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Journal of Zhejiang University-Science A(Applied Physics & Engineering) 2011年第7期12卷 552-560页

作者： hua QIAO wei-qiu chen Department of Engineering Mechanics Zhejiang University Hangzhou 310027 China

The Arlequin framework proposed by Ben Dhia in 1998 is a flexible and robust method for conducting global/local analysis of structures and materials.A penalty version of the Arlequin framework for the study of structural problems involving large deformation is considered *** implementation of the penalty-based Arlequin framework into ABAQUS is then explored and the corresponding Arlequin user element subroutine is *** nonlinear simulations of a cantilever beam and a shallow arch are conducted and the choice of the coupling operator with an appropriate penalty parameter is *** numerical results justify the feasibility of the proposed method,ensuring its further application to more complicated problems involving geometric or material nonlinearities.

关键词： Global/Local analysis Geometric nonlinear analysis Penalty-based Arlequin method User defined element

Wavelet network solution for the inverse kinematics problem in robotic manipulator

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Journal of Zhejiang University-Science A(Applied Physics & Engineering) 2006年第4期7卷 525-529页

作者： chen hua chen wei-shan XIE Tao School of Mechatronics Engineering Harbin Institute of Technology Harbin 150001 China

Wavelet network, a class of neural network consisting of wavelets, is proposed to solve the inverse kinematics problem in robotic manipulator. A wavelet network suitable for dealing with multi-input and multi-output system is constructed. The network is optimized by reducing the number of wavelets handling large dimension problem according to the sample data. The algorithms for sparseness analysis of input data and fitting wavelets to the output data with orthogonal method are introduced. Then Levenberg-Marquardt algorithm is used to train the network. Simulation results showed that this method is capable of solving the inverse kinematics problem for PUMA560.

关键词： Inverse kinematics problem Robotic manipulator Wavelet network

GAAD: A Gene and Autoimmiune Disease Association Database

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Genomics, Proteomics & Bioinformatics 2018年第4期16卷 252-261页

作者： Guanting Lu Xiaowen Hao wei-hua chen Shijie Mu Department of Blood Transfusion Tangdu Hospital Fourth Military Medical University MOE Key Laboratory of Molecular Biophysics Hubei Key Laboratory of Bioinformatics and Molecular-imaging Department of Bioinformatics and Systems Biology College of Life Science and Technology Huazhong University of Science and Technology

Autoimmune diseases （ADs） arise from an abnormal immune response of the body against substances and tissues normally present in the body. More than a hundred of ADs have been described in the literature so far. Although their etiology remains largely unclear, various types of ADs tend to share more associated genes with other types of ADs than with non-AD types. Here we present GAAD, a gene and AD association database. In GAAD, we collected 44,762 associations between 49 ADs and 4249 genes from public databases and MEDLINE documents. We manually verified the associations to ensure the quality and credibility. We reconstructed and recapitulated the relationships among ADs using their shared genes, which further validated the quality of our data. We also provided a list of significantly co-occurring gene pairs among ADs;with embedded tools, users can query gene co-occurrences and construct customized cooccurrence network with genes of interest. To make GAAD more straightforward to experimental biologists and medical scientists, we extracted additional information describing the associations through text mining, including the putative diagnostic value of the associations, type and position of gene polymorphisms, expression changes of implicated genes, as well as the phenotypical consequences, and grouped the associations accordingly. GAAD is freely available at http：//***.

关键词： Autoimmune diseases Disease-gene association Database Text mining

Preparation of n-Atom GHZ State and Implementation of Quantum-State Transfer via Cavity Decay

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Communications in Theoretical Physics 2008年第3期49卷 655-658页

作者： chen Li-Bo DU Qian-hua LIN Gong-wei chen Zhi-hua LIN Xiu-Min School of Physics and Optoelectronics Technology Fujian Normal University Fuzhou 350007 China

We propose schemes to prepare n-atom Greenberger-Horn-Zeilinger （GHZ） state via two-sided cavities interacting with single-photon pulses, and achieve quantum state transfer （QST） from one atom to another atom. Entanglement particle pair and the control of coupling between qu bits are of no need in the QST process. Some practical quantum noises only decrease the success probabilities of the schemes but have no influence on the fidelity of prepared state. In addition, the success probabilities of our schemes are close to unity in the ideal case.

