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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 | Fundamental Theories and Key Technologies for Smart andOptimal Manufacturing in the Process Industry显示文摘Given the significant requirements for transforming and promoting the process industry, we present themajor limitations of current petrochemical enterprises, including limitations in decision-making, produc-tion operation, efficiency and security, information integration, and so forth. To promote a vision of theprocess industry with efficient, green, and smart production, modern information technology should beutilized throughout the entire optimization process for production, management, and marketing. To focuson smart equipment in manufacturing processes, as well as on the adaptive intelligent optimization of themanufacturing process, operating mode, and supply chain management, we put forward several key scien-tific problems in engineering in a demand-driven and application-oriented manner, namely:intelligentsensing and integration of all process information, including production and management information; collaborative decision-making in the supply chain, industry chain, and value chain, driven by knowledge; cooperative control and optimization of plant-wide production processes via human-cyber-physical in-teraction; and Q life-cycle assessments for safety and environmental footprint monitoring, in addition totracing analysis and risk control. In order to solve these limitations and core scientific problems, we furtherpresent fundamental theories and key technologies for smart and optimal manufacturing in the processindustry. Although this paper discusses the process industry in China, the conclusions in this paper can beextended to the larocess industry around the world. | Feng Qian Weimin Zhong Wenli Du | 2017 | Engineering2017，3，2： | 23 |
| 3 | Study on co-cracking performance of different hydrocarbon mixture in a steam pyrolysis furnace显示文摘Co-cracking is a process where the mixtures of different hydrocarbon feedstocks are cracked in a steam pyrolysis furnace, and widely adopted in chemical industries. In this work, the simulations of the co-cracking of ethane and propane, and LPG and naphtha mixtures have been conducted, and the software packages of COILSIM1 D and Sim CO are used to account for the cracking process in a tube reactor. The effects of the mixing ratio, coil outlet temperature, and pressure on cracking performance have been discussed in detail. The co-cracking of ethane and propane mixture leads to a lower profitability than the cracking of single ethane or single propane. For naphtha, cracking with LPG leads to a higher profitability than single cracking of naphtha, and more LPG can produce a higher profitability. | Benfeng Yuan Jinlong Li Wenli Du Feng Qian | 2016 | Chinese Journal of Chemical Engineering2016，24，9： | 6 |
| 4 | A Hybrid Improved Genetic Algorithm and Its Application in Dynamic Optimization Problems of Chemical Processes显示文摘The solutions of dynamic optimization problems are usually very difficult due to their highly nonlinear and multidimensional nature. Genetic algorithm (GA) has been proved to be a feasible method when the gradient is difficult to calculate. Its advantage is that the control profiles at all time stages are optimized simultaneously, but its convergence is very slow in the later period of evolution and it is easily trapped in the local optimum. In this study, a hybrid improved genetic algorithm (HIGA) for solving dynamic optimization problems is proposed to overcome these defects. Simplex method (SM) is used to perform the local search in the neighborhood of the optimal solution. By using SM, the ideal searching direction of global optimal solution could be found as soon as possible and the convergence speed of the algorithm is improved. The hybrid algorithm presents some improvements, such as protecting the best individual, accepting immigrations, as well as employing adaptive crossover and Gaussian mutation operators. The efficiency of the proposed algorithm is demonstrated by solving several dynamic optimization problems. At last, HIGA is applied to the optimal production of secreted protein in a fed batch reactor and the optimal feed-rate found by HIGA is effective and relatively stable. | SUN Fan DU Wenli QI Rongbin QIAN Feng ZHONG Weimin | 2013 | Chinese Journal of Chemical Engineering2013，21，2： | 5 |
