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| 1 | clusterProfiler 4.0:A universal enrichment tool for interpreting omics data显示文摘Functional enrichment analysis is pivotal for interpreting highthroughput omics data in life science.It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible.To meet these requirements,we present here an updated version of our popular Bioconductor package,clusterProfiler 4.0.This package has been enhanced considerably compared with its original version published 9 years ago.The new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases.It also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and visualization.Other new features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists.We anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms. | Tianzhi Wu Erqiang Hu Shuangbin Xu Meijun Chen Pingfan Guo Zehan Dai Tingze Feng Lang Zhou Wenli Tang Li Zhan Xiaocong Fu Shanshan Liu Xiaochen Bo Guangchuang Yu | 2021 | The Innovation2021，2，3： | 40 |
| 2 | Research on the mechanics of underwater supersonic gas jets显示文摘An experimental research was carried out to study the fluid mechanics of underwater supersonic gas jets. High pressure air was injected into a water tank through converging-diverging nozzles (Laval nozzles). The jets were operated at different conditions of over-, full- and under-expansions. The jet sequences were visualized using a CCD camera. It was found that the injection of supersonic air jets into water is always accompanied by strong flow oscillation, which is related to the phenomenon of shock waves feedback in the gas phase. The shock wave feedback is different from the acoustic feedback when a supersonic gas jet discharges into open air, which causes screech tone. It is a process that the shock waves enclosed in the gas pocket induce a periodic pressure with large amplitude variation in the gas jet. Consequently, the periodic pressure causes the jet oscillation including the large amplitude expansion. Detailed pressure measurements were also conducted to verify the shock wave feedback phenomenon. Three kinds of measuring methods were used, i.e., pressure probe submerged in water, pressure measurements from the side and front walls of the nozzle devices respectively. The results measured by these methods are in a good agreement. They show that every oscillation of the jets causes a sudden increase of pressure and the average frequency of the shock wave feedback is about 5–10 Hz. | SHI HongHui1, WANG BoYi2 & DAI ZhenQing2 1 College of Mechanical Engineering and Automation, Zhejiang Sci-Tech University, Hangzhou 310018, China 2 State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China | 2010 | Science China(Physics,Mechanics & Astronomy)2010，53，3： | 22 |
| 3 | Research hotspots and effectiveness of repetitive transcranial magnetic stimulation in stroke rehabilitation显示文摘Repetitive transcranial magnetic stimulation, as a relatively new type of rehabilitation treatment, is a painless and non-invasive method for altering brain excitability. Repetitive transcranial magnetic stimulation has been widely used in the neurorehabilitation of stroke patients. Here, we used CiteSpace software to visually analyze 315 studies concerning repetitive transcranial magnetic stimulation for stroke rehabilitation from 1999 to 2019, indexed by Web of Science, to clarify the research hotspots in different periods and characterize the gradual process of discovery in this field. We found that four main points were generally accepted:(1) repetitive transcranial magnetic stimulation has a positive effect on motor function recovery in patients with subcortical stroke;(2) it may be more advantageous for stroke patients to receive low-frequency repetitive transcranial magnetic stimulation in the unaffected hemispheres than to receive high-frequency repetitive transcranial magnetic stimulation in affected hemisphere;(3) low-frequency repetitive transcranial magnetic stimulation has become a potential therapeutic tool for patients with non-fluent aphasia after chronic stroke for neurological rehabilitation and language recovery;and(4) there are some limitations to these classic clinical studies, such as small sample size and low test efficiency. Our assessment indicates that prospective, multi-center, large-sample, randomized controlled clinical trials are still needed to further verify the effectiveness of various repetitive transcranial magnetic stimulation programs for the rehabilitation of stroke patients. | Ai-Hua Xu Yong-Xin Sun | 2020 | Neural Regeneration Research2020，15，11： | 21 |
