• Korean Journal of Clinical Laboratory Science
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• v.55 no.4
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• pp.235-243
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• 2023

As next-generation sequencing has been developed and used widely, RNA-sequencing (RNA-seq) has rapidly emerged as the first choice of tools to validate global transcriptome profiling. With the significant advances in RNA-seq, various types of RNA-seq have evolved in conjunction with the progress in bioinformatic tools. On the other hand, it is difficult to interpret the complex data underlying the biological meaning without a general understanding of the types of RNA-seq and bioinformatic approaches. In this regard, this paper discusses the two main sections of RNA-seq. First, two major variants of RNA-seq are described and compared with the standard RNA-seq. This provides insights into which RNA-seq method is most appropriate for their research. Second, the most widely used RNA-seq data analyses are discussed: (1) exploratory data analysis and (2) pathway enrichment analysis. This paper introduces the most widely used exploratory data analysis for RNA-seq, such as principal component analysis, heatmap, and volcano plot, which can provide the overall trends in the dataset. The pathway enrichment analysis section introduces three generations of pathway enrichment analysis and how they generate enriched pathways with the RNA-seq dataset.

• Journal of the Korea Society for Simulation
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• v.33 no.1
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• pp.1-17
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• 2024

Forest management is known to beneficially influence stand structure and wood production, yet quantitative understanding as well as an illustrative depiction of the effects of different management approaches on tree growth and stand dynamics are still scarce. Long-term management of beech forests must balance public interests with ecological aspects. Efficient forest management requires the reliable prediction of tree growth change. We aimed to develop a novel hybrid simulation approach, which realistically simulates short- as well as long-term effects of different forest management regimes commonly applied, but not limited, to German low mountain ranges, including near-natural forest management based on single-tree selection harvesting. The model basically consists of three modules for (a) natural seedling regeneration, (b) mortality adjustment, and (c) tree growth simulation. In our approach, an existing validated growth model was used to calculate single year tree growth, and expanded on by including in a newly developed simulation process using calibrated modules based on practical experience in forest management and advice from the local forest. We included the following different beech forest-management scenarios that are representative for German low mountain ranges to our simulation tool: (1) plantation, (2) continuous cover forestry, and (3) reserved forest. The simulation results show a robust consistency with expert knowledge as well as a great comparability with mid-term monitoring data, indicating a strong model performance. We successfully developed a hybrid simulation that realistically reflects different management strategies and tree growth in low mountain range. This study represents a basis for a new model calibration method, which has translational potential for further studies to develop reliable tailor-made models adjusted to local situations in beech forest management.

• Korean Journal of Biological Psychiatry
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• v.6 no.2
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• pp.153-160
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• 1999

Animal models can provide a useful tool for the study of some aspects of psychiatric disorders and their treatment. The four criteria for the evaluation of animal models of psychiatric disorders are as following : 1) similarity of inducing conditions 2) similarity of behavioral state 3) common underlying neurobiological mechanisms 4) reversal by clinically effective treatment techniques. Several animal models have been proposed for schizophrenia : phenylethylamine model, L-dopa model, hallucinogen model, cocaine model, amphetamine model, phencyclidine model, noradrenergic reward system lesion model, reticular stimulation model, social isolation model, conditioned avoidance reaction, catalepsy test, paw test, self-stimulation paradigms, latent inhibition paradigms, blocking paradigms, prepulse inhibition of the startle reflex, rodent interaction, social behavior in monkeys, hippocampal damage, high ambient pressure, and models using selective breeding. Among them, animals with bilateral lesion of the hippocampus may provide an adequate animal model for several symptoms of schizophrenia, and ketamine model can reproduce negative symptoms and cognitive deficits as well as positive symptoms of schizophrenia. In conclusion, no model of schizophrenia is entirely representative of the disease, and findings gleaned from model systems must be cautiously interpreted. Furthermore, the process of developing and validating animal models must work in concert with the process to identify reliable measures of human phenomenology.

