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Molecular Dynamics Simulation of Persistent Slip Bands Formation in Nickel-base Superalloys

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International Journal of Automation and computing 2017年第1期14卷 68-79页

作者： Jian-Feng Huang Zhong-Lai Wang Er-Fu Yang Don McGlinchey yuan-xin Luo Yun Li Yi Chen School of Engineering and Built Environment Glasgow Caledonian UniversityGlasgow G4 0BAUK University of Electronic Science and Technology of China Chengdu 611731China Space Mechatronic Systems Technology Laboratory(SMe STech) Department of DesignManufacture and Engineering ManagementJames Weir BuildingUniversity of StrathclydeGlasgow G1 1X JUK College of Mechanical Engineering Chongqing UniversityChongqing 400044China School of Computer Science and Network Security Dongguan University of TechnologyDongguan 523808China

Persistent slip band （PSB） is an important and typical microstructure generated during fatigue crack initiation. Intensive work has been done to investigate the mechanisms of the formation of persistent slip bands since the 1950s when Wadsworth[1] observed the fatigue fracture in copper. Simulations have indicated that PSBs formation during fatigue crack initiation is related to the dislocation driving force and interaction. In this paper, a molecular dynamics （MD） simulation associated with embedded atom model （EAM） is applied to the PSBs formation in nickel-base superalloys with different microstructure and temperature under tensile- tensile loadings. Five MD models with different microstructure （pure 5/ phase and γ/γ＇ phase）, grain orientation （[1 0 0][0 1 0][0 0 1] and [1 1 1][1 0 1][1 2 1]） and simulation temperature （300 K, 600 K, 900 K） were built up in these simulations. Our results indicated that within the γ phase by massive dislocations, pile-up and propagation which can penetrate the grain. Also, it is found that the temperature will affect the material fatigue performance and blur PSBs appearance. The simulation results are in strong agreement with published experimental test result. This simulation is based on the work[2]. The highlights of the article include： 1） investigation of the PSB formation via molecular dynamics simulation with three different parameters, 2） conduct of a new deformation and velocity combination controlled simulation for the PSB formation, 3） high-performance computing of PSB formation, and 4） systematic analysis of the PSB formation at the atomic scale in which the dislocation plays a critical role.

关键词： Persistent slip bands （PSB） molecular dynamics superalloys computational simulation embedded atom model （EAM）.

Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome

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Plant Communications 2020年第1期1卷 147-163页

作者： Xiaoxuan Guo Xiaoning Zhang yuan Qin Yong-xin Liu Jingying Zhang Na Zhang Kun Wu Baoyuan Qu Zishan He xin Wang xinjian Zhang Stephane Hacquard Xiangdong Fu Yang Bai State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of Sciences(CAS)Beijing 100101China CAS-JIC Centre of Excellence for Plant and Microbial Science(CEPAMS) Institute of Genetics and Developmental BiologyChinese Academy of Sciences(CAS)Beijing 100101China College of Advanced Agricultural Sciences University of Chinese Academy of SciencesBeijing 100039China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of Sciences(CAS)Beijing 100101China College of Life Sciences University of Chinese Academy of SciencesBeijing100049China Shandong Provincial Key Laboratory of Applied Microbiology Ecology InstituteQilu University of Technology(Shandong Academy of Sciences)Jinan 250014China Max Planck Institute for Plant Breeding Research Cologne 50829Germany

Plant-associated microbes are critical for plant growth and survival under natural environmental conditions.To date,most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relative abundance of microbial taxa.However,this technique does not assess the total microbial load and the abundance of individual microbes relative to the amount of host plant tissues.Here,we report the development of a host-associated quantitative abundance profiling(HA-QAP)method that can accurately examine total microbial load and colonization of individual root microbiome members relative to host plants by the copy-number ratio of microbial marker gene to plant genome.We validate the HAQAP method using mock experiments,perturbation experiments,and metagenomic sequencing.The HA-QAP method eliminates the generation of spurious outputs in the classical method based on microbial relative abundance,and reveals the load of root microbiome to host plants.Using the HA-QAP method,we found that the copy-number ratios of microbial marker genes to plant genome range from 1.07 to 6.61 for bacterial 16S rRNA genes and from 0.40 to 2.26 for Fungal internal transcribed spacers in the root microbiome samples from healthy rice and wheat.Furthermore,using HA-QAP we found that an increase in total microbial load represents a key feature of changes in root microbiome of rice plants exposed to drought stress and of wheat plants with root rot disease,which significantly influences patterns of differential taxa and species interaction networks.Given its accuracy and technical feasibility,HA-QAP would facilitate our understanding of genuine interactions between root microbiome and plants.

