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Recent advances in enzyme-mediated peptide ligation

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Chinese Chemical Letters 2018年第7期29卷 1009-1016页

作者： Silin Xu Zhenguang zhao junfeng zhao Key Laboratory of Chemical Biology of Jiangxi Province College of Chemistry and Chemical EngineeringJiangxi Normal University The Institute of Chemistry The Hebrew University of Jerusalem State Key Laboratory of Elemento-Organic Chemistry Nankai University

Artificial synthesis and site-specific modification of peptides and proteins has evolved into an indispensable tool for protein engineers and chemical biologists. Chemical and enzymatic approaches to peptide ligation are important alternatives of recombinant DNA technology for protein synthesis and modification. Although as old as that of chemical procedures, enzyme-mediated peptide ligation is far less developed than that of chemical counterpart due to the difficult availability of peptide ***, this situation has been changed slowly with the fast development of biological techniques. In the past decades, several natural peptide ligases have been discovered. Protein engineering to improve the ligation efficiencies of the natural peptide ligase and to reverse the functionality of protease provide more powerful peptide ligases. In this review, the advances of enzyme-mediated peptide ligation and their application in protein synthesis and modification will be discussed.

关键词： Ligase Peptide synthesis Protein engineering Enzyme-mediated peptide ligation Site-specific protein modification

A Novel Two-Level Optimization Strategy for Multi-Debris Active Removal Mission in LEO

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Computer Modeling in Engineering & Sciences 2020年第1期122卷 149-174页

作者： junfeng zhao Weiming Feng Jianping Yuan Shandong University Jinan250031China Northwestern Polytechnical University Xi’an710072China National Key Laboratory of Aerospace Flight Dynamics Xi’an710072China

Recent studies of the space debris environment in Low Earth Orbit(LEO)have shown that the critical density of space debris has been reached in certain *** Active Debris Removal(ADR)mission,to mitigate the space debris density and stabilize the space debris environment,has been considered as a most effective *** this paper,a novel two-level optimization strategy for multi-debris removal mission in LEO is proposed,which includes the low-level and high-level optimization *** improve the overall performance of the multi-debris active removal mission and obtain multiple Pareto-optimal solutions,the ADR mission is seen as a Time-Dependant Traveling Salesman Problem(TDTSP)with two objective functions to minimize the total mission duration and the total propellant *** problem includes the sequence optimization to determine the sequence of removal of space debris and the transferring optimization to define the orbital *** optimization models for the two-level optimization strategy are built in solving the multi-debris removal mission,and the optimal Pareto solution is successfully obtained by using the non-dominated sorting genetic algorithm II(NSGA-II).Two test cases are presented,which show that the low level optimization strategy can successfully obtain the optimal sequences and the initial solution of the ADR mission and the high level optimization strategy can efficiently and robustly find the feasible optimal solution for long duration perturbed rendezvous problem.

关键词： Two-level optimization strategy active debris removal non-dominated sorting genetic algorithm bi-objective optimization LEO

Global Optimization Method Using SLE and Adaptive RBF Based on Fuzzy Clustering

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Chinese Journal of Mechanical Engineering 2012年第4期25卷 768-775页

作者： ZHU Huaguang LIU Li LONG Teng zhao junfeng School of Aerospace Engineering Beijing Institute of Technology Beijing 100081 China

High fidelity analysis models,which are beneficial to improving the design quality,have been more and more widely utilized in the modern engineering design optimization ***,the high fidelity analysis models are so computationally expensive that the time required in design optimization is usually *** order to improve the efficiency of optimization involving high fidelity analysis models,the optimization efficiency can be upgraded through applying surrogates to approximate the computationally expensive models,which can greately reduce the computation *** efficient heuristic global optimization method using adaptive radial basis function（RBF） based on fuzzy clustering（ARFC） is *** this method,a novel algorithm of maximin Latin hypercube design using successive local enumeration（SLE） is employed to obtain sample points with good performance in both space-filling and projective uniformity properties,which does a great deal of good to metamodels *** method is adopted for constructing the metamodels,and with the increasing the number of sample points the approximation accuracy of RBF is gradually *** fuzzy c-means clustering method is applied to identify the reduced attractive regions in the original design *** numerical benchmark examples are used for validating the performance of *** results demonstrates that for most application examples the global optima are effectively obtained and comparison with adaptive response surface method（ARSM） proves that the proposed method can intuitively capture promising design regions and can efficiently identify the global or near-global design *** method improves the efficiency and global convergence of the optimization problems,and gives a new optimization strategy for engineering design optimization problems involving computationally expensive models.

