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Transfer entropy

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https://www.readbyqxmd.com/read/28737914/dft-study-on-the-complexation-of-nota-as-a-bifunctional-chelator-with-radiometal-ions
#1
Fatima Y Adeowo, Bahareh Honarparvar, Adam A Skelton
1,4,7 triazacyclononane-1,4,7 triacetic acid (NOTA) is a key bifunctional chelator utilized for the complexation of metal ions in radiopharmaceutical applications; the ability of these chelators depends on the strength of their binding with ions. The focus of the present work is to evaluate the complexation of Cu2+, Ga3+, Sc3+ and In3+ radiometal ions with NOTA using density functional theory (B3LYP functional) and 6-311+G(2d,2p)/DGDZVP basis sets. The significant role of ion-water interactions in the chelation interaction energies in solution reflects the competition between ion-water and NOTA-ion interaction in the chelation process...
July 24, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28737389/glycosyl-cations-versus-allylic-cations-in-spontaneous-and-enzymatic-hydrolysis
#2
Phillip M Danby, Stephen G Withers
Enzymatic prenyl and glycosyl transfer are seemingly unrelated reactions that yield molecules and protein modifications with disparate biological functions. However, both reactions employ diphosphate-activated donors and each proceed via cationic spe-cies: allylic cations and oxocarbenium ions, respectively. In this study, we explore the relationship between these processes by preparing valienyl ethers to serve as glycoside mimics that are capable of allylic rather than oxocarbenium cation stabilization. Rate constants for spontaneous hydrolysis of aryl glycosides and their analogous valienyl ethers were found to be almost identical, as were the corresponding activation enthalpies and entropies...
July 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28711759/dft-study-of-the-interaction-between-dota-chelator-and-competitive-alkali-metal-ions
#3
E Frimpong, A A Skelton, B Honarparvar
1, 4, 7, 10-tetraazacyclododecane-1, 4, 7, 10-tetracetic acid (DOTA) is an important chelator for radiolabeling of pharmaceuticals. The ability of alkali metals found in the body to complex with DOTA and compete with radio metal ions can alter the radiolabeling process. Non-covalent interactions between DOTA complexed with alkali metals Li(+), Na(+), K(+) and Rb(+), are investigated with density functional theory using B3LYP and ωB97XD functionals. Conformational possibilities of DOTA were explored with a varying number of carboxylic pendant arms of DOTA in close proximity to the ions...
June 29, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28708870/assessment-of-resampling-methods-for-causality-testing-a-note-on-the-us-inflation-behavior
#4
Angeliki Papana, Catherine Kyrtsou, Dimitris Kugiumtzis, Cees Diks
Different resampling methods for the null hypothesis of no Granger causality are assessed in the setting of multivariate time series, taking into account that the driving-response coupling is conditioned on the other observed variables. As appropriate test statistic for this setting, the partial transfer entropy (PTE), an information and model-free measure, is used. Two resampling techniques, time-shifted surrogates and the stationary bootstrap, are combined with three independence settings (giving a total of six resampling methods), all approximating the null hypothesis of no Granger causality...
2017: PloS One
https://www.readbyqxmd.com/read/28702344/directional-information-flow-in-patients-with-alzheimer-s-disease-a-source-space-resting-state-meg-study
#5
M M A Engels, M Yu, C J Stam, A A Gouw, W M van der Flier, Ph Scheltens, E C W van Straaten, A Hillebrand
In a recent magnetoencephalography (MEG) study, we found posterior-to-anterior information flow over the cortex in higher frequency bands in healthy subjects, with a reversed pattern in the theta band. A disruption of information flow may underlie clinical symptoms in Alzheimer's disease (AD). In AD, highly connected regions (hubs) in posterior areas are mostly disrupted. We therefore hypothesized that in AD the information flow from these hub regions would be disturbed. We used resting-state MEG recordings from 27 early-onset AD patients and 26 healthy controls...
2017: NeuroImage: Clinical
https://www.readbyqxmd.com/read/28681604/sequential-proton-loss-electron-transfer-in-deactivation-of-iron-iv-binding-protein-by-tyrosine-based-food-components
#6
Ning Tang, Leif H Skibsted
The iron(IV) binding protein ferrylmyoglobin, MbFe(IV)═O, was found to be reduced by tyrosine based food components in aqueous solution through a sequential proton loss electron transfer reaction mechanism without binding to the protein as confirmed by isothermal titration calorimetry. Dopamine and epinephrine are the most efficient food components reducing ferrylmyoglobin to oxymyoglobin, MbFe(II)O2, and metmyoglobin, MbFe(III), as revealed by multivariate curve resolution alternating least-squares with second order rate constants of 33...