关键词： microbial load host-associated quantitative abundance profiling root microbiome

Social Functions of relaxed open-mouth display in golden snub-nosed monkeys(Rhinopithecus roxellana)

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Zoological Research 2019年第2期40卷 113-120页

作者： You-Ji Zhang Yi-xin Chen Hao-Chun Chen yuan Chen Hui Yao Wan-Ji Yang Xiang-Dong Ruan Zuo-Fu Xiang Institute of Evolutionary Ecology and Conservation Biology Central South University of Forestry & Technology College of Life Science and Technology Central South University of Forestry and Technology Shennongjia National Park National Forest Inventory and Design Institute

Relaxed open-mouth display serves important social Functions in relation to submission, reconciliation affiliation and reassurance among non-human primate societies; however, quantitative evidence on this behavior remains insufficient among multi-level social groups. From July to November 2016, we examined four potential Functions of the relaxed open-mouth display during pairwise, intra-unit social interactions among 18 free-ranging adult and sub-adult golden snub-nosed monkeys(Rhinopithecus roxellana) who belonged to three one-male, multi-female units(OMU) at Dalongtan, Shennongjia National Park China. Results showed that: compared with no relaxed open-mouth display,(1) the occurrence of displacement by a dominant individual approaching a subordinate was lower and the distance of the subordinate to the approaching dominant was shorter when the subordinate showed open-mouth display;(2) relaxed open-mouth display reduced the probability of continued attack for victims of aggression and allowed victims to achieve closer proximity to the aggressor during post-conflict periods;(3) relaxed open-mouth display by dominant individuals allowed them to achieve closer proximity to subordinates; and(4) the exchange of relaxed open-mouth display had a greater impact on the outcome of interactions than one individual alone giving this signal. These findings suggest that relaxed open-mouth display serves important Functions regarding submission, reconciliation, affiliation and reassurance in coordinating social interactions within OMUs in golden snub-nosed monkeys.

关键词： Golden snub-nosed monkey Open- mouth Submission Reconciliation Affiliation Reassurance

A high fidelity general purpose 3-D Monte Carlo particle transport program JMCT3.0

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Nuclear Science and Techniques 2022年第8期33卷 175-192页

作者： Li Deng Gang Li Bao-Yin Zhang Rui Li Ling-Yu Zhang xin Wang yuan-Gang Fu Dun-Fu Shi Peng Liu Yan Ma Dan-Hu Shangguan Ze-Hua Hu Sheng-Cheng Zhou Jing-Wen Shen Institute of Applied Physics and Computational Mathematics(IAPCM) Beijing 100094China CAEP Software Centre for High Performance Numerical Simulation(CAEP-SCNS) Beijing 100088China

JMCT is a large-scale,high-fidelity,three-dimensional general neutron–photon–electron–proton transport Monte Carlo software system.It was developed based on the combinatorial geometry parallel infrastructure JCOGIN and the adaptive structured mesh infrastructure JASMIN.JMCT is equipped with CAD modeling and visualizes the image output.It supports the geometry of the body and the structured/unstructured mesh.JMCT has most Functions,variance reduction techniques,and tallies of the traditional Monte Carlo particle transport codes.Two energy models,multi-group and continuous,are provided.In recent years,some new Functions and algorithms have been developed,such as Doppler broadening on-thefly(OTF),uniform tally density(UTD),consistent adjoint driven importance sampling(CADIS),fast criticality search of boron concentration(FCSBC)domain decomposition(DD),adaptive control rod moving(ACRM),and random geometry(RG)etc.The JMCT is also coupled with the discrete ordinate SNcode JSNT to generate source-biasing factors and weight-window parameters.At present,the number of geometric bodies,materials,tallies,depletion zones,and parallel processors are sufficiently large to simulate extremely complicated device problems.JMCT can be used to simulate reactor physics,criticality safety analysis,radiation shielding,detector response,nuclear well logging,and dosimetry calculations etc.In particular,JMCT can be coupled with depletion and thermal-hydraulics for the simulation of reactor nuclear-hot feedback effects.This paper describes the progress in advanced modeling,high-performance numerical simulation of particle transport,multiphysics coupled calculations,and large-scale parallel computing.

关键词： Advanced modeling High-performance numerical simulation Multi-physics coupled calculation Large-scale parallel computing JMCT

Altered intrinsic Functional connectivity of the primary visual cortex in youth patients with comitant exotropia: a resting state fMRI study

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International Journal of Ophthalmology(English edition) 2018年第4期11卷 668-673页

作者： Pei-Wen Zhu xin Huang Lei Ye Nan Jiang Yu-Lin Zhong Qing yuan Fu-Qing Zhou Yi Shao Department of Ophthalmology the First Affiliated Hospital of Nanchang University Eye Center Renmin Hospital of Wuhan University Wuhan University Department of Radiology the First Affiliated Hospital of Nanchang University

