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evolution analysis of Societal Risk Events by Risk Maps

Journal of Systems Science and Systems Engineering 2020年第4期29卷 454-467页

作者： Nuo Xu Xjjin Tang State Key Laboratory of Digital Publishing Technology Peking University Founder Group CoLtdBeijing 100871China Academy of Mathematics and Systems Science Chinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China Wangxuan Institute of Computer Technology Peking UniversityBeijing 100080China

Event evolution analysis which provides an effective approach to capture the main context of a story from explosive increased news texts has become the critical basis for many real applications,such as crisis and emergency management and decision making.Especially,the development of societal risk events which may cause some possible harm to society or individuals has been heavily concerned by both the government and the public.In order to capture the evolution and trends of societal risk events,this paper presents an improved algorithm based on the method of information maps.It contains an event-level cluster generation algorithm and an evaluation algorithm.The main work includes:1)Word embedding representation is adopted and event-level clusters are chosen as nodes of the events evolution chains which may comprehensively present the underlying structure of events.Meanwhile,clusters that consist of risk-labeled events enable to illustrate how events evolve along the time with transitions of risks.2)One real-world case,the event of"Chinese Red Cross",is studied and a series of experiments are conducted.3)An evaluation algorithm is proposed on the basis of indicators of map construction without massive human-annotated dataset.Our approach for event evolution analysis automatically generates a visual evolution of societal risk events,displaying a clear and structural picture of events development.

关键词： Risk maps evolution analysis Baidu hot news search words societal risk events

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深低温保存下高效抗冻多肽的合理设计和机理探讨

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Engineering 2024年第3期34卷 164-173页

作者： Haishan Qi Yihang Gao Lin Zhang Zhongxin Cui Xiaojie Sui Jianfan Ma Jing Yang Zhiquan Shu Lei Zhang Department of Biochemical Engineering School of Chemical Engineering and TechnologyFrontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(MOE)Tianjin UniversityTianjin 300350China School of Engineering and Technology University of Washington TacomaTacomaWA 98402USA

The development of effective antifreeze peptides to control ice growth has attracted a significant amount of attention yet still remains a great challenge.Here,we propose a novel design method based on in-depth investigation of repetitive motifs in various ice-binding proteins(IBPs)with evolution analysis.In this way,several peptides with notable antifreeze activity were developed.In particular,a designed antifreeze peptide named AVD exhibits ideal ice recrystallization inhibition(IRI),solubility,and biocompatibility,making it suitable for use as a cryoprotective agent(CPA).A mutation analysis and molecular dynamics(MD)simulations indicated that the Thr6 and Asn8 residues of the AVD peptide are fundamental to its ice-binding capacity,while the Ser18 residue can synergistically enhance their interaction with ice,revealing the antifreeze mechanism of AVD.Furthermore,to evaluate the cryoprotection potential of AVD,the peptide was successfully employed for the cryopreservation of various cells,which demonstrated significant post-freezing cell recovery.This work opens up a new avenue for designing antifreeze materials and provides peptide-based functional modules for synthetic biology.

关键词： Antifreeze peptides evolution analysis Ice recrystallization inhibition Molecular dynamics simulation Cryopreservation Synthetic biology

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evolution analysis of Influenza A（H1N1） Virus based on the Sequences of Swine Influenza Viruses

Evolution analysis of Influenza A（H1N1） Virus based on the...

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第二届全国微生物资源学术暨国家微生物资源平台运行服务研...

作者： Jiuru Zhao,Kou Zheng,Han Xia,Zhong Zhang,Zhaojun Fan,Shuang Tang,Tianxian Li(State Key Laboratory of Virology,Wuhan Institute of Virology,Chinese Academy of Sciences,Wuhan 430071,China.)

Based on the data from NCBI and the genome sequence of swine influenza virus（A/Swine/Hubei/01/2007（H1N1））,which was isolated from Hubei province of China in 2007,we constructed swine influenza virus data sets of Chinese mainland.The latest datasets contained 408 sequences of 51 swine viruses.Taking A/CaliforniA/04/2009（H1N1;CA/04/09） as representative strain,we analyzed the evolutionary relationship between novel H1N1 human influenza viruses and swine influenza viruses from Chinese mainland.The highest similarity of all 8 genes between the CA/04/09 and Chinese mainland swine influenza virus was 91%-96%,and the evolutionary distances between them were relatively far（0.10787-0.02965;average:0.05743）.The result showed that none of the viral genes in the gene pool of swine population in Chinese mainland was closed to those of novel H1N1 human influenza viruses.

