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Leading directions and effective distance of larch offspring dispersal at the upper treeline in the Northern and Polar Urals, Russia

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Forest Ecosystems 2024年第5期11卷 603-617页

作者： P.A.Moiseev V.L.Semerikov T.V.Semerikova D.S.Balakin I.B.Vorobiev S.O.Viuykhin Institute of plant and Animal Ecology Ural BranchRussian Academy of SciencesEkaterinburg620144Russia Center for Genetics and Life science Sirius University of Science and Technology354340SochiRussia

Climate has changed sufficiently over the last 150 years and forced out upper treeline advance at the most studied sites around the *** rate of advance has been extremely variable–from tens to hundreds meters in *** is because the degree at which tree frontal populations respond to climate change depends on the complex interaction of biological and physical *** resulting stand pattern is the consequence of the interaction between dispersal and survival functions.A few publications have addressed the question of how this pattern is *** order to understand how the spatial structure of tree stands was formed at the upper limit of their distribution in the Ural Mountains,we assessed the distance and direction of dispersal of offspring from maternal *** found that in frontal Larix sibirica ***,‘effective’dispersal of offspring ranges from 3 to 758 m(with a median of 20–33 m in open forest and 219 m in single-tree tundra in the Polar Urals and 107 m in open forest in the Northern Urals).We revealed that most of the offspring effectively dispersed not only in the direction of the prevailing winds,but also in the opposite direction up the slope,and the distance can reach 500–760 *** data obtained can be used to develop an individual-based model which is capable of simulating in detail the dynamics of tree stands at the upper limit of their growth and reliably predicting the future position and pattern of treeline ecotone as growth conditions continue to improve in the face of observed climate change.

关键词： Effective dispersal distance Upper treeline Parentage analysis Age estimation Terrestrial laser scanning Larix sibirica Ural mountains

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TaSRO1 interacts with TaVP1 to modulate seed dormancy and pre-harvest sprouting resistance in wheat

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Journal of Integrative plant Biology 2024年第1期66卷 36-53页

作者： Shupeng Liu Li Li Wenlong Wang Guangmin Xia Shuwei Liu Key lab.ratory of plant Development and Environmental Adaptation Biology Ministry of EducationSchool of Life ScienceShandong UniversityQingdao 266237China

Dormancy is an adaptive trait which prevents seeds from germinating under unfavorable environmental *** with weak dormancy undergo pre-harvest sprouting(PHS)which decreases grain yield and *** the genetic mechanisms that regulate seed dormancy and resistance to PHS is crucial for ensuring global food *** this study,we illustrated the function and molecular mechanism of TaSRO1 in the regulation of seed dormancy and PHS resistance by suppressing *** tasro1 mutants exhibited strong seed dormancy and enhanced resistance to PHS,whereas the mutants of tavp1 displayed weak *** evidence has shown that TaVP1 is epistatic to *** evidence has shown that TaSRO1 interacts with TaVP1 and represses the transcriptional activation of the PHS resistance genes TaPHS1 and ***,TaSRO1 undermines the synergistic activation of TaVP1 and TaABI5 in PHS resistance ***,we highlight the great potential of tasro1 alleles for breeding elite wheat cultivars that are resistant to PHS.

关键词： wheat seed dormancy pre-harvest sprouting(PHS) ABA signaling vivipary

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Endomembrane-biased dimerization of ABCG16 and ABCG25 transporters determines their substrate selectivity in ABA-regulated plant growth and stress responses

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Molecular plant 2024年第3期17卷 478-495页

作者： Yeling Zhou Yuzhu Wang Dong Zhang Jiansheng Liang institute of plant and Food science Department of BiologySchool of Life SciencesSouthern University of Science and Technology(SUSTech)Shenzhen 518055China Key lab.ratory of Molecular Design for plant Cell Factory of Guangdong Higher Education Institutes Southern University of Science and Technology(SUSTech)Shenzhen 518055China jiangsu Key lab.ratory of Crop Genetics and Physiology/Co-lnnovation Center for Modern Production Technology of Grain Crops Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhou 225009China

