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American Journal of Molecular Biology 2024年第2期14卷 54-65页

作者： Jianzhong Huang Peng Jia Xiaoju Zhong Xiuying Guan hongbin zhang Honglei Ruan Key Laboratory of Chronic Diseases Fuzhou Medical University Fuzhou China

Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes.

关键词： Coding Sequence Genomic Sequence Nicotiana benthamiana Plant Genes

Structural and Functional Insights into an Arabidopsis NBS-LRR Receptor in Nicotiana benthamiana

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American Journal of Molecular Biology 2024年第2期14卷 84-96页

作者： Jianzhong Huang Xiuying Guan Xiaoju Zhong Peng Jia hongbin zhang Honglei Ruan Key Laboratory of Chronic Diseases Fuzhou Medical University Fuzhou China

Nucleotide-binding site leucine-rich repeat receptors (NBS-LRR/NLRs) are crucial intracellular immune proteins in plants. Previous article reported a novel NLR protein SUT1 (SUPPRESSORS OF TOPP4-1, 1), which is involved in autoimmunity initiated by type one protein phosphatase 4 mutation (topp4-1) in Arabidopsis, however, its role in planta is still unclear. This study employed Nicotiana benthamiana, a model platform, to conduct an overall structural and functional analysis of SUT1 protein. The transient expression results revealed that SUT1 is a typical CNL (CC-NBS-LRR) receptor, both fluorescence data and biochemical results showed the protein is mainly anchored on the plasma membrane due to its N-terminal acylation site. Further truncation experiments announced that its CC (coiled-coil) domain possessed cell-death-inducing activity. The outcomes of point mutations analysis revealed that not only the CC domain, but also the full-length SUT1 protein, whose function and subcellular localization are influenced by highly conserved hydrophobic residues. These research outcomes provided favorable clues for elucidating the activation mechanism of SUT1.

关键词： CC-NBS-LRR Hypersensitive Response Nicotiana benthamiana Plasma Membrane Localization

Improving entity linking with two adaptive features

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Frontiers of Information Technology & Electronic Engineering 2022年第11期23卷 1620-1630页

作者： hongbin zhang Quan CHEN Weiwen zhang School of Computer Science and Technology Guangdong University of TechnologyGuangzhou 510006China

Entity linking(EL)is a fundamental task in natural language processing.Based on neural networks,existing systems pay more attention to the construction of the global model,but ignore latent semantic information in the local model and the acquisition of effective entity type information.In this paper,we propose two adaptive features,in which the first adaptive feature enables the local and global models to capture latent information,and the second adaptive feature describes effective information for entity type embeddings.These adaptive features can work together naturally to handle some uncertain entity type information for EL.Experimental results demonstrate that our EL system achieves the best performance on the AIDA-B and MSNBC datasets,and the best average performance on out-domain datasets.These results indicate that the proposed adaptive features,which are based on their own diverse contexts,can capture information that is conducive for EL.

关键词： Entity linking Local model Global model Adaptive features Entity type

Correspondence(reply):The application conditions of false discovery rate control

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Genes & Diseases 2023年第4期10卷 1145-1146页

作者： hongbin zhang Xin Le Tingxiu Xiang Cancer Center Daping HospitalArmy Medical University(Third Military Medical University)Chongqing 400042China Department of Oncology The First Affiliated Hospital of Chongqing Medical UniversityChongqing 400016China Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment Chongqing University Cancer HospitalChongqing 400030China

We have carefully read the correspondence“False Discov-ery Rate Control in Cancer Biomarker Selection”authored by Li.The author clarified the need of paying attention to the control of false discovery rate(FDR)when screening for cancer biomarkers.They expressed concerns about whether the 30 genes concluded in Figure 7 in our published paper“LPCAT1 functions as a novel prognostic molecular marker in hepatocellular carcinoma”call for FDR control.

关键词： false Cancer Figure

Influence of Selective Laser Melting Process Parameters on Microstructure and Properties of a Typical Ni-Based Superalloy

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Acta Metallurgica Sinica(English Letters) 2022年第10期35卷 1673-1687页

作者： Zhen Lu Chengcai zhang Nana Deng Haiping Zhou Ruirui Fang Kuidong Gao Yukuo Su hongbin zhang School of Materials Science and Engineering Harbin Institute of TechnologyHarbin150001China College of Mechanical and Electronic Engineering Shandong University of Science and TechnologyQingdao266590China Jier Machine-Tool Group Co.Ltd Jinan250022China

The influence of selective laser melting(SLM)process parameters on the microstructure and mechanical properties of a typical Ni-based superalloy was researched.The optimum parameters of P=170 W,V=0.8 m/s were determined,under which the SLMed samples exhibited both the largest relative density of 99.57%and the best mechanical properties,including the microhardness(329.3±3.8 HV),yield strength(726±8.1 MPa),ultimate tensile strength(900±5.9 MPa)and elongation((31.9±0.24)%).The average grain size ranges of SLMed samples are from 15.2 to 17.4μm,with a typical mixed grain structure.Owing to the high cooling rate and remelting during SLM process,a large number of low-angle grain boundaries(LAGBs),dislocations and sub-grains were formed,and the fraction of LAGBs reached above 65%.At the same time,the content of low-Σcoincidence site lattice(CSL)boundaries was mostly less than 1%,while there was almost noγ′phase precipitated in the matrix.The texture of SLMed samples was weak,and there was no obvious preferred growth direction.Combining with the microstructure characterization,both grain refinement strengthening and dislocation strengthening were considered as the main strengthening mechanisms.Moreover,the fracture mechanism of the optimum sample belonged to ductile fracture.

