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Approximate entropy

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https://www.readbyqxmd.com/read/28095421/approximate-inference-for-time-varying-interactions-and-macroscopic-dynamics-of-neural-populations
#1
Christian Donner, Klaus Obermayer, Hideaki Shimazaki
The models in statistical physics such as an Ising model offer a convenient way to characterize stationary activity of neural populations. Such stationary activity of neurons may be expected for recordings from in vitro slices or anesthetized animals. However, modeling activity of cortical circuitries of awake animals has been more challenging because both spike-rates and interactions can change according to sensory stimulation, behavior, or an internal state of the brain. Previous approaches modeling the dynamics of neural interactions suffer from computational cost; therefore, its application was limited to only a dozen neurons...
January 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28071779/diffusive-escape-through-a-narrow-opening-new-insights-into-a-classic-problem
#2
Denis S Grebenkov, Gleb Oshanin
We study the mean first exit time (Tε) of a particle diffusing in a circular or a spherical micro-domain with an impenetrable confining boundary containing a small escape window (EW) of an angular size ε. Focusing on the effects of an energy/entropy barrier at the EW, and of the long-range interactions (LRIs) with the boundary on the diffusive search for the EW, we develop a self-consistent approximation to derive for Tε a general expression, akin to the celebrated Collins-Kimball relation in chemical kinetics and accounting for both rate-controlling factors in an explicit way...
January 10, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28060517/thermodynamics-of-helix-coil-transitions-of-polyalanine-in-open-carbon-nanotubes
#3
Dylan Suvlu, Seneviratne Samaratunga, D Thirumalai, Jayendran C Rasaiah
Understanding structure formation in polypeptide chains and synthetic polymers encapsulated in pores is important in biology and nanotechnology. We present replica exchange molecular dynamics studies of the phase diagram for α-helix formation of capped polyalanine in nanotubes (NT) open to a water reservoir as a function of the NT diameter and hydrophobicity. A helix forms only in a narrow range of diameters, which surprisingly is comparable to the width of the ribosome tunnel. Increasing the hydrophobicity enhances helicity in the NT...
January 19, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28054595/relationship-between-structural-order-and-water-like-anomalies-in-metastable-liquid-silicon-ab-initio-molecular-dynamics
#4
G Zhao, J L Yan, Y J Yu, M C Ding, X G Zhao, H Y Wang
The relationship between structural order and water-like anomalies in tetrahedral liquids is still open. Here, first-principle molecular dynamics are performed to study it in metastable liquid Si. It is found that in T-P phase diagram, there indeed exists a structural anomaly region, which encloses density anomaly but not diffusivity anomaly. This is consistent with that of SW Si and BKS SiO2 but different from that of SPC/E water. Two-body excess entropy anomaly can neither capture the diffusivity, structural, and density anomalies, as it can in a two-scale potential fluid...
January 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28049307/communication-pseudoisomorphs-in-liquids-with-intramolecular-degrees-of-freedom
#5
Andreas Elmerdahl Olsen, Jeppe C Dyre, Thomas B Schrøder
Computer simulations show that liquids of molecules with harmonic intramolecular bonds may have "pseudoisomorphic" lines of approximately invariant dynamics in the thermodynamic phase diagram. We demonstrate that these lines can be identified by requiring scale invariance of the inherent-structure reduced-unit low-frequency vibrational spectrum evaluated for a single equilibrium configuration. This rationalizes why generalized excess-entropy scaling, density scaling, and isochronal superposition apply for many liquids with internal degrees of freedom...
December 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28047742/su-f-r-17-advancing-glioblastoma-multiforme-gbm-recurrence-detection-with-mri-image-texture-feature-extraction-and-machine-learning
#6
V Yu, D Ruan, D Nguyen, T Kaprealian, R Chin, K Sheng
PURPOSE: To test the potential of early Glioblastoma Multiforme (GBM) recurrence detection utilizing image texture pattern analysis in serial MR images post primary treatment intervention. METHODS: MR image-sets of six time points prior to the confirmed recurrence diagnosis of a GBM patient were included in this study, with each time point containing T1 pre-contrast, T1 post-contrast, T2-Flair, and T2-TSE images. Eight Gray-level co-occurrence matrix (GLCM) texture features including Contrast, Correlation, Dissimilarity, Energy, Entropy, Homogeneity, Sum-Average, and Variance were calculated from all images, resulting in a total of 32 features at each time point...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046883/su-f-r-21-the-stability-of-radiomics-features-on-4d-fdg-pet-ct-images
#7
C Ma
PURPOSE: The aim of our study was to perform a stability analysis of 4D PET-derived features in non-small cell lung carcinoma (NSCLC) based on six different respiratory phases. METHODS: The 4D FDG-PET/CT respiratory phases were labeled as T0%, T17%, T33%,T50%, T67%, T83% phases, with the T0% phase approximately corresponding to the normal end-inspiration. Lesions were manually delineated based on fused PET-CT, using a standardized clinical delineation protocol. Six texture parameters were analyzed...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28025649/biochemical-characterization-thermal-stability-and-partial-sequence-of-a-novel-exo-polygalacturonase-from-the-thermophilic-fungus-rhizomucor-pusillus-a13-36-obtained-by-submerged-cultivation
#8
Lucas Vinícius Trindade, Carla Desagiacomo, Maria de Lourdes Teixeira de Moraes Polizeli, André Ricardo de Lima Damasio, Aline Margarete Furuyama Lima, Eleni Gomes, Gustavo Orlando Bonilla-Rodriguez
This work reports the production of an exo-polygalacturonase (exo-PG) by Rhizomucor pusillus A13.36 in submerged cultivation (SmC) in a shaker at 45°C for 96 h. A single pectinase was found and purified in order to analyze its thermal stability, by salt precipitation and hydrophobic interaction chromatography. The pectinase has an estimated Mw of approximately 43.5-47 kDa and optimum pH of 4.0 but is stable in pH ranging from 3.5 to 9.5 and has an optimum temperature of 61°C. It presents thermal stability between 30 and 60°C, has 70% activation in the presence of Ca(2+), and was tested using citrus pectin with a degree of methyl esterification (DE) of 26%...
