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Modeling stochastic noise in gene regulatory systems

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Frontiers of Electrical and Electronic Engineering in China 2014年第1期9卷 1-29页

作者： Arwen Meister chao Du ye Henry Li Wing Hung Wong Computational Biology Lab Bio-X Program Stanford University Stanford CA 94305 USA

The Master equation is considered the gold standard for modeling the stochastic mechanisms of gene regulation in molecular detail, but it is too complex to solve exactly in most cases, so approximation and simulation methods are essential. However, there is still a lack of consensus about the best way to carry these out. To help clarify the situation, we review Master equation models of gene regulation, theoretical approximations based on an expansion method due to N.G. van Kampen and R. Kubo, and simulation algorithms due to D.T. Gillespie and P. Langevin. Expansion of the Master equation shows that for systems with a single stable steady-state, the stochastic model reduces to a deterministic model in a first-order approximation. Additional theory, also due to van Kampen, describes the asymptotic behavior of multistable systems. To support and illustrate the theory and provide further insight into the complex behavior of multistable systems, we perform a detailed simulation study comparing the various approximation and simulation methods applied to synthetic gene regulatory systems with various qualitative characteristics. The simulation studies show that for large stochastic systems with a single steady-state, deterministic models are quite accurate, since the probability distribution of the solution has a single peak tracking the deterministic trajectory whose variance is inversely proportional to the system size. In multistable stochastic systems, large fluctuations can cause individual trajectories to escape from the domain of attraction of one steady-state and be attracted to another, so the system eventually reaches a multimodal probability distribution in which all stable steady- states are represented proportional to their relative stability. However, since the escape time scales exponentially with system size, this process can take a very long time in large systems.

关键词： gene regulation stochastic modeling simulation Master equation Gillespie algorithm Langevin equation

Discovering Cathodic Biocompatibility for Aqueous Zn–MnO_(2) Battery:An Integrating Biomass Carbon Strategy

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Nano-Micro Letters 2024年第6期16卷 111-126页

作者： Wei Lv Zilei Shen Xudong Li Jingwen Meng Weijie Yang Fang Ding Xing Ju Feng ye Yiming Li Xuefeng Lyu Miaomiao Wang Yonglan Tian chao Xu Institute of Energy Power Innovation North China Electric Power UniversityBeijing 102206People’s Republic of China Department of Power Engineering School of EnergyPower and Mechanical EngineeringNorth China Electric Power UniversityBaoding 071003People’s Republic of China Key Laboratory of RNA Biology Institute of BiophysicsChinese Academy of SciencesBeijing 100101People’s Republic of China Collaborative Innovation Center of Integrated Exploitation of Bayan Obo Multi‑Metal Resources Inner Mongolia University of Science and TechnologyBaotou 014010People’s Republic of China

Developing high-performance aqueous Zn-ion batteries from sustainable biomass becomes increasingly vital for large-scale energy storage in the foreseeable future.Therefore,γ-MnO_(2) uniformly loaded on N-doped carbon derived from grapefruit peel is successfully fabricated in this work,and particularly the composite cathode with carbon carrier quality percentage of 20 wt%delivers the specific capacity of 391.2 mAh g^(−1)at 0.1 A g^(−1),outstanding cyclic stability of 92.17%after 3000 cycles at 5 A g^(−1),and remarkable energy density of 553.12 Wh kg^(−1) together with superior coulombic efficiency of~100%.Additionally,the cathodic biosafety is further explored specifically through in vitro cell toxicity experiments,which verifies its tremendous potential in the application of clinical medicine.Besides,Zinc ion energy storage mechanism of the cathode is mainly discussed from the aspects of Jahn–Teller effect and Mn domains distribution combined with theoretical analysis and experimental data.Thus,a novel perspective of the conversion from biomass waste to biocompatible Mn-based cathode is successfully developed.

关键词： Aqueous Zn-ion batteries Biocompatibility Jahn-Teller effect Mn domains γ-MnO_(2)

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中国超大城市户籍人口转化的实证研究

地理学报 2022年第2期77卷 369-380页

作者：叶超杨东阳赵江南华东师范大学地理科学学院中国现代城市研究中心上海200241 河南大学黄河文明与可持续发展研究中心开封475001

"十四五"时期到2030年,加快流动人口市民化是推进新型城镇化和实现共同富裕的关键。中国户籍人口城镇化率与常住人口城镇化率相差约18%,老龄化压力与劳动力市场缺口使大城市纷纷出台"抢人"政策,市民化程度亟待提升,焦点在北上广深等超... 详细信息

