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Search Results: 1 - 10 of 28553 matches for " Seul-Bi Lee "
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A Retroperitoneal Inflammatory Myofibroblastic Tumor Mimicking a Germ Cell Tumor of the Undescended Testis: A Case Report and Literature Review  [PDF]
Seul-Bi Lee, Jung-Hee Yoon, Seung-Ho Kim, Yedaun Lee, Jin-Soo Lee, Jung-Wook Seo
Advances in Computed Tomography (ACT) , 2016, DOI: 10.4236/act.2016.53004
Abstract: We report here a case of an inflammatory myofibroblastic tumor in the retroperitoneum, which mimicked a germ cell tumor of the undescended testis. A 75-year-old healthy man presented with a palpable abdominal mass. On the computed tomography image, there was large, well-defined soft tissue mass in the left side of the retroperitoneum, and there was no visible left testis or seminal vesicle. After contrast enhancement, the mass appeared to be relatively homogeneous, considering its large size. With ultrasonography, it appeared as a well-defined, hypoechoic mass with intratumoral vascularity. This solid mass was surgically diagnosed as an inflammatory myofibroblastic tumor.
Vegetation of mono-layer landfill cover made of coal bottom ash and soil by compost application  [PDF]
Seul Bi Lee, Sang Yoon Kim, Chan Yu, Soon-Oh Kim, Pil Joo Kim
Journal of Agricultural Chemistry and Environment (JACEN) , 2013, DOI: 10.4236/jacen.2013.23008
Abstract: Monolayer barriers called evapotranspiration (ET) covers were developed as alternative final cover systems in waste landfills but high-quality soil remains a limiting factor in these cover systems. Coal bottom ash was evaluated to be a very good alternative to soil in previous tests and a combination of soil (65% wt.wt-1) and coal bottom ash (35% wt.wt-1) was evaluated to be the most feasible materials for ET cover systems. In our pot test, selected manure compost as soil amendment for the composite ET cover system, which was made of soil and bottom ash at ca. 40 Mg.ha-1 application level was very effective to promote vegetation growth of three plants; namely, garden cosmos (Cosmosbipinnatus), Chinese bushclover (Lespedezacuneata), and leafy lespedeza (Lespedeza cyrtobotrya). To evaluate the effect of compost application on plant growth in an ET vegetative cover system, two couples of lysimeters, packed with soil and a mixture of soil and bottom ash, were installed in a pilot landfill cover system in 2007. Manure composts were applied at the rates of 0 and  40 Mg.ha-11before sowing the five plant species, i.e.indigo-bush (Amorphafruticosa), Japanese mugwort (Artemisia princeps, Arundinella hirta, Lespedezacuneata, and Lespedezacyrtobotrya). Unseeded native plant (green foxtail,Setaria viridis) was dominant in all treatments in the 1st year after installation while the growth of the sown plants significantly improved over the years. Total biomass productivity significantly increased with manure compost application, and more significantly increased in the composite ET cover made of soil and bottom ash treatment compared to the single soil ET cover, mainly due to more improved soil nutrient levels promoting vegetation growth and maintaining the vegetation system. The use of bottom ash as a mixing material in ET cover systems has a strong potential as an alternative to fine-grained soils, and manure compost addition can effectively enhance vegetative propagation in ET cover systems.
Prediction of ultra-high ON/OFF ratio nanoelectromechanical switching from covalently-bound C60 chains
Han Seul Kim,Jhinhwan Lee,Yong-Hoon Kim
Physics , 2013, DOI: 10.1016/j.carbon.2013.09.054
Abstract: Applying a first-principles computational approach, we have systematically analyzed the effects of [2+2] cycloaddition oligomerization of fullerene C60 chains on their junction electronic and charge transport properties. For hypothetical infinite C60 chains, we first establish that the polymerization can in principle increase conductance by several orders of magnitude due to the strong orbital hybridizations and band formation. On the other hand, our simulations of the constant-height scanning tunneling microscope (STM) configuration shows that, in agreement with the recent experimental conclusion, the junction electronic structure and device characteristics are virtually unaffected by the C60 chain oligomerization. We further predict that the switching characteristics including even the ON/OFF-state assignment will sensitively depend on the substrate metal species due to the Fermi-level pinning at the substrate-side contact and the subsequent energy level bending toward the STM tip-side contact. We finally demonstrate that a force-feedbacked nanoelectromechanical approach in which both of the C60-electrode distances are kept at short distances before and after switching operations can achieve a metal-independent and significantly improved switching performance due to the Fermi-level pinning in both contacts and the large intrinsic conductance switching capacity of the C60 chain oligomerization.
Distinct mechanisms of DNA sensing based on N-doped carbon nanotubes with enhanced conductance and chemical selectivity
Han Seul Kim,Seung Jin Lee,Yong-Hoon Kim
Physics , 2012, DOI: 10.1002/smll.201301225
Abstract: Carrying out first-principles calculations, we study N-doped capped carbon nanotube (CNT) electrodes applied to DNA sequencing. While we obtain for the face-on nucleobase junction configurations a conventional conductance ordering where the largest signal results from guanine according to its high highest occupied molecular orbital (HOMO) level, we extract for the edge-on counterparts a distinct conductance ordering where the low-HOMO thymine provides the largest signal. The edge-on mode is shown to operate based on a novel molecular sensing mechanism that reflects the chemical connectivity between N-doped CNT caps that can act both as electron donors and electron acceptors and DNA functional groups that include the hyperconjugated thymine methyl group.
