• Architectural research
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• v.11 no.2
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• pp.19-26
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• 2009

The effect of rebirthing technique on the genetic algorithm (GA)-based size optimization is investigated. The GA mimics the principles of nature and it can gradually improve structural design through biological operations such as fitness, selection, crossover and mutation. However, premature optimum has been often detected in the generic GA with continuous design variable. Since then, the so-called rebirthing technique has been proposed to avoid this problem. However, the performance of the rebirthing technique has not been reported. Therefore, the size optimizations of spatial structures are tackled to investigate the performance of the rebirthing technique on the generic GA. From numerical results, it is well proved that the rebirthing technique is very effective to produce the optimum values regardless of the values of parameters used in the GA operations.

• IMMUNE NETWORK
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• v.1 no.2
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• pp.151-161
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• 2001

Background: Inactivation in p53 tumor suppressor gene through a point mutation and deletion is one of the most frequent genetic changes found in human cancer, with 50% of an incidence. This high rate of mutation mostly suggests that the gene plays a central role in the development of cancer and the mutations detected so far were found in exons 5 to 8. Mutation of p53 locus produced accumulation of abnormal p53 protein, and negative regulation of cell proliferation and transcriptional activation as a suppressor of transformation were lost. In addition, inhibition of its normal cellular function of wild-type by mutant is an important step in tumorigenesis. Method: 4 colon cancer cell lines (SNU C1, C2A, C4, C5) were examined for mutation in exons 5 to 8 of the p53 tumor suppressor gene by PCR-SSCP analysis and expression pattern by western blotting and immunoprecipitation. p53-mediated transactivation ability were examined by CAT assay and base substitution of p53 in SNU C2A cell were detected by DNA sequencing. Results: 1) SNU C2A cell and SNU C5 cell were detected mobility shifts each in exon 5 and exon 7 of p53 gene by the PCR-SSCP method, implicating being of p53 mutation. 2) 3 colon cancer cell lines (SNU C1, SNU C2A, SNU C5) expressed wild type and mutant type p53 protein. 3) In northern blot experiment, SNU C2A and SNU C5 cell expressed high level of p53 mRNA. 4) Results of p53-mediated transactivation in colon cancer cell lines by CAT assay represented only SNU C2A cell has transcriptional activity. 5) DNA sequencing in SNU C2A cell showed missense mutation in codon 179 of one allele, histidine to arginine and wild type p53 in the other allele. Conclusion: Colon cancer cell lines showed correlation with mutation in p53 gene and accumulation of abnormal p53 protein. Colon cancer cell SNU C2A retained p53-mediated transactivation as heterozygous p53 with one mutant allele in 179 codon and the other wild-type allele.

• Genomics & Informatics
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• v.16 no.2
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• pp.22-29
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• 2018

Incorporation of unique barcodes into fission yeast gene deletion collections has enabled the identification of gene functions by growth fitness analysis. For fine tuning, it is important to examine barcode sequences, because mutations arise during strain construction. Out of 8,708 barcodes (4,354 strains) covering 88.5% of all 4,919 open reading frames, 7,734 barcodes (88.8%) were validated as high-fidelity to be inserted at the correct positions by Sanger sequencing. Sequence examination of the 7,734 high-fidelity barcodes revealed that 1,039 barcodes (13.4%) deviated from the original design. In total, 1,284 mutations (mutation rate of 16.6%) exist within the 1,039 mutated barcodes, which is comparable to budding yeast (18%). When the type of mutation was considered, substitutions accounted for 845 mutations (10.9%), deletions accounted for 319 mutations (4.1%), and insertions accounted for 121 mutations (1.6%). Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (~28%) and well above the predicted error of Sanger sequencing (~2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. When the mutation rate was analyzed by position within 20-mer barcodes using the 1,284 mutations from the 7,734 sequenced barcodes, there was no significant difference between up-tags and down-tags at a given position. The mutation frequency at a given position was similar at most positions, ranging from 0.4% (32/7,734) to 1.1% (82/7,734), except at position 1, which was highest (3.1%), as in budding yeast. Together, well-defined barcode sequences, combined with the next-generation sequencing platform, promise to make the fission yeast gene deletion library a powerful tool for understanding gene function.

