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Network Analysis Reveals A Signaling RegulatoryLoop in PIK3CA-mutated Breast Cancer Predicting Survival Outcome

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Genomics, Proteomics & Bioinformatics 2017年第2期15卷 121-129页

作者： Shauna R. McGee Chabane Tibiche mark Trifiro Edwin wang National Research Council Canada Montreal QC H4P 2R2 Canada Department of Experimental Medicine McGill University Montreal QC H3A 2B2 Canada Center for Bioinformatics McGill University Montreal QC H3G OB1 Canada Lady Davis Institute for Medical Research of the Jewish General Hospital Montreal QC H3T 1E2 Canada Center for Health Genomics and Informatics Calgary AB T2N 4N1 Canada Department of Biochemistry & Molecular Biology/Medical Genetics/Oncology University of Calgary Cumming School of Medicine Calgary AB T2N 4N1 Canada Alberta Children's Hospital Research Institute Calgary AB T2N 4N1 Canada Arnie Charbonneau Cancer Research Institute Calgary AB T2N 4N1 Canada O'Brien Institute for Public Health Calgary AB T2N 4N1 Canada

Mutated genes are rarely common even in the same pathological type between cancer patients and as such, it has been very challenging to interpret genome sequencing data and difficult to predict clinical outcomes. PIK3 CA is one of a few genes whose mutations are relatively popular in tumors. For example, more than 46.6% of luminal-A breast cancer samples have PIK3 CA mutated, whereas only 35.5% of all breast cancer samples contain PIK3 CA mutations. To understand the function of PIK3 CA mutations in luminal A breast cancer, we applied our recentlyproposed Cancer Hallmark Network Framework to investigate the network motifs in the PIK3CA-mutated luminal A tumors. We found that more than 70% of the PIK3CA-mutated luminal A tumors contain a positive regulatory loop where a master regulator(PDGF-D), a second regulator(FLT1) and an output node(SHC1) work together. Importantly, we found the luminal A breast cancer patients harboring the PIK3 CA mutation and this positive regulatory loop in their tumors have significantly longer survival than those harboring PIK3 CA mutation only in their tumors. These findings suggest that the underlying molecular mechanism of PIK3 CA mutations in luminal A patients can participate in a positive regulatory loop, and furthermore the positive regulatory loop(PDGF-D/FLT1/SHC1) has a predictive power for the survival of the PIK3 CAmutated luminal A patients.

关键词： Network analysis PIK3CA mutation Network motif Breast cancer Genome sequencing Survival

Measuring the resilience of an airport network

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Chinese Journal of Aeronautics 2019年第12期32卷 2694-2705页

作者： Yanjun wang Jianming ZHAN Xinhua XU Lishuai LI Ping CHEN mark HANSEN College of Civil Aviation Nanjing University of Aeronautics and AstronauticsNanjing 210016China Department of Aeronautics and Astronautics Massachusetts Institute of TechnologyCambridge 02139USA Air Traffic Management Bureau Beijing 100012China Xiamen Airlines Xiamen 361006China Department of Systems Engineering and Engineering Management City University of Hong KongKowloonHong KongChina State Key Laboratory of Air Traffic Management System and Technology Nanjing 210000China Department of Civil and Environmental Engineering University of CaliforniaBerkeleyCA 94720USA

Resilience is the ability of a system to withstand and stay operational in the face of an unexpected disturbance or unpredicted changes. Recent studies on air transport system resilience focus on topology characteristics after the disturbance and measure the robustness of the network with respect to connectivity. The dynamic processes occurring at the node and link levels are often ignored. Here we analyze airport network resilience by considering both structural and dynamical aspects. We develop a simulation model to study the operational performance of the air transport system when airports operate at degraded capacity rather than completely shutting down. Our analyses show that the system deteriorates soon after disruptive events occur but returns to an acceptable level after a period of time. Static resilience of the airport network is captured by a phase transition in which a small change to airport capacity will result in a sharp change in system punctuality. After the phase transition point, decreasing airport capacity has little impact on system performance. Critical airports which have significant influence on the performance of whole system are identified, and we find that some of these cannot be detected based on the analysis of network structural indicators alone. Our work shows that air transport system’s resilience can be well understood by combining network science and operational dynamics.

