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Supercoiled DNA Minicircles under Double-strand Breaks

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Chinese Journal of Polymer Science 2024年第9期42卷 1353-1359,I0007页

作者： ye-peng Qiao Chun-Lai Ren National Laboratory of Solid State Microstructures and Department of Physics Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210093China

Understanding how supercoiled DNA releases intramolecular stress is essential for its functional ***,the molecular mechanism underlying the relaxation process remains insufficiently *** we employed MD simulations based on the oxDNA2 model to investigate the relaxation process of a 336-base pair supercoiled minicircular DNA under double-strand breaks with two fixed *** simulations show that the conformational changes in the DNA occur continuously,with intramolecular stress release happening abruptly only when the DNA chain traverses the breakage *** relaxation process is influenced not only by the separation distance between the fixed ends but also their ***,we observe an inhibitory effect on the relaxation characterized by small angles,where short terminal loops impede DNA conformational adjustments,preserving the supercoiled *** findings elucidate the intricate interplay between DNA conformational change,DNA motion and intramolecular stress release,shedding light on the mechanisms governing the relaxation of supercoiled DNA at the molecular level.

关键词： Supercoiled DNA DNA minicircle DNA relaxation oxDNA model MD simulation

Joint Analysis of Recurrent Event Data with a Dependent Terminal Event

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Journal of Systems Science & Complexity 2017年第6期30卷 1443-1458页

作者： ye peng DAI Jiajia ZHU Jun School of Statistics University of International Business and Economics School of Mathematics and Statistics Guizhou University Institute of Applied Mathematics Academy of Mathematics and Systems Science Chinese Academy of Sciences

Recurrent event data frequently occur in many longitudinal studies, and the observation on recurrent events could be stopped by a terminal event such as death. This paper considers joint modeling and analysis of recurrent event and terminal event data through a common subject-specific frailty, in which the proportional intensity model is used for modeling the recurrent event process and the additive hazards model is used for modeling the terminal event time. Estimating equation approaches are developed for parameter estimation and asymptotic properties of the resulting estimators are established. In addition, some procedures are presented for model checking. The finite sample behavior of the proposed estimators is evaluated through simulation studies, and an application to a heart failure study is provided.

关键词： Additive hazards model estimating equation frailty recurrent events terminal event

Evolution and dynamics of a summertime penetrating front off the Zhejiang-Fujian coast,China

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Science China Earth Sciences 2022年第3期65卷 556-569页

作者： peng ye Jiliang XUAN Daji HUANG Ocean College Zhejiang UniversityZhoushan 316021China State Key Laboratory of Satellite Ocean Environment Dynamics Second Institute of OceanographyMinistry of Natural ResourcesHangzhou 310012China Key Laboratory of Tropical Marine Ecosystem and Bioresources Fourth Institute of OceanographyMinistry of Natural ResourcesBeihai 536000China

Penetrating fronts are frequently observed off the Zhejiang-Fujian coast,but their life cycles are poorly understood because of the lack of time series *** this study,Geostationary Ocean Color Imager data are used to describe the complete evolutionary process of a penetrating front,and the impacts of wind and circulation on evolution are *** on the horizontal coverage and the front of the penetrating water,the evolutionary process is divided into three stages of development,maturation and *** the development stage,the area of the penetrating water increases rapidly with eastward extension,and the penetrating front is well connected to the Zhejiang-Fujian coastal front in the southwestern *** the maturation stage,the penetrating water continues to extend eastward at a low speed and finally arrives at the Kuroshio area on the continental ***,the southwestern part of the penetrating front is gradually separated from the coastal *** the decay stage,the coverage of the penetrating water decreases rapidly,and the penetrating front disappears first in the *** this stage,the penetrating front is rarely moves east but completely separated from the coastal front south of 30°*** analysis suggests that the typhoon-induced southward extension of the Changjiang Diluted Water off the Zhejiang-Fujian coast is an important precondition for the generation of the penetrating *** eastward extension of the penetrating front during the development stage is mainly driven by a southwesterly wind,while in the maturation stage,it is affected by both the wind and the offshore branch of the Taiwan Warm *** detachment of penetrating water from coastal water is caused by the inshore branch of the Taiwan Warm *** tracer experiments confirm the wind and Taiwan Warm Current impacts on the eastward extension and detachment of penetrating *** addition,the Kuroshio frontal eddy may play an important role in