AIM： To evaluate the differences in the Functional connectivity（FC） of the primary visual cortex（V1） between the youth comitant exotropia（CE） patients and health subjects using resting Functional magnetic resonance imaging（f MRI） data.METHODS： Totally, 32 CEs（25 males and 7 females） and 32 healthy control subjects（HCs）（25 males and 7 females） were enrolled in the study and underwent the MRI scanning. Two-sample t-test was used to examine differences in FC maps between the CE patients and HCs. RESULTS： The CE patients showed significantly less FC between the left brodmann area（BA17） and left lingual gyrus/cerebellum posterior lobe, right middle occipital gyrus, left precentral gyrus/postcentral gyrus and right inferior parietal lobule/postcentral gyrus. Meanwhile, CE patients showed significantly less FC between right BA17 and right middle occipital gyrus（BA19, 37）.CONCLUSION： Our findings show that CE involves abnormal FC in primary visual cortex in many regions, which may underlie the pathologic mechanism of impaired Fusion and stereoscopic vision in CEs.

关键词： comitant exotropia Functional connectivity primary visual cortex spontaneous activity

Diversity in metagenomic sequences reveals new pathogenic Fungus associated with smut in Job's tears

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Journal of Integrative Agriculture 2020年第9期19卷 2257-2264页

作者： LI Xiang-dong SHI Ming PAN Hong LU Xiu-juan WEI Xin-Yuan LU Ping LIAN Qi-xian Fu Yu-hua Southwest Guizhou Institute of Karst Regional Development Xingyi 562400P.R.China Adlay of Engineering Technical Research Centre in Guizhou Xingyi 562400P.R.China Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081P.R.China xingyi Normal University for Nationalities Xingyi 562400P.R.China Guizhou Institute of Subtropical Crops Guizhou Academy of Agricultural SciencesXingyi 562400P.R.China

Smut is a serious disease in Job's tears,also known as adlay,and contributes to the reduction of crop yield in agricultural fields.In this study,the key pathogenic Fungi in adlay smut disease were first identified by internal transcribed spacer region(ITS)high-throughput sequencing and then used to elucidate the composition and diversity of the Fungal community in adlay smut.Results indicate that an abundance of operational taxonomic units(OTUs)were detected in the infected involucres of flowering plants and the OTUs were classified to nine phyla,20 classes,45 orders,90 families and 119 genera.A total of 4986 OTUs clustered together,sharing six core OTUs in all samples,while 145 OTUs were shared among four geographical groups.The Shannon and Simpson indices ranged from 0.137–1.629 and 0.357–0.970,respectively.Community diversity ranked as Anshun(AS)>Qinglong(QL)>xingren(XR)>xingyi(XY)among the four geographical groups by Shannon and Simpson indices,exhibiting complex community diversities among accessions and geographical groups.The richness and diversity data imply a weak relationship between the accession community richness and geographical origins of samples.Two closely related Fungal genera,Sporisorium and Ustilago,were implicated as causes of smut disease.The genus Sporisorium appears to be more commonly found among accessions and thus is more likely to be the Fungal pathogen causing smut in adlay.This work can facilitate strategies to control and prevent smut infection to improve adlay yield.

关键词： metagenomic ITS smut Job's tears

Multi-scale UDCT dictionary learning based highly undersampled MR image reconstruction using patch-based constraint splitting augmented Lagrangian shrinkage algorithm

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Frontiers of Information Technology & Electronic Engineering 2015年第12期16卷 1069-1087页

作者： Min yuan Bing-xin YANG Yi-de MA Jiu-wen ZHANG Fu-xiang LU Tong-feng ZHANG School of Information Science & Engineering Lanzhou University

Recently, dictionary learning(DL) based methods have been introduced to compressed sensing magnetic resonance imaging(CS-MRI), which outperforms pre-defined analytic sparse priors. However, single-scale trained dictionary directly from image patches is incapable of representing image features from multi-scale, multi-directional perspective, which influences the reconstruction performance. In this paper, incorporating the superior multi-scale properties of uniform discrete curvelet transform(UDCT) with the data matching adaptability of trained dictionaries, we propose a flexible sparsity framework to allow sparser representation and prominent hierarchical essential features capture for magnetic resonance(MR) images. Multi-scale decomposition is implemented by using UDCT due to its prominent properties of lower redundancy ratio, hierarchical data structure, and ease of implementation. Each sub-dictionary of different sub-bands is trained independently to form the multi-scale dictionaries. Corresponding to this brand-new sparsity model, we modify the constraint splitting augmented Lagrangian shrinkage algorithm(C-SALSA) as patch-based C-SALSA(PB C-SALSA) to solve the constraint optimization problem of regularized image reconstruction. Experimental results demonstrate that the trained sub-dictionaries at different scales, enforcing sparsity at multiple scales, can then be efficiently used for MRI reconstruction to obtain satisfactory results with Further reduced undersampling rate. Multi-scale UDCT dictionaries potentially outperform both single-scale trained dictionaries and multi-scale analytic transforms. Our proposed sparsity model achieves sparser representation for reconstructed data, which results in fast convergence of reconstruction exploiting PB C-SALSA. Simulation results demonstrate that the proposed method outperforms conventional CS-MRI methods in maintaining intrinsic properties, eliminating aliasing, reducing unexpected artifacts, and removing noise. It can achieve comparable performance of reconstruc

