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De Novo Design of a Highly Stable Ovoid TIM Barrel:Unlocking Pocket Shape towards Functional Design

BioDesign Research 2022年第1期2022卷 68-80页

作者： alexander E.chu Daniel Fernandez Jingjia Liu Raphael R.Eguchi Po-Ssu Huang Biophysics Program Stanford UniversityStanfordCAUSA Department of Bioengineering Stanford UniversityStanfordCAUSA Program in Chemistry EngineeringAnd Medicine for Human Health(ChEM-H)Stanford UniversityStanfordCAUSA Stanford ChEM-H Macromolecular Structure Knowledge CenterStanford UniversityStanfordCAUSA Department of Biochemistry Stanford UniversityStanfordCAUSA Bio-X Institute Stanford UniversityStanfordCAUSA

The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrelfold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel proteinhas been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the foldremains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold)symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbonesampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequencedesign protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences arehighly stable and fold to the designed barrel curvature as determined by a 2.1Å resolution crystal structure. The designs showrobustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in thehydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diversehydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major steptowards the de novo design of functional TIM barrels.

关键词： structure curvature backbone

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Evaluation of the role of H pylori infection in pathogenesis of gastric cancer by immunoblot assay

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World Journal of Gastroenterology 2006年第43期12卷 7029-7032页

作者： Kuo-Ching Yang alexander chu Chao-Sheng Liao Yu-Min Lin Gen-Min Wang Division of Gastroenterology Department of Internal Medicine Shin Kong Wu Ho-Su MemorialHospitalTaipei Taiwan China Taipei Medical University Taipei TaiwanChina

AIM： To elucidate the different serological reactions to H pylori using the immunoblotting technique for further understanding of its pathogenic role in gastric cancer. METHODS： A total of 54 patients were divided into two groups after upper gastrointestinal endoscopy： normal control group （25 patients） and gastric cancer group （29 patients）. Both groups were further divided into Hpylori （＋） and H pylori （-） subgroups based on the results of CLO test, Giemsa staining and culture. Sera were further analyzed with the immunoblotting technique （HelicoBIot 2.0, Genelabs Diagnostics, Singapore）. RESULTS： The positive rate of the immunoblotting test was as high as 88.9% in the H pylori （-） gastric cancer group and only 14.3% in the H pylori （-） normal control group with a statistically significant difference. CONCLUSION： The prevalence of H pylori infection is higher in gastric cancer patients than in the normal controls, suggesting that H pylori may play a role in the pathogenesis of gastric cancer.

关键词： Western blot Immunoblotting Gastric cancer Hpylori Enzyme-linked immunosorbent assay

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Fifth-Order A-WENO Path-Conservative Central-Upwind Scheme for Behavioral Non-Equilibrium Traffic Models

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Communications in Computational Physics 2023年第3期33卷 692-732页

作者： Shaoshuai chu alexander Kurganov Saeed Mohammadian Zuduo Zheng Department of Mathematics Southern University of Science and TechnologyShenzhen518055P.R.China Shenzhen International Center for Mathematics and Guangdong Provincial Key Laboratory of Computational Science and Material Design Southern University of Science and TechnologyShenzhen518055P.R.China School of Civil Engineering the University of QueenslandBrisbane Qld4072Australia.

Non-equilibrium hyperbolic traffic models can be derived as continuum approximations of car-following models and in many cases the resulting continuum models are *** leads to numerical difficulties,which seem to have discouraged further development of complex behavioral continuum models,which is a significant research *** this paper,we develop a robust numerical scheme that solves hyperbolic traffic flow models based on their non-conservative *** develop a fifth-order alternative weighted essentially non-oscillatory(A-WENO)finite-difference scheme based on the path-conservative central-upwind(PCCU)method for several non-equilibrium traffic flow *** order to treat the non-conservative product terms,we use a path-conservative *** this end,we first apply the recently proposed secondorder finite-volume PCCU scheme to the traffic flow models,and then extend this scheme to the fifth-order of accuracy via the finite-difference A-WENO *** designed schemes are applied to three different traffic flow models and tested on a number of challenging numerical *** schemes produce quite accurate results though the resolution achieved by the fifth-order A-WENO scheme is *** proposed scheme in this paper sets the stage for developing more robust and complex continuum traffic flow models with respect to human psychological factors.

关键词： Finite-difference A-WENO schemes finite-volume central-upwind schemes pathconservative central-upwind schemes non-oscillatory schemes continuum traffic flow model driver behavior.

