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Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids

Journal of Integrative Plant Biology 2024年第2期66卷 208-227页

作者： Zhaoxu Gao Yanning Su Le Chang Guanzhong Jiao Yang Ou Mei Yang Chao Xu pengtao Liu Zejia Wang Zewen Qi Wenwen Liu Linhua sun Guangming He Xing Wang Deng Hang He School of Advanced Agriculture Sciences and School of Life Sciences State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijing 100871China College of Grassland Science Beijing Forestry UniversityBeijing 100083China Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences in WeifangWeifang 261325China

In plants,the genome structure of hybrids changes compared with their parents,but the effects of these changes in hybrids remain elusive.Comparing reciprocal crosses between Col×C24 and C24×Col in Arabidopsis using high-throughput chromosome conformation capture assay(Hi-C)analysis,we found that hybrid three-dimensional(3D)chromatin organization had more long-distance interactions relative to parents,and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways.The interactions between euchromatin and heterochromatin were increased,and the compartment strength decreased in hybrids.In compartment domain(CD)boundaries,the distal interactions were more in hybrids than their parents.In the hybrids of CURLY LEAF(clf)mutants clfCol×clfC24and clfC24×clfCol,the heterosis phenotype was damaged,and the long-distance interactions in hybrids were fewer than in their parents with lower H3K27me3.ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type(WT)hybrids,which may have led to more long-distance interactions.In addition,the differentially expressed genes(DEGs)located in the boundaries of CDs and loop regions changed obviously in WT,and the functional enrichment for DEGs was different between WT and clf in the longdistance interactions and loop regions.Our findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.

关键词： 3D chromatin organization H3K27me3 homo-trans hybrids long-distanceinteractions

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Predict Blood Pressure by Photoplethysmogram with the Fluid-Structure Interaction Modeling

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Communications in Computational Physics 2022年第4期31卷 1114-1133页

作者： Jianhong Chen Wenrui Hao pengtao sun Lian Zhang Wilshire Advisors LLC Los AngelesCaliforniaUSA Department of Mathematics Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA Department of Mathematical Sciences University of Nevada Las VegasLas VegasNevadaUSA In-Chao Institute Ltd ShenzhenChina

Blood pressure(BP)has been identified as one of the main factors in cardiovascular disease and other related diseases.Then how to accurately and conveniently measure BP is important to monitor BP and to prevent hypertension.This paper proposes an efficient BP measurement model by integrating a fluid-structure interaction model with the photoplethysmogram(PPG)signal and developing a data-driven computational approach to fit two optimization parameters in the proposedmodel for each individual.The developed BPmodel has been validated on a public BP dataset and has shown that the average prediction errors among the root mean square error(RMSE),the mean absolute error(MAE),the systolic blood pressure(SBP)error,and the diastolic blood pressure(DBP)error are all below 5mmHg for normal BP,stage I,and stage II hypertension groups,and,prediction accuracies of the SBP and the DBP are around 96%among those three groups.

关键词： Blood pressure prediction fluid-structure interaction PPG

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An Augmented Lagrangian Uzawa IterativeMethod for Solving Double Saddle-Point Systems with Semidefinite(2,2)Block and its Application to DLM/FDMethod for Elliptic Interface Problems

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Communications in Computational Physics 2021年第6期30卷 124-143页

作者： Cheng Wang pengtao sun School of Mathematical Sciences Tongji UniversityShanghai 200092China Department of Mathematical Sciences University of Nevada Las Vegas4505Maryland ParkwayLas VegasNV 89154USA

.In this paper,an augmented Lagrangian Uzawa iterative method is developed and analyzed for solving a class of double saddle-point systems with semidefinite(2,2)block.Convergence of the iterativemethod is proved under the assumption that the double saddle-point problem exists a unique solution.An application of the iterative method to the double saddle-point systems arising from the distributed Lagrange multiplier/fictitious domain(DLM/FD)finite element method for solving elliptic interface problems is also presented,in which the existence and uniqueness of the double saddle-point system is guaranteed by the analysis of the DLM/FD finite element method.Numerical experiments are conducted to validate the theoretical results and to study the performance of the proposed iterative method.

