• Proceedings of the Computational Structural Engineering Institute Conference
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• 2001.04a
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• pp.335-342
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• 2001

In this paper, an improved Element-Free Galerkin (EFG) method is proposed by adding enrichment function to the standard EFG approximation and a discontinuity function is implemented in constructing the shape function across the crack surface. In this method, the singularity and the discontinuity of the crack are efficiently modeled by using initial node distribution to evaluate reliable stress intensity factor, though the standard EFG method requires placing additional nodes near the crack tip. The proposed method enables the initial node distribution to be kept without any additional nodal d.o.f. and expresses the asymptotic stress field near the crack tip successfully. Numerical example verifies the improvement and the effectiveness of the method.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.3
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• pp.1731-1735
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• 2013

Objective: We aimed to identify key genes, pathways and function modules in the development of diffuse large B-cell lymphoma (DLBCL) with microarray data and interaction network analysis. Methods: Microarray data sets for 7 DLBCL samples and 7 normal controls was downloaded from the Gene Expression Omnibus (GEO) database and differentially expressed genes (DEGs) were identified with Student's t-test. KEGG functional enrichment analysis was performed to uncover their biological functions. Three global networks were established for immune system, signaling molecules and interactions and cancer genes. The DEGs were compared with the networks to observe their distributions and determine important key genes, pathways and modules. Results: A total of 945 DEGs were obtained, 272 up-regulated and 673 down-regulated. KEGG analysis revealed that two groups of pathways were significantly enriched: immune function and signaling molecules and interactions. Following interaction network analysis further confirmed the association of DEGs in immune system, signaling molecules and interactions and cancer genes. Conclusions: Our study could systemically characterize gene expression changes in DLBCL with microarray technology. A range of key genes, pathways and function modules were revealed. Utility in diagnosis and treatment may be expected with further focused research.

• Journal of Korean Neurosurgical Society
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• v.65 no.5
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• pp.697-709
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• 2022

Objective : The present study aimed to identify the function of ischemic stroke (IS) patients' peripheral blood and its role in IS, explore the pathogenesis, and provide direction for clinical research progress by comprehensive bioinformatics analysis. Methods : Two datasets, including GSE58294 and GSE22255, were downloaded from Gene Expression Omnibus database. GEO2R was utilized to obtain differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs were performed using the database annotation, visualization and integrated discovery database. The protein-protein interaction (PPI) network of DEGs was constructed by search tool of searching interactive gene and visualized by Cytoscape software, and then the Hub gene was identified by degree analysis. The microRNA (miRNA) and miRNA target genes closely related to the onset of stroke were obtained through the miRNA gene regulatory network. Results : In total, 36 DEGs, containing 27 up-regulated and nine down-regulated DEGs, were identified. GO functional analysis showed that these DEGs were involved in regulation of apoptotic process, cytoplasm, protein binding and other biological processes. KEGG enrichment analysis showed that these DEGs mediated signaling pathways, including human T-cell lymphotropic virus (HTLV)-I infection and microRNAs in cancer. The results of PPI network and cytohubba showed that there was a relationship between DEGs, and five hub genes related to stroke were obtained : SOCS3, KRAS, PTGS2, EGR1, and DUSP1. Combined with the visualization of DEG-miRNAs, hsa-mir-16-5p, hsa-mir-181a-5p and hsa-mir-124-3p were predicted to be the key miRNAs in stroke, and three miRNAs were related to hub gene. Conclusion : Thirty-six DEGs, five Hub genes, and three miRNA were obtained from bioinformatics analysis of IS microarray data, which might provide potential targets for diagnosis and treatment of IS.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.12
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• pp.7221-7227
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• 2013

