• Genomics & Informatics
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• 제4권3호
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• pp.129-132
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• 2006

Toxicogenomics has recently emerged in the field of toxicology and the DNA microarray technique has become common strategy for predictive toxicology which studies molecular mechanism caused by exposure of chemical or environmental stress. Although microarray experiment offers extensive genomic information to the researchers, yet high dimensional characteristic of the data often makes it hard to extract meaningful result. Therefore we developed toxicant enrichment analysis similar to the common enrichment approach. We also developed web-based system graPT to enable considerable prediction of toxic endpoints of experimental chemical.

• Analytical Science and Technology
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• 제36권1호
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• pp.12-21
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• 2023

Protein glycation is vital to aging and disease. However, glycated proteins are low-abundant in plasma, rendering them difficult to identify using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Many studies have analyzed glycated peptides with high reproducibility. Here, glycated peptides in human serum were analyzed by LC-MS/MS using data-dependent acquisition (DDA) and parallel reaction monitoring (PRM). Boronic acid (BA) enrichment of in vitro glycated human serum peptides was performed. BA enrichment identified the most glycated peptides, and the glycated peptides of the more diversified proteins, excluding albumin, were analyzed. In PRM, glycated albumin PSMs were the most common, and this method exhibited the best reproducibility. The results of this study could help compare methods for identifying glycation-related biomarkers.

• Korean Journal of Adult Nursing
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• 제17권1호
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• pp.128-138
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• 2005

Purpose: As population of elderly people continues to grow, successful aging has risen to the top of the nursing science agenda. The successful aging includes maintenance of the cognitive and physical functions, as well as emotional well-beings. This study was carried out to evaluate effects of the environmental enrichments on cognition of institutionalized elderly. Method: The population was selected among the elderly aging over 65 residing at two of institutions. A quasi experimental design was used with non-equivalent control group. Study subjects were thirteen for each group. For the experimental group, physical, social and symbolic environmental enrichment program was provided for six weeks. The data were analyzed by repeated measure ANOVA and repeated measure ANCOVA using SPSS Win 11.0. Result: Compared to control group, the experimental group showed a significant difference on DSF(F=3.29, p=.046), and TMTA(F=4.76, p=.013) of cognitive function, and depression (F=5.56, p=.007) of emotional distress after 1 and 12 weeks of environmental enrichment program. Conclusion: Findings indicate that physical, social, and symbolic environmental enrichment was effective to partially prevent from cognitive decline, and to decrease emotional distress of elderly. As a nursing intervention, environmental enrichment program for elderly should be expanded for nursing practice to promote healthy aging and to offer support to the growing population of elderly. Further research should be conducted to evaluate the effect on the community elderly.

• Molecules and Cells
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• 제42권8호
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• pp.579-588
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• 2019

Gene set enrichment analysis (GSEA) is a popular tool to identify underlying biological processes in clinical samples using their gene expression phenotypes. GSEA measures the enrichment of annotated gene sets that represent biological processes for differentially expressed genes (DEGs) in clinical samples. GSEA may be suboptimal for functional gene sets; however, because DEGs from the expression dataset may not be functional genes per se but dysregulated genes perturbed by bona fide functional genes. To overcome this shortcoming, we developed network-based GSEA (NGSEA), which measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network. We found that NGSEA outperformed GSEA in identifying pathway gene sets for matched gene expression phenotypes. We also observed that NGSEA substantially improved the ability to retrieve known anti-cancer drugs from patient-derived gene expression data using drug-target gene sets compared with another method, Connectivity Map. We also repurposed FDA-approved drugs using NGSEA and experimentally validated budesonide as a chemical with anti-cancer effects for colorectal cancer. We, therefore, expect that NGSEA will facilitate both pathway interpretation of gene expression phenotypes and anti-cancer drug repositioning. NGSEA is freely available at www.inetbio.org/ngsea.

• Advances in environmental research
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• 제8권1호
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• pp.23-38
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• 2019

In this study, Malachite Green (MG) dye removal from synthetic wastewaters by adsorption process using raw boron enrichment waste (BEW) and it's modifications (with acid and ultrasound) were aimed. 81% MG removal was obtained by BEW at optimum equilibrium conditions (time: 40 min., dosage: 500 mg/dm³, pH: 5-6, speed: 200 rpm, 298 K). MG removal from wastewaters using acid modified boron enrichment waste (HBEW) was determined as 82% at optimum conditions (time: 20 min., dosage: 200 mg/dm³, pH: 10, speed: 200 rpm, 298 K). For ultrasound modified BEW (UBEW), the highest MG removal percent was achieved as 84% at optimum conditions (time: 30 min, dosage: 375 mg/ dm³, pH: 8, speed: 200 rpm, 298 K). The equilibrium data of Malachite Green was evaluated for BEW, HBEW and UBEW adsorbents by using sorption isotherms such as Langmuir, Freundlich and Temkin models, out of which Langmuir model (R² = 0.971, 0.987 and 0.984) gave better correlation and maximum adsorption capacity was found to be 147.05, 434.78 and 192.30 mg/g, respectively. The adsorption kinetics followed the pseudo-second-order kinetic equation for sorption of MG onto wastes. A look at thermodynamic data reveals that natural sorption is spontaneous and endothermic because of free negative energy exchange and positive change in enthalpy, respectively. The results indicated that boron enrichment waste, and HCl and ultrasound-modified boron enrichment waste served as good alternative adsorbents in dye removal from wastewater.