| 4 | New advances in virtual plant research显示文摘Virtual plants are computer simulations of the growth, development and deployment of plants in a three-dimensional space. Over the past 20 years, significant progress has been made in virtual plant modeling corresponding to the rapid advances in information technology. Virtual plant research has broad applications in agronomy, forestry, ecology, and remote sensing areas. In this review, we attempt to introduce the significance, modeling methodology, and main advances in virtual plant research and applications. The challenges associated with virtual plant modeling in agronomy applications, including the interaction mechanism between plant and environment and root system modeling, are also discussed. Insights into applications of virtual plants in agronomy are given in the areas of performing virtual experiments to accurately quantify the utilization of soil water and nutrients, to design crop ideotype on computers, and to improve crop planting. | Yan Guo Baoguo Li | 2001 | Chinese Science Bulletin2001，46，11： | 21 |
| 5 | A Liutex based definition and identification of vortex core center lines显示文摘Six core issues for vortex definition and identification concern with (1) the absolute strength,(2) the relative strength,(3) the rotational axis,(4) the vortex core center,(5) the vortex core size, and (6) the vortex boundary (Liu C. 2019). However, most of the currently popular vortex identification methods, including the Q criterion, the criterion and the Acj criterion etc., are Eulerian local region-type vortex identification criteria and can only approximately identify the vortex boundary by somewhat arbitrary threshold. On the other hand, the existing Eulerian local line-type methods, which seek to extract line-type features such as vortex core line, are not entirely satisfactory since most of these methods are based on vorticity or pressure minimum that will fail in many cases. The key issue is the lack of a reasonable mathematical definition for vortex core center. To address this issue, a Liutex (previously named Rortex) based definition of vortex core center is proposed in this paper. The vortex core center, also called vortex rotation axis line here, is defined as a line where the Liutex magnitude gradient vector is aligned with the Liutex vector, which mathematically implies that the cross product of the Liutex magnitude gradient vector and the Liutex vector on the line is equal to zero. Based on this definition, a novel three-step method for extracting vortex rotation axis lines is presented. Two test cases, namely the Burgers vortex and hairpin vortices, are examined to justify the proposed method. The results demonstrate that the proposed method can successfully identify vortex rotation axis lines without any user-specified threshold, so that the proposed method is very straightforward, robust and efficient. | Yi-sheng Gao Jian-ming Liu Yi-fei Yu Chaoqun Liu | 2019 | Journal of Hydrodynamics2019，31，3： | 19 |
| 6 | 词意辨析:可视化、视觉化、Visualization及信息图形显示文摘当我们翻开有关视觉化、可视化、信息图形的书籍或论文,会发现它们所列举的作品非常相似,并都指向英文单词'Visualization'。这四个相似度极高的词语形成了一片模糊的风景。本文通过词义考察、文献纪录分析来辨析这些词之间的关系,尝试辨识'可视化'与'视觉化'的正误、厘清'视觉化'与英文对应词'Visualization'的对应关系,并讨论'视觉化'与'信息图形'之间的本质差异,以期获得对此领域更明确而深入的理解。 | 向帆 | 2017 | 装饰2017，，4： | 19 |
| 7 | Flow visualization of silicon-based micro pulsating heat pipes显示文摘Two sets of silicon-based micro pulsating heat pipes(SMPHPs) with trapezoidal cross section having hydraulic diameters of 352 μm(#1) and 394 μm(#2) respectively were fabricated for the first time using MEMS technology.With FC-72 as the working fluid,the start-up,steady operation state,as well as flow patterns were investigated using a CCD camera.It was found that the start-up process of these two SMPHPs was rather rapid.At the start-up period,no nucleation was observed,and the vapor plugs at the evaporator U-bends were formed mainly due to the breakup of liquid slugs.At the steady operation state,self-sustained oscillation with large amplitudes dominated the flow behavior when the inclination angle varied from 10° to 90°,but the nucleate boiling and bulk circulation were observed only in SMPHP #2.While bubbly,slug/plug,annular/semi-annular,and wavy-annular flows were observed in both two SMPHPs,the injection flow only appeared in SMPHP #2. | QU Jian & WU HuiYing Key Laboratory for Power Machinery and Engineering of Ministry of Education,School of Mechanical Engineering,Shanghai Jiaotong University,Shanghai 200240,China | 2010 | Science China(Technological Sciences)2010，53，4： | 13 |
