• The Journal of Korean Society for Radiation Therapy
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• v.29 no.1
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• pp.19-26
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• 2017

Purpose: The application of density override is very important to minimize dose calculation errors by fiducial markers of metal material in proton treatment plan. However, density override with actual material of the fiducial marker could make problem such as inaccurate target contouring and compensator fabrication. Therefore, we perform density override with surrounding material instead of actual material and we intend to evaluate the usefulness of density override with surrounding material of the fiducial marker by analyzing the dose distribution according to the position, material of the fiducial marker and number of beams. Materials and Method: We supposed that the fiducial marker of gold, steel, titanium is located in 1.5, 2.5, 4.0, 6.0 cm from the proton beam's end of range using water phantom. Treatment plans were created by applying density override with the surrounding material and actual material of the fiducial marker. Also, a liver cancer patient who received proton therapy was selected. We located the fiducial marker of gold, steel, titanium in 0, 1.5, 3.5 cm from the proton beam's end of range and the treatment plans were created by same method with water phantom. Homogeneity Index(HI), Conformity Index(CI) and maximum dose of Organ At Risk(OAR) in Planning Target Volume(PTV) as the evaluation index were compared according to the material, position of the fiducial marker and number of beam. Results: The HI value was more decreased when density override with surrounding material of the fiducial marker was performed comparing with density override with actual material. Especially the HI value was increased when the fiducial marker was located farther from the proton beam's end of the range for a single beam and the fiducial marker's position was closer to isocenter for two or more beams. The CI value was close to 1 and OAR maximum dose was greatly reduced when density override with surrounding material of the fiducial marker was performed comparing with density override with actual material. Conclusion: Density override with surrounding material can be expected to achieve more precise proton therapy than density override with actual material of the fiducial marker and could increase the dose uniformity and target coverage and reduce the dose to surrounding normal tissues for the small fiducial markers used in clinical practice. Most of all, it is desirable to plan the treatment by avoiding the fiducial marker of metal material as much as possible. However, if the fiducial marker have on the beam path, density override of the surrounding material can be expected to achieve more precise proton therapy.

• Journal of Animal Science and Technology
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• v.63 no.6
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• pp.1232-1246
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• 2021

Recently, the cattle genome sequence has been completed, followed by developing a commercial single nucleotide polymorphism (SNP) chip panel in the animal genome industry. In order to increase statistical power for detecting quantitative trait locus (QTL), a number of animals should be genotyped. However, a high-density chip for many animals would be increasing the genotyping cost. Therefore, statistical inference of genotype imputation (low-density chip to high-density) will be useful in the animal industry. The purpose of this study is to investigate the effect of the reference population size and marker density on the imputation accuracy and to suggest the appropriate number of reference population sets for the imputation in Hanwoo cattle. A total of 3,821 Hanwoo cattle were divided into reference and validation populations. The reference sets consisted of 50k (38,916) marker data and different population sizes (500, 1,000, 1,500, 2,000, and 3,600). The validation sets consisted of four validation sets (Total 889) and the different marker density (5k [5,000], 10k [10,000], and 15k [15,000]). The accuracy of imputation was calculated by direct comparison of the true genotype and the imputed genotype. In conclusion, when the lowest marker density (5k) was used in the validation set, according to the reference population size, the imputation accuracy was 0.793 to 0.929. On the other hand, when the highest marker density (15k), according to the reference population size, the imputation accuracy was 0.904 to 0.967. Moreover, the reference population size should be more than 1,000 to obtain at least 88% imputation accuracy in Hanwoo cattle.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.12
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• pp.1912-1921
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• 2020

