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Transfer entropy

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https://www.readbyqxmd.com/read/29149201/the-influence-of-filtering-and-downsampling-on-the-estimation-of-transfer-entropy
#1
Immo Weber, Esther Florin, Michael von Papen, Lars Timmermann
Transfer entropy (TE) provides a generalized and model-free framework to study Wiener-Granger causality between brain regions. Because of its nonparametric character, TE can infer directed information flow also from nonlinear systems. Despite its increasing number of applications in neuroscience, not much is known regarding the influence of common electrophysiological preprocessing on its estimation. We test the influence of filtering and downsampling on a recently proposed nearest neighborhood based TE estimator...
2017: PloS One
https://www.readbyqxmd.com/read/29121044/information-theoretic-analysis-of-the-directional-influence-between-cellular-processes
#2
Sourabh Lahiri, Philippe Nghe, Sander J Tans, Martin Luc Rosinberg, David Lacoste
Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying interactions. Here, we use the transfer entropy (TE), an information-theoretic quantity that quantifies the directional influence between fluctuating variables in a model-free way. We present a theoretical approach to compute the transfer entropy, even when the noise has an extrinsic component or in the presence of feedback...
2017: PloS One
https://www.readbyqxmd.com/read/29117691/theory-of-molecular-nonadiabatic-electron-dynamics-in-condensed-phases
#3
Kazuo Takatsuka
In light of the rapid progress of ultrafast chemical dynamics driven by the pulse lasers having width as short as several tens of attoseconds, we herein develop a theory of nonadiabatic electron wavepacket dynamics in condensed phases, with which to directly track the dynamics of electronic-state mixing such as electron transfer in liquid solvents. Toward this goal, we combine a theory of path-branching representation for nonadiabatic electron wavepacket dynamics in vacuum {a mixed quantum-classical representation, Yonehara and Takatsuka [J...
November 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29111741/theoretical-probing-of-weak-anion-cation-interactions-in-certain-pyridinium-based-ionic-liquid-ion-pairs-and-the-application-of-molecular-electrostatic-potential-in-their-ionic-crystal-density-determination-a-comparative-study-using-density-functional-approach
#4
Aswathy Joseph, Vibin Ipe Thomas, Gaweł Żyła, Padmanabhan Sridharan Alapat, Suresh Mathew
A comprehensive study on the structure, nature of interaction and properties of six ionic pairs of 1-butylpyridinium and 1-butyl-4-methylpyridinium cations in combination with tetrafluoroborate (BF4-), chloride (Cl-) and bromide (Br-) anions have been carried out using Density Functional Theory (DFT). The anion-cation interaction energy (ΔEint), theoretical band gap, molecular orbital energy-order, DFT-based chemical activity descriptors: chemical potential (μ), chemical hardness (η) and electrophilicity index (ω) and distribution of density of states (DOS) of these ion-pairs were investigated...
November 7, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/29109413/plasticity-in-leader-follower-roles-in-human-teams
#5
Shinnosuke Nakayama, Manuel Ruiz Marín, Maximo Camacho, Maurizio Porfiri
In humans, emergence of leaders and followers is key to group performance, but little is known about the whys and hows of leadership. A particularly elusive question entails behavioral plasticity in leadership across social contexts. Addressing this question requires to eliminate social feedback between focal individuals and their partners in experiments that could illuminate the spontaneous emergence of social roles. We investigated plasticity in leader-follower roles in cooperation, where members choose the task toward a shared goal, and coordination, where members adjust their actions in real time based on social responsiveness...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29089554/reversible-tuning-of-magnetocaloric%C3%A2-ni-mn-ga-co-films-on-ferroelectric-pmn-pt-substrates
#6
Benjamin Schleicher, Robert Niemann, Stefan Schwabe, Ruben Hühne, Ludwig Schultz, Kornelius Nielsch, Sebastian Fähler
Tuning functional properties of thin caloric films by mechanical stress is currently of high interest. In particular, a controllable magnetisation or transition temperature is desired for improved usability in magnetocaloric devices. Here, we present results of epitaxial magnetocaloric Ni-Mn-Ga-Co thin films on ferroelectric Pb(Mg1/3Nb2/3)0.72Ti0.28O3 (PMN-PT) substrates. Utilizing X-ray diffraction measurements, we demonstrate that the strain induced in the substrate by application of an electric field can be transferred to the thin film, resulting in a change of the lattice parameters...
