• Journal of Environmental Health Sciences
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• v.50 no.2
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• pp.113-124
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• 2024

Background: The increasing need to minimize animal testing has sparked interest in alternative methods with more humane, cost-effective, and time-saving attributes. In particular, in silico-based computational toxicology is gaining prominence. Adverse outcome pathway (AOP) is a biological map depicting toxicological mechanisms, composed of molecular initiating events (MIEs), key events (KEs), and adverse outcomes (AOs). To understand toxicological mechanisms, predictive models are essential for AOP components in computational toxicology, including molecular structures. Objectives: This study reviewed the literature and investigated previous research cases related to AOP and in silico methodologies. We describe the results obtained from the analysis, including predictive techniques and approaches that can be used for future in silico-based alternative methods to animal testing using AOP. Methods: We analyzed in silico methods and databases used in the literature to identify trends in research on in silico prediction models. Results: We reviewed 26 studies related to AOP and in silico methodologies. The ToxCast/Tox21 database was commonly used for toxicity studies, and MIE was the most frequently used predictive factor among the AOP components. Machine learning was most widely used among prediction techniques, and various in silico methods, such as deep learning, molecular docking, and molecular dynamics, were also utilized. Conclusions: We analyzed the current research trends regarding in silico-based alternative methods for animal testing using AOPs. Developing predictive techniques that reflect toxicological mechanisms will be essential to replace animal testing with in silico methods. In the future, since the applicability of various predictive techniques is increasing, it will be necessary to continue monitoring the trend of predictive techniques and in silico-based approaches.

• Korean Chemical Engineering Research
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• v.62 no.3
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• pp.274-280
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• 2024

Machine learning techniques utilizing neural networks have been employed in various fields such as disease gene discovery and diagnosis, drug development, and prediction of drug-induced liver injury. Disease features can be investigated by molecular information of DNA. In this study, we developed a neural network to predict the length of DNA and the number of DNA species in mixture solution which are representative molecular information of DNA. In order to address the time-consuming limitations of gel electrophoresis as conventional analysis, we analyzed the dynamic data of a microfluidic concentrating device. The dynamic data were reconstructed into a spatiotemporal map, which reduced the computational cost required for training and prediction. We employed a convolutional neural network to enhance the accuracy to analyze the spatiotemporal map. As a result, we successfully performed single DNA length prediction as single-variable regression, simultaneous prediction of multiple DNA lengths as multivariable regression, and prediction of the number of DNA species in mixture as binary classification. Additionally, based on the composition of training data, we proposed a solution to resolve the problem of prediction bias. By utilizing this study, it would be effectively performed that medical diagnosis using optical measurement such as liquid biopsy of cell-free DNA, cancer diagnosis, etc.

• Journal of The Korean Association For Science Education
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• v.15 no.2
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• pp.213-222
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• 1995

Analyzing textbook is the first step for enhancing the level of biology education especially in Korea. Prior studies of textbook analysis have mostly dealt with such topics as terminology analysis, content analysis, relationship analysis of chapters, and comparative studies. However, not much attention was paid to concept system to be learned and to relevance of concepts chosen. Therefore, the purpose of this study is to clarify the concept system and to elucidate the relationship among concepts for effective learning. Novak's concept map was utilized as a theoretical framework for the analysis of chapter I of high school biology textbook. Concept map has several distinctive merits in many aspects such as teaching, learning, and evaluation. It not only makes the understanding of key concepts and proposition a lot easier, but also helps to link prior knowledge and new concepts more effectively. This study will be a basic material for improving textbook for effective biology learning. The conclusions of the study are as follows: 1. Concepts in subchapters were arranged unsystematically or they were overlapping. For more effective understanding, those items should be rearranged. 2. Key concepts are not arrayed properly according to their hierarchy. Therefore, it was hard for students to set up concept structure. 3. The concepts emphasized by bold letters were not selected properly in accordance with their importance. Appropriate concepts should be chosen. 4. Key concepts should be explained by using examples in everyday life for easy understanding. 5. Many concepts in molecular biology is too abstract to grasp their meaning. Therefore, many audio-visual materials should be used to aid concept building.