Objective: This study assessed genomic prediction accuracies based on different selection methods, evaluation procedures, training population (TP) sizes, heritability (h²) levels, marker densities and pedigree error (PE) rates in a simulated Korean beef cattle population. Methods: A simulation was performed using two different selection methods, phenotypic and estimated breeding value (EBV), with an h² of 0.1, 0.3, or 0.5 and marker densities of 10, 50, or 777K. A total of 275 males and 2,475 females were randomly selected from the last generation to simulate ten recent generations. The simulation of the PE dataset was modified using only the EBV method of selection with a marker density of 50K and a heritability of 0.3. The proportions of errors substituted were 10%, 20%, 30%, and 40%, respectively. Genetic evaluations were performed using genomic best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP) with different weighted values. The accuracies of the predictions were determined. Results: Compared with phenotypic selection, the results revealed that the prediction accuracies obtained using GBLUP and ssGBLUP increased across heritability levels and TP sizes during EBV selection. However, an increase in the marker density did not yield higher accuracy in either method except when the h² was 0.3 under the EBV selection method. Based on EBV selection with a heritability of 0.1 and a marker density of 10K, GBLUP and ssGBLUP_0.95 prediction accuracy was higher than that obtained by phenotypic selection. The prediction accuracies from ssGBLUP_0.95 outperformed those from the GBLUP method across all scenarios. When errors were introduced into the pedigree dataset, the prediction accuracies were only minimally influenced across all scenarios. Conclusion: Our study suggests that the use of ssGBLUP_0.95, EBV selection, and low marker density could help improve genetic gains in beef cattle.

• Journal of the Society of Naval Architects of Korea
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• v.51 no.1
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• pp.58-66
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• 2014

Numerical simulations for the flows containing free surface remain difficult problems because the drastic differences of physical properties of water and air, The difference of densities makes the solution instable in particular. For the stabilities of the solutions, the most typical methods to simulate free surface flows, such as Volume Of Fluid(VOF) and Level-Set(LS) methods, impose transient zones where the physical prosperities are continuously distributed. The thickness of the transient zone is the source of the numerical errors. The other side, marker-density method does not use such a transient zone. In the traditional marker-density method, however, the air velocities of free surface cells are extrapolated from the water velocity, and the pressures on the free surface are extrapolated from the air pressures for the stability of the solution. In this study, the marker-density method is modified for the decrease of such numerical errors. That is, the pressure on the free surface is determined to coincide with the pressure gradient terms of the governing equations, and the velocity of free surface cells are calculated with the governing equations. Two-dimensional steady spilling breakers behind of a submersed hydrofoil and three-dimensional spilling breaker near a wedge shaped ship model are simulated using INHAWAVE-II including the modified marker-density(MMD) method. The results are compared with the results of Fluent V6.3 including VOF method and several published research results.

• International Journal of Naval Architecture and Ocean Engineering
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• v.7 no.3
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• pp.610-625
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• 2015

In this paper the wave run-up around a circular column in regular waves is numerically calculated to investigate the applicability of the Modified Marker-Density (MMD) method to prediction of wave run-up around an offshore platform. The MMD method is one of the methods to define the highly nonlinear free surface. The governing equations are the Navier-Stokes equations and the continuity equation which are computed in Cartesian grid system. To validate incident waves generated by numerical simulation, those are compared with the solutions of the Stokes $5^{th}$ order wave theory. The wave run-up simulations are performed varying the steepness and period of incident waves as referred experimental data. The numerical results are compared to the experimental data and the results show good agreements.

• 한국전산유체공학회:학술대회논문집
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• 2005.10a
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• pp.213-217
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• 2005

In this study the water including sediment is assumed that the density is different from fresh water. And the phenomenon inhaled by low pressure around the pipe is numerically simulated in two dimension. The simulation is done using finite difference method in rectangular staggered mesh system and Navier-Stokes equations and continuty equation are employed as governing equations. The method of Irregular leg lengths and stars are adopted to satisfy boundary condition of body boundary. Marker-Density method is used to calculate the density of mixed flow. Also SGS turbulence model is applied to consider vortex smaller then grid at high Renolds number. This study is to analyze inhalation phenomenon of mixed flow with sediment and to verify the numerical method for mixed flow. To verify the numerical results are compared with experimental results

