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Identifying disease modules and components of viral infections based on multi-layer networks

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Science China(Information Sciences) 2016年第7期59卷 15-29页

作者： yuanyuan li Xiufen ZOU School of Mathematics and Statistics Wuhan University Computational Science Hubei Key Laboratory Wuhan University School of Science Wuhan Institute of Technology

With the emergence of multi-dimensional data, we can more comprehensively analyze the pathogenic mechanisms of complex diseases, and thereby improve the diagnosis, treatment and prevention of these *** study presents a novel multi-layer network-based strategy that integrates multi-dimensional data, and identifies disease-related modules and components of viral infections. We first propose a systematic method that constructs a virus-host interaction network with three layers: a viral protein layer, a host protein layer and a host gene layer. This method combines the data of high-throughput gene expression, viral protein interactions,virus-host interactions, protein-protein interactions and transcriptional regulatory relationships. To extract the underlying mechanisms of viral infections from the multi-layer networks, we identify the intra-layer and crosslayer modules, and investigate the conserved modules across multiple datasets. The essential components in the multi-layer networks are detected by singular-value decomposition. The identified conserved modules and essential components are combined into a functional enrichment analysis that reveals their contributions to influenza virus replication. By this analysis, we elucidate the common and specific mechanisms of the replication cycles of two influenza strains. By combining the different layers of information, we can comprehensively understand pathogenic mechanisms of complex diseases.

关键词： multi-dimensional data multi-layer network complex disease virus infection disease modules

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插芯结构对旋流冷却流动换热特性的影响

西安交通大学学报 2025年第1期59卷 105-115页

作者：何伟肖俊峰高松李园园于飞龙伍赫西安热工研究院有限公司西安710054

针对用于透平叶片前缘的旋流冷却结构,为了改善其冷气发展空间、提高综合冷却性能,提出了一种布置在冷却腔内的插芯结构。基于简化旋流冷却结构,采用数值模拟方法研究了插芯结构对旋流冷却靶面换热系数、综合冷却性能、流量分配、流动... 详细信息

针对用于透平叶片前缘的旋流冷却结构,为了改善其冷气发展空间、提高综合冷却性能,提出了一种布置在冷却腔内的插芯结构。基于简化旋流冷却结构,采用数值模拟方法研究了插芯结构对旋流冷却靶面换热系数、综合冷却性能、流量分配、流动结构等的改善效果和作用机理。结果表明:增设插芯结构后,在射流雷诺数5 000~20 000范围内,旋流冷却结构的靶面面积平均努塞尔数增加了5.9%~8.3%,综合冷效因子增加了5.2%~6.6%,吸力侧努塞尔数提高了14.8%~16.6%,相邻喷嘴间流量的最大差从18%削减到5%。插芯结构削减了上游射流在旋流腔轴心处的发展空间,抑制了旋流回流和旋流涡核的形成,降低了上游冷气对新鲜射流的干扰,强化了旋流对壁面边界层的削弱效果,从而有效增加了旋流结构的一致性并提高了靶面换热系数的强度和均匀性。

关键词：旋流冷却透平叶片内部冷却努塞尔数射流雷诺数

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Effect of carbon black on the dynamic moduli of asphalt mixtures and its master curves

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Frontiers of Structural and Civil Engineering 2019年第4期13卷 918-925页

作者： Chuangmin li Fanbo NING yuanyuan li Engineering Laboratory of Spatial Information Technology of Highway Geological Disaster Early Warning in Hunan Province Changsha University of Science & Technology Changsha 410114 China School of Traffic and Transportation Engineering Changsha University of Science &Technology Changsha 410114 China State Key Laboratory of Silicate Materials for Architectures Wuhan University of Technology Wuhan 430070 China

Modulus is one of the main parameters during the design of asphalt pavement structure, the newest specifications of China gives the dynamic moduli ranges of commonly used asphalt mixtures with base asphalt (BA) or styrene-butadiene-styrene modified asphalt (SBS MA), while the moduli ranges of mixtures with carbon black modified asphalt (CB MA) are not recommended. To investigate the CB effect on the dynamic moduli of CB MA mixtures, one commonly used asphalt mixture (AC-20) was designed with BA, SBS MA, and CB MA, respectively. Then, the uniaxial compression dynamic modulus tests were conducted at different temperatures and loading frequencies, the master curves of asphalt mixtures were analyzed based on the time-temperature equivalence principle. The results show that with increasing loading frequency, the temperature dependence of dynamic moduli of all asphalt mixtures tend to be less obvious. Both SBS and CB can decrease the temperature sensitivity of asphalt mixture, the SBS MA mixture has the lowest temperature sensitivity, followed by CB MA and BA mixture. In addition, CB and SBS can obviously improve the dynamic modulus of the BA mixture, enhance the anti-deformation performance of pavement structure, and the improvement effect of CB is almost the same with SBS.

