Genome-wide DNA methylation profiling in differentiating Crohn’s disease from intestinal tuberculosis

Wu Hao,Liu Hongchun,Liu Haining,Chen Yanjie,Liu Taotao,Shen Xizhong,Liu Lili 한국유전학회 2022 Genes & Genomics Vol.44 No.5

Background: Differential diagnosis of Crohn's disease (CD) and intestinal tuberculosis (ITB) is still difficult in clinical pratice. DNA methylation has been considered as a favorable area for biomarker exploration and identification. Objective: The purpose of the current study was to evaluate DNA methylation changes between CD and ITB. Methods: We performed a genome-wide association study to identify differentially methylated positions (DMPs), including 8 CD patients (before the initial of biologics or immunomodulators), 6 ITB patients, and 8 healthy controls (HCs), in whole blood DNA using the Infinium HumanMethylation850 BeadChip. Results: Patients in the CD group and ITB group were all observed with hypo-methylated changes compared with HCs. However, the CD group overlaps with the ITB group in DNA methylation, suggesting a stable epigenetic profile between the two diseases. The pathway enrichment analysis showed the alternation in inflammation-related pathway, immune system, and signal transduction. Focused on the DMPs located in the promoter region, further analysis indicated hypermethylation of cg03122532 (5'UTR of KCNJ15) could be a potential CD-specific biomarker. Conclusions: We identified specific differential methylation loci related to CD and ITB in blood DNA. DNA metylation as a important epigenetic modification could contribute to the pathogenesis study and biomarker exploration of the diseases.

Scattering Correction for Image Reconstruction in Flash Radiography

LIANGZHI CAO,Mengqi Wang,Hongchun Wu,Zhouyu Liu,Yuxiong Cheng,Hongbo Zhang 한국원자력학회 2013 Nuclear Engineering and Technology Vol.45 No.4

Scattered photons cause blurring and distortions in flash radiography, reducing the accuracy of image reconstruction significantly. The effect of the scattered photons is taken into account and an iterative deduction of the scattered photons is proposed to amend the scattering effect for image restoration. In order to deduct the scattering contribution, the flux of scattered photons is estimated as the sum of two components. The single scattered component is calculated accurately together with the uncollided flux along the characteristic ray, while the multiple scattered component is evaluated using correction coefficients pre-obtained from Monte Carlo simulations.The arbitrary geometry pretreatment and ray tracing are carried out based on the customization of AutoCAD. With the above model, an Iterative Procedure for image restORation code, IPOR, is developed. Numerical results demonstrate that the IPOR code is much more accurate than the direct reconstruction solution without scattering correction and it has a very high computational efficiency.

Effect of high-energy neutron source on predicting the proton beam current in the ADS design

Youqi Zheng,Xunzhao Li,,Hongchun Wu 한국원자력학회 2017 Nuclear Engineering and Technology Vol.49 No.8

The accelerator-driven subcritical system (ADS) is driven by a neutron source from spallation reactionsintroduced by the injected proton beam. Part of the neutron source has energy as high as a few hundredMeV to a few GeV. The effects of high-energy source neutrons (En > 20 MeV) are usually approximated byenergy cut-off treatment in practical core calculations, which can overestimate the predicted protonbeam current in the ADS design. This article intends to quantize this effect and propose a way to solvethis problem. To evaluate the effects of high-energy neutrons in the subcritical core, two models areestablished aiming to cover the features of current experimental facilities and industrial-scale ADS in thefuture. The results show that high-energy neutrons with En > 20 MeV are of small fraction (2.6%) in theneutron source, but their contribution to the source efficiency is about 23% for the large scale ADS. Basedon this, a neutron source efficiency correction factor is proposed. Tests show that the new correctionmethod works well in the ADS calculation. This method can effectively improve the accuracy of theprediction of the proton beam current.

