• Bulletin of the Korean Chemical Society
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• v.19 no.4
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• pp.422-428
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• 1998

In the present paper, we report a molecular dynamics (MD) simulation of non-rigid zeolite-A framework only as the base case for a consistent study of the role of intraframework interaction on several zeolite-A systems using the same technique in our previous studies of rigid zeolite-A frameworks. Usual bond stretching, bond angle bending, torsional rotational, and non-bonded Lennard-Jones and electrostatic interactions are considered as intraframework interaction potentials. The comparison of experimental and calculated structural parameters confirms the validity of our MD simulation for zeolite-A framework. The radial distribution functions of non-rigid zeolite-A framework atoms characterize the vibrational motion of the framework atoms. Mean square displacements are all periodic with a short period of 0.08 ps and a slow change in the amplitude of the vibration with a long period of 0.53 ps. The displacement auto-correlation (DAC) and neighbor-correlation (DNC) functions describe the up-and-down motion of the framework atoms from the center of α-cage and the back-and-forth motion on each ring window from the center of each window. The DAC and DNC functions of the framework atoms from the center of α-cage at the 8-ring windows have the same period of the up-and-down motion, but those functions from the center of 8-ring window at the 8-ring windows are of different periods of the back-and-forth motion.

• International Journal of Oral Biology
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• v.44 no.2
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• pp.62-70
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• 2019

Xylitol is well-known to have an anti-caries effect by inhibiting the replication of cariogenic bacteria. In addition, xylitol enhances saliva secretion. However, the precise molecular mechanism of xylitol on saliva secretion is yet to be elucidated. Thus, in this study, we aimed to investigate the stimulatory effect of xylitol on saliva secretion and to further evaluate the involvement of xylitol in muscarinic type 3 receptor (M3R) signaling. For determining these effects, we measured the saliva flow rate following xylitol treatment in healthy individuals and patients with dry mouth. We further tested the effects of xylitol on M3R signaling in human salivary gland (HSG) cells using real-time quantitative reverse-transcriptase polymerase chain reaction, immunoblotting, and immunostaining. Xylitol candy significantly increased the salivary flow rate and intracellular calcium release in HSG cells via the M3R signaling pathway. In addition, the expressions of M3R and aquaporin 5 were induced by xylitol treatment. Lastly, we investigated the distribution of M3R and aquaporin 5 in HSG cells. Xylitol was found to activate M3R, thereby inducing increases in $Ca^{2+}$ concentration. Stimulation of the muscarinic receptor induced by xylitol activated the internalization of M3R and subsequent trafficking of aquaporin 5. Taken together, these findings suggest a molecular mechanism for secretory effects of xylitol on salivary epithelial cells.

• The Korean Journal of Mycology
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• v.47 no.2
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• pp.95-104
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• 2019

The genus Ochrolechia is a widespread, lichen genus in Korea. Despite being common, little is known about the species diversity and geographical distribution of Ochrolechia. In this study, we detailed the identification procedure of the genus Ochrolechia in a Korean collection and provided the description of each species. Using 104 specimens collected from 2003 to 2017, we identified four species of the genus Ochrolechia via morphological and/or molecular phylogenetic analysis: O. parellula, O. trochophora, O. yasudae and O. akagiensis. Among them, O. akagiensis had not been previously reported in Korea. Moreover, the species identified as O. frigida and O. tartarea in past studies were corrected as O. yasudae and O. parellula, respectively, based on morphological and/or molecular evidence. Phylogenetic analysis using the internal transcribed spacer regions including 5.8S rRNA gene showed that the four species separated clearly, indicating that the morphological identification corresponds to the phylogenetic identification. We provide a taxonomic key for the four species of the genus Ochrolechia.

