entropy

Summary

Summary: The measure of that part of the heat or energy of a system which is not available to perform work. Entropy increases in all natural (spontaneous and irreversible) processes. (From Dorland, 28th ed)

Top Publications

  1. ncbi Protein activity regulation by conformational entropy
    Shiou Ru Tzeng
    Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
    Nature 488:236-40. 2012
  2. ncbi Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
    S D Dunn
    Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A 5C1
    Bioinformatics 24:333-40. 2008
  3. ncbi Physiological time-series analysis using approximate entropy and sample entropy
    J S Richman
    Department of Internal Medicine, University of Virginia Health Sciences Center, Charlottesville 22908, USA
    Am J Physiol Heart Circ Physiol 278:H2039-49. 2000
  4. ncbi A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility
    Jason H Moore
    Computational Genetics Laboratory, Department of Genetics, Dartmouth Hitchcock Medical Center, One Medical Center Dr, 706 Rubin Bldg, HB7937, Lebanon, NH 03756, USA
    J Theor Biol 241:252-61. 2006
  5. pmc QDMR: a quantitative method for identification of differentially methylated regions by entropy
    Yan Zhang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Nucleic Acids Res 39:e58. 2011
  6. ncbi Multiscale entropy analysis of complex physiologic time series
    Madalena Costa
    Cardiovascular Division, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
    Phys Rev Lett 89:068102. 2002
  7. ncbi Multiscale entropy analysis of biological signals
    Madalena Costa
    Margret and H A Rey Institute for Nonlinear Dynamics in Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 71:021906. 2005
  8. pmc Transfer entropy--a model-free measure of effective connectivity for the neurosciences
    Raul Vicente
    Max Planck Institute for Brain Research, Frankfurt, Germany
    J Comput Neurosci 30:45-67. 2011
  9. pmc Maximum entropy models for antibody diversity
    Thierry Mora
    Joseph Henry Laboratories of Physics and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 107:5405-10. 2010
  10. pmc A small world of neuronal synchrony
    Shan Yu
    Department of Neurophysiology, Max Planck Institute for Brain Research, D 60528 Frankfurt am Main, Germany
    Cereb Cortex 18:2891-901. 2008

Detail Information

Publications284 found, 100 shown here

  1. ncbi Protein activity regulation by conformational entropy
    Shiou Ru Tzeng
    Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
    Nature 488:236-40. 2012
    ..Here we show that changes in conformational entropy can determine whether protein-ligand interactions will occur, even among protein complexes with identical binding ..
  2. ncbi Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
    S D Dunn
    Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A 5C1
    Bioinformatics 24:333-40. 2008
    ..However, a high background composed of random noise and phylogenetic components interferes with the identification of coevolving positions...
  3. ncbi Physiological time-series analysis using approximate entropy and sample entropy
    J S Richman
    Department of Internal Medicine, University of Virginia Health Sciences Center, Charlottesville 22908, USA
    Am J Physiol Heart Circ Physiol 278:H2039-49. 2000
    b>Entropy, as it relates to dynamical systems, is the rate of information production...
  4. ncbi A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility
    Jason H Moore
    Computational Genetics Laboratory, Department of Genetics, Dartmouth Hitchcock Medical Center, One Medical Center Dr, 706 Rubin Bldg, HB7937, Lebanon, NH 03756, USA
    J Theor Biol 241:252-61. 2006
    ..e. class entropy removed) and reduced to a single attribute using MDR...
  5. pmc QDMR: a quantitative method for identification of differentially methylated regions by entropy
    Yan Zhang
    College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
    Nucleic Acids Res 39:e58. 2011
    ..to quantify methylation difference and identify DMRs from genome-wide methylation profiles by adapting Shannon entropy. QDMR was applied to synthetic methylation patterns and methylation profiles detected by methylated DNA ..
  6. ncbi Multiscale entropy analysis of complex physiologic time series
    Madalena Costa
    Cardiovascular Division, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
    Phys Rev Lett 89:068102. 2002
    ..We introduce a method to calculate multiscale entropy (MSE) for complex time series...
  7. ncbi Multiscale entropy analysis of biological signals
    Madalena Costa
    Margret and H A Rey Institute for Nonlinear Dynamics in Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 71:021906. 2005
    ..We describe in detail the basis and implementation of the multiscale entropy (MSE) method...
  8. pmc Transfer entropy--a model-free measure of effective connectivity for the neurosciences
    Raul Vicente
    Max Planck Institute for Brain Research, Frankfurt, Germany
    J Comput Neurosci 30:45-67. 2011
    ..Transfer entropy (TE) is an alternative measure of effective connectivity based on information theory...
  9. pmc Maximum entropy models for antibody diversity
    Thierry Mora
    Joseph Henry Laboratories of Physics and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 107:5405-10. 2010
    Recognition of pathogens relies on families of proteins showing great diversity. Here we construct maximum entropy models of the sequence repertoire, building on recent experiments that provide a nearly exhaustive sampling of the IgM ..
  10. pmc A small world of neuronal synchrony
    Shan Yu
    Department of Neurophysiology, Max Planck Institute for Brain Research, D 60528 Frankfurt am Main, Germany
    Cereb Cortex 18:2891-901. 2008
    ..To reconstruct the interaction network, we applied the Ising model based on the principle of maximum entropy. This allowed us to assess the interactions by measuring pairwise correlations and to assess the strength of ..
  11. ncbi AL2CO: calculation of positional conservation in a protein sequence alignment
    J Pei
    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA
    Bioinformatics 17:700-12. 2001
    ..Three conceptually different approaches (entropy-based, variance-based and matrix score-based) are implemented in the algorithm to define the conservation index...
  12. pmc Entropy as the driver of chromosome segregation
    Suckjoon Jun
    FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Rev Microbiol 8:600-7. 2010
    ..as a result of entropic forces, despite their strong confinement within the cell; in other words, we propose that entropy can act as a primordial physical force which drives chromosome segregation under the right physical conditions...
  13. ncbi Calculation of protein-ligand binding affinities
    Michael K Gilson
    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
    Annu Rev Biophys Biomol Struct 36:21-42. 2007
    ..of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches...
  14. pmc Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding
    Andrew T Fenley
    Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093 0736, USA
    Proc Natl Acad Sci U S A 109:20006-11. 2012
    ..These results establish the basis for a mechanism that we term entropy-enthalpy transduction (EET), in which the thermodynamic character of a local perturbation, such as enthalpic ..
  15. ncbi Atypical EEG complexity in autism spectrum conditions: a multiscale entropy analysis
    Ana Catarino
    Institute of Biophysics and Biomedical Engineering, Faculty of Sciences, University of Lisbon, Campo Grande 1749 016 Lisbon, Portugal
    Clin Neurophysiol 122:2375-83. 2011
    ..One recently developed measure of intrinsic complexity of biological systems is multiscale entropy (MSE)...
  16. pmc Differential network entropy reveals cancer system hallmarks
    James West
    Statistical Cancer Genomics, UCL Cancer Institute, University College London, London, United Kingdom
    Sci Rep 2:802. 2012
    ..a protein interaction network we here demonstrate that cancer cells are characterised by an increase in network entropy. In addition, we formally demonstrate that gene expression differences between normal and cancer tissue are ..
