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- 5. Statistical techniques forneuroscientists 1st Edition Young K. Truong Digital Instant Download Author(s): Young K. Truong, Mechelle M. Lewis ISBN(s): 9781466566149, 1466566140 Edition: 1 File Details: PDF, 8.55 MB Year: 2016 Language: english
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- 8. FRONTIERS IN NEUROSCIENCE SeriesEditor Sidney A. Simon, PhD Published Titles Apoptosis in Neurobiology Yusuf A. Hannun, MD, Professor of Biomedical Research and Chairman, Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina Rose-Mary Boustany, MD, tenured Associate Professor of Pediatrics and Neurobiology, Duke University Medical Center, Durham, North Carolina Neural Prostheses for Restoration of Sensory and Motor Function John K. Chapin, PhD, Professor of Physiology and Pharmacology, State University of New York Health Science Center, Brooklyn, New York Karen A. Moxon, PhD, Assistant Professor, School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, Pennsylvania Computational Neuroscience: Realistic Modeling for Experimentalists Eric DeSchutter, MD, PhD, Professor, Department of Medicine, University of Antwerp, Antwerp, Belgium Methods in Pain Research Lawrence Kruger, PhD, Professor of Neurobiology (Emeritus), UCLA School of Medicine and Brain Research Institute, Los Angeles, California Motor Neurobiology of the Spinal Cord Timothy C. Cope, PhD, Professor of Physiology, Wright State University, Dayton, Ohio Nicotinic Receptors in the Nervous System Edward D. Levin, PhD, Associate Professor, Department of Psychiatry and Pharmacology and Molecular Cancer Biology and Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, North Carolina Methods in Genomic Neuroscience Helmin R. Chin, PhD, Genetics Research Branch, NIMH, NIH, Bethesda, Maryland Steven O. Moldin, PhD, University of Southern California, Washington, D.C. Methods in Chemosensory Research
- 9. Sidney A. Simon,PhD, Professor of Neurobiology, Biomedical Engineering, and Anesthesiology, Duke University, Durham, North Carolina Miguel A.L. Nicolelis, MD, PhD, Professor of Neurobiology and Biomedical Engineering, Duke University, Durham, North Carolina The Somatosensory System: Deciphering the Brain’s Own Body Image Randall J. Nelson, PhD, Professor of Anatomy and Neurobiology, University of Tennessee Health Sciences Center, Memphis, Tennessee The Superior Colliculus: New Approaches for Studying Sensorimotor Integration William C. Hall, PhD, Department of Neuroscience, Duke University, Durham, North Carolina Adonis Moschovakis, PhD, Department of Basic Sciences, University of Crete, Heraklion, Greece New Concepts in Cerebral Ischemia Rick C.S. Lin, PhD, Professor of Anatomy, University of Mississippi Medical Center, Jackson, Mississippi DNA Arrays: Technologies and Experimental Strategies Elena Grigorenko, PhD, Technology Development Group, Millennium Pharmaceuticals, Cambridge, Massachusetts Methods for Alcohol-Related Neuroscience Research Yuan Liu, PhD, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland David M. Lovinger, PhD, Laboratory of Integrative Neuroscience, NIAAA, Nashville, Tennessee Primate Audition: Behavior and Neurobiology Asif A. Ghazanfar, PhD, Princeton University, Princeton, New Jersey Methods in Drug Abuse Research: Cellular and Circuit Level Analyses Barry D. Waterhouse, PhD, MCP-Hahnemann