关键词： global optimization Latin hypercube design radial basis function fuzzy clustering adaptive response surface method

Hydrocarbons in igneous rock of Brazil:A review

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Petroleum Research 2020年第3期5卷 265-275页

作者： Kangxu Ren junfeng zhao Qian Liu Jian zhao CNODC Brasil Petroleo e Gas Ltda Rio de Janeiro22250-040Brazil PetroChina Research Institute of Petroleum Exploration&Development Beijing100083China

Igneous rocks are widely developed in many hydrocarbon-bearing sedimentary basins in Brazil,and some igneous rocks play positive roles in the oil and gas accumulation *** so far,no industrial oil or gas flow is discovered in igneous rocks in Brazilian onshore *** present,in some literatures published by some researchers,cases of igneous reservoirs in Brazil are *** lithology of reservoirs in the Igarape Cuia oil and gas field,the oil and gas field of Urucu and the Barra Bonita gasfield,were previously thought to be volcanic rocks,but now are clastic rocks according to studies,and the igneous rocks in these three oil and gas field can only be acted as indirect and direct cap ***,igneous rock reservoirs in the Campos Basin and Santos Basin in the Brazilian offshore are briefly *** representative Badejo oilfield in the Campos Basin has igneous rock reservoirs dominated by basalts which are intercalated with thin layers of volcaniclastic and sedimentary rocks,the storage space are vesicules,fractures and vugular pores,and the porosity of hydrocarbon bearing interval basalt reservoirs ranges from 10%to 15%.In addition,for the Santos Basin,igneous rocks in this basin are dominated by basic rocks,some alkaline intrusive rocks develop good micro spaces,mainly crystal moldic pores,inter-and intra-crystal dissolution pores and fractures,better reservoir intervals are often concentrated such as at sections near to unconformity surfaces and can have porosity of 6%e9%or higher;local pre-salt igneous rock reservoirs in the Santos Basin have the necessary conditions for hydrocarbon accumulation and it will be a new target layer for hydrocarbon exploration.

关键词： Igneous reservoirs Badejo oilfield Pre-salt igneous rocks Offshore Campos basin Santos basin Brazil

An Orthogonal Approach to Reusable Component Discovery in Cloud Migration

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China Communications 2015年第5期12卷 134-151页

作者： zhao junfeng ZHOU Jiantao YANG Hongji LIU Guoping College of Computer Science Inner Mongolia University Hohhot Centre for Creative Computing Bath Spa University Bath Advanced Control and Network Technology Research Unit University of South Wales

As an innovative software application mode,Software as a service(SaaS) shows many attractive *** legacy system to SaaS can make outdated systems *** the process of migration,the existing valuable components need to be discovered and reused in order that the target system could be developed/integrated more *** innovative approach is proposed in this paper to extract the reusable components from legacy ***,implementation models of legacy system are recovered through reverse ***,function models are derived by vertical clustering,and then logical components are discovered by horizontal clustering based on the function ***,the reusable components with specific feature descriptions are *** experimental verification,the approach is considered to be efficient in reusable component discovery and to be helpful to migrating legacy system to SaaS.

关键词： legacy system architecture recovery horizontal clustering vertical clustering, reusable component

Toward accurate link between code and software documentation

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Science China(Information Sciences) 2018年第5期61卷 72-86页

作者： Yingkui CAO Yanzhen ZOU Yuxiang LUO Bing XIE junfeng zhao Key Laboratory of High Confidence Software Technologies Ministry of Education School of Electronics Engineering and Computer Science Peking University Beida (Binhai) Information Research

Recovering traceability links between source code and software documentation is an important research topic in software maintenance and software reuse. There have been a lot of research efforts in recovering traceability between documentation and code elements(class, interface, method, etc.), mostly based on program analysis. However, there are still a lot of noise links being established in existing work. In this paper, we propose a novel approach to classifying code elements, occurring in a document, into contextual code elements and salient code elements. As a result, we can filter the noise traceability links between a software document and its contextual code elements and get a higher quality link set. Our classifier is trained based on open source project Lucene’s source code and 1899 Stack Overflow answer documents about *** extract code elements from these documents and represent each of these code elements with a 7-dimension feature vector, then we use a decision-tree-based learning model to classify them as salient or not. In the experiments, we get a precision of 70.7% in recognizing the salient code elements of these documents and get12% improvement compared with Rigby’s work. We can filter out 56.5%～69.3% noise traceability links with different thresholds in our classifier. It can improve the quality of traceability links between source code and their related software documents in application.