  17. ncbi Granger causality and transfer entropy are equivalent for Gaussian variables
    Lionel Barnett
    Centre for Computational Neuroscience and Robotics, School of Informatics, University of Sussex, Brighton BN1 9QJ, United Kingdom
    Phys Rev Lett 103:238701. 2009
    ..More recently transfer entropy, an information-theoretic measure of time-directed information transfer between jointly dependent processes, has ..
  18. pmc TRENTOOL: a Matlab open source toolbox to analyse information flow in time series data with transfer entropy
    Michael Lindner
    MEG Unit, Brain Imaging Center, Goethe University, Frankfurt, Germany
    BMC Neurosci 12:119. 2011
    Transfer entropy (TE) is a measure for the detection of directed interactions. Transfer entropy is an information theoretic implementation of Wiener's principle of observational causality...
  19. ncbi A two-entropies analysis to identify functional positions in the transmembrane region of class A G protein-coupled receptors
    Kai Ye
    Division of Medicinal Chemistry, Leiden Amsterdam Center for Drug Research, Leiden University, Leiden, The Netherlands
    Proteins 63:1018-30. 2006
    ..Our method appears superior when compared to other bioinformatics approaches, such as the evolutionary trace method, entropy-variability plot, and correlated mutation analysis, both qualitatively and quantitatively.
  20. pmc Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways
    Paul C Whitford
    Center for Theoretical Biological Physics and Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
    RNA 16:1196-204. 2010
    ..that employ an all-atom, structure-based (Gō-like) model illuminate the interplay between configurational entropy and effective enthalpy during the accommodation process...
  21. ncbi Prediction of G-protein-coupled receptor classes in low homology using Chou's pseudo amino acid composition with approximate entropy and hydrophobicity patterns
    Q Gu
    College of Information Sciences and Technology, Donghua University, Shanghai 201620, China
    Protein Pept Lett 17:559-67. 2010
    We use approximate entropy and hydrophobicity patterns to predict G-protein-coupled receptors. Adaboost classifier is adopted as the prediction engine. A low homology dataset is used to validate the proposed method...
  22. ncbi Nonclassical splicing mutations in the coding and noncoding regions of the ATM Gene: maximum entropy estimates of splice junction strengths
    Laura Eng
    Department of Pathology and Laboratory Medicine, The David Geffen School of Medicine at UCLA, Los Angeles, California 90095 1732, USA
    Hum Mutat 23:67-76. 2004
    ..mutations in 12 A-T patients and compare cDNA changes to estimates of splice junction strengths based on maximum entropy modeling...
  23. pmc Pairwise maximum entropy models for studying large biological systems: when they can work and when they can't
    Yasser Roudi
    Gatsby Computational Neuroscience Unit, University College London, London, United Kingdom
    PLoS Comput Biol 5:e1000380. 2009
    ..Applied to neural data, the size of most systems studied so far is below the crossover point...
  24. pmc Weak pairwise correlations imply strongly correlated network states in a neural population
    Elad Schneidman
    Joseph Henry Laboratories of Physics, Princeton University, Princeton, New Jersey 08544, USA
    Nature 440:1007-12. 2006
    ..These maximum entropy models are equivalent to Ising models, and predict that larger networks are completely dominated by correlation ..
  25. ncbi Use of sample entropy approach to study heart rate variability in obstructive sleep apnea syndrome
    Haitham M Al-Angari
    Electrical and Computer Engineering Department, King Abdulaziz University, P O Box 80204, Jeddah, 21589, Saudi Arabia
    IEEE Trans Biomed Eng 54:1900-4. 2007
    Sample entropy, a nonlinear signal processing approach, was used as a measure of signal complexity to evaluate the cyclic behavior of heart rate variability (HRV) in obstructive sleep apnea syndrome (OSAS)...
  26. ncbi Engineering entropy-driven reactions and networks catalyzed by DNA
    David Yu Zhang
    Computation and Neural Systems, California Institute of Technology, MC 136 93, 1200 East California Boulevard, Pasadena, CA91125, USA
    Science 318:1121-5. 2007
    ..This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and ..
  27. ncbi Accurate estimation of entropy in very short physiological time series: the problem of atrial fibrillation detection in implanted ventricular devices
    Douglas E Lake
    Cardiovascular Division, Department of Internal Medicine, and Cardiovascular Research Center, University of Virginia Health System, Charlottesville, Virginia, USA
    Am J Physiol Heart Circ Physiol 300:H319-25. 2011
    b>Entropy estimation is useful but difficult in short time series...
  28. pmc Stimulus-dependent maximum entropy models of neural population codes
    Einat Granot-Atedgi
    Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 9:e1002922. 2013
    ..We introduce the stimulus-dependent maximum entropy (SDME) model-a minimal extension of the canonical linear-nonlinear model of a single neuron, to a pairwise-..
  29. ncbi Information theory, novelty and hippocampal responses: unpredicted or unpredictable?
    Bryan A Strange
    Wellcome Department of Imaging Neuroscience, Functional Imaging Laboratory, Institute of Neurology, 12 Queen Square, London WC1N 3BG, UK
    Neural Netw 18:225-30. 2005
    ..In particular, entropy measures the expected uncertainty of events in a given context...
  30. pmc Protein flexibility and conformational entropy in ligand design targeting the carbohydrate recognition domain of galectin-3
    Carl Diehl
    Center for Molecular Protein Science, Biophysical Chemistry, Lund University, P O Box 124, SE 22100 Lund, Sweden
    J Am Chem Soc 132:14577-89. 2010
    ..Despite the fundamental importance of both enthalpy and entropy in driving ligand binding, the role of conformational entropy is rarely addressed in drug design...
  31. ncbi Common input explains higher-order correlations and entropy in a simple model of neural population activity
    Jakob H Macke
    Gatsby Computational Neuroscience Unit, University College London, London, United Kingdom
    Phys Rev Lett 106:208102. 2011
    ..to large changes in higher-order redundancies, and that the resulting interactions have a strong impact on the entropy, sparsity, and statistical heat capacity of the population...
  32. pmc Analysis of kinetics using a hybrid maximum-entropy/nonlinear-least-squares method: application to protein folding
    Peter J Steinbach
    Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA
    Biophys J 82:2244-55. 2002
    A hybrid analysis that combines the maximum entropy method (MEM) with nonlinear least squares (NLS) fitting has been developed to interpret a general time-dependent signal...
  33. pmc Entropy-driven spatial organization of highly confined polymers: lessons for the bacterial chromosome
    Suckjoon Jun
    Stichting voor Fundamenteel Onderzoek der Materie FOM Institute for Atomic and Molecular Physics AMOLF, Kruislaan 407, 1098 SJ, Amsterdam, The Netherlands
    Proc Natl Acad Sci U S A 103:12388-93. 2006
    ..topologically distinct domains of a polymer complex effectively repel each other to maximize their conformational entropy, suggesting that duplicated circular chromosomes could partition spontaneously...