• Journal of Gifted/Talented Education
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• 제13권3호
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• pp.87-120
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• 2003

The purpose of this study is to verify empirically whether or not the linguistically creative problem-solving ability progress by developing and applying an enrichment learning program for the verbally gifted elementary school students. The total number of the verbally gifted students who participated in this study were 60 children. Half of them were subjects for evaluating the appropriateness of the enrichment learning program and the verbally creative problem-solving ability test developed by the researcher. The other half were divided into three groups for applying the teaching materials by Korean Educational Development Institute, the enrichment learning program by the present researcher, and the textbook enrichment program. The data were analyzed by the statistical method of repeated measures ANOVA. The results were as follows: First, the enrichment learning program developed by this researcher has greatly contributed to the advancement of verbally creative problem-solving ability. The program was especially effective in reading and writing, but not in speaking. second, the sub-category of reading includes factual, inferential·critical, and imaginary understanding. Among them, factual and imaginary understanding had not significantly advanced, while inferential·critical understanding had significant progression. Third, it was found that both logical and creative expression did not improve significantly by the enrichment learning program developed by the present researcher. Speaking is difficult to instruct. In conclusion, it was found that the systematic enrichment learning program was effective in developing language skills of the verbally gifted elementary school children. It was also proved to be more effective to teach them reading and writing together in everyday life. Also, it was turned out that continuous development of the enrichment learning program for the verbally gifted students is needed.

• BMB Reports
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• 제45권2호
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• pp.120-125
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• 2012

We have developed a biologist-friendly, Java GUI application (GoBean) for GO term enrichment analysis. It was designed to be a comprehensive and flexible GUI tool for GO term enrichment analysis, combining the merits of other programs and incorporating extensive graphic exploration of enrichment results. An intuitive user interface with multiple panels allows for extensive visual scrutiny of analysis results. The program includes many essential and useful features, such as enrichment analysis algorithms, multiple test correction methods, and versatile filtering of enriched GO terms for more focused analyses. A unique graphic interface reflecting the GO tree structure was devised to facilitate comparisons of multiple GO analysis results, which can provide valuable insights for biological interpretation. Additional features to enhance user convenience include built in ID conversion, evidence code-based gene-GO association filtering, set operations of gene lists and enriched GO terms, and user -provided data files. It is available at http://neon.gachon.ac.kr/GoBean/.

• Genomics & Informatics
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• 제5권3호
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• pp.133-136
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• 2007

The Gene Set network viewer (GSnet) visualizes the functional enrichment of a given gene set with a protein interaction network and is implemented as a plug-in for the Cytoscape platform. The functional enrichment of a given gene set is calculated using a hypergeometric test based on the Gene Ontology annotation. The protein interaction network is estimated using public data. Set operations allow a complex protein interaction network to be decomposed into a functionally-enriched module of interest. GSnet provides a new framework for gene set analysis by integrating a priori knowledge of a biological network with functional enrichment analysis.

• Nuclear Engineering and Technology
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• 제47권5호
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• pp.596-607
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• 2015

In this paper, we describe a computer program, iBEST (inverse Burnup ESTimator), that we developed to accurately estimate the burnup histories of spent nuclear fuels based on sample measurement data. The burnup history parameters include initial uranium enrichment, burnup, cooling time after discharge from reactor, and reactor type. The program uses algebraic equations derived using the simplified burnup chains of major actinides for initial estimations of burnup and uranium enrichment, and it uses the ORIGEN-S code to correct its initial estimations for improved accuracy. In addition, we newly developed a stable bisection method coupled with ORIGEN-S to correct burnup and enrichment values and implemented it in iBEST in order to fully take advantage of the new capabilities of ORIGEN-S for improving accuracy. The iBEST program was tested using several problems for verification and well-known realistic problems with measurement data from spent fuel samples from the Mihama-3 reactor for validation. The test results show that iBEST accurately estimates the burnup history parameters for the test problems and gives an acceptable level of accuracy for the realistic Mihama-3 problems.

• Korean Journal of Fisheries and Aquatic Sciences
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• 제46권4호
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• pp.424-436
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• 2013

Organic enrichment was investigated in surface sediments from the Yeoja and Gangjin Bays of Korea, which contain dense shellfish farms, in order to evaluate the contamination status and temporal changes in shellfish farming along these coasts. The degree of organic enrichment was determined using geochemical indicators (chemical oxygen demand, ignition loss, acid volatile sulfide, total organic carbon in sediments, and total nitrogen in sediments, ammonium and nitrate in pore water, and bioluminescence inhabitation for sediments). Temporal changes in organic enrichment conditions were detected by comparing our 2012 data to those previously reported from a survey conducted in 1999/2000. Organic enrichment was significantly higher in September than in May and July, in Gangjin Bay than in Yeoja Bay, and significantly higher in shellfish farms than in reference sites not used to culture shellfish. Ammonium concentrations in pore water were two orders of magnitude greater than nitrate concentrations, suggesting that these bays represent nitrogen-reducing environments.