• Archives of Pharmacal Research
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• v.24 no.5
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• pp.455-465
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• 2001

The highly potent cytotoxic DNA-DNA cross-linker consists of two cyclopropa[c]pyrrolo[3,4-3]indol-4(5H)-ones insoles [(+)-CPI-I] joined by a bisamido pyrrole (abbreviated to "Pyrrole"). The Pyrrole is a synthetic analog of Bizelesin, which is currently in phase II clinical trials due to its excellent in vivo antitumor activity. The Pyrrole has 10 times more potent cytotoxicity than Bizelesin and mostly form DNA-DNA interstrand cross-links through the N3 of adenines spaced 7 bp apart. The Pyrrole requires a centrally positioned GC base pair for high cross-linking reactivity (i.e., $5^1$-T$AT_2$A*-$3^1$), while Bizelesin prefers purely AT-rich sequences (i.e., $5^1$-T$AT_4$A*-$3^1$, where /(equation omitted) represents the cross-strand adenine alkylation and A* represents an adenine alkylation) (Park et al., 1996). In this study, the high-field $^1$H-NMR and rMD studies are conducted on the 1 1-mer DNA duplex adduct of the Pyrrole where the 5′(equation omitted)TAGTTA*-3′sequence is cross-linked by the drug. A severe structural perturbation is observed in the intervening sequences of cross-linking site, while a normal B-DNA structure is maintained in the region next to the drug-modified adenines. Based upon these observations, we propose that the interplay between the bisamido pyrrole unit of the drug and central C/C base pair (hydrogen-bonding interactions) is involved in the process of cross-linking reaction, and sequence specificity is the outcome of those interactions. This study suggests a mechanism for the sequence specific cross-linking reaction of the Pyrrole, and provides a further insight to develop new DNA sequence selective and distortive cross-linking agents.

• Journal of Microbiology and Biotechnology
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• v.22 no.4
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• pp.470-478
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• 2012

Recent genome comparisons of E. coli B and K-12 strains have indicated that the makeup of the cell envelopes in these two strains is quite different. Therefore, we analyzed and compared the envelope proteomes of E. coli BL21(DE3) and MG1655. A total of 165 protein spots, including 62 nonredundant proteins, were unambiguously identified by two-dimensional gel electrophoresis and mass spectrometry. Of these, 43 proteins were conserved between the two strains, whereas 4 and 16 strain-specific proteins were identified only in E. coli BL21(DE3) and MG1655, respectively. Additionally, 24 proteins showed more than 2-fold differences in intensities between the B and K-12 strains. The reference envelope proteome maps showed that E. coli envelope mainly contained channel proteins and lipoproteins. Interesting proteomic observations between the two strains were as follows: (i) B produced more OmpF porin with a larger pore size than K-12, indicating an increase in the membrane permeability; (ii) B produced higher amounts of lipoproteins, which facilitates the assembly of outer membrane ${\beta}$-barrel proteins; and (iii) motility- (FliC) and chemotaxis-related proteins (CheA and CheW) were detected only in K-12, which showed that E. coli B is restricted with regard to migration under unfavorable conditions. These differences may influence the permeability and integrity of the cell envelope, showing that E. coli B may be more susceptible than K-12 to certain stress conditions. Thus, these findings suggest that E. coli K-12 and its derivatives will be more favorable strains in certain biotechnological applications, such as cell surface display or membrane engineering studies.

• Macromolecular Research
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• v.16 no.8
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• pp.695-703
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• 2008

Nanoparticles have tremendous potential in cancer prevention, detection and augmenting existing treatments. They can target tumors, carry imaging capability to document the presence of tumors, sense pathophysiological defects in tumor cells, deliver therapeutic genes or drugs based on the tumor characteristics, respond to external triggers to release an appropriate agent, document the tumor response, and identify the residual tumor cells. Nanoparticles < 30 nanometers in diameter show unexpected and unique properties. Furthermore, particles < 5 nanometers in size can easily penetrate cells as well as living tissues and organs. This study evaluated the safety of nano materials in a living body and the relationship between the living tissue and synthetic nano materials by examining the in-vitro cytotoxicity of poly(lactic-co-glycolic) acid (PLGA) nano-spheres and fluorescein isothiocynate(FITC)-labeled dendrimers as polymer nanoparticles. PLGA was chosen because it has been used extensively for biodegradable nanoparticles on account of its outstanding bio-compatibility and its acceptance as an FDA approved material. The dendrimer was chosen because it can carry a molecule that recognizes cancer cells, a therapeutic agent that can kill those cells, and a molecule that recognizes the signals of cell death. Cytotoxicity in L929 mouse fibroblasts was monitored using MTT assay. Microscopic observations were also carried out to observe cell growth. All assays yielded meaningful results and the PLGA nanoparticles showed less cytotoxicity than the dendrimer. These nano-particles ranged in size from 10 to 100 nm according to microscopy and spectroscopic methods.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.8 no.2
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• pp.132-137
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• 2003