  34. ncbi Transfer entropy in magnetoencephalographic data: quantifying information flow in cortical and cerebellar networks
    Michael Wibral
    Goethe University, Brain Imaging Center, MEG Unit, Heinrich Hoffmann Strasse 10, 60528 Frankfurt, Germany
    Prog Biophys Mol Biol 105:80-97. 2011
    ..Ideally, this method should not require a pre-specified model of the interaction. Transfer entropy--an information theoretic implementation of Wiener-type causality--is a method for the investigation of causal ..
  35. ncbi Predicting survival in heart failure case and control subjects by use of fully automated methods for deriving nonlinear and conventional indices of heart rate dynamics
    K K Ho
    Cardiovascular Division, Beth Israel Deaconess Medical Center, Boston, Mass 02215 5491, USA
    Circulation 96:842-8. 1997
    ..Despite much recent interest in quantification of heart rate variability (HRV), the prognostic value of conventional measures of HRV and of newer indices based on nonlinear dynamics is not universally accepted...
  36. ncbi Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactions
    J D Dunitz
    Organic Chemistry Laboratory, Swiss Federal Institute of Technology, Zurich, Switzerland
    Chem Biol 2:709-12. 1995
    Enthalpy-entropy compensation is a general feature of many chemical reactions and processes in biological systems, but its origin has remained obscure...
  37. pmc Entropy explains aging, genetic determinism explains longevity, and undefined terminology explains misunderstanding both
    Leonard Hayflick
    PLoS Genet 3:e220. 2007
  38. pmc Conformational entropy in molecular recognition by proteins
    Kendra King Frederick
    Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Nature 448:325-9. 2007
    ..Historically it has been virtually impossible to experimentally estimate changes in protein conformational entropy, a potentially important component of the free energy of protein association...
  39. pmc Predicting the current and future potential distributions of lymphatic filariasis in Africa using maximum entropy ecological niche modelling
    Hannah Slater
    Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
    PLoS ONE 7:e32202. 2012
    ..literature in conjunction with five predictive environmental/climatic and demographic variables, and a maximum entropy niche modelling method to construct the first ecological niche maps describing potential distribution and burden ..
  40. pmc Is information a proper observable for biological organization?
    G Longo
    CREA, Ecole Polytechnique, 32 Boulevard Victor, 75015 Paris, France
    Prog Biophys Mol Biol 109:108-14. 2012
    ..Our analysis concentrates on the development of information theories in mathematics and on the differences between these theories regarding the relationship among complexity, information and entropy.
  41. pmc Coupled mutation finder: a new entropy-based method quantifying phylogenetic noise for the detection of compensatory mutations
    Mehmet Gültas
    Institute of Computer Science, University of Gottingen, Goldschmidtstr 7, Gottingen, 37077, Germany
    BMC Bioinformatics 13:225. 2012
    ..In this study, we developed a new method, the Coupled Mutation Finder (CMF) quantifying the phylogenetic noise for the detection of compensatory mutations...
  42. ncbi Identifying protein complexes in protein-protein interaction networks by using clique seeds and graph entropy
    Bolin Chen
    Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK, Canada
    Proteomics 13:269-77. 2013
    ..The performance of this seed-selection strategy and the result-modification approach are tested by using the entropy-based algorithm, which is currently the best seed-growth style algorithm to detect protein complexes from PPI ..
  43. ncbi Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle
    Andrea Cavalli
    Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
    J Chem Phys 138:094112. 2013
    ..by nuclear Overhauser effects by showing that it generates ensembles of conformations according to the maximum entropy principle...
  44. ncbi Comparison of entropy-based regularity estimators: application to the fetal heart rate signal for the identification of fetal distress
    Manuela Ferrario
    Dipartimento di Bioingegneria, University Politecnico di Milano, Italy
    IEEE Trans Biomed Eng 53:119-25. 2006
    This paper considers the multiscale entropy (MSE) approach for estimating the regularity of time series at different scales...
  45. ncbi Evaluating information transfer between auditory cortical neurons
    Boris Gourévitch
    Department of Physiology and Biophysics and Department of Psychology, University of Calgary, Calgary, Alberta, Canada
    J Neurophysiol 97:2533-43. 2007
    Transfer entropy, presented as a new tool for investigating neural assemblies, quantifies the fraction of information in a neuron found in the past history of another neuron. The asymmetry of the measure allows feedback evaluations...
  46. ncbi Entropy in protein folding and in protein-protein interactions
    G P Brady
    Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Curr Opin Struct Biol 7:215-21. 1997
    The reduction of conformational entropy is a major barrier that has to be overcome in protein folding and binding. Changes in solvent entropy are also a major factor...
  47. ncbi The effect of orthostatic stress on multiscale entropy of heart rate and blood pressure
    Zuzana Turianikova
    Department of Physiology, Jessenius Faculty of Medicine, Comenius University, Martin, Slovak Republic
    Physiol Meas 32:1425-37. 2011
    ..Multiscale entropy (MSE) analysis has been developed to quantify the complexity of a time series over multiple time scales...
  48. ncbi Multiscale entropy and detrended fluctuation analysis of QT interval and heart rate variability during normal pregnancy
    Mathias Baumert
    School of Electrical and Electronic Engineering, University of Adelaide, Adelaide 5005, Australia
    Comput Biol Med 42:347-52. 2012
    ..Heart rate and QT variability were quantified using multiscale entropy (MSE) and detrended fluctuation analyses (DFA)...
  49. pmc A thermodynamic approach to the affinity optimization of drug candidates
    Ernesto Freire
    Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
    Chem Biol Drug Des 74:468-72. 2009
    ..As the binding affinity is a function of two quantities, the binding enthalpy and the binding entropy, it is evident that a more efficient optimization would be accomplished if both quantities were considered and ..
  50. pmc Cellular network entropy as the energy potential in Waddington's differentiation landscape
    Christopher R S Banerji
    1 Statistical Cancer Genomics, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, United Kingdom 2 Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London WC1E6BT United Kingdom
    Sci Rep 3:3039. 2013
    ..Here we adopt a systems view and consider the sample's network entropy, a measure of signaling pathway promiscuity, computable from a sample's genome-wide expression profile...
  51. ncbi Topological entropy of DNA sequences
    David Koslicki
    Department of Mathematics, Pennsylvania State University, State College, PA 16801, USA
    Bioinformatics 27:1061-7. 2011
    Topological entropy has been one of the most difficult to implement of all the entropy-theoretic notions. This is primarily due to finite sample effects and high-dimensionality problems...
  52. ncbi Intrinsic adaptation in autonomous recurrent neural networks
    Dimitrije Marković
    Institute for Theoretical Physics, J W Goethe University, 60438 Frankfurt am Main, Hessen, Germany
    Neural Comput 24:523-40. 2012
    ..neural parameters, such as the threshold and the gain, and is driven by the optimization of the information entropy. We observe, in the presence of the intrinsic adaptation processes, three distinct and globally attracting ..
  53. ncbi Non-stationarities significantly distort short-term spectral, symbolic and entropy heart rate variability indices
    Valentina Magagnin
    Laboratorio di Modellistica di Sistemi Complessi, Dipartimento di Tecnologie per la Salute, Istituto Ortopedico Galeazzi, Universita degli Studi di Milano, Via R Galeazzi 4, Milan, Italy
    Physiol Meas 32:1775-86. 2011
    ..The aim of our study is to quantify the potential bias of spectral, symbolic and entropy HRV indices due to non-stationarities...
