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Ligand-directed profiling of organelles with internalizing phage libraries

Current Protocols in Protein Science 2015年第1期2015卷 30.4.1-30.4.30页

作者： Dobroff, Andrey S. Range, Roberto Guzman-Roja, Liliana Salmeron, Carolina C. Gelovani, Juri G. Sidman, Richard L. Bologa, Cristian G. Oprea, Tudor I. Brinker, C. Jeffrey Pasqualini, Renata Arap, Wadih Division of Hematology/Oncology Department of Internal Medicine University of New Mexico School of Medicine Albuquerque NM United States Division of Molecular Medicine Department of Internal Medicine University of New Mexico School of Medicine Albuquerque NM United States Cancer Research Program Houston Methodist Research Institute Houston TX United States Department of Biomedical Engineering Wayne State University Detroit MI United States Department of Neurology Beth Israel Deaconess Medical Center Harvard Medical School Boston MA United States Translational Informatics Division Department of Internal Medicine University of New Mexico School of Medicine Albuquerque NM United States Department of Chemical and Nuclear Engineering The University of New Mexico Cancer Center Albuquerque NM United States

Phage display is a resourceful tool to, in an unbiased manner, discover and characterize functional protein-protein interactions, create vaccines, and engineer peptides, antibodies, and other proteins as targeted diagnostic and/or therapeutic agents. Recently, our group has developed a new class of internalizing phage (iPhage) for ligand-directed targeting of organelles and to identify molecular pathways within live cells. This unique technology is suitable for applications ranging from fundamental cell biology to drug development. This unit describes the methods for generating and screening the iPhage display system, and explains how to select and validate candidate internalizing homing peptide. © 2014 by John Wiley & Sons, Inc.

关键词： Intracellular receptors Intracellular targeting Mammalian cells Organelles Penetratin Peptides Phage display Proteomics

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The γ-ray spectrum of the core of Centaurus A as observed with H.E.S.S. and Fermi-LAT