| 8 | 基于OpenGL的三维可视化方法研究显示文摘随着三维技术的飞速发展和广泛应用,许多应用工程领域都出现了虚拟现实、科学计算可视化等三维仿真处理的应用要求。据此论文介绍了OpenGL的特点和工作原理,详细论述了如何建立VC和OpenGL库应用接口及进行三维图形开发的具体步骤和基本过程,最后通过三维地形图绘制实例的过程分析,便于用户理解运用。 | 潘忠英 | 2014 | 计算机与数字工程2014，42，3： | 11 |
| 9 | 混合现实技术在医学手术可视化中的应用研究(英文)显示文摘With the continuous progress of virtual simulation technology,medical surgery visualization system has been developed from two-dimensional to three-dimensional,from digital to network and intelligentization.The visualization system with mixed reality technology will also be used in all stage of medical surgery,such as case discussion,surgical planning,intraoperative guidance,post-operative evaluation,rehabilitation,so as to further promote high intelligence,high precision of medical surgery,and consequently improve effectiveness of treatment and quality of medical service.This paper discusses the composition and technical characteristics of medical operation visualization system based on mixed reality technology,and introduces some typical applications of mixed reality technology in medical operation visualization,which provides a new perspective for the application of mixed technology in medical surgery. | 高原 谭珂 孙坚 姜涛 邹晓文 | 2019 | Chinese Medical Sciences Journal2019，34，2： | 11 |
| 10 | 基于Visualization Toolkit的数字化人体骨骼系统的重建与可视化显示文摘在人体骨骼系统的三维可视化过程中 ,将二维CT数据重建生成理想的三维骨骼数据是非常重要的一环。作者应用可视化工具VisualizationToolkit (VTK)和VC ++实现了二维数据的三维重建、面片削减、连通性检测、三维平滑等一系列功能。与利用OpenGL等工具重建得到的骨骼数据相比 ,不但准确度和视觉效果有了显著改善 ,数据量也大大减小。VTK在人体骨骼系统的重建及处理工作中取得的良好效果表明 ,它是医学图像重建和处理的有力工具之一 ,具有使用灵活 ,功能强大的优点 ,值得推广。 | 费晓璐 张志广 李银波 | 2002 | 北京生物医学工程2002，21，4： | 11 |
| 11 | Visualization Toolkit及其在三维体重建中的应用显示文摘本文介绍了 the Visualization Toolkit(VTK)工具的基本概念 ,总体框架 ,命名规则 ,宏文件 ,创建和删除 ,源目标 ,文件格式 ,以及用 CT切片重建脑体三维模型的示例方法。 | 吴建明 施鹏飞 | 2002 | 微型电脑应用2002，18，8： | 11 |
| 12 | Theory and practice of construction simulation for high rockfill dam显示文摘Construction simulation for high rockfill dam (CSHRD) is the technology that takes advantage of computer simulation to observe and analyze a complex construction process, which is useful for construction design and management. In this paper, the domestic and oversea research status of CSHRD is reviewed firstly, along with introduction of their present achievements and deficiencies, and the CSHRD theory is also described. Then, considering the influence of many stochastic factors, integrated simulation for high rockfill dam construction (HRDC) is presented with technologies of cycle operation network (CYCLONE) and computer simulation. It rationally combines two subsystems in HRDC, namely haulage and placement of rockfill subsystem, which reflects the actual construction objectively. Important parameters, such as the haulage intensity and traffic density, are obtained, and the process of CSHRD is represented intuitively in dynamic visualization. All of these help engineers to make rapid decisions in HRDC scientifically. | ZHONG DengHua ZHANG Ping WU KangXin | 2007 | Science China(Technological Sciences)2007，50，z1： | 10 |
| 13 | CAD and CAE Integration Through Scientific Visualization Techniques for Illumination Design显示文摘Engineers tend to use different software to perform tasks such as geometry modeling, database management, numerical analysis, and visualization. This may cause decrease of productivity and loss of information during the conversion process between different data file formats. This paper presents a computer aided design (CAD) and computer aided engineering (CAE) system integration using scientific visualization tools and techniques. It deals with the development of a 3D CAD add-in for lighting analysis which uses the CAD model as 3D interface for creating a lighting scheme, processing, and visualizing 2D or 3D illuminance fields. Visualization features as color and contour mapping were developed using the visualization toolkit (VTK) toolkit. The application integrates all functionalities of the 3D CAD with tools for light sources database management, pre-processing, processing, and post-processing of illuminance fields in a single environment. This approach increases productivity and eliminates the need for different software. | Tiago Martinuzzi Buriol Sergio Scheer | 2008 | Tsinghua Science and Technology2008，13，S1： | 10 |