关键词： traceability link code element software document contextual code element salient codeelement

Biochemical Characterization of an Arginine 2,3-Aminomutase with Dual Substrate Specificity

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Chinese Journal of Chemistry 2020年第9期38卷 959-962页

作者： junfeng zhao Wenjuan Ji Xinjian Ji Qi Zhang Department of Chemistry Fudan University2005 Songhu RoadShanghai 200438China

Summary of main observation and conclusion The radical S-adenosylmethionine(SAM)aminomutases represent an important pathway for the biosynthesis of p-amino *** this study,we report biochemical characterization of BlsG involved in blasticidin S biosynthesis as a radical SAM arginine 2,*** showed that BlsG acts on both£-arginine and L-lysine with comparable catalytic *** dual substrate specificity was also observed for the lysine 2,3-aminomutase from Escherichia coli(LAMec).The catalytic efficiency of LAMEc is similar to that of BlsG,but is significantly lower than that of the enzyme from Clostridium subterminale(LAMcs),which acts only on L-lysine rather than on ***,we showed that enzymes can be grouped into two major phylogenetic clades,each corresponding to a certain C3 stereochemistry of the P-amino acid *** study expands the radical SAM aminomutase members and provides insights into enzyme evolution,supporting a trade-off between substrate promiscuity and catalytic efficiency.

关键词： radical catalytic conclusion

Particle Swarm Optimization Applied to Some Anti-Windup Problems

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Journal of Beijing Institute of Technology 2019年第3期28卷 477-490页

作者： Aojia Ma Lei Zhang junfeng zhao Yahui Li Feng Gao China Academy of Launch Vehicle Technology

The particle swarm optimization (PSO) algorithm is introduced to deal with some open anti-windup problems, i.e., determining the initial condition when applying the iterative algorithm to enlarge the estimate of the domain of attraction, determining the design point in the delayed anti-windup scheme, and determining the design point and the weighting factors in the multi-stage anti-windup scheme. Therefore, the corresponding PSO-based algorithms are proposed. Unlike the traditional methods in which the free design parameters can only be selected by trial and error with the available computational results, the PSO-based algorithms provide a systematic way to determine these parameters. In addition, the algorithms are easy to be implemented and are very likely to find the desirable parameters that further improve the anti-windup closed-loop performances. Simulation results are presented to validate the effectiveness and advantages of the proposed method.

关键词： anti-windup particle swarm optimization(PSO) intelligent algorithm

Petrologic and REE Geochemical Characters of Burnt Rocks

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Acta Geologica Sinica(English Edition) 2008年第2期82卷 392-398页

作者： HUANG Lei LIU Chiyang YANG Lei zhao junfeng FANG Jianjun State Key Laboratory of-Continental Dynamics （Northwest University）~Institute of Petroliferous Basin of Northwest University Xi＇ an Shaanxi 710069

The study of burnt rocks is beneficial to the discussion on the tectonic movement, paleoclimate and paleogeography that coal seams are subjected to after they were formed. In order to obtain the basic data on the features of the burnt rocks, a systematic study of petrology and REE geochemistry on burnt rocks in Shenmu, Northern Shaanxi Province has been done, using the methods of SEM, EDS, susceptibility measurements and ICP-MS. The burnt rocks are divided into two series in the section： the melted rocks and the baked rocks. SEM and EDS analyses reveal that all the minerals show burnt and melted traces, and there are no clay minerals except illite found in the burnt rocks. Susceptibility measurements reveal that the burnt rocks have abnormally high susceptibility values, whereas a geochemical analysis shows that the REE distribution pattern of burnt rocks is similar to that of sedimentary rocks （initial rocks）. In the longitudinal section, with increasing degree of burning （from baked rocks to melted rocks）, the ∑REE gradually decreases, and the total REE of melted rocks is obviously lower than that of baked rocks. Besides, the melted rocks show apparent negative Ce anomalies, while the baked rocks show no anomaly of Ce, and sometimes even show positive anomalies.

关键词： burnt rock mineral petrology susceptibility REE negative Ce anomaly