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Continuous and Discrete Similarity Coefficient for Identifying Essential Proteins Using Gene Expression Data

Big Data Mining and Analytics 2023年第2期6卷 185-200页

作者： Jiancheng Zhong zuohang qu Ying Zhong Chao Tang Yi Pan College of Information Science and Engineering Hunan Normal UniversityChangsha 410081China Faculty of Computer Science and Control Engineering Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences ShenzhenGuangzhou 518055China

Essential proteins play a vital role in biological processes,and the combination of gene expression profiles with Protein-Protein Interaction(PPI)networks can improve the identification of essential ***,gene expression data are prone to significant fluctuations due to noise interference in topological *** this work,we discretized gene expression data and used the discrete similarities of the gene expression spectrum to eliminate noise *** then proposed the Pearson Jaccard coefficient(PJC)that consisted of continuous and discrete similarities in the gene expression *** the graph theory as the basis,we fused the newly proposed similarity coefficient with the existing network topology prediction algorithm at each protein node to recognize essential *** strategy exhibited a high recognition rate and good *** validated the new similarity coefficient PJC on PPI datasets of Krogan,Gavin,and DIP of yeast species and evaluated the results by receiver operating characteristic analysis,jackknife analysis,top analysis,and accuracy *** with that of node-based network topology centrality and fusion biological information centrality methods,the new similarity coefficient PJC showed a significantly improved prediction performance for essential proteins in DC,IC,Eigenvector centrality,subgraph centrality,betweenness centrality,closeness centrality,NC,PeC,and *** also compared the PJC coefficient with other methods using the NF-PIN algorithm,which predicts proteins by constructing active PPI networks through dynamic gene *** experimental results proved that our newly proposed similarity coefficient PJC has superior advantages in predicting essential proteins.

关键词： Protein-Protein Interaction(PPI)network continuous and discrete similarity coefficient essential proteins

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基于动态网络切分的关键蛋白质预测方法

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计算机研究与发展 2022年第7期59卷 1569-1588页

作者：钟坚成方卓瞿佐航钟颖彭玮潘毅湖南师范大学信息科学与工程学院长沙410081 昆明理工大学信息工程与自动化学院昆明650500 中国科学院深圳理工大学计算机与控制工程学院广东深圳518055

关键蛋白质作为蛋白质中的关键物质,不仅对研究细胞生长调控有着重要意义,也为更深层次的疾病研究奠定理论基础.目前,针对关键蛋白质的识别方法大多为应用基因表达信息和蛋白质相互作用网络,提出识别关键蛋白质的静态和动态网络方法,但... 详细信息

关键蛋白质作为蛋白质中的关键物质,不仅对研究细胞生长调控有着重要意义,也为更深层次的疾病研究奠定理论基础.目前,针对关键蛋白质的识别方法大多为应用基因表达信息和蛋白质相互作用网络,提出识别关键蛋白质的静态和动态网络方法,但这些方法未考虑基因表达调控的周期性规律,无法准确地刻画受基因周期调控的蛋白质网络.为此,在基因表达动态性的基础上引入了基因周期性表达的概念,提出了一种动态网络切分方法.该方法通过构建基因“活性”表达矩阵,利用切分后的“活性”表达矩阵作用于蛋白质相互作用网络,从而形成蛋白质周期子网络,最终综合各周期子网络来衡量蛋白质结点在网络中的重要性.实验结果表明,该方法在酵母、大肠杆菌和人类膀胱数据中可以有效地提高关键蛋白质预测率.

关键词：关键蛋白质蛋白质相互作用网络动态网络周期子网络动态基因表达

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Time-Periodic Solutions to quasilinear Hyperbolic Systems on General Networks

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Chinese Annals of Mathematics,Series B 2024年第1期45卷 41-72页

作者： Peng qu School of Mathematical Sciences Fudan UniversityShanghai 200433China

For quasilinear hyperbolic systems on general networks with time-periodic boundary-interface conditions with a dissipative structure,the existence and stability of the time-periodic classical solutions are discussed.