• Korean Journal of Otorhinolaryngology-Head and Neck Surgery
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• v.61 no.11
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• pp.600-604
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• 2018

Background and Objectives This study aimed to identify a reliable preoperative predictive factor for the development of thyroid cancer in patients with atypia of undetermined significance (AUS) identified by fine needle aspiration biopsy (FNAB). Subjects and Method This was a retrospective cohort study. Two hundred and ninety-nine patients diagnosed with AUS by preoperative FNAB who underwent curative thyroid surgery at our institution between September 2005 and February 2014 were analyzed. Clinical, radiological and molecular features were investigated as preoperative predictors for postoperative permanent malignant pathology. Results The final pathologic results revealed 36 benign tumors including nodular hyperplasia, follicular adenoma, adenomatous goiter, nontoxic goiter, and lymphocytic thyroiditis, as well as 263 malignant tumors including 1 follicular carcinoma and 1 invasive follicular carcinoma; the rest were papillary thyroid carcinomas. The malignancy rate was 87.9%. The following were identified as risk factors for malignancy by univariate analysis: $BRAF^{V600E}$ gene mutation, specific ultrasonographic findings including smaller nodule size, low echogenicity of the nodule, and irregular or spiculated margin (p<0.05). Multivariate analysis revealed that only $BRAF^{V600E}$ mutation was a statistically significant risk factor for malignancy (p<0.05). When $BRAF^{V600E}$ mutation was positive, 98.5% of enrolled patients developed malignant tumors. In addition, the diagnostic rate of malignancy in these cases was approximately 16-fold higher than BRAF-negative cases. Conclusion Patients with AUS thyroid nodules should undergo $BRAF^{V600E}$ gene mutation analysis to improve diagnostic accuracy and if the mutation is confirmed, surgery is recommended due to the high risk of malignancy.

• Biomedical Science Letters
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• v.29 no.4
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• pp.302-313
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• 2023

Y chromosomal short tandem repeat (Y-STR) markers have been developed continuously to complement forensic DNA analyses and population genetic studies. Initially, we collected data from previously reported Korean population Y-STR haplotype studies on 1133 individuals. We then conducted a marker expansion analysis using a dataset from the Y-STR Haplotype Reference Database (YHRD), covering up to 29 Y-STRs, referred to as Ymax. Additionally, we examined the impact of rapidly mutating (RM) Y-STRs included in this expanded marker set on the discrimination capacity. We observed that marker expansions both with (0.9896), and without (0.9510), RM Y-STR improved the discrimination capacity. Subsequently, we focused on 16 individuals belonging to seven distinct groups sharing identical haplotypes. These particular haplotypes had been previously identified among 476 unrelated males using 23 Y-STR markers from the PowerPlex^® Y23 System. We expanded the marker panel up to Ymax to explore how discrimination improved with an expansion of Y-STR markers for these 16 individuals. Among the expanded markers, DYS627, which had high discriminatory power, had a high mutation rate (1.10 × 10^-2) and high gene diversity (0.83). In contrast, DYF387S1 displayed high gene diversity (0.95) but a relatively low mutation rate (2.80 × 10^-3). We propose that these findings will be valuable in the selection of suitable Y-STR markers, depending on the objectives of forensic analyses. Additionally, the presence of frequently observed Y-haplotypes in Korean population will facilitate statistical interpretation in Y-STR DNA profiling.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.41 no.3
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• pp.348-353
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• 1996