关键词： Zhejiang-Fujian Coast Chlorophyll-a Penetrating front Evolution process Taiwan Warm Current

A class of weighted estimating equations for additive hazards models with covariates missing at random

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Science China Mathematics 2022年第3期65卷 583-602页

作者： Jin Jin peng ye Liuquan Sun Institute of Applied Mathematics Academy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China School of Mathematical Sciences University of Chinese Academy of SciencesBeijing 100049China School of Statistics University of International Business and EconomicsBeijing 100029China

Missing covariate data arise frequently in biomedical *** this article,we propose a class of weighted estimating equations for the additive hazards regression model when some of the covariates are missing at ***-specific and subject-specific weights are incorporated into the formulation of weighted estimating *** results are established for estimating selection probabilities that cover both parametric and non-parametric modelling *** resulting estimators have closed forms and are shown to be consistent and asymptotically *** studies indicate that the proposed estimators perform well for practical *** application to a mouse leukemia study is illustrated.

关键词： additive hazards model censored data kernel smoothing missing at random weighted estimating equation

Deep learning models for spatial relation extraction in text

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Geo-Spatial Information Science 2023年第1期26卷 58-70页

作者： Kehan Wu Xueying Zhang Yulong Dang peng ye Key Laboratory of Virtual Geographic Environment(Nanjing Normal University) Ministry of EducationNanjingChina Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application NanjingChina Urban Planning and Development Institute Yangzhou UniversityYangzhouChina College of Civil Science and Engineering Yangzhou UniversityYangzhouChina

Spatial relation extraction is the process of identifying geographic entities from text and determining their corresponding spatial *** spatial relation extraction mainly uses rule-based pattern matching,supervised learning-based or unsupervised learning-based ***,these methods suffer from poor time-sensitive,high labor cost and high dependence on large-scale *** the development of pre-trained language models greatly alleviating the shortcomings of traditional methods,supervised learning methods incorporating pre-trained language models have become the mainstream relation extraction *** extraction and joint extraction,as the two most dominant ideas of relation extraction,both have obtained good performance on different datasets,and whether to share the contextual information of entities and relations is the main differences between the two *** this paper,we compare the performance of two ideas oriented to spatial relation extraction based on Chinese corpus data in the field of geography and verify which method based on pre-trained language models is more suitable for Chinese spatial relation *** fine-tuned the hyperparameters of the two models to optimize the extraction accuracy before the comparison *** results of the comparison experiments show that pipeline extraction performs better than joint extraction of spatial relation extraction for Chinese text data with sentence granularity,because different tasks have different focus on contextual information,and it is difficult to take account into the needs of both tasks by sharing contextual *** addition,we further compare the performance of the two models with the rule-based template approach in extracting topological,directional and distance relations,summarize the shortcomings of this experiment and provide an outlook for future work.

关键词： Spatial relation extraction pre-trained language model pipeline extraction joint extraction

Patterns and mechanism of wintertime penetrating fronts in the East China Sea

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Science China Earth Sciences 2024年第11期67卷 3500-3514页

作者： peng ye Daji HUANG Jiliang XUAN Shuangyan HE Ocean College Zhejiang UniversityZhoushan 316021China State Key Laboratory of Satellite Ocean Environment Dynamics Second Institute of OceanographyMinistry of Natural ResourcesHangzhou 310012China Guangxi Key Laboratory of Beibu Gulf Marine Resources Environment and Sustainable DevelopmentFourth Institute of OceanographyMinistry of Natural ResourcesBeihai 536015China

