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Implicit Quadrature-Free Direct Reconstruction Method for Efficient Scale-Resolving Simulations

Communications in Computational Physics 2023年第4期33卷 992-1034页

作者： Hojun You juhyun kim Chongam kim Department of Aerospace System Engineering Sejong UniversitySeoul 05006Republic of Korea Department of Aerospace Engineering Seoul National UniversitySeoul 08826Republic of Korea Institute ofAdvanced Aerospace Technology SeoulNationalUniversitySeoul 08826Republic of Korea

The present study develops implicit physical domain-based discontinuous Galerkin(DG)methods for efficient scale-resolving simulations on mixed-curved *** methods are essential to handle stiff systems in many scale-resolving simulations of interests in computational science and *** physical domain-based DGmethod can achieve high-order accuracy using the optimal bases set and preserve the required accuracy on *** using the quadraturebased DG method,these advantages are overshadowed by severe computational costs on mixed-curved meshes,making implicit scale-resolving simulations *** address this issue,the quadrature-free direct reconstruction method(DRM)is extended to the implicit DG *** this approach,the generalized reconstruction approximates non-linear flux functions directly in the physical domain,making the computing-intensive numerical integrations precomputable at a preprocessing *** DRM operator is applied to the residual computation in the matrix-free *** DRM operator can be further extended to the system matrix computation for the matrix-explicit Krylov subspace method and ***,the A-stable Rosenbrock-type Runge–Kutta methods are adopted to achieve high-order accuracy in *** verification and validation from the manufactured solution to implicit large eddy simulations are *** computed results confirm that the proposed method significantly improves computational efficiency compared to the quadrature-based method while accurately resolving detailed unsteady flow features that are hardly captured by scale-modeled simulations.

关键词： Direct reconstruction method implicit Runge-Kutta method quadrature-free method discontinuous Galerkin method implicit large eddy simulation high performance computing

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condLSTM-Q: A novel deep learning model for predicting COVID-19 mortality in fine geographical scale

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Quantitative Biology 2022年第2期10卷 125-138页

作者： HyeongChan Jo juhyun kim Tzu-Chen Huang Yu-Li Ni Division of Biology and Biological Engineering CaltechPasadena CA 91125USA The Division of Physics Mathematics and AstronomyCaltechPasadena CA 91125USA Walter Burke Institute for Theoretical Physics CaltechPasadena CA 91125USA

Background: Modern machine learning-based models have not been harnessed to their total capacity for disease trend predictions prior to the COVID-19 pandemic. This work is the first use of the conditional RNN model in predicting disease trends that we know of during development that complemented classical epidemiological ***: We developed the long short-term memory networks with quantile output (condLSTM-Q) model for making quantile predictions on COVID-19 death ***: We verified that the condLSTM-Q was accurately predicting fine-scale, county-level daily deaths with a two-week window. The model’s performance was robust and comparable to, if not slightly better than well-known, publicly available models. This provides unique opportunities for investigating trends within the states and interactions between counties along state borders. In addition, by analyzing the importance of the categorical data, one could learn which features are risk factors that affect the death trend and provide handles for officials to ameliorate the ***: The condLSTM-Q model performed robustly, provided fine-scale, county-level predictions of daily deaths with a two-week window. Given the scalability and generalizability of neural network models, this model could incorporate additional data sources with ease and could be further developed to generate other valuable predictions such as new cases or hospitalizations intuitively.

关键词： COVID-19 machine learning deep learning epidemiology time series forecast

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Oncology Research 2024年第2期32卷 421-432页

作者： SEUNG-HEE GWAK juhyun LEE EUNJI OH DOHYUN LEE WONSHIK HAN JONGMIN kim KYONG-TAI kim Department of Life Sciences Pohang University of Science and TechnologyPohang37673Korea R&D Center NovMetaPharma Co.Ltd.Pohang37668Korea Department of Surgery and Cancer Research Institute Seoul National University College of MedicineSeoul03080Korea Generative Genomics Research Center Global Green Research&Development CenterHandong Global UniversityPohang37554Korea

Genetic information is transcribed from genomic DNA to mRNA,which is then translated into threedimensional *** can undergo various post-transcriptional modifications,including RNA editing that alters mRNA sequences,ultimately affecting protein *** this study,RNA editing was identified at the 499th base(c.499)of human vaccinia-related kinase 2(VRK2).This RNA editing changes the amino acid in the catalytic domain of VRK2 from isoleucine(with adenine base)to valine(with guanine base).Isoleucine-containing VRK2 has higher kinase activity than the valine-containing VRK2,which leads to an increase in tumor cell *** we reported that VRK2 directly interacts with dystrobrevin-binding protein(dysbindin)and results in reducing its ***,we demonstrate that isoleucine-containing VRK2 decreases the level of dysbindin than valinecontaining *** interacts with cyclin D and thereby regulates its expression and *** reduction in the level of dysbindin by isoleucine-containing VRK2 further enhances the cyclin D expression,resulting in increased tumor growth and reduction in survival *** has also been observed that in patient samples,VRK2 level was elevated in breast cancer tissue compared to normal breast ***,the isoleucine form of VRK2 exhibited a greater increase in breast cancer ***,it is concluded that VRK2,especially dependent on the 167th variant amino acid,can be one of the indexes of tumor progression and proliferation.