"十四五"时期到2030年,加快流动人口市民化是推进新型城镇化和实现共同富裕的关键。中国户籍人口城镇化率与常住人口城镇化率相差约18%,老龄化压力与劳动力市场缺口使大城市纷纷出台"抢人"政策,市民化程度亟待提升,焦点在北上广深等超大城市。超大城市每年户籍人口转化数相差很大,学界对此缺乏研究,使得城市每年能"化"多少户籍人口成为重要学术问题。本文结合自然和社会两个视角,选取简明指标,构建可能—满意度模型,测算4个超大城市年均户籍城镇化转化缺口,构建面板数据模型实证分析超大城市户籍缺口的主导因素。影响超大城市户籍人口转化的因素主要是医疗、教育和供水。城乡治理亟需转变被动和僵化的制度安排,实现弹性的常态化治理。

关键词：城镇化市民化城市可持续治理中国

Low Resource Chinese Geological Text Named Entity Recognition Based on Prompt Learning

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Journal of Earth Science 2024年第3期35卷 1035-1043页

作者： Hang He chao Ma Shan ye Wenqiang Tang Yuxuan Zhou Zhen Yu Jiaxin Yi Li Hou Mingcai Hou State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation Institute of Sedimentary GeologyCollege of Computer Science and Cyber SecurityChengdu University of TechnologyChengdu 610059China Key Laboratory of Deep-Time Geography and Environment Reconstruction and Applications of Ministry of Natural Resources Chengdu University of TechnologyChengdu 610059China School of Information Engineering China University of Geosciences(Beijing)Beijing 100083China

Geological reports are a significant accomplishment for geologists involved in geological investigations and scientific research as they contain rich data and textual information.With the rapid development of science and technology,a large number of textual reports have accumulated in the field of geology.However,many non-hot topics and non-English speaking regions are neglected in mainstream geoscience databases for geological information mining,making it more challenging for some researchers to extract necessary information from these texts.Natural Language Processing(NLP)has obvious advantages in processing large amounts of textual data.The objective of this paper is to identify geological named entities from Chinese geological texts using NLP techniques.We propose the RoBERTa-Prompt-Tuning-NER method,which leverages the concept of Prompt Learning and requires only a small amount of annotated data to train superior models for recognizing geological named entities in low-resource dataset configurations.The RoBERTa layer captures context-based information and longer-distance dependencies through dynamic word vectors.Finally,we conducted experiments on the constructed Geological Named Entity Recognition(GNER)dataset.Our experimental results show that the proposed model achieves the highest F1 score of 80.64%among the four baseline algorithms,demonstrating the reliability and robustness of using the model for Named Entity Recognition of geological texts.

关键词： Prompt Learning Named Entity Recognition(NER) low resource geological text text information mining big data geology.

Overlaying welding technology and performance of axle tube remanufacturing

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Advances in Manufacturing 2013年第2期1卷 143-150页

作者： Shou-Xu Song Yun-Dong Liu Qing-Di Ke ye-chao Shen School of Mechanical and Auto Engineering Hefei University of Technology

Screw failure is one of the main scrap forms for rear axle tube, and thread turning after surfacing is a common means of remanufacturing. This paper takes rear axle tube as the main research topic, which is made of 40Mn and provided by an axle company. Manual electric arc welding, CO2 shielded arc welding and argon shielded arc welding are carried to overlay the damaged thread. The deposited metal consists of two welding material lays. Welding process and overlay properties are characterized by the test and analysis of microstructure, residual stress and hardness of surfacing layers. The results show that argon shielded arc welding is an effective method to repair the failure thread; its microstructure of fusion area is meticulous and uniform; its residual compressive stress （absolute value） of welding surface is the biggest among the three welding methods; its hardness curve is relatively fiat and appropriate for turning.

关键词： Surfacing Remanufacturing Metallographicstructure Residual stress Hardness

First total synthesis,antitumor evaluation and target identification of mornaphthoate E:A new tubulin inhibitor template acting on PI3K/Akt signaling pathway

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Acta Pharmaceutica Sinica B 2024年第5期14卷 2177-2193页

作者： Peipei Shan Tao ye Ying-De Tang Hui Song chao Wang Kongkai Zhu Feifei Yang Shi-Lei Zhang Pei-Wen Su Shuanhu Gao Hua Zhang Institute of Translational Medicine the Affiliated Hospital of Qingdao UniversityCollege of MedicineQingdao UniversityQingdao 266021China School of Biological Science and Technology University of JinanJinan 250022China Advanced Medical Research Institute Cheeloo College of MedicineShandong UniversityJinan 250012China College of Pharmaceutical Sciences Soochow UniversitySuzhou 215127China School of Chemistry and Molecular Engineering East China Normal UniversityShanghai 200062China

Mornaphthoate E(MPE)is a prenylated naphthoic acid methyl ester isolated from the roots of a famous Chinese medicinal plant Morinda officinalis and shows remarkable cytotoxicity against several human tumor cell lines.In the current project,the first total synthesis of(±)-MPE was achieved in seven steps and 5.6%overall yield.Then the in vitro anti-tumor activity of MPE was first assessed for both enantiomers in two breast cancer cells,with the levoisomer exerting slightly better potency.The in vivo anti-tumor effect was further verified by applying the racemate in an orthotopic autograft mouse model.Notably,MPE exerted promising anti-metastasis activity both in vitro and in vivo and showed no obvious toxicity on mice at the therapeutic dosage.Mechanistic investigations demonstrated that MPE acted as a tubulin polymerization stabilizer and disturbed the dynamic equilibrium of microtubules via regulating PI3K/Akt signaling.In conclusion,our work has provided a new chemical template for the future design and development of next-generation tubulin-targeting chemotherapies.