  54. pmc Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design
    John D Chodera
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Annu Rev Biophys 42:121-42. 2013
    ..between small molecules and biomolecular targets have generated renewed interest in the phenomenon of entropy-enthalpy compensation...
  55. ncbi Fast and accurate computation schemes for evaluating vibrational entropy of proteins
    Beisi Xu
    State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, The Chinese Academy of Sciences, Dalian, China
    J Comput Chem 32:3188-93. 2011
    Standard normal mode analysis (NMA) method is able to calculate vibrational entropy of proteins, but it is computationally intensive, especially for large proteins...
  56. ncbi An entropy-based approach for testing genetic epistasis underlying complex diseases
    Guolian Kang
    Department of Statistics and Probability, East Lansing, Michigan State University, MI 48824, USA
    J Theor Biol 250:362-74. 2008
    ..In this article, we introduce a new approach for testing genetic epistasis in multiple loci using an entropy-based statistic for a case-only design. The entropy-based statistic asymptotically follows a chi(2) distribution...
  57. pmc Nonadditivity in conformational entropy upon molecular rigidification reveals a universal mechanism affecting folding cooperativity
    Oleg K Vorov
    Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
    Biophys J 100:1129-38. 2011
    ..classical helix-coil transition theories, the folding mechanism derives from nonadditivity in conformational entropy caused by rigidification of molecular structure as intramolecular cross-linking interactions form along the ..
  58. pmc A comparison of pain level and entropy changes following core stability exercise intervention
    Taero Lee
    Department of Healthcare Management, College of Health Science, Korea University, Seoul, Republic of Korea
    Med Sci Monit 17:CR362-8. 2011
    ..We examined whether the observed Shannon (information) entropy, as compared with median frequency (MF), was able to differentiate fatigability of the thoracic and lumbar parts ..
  59. ncbi Maximum entropy: a complement to Tikhonov regularization for determination of pair distance distributions by pulsed ESR
    Yun Wei Chiang
    Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 1301, USA
    J Magn Reson 177:184-96. 2005
    ..The Shannon-Jaynes entropy of a probability distribution provides an intrinsic non-negativity constraint on the probability distribution and ..
  60. ncbi Spectral entropy measurement of patient responsiveness during propofol and remifentanil. A comparison with the bispectral index
    A L G Vanluchene
    Department of Anaesthesia, Gent University Hospital, De Pintelaan 185, B 9000 Gent, Belgium
    Br J Anaesth 93:645-54. 2004
    We compared two spectral entropies, state entropy (SE) and response entropy (RE), based on the irregularity of the EEG, to measure loss of response to verbal command (LOR(verbal)) and noxious stimulus (LOR(noxious)) with the bispectral ..
  61. ncbi Evaluation of EEG localization methods using realistic simulations of interictal spikes
    C Grova
    Montreal Neurological Institute, McGill University, EEG Department, Room 009d, 3801 University Street, Montreal, Quebec, Canada H3A 2B4
    Neuroimage 29:734-53. 2006
    ..MSP), cortical LORETA with or without additional minimum norm regularization, and two derivations of the maximum entropy on the mean (MEM) approach...
  62. ncbi Entropy-driven cAMP-dependent allosteric control of inhibitory interactions in exchange proteins directly activated by cAMP
    Rahul Das
    Department of Chemistry, Biochemistry, and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
    J Biol Chem 283:19691-703. 2008
    ....
  63. pmc Connections between classical and parametric network entropies
    Matthias Dehmer
    Institute for Bioinformatics and Translational Research, UMIT, Hall in Tirol, Austria
    PLoS ONE 6:e15733. 2011
    ..The inequalities established in this paper relating classical and parametric measures lay a foundation for systematic classification of entropy-based measures of graph complexity.
  64. ncbi Assessment of non-invasive time and frequency atrial fibrillation organization markers with unipolar atrial electrograms
    Raul Alcaraz
    Innovation in Bioengineering Research Group, University of Castilla La Mancha, Campus Universitario, Cuenca, Spain
    Physiol Meas 32:99-114. 2011
    ..ECG and AEG signals, AF organization has been computed by applying a nonlinear regularity index, such as sample entropy (SampEn), to the atrial activity (AA) and to its fundamental waveform, defined as the main atrial wave (MAW)...
  65. ncbi Statistical analysis of the cancer cell's molecular entropy using high-throughput data
    Wessel N van Wieringen
    Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
    Bioinformatics 27:556-63. 2011
    As cancer progresses, DNA copy number aberrations accumulate and the genomic entropy (chromosomal disorganization) increases...
  66. ncbi Accounting for conformational entropy in predicting binding free energies of protein-protein interactions
    Hetunandan Kamisetty
    Computer Science Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
    Proteins 79:444-62. 2011
    ..often marginally stable, so one must examine the balance between the change in enthalpy, ΔH, and the change in entropy, ΔS, when investigating known complexes, characterizing the effects of mutations, or designing optimized ..
  67. pmc Altered neural and behavioral dynamics in Huntington's disease: an entropy conservation approach
    S Lee Hong
    Department of Kinesiology, Indiana University, Bloomington, Indiana, United States of America
    PLoS ONE 7:e30879. 2012
    ..The aim of this study was to test the patterns of unpredictability in brain and behavior in wild-type (WT) and R6/2 mice...
  68. ncbi The concept of structural entropy in tissue-based diagnosis
    Klaus Kayser
    UICC Telepathology Consultation Center, Charite, Berlin, Germany
    Anal Quant Cytol Histol 29:296-308. 2007
    The concept of entropy is described and its characteristics discussed as applied in tissue-based diagnosis. The concept of entropy includes at least 2 points of view--thermodynamic and informatics perspectives...
  69. pmc Gaining ligand selectivity in thyroid hormone receptors via entropy
    Leandro Martinez
    Instituto de Quimica, Universidade Estadual de Campinas, SP 13084 862, Campinas, Brazil
    Proc Natl Acad Sci U S A 106:20717-22. 2009
    ..Similar effects could potentially be exploited in nuclear receptor drug design...
  70. pmc Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes
    Xiaohui Cang
    Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah, USA
    Nucleic Acids Res 39:4499-512. 2011
    ..This leads to smaller energy differences between different geometries and helps explain the extreme structural polymorphism of the human telomeric G-quadruplexes...
  71. ncbi Aging of the brain, entropy, and Alzheimer disease
    David A Drachman
    Department of Neurology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
    Neurology 67:1340-52. 2006
    ..The effect of ARCs on the brain is seen as the biologic manifestation of increasing entropy, an approach that helps to explain the progressive decline of neural and cognitive function over time; the ..
  72. ncbi Prediction of spatiotemporal patterns of neural activity from pairwise correlations
    O Marre
    Unité de neurosciences intégratives et computationnelles UNIC, UPR CNRS 2191, Gif sur Yvette, France
    Phys Rev Lett 102:138101. 2009
    ..Using a maximum entropy principle with a Markovian assumption, we obtain a model that accounts for both spatial and temporal pairwise ..
