Classifying epileptic EEG signals with delay permutation entropy and Multi-Scale K-means.

PubMed

Zhu, Guohun; Li, Yan; Wen, Peng Paul; Wang, Shuaifang

2015-01-01

Most epileptic EEG classification algorithms are supervised and require large training datasets, that hinder their use in real time applications. This chapter proposes an unsupervised Multi-Scale K-means (MSK-means) MSK-means algorithm to distinguish epileptic EEG signals and identify epileptic zones. The random initialization of the K-means algorithm can lead to wrong clusters. Based on the characteristics of EEGs, the MSK-means MSK-means algorithm initializes the coarse-scale centroid of a cluster with a suitable scale factor. In this chapter, the MSK-means algorithm is proved theoretically superior to the K-means algorithm on efficiency. In addition, three classifiers: the K-means, MSK-means MSK-means and support vector machine (SVM), are used to identify seizure and localize epileptogenic zone using delay permutation entropy features. The experimental results demonstrate that identifying seizure with the MSK-means algorithm and delay permutation entropy achieves 4. 7 % higher accuracy than that of K-means, and 0. 7 % higher accuracy than that of the SVM.

Estimation of absolute solvent and solvation shell entropies via permutation reduction

NASA Astrophysics Data System (ADS)

Reinhard, Friedemann; Grubmüller, Helmut

2007-01-01

Despite its prominent contribution to the free energy of solvated macromolecules such as proteins or DNA, and although principally contained within molecular dynamics simulations, the entropy of the solvation shell is inaccessible to straightforward application of established entropy estimation methods. The complication is twofold. First, the configurational space density of such systems is too complex for a sufficiently accurate fit. Second, and in contrast to the internal macromolecular dynamics, the configurational space volume explored by the diffusive motion of the solvent molecules is too large to be exhaustively sampled by current simulation techniques. Here, we develop a method to overcome the second problem and to significantly alleviate the first one. We propose to exploit the permutation symmetry of the solvent by transforming the trajectory in a way that renders established estimation methods applicable, such as the quasiharmonic approximation or principal component analysis. Our permutation-reduced approach involves a combinatorial problem, which is solved through its equivalence with the linear assignment problem, for which O(N3) methods exist. From test simulations of dense Lennard-Jones gases, enhanced convergence and improved entropy estimates are obtained. Moreover, our approach renders diffusive systems accessible to improved fit functions.

Multiscale permutation entropy analysis of electrocardiogram

NASA Astrophysics Data System (ADS)

Liu, Tiebing; Yao, Wenpo; Wu, Min; Shi, Zhaorong; Wang, Jun; Ning, Xinbao

2017-04-01

To make a comprehensive nonlinear analysis to ECG, multiscale permutation entropy (MPE) was applied to ECG characteristics extraction to make a comprehensive nonlinear analysis of ECG. Three kinds of ECG from PhysioNet database, congestive heart failure (CHF) patients, healthy young and elderly subjects, are applied in this paper. We set embedding dimension to 4 and adjust scale factor from 2 to 100 with a step size of 2, and compare MPE with multiscale entropy (MSE). As increase of scale factor, MPE complexity of the three ECG signals are showing first-decrease and last-increase trends. When scale factor is between 10 and 32, complexities of the three ECG had biggest difference, entropy of the elderly is 0.146 less than the CHF patients and 0.025 larger than the healthy young in average, in line with normal physiological characteristics. Test results showed that MPE can effectively apply in ECG nonlinear analysis, and can effectively distinguish different ECG signals.

Estimating Temporal Causal Interaction between Spike Trains with Permutation and Transfer Entropy

PubMed Central

Li, Zhaohui; Li, Xiaoli

2013-01-01

Estimating the causal interaction between neurons is very important for better understanding the functional connectivity in neuronal networks. We propose a method called normalized permutation transfer entropy (NPTE) to evaluate the temporal causal interaction between spike trains, which quantifies the fraction of ordinal information in a neuron that has presented in another one. The performance of this method is evaluated with the spike trains generated by an Izhikevich’s neuronal model. Results show that the NPTE method can effectively estimate the causal interaction between two neurons without influence of data length. Considering both the precision of time delay estimated and the robustness of information flow estimated against neuronal firing rate, the NPTE method is superior to other information theoretic method including normalized transfer entropy, symbolic transfer entropy and permutation conditional mutual information. To test the performance of NPTE on analyzing simulated biophysically realistic synapses, an Izhikevich’s cortical network that based on the neuronal model is employed. It is found that the NPTE method is able to characterize mutual interactions and identify spurious causality in a network of three neurons exactly. We conclude that the proposed method can obtain more reliable comparison of interactions between different pairs of neurons and is a promising tool to uncover more details on the neural coding. PMID:23940662

Refined composite multiscale weighted-permutation entropy of financial time series

NASA Astrophysics Data System (ADS)

Zhang, Yongping; Shang, Pengjian

2018-04-01

For quantifying the complexity of nonlinear systems, multiscale weighted-permutation entropy (MWPE) has recently been proposed. MWPE has incorporated amplitude information and been applied to account for the multiple inherent dynamics of time series. However, MWPE may be unreliable, because its estimated values show large fluctuation for slight variation of the data locations, and a significant distinction only for the different length of time series. Therefore, we propose the refined composite multiscale weighted-permutation entropy (RCMWPE). By comparing the RCMWPE results with other methods' results on both synthetic data and financial time series, RCMWPE method shows not only the advantages inherited from MWPE but also lower sensitivity to the data locations, more stable and much less dependent on the length of time series. Moreover, we present and discuss the results of RCMWPE method on the daily price return series from Asian and European stock markets. There are significant differences between Asian markets and European markets, and the entropy values of Hang Seng Index (HSI) are close to but higher than those of European markets. The reliability of the proposed RCMWPE method has been supported by simulations on generated and real data. It could be applied to a variety of fields to quantify the complexity of the systems over multiple scales more accurately.

Generalized composite multiscale permutation entropy and Laplacian score based rolling bearing fault diagnosis

NASA Astrophysics Data System (ADS)

Zheng, Jinde; Pan, Haiyang; Yang, Shubao; Cheng, Junsheng

2018-01-01

Multiscale permutation entropy (MPE) is a recently proposed nonlinear dynamic method for measuring the randomness and detecting the nonlinear dynamic change of time series and can be used effectively to extract the nonlinear dynamic fault feature from vibration signals of rolling bearing. To solve the drawback of coarse graining process in MPE, an improved MPE method called generalized composite multiscale permutation entropy (GCMPE) was proposed in this paper. Also the influence of parameters on GCMPE and its comparison with the MPE are studied by analyzing simulation data. GCMPE was applied to the fault feature extraction from vibration signal of rolling bearing and then based on the GCMPE, Laplacian score for feature selection and the Particle swarm optimization based support vector machine, a new fault diagnosis method for rolling bearing was put forward in this paper. Finally, the proposed method was applied to analyze the experimental data of rolling bearing. The analysis results show that the proposed method can effectively realize the fault diagnosis of rolling bearing and has a higher fault recognition rate than the existing methods.

A practical comparison of algorithms for the measurement of multiscale entropy in neural time series data.

