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Identification of differential gene expression for microarray data using recursive random forest

Chinese Medical Journal 2008年第24期121卷 2492-2496页

作者： wu Xiao-yan wu zhen-yu LI Kang Department of Biostatistics College of Public Health Harbin Medical University Harbin Heilongjiang 150081 China

Background The major difficulty in the research of DNA microarray data is the large number of genes compared with the relatively small number of samples as well as the complex data structure. Random forest has received much attention recently; its primary characteristic is that it can form a classification model from the data with high dimensionality. However, optimal results can not be obtained for gene selection since it is still affected by undifferentiated genes. We proposed recursive random forest analysis and applied it to gene selection. Methods Recursive random forest, which is an improvement of random forest, obtains optimal differentiated genes after step by step dropping of genes which, according to a certain algorithm, have no effects on classification. The method has the advantage of random forest and provides a gene importance scale as well. The value of the area under the curve （AUC） of the receiver operating characteristic （ROC） curve, which synthesizes the information of sensitivity and specificity, is adopted as the key standard for evaluating the performance of this method. The focus of the paper is to validate the effectiveness of gene selection using recursive random forest through the analysis of five microarray datasets; colon, prostate, leukemia, breast and skin data. Results Five microarray datasets were analyzed and better classification results have been attained using only a few genes after gene selection. The biological information of the selected genes from breast and skin data was confirmed according to the National Center for Biotechnology Information （NCBI）. The results prove that the genes associated with diseases can be effectively retained by recursive random forest. Conclusions Recursive random forest can be effectively applied to microarray data analysis and gene selection. The retained genes in the optimal model provide important information for clinical diagnoses and research of the biological mechanism of diseases.

关键词： microarray gene selection recursive random forest

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Speed aware self-adapting and reconfigurable routing mechanism in MANET

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High Technology Letters 2012年第3期18卷 321-325页

作者： Zhang Qinjuan wu Muqing zhen yan Laboratory of Network System Architecture and Convergence Beijing University of Posts and Telecommunications Beijing 100876 P. R. China

A self-adapting and reconfigurable routing mechanism is proposed according to the average moving speed of the nodes in mobile ad hoc network （MANET）. This mechanism is based on the perception of moving speed and a predesigned selection metric to choose the optimal routing protocol. The routing evaluation and selection metric is derived by OPNET simulations. AODV and OLSR are used as the example to show the process of this mechanism with the moving speed varying. The routing protocol can be configured without central configuration and human management. Besides, the overhead of the mechanism is reasonable and doesnot affect the quality of service （QoS） of the traffic in the network. Results show that the optimal routing protocol can be configured adaptively according to the speed so that better performance than end-to-end delay and packet delivery ratio. a specific protocol can be obtained in terms of

关键词： speed aware self-adapting reconfiguration mobile ad hoc network (MANET)

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Configuring single-layer MXene nanosheet onto natural wood fiber via C-Ti-C covalent bonds for high-stability Li-S batteries

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Journal of Energy Chemistry 2024年第8期95卷 701-711,I0016页

作者： yangyang Chen Yu Liao Ying wu Lei Li zhen Zhang Sha Luo Yiqiang wu yan Qing College of Materials Science and Technology Central South University of Forestry and TechnologyChangsha 410004HunanChina

Lithium-sulfur batteries(LSBs)are considered promising candidates for next-generation battery technologies owing to their outstanding theoretical energy density and ***,the low conductivity and polysulfide shuttling effect of S cathodes severely hamper the practical performance of ***,in situ-generated single layer MXene nanosheet/hierarchical porous carbonized wood fiber(MX/PCWF)composites are prepared via a nonhazardous eutectic activation strategy coupled with pyrolysis-induced gas *** unique architecture,wherein single layer MXene nanosheets are constructed on carbonized wood fiber walls,ensures rapid polysulfide conversion and continuous electron transfer for redox *** C-Ti-C bonds formed between MXene and PCWF can considerably expedite the conversion of polysulfides,effectively suppressing the shuttle *** impressive capacity of 1301.1 m A h g^(-1)at 0.5 C accompanied by remarkable stability is attained with the MX/PCWF host,as evidenced by the capacity maintenance of 722.6 m A h g^(-1)after 500 ***,the MX/PCWF/S cathode can still deliver a high capacity of 886.8 m A h g^(-1)at a high S loading of 5.6 mg cm^(-2).The construction of two-dimensional MXenes on natural wood fiber walls offers a competitive edge over S-based cathode materials and demonstrates a novel strategy for developing high-performance batteries.

