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Scaling Notebooks as Re-configurable Cloud workflows

Data Intelligence 2022年第2期4卷 409-425页

作者： Yuandou wang Spiros Koulouzis Riccardo Bianchi Na Li Yifang Shi Joris Timmermans w.daniel kissling Zhiming Zhao Multiscale Networked Systems Informatics InstituteUniversity of Amsterdam1098XH AmsterdamThe Netherlands Life watch ERIC Virtual Lab&InnovationCenter(VLIC)Science Park 9041098XH AmsterdamThe Netherlands Institute for Biodiversity and Ecosystem Dynamics(IBED) 1098xH AmsterdamThe Netherlands

Literate computing environments,such as the Jupyter(i.e.,Jupyter Notebooks,JupyterLab,and JupyterHub),have been widely used in scientific studies;they allow users to interactively develop scientific code,test algorithms,and describe the scientific narratives of the experiments in an integrated *** scale up scientific analyses,many implemented Jupyter environment architectures encapsulate the whole Jupyter notebooks as reproducible units and autoscale them on dedicated remote infrastructures(e.g.,highperformance computing and cloud computing environments).The existing solutions are stl limited in many ways,e.g.,1)the workflow(or pipeline)is implicit in a notebook,and some steps can be generically used by different code and executed in parallel,but because of the tight cell structure,all steps in the Jupyter notebook have to be executed sequentially and lack of the flexibility of reusing the core code fragments,and 2)there are performance bottlenecks that need to improve the parallelism and scalability when handling extensive input data and complex *** this work,we focus on how to manage the workflow in a notebook *** 1)encapsulate the reusable cells as RESTful services and containerize them as portal components,2)provide a composition tool for describing workflow logic of those reusable components,and 3)automate the execution on remote cloud ***,we validate the solution's usability via a use case from the Ecology and Earth Science domain,illustrating the processing of massive Light Detection and Ranging(LiDAR)*** demonstration and analysis show that our method is feasible,but that it needs further improvement,especially on integrating distributed workflow scheduling,automatic deployment,and execution to develop as a mature approach.

关键词： Scientific experiments Jupyter Notebooks workflow management Ecosystem structure data products Cloud Scalability

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Phenology of high-arctic butterflies and their floral resources： Species-specific responses to climate change

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Current Zoology 2014年第2期60卷 243-251页

作者： Toke T.HФYE Anne ESKILDSEN Rikke R. HANSEN Joseph J.BOwDEN Niels M.SCHMIDT w.daniel kissling Aarhus Institute of Advanced Studies Hoegh-Guldbergs Gade 6B bldgs. 1630-1632 DK-8000 Aarhus C Denmark Department ofBioscience Kalo Aarhus University Grenaivej 14 DK-8410 Ronde Denmark Arctic Research Centre Aarhus University C.F. Mollers Allé 8 bldg. 1110 DK-8000 Aarhus C Denmark Department of Bioscience Aarhus Aarhus University Ny Munkegade bldg. 1540 DK-8000 Aarhus C Denmark Department of Bioscience Aarhus University Frederiksborgvej 399 DK-4000 Roskilde Denmark Institute for Biodiversity and Ecosystem Dynamics (IBED) University of Amsterdam P.O. Box 94248 1090 GE AmsterdamThe Netherlands

Current global warming is particularly pronounced in the Arctic and arthropods are expected to respond rapidly to these changes. Long-term studies of individual arthropod species from the Arctic are, however, virtually absent. we examined butterfly specimens collected from yellow pitfall traps over 14 years （1996-2009） at Zackenberg in high-arctic, north-east Greenland. Specimens were previously sorted to the family level. we identified them to the species level and examined long-term species-specific phenological responses to recent summer wanning. Two species were rare in the samples （Polaris fritillary Boloria polaris and Arctic blue Plebejus glandon） and statistical analyses of phenological responses were therefore restricted to the two most abundant species （Arctic fritillary, B. chariclea and Northern clouded yellow Colias hecla）. Our analyses demonstrated a trend towards earlier flight seasons in B. chariclea, but not in C. hecla. The timing of onset, peak and end of the flight season in B. chariclea were closely related to snowmelt, July temperature and their interaction, whereas onset, peak and end of the flight season in C. hecla were only related to timing of snowmelt. The duration of the butterfly flight season was significantly positively related to the temporal overlap with floral resources in both butterfly species. we further demonstrate that yellow pitfall traps are a useful alternative to transect walks for butterfly recording in tundra habitats. More phenological studies of Arctic arthropods should be carded out at the species level and ideally be analysed in context with interacting species to assess how ongoing climate change will affect Arctic biodiversity in the near future [Current Zoology 60 （2）： 243-251, 2014].