Observations of internal waves in the southwest coastal waters of Korea have been made using a mooring measurement and satellite SAR together. From May 28 to May 30 in 2002, thermistor chains with RCM and ADCP mooring measurements were carried out at 10 kin west of Ocheong-Do, together with a CTD field sur-vey on the surrounding waters. Also, a SAR image was acquired on May 29 at 06:53. The data from the in-situ measurement show several internal wave packets passing through the mooring point and the SAR image reveals numbers of internal wave packets distributed around the point. Temporal and spatial characteristics of internal waves in the southwest coastal waters were analyzed using the data from mooring measurement, SAR image, and the K-dv equation. The internal waves are important phenomena in terms of physical oceanography and military as well as marine biology. They should be considered as one of important features in the southwest coastal waters in summer.

• Journal of Korean Society on Water Environment
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• v.39 no.1
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• pp.1-8
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• 2023

Monitoring and prediction of water quality are essential for effective river pollution prevention and water quality management. In this study, a multi-classification model was developed to predict chlorophyll-a (Chl-a) level in rivers. A model was developed using CatBoost, a novel ensemble machine learning algorithm. The model was developed using hourly field monitoring data collected from January 1 to December 31, 2015. For model development, chl-a was classified into class 1 (Chl-a≤10 ㎍/L), class 2 (10<Chl-a≤50 ㎍/L), and class 3 (Chl-a>50 ㎍/L), where the number of data used for the model training were 27,192, 11,031, and 511, respectively. The macro averages of precision, recall, and F1-score for the three classes were 0.58, 0.58, and 0.58, respectively, while the weighted averages were 0.89, 0.90, and 0.89, for precision, recall, and F1-score, respectively. The model showed relatively poor performance for class 3 where the number of observations was much smaller compared to the other two classes. The imbalance of data distribution among the three classes was resolved by using the synthetic minority over-sampling technique (SMOTE) algorithm, where the number of data used for model training was evenly distributed as 26,868 for each class. The model performance was improved with the macro averages of precision, rcall, and F1-score of the three classes as 0.58, 0.70, and 0.59, respectively, while the weighted averages were 0.88, 0.84, and 0.86 after SMOTE application.

• Journal of Ocean Engineering and Technology
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• v.38 no.2
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• pp.64-73
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• 2024

Oil spills pose significant threats to marine ecosystems, human health, socioeconomic aspects, and coastal communities. Accurate real-time predictions of oil slick transport along coastlines are paramount for quick preparedness and response efforts. This study used an open-source OpenOil numerical model to simulate the fate and trajectories of oil slicks released during the 2007 Hebei Spirit accident along the Korean coasts. Six combinations of input parameters, derived from a five-day met-ocean dataset incorporating various hydrodynamic, meteorological, and wave models, were investigated to determine the input variables that lead to the most reasonable results. The predictive performance of each combination was evaluated quantitatively by comparing the dimensions and matching rates between the simulated and observed oil slicks extracted from synthetic aperture radar (SAR) data on the ocean surface. The results show that the combination incorporating the Hybrid Coordinate Ocean Model (HYCOM) for hydrodynamic parameters exhibited more substantial agreement with the observed spill areas than Copernicus Marine Environment Monitoring Service (CMEMS), yielding up to 88% and 53% similarity, respectively, during a more than four-day oil transportation near Taean coasts. This study underscores the importance of integrating high-resolution met-ocean models into oil spill modeling efforts to enhance the predictive accuracy regarding oil spill dynamics and weathering processes.

