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redPATH:Reconstructing the Pseudo Development Time of Cell Lineages in Single-cell RNA-seq Data and Applications in Cancer

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Genomics, Proteomics & Bioinformatics 2021年第2期19卷 292-305页

作者： Kaikun Xie zehua liu Ning Chen Ting Chen Institute for Artificial Intelligence State Key Lab of Intelligent Technology and SystemsDepartment of Computer Science and TechnologyTsinghua UniversityBeijing 100084China Tsinghua-Fuzhou Institute of Digital Technology Beijing National Research Center for Information Science and TechnologyTsinghua UniversityBeijing 100084China Center for Computational and Integrative Biology Massachusetts General HospitalHarvard Medical SchoolBostonMA 02114USA Department of Molecular Biology Massachusetts General HospitalHarvard Medical SchoolBostonMA 02114USA Broad Institute of Massachusetts Institute of Technology and Harvard CambridgeMA 02142USA

The recent advancement of single-cell RNA sequencing(scRNA-seq)technologies facilitates the study of cell lineages in developmental processes and *** this study,we developed a computational method,called redPATH,to reconstruct the pseudo developmental time of cell lineages using a consensus asymmetric Hamiltonian path ***,we developed a novel approach to visualize the trajectory development and implemented visualization methods to provide biological *** validated the performance of redPATH by segmenting different stages of cell development on multiple neural stem cell and cancer datasets,as well as other single-cell transcriptome *** particular,we identified a stem cell-like subpopulation in malignant glioma *** cells express known proliferative markers,such as GFAP,ATP1A2,IGFBPL1,and ALDOC,and remain silenced for quiescent markers such as ***,we identified MCL1 as a significant gene that regulates cell apoptosis and CSF1R for reprogramming macrophages to control tumor *** conclusion,redPATH is a comprehensive tool for analyzing scRNA-seq datasets along the pseudo developmental *** is available at https://***/tinglabs/redPATH.

关键词： Single-cell pseudotime reconstruction Consensus Hamiltonian path Cell differentiation Cell proliferation Cell development and diseases

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The effect of porosity on the mechanical properties of 3D-printed triplyperiodic minimal surface (TPMS) bioscaffold

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Bio-Design and Manufacturing 2019年第4期2卷 242-255页

作者： Zizhen Cai zehua liu Xiaodong Hu Hekun Kuang Jinsong Zhai Department of Materials Engineering Faculty of Applied ScienceUniversity of British Columbia2329 West MallVancouverBC V6T 1Z4Canada

Prevailing tissue degeneration caused by musculoskeletal maladies poses a great demand on bioscaffolds,which are artificial,biocompatible structures implanted into human bodies with appropriate mechanical *** advances in additive manufacturing,i.e.,3D printing,facilitated the fabrication of bioscaffolds with unprecedented geometrical complexity and size flexibility and allowed for the fabrication of topologies that would not have been achieved *** our work,we explored the effect of porosity on themechanical properties of a periodic cellular *** structure was derived from the mathematically created triply periodic minimal surface(TPMS),namely the Sheet-Diamond ***,we employed a series of software including MathMod,Meshmixer,Netfabb and Cura to design the ***,we utilized additive manufacturing technology to fabricate the cellular structures with designated ***,we performed compressive testing to deduce the mechanical properties of each cellular *** showed that,in comparison with the highporosity group,the yield strength of the low-porosity group was 3 times higher,and the modulus was 2.5 times *** experiments revealed a specific relationship between porosity and Young’s modulus of PLA-made Sheet-Diamond TPMS ***,it was observed that the high-and low-porosity structures failed through distinctive mechanisms,with the former breaking down via buckling and the latter via micro-fracturing.

关键词： Additive manufacturing(AM/3D printing) Triply periodic minimal surface(TPMS) Bioscaffolding

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Roles and Functions of Tourism Destinations in Tourism Region of South Anhui:A Tourist Flow Network Perspective

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Chinese Geographical Science 2012年第6期22卷 755-764页

作者： liu Fajian ZHANG Jinhe ZHANG Jie CHEN Dongdong liu zehua LU Song School of Geographic Science Nanjing University Nanjing 210093 China School of Business Anhui University Hefei 230601 China Anhui Broadcasting Movie and Television College Hefei 230011 China College of Territorial Resources and Tourism Anhui Normal University Wuhu 241003 China

Theoretic and practical significance has been highlighted in the research of the roles and functions of destinations,as destinations are restricted by the spatial structure based on tourist flow network from the perspective of *** article conducted an empirical analysis for Tourism Region of South Anhui(TRSA) and revealed the necessity and feasibility of studying the roles and functions of destinations from tourist flow network's *** automorphic equivalence analysis and centrality analysis were used to classify 16 destinations in TRSA into six role types:tourist flow distribution center,hub of tourist flows,passageway destination,common touring destination,attached touring destination,and nearly isolated *** suggestions were given on suitable infrastructure construction and destinations service designs according to their functions in *** destination role positioning was based on tourist flow network structure in integral and macroscopic *** provided an important reference for the balanced and harmonious development of all the destinations of *** addition,this article verified the applicability of social network analysis on tourist flow research in local scale,and expanded this method to destination role and function positioning.