arXiv

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arXiv 2018年

作者： Abdalla, H. Abramowski, A. Aharonian, F. Benkhali, F. Ait Angüner, E.O. Arakawa, M. Armand, C. Arrieta, M. Backes, M. Balzer, A. Barnard, M. Becherini, Y. Tjus, J. Becker Berge, D. Bernhard, S. Bernlöhr, K. Blackwell, R. Böttcher, M. Boisson, C. Bolmont, J. Bonnefoy, S. Bordas, P. Bregeon, J. Brun, F. Brun, P. Bryan, M. Büchele, M. Bulik, T. Capasso, M. Caroff, S. Carosi, A. Casanova, S. Cerruti, M. Chakraborty, N. Chaves, R.C.G. Chen, A. Chevalier, J. Colafrancesco, S. Condon, B. Conrad, J. Davids, I.D. Decock, J. Deil, C. Devin, J. deWilt, P. Dirson, L. Djannati-Ataï, A. Donath, A. O’C. Drury, L. Dyks, J. Edwards, T. Egberts, K. Emery, G. Ernenwein, J.-P. Eschbach, S. Farnier, C. Fegan, S. Fernandes, M.V. Fiasson, A. Fontaine, G. Funk, S. Füßling, M. Gabici, S. Gallant, Y.A. Garrigoux, T. Gaté, F. Giavitto, G. Glawion, D. Glicenstein, J.F. Gottschall, D. Grondin, M.-H. Hahn, J. Haupt, M. Hawkes, J. Heinzelmann, G. Henri, G. Hermann, G. Hinton, J.A. Hofmann, W. Hoischen, C. Holch, T.L. Holler, M. Horns, D. Ivascenko, A. Iwasaki, H. Jacholkowska, A. Jamrozy, M. Jankowsky, D. Jankowsky, F. Jingo, M. Jouvin, L. Jung-Richardt, I. Kastendieck, M.A. Katarzyński, K. Katsuragawa, M. Katz, U. Kerszberg, D. Khangulyan, D. Khélifi, B. King, J. Klepser, S. Klochkov, D. Kluźniak, W. Komin, Nu. Kosack, K. Krakau, S. Kraus, M. Krüger, P.P. Laffon, H. Lamanna, G. Lau, J. Lefaucheur, J. Lemière, A. Lemoine-Goumard, M. Lenain, J.-P. Leser, E. Lohse, T. Lorentz, M. Liu, R. López-Coto, R. Lypova, I. Malyshev, D. Marandon, V. Marcowith, A. Mariaud, C. Marx, R. Maurin, G. Maxted, N. Mayer, M. Meintjes, P.J. Meyer, M. Mitchell, A.M.W. Moderski, R. Mohamed, M. Mohrmann, L. Morå, K. Moulin, E. Murach, T. Nakashima, S. de Naurois, M. Ndiyavala, H. Niederwanger, F. Niemiec, J. Oakes, L. O’Brien, P. Odaka, H. Ohm, S. Ostrowski, M. Oya, I. Padovani, M. Panter, M. Parsons, R.D. Pekeur, N.W. Pelletier, G. Perennes, C. Petrucci, P.-O. Centre for Space Research North-West University Potchefstroom2520 South Africa Universität Hamburg Institut für Experimentalphysik Luruper Chaussee 149 HamburgD 22761 Germany Max-Planck-Institut für Kernphysik P.O. Box 103980 HeidelbergD 69029 Germany Dublin Institute for Advanced Studies 31 Fitzwilliam Place Dublin 2 Ireland National Academy of Sciences of the Republic of Armenia Marshall Baghramian Avenue 24 Yerevan0019 Armenia Instytut Fizyki JĄdrowej PAN ul. Radzikowskiego 152 Kraków31-342 Poland Department of Physics Rikkyo University 3-34-1 Nishi-Ikebukuro Toshima-ku Tokyo171-8501 Japan Laboratoire d’Annecy de Physique des Particules Université Savoie Mont-Blanc CNRS/IN2P3 Annecy-le-VieuxF-74941 France LUTH Observatoire de Paris PSL Research University CNRS Université Paris Diderot 5 Place Jules Janssen Meudon92190 France University of Namibia Department of Physics Private Bag 13301 Windhoek Namibia GRAPPA Anton Pannekoek Institute for Astronomy University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Department of Physics and Electrical Engineering Linnaeus University Växjö351 95 Sweden Institut für Theoretische Physik Lehrstuhl IV: Weltraum und Astrophysik Ruhr-Universität Bochum BochumD 44780 Germany DESY ZeuthenD-15738 Germany Institut für Astro- und Teilchenphysik Leopold-Franzens-Universität Innsbruck InnsbruckA-6020 Austria School of Physical Sciences University of Adelaide Adelaide5005 Australia 4 place Jussieu Paris Cedex 5F-75252 France Laboratoire Univers et Particules de Montpellier Université Montpellier CNRS/IN2P3 CC 72 Place Eugène Bataillon Montpellier Cedex 5F-34095 France Université Bordeaux CNRS/IN2P3 Centre d’Études Nucléaires de Bordeaux Gradignan Gradignan33175 France IRFU CEA Université Paris-Saclay Gif-sur-YvetteF-91191 France Friedrich-Alexander-Universität Erlangen-Nürnberg Erlangen Centre for Astroparticle Physics Erwin-Rommel-Str. 1 ErlangenD 91058 Germany Astronomica

