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KLF4 facilitates chromatin accessibility remodeling in porcine early embryos

Science China(Life Sciences) 2024年第1期67卷 96-112页

作者： Wei Zhu Guowei Bu ruifeng hu Jixiang Zhang Lianyong Qiao Kai Zhou Tingting Wang Qiao Li Jingjing Zhang Linhui Wu Yali Xie Taotao hu Shichun Yang Jiaqi Guan Xiaoyu Chu Juanjuan Shi Xia Zhang Falong Lu Xin Liu Yi-Liang Miao Institute of Stem Cell and Regenerative Biology College of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhan 430070China Key Laboratory of Agricultural Animal Genetics Breeding and Reproduction(Huazhong Agricultural University)Ministry of EducationWuhan 430070China State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental BiologyInnovative Academy of Seed DesignChinese Academy of SciencesBeijing 100101China Frontiers Science Center for Animal Breeding and Sustainable Production Huazhong Agricultural UniversityWuhan 430070China hubei Hongshan Laboratory Wuhan 430070China

Chromatin accessibility remodeling driven by pioneer factors is critical for the development of early embryos.Current studies have illustrated several pioneer factors as being important for agricultural animals,but what are the pioneer factors and how the pioneer factors remodel the chromatin accessibility in porcine early embryos is not clear.By employing low-input DNase-seq(liDNase-seq),we profiled the landscapes of chromatin accessibility in porcine early embryos and uncovered a unique chromatin accessibility reprogramming pattern during porcine preimplantation development.Our data revealed that KLF4 played critical roles in remodeling chromatin accessibility in porcine early embryos.Knocking down of KLF4 led to the reduction of chromatin accessibility in early embryos,whereas KLF4 overexpression promoted the chromatin openness in porcine blastocysts.Furthermore,KLF4 deficiency resulted in mitochondrial dysfunction and developmental failure of porcine embryos.In addition,we found that overexpression of KLF4 in blastocysts promoted lipid droplet accumulation,whereas knockdown of KLF4 disrupted this process.Taken together,our study revealed the chromatin accessibility dynamics and identified KLF4 as a key regulator in chromatin accessibility and cellular metabolism during porcine preimplantation embryo development.

关键词： porcine embryos liDNase-seq chromatin accessibility KLF4 mitochondrion lipid droplets

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Palladium Nanoparticles/Graphdiyne Oxide Nanocomposite with Excellent Peroxidase-like Activity and Its Application for Glutathione Detection

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Chemical Research in Chinese Universities 2022年第2期38卷 529-534页

作者： LAN Weifei hu ruifeng huANG Danrong DONG Xu SHEN Gangyi CHANG Shan DAI Dongsheng School of Pharmacy Minzu University of ChinaBeijing 100081P.R.China Institute of Chemistry Chinese Academy of SciencesBeijing 100190P.R.China Institute of Bioinformatics and Medical Engineering School of Electrical and Information EngineeringJiangsu University of TechnologyChangzhou 213001P.R.China

In this study, palladium nanoparticles loaded graphdiyne oxide (Pd/GDYO) nanocomposite were fabricated by in-situ reduction of palladium chloride in the dispersion of GDYO, and characte-rized by Raman spectra, transmission electron microscopy, X-ray diffraction and X-ray photoelectron spectroscopy. The synthesized Pd/GDYO was first found to have catalytic activities similar to those of the peroxidase enzyme, which can catalyze the oxidation of peroxidase substrate 3,3',5,5'-tetramethylbenzidine(TMB) in the presence of hydrogen peroxide(H2O2). Steady-state kinetic studies showed that the catalytic reaction of Pd/GDYO follows a ping-pong mechanism, and Pd/GDYO has a stronger activity to TMB with a Michaelis constant(Km) value of 5.32×10-4 mmol/L. Based on the shielding effect of glutathione(GSH) on the Pd/GDYO-H2O2-TMB reaction system, a colorimetric detection method for GSH was deve-loped with a wide linear range from 0.1 μmol/L to 40 μmol/L and a limit of detection of 0.1 μmol/L. The method was successfully applied for fast and accurate detection of GSH in injection powder drugs. It was expected that this peroxidase-like Pd/GDYO nano- composite would have wide applications in the fields of biomedicine and environmental chemistry.

关键词： Palladium nanoparticle/graphdiyne oxide nanocomposite Peroxidase-like activity Colorimetric detection Glutathione

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Study on thermal wave based on the thermal mass theory

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Science China(Technological Sciences) 2009年第6期52卷 1786-1792页

作者： hu ruifeng CAO BingYang Key Laboratory for Thermal Science and Power Engineering of Ministry of Education Department of Engeering MechanicsTsinghua UniversityBeijing 100084China

The conservation equations for heat conduction are established based on the concept of thermal mass.We obtain a general heat conduction law which takes into account the spatial and temporal inertia of thermal mass.The general law introduces a damped thermal wave equation.It reduces to the well-known CV model when the spatial inertia of heat flux and temperature and the temporal inertia of temperature are neglected,which indicates that the CV model only considers the temporal inertia of heat flux.Numerical simulations on the propagation and superposition of thermal waves show that for small thermal perturbation the CV model agrees with the thermal wave equation based on the thermal mass theory.For larger thermal perturbation,however,the physically impossible phenomenon pre-dicted by CV model,i.***.the negative temperature induced by the thermal wave superposition,is eliminated by the general heat conduction law,which demonstrates that the present heat conduction law based on the thermal mass theory is more reasonable.