• Journal of Food Hygiene and Safety
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• v.22 no.4
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• pp.338-345
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• 2007

This study surveyed on the actual conditions of using sanitizers and disinfectants for improvements of sanitization on food utensils at 105 school and 20 industry foodservice operations. The questionnaire which was administered to 125 foodservices was used as a mail or visitation method. The answers of asking "Perception on temporary authorization system of sanitizers and disinfectants on food utensils" were 75% in contract managed school foodservices, 81.8% in self operated school foodservices, and 50% in industry. Main factors to choose sanitizers were sterilizing power (38.6%, 28.6%, 38.9%) and safety (32.6%, 46.1%, 33.3%) at every foodservices. Keeping ratio of sanitizers and disinfectants guidelines in contract managed school, self operated school and industry foodservices were 64.8%, 52% and 73.7%, respectively. If easy and practical guideline is developed, most foodservices replied to use if for disinfection of foodservices. Most of the foodservices were not only knowing sanitizers and disinfectants but also possessing a guideline. However, they didn't perform disinfection according to the guideline due to its complexity. Consequently, we suggest that it is necessary to provide an easy and practical "sanitizers and disinfectants guideline" and useful information.

• Korean Journal of Food Science and Technology
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• v.43 no.5
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• pp.544-552
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• 2011

The purpose of this study was to develop an analytical method for determining 15 polycyclic aromatic hydrocarbons (PAHs) of EU priority using gas chromatography (GC)-tandem mass spectrometry (MS). The PAHs in ground coffee were analyzed after being extracted using methods such as saponification-liquid-liquid extraction, Soxhlet extraction, and solid-liquid extraction. The solid-liquid extraction method showed the greatest repeatability and most efficient reduction of the matrix effect. GC-tandem MS for the quantification of the 15 PAHs showed better resolution and lower limit of detections (LODs) than GC-MS-selected ion monitoring (SIM) and high performance liquid chromatography with fluorescence detector. LODs of this method for the ground coffee types were 0.002-0.1 ${\mu}g/kg$ and limit of quantifications (LOQs) were 0.006-0.2 ${\mu}g/kg$ The recoveries ranged from 52.6 to 93.3%. Forty-six commercial types of ground coffee were analyzed to determine their PAHs contamination levels. PAHs concentration ranged from ND to 5.988 ${\mu}g/kg$. This study was conducted with toxicity equivalence factors, the U.S. EPA recommendation to identify dietary risks for PAHs in different types of coffee. The estimated average daily dose of PAHs was $5.24{\times}10^{-8}$ mg/kg body weight/day.

• Journal of the Korean Society of Food Science and Nutrition
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• v.38 no.12
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• pp.1691-1698
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• 2009

The purpose of this study was to investigate the antioxidative and antiallergic effects of persimmon leaf extract. Antioxidative and anti-inflammatory effects of the crude persimmon leaf extract (PLE) and the partially purified persimmon leaf extract (PPLE) were determined in in vitro assays by using 1,1-diphenyl-2-picrylhydrazyl (DPPH) and superoxide anion radicals, and 5-lipoxygenase (5-LO) and cyclooxygenase (COX). Total phenols and total flavonoid levels of PLE and PPLE were $230.0{\pm}19.6$ mg/g and $475.5{\pm}38.7$ mg/g, and $34.8{\pm}6.5$ mg/g and $78.8{\pm}3.6$ mg/g, respectively. DPPH and superoxide radical-scavenging activities ($SC_{50}$) of the PLE and PPLE were $23.8{\pm}3.2$ ppm and $10.0{\pm}1.3$ ppm, and $47.6{\pm}3.4$ ppm and $22.4{\pm}3.3$ ppm, respectively. Inhibitory activities ($IC_{50}$) of PLE and PPLE against 5-LO, COX-1 and COX-2 were $77.1{\pm}11.7$, $38.6{\pm}7.0$ ppm, $47.4{\pm}7.7$, $25.3{\pm}6.3$ ppm, and $129.5{\pm}5.5$, $84.5{\pm}2.3$ ppm, respectively. Moreover, two extracts inhibited dose-dependently NO production in LPS-stimulated RAW 264.7 cells, and also effectively inhibited the cutaneous anaphylaxis reaction activated by anti-dinitrophenyl IgE antibody in mice. These results suggest that PLE and PPLE may be useful for phytochemical materials for prevention and treatment of radical-mediated pathological and allergy diseases.