• Journal of the Korean Society for Marine Environment & Energy
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• v.15 no.3
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• pp.208-218
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• 2012

Numerical simulation technique has been developed to calculate microwave backscattering from water surface. The simulation plays a role of a substitute for experiments. Validation of the simulation was shown by comparing with experimental results. Water area observations by microwave radar have been simulated to evaluate algorithms and systems. Furthermore, the simulation can be used to understand microwave scattering mechanism on the water surface. The simulation has applied to the various methods for water area observations, and the utilizations of the simulation are introduced in this paper. In the case of fixed radar, we show following examples, 1. Radar image with a pulse Doppler radar, 2. Effect of microwave irradiation width and 3. River observation (Water level observation). In addition, another application (4.Synthetic aperture radar image) is also described. The details of the applications are as follows. 1. Radar image with a pulse Doppler radar: A new system for the sea surface observation is suggested by the simulation. A pulse Doppler radar is assumed to obtain radar images that display amplitude and frequency modulation of backscattered microwaves. The simulation results show that the radar images of the frequency modulation is useful to measure sea surface waves. 2. Effect of microwave irradiation width: It is reported (Rheem[2008]) that microwave irradiation width on the sea surface affects Doppler spectra measured by a CW (Continuous wave) Doppler radar. Therefore the relation between the microwave irradiation width and the Doppler spectra is evaluated numerically. We have shown the suitable condition for wave height estimation by a Doppler radar. 3. River observation (Water level observation): We have also evaluated algorithms to estimate water current and water level of river. The same algorithms to estimate sea surface current and sea surface level are applied to the river observation. The simulation is conducted to confirm the accuracy of the river observation by using a pulse Doppler radar. 4. Synthetic aperture radar (SAR) image: SAR images are helpful to observe the global sea surface. However, imaging mechanisms are complicated and validation of analytical algorithms by SAR images is quite difficult. In order to deal with the problems, SAR images in oceanic scenes are simulated.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.23 no.4
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• pp.153-178
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• 2018

Most operational uses of wind speed data require measurements at, or estimates generated for, the reference height of 10 m above mean sea level (AMSL). On the Ieodo Ocean Research Station (IORS), wind speed is measured by instruments installed on the lighthouse tower of the roof deck at 42.3 m AMSL. This preliminary study indicates how these data can best be converted into synthetic 10 m wind speed data for operational uses via the Korea Hydrographic and Oceanographic Agency (KHOA) website. We tested three well-known conventional empirical neutral wind profile formulas (a power law (PL); a drag coefficient based logarithmic law (DCLL); and a roughness height based logarithmic law (RHLL)), and compared their results to those generated using a well-known, highly tested and validated logarithmic model (LMS) with a stability function (${\psi}_{\nu}$), to assess the potential use of each method for accurately synthesizing reference level wind speeds. From these experiments, we conclude that the reliable LMS technique and the RHLL technique are both useful for generating reference wind speed data from IORS observations, since these methods produced very similar results: comparisons between the RHLL and the LMS results showed relatively small bias values ($-0.001m\;s^{-1}$) and Root Mean Square Deviations (RMSD, $0.122m\;s^{-1}$). We also compared the synthetic wind speed data generated using each of the four neutral wind profile formulas under examination with Advanced SCATterometer (ASCAT) data. Comparisons revealed that the 'LMS without ${\psi}_{\nu}^{\prime}$ produced the best results, with only $0.191m\;s^{-1}$ of bias and $1.111m\;s^{-1}$ of RMSD. As well as comparing these four different approaches, we also explored potential refinements that could be applied within or through each approach. Firstly, we tested the effect of tidal variations in sea level height on wind speed calculations, through comparison of results generated with and without the adjustment of sea level heights for tidal effects. Tidal adjustment of the sea levels used in reference wind speed calculations resulted in remarkably small bias (<$0.0001m\;s^{-1}$) and RMSD (<$0.012m\;s^{-1}$) values when compared to calculations performed without adjustment, indicating that this tidal effect can be ignored for the purposes of IORS reference wind speed estimates. We also estimated surface roughness heights ($z_0$) based on RHLL and LMS calculations in order to explore the best parameterization of this factor, with results leading to our recommendation of a new $z_0$ parameterization derived from observed wind speed data. Lastly, we suggest the necessity of including a suitable, experimentally derived, surface drag coefficient and $z_0$ formulas within conventional wind profile formulas for situations characterized by strong wind (${\geq}33m\;s^{-1}$) conditions, since without this inclusion the wind adjustment approaches used in this study are only optimal for wind speeds ${\leq}25m\;s^{-1}$.