关键词： GHZ state quantum state transfer cavity

Effects of PAHs on Biotransformation Enzymatic Activities in Fish

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Chemical Research in Chinese Universities 2011年第3期27卷 413-416页

作者： LU Guang-hua chen wei LI Ying ZHU Zhi Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes Ministry of Education College of Environment Hohai University Nanjing 210098 P. R. China

Biotransformation and detoxification responses to the exposure to five polycyclic aromatic hydrocarbons were investigated in crucian（Carassius auratus）. Juvenile crucian were treated with a single intraperitoneal injection of each compound at dosages of 0.1, 1.0, 2.0, 5.0 and 8.0（or 10.0） mg/kg and sacrificed 15 d later to determine 7-ethoxyresorufin-O-deethylase（EROD） and glutathione S-transferases（GST） activities in gill S9 fractions. EROD activity is significantly increased by benzo（b）fluoranthene and indeno（1,2,3-cd）pyrene at all the doses. High dosages of PAHs induced GST activity and the inducing ability of them increased in the following order： fluorene fluorantheneindeno（1,2,3-cd）pyrenebenzo（g,h,i）perylenebenzo（b）fluoranthene. In all the cases, dose dependence appeared to exist. The gill EROD and GST in Carassius auratus are useful biomarkers to estimate sub-acute toxicity of both polycyclic aromatic hydrocarbons（PAHs） and PAHs-like compounds.

关键词： Polycyclic aromatic hydrocarbon Gill 7-Ethoxyresorufin-O-deethylase activity Glutathione S-transferases activity

Osteochondral Integrated Scaffolds with Gradient Structure by 3D Printing Forming

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International Journal of Automation and computing 2015年第2期12卷 220-228页

作者： wei-hua chen Yuan-Yuan Liu Fu-hua Zhang Yong-Ze Yu Hai-Ping chen Qing-Xi Hu Rapid Manufacturing Engineering Center Shanghai University

Recently in the area of biological manufacturing and rapid prototyping manufacturing, the bone scaffolds based on the additive manufacturing in repairing bone defects have been paid more and more attention. In the process of preparation, path planning directly affects the structure, performance as well as the final bone cell culture conditions. Due to the special natural bone scaffold structural characteristic, the traditional rapid prototyping(RP) path planning is not fully suitable for the preparation of bone scaffolds. In this paper, based on the 3D printing extrusion forming technology, a method of path planning for osteochondral integrated scaffolds with gradient structure is put forward, which provides a theoretical basis for bone-scaffold modeling and practical preparation. The implementation of the path planning processing system makes it possible to process data automatically from the initial stereo lithography(STL) model of the actual bone defect part by computer X-ray tomography technique(CT) scan or modeling,to generate the path code and to generate the final machining information after post-processing. This work provides some guidelines for independent research and development of automation equipment for biological manufacturing preparation and software *** experiment and test results have verified the validity of the path planning method and the good properties of the bone scaffolds with gradient structures.

关键词： 3D printing biological bone-scaffold path planning additive manufacturing tissue engineering.

Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-free Mice

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Genomics, Proteomics & Bioinformatics 2022年第2期20卷 382-393页

作者： Yanze Li Wenming Cao Na L Gao Xing-Ming Zhao wei-hua chen MOE Key Laboratory of Molecular Biophysics Hubei Key Laboratory of Bioinformatics and Molecular-imagingDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China Institute of Science and Technology for Brain-Inspired Intelligence(ISTBI) Fudan UniversityShanghai 200433China College of Life Science Henan Normal UniversityXinxiang 453007China

Fecal microbiota transplantation(FMT)of human fecal samples into germ-free(GF)mice is useful for establishing causal relationships between the gut microbiota and human ***,due to the intrinsic differences between human and mouse intestines and the different diets of the two organisms,it may not be possible to replicate human phenotypes in mice through FMT;similarly,treatments that are effective in mouse models may not be effective in *** this study,we aimed to identify human gut microbes that undergo significant and consistent changes(i.e.,in relative abundances)after transplantation into GF mice in multiple experimental *** collected 16S rDNA-seq data from four published studies and analyzed the gut microbiota profiles from 1713 human–mouse ***,on average,we found that only 47%of the human gut microbes could be re-established in mice at the species level,among which more than 1/3 underwent significant changes(referred to as“variable taxa”).Most of the human gut microbes that underwent significant changes were consistent across multiple human–mouse pairs and experimental ***,about 1/3 of human samples changed their enterotypes,i.e.,significant changes in their leading species after *** fed with a controlled diet showed a lower enterotype change rate(23.5%)than those fed with a noncontrolled diet(49.0%),suggesting a possible solution for *** of the variable taxa have been reported to be implicated in human diseases,with some recognized as the causative *** results highlight the challenges of using a mouse model to replicate human gut microbiota-associated phenotypes,provide useful information for researchers using mice in gut microbiota studies,and call for additional validations after *** online database named FMT-DB is publicly available at http://***/#/.