关键词： tourist flow network equivalence model roles functions centrality analysis Tourism Region of South Anhui

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Duple-EDA and sample density balancing

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Science in China(Series F) 2009年第9期52卷 1640-1650页

作者： CAI YunPeng XU Hua SUN XiaoMin JIA PeiFa liu zehua State Key Laboratory on Intelligent Technology and Systems Tsinghua National Laboratory for Information Science and Technology Department of Computer Science and Technology Tsinghua University Beijing 100084 China School of Computer Engineering Nanyang Technological University Singapore 639798 Singapore

In this paper, a new method is proposed to overcome the problem of local optima traps in a class of evolutionary algorithms, called estimation of distribution algorithms （EDAs）, in real-valued function optimization. The Duple-EDA framework is proposed in which not only the current best solutions but also the search history are modeled, so that long-term feedback can be taken into account. Sample Density Balancing （SDB） is proposed under the framework to alleviate the drift phenomenon in EDA. A selection scheme based on Pareto ranking considering both the fitness and the historical sample density is adopted, which prevents the algorithm from repeatedly sampling in a small region and directs it to explore potentially optimal regions, thus helps it avoid being stuck into local optima. An MBOA （mixed Bayesian optimization algorithm） version of the framework is implemented and tested on several benchmark problems. Experimental results show that the proposed method outperforms a standard niching method in these benchmark problems.

关键词： evolutionary computation estimation of distribution algorithm Boltzmann selection

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Crosstalk in polymer microelectrode arrays

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Nano Research 2021年第9期14卷 3240-3247页

作者： Yi Qiang Wen Gu zehua liu Shanchuan Liang Jae Hyeon Ryu Kyung Jin Seo Wentai liu Hui Fang Department of Electrical and Computer Engineering Northeastern UniversityBostonMA 02115USA Department of Bioengineering University of CaliforniaLos AngelesLos AngelesCA 90095USA Department of Bioengineering Northeastern UniversityBostonMA 02115USA

Thin-film polymer microelectrcxje arrays(MEAs)facilitate the high-resolution neural recording with its superior mechanical ***,the densely packed electrodes and interconnects along with the ultra-thin polymeric encapsulation/substrate layers give rise to non-negligible crosstalk,which could result in severe interference in the neural signal *** to the lack of standardized characterization or modeling of crosstalk in neural electrode arrays,to date,crosstalk in polymer MEAs remains poorly *** this work,the crosstalk between two adjacent polymer microelectrodes is measured experimentally and modeled using equivalent ***,this study demonstrated a two-well measuring platform and systematically characterized the crosstalk in polymer microelectrodes with true isolation of the victim channel and precise control of its grounding condition.A simple,unified equation from detailed circuit modeling was proposed to calculate the crosstalk in different *** element analysis(FEA)analysis was conducted further to explore the crosstalk in more aggressively scaled polymer electrode *** addition to standardizing neural electrode array crosstalk characterization,this study not only reveals the dependence of the crosstalk in polymer MEAs on a variety of key device parameters but also provides general guidelines for the design of thin polymer MEAs for high-quality neural signal recording.

关键词： crosstalk effect flexible microelectrodes equivalent circuit modelling finite element analysis polymer

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Vertically stacked holey graphene/polyaniline heterostructures with enhanced energy storage for on-chip micro-supercapacitors

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Nano Research 2016年第4期9卷 1012-1021页

作者： Xiaocong Tian Bei Xiao Xu Xu Lin Xu zehua liu Zhaoyang Wang Mengyu Yan Qiulong Wei Liqiang Mai State Key Laboratory of Advanced Technology for Materials Synthesis and Processing Wuhan University of Technology Wuhan 430070 China Department of Chemistry and Biochemistry University of California Los Angeles California 90095 USA Department of Chemistry and Chemical Biology Harvard University Cambridge Massachusetts 02138 USA These authors contributed equally to this work.

Planar micro-supercapacitors （MSCs） have drawn extensive research attention owing to their unique structural design and size compatibility for microelectronic devices. Graphene has been widely used to improve the performance of microscale electrochemical capacitors. However, investigations of an intrinsic electrochemical mechanism for graphene-based microscale devices are still not sufficient. Here, micro-supercapacitors with various typical architectures are fabricated as models to study the graphene effect, and their electrochemical performance is also evaluated. The results show that ionic accessibility and adsorption are greatly improved after the introduction of the holey graphene intermediate layer. This study provides a new route to understand intrinsic electrochemical behaviors and possesses exciting potential for highly efficient on-chip micro-energy storage.