University, Philadelphia, Pennsylvania Functional and Neural Mechanisms of Interval Timing Warren H. Meck, PhD, Professor of Psychology, Duke University, Durham, North Carolina Biomedical Imaging in Experimental Neuroscience Nick Van Bruggen, PhD, Department of Neuroscience Genentech, Inc. Timothy P.L. Roberts, PhD, Associate Professor, University of Toronto, Canada The Primate Visual System John H. Kaas, Department of Psychology, Vanderbilt University, Nashville, Tennessee Christine Collins, Department of Psychology, Vanderbilt University, Nashville, Tennessee
- 10. Neurosteroid Effects inthe Central Nervous System Sheryl S. Smith, PhD, Department of Physiology, SUNY Health Science Center, Brooklyn, New York Modern Neurosurgery: Clinical Translation of Neuroscience Advances Dennis A. Turner, Department of Surgery, Division of Neurosurgery, Duke University Medical Center, Durham, North Carolina Sleep: Circuits and Functions Pierre-Hervé Luppi, Université Claude Bernard, Lyon, France Methods in Insect Sensory Neuroscience Thomas A. Christensen, Arizona Research Laboratories, Division of Neurobiology, University of Arizona, Tuscon, Arizona Motor Cortex in Voluntary Movements Alexa Riehle, INCM-CNRS, Marseille, France Eilon Vaadia, The Hebrew University, Jerusalem, Israel Neural Plasticity in Adult Somatic Sensory-Motor Systems Ford F. Ebner, Vanderbilt University, Nashville, Tennessee Advances in Vagal Afferent Neurobiology Bradley J. Undem, Johns Hopkins Asthma Center, Baltimore, Maryland Daniel Weinreich, University of Maryland, Baltimore, Maryland The Dynamic Synapse: Molecular Methods in Ionotropic Receptor Biology Josef T. Kittler, University College, London, England Stephen J. Moss, University College, London, England Animal Models of Cognitive Impairment Edward D. Levin, Duke University Medical Center, Durham, North Carolina Jerry J. Buccafusco, Medical College of Georgia, Augusta, Georgia The Role of the Nucleus of the Solitary Tract in Gustatory Processing Robert M. Bradley, University of Michigan, Ann Arbor, Michigan Brain Aging: Models, Methods, and Mechanisms David R. Riddle, Wake Forest University, Winston-Salem, North Carolina Neural Plasticity and Memory: From Genes to Brain Imaging Frederico Bermudez-Rattoni, National University of Mexico, Mexico City, Mexico Serotonin Receptors in Neurobiology Amitabha Chattopadhyay, Center for Cellular and Molecular Biology, Hyderabad, India TRP Ion Channel Function in Sensory Transduction and Cellular Signaling Cascades
- 11. Wolfgang B. Liedtke,MD, PhD, Duke University Medical Center, Durham, North Carolina Stefan Heller, PhD, Stanford University School of Medicine, Stanford, California Methods for Neural Ensemble Recordings, Second Edition Miguel A.L. Nicolelis, MD, PhD, Professor of Neurobiology and Biomedical Engineering, Duke University Medical Center, Durham, North Carolina Biology of the NMDA Receptor Antonius M. VanDongen, Duke University Medical Center, Durham, North Carolina Methods of Behavioral Analysis in Neuroscience Jerry J. Buccafusco, PhD, Alzheimer’s Research Center, Professor of Pharmacology and Toxicology, Professor of Psychiatry and Health Behavior, Medical College of Georgia, Augusta, Georgia In Vivo Optical Imaging of Brain Function, Second Edition Ron Frostig, PhD, Professor, Department of Neurobiology, University of California, Irvine, California Fat Detection: