• 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.

• Archives of Craniofacial Surgery
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• v.14 no.2
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• pp.89-95
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• 2013

Background: If patients have a better understanding about their problem and treatment, compliance and satisfaction with treatment will increase. For this purpose, simple repeated explanations regarding a patients' problem and treatment are essential. Critical pathway (CP) has a very wide range in medicine with the exception of the plastic surgery field. The authors developed a CP for facial bone fractures and implemented it clinically. The aim of this study was to evaluate the effectiveness of the CP on the degree of recognition of the problem along with patient satisfaction with the treatment process. Methods: From May 2011 to October 2011, a total of 82 patients suffering from facial bone fractures were studied. The CP for facial bone fractures was developed by plastic surgeons, residents and nurses. Subsequently, the authors investigated the degree of recognition of the disease and patient satisfaction with the treatment through the use of a questionnaire. The authors compared the score of the questionnaires before and after implementation of the clinical pathway. Results: The degree of the recognition of the problem changed from 3.1 to 4.2 (p<0.001). Further, the degree of satisfaction with the treatment process changed from 3.6 to 4.3 (p<0.05). Overall, there was a two point increase in improvement. Conclusion: Implementation of the CP for facial bone fractures was effective in improving the degree of recognition and satisfaction. The authors expect that hereafter, the CP for facial bone fractures will be implemented actively in the plastic surgery field.

• Journal of Korean Neurosurgical Society
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• v.30 no.5
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• pp.561-566
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• 2001

Objective : The purpose of this study are to evaluate the effectiveness of Gamma Knife radiosurgery(GKS) as a treatment of craniopharyngioma and to investigate the proper dose planning technique in GKS for craniopharyngioma. Method : Between May 1992 and March 1999, seven Gamma Knife radiosurgical procedures were done for residual tumor mass of 6 patients with craniopharyngioma after microsurgical resection. Conventional radiation therapy was not performed. In this study, their clinical, radiological and radiosurgical data were analyzed and the radiation dosage to the optic pathway, hypothalamus, pituitary stalk, and cavernous sinus were calculated and correlation with clinical outcome was evaluated. The mean follow-up period was 33.5 months(12.3-55.2 months). Result : The mean tumor volume was 4.4cc(0.4-18.0cc) and the maximum radiation dose ranged from 14 to 32 Gy(mean 20.9Gy). The radiation was given with isodose curve, 50-90% and the marginal dose varied within 8-22.4Gy(mean 12.7Gy). The mean number of isocenter was 4.3(1-12). The tumor was well controlled in all cases. In 5 of 7 cases, the size of tumor decreased to 10-50% of pre-GKS volume and remaining two showed no volume change. The mean dose to optic pathway was 5.7Gy(5.1-11.2Gy) and there were no complications. Conclusion : GKS seems to be effective for control of craniopharyngioma as an adjuvant treatment after microsurgical resection and even suboptimal dose for tumor margin is considered to be enough for tumor control. It is safe with careful dose planning to protect surrounding important structures, especially optic pathway. We believe conventional radiation therapy should be avoided because it has limitation for dose planning of additional treatments such as radiosurgery or intracystic instillation of radioisotope in case of recurrence.

• The Journal of Pediatrics of Korean Medicine
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• v.37 no.3
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• pp.1-16
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• 2023

Objectives We aimed to investigate the effectiveness of the Korean medical critical pathway (CP) in treating childhood anorexia. Methods In total, 21 patients who met the criteria and agreed to provide information were assigned to the CP group, while 24 patients who met the criteria, agreed to provide information, but disagreed with CP application were assigned to the non-CP group. Demographic, clinical, and economic indices were compared between the two groups. Clinical indices before and after treatment were also compared between the two groups. Results In the CP group, height, weight, body mass index (BMI), BMI percentile, and food approach (FAP) increased significantly after treatment, and numeric rating scale (NRS) and food avoidance (FAV) scores decreased significantly. In the non-CP group, height, weight, weight percentile, BMI, BMI percentile, and FAP increased significantly, whereas NRS and FAV decreased significantly after treatment. Compared to the non-CP group, CP application increased FAP and decreased FAV, medical expenses per consultation, and the total treatment period. Conclusions The application of the Korean medical critical pathway for childhood anorexia is an effective cure system that decreases overall medical expenses with good-quality treatment by means of the standardization of medical practices.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4241-4244
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• 2012

