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Observation of a single protein by ultrafast X-ray diffraction

Light(Science & Applications) 2024年第1期13卷 80-90页

作者： Tomas Ekeberg Dameli Assalauova Johan Bielecki Rebecca Boll Benedikt J.Daurer Lutz A.Eichacker Linda E.Franken Davide E.Galli Luca Gelisio Lars Gumprecht Laura H.Gunn Janos Hajdu Robert Hartmann Dirk Hasse Alexandr Ignatenko Jayanath Koliyadu Olena Kulyk Ruslan Kurta Markus Kuster Wolfgang Lugmayr Jannik Lübke Adrian P.Mancuso Tommaso Mazza Carl Nettelblad Yevheniy Ovcharenko daniel E.Rivas Max Rose Amit K.Samanta Philipp Schmidt Egor Sobolev Nicusor Timneanu Sergey Usenko daniel westphal Tamme Wollweber Lena Worbs Paul Lourdu Xavier Hazem Yousef Kartik Ayyer Henry N.Chapman Jonas A.Sellberg Carolin Seuring Ivan A.Vartanyants Jochen Küpper Michael Meyer Filipe R.N.C.Maia Laboratory of Molecular Biophysics Department of Cell and Molecular BiologyUppsala UniversityHusargatan 3(Box 596)SE-75124 UppsalaSweden Deutsches Electronen-Synchrotron DESY Notkestrasse 8522607 HamburgGermany European XFEL Holzkoppel 422869 SchenefeldGermany Diamond Light Source Harwell Science&Innovation CampusDidcot OX110DEUK University of Stavanger Centre Organelle ResearchRichard-Johnsensgate 44021 StavangerNorway Leibniz Institute for Experimental Virology(HPI) Centre for Structural Systems BiologyNotkestraße 8522607 HamburgGermany Dipartimento di Fisica“Aldo Pontremoli” Universitàdegli Studi di Milanovia Celoria 1620133 MilanoItaly Center for Free-Electron Laser Science DESY22607 HamburgGermany Plant Biology Section School of Integrative Plant ScienceCornell UniversityIthacaNY 14853USA PNSensor GmbH Otto-Hahn-Ring 6D-81739 MünchenGermany Biomedical and X-Ray Physics Department of Applied PhysicsAlbaNova University CenterKTH Royal Institute of TechnologySE-10691 StockholmSweden ELI Beamlines/IoP Institute of Physics AS CR v.v.i.Na Slovance 218221 Prague 8Czech Republic Multi-User CryoEM Facility Centre for Structural Systems BiologyNotkestr.8522607 HamburgGermany University Medical Center Hamburg-Eppendorf(UKE) Martinistrasse 5220246 HamburgGermany The Hamburg Center for Ultrafast Imaging Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of Physics Universität HamburgLuruper Chaussee 14922761 HamburgGermany Department of Chemistry and Physics La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVIC 3086Australia Division of Scientific Computing Science for Life LaboratoryDepartment of Information TechnologyUppsala UniversityBox 337SE-75105 UppsalaSweden European Molecular Biology Laboratory c/o DESYNotkestrasse 8522607 HamburgGermany Department of Physics and Astronomy Uppsala UniversityBox 516SE-75120 UppsalaSweden Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 14922761 HamburgGe

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired *** was one of the arguments for building X-ray free-electron *** to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably *** was first demonstrated on biological samples a decade ago on the giant *** then,a large collaboration has been pushing the limit of the smallest sample that can be *** ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of *** we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single *** the pattern,it is possible to determine the approximate orientation of the *** experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.