关键词： Time-periodic solution quasilinear hyperbolic system General net-work Classical solution Asymptotic stability

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Flat jet electrochemical milling of TC4 alloy with tailoring backward parallel flow

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Chinese Journal of Aeronautics 2024年第4期37卷 574-592页

作者： Huanghai KONG Ningsong qu College of Mechanical and Electrical Engineering Nanjing University of Aeronautics and AstronauticsNanjing 210016China

In flat jet electrochemical milling, the electrolyte forms a backward parallel flow after impacting the workpiece, resulting in a weak current density distribution on the workpiece. Poor surface quality usually occurs on the machined titanium alloy surface because it inevitably suffers from the weak current density. In this study, a method of flat jet electrochemical milling with tailoring the backward parallel flow was proposed to eliminate the negative effects caused by the weak current density. Multiphysics simulations are carried out to comprehend the mechanism of flat jetEC milling with tailoring backward parallel flow and better construct the novel tool *** on flat jet electrochemical milling of TC4 alloy with and without tailoring backward parallel flow are conducted. The results reveal that, compared with flat jet electrochemical milling without tailoring backward parallel flow, the recommended tool reduces the surface roughness by86% to 93%, and improves the material removal rate by 93% to 163% with different feed ***, the recommended tool is more conducive to maintaining the inherent hardness of the material. Finally, a surface with low Sa of 0.37 μm is obtained.

关键词： Flat jet electrochemical milling TC4 alloy Surface roughness Micro-hardness Material removal rate

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Pathways toward a pollution-free planet and challenges

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Frontiers of Environmental Science & Engineering 2024年第6期18卷 3-8页

作者： Jiuhui qu Jiaping Chen School of Environment Tsinghua UniversityBeijing 100084China College of Chemistry and Environmental Engineering Shenzhen UniversityShenzhen 518060China

The mission of“Establishment of Zero-Pollution Earth”defined by United Nations Environment Programme aims at creation of a clean,safe and prosperous home for all human *** is of rational choice from each individual to protect our environment and demonstrates our great ambition to achieve our *** key message given in this article is that,zero pollution does not mean no discharge of pollutants and instead it can be achievable through optimizing and controlling a sound balance between pollutants discharge and capacities of decontamination through treatment and natural environmental accumulation,which can be termed as“Principle of Equilibrium”between pollution and *** on this principle,we propose and illustrate several key factors and synergistic pathways toward a pollution-free planet:quantitative determination on purification and wastewater;source control through green measures;minimization of negative side-effects;precise management through digitalized systems;and keeping sound balance between pollutants and natural *** should be noted that we would face a series of difficulties and challenges in moving forward to“Zero-Pollution Earth”.We should further develop theories,principles and tools to achieve the balance between quantity of pollutants and decontamination *** should work together to break through the bottleneck limited by“Principle of equilibrium”to establish new environmental remediation systems leading to“Zero-Pollution Earth”.

关键词： Wastewater treatment Resources Recovery Greenhouse gases Energy Pollution-free

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Different Types of Bone Fractures Observed by Terahertz Time-Domain Spectroscopy

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Acta Mechanica Solida Sinica 2024年第3期37卷 468-477页

作者： Minghao Zhang Xianjia Meng Zhiyong Wang Chuanyong qu Chuan qu Donghui Fu Department of Mechanics Tianjin UniversityTianjin300072China Tianjin Key Laboratory of Modern Engineering Mechanics Tianjin300072China