PubMed

Kuntzelman, Karl; Jack Rhodes, L; Harrington, Lillian N; Miskovic, Vladimir

2018-06-01

There is a broad family of statistical methods for capturing time series regularity, with increasingly widespread adoption by the neuroscientific community. A common feature of these methods is that they permit investigators to quantify the entropy of brain signals - an index of unpredictability/complexity. Despite the proliferation of algorithms for computing entropy from neural time series data there is scant evidence concerning their relative stability and efficiency. Here we evaluated several different algorithmic implementations (sample, fuzzy, dispersion and permutation) of multiscale entropy in terms of their stability across sessions, internal consistency and computational speed, accuracy and precision using a combination of electroencephalogram (EEG) and synthetic 1/ƒ noise signals. Overall, we report fair to excellent internal consistency and longitudinal stability over a one-week period for the majority of entropy estimates, with several caveats. Computational timing estimates suggest distinct advantages for dispersion and permutation entropy over other entropy estimates. Considered alongside the psychometric evidence, we suggest several ways in which researchers can maximize computational resources (without sacrificing reliability), especially when working with high-density M/EEG data or multivoxel BOLD time series signals. Copyright © 2018 Elsevier Inc. All rights reserved.

Information Measures for Multisensor Systems

DTIC Science & Technology

2013-12-11

permuted to generate spectra that were non- physical but preserved the entropy of the source spectra. Another 1000 spectra were constructed to mimic co...Research Laboratory (NRL) has yielded probabilistic models for spectral data that enable the computation of information measures such as entropy and...22308 Chemical sensing Information theory Spectral data Information entropy Information divergence Mass spectrometry Infrared spectroscopy Multisensor

Folding behavior of ribosomal protein S6 studied by modified Go¯ -like model

NASA Astrophysics Data System (ADS)

Wu, L.; Zhang, J.; Wang, J.; Li, W. F.; Wang, W.

2007-03-01

Recent experimental and theoretical studies suggest that, although topology is the determinant factor in protein folding, especially for small single-domain proteins, energetic factors also play an important role in the folding process. The ribosomal protein S6 has been subjected to intensive studies. A radical change of the transition state in its circular permutants has been observed, which is believed to be caused by a biased distribution of contact energies. Since the simplistic topology-only Gō -like model is not able to reproduce such an observation, we modify the model by introducing variable contact energies between residues based on their physicochemical properties. The modified Gō -like model can successfully reproduce the Φ -value distributions, folding nucleus, and folding pathways of both the wild-type and circular permutants of S6. Furthermore, by comparing the results of the modified and the simplistic models, we find that the hydrophobic effect constructs the major force that balances the loop entropies. This may indicate that nature maintains the folding cooperativity of this protein by carefully arranging the location of hydrophobic residues in the sequence. Our study reveals a strategy or mechanism used by nature to get out of the dilemma when the native structure, possibly required by biological function, conflicts with folding cooperativity. Finally, the possible relationship between such a design of nature and amyloidosis is also discussed.

Revisiting the European sovereign bonds with a permutation-information-theory approach

NASA Astrophysics Data System (ADS)

Fernández Bariviera, Aurelio; Zunino, Luciano; Guercio, María Belén; Martinez, Lisana B.; Rosso, Osvaldo A.

2013-12-01

In this paper we study the evolution of the informational efficiency in its weak form for seventeen European sovereign bonds time series. We aim to assess the impact of two specific economic situations in the hypothetical random behavior of these time series: the establishment of a common currency and a wide and deep financial crisis. In order to evaluate the informational efficiency we use permutation quantifiers derived from information theory. Specifically, time series are ranked according to two metrics that measure the intrinsic structure of their correlations: permutation entropy and permutation statistical complexity. These measures provide the rectangular coordinates of the complexity-entropy causality plane; the planar location of the time series in this representation space reveals the degree of informational efficiency. According to our results, the currency union contributed to homogenize the stochastic characteristics of the time series and produced synchronization in the random behavior of them. Additionally, the 2008 financial crisis uncovered differences within the apparently homogeneous European sovereign markets and revealed country-specific characteristics that were partially hidden during the monetary union heyday.

Multiscale permutation entropy analysis of laser beam wandering in isotropic turbulence.

PubMed

Olivares, Felipe; Zunino, Luciano; Gulich, Damián; Pérez, Darío G; Rosso, Osvaldo A

2017-10-01

We have experimentally quantified the temporal structural diversity from the coordinate fluctuations of a laser beam propagating through isotropic optical turbulence. The main focus here is on the characterization of the long-range correlations in the wandering of a thin Gaussian laser beam over a screen after propagating through a turbulent medium. To fulfill this goal, a laboratory-controlled experiment was conducted in which coordinate fluctuations of the laser beam were recorded at a sufficiently high sampling rate for a wide range of turbulent conditions. Horizontal and vertical displacements of the laser beam centroid were subsequently analyzed by implementing the symbolic technique based on ordinal patterns to estimate the well-known permutation entropy. We show that the permutation entropy estimations at multiple time scales evidence an interplay between different dynamical behaviors. More specifically, a crossover between two different scaling regimes is observed. We confirm a transition from an integrated stochastic process contaminated with electronic noise to a fractional Brownian motion with a Hurst exponent H=5/6 as the sampling time increases. Besides, we are able to quantify, from the estimated entropy, the amount of electronic noise as a function of the turbulence strength. We have also demonstrated that these experimental observations are in very good agreement with numerical simulations of noisy fractional Brownian motions with a well-defined crossover between two different scaling regimes.

Permutation Entropy Applied to Movement Behaviors of Drosophila Melanogaster

NASA Astrophysics Data System (ADS)

Liu, Yuedan; Chon, Tae-Soo; Baek, Hunki; Do, Younghae; Choi, Jin Hee; Chung, Yun Doo

Movement of different strains in Drosophila melanogaster was continuously observed by using computer interfacing techniques and was analyzed by permutation entropy (PE) after exposure to toxic chemicals, toluene (0.1 mg/m3) and formaldehyde (0.01 mg/m3). The PE values based on one-dimensional time series position (vertical) data were variable according to internal constraint (i.e. strains) and accordingly increased in response to external constraint (i.e. chemicals) by reflecting diversity in movement patterns from both normal and intoxicated states. Cross-correlation function revealed temporal associations between the PE values and between the component movement patterns in different chemicals and strains through the period of intoxication. The entropy based on the order of position data could be a useful means for complexity measure in behavioral changes and for monitoring the impact of stressors in environment.

EEG entropy measures in anesthesia

PubMed Central

Liang, Zhenhu; Wang, Yinghua; Sun, Xue; Li, Duan; Voss, Logan J.; Sleigh, Jamie W.; Hagihira, Satoshi; Li, Xiaoli