关键词： smallest intense ultrafast

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Testing and modelling of transient adhesion phenomena in rolling-sliding contacts

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Friction 2024年第5期12卷 1016-1027页

作者： daniel KVARDA Alexander MEIERHOFER Klaus SIX Faculty of Mechanical Engineering Brno University of TechnologyBrno61669Czech Republic Virtual Vehicle Research GmbH Graz8010Austria

Transient adhesion effects in rolling–sliding contacts influence all aspects of train–track *** is of high importance specifically when these effects result in critically low adhesion,which poses a risk to traction and braking of railway *** study presents a model that can replicate the transient changes of the coefficient of adhesion with tested water and solid particle *** experimental data for the model are measured using a commercial ball-on-disc *** experimental results showed a liquid reservoir in front of the contact area that slowly reduces in *** observation was used in the modelling approach to divide the calculation into two stages where the reservoir is present and when it *** model was able to reproduce the occurrence of low adhesion region seen in experimental results with different particle concentrations.

关键词： coefficient of adhesion tribology transient effects wheel-rail contact

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Energy model based on solar potential and the production of electrical energy through living plants’photosynthesis

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Clean Energy 2024年第3期8卷 116-126页

作者： Raymond daniel Rodriguez Martinez Department of Industrial Production Faculty of EngineeringUniversidad Metropolitana1073 CaracasVenezuela

Developing a sustainable energy model is imperative considering the current trend towards decarbonizing sectors *** this purpose,Venezuela was used as a reference to propose an energy model focused on taking advantage of plant photosynthesis through microbial-vegetable fuel cells together with an agro-photovoltaic system to enhance energy and agricultural *** production from the cells was estimated using an average power density of 264 mW/m^(2) over 4%of the areas destined for crops in the entire Venezuelan region,obtaining an annual production of 19.889 GWh/*** contrast,the energy production of the agro-photovoltaic system was modelled using PVsyst software on 50%of the area used for the cells distributed throughout the states of Anzoátegui,Guárico,Monagas and Portuguesa according to their meteorological conditions,solar irradiation and agricultural activity,resulting in 3703417 GWh/*** resulting whole system proved to be able to cover>10 times the installed electricity generation capacity at a national level and,together with the tremendous scalability of the microbial fuel cells,it shows that Venezuela has a high potential for the production and distribution of clean energy.

关键词： ecosystems microbial fuel cell microorganisms renewable sustainability

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Beyond the code:the role of histone methylation in cancer resistance and therapy

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Signal Transduction and Targeted Therapy 2024年第7期9卷 2837-2839页

作者： daniel Noerenberg Frederik Damm Charité–Universitätsmedizin Berlin corporate member of Freie Universität BerlinHumboldt Universität zu Berlinand Berlin Institute of HealthDepartment of HematologyOncologyand Cancer ImmunologyBerlinGermany German Cancer Consortium(Deutsches Konsortium für Translationale Krebsforschung DKTK)Partner SiteBerlinGermany

In a recently published paper in Nature,Yamagishi et *** a comprehensive exploration on the mechanistic basis and subsequent emergence of resistance of targeting histone H3 lysine trimethylation(H3K27me3)using the EZH... 详细信息

关键词： EZH2 resistance

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Plant-microbial fuel cell for electrical generation through living plants: an internal resistance insight into the plant species used

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Clean Energy 2024年第5期8卷 45-53页

作者： Raymond daniel Rodriguez Martinez Department of Industrial Production Faculty of EngineeringUniversidad Metropolitana1073 CaracasVenezuela

Climate change is a global threat,the presence of which has encouraged the development and implementation of renewable energies,including plant–microbial fuel cells,which could generate 6629568–33147840 MWh per year due to their large-scale *** of the main challenges associated with microbial cells is internal resistance—a parameter whose magnitude is influenced by sev-eral *** the case of plant–microbial fuel cells,adding a plant positively affects the mitigation of internal ***,the species employed is expected to play an important *** the present study,the objective was to determine as a general reference the internal resistance of cells using various plant species,among which were tomato(Solanum lycopersicum),black beans(Phaseolus vulgaris),aloe vera(Aloe vera),corn(Zea mays),and moss(Dicranidae).For this purpose,an experimental procedure was carried out to compare the manual voltage measurements with a free cell concerning the voltage obtained by adding an external resistor in *** internal resistance values were determined as a function of the measured voltage,obtaining 177,179,175,324,and 233 kΩfor aloe vera,corn,tomato,black beans,and moss,*** this,it was shown that the roots of the plants represent an essen-tial addition to the internal resistance of the cell in the short *** contrast,plants with a C4 photosynthetic metabolism are more favourable,while C3 plants can also benefit from internal resistance during a more extended period of rhizodeposition.