关键词： Double saddle-point problem augmented Lagrangian Uzawa method elliptic interface problem distributed Lagrange multiplier/fictitious domain(DLM/FD)method

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Phase Field Model of Thermo-Induced Marangoni Effects in the Mixtures and its Numerical Simulations with Mixed Finite Element Method

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Communications in Computational Physics 2009年第10期6卷 1095-1117页

作者： pengtao sun Chun Liu Jinchao Xu Department of Mathematical Sciences University of NevadaLas Vegas4505 Maryland ParkwayLas VegasNV 89154USA Department of Mathematics The Pennsylvania State UniversityUniversity ParkPA 16802USA

In this paper,we study the Marangoni effects in the mixture of two Newtonian fluids due to the thermo-induced surface tension heterogeneity on the interface.We employ an energetic variational phase field model to describe its physical phenomena,and obtain the corresponding governing equations defined by a modi-fied Navier-Stokes equations coupled with phase field and energy transport.A mixed Taylor-Hood finite element discretization together with full Newton’s method are applied to this strongly nonlinear phase field model on a specific domain.Under different boundary conditions of temperature,the resulting numerical solutions illustrate that the thermal energy plays a fundamental role in the interfacial dynamics of two-phase flows.In particular,it gives rise to a dynamic interfacial tension that depends on the direction of temperature gradient,determining the movement of the interface along a sine/cosine-like curve.

关键词： Phase field Navier-Stokes equations Marangoni effects temperature dependent surface tension mixed Taylor-Hood finite element Newton’s method

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Distributed Lagrange Multiplier/Fictitious Domain Finite Element Method for a Transient Stokes Interface Problem with Jump Coefficients

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Computer Modeling in Engineering & Sciences 2019年第4期119卷 35-62页

作者： Andrew Lundberg pengtao sun Cheng Wang Chen-song Zhang Department of Mathematical Sciences University of NevadaLas Vegas4505 Maryland ParkwayLas VegasNV 89154USA School of Mathematical Sciences Tongji UniversityShanghaiChina LSEC&NCMIS Academy of Mathematics and System ScienceBeijingChina

The distributed Lagrange multiplier/fictitious domain(DLM/FD)-mixed finite element method is developed and analyzed in this paper for a transient Stokes interface problem with jump coefficients.The semi-and fully discrete DLM/FD-mixed finite element scheme are developed for the first time for this problem with a moving interface,where the arbitrary Lagrangian-Eulerian(ALE)technique is employed to deal with the moving and immersed subdomain.Stability and optimal convergence properties are obtained for both schemes.Numerical experiments are carried out for different scenarios of jump coefficients,and all theoretical results are validated.

关键词： Transient Stokes interface problem jump coefficients distributed Lagrange multiplier fictitious domain method mixed finite element an optimal error estimate stability

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Numerical Study of a 3D Two-Phase PEM Fuel Cell Model Via a Novel Automated Finite Element/Finite Volume Program Generator

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Communications in Computational Physics 2012年第1期11卷 65-98页

作者： pengtao sun Su Zhou Qiya Hu Guoping Liang Department of Mathematical Sciences University of NevadaLas Vegas4505Maryland ParkwayLas VegasNV 89154USA Department of Fuel Cell Power Systems Tongji University(Jiading campus)4800 Caoan RoadShanghai 201804China Institute of Computational Mathematics and Scientific Engineering Computing Chinese Academy of SciencesBeijing 100080China Institute of Mathematics Academy of Mathematics and Systems SciencesChinese Academy of SciencesBeijing 100080China.