2015-01-01

Highlights: ► Twelve entropy indices were systematically compared in monitoring depth of anesthesia and detecting burst suppression.► Renyi permutation entropy performed best in tracking EEG changes associated with different anesthesia states.► Approximate Entropy and Sample Entropy performed best in detecting burst suppression. Objective: Entropy algorithms have been widely used in analyzing EEG signals during anesthesia. However, a systematic comparison of these entropy algorithms in assessing anesthesia drugs' effect is lacking. In this study, we compare the capability of 12 entropy indices for monitoring depth of anesthesia (DoA) and detecting the burst suppression pattern (BSP), in anesthesia induced by GABAergic agents. Methods: Twelve indices were investigated, namely Response Entropy (RE) and State entropy (SE), three wavelet entropy (WE) measures [Shannon WE (SWE), Tsallis WE (TWE), and Renyi WE (RWE)], Hilbert-Huang spectral entropy (HHSE), approximate entropy (ApEn), sample entropy (SampEn), Fuzzy entropy, and three permutation entropy (PE) measures [Shannon PE (SPE), Tsallis PE (TPE) and Renyi PE (RPE)]. Two EEG data sets from sevoflurane-induced and isoflurane-induced anesthesia respectively were selected to assess the capability of each entropy index in DoA monitoring and BSP detection. To validate the effectiveness of these entropy algorithms, pharmacokinetic/pharmacodynamic (PK/PD) modeling and prediction probability (Pk) analysis were applied. The multifractal detrended fluctuation analysis (MDFA) as a non-entropy measure was compared. Results: All the entropy and MDFA indices could track the changes in EEG pattern during different anesthesia states. Three PE measures outperformed the other entropy indices, with less baseline variability, higher coefficient of determination (R2) and prediction probability, and RPE performed best; ApEn and SampEn discriminated BSP best. Additionally, these entropy measures showed an advantage in computation efficiency compared with MDFA. Conclusion: Each entropy index has its advantages and disadvantages in estimating DoA. Overall, it is suggested that the RPE index was a superior measure. Investigating the advantages and disadvantages of these entropy indices could help improve current clinical indices for monitoring DoA. PMID:25741277

EEG entropy measures indicate decrease of cortical information processing in Disorders of Consciousness.

PubMed

Thul, Alexander; Lechinger, Julia; Donis, Johann; Michitsch, Gabriele; Pichler, Gerald; Kochs, Eberhard F; Jordan, Denis; Ilg, Rüdiger; Schabus, Manuel

2016-02-01

Clinical assessments that rely on behavioral responses to differentiate Disorders of Consciousness are at times inapt because of some patients' motor disabilities. To objectify patients' conditions of reduced consciousness the present study evaluated the use of electroencephalography to measure residual brain activity. We analyzed entropy values of 18 scalp EEG channels of 15 severely brain-damaged patients with clinically diagnosed Minimally-Conscious-State (MCS) or Unresponsive-Wakefulness-Syndrome (UWS) and compared the results to a sample of 24 control subjects. Permutation entropy (PeEn) and symbolic transfer entropy (STEn), reflecting information processes in the EEG, were calculated for all subjects. Participants were tested on a modified active own-name paradigm to identify correlates of active instruction following. PeEn showed reduced local information content in the EEG in patients, that was most pronounced in UWS. STEn analysis revealed altered directed information flow in the EEG of patients, indicating impaired feed-backward connectivity. Responses to auditory stimulation yielded differences in entropy measures, indicating reduced information processing in MCS and UWS. Local EEG information content and information flow are affected in Disorders of Consciousness. This suggests local cortical information capacity and feedback information transfer as neural correlates of consciousness. The utilized EEG entropy analyses were able to relate to patient groups with different Disorders of Consciousness. Copyright © 2015 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

Credit market Jitters in the course of the financial crisis: A permutation entropy approach in measuring informational efficiency in financial assets

NASA Astrophysics Data System (ADS)

Siokis, Fotios M.

2018-06-01

We explore the evolution of the informational efficiency for specific instruments of the U.S. money, bond and stock exchange markets, prior and after the outbreak of the Great Recession. We utilize the permutation entropy and the complexity-entropy causality plane to rank the time series and measure the degree of informational efficiency. We find that after the credit crunch and the collapse of Lehman Brothers the efficiency level of specific money market instruments' yield falls considerably. This is an evidence of less uncertainty included in predicting the related yields throughout the financial disarray. Similar trend is depicted in the indices of the stock exchange markets but efficiency remains in much higher levels. On the other hand, bond market instruments maintained their efficiency levels even after the outbreak of the crisis, which could be interpreted into greater randomness and less predictability of their yields.

Refined two-index entropy and multiscale analysis for complex system

NASA Astrophysics Data System (ADS)

Bian, Songhan; Shang, Pengjian

2016-10-01

As a fundamental concept in describing complex system, entropy measure has been proposed to various forms, like Boltzmann-Gibbs (BG) entropy, one-index entropy, two-index entropy, sample entropy, permutation entropy etc. This paper proposes a new two-index entropy Sq,δ and we find the new two-index entropy is applicable to measure the complexity of wide range of systems in the terms of randomness and fluctuation range. For more complex system, the value of two-index entropy is smaller and the correlation between parameter δ and entropy Sq,δ is weaker. By combining the refined two-index entropy Sq,δ with scaling exponent h(δ), this paper analyzes the complexities of simulation series and classifies several financial markets in various regions of the world effectively.

Permutation auto-mutual information of electroencephalogram in anesthesia

NASA Astrophysics Data System (ADS)

Liang, Zhenhu; Wang, Yinghua; Ouyang, Gaoxiang; Voss, Logan J.; Sleigh, Jamie W.; Li, Xiaoli

2013-04-01

Objective. The dynamic change of brain activity in anesthesia is an interesting topic for clinical doctors and drug designers. To explore the dynamical features of brain activity in anesthesia, a permutation auto-mutual information (PAMI) method is proposed to measure the information coupling of electroencephalogram (EEG) time series obtained in anesthesia. Approach. The PAMI is developed and applied on EEG data collected from 19 patients under sevoflurane anesthesia. The results are compared with the traditional auto-mutual information (AMI), SynchFastSlow (SFS, derived from the BIS index), permutation entropy (PE), composite PE (CPE), response entropy (RE) and state entropy (SE). Performance of all indices is assessed by pharmacokinetic/pharmacodynamic (PK/PD) modeling and prediction probability. Main results. The PK/PD modeling and prediction probability analysis show that the PAMI index correlates closely with the anesthetic effect. The coefficient of determination R2 between PAMI values and the sevoflurane effect site concentrations, and the prediction probability Pk are higher in comparison with other indices. The information coupling in EEG series can be applied to indicate the effect of the anesthetic drug sevoflurane on the brain activity as well as other indices. The PAMI of the EEG signals is suggested as a new index to track drug concentration change. Significance. The PAMI is a useful index for analyzing the EEG dynamics during general anesthesia.

Exact Test of Independence Using Mutual Information

DTIC Science & Technology

2014-05-23

1000 × 0.05 = 50. Entropy 2014, 16 2844 Importantly, the permutation test, which does not preserve Markov order, resulted in 489 Type I errors! Using...Block 13 ARO Report Number Block 13: Supplementary Note © 2014 . Published in Entropy , Vol. Ed. 0 16, (7) (2014), (, (7). DoD Components reserve a...official Department of the Army position, policy or decision, unless so designated by other documentation. ... Entropy 2014, 16, 2839-2849; doi:10.3390

Monitoring the Depth of Anesthesia Using a New Adaptive Neurofuzzy System.

PubMed

Shalbaf, Ahmad; Saffar, Mohsen; Sleigh, Jamie W; Shalbaf, Reza

2018-05-01

Accurate and noninvasive monitoring of the depth of anesthesia (DoA) is highly desirable. Since the anesthetic drugs act mainly on the central nervous system, the analysis of brain activity using electroencephalogram (EEG) is very useful. This paper proposes a novel automated method for assessing the DoA using EEG. First, 11 features including spectral, fractal, and entropy are extracted from EEG signal and then, by applying an algorithm according to exhaustive search of all subsets of features, a combination of the best features (Beta-index, sample entropy, shannon permutation entropy, and detrended fluctuation analysis) is selected. Accordingly, we feed these extracted features to a new neurofuzzy classification algorithm, adaptive neurofuzzy inference system with linguistic hedges (ANFIS-LH). This structure can successfully model systems with nonlinear relationships between input and output, and also classify overlapped classes accurately. ANFIS-LH, which is based on modified classical fuzzy rules, reduces the effects of the insignificant features in input space, which causes overlapping and modifies the output layer structure. The presented method classifies EEG data into awake, light, general, and deep states during anesthesia with sevoflurane in 17 patients. Its accuracy is 92% compared to a commercial monitoring system (response entropy index) successfully. Moreover, this method reaches the classification accuracy of 93% to categorize EEG signal to awake and general anesthesia states by another database of propofol and volatile anesthesia in 50 patients. To sum up, this method is potentially applicable to a new real-time monitoring system to help the anesthesiologist with continuous assessment of DoA quickly and accurately.

