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Rapid and Efficient Assembly of Transcription Activator-Like Effector Genes by user Cloning

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Journal of Genetics and Genomics 2014年第6期41卷 339-347页

作者： Song Wang Wei Li Shuo Wang Baoyang Hu State Key Laboratory of Reproductive Biology Institute of Zoology Chinese Academy of Sciences University of the Chinese Academy of Sciences Nanjing Agricultural University

Transcription activator-like effectors （TALEs） that were related to bacteria immune system have lately been employed in a promising approach of precise gene targeting. Because of the repetitive characteristics of TALEs, existing TALE assembly methods are either very complicated, time-consuming, or too tricky to be handled in common labs. Here, we reported a rapid, efficient and easy method for TALE assembly. This method takes advantage of uracil-specific excision reagent （user）, an enzyme that can cleave DNA constructs and create long, unique single-strand DNA overhangs. Upon user treatment, the overhangs on each individual TALE repeat unit can be rejoined hierarchically to form pentamers in a ligation-independent manner. Eventually, three pentamers are assembled into a full TALE construct by Golden Gate cloning. TALE nucleases （TALENs） generated with this method exhibit high genome-editing activity in human cells such as HEK293FT cells. Using this method, we have successfully synthesized three TALEN pairs targeting endogenous Tetl locus, and proved that all can specifically target Tetl gene, though in various degree. Comparing to other methods of TALEN assembly, this one is much less labor intensive and fairly faster, and positive clones can be obtained at high efficiency within only two days. We thus contribute to an easier approach for effective TALENs synthesis, which may highly facilitate the wide application of TALEN technology in genome editing, especially for human cells that require precise targeting.

关键词： TAL effector TALENs user Tetl Golden Gate cloning

user Account Linkage Across Multiple Platforms with Location Data

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Journal of Computer Science & Technology 2020年第4期35卷 751-768页

作者： Wei Chen Weiqing Wang Hongzhi Yin Jun-Hua Fang Lei Zhao Institute of Artificial Intelligence School of Computer Science and TechnologySoochow UniversitySuzhou 215006China Faculty of Information Technology Monash UniversityMelbourne 3000Australia School of Information Technology and Electrical Engineering The University of QueenslandBrisbane 4072Australia

Linking user accounts belonging to the same user across different platforms with location data has received significant attention,due to the popularization of GPS-enabled devices and the wide range of applications benefiting from user account linkage(e.g.,cross-platform user profiling and recommendation).Different from most existing studies which only focus on user account linkage across two platforms,we propose a novel model ULMP(i.e.,user account linkage across multiple platforms),with the goal of effectively and efficiently linking user accounts across multiple platforms with location data.Despite of the practical significance brought by successful user linkage across multiple platforms,this task is very challenging compared with the ones across two platforms.The major challenge lies in the fact that the number of user combinations shows an explosive growth with the increase of the number of platforms.To tackle the problem,a novel method GTkNN is first proposed to prune the search space by efficiently retrieving top-k candidate user accounts indexed with well-designed spatial and temporal index structures.Then,in the pruned space,a match score based on kernel density estimation combining both spatial and temporal information is designed to retrieve the linked user accounts.The extensive experiments conducted on four real-world datasets demonstrate the superiority of the proposed model ULMP in terms of both effectiveness and efficiency compared with the state-of-art methods.

关键词： user account linkage multiple platform check-in record

Electric Vehicle Charging Simulation Framework Considering Traffic,user,and Power Grid

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Journal of Modern Power Systems and Clean Energy 2021年第3期9卷 602-611页

作者： Weicheng Liu Xujiang Shi Jianfeng Zhao Xiao-Ping Zhang Ying Xue the School of Electrical Engineering Southeast UniversityNanjing 210096China the Department of Electronic Electrical and System EngineeringSchool of EngineeringUniversity of BirminghamBirminghamUK

The traffic and user have significant impacts on the electric vehicle(EV)charging load but are not considered in the existing research.We propose a novel integrated simulation framework considering the traffic,the user,and power grid as well as the EV traveling,parking and charging based on cellular automaton(CA).The traffic is modeled by the traffic module of the proposed framework based on CA,while the power grid and user are modeled in the EV charging module.The traffic flow,user’s charging preference,user’s charging satisfaction,and the total supply capability(TSC)in the surveyed region are considered in the proposed framework.Two cases are carried out to show the interactions between the user and power grid.It is shown that the proposed framework can accurately simulate the interactions among traffic situation,user's behavior and TSC,which are significantly lacking in the existing research.The proposed framework is scalable in considering additional interrelated elements.