关键词： micro-supercapacitors holey graphene heterostructures ionic accessibility intrinsic electrochemical behaviors

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Capacitance and voltage matching between MnO2 nanoflake cathode and Fe2O3 nanoparticle anode for high-performance asymmetric micro-supercapacitors

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Nano Research 2017年第7期10卷 2471-2481页

作者： zehua liu Xiaocong Tian Xu Xu Liang He Mengyu Yan Chunhua Han Yan Li Wei Yang Liqiang Mai State Key Laboratory of Advanced Technology for Materials Synthesis and Processing Wuhan University of Technology Wuhan 430070 China Department of Chemistry University of California Berkeley CA 94720 USA

Planar micro-supercapacitors show great potential as the energy storage unit in miniaturized electronic devices. Asymmetric structures have been widely inves- tigated in micro-supercapacitors, and carbon-based materials are commonly applied in the electrodes. To integrate different metal oxides in both electrodes in micro-supercapacitors, the critical challenge is the pairing of different faradic metal oxides. Herein, we propose a strategy of matching the voltage and capadtance of two faradic materials that are fully integrated into one high-performance asymmetric micro-supercapacitor by a facile and controllable fabrication process. The fabricated micro-supercapacitors employ MnO2 as the positive active material and Fe203 as the negative active material, respectively. The planar asymmetric micro-supercapacitors possess a high capacitance of 60 F-cm-3, a high energy density of 12 ***-3, and a broad operation voltage range up to 1.2 V.

关键词： MnO2 nanoflake Fe2O3 nanoparticle asymmetric electrodes micro-supercapacitors

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Design, Synthesis and Antitumor Activity of Pyrrolopyrazinone-chalcone Hybrids

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Chemical Research in Chinese Universities 2014年第4期30卷 624-631页

作者： MENG Ying ZHANG Hongwei liu zehua ZENG Shanchao SUN Chiyu ZHANG Lijuan ZHAO Mingming WANG Guan JIANG Mengying SHI Wei SONG Hongrui 10016 P. R. China Key Laboratory for Molecular Enzymology & Engineering Ministry of Education Jilin University Changchun 130012 P. R. China

A series of pyrrolopyrazinone-chalcone hybrids（12a-12q） was designed,synthesized and screened for their antitumor activity against SKOV-3,A549 and HeLa cell lines in *** with the pyrrolopyrazinone（10a） and 5-fluorouracil（5-FU）,nearly all the tested compounds showed significantly-improved antitumor *** most promising compounds 12e and 12k（IC50=0.25 and 0.88 μmol/L） respectively show activities of 123and 35 times that of compound 10a（IC50=30.74 μmol/L） against HeLa cell *** result reveals that the presence of chalcone moiety is beneficial to their activity and selectivity.

关键词： Pyrrolopyrazinone-chalcone hybrid Antitumor Marine sponge Combination principle

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关于历史是非认识的几个问题

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史学月刊 2016年第1期 5-13页

作者：刘泽华南开大学中国社会史研究中心教授天津300350

历史学是一种认识学,一方面求"映像",另一方面认识者的主观因素不可避免地掺入;历史本身不会变化,但它又是活的,它的影响像血液流动一样,或多或少流传于后世,并与新的因素形成再组合;对历史进行认识的人也在流动和变化。因此历史认识中... 详细信息

历史学是一种认识学,一方面求"映像",另一方面认识者的主观因素不可避免地掺入;历史本身不会变化,但它又是活的,它的影响像血液流动一样,或多或少流传于后世,并与新的因素形成再组合;对历史进行认识的人也在流动和变化。因此历史认识中的"是非"也在不断地更化,所以"是非"观基本上是个体性的。由于个性包含着某些共性,或多或少被另外一些人采纳,由此也会形成群体性的共识。历史"是非"靠真实的、全面的史料支撑,任何行政权力的判定也必须靠此来检验。

关键词：历史是非认识历史规律阶级一共同体丛林法则

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从观念“定势”中走出来的尝试——研讨历史的思想自述之三

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首都师范大学学报（社会科学版） 2013年第5期 1-7页

作者：刘泽华南开大学中国社会史研究中心

《先秦政治思想史》的撰写(1979—1983年),是其时作者从传统思想"定势"中走出来的一次尝试。作者之所以将中国政治思想史作为研究对象,是希望反思"文革"和专制主义的影响,重新核检中国的政治观念。该书对若干历史理论进行探索,提出政治... 详细信息

《先秦政治思想史》的撰写(1979—1983年),是其时作者从传统思想"定势"中走出来的一次尝试。作者之所以将中国政治思想史作为研究对象,是希望反思"文革"和专制主义的影响,重新核检中国的政治观念。该书对若干历史理论进行探索,提出政治思想既有阶级性也有社会性、君主专制是政治思想的主体等观点,探讨价值、是非的判定标准,尝试以人性论等作为分析的起点,拓宽政治思想研究对象的内容。

关键词： 80年代史学《先秦政治思想史》历史理论

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