Detecting the chaotic nature in a transitional boundary layer using symbolic information-theory quantifiers.

PubMed

Zhang, Wen; Liu, Peiqing; Guo, Hao; Wang, Jinjun

2017-11-01

The permutation entropy and the statistical complexity are employed to study the boundary-layer transition induced by the surface roughness. The velocity signals measured in the transition process are analyzed with these symbolic quantifiers, as well as the complexity-entropy causality plane, and the chaotic nature of the instability fluctuations is identified. The frequency of the dominant fluctuations has been found according to the time scales corresponding to the extreme values of the symbolic quantifiers. The laminar-turbulent transition process is accompanied by the evolution in the degree of organization of the complex eddy motions, which is also characterized with the growing smaller and flatter circles in the complexity-entropy causality plane. With the help of the permutation entropy and the statistical complexity, the differences between the chaotic fluctuations detected in the experiments and the classical Tollmien-Schlichting wave are shown and discussed. It is also found that the chaotic features of the instability fluctuations can be approximated with a number of regular sine waves superimposed on the fluctuations of the undisturbed laminar boundary layer. This result is related to the physical mechanism in the generation of the instability fluctuations, which is the noise-induced chaos.

Detecting the chaotic nature in a transitional boundary layer using symbolic information-theory quantifiers

NASA Astrophysics Data System (ADS)

Zhang, Wen; Liu, Peiqing; Guo, Hao; Wang, Jinjun

2017-11-01

The permutation entropy and the statistical complexity are employed to study the boundary-layer transition induced by the surface roughness. The velocity signals measured in the transition process are analyzed with these symbolic quantifiers, as well as the complexity-entropy causality plane, and the chaotic nature of the instability fluctuations is identified. The frequency of the dominant fluctuations has been found according to the time scales corresponding to the extreme values of the symbolic quantifiers. The laminar-turbulent transition process is accompanied by the evolution in the degree of organization of the complex eddy motions, which is also characterized with the growing smaller and flatter circles in the complexity-entropy causality plane. With the help of the permutation entropy and the statistical complexity, the differences between the chaotic fluctuations detected in the experiments and the classical Tollmien-Schlichting wave are shown and discussed. It is also found that the chaotic features of the instability fluctuations can be approximated with a number of regular sine waves superimposed on the fluctuations of the undisturbed laminar boundary layer. This result is related to the physical mechanism in the generation of the instability fluctuations, which is the noise-induced chaos.

Permutation entropy analysis of financial time series based on Hill's diversity number

NASA Astrophysics Data System (ADS)

Zhang, Yali; Shang, Pengjian

2017-12-01

In this paper the permutation entropy based on Hill's diversity number (Nn,r) is introduced as a new way to assess the complexity of a complex dynamical system such as stock market. We test the performance of this method with simulated data. Results show that Nn,r with appropriate parameters is more sensitive to the change of system and describes the trends of complex systems clearly. In addition, we research the stock closing price series from different data that consist of six indices: three US stock indices and three Chinese stock indices during different periods, Nn,r can quantify the changes of complexity for stock market data. Moreover, we get richer information from Nn,r, and obtain some properties about the differences between the US and Chinese stock indices.

Double symbolic joint entropy in nonlinear dynamic complexity analysis

NASA Astrophysics Data System (ADS)

Yao, Wenpo; Wang, Jun

2017-07-01

Symbolizations, the base of symbolic dynamic analysis, are classified as global static and local dynamic approaches which are combined by joint entropy in our works for nonlinear dynamic complexity analysis. Two global static methods, symbolic transformations of Wessel N. symbolic entropy and base-scale entropy, and two local ones, namely symbolizations of permutation and differential entropy, constitute four double symbolic joint entropies that have accurate complexity detections in chaotic models, logistic and Henon map series. In nonlinear dynamical analysis of different kinds of heart rate variability, heartbeats of healthy young have higher complexity than those of the healthy elderly, and congestive heart failure (CHF) patients are lowest in heartbeats' joint entropy values. Each individual symbolic entropy is improved by double symbolic joint entropy among which the combination of base-scale and differential symbolizations have best complexity analysis. Test results prove that double symbolic joint entropy is feasible in nonlinear dynamic complexity analysis.

Inferring the Presence of Reverse Proxies Through Timing Analysis

DTIC Science & Technology

2015-06-01

16 Figure 3.2 The three different instances of timing measurement configurations 17 Figure 3.3 Permutation of a web request iteration...Their data showed that they could detect at least 6 bits of entropy between unlike devices and that it was enough to determine that they are in fact...depending on the permutation being executed so that every iteration was conducted under the same distance 15 City   Lat   Long   City   Lat   Long

Multiscale permutation entropy analysis of EEG recordings during sevoflurane anesthesia

NASA Astrophysics Data System (ADS)

Li, Duan; Li, Xiaoli; Liang, Zhenhu; Voss, Logan J.; Sleigh, Jamie W.

2010-08-01

Electroencephalogram (EEG) monitoring of the effect of anesthetic drugs on the central nervous system has long been used in anesthesia research. Several methods based on nonlinear dynamics, such as permutation entropy (PE), have been proposed to analyze EEG series during anesthesia. However, these measures are still single-scale based and may not completely describe the dynamical characteristics of complex EEG series. In this paper, a novel measure combining multiscale PE information, called CMSPE (composite multi-scale permutation entropy), was proposed for quantifying the anesthetic drug effect on EEG recordings during sevoflurane anesthesia. Three sets of simulated EEG series during awake, light and deep anesthesia were used to select the parameters for the multiscale PE analysis: embedding dimension m, lag τ and scales to be integrated into the CMSPE index. Then, the CMSPE index and raw single-scale PE index were applied to EEG recordings from 18 patients who received sevoflurane anesthesia. Pharmacokinetic/pharmacodynamic (PKPD) modeling was used to relate the measured EEG indices and the anesthetic drug concentration. Prediction probability (Pk) statistics and correlation analysis with the response entropy (RE) index, derived from the spectral entropy (M-entropy module; GE Healthcare, Helsinki, Finland), were investigated to evaluate the effectiveness of the new proposed measure. It was found that raw single-scale PE was blind to subtle transitions between light and deep anesthesia, while the CMSPE index tracked these changes accurately. Around the time of loss of consciousness, CMSPE responded significantly more rapidly than the raw PE, with the absolute slopes of linearly fitted response versus time plots of 0.12 (0.09-0.15) and 0.10 (0.06-0.13), respectively. The prediction probability Pk of 0.86 (0.85-0.88) and 0.85 (0.80-0.86) for CMSPE and raw PE indicated that the CMSPE index correlated well with the underlying anesthetic effect. The correlation coefficient for the comparison between the CMSPE index and RE index of 0.84 (0.80-0.88) was significantly higher than the raw PE index of 0.75 (0.66-0.84). The results show that the CMSPE outperforms the raw single-scale PE in reflecting the sevoflurane drug effect on the central nervous system.