Microcracks are common in compact bone,but their continued propagation can lead to macroscopic *** microcracks cannot be visualized radiographically,necessitating alternative noninvasive methods to identify excessive microcracking and prevent *** this study,terahertz time-domain spectroscopy(THz-TDS)was used to examine bone interiors near cracks resulting from loading in bovine tibia *** loading configurations,such as impact,quasi-static loading,and fatigue loading,known to induce different types of micro-scale damage,were *** values of refractive index and absorption coefficient of the bone samples were then determined from the THz-TDS spectra acquired before loading and after *** study revealed that different loading configurations led to varying terahertz optical coefficients associated with various types of bone ***,the refractive index notably increased under fatigue loading but remained relatively stable during quasi-static *** absorption coefficient of bone decreased only under fatigue ***,samples were subjected to axial and radial impacts without sustaining *** indicated that in the undamaged state,the change in refractive index was smaller compared to after impact failure,while the change in absorption coefficient remained consistent after *** radial impact loading,changes in refractive index and absorption coefficient were significantly more pronounced than under axial *** to loading,the measured value of refractive index was 2.72±0.11,and the absorption coefficient was 6.33±0.09 mm^(−1)at 0.5 THz.

关键词： Terahertz time-domain spectroscopy Bone Microdamage Noninvasive method

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Physiological and psychological responses to tended plant communities with varying color characteristics

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Journal of Forestry Research 2024年第1期35卷 183-201页

作者： Siyuan Zheng Yanzhen Zhou Haiyan qu School of Architecture and Urban Planning Shenyang Jianzhu UniversityShenyang 110168People’s Republic of China

Exposure to plants has been reported to promote health and reduce stress,and plant color has direct impacts on physical and mental *** used images of common types of tended plant communities in Shenyang,China,with combinations of yellow,green,and red foliage,as experimental stimuli.A total of 27 images were used as visual *** used electroencephalography to measureαwave activity(8-13 Hz)in 40 subjects while they viewed visual *** data were combined with subjective questionnaire data to analyze the relaxing effect of images of tended plant communities with different color types and proportions on *** results revealed that,although there were slight differences between the electroencephalography and psychological findings,women were significantly more relaxed than men after viewing the *** and psychological responses varied with the types and proportions of colors in the tended plant communities:those of foliage with combinations of two or three colors induced stronger responses than images with a single ***,(1)for one-color plant communities,green or yellow plant communities induced a stronger relaxation effect than red plant communities;(2)for two-color plant communities,the optimal color proportion was 55%+45%,and the green+yellow and green+red color combinations induced a stronger relaxation effect;(3)for three-color plant communities,the relaxation effect was strongest when the color proportion was 55%green+25%yellow+20%*** data would provide a plant color matching in future plant landscape design,which may be helpful for creating healthy and relaxing environments.

关键词： Plant community Color type Color ratio Electroencephalography Subjective questionnaire

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Digital Twin Technology of Human-Machine Integration in Cross-Belt Sorting System

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Chinese Journal of Mechanical Engineering 2024年第2期37卷 195-212页

作者： Yanbo qu Ning Zhao Haojue Zhang School of Mechanical Engineering University of Science and Technology BeijingBeijing 100083China Institute of Microelectronics of the Chinese Academy of Sciences Beijing 100029China Wayzim Technology Co. LtdWuxi 214108China Business School Beijing Technology and Business UniversityBeijing 100048China

The Chinese express delivery industry processes nearly 110 billion items in 2022,averaging an annual growth rate of 200%.Among the various types of sorting systems used for handling express items,cross-belt sorting systems stand out as the most ***,despite their high degree of automation,the workload for operators has intensified owing to the surging volume of express *** the era of Industry 5.0,it is imperative to adopt new technologies that not only enhance worker welfare but also improve the efficiency of cross-belt *** a balance between efficiency in handling express items and operator well-being is *** twin technology offers a promising solution in this respect.A realization method of a human-machine integrated digital twin is proposed in this study,enabling the interaction of biological human bodies,virtual human bodies,virtual equipment,and logistics equipment in a closed loop,thus setting an operating *** technologies in the proposed framework include a collection of heterogeneous data from multiple sources,construction of the relationship between operator fatigue and operation efficiency based on physiological measurements,virtual model construction,and an online optimization module based on real-time *** feasibility of the proposed method was verified in an express distribution center.