October 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29060888/propofol-induced-sedation-diminishes-the-strength-of-frontal-parietal-occipital-eeg-network
#7
Dheeraj Rathee, Hubert Cecotti, Girijesh Prasad
The level of conscious experience can be effectively and reversibly altered by the administration of sedative agents. Several studies attempted to explore the variations in frontal-parietal network during propofol-induced sedation. However, contradictory outcomes warrant further investigations. In this study, we implemented the Neural Gas algorithm-based delay symbolic transfer entropy (NG-dSTE) for investigation of frontal-parietal-occipital (F-P-O) network using scalp EEG signals recorded during altered levels of consciousness...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/29033799/a-critical-assessment-of-directed-connectivity-estimates-with-artificially-imposed-causality-in-the-supramammillary-septo-hippocampal-circuit
#8
Calvin K Young, Ming Ruan, Neil McNaughton
Algorithms for estimating directed connectivity have become indispensable to further understand the neurodynamics between functionally coupled brain areas. The evaluation of directed connectivity on the propagation of brain activity has largely been based on simulated data or toy models, where various hidden properties of neurophysiological data may not be fully recapitulated. In this study, directionality was unequivocally manipulated in the freely moving rat in a unique dataset, where normal oscillatory interactions between the supramammillary nucleus (SuM) and hippocampus (HPC) were attenuated by temporary medial septal (MS) inactivation, and replaced by electrical stimulation of the fornix to evaluate the performance of several directed connectivity assessment methods...
2017: Frontiers in Systems Neuroscience
https://www.readbyqxmd.com/read/28988388/spicodyn-a-toolbox-for-the-analysis-of-neuronal-network-dynamics-and-connectivity-from-multi-site-spike-signal-recordings
#9
Vito Paolo Pastore, Aleksandar Godjoski, Sergio Martinoia, Paolo Massobrio
We implemented an automated and efficient open-source software for the analysis of multi-site neuronal spike signals. The software package, named SPICODYN, has been developed as a standalone windows GUI application, using C# programming language with Microsoft Visual Studio based on .NET framework 4.5 development environment. Accepted input data formats are HDF5, level 5 MAT and text files, containing recorded or generated time series spike signals data. SPICODYN processes such electrophysiological signals focusing on: spiking and bursting dynamics and functional-effective connectivity analysis...
October 7, 2017: Neuroinformatics
https://www.readbyqxmd.com/read/28966550/entropy-information-of-cardiorespiratory-dynamics-in-neonates-during-sleep
#10
Maristella Lucchini, Nicolò Pini, William P Fifer, Nina Burtchen, Maria G Signorini
Sleep is a central activity in human adults and characterizes most of the newborn infant life. During sleep, autonomic control acts to modulate heart rate variability (HRV) and respiration. Mechanisms underlying cardiorespiratory interactions in different sleep states have been studied but are not yet fully understood. Signal processing approaches have focused on cardiorespiratory analysis to elucidate this co-regulation. This manuscript proposes to analyze heart rate (HR), respiratory variability and their interrelationship in newborn infants to characterize cardiorespiratory interactions in different sleep states (active vs...
May 2017: Entropy
https://www.readbyqxmd.com/read/28963049/histogram-analysis-parameters-identify-multiple-associations-between-dwi-and-dce-mri-in-head-and-neck-squamous-cell-carcinoma
#11
Hans Jonas Meyer, Leonard Leifels, Stefan Schob, Nikita Garnov, Alexey Surov
OBJECTIVE: Nowadays, multiparametric investigations of head and neck squamous cell carcinoma (HNSCC) are established. These approaches can better characterize tumor biology and behavior. Diffusion weighted imaging (DWI) can by means of apparent diffusion coefficient (ADC) quantitatively characterize different tissue compartments. Dynamic contrast-enhanced magnetic resonance imaging (DCE MRI) reflects perfusion and vascularization of tissues. Recently, a novel approach of data acquisition, namely histogram analysis of different images is a novel diagnostic approach, which can provide more information of tissue heterogeneity...
September 28, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28950488/specific-transfer-entropy-and-other-state-dependent-transfer-entropies-for-continuous-state-input-output-systems
#12
David Darmon, Paul E Rapp
Since its original formulation in 2000, transfer entropy has become an invaluable tool in the toolbox of nonlinear dynamicists working with empirical data. Transfer entropy and its generalizations provide a precise definition of uncertainty and information transfer that are central to the coupled systems studied in nonlinear science. However, a canonical definition of state-dependent transfer entropy has yet to be introduced. We introduce a candidate measure, the specific transfer entropy, and compare its properties to both total and local transfer entropy...
August 2017: Physical Review. E
https://www.readbyqxmd.com/read/28933544/conformational-dynamics-and-exchange-kinetics-of-n-formyl-and-n-acetyl-groups-substituting-3-amino-3-6-dideoxy-%C3%AE-d-galactopyranose-a-sugar-found-in-bacterial-o-antigen-polysaccharides
#13
Olof Engström, Hani Mobarak, Jonas Ståhle, Göran Widmalm
Three dimensional shape and conformation of carbohydrates are important factors in molecular recognition events and the N-acetyl group of a monosaccharide residue can function as a conformational gatekeeper whereby it influences the overall shape of the oligosaccharide. NMR spectroscopy and quantum mechanics (QM) calculations are used herein to investigate both the conformational preferences and the dynamic behavior of N-acetyl and N-formyl substituents of 3-amino-3,6-dideoxy-α-d-galactopyranose, a sugar and substitution pattern found in bacterial O-antigen polysaccharides...