关键词： Selective laser melting Ni-based superalloy Relative density Microstructure Mechanical property

Autonomous atomic Hamiltonian construction and active sampling of X-ray absorption spectroscopy by adversarial Bayesian optimization

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npj Computational Materials 2023年第1期9卷 1890-1900页

作者： Yixuan zhang Ruiwen Xie Teng Long Damian Günzing Heiko Wende Katharina J.Ollefs hongbin zhang Institute of Materials Science Technical University of Darmstadt64287 DarmstadtGermany School of Materials Science and Engineering Shandong University250061 JinanChina Faculty of Physics University of Duisburg-Essen47057 DuisburgGermany

X-ray absorption spectroscopy(XAS)is a well-established method for in-depth characterization of electronic structure.In practice hundreds of energy-points should be sampled during the measurements,and most of them are redundant.Additionally,it is also tedious to estimate reasonable parameters in the atomic Hamiltonians for mechanistic understanding.We implement an Adversarial Bayesian optimization(ABO)algorithm comprising two coupled BOs to automatically fit the many-body model Hamiltonians and to sample effectively based on active learning(AL).Taking NiO as an example,we find that less than 30 sampling points are sufficient to recover the complete XAS with the corresponding crystal field and charge transfer models,which can be selected based on intuitive hypothesis learning.Further applications on the experimental XAS spectra reveal that less than 80 sampling points give reasonable XAS and reliable atomic model parameters.Our ABO algorithm has a great potential for future applications on automated physics-driven XAS analysis and AL sampling.

关键词： structure Hamiltonian absorption

Thermal Deformation Behavior and Processing Map of a Novel CrFeNiSi_(0.15)Medium Entropy Alloy

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Acta Metallurgica Sinica(English Letters) 2023年第11期36卷 1870-1882页

作者： hongbin zhang Kang Chen Zhongwei Wang Haiping Zhou Chengcheng Shi Shengxue Qin Jie Liu Tingjun Lv Jian Xu College of Mechanical and Electronic Engineering Shandong University of Science and TechnologyQingdao266590China School of Mechanical Engineering Shandong University of TechnologyZibo255000China Zibo Yuan Xu Metallurgical Machinery Co LtdZibo255120China

The thermal deformation behavior of a novel CrFeNiSi_(0.15)medium entropy alloy(MEA)was studied via isothermal compression experiments,with the processing parameter range of 900–1200℃and 0.001–1 s^(−1).According to experimental data,the modified constitutive equation had been obtained,which precisely predicted the flow behavior of CrFeNiSi_(0.15)MEA during thermal deformation.At the same time,the processing map was established on the basis of the dynamic material model(DMM)theory.According to the map,the optimal processing parameters were determined at 1130–1200℃/0.06–1 s−1,under which the power dissipation efficiency could reach above 34%.The peak efficiency was above 38%,which occurred at 1200℃/1 s^(−1).In such parameter,complete dynamic recrystallization(DRX)also occurred.The flow instability of CrFeNiSi_(0.15)MEA was estimated to occur at 900–985℃/0.12–1 s^(−1),which was shown as grain boundaries cracking.Furthermore,both the continuous DRX(CDRX)and discontinuous DRX(DDRX)occurred simultaneously during thermal deformation.Meanwhile,some twins were also newly formed during DRX process,most of which were primary twins.The occurrence of twinning was beneficial to promote the development of DRX behavior.

关键词： Medium entropy alloys Thermal deformation behavior Constitutive model Processing maps

First-principles investigation of the significant anisotropy and ultrahigh thermoelectric efficiency of a novel two-dimensional Ga_(2)I_(2)S_(2) at room temperature

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International Journal of Extreme Manufacturing 2022年第2期4卷 100-112页

作者： Zheng Chang Ke Liu Zhehao Sun Kunpeng Yuan Shuwen Cheng Yufei Gao Xiaoliang zhang Chen Shen hongbin zhang Ning Wang Dawei Tang Key Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of Education School of Energy and Power EngineeringDalian University of TechnologyDalian 116024People’s Republic of China Research Office of Propulsion Technology Expace Technology Corporation LimitedBeijing 100176People’s Republic of China Research School of Chemistry Australian National UniversityCanberraACT 2601Australia School of Metallurgy Northeastern UniversityShenyang 100819People’s Republic of China Institut fur Materialwissenschaft Technische Universitat DarmstadtDarmstadt 64283Germany School of Physics University of Electronic Science and Technology of ChinaChengdu 610054People’s Republic of China

