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Simplifying the Nonlinear Continuous Time-Cost Tradeoff Problem

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Journal of Systems Science & Complexity 2017年第4期30卷 901-920页

作者： SU Zhixiong qi jianxun WEI Hanying Business Administration College Nanchang Institute of Technology School of Economics and Management North China Electric Power University

Equivalent simplification is an effective method for solving large-scale complex problems. In this paper, the authors simplify a classic project scheduling problem, which is the nonlinear continuous time-cost tradeoff problem(TCTP). Simplifying TCTP is a simple path problem in a critical path method(CPM) network. The authors transform TCTP into a simple activity float problem and design a complex polynomial algorithm for its solution. First, the authors discover relationships between activity floats and path lengths by studying activity floats from the perspective of path instead of ***, the authors perform simplification and improve the efficiency and accuracy of the solution by deleting redundant activities and narrowing the duration intervals of non-redundant activities. Finally,the authors compare our method with current methods. The relationships between activity floats and path lengths provide new approaches for other path and correlative project problems.

关键词： Activity floats CPM networks operational research simplification time-cost tradeoff.

Prediction of nonregular secondary structures of proteins based on wavelet analysis

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Chinese Science Bulletin 2002年第11期47卷 918-923页

作者： jianxun qi Yi Xiao Huazhong Univ Sci & Technol Dept Phys Wuhan 430074 Peoples R China

The secondary structures of proteins fall into two classes: regular structure and nonregular structure. Helices and sheets are termed 'regular' structures because their residues have repeating main-chain torsion angles, and their backbone N-H and C-O groups are arranged in a periodic pattern of hydrogen bonding. In contrast, the remaining structures with nonrepeating backbone torsion angles are called nonregular secondary structures. In this note, we performed an extensive sequence analysis of nonregular secondary structures and showed that these nonregular parts could be effectively predicted by continuous wavelet transform.

关键词： nonregular secondary structure a helix P strand turn hydrophobicity continuous wavelet transform.

Targeting multiple epitopes on the spike protein:a new hope for COVID-19 antibody therapy

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Signal Transduction and Targeted Therapy 2020年第1期5卷 778-779页

作者： Yeping Sun Bostjan Kobe jianxun qi CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of Sciences100101 BeijingChina School of Chemistry and Molecular Biosciences University of QueenslandBrisbaneQLD 4072Australia Savaid Medical School University of the Chinese Academy of Sciences100049 BeijingChina

Lihong Liu et al.1 from Columbia University recently reported in Nature the isolation of a collection of 19 SARS-CoV-2-neutralizing monoclonal antibodies(mAbs)from five infected patients with high plasma virus-neutralizing *** antibodies can neutralize SARS-CoV-2 in vitro,and nine of them exhibited exquisite potency,with 50%virus-inhibitory concentrations of 9 ng/mL or *** strategy for isolation of these antibodies included sorting SARS-CoV-2 spike protein(S)-specific memory B cells by flow cytometry and single-cell sequencing.

关键词： al antibodies neutral

AN EXTENDED MODEL FOR PROJECT PORTFOLIO SELECTION WITH PROJECT DIVISIBILITY AND INTERDEPENDENCY

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Journal of Systems Science and Systems Engineering 2016年第1期25卷 119-138页

作者： Xingmei Li Shu-Cherng Fang Xiaoling Guo Zhibin Deng jianxun qi School of Economics and Management North China Electric Power University Beijing 102206 China Industrial and Systems Engineering Department North Carolina State University Raleigh NC 27695 USA College of Engineering andlnformation Technology University of Chinese Academy of Sciences Beijing100049 China School of Management University of Chinese Academy of Sciences Beijing 100190 China Key Laboratory of Big Data Mining and Knowledge Management Chinese Academy of Sciences Beijing 100190 China

In this paper, we develop an extended model for the project portfolio selection problem over a planning horizon with multiple time periods. The model incorporates the factors of project divisibility and interdependency at the same time for real-life applications. The project divisibility is considered as a strategy, not an unfortunate event as in the literature, in choosing the best execution schedule for the projects, and the classical concept of＂project interdependencies＂ among fully executed projects is then extended to the portions of executed projects. Additional constraints of reinvestment consideration, setup cost, cardinality restriction, precedence relationship and scheduling are also included in the model. For efficient computations, an equivalent mixed integer linear programming representation of the proposed model is derived. Numerical examples under four scenarios are presented to highlight the characteristics of the proposed model. In particular, the positive effects of project divisibility are shown for the first time.