| 14 | A methodology for 3D modeling and visualization of geological objects显示文摘Geological body structure is the product of the geological evolution in the time dimension, which is presented in 3D configuration in the natural world. However, many geologists still record and process their geological data using the 2D or 1D pattern, which results in the loss of a large quantity of spatial data. One of the reasons is that the current methods have limitations on how to express underground geological objects. To analyze and interpret geological models, we present a layer data model to organize different kinds of geological datasets. The data model implemented the unification expression and storage of geological data and geometric models. In addition, it is a method for visualizing large-scaled geological datasets through building multi-resolution geological models rapidly, which can meet the demand of the operation, analysis, and interpretation of 3D geological objects. It proves that our methodology is competent for 3D modeling and self-adaptive visualization of large geological objects and it is a good way to solve the problem of integration and share of geological spatial data. | ZHANG LiQiang TAN YuMin KANG ZhiZhong RUI XiaoPing ZHAO YuanYuan LIU Liu | 2009 | Science China Earth Sciences2009，52，7： | 9 |
| 15 | Usefulness of three-dimensional visualization technology in minimally invasive treatment for infected necrotizing pancreatitis显示文摘AIM To explore the value of three-dimensional(3 D) visualization technology in the minimally invasive treatment for infected necrotizing pancreatitis(INP). METHODS Clinical data of 18 patients with INP, who were admitted to the PLA General Hospital in 2017, were retrospectively analyzed. Two-dimensional images of computed tomography were converted into 3 D images based on 3 D visualization technology. The size, number, shape and position of lesions and their relationship with major abdominal vasculature were well displayed. Also, percutaneous catheter drainage(PCD) number and puncture paths were designed through virtual surgery(percutaneous nephroscopic necrosectomy) based on the principle of maximum removal of infected necrosis conveniently.RESULTS Abdominal 3 D visualization images of all the patients were well reconstructed, and the optimal PCD puncture paths were well designed. Infected necrosis was conveniently removed in abundance using a nephroscope during the following surgery, and the median operation time was 102(102 ± 20.7) min. Only 1 patient underwent endoscopic necrosectomy because of residual necrosis. CONCLUSION The 3 D visualization technology could optimize the PCD puncture paths, improving the drainage effect in patients with INP. Moreover, it significantly increased the efficiency of necrosectomy through the rigid nephroscope. As a result, it decreased operation times and improved the prognosis. | Peng-Fei Wang Zhi-Wei Liu Shou-Wang Cai Jun-Jun Su Lei He Jian Feng Xian-Lei Xin Shi-Chun Lu | 2018 | World Journal of Gastroenterology2018，24，17： | 7 |
| 16 | China Digital Ocean Prototype System显示文摘Digital Ocean is a new research domain of Digital Earth.Because of the spatiotemporal,three-dimensional(3D)and intrinsically dynamic nature of ocean data,it is more difficult to make a breakthrough in this domain.The construction of the China Digital Ocean Prototype System(CDOPS)pushes Digital Ocean a step forward from its operation as a mere concept to its achievement as a realistic system.In this paper,the technical framework of the CDOPS is discussed,including its data,function,and application layers.Then,two key technologies are studied in detail that will enable the construction of the 3D ocean environment and the visualization of the ocean model output data.Practical demonstrations show that the CDOPS provides a technical reference for the development of Digital Ocean.This paper is based on an ongoing research project of the development of CDOPS that aims at the facilitation,integration,sharing,accessing,visualization,and use of the ocean data and model computing data from the Digital Earth perspective. | Xin Zhang Wen Dong Sihai Li Jiancheng Luo Tianhe Chi | 2011 | International Journal of Digital Earth2011，4，3： | 7 |