Taste, Texture, and Post Ingestive Effects Jean-Pierre Montmayeur, PhD, Centre National de la Recherche Scientifique, Dijon, France Johannes le Coutre, PhD, Nestlé Research Center, Lausanne, Switzerland The Neurobiology of Olfaction Anna Menini, PhD, Neurobiology Sector International School for Advanced Studies, (S.I.S.S.A.), Trieste, Italy Neuroproteomics Oscar Alzate, PhD, Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, North Carolina Translational Pain Research: From Mouse to Man Lawrence Kruger, PhD, Department of Neurobiology, UCLA School of Medicine, Los Angeles, California Alan R. Light, PhD, Department of Anesthesiology, University of Utah, Salt Lake City, Utah Advances in the Neuroscience of Addiction Cynthia M. Kuhn, Duke University Medical Center, Durham, North Carolina George F. Koob, The Scripps Research Institute, La Jolla, California Neurobiology of Huntington’s Disease: Applications to Drug Discovery Donald C. Lo, Duke University Medical Center, Durham, North Carolina Robert E. Hughes, Buck Institute for Age Research, Novato, California Neurobiology of Sensation and Reward
- 12. Jay A. Gottfried,Northwestern University, Chicago, Illinois The Neural Bases of Multisensory Processes Micah M. Murray, CIBM, Lausanne, Switzerland Mark T. Wallace, Vanderbilt Brain Institute, Nashville, Tennessee Neurobiology of Depression Francisco López-Muñoz, University of Alcalá, Madrid, Spain Cecilio Álamo, University of Alcalá, Madrid, Spain Astrocytes: Wiring the Brain Eliana Scemes, Albert Einstein College of Medicine, Bronx, New York David C. Spray, Albert Einstein College of Medicine, Bronx, New York Dopamine–Glutamate Interactions in the Basal Ganglia Susan Jones, University of Cambridge, United Kingdom Alzheimer’s Disease: Targets for New Clinical Diagnostic and Therapeutic Strategies Renee D. Wegrzyn, Booz Allen Hamilton, Arlington, Virginia Alan S. Rudolph, Duke Center for Neuroengineering, Potomac, Maryland The Neurobiological Basis of Suicide Yogesh Dwivedi, University of Illinois at Chicago Transcranial Brain Stimulation Carlo Miniussi, University of Brescia, Italy Walter Paulus, Georg-August University Medical Center, Göttingen, Germany Paolo M. Rossini, Institute of Neurology, Catholic University of Rome, Italy Spike Timing: Mechanisms and Function Patricia M. Di Lorenzo, Binghamton University, Binghamton, New York Jonathan D. Victor, Weill Cornell Medical College, New York City, New York Neurobiology of Body Fluid Homeostasis: Transduction and Integration Laurival Antonio De Luca Jr., Sâo Paulo State University–UNESP, Araraquara, Brazil Jose Vanderlei Menani, Sâo Paulo State University–UNESP, Araraquara, Brazil Alan Kim Johnson, The University of Iowa, Iowa City, Iowa Neurobiology of Chemical Communication Carla Mucignat-Caretta, University of Padova, Padova, Italy Itch: Mechanisms and Treatment E. Carstens, University of California, Davis, California Tasuku Akiyama, University of California, Davis, California
- 13. Translational Research inTraumatic Brain Injury Daniel Laskowitz, Duke University, Durham, North Carolina Gerald Grant, Duke University, Durham, North Carolina Statistical Techniques for Neuroscientists Young K. Truong, University of North Carolina, Chapel Hill, North Carolina Mechelle M. Lewis, Pennsylvania State University, Hershey, Pennsylvania