The complexity of gene expression dynamics revealed by permutation entropy

PubMed Central

2010-01-01

Background High complexity is considered a hallmark of living systems. Here we investigate the complexity of temporal gene expression patterns using the concept of Permutation Entropy (PE) first introduced in dynamical systems theory. The analysis of gene expression data has so far focused primarily on the identification of differentially expressed genes, or on the elucidation of pathway and regulatory relationships. We aim to study gene expression time series data from the viewpoint of complexity. Results Applying the PE complexity metric to abiotic stress response time series data in Arabidopsis thaliana, genes involved in stress response and signaling were found to be associated with the highest complexity not only under stress, but surprisingly, also under reference, non-stress conditions. Genes with house-keeping functions exhibited lower PE complexity. Compared to reference conditions, the PE of temporal gene expression patterns generally increased upon stress exposure. High-complexity genes were found to have longer upstream intergenic regions and more cis-regulatory motifs in their promoter regions indicative of a more complex regulatory apparatus needed to orchestrate their expression, and to be associated with higher correlation network connectivity degree. Arabidopsis genes also present in other plant species were observed to exhibit decreased PE complexity compared to Arabidopsis specific genes. Conclusions We show that Permutation Entropy is a simple yet robust and powerful approach to identify temporal gene expression profiles of varying complexity that is equally applicable to other types of molecular profile data. PMID:21176199

Effects of propofol, sevoflurane, remifentanil, and (S)-ketamine in subanesthetic concentrations on visceral and somatosensory pain-evoked potentials.

PubMed

Untergehrer, Gisela; Jordan, Denis; Eyl, Sebastian; Schneider, Gerhard

2013-02-01

Although electroencephalographic parameters and auditory evoked potentials (AEP) reflect the hypnotic component of anesthesia, there is currently no specific and mechanism-based monitoring tool for anesthesia-induced blockade of nociceptive inputs. The aim of this study was to assess visceral pain-evoked potentials (VPEP) and contact heat-evoked potentials (CHEP) as electroencephalographic indicators of drug-induced changes of visceral and somatosensory pain. Additionally, AEP and electroencephalographic permutation entropy were used to evaluate sedative components of the applied drugs. In a study enrolling 60 volunteers, VPEP, CHEP (amplitude N2-P1), and AEP (latency Nb, amplitude Pa-Nb) were recorded without drug application and at two subanesthetic concentration levels of propofol, sevoflurane, remifentanil, or (s)-ketamine. Drug-induced changes of evoked potentials were analyzed. VPEP were generated by electric stimuli using bipolar electrodes positioned in the distal esophagus. For CHEP, heat pulses were given to the medial aspect of the right forearm using a CHEP stimulator. In addition to AEP, electroencephalographic permutation entropy was used to indicate level of sedation. With increasing concentrations of propofol, sevoflurane, remifentanil, and (s)-ketamine, VPEP and CHEP N2-P1 amplitudes decreased. AEP and electroencephalographic permutation entropy showed neither clinically relevant nor statistically significant suppression of cortical activity during drug application. Decreasing VPEP and CHEP amplitudes under subanesthetic concentrations of propofol, sevoflurane, remifentanil, and (s)-ketamine indicate suppressive drug effects. These effects seem to be specific for analgesia.

Comparing vector-based and Bayesian memory models using large-scale datasets: User-generated hashtag and tag prediction on Twitter and Stack Overflow.

PubMed

Stanley, Clayton; Byrne, Michael D

2016-12-01

The growth of social media and user-created content on online sites provides unique opportunities to study models of human declarative memory. By framing the task of choosing a hashtag for a tweet and tagging a post on Stack Overflow as a declarative memory retrieval problem, 2 cognitively plausible declarative memory models were applied to millions of posts and tweets and evaluated on how accurately they predict a user's chosen tags. An ACT-R based Bayesian model and a random permutation vector-based model were tested on the large data sets. The results show that past user behavior of tag use is a strong predictor of future behavior. Furthermore, past behavior was successfully incorporated into the random permutation model that previously used only context. Also, ACT-R's attentional weight term was linked to an entropy-weighting natural language processing method used to attenuate high-frequency words (e.g., articles and prepositions). Word order was not found to be a strong predictor of tag use, and the random permutation model performed comparably to the Bayesian model without including word order. This shows that the strength of the random permutation model is not in the ability to represent word order, but rather in the way in which context information is successfully compressed. The results of the large-scale exploration show how the architecture of the 2 memory models can be modified to significantly improve accuracy, and may suggest task-independent general modifications that can help improve model fit to human data in a much wider range of domains. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Regional Value Analysis at Threat Evaluation

DTIC Science & Technology

2014-06-01

targets based on information entropy and fuzzy optimization theory. in Industrial Engineering and Engineering Management (IEEM), 2011 IEEE...Assignment by Virtual Permutation and Tabu Search Heuristics. Systems, Man, and Cybernetics, Part C: Applications and Reviews, IEEE Transactions on, 2010

Permutation entropy with vector embedding delays

NASA Astrophysics Data System (ADS)

Little, Douglas J.; Kane, Deb M.

2017-12-01

Permutation entropy (PE) is a statistic used widely for the detection of structure within a time series. Embedding delay times at which the PE is reduced are characteristic timescales for which such structure exists. Here, a generalized scheme is investigated where embedding delays are represented by vectors rather than scalars, permitting PE to be calculated over a (D -1 ) -dimensional space, where D is the embedding dimension. This scheme is applied to numerically generated noise, sine wave and logistic map series, and experimental data sets taken from a vertical-cavity surface emitting laser exhibiting temporally localized pulse structures within the round-trip time of the laser cavity. Results are visualized as PE maps as a function of embedding delay, with low PE values indicating combinations of embedding delays where correlation structure is present. It is demonstrated that vector embedding delays enable identification of structure that is ambiguous or masked, when the embedding delay is constrained to scalar form.

Spatiotemporal Permutation Entropy as a Measure for Complexity of Cardiac Arrhythmia

NASA Astrophysics Data System (ADS)

Schlemmer, Alexander; Berg, Sebastian; Lilienkamp, Thomas; Luther, Stefan; Parlitz, Ulrich

2018-05-01

Permutation entropy (PE) is a robust quantity for measuring the complexity of time series. In the cardiac community it is predominantly used in the context of electrocardiogram (ECG) signal analysis for diagnoses and predictions with a major application found in heart rate variability parameters. In this article we are combining spatial and temporal PE to form a spatiotemporal PE that captures both, complexity of spatial structures and temporal complexity at the same time. We demonstrate that the spatiotemporal PE (STPE) quantifies complexity using two datasets from simulated cardiac arrhythmia and compare it to phase singularity analysis and spatial PE (SPE). These datasets simulate ventricular fibrillation (VF) on a two-dimensional and a three-dimensional medium using the Fenton-Karma model. We show that SPE and STPE are robust against noise and demonstrate its usefulness for extracting complexity features at different spatial scales.

Distributed Sensing and Processing Adaptive Collaboration Environment (D-SPACE)

DTIC Science & Technology

2014-07-01

to the query graph, or subgraph permutations with the same mismatch cost (often the case for homogeneous and/or symmetrical data/query). To avoid...decisions are generated in a bottom-up manner using the metric of entropy at the cluster level (Figure 9c). Using the definition of belief messages...for a cluster and a set of data nodes in this cluster , we compute the entropy for forward and backward messages as (,) = −∑ (

Amplitude-aware permutation entropy: Illustration in spike detection and signal segmentation.