Penetrating fronts play an important role in the cross-shelf transport of terrestrial materials in the East China Sea(ECS). Using long-term satellite remote sensing data and numerical simulation data, the most likely period of occurrence and region of the penetrating fronts in the western ECS are analyzed in this study, and the evolutionary process and mechanism are also investigated. The statistical results of satellite-derived chlorophyll data from 1998 to 2022(25 years) reveal that penetrating fronts occur most frequently near 27°N in winter, with the frequencies of occurrence in January, February and March being 47%,65% and 64%, respectively. Backward Lagrangian tracer experiments demonstrate that the penetrating water near 27°N originate from three different regions. The core penetrating low-salinity water originates from the Zhejiang-Fujian coast, while the northern marginal water originates from the northern part of Taiwan Island, and the southern marginal water originates from the central Taiwan Strait. Mechanism analysis reveals that the core penetrating low-salinity water evolves in three successive ***, under the influence of the Zhejiang-Fujian Coastal Current driven by strong northeasterly winds, the low-salinity water along the Zhejiang-Fujian coast moves southwestward parallel to the coastline and accumulates in the western Taiwan ***, during the relaxation stage of the northeasterly wind, the northeastward Taiwan Strait Current strengthens, and the lowsalinity water accumulated in the western Taiwan Strait moves to the northeast. Third, when the northeastward-moving lowsalinity water runs into the Western Kuroshio Branch off the northeastern Taiwan Island, the low-salinity water is rapidly stretched eastward, and a significant penetrating front eventually appears. Since the synoptic northeasterly wind and the Western Kuroshio Branch are dominant dynamic factors in this region during wintertime, we believe that the synoptic winterti

关键词： Penetrating fronts Satellite-derived chlorophyll Lagrangian tracer experiments Synoptic-scale fluctuation Western Kuroshio Branch

N-Soliton Solutions of(2+1)-Dimensional Non-isospectral AKNS System

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Communications in Theoretical Physics 2008年第11期50卷 1181-1184页

作者： ZHANG Xiao-Xian SUN ye-peng Department of Mathematics Lanzhou City University Lanzhou 730070 China School of Statistics and Mathematics Shandong Economic University Jinan 250014 China

The bilinear form of the （2＋1）-dimensional non-isospectral AKNS system is derived. Its N-soliton solutions are obtained by using the Hirota method. As a reduction, a （2＋1）-dimensional non-isospectral Schrodinger... 详细信息

关键词： non-isospectral AKNS system Hirota method N-soliton solution non-isospectral Schrodinger equation

Site response in the Qionghai Basin in the Wenchuan earthquake

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Earthquake Engineering and Engineering Vibration 2013年第2期12卷 195-199页

作者： Wang Haiyun Xie Lili Wang Suyang ye peng Key Laboratory of Earthquake Engineering and Engineering Vibration Institute of Engineering MechanicsChina Earthquake Administration

Amplification effects of soil site response can significantly impact ground motions, and must be considered in the seismic fortification of buildings/structures to prevent or mitigate this potential seismic hazard. Utilizing acceleration time histories from the main shock of the Wenchuan earthquake recorded at four stations （i.e., one on bedrock and three on soil） in the Qionghai Basin, the site responses from three soil sites are studied by using the traditional spectral ratio method. The bedrock site is selected as a reference site. This study found that peak ground accelerations （PGAs） on the soil sites are much larger than on bedrock, with EW, NS and UD components of 3.96-6.58, 6.27-10.98, and 3.17-6.66 times those of the bedrock site, respectively. The amplification effects of the soil sites on ground motions in the frequency range of 0.1 Hz to 10 Hz are significant, depending on the thickness of the soil layer and the frequency content of the site. A significant amplification occurs with high frequency components of ground motion at shallow soil sites, and low and high frequency components of ground motion at intermediate soil sites.

关键词： site response traditional spectral ratio method acceleration time history Qionghai Basin Wenchuan earthquake

The Extension Dimension of Subcategories and Recollements of Abelian Categories

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Acta Mathematica Sinica,English Series 2024年第4期40卷 1042-1058页

作者： Xin MA ye Yang peng Zhao Yong HUANG College of Science Henan University of EngineeringZhengzhou 451191P.R.China Department of Mathematics Nanjing UniversityNanjing 210093P.R.China

We investigate the behavior of the extension dimension of subcategories of abelian categories under ***Λ',Λ,Λ"be art in algebras such that(modΛ',mod A,modΛ")is a recollement,and let D'and D"be subcategories of modΛand modΛ"*** any n,m≥0,under some conditions,we get dimΩ^(k)(D)≤dimΩ^(n)(D')+dimΩ^(m)(D")+1,where k=max{m,n}and D is the subcategory of modΛglued by D'and D";moreover,we give a sufficient condition such that the converse inequality holds *** applications,some results for Igusa-Todorov subcategories and syzygy finite sub categories are obtained.

关键词： Recollements extension dimension Igusa–Todorov subcategories syzygy finite subcategories