• Toxicological Research
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• v.34 no.4
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• pp.303-310
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• 2018

The methods of applied genetic toxicology are changing from qualitative hazard identification to quantitative risk assessment. Recently, quantitative analysis with point of departure (PoD) metrics and benchmark dose (BMD) modeling have been applied to in vitro genotoxicity data. Two software packages are commonly used for BMD analysis. In previous studies, we performed quantitative dose-response analysis by using the PROAST software to quantitatively evaluate the mutagenicity of four piperidine nitroxides with various substituent groups on the 4-position of the piperidine ring and six cigarette whole smoke solutions (WSSs) prepared by bubbling machine-generated whole smoke. In the present study, we reanalyzed the obtained genotoxicity data by using the EPA's BMD software (BMDS) to evaluate the inter-platform quantitative agreement of the estimates of genotoxic potency. We calculated the BMDs for 10%, 50%, and 100% (i.e., a two-fold increase), and 200% increases over the concurrent vehicle controls to achieve better discrimination of the dose-responses, along with their BMDLs (the lower 95% confidence interval of the BMD) and BMDUs (the upper 95% confidence interval of the BMD). The BMD values and rankings estimated in this study by using the EPA's BMDS were reasonably similar to those calculated in our previous studies by using PROAST. These results indicated that both software packages were suitable for dose-response analysis using the mouse lymphoma assay and that the BMD modeling results from these software packages produced comparable rank orders of the mutagenic potency.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.9
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• pp.1217-1220
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• 2005

Random amplified polymorphic DNA (RAPD-PCR) analysis of 56 animals of four different genetic groups of dwarf cattle in Kerala was done as a single step analysis. Bandsharing (BS) values were calculated for animals of each group and between groups as an analytical tool to find out genetic variation among animals. The different factors affecting BS values were estimated using Harvey''s Least squares analysis. The effects of genetic group, Guanine-cytosine (GC) content of primer and gel on BS values were found significant. Bandsharing values of Kasargode-Highrange dwarf animals were significantly different from Vechur, Vatakara and their combinations. The Vechur, Vatakara and Vechur-Vatakara combinations were found to be more uniform (high BS value) compared with other combinations. The bandsharing value was lowest with primers of GC content 90% and highest with 80% GC content. The effect of gel on BS value points to the need of adjustments of gel factor for calculation of BS values.

• Genomics & Informatics
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• v.11 no.1
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• pp.46-51
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• 2013

Normal-karyotype acute myeloid leukemia (NK-AML) is a highly malignant and cytogenetically heterogeneous hematologic cancer. We searched for somatic mutations from 10 pairs of tumor and normal cells by using a highly efficient and reliable analysis workflow for whole-exome sequencing data and performed association tests between the NK-AML and somatic mutations. We identified 21 nonsynonymous single nucleotide variants (SNVs) located in a coding region of 18 genes. Among them, the SNVs of three leukemia-related genes (MUC4, CNTNAP2, and GNAS) reported in previous studies were replicated in this study. We conducted stepwise genetic risk score (GRS) models composed of the NK-AML susceptible variants and evaluated the prediction accuracy of each GRS model by computing the area under the receiver operating characteristic curve (AUC). The GRS model that was composed of five SNVs (rs75156964, rs56213454, rs6604516, rs10888338, and rs2443878) showed 100% prediction accuracy, and the combined effect of the three reported genes was validated in the current study (AUC, 0.98; 95% confidence interval, 0.92 to 1.00). Further study with large sample sizes is warranted to validate the combined effect of these somatic point mutations, and the discovery of novel markers may provide an opportunity to develop novel diagnostic and therapeutic targets for NK-AML.

• Korean Journal of Remote Sensing
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• v.34 no.1
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• pp.151-166
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• 2018

This paper compares the four selections of performance used in the application of genetic algorithms (GAs) to automatically optimize multispectral pixel cluster for unsupervised classification from KOMPSAT-3 data, since the selection among three main types of operators including crossover and mutation is the driving force to determine the overall operations in the clustering GAs. Experimental results demonstrate that the tournament selection obtains a better performance than the other selections, especially for both the number of generation and the convergence rate. However, it is computationally more expensive than the elitism selection with the slowest convergence rate in the comparison, which has less probability of getting optimum cluster centers than the other selections. Both the ranked-based selection and the proportional roulette wheel selection show similar performance in the average Euclidean distance using the pixel clustering, even the ranked-based is computationally much more expensive than the proportional roulette. With respect to finding global optimum, the tournament selection has higher potential to reach the global optimum prior to the ranked-based selection which spends a lot of computational time in fitness smoothing. The tournament selection-based clustering GA is used to successfully classify the KOMPSAT-3 multispectral data achieving the sufficient the matic accuracy assessment (namely, the achieved Kappa coefficient value of 0.923).

• Journal of Species Research
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• v.1 no.2
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• pp.224-231
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• 2012

To assess the genetic diversity of Aconitum coreanum (Ranunculaceae) populations in Korea, we have amplified and sequenced eight organellar marker regions, and developed and analyzed microsatellite markers. No sequence variation was detected from the eight organellar markers. Ten microsatellites were developed using Next Generation Sequencing and two microsatellite markers, AK_CA03 and AK_CT07, were identified polymorphic and applied for 143 individuals of twelve A. coreanum populations. Four and five alleles were detected for the two microsatellite loci, respectively, and number of migrants ($N_m$) was estimated as 1.12586. Two microsatellite marker loci showed $F_{ST}$ of 0.205 and 0.275, respectively. The heterozygosity deficit, low level of among-population differentiation, small size of gene flow, and lack of sequence variation of the organellar markers suggest that A. coreanum is reproductively isolated from other Aconitum species and there has been continuous gene flow among the populations of A. coreanum or it has dispersed relatively recently after speciation. Though population pairwise $F_{ST}$'s presented significant geographic structure, further sampling and study will be necessary to confirm this.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.6
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• pp.3001-3006
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• 2016