关键词： Arctic Arthropod Flight period Greenland Pitfall trap Zackenberg

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Twisted fiber microfluidics:a cutting-edge approach to 3D spiral devices

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Microsystems & Nanoengineering 2024年第1期10卷 193-202页

作者： Shunsuke Kato daniel w.Carlson Amy Q.Shen Yuanyuan Guo Department of Electrical Information and Physics EngineeringSchool of EngineeringTohoku UniversityAoba-kuSendai 980-8579 MiyagiJapan Micro/Bio/Nanofluidics Unit Okinawa Institute of Science and TechnologyOnnaKunigami-gun 904-0495 OkinawaJapan Frontier Research Institute for Interdisciplinary Sciences(FRIS) Tohoku UniversityAoba-kuSendai 980-0845 MiyagiJapan Graduate School of Biomedical Engineering Tohoku UniversityAoba-kuSendai 980-8579 MiyagiJapan Department of Physiology Graduate School of MedicineTohoku UniversityAoba-kuSendai 980-8575 MiyagiJapan

The development of 3D spiral microfluidics has opened new avenues for leveraging inertial focusing to analyze small fluid volumes,thereby advancing research across chemical,physical,and biological *** traditional straight microchannels rely solely on inertial lift forces,the novel spiral geometry generates Dean drag forces,eliminating the necessity for external fields in fluid ***,fabricating 3D spiral microfluidics remains a labor-intensive and costly endeavor,hindering its widespread ***,conventional lithographic methods primarily yield 2D planar devices,thereby limiting the selection of materials and geometrical *** address these challenges,this work introduces a streamlined fabrication method for 3D spiral microfluidic devices,employing rotational force within a miniaturized thermal drawing process,termed as *** innovation allows for rapid prototyping of twisted fiber-based microfluidics featuring versatility in material selection and heightened geometric *** validate the performance of these devices,we combined computational modeling with microtomographic particle image velocimetry(uTPiM)to comprehensively characterize the 3D flow *** results corroborate the presence of a steady secondary flow,underscoring the effectiveness of our *** 3D spiral microfluidics platform paves the way for exploring intricate microflow dynamics,with promising applications in areas such as drug delivery,diagnostics,and lab-on-a-chip systems.

关键词： thereby straight twisted

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Determining minimum sample size for the conditioned Latin hypercube sampling algorithm

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Pedosphere 2024年第3期34卷 530-539页

作者： daniel D.SAURETTE Asim BISwAS Richard J.HECK Adam w.GILLESPIE Aaron A.BERG School of Environmental Sciences University of Guelph50 Stone Rd EastGuelph ON N1G 2W1(Canada) Ontario Ministry of Agriculture Food and Rural Affairs1 Stone Rd WestGuelph ON N1G 2Y4(Canada) Geography Environment&GeomaticsUniversity of Guelph50 Stone Rd EastGuelph ON N1G 2W1(Canada)

In digital soil mapping(DSM),a fundamental assumption is that the spatial variability of the target variable can be explained by the predictors or environmental *** to adequately sample the predictors have been well documented,with the conditioned Latin hypercube sampling(cLHS)algorithm receiving the most attention in the DSM *** advances in sampling design,a critical gap remains in determining the number of samples required for DSM *** propose a simple workflow and function coded in R language to determine the minimum sample size for the cLHS algorithm based on histograms of the predictor variables using the Freedman-Diaconis rule for determining optimal bin *** preprocessing was included to correct for multimodal and non-normally distributed data,as these can affect sample size determination from the *** on a user-selected quantile range(QR)for the sample plan,the densities of the histogram bins at the upper and lower bounds of the QR were used as a scaling factor to determine minimum sample *** technique was applied to a field-scale set of environmental covariates for a well-sampled agricultural study site near Guelph,Ontario,Canada,and tested across a range of *** results showed increasing minimum sample size with an increase in the QR *** sample size increased from 44 to 83 when the QR increased from 50% to 95% and then increased exponentially to 194 for the 99%*** technique provides an estimate of minimum sample size that can be used as an input to the cLHS algorithm.

关键词： bin width digital soil mapping normal distribution quantile range sampling design

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Anneal-free ultra-low loss silicon nitride integrated photonics

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Light(Science & Applications) 2024年第8期13卷 1565-1577页

作者： Debapam Bose Mark w.Harrington Andrei Isichenko Kaikai Liu Jiawei wang Nitesh Chauhan Zachary L.Newman daniel J.Blumenthal Department of Electrical and Computer Engineering University of California Santa BarbaraSanta BarbaraCA 93106USA Octave Photonics LouisvilleCO 80027USA

Heterogeneous and monolithic integration of the versatile low-loss silicon nitride platform with low-temperature materials such as silicon electronics and photonics,III–V compound semiconductors,lithium niobate,organics,and glasses has been inhibited by the need for high-temperature annealing as well as the need for different process flows for thin and thick *** techniques are needed to maintain the state-of-the-art losses,nonlinear properties,and CMOS-compatible processes while enabling this next generation of 3D silicon nitride *** report a significant advance in silicon nitride integrated photonics,demonstrating the lowest losses to date for an anneal-free process at a maximum temperature 250℃,with the same deuterated silane based fabrication flow,for nitride and oxide,for an order of magnitude range in nitride thickness without requiring stress mitigation or *** report record low anneal-free losses for both nitride core and oxide cladding,enabling 1.77 dBm-1 loss and 14.9 million Q for 80 nm nitride core waveguides,more than half an order magnitude lower loss than previously reported sub 300℃ *** 800 nm-thick nitride,we achieve as good as 8.66 dBm-1 loss and 4.03 million Q,the highest reported Q for a low temperature processed resonator with equivalent device area,with a median of loss and Q of 13.9 dBm-1 and 2.59 million each *** demonstrate laser stabilization with over 4 orders of magnitude frequency noise reduction using a thin nitride reference cavity,and using a thick nitride micro-resonator we demonstrate OPO,over two octave supercontinuum generation,and four-wave mixing and parametric gain with the lowest reported optical parametric oscillation threshold per unit resonator *** results represent a significant step towards a uniform ultra-low loss silicon nitride homogeneous and heterogeneous platform for both thin and thick waveguides capable of linear and nonlinear photonic circuits and integrat

关键词： resonator thick free

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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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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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