July 18, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28676748/regularity-of-center-of-pressure-trajectories-in-expert-gymnasts-during-bipedal-closed-eyes-quiet-standing
#7
Brice Isableu, Petra Hlavackova, Bruno Diot, Nicolas Vuillerme
We compared postural control of expert gymnasts (G) to that of non-gymnasts (NG) during bipedal closed-eyes quiet standing using conventional and nonlinear dynamical measures of center of foot pressure (COP) trajectories. Earlier findings based on COP classical variables showed that gymnasts exhibited a better control of postural balance but only in demanding stances. We examined whether the effect of expertise in Gymnastic can be uncovered in less demanding stances, from the analysis of the dynamic patterns of COP trajectories...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28668020/adsorption-and-encapsulation-of-flexible-polyelectrolytes-in-charged-spherical-vesicles
#8
H R Shojaei, M Muthukumar
We present a theory of adsorption of flexible polyelectrolytes on the interior and exterior surfaces of a charged vesicle in an electrolyte solution. The criteria for adsorption and the density profiles of the adsorbed polymer chain are derived in terms of various characteristics of the polymer, vesicle, and medium, such as the charge density and length of the polymer, charge density and size of the vesicle, electrolyte concentration and dielectric constant of the medium. For adsorption inside the vesicle, the competition between the loss of conformational entropy and gain in adsorption energy results in two kinds of encapsulated states, depending on the strength of the polymer-vesicle interaction...
June 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28653659/continuous-assessment-of-schizophrenia-using-heart-rate-and-accelerometer-data
#9
Erik Reinertsen, Maxim Osipov, Chengyu Liu, John M Kane, Georgios Petrides, Gari D Clifford
OBJECTIVE: Schizophrenia has been associated with changes in heart rate (HR) and physical activity measures. However, the relationship between analysis window length and classifier accuracy using these features has yet to be quantified. APPROACH: Here we used objective HR and activity data to classify contiguous days of data as belonging to a schizophrenia patient or a healthy control. HR and physical activity recordings were made on 12 medicated subjects with schizophrenia and 12 healthy controls...
June 27, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28628618/solving-the-influence-maximization-problem-reveals-regulatory-organization-of-the-yeast-cell-cycle
#10
David L Gibbs, Ilya Shmulevich
The Influence Maximization Problem (IMP) aims to discover the set of nodes with the greatest influence on network dynamics. The problem has previously been applied in epidemiology and social network analysis. Here, we demonstrate the application to cell cycle regulatory network analysis for Saccharomyces cerevisiae. Fundamentally, gene regulation is linked to the flow of information. Therefore, our implementation of the IMP was framed as an information theoretic problem using network diffusion. Utilizing more than 26,000 regulatory edges from YeastMine, gene expression dynamics were encoded as edge weights using time lagged transfer entropy, a method for quantifying information transfer between variables...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28628313/tunneling-kinetics-and-nonadiabatic-proton-coupled-electron-transfer-in-proteins-the-effect-of-electric-fields-and-anharmonic-donor-acceptor-interactions
#11
Bridget Salna, Abdelkrim Benabbas, Douglas Russo, Paul M Champion
A proper description of proton donor-acceptor (D-A) distance fluctuations is crucial for understanding tunneling in proton-coupled electron transport (PCET). The typical harmonic approximation for the D-A potential results in a Gaussian probability distribution, which does not appropriately reflect the electronic repulsion forces that increase the energetic cost of sampling shorter D-A distances. Because these shorter distances are the primary channel for thermally activated tunneling, the analysis of tunneling kinetics depends sensitively on the inherently anharmonic nature of the D-A interaction...
July 11, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28621540/accurate-prediction-of-the-hydration-free-energies-of-20-salts-through-adaptive-force-matching-and-the-proper-comparison-with-experimental-references
#12
Jicun Li, Feng Wang
Simple pairwise potentials for five alkali ions and four halide ions were developed by only fitting to ab initio MP2 forces with the adaptive force matching (AFM) method. Without fitting to any experimental information, the AFM models predict the hydration free energies of all 10 fluoride and chloride salts formed by these ions within 1.5% of experimental references. The predicted hydration free energies for the 10 bromide and iodide salts are within 5-6% of experimental references with the larger error likely due to the neglect of explicit treatment of polarization and charge transfer...
June 29, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28618513/recurrence-measure-of-conditional-dependence-and-applications
#13
Antônio M T Ramos, Alejandro Builes-Jaramillo, Germán Poveda, Bedartha Goswami, Elbert E N Macau, Jürgen Kurths, Norbert Marwan
Identifying causal relations from observational data sets has posed great challenges in data-driven causality inference studies. One of the successful approaches to detect direct coupling in the information theory framework is transfer entropy. However, the core of entropy-based tools lies on the probability estimation of the underlying variables. Here we propose a data-driven approach for causality inference that incorporates recurrence plot features into the framework of information theory. We define it as the recurrence measure of conditional dependence (RMCD), and we present some applications...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28613876/origin-of-the-non-arrhenius-behavior-of-the-rates-of-enzymatic-reactions
#14
Subhendu Roy, Patrick Schopf, Arieh Warshel
The origin of the non-Arrhenius behavior of the rate constant for hydride transfer enzymatic reactions has been a puzzling problem since its initial observation. This effect has been used originally to support the idea that enzymes work by dynamical effects and more recently to suggest an entropy funnel model. Our analysis, however, has advanced the idea that the reason for the non-Arrhenius trend reflects the temperature dependence of the rearrangements of the protein polar groups in response to the change in the charge distribution of the reacting system during the transition from the ground state (GS) to the transition state (TS)...