• Geophysics and Geophysical Exploration
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• v.8 no.1
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• pp.26-33
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• 2005

Inversion of multi-mode surface-wave phase velocity for shallow engineering site investigation has received much attention in recent years. A sensitivity analysis and inversion of both synthetic and field data demonstrates the greater effectiveness of this method over employing the fundamental mode alone. Perturbation of thickness and shear-wave velocity parameters in multi-modal Rayleigh wave phase velocities revealed that the sensitivities of higher modes: (a) concentrate in different frequency bands, and (b) are greater than the fundamental mode for deeper parameters. These observations suggest that multi-mode phase velocity inversion can provide better parameter discrimination and imaging of deep structure, especially with a velocity reversal, than can inversion of fundamental mode data alone. An inversion of the theoretical phase velocities in a model with a low velocity layer at 20 m depth can only image the soft layer when the first higher mode is incorporated. This is especially important when the lowest measurable frequency is only 6 Hz. Field tests were conducted at sites surveyed by borehole and PS logging. At the first site, an array microtremor survey, often used for deep geological surveying in Japan, was used to survey the soil down to 35 m depth. At the second site, linear multichannel spreads with a sledgehammer source were recorded, for an investigation down to 12 m depth. The f-k power spectrum method was applied for dispersion analysis, and velocities up to the second higher mode were observed in each test. The multi-mode inversion results agree well with PS logs, but models estimated from the fundamental mode alone show f large underestimation of the depth to shallow soft layers below artificial fill.

• Journal of Korean Neurosurgical Society
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• v.64 no.4
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• pp.562-574
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• 2021

Objective : This study is to evaluate the efficacy and safety of demineralized bone matrix (DBM) gel versus DBM gel with recombinant human bone morphogenetic protein-2 (rhBMP-2) used in transforaminal lumbar interbody fusion (TLIF). Methods : This study was designed as a prospective, multi-center, double-blind method, randomized study. All randomized subjects underwent TLIF with DBM gel with rhBMP-2 group (40 patients) as an experimental group or DBM gel group (36 patients) as a control group. Post-operative observations were performed at 12, 24, and 48 weeks. The spinal fusion rate on computed tomography scans and X-rays films, Visual analog scale pain scores, Oswestry disability index and SF-36 quality of life (QOL) scores were used for the efficacy evaluation. The incidence rate of adverse device effects (ADEs) and serious adverse device effects (SADEs) were used for safety evaluation. Results : The spinal fusion rate at 12 weeks for the DBM gel with rhBMP-2 group was higher with 73.68% compared to 58.82% for the DBM gel group. The 24 and 48 weeks were 72.22% and 82.86% for the DBM gel with rhBMP-2 group and 78.79% and 78.13%, respectively, for the DBM gel group. However, there were no significant differences between two groups in the spinal fusion rate at 12, 24, and 48 weeks post-treatment (p=0.1817, p=0.5272, p=0.6247). There was no significant difference between the two groups in the incidence rate of ADEs (p=0.3836). For ADEs in the experimental group, 'Pyrexia' (5.00%) was the most common ADE, followed by 'Hypesthesia', 'Paresthesia', 'Transient peripheral paralysis', 'Spondylitis' and 'Insomnia' (2.50%, respectively). ADEs reported in control group included 'Pyrexia', 'Chest discomfort', 'Pain', 'Osteoarthritis', 'Nephropathy toxic', 'Neurogenic bladder', 'Liver function analyses' and 'Urticaria' (2.86%, respectively). There was no significant difference between the two groups in the incidence rate of SADEs (p=0.6594). For SADE in the experimental group, ''Pyrexia' and 'Spondylitis' were 2.50%. SADE reported in the control group included 'Chest discomfort', 'Osteoarthritis' and 'Neurogenic bladder'. All SADEs described above were resolved after medical treatment. Conclusion : This study demonstrated that the spinal fusion rates of DBM gel group and DBM gel with rhBMP-2 group were not significantly different. But, this study provides knowledge regarding the earlier postoperative effect of rhBMP-2 containing DBM gel and also supports the idea that the longer term follow-up results are essential to confirm the safety and effectiveness.