Numerical methods of a 3D multiphysics,two-phase transport model of proton exchange membrane fuel cell(PEMFC)is studied in this paper.Due to the coexistence of multiphase regions,the standard finite element/finite volume method may fail to obtain a convergent nonlinear iteration for a two-phase transport model of PEMFC[49,50].By introducing Kirchhoff transformation technique and a combined finite element-upwind finite volume approach,we efficiently achieve a fast convergence and reasonable solutions for this multiphase,multiphysics PEMFC model.Numerical implementation is done by using a novel automated finite element/finite volume programgenerator(FEPG).By virtue of a high-level algorithmdescription language(script),component programming and human intelligence technologies,FEPG can quickly generate finite element/finite volume source code for PEMFC simulation.Thus,one can focus on the efficient algorithm research without being distracted by the tedious computer programming on finite element/finite volume methods.Numerical success confirms that FEPG is an efficient tool for both algorithm research and software development of a 3D,multiphysics PEMFC model with multicomponent and multiphase mechanism.

关键词： Proton exchange membrane fuel cell two-phase transport Kirchhoff transformation finite element finite volume automated programgenerator algorithmdescription language script

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Fast Numerical Simulation of Two-Phase Transport Model in the Cathode of a Polymer Electrolyte Fuel Cell

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Communications in Computational Physics 2009年第6期6卷 49-71页

作者： pengtao sun Guangri Xue Chaoyang Wang Jinchao Xu Department of Mathematical Sciences University of NevadaLas Vegas4505 Maryland ParkwayLas VegasNV 89154USA Department of Mathematics The Pennsylvania State UniversityUniversity ParkPA 16802USA Departments of Mechanical Engineering and Materials Science and Engineering Electrochemical Engine Center(ECEC)The Pennsylvania State UniversityUniversity ParkPA 16802USA Laboratory of Mathematics and Applied Mathematics School of Mathematical SciencesPeking UniversityBeijing 100871China

In this paper,we apply streamline-diffusion and Galerkin-least-squares fi-nite element methods for 2D steady-state two-phase model in the cathode of polymer electrolyte fuel cell(PEFC)that contains a gas channel and a gas diffusion layer(GDL).This two-phase PEFC model is typically modeled by a modified Navier-Stokes equation for the mass and momentum,with Darcy’s drag as an additional source term in momentum for flows through GDL,and a discontinuous and degenerate convectiondiffusion equation for water concentration.Based on the mixed finite element method for the modified Navier-Stokes equation and standard finite element method for water equation,we design streamline-diffusion and Galerkin-least-squares to overcome the dominant convection arising from the gas channel.Meanwhile,we employ Kirchhoff transformation to deal with the discontinuous and degenerate diffusivity in water concentration.Numerical experiments demonstrate that our finite element methods,together with these numerical techniques,are able to get accurate physical solutions with fast convergence.

关键词： Two-phase model polymer electrolyte fuel cell Kirchhoff transformation convection dominated diffusion problem streamline diffusion Galerkin-least-squares

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Applications of multiresolution analysis in Besov-Q type spaces and Triebel-Lizorkin-Q type spaces

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Frontiers of Mathematics in China 2022年第3期17卷 373-435页

作者： pengtao LI Wenchang sun School of Mathematics and Statistics Qingdao UniversityQingdao 266071China School of Mathematical Sciences Nankai UniversityTianjin 300000China

In this survey,we give a neat summary of the applications of the multi-resolution analysis to the studies of Besov-Q type spaces B_(p,q)^(γ1,γ2) (R^(n))and Triebel-Lizorkin-Q type spaces B_(p,q)^(γ1,γ2) (R^(n)).We will state briefly the recent progress on the wavelet characterizations,the boundedness of Calderon-Zygmund operators,the boundary value problem of B_(p,q)^(γ1,γ2) (R^(n)) and F_(p,q)^(γ1,γ2) (R^(n)).We also present the recent developments on the well-posedness of fluid equations with small data in B_(p,q)^(γ1,γ2) (R^(n))and F_(p,q)^(γ1,γ2) (R^(n)).