关键词： dynamic modulus carbon black master curve modified asphalt asphalt mixture

Explicit Analytical Solutions of Radial Permeable Power Rate Flow

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Chinese Journal of Mechanical Engineering 2011年第2期24卷 220-223页

作者： li yuanyuan CAI Ruixian Institute of Engineering Thermophysics Chinese Academy of Sciences Beijing 100190 China

The research of different kinds of permeable non-Newtonian fluid flow is increasing day by day owing to the development of science,technology and production *** is most common to use power rate equation to describe such ***,this equation is nonlinear and very difficult to derive explicit exact analytical ***,people can only derive approximate solutions with numerical ***,an advanced separating variables method which can derive exact analytical solutions easier is developed by Academician CAI Ruixian（the method of separating variables with addition）.It is assumed that the unknown variable may be indicated as the sum of one-dimensional functions rather than the product in the common method of separating *** method is used to solve the radial permeable power rate flow unsteady nonlinear equations on account of making the process *** concise（no special functions and infinite series） exact analytical solutions is derived with the new method about this flow to develop the theory of non-Newtonian permeable fluid,which are exponential solution,two-dimensional function with time and radius,logarithmic solution,and double logarithmic solution,*** addition,the method of separating variables with addition is developed and applied instead of the conventional multiplication *** is proven to be promising and encouraging by the *** solutions yielded will be valuable to the theory of the permeable power rate flow and can be used as standard solutions to check numerical methods and their differencing schemes,grid generation ways,*** also can be used to verify the accuracy,convergency and stability of the numerical solutions and to develop the numerical computational approaches.

关键词： non-Newtonian fluid analytical solution permeable power rate flow method of separating variables with addition

Developing a novel quantitative parameter for characterizing spatial distribution of fish following exposure to chemicals and wastewater:Behavioral Gini coefficient

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Journal of Environmental Sciences 2024年第7期141卷 129-138页

作者： Xuanyue Chen yuanyuan li Zhanfen Qin State Key Laboratory of Environmental Chemistry and Ecotoxicology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China University of Chinese Academy of Sciences Beijing 100049China

While the spatial distribution pattern of fish is increasingly used for toxicological test o chemicals or wastewater,no ideal parameter is available for quantitative assessment of spa tial distribution,especially uneven distribution with multiple ***,to develop a quantitative assessment parameter for spatial distribution,the zebrafish were exposed to ethanol,pentylenetetrazole(PTZ),paraquat dichloride(paraquat)and wastewater,followed by a behavioral test in a narrow *** data was acquired and analyzed by id Tracker and *** comparing the effects of all treatments on behavior parameters we confirmed that the spatial distribution was more easily altered rather than general loco motor parameters,e.g.0.7-70 mg/L PTZ and 5-20 mg/L paraquat being effective for altering spatial distribution but having little effects on general locomotor *** on the heatmap,i.e.,the cumulative proportion of grids and that of frequency in grids,we calcu lated the behavioral Gini coefficient(G_(b))for quantitative assessment of fish spatial distri *** Gini coefficient ranged from zero to 1,with larger values meaning poorer even ness of spatial *** note,G_(b)showed smaller coefficient of variations(CV)with3%-19%between replicate tanks in all treatments than the highest frequency(4%-79%),dis playing well ***,G_(b)addressed the challenge of the complicated heatmap with multiple ***,the behavioral Gini coefficient we established is an idea parameter to quantitatively assess spatial distribution of fish shoal,which is expected to be applied in toxicity testing for chemicals and wastewater and automatic quality monitoring for surface water and aquaculture water.

关键词： Zebrafish Behavioral test Spatial distribution Behavioral Gini coefficient

Unsteady 3D algebraically explicit analytical solutions for bio-heat transfer equations

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Science China(Technological Sciences) 2011年第2期54卷 362-368页

作者： li yuanyuan CAI RuiXian Institute of Engineering Thermophysics Chinese Academy of Sciences Beijing 100190 China Graduate University of Chinese Academy of Sciences Beijing 100039 China

Reasonable unsteady three-dimensional explicit analytical solutions are derived with different methods for the widely used bio-heat transfer equation–Pennes *** condition to decide temperature oscillation is obtained in this *** other cases the temperature would vary monotonously along geometric coordinates as time goes *** have been very few open reports of explicit unsteady multidimensional exact analytical solutions published in *** its irreplaceable theoretical value,the analytical solution can also serve as standard solution to check numerical calculation,and therefore promote the development of numerical method of computational heat *** addition,some new special methods have been given originally and deserved further attention.