关键词： Air transport Complex networks Network resilience Resilience indicator Transportation resilience

‘Face’and psychological processes of laid-off workers in transitional China

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Family Medicine and Community Health 2016年第3期4卷 51-63页

作者： Bingxin wang Kenneth mark Greenwood Faculty of Health Engineering and ScienceEdith Cowan UniversityWestern AustraliaAustralia James Cook University Singapore Singapore Department of Clinical Psychology Beijing Anding HospitalCapital Medical UniversityBeijingChina

Objective:The objective was to explore the psychological experiences of laid-off workers in contemporary transitional China and to formulate a theoretical model of ***:In-depth interviews of 26 laid-off workers were conducted and analysed using grounded theory ***:Four themes underline the psychological processes of these laid-off workers-feeling of loss,feeling of physical pain,feeling of fatalism,and final *** are characterized by Chinese culture and its philosophy-feeling of loss is dominated by their loss of face(diu mi-anzi),physical pain is a somatization of their mental painfulness,their fatalism is traced back to the Chinese ancient theocratic concept of Tian Ming,and their acceptance of reality to their final making face(zheng mianzi)is sourced from both Confucianism and ***:The psychological experience of laid-off workers(or unemployed workers)is likely to have varied manifestations in different cultural *** psychological processes of Chinese laid-off workers(or unemployed workers)might be different from those of laid-off workers in Western countries.A therapeutic intervention to cater for the needs of laid-off workers derived from the four themes might be effective.

关键词： laid-off workers unemployed workers state-owned enterprises psychological process China

Modelling of the Whole Process of a University Campus CHP Power Plant and Dynamic Performance Study

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International Journal of Automation and computing 2016年第1期13卷 53-63页

作者： Yue wang Akmaral Bermukhambetova Ji-Hong wang mark Donner Jun-Fu Lv Qi-Rui Gao School of Engineering University of Warwick Coventry CV4 7AL UK Laboratory of Intelligent Systems and Energy Emeiency Nazarbayev University Astana 010000 Kazakhstan Department of Thermal Engineering Tsinghua University Beijing 100084 China

Combined heat and power （CHP） refers to a process/system designed to utilize the waste or residual heat from a power generation process. Thus, a CHP plant can produce both electricity and heat. The nature of such a combination makes the process more complex than any single power generation process or boiler heating system. The paper focuses on modelling study and analysis of energy efficiency of the University of Warwick micro-CHP power plant. In this CHP modelling study, a gas turbine module is built to provide driving power and methane is used as fuel gas. Heat recovery system and auxiliary boiler modules are developed for thermal power generation. All the sub-systems are validated by comparing the simulation results with the operating data collected from the CHP plant. The dynamic performance of the key CHP process outputs is studied with respect to the variation of the input syngas stream, including electricity generation, thermal power output and water output temperature. Simplified controllers are also applied to the gas engineheat recovery subsystem and auxiliary boiler. Simulation results with/without feedback control are both analyzed. The study has highlighted the key factors which influence the plant performance and suggested the strategy for potential energy efficiency improvement.

关键词： Combined heat and power (CHP) dynamic performance gas engine boiler thermal power.

Immunocamouflage of latex surfaces by grafted methoxypoly(ethylene glycol)(mPEG):Proteomic analysis of plasma protein adsorption

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Science China(Life Sciences) 2012年第3期55卷 191-201页

作者： LE Yevgeniya LI Li wang DunCheng SCOTT mark D Canadian Blood Services Vancouver V6T 1Z3 Canada Centre for Blood Research University of British Columbia Vancouver V6T 1Z3 Canada Department of Pathology and Laboratory Medicine University of British Columbia Vancouver V6T 1Z3 Canada

Grafting of methoxypoly(ethylene glycol)(mPEG) to cells and biomaterials is a promising non-pharmacological immunomodulation ***,due to the labile nature of cells,surface-plasma interactions are poorly understood;hence,a latex bead model was *** of beads resulted in a density and molecular weight dependent decrease in total adsorbed protein with a net reduction from(159.9±6.4) ng cm-2 on bare latex to(18.4±0.8) and(52.3±5.3) ng cm-2 on PEGylated beads(1 mmol L-1 of 2 or 20 kD SCmPEG,respectively).SDS-PAGE and iTRAQ-MS analysis revealed differential compositions of the adsorbed protein layer on the PEGylated latex with a significant reduction in the compositional abundance of proteins involved in immune system ***,the biological efficacy of immunocamouflaged cells and materials is mediated by both biophysical obfuscation of antigens and reduced surface-macromolecule interactions.