Centaurus A (Cen A) is the nearest radio galaxy discovered as a very-high-energy (VHE;100 GeV-100 TeV) γ-ray source by the High Energy Stereoscopic System (H.E.S.S.). It is a faint VHE γ-ray emitter, though its VHE flux exceeds both the extrapolation from early Fermi-LAT observations as well as expectations from a (misaligned) single-zone synchrotron-self Compton (SSC) description. The latter satisfactorily reproduces the emission from Cen A at lower energies up to a few GeV. New observations with H.E.S.S., comparable in exposure time to those previously reported, were performed and eight years of Fermi-LAT data were accumulated to clarify the spectral characteristics of the γ-ray emission from the core of Cen A. The results allow us for the first time to achieve the goal of constructing a representative, contemporaneous γ-ray core spectrum of Cen A over almost five orders of magnitude in energy. Advanced analysis methods, including the template fitting method, allow detection in the VHE range of the core with a statistical significance of 12σ on the basis of 213 hours of total exposure time. The spectrum in the energy range of 250 GeV-6 TeV is compatible with a power-law function with a photon index Γ = 2.52 ± 0.13stat ± 0.20sys. An updated Fermi-LAT analysis provides evidence for spectral hardening by ∆Γ 0.4 ± 0.1 at γ-ray energies above 2.8+1.0−0.6 GeV at a level of 4.0σ. The fact that the spectrum hardens at GeV energies and extends into the VHE regime disfavour a single-zone SSC interpretation for the overall spectral energy distribution (SED) of the core and is suggestive of a new γ-ray emitting component connecting the high-energy emission above the break energy to the one observed at VHE energies. The absence of significant variability at both GeV and TeV energies does not yet allow disentanglement of the physical 1 nature of this component, though a jet-related origin is possible and a simple two-zone SED model fit is provided to this end. Copyright © 2018,

关键词： Gamma rays

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Dynamic Bandwidth Distribution for Entertainment Vehicular Networks Applications

Dynamic Bandwidth Distribution for Entertainment Vehicular N...

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International Conference on Advanced Information Networking and Applications Workshops (AINAW)

作者： Ronan D. Mendonça Thais R.M. Braga Silva Fabrício A. Silva Linnyer B. Ruiz Antonio A.F. Loureiro Graduate Program in Electrical Engineering Federal University of Minas Gerais Campus Florestal - Fed. Univ. of Vicosa Vicosa Brazil Computer Science Department Federal University of Minas Gerais Department of Informatics State University of Maringa

Vehicular networks will play an important role in future smart cities. Connected vehicles will be able to provide entertainment content to their users in order to make traffic situations more enjoyable. However, the amount of bandwidth available to the vehicles may not be enough to satisfy all of them. In this case, we can say that a conflict of interest occurred and then must the solved as fair as possible. In this work, we propose a solution to solve this kind of collective conflict. Our solution balances users' satisfaction with resources consumption as it is capable of choosing the most adequate resolution algorithm based on the current application's situation. The results showed that with our solution it was possible to achieve adequate satisfaction levels, with low response time and controlled network usage.

关键词： Vehicles Bandwidth Entertainment industry Protocols Time factors Vehicle dynamics Heuristic algorithms

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Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016 : Cadiz, KY, USA. 8-10 April 2016

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BMC bioinformatics 2016年第SUPPL 10期17卷 297页