October 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28916452/symbolic-dynamics-of-animal-interaction
#14
Maurizio Porfiri, Manuel Ruiz Marín
Since its introduction nearly two decades ago, transfer entropy has contributed to an improved understanding of cause-and-effect relationships in coupled dynamical systems from raw time series. In the context of animal behavior, transfer entropy might help explain the determinants of leadership in social groups and elucidate escape response to predator attacks. Despite its promise, the potential of transfer entropy in animal behavior is yet to be fully tested, and a number of technical challenges in information theory and statistics remain open...
December 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28911681/study-on-the-interaction-of-bioactive-compound-s-allyl-cysteine-from-garlic-with-serum-albumin
#15
Yue-E Sun, Wei-Dong Wang
Multispectroscopic techniques were used to investigate the interaction of S-allyl cysteine (SAC) from garlic with human serum albumin (HSA). UV-Vis absorption measurements prove the formation of the HSA-SAC complex. An analysis of fluorescence spectra revealed that in the presence of SAC, the quenching mechanism of HSA is considered static. The quenching rate constant Kq, KSV, and the binding constant KA were estimated. According to the Van't Hoff equation, the thermodynamic parameters enthalpy change (ΔH) and entropy change (ΔS) were calculated to be -1...
April 2017: Journal of Food and Drug Analysis
https://www.readbyqxmd.com/read/28869520/multi-scale-low-entropy-method-for-optimizing-the-processing-parameters-during-automated-fiber-placement
#16
Zhenyu Han, Shouzheng Sun, Hongya Fu, Yunzhong Fu
Automated fiber placement (AFP) process includes a variety of energy forms and multi-scale effects. This contribution proposes a novel multi-scale low-entropy method aiming at optimizing processing parameters in an AFP process, where multi-scale effect, energy consumption, energy utilization efficiency and mechanical properties of micro-system could be taken into account synthetically. Taking a carbon fiber/epoxy prepreg as an example, mechanical properties of macro-meso-scale are obtained by Finite Element Method (FEM)...
September 3, 2017: Materials
https://www.readbyqxmd.com/read/28863488/detection-of-coupling-delay-a-problem-not-yet-solved
#17
David Coufal, Jozef Jakubík, Nikola Jajcay, Jaroslav Hlinka, Anna Krakovská, Milan Paluš
Nonparametric detection of coupling delay in unidirectionally and bidirectionally coupled nonlinear dynamical systems is examined. Both continuous and discrete-time systems are considered. Two methods of detection are assessed-the method based on conditional mutual information-the CMI method (also known as the transfer entropy method) and the method of convergent cross mapping-the CCM method. Computer simulations show that neither method is generally reliable in the detection of coupling delays. For continuous-time chaotic systems, the CMI method appears to be more sensitive and applicable in a broader range of coupling parameters than the CCM method...
August 2017: Chaos
https://www.readbyqxmd.com/read/28862457/reaction-paths-and-chemical-activation-reactions-of-2-methyl-5-furanyl-radical-with-3-o2
#18
Jason M Hudzik, Joseph W Bozzelli
Interest in high-energy substituted furans has been increasing due to their occurrence in biofuel production and their versatility in conversion to other useful products. Methylfurans are the simplest substituted furans and understanding their reaction pathways, thermochemical properties, including intermediate species stability, and chemical kinetics would aid in the study of larger furans. Furan ring C-H bonds have been shown to be extremely strong, approximately 120 kcal mol(-1), due in part to the placement of the oxygen atom and aromatic-like resonance, both within the ring...
September 26, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28858857/maximum-entropy-analysis-of-polarized-fluorescence-decay-of-e-gfp-in-aqueous-solution
#19
Eugene G Novikov, Victor V Skakun, Jan Willem Borst, Antonie J W G Visser
The Maximum Entropy Method (MEM) was used for the analysis of polarized fluorescence decays of enhanced green fluorescent protein (EGFP) in buffered water/glycerol mixtures, obtained with time-correlated single-photon counting (Visser et al., Methods Appl. Fluoresc. 4 (2016) 035002). To this end, we used a general-purpose software module of MEM that was earlier developed to analyze (complex) laser photolysis kinetics of ligand rebinding reactions in oxygen binding proteins. We demonstrate that the MEM software provides reliable results and is easy to use for the analysis of both total fluorescence decay and fluorescence anisotropy decay of aqueous solutions of EGFP...
August 31, 2017: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28845049/reactive-molecular-dynamics-models-from-ab-initio-molecular-dynamics-data-using-relative-entropy-minimization
#20
Christopher Arntsen, Chen Chen, Gregory A Voth
We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields...
September 1, 2017: Chemical Physics Letters
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