关键词： climate change energy microorganism renewable source voltage

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Assessment of scale interactions associated with wake meandering using bispectral analysis methodologies

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Theoretical & Applied Mechanics Letters 2024年第2期14卷 65-75页

作者： Dinesh Kumar Kinjangi daniel Foti Department of Mechanical Engineering University of MemphisMemphisTennesseeUSA

Large atmospheric boundary layer fluctuations and smaller turbine-scale vorticity dynamics are separately hypothesized to initiate the wind turbine wake meandering phenomenon,a coherent,dynamic,turbine-scale oscillation of the far *** interactions,the mechanism of energy transfers between scales,manifest as triples of wavenumbers or frequencies and can be characterized through bispectral *** bispectrum,which correlates the two frequencies to their sum,is calculated by two recently developed multi-dimensional modal decomposition methods:scale-specific energy transfer method and bispectral mode ***-eddy simulation of a utility-scale wind turbine in an atmospheric boundary layer with a broad range of large length-scales is used to acquire instantaneous velocity *** bispectrum from both methods identifies prominent upwind and wake meandering interactions that create a broad range of energy scales including the wake meandering *** coherent kinetic energy associated with the interactions shows strong correlation between upwind scales and wake meandering.

关键词： Wind turbine wake Mode decomposition Bispectral analysis

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Numerical study on the use of soft material walls to enhance seismic performance of an existing tunnel

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Underground Space 2024年第2期15卷 90-112页

作者： Qiangqiang Sun Menghao Hou daniel Dias Institute of Geotechnical Engineering College of Civil Engineering and ArchitectureHebei UniversityBaoding 071002China Laboratory 3SR CNRS UMR 5521Grenoble Alpes UniversityGrenoble 38000France

Seismic risk is one of the biggest challenges for tunnel safety,and several mitigation techniques have been proposed to enhance the seismic performance of existing *** paper aims to investigate the effectiveness of an innovative approach for reducing the seismic risk of existing tunnels by using soft material walls(SMW)symmetrically installed in the surrounding *** investigation is performed with a two-dimensional numerical model and the effectiveness of SMW in mitigating the seismic-induced lining forces is quantitatively evaluated by reduction *** influences of nonlinear properties of soil,SMW and tunnel lining on the isolation effectiveness are also *** parametric studies show that the computed reduction ratio is strongly affected by the modulus ratio between the SMW and the soil,the wall geometric parameter,and the flexibility *** is more effective for the thick and soft isolation walls that are inserted near a stiff tunnel in the soft *** tunnel seismic response can be reduced by up to 50%for the scenarios ***,the parametric study identifies an optimum normalized depth of SMW and recommends a relation between the maximum isolation effect and the flexibility ***,simple charts are suggested in this work for estimating the isolation effect in specific conditions of the soil and the *** these lines,the results of this work may be used in the seismic retrofitting of an existing tunnel,aiding the preliminary design of the isolation walls.

关键词： Tunnels Earthquakes Seismic analysis Isolation walls Soft material

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Fundamental error in tree-based machine learning model selection for reservoir characterisation

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Energy Geoscience 2024年第2期5卷 214-224页

作者： daniel Asante Otchere Centre of Excellence in Subsurface Seismic Imaging and Hydrocarbon Prediction Universiti Teknologi PETRONAS32610Seri IskandarPerak Darul RidzuanMalaysia