关键词： Industry 5.0 Cross-belt sorting system Human-machine integrated Digital twin Online optimization

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Bacterial Cellulose/Zwitterionic Dual-network Porous Gel Polymer Electrolytes with High Ionic Conductivity

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Journal of Wuhan University of Technology(Materials Science) 2024年第3期39卷 596-605页

作者：侯朝霞 WANG Haoran qu Chenying Liaoning Province Key Laboratory of Micro-nano Materials Research and Development School of Mechanical EngineeringShenyang UniversityShenyang 110044China

Bacterial cellulose(BC)was innovatively combined with zwitterionic copolymer acrylamide and sulfobetaine methacrylic acid ester[P(AM-co-SBMA)]to build a dual-network porous structure gel polymer electrolytes(GPEs)with high ionic *** dual network structure BC/P(AM-co-SBMA)gels were formed by a simple one-step polymerization *** results show that ionic conductivity of BC/P(AM-co-SBMA)GPEs at the room temperature are 3.2×10^(-2) S/cm@1 M H_(2)SO_(4),4.5×10^(-2) S/cm@4 M KOH,and 3.6×10^(-2) S/cm@1 M NaCl,*** active carbon(AC)as the electrodes,BC/P(AM-co-SBMA)GPEs as both separator and electrolyte matrix,and 4 M KOH as the electrolyte,a symmetric solid supercapacitors(SSC)(AC-GPE-KOH)was assembled and *** specific capacitance of AC electrode is 173 F/g and remains 95.0%of the initial value after 5000 cycles and 86.2%after 10,000 cycles.

关键词： bacterial cellulose zwitterion gel polymer electrolytes ionic conductivity dual-network structure

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Effects of wind speed,underlying surface,and seed morphological traits on the secondary seed dispersal in the Tengger Desert,China

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Journal of Arid Land 2024年第4期16卷 531-549页

作者： qu Wenjie ZHAO Wenzhi YANG Xinguo WANG Lei ZHANG Xue qu Jianjun Northwest Institute of Eco-Environment and Resources Chinese Academy of SciencesLanzhou 730000China Key Laboratory of Restoration and Reconstruction of Degraded Ecosystems in Northwestern China of Ministry of Education Ningxia UniversityYinchuan 750021China University of Chinese Academy of Sciences Beijing 100049China School of Ecology and Environment Ningxia UniversityYinchuan 750021China

The maintenance of sand-fixing vegetation is important for the stability of artificial sand-fixing systems in which seed dispersal plays a key *** on field wind tunnel experiments using 11 common plant species on the southeastern edge of the Tengger Desert,China,we studied the secondary seed dispersal in the fixed and semi-fixed sand dunes as well as in the mobile dunes in order to understand the limitations of vegetation regeneration and the maintenance of its *** results indicated that there were significant variations among the selected 11 plant species in the threshold of wind speed(TWS).The TWS of Caragana korshinskii was the highest among the 11 plant species,whereas that of Echinops gmelinii was the *** morphological traits and underlying surface could generally explain the *** the secondary seed dispersal processes,the proportions of seeds that did not disperse(no dispersal)and only dispersed over short distance(short-distance dispersal within the wind tunnel test section)were significantly higher than those of seeds that were buried(including lost seeds)and dispersed over long distance(long-distance dispersal beyond the wind tunnel test section).Compared with other habitats,the mobile dunes were the most difficult places for secondary seed *** seeds were the easiest to be found in the semi-fixed sand dunes,whereas fixed sand dunes were the best sites for seeds that dispersed over long *** results of linear mixed models showed that after controlling the dispersal distance,smaller and rounder seeds dispersed *** index and wind speed were the two significant influencing factors on the burial of *** explanatory power of wind speed,underlying surface,and seed morphological traits on the seeds that did not disperse and dispersed over short distance was far greater than that on the seeds that were buried and dispersed over long distance,implying that the processes and mechanisms of burial and lo

关键词： seed dispersal seed morphological traits wind speed vegetation regeneration wind tunnel Tengger Desert

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