关键词： Pennes equation temperature oscillation three-dimensional unsteady analytical solutions

Morphological Tracing and Functional Identification of Monosynaptic Connections in the Brain:A Comprehensive Guide

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Neuroscience Bulletin 2024年第9期40卷 1364-1378页

作者： yuanyuan li yuanyuan Fang Kaiyuan li Hongbin Yang Shumin Duan li Sun Affiliated Mental Health Center and Hangzhou Seventh People’s Hospital and School of Brain Science and Brain Medicine Zhejiang University School of MedicineHangzhou310058China liangzhu Laboratory MOE Frontier Science Center for Brain Science and Brain-machine IntegrationState Key Laboratory of Brain-machine IntelligenceZhejiang UniversityHangzhou311121China NHC and CAMS Key Laboratory of Medical Neurobiology Zhejiang UniversityHangzhou310058China Department of Neurobiology and Department of Neurology of the Second Affiliated Hospital Zhejiang University School of MedicineHangzhou310058China Institute of Basic Medical Sciences Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100005China

Behavioral studies play a crucial role in unraveling the mechanisms underlying brain *** advances in optogenetics,neuronal typing and labeling,and circuit tracing have facilitated the dissection of the neural circuitry involved in various important *** identification of monosynaptic connections,both upstream and downstream of specific neurons,serves as the foundation for understanding complex neural circuits and studying behavioral ***,the practical implementation and mechanistic understanding of monosynaptic connection tracing techniques and functional identification remain challenging,particularly for inexperienced *** application of these methods and misinterpretation of results can impede experimental progress and lead to erroneous *** this paper,we present a comprehensive description of the principles,specific operational details,and key steps involved in tracing anterograde and retrograde monosynaptic *** outline the process of functionally identifying monosynaptic connections through the integration of optogenetics and electrophysiological techniques,providing practical guidance for researchers.

关键词： Trans-monosynaptic Retrograde Anterograde Viral tool Neural circuit Optogenetics Electrophysiology

A Review on the Coupled Method of Using the Magnetic and Acoustic Fields for Biological Tissue Imaging

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Chinese Journal of Electrical Engineering 2023年第1期9卷 47-60页

作者： yuanyuan li Guoqiang liu Institute of Electrical Engineering Chinese Academy of SciencesBeijing 100190China Institute of Electrical Engineering and Advanced Electromagnetic Drive Technology Qilu ZhongkeJinan 250102China School of Electronic Electrical and Communication Engineering University of Chinese Academy of SciencesBeijing 100049China

Magnetic field and acoustic field coupled imaging methods mainly include magnetoacoustic tomography,magneto-acousto-electrical tomography,and thermoacoustic tomography,all of which non-invasively achieve the electrical conductivity imaging of tissues with a resolution of up to the millimeter *** principles of these three imaging methods and the research progress in the last two decades are ***,the principles of the three magnetic and acoustic field coupled methods are individually *** progress in medical electromagnetic imaging is further elaborated,and finally the future directions and summary of the coupled imaging methods are summarized.

关键词： Biomedical imaging electromagnetic field acoustic field electrical conductivity coupled method

A simple strategy for constructing acylhydrazone photochromic system with visible color/emission change and its application in photo-patterning

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Chinese Chemical Letters 2020年第12期31卷 3271-3275页

作者： yuanyuan liu Qiuchen Peng yuanyuan li Hongwei Hou Kai li Green Catalysis Center College of ChemistryZhengzhou UniversityZhengzhou 450001China School of Chemistry and Chemical Engineering Henan University of TechmologyZhengzhou 450001China

As a potential photochromic system,acylhydrazones exhibit many outstanding adva ntages including low cost,simple synthesis and high modifiability compared with some classic photochromic ***,the absorption wavelengths of acylhydrazones usually locate in ultraviolet regio n,which makes the band separation between the absorbance maxima of its irradiated and unirradiated forms cannot be observed by naked eyes and greatly limits their practical *** this work,a simple strategy for constructing acylhydrazone photochromic system with visible color/emission change is *** 6 G hydrazine-2-aldehyde-pyridine Schiff base(compound 3)is designed and synthesized by combining acylhydrazone with Rhodamine 6 G *** introduction of Rhodamine 6 G moiety to 3 not only makes it remain all the advantages of acylhydrazone photochromic system but also exhibits visible photo-induced color/emission changes both in solution and in a solid ***,3 exhibits reversible photochromic property with good fatigue re sistance,which makes it an excellent candidate for p hoto-patterning.

关键词： Photochromism Acylhydrazone Rhodamine6G E/Z isomerization Photo-patternin