• Mycobiology
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• v.47 no.1
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• pp.76-86
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• 2019

Scab disease caused by Venturia nashicola is of agroeconomic importance in cultivation of Asian pear. However, little is known about the degree of genetic diversity in the populations of this pathogen. In this study, we collected 55 isolates from pear scab lesions in 13 major cultivation areas in Korea and examined the diversity using sequences of internal transcribed spacer (ITS) region, ${\beta}$-tubulin (TUB2), and translation elongation factor-$1{\alpha}$ ($TEF-1{\alpha}$) genes as molecular markers. Despite a low level of overall sequence variation, we found three distinctive subgroups from phylogenetic analysis of combined ITS, TUB2, and $TEF-1{\alpha}$ sequences. Among the three subgroups, subgroup 1 (60% of isolates collected) was predominant compared to subgroup 2 (23.6%) or subgroup 3 (16.4%) and was distributed throughout Korea. To understand the genetic diversity among the subgroups, RAPD analysis was performed. The isolates yielded highly diverse amplicon patterns and none of the defined subgroups within the dendrogram were supported by bootstrap values greater than 30%. Moreover, there is no significant correlation between the geographical distribution and the subgroups defined by molecular phylogeny. Our data suggest a low level of genetic diversification among the populations of V. nashicola in Korea.

• Proceedings of the Korean Society for Technology of Plasticity Conference
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• 1999.03b
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• pp.173-178
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• 1999

In this study MD simulations have been performed to observe the behavior of a grain boundary in an a-Fe plate under 2-dimensional loading. In MD simulation the acceleration of every molecule can be achieved from the potential energy and the force interacting between each molecule and the integration of the motion equation by using Verlet method gives the displacement of each molecule. Initially four a-Fe rectangular plates having different misorientation angles of grain boundary were modeled by using the Johnson potential and Morse potential We compared the potential energy of the grain boundary system with that of the perfect structure model. Also we could obtain the width of the grain boundary by investigating the local potential energy distribution. The tensile loading for each grain boundary models was applied and the behavior of grin boundary was studied. From this study it was clarified that in the case using Johnson potential the obvious fracture mechanism occurs along the grain boundary in the case of Morse potential the diffusion of the grain boundary appears instead of the grain boundary fracture.

• BMB Reports
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• v.56 no.4
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• pp.252-257
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• 2023

The hypoxia-inducible factor-1α (HIF-1α) is a key regulator of hypoxic stress under physiological and pathological conditions. HIF-1α protein stability is tightly regulated by the ubiquitin-proteasome system (UPS) and autophagy in normoxia, hypoxia, and the tumor environment to mediate the hypoxic response. However, the mechanisms of how the UPS and autophagy interplay for HIF-1α proteostasis remain unclear. Here, we found a HIF-1α species propionylated at lysine (K) 709 by p300/CREB binding protein (CBP). HIF-1α stability and the choice of degradation pathway were affected by HIF-1α propionylation. K709-propionylation prevented HIF-1α from degradation through the UPS, while activated chaperon-mediated autophagy (CMA) induced the degradation of propionylated and nonpropionylated HIF-1α. CMA contributed to HIF-1α degradation in both normoxia and hypoxia. Furthermore, the pan-cancer analysis showed that CMA had a significant positive correlation with the hypoxic signatures, whereas SIRT1, responsible for K709-depropionylation correlated negatively with them. Altogether, our results revealed a novel mechanism of HIF-1α distribution into two different degradation pathways.

• Journal of Radiopharmaceuticals and Molecular Probes
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• v.8 no.2
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• pp.113-118
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• 2022

Gadolinium neutron capture therapy (Gd-NCT) is a precision radiation therapy that kills cancer cells using the neutron capture reaction that occurs when ¹⁵⁷Gd hits thermal neutrons. ¹⁵⁷Gd has the highest thermal neutron capture cross section of 254,000 barns among stable isotopes in the periodic table. Another stable isotope, ¹⁵⁵Gd, also has a high thermal neutron trapping area (~ 60,700 barns), so gadolinium that exists in nature can be used as a Gd-NCT drug. Gd-NCT is a mixed kinetic energy of low-energy and high-energy ionizing particles, which can be uniformly distributed throughout the tumor tissue, thereby solving the disadvantage of heterogeneous dose distribution in tumor tissue. The Gd complexes of small-sized molecule are widely used as contrast agents for magnetic resonance imaging (MRI) in clinical practice. Therefore, these compounds can be used not only for diagnosis but also therapy when considering the concept of Gd-NCT. This multifunctional trial can look forward to new medical advance into NCT clinical practices. In this review, we introduce gadolinium compounds suitable for Gd-NCT and describe the necessity of image guided Gd-NCT.