| 5 | Hot deformation characterization of as-homogenized Al-Cu-Li X2A66 alloy through processing maps and microstructural evolution显示文摘Uniaxial compression tests were carried out on an Al-Cu-Li alloy at a temperature range of 300–500℃ and a strain rate range of 0.001–10 s^-1. Four representative instability maps based on Gegel, AlexanderMalas(A-M), Kumar-Prasad(K-P) and Murty-Rao(M-R) criteria were constructed. Through formula deduction and microstructural observation, it can be concluded that M-R criterion is more accurate than K-P criterion, and the first two criteria are better than Gegel and A-M criteria. From a power dissipation map and a M-R instability map, the optimized processing parameters are 480–500℃/0.001–0.1 s^-1 and 420–480℃/0.1-1 s^-1. The corresponding microstructural analysis shows that dynamic recovery and partial dynamic recrystallization are main dynamic softening mechanisms. Transmission electron microscopy observation indicated that a large number of primary coarse T1(Al2 Cu Li) particles precipitated in the homogenized specimen. After deformation at 500℃, most of the primary T1 particles dissolved back into the matrix, and secondary fine T1 particles precipitated at deformation-induced dislocations, high angle grain boundaries and other dispersed particles. | Liwei Zhong Wenli Gao Zhaohui Feng Zheng Lu Congcong Zhu | 2019 | Journal of Materials Science & Technology2019，35，10： | 5 |
| 6 | Total plant performance evaluation based on big data: Visualization analysis of TE process显示文摘The performance evaluation of the process industry, which has been a popular topic nowadays, can not only find the weakness and verify the resilience and reliability of the process, but also provide some suggestions to improve the process benefits and efficiency. Nevertheless, the performance assessment principally concentrates upon some parts of the entire system at present, for example the controller assessment. Although some researches focus on the whole process, they aim at discovering the relationships between profit, society, policies and so forth, instead of relations between overall performance and some manipulated variables, that is, the total plant performance. According to the big data of different performance statuses, this paper proposes a hierarchical framework to select some structured logic rules from monitored variables to estimate the current state of the process. The variables related to safety and profits are regarded as key factors to performance evaluation. To better monitor the process state and observe the performance variation trend of the process, a classificationvisualization method based on kernel principal component analysis(KPCA) and self-organizing map(SOM) is established. The dimensions of big data produced by the process are first reduced by KPCA and then the processed data will be mapped into a two-dimensional grid chart by SOM to evaluate the performance status. The monitoring method is applied to the Tennessee Eastman process. Monitoring results indicate that off-line and on-line performance status can be well detected in a two-dimensional diagram. | Mengyao Li Wenli Du Feng Qian Weiming Zhong | 2018 | Chinese Journal of Chemical Engineering2018，26，8： | 4 |
| 7 | Experimental investigation on dilatancy behavior of water-saturated sandstone显示文摘It is important to study the dilatancy property of water-saturated rock for understanding the engineering behavior of loaded rock mass. This study carried out the uniaxial and triaxial compressive experiments on the water-saturated red sandstone, analyzed the influences of confining pressure and pore pressure on dilatancy property of water-saturated rock, and discussed the reasonable basis of the stress of dilatancy onset as a strength design parameter of rock engineering, finally established the prediction model of the stress of dilatancy onset under the impacts of confining pressure and pore pressure. The results show that the strength parameters(the stress of dilatancy onset and peak strength) and deformation parameters(axial strain and circumferential strain) of water-saturated sandstone increase with the confining pressure, and the relations can be fitted with a positive linear function. The cohesion and internal friction angle obtained from the stress of dilatancy onset decrease by 11.57% and 7.33%, respectively, when compared with those obtained from the peak strength. The strength parameters and deformation parameters of water-saturated sandstone decrease basically with the increase of pore pressure, in which the relations between strength parameters or axial strain and pore pressure can be fitted with a negative linear function. However, the relation between the peak circumferential strain and the pore pressure should be characterized by a negative exponential function, and the circumferential strain at dilatancy onset isn't affected by the pore pressure. | Jiangyu Wu Meimei Feng Bangyong Yu Wenli Zhang Xiaoyan Ni Guansheng Han | 2018 | International Journal of Mining Science and Technology2018，28，2： | 4 |