PubMed

Azami, Hamed; Escudero, Javier

2016-05-01

Signal segmentation and spike detection are two important biomedical signal processing applications. Often, non-stationary signals must be segmented into piece-wise stationary epochs or spikes need to be found among a background of noise before being further analyzed. Permutation entropy (PE) has been proposed to evaluate the irregularity of a time series. PE is conceptually simple, structurally robust to artifacts, and computationally fast. It has been extensively used in many applications, but it has two key shortcomings. First, when a signal is symbolized using the Bandt-Pompe procedure, only the order of the amplitude values is considered and information regarding the amplitudes is discarded. Second, in the PE, the effect of equal amplitude values in each embedded vector is not addressed. To address these issues, we propose a new entropy measure based on PE: the amplitude-aware permutation entropy (AAPE). AAPE is sensitive to the changes in the amplitude, in addition to the frequency, of the signals thanks to it being more flexible than the classical PE in the quantification of the signal motifs. To demonstrate how the AAPE method can enhance the quality of the signal segmentation and spike detection, a set of synthetic and realistic synthetic neuronal signals, electroencephalograms and neuronal data are processed. We compare the performance of AAPE in these problems against state-of-the-art approaches and evaluate the significance of the differences with a repeated ANOVA with post hoc Tukey's test. In signal segmentation, the accuracy of AAPE-based method is higher than conventional segmentation methods. AAPE also leads to more robust results in the presence of noise. The spike detection results show that AAPE can detect spikes well, even when presented with single-sample spikes, unlike PE. For multi-sample spikes, the changes in AAPE are larger than in PE. We introduce a new entropy metric, AAPE, that enables us to consider amplitude information in the formulation of PE. The AAPE algorithm can be used in almost every irregularity-based application in various signal and image processing fields. We also made freely available the Matlab code of the AAPE. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Extending Differential Fault Analysis to Dynamic S-Box Advanced Encryption Standard Implementations

DTIC Science & Technology

2014-09-18

entropy . At the same time, researchers strive to enhance AES and mitigate these growing threats. This paper researches the extension of existing...the algorithm or use side channels to reduce entropy , such as Differential Fault Analysis (DFA). At the same time, continuing research strives to...the state matrix. The S-box is an 8-bit 16x16 table built from an affine transformation on multiplicative inverses which guarantees full permutation (S

A permutation information theory tour through different interest rate maturities: the Libor case.

PubMed

Bariviera, Aurelio Fernández; Guercio, María Belén; Martinez, Lisana B; Rosso, Osvaldo A

2015-12-13

This paper analyses Libor interest rates for seven different maturities and referred to operations in British pounds, euros, Swiss francs and Japanese yen, during the period 2001-2015. The analysis is performed by means of two quantifiers derived from information theory: the permutation Shannon entropy and the permutation Fisher information measure. An anomalous behaviour in the Libor is detected in all currencies except euros during the years 2006-2012. The stochastic switch is more severe in one, two and three months maturities. Given the special mechanism of Libor setting, we conjecture that the behaviour could have been produced by the manipulation that was uncovered by financial authorities. We argue that our methodology is pertinent as a market overseeing instrument. © 2015 The Author(s).

Measuring the uncertainty of coupling

NASA Astrophysics Data System (ADS)

Zhao, Xiaojun; Shang, Pengjian

2015-06-01

A new information-theoretic measure, called coupling entropy, is proposed here to detect the causal links in complex systems by taking into account the inner composition alignment of temporal structure. It is a permutation-based asymmetric association measure to infer the uncertainty of coupling between two time series. The coupling entropy is found to be effective in the analysis of Hénon maps, where different noises are added to test its accuracy and sensitivity. The coupling entropy is also applied to analyze the relationship between unemployment rate and CPI change in the U.S., where the CPI change turns out to be the driving variable while the unemployment rate is the responding one.

Cipher image damage and decisions in real time

NASA Astrophysics Data System (ADS)

Silva-García, Victor Manuel; Flores-Carapia, Rolando; Rentería-Márquez, Carlos; Luna-Benoso, Benjamín; Jiménez-Vázquez, Cesar Antonio; González-Ramírez, Marlon David

2015-01-01

This paper proposes a method for constructing permutations on m position arrangements. Our objective is to encrypt color images using advanced encryption standard (AES), using variable permutations means a different one for each 128-bit block in the first round after the x-or operation is applied. Furthermore, this research offers the possibility of knowing the original image when the encrypted figure suffered a failure from either an attack or not. This is achieved by permuting the original image pixel positions before being encrypted with AES variable permutations, which means building a pseudorandom permutation of 250,000 position arrays or more. To this end, an algorithm that defines a bijective function between the nonnegative integer and permutation sets is built. From this algorithm, the way to build permutations on the 0,1,…,m-1 array, knowing m-1 constants, is presented. The transcendental numbers are used to select these m-1 constants in a pseudorandom way. The quality of the proposed encryption according to the following criteria is evaluated: the correlation coefficient, the entropy, and the discrete Fourier transform. A goodness-of-fit test for each basic color image is proposed to measure the bits randomness degree of the encrypted figure. On the other hand, cipher images are obtained in a loss-less encryption way, i.e., no JPEG file formats are used.

Value Focused Thinking Applications to Supervised Pattern Classification With Extensions to Hyperspectral Anomaly Detection Algorithms

DTIC Science & Technology

2015-03-26

performing. All reasonable permutations of factors will be used to develop a multitude of unique combinations. These combinations are considered different...are seen below (Duda et al., 2001). Entropy impurity: () = −�P�ωj�log2P(ωj) j (9) Gini impurity: () =�()�� = 1 2 ∗ [1...proportion of one class to another approaches 0.5, the impurity measure reaches its maximum, which for Entropy is 1.0, while it is 0.5 for Gini and

Phase Transitions in Definite Total Spin States of Two-Component Fermi Gases.

PubMed

Yurovsky, Vladimir A

2017-05-19

Second-order phase transitions have no latent heat and are characterized by a change in symmetry. In addition to the conventional symmetric and antisymmetric states under permutations of bosons and fermions, mathematical group-representation theory allows for non-Abelian permutation symmetry. Such symmetry can be hidden in states with defined total spins of spinor gases, which can be formed in optical cavities. The present work shows that the symmetry reveals itself in spin-independent or coordinate-independent properties of these gases, namely as non-Abelian entropy in thermodynamic properties. In weakly interacting Fermi gases, two phases appear associated with fermionic and non-Abelian symmetry under permutations of particle states, respectively. The second-order transitions between the phases are characterized by discontinuities in specific heat. Unlike other phase transitions, the present ones are not caused by interactions and can appear even in ideal gases. Similar effects in Bose gases and strong interactions are discussed.

Monitoring the informational efficiency of European corporate bond markets with dynamical permutation min-entropy

NASA Astrophysics Data System (ADS)

Zunino, Luciano; Bariviera, Aurelio F.; Guercio, M. Belén; Martinez, Lisana B.; Rosso, Osvaldo A.