2016: BioMed Research International
https://www.readbyqxmd.com/read/28012675/saccadic-entropy-of-head-impulses-in-acute-unilateral-vestibular-loss
#9
Li-Chun Hsieh, Hung-Ching Lin, Guo-She Lee
BACKGROUND/PURPOSE: To evaluate the complexity of vestibular-ocular reflex (VOR) in patients with acute unilateral vestibular loss (AUVL) via entropy analysis of head impulses. METHODS: Horizontal head impulse test (HIT) with high-velocity alternating directions was used to evaluate 12 participants with AUVL and 16 healthy volunteers. Wireless electro-oculography and electronic gyrometry were used to acquire eye positional signals and head velocity signals. The eye velocity signals were then obtained through differentiation, band-pass filtering...
December 21, 2016: Journal of the Formosan Medical Association, Taiwan Yi Zhi
https://www.readbyqxmd.com/read/27996253/efficient-approximation-of-ligand-rotational-and-translational-entropy-changes-upon-binding-for-use-in-mm-pbsa-calculations
#10
Ido Y Ben-Shalom, Stefania Pfeiffer-Marek, Karl-Heinz Baringhaus, Holger Gohlke
A major uncertainty in binding free energy estimates for protein-ligand complexes by methods such as MM-PB(GB)SA or docking scores results from neglecting or approximating changes in the configurational entropies (ΔSconfig.) of the solutes. In MM/PB(GB)SA-type calculations, ΔSconfig. has usually been estimated in the rigid rotor, harmonic oscillator approximation. Here, we present the development of a computationally efficient method (termed BEERT) to approximate ΔSconfig. in terms of the reduction in translational and rotational freedom of the ligand upon protein-ligand binding (ΔSR/T), starting from the flexible molecule approach...
January 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/27994467/diminished-autonomic-neurocardiac-function-in-patients-with-generalized-anxiety-disorder
#11
Kyungwook Kim, Seul Lee, Jong-Hoon Kim
BACKGROUND: Generalized anxiety disorder (GAD) is a chronic and highly prevalent disorder that is characterized by a number of autonomic nervous system symptoms. The purpose of this study was to investigate the linear and nonlinear complexity measures of heart rate variability (HRV), measuring autonomic regulation, and to evaluate the relationship between HRV parameters and the severity of anxiety, in medication-free patients with GAD. METHODS: Assessments of linear and nonlinear complexity measures of HRV were performed in 42 medication-free patients with GAD and 50 healthy control subjects...
2016: Neuropsychiatric Disease and Treatment
https://www.readbyqxmd.com/read/27987340/ethnic-analogies-and-differences-in-fetal-heart-rate-variability-signal-a-retrospective-study
#12
Salvatore Tagliaferri, Francesca Giovanna Esposito, Rosa Fagioli, Marco Di Cresce, Lucia Sacchi, Maria Gabriella Signorini, Marta Campanile, Pasquale Martinelli, Giovanni Magenes
AIM: We aimed to analyze computerized cardiotocographic (cCTG) parameters (including fetal heart rate baseline, short-term variability, Delta, long-term irregularity [LTI], interval index [II], low frequency [LF], movement frequency [MF], high frequency [HF], and approximate entropy [ApEn]) in physiological term pregnancies in order to correlate them with ethnic differences. The clinical meaning of numerical parameters may explain physiological or paraphysiological phenomena that occur in fetuses of different ethnic origins...
