_{H}S107$ and $V_{H}J558$ probes. The analyzed results clearly demonstrate that the level of each different $V_H$ gene family expression is dependent upon the complexity or size of that family. These findings are also extended to the level of $V_H$ gene family expression in separated bone marrow B cells depend upon the various stage of differentiation and conclude no preferential utilization of specific $V_H$ gene family. Thus, the utilization of VH gene segments in B lymphocyte of adult BALB/c mice is random and is not regulated or changed during the differentiation of B cells.

• Geophysics and Geophysical Exploration
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• v.14 no.1
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• pp.98-104
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• 2011

Numerical simulation in exploration geophysics provides important insights into subsurface wave propagation phenomena. Although elastic wave simulations take longer to compute than acoustic simulations, an elastic simulator can construct more realistic wavefields including shear components. Therefore, it is suitable for exploration of the responses of elastic bodies. To overcome the long duration of the calculations, we use a Graphic Processing Unit (GPU) to accelerate the elastic wave simulation. Because a GPU has many processors and a wide memory bandwidth, we can use it in a parallelised computing architecture. The GPU board used in this study is an NVIDIA Tesla C1060, which has 240 processors and a 102 GB/s memory bandwidth. Despite the availability of a parallel computing architecture (CUDA), developed by NVIDIA, we must optimise the usage of the different types of memory on the GPU device, and the sequence of calculations, to obtain a significant speedup of the computation. In this study, we simulate two- (2D) and threedimensional (3D) elastic wave propagation using the Finite-Difference Time-Domain (FDTD) method on GPUs. In the wave propagation simulation, we adopt the staggered-grid method, which is one of the conventional FD schemes, since this method can achieve sufficient accuracy for use in numerical modelling in geophysics. Our simulator optimises the usage of memory on the GPU device to reduce data access times, and uses faster memory as much as possible. This is a key factor in GPU computing. By using one GPU device and optimising its memory usage, we improved the computation time by more than 14 times in the 2D simulation, and over six times in the 3D simulation, compared with one CPU. Furthermore, by using three GPUs, we succeeded in accelerating the 3D simulation 10 times.

• Journal of the Korean Institute of Landscape Architecture
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• v.37 no.2
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• pp.90-103
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• 2009

The poem 'Kyungjusipiyung(慶州十二詠)' written by Seo, Geo-jeong(徐居正) describes sentiments felt for the ruined historical and cultural landscape of Silla's capital city, Kyungju. It differs from the existing 'Eight Sceneries(八景)' as it conveys the strong metaphorical aesthetics of ruins as the episodes and figures are sung, as well as the myths and stories related to the representative holy places of the Silla culture: Gyelim(鷄林), Banwolseong(半月城), Najeong(蘿井), Oneung(五陵), Geumosan(金鰲山), the scenic beauty of deep placeness, Poseokjeong(鮑石亭), Mooncheon(蚊川), Cheomseongdae(瞻星臺), Boonhwangsa(芬皇寺), Youngmyosa(靈妙寺) and Grave of the General Kim Yu-Sin(金庾信墓). Compared with the former "Eight Sceneries" Poems, including Seo Geojeong's 'Kyungjusipiyung', there is a difference in the content of theme recitation, as well as in structure and form, especially with the deep impression of the classical features of the meanings and acts. The sequence of theme recitation seems to be composed of more than two visual corridors visited during trips that last longer than two days. The dominant emotions expresses in this poem, through written in the spring, are regret and sadness such as 'worn', 'broken and ruined', 'old and sad', without touching on the beauty of nature and the taste for life that is found in most of the Eight Sceneries Poems. Thus, the feelings of the reciter himself, Seo, Geo-jeong, about the described sceneries and their symbolism are more greatly emphasized than the beauty of form. The characteristic aspect of his experiences of ruins expressed from 'Kyungjusipiyung' is that the experiences were, first of all, qualitative of the aura conveyed; that is, the quality omnipresent throughout the culture of Silla as reflected in the twelve historical and cultural landscapes. In this poem, the cultural ruins of the invisible dimension such as the myths and legends are described by repetition, parallelism, juxtaposition, reflection and admiration from the antiphrases, as well as the civilized ruins of the visible dimension such as the various sceneries and features of Kyungju. This seems to be characteristic of the methods by which Seo, Geo-jeong appreciates 'Silla' in the poem 'Kyungjusipiyung'. Ruins as an Aesthetic Object imply the noble pride of Seo, Geo-jeong in identifying himself with the great nature of ruins. In 'Kyungjusipiyung', the images of the ruins of Silla and Kyungju are interspersed in spite of his positive recognition of 'the village of Kyungju' based on his records. However, though the concept of ruins has a pessimistic tone connoting the road of extinction and downfall, the aspect here seems to ambivalently contain the desire to recover and revive Kyungju through the Chosun Dynasty as adominant influence on the earlier Chosun's literary tide. The aesthetics of the scenery found in Seo, Geo-jeong's 'Kyungjusipiyung' contain the strongest of metaphor and symbolism by converting the experiences of the paradoxical ruins into the value of reflective experiences.

