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https://www.readbyqxmd.com/read/28628618/solving-the-influence-maximization-problem-reveals-regulatory-organization-of-the-yeast-cell-cycle
#1
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 28,000 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 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28628313/tunneling-kinetics-and-non-adiabatic-proton-coupled-electron-transfer-in-proteins-the-effect-of-electric-fields-and-anharmonic-donor-acceptor-interactions
#2
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...
June 19, 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
#3
Jicun Li, Feng Wang
Simple pair-wise 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 reference. 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 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28618513/recurrence-measure-of-conditional-dependence-and-applications
#4
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/on-the-origin-of-non-arrhenius-behavior-of-the-rates-of-enzymatic-reactions
#5
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 the change in the charge distribution of the reacting system, during the transition from the ground state (GS) to the transition state (TS)...
June 14, 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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28523598/study-on-the-interaction-of-chromate-with-bovine-serum-albumin-by-spectroscopic-method
#12
Hongguang Cao, Yanli Yi
The interaction between two chromates [sodium chromate (Na2CrO4) and potassium chromate K2CrO4)] and bovine serum albumin (BSA) in physiological buffer (pH 7.4) was investigated by the fluorescence quenching technique. The results of fluorescence titration revealed that two chromates could strongly quench the intrinsic fluorescence of BSA through a static quenching procedure. The apparent binding constants K and number of binding sites n of chromate with BSA were obtained by the fluorescence quenching method...
May 18, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28507235/assessing-the-strength-of-cardiac-and-sympathetic-baroreflex-controls-via-transfer-entropy-during-orthostatic-challenge
#13
Alberto Porta, Andrea Marchi, Vlasta Bari, Beatrice De Maria, Murray Esler, Elisabeth Lambert, Mathias Baumert
The study assesses the strength of the causal relation along baroreflex (BR) in humans during an incremental postural challenge soliciting the BR. Both cardiac BR (cBR) and sympathetic BR (sBR) were characterized via BR sequence approaches from spontaneous fluctuations of heart period (HP), systolic arterial pressure (SAP), diastolic arterial pressure (DAP) and muscle sympathetic nerve activity (MSNA). A model-based transfer entropy method was applied to quantify the strength of the coupling from SAP to HP and from DAP to MSNA...
June 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28505709/causal-influence-in-linear-langevin-networks-without-feedback
#14
Andrea Auconi, Andrea Giansanti, Edda Klipp
The intuition of causation is so fundamental that almost every research study in life sciences refers to this concept. However, a widely accepted formal definition of causal influence between observables is still missing. In the framework of linear Langevin networks without feedback (linear response models) we propose a measure of causal influence based on a new decomposition of information flows over time. We discuss its main properties and we compare it with other information measures like the transfer entropy...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28504948/substructural-regularization-with-data-sensitive-granularity-for-sequence-transfer-learning
#15
Shichang Sun, Hongbo Liu, Jiana Meng, C L Philip Chen, Yu Yang
Sequence transfer learning is of interest in both academia and industry with the emergence of numerous new text domains from Twitter and other social media tools. In this paper, we put forward the data-sensitive granularity for transfer learning, and then, a novel substructural regularization transfer learning model (STLM) is proposed to preserve target domain features at substructural granularity in the light of the condition of labeled data set size. Our model is underpinned by hidden Markov model and regularization theory, where the substructural representation can be integrated as a penalty after measuring the dissimilarity of substructures between target domain and STLM with relative entropy...
May 12, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28470287/a-theoretical-study-on-hot-charge-transfer-states-and-dimensional-effects-of-organic-photocells-based-on-an-ideal-diode-model
#16
Tomomi Shimazaki, Takahito Nakajima
This paper discusses an ideal diode model with hot charge-transfer (CT) states to analyze the power conversion efficiency of an organic photocell. A free carrier generation mechanism via sunlight in an organic photocell consists of four microscopic processes: photon absorption, exciton dissociation, CT, and charge separation. The hot CT state effect has been actively investigated to understand the charge separation process. We previously reported a theoretical method to calculate the efficiency of the charge separation process via a hot CT state (T...
May 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28456171/on-the-role-of-the-entorhinal-cortex-in-the-effective-connectivity-of-the-hippocampal-formation
#17
Víctor J López-Madrona, Fernanda S Matias, Ernesto Pereda, Santiago Canals, Claudio R Mirasso
Inferring effective connectivity from neurophysiological data is a challenging task. In particular, only a finite (and usually small) number of sites are simultaneously recorded, while the response of one of these sites can be influenced by other sites that are not being recorded. In the hippocampal formation, for instance, the connections between areas CA1-CA3, the dentate gyrus (DG), and the entorhinal cortex (EC) are well established. However, little is known about the relations within the EC layers, which might strongly affect the resulting effective connectivity estimations...
April 2017: Chaos
https://www.readbyqxmd.com/read/28439520/relationship-between-relative-cerebral-blood-flow-relative-cerebral-blood-volume-and-relative-cerebral-metabolic-rate-of-oxygen-in-the-preterm-neonatal-brain
#18
Mina Nourhashemi, Guy Kongolo, Mahdi Mahmoudzadeh, Sabrina Goudjil, Fabrice Wallois
The mechanisms responsible for coupling between relative cerebral blood flow (rCBF), relative cerebral blood volume (rCBV), and relative cerebral metabolic rate of oxygen ([Formula: see text]), an important function of the microcirculation in preterm infants, remain unclear. Identification of a causal relationship between rCBF-rCBV and [Formula: see text] in preterms may, therefore, help to elucidate the principles of cortical hemodynamics during development. We simultaneously recorded rCBF and rCBV and estimated [Formula: see text] by two independent acquisition systems: diffuse correlation spectroscopy and near-infrared spectroscopy, respectively, in 10 preterms aged between 28 and 35 weeks of gestational age...
April 2017: Neurophotonics
https://www.readbyqxmd.com/read/28435963/thermodynamic-and-morphological-characterization-of-turing-patterns-in-non-isothermal-reaction-diffusion-systems
#19
Horacio Serna, Alberto P Muñuzuri, Daniel Barragán
The effect of temperature on the bifurcation diagram and Turing instability domain under non isothermal conditions is studied in the reversible Gray-Scott model. After adding the energy balance to the cubic autocatalytic model, the thermostat temperature and heat transfer coefficient are used as control parameters in the Turing pattern formation. The patterns obtained in the domain of the thermal parameter are characterized by quantifying the overall entropy generation rate and two topological indices; Shannon entropy and Minkowski functionals...
June 7, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28430108/a-network-physiology-approach-to-the-assessment-of-the-link-between-sinoatrial-and-ventricular-cardiac-controls
#20
Alberto Porta, Vlasta Bari, Beatrice De Maria, Mathias Baumert
A network physiology approach to evaluate the strength of the directed interactions among cardiac controls at sinoatrial and ventricular levels and respiration (R) is proposed. The network is composed of three nodes (i.e. sinoatrial and ventricular cardiac controls and R) and their activity is exemplified by the variability of heart period (HP), the variability of the duration of the electrical activity of the heart approximated as the temporal distance between Q-wave onset and T-wave end or apex (i.e. QTe or QTa) and thoracic movements respectively...
April 21, 2017: Physiological Measurement
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