• BMB Reports
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• v.35 no.4
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• pp.377-383
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• 2002

Arsenic trioxide ($As_O_3$) was recently demonstrated to be an effective inducer of apoptosis in patients with relapsed acute promyelocytic leukemia (APL) as well as patients with APL in whom all-trans-retinoic acid and conventional chemotherapy failed. Chronic myelogenous leukemia cells are highly resistant to chemotherapeutic drugs. To determine if $As_O_3$ might be useful for the treatment of chronic myelogenous leukemia, we examined the ability of $As_O_3$ to induce apoptosis in K562 cells. In vitro cytotoxicity of $As_O_3$ was evaluated in K562 cells by a MTT assay: the $IC_50$ value for $As_O_3$ was determined to be $10\;{\mu}m$. When analyzed by agarose gel electorphoresis, the DNA fragments became evident after incubation of the cells with $20\;{\mu}m$ $As_O_3$ for 24 h. We also found morphological changes and chromatin condensation of the cells undergoing apoptosis. Activation of caspase-3 was observed 6 h after treatment with $20\;{\mu}m$ $As_O_3$ by a Western blot analysis. Next, we examined the MAP kinase-signaling pathway of $As_O_3$-induced apoptosis in K562 cells. $As_O_3$ at $10\;{\mu}m$ strongly induced the activation of p38, inhibited $As_O_3$ induced apoptotic cell death. These results suggest that $As_O_3$ is able to induce the apoptotic activity in K562 cells, and its apoptotic mechanism may be associated with the activation of p38.

• The Journal of Korean Medicine
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• v.27 no.1 s.65
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• pp.23-35
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• 2006

Objectives : This study was conducted to investigate the inhibitory effects of Gaejibokryunghwan on cell proliferation in HeLa cells. Methods : Human uterine cervical carcinoma HeLa cells were cultured in the 1%, 5% and 10% concentration of Gaejibokryunghwan extract solution. All three were cultured for 24 hours, 48 hours and 72 hours each, to examine the inhibitory effects of Gaejibokryunghwan. Afterwards, we drew out the effect of Gaejibokryunghwan extract solution by making 5 analysis. First analysis was to measure the proliferation rate of cells. Second was FACS analysis. Third was to estimate the activity or caspase-3. Fourth, we used XTT assay to analyze the activation or cells. Ana lastly, a molecular biological method was used to determine activation of MAP kinase in the HeLa cells. Results : After 24, 48 and 72 hours cultivation, the proliferation of HeLa cells showed the dose-dependent decrease in all Gaejibokryunghwan extract solution groups compared to the control group. In the FACS analysis, Gaejibokryunghwan extract solution groups showed increased caspase expression compared to the control group, except for the group for 48 and 72 hours in 1 % concentrate. Caspase-3 activities were increased in all, except tile group cultured for 24 hours in 5% concentrate and the groups cultured for 48 hours in 1% and 5% concentrate. In the XTT study, 1% Gaejibokryunghwan extract solution groups showed increase compared to the control group, but other Gaejibokryunghwan extract solution containing groups showed significant decrease compared to the control after 24, 48 and 72 hours of cultivation. The expressions of MAP kinase were decreased in all Gaejibokryunghwan extract solution containing groups compared to the control group after 24, 48 and 72 hours of cultivation. Conclusions : From this study, we could suggest that Gaejibokryunghwan be available to the inhibition of proliferation of human cervical carcinoma cell line, HeLa cells in vitro.