关键词： thermal wave thermal mass theory non-Fourier heat conduction CV model

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Modelling the spreading rate of controlled communicable epidemics through an entropy-based thermodynamic model

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Science China(Physics,Mechanics & Astronomy) 2013年第11期56卷 2143-2150页

作者： WANG WenBin WU ZiNiu WANG ChunFeng hu ruifeng Department of Engineering Mechanics Tsinghua University School of Electro-Mechanical Engineering Xidian University

A model based on a thermodynamic approach is proposed for predicting the dynamics of communicable epidemics assumed to be governed by controlling eforts of multiple scales so that an entropy is associated with the system.All the epidemic details are factored into a single and time-dependent coefcient,the functional form of this coefcient is found through four constraints,including notably the existence of an inflexion point and a maximum.The model is solved to give a log-normal distribution for the spread rate,for which a Shannon entropy can be defined.The only parameter,that characterizes the width of the distribution function,is uniquely determined through maximizing the rate of entropy production.This entropy-based thermodynamic(EBT)model predicts the number of hospitalized cases with a reasonable accuracy for SARS in the year 2003.This EBT model can be of use for potential epidemics such as avian influenza and H7N9 in China.

关键词：热力学模型传播速率信息熵流行病传染性控制建模对数正态分布

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Review of shock wave detection method in CFD post-processing

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Chinese Journal of Aeronautics 2013年第3期26卷 501-513页

作者： Wu Ziniu Xu Yizhe Wang Wenbin hu ruifeng School of Aerospace Tsinghua University

In the present computational fluid dynamics （CFD） community, post-processing is regarded as a procedure to view parameter distribution, detect characteristic structure and reveal physical mechanism of fluid flow based on computational or experimental results. Field plots by contours, iso-surfaces, streamlines, vectors and others are traditional post-processing techniques. While the shock wave, as one important and critical flow structure in many aerodynamic problems, can hardly be detected or distinguished in a direct way using these traditional methods, due to possible confusions with other similar discontinuous flow structures like slip line, contact discontinuity, etc. Therefore, method for automatic detection of shock wave in post-processing is of great importance for both academic research and engineering applications. In this paper, the current status of methodologies developed for shock wave detection and implementations in post-processing platform are reviewed, as well as discussions on advantages and limitations of the existing methods and proposals for further studies of shock wave detection method. We also develop an advanced post-processing software, with improved shock detection.

关键词： Aerodynamics Automatic detection Computational fluid dynamics Shock wave Post-processing

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Space Debris Reentry Analysis Methods and Tools

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Chinese Journal of Aeronautics 2011年第4期24卷 387-395页

作者： WU Ziniua hu ruifeng QU Xi WANG Xiang WU Zhe School of Aerospace Tsinghua University Beijing 100084 China China Academy of Space Technology Beijing 100094 China

The reentry of uncontrolled spacecraft may be broken into many pieces of debris at an altitude in the range of 75-85 km. The surviving fragments could pose great hazard and risk to ground and people. In recent years, methods and tools for predicting and analyzing debris reentry and ground risk assessment have been studied and developed in National Aeronautics and Space Ad-ministration （NASA）, European Space Agency （ESA） and other organizations, including the group of the present authors. This paper reviews the current progress on this topic of debris reentry briefly. We outline the Monte Carlo method for uncertainty analysis, breakup prediction, and parameters affecting survivability of debris. The existing analysis tools can be classified into two categories, i.e. the object-oriented and the spacecraft-oriented methods, the latter being more accurate than the first one. The past object-oriented tools include objects of only simple shapes. For more realistic simulation, here we present an object-oriented tool debris reentry and ablation prediction system （DRAPS） developed by the present authors, which introduces new object shapes to 15 types, as well as 51 predefined motions and relevant aerodynamic and aerothermal models. The aerodynamic and aerothermal models in DRAPS are validated using direct simulation Monte Carlo （DSMC） method.