Over the past two decades,machine learning techniques have been extensively used in predicting reservoir *** this approach has significantly contributed to the industry,selecting an appropriate model is still challenging for most *** solely on statistical metrics to select the best model for a particular problem may not always be the most effective *** study encourages researchers to incorporate data visualization in their analysis and model selection *** evaluate the suitability of different models in predicting horizontal permeability in the Volve field,wireline logs were used to train Extra-Trees,Ridge,Bagging,and XGBoost *** Random Forest feature selection technique was applied to select the relevant logs as inputs for the *** on statistical metrics,the Extra-Trees model achieved the highest test accuracy of 0.996,RMSE of 19.54 mD,and MAE of 3.18 mD,with XGBoost coming in ***,when the results were visualised,it was discovered that the XGBoost model was more suitable for the problem being *** XGBoost model was a better predictor within the sandstone interval,while the Extra-Trees model was more appropriate in non-sandstone *** this study aims to predict permeability in the reservoir interval,the XGBoost model is the most *** contrasting results demonstrate the importance of incorporating data visualisation techniques as an evaluation *** the heterogeneity of the subsurface,relying solely on statistical metrics may not be sufficient to determine which model is best suited for a particular problem.

关键词： Data visualisation Permeability Machine learning Statistical metrics

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Online Demand Response Characterization Based on Variability in Customer Behavior

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Journal of Modern Power Systems and Clean Energy 2024年第3期12卷 936-946页

作者： Lester Marrero daniel Sbárbaro Luis García-Santander the Department of Electrical Engineering University of ConcepciónConcepción 4070409Chile

This paper proposes an online framework to characterize demand response(DR)over *** proposed framework facilitates obtaining and updating the daily consumption patterns of *** essential concept of response profile class(RPC)is introduced for characterization and complemented by the measure of the variability in customer *** paper uses a modified version of the incremental clustering by fast search and find of density peaks(CFSFDP)algorithm for daily profiles,considering the multivariate normal kernel density estimator and incremental forms of the Davies-Bouldin(i DB)and Xie-Beni(i XB)validity *** studies conducted using real-world and simulated daily profiles of residential and commercial Chilean end-users have demonstrated how the proposed framework can continuously characterize *** proposed framework is proven to achieve realistic customer models for effective energy management by estimating the customer response to price signals at the distribution system operator(DSO)level.

关键词： Demand response(DR) incremental indice online characterization online clustering response profile class(RPC)

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Comprehensive review of hepatocellular carcinoma with portal vein tumor thrombus:State of art and future perspectives

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Hepatobiliary & Pancreatic Diseases International 2024年第3期23卷 221-227页

作者： Paschalis Gavriilidis Timothy M Pawlik daniel Azoulay Department of Surgery Colchester General HospitalTurner RoadColchester CO45JLUK Department of Surgery The Ohio State Wexner Medical CenterJames Comprehensive Cancer CenterColumbusOHUSA Department of Hepato-Biliary and Liver Transplantation surgery Paul Brousse University HospitalParis-Saclay UniversityVillejuif 94800France

Background:Despite advances in the diagnosis of patients with hepatocellular carcinoma(HCC),70%-80%of patients are diagnosed with advanced stage *** vein tumor thrombus(PVTT)is among the most ominous signs of advanced stage disease and has been associated with poor survival if *** sources:A systematic search of MEDLINE(PubMed),Embase,Cochrane Library and Database for Systematic Reviews(CDSR),Google Scholar,and National Institute for Health and Clinical Excellence(NICE)databases until December 2022 was conducted using free text and MeSH terms:hepatocellular carcinoma,portal vein tumor thrombus,portal vein thrombosis,vascular invasion,liver and/or hepatic resection,liver transplantation,and systematic ***:Centers of surgical excellence have reported promising results related to the individualized surgical management of portal thrombus versus arterial chemoembolization or systemic *** elements to the individualized surgical management of HCC and portal thrombus include precise classification of the portal vein tumor thrombus,accurate identification of the subgroups of patients who may benefit from resection,as well as meticulous surgical *** review addressed five specific areas:(a)formation of PVTT;(b)classifications of PVTT;(c)controversies related to clinical guidelines;(d)surgical treatments versus non-surgical approaches;and(e)characterization of surgical techniques correlated with classifications of ***:Current evidence from Chinese and Japanese high-volume centers demonstrated that patients with HCC and associated PVTT can be managed with surgical resection with acceptable results.

关键词： Hepatectomy Liver surgery Liver neoplasms Portal vein tumor thrombus

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