关键词： Lithium-sulfur batteries S cathodes MXene nanosheets Wood fiber C-Ti-C bonds

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A data-driven approach to RUL prediction of tools

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Advances in Manufacturing 2024年第1期12卷 6-18页

作者： Wei Li Liang-Chi Zhang Chu-Han wu yan Wang zhen-Xiang Cui Chao Niu Department of Mechanical Engineering University College LondonLondonWC1E 7JEUK Shenzhen Key Laboratory of Cross-Scale Manufacturing Mechanics Southern University of Science and TechnologyShenzhen518055GuangdongPeople’s Republic of China SUSTech Institute for Manufacturing Innovation Southern University of Science and TechnologyShenzhen518055GuangdongPeople’s Republic of China Department of Mechanics and Aerospace Engineering Southern University of Science and TechnologyShenzhen518055GuangdongPeople’s Republic of China School of Mechanical and Manufacturing Engineering The University of New South WalesKensingtonNSW2052Australia Baoshan Iron&Steel Co. Ltd.Shanghai200941People’s Republic of China

An effective and reliable prediction of the remaining useful life(RUL)of a tool is important to a metal forming process because it can significantly reduce unexpected maintenance,avoid machine shutdowns and increase system *** study proposes a new data-driven approach to the RUL prediction for metal forming processes under multiple contact sliding *** data-driven approach took advantage of bidirectional long short-term memory(BLSTM)and convolutional neural networks(CNN).A pre-trained lightweight CNN-based network,WearNet,was re-trained to classify the wear states of workpiece surfaces with a high accuracy,then the classification results were passed into a BLSTM-based regression model as inputs for RUL *** experimental results demonstrated that this approach was able to predict the RUL values with a small error(below 5%)and a low root mean square error(RMSE)(around 1.5),which was more superior and robust than the other state-of-the-art methods.

关键词： Remaining useful life(RUL) Bidirectional long short-term memory(BLSTM) Data-driven approach Metal forming

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Effects of CO_2 enrichment and spikelet removal on rice quality under open-air field conditions

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Journal of Integrative Agriculture 2016年第9期15卷 2012-2022页

作者： JING Li-quan wu yan-zhen ZHUANG Shi-teng WANG Yun-xia ZHU Jian-guo WANG Yu-long yanG Lian-xin Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops Yangzhou University College of Environmental Science and Engineering Yangzhou University State Key Laboratory of Soil and Sustainable Agriculture/Institute of Soil Science Chinese Academy of Sciences

The increase of atmospheric carbon dioxide（CO_2） concentration adversely affect several quality traits of rice grains, but the biochemical mechanism remains unclear. The objectives of this study were to determine how changes in the source-sink relationship affected rice quality. Source-sink manipulation was achieved by free-air CO_2 enrichment from tillering to maturity and partial removal of spikelet at anthesis using a japonica rice cultivar wuyunjing 23. Enrichment with CO_2 decreased the head rice percentage and protein concentration of milled rice, but increased the grain chalkiness. In contrast, spikelet removal resulted in a dramatic increase in the head rice percentage and protein concentration, and much less grain chalkiness. Neither CO_2 enrichment nor spikelet removal affected the starch content, but the distribution of starch granule size showed distinct treatment effects. O n average, spikelet removal decreased the percentage of starch granules of diameter 〉10 and 5–10 μm by 23.6 and 5.6%, respectively, and increased those with a diameter of 2–5 and 〈2 μm by 4.6 and 3.3%, respectively. In contrast, CO_2 elevation showed an opposite response： increasing the proportion of large starch granules（〉5 μm） and decreasing that of 〈5 μm. The starch pasting properties were affected by spikelet removal much more than by CO_2 elevation. These results indicated that the protein concentration and starch granule size played a role in chalkiness formation under these experimental conditions.