  73. pmc Increased entropy of signal transduction in the cancer metastasis phenotype
    Andrew E Teschendorff
    Medical Genomics Group, Paul O Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
    BMC Syst Biol 4:104. 2010
    ..However, relatively little is known as to what network features differ between the cancer and normal cell physiologies, or between different cancer cell phenotypes...
  74. ncbi Information domain analysis of cardiovascular variability signals: evaluation of regularity, synchronisation and co-ordination
    A Porta
    Dipartimento di Scienze Precliniche, Universita degli Studi di Milano, Italy
    Med Biol Eng Comput 38:180-8. 2000
    ..This approach is based on conditional entropy and is specifically designed to deal with a small amount of data (a few hundred samples)...
  75. ncbi Symbolic transfer entropy
    Matthäus Staniek
    Department of Epileptology, Neurophysics Group, University of Bonn, Sigmund Freud Strasse 25, Bonn, Germany
    Phys Rev Lett 100:158101. 2008
    We propose to estimate transfer entropy using a technique of symbolization...
  76. pmc Extending transfer entropy improves identification of effective connectivity in a spiking cortical network model
    Shinya Ito
    Department of Physics, Indiana University, Bloomington, Indiana, United States of America
    PLoS ONE 6:e27431. 2011
    Transfer entropy (TE) is an information-theoretic measure which has received recent attention in neuroscience for its potential to identify effective connectivity between neurons...
  77. pmc Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family
    Beth G Wensley
    Department of Chemistry, University of Cambridge, MRC Centre for Protein Engineering, Lensfield Rd, Cambridge CB2 1EW UK
    Nature 463:685-8. 2010
    ..Simple folding models show that folding is significantly influenced by chain entropy; proteins in which the contacts are local fold quickly, owing to the low entropy cost of forming stabilizing, ..
  78. ncbi Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach
    Vasyl Pihur
    Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY 40202, USA
    Bioinformatics 23:1607-15. 2007
    ..An automated and objective way of reconciling the rankings is needed...
  79. pmc A large scale analysis of information-theoretic network complexity measures using chemical structures
    Matthias Dehmer
    Institute for Bioinformatics and Translational Research, UMIT, Hall in Tyrol, Austria
    PLoS ONE 4:e8057. 2009
    ..Generally, a high uniqueness is an important and desirable property when designing novel topological descriptors having the potential to be applied to large chemical databases...
  80. ncbi Comparative evaluation of the Datex-Ohmeda S/5 Entropy Module and the Bispectral Index monitor during propofol-remifentanil anesthesia
    Gunter N Schmidt
    Department of Anesthesiology, University Hospital Hamburg Eppendorf, Hamburg, Germany
    Anesthesiology 101:1283-90. 2004
    ..The Datex-Ohmeda S/5 Entropy Module (Datex-Ohmeda Division, Instrumentarium Corp...
  81. ncbi DNA binding of a non-sequence-specific HMG-D protein is entropy driven with a substantial non-electrostatic contribution
    Anatoly I Dragan
    Department of Biology, Johns Hopkins University, Mudd Hall, 3400 N Charles Street, Baltimore, MD 21218 2685, USA
    J Mol Biol 331:795-813. 2003
    ..e. DNA binding is a completely entropy-driven process...
  82. pmc Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    Daniel R Caffrey
    Pfizer Discovery Technology Center, Cambridge, Massachusetts 02139, USA
    Protein Sci 13:190-202. 2004
    ....
  83. pmc Potential landscape and flux framework of nonequilibrium networks: robustness, dissipation, and coherence of biochemical oscillations
    Jin Wang
    State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People s Republic of China
    Proc Natl Acad Sci U S A 105:12271-6. 2008
    ..We also found that the entropy production of the whole network, characterizing the dissipation costs from the combined effects of both ..
  84. ncbi Elevations in local gamma activity are accompanied by changes in the firing rate and information coding capacity of neurons in the region of the subthalamic nucleus in Parkinson's disease
    Alek Pogosyan
    Sobell Department of Motor Neuroscience and Movement Disorders, Institute of Neurology, Queen Square, London, WCIN 3BG, UK
    Exp Neurol 202:271-9. 2006
    ..Changes in the median firing frequency, entropy and baud were determined during spontaneous variations in the level of simultaneously recorded LFP gamma activity ..
  85. ncbi Wavelet entropy: a new tool for analysis of short duration brain electrical signals
    O A Rosso
    Facultad de Ciencias Exactas y Naturales, Instituto de Calculo, Universidad de Buenos Aires, Pabellon II, Ciudad Universitaria, 1428, Buenos Aires, Argentina
    J Neurosci Methods 105:65-75. 2001
    ..It takes as a basic element the ODWT of the EEG signal, and defines the relative wavelet energy, the wavelet entropy (WE) and the relative wavelet entropy (RWE)...
  86. ncbi Structural and thermodynamic strategies for site-specific DNA binding proteins
    L Jen-Jacobson
    Department of Biological Sciences University of Pittsburgh, Pittsburgh, PA 15260, USA
    Structure 8:1015-23. 2000
    ..A better understanding of the structural and energetic engineering principles might lead to rational methods for modification or design of such proteins...
  87. pmc Entropy bounds for hierarchical molecular networks
    Matthias Dehmer
    Institute of Discrete Mathematics and Geometry, Vienna University of Technology, Vienna, Austria
    PLoS ONE 3:e3079. 2008
    In this paper we derive entropy bounds for hierarchical networks...
  88. ncbi Basin entropy in Boolean network ensembles
    Peter Krawitz
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Phys Rev Lett 98:158701. 2007
    ..We introduce a novel network parameter, the basin entropy, as a measure of the complexity of information that such a system is capable of storing...
  89. ncbi A maximum entropy model applied to spatial and temporal correlations from cortical networks in vitro
    Aonan Tang
    Department of Physics, Indiana University, Bloomington, Indiana 47405, USA
    J Neurosci 28:505-18. 2008
    ..To explain these correlated network states, two groups recently applied a second-order maximum entropy model that used only observed firing rates and pairwise interactions as parameters (Schneidman et al...
  90. ncbi Human midbrain sensitivity to cognitive feedback and uncertainty during classification learning
    A R Aron
    Dept of Psychology and Brain Research Institute, University of California Los Angeles, CA 90065, USA
    J Neurophysiol 92:1144-52. 2004
    ..Purely cognitive feedback apparently engages the same regions as rewarding stimuli, consistent with a broader characterization of this network...
  91. pmc ROKU: a novel method for identification of tissue-specific genes
    Koji Kadota
    Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
    BMC Bioinformatics 7:294. 2006
    ..One of the important goals of microarray research is the identification of genes whose expression is considerably higher or lower in some tissues than in others. We would like to have ways of identifying such tissue-specific genes...
  92. pmc Ligand binding to protein-binding pockets with wet and dry regions
    Lingle Wang
    Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
    Proc Natl Acad Sci U S A 108:1326-30. 2011
    ....