• KSBB Journal
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• v.24 no.4
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• pp.327-333
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• 2009

The antioxidant and anti-inflammatory activities of ethanol extract of Malus micromalus were studied in vitro. Ethanol extract of M. micromalus showed scavenging effects on 1,1-diphenyl-2-picrylhydrazyl (DPPH) and nitric oxide (NO) radicals. In addition, ethanol extract of M. micromalus inhibited the generation of superoxide anion ($O_2^-$) radical and uric acid by xanthine oxidase. We also investigated the effect of ethanol extract of M. micromalus on NO production in a lipopolysaccharide (LPS)-stimulated murine macrophage RAW 264.7 cells. Ethanol extract of M. micromalus significantly inhibited NO production and this inhibitory action was not due to the cytotoxicity. The expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) was markedly down-regulated by ethanol extract of M. micromalus. These results indicate that the inhibitory action of ethanol extract of M. micromalus on NO production in LPS-stimulated macropages might be due in part to abrogation of iNOS and COX-2 protein induction. Taken together, this study suggests that ethanol extract of M. micromalus could contribute to the chemoprevention and therapy of oxidative stress and inflammation.

• Economic and Environmental Geology
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• v.54 no.1
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• pp.21-33
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• 2021

The purpose of this study is to determine the order of priority for the use of amendments, matching the optimal amendment to the specific site in Korea. This decision-making process must prioritize the stabilization and economic efficiency of amendment for heavy metals and metalloid based on domestic site contamination scenarios. For this study, total 5 domestic heavy metal contaminated sites were selected based on different pollution scenarios and 13 amendments, which were previously studied as the soil stabilizer. Batch extraction experiments were performed to quantify the stabilization efficiency for 8 heavy metals (including As and Hg) for 5 soil samples, representing 5 different pollution scenarios. For each amendment, the analyses using XRD and XRF to identify their properties, the toxicity characteristics leaching procedure (TCLP) test, and the synthetic precipitation leaching procedure (SPLP) test were also conducted to evaluate the leaching safety in applied site. From results of batch experiments, the amendments showing > 20% extraction lowering efficiency for each heavy metal (metalloid) was selected and the top 5 ranked amendments were determined at different amount of amendment and on different extraction time conditions. For each amendment, the total number of times ranked in the top 5 was counted, prioritizing the feasible amendment for specific domestic contaminated sites in Korea. Mine drainage treatment sludge, iron oxide, calcium oxide, calcium hydroxide, calcite, iron sulfide, biochar showed high extraction decreasing efficiency for heavy metals in descending order. When the economic efficiency for these amendments was analyzed, mine drainage treatment sludge, limestone, steel making slag, calcium oxide, calcium hydroxide were determined as the priority amendment for the Korean field application in descending order.

• Radiation Oncology Journal
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• v.16 no.3
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• pp.311-323
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• 1998