Mutation tachniques inducing more useful mutations and reducing somatic effects need to be improved for crop breeding. Seeds of barley varieties ; Dema, Grosso were treated with two types of mutagens ; 1) chemical treatment: single treatment or double treatment of two mutagens (N-nitroso-N-methylurea ; MNH, Sodium Azide; NaN$_3$) 2) gamma ray irradiation treatment. After treatment, half of seeds were used for germination test and half of seeds were sown to the field. With the higher dose of mutagen both chemical and gamma ray were plants treated, the higher rate of growth reduction rate was in M$_1$ seedling. In chemical treatment, germination rate of seeds, growth rate of coleoptile and root in double treatment of chemical mutagens were better than single treatments, especially in same dose. Growth inhibition rate of plant in double treatment of 1.0mM MNH(0.5mM MNH + 0.5mM MNH), for example, were less than one of plants of single treatment of 1.0mM MNH in pot and petri dish test. Growth reduction rate of culm and fertility rate in M$_1$ plants double treated in same dose of single treatment were also less than single one. With the higher dose of mutagen both chemical and gamma ray were plants treated, the higher frequency of chlorophyll mutants was in M$_2$ seedling. The rate of chlorophyll mutants in double treatment of chemical mutagens were higher than single treatment. Double treatment methods can be a improved method for induction of new good mutants, which were induced more useful mutations and reduced harmful somatic effects.

• Korean Journal of Bronchoesophagology
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• v.9 no.2
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• pp.36-43
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• 2003

Background and objectives; Esophageal cancer is one of the most malignant tumors and has a poor prognosis. Many clinical studies have been tried for improving prognosis of esophageal cancer. Some clinical studies used molecular markers as the predictor of prognosis & the indicator for the choice of multimodality treatments. We investigated the relationship between some molecular markers, including p53 mutation, expression of bc12, Ki67 index, expression of E-Cadherin and the prognosis of esophageal cancer, Materials and Method; The materials used in this study were the tumor specimens from 72 esophageal cancer patients who underwent esophagectomy from 1987 to 2002 in our institute. The mutation of p53, expression of bc12, Ki67 index, and expression of E-cadherin were examined by using the tissue array and immunohistochemical staining method. The patients were subgrouped into higher Ki67 index group if the index was higher than 30. The patients were also subgrouped into grade 1(>90%), grade 2(50∼90%), grade 3 (10∼50%), and grade 4(<10%) according to the rate of E-Cadherin expression. We studied the relationship between the rates of immunohistochemical staining and the survival rate. Results: Seventy two tumor specimens from 72 patients were studied. (mean age ; 59.6 years, male female = 69 : 3) The histologic type of the specimens was all squamous cell carcinoma. The patient's number of stage IIA, IIB, and Ⅳ was 30, 37, and 7 respectively, Thirty patients were alive and overall 5 year-survival rate was 28%. The mutation of p53 was shown in 54.2% of the patients. Five year survival rates of negative and positive groups were 29% and 28% respectively.(p=0.4) Expression of bc12 gene was found in 13.9% of the specimens. Five year survival rates of negative and positive groups were 30% and 21%.(p=0.3) Higher Ki67 index was correlated to poorer differentiation.(p=0.05) Five year survival rates of higher and lower groups of Ki67 index were 47% and 30%.(p=0.15) Higher expression rate of E-Cadherin showed better differentiation.(p=0.04). However we couldn't find any survival differences between these 4 groups.(p=0.23) Conclusion; We could not find any molecular markers meaningful in the prognosis of esophageal cancer patients. We just found the tumor markers correlated to the differentiation of esophageal cancer. However, we knew that we need further study with some more samples to stratify other important prognostic factors of esophageal cancer.