关键词： Project management project portfolio selection problem project divisibility project interdependency

An octamer of enolase from Streptococcus suis

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Protein & Cell 2012年第10期3卷 769-780页

作者： qiong Lu Hao Lu jianxun qi Guangwen Lu George F Gao CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Graduate University Chinese Academy of SciencesBeijing 100049China Research Network of Immunity and Health(RNIH) Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing 100101China Laboratory of Protein Engineering and Vaccines Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin 300308China

Enolase is a conserved cytoplasmic metalloenzyme existing universally in both eukaryotic and prokaryotic *** enzyme can also locate on the cell surface and bind to plasminogen,via which contributing to the mucosal surface localization of the bacterial pathogens and assisting the invasion into the host *** functions of the eukaryotic enzymes on the cell surface expression(including T cells,B cells,neutrophils,monocytoes,neuronal cells and epithelial cells)are not *** suis serotype 2(*** 2,SS2)is an important zoonotic pathogen which has recently caused two large-scale outbreaks in southern China with severe streptococcal toxic shock syndrome(STSS)never seen before in human *** recently identified the SS2 enolase as an important protective antigen which could protect mice from fatal *** 2 *** this study,a 2.4-angstrom structure of the SS2 enolase is solved,revealing an octameric arrangement in the *** further demonstrated that the enzyme exists exclusively as an octamer in solution via a sedimentation *** results indicate that the octamer is the biological unit of SS2 enolase at least in vitro and most likely in vivo as *** is,to our knowledge,the first comprehensive characterization of the SS2 enolase octamer both structurally and biophysically,and the second octamer enolase structure in addition to that of Streptococcus *** also investigated the plasminogen binding property of the SS2 enzyme.

关键词： enolase octamer Streptococcus suis structure plasminogen binding

Structure and receptor-binding properties of an airborne transmissible avian infl uenza A virus hemagglutinin H5(VN1203mut)

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Protein & Cell 2013年第7期4卷 502-511页

作者： Xishan Lu Yi Shi Wei Zhang Yanfang Zhang jianxun qi George F Gao College of Veterinary Medicine China Agricultural UniversityBeijing 100193China Research Network of Immunity and Health(RNIH) Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Chinese Academy of SciencesBeijing 100049China Laboratory of Protein Engineering and Vaccines Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjin 300308China National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention(China CDC)Beijing 102206China

Avian infl uenza A virus continues to pose a global threat with occasional H5N1 human infections,which is em-phasized by a recent severe human infection caused by avian-origin H7N9 in *** these viruses do not transmit effi ciently in human *** a few ami-no acid substitutions of the hemagglutinin H5 protein in the laboratory,two H5 mutants have been shown to obtain an air-borne transmission in a mammalian ferret *** in this study one of the mutant H5 proteins devel-oped by Kawaoka’s group(VN1203mut)was expressed in a baculovirus system and its receptor-binding properties were *** herein show that the VN1203mut had a dramatically reduced binding affi nity for the avianα2,3-linkage receptor compared to wild type but showed no detectable increase in affi nity for the humanα2,6-linkage receptor,using Surface Plasmon Resonance ***,the crystal structures of the VN1203mut and its complexes with either human or avian receptors demon-strate that the VN1203mut binds the human receptor in the same binding manner(cis conformation)as seen for the HAs of previously reported 1957 and 1968 pandemic influenza *** receptor binding and crystallo-graphic data shown here further confi rm that the ability to bind the avian receptor has to decrease for a higher hu-man receptor binding affi *** the Q226L substitution is shown important for obtaining human receptor binding,we suspect that the newly emerged H7N9 binds human receptor as H7 has a Q226L substitution.

关键词： airborne transmission H5 avian infl uenza structure receptor binding

A dimeric structure of PD-L1: functional units or evolutionary relics?

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Protein & Cell 2010年第2期1卷 153-160页

作者： Yong Chen Peipei Liu Feng Gao Hao Cheng jianxun qi George F.Gao CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of Sciences(CASPMI)Beijing 100101China College of Life Sciences Graduate UniversityChinese Academy of SciencesBeijing 100049China Institute of Biophysics Chinese Academy of SciencesBeijing 100101China China-Japan Joint Laboratory of Molecular Immunology and Molecular Microbiology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

PD-L1 is a member of the B7 protein family,most of whose members so far were identified as dimers in a solution and crystalline state,either complexed or uncomplexed with their ligand(s).The binding of PD-L1 with its receptor PD-1(CD279)delivers an inhibitory signal regulating the T cell *** with the Garboczi group,we successfully solved another structure of human PD-L1(hPD-L1).Our protein crystallized in the space group of C222_(1) with two hPD-L1 molecules per asymmetric *** comparison of reported B7 structures,we have found some intrinsic factors involved in the interaction of these two *** on these results,we tend to believe this uncomplexed hPD-L1 structure demonstrated its potential dimeric state in solution,althougt it could just be an evolutionary relic,too weak to be detected under present technology,or still a functional unit deserved our attentions.