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Correlative spatter and vapour depression dynamics during laser powder bed fusion of an Al-Fe-Zr alloy

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International Journal of Extreme Manufacturing 2024年第5期6卷 298-310页

作者： Da Guo Rubén Lambert-Garcia Samy Hocine Xianqiang Fan Henry Greenhalgh Ravi Shahani Marta Majkut alexander Rack Peter D Lee chu Lun Alex Leung UCL Mechanical Engineering University College LondonLondon WC1E 7JEUnited Kingdom Research Complex at Harwell Harwell CampusDidcot OX110FAUnited Kingdom HiETA Technologies Bristol BS167FRUnited Kingdom Constellium Technology Centre 38341 VoreppeFrance ESRF—The European Synchrotron 38000 GrenobleFrance

Spatter during laser powder bed fusion(LPBF)can induce surface defects,impacting the fatigue performance of the fabricated ***,we reveal and explain the links between vapour depression shape and spatter dynamics during LPBF of an Al-Fe-Zr aluminium alloy using high-speed synchrotron x-ray *** quantify the number,trajectory angle,velocity,and kinetic energy of the spatter as a function of vapour depression zone/keyhole morphology under industry-relevant processing *** depression zone/keyhole morphology was found to influence the spatter ejection angle in keyhole versus conduction melting modes:(i)the vapour-pressure driven plume in conduction mode with a quasi-semi-circular depression zone leads to backward spatter whereas;and(ii)the keyhole rear wall redirects the gas/vapour flow to cause vertical spatter ejection and rear rim droplet *** the opening of the keyhole or vapour depression zone can reduce entrainment of solid *** discover a spatter-induced cavity mechanism in which small spatter particles are accelerated towards the powder bed after laser-spatter interaction,inducing powder denudation and cavities on the printed *** quantifying these laser-spatter interactions,we suggest a printing strategy for minimising defects and improving the surface quality of LPBF parts.

关键词： spatter vapour depression x-ray imaging defects surface quality

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Experimental mapping of short-wavelength phonons in proteins

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The Innovation 2022年第1期3卷 97-103页

作者： Utsab R.Shrestha Eugene Mamontov Hugh M.O’Neill Qiu Zhang alexander I.Kolesnikov Xiangqiang chu UT/ORNL Center for Molecular Biophysics Biosciences DivisionOak Ridge National LaboratoryOak RidgeTN 37831USA Neutron Scattering Division Oak Ridge National LaboratoryOak RidgeTN 37831USA Department of Nuclear Science and Technology Graduate School of China Academy of Engineering PhysicsBeijing 100193China

Phonons are quasi-particles,observed as lattice vibrations in periodic materials,that often dampen in the presence of structural ***,phonon-like collective excitations exist in highly complex systems,such as proteins,although the origin of such collective motions has remained *** we present a picture of temperature and hydration dependence of collective excitations in green fluorescent protein(GFP)obtained by inelastic neutron *** results provide evidence that such excitations can be used as a measure of flexibility/softness and are possibly associated with the protein’s ***,we show that the hydration water in GFP interferes with the phonon propagation pathway,enhancing the structural rigidity and stability of GFP.

关键词： scattering collective excitation

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Ultra-sensitive hybrid diamond nanothermometer

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National Science Review 2021年第5期8卷 76-84页

作者： chu-Feng Liu Weng-Hang Leong Kangwei Xia Xi Feng Amit Finkler Andrej Denisenko J?rg Wrachtrup Quan Li Ren-Bao Liu Department of Physics The Chinese University of Hong Kong 3rd Institute of Physics and Center for Applied Quantum Technologies University of Stuttgart Department of Chemical and Biological Physics Weizmann Institute of Science Max Planck Institute for Solid State Research The Hong Kong Institute of Quantum Information Science and Technology The Chinese University of Hong Kong

Nitrogen-vacancy（NV） centers in diamond are promising quantum sensors because of their long spin coherence time under ambient conditions. However, their spin resonances are relatively insensitive to non-magnetic parameters such as temperature. A magnetic-nanoparticle-nanodiamond hybrid thermometer, where the temperature change is converted to the magnetic field variation near the Curie temperature, were demonstrated to have enhanced temperature sensitivity(11 m K Hz-1/2)（Wang N, Liu G-Q and Leong W-H et al. Phys Rev X 2018; 8: 011042）, but the sensitivity was limited by the large spectral broadening of ensemble spins in nanodiamonds. To overcome this limitation, here we show an improved design of a hybrid nanothermometer using a single NV center in a diamond nanopillar coupled with a single magnetic nanoparticle of copper-nickel alloy, and demonstrate a temperature sensitivity of 76 μK Hz-1/*** hybrid design enables detection of 2 m K temperature changes with temporal resolution of 5 ms. The ultra-sensitive nanothermometer offers a new tool to investigate thermal processes in nanoscale systems.

