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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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Measurements of Fog Water Deposition on the California Central Coast

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Atmospheric and Climate Sciences 2012年第4期2卷 525-531页

作者： Cyrus Hiatt daniel fernandez Christopher Potter California State University Monterey Bay Seaside United States of America NASA Ames Research Center Moffett Field United States of America

Fog deposition is a notable component of the water budget of herbaceous-shrub ecosystems on the central and southern coastal regions of California. This paper presents an analysis of fog water deposition rates and meteorological controls in Big Sur, California. Mesh-screen fog collectors were installed the Brazil Ranch weather station sites to measure fog water during the summer seasons of 2010 and 2011. Fog deposition occurred during 73% of days recorded in 2010 and 87% of days recorded in 2011. The daily average deposition rate was 2.29 L/m2 in 2010 and 3.86 L/m2 in 2011. The meteorological variables which had the greatest influence on prediction of fog deposition were wind speed, wind direction, and the dew-point depression (difference between air temperature and dew point). Based on these results, we hypothesize that high rates of summer fog deposition help sustain the productivity of California coastal vegetation through periods of low rainfall.

关键词： Fog Deposition California Styling Water Budget

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Effectiveness of a course in the control of tobacco use for university health students: A quasi-experimental community intervention trial

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Open Journal of Nursing 2013年第4期3卷 351-357页

作者： daniel fernandez Antonio Molina Vicente Martin Beatriz Ordas Jose Manuel De Luis Leon University Hospital University of Leon Leon Spain

Introduction: The aim of the study was to evaluate the effectiveness of a tobacco control course in the reduction of prevalence and the improvement of knowledge and attitudes among university health students. Method: Quasi-experimental study on a community based intervention. Interventional campus students received a tobacco control course in the first year of the degree. Data were collected by Self-Answered Questionnaire during three academic years in two graduations years among health students in both campuses. Results: 84.4% of students participated in the study. In both campuses tobacco use was reduced, not significantly, above all in those joining courses from origins other than baccalaureate. In the intervention and control campus showed an increase in the nicotine dependency according to Fagerstr?m test and a little change in motivation according toRichmondtest. The regression model best explaining the improving of the knowledge included academic course mainly and campus and academic background too. With regard to opinions and beliefs tobacco use was not influenced, being associated in general to the academic course. Conclusions: A specific tobacco control course did not change prevalence of tobacco, nicotine dependence and motivation to give up. The improvement in knowledge was associated with academic course in both campuses. We recommend to commence smoking cessation strategies in university health students.

关键词： Tobacco Students Nursing University Intervention

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

Energy Geoscience

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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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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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