关键词： space debris reentry ablation breakup risk assessment aerodynamics

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Inner-outer decomposition of wall shear stress fluctuations in turbulent channels

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Theoretical & Applied Mechanics Letters 2022年第2期12卷 132-136页

作者： Limin Wang ruifeng hu Center for Particle-Laden Turbulence Key Laboratory of Mechanics on Disaster and Environment in Western ChinaMinistry of EducationCollege of Civil Engineering and MechanicsLanzhou UniversityLanzhou 730000China

Fluctuating wall shear stress in turbulent channel flows is decomposed into small-scale and large-scale components.The large-scale fluctuating wall shear stress is computed as the footprints of the outer turbulent motions,and the small-scale one is obtained by subtracting the large-scale one from the total,which fully remove the outer influences.We show that the statistics of the small-scale fluctuating wall shear stress is Reynolds number independent at the friction Reynolds number larger than 1000,while which is Reynolds number dependent or the low-Reynolds-number effect exists at the friction Reynolds number smaller than 1000.Therefore,a critical Reynolds number that defines the emergence of universal small-scale fluctuating wall shear stress is proposed to be 1000.The total and large-scale fluctuating wall shear stress intensities approximately follow logarithmic-linear relationships with Reynolds number,and empirical fitting expressions are given in this work.

关键词： Turbulent boundary layer Wall shear stress Inner-outer decomposition

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云南省地质灾害气象风险预警技术改进及应用检验

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灾害学 2024年第2期39卷 85-91页

作者：杨竹云许彦艳李华宏杨迎冬胡瑞峰夏龙松刘博文魏蕾云南省气象台云南昆明650034 中国气象局横断山区(低纬高原)灾害性天气研究中心云南昆明650034 云南省地质环境监测院云南昆明650216 云南省地质调查院(云南省地质科学研究院) 云南昆明650216 双江县气象局云南双江677399

利用2014—2022年云南省地质灾害数据和气象降水资料,开展有效降水量致灾概率研究,并结合地质灾害易发因子,分区建立了新一代精细化地质灾害气象风险预警模型,并对模型性能开展了应用检验。结果表明:新建的地质灾害气象风险预警模型提... 详细信息

利用2014—2022年云南省地质灾害数据和气象降水资料,开展有效降水量致灾概率研究,并结合地质灾害易发因子,分区建立了新一代精细化地质灾害气象风险预警模型,并对模型性能开展了应用检验。结果表明:新建的地质灾害气象风险预警模型提高了预警产品的时空分辨率和准确率,应用效果良好。模型能提前较好地反映出区域性强降水过程背景下的气象风险预警等级;对较难预报的局地强降水,也可以通过实时更新的监测预警产品给出风险加强的趋势,提前发出地质灾害气象风险预警信息;能直接客观反映出极端强降水背景下的气象风险高级别预警,起到较好的预警提示作用。

关键词：云南地质灾害预警模型致灾概率检验

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Large eddy simulation of high-Reynolds-number atmospheric boundary layer flow with improved near-wall correction

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Applied Mathematics and Mechanics(English Edition) 2020年第1期41卷 33-50页

作者： Shengjun FENG Xiaojing ZHENG ruifeng hu Ping WANG Key Laboratory of Mechanics on Disaster and Environment in Western China Ministry of EducationCollege of Civil Engineering and MechanicsLanzhou UniversityLanzhou 730000China Research Center for Applied Mechanics School of Mechano-Electronic EngineeringXidian UniversityXi’an 710071China

It is highly attractive to develop an efficient and flexible large eddy simulation(LES)technique for high-Reynolds-number atmospheric boundary layer(ABL)simulation using the low-order numerical scheme on a relatively coarse grid,that could reproduce the logarithmic profile of the mean velocity and some key features of large-scale coherent structures in the outer layer.In this study,an improved near-wall correction scheme for the vertical gradient of the resolved streamwise velocity in the strain-rate tensor is proposed to calculate the eddy viscosity coefficient in the subgrid-scale(SGS)model.The LES code is realized with a second-order finite-difference scheme,the scale-dependent dynamic SGS stress model,the equilibrium wall stress model,and the proposed correction scheme.Very-high-Reynolds-number ABL flow simulation under the neutral stratification condition is conducted to assess the performance of the method in predicting the mean and fluctuating characteristics of the rough-wall turbulence.It is found that the logarithmic profile of the mean streamwise velocity and some key features of large-scale coherent structures can be reasonably predicted by adopting the proposed correction method and the low-order numerical scheme.

关键词： atmospheric boundary layer near-wall correction large-eddy simulation(LES) very-large-scale motion

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Aerodynamic map for soft and hard hypersonic level flight in near space

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Acta Mechanica Sinica 2009年第4期25卷 571-575页

作者： ruifeng hu Ziniu Wu Zhe Wu Xiaoxin Wang Zhongwei Tian School of Aerospace, Tsinghua University, 100084 Beijing, China School of Aerospace Tsinghua University Beijing China

In this note, we design a velocity-altitude map for hypersonic level flight in near space of altitude 20-100 km. This map displays aerodynamic-related parameters associated with near space level flight, schematically or quantitatively. Various physical conditions for the near-space level flight are then characterized, including laminar or turbulent flow, rarefaction or continuous flow, aerodynamic heating, as well as conditions for sustaining level flight with and without orbital effect. This map allows one to identify conditions to have soft flight or hard flight, and this identification would be helpful for making correct planning on detailed studies of aerodynamics or making initial design of near space vehicles.

关键词： Near space Aerodynamics Hypersonic Level flight Soft flow

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