The lung adenocarcinoma is considered more aggressive than other types of non-small cell lung cancer. As metabolites of tryptophan degradation along the kynurenine pathway, including kynurenic acid, have been shown to induce immunosuppression and facilitate escape of tumor cells from immune surveillance, a hypothesis was set up that differences in biological behavior between types of lung cancer may be associated with altered activity of the kynurenine metabolic pathway. The aim of the study was to determine kynurenic acid levels in the serum of patients with bronchial adenocarcinoma for comparison with other types of non-small cell lung cancer. A total of 227 patients with non-small cell lung cancer were enrolled in the study, including 71 with adenocarcinoma and 96 with squamous cell carcinoma. Serum kynurenic acid concentration was determined with use of high performance liquid chromatography and fluorometry. The level of kynurenic acid in the serum of patients with adenocarcinoma was significantly higher than in those with squamous cell lung cancer ($107.1{\pm}62.8$ pmol/ml; 95%CI: 92.4 to 132.3 pmol/ml versus $82.1{\pm}47.6$ pmol/ml; 95%CI: 78.5 to 91.2 pmol/ml, respectively; p = 0.027). Differences between other histological types of lung cancer were insignificant. We conclude that increased activity of kynurenine metabolic pathway manifested by elevated serum kynurenic acid level may be one of the factors associated with clinically distinct biological behavior of adenocarcinoma, in particular high invasiveness and rapid progression.

• Journal of the Korean Data and Information Science Society
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• v.21 no.1
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• pp.43-50
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• 2010

In this study, we propose a new order selection method for clinical pathway development in acute appendectomy. This method is based on the lift concept which is popular in association rule discovery and, starting from the orders with more frequencies, sequentially removes the negatively associated orders which have lift values somewhat less than one. The orders in acute appendectomy we consider in this study are test and medical treatment items respectively, and since there are different order patterns before, during, and after operation, three different order selections are made for each. The selection results are somewhat different from those selected only by the order of more frequencies. Specifically, the selection results of two methods are different in 1 or 2 orders for medical treatment items and in maximum 5 orders for test items, respectively.

• Biomedical Science Letters
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• v.24 no.3
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• pp.213-220
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• 2018

Triglyceride (TG) is known to be associated with inflammatory disease including atherosclerosis. In a variety of atherosclerosis models, T lymphocytes are localized in the earliest lesions of atherosclerosis. T cell associated cytokines such as $TNF-{\alpha}$ and $IFN-{\gamma}$ have pre-dominant inflammatory effects in chronic vascular diseases. In our previous study, we found that the expression of $TNF-{\alpha}$ and its receptor, $TNF-{\alpha}R$ was increased when Jurkat T lymphocyte cell lines were exposed to TGs. Therefore, experiments were conducted to determine which cell signaling pathway are involved in the increase of $TNF-{\alpha}$ and $TNF-{\alpha}R$ expression by TGs. To identify signal transduction pathways involved in TG-induced upregulation of $TNF-{\alpha}$, we treated TG-exposed Jurkat T cells with specific inhibitors for MEK1, PI3K, $NF-{\kappa}B$ and PKC. We found that inhibition of the MEK1 pathway blocked TG-induced upregulation of $TNF-{\alpha}$. However, the expression level of $TNF-{\alpha}R$ did not change with any signal transduction inhibitor. Based on this observation, we suggest that increase of exogenous TG induces increase of $TNF-{\alpha}$ expression through MEK1 pathway in Jurkat T cells. In addition, it was confirmed that the increase of $TNF-{\alpha}$ and $TNF-{\alpha}R$ expression by TGs occurs via different pathways.

