• Title, Summary, Keyword: mutation

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Developing a new mutation operator to solve the RC deep beam problems by aid of genetic algorithm

  • Kaya, Mustafa
    • Computers and Concrete
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    • v.22 no.5
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    • pp.493-500
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    • 2018
  • Due to the fact that the ratio of their height to their openings is very large compared to normal beams, there are difficulties in the design and analysis of deep beams, which differ in behavior. In this study, the optimum horizontal and vertical reinforcement diameters of 5 different beams were determined by using genetic algorithms (GA) due to the openness/height ratio (L/h), loading condition and the presence of spaces in the body. In this study, the effect of different mutation operators and improved double times sensitive mutation (DTM) operator on GA's performance was investigated. In the study following random mutation (RM), boundary mutation (BM), non-uniform random mutation (NRM), Makinen, Periaux and Toivanen (MPT) mutation, power mutation (PM), polynomial mutation (PNM), and developed DTM mutation operators were applied to five deep beam problems were used to determine the minimum reinforcement diameter. The fitness values obtained using developed DTM mutation operator was higher than obtained from existing mutation operators. Moreover; obtained reinforcement weight of the deep beams using the developed DTM mutation operator lower than obtained from the existing mutation operators. As a result of the analyzes, the highest fitness value was obtained from the applied double times sensitive mutation (DTM) operator. In addition, it was found that this study, which was carried out using GAs, contributed to the solution of the problems experienced in the design of deep beams.

Statistical Investigation on Class Mutation Operators

  • Ma, Yu-Seung;Kwon, Yong-Rae;Kim, Sang-Woon
    • ETRI Journal
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    • v.31 no.2
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    • pp.140-150
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    • 2009
  • Although mutation testing is potentially powerful, it is a computationally expensive testing method. To investigate how we can reduce the cost of object-oriented mutation testing, we have conducted empirical studies on class mutation operators. We applied class mutation operators to 866 classes contained in six open-source programs. An analysis of the number and the distribution of class mutants generated and preliminary data on the effectiveness of some operators are provided. Our study shows that the overall number of class mutants is smaller than for traditional mutants, which offers the possibility that class mutation can be made practically affordable.

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Mutation analyses in Korean patients with MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes)

  • Yoo, Han-Wook;Kim, Gu-Hwan;Ko, Tae-Sung
    • Journal of Genetic Medicine
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    • v.1 no.1
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    • pp.39-43
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    • 1997
  • The mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) is inherited maternally, in which the MTTL1*MELAS 3243 mutation has been most commonly found as a heteroplasmy of A to G point mutation in the $tRNA^{Leu(UUR)}$ gene. The MTTL1*MELAS 3271 mutation is known to be the second common mutation, though clinical features of both mutations are not remarkably different. Recently, a variety of minor mutations have been reported in patients with MELAS. In this study, major efforts have been made to investigate the allele frequency of major three mutations including MTTL1*MELAS 3243, 3252, 3271 in 10 Korean families with MELAS probands. The PCR and subsequent direct sequencing of the PCR product in the regions spanning these three mutation sites were employed to identify the mutation in each proband. All family members have been screened for the presence of these three mutations by PCR-RFLP assay using Apa I, Acc I and Bfr I restriction enzymes. The MTTL1*MELAS 3243 mutation was most commonly found (7 out of 10 families tested) followed by the MTTL1*MELAS 3271 which was identified in 1 out of 10 families. In the remaining 2 families none of three mutations were found, indicating the presence of either nuclear mutation or yet unidentified mitochondrial DNA mutation in these families.

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Mutation Analysis of Wilson Disease Gene: Arg778Leu Mutation in Korean Children (윌슨 유전자의 돌연변이 분석: 한국 윌슨병 환자에서의 Arg778Leu 돌연변이)

  • Seo, Jeong-Kee;Kim, Jong-Won
    • Pediatric Gastroenterology, Hepatology & Nutrition
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    • v.2 no.2
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    • pp.164-168
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    • 1999
  • Background: Wilson disease (WD) is an autosomal recessive disorder of copper transport and characterized by degenerative changes in the brain, liver dysfunction, and Kayser-Fleischer rings due to toxic accumulation of copper. Since the identification of Wilson disease gene (ATP7B), more than 80 mutations have been detected among the different ethnic groups. Methods: Twenty three children with Wilson disease were included in this study. They were all diagnosed by low serum ceruloplasmin and increased 24 hour urinary copper excretion with characteristic clinical findings. We analysed WD gene mutation by assessing the nucleotide sequence of exon 7, 8, 9 and 10 including intron-exon boundaries of ATP7B gene from genomic DNA. Results: Arg778Leu mutation was identified in 16 WD patients; three were homozygous and 13 were heterozygous for this mutation. Of the 46 alleles, 19 alleles had a Arg778Leu mutation (19/46=41%). Homozygote patients had neurologic forms of WD. Arg778Leu mutation was not found among 50 normal healthy persons. Conclusion: Arg778Leu mutation is a common mutation in Korean WD gene. Arg778Leu mutation screening might be used as a useful supplementary diagnostic test in some patients to confirm Wilson disease in Korea.