  93. ncbi Entropy-accelerated exact clustering of protein decoys
    Francois Berenger
    Zhang Initiative Research Unit, Advanced Science Institute, RIKEN, Wako, Saitama, Japan
    Bioinformatics 27:939-45. 2011
    ..Typically, only a reduced set of decoys using energy filtering is subjected to clustering analysis. A fast clustering method for a large decoy set would be beneficial to protein structure prediction and this still poses a challenge...
  94. ncbi Comparison between approximate entropy, correntropy and time reversibility: application to uterine electromyogram signals
    Mahmoud Hassan
    UMR CNRS 6600, Biomécanique et Bio ingénierie, Universite de Technologie de Compiegne, Compiegne, France
    Med Eng Phys 33:980-6. 2011
    ..In this paper we compare three methods widely used in nonlinearity detection: approximate entropy, correntropy and time reversibility...
  95. ncbi Calculation of configurational entropy with a Boltzmann-quasiharmonic model: the origin of high-affinity protein-ligand binding
    Kyle W Harpole
    Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, United States
    J Phys Chem B 115:9461-72. 2011
    Accurate assessment of configurational entropy remains a large challenge in biology. While many methods exist to calculate configurational entropy, there is a balance between accuracy and computational demands...
  96. ncbi Fast computation of sample entropy and approximate entropy in biomedicine
    Yu Hsiang Pan
    Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, 2 Pei Ning Road, Keelung 20224, Taiwan
    Comput Methods Programs Biomed 104:382-96. 2011
    Both sample entropy and approximate entropy are measurements of complexity...
  97. pmc Apomorphine reduces subthalamic neuronal entropy in parkinsonian patients
    M Lafreniere-Roula
    Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
    Exp Neurol 225:455-8. 2010
    ..Here we examine the entropy of subthalamic neurons in PD patients undergoing stereotactic surgery for deep brain stimulation (DBS)...
  98. ncbi Generalized scalar measures for diffusion MRI using trace, variance, and entropy
    Evren Ozarslan
    Department of Physics, University of Florida, P O Box 118440, Gainesville, FL 32611, USA
    Magn Reson Med 53:866-76. 2005
    ..Simulations suggested that a lower-rank tensor model may produce artificially low anisotropy values in voxels with complex structure. This was confirmed with a spin-echo experiment performed on an excised rat brain...
  99. pmc Nonequilibrium generation of information in copolymerization processes
    David Andrieux
    Center for Nonlinear Phenomena and Complex Systems, Universite Libre de Bruxelles, Code Postal 231, Campus Plaine, B 1050 Brussels, Belgium
    Proc Natl Acad Sci U S A 105:9516-21. 2008
    ..This shows in particular how information acquisition results from the interplay between stored patterns and dynamical evolution in nonequilibrium environments. In addition, we apply these results to the process of DNA replication...
  100. ncbi Conformational constraint in protein ligand design and the inconsistency of binding entropy
    D Gomika Udugamasooriya
    Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
    Biopolymers 89:653-67. 2008
    ..expectation of improving affinity, justified by the theoretical possibility that an unfavorable change in binding entropy will be reduced...
  101. ncbi A comparison of state and response entropy versus bispectral index values during the perioperative period
    Paul F White
    Department of Anesthesiology and Pain Management, University of Texas, Southwestern Medical Center at Dallas, Texas 75390 9068, USA
    Anesth Analg 102:160-7. 2006
    ..We designed this clinical study to test the hypothesis that use of the spectral entropy (Entropy) module is associated with less frequent intraoperative interference with the displayed indices than the ..

Research Grants63

  1. Mechanisms of Viral DNA Packaging
    CARLOS JOSE BUSTAMANTE; Fiscal Year: 2013
    ..density-overcoming energetic penalties due to electrostatics repulsion, DNA bending stiffness, and entropy. Because this motor is comprised of a pentameric ring of ASCE ATPases, its study will shed important light into ..
  2. NEURONAL BASIS UNDERLYING VOLATILE ANESTHETIC INDUCED HYPNOSIS
    MAX KELZ; Fiscal Year: 2013
    ..of VLPO cause resistance to anesthetic hypnosis as determined by righting reflex assays and processed EEG entropy. Finally, we will determine if light-induced depolarization of VLPO causes hypersensitivity to anesthetic ..
  3. Integrated Desktop Software for Management of Hepatitic C Data
    Johanna C Craig; Fiscal Year: 2010
    ..In Phase II we will develop additional tools for mutation tracking, report generation and entropy measurement, and we will develop statistical routines and security and installation packages...
  4. Topoisomerases and Chromosome Segregation
    Kenneth J Marians; Fiscal Year: 2012
    ..transertion (the coupling of transcription and co-translational insertion of proteins into the membrane], and entropy. And the role of the recently discovered MreB cytoskeleton remains unclear...
  5. Fluorescence Fluctuation Spectroscopy for von Willebrand Factor Multimer Analysis
    Michael J Levene; Fiscal Year: 2010
    ..Maximum entropy regularization has been used for multi-parameter FCS (MEMFCS) fits;we will develop our own MEMFCS algorithm to ..
  6. Biophysical Characterization of PDX1 interactions with DNA and other transcriptio
    Monique Bastidas; Fiscal Year: 2013
    ..Based on all ITC data, a catalogue of the binding affinity, stoichiometry, entropy of binding, free energy of the reaction, change in heat capacity and apparent binding enthalpy will be generated...
  7. Consequences of Cardiac Arrest: Brain Injury
    NITISH VYOMESH THAKOR; Fiscal Year: 2013
    ..of cortical somatosensory evoked potentials (SSEP) will track recovery of normal thalamocortical coupling, and c) entropy-based quantitative EEG (qEEG) analysis will capture sequential changes in thalamocortical coupling during ..
  8. Reversible dimerization of a CLC transporter: A model for membrane protein foldin
    Janice L Robertson; Fiscal Year: 2013
    ..The second hypothesis is that interactions are driven by increased entropy of lipids upon helix association...
  9. Reversible dimerization of a CLC transporter: A model for membrane protein foldin
    Janice L Robertson; Fiscal Year: 2013
    ..The second hypothesis is that interactions are driven by increased entropy of lipids upon helix association...
  10. Mechanisms of Allosteric Influence on Enzymes Activity
    GREGORY DUNCAN REINHART; Fiscal Year: 2012
    ..The second question is whether the entropy change that contributes to the action of an allosteric ligand is related to changes in enzyme dynamics...
  11. Thermodynamics and kinetics of DNA-ligand binding probed by DNA overstretching
    Andreas Hanke; Fiscal Year: 2013
    ..of length and time scales spanned by the process, and by the difficulty in computing the accompanying change in entropy. To better understand the fundamental biophysics involved in crossing length and times scales from the atomistic ..
  12. Integrated software application for management of Hepatitis C Virus data
    Johanna C Craig; Fiscal Year: 2013
    ..In this Phase II work, we will develop additional tools for mutation tracking, report generation and entropy measurement, and we will develop statistical routines and security and installation packages...
  13. Brain Monitoring and Therapeutic Hypothermia after Cardiac Arrest
    Xiaofeng Jia; Fiscal Year: 2013
    ..We test the hypotheses that a) qEEG analysis, based on our novel entropy based algorithms, will capture electrophysiological recovery to pre-CA baseline, and b) sequential recovery in ..