关键词： nano-thermometry diamond nitrogen-vacancy center quantum sensing magnetic nanoparticle

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Threats of Zika virus transmission for Asia and its Hindu-Kush Himalayan region

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Infectious Diseases of Poverty 2018年第1期7卷 387-393页

作者： Meghnath Dhimal Sushma Dahal Mandira Lamichhane Dhimal Shiva Raj Mishra Khem BKarki Krishna Kumar Aryal Ubydul Haque Md Iqbal Kabir Pradeep Guin Azeem Mehmood Butt Harapan Harapan Qi-Yong Liu Cordia chu Doreen Montag David alexander Groneberg Basu Dev Pandey Ulrich Kuch Ruth Muller Nepal Health Research Council(NHRC) Ramshah PathKathmanduNepal Institute of Occupational edicine Social Medicine and Environmental MedicineGoethe UniversityFrankfurt am MainGermany Faculty of Social Sciences Goethe UniversityFrankfurt am MainGermany The University of Queensland BrisbaneAustralia Department of Public Health Baldwin Wallace UniversityBereaOhioUSA Department of Epidemiology National Institute of Preventive and Social MedicineMinistry of Health and Family WelfareDhakaBangladesh Public Health Foundation of India GurgaonHaryanaIndia Centre for Environmental Health GurgaonHaryanaIndia Translational Genomics Laboratory Department of BiosciencesCOMSATS Institute of Information Technology(CIIT)Islamabad 45550Pakistan Medical Research Unit School of MedicineSyiah Kuala UniversityBanda AcehIndonesia WHO Collaborating Centre for Vector Surveillance and Management SKLIDCCIDICDCChina CDCBeijingChina Centre for Environment and Population Health Griffith UniversityNathanQueenslandAustralia Barts and the London School of Medicine Centre for Primary Care and Public HealthQueen Mary University of LondonLondonUK Department of Health Services Ministry of HealthGovernment of NepalKathmanduNepal

Asia and its Hindu Kush Himalayan(HKH)region is particularly vulnerable to environmental change,especially climate and land use changes further influenced by rapid population growth,high level of poverty and unsustainable *** has been a hotspot of dengue fever and chikungunya mainly due to its dense human population,unplanned urbanization and *** an urban cycle,dengue virus(DENV)and chikungunya virus(CHIKV)are transmitted by Aedes aegypti and *** mosquitoes which are also competent vectors of Zika virus(ZIKV).Over the last decade,DENV and CHIKV transmissions by *** have extended to the Himalayan countries of Bhutan and Nepal and ZIKV could follow in the footsteps of these viruses in the HKH *** already established distribution of human-biting Aedes mosquito vectors and a naïve population with lack of immunity against ZIKV places the HKH region at a higher risk of *** of the countries in the HKH region have already reported ZIKV *** have documented an increasing threat of ZIKV in Asia and its HKH region because of the high abundance and wide distribution of human-biting mosquito vectors,climate change,poverty,report of indigenous cases in the region,increasing numbers of imported cases and a naïve population with lack of immunity against *** outbreak anywhere is potentially a threat ***,in order to ensure international health security,all efforts to prevent,detect,and respond to ZIKV ought to be intensified now in Asia and its HKH *** prepare for possible ZIKV outbreaks,Asia and the HKH region can also learn from the success stories and strategies adopted by other regions and countries in preventing ZIKV and associated *** future control strategies for DENV,CHIKV and ZIKV should be considered in tandem with the threat to human well-being that is posed by other emerging and re-emerging vector-borne and zoonotic diseases,and by the continuing urgent need to strengthen public

关键词： Aedes aegypti Aedes albopictus Dengue virus Chikungunya virus Hindu Kush Himalayas Mountain Poverty Zika virus

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Impact of T_(i)/T_(e )ratio on ion transport based on EAST H-mode plasmas

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Plasma Science and Technology 2024年第4期26卷 68-78页

作者：刘建文臧庆梁云峰陈佳乐邬潇河 alexander KNIEPS 扈嘉辉金仡飞张斌储宇奇刘海庆吕波段艳敏李妙辉陈颖杰龚先祖 the EAST Team Institute of Plasma Physics Chinese Academy of SciencesHefei 230031People’s Republic of China University of Science and Technology of China Hefei 230026People’s Republic of China Forschungszentrum Jülich GmbH Institut für Energie-und Klimaforschung-PlasmaphysikPartner of the Trilateral Euregio Cluster(TEC)Jülich 52425Germany