作者： Eric C. Rouchka Julia H. Chariker Benjamin J. Harrison Juw Won Park Xueyuan Cao Stanley Pounds Susana Raimondi James Downing Raul Ribeiro Jeffery Rubnitz Jatinder Lamba Bernie J. Daigle Deborah Burgess Stephanie Gehrlich John C. Carmen Nicholas Johnson Chandrakanth Emani Kalpani De Silva Michael P. Heaton Theodore S. Kalbfleisch Teeradache Viangteeravat Rahul Mudunuri Oluwaseun Ajayi Fatih Şen Eunice Y. Huang Mohammad Mohebbi Luaire Florian Douglas J. Jackson John F. Naber AKM Sabbir Sally R. Ellingson Yuping Lu Charles A Phillips Michael A. Langston Rahul K. Sevakula Raghuveer Thirukovalluru Nishchal K. Verma Yan Cui Mohammed Sayed Jing Wang Qi Liu Yu Shyr Xiaofei Zhang Naresh Prodduturi Gavin R. Oliver Diane Grill Jie Na Jeanette Eckel-Passow Eric W. Klee Michael M. Goodin Mark Farman Harrison Inocencio Chanyong Jang Jerzy W. Jaromczyk Neil Moore Kelly Sovacool Leon Dent Mike Izban Sammed Mandape Shruti Sakhare Siddharth Pratap Dana Marshall M Scotty DePriest James N. MacLeod Hanady Adam Ethan Blandford Joel Campbell Joshua Castlen Brittany Dixon Ginger Gilbert Aaron Hall Philip Kreisle Jessica Lasher Bethany Oakes Allison Speer Maximilian Valentine Naga Satya V. Rao Nagisetty Rony Jose Robert Rooney David Hains Department of Computer Engineering and Computer Science University of Louisville Duthie Center for Engineering Louisville USA Kentucky Biomedical Research Infrastructure (KBRIN) Bioinformatics Core Louisville USA Department of Psychological and Brain Sciences University of Louisville Louisville USA Department of Anatomical Sciences and Neurobiology University of Louisville Louisville USA Department of Biostatistics St. Jude Children’s Research Hospital Memphis USA Department of Pathology St. Jude Children’s Research Hospital Memphis USA Department of Oncology St. Jude Children’s Research Hospital Memphis USA Department of Pharmacotherapy and Translational Research College of Pharmacy University of Florida Gainesville USA Department of Biological Sciences University of Memphis Memphis USA Department of Computer Science University of Memphis Memphis USA Department of Computer Science Northern Kentucky University Highland Heights USA Department of Biological Sciences Northern Kentucky University Highland Heights USA Department of Biology Western Kentucky University Bowling Green USA Interdisciplinary Studies Program: Specialization in Bioinformatics University of Louisville Louisville USA United States Department of Agriculture Agricultural Research Service United States Meat Animal Research Center Clay Center USA Department of Biochemistry and Molecular Genetics School of Medicine University of Louisville Louisville USA Biomedical Informatics Core Children’s Foundation Research Institute Memphis USA Department of Pediatrics University of Tennessee Health Science Center Memphis USA Department of Electrical and Computer Engineering University of Louisville Louisville USA Department of Computer Science University of Kentucky Lexington USA Division of Biomedical Informatics College of Medicine University of Kentucky Lexington USA Department of Electrical Engineering and Computer Science University of Tennessee Knoxville USA Department of Electrical E

I1 Proceedings of the Fifteenth Annual UT- KBRIN Bioinformatics Summit 2016 Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park P1 CC-PROMISE: Projection onto the Most Interesting Statistical Evidence (PROMISE) with Canonical Correlation to integrate gene expression and methylation data with multiple pharmacologic and clinical endpoints Xueyuan Cao, Stanley Pounds, Susana Raimondi, James Downing, Raul Ribeiro, Jeffery Rubnitz, Jatinder Lamba P2 Integration of microRNA-mRNA interaction networks with gene expression data to increase experimental power Bernie J Daigle, Jr. P3 Designing and writing software for in silico subtractive hybridization of large eukaryotic genomes Deborah Burgess, Stephanie Gehrlich, John C Carmen P4 Tracking the molecular evolution of Pax gene Nicholas Johnson; Chandrakanth Emani P5 Identifying genetic differences in thermally dimorphic and state specific fungi using in silico genomic comparison Stephanie Gehrlich, Deborah Burgess, John C Carmen P6 Identification of conserved genomic regions and variation therein amongst Cetartiodactyla species using next generation sequencing Kalpani De Silva, Michael P Heaton, Theodore S Kalbfleisch P7 Mining physiological data to identify patients with similar medical events and phenotypes Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun Ajayi, Fatih Şen, Eunice Y Huang P8 Smart brief for home health monitoring Mohammad Mohebbi, Luaire Florian, Douglas J Jackson, John F Naber P9 Side-effect term matching for computational adverse drug reaction predictions AKM Sabbir, Sally R Ellingson P10 Enrichment vs robustness: A comparison of transcriptomic data clustering metrics Yuping Lu, Charles A Phillips, Michael A Langston P11 Deep neural networks for transcriptome-based cancer classification Rahul K Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui P12 Motif discovery using K-means clustering Mohammed Sayed, Juw Won Park P13 Large scale discovery of active enhancers from nasce

关键词： True Negative Differential Expression UCSC Genome Browser Laboratory Information Management System Biomedical informatics

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Lungs anomaly detection by filtered back projection reconstruction method in electrical impedance tomography

Lungs anomaly detection by filtered back projection reconstr...