  14. NMR Studies of Protein Side-Chain Dynamics
    MARK A RANCE; Fiscal Year: 2012
    ..Side chains can make significant contributions to the configurational entropy of a protein, thereby modulating the thermodynamics of protein function...
  15. Engineering of Proteins for Crystallography
    Adam Godzik; Fiscal Year: 2013
    ..that protein crystallization can be rationally induced by surface engineering based on the premise of surface entropy reduction (SER), i.e...
  16. Mechanical and Dynamical Regulation of Protein Kinases
    CHRISTOPHER LEE MCCLENDON; Fiscal Year: 2013
    ..A covariance of mechanical stress approach will be developed along with transfer entropy analysis in internal coordinates to identify mechanistic cause and effect in active site opening, the rate- ..
  17. Structural and Biochemical Characterization of the S. cerevisiae RNA Exosome
    ELIZABETH VICTORINA WASMUTH; Fiscal Year: 2013
    ..strategy will facilitate reconstitution of the 9-, 10-, and 11-subunit exosome complexes that better mimic their cellular counterparts in addition to providing samples more amenable to crystallization through surface entropy reduction.
  18. Dynamics &energetics of p38a kinase regulation by ligands
    A Joshua Wand; Fiscal Year: 2013
    ..enabled the use of measures-of-motion between conformational states of a protein as a proxy for conformational entropy. There is now a strong indication from recent studies utilizing this approach that changes in conformational ..
  19. EEG Complexity Trajectory as an Early Biomarker for Autism
    William J Bosl; Fiscal Year: 2013
    ..Our hypothesis is that multiscale entropy (MSE) is one measure of signal complexity that will reveal distinct, measurable differences between normally ..
  20. Imaging Taste in Ensembles of Afferent Neurons
    Stephen D Roper; Fiscal Year: 2013
    ..We will measure the breadth of tuning, concentration-response relations and entropy for gustatory geniculate ganglion cells (Aim 1)...
  21. A MULTIDISCIPLINARY APPROACH TO PEPTIDE-BASED ANTAGONISTS OF PCNA
    Zhihao Zhuang; Fiscal Year: 2011
    ..monovalent ligands for optimized interaction at multiple sites on the target to maximize favorable enthalpy and entropy without introducing the significant entropic or enthalpic penalties commonly observed in polyvalency;and (c) ..
  22. Accurate and Efficient Measures for HIV Incidence
    Marcello Pagano; Fiscal Year: 2013
    ..To address these shortcomings, we first introduce a novel entropy measure associated with the viral genome, which will distinguish between recent and long term infections among ..
  23. Dynamic markers of intraoperative instability
    Balachundhar Subramaniam; Fiscal Year: 2013
    ..The data will be deidentified and analyzed with multi scale entropy. The entropy data will be tested for its MAE predictive ability and compared to the traditional STS risk indices ..
  24. A new interpretation of solute effects on biological equilibria
    Daryl K Eggers; Fiscal Year: 2013
    ..Enthalpy and entropy values of bulk water will be measured and tabulated for many solutions of interest, including neutral salts, ..
  25. Permissive Specificity in Peptide Binding to HLA-DR
    JACK A GORSKI; Fiscal Year: 2012
    ..by thermodynamic phenomena, in particular the presence of cooperativity and the occurrence of isothermal entropy-enthalpy compensation (iEEC)...
  26. Fluctuations and entropy in the energetics and function of protein complexes
    A Joshua Wand; Fiscal Year: 2013
    ..entities, that their internal motion is an expression of an inherent and significant amount of conformational entropy and that changes in conformation entropy can greatly influence the energetics of protein function...
  27. Purchase of an Isothermal Titration Calorimeter
    ROBERT TODD BATEY; Fiscal Year: 2010
    ..advantages over others, including that it can obtain information about the binding affinity, enthalpy and entropy of reaction and stoichiometry of the reaction in a single experiment and that it does not require the labeling of ..
  28. Mechanical Stress and the Heat-Treatment of Soft Tissue
    JAY HUMPHREY; Fiscal Year: 2003
    ..This reveals that loading influences the process via the activation entropy, not energy. No prior clinical trial of a heating device or strategy has accounted for this coupling...
  29. SEQUENCE SPECIFIC DNA PROTEIN INTERACTIONS
    Linda Jen Jacobson; Fiscal Year: 2010
    ..and kinetic basis for a quantitative understanding of the changes in free energy (AG), enthalpy (AH) and entropy (AS0) in formation of protein-DNA complexes...
  30. METABOLISM AND NUTRITION OF IRON AND OTHER TRACE METALS
    PAUL SALTMAN; Fiscal Year: 1993
    ..to Cu(ll) requires site-specific binding to favorably modify both the half-cell potential of the Cu(ll) and the entropy of ligands surrounding the metal...
  31. Cardiovascular Variability and Control in Early Sepsis
    SAMUEL MORRIS BROWN; Fiscal Year: 2013
    ..hypothesizes that spectral and non-linear measures of cardiovascular variability like spectral power, sample entropy, and fractal exponents will predict recovery of cardiovascular homeostasis by 24 hours after presentation in ..
  32. High throughput measurement of envelope gene diversity for an HIV incidence assay
    SATISH KUMAR PILLAI; Fiscal Year: 2013
    ..how well AmpliCot measurements correlate with viral sequence complexity, sequence diversity, and Shannon entropy (a measure of sequence complexity weighted for relative abundance), with comparison to deep sequencing as a gold ..
  33. Spatial Epidemiology of Syphilis and Gonorrhea in North Carolina
    William C Miller; Fiscal Year: 2010
    ..Our primary strategy will use Bayesian Maximum Entropy models, incorporating both spatial and temporal data...
  34. REM SLEEP AND MEMORY
    Gina R Poe; Fiscal Year: 2013
    ..reactivation events for changes indicative of plasticity, like burst spike attenuation changes, Causal Entropy and Functional Clustering...
  35. Novel markers of synchrony in the evaluation of cardiac resynchronization therapy
    KURT STEPHEN HOFFMAYER; Fiscal Year: 2011
    ..parameters of ventricular synchrony including ECGI electrical synchrony index (Esyn) and ERNA-synchrony (S) and entropy (E) pre and post CRT implantation (8-12)...
  36. Accelerated Determination of 3D Structures of Proteins and Complexes
    Chris Sander; Fiscal Year: 2013
    ..team, extracts evolutionary residue-residue couplings from multiple sequence alignments, using a maximum entropy method...
  37. Multi-Scale Integration of Extracellular Matrix Mechanics in Vascular Remodeling
    YANHANG KATHERINE ZHANG; Fiscal Year: 2013
    ..A freely joined chain (FJC) model will be adopted to describe the possible configurations, thus entropy, of a fiber during stretching...
  38. Collaborative experimental &computational studies of conformational transitions
    Dorothee Kern; Fiscal Year: 2013
    ..Furthermore, determining interconversion entropy and entropy changes for these enzymes adapted to extreme environments may shed light on the evolutionary ..