ATP-binding cassette(ABC)transporters are integral membrane proteins that have evolved diverse func-tions fulfilled via the transport of various *** Arabidopsis,the G subfamily of ABC proteins is particularly abundant and participates in multiple signaling pathways during plant development and stress *** this study,we revealed that two Arabidopsis ABCG transporters,ABCG16 and ABCG25,engage in ABA-mediated stress responses and early plant growth through endomembrane-specific dimerization-coupled transport of ABA and ABA-glucosyl ester(ABA-GE),*** first revealed that ABCG16 contributes to osmotic stress tolerance via ABA *** specifically,ABCG16 induces cellular ABA efflux in both yeast and plant *** FRET analysis,we showed that ABCG16 forms oblig-atory homodimers for ABA export activity and that the plasma membrane-resident ABCG16 homodimers specifically respond to ABA,undergoing notable conformational ***,we demonstrated that ABCG16 heterodimerizes with ABCG25 at the endoplasmic reticulum(ER)membrane and facilitates the ER entry of ABA-GE in both Arabidopsis and tobacco *** specific responsiveness of the ABCG16-ABCG25 heterodimer to ABA-GE and the superior growth of their double mutant support an inhib-itory role of these twoABCGs in early seedling establishment via regulation of ABA-GE translocation across the ER *** endomembrane-specific analysis of the FRET signals derived from the homo-or heterodimerized ABcG complexes allowed us to link endomembrane-biased dimerization to the transloca-tion of distinct substrates by ABcG transporters,providing a prototypic framework for understanding the omnipotence of ABcG transporters in plant development and stress responses.

关键词： abscisic acid ABCG transporter dimerization endomembrane substrate selectivity

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A survey on dynamic graph processing on GPUs: concepts, terminologies and systems

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Frontiers of Computer science 2024年第4期18卷 1-23页

作者： Hongru GAO Xiaofei LIAO Zhiyuan SHAO Kexin LI Jiajie CHEN Hai JIN National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System lab.Cluster and Grid Computing lab School of Computer Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China Zhejiang lab Hangzhou 311121China

Graphs that are used to model real-world entities with vertices and relationships among entities with edges,have proven to be a powerful tool for describing real-world problems in *** most real-world scenarios,entities and their relationships are subject to constant *** that record such changes are called dynamic *** recent years,the widespread application scenarios of dynamic graphs have stimulated extensive research on dynamic graph processing systems that continuously ingest graph updates and produce up-to-date graph analytics *** the scale of dynamic graphs becomes larger,higher performance requirements are demanded to dynamic graph processing *** the massive parallel processing power and high memory bandwidth,GPUs become mainstream vehicles to accelerate dynamic graph processing ***-based dynamic graph processing systems mainly address two challenges:maintaining the graph data when updates occur(i.e.,graph updating)and producing analytics results in time(i.e.,graph computing).In this paper,we survey GPU-based dynamic graph processing systems and review their methods on addressing both graph updating and graph *** comprehensively discuss existing dynamic graph processing systems on GPUs,we first introduce the terminologies of dynamic graph processing and then develop a taxonomy to describe the methods employed for graph updating and graph *** addition,we discuss the challenges and future research directions of dynamic graph processing on GPUs.

关键词： dynamic graphs graph processing graph algorithms GPUs

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Modularly assembled multiplex prime editors for simultaneous editing of agronomically important genes in rice

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plant Communications 2024年第2期5卷 67-78页

作者： Ajay Gupta Bo Liu Saad Raza Qi-Jun Chen Bing Yang Division of plant science and Technology Bond Life Sciences CenterUniversity of MissouriColumbiaMO 65211USA State Key lab.ratory of plant Physiology and Biochemistry College of Biological SciencesChina Agricultural UniversityBeijing 100193China Center for Crop Functional Genomics and Molecular Breeding China Agricultural UniversityBeijing 100193China Donald Danforth plant science Center St.LouisMO 63132USA