Background: The cancer progression of oral leukoplakia is an important watchpoint in the follow-up observation of the patients. However, potential malignancies of oral leukoplakia cannot be estimated by histopathologic assessment alone. We evaluated genetic abnormalities at the level of copy number variation (CNV) to investigate the risk for developing cancer in oral leukoplakias. Materials and Methods: The current study used 27 oral leukoplakias with histological evidence of dysplasia. The first group (progressing dysplasia) consisted of 7 oral lesions from patients with later progression to cancer at the same site. The other group (non-progressing dysplasia) consisted of 20 lesions from patients with no occurrence of oral cancer and longitudinal follow up (>7 years). We extracted DNA from Formalin-Fixed Paraffin-Embedded (FFPE) samples and examined chromosomal loci and frequencies of CNVs using Taqman copy number assays. Results: CNV frequently occurred at 3p, 9p, and 13q loci in progressing dysplasia. Our results also indicate that CNV at multiple loci-in contrast to single locus occurrences-is characteristic of progressing dysplasia. Conclusions: This study suggests that genetic abnormalities of the true precancer demonstrate the progression risk which cannot be delineated by current histopathologic diagnosis.

• Animal Bioscience
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• v.35 no.7
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• pp.949-954
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• 2022

Objective: The present study is aimed at phenotypic characterization and mitochondrial d-loop analysis of indigenous "Diara" buffalo population, which are mostly confined to the villages on the South and North Gangetic marshy plains in the Bihar state of India. These buffaloes are well adapted and are best suited for ploughing and puddling the wet fields meant for paddy cultivation. Methods: Biometric data on 172 buffaloes were collected using a standard flexible tape measure. Animals are medium in size; the typical morphometric features are long head with a broad forehead and moderately long and erect ears. Genomic DNA was isolated from unrelated animals. The mtDNA d-loop 358-bp sequence data was generated and compared with 338 sequences belonging to riverine and swamp buffaloes. Results: Based on the mitochondrial d-loop analysis the Diara buffaloes were grouped along with the haplotypes reported for riverine buffalo. Sequence analysis revealed the presence of 7 mitochondrial D loop haplotypes with haplotype diversity of 0.9643. Five of the haplotypes were shared with established swamp breeds and with Buffalo population of Orissa in India. Conclusion: Morphometric analyses clearly shows distinguishing features like long and broad forehead which may be useful in identification. The germplasm of Diara buffalo is much adapted to the marshy banks of river Ganga and its tributaries. It constitutes a valuable genetic resource which needs to be conserved on priority basis.

• Structural Engineering and Mechanics
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• v.87 no.3
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• pp.211-219
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• 2023

The structural health of a pipeline is usually assessed by visual inspection. In addition to the fact that this method is expensive and time consuming, inspection of the whole structure is not possible due to limited access to some points. Therefore, adopting a damage detection method without the mentioned limitations is important in order to increase the safety of the structure. In recent years, vibration-based methods have been used to detect damage. These methods detect structural defects based on the fact that the dynamic responses of the structure will change due to damage existence. Therefore, the location and extent of damage, before and after the damage, are determined. In this study, fuzzy genetic algorithm has been used to monitor the structural health of the pipeline to create a fuzzy automated system and all kinds of possible failure scenarios that can occur for the structure. For this purpose, the results of an experimental model have been used. Its numerical model is generated in ABAQUS software and the results of the analysis are used in the fuzzy genetic algorithm. Results show that the system is more accurate in detecting high-intensity damages, and the use of higher frequency modes helps to increase accuracy. Moreover, the system considers the damage in symmetric regions with the same degree of membership. To deal with the uncertainties, some error values are added, which are observed to be negligible up to 10% of the error.

• Nuclear Engineering and Technology
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• v.56 no.2
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• pp.644-654
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• 2024

After the Tohoku earthquake and tsunami (Japan, 2011), regulatory efforts to mitigate external hazards have increased both the safety requirements and the total capital cost of nuclear power plants (NPPs). In these circumstances, identifying not only disaster robustness but also cost-effective capacity setting of NPPs has become one of the most important tasks for the nuclear power industry. A few studies have been performed to relocate the seismic capacity of NPPs, yet the effects of multiple hazards have not been accounted for in NPP capacity optimization. The major challenges in extending this problem to the multihazard dimension are (1) the high computational costs for both multihazard risk quantification and system-level optimization and (2) the lack of capital cost databases of NPPs. To resolve these issues, this paper proposes an effective method that identifies the optimal multihazard capacity of NPPs using a multi-objective genetic algorithm and the two-stage direct quantification of fault trees using Monte Carlo simulation method, called the two-stage DQFM. Also, a capacity-based indirect capital cost measure is proposed. Such a proposed method enables NPP to achieve safety and cost-effectiveness against multi-hazard simultaneously within the computationally efficient platform. The proposed multihazard capacity optimization framework is demonstrated and tested with an earthquake-tsunami example.

• The Transactions of The Korean Institute of Electrical Engineers
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• v.62 no.11
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• pp.1505-1510
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• 2013

This paper presents a method for determining the optimal placement of distributed generation units considering voltage sags. In general, the existing methods for distributed generation placement do not consider power quality problems such as voltage sags. In this paper, a novel method based on both genetic algorithm and voltage sag assessment is proposed for determining the placement of distributed generation unit. In the proposed method, the optimal placement is determined to minimize voltage sag effects and system losses.