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Basophile:Accurate Fragment charge State Prediction Improves Peptide Identification Rates

Genomics, Proteomics & Bioinformatics 2013年第2期11卷 86-95页

作者： Dong Wang Surendra Dasari Matthew c.chambers Jerry D.Holman Kan chen daniel c.liebler daniel J.Orton Samuel O.Purvine Matthew E.Monroe chang Y.chung Kristie L.Rose David L.Tabb Department of Biomedical Informatics Vanderbilt University Medical Center Division of Biomedical Statistics and Informatics Mayo Clinic Department of Biochemistry Vanderbilt University Medical Center Biological Sciences Division and Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Department of Pharmacology Vanderbilt University Medical Center Vanderbilt-Ingram cancer center Vanderbilt University School of Medicine

In shotgun proteomics, database search algorithms rely on fragmentation models to pre- dict fragment ions that should be observed for a given peptide sequence. The most widely used strat- egy （Naive model） is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmen- tation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during cID/higher- energy collision induced dissociation （HcD） of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% （on average） over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.

关键词： Fragmentation Basicity Fragment size Ordinal regression

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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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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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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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Floristic composition and edaphic relationships in ferruginous campo rupestre reference ecosystems

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Journal of Mountain Science 2024年第3期21卷 719-733页

作者： G.Wilson FERNANDES Letícia RAMOS Dario c.PAIVA Jéssica cUNHA-BLUM Vanessa Matos GOMES daniel NEGREIROS Ecologia Evolutiva&Biodiversidade Departamento de GenéticaEcologia e Evolução/ICBUniversidade Federal de Minas Gerais31270-901Belo HorizonteMGBrazil Knowledge center for Biodiversity 31270-901Belo HorizonteMGBrazil Department of Biological Sciences Institute of EnvironmentFlorida International UniversityMiamiFL 33199USA Programa de Pós Graduação em Biodiversidade e Uso dos Recursos Naturais Universidade Estadual de Montes ClarosMontes ClarosMGBrazil Laboratório de Estudo das Relações Solo-Planta Departamento de SolosUniversidade Federal Rural do Rio de JaneiroSeropédicaRGBrazil

Land use change and occupation have led to modifications in the environment causing loss of biodiversity and ecosystem services throughout the *** environments with high economic relevance,such as the ferruginous campo rupestre(rupestrian grassland known as canga in Brazil),are even more susceptible to severe impacts due to their extreme habitat conditions and low *** determination of reference ecosystems based on the intrinsic characteristics of the ecosystem is essential for conservation as well as to the implementation of ecological *** proposed the reference ecosystem of the three main types of habitats of the ferruginous campo rupestre based on their floristic *** described the floristic composition of each habitat and evaluated the physicochemical properties of the soils and the relationship between plants and *** three habitats showed high diversity of plant species and many endemic species,such as chamaecrista choriophylla,cuphea pseudovaccinium,Lychnophora pinaster,and Vellozia *** distribution of vegetation was strongly related with the edaphic characteristics,with a set of species more adapted to high concentration of base saturation,fine sand,organic carbon,and iron,while another set of species succeeded in more acidic soils with higher S and silt *** provide support for the contention that the ferruginous campo rupestre is a mosaic of different habitats shaped by intrinsic local *** to recognize the floristic composition of each particular habitat can lead to inappropriate restoration,increased habitat homogenization and increased loss of biodiversity and ecosystem *** study also advances the knowledge base for building the reference ecosystem for the different types of ferruginous campo rupestre habitats,as well as a key database for highlighting those species contribute most to community assembly in this diverse and threatened tropical mountain ecosystem.