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Sensitivity and Usefulness of VE1 Immunohistochemical Staining in Acral Melanomas with BRAF Mutation

  • Suh, Min Song;Choi, Yoo Duk;Lee, Jee-Bum;Lee, Seung-Chul;Won, Young Ho;Yun, Sook Jung
    • Annals of dermatology
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    • v.30 no.5
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    • pp.556-561
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    • 2018
  • Background: Acral melanomas are known to have a low frequency of BRAF mutation, in contrary to higher KIT mutation. Recently, VE1 immunostaining was reported to have a good correlation with BRAF mutation status. Objective: We aimed to evaluate the clinicopathological features of BRAF-mutated acral melanomas and validate the correlation of the VE1 immunohistochemical stains in those cases. Methods: The clinical features (age, sex, anatomical site), and histopathological characteristics of 41 patients with acral melanoma were evaluated. We performed a next-generation sequencing to detect BRAF mutation status. We also determined the correlation of VE1 immunohistochemical staining with BRAF mutation status. Results: Among 19 acral melanomas with BRAF mutation, common histopathological subtype was acral lentiginous melanoma (8/19, 42%) and nodular melanoma (8/19, 42%) and superficial spreading melanoma (3/19, 16%) followed. VE1 immunostaining results were positive in all 15 cases with BRAF V600E mutation (sensitivity 100%), and negative in 4 cases of BRAF non-V600E mutation. However, VE1 immunostaining was negative in all 22 patients with BRAF wild-type. Conclusion: VE1 immunostaining had a good correlation with BRAF V600E mutation status.

Mutations of the Epidermal Growth Factor Receptor Gene in Triple-Negative Breast Cancer

  • Kim, Aeri;Jang, Min Hye;Lee, Soo Jung;Bae, Young Kyung
    • Journal of Breast Cancer
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    • v.20 no.2
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    • pp.150-159
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    • 2017
  • Purpose: Epidermal growth factor receptor (EGFR) is considered a potential therapeutic target for anti-EGFR therapy in triple-negative breast cancer (TNBC). However, the frequency of EGFR gene mutation in TNBC is low and varies with ethnicity. This study aimed to investigate the incidence of EGFR gene mutation in TNBC. Methods: EGFR protein expression was evaluated by immunohistochemistry in tissue microarrays of 493 TNBC cases using four different primary antibodies, which included mutation-specific antibodies. For cases with an immunoreactivity level ${\geq}1+$, we performed pyrosequencing analysis for EGFR gene mutation. A case was considered mutation-positive when its mutation frequency minus its limit of detection (LOD) was >10%. Cases with mutation frequency higher than LOD were assessed for EGFR gene mutation status using the Cobas assay and by peptide nucleic acid-mediated polymerase chain reaction (PNA-clamping). Results: Among 493 TNBCs, 148 (30.0%) exhibited staining ${\geq}1$+ for EGFR, including 78 with 1+, 49 with 2+, and 21 with 3+. Positive EGFR expression (${\geq}2+$) was significantly associated with lymphovascular invasion (p=0.010), but not with overall survival (p=0.444) or disease-free survival (p=0.388). None of the 493 TNBCs harbored an EGFR gene mutation. Among 148 cases with an EGFR staining result ${\geq}1+$, five (3.4%) showed mutation frequencies (4.4%-10.9%) higher than LOD (2.6%-4.3%) in exons 19 (L747_P753>Q) or 21 (L858R and L861Q) as determined by pyrosequencing. However, Cobas and PNA-clamping failed to detect the presence of EGFR gene mutation in these five cases. Conclusion: No activating mutation of EGFR gene of clinical significance was observed in 148 TNBC cases using three commercially available methods. Thus, EGFR gene mutation appears to be an extremely rare event in patients with TNBC.

Prognostic Value of MGMT Promoter Methylation and TP53 Mutation in Glioblastomas Depends on IDH1 Mutation

  • Wang, Kai;Wang, Yin-Yan;Ma, Jun;Wang, Jiang-Fei;Li, Shao-Wu;Jiang, Tao;Dai, Jian-Ping
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.24
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    • pp.10893-10898
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    • 2015
  • Several molecular markers have been proposed as predictors of outcome in patients with glioblastomas. We investigated the prognostic significance of $O^6$-methylguanine-DNA methyltransferase (MGMT) promoter methylation and TP53 mutation status dependent on isocitrate dehydrogenase 1 (IDH1) mutation in glioblastoma patients. A cohort of 78 patients with histologically confirmed glioblastomas treated with radiation therapy and chemotherapy were reviewed retrospectively. We evaluated the prognostic value of MGMT promoter methylation and TP53 mutation status with regard to progression-free survival (PFS) and overall survival (OS). It was revealed that mutations in IDH1, promoter methylation of MGMT, TP53 mutation, age, Karnofsky performance status (KFS), and extension of resection were independent prognostic factors. In patients with an IDH1 mutation, those with an MGMT methylation were associated with longer PFS (p=0.016) and OS (p=0.013). Nevertheless, the presence of TP53 mutation could stratify the PFS and OS of patients with IDH1 wild type (p=0.003 and 0.029 respectively, log-rank). The MGMT promoter methylation and TP53 mutation were associated with a favorable outcome of patients with and without mutant IDH1, respectively. The results indicate that glioblastomas with MGMT methylation or TP53 mutations have improved survival that may be influenced by IDH1 mutation status.