Prime editing(PE)technology enables precise alterations in the genetic code of a genome of *** offers great potential for identifying major agronomically important genes in plants and editing them into superior variants,ideally targeting multiple loci simultaneously to realize the collective effects of the ***,we report the development of a modular assembly-based multiplex PE system in rice and demon-strate its efficacy in editing up to four genes in a single transformation *** duplex PE(DPE)system achieved a co-editing efficiency of 46.1%in the T0 generation,converting TFIIAg5 to xa5 and xa23 to *** resulting double-mutant lines exhibited robust broad-spectrum resistance against multiple Xanthomonas oryzae pathovar oryzae(Xoo)strains in the T1 *** addition,we success-fully edited OsEPSPS1 to an herbicide-tolerant variant and OsSWEET11a to a Xoo-resistant allele,achieving a co-editing rate of 57.14%.Furthermore,with the quadruple PE(QPE)system,we edited four genes—two for herbicide tolerance(OsEPSPS1 and OsALS1)and two for Xoo resistance(TFIIAg5 and OsSWEET11a)—using one construct,with a co-editing efficiency of 43.5%for all four genes in the T0 *** performed multiplex PE usingfive more constructs,including two for triplex PE(TPE)and three for QPE,each targeting a different set of *** editing rates were dependent on the activity of pegRNA and/or *** instance,optimization of ngRNA increased the PE rates for one of the targets(OsSPL13)from 0%to 30%but did not improve editing at another target(OsGS2).Overall,our modular assembly-based system yielded high PE rates and streamlined the cloning of PE reagents,making it feasible for more lab. to utilize PE for their editing *** have significant implications for advancing gene editing techniques in plants and may pave the way for future agricultural applications.

关键词： prime editing rice bacterial blight herbicide tolerance multiplex genome editing

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What can we learn from quality assurance badges in open-source software?

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science China(Information sciences) 2024年第4期67卷 146-163页

作者： Feng LI Yiling LOU Xin TAN Zhenpeng CHEN Jinhao DONG Yang LI Xuanzhi WANG Dan HAO Lu ZHANG MoE Key lab.of HCST School of Computer SciencePeking University Department of Computer science Purdue University School of Computer science & Engineering Beihang University(BUAA) Department of Computer science University College London(UCL)

In the development of open-source software(OSS), many developers use badges to give an overview of the software and share some key features/metrics conveniently. Among various badges, quality assurance(QA) badges make up a large proportion and are the most prevalent because QA is of vital importance in software development, and ineffective QA may lead to anomalies or defects. In this paper, we focus on QA badges in open-source projects, which present quality assurance information directly and instantly,and aim to produce some interesting findings and provide practical implications. We collect and analyze 100000 projects written in popular programming languages from GitHub and conduct a comprehensive empirical study both inside and outside QA badges. Inside QA badges, we build a category classification for all QA badges based on the properties they focus on, which shows the types of QA badges developers use. Then,we analyze the frequency of the properties that QA badges focus on, and property combinations, too, which present their use status. We find that QA badges focus on various properties while developers give different preferences to different properties. The use status also differs between different programming languages. For example, projects written in C focus on Security to a great extent. Our findings also provide implications for developers and badge providers. Outside QA badges, we conduct a correlation analysis between QA badges and some software metrics that have potential relationships with code quality, contribution quality, and popularity. We find that QA badges have statistically significant correlations with various software metrics.

关键词： quality assurance badge open-source software code quality empirical study

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Characteristics of long-distance mobile mRNAs from shoot to root in grafted plant species

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Horticultural plant Journal 2024年第1期10卷 25-37页

作者： Mengmeng Fu Zhen Xu Huaying Ma Yifan Hao Ji Tian Yi Wang Xinzhong Zhang Xuefeng Xu Zhenhai Han Ting Wu College of Horticulture China Agricultural UniversityBeijing 100193China plant science and Technology College Beijing University of AgricultureBeijing 102206China

Thousands of long-distance mobile mRNAs were identified from different grafting systems,based on high-throughput sequencing ***,the long-distance delivery of RNAs was proved to involve multiple ***,we analyzed the homology,motif,and tRNA-like structure(TLS)of long-distance mobile mRNAs identified by RNA-seq as well as the RNA-binding protein(RBP)in nine grafting combinations including Arabidopsis thaliana,Vitis vinifera,Cucumis sativus,Citrullus lanatus,Nicotiana benthamiana,Malus domestica,Pyrus spp.,Glycine max and Phaseolus *** several mRNAs were found to be shared in herbaceous,woody,and related species,the vast majority of long-distance mobile mRNAs were *** non-specific movement-related motifs were identified,while the TLS was not necessary for mRNA long distance *** addition,we found that RBPs were conserved among herbaceous and woody plants as well as related *** paper reports a further in-depth analysis of the endogenous mechanisms by which the species-specific transportable m RNAs were selected by bioinformatics,in order to provide insights for future research on long-distance mobile mRNAs.