Background: Fascin, an actin-bundling protein forming actin bundles including filopodia and stress fibers, is overexpressed in multiple human epithelial cancers including esophageal squamous cell carcinoma (ESCC). Previously we conducted a microarray experiment to analyze fascin knockdown by RNAi in ESCC. Method: In this study, the differentially expressed genes from mRNA expression profilomg of fascin knockdown were analyzed by multiple bioinformatics methods for a comprehensive understanding of the role of fascin. Results: Gene Ontology enrichment found terms associated with cytoskeleton organization, including cell adhesion, actin filament binding and actin cytoskeleton, which might be related to fascin function. Except GO categories, the differentially expressed genes were annotated by 45 functional categories from the Functional Annotation Chart of DAVID. Subpathway analysis showed thirty-nine pathways were disturbed by the differentially expressed genes, providing more detailed information than traditional pathway enrichment analysis. Two subpathways derivated from regulation of the actin cytoskeleton were shown. Promoter analysis results indicated distinguishing sequence patterns and transcription factors in response to the co-expression of downregulated or upregulated differentially expressed genes. MNB1A, c-ETS, GATA2 and Prrx2 potentially regulate the transcription of the downregulated gene set, while Arnt-Ahr, ZNF42, Ubx and TCF11-MafG might co-regulate the upregulated genes. Conclusions: This multiple bioinformatic analysis helps provide a comprehensive understanding of the roles of fascin after its knockdown in ESCC.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.35 no.5
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• pp.267-275
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• 2022

Using a nonconforming mesh in enrichment methods results in several numerical issues induced by discontinuities and singularities found within the solution spaces, including the computational overhead during integration. In this study, we present a novel enrichment technique based on the selective expansion technique of moment fitting (Düster and Allix, 2020). In particular, two modifications are proposed to address the inefficiency during the integration process. First, a feedforward artificial neural network is introduced to correlate the implicit functions and integration moments. Through numerical examples, it is shown that the efficiency of the method is greatly improved when compared with existing expansion techniques, whereas the solution accuracy is maintained. Additionally, the finite element and domain representation grids are separated, which in turn improves the solution accuracy even for coarse mesh conditions.

• Journal of Periodontal and Implant Science
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• v.52 no.2
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• pp.127-140
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• 2022

Purpose: In dental avulsion, delayed replantation usually has an uncertain prognosis. After tooth replantation, complex inflammatory responses promote a return to periodontal tissue homeostasis. Various types of cytokines are produced in the inflammatory microenvironment, and these cytokines determine the periodontal tissue response. This study aimed to identify the gene expression profiles of replanted teeth and evaluate the functional differences between immediate and delayed replantation. Methods: Maxillary molars from Sprague-Dawley rats were extracted, exposed to a dry environment, and then replanted. The animals were divided into 2 groups according to the extra-oral time: immediate replantation (dry for 5 minutes) and delayed replantation (dry for 60 minutes). Either 3 or 7 days after replantation, the animals were sacrificed. Periodontal soft tissues were harvested for mRNA sequencing. Hallmark gene set enrichment analysis was performed to predict the function of gene-gene interactions. The normalized enrichment score (NES) was calculated to determine functional differences. Results: The hallmark gene sets enriched in delayed replantation at 3 days were oxidative phosphorylation (NES=2.82, Q<0.001) and tumor necrosis factor-alpha (TNF-α) signaling via the nuclear factor kappa light chain enhancer of activated B cells (NF-κB) pathway (NES=1.52, Q=0.034). At 7 days after delayed replantation, TNF-α signaling via the NF-κB pathway (NES=-1.82, Q=0.002), angiogenesis (NES=-1.66, Q=0.01), and the transforming growth factor-beta signaling pathway (NES=-1.46, Q=0.051) were negatively highlighted. Conclusions: Differentially expressed gene profiles were significantly different between immediate and delayed replantation. TNF-α signaling via the NF-κB pathway was marked during the healing process. However, the enrichment score of this pathway changed in a time-dependent manner between immediate and delayed replantation.

• Physical Therapy Korea
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• v.14 no.3
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• pp.48-56
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• 2007

Environmental Enrichment (EE) alone is not capable of enhancing the fine digit and the forelimb functions. Therefore, we applied modified constraint-induced movement therapy (mCIMT) under the influence of EE to assess its effect on promoting improved forelimb sensorimotor functions. Focal ischemic brain injury was produced in Sprague-Dawley rats (60 rats, $250{\pm}50$ g) through middle cerebral artery occlusion (MCAO). Before MCAO induction, all rats were trained in modified limb placing tests and reaching tasks for 1 week. Then they were randomly divided into three groups: Group I: application of standard environment (SE) after MCAO induction (n=20), Group II: application of EE after MCAO induction (n=20), Group III: MCAO+EE, mCIMT and task-oriented training that was initiated at 10th day after MCAO induction (n=20). We also applied mCIMT (between 9 AM and 5 PM/daily) which included restraining the forelimb ipsilateral to the lesion using the 'Jones & Schallert' method. We assessed the change of modified limb placing, single pellet reaching test and the immunoreactivity of BDNF by immunohistochemistry (pre, 1st, 5th, 10th and 20th day). Group I showed no improved outcome, whereas group II and III significantly improved on the use of the forelimb and the immunoreactivity. The qualitative analysis of the skilled reaching test, of group III showed the greatest improvement in the fine digit and the forelimb function. These results suggest that EE combined with mCIMT is more functional in promoting enhanced fine digit and forelimb functional movements.