关键词： Multiresolution analysis regular wavelet Besov-Q type spaces Triebel-Lizorkin-Q type spaces

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基于文本图像修正的两阶段船名识别框架

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电子测量与仪器学报 2024年第2期38卷 30-39页

作者：卢鹏涛蒋雯黄菊孙水发汪方毅湖北省水电工程智能视觉监测重点实验室宜昌443002 三峡大学计算机与信息学院宜昌443002 长江宜昌通信管理局宜昌443001 杭州师范大学杭州311121

船舶名称(牌照)识别在水路运输系统中发挥着重要的作用。针对船舶名称在内河航道中目标较小且航道两岸观测船舶存在较大倾斜角度导致难以识别的问题,提出一个以自然场景文本检测算法(differentiable binarization,DB)和文本识别算法(con... 详细信息

船舶名称(牌照)识别在水路运输系统中发挥着重要的作用。针对船舶名称在内河航道中目标较小且航道两岸观测船舶存在较大倾斜角度导致难以识别的问题,提出一个以自然场景文本检测算法(differentiable binarization,DB)和文本识别算法(convolutional recurrent neural network,CRNN)为基础的船舶名称自动识别框架(automatic ship name identification,ASNI),ASNI包括以下3个部分:船名检测、文本图像修正和识别,其中,船名文本图像修正由船名矫正模块和超分辨率重建模块构成。首先,该框架利用DB算法对图像船名候补区域特征进行自适应尺度融合处理获取特征图,通过特征映射预测生成的二值图像寻找连接区域,以此获得船名感兴趣区域(ROI)。其次,在船名检测之后引入船名矫正模块,基于透视变换对ROI中船名不规则文本进行矫正。此外,设计超分辨率重建模块,对矫正后的船名图像进行超分辨率重建处理,以提高船名图像的分辨率。最后,利用CRNN算法对文本图像修正后的ROI中船名进行识别得到最终结果。通过在内河航道船舶数据集(ship license plate,SLP)上进行训练和测试,最终实验结果显示,ASNI框架对船舶识别的平均准确率为87.50%,相比于基础框架提升了3.12%。本文设计的框架有效解决了因分辨率不足和倾斜导致船舶识别不准确的问题,相比基础框架,ASNI有更好的识别效果。

关键词：船舶名称识别文本检测透视变换超分辨率

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基于多特征融合的煤自燃温度深度预测模型

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中国矿业 2024年第2期33卷 84-90页

作者：王斌贾澎涛郭风景孙刘咏林开义陕西建新煤化有限责任公司陕西黄陵727300 西安科技大学计算机科学与技术学院陕西西安710054 陕西陕煤蒲白矿业有限公司陕西蒲城715517

为了有效预防煤矿采空区煤自燃灾害,提高煤自燃灾害预测模型精度,提出了基于多特征融合的煤自燃温度深度预测模型。首先,通过自编码器网络对煤自燃数据的每一个特征进行降噪处理,增强数据的鲁棒性;其次,按时间序列顺序将降噪后的数据转... 详细信息

为了有效预防煤矿采空区煤自燃灾害,提高煤自燃灾害预测模型精度,提出了基于多特征融合的煤自燃温度深度预测模型。首先,通过自编码器网络对煤自燃数据的每一个特征进行降噪处理,增强数据的鲁棒性;其次,按时间序列顺序将降噪后的数据转成二维特征矩阵,采用滑动窗口对特征矩阵进行切片,并采用深度学习中的卷积神经网络提取特征矩阵上的有效特征,进行特征数据融合,在降噪和特征提取与融合的过程中采用差分进化算法对降噪自编码器和卷积神经网络的参数进行优化;最后,将融合后的数据输入门控循环单元神经网络进行煤自燃温度预测。实验结果表明,降噪后和特征融合后的数据在平均绝对误差上比直接采用原始数据预测误差分别降低6.55%和69.26%,均方根误差分别降低13.23%和63.49%,说明经过编码器降噪以及特征融合处理后能够有效提升煤自燃温度预测的准确度。

关键词：煤自燃深度学习卷积神经网络预测差分进化算法

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