关键词： Electric vehicle(EV) integrated simulation framework cellular automaton traffic user power grid

Generic user revocation systems for attribute-based encryption in cloud storage

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Frontiers of Information Technology & Electronic Engineering 2018年第11期19卷 1362-1384页

作者： Genlang CHEN Zhiqian XU Hai JIANG Kuan-ching LI Institute of Ningbo Technology Zhejiang University Independent Scholar Department of Computer Science Arkansas State University Department of Computer Science and Information Engineering Providence University

Cloud-based storage is a service model for businesses and individual users that involves paid or free storage resources. This service model enables on-demand storage capacity and management to users anywhere via the Internet. Because most cloud storage is provided by third-party service providers, the trust required for the cloud storage providers and the shared multi-tenant environment present special challenges for data protection and access control. Attribute-based encryption(ABE) not only protects data secrecy, but also has ciphertexts or decryption keys associated with fine-grained access policies that are automatically enforced during the decryption process. This enforcement puts data access under control at each data item level. However, ABE schemes have practical limitations on dynamic user revocation. In this paper, we propose two generic user revocation systems for ABE with user privacy protection, user revocation via ciphertext re-encryption(UR-CRE) and user revocation via cloud storage providers(UR-CSP), which work with any type of ABE scheme to dynamically revoke users.

关键词： Attribute-based.encryption Generic user revocation user privacy Cloud storage Access control

user-Oriented Hybrid Opportunistic Network Design

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中国通信：英文版 2015年第11期12卷 119-133页

作者： ZHANG Yong LI Jin SONG Mei YANG Ming Beijing Key Laboratory of Work Safety Intelligent Monitoring Beijing University of Posts and Telecommunications Beijing Information Science & Technology University

To improve the end-to-end Successful Delivery Probability(SDP) of mobile nodes in opportunistic network,hybrid Opportunistic Network(OppNet) architecture using Fix Infrastructure Nodes(FINs) is proposed.As enhanced OppNet serving for special users,the network planning and design should take user's mobility behavior into account.We adopt collected users' mobility records,analyze users' stay pattern,and establish Message Exchange Points(MEPs) where FINs should be installed.Our solution includes MEPs detection algorithm,Maximum end-to-end Success Delivery Probability(MSDP) detection algorithm,and simulated annealing algorithm.After data preprocessing,MEPs detection algorithm detects feasible locations from users' trajectory records where not more than one user visit frequently.End to end SDPs of these feasible MEPs are evaluated using MSDP detection algorithm.To reduce the computation complexity,a simulated annealing algorithm to select optimal FIN locations in a large number of feasible MEPs is given.The evaluation experiments based on reallife trajectory dataset verify our proposal can achieve better E2 E SDP gain than "most visitors" strategy and "max residence probability" strategy.

关键词： opportunistic network network architecture user mobility

Modified stochastic user-equilibrium assignment algorithm for urban rail transit under network operation

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Journal of Central South University 2013年第10期20卷 2897-2904页

作者：朱炜胡昊徐瑞华洪玲 Center of Transportation Research School of Naval ArchitectureOcean and Civil EngineeringShanghai Jiao Tong University School of Transportation Engineering Tongji University

Based on the framework of method of successive averages(MSA), a modified stochastic user-equilibrium assignment algorithm was proposed, which can be used to calculate the passenger flow distribution of urban rail transit(URT) under network operation. In order to describe the congestion's impact to passengers' route choices, a generalized cost function with in-vehicle congestion was set up. Building on the k-th shortest path algorithm, a method for generating choice set with time constraint was embedded, considering the characteristics of network operation. A simple but efficient route choice model, which was derived from travel surveys for URT passengers in China, was introduced to perform the stochastic network loading at each iteration in the algorithm. Initial tests on the URT network in Shanghai City show that the methodology, with rational calculation time, promises to compute more precisely the passenger flow distribution of URT under network operation, compared with those practical algorithms used in today's China.