• Clinical and Experimental Reproductive Medicine
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• v.46 no.2
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• pp.76-86
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• 2019

Objective: This study was performed to explore the possibility that each oocyte and its surrounding cumulus cells might have different genetic expression patterns that could affect human reproduction. Methods: Differential gene expression analysis was performed for 10 clusters of cumulus cells obtained from 10 cumulus-oocyte complexes from 10 patients. Same procedures related to oocyte maturation, microinjection, and microarray analyses were performed for each group of cumulus cells. Two differential gene expression analyses were performed: one for the outcome of clinical pregnancy and one for the outcome of live birth. Results: Significant genes resulting from these analyses were selected and the top 20 affected pathways in each group were analyzed. Circadian entrainment is determined to be the most affected pathway for clinical pregnancy, and proteoglycans in cancer pathway is the most affected pathway for live birth. Circadian entrainment is also amongst the 12 pathways that are found to be in top 20 affected pathways for both outcomes, and has both lowest p-value and highest number of times found count. Conclusion: Although further confirmatory studies are necessary, findings of this study suggest that these pathways, especially circadian entrainment in cumulus cells, may be essential for embryo development and pregnancy.

• Journal of Ginseng Research
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• v.46 no.2
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• pp.235-247
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• 2022

Background: Ginsenoside Rg3 is one of the main active ingredients in ginseng. Here, we aimed to confirm its protective effect on the heart function in transverse aortic coarctation (TAC)-induced heart failure mice and explore the potential molecular mechanisms involved. Methods: The effects of ginsenoside Rg3 on heart and mitochondrial function were investigated by treating TAC-induced heart failure in mice. The mechanism of ginsenoside Rg3 for improving heart and mitochondrial function in mice with heart failure was predicted through integrative analysis of the proteome and plasma metabolome. Glucose uptake and myocardial insulin sensitivity were evaluated using micro-positron emission tomography. The effect of ginsenoside Rg3 on myocardial insulin sensitivity was clarified by combining in vivo animal experiments and in vitro cell experiments. Results: Treatment of TAC-induced mouse models with ginsenoside Rg3 significantly improved heart function and protected mitochondrial structure and function. Fusion of metabolomics, proteomics, and targeted metabolomics data showed that Rg3 regulated the glycolysis process, and Rg3 not only regulated glucose uptake but also improve myocardial insulin resistance. The molecular mechanism of ginsenoside Rg3 regulation of glucose metabolism was determined by exploring the interaction pathways of AMPK, insulin resistance, and glucose metabolism. The effect of ginsenoside Rg3 on the promotion of glucose uptake in IR-H9c2 cells by AMPK activation was dependent on the insulin signaling pathway. Conclusions: Ginsenoside Rg3 modulates glucose metabolism and significantly ameliorates insulin resistance through activation of the AMPK pathway.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.15
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• pp.6321-6326
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• 2014

${\alpha}$-Methyl-n-butylshikonin (MBS), one of the active components in the root extracts of Lithospermum erythrorhizon, posses antitumor activity. In this study, we assess the molecular mechanisms of MBS in causing apoptosis of SW620 cells. MBS reduced the cell viability of SW620 cells in a dose-and time-dependent manner and induced cell apoptosis. Treatment of SW620 cells with MBS down-regulated the expression of Bcl-2 and up-regulated the expression of Bak and caused the loss of mitochondrial membrane potential. Additionally, MBS treatment led to activation of caspase-9, caspase-8 and caspase-3, and cleavage of PARP, which was abolished by pretreatment with the pan-caspase inhibitor Z-VAD-FMK. MBS also induced significant elevation in the phosphorylation of JNK and p38. Pretreatment of SW620 cells with specific inhibitors of JNK (SP600125) and p38 (SB203580) abrogated MBS-induced apoptosis. Our results demonstrated that MBS inhibited growth of colorectal cancer SW620 cells by inducing JNK and p38 signaling pathway, and provided a clue for preclinical and clinical evaluation of MBS for colorectal cancer therapy.