At the EAST tokamak, the ion temperature(T_(i)) is observed to be clamped around 1.25 keV in electron cyclotron resonance(ECR)-heated plasmas, even at core electron temperatures up to 10 keV(depending on the ECR heating power and the plasma density). This clamping results from the lack of direct ion heating and high levels of turbulence-driven transport. Turbulent transport analysis shows that trapped electron mode and electron temperature gradient-driven modes are the most unstable modes in the core of ECR-heated H-mode plasmas. Nevertheless, recently it was found that the T_(i)/T_(e)ratio can increase further with the fraction of the neutral beam injection(NBI) power, which leads to a higher core ion temperature(Ti0). In NBI heating-dominant H-mode plasmas, the ion temperature gradient-driven modes become the most unstable ***, a strong and broad internal transport barrier(ITB) can form at the plasma core in high-power NBI-heated H-mode plasmas when the T_(i)/T_(e)ratio approaches ~1, which results in steep core Teand Tiprofiles, as well as a peaked neprofile. Power balance analysis shows a weaker Teprofile stiffness after the formation of ITBs in the core plasma region, where Ticlamping is broken,and the core Tican increase further above 2 keV, which is 80% higher than the value of Ticlamping in ECR-heated plasmas. This finding proposes a possible solution to the problem of Ticlamping on EAST and demonstrates an advanced operational regime with the formation of a strong and broad ITB for future fusion plasmas dominated by electron heating.

关键词： ion temperature clamping transport neutral beam injection stiffness internal transport barrier

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High-silica faujasite zeolite-tailored metal encapsulation for the low-temperature production of pentanoic biofuels

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Journal of Energy Chemistry 2024年第1期88卷 552-560,I0012页

作者： Wenhao Cui Yuanshuai Liu Pengfei Guo Zhijie Wu Liqun Kang Huawei Geng Shengqi chu Linying Wang Dong Fan Zhenghao Jia Haifeng Qi Wenhao Luo Peng Tian Zhongmin Liu National Engineering Research Center of Lower-Carbon Catalysis Technology Dalian National Laboratory for Clean EnergyDalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023LiaoningChina University of Chinese Academy of Sciences Beijing 100049China Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of SciencesQingdao 266101ShandongChina College of Chemistry and Chemical Engineering Inner Mongolia UniversityHohhot 010021Inner MongoliaChina State Key Laboratory of Heavy Oil Processing and Key Laboratory of Catalysis of CNPC China University of PetroleumBeijing 102249China Department of Inorganic Spectroscopy Max Planck Institute for Chemical Energy ConversionMülheim an der Ruhr 45470Germany Beijing Synchrotron Radiation Facility Institute of High Energy PhysicsChinese Academy of SciencesBeijing 100049China Division of Energy Research Resources Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023LiaoningChina Leibniz-Institut für Katalyse Albert-Einstein-Straβe 29aRostock 18059Germany

Zeolite-encapsulated metal nanoclusters are at the heart of bifunctional catalysts,which hold great potential for petrochemical conversion and the emerging sustainable ***,efficient encapsulation of metal nanoclusters into a high-silica zeolite Y in particular with good structural integrity still remains a significant ***,we have constructed Ru nanoclusters(~1 nm)encapsulated inside a high-silica zeolite Y(SY)with a SiO_(2)/Al_(2)O_(3) ratio(SAR)of 10 via a cooperative strategy for direct zeolite synthesis and a consecutive impregnation for metal *** with the benchmark Ru/H-USY and other analogues,the as-prepared Ru/H-SY markedly boosts the yields of pentanoic biofuels and stability in the direct hydrodeoxygenation of biomass-derived levulinate even at a mild temperature of 180℃,which are attributed to the notable stabilization of transition states by the enhanced acid accessibility and properly sized constraints of zeolite cavities owing to the good structural integrity.

关键词： High-silica zeolite Y Metal encapsulation Bifunctional catalysis Hydrodeoxygenation Biofuels

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技术问答解决技术问题

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空中英语教室（高级版．彭蒙惠英语） 2019年第3期 12-13,39,40页

作者： Steve alexander Tribune Content Agency, LLC. OLIVE chu(PAGE DESIGN) 马励(译) 不详

如何安全储存iPhone照片问:我朋友的iPhone 5和我的iPhone SE—直提示我们,手机的储存容量不够存储更多照片,所以我们很不情愿地删除了大量照片,但是仍然收到警告我们能怎么办?

关键词： iPhone 技术安全储存储存容量照片手机

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