July 5, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28604250/synthesis-characterization-in-silico-admet-prediction-and-protein-binding-analysis-of-a-novel-zinc-ii-schiff-base-complex-application-of-multi-spectroscopic-and-computational-techniques
#15
Somaye Shahraki, Fereshteh Shiri, Maryam Saeidifar
By reaction of 1,2-diaminocyclohexane with the 2,3-butanedione monoxime in the presence of ZnCl2, a new Schiff base complex was obtained. This complex was characterized by elemental analyses, FT-IR, (1)H NMR, UV-Vis and conductivity measurements. The reactivity of this complex to human serum albumin (HSA) under simulative physiological conditions was studied by spectroscopic and molecular docking analysis. Experimental results at various temperatures indicated that the intrinsic fluorescence of protein was quenched through a static quenching mechanism...
June 12, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28585624/exploiting-the-biomimetic-and-luminescence-properties-of-multivalent-dendrimer-semiconductor-nanohybrid-materials-in-the-ultra-low-level-determination-of-folic-acid
#16
Somashree Kundu, Susmita Maiti, Tushar Kanti Das, Debasmita Ghosh, Chandra Nath Roy, Abhijit Saha
In view of the enhanced generation of folate receptors in cancerous cells and diseases linked to the deficiency of folic acid, such as anemia, mental devolution, congenital malformation, etc., the development of a simple method for the ultra-sensitive determination of folic acid remains a long-standing issue for practical applications in medicine and biotechnology. Thus, the proposed luminescence based strategy involving multifunctional poly(amidoamine) (PAMAM) dendrimer encapsulated quantum dots (QDs) as a probe provides a simple, fast and efficient method for the selective determination of folic acid at the nano-molar level...
June 6, 2017: Analyst
https://www.readbyqxmd.com/read/28570661/breakdown-of-local-information-processing-may-underlie-isoflurane-anesthesia-effects
#17
Patricia Wollstadt, Kristin K Sellers, Lucas Rudelt, Viola Priesemann, Axel Hutt, Flavio Fröhlich, Michael Wibral
The disruption of coupling between brain areas has been suggested as the mechanism underlying loss of consciousness in anesthesia. This hypothesis has been tested previously by measuring the information transfer between brain areas, and by taking reduced information transfer as a proxy for decoupling. Yet, information transfer is a function of the amount of information available in the information source-such that transfer decreases even for unchanged coupling when less source information is available. Therefore, we reconsidered past interpretations of reduced information transfer as a sign of decoupling, and asked whether impaired local information processing leads to a loss of information transfer...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28562820/entropy-generation-minimization-analysis-of-active-magnetic-regenerators
#18
Paulo V Trevizoli, Jader R Barbosa
A performance assessment of active magnetocaloric regenerators using entropy generation minimization is presented. The model consists of the Brinkman-Forchheimer equation to describe the fluid flow and coupled energy equations for the fluid and solid phases. Entropy generation contributions due to axial heat conduction, fluid friction and interstitial heat transfer are considered. Based on the velocity and temperature profiles, local rates of entropy generation per unit volume were integrated to give the cycle-average entropy generation in the regenerator, which is the objective function of the optimization procedure...
May 2017: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/28539247/horizontal-visibility-graph-transfer-entropy-hvg-te-a-novel-metric-to-characterize-directed-connectivity-in-large-scale-brain-networks
#19
Meichen Yu, Arjan Hillebrand, Alida A Gouw, Cornelis J Stam
We propose a new measure, horizontal visibility graph transfer entropy (HVG-TE), to estimate the direction of information flow between pairs of time series. HVG-TE quantifies the transfer entropy between the degree sequences of horizontal visibility graphs derived from original time series. Twenty-one Rössler attractors unidirectionally coupled in the posterior-to-anterior direction were used to simulate 21-channel Electroencephalography (EEG) brain networks and validate the performance of the HVG-TE. We showed that the HVG-TE is robust to different levels of coupling strengths between the coupled Rössler attractors, a wide range of time delays, different sample sizes, the effects of noise and linear mixing, and the choice of reference for EEG data...
May 21, 2017: NeuroImage
https://www.readbyqxmd.com/read/28529761/developing-and-evaluating-a-mobile-driver-fatigue-detection-network-based-on-electroencephalograph-signals
#20
Jinghai Yin, Jianfeng Hu, Zhendong Mu
The rapid development of driver fatigue detection technology indicates important significance of traffic safety. The authors' main goals of this Letter are principally three: (i) A middleware architecture, defined as process unit (PU), which can communicate with personal electroencephalography (EEG) node (PEN) and cloud server (CS). The PU receives EEG signals from PEN, recognises the fatigue state of the driver, and transfer this information to CS. The CS sends notification messages to the surrounding vehicles...
February 2017: Healthcare Technology Letters
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