  39. Racial and Ethnic Diversity in American Communities, 1980-2010
    Barrett A Lee; Fiscal Year: 2013
    ..At the community level, we will employ the entropy index, a 'majority rule'compositional typology, transition matrices, cohort analysis, and growth ..
  40. ITC: Isothermal Titration Calorimeter
    ROBERT THOMPSON CLUBB; Fiscal Year: 2012
    ..The information obtained includes the binding stoichiometry, affinity, enthalpy and entropy. Access to this technology is lacking at UCLA as the campus contains only a single older-generation ..
  41. Statistical Mechanics of RNA Folding
    Shi Jie Chen; Fiscal Year: 2013
    ..A key advantage of the approach is the completeness and certainty in conformational sampling (entropy). Incorrect entropy results in poor predictions...
  42. DNA circuits for point-of-care diagnostics
    Andrew D Ellington; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): We propose to adapt novel, entropy-driven DNA circuitry that has only recently been developed to pressing needs in point-of-care diagnostics...
  43. Optimizing Therapeutic Index of mAb-IFN_alpha Molecule to Treat Lymphoma
    SANJAY DEEP KHARE; Fiscal Year: 2012
    ..or none ofthe intrinsic binding energy of IFN[unreadable] for its receptor has to be used to pay the cost of entropy loss incurred when the bound IFN[unreadable] is localized on the cell surface...
  44. Uncertainty, Cognitive Control, and the Brain
    Jin Fan; Fiscal Year: 2013
    ..We argue that conflict is only a special case of uncertainty that can be quantified as information entropy, based on an information theory framework...
  45. Design of inhibitors targeted to the CD4 binding site on HIV-1 gp120
    Asim K Debnath; Fiscal Year: 2013
    ..In Aim-2, thermodynamic and kinetic properties such as enthalpy, entropy, on- and off-rates and binding affinity (KD) will be measured as well as their antiviral potency and toxicity...
  46. MOLECULAR RECOGNITION IN THE STREPTAVIDIN BIOTIN SYSTEM
    Patrick Stayton; Fiscal Year: 2002
    ..interact with? For example, do residues contacting portions of a ligand expected to have high configurational entropy (such as the valeric acid tails of biotin) have a different energetic challenge than those residues contacting ..
  47. MOLECULAR RECOGNITION IN THE STREPTAVIDIN BIOTIN SYSTEM
    Patrick Stayton; Fiscal Year: 2001
    ..interact with? For example, do residues contacting portions of a ligand expected to have high configurational entropy (such as the valeric acid tails of biotin) have a different energetic challenge than those residues contacting ..
  48. Blood flow oscillations and early detection of pressure ulcers in older adults
    Yih Kuen Jan; Fiscal Year: 2010
    ..Nonlinear analyses include Hurst exponent, detrended fluctuation analysis, correlation dimension, sample entropy, and Lyapunov exponent...
  49. Innovative Ultrasound Technology in Neuromuscular Disease
    Seward B Rutkove; Fiscal Year: 2013
    ..radiofrequency data, computer-assisted image segmentation, and volumetric, electrographic, anisotropic, and entropy-based analyses...
  50. THEORY AND MODELING OF NONCOVALENT BINDING
    Michael K Gilson; Fiscal Year: 2013
    ..The second part is to study the changes in entropy that occur when molecules bind...
  51. PROTEIN INTERACTIONS FROM SOLID MODEL COMPOUND
    STANLEY GILL; Fiscal Year: 1992
    ..the thermodynamic properties of the dissolution process, namely the free energy change, the enthalpy change, the entropy change, and the heat capacity change for simple compounds composed of amino acids...
  52. OPIOID RECEPTOR CONSTANTS IN VITRO--TEMPERATURE
    Frank Porreca; Fiscal Year: 1990
    ..e., changes in Gibbs free energy reflected as changes in enthalpy and entropy. Agonists and antagonists may bind to receptors differently, with only agonists able to possibly induce a ..
  53. Development of Protein Surface Binding, Low Entropy Oligomers
    Christian E Schafmeister; Fiscal Year: 2013
    ..by applicant): We will test the hypothesis that we can rapidly develop oligomeric ligands with low conformational entropy that bind shallow crevices and grooves on protein surfaces with high affinity (Kd <10 nM) by sequentially ..
  54. Processing of complex stimuli in the primary sensory cortex.
    Alejandro Ramirez; Fiscal Year: 2013
    ..Through the use of a maximum noise entropy model, we are able to calculate the optimal stimulus for a L2/3 neuron online, and then deliver the stimulus back ..
  55. SYNTHETIC STUDIES OF PROTEIN STABILITY AND FOLDING
    George Barany; Fiscal Year: 2001
    ..The crosslink is designed with the ideal that its primary function is to restrict the mobility (entropy) of the chain, rather than to stabilize folded structure...
  56. Signaling Proteins: Binding Studies and Peptide Mimetics
    Mark Spaller; Fiscal Year: 2006
    ..calorimetry (ITC), a powerful method that provides a thorough thermodynamic profile for binding (enthalpy, entropy, free energy, and dissociation constants)...
  57. INTERPHASE SOLUBILITY AND CHROMATOGRAPHIC RETENTION
    John Dorsey; Fiscal Year: 1990
    ..experiments in bilayers confirm the predicted expulsion of solute with surface denisty, due to configurational entropy. We have developed new methods for synthesizing bonded phases of varying surface density, and have shown ..
  58. Multimodal Resting State Network Tools
    Mark E Pflieger; Fiscal Year: 2012
    ..based on fMRI connectivity will be used to inform two complementary EMEG source estimation methods: A maximum entropy source covariance source estimator (MaxEntCov) provides a globally consistent solution, and a dual vector ..
  59. SOCIO-ECONOMIC IMPACT OF GATED COMMUNITIES ON AMERICAN CITIES
    ELENA VESSELINOV; Fiscal Year: 2009
    ..and economic residential segregation in urban regions? We examine this question by constructing dissimilarity and entropy indices at metropolitan level and then by applying spatial analysis of social distance at neighborhood level...
  60. Maximum Entropy Deconvolution for Resolution &Sensitivity Enhancement in Bio-NMR
    Jeffrey C Hoch; Fiscal Year: 2013
    ..Anecdotal examples of simultaneously improving sensitivity and resolution in one dimension using maximum entropy deconvolution have been reported, but the gains achieved with this approach are typically modest...
  61. PathMiner: Web Telemicroscopy & Intelligent Databases
    DAVID FORAN; Fiscal Year: 2004
    ..It features entropy-based, auto-focusing, shared graphics, and messaging...
  62. Accounting for Water Structure and Thermodynamics in Computer-Aided Drug Design
    Michael K Gilson; Fiscal Year: 2013
    ..discretize the equations of inhomogeneous solvation theory (IST), up to second order, onto 3D grids of energy and entropy in a targeted binding site...
  63. Dynamics of Sleep Fragmentation in the Elderly
    Eugene Bruce; Fiscal Year: 2009
    ..Preliminary results show that Sample Entropy of the C3A2 EEG signal varies systematically with sleep state, being highest in Wake and lowest in stage 3-4, and ..