SCATTERING CORRECTION FOR IMAGE RECONSTRUCTION IN FLASH RADIOGRAPHY

Cao, Liangzhi,Wang, Mengqi,Wu, Hongchun,Liu, Zhouyu,Cheng, Yuxiong,Zhang, Hongbo Korean Nuclear Society 2013 Nuclear Engineering and Technology Vol.45 No.4

Scattered photons cause blurring and distortions in flash radiography, reducing the accuracy of image reconstruction significantly. The effect of the scattered photons is taken into account and an iterative deduction of the scattered photons is proposed to amend the scattering effect for image restoration. In order to deduct the scattering contribution, the flux of scattered photons is estimated as the sum of two components. The single scattered component is calculated accurately together with the uncollided flux along the characteristic ray, while the multiple scattered component is evaluated using correction coefficients pre-obtained from Monte Carlo simulations.The arbitrary geometry pretreatment and ray tracing are carried out based on the customization of AutoCAD. With the above model, an Iterative Procedure for image restORation code, IPOR, is developed. Numerical results demonstrate that the IPOR code is much more accurate than the direct reconstruction solution without scattering correction and it has a very high computational efficiency.

Resonance Elastic Scattering and Interference Effects Treatments in Subgroup Method

Li, Yunzhao,He, Qingming,Cao, Liangzhi,Wu, Hongchun,Zu, Tiejun Korean Nuclear Society 2016 Nuclear Engineering and Technology Vol.48 No.2

Based on the resonance integral (RI) tables produced by the NJOY program, the conventional subgroup method usually ignores both the resonance elastic scattering and the resonance interference effects. In this paper, on one hand, to correct the resonance elastic scattering effect, RI tables are regenerated by using the Monte Carlo code, OpenMC, which employs the Doppler broadening rejection correction method for the resonance elastic scattering. On the other hand, a fast resonance interference factor method is proposed to efficiently handle the resonance interference effect. Encouraging conclusions have been indicated by the numerical results. (1) For a hot full power pressurized water reactor fuel pin-cell, an error of about +200 percent mille could be introduced by neglecting the resonance elastic scattering effect. By contrast, the approach employed in this paper can eliminate the error. (2) The fast resonance interference factor method possesses higher precision and higher efficiency than the conventional Bondarenko iteration method. Correspondingly, if the fast resonance interference factor method proposed in this paper is employed, the $k_{inf}$ can be improved by ~100 percent mille with a speedup of about 4.56.

On the equivalence of reaction rate in energy collapsing of fast reactor code SARAX

Xiao, Bowen,Wei, Linfang,Zheng, Youqi,Zhang, Bin,Wu, Hongchun Korean Nuclear Society 2021 Nuclear Engineering and Technology Vol.53 No.3

Scattering resonance of medium mass nuclides leads complex spectrum in the fast reactor, which requires thousands of energy groups in the spectrum calculation. When the broad-group cross sections are collapsed, reaction rate cannot be completely conserved. To eliminate the error from energy collapsing, the Super-homogenization method in energy collapsing (ESPH) was employed in the fast reactor code SARAX. An ESPH factor was derived based on the ESPH-corrected SN transport equation. By applying the factor in problems with reflective boundary condition, both the effective multiplication factor and reaction rate were conserved. The fixed-source iteration was used to ensure the stability of ESPH iteration. However, in the energy collapsing process of SARAX, the vacuum boundary condition was adopted, which was necessary for fast reactors with strong heterogeneity. To further reduce the error caused by leakage, an additional conservation factor was proposed to correct the neutron current in energy collapsing. To evaluate the performance of ESPH with conservation factor, numerical benchmarks of fast reactors were calculated. The results of broad-group calculation agreed well with the direct full-core Monte-Carlo calculation, including the effective multiplication factor, radial power distribution, total control rod worth and sodium void worth.