- 14. STATISTICAL TECHNIQUES FOR NEUROSCIENTISTS Editedby Young K. Truong The University of North Carolina at Chapel Hill, USA Mechelle M. Lewis Pennsylvania State University, Hershey, Pennsylvania, USA
- 15. CRC Press Taylor &Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2016 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed on acid-free paper Version Date: 20160127 International Standard Book Number-13: 978-1-4665-6614-9 (Hardback) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Library of Congress Cataloging-in-Publication Data Names: Truong, Young K., editor. Title: Statistical techniques for neuroscientists / editor, Young K. Truong. Other titles: Frontiers in neuroscience (Boca Raton, Fla.) Description: Boca Raton : Taylor & Francis, 2016. | Series: Frontiers in neuroscience | Includes bibliographical references and index. Identifiers: LCCN 2016003627 | ISBN 9781466566149 (alk. paper) Subjects: | MESH: Statistics as Topic | Neurosciences Classification: LCC RC337 | NLM WL 16 | DDC 616.80072/7--dc23 LC record available at http://lccn.loc.gov/2016003627 Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com
- 16. Dedication To David R.Brillinger and Chuck J. Stone and my lovely Psyche Lee
- 17. Contents Preface Editors Contributors List of Figures Listof Tables PART I Statistical Analysis of Neural Spike Train Data Chapter 1 Statistical Modeling of Neural Spike Train Data Ruiwen Zhang, Shih-Chieh Lin, Haipeng Shen, and Young K. Truong 1.1 Introduction 1.2 Point Process and Conditional Intensity Function 1.3 The Likelihood Function of a Point Process Model 1.4 Continuous State-Space Model 1.4.1 Kernel Smoothing 1.4.2 Adaptive Kernel Smoothing 1.4.3 Kernel Bandwidth Optimization 1.4.4 Smoothing Splines 1.4.5 Real Data Analysis 1.5 M-Files for Simulation 1.6 M-Files for Real Data 1.7 R Files for Real Data Bibliography Chapter 2 Regression Spline Model for Neural Spike Train Data Ruiwen Zhang, Shih-Chieh Lin, Haipeng Shen, and Young K. Truong 2.1 Introduction 2.2 Linear Models for the Conditional Log-Intensity Function 2.3 Maximum Likelihood Estimation 2.4 Simulation Studies 2.4.1 Case 1: Fixed Number of Basis Functions 2.4.2 Case 2: Adaptive Knots Selection 2.5 Data Analysis 2.6 Conclusion 2.6.1 A Parametric Model for Interacting Neurons 2.7 R Code for Real Data Analysis 2.8 R Code for Simulation Bibliography PART II Statistical Analysis of fMRI Data
- 18. Chapter 3 AHypothesis Testing Approach for Brain Activation Wenjie Chen, Haipeng Shen, and Young K. Truong 3.1 Introduction 3.1.1 Model 3.1.2 Ordinary Least Square Estimate 3.1.2.1 Window Estimate 3.2 Hypothesis Testing 3.2.1 Key Concepts 3.2.2 Testing the Linearity 3.2.3 Testing the Effect from a Specific Stimulus 3.2.4 Detecting the Activation 3.2.5 Testing the Difference between HRF 3.2.6 Remarks 3.3 Simulation 3.4 Real Data Analysis 3.4.1 Auditory Data 3.4.2 Event-Related Visual Data 3.5 Discussion 3.6 Software: R Bibliography Chapter 4 An Efficient Estimate of HRF Wenjie Chen, Haipeng Shen, and Young K. Truong 4.1 Introduction 4.1.1 Experiment Design for Detecting HRF 4.1.2 General Guideline for Estimating HRF 4.1.3 The General Linear Model Framework 4.1.4 HRF Modeling 4.1.4.1 Time-Domain Methods 4.1.4.2 Frequency-Domain Methods 4.1.4.3 Comparison of the Current Methods 4.2 TFE Method: WLS Estimate 4.3 Simulation 4.3.1 Simulation 1: WLS 4.3.2 Simulation 2: Comparison 4.4 Real Data Analysis 4.5 Software: R Bibliography Chapter 5 Independent Component Analysis: An Overview Dong Wang, Seonjoo Lee, Haipeng Shen, and Young K. Truong 5.1 Introduction 5.2 Neuroimaging Data Analysis 5.3 Single-Subject and the Group Structure Assumptions 5.4 Homogeneous in Space 5.5 Homogeneous in Both Space and Time 5.6 Homogeneous in Both Space and Time with Subject-Specific Weights 5.7 Inhomogeneous in Space 5.8 Approaches with Multiple Group Structures 5.9 Software
