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Corrigendum to‘The power of“controllers”:Transposon-mediated duplicated genes evolve towards neofunctionalization’[Journal of Genetics and Genomics(2023)50,462–472]

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Journal of Genetics and Genomics 2024年第1期51卷 109-109页

作者： Huijing Ma Mengxia Wang Yong E.Zhang shengjun tan Key Laboratory of Zoological Systematics and Evolution&State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China CAS Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China Chinese Institute for Brain Research Beijing 102206China

This corrigendum clarifies information in the review‘The power of“controllers”:Transposon-mediated duplicated genes evolve towards neofunctionalization’by Ma et al.(2023).The word“controllers”throughout the paper should be corrected into“controlling elements”:*** title‘The power of“controllers”:Transposon-mediated duplicated genes evolve towards neofunctionalization’should be corrected into‘The power of“controlling elements”:Transposon-mediated duplicated genes evolve towards neofunctionalization’.

关键词： controllers power evolve

The power of“controllers”:Transposon-mediated duplicated genes evolve towards neofunctionalization

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Journal of Genetics and Genomics 2023年第7期50卷 462-472页

Since the discovery of the first transposon by *** McClintock,the prevalence and diversity of transposable elements(TEs)have been gradually *** fundamental genetic components,TEs drive organismal evolution not only by contributing functional sequences(e.g.,regulatory elements or“controllers”as phrased by ***)but also by shuffling genomic *** the latter respect,TE-mediated gene duplications have contributed to the origination of new genes and attracted extensive *** response to the development of this field,we herein attempt to provide an overview of TEmediated duplication by focusing on common rules emerging across duplications generated by different TE ***,despite the huge divergence of transposition machinery across TEs,we identify three common features of various TE-mediated duplication mechanisms,including end bypass,template switching,and recurrent *** three features lead to one common functional outcome,namely,TE-mediated duplicates tend to be subjected to exon shuffling and ***,the intrinsic properties of the mutational mechanism constrain the evolutionary trajectories of these *** finally discuss the future of this field including an in-depth characterization of both the duplication mechanisms and functions of TE-mediated duplicates.

关键词： Transposable elements Gene duplication New gene origination End bypass Template switching Exon shuffling Neofunctionalization Mutational constraint

Increased complexity of gene structure and base composition in vertebrates

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Journal of Genetics and Genomics 2011年第7期38卷 297-305页

作者： Ying Wu Huizhong Yuan shengjun tan Jian-Qun Chen Dacheng Tian Haiwang Yang State Key Laboratory of Pharmaceutical Biotechnology Department of Biology Nanjing University Nanjing 210093 China

How the structure and base composition of genes changed with the evolution of vertebrates remains a puzzling question. Here we analyzed 895 orthologous protein-coding genes in six multicellular animals： human, chicken, zebrafish, sea squirt, fruit fly, and worm. Our analyses reveal that many gene regions, particularly intron and 3~ UTR, gradually expanded throughout the evolution of vertebrates from their invertebrate ancestors, and that the number of exons per gene increased. Studies based on all protein-coding genes in each genome provide consistent results. We also find that GC-content increased in many gene regions （especially 5＇ UTR） in the evolution of endotherms, except in coding-exons. Analysis of individual genomes shows that 3t UTR demonstrated stronger length and GC-content correlation with intron than 5~ UTR, and gene with large intron in all six species demonstrated relatively similar GC-content. Our data indicates a great increase in complexity in vertebrate genes and we propose that the requirement for morphological and functional changes is probably the driving force behind the evolution of structure and base composition complexity in multicellular animal genes.

关键词： GC-content Gene structure Intron UTR Vertebrate Endotherm

Innovation and Firm Co-ownership Network in China’s Electric Vehicle Industry

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Chinese Geographical Science 2024年第2期34卷 195-209页

作者： JIN Zerun ZHU shengjun College of Urban and Environmental Sciences Peking UniversityBeijing 100871China Laboratory for Earth Surface Pro-cesses of the Ministry of Education Peking UniversityBeijing 100871China

Firms are embedded in complex networks,where diverse ideas combine and generate new *** of firms are of-ten seen as critical external resources that have significant influence on firm *** current literature tends to focus on the rela-tionship between firms and their shareholders,while paying less attention to the connections between firms with the same *** article identifies two types of network spillover effects,intra-city network effect and inter-city network effect,by visualizing the co-ownership networks in China’s electric vehicle(EV)*** find that firms with the same shareholders,which are defined as co-owned EV firms,are more innovative than non-co-owned ***,there are two dominant types of firm co-ownership ties formed by corporate and financial institution *** corporate shareholders help exploiting local tacit knowledge,financial institutions are more active in bridging inter-city *** conclusion is confirmed at both firm and city *** paper theor-izes the firm co-ownership network as a new form of institutional proximity and tested the result *** policy consideration,we have emphasized the importance of building formal or informal inter-firm network,and the government should further enhance the knowledge flow channel by institutional construction.