The JFNK method for the PWR's transient simulation considering neutronics, thermal hydraulics and mechanics

He, Qingming,Zhang, Yijun,Liu, Zhouyu,Cao, Liangzhi,Wu, Hongchun Korean Nuclear Society 2020 Nuclear Engineering and Technology Vol.52 No.2

A new task of using the Jacobian-Free-Newton-Krylov (JFNK) method for the PWR core transient simulations involving neutronics, thermal hydraulics and mechanics is conducted. For the transient scenario of PWR, normally the Picard iteration of the coupled coarse-mesh nodal equations and parallel channel TH equations is performed to get the transient solution. In order to solve the coupled equations faster and more stable, the Newton Krylov (NK) method based on the explicit matrix was studied. However, the NK method is hard to be extended to the cases with more physics phenomenon coupled, thus the JFNK based iteration scheme is developed for the nodal method and parallel-channel TH method. The local gap conductance is sensitive to the gap width and will influence the temperature distribution in the fuel rod significantly. To further consider the local gap conductance during the transient scenario, a 1D mechanics model is coupled into the JFNK scheme to account for the fuel thermal expansion effect. To improve the efficiency, the physics-based precondition and scaling technique are developed for the JFNK iteration. Numerical tests show good convergence behavior of the iterations and demonstrate the influence of the fuel thermal expansion effect during the rod ejection problems.

The applicability study and validation of TULIP code for full energy range spectrum

Chen Wenjie,Du Xianan,Wang Rong,Zheng Youqi,Wang Yongping,Wu Hongchun 한국원자력학회 2023 Nuclear Engineering and Technology Vol.55 No.12

NECP-SARAX is a neutronics analysis code system for advanced reactor developed by Nuclear Engineering Computational Physics Laboratory of Xi’an Jiaotong University. In past few years, improvements have been implemented in TULIP code which is the cross-section generation module of NECP-SARAX, including the treatment of resonance interface, considering the self-shielding effect in non-resonance energy range, hyperfine group method and nuclear library with thermal scattering law. Previous studies show that NECP-SARAX has high performance in both fast and thermal spectrum system analysis. The accuracy of TULIP code in fast and thermal spectrum system analysis is demonstrated preliminarily. However, a systematic verification and validation is still necessary. In order to validate the applicability of TULIP code for full energy range, 147 fast spectrum critical experiment benchmarks and 170 thermal spectrum critical experiment benchmarks were selected from ICSBEP and used for analysis. The keff bias between TULIP code and reference value is less than 300 pcm for all fast spectrum benchmarks. And that bias keeps within 200 pcm for thermal spectrum benchmarks with neutronmoderating materials such as polyethylene, beryllium oxide, etc. The numerical results indicate that TULIP code has good performance for the analysis of fast and thermal spectrum system

Homogenized cross-section generation for pebble-bed type high-temperature gas-cooled reactor using NECP-MCX

Qin Shuai,Li Yunzhao,He Qingming,Cao Liangzhi,Wang Yongping,Wu Yuxuan,Wu Hongchun 한국원자력학회 2023 Nuclear Engineering and Technology Vol.55 No.9

In the two-step analysis of Pebble-Bed type High-Temperature Gas-Cooled Reactor (PB-HTGR), the lattice physics calculation for the generation of homogenized cross-sections is based on the fuel pebble. However, the randomly-dispersed fuel particles in the fuel pebble introduce double heterogeneity and randomness. Compared to the deterministic method, the Monte Carlo method which is flexible in geometry modeling provides a high-fidelity treatment. Therefore, the Monte Carlo code NECP-MCX is extended in this study to perform the lattice physics calculation of the PB-HTGR. Firstly, the capability for the simulation of randomly-dispersed media, using the explicit modeling approach, is developed in NECP-MCX. Secondly, the capability for the generation of the homogenized cross-section is also developed in NECP-MCX. Finally, simplified PB-HTGR problems are calculated by a two-step neutronics analysis tool based on Monte Carlo homogenization. For the pebble beds mixed by fuel pebble and graphite pebble, the bias is less than 100 pcm when compared to the high-fidelity model, and the bias is increased to 269 pcm for pebble bed mixed by depleted fuel pebble. Numerical results show that the Monte Carlo lattice physics calculation for the two-step analysis of PB-HTGR is feasible.