- 19. 5.10 Conclusion Bibliography Chapter 6Polynomial Spline Independent Component Analysis with Application to fMRI Data Atsushi Kawaguchi and Young K. Truong 6.1 Introduction 6.2 Method 6.3 Simulation Study 6.4 Application 6.5 Discussions and Conclusions 6.6 Logspline Density Estimation 6.6.1 Methodology 6.6.2 Numerical Results 6.7 Stochastic EM Algorithm 6.8 Software: R 6.8.1 Example.R 6.8.2 MLICA.r 6.8.3 a24random.r 6.8.4 amarimetric.r 6.8.5 logsplinederivative.r 6.8.6 pdfunction.r 6.8.7 UniOrthoMat4multi.r Bibliography Chapter 7 Colored Independent Component Analysis Seonjoo Lee, Haipeng Shen, and Young K. Truong 7.1 Introduction 7.2 Colored Independent Component Analysis 7.3 Stationary Time Series Models 7.3.1 White Noise 7.3.2 Moving-Average Processes 7.3.3 Autoregressive Processes 7.3.4 Autoregressive and Moving-Average Processes 7.3.5 Harmonic Processes 7.4 Stationary Colored Source Models 7.5 Maximum Likelihood Estimation 7.6 ColoredICA R-Package 7.7 Resting-State EEG Data Analysis 7.8 M-Files 7.8.1 aic unit 7.8.2 aic unit2 7.8.3 amari distanceW 7.8.4 assignspec.m 7.8.5 cICA-xarma2 7.8.6 calculateAIC.m 7.8.7 colorICA-pmm 7.8.8 colorICA-pmm4 7.8.9 dexprand.m 7.8.10 estimateAR.m 7.8.11 getspec2.m
- 20. 7.8.12 model-select-MM 7.8.13 specAR.m 7.8.14whiteICA.m Bibliography Chapter 8 Group Blind Source Separation (GBSS) Dong Wang, Haipeng Shen, and Young K. Truong 8.1 Introduction 8.2 Background on ICA and PICS 8.2.1 Preliminaries 8.2.2 Independent Component Analysis (ICA) 8.2.3 Parametric Independent Colored Sources (PICS) 8.3 Group Parametric Independent Colored Sources (GPICS) 8.4 Simulations 8.4.1 Blind Source Separation 8.5 Real Data Analysis 8.6 Discussions and Conclusions 8.7 M-Files 8.7.1 GCICA H10 8.7.2 GCICA H01 8.7.3 GCICA H00 8.7.4 GCICA H11 Bibliography Chapter 9 Diagnostic Probability Modeling for Longitudinal Structural Brain MRI Data Analysis Atsushi Kawaguchi 9.1 Introduction 9.2 Methods 9.2.1 Notation and Conceptual Model 9.2.2 Spatial Modeling 9.2.3 Temporal Modeling 9.2.4 Final Model 9.3 Application 9.4 ROC Analysis 9.5 Summary and Conclusion 9.6 Software Implementation Bibliography Chapter 10 Supervised SVD of fMRI Data with Time-Varying Frequency Components Avner Halevy and Young K. Truong 10.1 Introduction 10.2 Independent Component Analysis (ICA) 10.2.1 Overview of ICA 10.2.2 ICA for fMRI 10.2.3 Dimension Reduction 10.3 Supervised SVD 10.3.1 Low Rank Approximation 10.3.2 Supervised SVD 10.4 Extension to Time-Varying Frequency
- 21. Exploring the Varietyof Random Documents with Different Content