关键词： H1N1 influenza virus Swine influenza virus Blast evolution analysis

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Insight into the characteristics of an important evolutionary model bird(Geospiza magnirostris)mitochondrial genome through comparison

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BIOCELL 2022年第7期46卷 1733-1746页

作者： ZHENGGANG XU LIANG WU JIAHAO CHEN YUNLIN ZHAO CHONGXUAN HAN TIAN HUANG GUIYAN YANG Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster College of ForestryNorthwest A&F UniversityYangling712100China Engineering Research Center for Internet of Animals Changsha410000China Key Laboratory of Forestry Remote Sensing Based Big Data&Ecological Security for Hunan Province Central South University of Forestry and TechnologyChangsha410004China

Darwin’s finches are the most classic case of evolution.Early studies on the evolution of this species were mainly based on morphology.Until now,the mitochondrial genome of Geospiza magnirostris has been sequenced and the study explored the characteristics of the complete genome of G.magnirostris and verified the evolutionary position of it.The 13 PCGs initiated by ATN codons.The stop codons of three PCGs(ND2,COX3 and ND4)were incomplete,with only T-or TA-replacing complete form TAA or TAG.All the tRNA genes expressed a typical cloverleaf secondary structure,except for tRNA^(Ser1)(AGY),whose dihydrouridine(DHU)arm was lack and instead with a simple loop.In the sequence of the control region of G.magnirostris,we found six simple repeat tandem sequences with a total length of 42 bp.Two characteristic conserved overlapping junction(ATGCTAA)and(CAAGAAAG)were observed as reported for eight selected Passeriformes birds.A special conserved overlapping junction(ATCTTACC)involved in mitochondrial transcription termination was found between tRNA^(Tyr) and COX1 in G.magnirostris’s control region.Four most frequently used amino acids in G.magnirostris’s PCGs were Leu1(CUN),Ile,Thr,Ala.The codon usage of G.magnirostris was relatively average,and there was no particular bias.The ratio Ka/Ks results showed that G.magnirostris receives less natural selection pressure.The phylogenetic relationships and cluster analysis of relative codon usage showed that G.magnirostris and Thraupis episcopus clustered in one branch.The phylogenetic position of G.magnirostris was consistent with the traditional taxonomic of Thraupis.The results supported the conclusion that G.magnirostris belongs to the morphological classification of the family Thraupidae.

关键词： Geospiza magnirostris Mitochondrial genome Comparative analysis evolution analysis Phylogenetic relationships

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Rational design of generic primers used for genome clone of norovirus Gil

Rational design of generic primers used for genome clone of ...

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2012年鄂粤微生物学学术年会——湖北省暨武汉微生物学...

作者： Liang Xue Qingping Wu Xiaoxia Kou Jumei Zhang Guangdong Institute of Microbiology State Key Laboratory of Applied Microbiology(Ministry-Guangdong Province Jointly Breeding Base)South ChinaGuangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Open Laboratory of Applied Microbiology School of Bioscience and Bioengineering South China University of Technology

Background:Noroviruses are regarded as the major cause of epidemic diarrhea all over the world,and recent studies have revealed that rapid evolution promotes the viruses occur outbreaks constantly in the last three decades.But the lack of suitable reproduction and culture in vitro system hindered the development of virus research. Methods and Findings:In the present study,an easy method was established to amplify and clone the full length genome of norovirus Gil.Ninety-six reference norovirus Gil genome were collected from GenBank,by conservative analysis,the full length genome was cut into three fragments and amplified by the corresponding primers(Fragment A:N1F/N2819R,fragment B:N2489F/COG2R,fragment C: COG2F/Adaptor).Furthermore,to prove its availability,two stains of different genotypes collected from clinical samples,including Gil.4 and Gil.6 were cloned followed the novel method. Conclusions and Significance:The three-fragment-clone method is a useful tool to collect more genome information of norovirus strains,which would be the foundation of evolution and antivirus research.

关键词： norovirus genome clone rational design evolution analysis

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