关键词： urban rail transit stochastic user equilibrium assignment algorithm method of successive averages network operation

user Selection Algorithms for Lowering Cross-Tier Interference in Heterogeneous Network

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China Communications 2016年第S1期13卷 116-123页

作者： CHE Linlin HAO Conghui HAN Dongsheng CHEN Zhixiong School of Electrical and Electronic Engineering North China Electric Power University

To lower the cross-tier intercell interference(ICI) between macrocell and microcell,three user selection algorithms for the heterogeneous network were proposed in this paper, assuming full knowledge of channelstate information at the transmitter. Algorithm 1 chooses microcell users whose interference channel matrix is parallel to that of a known user and targets at increasing user SINR. Algorithm 2 takes effect of chordal distance-channel norm balance on the system into account and predetermines the available user set from which it can choose service users. With comprehensive considerations to effect of interference signal and useful signal on system, Algorithm 3 set a weighting function as the objective function of user selection. Simulation results demonstrated that all three proposed algorithms could achieve user diversity gain while lowering cross-tier interference.

关键词： user selection cross-tier interference chordal distance channel norm heterogeneous network

shinyChromosome:An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes

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Genomics, Proteomics & Bioinformatics 2019年第5期17卷 535-539页

作者： Yiming Yu Wen Yao Yuping Wang Fangfang Huang National Key Laboratory of Wheat and Maize Crop Science College of Life SciencesHenan Agricultural UniversityZhengzhou 450002China National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research(Wuhan)Huazhong Agricultural UniversityWuhan 430070China

Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes.Currently,there is no specialized graphical user interface(GUI)designed to produce non-circular whole genome diagrams,and the use of existing tools requires considerable coding effort from users.Moreover,such tools also require improvement,including the addition of new functionalities.To address these issues,we developed a new R/Shiny application,named shiny Chromosome,as a GUI for the interactive creation of non-circular whole genome diagrams.shiny Chromosome can be easily installed on personal computers for own use as well as on local or public servers for community use.Publication-quality images can be readily generated and annotated from user input using diverse widgets.shiny Chromosome is deployed at http://150.***.59.144:3838/shiny Chromosome/,http://shiny ***,and https://yimingyu.***.io/shiny Chromosome for online use.The source code and manual of shiny Chromosome are freely available at https://***/venyao/shiny Chromosome.

关键词： Genomic data visualization Non-circular whole genome plot Shiny application Graphical user interface shiny Chromosome

DFTracker: detecting double-fetch bugs by multi-taint parallel tracking

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Frontiers of Computer Science 2019年第2期13卷 247-263页

作者： Pengfei WANG Kai LU Gen LI Xu ZHOU Science and Technology on Parallel and Distributed Processing Laboratory National University of Defense Technology Changsha 410073 China College of Computer National University of Defense Technology Changsha 410073 China Collaborative Innovation Center of High Performance Computing National University of Defense Technology Changsha 410073 China

A race condition is a common trigger for concurrency bugs. As a special case, a race condition can also occur across the kernel and user space causing a doublefetch bug, which is a field that has received little research attention. In our work, we first analyzed real-world doublefetch bug cases and extracted two specific patterns for doublefetch bugs. Based on these patter ns, we proposed an approach of multi-taint parallel tracking to detect double-fetch bugs. We also implemented a prototype called DFTracker (doublefetch bug tracker), and we evaluated it with our test suite. Our experiments demonstrated that it could effectively find all the double-fetch bugs in the test suite including eight realworld cases with no false negatives and minor false positives. In addition, we tested it on Linux kernel and found a new double-fetch bug. The execution overhead is approximately 2x for single-file cases and approximately 9x for the whole kernel test, which is acceptable. To the best of the authors1 knowledge, this work is the first to introduce multi-taint parallel tracking to double-fetch bug detection—an innovative method that is specific to double-fetch bug features—and has better path coverage as well as lower runtime overhead than the widely used dynamic approaches.

关键词： multi-taint parallel tracking double fetch race condition between kernel and user time of check to time of use real-world case analysis Clang Static Analyzer