• The Korean Journal of Petroleum Geology
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• v.4 no.1_2 s.5
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• pp.27-39
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• 1996

In the Cretaceous, the Gulf Coast Basin evolved as a marginal sag basin. Thick clastic and carbonate sequences cover the disturbed and diapirically deformed salt layer. In the Cretaceous the salinities of the Gulf Coast Basin probably matched the Holocene Persian Gulf, as is evidenced by the widespread development of supratidal anhydrite. The major Lower Cretaceous reservoir formations are the Cotton Valley, Hosston, Travis Peak siliciclastics, and Sligo, Trinity (Pine Island, Pearsall, Glen Rose), Edwards, Georgetown/Buda carbonates. Source rocks are down-dip offshore marine shales and marls, and seals are either up-dip shales, dense limestones, or evaporites. During this period, the entire Gulf Basin was a shallow sea which to the end of Cretaceous had been rimmed to the southwest by shallow marine carbonates while fine-grained terrigengus clastics were deposited on the northern and western margins of the basin. The main Upper Cretaceous reservoir groups of the Gulf Coast, which were deposited in the period of a major sea level .rise with the resulting deep water conditions, are Woodbinefruscaloosa sands, Austin chalk and carbonates, Taylor and Navarro sandstones. Source rocks are down-dip offshore shales and seals are up-dip shales. Major trap types of the Lower and Upper Cretaceous include salt-related anticlines from low relief pillows to complex salt diapirs. Growth fault structures with rollover anticlines on downthrown fault blocks are significant Gulf Coast traps. Permeability barriers, up-dip pinch-out sand bodies, and unconformity truncations also play a key role in oil exploration from the Cretaceous Gulf Coast reservoirs. The sedimentary sequences of the major Cretaceous reseuoir rocks are a good match to the regressional phases on the global sea level cuwe, suggesting that the Cretaceous Gulf Coast sedimentary stratigraphy relatively well reflects a response to eustatic sea level change throughout its history. Thus, of the three main factors controlling sedimentation (tectonic subsidence, sediment input, and eustatic sea level change) in the Gulf Coast Basin, sea-level ranks first in the period.

• KSCE Journal of Civil and Environmental Engineering Research
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• v.40 no.3
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• pp.273-283
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• 2020

Because of climate change, the occurrence of localized and heavy rainfall is increasing. It is important to predict floods in urban areas that have suffered inundation in the past. For flood prediction, not only numerical analysis models but also machine learning-based models can be applied. The LSTM (Long Short-Term Memory) neural network used in this study is appropriate for sequence data, but it demands a lot of data. However, rainfall that causes flooding does not appear every year in a single urban basin, meaning it is difficult to collect enough data for deep learning. Therefore, in addition to the rainfall observed in the study area, the observed rainfall in another urban basin was applied in the predictive model. The LSTM neural network was used for predicting the total overflow, and the result of the SWMM (Storm Water Management Model) was applied as target data. The prediction of the inundation map was performed by using logistic regression; the independent variable was the total overflow and the dependent variable was the presence or absence of flooding in each grid. The dependent variable of logistic regression was collected through the simulation results of a two-dimensional flood model. The input data of the two-dimensional flood model were the overflow at each manhole calculated by the SWMM. According to the LSTM neural network parameters, the prediction results of total overflow were compared. Four predictive models were used in this study depending on the parameter of the LSTM. The average RMSE (Root Mean Square Error) for verification and testing was 1.4279 ㎥/s, 1.0079 ㎥/s for the four LSTM models. The minimum RMSE of the verification and testing was calculated as 1.1655 ㎥/s and 0.8797 ㎥/s. It was confirmed that the total overflow can be predicted similarly to the SWMM simulation results. The prediction of inundation extent was performed by linking the logistic regression with the results of the LSTM neural network, and the maximum area fitness was 97.33 % when more than 0.5 m depth was considered. The methodology presented in this study would be helpful in improving urban flood response based on deep learning methodology.