• Journal of Ginseng Research
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• v.46 no.6
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• pp.750-758
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• 2022

Background: Mild cognitive impairment (MCI) is a transitional condition between normality and dementia. Ginseng is known to have effects on attenuating cognitive deficits in neurogenerative diseases. Ginsenosides are the main bioactive component of ginseng, and their protein targets have not been fully understood. Furthermore, no thorough analysis is reported in ginsenoside-related protein targets in MCI. Methods: The candidate protein targets of ginsenosides in brain tissues were identified by drug affinity responsive target stability (DARTS) coupled with label-free liquid chromatography-mass spectrometry (LC-MS) analysis. Network pharmacology approach was used to collect the therapeutic targets for MCI. Based on the above-mentioned overlapping targets, we built up a proteineprotein interaction (PPI) network in STRING database and conducted gene ontology (GO) enrichment analysis. Finally, we assessed the effects of ginseng total saponins (GTS) and different ginsenosides on mitochondrial function by measuring the activity of the mitochondrial respiratory chain complex and performing molecular docking. Results: We screened 2526 MCI-related protein targets by databases and 349 ginsenoside-related protein targets by DARTS. On the basis of these 81 overlapping genes, enrichment analysis showed the mitochondria played an important role in GTS-mediated MCI pharmacological process. Mitochondrial function analysis showed GTS, protopanaxatriol (PPT), and Rd increased the activities of complex I in a dose-dependent manner. Molecular docking also predicted the docking pockets between PPT or Rd and mitochondrial respiratory chain complex I. Conclusion: This study indicated that ginsenosides might alleviate MCI by targeting respiratory chain complex I and regulating mitochondrial function, supporting ginseng's therapeutic application in cognitive deficits.

• BMB Reports
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• v.41 no.3
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• pp.194-203
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• 2008

Nitrosative modifications regulate cellular signal transduction and pathogenesis of inflammatory responses and neuro-degenerative diseases. Protein tyrosine nitration is a biomarker of oxidative stress and also influences protein structure and function. Recent advances in mass spectrometry have made it possible to identify modified proteins and specific modified amino acid residues. For analysis of nitrated peptides with low yields or only a subset of peptides, affinity 'tags' can be bait for 'fishing out' target analytes from complex mixtures. These tagged peptides are then extracted to a solid phase, followed by mass analysis. In this review, we focus on protein tyrosine modifications caused by nitrosative stresses and proteomic methods for selective enrichment and identification of nitrosative protein modifications.

• Journal of Korean Academy of Nursing
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• v.32 no.3
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• pp.305-316
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• 2002

This study examined the crisis experiencing by middle - aged women and tried to understand their lived experiences also explored the nature of their crisis. Method: The data was collected from 7 participants living in Incheon and Seoul from Sep. 2000 to Feb. 2001. The analysis of the data was made the phenomenological analytic method suggested by Giorgi. Result: The meanings of the lived experiences of the middle - aged women's crisis ; Impatience about decreased physical function : an attack of a disease, decreased strength, decreased quickness, decreased desire, increased concern of health, poor memory, easy fatigue, change of appearance, change of conjugal relations, sense of loss. Psychological, emotional disturbances : sense of emptiness, regret, sharpness, feeling gloomy, fear of dying, loneliness, feeling the want, loss of confidence. Attitude of active life : reinforcement of self experience, enrichment of understanding, search of self satisfaction, search of self development, development of support system, management of independent life. Envy feeling from relative comparison : feeling of comfort, unsatisfaction to the husband, yearning for youth. Conclusion: Therefore, the program should be developed for the program of physical, psychological, and emotional health and expansion of social role of the middle - aged women.