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2013 3rd International Conference on Instrumentation, Control and Automation, ICA 2013

作者： Ain, Khusnul Kurniadi, Deddy Suprijanto, S. Santoso, Oerip Engineering Physics Program Indonesia Informatics Program Institut Teknologi Bandung Bandung Indonesia Physics Departement Airlangga University Surabaya Indonesia

ISBN: (纸本)9781467357982

The electrical impedance tomography (EIT) is a promising imaging modality for early detection of lung disease. Several advantages of EIT imaging, such as save, simple and low cost. However, the better reconstruction method is still under investigated. The paper proposed filtered back projection to produce an anomaly image in the lungs. The method is applied to reconstruct an image from relative potential data of expiration and inspiration and also on normal lung and lung with anomaly. The simulation shows that the reconstruction method of filtered back projection from the relative potential data of expiration and inspiration have not been able to detect any anomalies, but from the relative potential data of normal lungs and lungs with anomaly is able to detect the presence and position of anomaly although have not been able to distinguish the size of the anomaly. © 2013 IEEE.

关键词： Electric impedance tomography

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Body machine interfaces for neuromotor rehabilitation: A case study

Body machine interfaces for neuromotor rehabilitation: A cas...

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Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Camilla Pierella Farnaz Abdollahi Ali Farshchiansadegh Jessica Pedersen David Chen Ferdinando A. Mussa-Ivaldi Maura Casadio Department of Physiology Northwestern University Evanston IL Department of Informatics Bioengineering Robotics and Systems Engineering University of Genoa Genoa Italy Sensory Motor Performance Program Rehabilitation Institute of Chicago Chicago IL 60611 Department of Biomedical Engineering Northwestern University Evanston IL Rehabilitation Institute of Chicago Chicago Illinois

High-level spinal cord injury (SCI) survivors face every day two related problems: recovering motor skills and regaining functional independence. Body machine interfaces (BoMIs) empower people with sever motor disabilities with the ability to control an external device, but they also offer the opportunity to focus concurrently on achieving rehabilitative goals. In this study we developed a portable, and low-cost BoMI that addresses both problems. The BoMI remaps the user's residual upper body mobility to the two coordinates of a cursor on a computer monitor. By controlling the cursor, the user can perform functional tasks, such as entering text and playing games. This framework also allows the mapping between the body and the cursor space to be modified, gradually challenging the user to exercise more impaired movements. With this approach, we were able to change the behavior of our SCI subject, who initially used almost exclusively his less impaired degrees of freedom - on the left side - for controlling the BoMI. At the end of the few practice sessions he had restored symmetry between left and right side of the body, with an increase of mobility and strength of all the degrees of freedom involved in the control of the interface. This is the first proof of concept that our BoMI can be used to control assistive devices and reach specific rehabilitative goals simultaneously.

关键词： Sensors Shoulder Training Aerospace electronics Wireless communication Standards Spinal cord injury

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Dynamic timeout power policy for network interfaces

Dynamic timeout power policy for network interfaces

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IEEE International Conference on Consumer Electronics - Berlin (ICCE-Berlin)

作者： Bruna M. J. C. Vilar Fabiano De M Silva Saulo O. D. Luiz J. J. Silva Hyggo Almeida Angelo Perkusich Post-Graduate Program in Electrical Engineering - PPgEE COPELE Embedded Systems and Pervasive Computing Laboratory Universidade Federal de Campina Grande Campina Grande PB BR Center of Electrical Engineering and Informatics Federal University of Campina Grande Campina Grande Brazil Embedded Systems and Pervasive Computing Laboratory Federal University of Campina Grande

Network interfaces are present in a variety of battery powered computer systems, such as notebooks, ultrabooks, tablets and mobile phones. Considering that the battery life is still a constraint, there are opportunities for power management by reducing the power consumption of idle network interfaces. In this work, a dynamic timeout power policy for network interfaces is presented, incorporating workload estimation and a problem optimization at runtime, thus providing power savings and suitable performance.