December 17, 2016: Journal of Obstetrics and Gynaecology Research
https://www.readbyqxmd.com/read/27977203/color-in-bridge-substituted-cyanines
#13
Seth Olsen
Theories of color in cyanine dyes have evolved around the idea of a "resonance" of structures with distinct bonding and charge localization. Understanding the emergence of resonance models from the underlying many-electron problem remains a central issue for these systems. Here, the issue is addressed using a maximum-entropy approach to valence-bond representations of state-averaged complete-active space self-consistent field models. The approach allows calculation of energies and couplings of high-energy valence-bond structures that mediate superexchange couplings and chemical bonding...
December 29, 2016: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/27967057/stochastic-disks-that-roll
#14
Miranda Holmes-Cerfon
We study a model of rolling particles subject to stochastic fluctuations, which may be relevant in systems of nano- or microscale particles where rolling is an approximation for strong static friction. We consider the simplest possible nontrivial system: a linear polymer of three disks constrained to remain in contact and immersed in an equilibrium heat bath so the internal angle of the polymer changes due to stochastic fluctuations. We compare two cases: one where the disks can slide relative to each other and the other where they are constrained to roll, like gears...
November 2016: Physical Review. E
https://www.readbyqxmd.com/read/27951672/computational-methods-for-configurational-entropy-using-internal-and-cartesian-coordinates
#15
Simon Hikiri, Takashi Yoshidome, Mitsunori Ikeguchi
The configurational entropy of solute molecules is a crucially important quantity to study various biophysical processes. Consequently, it is necessary to establish an efficient quantitative computational method to calculate configurational entropy as accurately as possible. In the present paper, we investigate the quantitative performance of the quasi-harmonic and related computational methods, including widely used methods implemented in popular molecular dynamics (MD) software packages, compared with the Clausius method, which is capable of accurately computing the change of the configurational entropy upon temperature change...
December 13, 2016: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/27940288/binarized-cross-approximate-entropy-in-crowdsensing-environment
#16
Tamara Skoric, Omer Mohamoud, Branislav Milovanovic, Nina Japundzic-Zigon, Dragana Bajic
OBJECTIVES: Personalised monitoring in health applications has been recognised as part of the mobile crowdsensing concept, where subjects equipped with sensors extract information and share them for personal or common benefit. Limited transmission resources impose the use of local analyses methodology, but this approach is incompatible with analytical tools that require stationary and artefact-free data. This paper proposes a computationally efficient binarised cross-approximate entropy, referred to as (X)BinEn, for unsupervised cardiovascular signal processing in environments where energy and processor resources are limited...
December 1, 2016: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/27930289/unified-framework-for-information-integration-based-on-information-geometry
#17
Masafumi Oizumi, Naotsugu Tsuchiya, Shun-Ichi Amari
Assessment of causal influences is a ubiquitous and important subject across diverse research fields. Drawn from consciousness studies, integrated information is a measure that defines integration as the degree of causal influences among elements. Whereas pairwise causal influences between elements can be quantified with existing methods, quantifying multiple influences among many elements poses two major mathematical difficulties. First, overestimation occurs due to interdependence among influences if each influence is separately quantified in a part-based manner and then simply summed over...
December 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27929045/fractal-based-analysis-of-the-influence-of-odorants-on-heart-activity
#18
Hamidreza Namazi, Vladimir V Kulish
An important challenge in heart research is to make the relation between the features of external stimuli and heart activity. Olfactory stimulation is an important type of stimulation that affects the heart activity, which is mapped on Electrocardiogram (ECG) signal. Yet, no one has discovered any relation between the structures of olfactory stimuli and the ECG signal. This study investigates the relation between the structures of heart rate and the olfactory stimulus (odorant). We show that the complexity of the heart rate is coupled with the molecular complexity of the odorant, where more structurally complex odorant causes less fractal heart rate...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924257/a-unified-statistical-model-of-protein-multiple-sequence-alignment-integrating-direct-coupling-and-insertions
#19
Akira R Kinjo
The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically model the MSA incorporating both short-range and long-range correlations as well as insertions, I have derived a lattice gas model of the MSA based on the principle of maximum entropy. The partition function, obtained by the transfer matrix method with a mean-field approximation, accounts for all possible alignments with all possible sequences...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27923290/computerised-analysis-of-antepartum-foetal-heart-parameters-new-reference-ranges
#20
Natascia Giuliano, Maria Laura Annunziata, Francesca Giovanna Esposito, Salvatore Tagliaferri, Andrea Di Lieto, Giovanni Magenes, Maria Gabriella Signorini, Marta Campanile, Domenico Arduini
We selected 4012 cCTG records (one trace for each patient) performed in healthy pregnancies from 30th to 42nd gestational week using foetal heart rate (FHR), short-term variability (STV), long-term irregularity (LTI), Delta, approximate entropy (ApEn), spectral components as low frequency (LF), median frequency (MF), high frequency (HF) and LF/(HF + MF) ratio were analysed. Reference nomograms were created and sensitivity and specificity for the prediction of foetal compromise were calculated which were 90% and 89%, respectively...
December 6, 2016: Journal of Obstetrics and Gynaecology: the Journal of the Institute of Obstetrics and Gynaecology
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