| 8 | Galectin-3-centered paracrine network mediates cardiac inflammation and fibrosis upon β-adrenergic insult显示文摘Rapid over-activation of β-adrenergic receptors (β-AR) following acute stress initiates cardiac inflammation and injury by activating interleukin-18 (IL-18),however,the process of inflammation cascades has not been fully illustrated.The present study aimed to determine the mechanisms of cardiac inflammatory amplification following acute sympathetic activation.With bioinformatics analysis,galectin-3 was identified as a potential key downstream effector of β-AR and IL-18 activation.The serum level of galectin-3 was positively correlated with norepinephrine or IL-18 in patients with chest pain.In the heart of mice treated with β-AR agonist isoproterenol (ISO,5 mg kg^(-1)),galectin-3 expression was upregulated markedly later than IL-18 activation,and Nlrp3^(-/-)and Il18^(-/-)mice did not show ISO-induced galectin-3 upregulation.It was further revealed that cardiomyocyte-derived IL-18 induced galectin-3 expression in macrophages following ISO treatment.Moreover,galectin-3deficiency suppressed ISO-induced cardiac inflammation and fibrosis without blocking ISO-induced IL-18 increase.Treatment with a galectin-3 inhibitor,but not a β-blocker,one day after ISO treatment effectively attenuated cardiac inflammation and injury.In conclusion,galectin-3 is upregulated to exaggerate cardiac inflammation and injury following acute β-AR activation,a galectin-3 inhibitor effectively blocks cardiac injury one day after β-AR insult. | Guomin Hu Jimin Wu Huijun Gu Xiangning Deng Wenli Xu Shan Feng Shuaixing Wang Yao Song Zhengda Pang Xiuling Deng Aleksandr E.Vendrov Nageswara R.Madamanchi Marschall S.Runge Xinyu Wang Youyi Zhang Han Xiao Erdan Dong | 2023 | Science China(Life Sciences)2023，66，5： | 3 |
| 9 | Solving chemical dynamic optimization problems with ranking-based differential evolution algorithms显示文摘Dynamic optimization problems(DOPs) described by differential equations are often encountered in chemical engineering. Deterministic techniques based on mathematic programming become invalid when the models are non-differentiable or explicit mathematical descriptions do not exist. Recently, evolutionary algorithms are gaining popularity for DOPs as they can be used as robust alternatives when the deterministic techniques are invalid. In this article, a technology named ranking-based mutation operator(RMO) is presented to enhance the previous differential evolution(DE) algorithms to solve DOPs using control vector parameterization. In the RMO, better individuals have higher probabilities to produce offspring, which is helpful for the performance enhancement of DE algorithms. Three DE-RMO algorithms are designed by incorporating the RMO. The three DE-RMO algorithms and their three original DE algorithms are applied to solve four constrained DOPs from the literature. Our simulation results indicate that DE-RMO algorithms exhibit better performance than previous non-ranking DE algorithms and other four evolutionary algorithms. | Xu Chen Wenli Du Feng Qian | 2016 | Chinese Journal of Chemical Engineering2016，24，11： | 3 |
| 10 | Genotypic variation in spatiotemporal distribution of canopy light interception in relation to yield formation in cotton显示文摘Background: Within-canopy interception of photosynthetically active radiation(PAR) impacts yield and other agronomic traits in cotton(Gossypium hirsutum L.). Field experiments were conducted to investigate the influence of 6 cotton varieties(they belong to 3 different plant types) on yield, yield distribution, light interception(LI), LI distribution and the relationship between yield formation and LI in Anyang, Henan, in 2014 and 2015.Result: The results showed that cotton cultivars with long branches(loose-type) intercepted more LI than did cultivars with short branches(compact-type), due to increased LI in the middle and upper canopy. Although loose-type varieties had greater LI, they did not yield significantly higher than compact-type varieties, due to decreased harvest index. Therefore, improving the harvest index by adjusting the source-to-sink relationship may further increase cotton yield for loose-type cotton. In addition, there was a positive relationship between reproductive organ biomass accumulation and canopy-accumulated LI, indicating that enhancing LI is important for yield improvement for each cultivar. Furthermore, yield distribution within the canopy was significantly linearly related to vertical LI distribution.Conclusion: Therefore, optimizing canopy structure of different plant type and subsequently optimizing LI distribution within the cotton canopy can effectively enhance the yield. | XING Fangfang HAN Yingchun FENG Lu ZHI Xiaoyu WANG Guoping YANG Beifang FAN Zhengyi LEI Yaping DU Wenli WANG Zhanbiao XIONG Shiwu LI Xiaofei Ll Yabing | 2018 | Journal of Cotton Research2018，1，3： | 3 |