关键词： VRK2 Kinase activity Breast cancer Tumor RNA editing Cell proliferation Cell growth

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The effects of single versus combined therapy using LIM-kinase 2 inhibitor and type 5 phosphodiesterase inhibitor on erectile function in a rat model of cavernous nerve injury-induced erectile dysfunction

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Asian Journal of Andrology 2019年第5期21卷 493-500页

作者： Min Chui Cho Junghoon Lee juhyun Park Sohee Oh Ji Sun Chai Hwancheol Son Jae-Seung Paick Soo Woong kim Department of Urology Seoul National University College of MedicineSMG-SNU Boramae Medical CenterSeoul 07061Korea Department of Urology Seoul National University College of MedicineSeoul National University HospitalSeoul 03080Korea Department of Biostatistics Seoul National University College of MedicineSMG-SNU Boramae Medical CenterSeoul 07061Korea

We aimed to determine whether combination of LIM-kinase 2 inhibitor(LIMK2i)and phosphodiesterase type-5 inhibitor(PDE5i)could restore erectile function through suppressing cavernous fibrosis and improving caver nous apoptosis in a rat model of cavernous nerve crush injury(CNCI).Seventy 12-week-old Sprague-Dawley rats were equally distributed into five groups as follows:(1)sham surgery(Group S),(2)CNCI(Group I),(3)CNCI treated with daily intraperitoneal administration of 10.0 mg kg^-1 LIMK2i(Group I+L),(4)daily oral administration of 20.0 mg kg-1 udenafil,PDE5i(Group I+U),and(5)combined administration of 10.0 mg kg^-1 LIMK2i and 20.0 mg kg^-1 udenafil(Group I+L+U).Rats in Groups I+L,I+U,and I+L+U were treated with respective regimens for 2 weeks after *** 2 weeks after surgery,erectile response was assessed using *** tissues were processed for histological studies and western *** I showed lower intracavernous pressure(ICP)/mean arterial pressure(MAP),lower area under the curve(AUC)/MAP,decreased immunohistochemical staining for alpha-smooth muscle(SM)actin,higher apoptotic index,lower SM/collagen ratio,increased phospho-LIMK2-positive fibroblasts,decreased protein kinase B/endothelial nitric oxide synthase(Akt/eNOS)phosphorylation,increased LIMK2/cofilin phosphorylation,and increased protein expression of fibronectin,compared to Group *** all three treatment groups,erectile responses,protein expression of fibronectin,and SM/collagen ratio were *** I+L+U showed greater improvement in erectile response than Group I+*** content and apoptotic index in Groups I+U and I+L+U were improved compared to those in Group ***,Group I+L did not show a significant improvement in SM content or apoptotic *** number of phospho-LIMK2-positive fibroblasts was normalized in Groups I+L and I+L+U,but not in Group I+***/eNOS phosphorylation was improved in Groups I+U and I+L+U,but not in Group I+***2/cofilin phosphorylation was i

关键词： apoptosis erectile dysfunction fibrosis LIM kinase phosphodiesterase

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Role of inhibiting LIM-kinase2 in improving erectile function through suppression of corporal fibrosis in a rat model of cavernous nerve injury

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Asian Journal of Andrology 2018年第4期20卷 372-378页

作者： juhyun Park Sung Yong Cho Kwanjin Park Ji Sun Chai Hwancheol Son Soo Woong kim Jae-Seung Paick Min Chul Cho Department of Urology Seoul National University College of Medicine SMG-SNU Boramae Medical Center Seoul 03080 Korea Department of Urology Seoul Nationa University College of Medicine Seoul National University Hospital Seoul 07061 Korea

We evaluated whether LIM-kinase 2 inhibitor （LIMK2i） could improve erectile function by suppressing corporal fibrosis through the normalization of the Rho-associated coiled-coil protein kinase 1 （ROCK1）/LIMK2/Cofilin pathway in a rat model of cavernous nerve crush injury （CNCl）. Sixty 11-week-old male Sprague-Dawley rats were divided equally into five groups： sham surgery （S）, CNCl （I）, and CNCl treated with low-dose （L）, medium-dose （M）, and high-dose （H） LIMK2i. The L, M, and H groups were treated with a daily intraperitoneal injection of LIMK2i （2.5, 5.0, and 10.0 mg kg-1 body weight, respectively） for 1 week after surgery. The erectile response was assessed using electrostimulation at 1 week, postoperatively. Penile tissues were processed for Masson＇s trichrome staining, double immunofluorescence, and Western blot assay. Erectile responses in the H group improved compared with the I group, while the M group showed only partial improvement. A significantly decreased smooth muscle/collagen ratio and an increased content of fibroblasts positive for phospho-/IMK2 were noted in the I group. The M and H groups revealed significant improvements in histological alterations and the dysregulated LIMK2/Cofilin pathway, except for LIMK2 phosphorylation in the M group. The inhibition of LIMK2 did not affect the ROCK1 protein expression. The content of fibroblasts positive for phospho-LIMK2 in the H group returned to the level found in the S group, whereas it did not in the M group. However, the L group did not exhibit such improvements. Our data suggest that the inhibition of LIMK2, particularly with administration of 10.0 mg kg^-1 body weight LIMK2i, can improve corporal fibrosis and erectile function by normalizing the LIMK2/Cofilin pathway.

关键词： erectile dysfunction fibrosis LIM kinase penis prostatectomy

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