关键词： Compressed sensing(CS) Magnetic resonance imaging(MRI) Uniform discrete curvelet transform(UDCT) Multi-scale dictionary learning(MSDL) Patch-based constraint splitting augmented Lagrangian shrinkage algorithm(PB C-SALSA)

Tumor suppressor genes on frequently deleted chromosome 3p in nasopharyngeal carcinoma

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Chinese Journal of Cancer 2012年第5期31卷 215-222页

作者： Juan Chen Li Fu Li-Yi Zhang Dora L. Kwong Li Yan xin-yuan Guan Department of Clinical Oncology The University of Hong Kong Hong Kong P. R. China Cancer Center Union Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan Hubei 430023 P. R. China State Key Laboratory of Oncology in South China Sun Yat-sen University Cancer Center Guangzhou Guangdong 510060 P. R. China.

Nasopharyngeal carcinoma (NPC) is among the most common malignancies in southern China.Deletion of genomic DNA,which occurs during the complex pathogenesis process for NPC,represents a pivotal mechanism in the inactivation of tumor suppressor genes (TSGs).In many circumstances,loss of TSGs can be detected as diagnostic and prognostic markers in cancer.The short arm of chromosome 3 (3p) is a frequently deleted chromosomal region in NPC,with 3p21.1-21.2 and 3p25.2-26.1 being the most frequently deleted minimal regions.In recent years,our research group and others have focused on the identification and characterization of novel target TSGs at 3p,such as RASSF1A,BLU,RBMS3,and CHL1,in the development and progression of NPC.In this review,we summarize recent findings of TSGs at 3p and discuss some of these genes in detail.A better understanding of TSGs at 3p will significantly improve our understanding of NPC pathogenesis,diagnosis,and treatment.

关键词： 3号染色体抑癌基因鼻咽癌删除全国人民代表大会基因组DNA 肿瘤抑制基因发病机制

The role of NF-κB activation in lipopolysacchavide induced keratitis in rats

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Chinese Medical Journal 2005年第22期118卷 1893-1899页

作者： WU xin-yi HAN Shao-ping REN Mei-yu CHANG yuan YU Fu-xin Department of Ophthalmology Qilu Hospital Shandong UniversityJi＇nan 250012 China

Background Nuclear factor-kappa B （NF-kB） is elevated in regulating transcription of many cytokines and inflammatory mediators. The purpose of this study was to investigate the activation and the significance NF-KB in lipopolysaccharide （LPS） induced keratitis.Methods LPS induced keratitis model was based on Wistar rats. At 0. 5, 1, 3, 6, 12, 24 or 72 hours after LPS treatment, the rat corneas were observed with a slit lamp microscope, then the rats were sacrificed and their corneas were excised for routine histological analysis. The expression of NF-kB was detected with immunohistochemical staining. The change identified by reverse transcriptase polymerase of tumour necrosis factors-α （TNF-α） mRNA expression was chain reaction （RT-PCR）. Results Histological findings demonstrated that LPS treated corneas showed significant changes in corneal structure. Corneal edema, pronounced inflammatory cells infiltration and inordinate collagen fibres were observed. Immunohistochemical results showed that the expression of NF-kB and its activation obviously increased after LPS treatment compared with the normal group and control group. Positive cells could be observed at 0. 5 hour and peak expression of NF-kB was observed between 3 hours and 12 hours after infection, but returned to or approached normal level by 72 hours. RT-PCR showed that the level of TNF-α mRNA began to increase 0. 5 hour after LPS treatment, peaked at 6 hours and then subsided by 72 hours. NF-kB had a positive correlation with the expression of TNF-α mRNA （r=0. 964, P 〈 0. 01 ） , both NF-kB and TNF-α had a strong positive correlation with the degree of inflammatory response in LPS treated corneas （ r=0. 929, P 〈 0. 01 ; r=0. 587, P 〈 0.05, respectively）. Conclusions The activation of NF-kB was increased keratitis by promoting overexpression of TNF-α mRNA. LPS-associated keratitis in rats. in LPS treated corneas and was elevated in LPS induced NF-kB may play an important role in the pathogenesis ofLPS-associated keratitis in rats.

关键词： keratitis·lipopolysaccharides tumour necrosis factors NF-kappa B