关键词： firm co-ownership intra-city network inter-city network technological innovation electric vehicle China

Robust AUC maximization for classification with pairwise confidence comparisons

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Frontiers of Computer Science 2024年第4期18卷 73-83页

作者： Haochen SHI Mingkun XIE shengjun HUANG College of Computer Science and Technology Nanjing University of Aeronautics and AstronauticsNanjing 211106China College of Electronic and Information Engineering Nanjing University of Aeronautics and AstronauticsNanjing 211106China MIIT Key Laboratory of Pattern Analysis and Machine Intelligence Nanjing 211106China

Supervised learning often requires a large number of labeled examples,which has become a critical bottleneck in the case that manual annotating the class labels is *** mitigate this issue,a new framework called pairwise comparison(Pcomp)classification is proposed to allow training examples only weakly annotated with pairwise comparison,i.e.,which one of two examples is more likely to be *** previous study solves Pcomp problems by minimizing the classification error,which may lead to less robust model due to its sensitivity to class *** this paper,we propose a robust learning framework for Pcomp data along with a pairwise surrogate loss called *** provides an unbiased estimator to equivalently maximize AUC without accessing the precise class ***,we prove the consistency with respect to AUC and further provide the estimation error bound for the proposed *** studies on multiple datasets validate the effectiveness of the proposed method.

关键词： method. pairwise weakly

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Tsinghua Science and Technology 2024年第4期29卷 971-984页

作者： Yuze Peng shengjun Xu Qingkun Chen Wenjin Huang Yihua Huang School of Electronics and Information Technology Sun Yat-sen UniversityGuangzhou 510006China Guangdong Provincial Key Laboratory of Optoelectronic Information Processing Chips and Systems Sun Yat-sen UniversityGuangzhou 510006Chinaand Southern Marine Science and Engineering Guangdong LaboratoryZhuhai 519080China

Popularity plays a significant role in the recommendation system. Traditional popularity is only defined as a static ratio or metric (e.g., a ratio of users who have rated the item and the box office of a movie) regardless of the previous trends of this ratio or metric and the attribute diversity of items. To solve this problem and reach accurate popularity, we creatively propose to extract the popularity of an item according to the Proportional Integral Differential (PID) idea. Specifically, Integral (I) integrates a physical quantity over a time window, which agrees with the fact that determining the attributes of items also requires a long-term observation. The Differential (D) emphasizes an incremental change of a physical quantity over time, which coincidentally caters to a trend. Moreover, in the Session-Based Recommendation (SBR) community, many methods extract session interests without considering the impact of popularity on interest, leading to suboptimal recommendation results. To further improve recommendation performance, we propose a novel strategy that leverages popularity to enhance the session interest (popularity-aware interest). The proposed popularity by PID is further used to construct the popularity-aware interest, which consistently improves the recommendation performance of the main models in the SBR community. For STAMP, SRGNN, GCSAN, and TAGNN, on Yoochoose1/64, the metric P@20 is relatively improved by 0.93%, 1.84%, 2.02%, and 2.53%, respectively, and MRR@20 is relatively improved by 3.74%, 1.23%, 2.72%, and 3.48%, respectively. On Movieslen-1m, the relative improvements of P@20 are 7.41%, 15.52%, 8.20%, and 20.12%, respectively, and that of MRR@20 are 2.34%, 12.41%, 20.34%, and 19.21%, respectively.

关键词： popularity Proportional Integral Differential(PID) algorithm session-based recommendation user’s interests

Cause analysis of expressway traffic accidents based on accident statistics of Hunan provincial expressway in 2012-2018

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Transportation Safety and Environment 2024年第1期6卷 83-92页

作者： Xinyu Liu shengjun Huang Qun Chen Business school Foshan UniversityFoshan 528225GuangdongChina School of Traffic and Transportation Engineering Central South UniversityChangsha 410075HunanChina Hunan Provincial Expressway Traffic Police Station Law Enforcement DepartmentChangsha 410007HunanChina

Based on the 2012–2018 accident statistics on the Hunan Provincial Expressway in China,this paper analyses the proportion to which various factors contribute to accidents,as well as the trends over *** 2012 to 2018,the total number of general procedure handling accidents(*** accidents)increased first and then decreased,while the number of accidents and deaths per 1000 kilometres decreased year by *** total number of simple procedure handling accidents(*** accidents)increased year by year,but the number of accidents per 1000 kilometres remained relatively ***,fatigued driving,improper driving operation,failure to maintain a safe distance from the preceding vehicle and pedestrians entering the expressway are the main causes of general procedure handling *** to maintain a safe distance from the preceding vehicle as required and improper driving operation accounted for approximately 2/3 of the simple procedure handling *** view of the accidents caused by these factors,how to use law enforcement,education,science and technology and facilities construction to further reduce the occurrence of expressway traffic accidents is discussed.