关键词： rice free-air CO_2 enrichment sink removal quality starch granule size

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Rational surface charge engineering of haloalkane dehalogenase for boosting the enzymatic performance in organic solvent solutions

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Chinese Journal of Chemical Engineering 2024年第1期65卷 276-285页

作者： Yin wu yan Sun Department of Biochemical Engineering School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology(Ministry of Education)Tianjin UniversityTianjin 300350China

Biocatalysis in organic solvents(OSs)has numerous important applications,but native enzymes in OSs often exhibit limited catalytic ***,we proposed a computation-aided surface charge engineering strategy to improve the catalytic performance of haloalkane dehalogenase DhaA in OSs based on the energetic analysis of substrate binding to the DhaA *** variants with enhanced OS resistance were obtained by replacing negative charged residues on the surface with positive charged residue(Arg).Particularly,a four-substitution variant E16R/E93R/E121R/E257R exhibited the best catalytic performance(five-fold improvement in OS resistance and seven-fold half-life increase in 40%(vol)dimethylsulfoxide).As a result,the overall catalytic performance of the variant could be at least 26 times higher than the wild-type *** spectroscopy and molecular dynamics simulation studies revealed that the residue substitution mainly enhanced OS resistance from four aspects:(a)improved the overall structural stability,(b)increased the hydrophobicity of the local microenvironment around the catalytic triad,(c)enriched the hydrophobic substrate around the enzyme molecule,and(d)lowered the contact frequency between OS molecules and the catalytic *** findings validate that computationaided surface charge engineering is an effective and ingenious rational strategy for tailoring enzyme performance in OSs.

关键词： Surface charge engineering Organic solvent resistance Molecular dynamics simulation Haloalkane dehalogenase

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Root cause of corrosion failure of tin coating on wire clamp in marine atmosphere

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Journal of Iron and Steel Research International 2024年第4期31卷 998-1014页

作者： zhen Zhong Wang-yan Ly Teng-yuan Liu Yi Xie yang yang zhen-zhu Wang Deng-ke Li Xiao-bo Li Tang-qing wu School of Materials Science and Engineering Xiangtan UniversityXiangtan 411105HunanChina Electric Power Research Institute of Guangdong Power Grid Co. Ltd.Guangzhou 510080GuangdongChina Shenyang National L aboratory for Materials Science Institute of Metal ResearchChinese Academy of SciencesShenyang 110016LiaoningChina School of Materials Science and Engineering.University of Science and Technology of China Shenyang 110016LiaoningChina Electric Power Research Institute State Grid Hunan Electric Power CompanyChangsha 410007HunanChina School of Mechanical Engineering and Mechanics Xiangtan UniversityXiangtan 411105HunanChina School of Information Science and Engineering Changsha Normal UniversityChangsha 410199HunanChina

The failure cause of a tinned copper wire clamp in marine atmosphere was studied systematically by X-ray photoelectron spectroscopy,scanning electron microscopy with energy dispersive spectroscopy and electrochemical *** main components of the green rust on the surface of the damaged wire clamp are SnO_(2),CuO,Cu_(2)Cl(OH)_(3) and CuCO(OH)_(2).Much of green rust distributes at the platform edge along the axial direction on the crimp connection,and severe corrosion and corrosion pits occur at the platform edge zone along the axial *** enriching Cl-at the marine atmosphere and the existing O_(2) in air collectively enhance the corrosion process of the tin coating and the copper *** element model results show that the residual stress and strain of the tin coating are the largest at the platform edge along the axial direction on the crimp connection,and the corresponding electrode potential of the tin coating at this zone drops *** above results indicate that the residual strain increases the driving force of the corrosion electrochemical reactions and accelerates the corrosion rate and the pit corrosion of the tin coating at this zone.