关键词： Heuristic algorithms Network interfaces Power demand Optimization Mobile handsets Internet Stochastic processes

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0.9 V, 5 nW, 9 ppm/oC resistorless sub-bandgap voltage reference in 0.18μm CMOS

0.9 V, 5 nW, 9 ppm/oC resistorless sub-bandgap voltage refer...

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IEEE Latin American Symposium on Circuits and Systems (LASCAS)

作者： Oscar E. Mattia Hamilton Klimach Sergio Bampi Microelectronics Graduate Program Federal University of Rio Grande do Porto Alegre RS Brazil Electrical Engineering Department Sul Federal University of Rio Grande do Porto Alegre RS Brazil Informatics Institute Federal University of Rio Grande do Porto Alegre RS Brazil

In this work a novel resistorless sub-bandgap voltage reference (BGR) is introduced. It is a self-biased and small area topology that works in the nano-ampere current consumption range, and under 1 V of power supply. The analytical behavior of the circuit is described, and simulation results for a standard 0.18 μm CMOS process are analysed. A reference voltage of 479 mV is demonstrated, with a temperature coefficient of 8.79 ppm/°C for the 0 to 125°C range, while the power consumption of the whole circuit is 4.86 nW under a 0.9 V power supply at 27 o C. The estimated silicon area is 0.0012 mm 2 .

关键词： MOSFET Threshold voltage Topology Junctions Photonic band gap

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A Body Machine Interface based on Inertial Sensors

A Body Machine Interface based on Inertial Sensors

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Annual International Conference of the IEEE engineering in Medicine and Biology Society

作者： Ali Farshchiansadegh Farnaz Abdollahi David Chen Mei-Hua Lee Jessica Pedersen Camilla Pierella Elliot J. Roth Ismael Seanez Gonzalez Elias B. Thorp Ferdinando A. Mussa-Ivaldi Department of Biomedical Engineering Northwestern University Evanston IL Sensory Motor Performance Program Rehabilitation Institute of Chicago Chicago IL Rehabilitation Institute of Chicago Chicago Illinois Department of Kinesiology Michigan State University East Lansing MI Department of Physiology Northwestern University Evanston IL Department of Informatics Bioengineering Robotics and Systems Engineering University of Genoa Genoa Italy

Spinal cord injury (SCI) survivors generally retain residual motor and sensory functions, which provide them with the means to control assistive devices. A body-machine interface (BoMI) establishes a mapping from these residual body movements to control commands for an external device. In this study, we designed a BoMI to smooth the way for operating computers, powered wheelchairs and other assistive technologies after cervical spinal cord injuries. The interface design included a comprehensive training paradigm with a range of diverse functional activities to enhance motor learning and retention. Two groups of SCI survivors and healthy control subjects participated in the study. The results indicate the effectiveness of the developed system as an alternative pathway for individuals with motor disabilities to control assistive devices while engaging in functional motor activity.

关键词： Wheelchairs Training Games Aerospace electronics Spinal cord injury Injuries Sensors

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Bound Analysis Through HDMR for Multivariate Data Modelling - CMMSE

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Journal of Mathematical Modelling and Algorithms 2013年第3期12卷 265-276页

作者： Tunga, M.Alper Demiralp, Metin Software Engineering Department Bahçeşehir University 34349 Istanbul Beşiktaş Turkey Informatics Institute Computational Science and Engineering Program Istanbul Technical University 34469 Istanbul Maslak Turkey

Multivariate data modelling problems consist of a number of nodes with associated function (class) values. The main purpose of these problems is to construct an analytical model to represent the characteristics of the problem under consideration. Because the devices, tools, and/or algorithms used to collect the data may have incapabilities or limited capabilities, the data set is likely to contain unavoidable errors. That is, each component of data is reliable only within an interval which contains the data value. To this end, when an analytical structure is needed for the given data, a band structure should be determined instead of a unique structure. As the multivariance of the given data set increases, divide-and-conquer methods become important in multivariate modelling problems. HDMR based methods allow us to partition the given multivariate data into less variate data sets to reduce the complexity of the given problem. This paper focuses on Interval Factorized HDMR method developed to determine an approximate band structure for a given multivariate data modelling problem having uncertainties on its nodes and function values. © 2012 Springer Science+Business Media B.V.

关键词： Approximation Bound analysis High dimensional model representation Interpolation Multidimensional problems Multivariate functions

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