关键词： expressway traffic accident cause analysis

Analysis of quality-related proteins in golden pompano(Trachinotus ovatus)fillets with modified atmosphere packaging under superchilling storage

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Food Science and Human Wellness 2024年第4期13卷 2253-2265页

作者： Chuang Pan Xiaofan Zhang shengjun Chen Yong Xue Yanyan Wu Yueqi Wang Di Wang South China Sea Fisheries Research Institute Chinese Academy of Fishery SciencesKey Laboratory of Aquatic Product ProcessingMinistry of Agriculture and Rural AffairsNational R&D Centre for Aquatic Product ProcessingGuangzhou 510300China Co-Innovation Center of Jiangsu Marine Bio-industry Technology Jiangsu Ocean UniversityLianyungang 222005China Collaborative Innovation Center of Seafood Deep Processing Dalian Polytechnic UniversityDalian 116034China Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province Sanya Tropical Fisheries Research InstituteSanya 572018China College of Food Science and Engineering Ocean University of ChinaQingdao 266003China

Here,we aimed to study the changes in proteome of golden pompano fillets during post-mortem *** mass tags(TMT)-labeled quantitative proteomic strategy was applied to investigate the relationships between protein changes and quality characteristics of modified atmosphere packaging(MAP)fillets during superchilling(-3°C)*** electron microscopy was used to show that the muscle histology microstructure of fillets was damaged to varying degrees,and low-field nuclear magnetic resonance was used to find that the immobilized water and free water in the muscle of fillets changed *** sulfhydryl content,TCA-soluble peptides and Ca2+-ATPase activity also showed that the fillet protein had a deterioration by oxidation and *** Fresh(FS),MAP,and air packaging(AP)groups were *** of 150 proteins were identified as differential abundant proteins(DAPs)in MAP/FS,while 209 DAPs were in AP/FS *** KEGG pathway analysis indicated that most DAPs were involved in binding proteins and protein *** analysis found that 52 DAPs were correlated with quality *** them,8 highly correlated DAPs are expected to be used as potential quality markers for protein oxidation and water-holding *** results provide a further understanding of the muscle deterioration mechanism of packaging golden pompano fillets during superchilling.

关键词： tandem mass tags(TMT)proteomics Trachinotus ovatus Modified atmosphere packaging Superchilling storage Low-field nuclear magnetic resonance Protein deterioration

Dual-additives enable stable electrode-electrolyte interfaces for long life Li-SPAN batteries

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Chinese Chemical Letters 2024年第5期35卷 459-465页

作者： Zhenqiang Guo Huicong Yang Qian Wei shengjun Xu Guangjian Hu Shuo Bai Feng Li School of Materials Science and Engineering University of Science and Technology of ChinaShenyang 110016China Shenyang National Laboratory for Materials Science Institute of Metal ResearchChinese Academy of SciencesShenyang 110016China Department of Biochemistry and Molecular Biology College of Life ScienceChina Medical UniversityShenyang 110122China Dalian National Laboratory for Clean Energy Dalian 116023China Shenyang King Power Technology Co. Ltd.Shenyang 110016China

Sulfurized polyacrylonitrile(SPAN)is proposed as a promising cathode material for lithium sulfur ***,the continuous side reactions at the electrolyte-electrode interfaces as well as the slow redox kinetics of SPAN cathode deteriorate the electrochemical *** this study,an electrolyte with dual-additives comprising 2-fluoropyridine(2-FP)and lithium difluorobis(oxalato)phosphate(LiDFBOP)was used to improve the performance of Li||SPAN cells.2-FP has a lower lowest occupied molecular orbital energy than that of the solvents in the electrolyte,leading to its prior reduction.A LiF-rich film can be formed on the electrode,effectively improving the stability of the electrolyte-electrode interfaces and prolonging the ***,LiDFBOP could form an electrolyte-electrode interface film containing a large amount of Li_(x)PO_(y)F_(z) species,compensating for the kinetic deterioration caused by the lower ionic conductive of LiF formed at the electrolyte-electrode ***,an electrode-interface film with good chemical stability and high Li^(+) transport was established by LiF and Li_(x)PO_(y)F_(z)-rich *** Li||SPAN cell with the electrolyte containing dual-additives demonstrates an excellent capacity retention of 97.5%after 200 cycles at 1.0 C,25℃,comparing to 56.2%capacity retention without ***,the rate capacities of cells with dual-additives can reach 1128.1 mAh/g at 5 C,comparing to only 813.5 mAh/g using electrolyte without *** results shown that the dual-additives in electrolyte provide a promising strategy for practical application of lithium sulfur batteries with SPAN cathodes.

关键词： Sulfurized polyacrylonitrile Lithium metal Interface film 2-Fluoropyridine Difluorobis(oxalato)phosphate