Population Genetic Structure and Evidence of Demographic Expansion of the Ayu (Plecoglossus altivelis) in East Asia
Ye-Seul Kwan,Hye-Kyung Song,Hyun-Jung Lee,Wan-Ok Lee
Animal Systematics, Evolution and Diversity , 2012, DOI: http://dx.doi.org/10.5635/ased.2012.28.4.279
Abstract: Plecoglossus altivelis (ayu) is an amphidromous fish widely distributed in Northeastern Asia from the East China Sea to the northern Japanese coastal waters, encompassing the Korean Peninsula within its range. The shore lines of northeastern region in Asia have severely fluctuated following glaciations in the Quaternary. In the present study, we investigate the population genetic structure and historical demographic change of P. altivelis at a population level in East Asia. Analysis of molecular variance (AMOVA) based on 244 mitochondrial control region DNA sequences clearly showed that as the sampling scope extended to a larger geographic area, genetic differentiation began to become significant, particularly among Northeastern populations. A series of hierarchical AMOVA could detect the genetic relationship of three closely located islands between Korea and Japan that might have been tightly connected by the regional Tsushima current. Neutrality and mismatch distribution analyses revealed a strong signature of a recent population expansion of P. altivelis in East Asia, estimated at 126 to 391 thousand years ago during the late Pleistocene. Therefore it suggests that the present population of P. altivelis traces back to its approximate demographic change long before the last glacial maximum. This contrasts our a priori expectation that the most recent glacial event might have the most crucial effect on the present day demography of marine organisms through bottleneck and subsequent increase of effective population size in this region.
Loss of CclA, required for histone 3 lysine 4 methylation, decreases growth but increases secondary metabolite production in Aspergillus fumigatus
Jonathan M. Palmer,Jin Woo Bok,Seul Lee,Taylor?R.T. Dagenais
PeerJ , 2013, DOI: 10.7717/peerj.4
Abstract: Secondary metabolite (SM) production in filamentous fungi is mechanistically associated with chromatin remodeling of specific SM clusters. One locus recently shown to be involved in SM suppression in Aspergillus nidulans was CclA, a member of the histone 3 lysine 4 methylating COMPASS complex. Here we examine loss of CclA and a putative H3K4 demethylase, HdmA, in the human pathogen Aspergillus fumigatus. Although deletion of hdmA showed no phenotype under the conditions tested, the cclA deletant was deficient in tri- and di-methylation of H3K4 and yielded a slowly growing strain that was rich in the production of several SMs, including gliotoxin. Similar to deletion of other chromatin modifying enzymes, ΔcclA was sensitive to 6-azauracil indicating a defect in transcriptional elongation. Despite the poor growth, the ΔcclA mutant had wild-type pathogenicity in a murine model and the Toll-deficient Drosophila model of invasive aspergillosis. These data indicate that tri- and di-methylation of H3K4 is involved in the regulation of several secondary metabolites in A. fumigatus, however does not contribute to pathogenicity under the conditions tested.
Carbon nanobuds based on carbon nanotube caps: A first-principles study
Ji Il Choi,Hyo Seok Kim,Han Seul Kim,Ga In Lee,Jeung Ku Kang,Yong-Hoon Kim
Physics , 2015, DOI: 10.1039/C5NR07188G
Abstract: Based on density functional theory calculations, we here show that the formation of a fullerene C$_{60}$ carbon "nanobud" (CNB) on carbon nanotube (CNT) caps is energetically more favorable than that on CNT sidewalls. The dominant CNB formation mode for CNT caps is found to be the [2+2] cycloaddition reaction as in the conventional CNT sidewall case. However, it is identified to be exothermic in contrast to the endothermic reaction on CNT sidewalls. Computed reaction pathways further demonstrate that the formation (dissociation) barrier for the CNT cap-based CNB is slightly lower (significantly higher) than that of the CNT sidewall-based CNB, indicating an easier CNB formation as well as a higher structural stability. Additionally, performing matrix Green's function calculations, we study the charge transport properties of the CNB/metal electrode interfaces, and show that the C$_{60}$ bonding to the CNT cap or open end induces resonant transmissions near the Fermi level. It is also found that the good electronic linkage in the CNT cap-C$_{60}$ cycloaddition bonds results in the absence of quantum interference patterns, which contrasts the case of the CNB formed on an open-ended CNT that shows a Fano resonance profile.