• Journal of Radiopharmaceuticals and Molecular Probes
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• v.7 no.2
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• pp.113-118
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• 2021

Chitosan is a polysaccharide derived from chitin by deacetylation. Chitosan is non-toxic, biodegradable, and biocompatible, so that it can be used in wide variety of medical applications such as wound healing and antimicrobial biomaterials. It also used as dermal fillers due to its ability to inject with liquid formulations. For investigation on in vivo distribution of these chitosans, Bolton-Hunter-conjugated chitosan (Chitosan-BH) was synthesized by the reaction between the primary amino group of chitosan and N-hydroxysuccinimide ester group of Bolton-Hunter reagent. Then Chitosan-BH was radiolabeled with ¹²⁵I (Chitosan-BH-¹²⁵I) using a Chloramine-T method. The effects of each radiolabeling step on the radiolabeling yield of the final product were tested. The results showed that purification step had significant effects on the radiolabeling yield of the final product. Finally, SPECT/CT images were obtained to evaluate in vivo uptake of the radiolabeled chitosan (Chitosan-BH-¹²⁵I) in several organs. The highest uptake was found in the site of injection at 21 days post-injection. The results of this study suggest that chitosan is expected to be useful for biomaterials of dermal fillers.

• Journal of Korea Artificial Intelligence Association
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• v.2 no.1
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• pp.7-14
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• 2024

In this paper, we explore the application of RNA-sequencing data and ensemble machine learning to predict lung cancer and treatment strategies for lung cancer, a leading cause of cancer mortality worldwide. The research utilizes Random Forest, XGBoost, and LightGBM models to analyze gene expression profiles from extensive datasets, aiming to enhance predictive accuracy for lung cancer prognosis. The methodology focuses on preprocessing RNA-seq data to standardize expression levels across samples and applying ensemble algorithms to maximize prediction stability and reduce model overfitting. Key findings indicate that ensemble models, especially XGBoost, substantially outperform traditional predictive models. Significant genetic markers such as ADGRF5 is identified as crucial for predicting lung cancer outcomes. In conclusion, ensemble learning using RNA-seq data proves highly effective in predicting lung cancer, suggesting a potential shift towards more precise and personalized treatment approaches. The results advocate for further integration of molecular and clinical data to refine diagnostic models and improve clinical outcomes, underscoring the critical role of advanced molecular diagnostics in enhancing patient survival rates and quality of life. This study lays the groundwork for future research in the application of RNA-sequencing data and ensemble machine learning techniques in clinical settings.

• Korean Journal of Veterinary Service
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• v.47 no.1
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• pp.41-48
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• 2024

Feline bocavirus (FBoV) is considered an emerging pathogen recently identified in domestic cats worldwide. To date, three species of FBoVs (FBoV-1, FBoV-2, and FBoV-3) have been reported, but there are no reports identifying FBoVs in Korea. In this study, we detected novel FBoVs for the first time in Korea in captive wild felids (four European lynx and a lion) kept at Seoul Zoo. In FBoV-positive fecal samples, not only singular infections but also dual or triple infections with three different species of FBoVs were confirmed, suggesting that three species of FBoVs are already introduced and co-circulated in susceptible host animals in Korea. These results will help expand our understanding of the geographical distribution and host susceptibility of novel FBoVs. Further studies are necessary to determine the infection status of FBoVs in domestic cats and the genetic characteristics of the viruses circulating in Korea.