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.2
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• pp.162-172
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• 2011

In this paper, simulation was used to determine accuracies of genomic breeding values for polygenic traits associated with many thousands of markers obtained from high density genome scans. The statistical approach was based upon stochastically simulating a pedigree with a specified base population and a specified set of population parameters including the effective and noneffective marker distances and generation time. For this population, marker and quantitative trait locus (QTL) genotypes were generated using either a single linkage group or multiple linkage group model. Single nucleotide polymorphism (SNP) was simulated for an entire bovine genome (except for the sex chromosome, n = 29) including linkage and recombination. Individuals drawn from the simulated population with specified marker and QTL genotypes were randomly mated to establish appropriate levels of linkage disequilibrium for ten generations. Phenotype and genomic SNP data sets were obtained from individuals starting after two generations. Genetic prediction was accomplished by statistically modeling the genomic relationship matrix and standard BLUP methods. The effect of the number of linkage groups was also investigated to determine its influence on the accuracy of breeding values for genomic selection. When using high density scan data (0.08 cM marker distance), accuracies of breeding values on juveniles were obtained of 0.60 and 0.82, for a low heritable trait (0.10) and high heritable trait (0.50), respectively, in the single linkage group model. Estimates of 0.38 and 0.60 were obtained for the same cases in the multiple linkage group models. Unexpectedly, use of BLUP regression methods across many chromosomes was found to give rise to reduced accuracy in breeding value determination. The reasons for this remain a target for further research, but the role of Mendelian sampling may play a fundamental role in producing this effect.

• 한국전산유체공학회:학술대회논문집
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• 2005.10a
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• pp.195-199
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• 2005

Wave breaking phenomenon near the fore body of a ship is numerically simulated. The ship advance with uniform velocity in calm water. For the simulation, incompressible Navier-Stokes equations and continuity equation are adopted as governing equations. The simulation is carried out in staggered variable mesh system with finite difference method. Marker and Cell(MAC) method and Marker-Density method are employed to track the free surface. Body boundary conditions are satisfied with the adoption of porosity method and no-slip condition on the hull surface. The ship model has a wedge type fore-body, and the computational domain is an appropriate region around the fore-body. The computation results are compared with some experimental results. Also the difference of the free surface tracking methods are discussed.

• 한국전산유체공학회:학술대회논문집
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• 2004.03a
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• pp.119-125
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• 2004

Unsteady nonlinear wave motions on the free surface over a plane beach of constant slope are numerically simulated using a finite difference method in rectangular grid system. Two-dimensional Navier-Stokes equations and the continuity equation are used for the computations. Irregular leg lengths and stars are employed near the boundaries of body and free surface to satisfy the boundary conditions. Also, the free surface which consists of markers or segments is determined every time step with the satisfaction of kinematic and dynamic free surface conditions. Moreover, marker-density method is also adopted to allow plunging jets impinging on the free surface. The second-order Stokes wave theory and solitary wave theory are employed for the generation of waves on the inflow boundary. For the simulation of wave breaking phenomena, the computations are carried out with the plane beach of constant slope in surf zone. The results are compared with each other. The marker-density method is better then the hybrid method. Also they are compared with other existing experimental results. The Agreement between the experimental data and the computation results is good.

• Journal of the Society of Naval Architects of Korea
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• v.53 no.1
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• pp.1-9
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• 2016

It is important to research and understand the physical phenomenon around a semi-submersible offshore structure on waves and currents because the wave run-up and load occurs owing to the waves and currents. In this study, the numerical simulations are performed about flow around a fixed semi-submersible offshore structure. The Modified Marker-density method is adopted in the present computation procedure, this method is one of the various methods to define the free-surface. The present computation results are compared with existing experimental and numerical simulation(VOF method) results. And, the computation results are relatively coincident with the existing results of model test and numerical simulation by VOF method.