关键词： Mornaphthoate E Tubulin inhibitor Antitumor Anti-metastasis Breast cancer PI3K/Akt

Chlorogenic acid attenuates virulence factors and pathogenicity of Pseudomonas aeruginosa by regulating quorum sensing

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Chlorogenic acid attenuates virulence factors and pathogenic...

Experimental Characterization of Dual-Frequency Capacitively Coupled Plasma with Inductive Enhancement in Argon

华东六省一市生物化学与分子生物学会联盟2019年学术与...

作者： Hong Wang Weihua Chu chao ye Bruno Gaeta Huimin Tao Min Wang Zheng Qiu

Quorum sensing(QS) is a cell-to-cell communication that is used by bacteria to regulate collective behaviors.Quorum sensing controls virulence factor production in many bacterial species and it is regarded as an attractive target to combat bacterial pathogenicity,especially against antibiotic-resistant bacteria.Chlorogenic acid(CA),abundant in fruits,vegetables,and Chinese herbs,processes multiple activities.In this research,we explored its quorum sensing quenching activity.In Pseudomonas aeruginosa,CA significantly inhibited the formation of biofilm,the ability of swarming,and virulence factors including protease and elastase activities and rhamnolipid and pyocyanin production.CA showed similar inhibitory effects in Chromobacterium violaceum on its biofilm formation,swarming motility,chitinolytic activity and violacein production.We examined the expression of QS-related genes in P.aeruginosa and found these genes were all down regulated by CA treatment.Computational modeling revealed that CA can form hydrogen bonds with all three QS receptors.Caenorhabditis elegans and mouse infection models were employed to explore the anti-virulence ability of CA and its effect on pathogenesi sprocess in vivo.CA extended the survival period and reduced the quantity of P.aeruginosa in nematode gut,showing a moderate protective effect on C.elegans.In mice wound model,CA-treated groups showed an accelerating healing rate and the bacteria number in wound area was also decreased by CA treatment.It is suggested by our research that CA has potential to be used as an anti-virulence factor in P.aeruginosa infection.

关键词： chlorogenic acid quorum sensing inhibitor Pseudomonas aeruginosa anti-virulence

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Plasma Science and Technology 2013年第10期15卷 1002-1005页

作者： BAI Yang JIN Chenggang YU Tao WU Xuemei ZHUGE Lanjian NING Zhaoyuan ye chao GE Shuibing School of Physics Science and Technology Soochow University Suzhou 215006 China Analysis and Testing Center Soochow U-niversity Suzhou 215123 China

The dual-frequency capacitively coupled plasma （DF-CCP） with inductive enhancement system is a newly designed plasma reactor. Different from the conventional inductively coupled plasma （ICP） reactors, now a radio frequency （rf） power is connected to an antenna placed outside the chamber with a one-turn bare coil placed between two electrodes in DF-CCP. This paper gives a detailed description of its structure of discharges in this apparatus were made via a Moreover, investigations on some characteristics Langmuir probe.

关键词： one-turn bare coil inductively coupled plasm dual-frequency capacitivelycoupled plasma Langmuir probe electron energy probability function

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朝向人文主义的世界:段义孚的思想遗产

人文地理 2023年第2期38卷 44-50,96页

作者：叶超吴佩瑾华东师范大学地理科学学院上海200241

作为西方地理学的重要流派,人文主义地理学在20世纪80年代后发展相对乏力,在中国相关研究则更为迟滞。缺乏人文主义也使现实世界陷入多重危机。2022年,人文主义地理学奠基者段义孚的逝世使我们思考其思想遗产的问题,在中国如何发扬和实... 详细信息

作为西方地理学的重要流派,人文主义地理学在20世纪80年代后发展相对乏力,在中国相关研究则更为迟滞。缺乏人文主义也使现实世界陷入多重危机。2022年,人文主义地理学奠基者段义孚的逝世使我们思考其思想遗产的问题,在中国如何发扬和实践人文主义地理学变得尤其重要。无论对于学术、实践或生活,如何朝向人文主义已成为义孚之后的关键问题。本文通过重新梳理段义孚的学思历程及其与地方的关系,发现人文主义是学术与地方、自我与世界、思想与实践交互塑造的产物,它不仅是一种世界观,更是超越现实世界的探索与行动。朝向人文主义世界的主要路径在于构建真实自我与世界的关联,探寻地方价值与普世主义的平衡点,走出狭隘的学科本位主义以及超越凡俗生活的渴望与努力。

关键词：人文主义地理学经验地理学思想段义孚