2016-08-01

In this paper the permutation min-entropy has been implemented to unveil the presence of temporal structures in the daily values of European corporate bond indices from April 2001 to August 2015. More precisely, the informational efficiency evolution of the prices of fifteen sectorial indices has been carefully studied by estimating this information-theory-derived symbolic tool over a sliding time window. Such a dynamical analysis makes possible to obtain relevant conclusions about the effect that the 2008 credit crisis has had on the different European corporate bond sectors. It is found that the informational efficiency of some sectors, namely banks, financial services, insurance, and basic resources, has been strongly reduced due to the financial crisis whereas another set of sectors, integrated by chemicals, automobiles, media, energy, construction, industrial goods & services, technology, and telecommunications has only suffered a transitory loss of efficiency. Last but not least, the food & beverage, healthcare, and utilities sectors show a behavior close to a random walk practically along all the period of analysis, confirming a remarkable immunity against the 2008 financial crisis.

Permutation entropy of finite-length white-noise time series.

PubMed

Little, Douglas J; Kane, Deb M

2016-08-01

Permutation entropy (PE) is commonly used to discriminate complex structure from white noise in a time series. While the PE of white noise is well understood in the long time-series limit, analysis in the general case is currently lacking. Here the expectation value and variance of white-noise PE are derived as functions of the number of ordinal pattern trials, N, and the embedding dimension, D. It is demonstrated that the probability distribution of the white-noise PE converges to a χ^{2} distribution with D!-1 degrees of freedom as N becomes large. It is further demonstrated that the PE variance for an arbitrary time series can be estimated as the variance of a related metric, the Kullback-Leibler entropy (KLE), allowing the qualitative N≫D! condition to be recast as a quantitative estimate of the N required to achieve a desired PE calculation precision. Application of this theory to statistical inference is demonstrated in the case of an experimentally obtained noise series, where the probability of obtaining the observed PE value was calculated assuming a white-noise time series. Standard statistical inference can be used to draw conclusions whether the white-noise null hypothesis can be accepted or rejected. This methodology can be applied to other null hypotheses, such as discriminating whether two time series are generated from different complex system states.

Characterising Dynamic Instability in High Water-Cut Oil-Water Flows Using High-Resolution Microwave Sensor Signals

NASA Astrophysics Data System (ADS)

Liu, Weixin; Jin, Ningde; Han, Yunfeng; Ma, Jing

2018-06-01

In the present study, multi-scale entropy algorithm was used to characterise the complex flow phenomena of turbulent droplets in high water-cut oil-water two-phase flow. First, we compared multi-scale weighted permutation entropy (MWPE), multi-scale approximate entropy (MAE), multi-scale sample entropy (MSE) and multi-scale complexity measure (MCM) for typical nonlinear systems. The results show that MWPE presents satisfied variability with scale and anti-noise ability. Accordingly, we conducted an experiment of vertical upward oil-water two-phase flow with high water-cut and collected the signals of a high-resolution microwave resonant sensor, based on which two indexes, the entropy rate and mean value of MWPE, were extracted. Besides, the effects of total flow rate and water-cut on these two indexes were analysed. Our researches show that MWPE is an effective method to uncover the dynamic instability of oil-water two-phase flow with high water-cut.

Analysis of HD 73045 light curve data

NASA Astrophysics Data System (ADS)

Das, Mrinal Kanti; Bhatraju, Naveen Kumar; Joshi, Santosh

2018-04-01

In this work we analyzed the Kepler light curve data of HD 73045. The raw data has been smoothened using standard filters. The power spectrum has been obtained by using a fast Fourier transform routine. It shows the presence of more than one period. In order to take care of any non-stationary behavior, we carried out a wavelet analysis to obtain the wavelet power spectrum. In addition, to identify the scale invariant structure, the data has been analyzed using a multifractal detrended fluctuation analysis. Further to characterize the diversity of embedded patterns in the HD 73045 flux time series, we computed various entropy-based complexity measures e.g. sample entropy, spectral entropy and permutation entropy. The presence of periodic structure in the time series was further analyzed using the visibility network and horizontal visibility network model of the time series. The degree distributions in the two network models confirm such structures.

Characterization of Early Partial Seizure Onset: Frequency, Complexity and Entropy

PubMed Central

Jouny, Christophe C.; Bergey, Gregory K.

2011-01-01

Objective A clear classification of partial seizures onset features is not yet established. Complexity and entropy have been very widely used to describe dynamical systems, but a systematic evaluation of these measures to characterize partial seizures has never been performed. Methods Eighteen different measures including power in frequency bands up to 300Hz, Gabor atom density (GAD), Higuchi fractal dimension (HFD), Lempel-Ziv complexity, Shannon entropy, sample entropy, and permutation entropy, were selected to test sensitivity to partial seizure onset. Intracranial recordings from forty-five patients with mesial temporal, neocortical temporal and neocortical extratemporal seizure foci were included (331 partial seizures). Results GAD, Lempel-Ziv complexity, HFD, high frequency activity, and sample entropy were the most reliable measures to assess early seizure onset. Conclusions Increases in complexity and occurrence of high-frequency components appear to be commonly associated with early stages of partial seizure evolution from all regions. The type of measure (frequency-based, complexity or entropy) does not predict the efficiency of the method to detect seizure onset. Significance Differences between measures such as GAD and HFD highlight the multimodal nature of partial seizure onsets. Improved methods for early seizure detection may be achieved from a better understanding of these underlying dynamics. PMID:21872526

Bubble Entropy: An Entropy Almost Free of Parameters.

PubMed

Manis, George; Aktaruzzaman, Md; Sassi, Roberto

2017-11-01

Objective : A critical point in any definition of entropy is the selection of the parameters employed to obtain an estimate in practice. We propose a new definition of entropy aiming to reduce the significance of this selection. Methods: We call the new definition Bubble Entropy . Bubble Entropy is based on permutation entropy, where the vectors in the embedding space are ranked. We use the bubble sort algorithm for the ordering procedure and count instead the number of swaps performed for each vector. Doing so, we create a more coarse-grained distribution and then compute the entropy of this distribution. Results: Experimental results with both real and synthetic HRV signals showed that bubble entropy presents remarkable stability and exhibits increased descriptive and discriminating power compared to all other definitions, including the most popular ones. Conclusion: The definition proposed is almost free of parameters. The most common ones are the scale factor r and the embedding dimension m . In our definition, the scale factor is totally eliminated and the importance of m is significantly reduced. The proposed method presents increased stability and discriminating power. Significance: After the extensive use of some entropy measures in physiological signals, typical values for their parameters have been suggested, or at least, widely used. However, the parameters are still there, application and dataset dependent, influencing the computed value and affecting the descriptive power. Reducing their significance or eliminating them alleviates the problem, decoupling the method from the data and the application, and eliminating subjective factors. Objective : A critical point in any definition of entropy is the selection of the parameters employed to obtain an estimate in practice. We propose a new definition of entropy aiming to reduce the significance of this selection. Methods: We call the new definition Bubble Entropy . Bubble Entropy is based on permutation entropy, where the vectors in the embedding space are ranked. We use the bubble sort algorithm for the ordering procedure and count instead the number of swaps performed for each vector. Doing so, we create a more coarse-grained distribution and then compute the entropy of this distribution. Results: Experimental results with both real and synthetic HRV signals showed that bubble entropy presents remarkable stability and exhibits increased descriptive and discriminating power compared to all other definitions, including the most popular ones. Conclusion: The definition proposed is almost free of parameters. The most common ones are the scale factor r and the embedding dimension m . In our definition, the scale factor is totally eliminated and the importance of m is significantly reduced. The proposed method presents increased stability and discriminating power. Significance: After the extensive use of some entropy measures in physiological signals, typical values for their parameters have been suggested, or at least, widely used. However, the parameters are still there, application and dataset dependent, influencing the computed value and affecting the descriptive power. Reducing their significance or eliminating them alleviates the problem, decoupling the method from the data and the application, and eliminating subjective factors.