关键词： PD-L1 crystal structure dimer costimulatory molecules B7 family

Structural Basis of SARS-CoV-2 Polymerase Inhibition by Favipiravir

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The Innovation 2021年第1期2卷 164-172页

作者： qi Peng Ruchao Peng Bin Yuan Min Wang Jingru Zhao Lifeng Fu jianxun qi Yi Shi CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijingChina Savaid Medical School University of Chinese Academy of SciencesBeijingChina Center for Influenza Research and Early-warning(CASCIRE) CAS-TWAS Center of Excellence for Emerging Infectious Disease(CEEID)Chinese Academy of SciencesBeijingChina Chongqing Key Laboratory of Neurodegenerative Diseases Chongqing General HospitalUniversity of Chinese Academy of SciencesChongqingChina College of Basic Medicine Jilin UniversityChangchunChina

The outbreak of severe acute respiratory syndrome coronavirus 2(SARSCoV-2)has developed into an unprecedented global *** analogs,such as Remdesivir and Favipiravir,can serve as the firstline broad-spectrum antiviral drugs by targeting the viral ***,the underlying mechanisms for the antiviral efficacies of these drugs are far from well ***,we reveal that Favipiravir,as a pyrazine derivative,could be incorporated into the viral RNA products by mimicking both adenine and guanine *** drug thus inhibits viral replication mainly by inducing mutations in progeny RNAs,different from Remdesivir or other RNA-terminating nucleoside analogs that impair the elongation of RNA *** further determined the cryo-EM structure of Favipiravir bound to the replicating polymerase complex of SARSCoV-2 in the pre-catalytic *** structure provides a missing snapshot for visualizing the catalysis dynamics of coronavirus polymerase,and reveals an unexpected base-pairing pattern between Favipiravir and pyrimidine residues that may explain its capacity for mimicking both adenine and guanine *** findings shed light on the mechanism of coronavirus polymerase catalysis and provide a rational basis for developing antiviral drugs to combat the SARS-CoV-2 pandemic.

关键词： SARS-CoV-2 Favipiravir cryo-EM polymerase pre-catalytic state

Crystal structures of RNA-dependent RNA polymerases from Jingmen tick virus and Alongshan virus

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hLife 2024年第1期2卷 18-31页

作者： Zhenyang Liu qi Peng Pu Han Lu Kuai jianxun qi Yi Shi CAS Key Laboratory of Pathogen Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijingChina Beijing Life Science Academy BeijingChina International Institute of Vaccine Research and Innovation Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina Center for Influenza Research and Early-warning CAS-TWAS Center of Excellence for Emerging Infectious DiseaseChinese Academy of SciencesBeijingChina Research Unit of Adaptive Evolution and Control of Emerging Viruses Chinese Academy of Medical SciencesBeijingChina

Jingmenviruses are a group of flavi-like viruses with segmented genome and have been found in various types of hosts,including humans,cattle,monkeys,bats,rodents,sheep,ticks,mosquitoes and ***,including the Jingmen tick virus(JMTV)and Alongshan virus(ALSV),have been associated with febrile illness and flu-like symptoms in *** polymerase plays critical roles in genome replication and transcription and is an ideal target for antiviral ***,we determined the crystal structures of RNA-dependent RNA polymerase(RdRp)domains of JMTV and ALSV at 2.6Åand 3.2Åresolutions,*** overall structures of JMTV and ALSV RdRp domains are similar to those from the typical unsegmented viruses in Flaviviridae family,especially the Flavivirus *** and ALSV RdRps can be divided into three subdomains and the catalytical Motif A-G are conserved like the typical flaviviruses,whereas the zinc-binding pockets are absent from the JMTV and ALSV *** 50-ends of jingmenvirus genomes are varied in length and sequence,and a highly conserved 8-nucleotide element located on the tip of stem loop A was identified and shown to be required for binding with RdRp and performing de novo replication *** findings provide important structural insights into RdRp of segmented flavivirus and reveal the key region of virus genome responsible for replication initiation,which would promote molecular understanding of segmented flavivirus replication and the structure-based design of antiviral drugs against flaviviruses.

关键词： Jingmenviruses X-rays RNA-dependent RNA polymerase replication