关键词： PEGylation immunocamouflage iTRAQ mass spectrometry polystyrene latex protein adsorption proteomics meth-oxypoly(ethylene glycol) polymer

Id2 epigenetically controls CD8^(+)T-cell exhaustion by disrupting the assembly of the Tcf3-LSD1 complex

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Cellular & Molecular Immunology 2024年第3期21卷 292-308页

作者： Yiming Li Mingwei Han Haolin Wei Wan Huang Zhinan Chen Tianjiao Zhang Meirui Qian Lin Jing Gang Nan Xiuxuan Sun Shuhui Dai Kun wang Jianli Jiang Ping Zhu Liang Chen Department of Cell Biology of National Translational Science Center for Molecular Medicine and Department of Clinical Immunology of Xijing Hospital Fourth Military Medical UniversityXi’anShaanxi 710032China State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases GanzhouJiangxi341000Xi’anShaanxi 710032China School of Medicine Shanghai UniversityShanghai 200444China

CD8^(+)T-cell exhaustion is a state of dysfunction that promotes tumor progression and is marked by the generation of Slamf6^(+)progenitor exhausted(Tex^(prog))and Tim-^(3+)terminally exhausted(Tex^(term))*** of DNA binding protein 2(Id2)has been shown to play important roles in T-cell development and CD8^(+)T-cell ***,the role of Id2 in CD8^(+)T-cell exhaustion is ***,we found that Id2 transcriptionally and epigenetically regulates the generation of Texprog cells and their conversion to Texterm *** deletion of Id2 dampens CD8^(+)T-cell-mediated immune responses and the maintenance of stem-like CD8^(+)T-cell subpopulations,suppresses PD-1 blockade and increases tumor ***,through its HLH domain,Id2 binds and disrupts the assembly of the Tcf3-Tal1 transcriptional regulatory complex,and thus modulates chromatin accessibility at the Slamf6 promoter by preventing the interaction of Tcf3 with the histone lysine demethylase ***,Id2 increases the abundance of the permissive H3K4me2 mark on the Tcf3-occupied E-boxes in the Slamf6 promoter,modulates chromatin accessibility at the Slamf6 promoter and epigenetically regulates the generation of Slamf6+Texprog *** LSD1 inhibitor GSK2879552 can rescue the Id2 knockout phenotype in tumor-bearing *** of LSD1 increases the abundance of Slamf6^(+)Tim-3^(−)Tex^(prog) cells in tumors and the expression level of Tcf1 in Id2-deleted CD8+T *** study demonstrates that Id2-mediated transcriptional and epigenetic modification drives hierarchical CD8^(+)T-cell exhaustion,and the mechanistic insights gained may have implications for therapeutic intervention with tumor immune evasion.

关键词： Id2 T-cell exhaustion Epigenetic modification Immune evasion

Long-term agricultural activity affects anthropogenic soil on the Chinese Loess Plateau

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Journal of Arid Land 2017年第5期9卷 678-687页

作者： LI Xiaoyun wang Yiquan mark E REYNOLDS LI Xiaoping LU Xinwei School of Geography and Tourism Shaanxi Normal University Xi'an 710119 China SNNU-JSU Joint Research Center for Nano-environment Science and Health Xi'an 710119 China College of Resources and Environment Northwest A&F University Yangling 712100 China Stockbridge School of Agriculture University of Massachusetts Massachusetts 01003 USA

Anthropogenic activities largely influence the soil quality of agricultural fields and the composition of soil. Samples of typical anthropogenic Loutu soil in the Guanzhong area of the Loess Plateau, Shaanxi Province, China were collected and measured for soil compaction, bulk density, total organic carbon（TOC）, active organic carbon（AOC）, and soil enzyme activities to investigate spatial variations in soil quality. The results indicate that soil compaction and bulk density increased with increasing distance from the farm village, whereas soil TOC, AOC, and soil enzyme activities firstly increased and subsequently decreased with increasing distance from the farm village. All of the tested parameters presented clear concentric distribution. Vertically, soil compaction and bulk density in the topsoil were lower than those in the subsoil, but all other tested parameters in the topsoil were significantly higher than those in the subsoil. In addition, there was a significant positive correlation between organic carbon content and enzyme activities, confirming that the spatial distribution of Loutu soil characteristics has been affected by long-term anthropogenic activities to some extent. The results of this study imply that the use of farmyard manure and appropriate deep plowing are important and effective ways to maintain and improve soil quality.