A compound heterozygous mutation in the FMO3 gene: the first pediatric case causes fish odor syndrome in Korea

  • Kim, Ji Hyun;Cho, Sung Min;Chae, Jong-Hee
    • Clinical and Experimental Pediatrics
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    • v.60 no.3
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    • pp.94-97
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    • 2017
  • Trimethylaminuria (TMAuria), known as "fish odor syndrome," is a congenital metabolic disorder characterized by an odor resembling that of rotting fish. This odor is caused by the secretion of trimethylamine (TMA) in the breath, sweat, and body secretions and the excretion of TMA along with urine. TMAuria is an autosomal recessive disorder caused by mutations in flavin-containing monooxygenase 3 (FMO3). Most TMAuria cases are caused by missense mutations, but nonsense mutations have also been reported in these cases. Here, we describe the identification of a novel FMO3 gene mutation in a patient with TMAuria and her family. A 3-year-old girl presented with a strong corporal odor after ingesting fish. Genomic DNA sequence analysis revealed that she had compound heterozygous FMO3 mutations; One mutation was the missense mutation p.Val158Ile in exon 3, and the other was a novel nonsense mutation, p.Ser364X, in exon 7 of the FMO3 gene. Familial genetic analyses showed that the p.Val158Ile mutation was derived from the same allele in the father, and the p.Ser364X mutation was derived from the mother. This is the first description of the p.Ser364X mutation, and the first report of a Korean patient with TMAuria caused by novel compound heterozygous mutations.

Colon Cancer Prevention by Detection of APC Gene Mutation in a Family with Attenuated Familial Adenomatous Polyposis

  • Poovorawan, Kittiyod;Suksawatamnuay, Sirinporn;Sahakitrungruang, Chucheep;Treeprasertsuk, Sombat;Wisedopas, Naruemon;Komolmit, Piyawat;Poovorawan, Yong
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.10
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    • pp.5101-5104
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    • 2012
  • Background: Genetic mutation is a significant factor in colon CA pathogenesis. Familial adenomatous polyposis (FAP) is an autosomal dominant hereditary disease characterized by multiple colorectal adenomatous polyps affecting a number of cases in the family. This report focuses on a family with attenuated familial adenomatous polyposis (AFAP) with exon 4 mutation, c.481C>T p.Q161X of the APC gene. Methods: We analyzed 20 members of a family with AFAP. Clinical and endoscopic data were collected for phenotype determination. Genetic analysis was also performed by direct sequencing of the APC gene. Result: Five patients with a phenotype of AFAP were found. Endoscopic polyposis was demonstrated among the second generation with genotype mutation of the disease (age > 50 years) consistent with delayed phenotypic adenomatous polyposis in AFAP. APC gene mutation was identified in exon 4 of the APC gene, with mutation points of c.481C>T p.Q161X. Laparoscopic subtotal colectomy was performed to prevent carcinogenesis. Conclusion: A family with attenuated familial adenomatous polyposis of APC related to exon 4 mutation, c.481C>T p.Q161X, was reported and the phenotypic finding was confirmed by endoscopic examination. Genetic mutation analysis might be advantageous in AFAP for long term colon cancer prevention and management due to subtle or asymptomatic phenotype presentation in early adulthood.

A genetic algorithm with uniform crossover using variable crossover and mutation probabilities (동적인 교차 및 동연변이 확률을 갖는 균일 교차방식 유전 알고리즘)

  • Kim, Sung-Soo;Woo, Kwang-Bang
    • Journal of Institute of Control, Robotics and Systems
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    • v.3 no.1
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    • pp.52-60
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    • 1997
  • In genetic algorithms(GA), a crossover is performed only at one or two places of a chromosome, and the fixed probabilities of crossover and mutation have been used during the entire generation. A GA with dynamic mutation is known to be superior to GAs with static mutation in performance, but so far no efficient dynamic mutation method has been presented. Accordingly in this paper, a GA is proposed to perform a uniform crossover based on the nucleotide(NU) concept, where DNA and RNA consist of NUs and also a concrete way to vary the probabilities of crossover and mutation dynamically for every generation is proposed. The efficacy of the proposed GA is demonstrated by its application to the unimodal, multimodal and nonlinear control problems, respectively. Simulation results show that in the convergence speed to the optimal value, the proposed GA was superior to existing ones, and the performance of GAs with varying probabilities of the crossover and the mutation improved as compared to GAs with fixed probabilities of the crossover and mutation. And it also shows that the NUs function as the building blocks and so the improvement of the proposed algorithm is supported by the building block hypothesis.

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