Purpose : Prospective, single arm, Phase I/II clinical trial was performed to assess the efficacy and toxicity of the concurrent chemotherapy and definitive radiotherapy (RT) in patients with previously untreated locally advanced carcinoma of the uterine cervix. Methods and Materials : From Mar 1992 to January 1997, a total of 73 patients with advanced cervical carcinoma were entered on the protocol but 5 patients were excluded in analysis because of patients' refusal of treatment. Their ages ranged from 31 to 77 years, median 58 years. The International Federation of Gynecology and Obstetrics (FIGO) stage distribution was as follows: IIB 46, IIIA 2, IIIB 15 and IVA 5. RT consisted of external beam irradiation to 4,140-5,040 cGy/23-28 fractions plus high dose rate intracavitary treatments to deliver a dose of 30-35 Gy to point A in 6-7 fractions. During the intracavitary treatments parametrial boost was delivered for point B dose of 60 Gy in stage IIB and 65 Gy in stage IIIB. Two cycles of concurrent 5-fluorouracil and cisplatin (FP) chemotherapy (5-fluorouracil 1,000 mg/$m^2$/day continuous infusion for 4 days, day 1-4, 29-32 and cisplatin 20 mg/$m^2$/day intravenous bolus for 3 days day 1-3, 29-31) administered starting on day 1 of RT. Results : The median follow-up was 24 months (range 4-68+). Sixty-four patients were evaluable for survival rate in this protocol: The 5-year actuarial and disease-free survival rate were 52$\%$ and 64$\%$, respectively. The 5-rear actuarial survival for stage IIB and III+IVA patients were 58$\%$ and 36$\%$, respectively The 5-year disease-free survival rate for stage IIB and III+IVA patients were 71$\%$ and 40$\%$, respectively. Of the 68 patients evaluated for patterns of failure, overall recurrence rate was 27.9$\%$ (19/68) : local failure in 5.9$\%$ (4/68), distant metastasis in 10.3$\%$ (7/68) and both in 11.8$\%$ (8/68). Of the 64 patients evaluated for response at one month after the completion of treatment the complete response rate was 78$\%$ (50/64). Concurrent chemoradiation appear to be a well-tolerated regimen but there were two treatment-related deaths. Conclusion : Concurrent chemotherapy of FP with high-dose definitive RT in locally advanced carcinoma of the uterine cervix is feasible and effective with acceptable toxicities. This chemoradiation regimen may offer a modest survival benefit for advanced stage. Further follow-up of these patients will evaluate the impact of this regimen on the long-term local control and their survival.

• Journal of Korean Society of Transportation
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• v.20 no.7
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• pp.155-166
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• 2002

Since 1990s. there has been an increasing number of traffic accidents at intersection. which requires more urgent measures to insure safety on intersection. This study set out to analyze the road conditions, traffic conditions and traffic operation conditions on signalized intersection. to identify the elements that would impose obstructions in safety, and to develop a traffic accident prediction model to evaluate the safety of an intersection using the cop relation between the elements and an accident. In addition, the focus was made on suggesting appropriate traffic safety policies by dealing with the danger elements in advance and on enhancing the safety on the intersection in developing a traffic accident prediction model fir a signalized intersection. The data for the study was collected at an intersection located in Wonju city from January to December 2001. It consisted of the number of accidents, the road conditions, the traffic conditions, and the traffic operation conditions at the intersection. The collected data was first statistically analyzed and then the results identified the elements that had close correlations with accidents. They included the area pattern, the use of land, the bus stopping activities, the parking and stopping activities on the road, the total volume, the turning volume, the number of lanes, the width of the road, the intersection area, the cycle, the sight distance, and the turning radius. These elements were used in the second correlation analysis. The significant level was 95% or higher in all of them. There were few correlations between independent variables. The variables that affected the accident rate were the number of lanes, the turning radius, the sight distance and the cycle, which were used to develop a traffic accident prediction model formula considering their distribution. The model formula was compared with a general linear regression model in accuracy. In addition, the statistics of domestic accidents were investigated to analyze the distribution of the accidents and to classify intersections according to the risk level. Finally, the results were applied to the Spearman-rank correlation coefficient to see if the model was appropriate. As a result, the coefficient of determination was highly significant with the value of 0.985 and the ranks among the intersections according to the risk level were appropriate too. The actual number of accidents and the predicted ones were compared in terms of the risk level and they were about the same in the risk level for 80% of the intersections.