关键词： Germ-free mice Fecal microbiota transplantation Gut microbe Enterotype 16S rDNA

Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes

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Genomics, Proteomics & Bioinformatics 2021年第6期19卷 949-957页

作者： Na L.Gao Zilong He Qianhui Zhu Puzi Jiang Songnian Hu wei-hua chen Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular-imagingDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China Institute for Computer Science and Cluster of Excellence on Plant Sciences Heinrich Heine UniversityD-40225 DuesseldorfGermany CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Beijing Advanced Innovation Center for Big Data-Based Precision Medicine Interdisciplinary Innovation Institute of Medicine and EngineeringBeihang UniversityBeijing 100191China University of Chinese Academy of Sciences Beijing 100049China

Coding regions have complex interactions among multiple selective forces,which are manifested as biases in nucleotide *** studies have revealed a decreasing GC gradient from the 5′-end to 3′-end of coding regions in various *** confirmed that this gradient is universal in eukaryotic genes,but the decrease only starts from the~25th *** trend is mostly found in nonsynonymous(ns)sites at which the GC gradient is universal across the eukaryotic *** GC contents at ns sites result in cheaper amino acids,indicating a universal selection for energy efficiency toward the N-termini of encoded *** a genome,the decreasing GC gradient is intensified from lowly to highly expressed genes(more and more protein products),further supporting this *** reveals a conserved selective constraint for cheaper amino acids at the translation start that drives the increased GC contents at ns *** GC contents can facilitate transcription but result in a more stable local secondary structure around the start codon and subsequently impede translation ***,the GC gradients at four-fold and two-fold synonymous sites vary across *** could decrease or increase,suggesting different constraints acting at the GC contents of different codon sites in different *** study reveals that the overall GC contents at the translation start are consequences of complex interactions among several major biological processes that shape the nucleotide sequences,especially efficient energy usage.

关键词： Macroevolution Prioritization of selective forces Energy efficiency Transcription Translation initiation

A 2.5-dimensional Analytical Model of Cold Leveling for Plates with Transverse Wave Defects

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Journal of Iron and Steel Research International 2015年第8期22卷 664-671页

作者： wei-hua chen Juan LIU Zhen-shan CUI Ying-jie WANG Ying-rui WANG National Die & Mold CAD Engineering Research Center Shanghai Jiaotong University Baosteel Co. Ltd.

Waves occurring in cold-rolled plates or sheets can be divided into longitudinal and transverse waves. Classical leveling theories merely solve the problem of longitudinal waves, while no well accepted method can be employed for transverse waves. In order to investigate the essential deformation law of leveling for plates with transverse waves, a 2.5-dimensional （2.5- D） analytical approach was proposed. In this model, the plate was transversely divided into some strips with equal width; the strips are considered to be in the state of plane strain and each group of adjacent strips are assumed to be deformation compatible under stress. After calculation, the bending deformation of each strip and the leveling effect of overall plate were obtained by comprehensNe consideration of various strips along with the width. Bending of roller is a main approach to eliminate the transverse waves, which is widely accepted by the industry, but the essential effect of bending of roller on the deformation of plates and the calculation of bending of roller are unknown. According to the 2.5-D analytical model, it can be found that, for plates, it is neutral plane offsetting and middle plane elongation or contraction under inner stress that can effectively improve plate shape. Taking double side waves as an example, the appropriate values of bending of roller were obtained by the 2.5-D analytical model related to different initial unevenness, which was applicable to the current on-line adjusting of bending of roller in rolling industry.

关键词： plate leveling 2.5-dimensional analytical model transverse wave middle plane deformation

Fabrication of hierarchical polycaprolactone/gel scaffolds via combined 3D bioprinting and electrospinning for tissue engineering

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Advances in Manufacturing 2014年第3期2卷 231-238页

作者： Yong-Ze Yu Lu-Lu Zheng Hai-Ping chen wei-hua chen Qing-Xi Hu Rapid Manufacturing Engineering Center Shanghai University

It is a severe challenge to construct 3D scaf- folds which hold controllable pore structure and similar morphology of the natural extracellular matrix （ECM）. In this study, a compound technology is proposed by com- bining the 3D bioprinting and electrospinning process to fabricate 3D scaffolds, which are composed by orthogonal array gel microfibers in a grid-like arrangement and inter- calated by a nonwoven structure with randomly distributed polycaprolactone （PCL） nanofibers. Human adipose- derived stem cells （hASCs） are seeded on the hierarchical scaffold and cultured 21 d for in vitro study. The results of cells culturing show that the microfibers structure with controlled pores can allow the easy entrance of cells and the efficient diffusion of nutrients, and the nanofiber webs layered in the scaffold can significantly improve initial cell attachment and proliferation. The present work demon- strates that the hierarchical PCL/gel scaffolds consisting of controllable 3D architecture with interconnected pores and biomimetic nanofiber structures resembling the ECM can be designed and fabricated by the combination of 3D bioprinting and electrospinning to improve biological per- formance in tissue engineering applications.

关键词： Hierarchical scaffold 3D bioprinting Electrospinning Tissue engineering