关键词： Tin coating Marine atmosphere Residual strain-Chloride ion Corrosion failure

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Sobolev Mapping of the Bergman Projections on Generalized Hartogs Triangles

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Acta Mathematica Sinica,English Series 2024年第2期40卷 451-466页

作者： Hong yan LIU zhen Han TU School of Mathematics and Statistics Wuhan UniversityWuhan 430072P.R.China

In this paper,we investigate Sobolev mapping properties of the Bergman *** domain we focus on is defined byΩm/n:={(z,w)∈C^(1+N):|w1|<|z|m1/n1<1,…|wN|<|z|/m_(N)/n_(N)<1},where m=(m1,…mN)∈(Z^(+))^(N),n=(n1,…nN)∈(Z^(+))N,N∈Z^(+).Sobolev irregularity of the Bergman projections on 2 is *** also prove some Sobolev regularity results of the Bergman projections onΩm/n for m=(1,…1).

关键词： Bergman projections generalized Hartogs triangles Sobolev spaces

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Super-Resolution Fluorescence Microscopy for Cilia Investigation and Ciliopathy Diagnosis(Invited)

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激光与光电子学进展 2024年第6期61卷 260-271页

作者： Liu zhen wu yang Division of Life Science The Hong Kong University of Science and TechnologyHong KongChina

The last two decades have witnessed the invention and development of super-resolution microscopy(SRM)that breaks the diffraction limit of light and pushes the fluorescence microscopy resolution to several *** SRM is widely used in biological studies,such as resolving subdiffraction structures,molecular mapping,tracking single molecules,probing protein-protein interactions,and observing organelle dynamics,its direct application in translational medicine,such as disease diagnosis,is still *** their small size,cilia play a crucial role as organelles in cell signaling and motility,with defects in cilia leading to *** to other miniature organelles and macromolecular complexes,cilia are ideal for super-resolution *** this review,we will 1)introduce cilia and ciliopathy,2)show how SRM extends our knowledge of cilia,and 3)focus on how SRM improves the diagnosis of motile ciliopathies.

关键词： diagnosis limit spite

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An interlaminar damage shell model for typical composite structures

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Chinese Journal of Aeronautics 2024年第1期37卷 118-137页

作者： Jie ZHOU zhen wu zhengliang LIU Xiaohui REN School of Aeronautics Northwestern Polytechnical UniversityXi’an 710072China National Key Laboratory of Strength and Structural Integrity Xi’an 710065China School of Mechanical Engineering Xi’an Aeronautical UniversityXi’an 710065China

Using the plate/shell elements in commercial software,accurate analysis of interlaminar initial damage in typical composite structures is still a challenging *** propose an accurate and efficient model for analysis of interlaminar initial damage,the following work is carried out:(A)A higher-order theory is firstly proposed by introducing the local Legendre polynomials,and then a novel shell element containing initial damage prediction is developed,which can directly predict transverse shear stresses without any postprocessing *** variables at each node are independent of number of layers,so the proposed model is more efficient than the 3D-FEM.(B)Compression experiment is carried out to verify the capability of the proposed *** results obtained from the proposed model are in good agreement with experimental data.(C)Several examples have been analyzed to further assess the capability of the proposed model by comparing to the 3D-FEM ***,accuracy and efficiency have been evaluated in different damage criterion by comparing with the selected *** numerical results show that the proposed model can well predict the initial interlaminar damage as well as other ***,the model is implemented with UEL subroutine,so that the present approach can be readily utilized to analyze the initial damage in typical composite structures.

关键词： Compression experiment Finite element method Initial damage Interlaminar stress Plate/shell element

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