Two-dimensional(2D)thermoelectric(TE)materials have been widely developed;however,some 2D materials exhibit isotropic phonon,electron transport properties,and poor TE performance,which limit their application scope.Thus,exploring excellent anisotropic and ultrahigh-performance TE materials are very warranted.Herein,we first investigate the phonon thermal and TE properties of a novel 2D-connectivity ternary compound named Ga2I2S2.This paper comprehensively studies the phonon dispersion,phonon anharmonicity,lattice thermal conductivity,electronic structure,carrier mobility,Seebeck coefficient,electrical conductivity,and the dimensionless figure of merit(ZT)versus carrier concentration for 2D Ga_(2)I_(2)S_(2).We conclude that the in-plane lattice thermal conductivities of Ga_(2)I_(2)S_(2) at room temperature(300 K)are found to be 1.55 W mK^(−1) in the X-axis direction(xx-direction)and 3.82 W mK^(−1)in the Y-axis direction(yy-direction),which means its anisotropy ratio reaches 1.46.Simultaneously,the TE performance of p-type and n-type doping 2D Ga2I2S2 also shows significant anisotropy,giving rise to the ZT peak values of p-type doping in xx-and yy-directions being 0.81 and 1.99,respectively,and those of n-type doping reach ultrahigh values of 7.12 and 2.89 at 300 K,which are obviously higher than the reported values for p-type and n-type doping ternary compound Sn2BiX(ZT∼1.70 and∼2.45 at 300 K)(2020 Nano Energy 67104283).This work demonstrates that 2D Ga_(2)I_(2)S_(2) has high anisotropic TE conversion efficiency and can also be used as a new potential room-temperature TE material.

关键词： thermoelectricity strong anisotropy two-dimensional materials room temperature first-principles calculation

Epidemiological Investigation of an Inhalational Anthrax Patient Traveling for Medical Treatment in Beijing Municipality,China,August 2021

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China CDC weekly 2022年第1期4卷 4-7页

作者： Changying Lin Xiangfeng Dou Daitao zhang Yinqi Sun Huiqiang Han Chunzhi Chen Xiaojun zhang Shuang Li Yanwei Chen hongbin zhang Bin Wang Zhichao Liang Xin zhang Feng Wei Jiangli Wang Feng Liu Quanyi Wang Jian Shi Peng Yang Beijing Center for Disease Control and Prevention BeijingChina Hebei Provincial Center for Disease Control and Prevention ShijiazhuangHebeiChina Chengde Center for Disease Control and Prevention ChengdeHebeiChina Haidian District Center of Disease Control and Prevention HaidianBeijingChina Weichang County Center for Disease Control and Prevention ChengdeHebeiChina.

Summary What is already known about this topic?Inhalational anthrax,also known as pulmonary anthrax,is an infectious disease caused by Bacillus anthracis.The patients are usually infected by inhaling aerosolized B.anthracis spores from dead animals or animal products.Compared to cutaneous anthrax,inhalational anthrax is rare and deadly and few cases in China were reported.What is added by this report?This report covers all information of clinical features,laboratory testing,and epidemiological characteristics as well as exposure history of a recent primary inhalational anthrax patient who was seeking medical treatment in Beijing Municipality in August 2021.New laboratory techniques,including second-generation sequencing,polymerase chain reaction,and rapid test for serum antibody,played an important role in the process.What are the implications for public health practice?The information provided in this report,including the correct sample type,epidemiological investigation details,and application of the new diagnostic criteria of anthrax,could assist public health professionals in dealing with anthrax epidemics.

关键词： clinical details dealing

Seed-induced synthesis of functional MFI zeolite materials:Method development,crystallization mechanisms,and catalytic properties

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Frontiers of Chemical Science and Engineering 2020年第2期14卷 143-158页

作者： Zhaoqi Ye hongbin zhang Yahong zhang Yi Tang Department of Chemistry Shanghai Key Laboratory of Molecular Catalysis and Innovative MaterialsLaboratory of Advanced Materialsand Collaborative Innovation Center of Chemistry for Energy MaterialsFudan UniversityShanghai 200433China Institute for Preservation of Chinese Ancient Books Fudan University LibraryFudan UniversityShanghai 200433China

As an important zeolite material,MFI zeolites,as well as their controllable synthesis,are of great interest in both basic and applied science.Among the developed synthetic approaches,the seed-induced method has gradually evolved into a facile,low-cost,and even green alternative to give zeolites the desirable physicochemical properties.In this review,we briefly summarize the development of seed-induced syntheses of diverse functional MFI zeolites,where the“living”seed crystals not only direct the formation of zeolitic framework but also function as special“templates”or“units”to fine-tune the zeolite materials with diverse sizes,shapes,compositions,morphologies and pore structures.Moreover,on the basis of their structural features and crystallization behaviors in seed-induced synthesis,we reveal the roles of seeds and discuss the related crystallization mechanisms including both classical and non-classical pathways.We also want to guide readers to investigate the structure-performance relationships between these functional MFI zeolite catalysts and suitable catalytic reactions.

关键词： seed-induced synthesis MFI zeolite synthesis mechanism catalytic property