关键词： anthropogenic soil spatial variation organic carbon enzyme activity soil quality

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带有时间戳的着色逻辑Petri网

计算机科学与探索 2024年第7期18卷 1776-1791页

作者：王嘉丰徐贤华东理工大学信息科学与工程学院上海200237

针对扩展着色逻辑Petri网存在的表达能力弱以及适用范围窄的问题,提出了一个新的Petri网模型,即带有时间戳的着色逻辑Petri网。首先,将颜色进行实例化以及将变量用于构建有向边上的表达式使得模型能够传递复杂的数据流。其次,引入全局... 详细信息

针对扩展着色逻辑Petri网存在的表达能力弱以及适用范围窄的问题,提出了一个新的Petri网模型,即带有时间戳的着色逻辑Petri网。首先,将颜色进行实例化以及将变量用于构建有向边上的表达式使得模型能够传递复杂的数据流。其次,引入全局时间以及令牌的时间戳等概念为变迁使能规则增加时间上的约束,使得模型能够用于模拟实时系统。再次,定义库所约束函数并为变迁使能规则增加输出库所上的约束,使得模型能够适用于存储资源有限的场景。接着,提出基于逻辑变迁输入输出矩阵的匹配法,降低逻辑输入变迁的使能判定计算开销并简化逻辑输出变迁的使能判定计算过程。然后,重新定义适用于三类变迁的使能判定条件以及适用于三类库所的标记更新方法,解决原有模型语义在新模型中不适用的问题。最后,通过实例说明新的Petri网模型具有更强的表达能力和适用范围,它能够适用于传递复杂数据流、存储资源有限、实时的且包含批处理选择结构的系统。

关键词： Petri网时间戳着色令牌逻辑变迁

Laser directed energy deposited, ultrafine-grained functional titanium-copper alloys tailored for marine environments: Antibacterial and anti-microbial corrosion studies

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Journal of Materials Science & Technology 2023年第35期166卷 21-33页

作者： Jiaqi Li Duyao Zhang Xiaobo Chen Dake Xu Dong Qiu Fuhui wang mark Easton Shenyang National Laboratory for Materials Science Northeastern UniversityShenyang 110819China Key Laboratory for Anisotropy and Texture of Materials(Ministry of Education) School of Materials Science and EngineeringNortheastern UniversityShenyang 110819China School of Engineering Centre for Additive ManufacturingRMIT UniversityMelbourneVIC 3000Australia

The microorganism-rich nature of the ocean imposes great challenges to the structural integrity of met-als over their service lifespan,including titanium(Ti)alloys,which are usually prone to microbiologically influenced corrosion(MIC).So,multifunctional anti-MIC Ti alloys need to be developed and *** paper investigates the effect of copper(Cu)concentration on the MIC resistance of a series of additively manufactured,ultrafine-grained Ti-x Cu(x=3.5,6.5 and 8.5 in wt.%)*** dependence of the cor-rosion resistance and MIC resistance on the Cu concentration of Ti-Cu alloy is interpreted considering all conceivable *** mechanisms for excellent corrosion resistance of Ti-Cu alloy in seawater are attributed to the strong passive film and small surface potential difference between ***-tural characterization reveals that uniformly distributed,nanosized Ti_(2) Cu phase led to increased reactive oxygen species in the bacterial membrane,which is the root reason for the superb anti-bacterial property(99.2%)for *** to pure Ti and Ti-6Al-4V,Ti-8.5Cu alloy features both high strength(yield stress>1000 MPa)and the best MIC resistance(97.5%).The combination of such balanced properties enables this functional 3D printed Ti-Cu alloy to become an ideal material for load-bearing applications in the marine environment.

关键词： Multifunctional titanium alloys Additive manufacturing Ultrafine grains Microbiologically influenced corrosion resistance Mechanical property Antibacterial property