• Tuberculosis and Respiratory Diseases
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• v.73 no.6
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• pp.303-311
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• 2012

Background: This study was designed to analyze the efficacy of gefitinib as a second-line therapy, according to the clinical characteristics in Korean patients with non-small-cell lung cancer (NSCLC). Methods: In this Phase IV observational study, we recruited patients, previously failed first-line chemotherapy, who had locally advanced or metastatic NSCLC, and who were found to be either epidermal growth factor receptor (EGFR) mutation-positive or satisfied 2 or more of the 3 characteristics: adenocarcinoma, female, and non-smoker. These patients were administered with gefitinib 250 mg/day, orally. The primary endpoints were to evaluate the objective response rate (ORR) and to determine the relationship of ORRs, depending on each patient's characteristics of modified intent-to-treat population. Results: A total of 138 patients participated in this study. One subject achieved complete response, and 42 subjects achieved partial response (ORR, 31.2%). The subgroup analysis demonstrated that the ORR was significantly higher in patients with EGFR mutation-positive, compared to that of EGFR mutation-negative (45.8% vs. 14.0%, p=0.0004). In a secondary efficacy variable, the median progression-free survival (PFS) was 5.7 months (95% confidence interval, 3.9~8.4 months) and the 6-month PFS and overall survival were 49.6% and 87.9%, respectively. The most common reported adverse events were rash (34.4%), diarrhea (26.6%), pruritus (17.5%), and cough (15.6%). Conclusion: Gefitinib was observed in anti-tumor activity with favorable tolerability profile as a second-line therapy in these selected patients. When looking at EGFR mutation status, EGFR mutation-positive showed strong association with gefitinib by greater response and prolonged PFS, compared with that of EGFR mutation-negative.

• Korean Journal of Clinical Laboratory Science
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• v.46 no.2
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• pp.59-63
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• 2014

The death toll of Colorectal Carcinoma in Korea was 1,826 and 7,721 in the years 1992 and 2011, respectively. This rate of increase was shown to be more than 4.23 times higher than that of any other form of cancer. Therefore, Colorectal Carcinoma requires various diagnostic methods, and Microsatellite Instability (MSI) was applied as a new diagnostic tool. From this study with several microsatellite markers, only marker #13 was detected and observed D13S160 13% (4/30), D13S292 13% (4/30), D13S153 10% (3/30) in order. From the results of amplication with microsatellite marker, D13S292 37% (11/30), D13S153 33% (10/30), D13S160 33% (10/30) in order were shown. The appearance of a genetic mutation, which depends on the loci of Colorectal Carcinoma, was shown amplication from rectal cancer (3.77) which was higher than that of right Colorectal Carcinoma (2.08) (p<0.018). The genetic mutation with lymph node (4.13) appeared higher than normal (1.93) (p<0.001). There were no great differences in the genetic mutation dependent on disease, histological classification and increased group of serum CEA. Accordingly, it is suggested that the correct primers, which can evaluate MSI well from colorectal carcinoma, should be chosen and that MSI be considered a good prognosis and quality control tool.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.122-133
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• 2016

While ion beams are widely used in plant breeding, little is known about the sensitivity of Lavandula angustifolia (lavender) to ionizing radiation. To compare the biological effects of different types of ionizing radiation on the germination and survival rates of lavender, we exposed lavender seeds to gamma rays, 3 MeV electron beams, and 1.89 MeV proton ion beams. We observed that the seed germination rate decreased with increasing dosages of all three types of ionizing radiation. The malformation rate of lavender seedlings exposed to electron beams and gamma rays increased with increasing radiation dosage. By contrast, the effect of the accelerated proton beams on the malformation rate was negatively correlated with the dosage used. The survival rate of lavender seedlings exposed to the three types of ionizing radiation decreased in a dose-dependent manner. In addition, the survival rate of seedlings irradiated with proton and electron beams decreased more slowly than did that of seedlings irradiated with gamma rays. The half-lethal dose of gamma rays, electron beams, and proton beams was determined to be 48.1 Gy, 134.3 Gy, and 277.8 Gy, respectively, and the most suitable proton-ion energy for lavender seeds in terms of penetration depth was determined to be 5 MeV. These findings provide valuable information for the breeding of lavender by radiation mutation.