关键词： Grafting combination Long-distance mobile mRNA TLS RNA binding proteins

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Movement of ACC oxidase 3 mRNA from seeds to flesh promotes fruit ripening in apple

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Molecular plant 2024年第8期17卷 1221-1235页

作者： Ting Wang Yi Zheng Chen Xu Yulin Deng Xinyi Hao Zicheng Chu Ji Tian Yi Wang Xinzhong Zhang Zhenhai Han Ting Wu College of Horticulture China Agricultural UniversityBeijingChina plant science and Technology College Bioinformatics CenterBeijing University of AgricultureBeijingChina

Xenia,the phenomenon in which the pollen genotype directly affects the phenotypic characteristics of maternal tissues(i.e.,fruit ripening),has applications in crop production and ***,the underlying molecular mechanism has yet to be ***,we investigated whether mobile mRNAs from the pollen affect the ripening and quality-related characteristics of the fruit using cross-pollination between distinct Malus domestica(apple)*** demonstrated that hundreds of mobile mRNAs originating fromthe seeds are deliveredto *** themovementof one of these mRNAs,AcC oxidase 3(MdAco3),is coordinated with fruit *** acid treatment,which can cause plasmodesmal closure,blocks MdAcO3 movement,indicating that MdAcO3 transcripts may move through the *** assess the role of mobile MdAcO3 transcripts in apple fruit,we created MdACO3-GFP-expressing apple seeds using MdACO3-GFP-overexpressing pollen for pollination and showed that MdACO3 transcripts in the transgenic seeds move to the flesh,where they promote fruit ***,we demonstrated that MdAco3 can be transported from the seeds to fruit in the fleshy-fruited species tomato and *** results underscore the potential of mobile mRNAs from seeds to influence fruit characteristics,providing an explanation for the xenia ***,our findings highlight the feasibility of leveraging diverse pollen genomic resources,without resorting to genome editing,to improve fruitquality.

关键词： fruit ripening xenia ACO3 mobile RNA seed(to flesh)

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Precise control of page cache for containers

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Frontiers of Computer science 2024年第2期18卷 17-30页

作者： Kun WANG Song WU Shengbang LI Zhuo HUANG Hao FAN Chen YU Hai JIN National Engineering Research Center for Big Data Technology and System Services Computing Technology and System LabCluster and Grid Computing Lab School of Computer Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China

Container-based virtualization isbecoming increasingly popular in cloud computing due to its efficiency and *** isolation is a fundamental property of *** works have indicated weak resource isolation could cause significant performance degradation for containerized applications and enhanced resource ***,current studies have almost not discussed the isolation problems of page cache which is a key resource for *** leverage memory cgroup to control page cache ***,existing policy introduces two major problems in a container-based ***,containers can utilize more memory than limited by their cgroup,effectively breaking memory ***,the Os kernel has to evict page cache to make space for newly-arrived memory requests,slowing down containerized *** paper performs an empirical study of these problems and demonstrates the performance impacts on containerized *** we propose pCache(precise control of page cache)to address the problems by dividing page cache into private and shared and controlling both kinds of page cache separately and *** do so,pCache leverages two new technologies:fair account(f-account)and evict on demand(EoD).F-account splits the shared page cache charging based on per-container share to prevent containers from using memory for free,enhancing memory *** EoD reduces unnecessary page cache evictions to avoid the performance *** evaluation results demonstrate that our system can effectively enhance memory isolation for containers and achieve substantial performance improvement over the original page cache management policy.

关键词： page cache memory cgroup container isolation cloud computing

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An abundant valuable resource for salt-tolerance allele hunting in rice

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plant Communications 2024年第4期5卷 127-128页

作者： Nai-Qian Dong Hong-Xuan Lin National Key lab.ratory of plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China University of the Chinese Academy of sciences Beijing 100049China School of Life science and Technology ShanghaiTech UniversityShanghai 201210China

Soil salinity is a major abiotic stressor that limits plant growth and crop productivity ***,soil salinity is predictably increasing owing to global climate change,over-fertilization,and various farm irrigation ***,there are more than 833 million hectares of salt-affected soils around the globe(8.7%of the planet),accounting for approximately 20%–50%of irrigated soils and posing a significant threat to food production and security for over 1.5 billion people worldwide as a result of salt-induced land degradation(FAO,2021;https://***/global-soil-partnership/resources/highlights/detail/en/c/1445579/).

关键词： soil salinity abundant

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