关键词： canga Ecological restoration Extreme ecosystem Non-forest ecosystems Rupestrian grassland Taxon environment relationships

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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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characterization of Arroyo Verde Epithermal Deposit:Paragenesis,Mineral Geochemistry,Geochronology and Fluid Inclusions in Lower chon Aike Volcanism,Argentina

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Journal of Earth Science 2024年第1期35卷 62-84页

作者： cecilia Pavón Pivetta Leonardo Benedini Paulo Marcos Ma.Agustina cócola Mercedes Virginia Barros daniel Gregori Leonardo Strazzere Anderson costa dos Santos Mauro c.Geraldes Instituto Geologico del Sur(INGEOSUR) Universidad Nacional del Sur(UNS)-Consejo Nacional de Investigaciones Cientificas y Tecnicas(CONICET)Bahia Blanca 8000Argentina Dpto.de Geologia Universidad Nacional del Sur(UNS)Bahia Blanca 8000Argentina Universidad Nacional de Rio Negro Instituto de Investigacion en Paleobiologia y GeologiaGeneral Roca 8332Argentina Universidade do Estado do Rio de Janeiro Faculdade de GeologiaDepartamento de Mineralogia e Petrologia igneaRiodeJaneiro20559-900Brazil Geobiotec Departamento de GeocienciasUniversidade de AveiroAveiro 3800-002Portuga

Arroyo Verde epithermal deposit,in the North Patagonia region of Argentina,is located within the Lower chon Aike volcanism and is developed between 192.6±2.5 Ma(mineralization host rock)and 189.5±2.6 Ma(overlying lava).Marifil volcanic complex is the host rock for these veins,veinlets and *** particular small deposit has developed low to intermediate sulphidation characteristics,with gangue mineral textures associated with several ore *** probe microanalysis determines electrum,silver minerals such as acanthite,and tetrahedrite,related Ag-cu minerals like jalpaite,mckinstryite,stromeyerite,and base metals like chalcopyrite,sphalerite,galena and *** inclusions in quartz of two out of five events indicate that these Low Jurassic veins were formed due to subtle boiling and dilution mechanisms and by low-salinity(3.4 wt.%to 6.7 wt.%Nacl Eq)magmatic-hydrothermal fluid at 225 to 310℃.The fluid inclusion measurements that indicate boiling(Event 3)were plotted,and based on this data,we interpret that the Arroyo Verde deposit has been eroded between 550 and 700 *** particular character has not been previously recorded for other sectors of the eastern north Patagonian region.

关键词： epithermal deposit Ag minerals mineral geochemistry fluid inclusions chon Aike geochronology

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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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Probabilistic analysis of tunnel face seismic stability in layered rock masses using Polynomial chaos Kriging metamodel

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第7期16卷 2678-2693页

作者： Jianhong Man Tingting Zhang Hongwei Huang daniel Dias Department of Geotechnical Engineering Key Laboratory of Geotechnical and Underground Engineering of Ministry of EducationCollege of Civil EngineeringTongji UniversityShanghai200092China Grenoble Alpes 3SR LabCNRS UMR 5521Grenoble38000France

Face stability is an essential issue in tunnel design and *** rock masses are typical and ubiquitous;uncertainties in rock properties always *** view of this,a comprehensive method,which combines the Upper bound Limit analysis of Tunnel face stability,the Polynomial chaos Kriging,the Monte-carlo Simulation and Analysis of covariance method(ULT-PcK-MA),is proposed to investigate the seismic stability of tunnel faces.A two-dimensional analytical model of ULT is developed to evaluate the virtual support force based on the upper bound limit *** efficient probabilistic analysis method PcK-MA based on the adaptive Polynomial chaos Kriging metamodel is then implemented to investigate the parameter uncertainty *** input parameters,including geological strength indices,uniaxial compressive strengths and constants for three rock formations,and the horizontal seismic coefficients,are treated as random *** effects of these parameter uncertainties on the failure probability and sensitivity indices are *** addition,the effects of weak layer position,the middle layer thickness and quality,the tunnel diameter,the parameters correlation,and the seismic loadings are investigated,*** results show that the layer distributions significantly influence the tunnel face probabilistic stability,particularly when the weak rock is present in the bottom *** efficiency of the proposed ULT-PcK-MA is validated,which is expected to facilitate the engineering design and construction.

关键词： Tunnel face stability Layered rock masses Polynomial chaos Kriging(PcK) Sensitivity index Seismic loadings

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