Loss of the Promyelocytic Leukemia Protein in Gastric Cancer: Implications for IP-10 Expression and Tumor-Infiltrating Lymphocytes
Hee Ja Kim, Dong Eun Song, Seul Ye Lim, Sung-Hee Lee, Jihee Lee Kang, Sun Jung Lee, Etty N. Benveniste, Youn-Hee Choi
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026264
Abstract: Gastric cancer is one of the most common causes of cancer-related mortality worldwide. Expression of the tumor suppressor, promyelocytic leukemia (PML) protein, is reduced or abolished in gastric carcinomas, in association with an increased level of lymphatic invasion, development of higher pTNM staging, and unfavorable prognosis. Herein, we investigated the relationship between the extent of tumor-infiltrating lymphocytes and the status of PML protein expression in advanced gastric carcinoma. We observed higher numbers of infiltrating T-cells in gastric carcinoma tissues in which PML expression was reduced or abolished, compared to tissues positive for PML. The extent of T-cell migration toward culture supernatants obtained from interferon-gamma (IFN-γ-stimulated gastric carcinoma cell lines was additionally affected by expression of PML in vitro. Interferon-gamma-inducible protein 10 (IP-10/CXCL10) expression was increased in gastric carcinoma tissues displaying reduced PML levels. Moreover, both Pml knockout and knockdown cells displayed enhanced IP-10 mRNA and protein expression in the presence of IFN-γ. PML knockdown increased IFN-γ-mediated Signal Transducer and Activator of Transcription-1 (STAT-1) binding to the IP-10 promoter, resulting in elevated transcription of the IP-10 gene. Conversely, PML IV protein expression suppressed IP-10 promoter activation. Based on these results, we propose that loss of PML protein expression in gastric cancer cells contributes to increased IP-10 transcription via enhancement of STAT-1 activity, which, in turn, promotes lymphocyte trafficking within tumor regions.
Stouffer’s Test in a Large Scale Simultaneous Hypothesis Testing
Sang Cheol Kim, Seul Ji Lee, Won Jun Lee, Young Na Yum, Joo Hwan Kim, Soojung Sohn, Jeong Hill Park, Jeongmi Lee, Johan Lim, Sung Won Kwon
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0063290
Abstract: In microarray data analysis, we are often required to combine several dependent partial test results. To overcome this, many suggestions have been made in previous literature; Tippett’s test and Fisher’s omnibus test are most popular. Both tests have known null distributions when the partial tests are independent. However, for dependent tests, their (even, asymptotic) null distributions are unknown and additional numerical procedures are required. In this paper, we revisited Stouffer’s test based on z-scores and showed its advantage over the two aforementioned methods in the analysis of large-scale microarray data. The combined statistic in Stouffer’s test has a normal distribution with mean 0 from the normality of the z-scores. Its variance can be estimated from the scores of genes in the experiment without an additional numerical procedure. We numerically compared the errors of Stouffer’s test and the two p-value based methods, Tippett’s test and Fisher’s omnibus test. We also analyzed our microarray data to find differentially expressed genes by non-genotoxic and genotoxic carcinogen compounds. Both numerical study and the real application showed that Stouffer’s test performed better than Tippett’s method and Fisher’s omnibus method with additional permutation steps.
Investigating the Different Mechanisms of Genotoxic and Non-Genotoxic Carcinogens by a Gene Set Analysis
Won Jun Lee, Sang Cheol Kim, Seul Ji Lee, Jeongmi Lee, Jeong Hill Park, Kyung-Sang Yu, Johan Lim, Sung Won Kwon
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0086700
Abstract: Based on the process of carcinogenesis, carcinogens are classified as either genotoxic or non-genotoxic. In contrast to non-genotoxic carcinogens, many genotoxic carcinogens have been reported to cause tumor in carcinogenic bioassays in animals. Thus evaluating the genotoxicity potential of chemicals is important to discriminate genotoxic from non-genotoxic carcinogens for health care and pharmaceutical industry safety. Additionally, investigating the difference between the mechanisms of genotoxic and non-genotoxic carcinogens could provide the foundation for a mechanism-based classification for unknown compounds. In this study, we investigated the gene expression of HepG2 cells treated with genotoxic or non-genotoxic carcinogens and compared their mechanisms of action. To enhance our understanding of the differences in the mechanisms of genotoxic and non-genotoxic carcinogens, we implemented a gene set analysis using 12 compounds for the training set (12, 24, 48 h) and validated significant gene sets using 22 compounds for the test set (24, 48 h). For a direct biological translation, we conducted a gene set analysis using Globaltest and selected significant gene sets. To validate the results, training and test compounds were predicted by the significant gene sets using a prediction analysis for microarrays (PAM). Finally, we obtained 6 gene sets, including sets enriched for genes involved in the adherens junction, bladder cancer, p53 signaling pathway, pathways in cancer, peroxisome and RNA degradation. Among the 6 gene sets, the bladder cancer and p53 signaling pathway sets were significant at 12, 24 and 48 h. We also found that the DDB2, RRM2B and GADD45A, genes related to the repair and damage prevention of DNA, were consistently up-regulated for genotoxic carcinogens. Our results suggest that a gene set analysis could provide a robust tool in the investigation of the different mechanisms of genotoxic and non-genotoxic carcinogens and construct a more detailed understanding of the perturbation of significant pathways.
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