• BMB Reports
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• v.31 no.6
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• pp.560-564
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• 1998

Echinomycin-7 is an echinomycin derivative, Smethylated sulfonium perchlorate of echinomycin. We studied the in vitro cytotoxicity and in vivo antitumor activity of echinomycin-7 against P388 leukemia cells and compared the results with echinomycin. With respect to the cytotoxic effects, echinomycin-7 had cell line-dependent $IC_{50}$ values while echinomycin had similar values to several tumor cell lines. Also, in vivo antitumor activities were observed in tumor-bearing mice treated with both agents, which showed that echinomycin-7 had a broad therapeutic dose range. We also observed the apoptosis on leukemia cells treated with echinomycin-7 which exihibited the ladder pattern of DNA on electrophoresis. In addition to apoptosis, echinomycin-7 arrested $G_1/S$ phases of the cell cycle at the same time. We then examined the signaling pathway of echinomycin-7-induced apoptosis and showed that ERK of the MAP kinase family was activated and translocated into the nucleus by echinomycin-7 stimulation. This study suggests that echinomycin-7 acts as an antitumor agent through in vitro cytotoxicity and has in vivo antitumor activity against leukemia cells, and that the echinomycin-7- induced apoptosis might involve signal transduction via MAP kinases.

• The Journal of Korean Obstetrics and Gynecology
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• v.19 no.2
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• pp.34-48
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• 2006

Purpose : This study was conducted to investigate the inhibitory effects of Dangguijakyaksan on cell proliferation in HeLa cells. Methods : Human uterine cervical carcinoma HeLa cells were cultured in the 1%, 5% and 10% concentration of Dangguijakyaksan extract solution for 24 hours, 48 hours and 72 hours for the direct inhibitory effects of Dangguijakyaksan. Afterwards, we executed the analysis of the effect of Dangguijakyaksan extract solution on cell proliferation inhibition using XTT assay, molecular biological method through MAP kinase activity and FACS analysis of caspase activity in the HeLa cells. Results : After 24, 48 and 72 hours cultivation, Dangguijakyaksan extract solution group showed significant decrease of HeLa cells except 1% solution after 24 hours compared with the control group. In the FACS analysis, Dangguijakyaksan extract solution groups showed increase of caspase activity except 1% solution after 48 hours compared with the control group. In the XTT assay, the caspase-3 activities were increased in Dangguijakyaksan extract solution groups except 1% solution after 24 hours in a dose-dependent manner. In the XTT study, cell activities were significantly decreased in 10% Dangguijakyaksan extract solution groups after 48 and 72 hours cultivation compared with the control group. In all Dangguijakyaksan extract solution groups, The activities of MAP kinase were decreased after 24, 48 and 72 hours cultivation compared with the control group. Conclusion : It could be concluded that Dangguijakyaksan is available to the inhibition of proliferation of human cervical carcinoma cell line in vitro.

• Korean Chemical Engineering Research
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• v.43 no.3
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• pp.412-418
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• 2005

The tube thickness map of water wall has been measured in a commercial circulating fluidized bed combustor (200 ton steam/hr, $4.97{\times}9.90{\times}28.98m$ height) with ultrasonic method and tube erosion has been discussed. Severe tube erosion took place in the splash region on all waterwalls including wingwalls. Erosion on the lower part of front and rear walls, close to both side walls, was more serious than other places. Erosion of some tubes around the gas exit was found to be noticible. Tube erosion increased on the wingwall as the position of the tube become closer to the center of the combustor crosssection.

• Journal of Animal Science and Technology
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• v.56 no.7
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• pp.23.1-23.7
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• 2014