- 22. Photo. Braun, Clémentet Cie. [To face p. 69. Plate 35.—Figure of Adam, from The Creation of Man Michael Angelo, Sistine Chapel, Vatican, Rome and paint as well, so leaving this portion in a clean-looking or light state; and if we bear in mind that the background work has in all probability been painted much more thinly, or with less impasto, than the figures, we can easily imagine that in the parts under notice there has always been less body of colour to be destroyed by the cleaners. It is also noticeable that where a blue or grey colour has been used in the draperies, the painting of such parts has badly perished, which suggests that either a vegetable or a copper-blue pigment has been used, instead of a cobalt or an ultramarine blue, or that these parts have been afterwards repainted in tempera. The other frescos in this room, the “Mount Parnassus,” and the “Prudence, Fortitude and Temperance,” are in a much better state than the “School of Athens.” Michael Angelo’s great work in fresco, on the ceiling of the Sistine Chapel, is still, fortunately, in a fairly good state, but the “Last Judgment,” on the altar wall, is very grimy, and in a much blackened state. One cannot help thinking
- 23. that a gooddeal of the dirt could be removed from this work by a little judicious cleaning. THE END
- 24. INDEX A, B, C,D, E, F, G, H, I, K, L, M, P, R, S, T, U, V, W. Andrea del Sarto, 63-64 Architecture, 1 Architecture, principles of, 6 Arts of Peace fresco, 34 Arts of War fresco, 33-34 Bardi Chapel, Santa Croce, Florence, 39-40 Benozzo Gozzoli, 51-53 Borgia apartments, Vatican, 56-58 Brancacci Chapel, Carmelite Church, 47-49 Brera Palace, Milan, frescos at, 64-65 Brown, Ford Madox, 32 Brushes for fresco, 20 Buon-fresco, 9 Campo Santa, Pisa, 52 Cartoons, 16, 17, 24, 56 Cenacolo by Ghirlandajo, 61-62 Cnossus, 10 Colour sketches, 16, 36 Colours for buon-fresco, 17-19 Design in objects of general utility, 5 Drapery painting, 28-29 Egyptian tempera, 11 Encaustic painting, 9 Filippino Lippi, 47 Flesh painting, 25-27 Foundling Hospital, Florence, 59-60 Fra Angelico, 44-46 Fresco-buono, 12 Fresco-secco, 8, 11
- 25. Fresco, systems andmethods, 8 Gaudenzio Ferrari, 66-67 Ghirlandajo, Domenico, 59-61 Giotto, 39-43 Giovanni da Udine, 57-58 Gloucester Cathedral, 31 Houses of Parliament frescos, 30 Intonaco, 15 Keim’s process, 9 Last Judgment fresco, 68 Leighton, Lord, 32-33 Luini, Bernardino, 64-66 Lyndhurst Church fresco, 32 Masaccio, 47-49 Masolino da Panicale, 47 Method of execution in buon-fresco, 23 Method of execution in spirit fresco, 36-37 Michael Angelo, 38, 50, 54, 68 Monastery of St. Mark frescos, 44-46, 61 Monumental painting, essentials of, 4 Mosaics, 3 Mycene, 10 Painting, 2 Parry, Gambier, 53 Perina del Vaga, 57-58 Perugino, 53-55 Pinturicchio, 56-58 Pompeii, 11 Poynter, Sir E. J., Bart., P.R.A., 16, 30 Raffaelle, 49, 67, 69 Retouching, 27
- 26. Riccardi palace, 51 Ruskin,53 Santa Maria della Grazie, Milan, 66-67 Santa Maria Maddalena de Pazzi, 54 Santa Maria Novella, Florence, 39, 61 Santissima Annunziata, Church of the, 63 St. Ambrogio, Milan, 66-67 St. Catherine of Alexandria, 58 St. Maurizo Church (Monastero Maggiore), 66 St. Stephen’s, Dulwich, 71 Saronno, Church of the Santuario, 66-67 School of Athens fresco, 68 Simon Memmi, 53 Sistine Chapel, 38, 54, 59 Spanish Chapel, 53 Spirit fresco, 31 Spirit fresco medium, 38 Spirit fresco painting, 9 Tempera painting, 9 Test brick for colour, 22 Thera, 10 Tiryns, 10 Undercoating, or ground tint, 21 Vasari, 40, 50, 56 Vatican, Loggia of the, 58 Victoria and Albert Museum, 33 Walls for fresco paintings, 14, 33 Walls, preparation of, 14, 33-34 Water-glass fresco, 9 Richard Clay & Sons, Limited, London and Bungay.
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