| 11 | Efficient Leave-One-Out Strategy for Supervised Feature Selection显示文摘Feature selection is a key task in statistical pattern recognition.Most feature selection algorithms have been proposed based on specific objective functions which are usually intuitively reasonable but can sometimes be far from the more basic objectives of the feature selection.This paper describes how to select features such that the basic objectives,e.g.,classification or clustering accuracies,can be optimized in a more direct way.The analysis requires that the contribution of each feature to the evaluation metrics can be quantitatively described by some score function.Motivated by the conditional independence structure in probabilistic distributions,the analysis uses a leave-one-out feature selection algorithm which provides an approximate solution.The leave-oneout algorithm improves the conventional greedy backward elimination algorithm by preserving more interactions among features in the selection process,so that the various feature selection objectives can be optimized in a unified way.Experiments on six real-world datasets with different feature evaluation metrics have shown that this algorithm outperforms popular feature selection algorithms in most situations. | Dingcheng Feng Feng Chen Wenli Xu | 2013 | Tsinghua Science and Technology2013，18，6： | 2 |
| 12 | Performance monitoring of non-gaussian chemical processes with modes-switching using globality-locality preserving projection显示文摘 | Xin Peng Yang Tang Wenli Du Feng Qian | 2017 | Frontiers of Chemical Science and Engineering2017，11，3： | 2 |
| 13 | Onlinediscriminative object tracking with local sparse representation显示文摘 | WANG Qing CHEN Feng XU Wenli | 2012 | IEEE Workshop on the Applications of Computer Vision2012，12，4： | 1 |
| 14 | Development of akinetic model for industrial oxidation of p-xylene by RBF-PLSand CCA显示文摘 | YAN Xuefeng DU Wenli QIAN Feng | 2004 | AIChE Journal:Process Systems Engineering2004，50，6： | 1 |
| 15 | A chromosome-scale genome assembly of Dasypyrum villosum provides insights into its application as a broad-spectrum disease resistance resource for wheat improvement显示文摘Dasypyrum villosum is one of the most valuable gene resources in wheat improvement,especially for disease resistance.The mining of favorable genes from D.villosum is frustrated by the lack of a whole genome sequence.In this study,we generated a doubled-haploid line,91C43^(DH),using microspore culture and obtained a 4.05-GB high-quality,chromosome-scale genome assembly for D.villosum.The assembly contains39727 high-confidence genes,and 85.31% of the sequences are repetitive.Two reciprocal translocation events were detected,and 7VS-4VL is a unique translocation in D.villosum.The prolamin seed storage protein-coding genes were found to be duplicated;in particular,the genes encoding low-molecular-weight glutenin at the Glu-V3 locus were significantly expanded.RNA sequencing(RNA-seq)analysis indicated that,after Blumeria graminearum f.sp tritici(Bgt)inoculation,there were more upregulated genes involved in the pattern-triggered immunity and effector-triggered immunity defense pathways in D.villosum than in Triticum urartu.MNase hypersensitive sequencing(MH-seq)identified two Bgt-inducible MH sites(MHSs),one in the promoter and one in the 3'terminal region of the powdery mildew resistance(Pm)gene NLR1-V.Each site had two subpeaks and they were termed MHS1(MHS1.1/1.2)and MHS2(MHS2.1/2.2).Bgt-inducible MHS2.2 was uniquely present in D.villosum,and MHS1.1 was more inducible in D.villosum than in wheat,suggesting that MHSs may be critical for regulation of NLR1-V expression and plant defense.In summary,this study provides a valuable genome resource for functional genomics studies and wheat-D.villosum introgression breeding.The identified regulatory mechanisms may also be exploited to develop new strategies for enhancing Pm resistance by optimizing gene expression in wheat. | Xu Zhang Haiyan Wang Haojie Sun Yingbo Li Yilong Feng Chengzhi Jiao Mengli Li Xinying Song Tong Wang Zongkuan Wang Chunxia Yuan Li Sun Ruju Lu Wenli Zhang Jin Xiao Xiue Wang | 2023 | Molecular Plant2023，16，2： | 1 |
| 16 | Development of a Kinetic Model for Industrial Oxidation of p-Xylene by RBF-PLS and CGA显示文摘 | Yan Xuefeng Du Wenli Qian Feng | 2004 | AIChE Journal2004，50，6： | 1 |
| 17 | Global Existence of Solutions to Fuzzy Voherra Integral Equations显示文摘 | ZHANG Dongkai FENG Wenli QIU Jiqing | 2009 | ICIC Express Letters2009，3，3： | 1 |
| 18 | Treatment of Irreducible Old Atlantoaxial Subluxation With Cable-Dragged Reduction and Cantilever Beam Internal Fixation显示文摘 | Xi Liu Hao Liu Tao Li Quan Gong Yueming Song Limin Liu Rui Shi Xiaodan Zhao Wenli Zhang Ganjun Feng Beiyu Wang | 2011 | Spine2011，，15： | 1 |
| 19 | Development of a kinetic model for industrial oxidation of p-xylene by RBF-PLS andCGA显示文摘 | Yan Xuefeng Du Wenli Qian Feng | 2004 | AIChEjournal2004，50，6： | 1 |
| 20 | Simultaneous reduction of vanadium (V) and chromium (VI) with enhanced energy recovery based on microbial fuel cell technology显示文摘 | Baogang Zhang Chuanping Feng Jinren Ni Jing Zhang Wenli Huang | 2012 | Journal of Power Sources2012，，： | 1 |
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