Background: Scanning of the genome for selection signatures between breeds may play important role in understanding the underlie causes for observable phenotypic variations. The discovery of high density single nucleotide polymorphisms (SNPs) provide a useful starting point to perform genome-wide scan in pig populations in order to identify loci/candidate genes underlie phenotypic variation in pig breeds and facilitate genetic improvement programs. However, prior to this study genomic region under selection in commercially selected Berkshire and Korean native pig breeds has never been detected using high density SNP markers. To this end, we have genotyped 45 animals using Porcine SNP60 chip to detect selection signatures in the genome of the two breeds by using the $F_{ST}$ approach. Results: In the comparison of Berkshire and KNP breeds using the FDIST approach, a total of 1108 outlier loci (3.48%) were significantly different from zero at 99% confidence level with 870 of the outlier SNPs displaying high level of genetic differentiation ($F_{ST}{\geq}0.490$). The identified candidate genes were involved in a wide array of biological processes and molecular functions. Results revealed that 19 candidate genes were enriched in phosphate metabolism (GO: 0006796; ADCK1, ACYP1, CAMK2D, CDK13, CDK13, ERN1, GALK2, INPP1; MAK, MAP2K5, MAP3K1, MAPK14, P14KB, PIK3C3, PRKC1, PTPRK, RNASEL, THBS1, BRAF, VRK1). We have identified a set of candidate genes under selection and have known to be involved in growth, size and pork quality (CART, AGL, CF7L2, MAP2K5, DLK1, GLI3, CA3 and MC3R), ear morphology and size (HMGA2 and SOX5) stress response (ATF2, MSRB3, TMTC3 and SCAF8) and immune response (HCST and RYR1). Conclusions: Some of the genes may be used to facilitate genetic improvement programs. Our results also provide insights for better understanding of the process and influence of breed development on the pattern of genetic variations.

• Proceedings of the Korea Environmental Mutagen Society Conference
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• 2002.11a
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• pp.14-40
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• 2002

15-Deoxy-${\Delta}^{12, 14}$-prostaglandin $J_2$ (15-deoxy-$PGJ_2$), a naturally occurring ligand activates the peroxisome proliferator-activated $receptor-{\gamma}(PPAR-{\gamma}$). Activation of $PPAR-{\gamma}$ has been found to induce cell differentiation such as adipose cell and macrophage. Here it was investigated whether 15-deoxy-$PGJ_2$ has neuronal cell differentiation and possible underlying molecular mechanisms. Dopaminergic differentiating PC 12 cells treated with 15-deoxy-$PGJ_2$ (0.2 to 1.6 ${\mu}M$) alone showed measurable neurite extension and expression of neurofilament, markers of cell differentiation. However much greater extent of neurite extension and expression of neurofilament was observed in the presence of NGF (50 ng/ml). In parallel with its increasing effect on the neurite extension and expression of neurofilament, 15-deoxy-$PGJ_2$ enhanced NGF-induced p38 MAP kinase expression and its phosphorylation in addition to the activation of transcription factor AP-1 in a dose dependent manner. Moreover, pretreatment of SD 203580, a specific inhibitor of p38 MAP kinase inhibited the promoting effect of 15-deoxy-$PGJ_2$(0.8 ${\mu}M$) on NGF-induced neurite extension. This inhibition correlated well with the ability of SB203580 to inhibit the enhancing effect of 15-deoxy-$PGJ_2$ on the expression of p38 MAP kinase and activation of AP-1, The promoting ability of 15-deoxy-$PGJ_2$ did not occur through $PPAR-{\gamma}$, as synthetic PPAR-${\gamma}$ agonist andantagonist did not change the neurite promoting effect of 15-deoxy-PGJ$_2$. In addition, contrast to other cells (embryonic midbrain and SK-N-MC cells), $PPAR-{\gamma}$ was not expressed in PC-12 cells. Other structure related prostaglandins, PGD$_2$ and $PGE_2$ acting via a cell surface G-protein-coupled receptor (GPCR) did not increase basal or NGF-induced neurite extension. Moreover, GPCR (EP and DP receptor) antagonists did not alter the promoting effect of f 5-deoxy-$PGJ_2$ on neurite extension and activation of p38 MAP kinase, suggesting that the promoting effect of 15-deoxy-$PGJ_2$ may not be mediated GPCR. These data demonstrate that activation of p38 MAP kinase in conjunction with AP-1 single pathway may be important in the promoting activity of 15-deoxy-$PGJ_2$ cells.