| 17 | Multislice CT virtual intravascular endoscopy of aortic dissection:A pictorial essay显示文摘AIM:To present our experience of using 3D virtual intravascular endoscopy(VIE) to characterize and evaluate the intraluminal appearances of aortic dissection.METHODS:Ten patients with known aortic dissection underwent dual-source computed tomography angiography and were included in the study.In addition to 2D axial and multiplanar reformatted images as well as 3D reconstructions,VIE images were created in each patient to demonstrate intraluminal views of the aorta and its branches,origin of artery branches and artery branch involvement by aortic dissection.RESULTS:Stanford A dissection was found in 8 patients and B dissection in the remaining 2 patients.VIE images were successfully generated in all of the patients with excellent visualization of the normal anatomical structures,intimal flap and intimal entrance tear,communication between true and false lumens,as well as assessment of the extent of aortic dissection.CONCLUSION:Our preliminary experience suggests that VIE could be used as a complementary tool to assist radiologists accurately evaluate aortic dissection so that better patient management can be achieved. | Zhonghua Sun Yan Cao | 2010 | World Journal of Radiology2010，2，11： | 7 |
| 18 | Galilean invariance of Omega vortex identification method显示文摘In the new vortex identification method(Liu et al.2016)to represent the rotation level and capture and visualize the vortices,proposed in our previous study,the independence of the reference frame and the Galilean invariant were not proved.In the present study,the Galilean invariance of the omega vortex identification method is proved and several examples are presented to verify the conclusion. | Jian-ming Liu Yi-qian Wang Yi-sheng Gao Chaoqun Liu | 2019 | Journal of Hydrodynamics2019，31，2： | 6 |
| 19 | Visualization and quantification of water movement in porous cement-based materials by real time thermal neutron radiography:Theoretical analysis and experimental study显示文摘Water movement in porous cement-based materials is of great importance when studying their deterioration processes and durability.Many traditional methods based on mass changes,electricity or nuclear magnetic resonances are available for studying water transport in cement-based materials.In this research,an advanced technique i.e.thermal neutron radiography was utilized to achieve visualization and quantification of time dependent water movement including water penetration and moisture vapor in porous cement-based materials through theoretical analysis and experimental study.Because thermal neutrons ex-perience a strong attenuation by hydrogen,neutron radiography exhibits high sensitivity to small amounts of water.A neutron transmission analysis for quantitative evaluation of raw radiographic measurements was developed and optimized based on point scattered functions(PScF).The determinations of the real time and space dependent water penetration into uncracked and cracked mortar samples,as well as the drying process have been presented in this paper.It is illustrated that thermal neutron radiography can be a useful research tool for visualization and quantification of water movement in porous building materials.The obtained results will help us to better understand deteriorating processes of cement-based materials and to find ways to improve their durability. | ZHANG Peng1,WITTMANN F H1,2,ZHAO TieJun1,LEHMANN E3 & JIN ZuQuan1 1 Center for Durability & Sustainability Studies of Shandong Province,Qingdao Technological University,Qingdao 266033,China 2 Aedificat Institute Freiburg,Freiburg D-79100,Germany 3 Department of Spallation Neutron Source(ASQ),Paul Scherrer Institute,Villigen PSI CH-5232,Switzerland | 2010 | Science China(Technological Sciences)2010，53，5： | 6 |
| 20 | Design and Implementation of National Meteorological Service Platform显示文摘In order to change the distributed status of the meteorological service platform,based on the integration of the self-built service platforms including meteorology,climate,observation and service,National Meteorological Information Center( NMIC) constructs National Meteorological Service Platform( NMSP). NMSP is a unified national meteorological service platform to provide browsing,searching and displaying of observation,weather forecasting,warning information,historical climate data and network information. NMSP uses the MVC design pattern.For adapting the characteristics of meteorological application,above J2 EE application framework( Struts + Spring + Hibernate),NMSP encapsulates data exchange module which improves flexibility and efficiency of the system development. On March 2015,NMSP( version 2. 0)has been on operational running,which covers six core sections,nearly 100 sub-modules,2000 kinds of service products. It plays an effective supporting role on various types of meteorological service. | Zhiqiang ZHANG Qiang ZHANG Xing HU Xuelei NI | 2016 | Asian Agricultural Research2016，8，9： | 6 |
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