A Versatile Platform for Nanotechnology Based on Circular Permutation of a Chaperonin Protein

NASA Technical Reports Server (NTRS)

Paavola, Chad; McMillan, Andrew; Trent, Jonathan; Chan, Suzanne; Mazzarella, Kellen; Li, Yi-Fen

2004-01-01

A number of protein complexes have been developed as nanoscale templates. These templates can be functionalized using the peptide sequences that bind inorganic materials. However, it is difficult to integrate peptides into a specific position within a protein template. Integrating intact proteins with desirable binding or catalytic activities is an even greater challenge. We present a general method for modifying protein templates using circular permutation so that additional peptide sequence can be added in a wide variety of specific locations. Circular permutation is a reordering of the polypeptide chain such that the original termini are joined and new termini are created elsewhere in the protein. New sequence can be joined to the protein termini without perturbing the protein structure and with minimal limitation on the size and conformation of the added sequence. We have used this approach to modify a chaperonin protein template, placing termini at five different locations distributed across the surface of the protein complex. These permutants are competent to form the double-ring structures typical of chaperonin proteins. The permuted double-rings also form the same assemblies as the unmodified protein. We fused a fluorescent protein to two representative permutants and demonstrated that it assumes its active structure and does not interfere with assembly of chaperonin double-rings.

A Novel Bearing Multi-Fault Diagnosis Approach Based on Weighted Permutation Entropy and an Improved SVM Ensemble Classifier.

PubMed

Zhou, Shenghan; Qian, Silin; Chang, Wenbing; Xiao, Yiyong; Cheng, Yang

2018-06-14

Timely and accurate state detection and fault diagnosis of rolling element bearings are very critical to ensuring the reliability of rotating machinery. This paper proposes a novel method of rolling bearing fault diagnosis based on a combination of ensemble empirical mode decomposition (EEMD), weighted permutation entropy (WPE) and an improved support vector machine (SVM) ensemble classifier. A hybrid voting (HV) strategy that combines SVM-based classifiers and cloud similarity measurement (CSM) was employed to improve the classification accuracy. First, the WPE value of the bearing vibration signal was calculated to detect the fault. Secondly, if a bearing fault occurred, the vibration signal was decomposed into a set of intrinsic mode functions (IMFs) by EEMD. The WPE values of the first several IMFs were calculated to form the fault feature vectors. Then, the SVM ensemble classifier was composed of binary SVM and the HV strategy to identify the bearing multi-fault types. Finally, the proposed model was fully evaluated by experiments and comparative studies. The results demonstrate that the proposed method can effectively detect bearing faults and maintain a high accuracy rate of fault recognition when a small number of training samples are available.

Folding pathway of a multidomain protein depends on its topology of domain connectivity

PubMed Central

Inanami, Takashi; Terada, Tomoki P.; Sasai, Masaki

2014-01-01

How do the folding mechanisms of multidomain proteins depend on protein topology? We addressed this question by developing an Ising-like structure-based model and applying it for the analysis of free-energy landscapes and folding kinetics of an example protein, Escherichia coli dihydrofolate reductase (DHFR). DHFR has two domains, one comprising discontinuous N- and C-terminal parts and the other comprising a continuous middle part of the chain. The simulated folding pathway of DHFR is a sequential process during which the continuous domain folds first, followed by the discontinuous domain, thereby avoiding the rapid decrease in conformation entropy caused by the association of the N- and C-terminal parts during the early phase of folding. Our simulated results consistently explain the observed experimental data on folding kinetics and predict an off-pathway structural fluctuation at equilibrium. For a circular permutant for which the topological complexity of wild-type DHFR is resolved, the balance between energy and entropy is modulated, resulting in the coexistence of the two folding pathways. This coexistence of pathways should account for the experimentally observed complex folding behavior of the circular permutant. PMID:25267632

Complexity-entropy causality plane: A useful approach for distinguishing songs

NASA Astrophysics Data System (ADS)

Ribeiro, Haroldo V.; Zunino, Luciano; Mendes, Renio S.; Lenzi, Ervin K.

2012-04-01

Nowadays we are often faced with huge databases resulting from the rapid growth of data storage technologies. This is particularly true when dealing with music databases. In this context, it is essential to have techniques and tools able to discriminate properties from these massive sets. In this work, we report on a statistical analysis of more than ten thousand songs aiming to obtain a complexity hierarchy. Our approach is based on the estimation of the permutation entropy combined with an intensive complexity measure, building up the complexity-entropy causality plane. The results obtained indicate that this representation space is very promising to discriminate songs as well as to allow a relative quantitative comparison among songs. Additionally, we believe that the here-reported method may be applied in practical situations since it is simple, robust and has a fast numerical implementation.

Symmetric encryption algorithms using chaotic and non-chaotic generators: A review

PubMed Central

Radwan, Ahmed G.; AbdElHaleem, Sherif H.; Abd-El-Hafiz, Salwa K.

2015-01-01

This paper summarizes the symmetric image encryption results of 27 different algorithms, which include substitution-only, permutation-only or both phases. The cores of these algorithms are based on several discrete chaotic maps (Arnold’s cat map and a combination of three generalized maps), one continuous chaotic system (Lorenz) and two non-chaotic generators (fractals and chess-based algorithms). Each algorithm has been analyzed by the correlation coefficients between pixels (horizontal, vertical and diagonal), differential attack measures, Mean Square Error (MSE), entropy, sensitivity analyses and the 15 standard tests of the National Institute of Standards and Technology (NIST) SP-800-22 statistical suite. The analyzed algorithms include a set of new image encryption algorithms based on non-chaotic generators, either using substitution only (using fractals) and permutation only (chess-based) or both. Moreover, two different permutation scenarios are presented where the permutation-phase has or does not have a relationship with the input image through an ON/OFF switch. Different encryption-key lengths and complexities are provided from short to long key to persist brute-force attacks. In addition, sensitivities of those different techniques to a one bit change in the input parameters of the substitution key as well as the permutation key are assessed. Finally, a comparative discussion of this work versus many recent research with respect to the used generators, type of encryption, and analyses is presented to highlight the strengths and added contribution of this paper. PMID:26966561

Development of isothermal-isobaric replica-permutation method for molecular dynamics and Monte Carlo simulations and its application to reveal temperature and pressure dependence of folded, misfolded, and unfolded states of chignolin

NASA Astrophysics Data System (ADS)

Yamauchi, Masataka; Okumura, Hisashi

2017-11-01

We developed a two-dimensional replica-permutation molecular dynamics method in the isothermal-isobaric ensemble. The replica-permutation method is a better alternative to the replica-exchange method. It was originally developed in the canonical ensemble. This method employs the Suwa-Todo algorithm, instead of the Metropolis algorithm, to perform permutations of temperatures and pressures among more than two replicas so that the rejection ratio can be minimized. We showed that the isothermal-isobaric replica-permutation method performs better sampling efficiency than the isothermal-isobaric replica-exchange method and infinite swapping method. We applied this method to a β-hairpin mini protein, chignolin. In this simulation, we observed not only the folded state but also the misfolded state. We calculated the temperature and pressure dependence of the fractions on the folded, misfolded, and unfolded states. Differences in partial molar enthalpy, internal energy, entropy, partial molar volume, and heat capacity were also determined and agreed well with experimental data. We observed a new phenomenon that misfolded chignolin becomes more stable under high-pressure conditions. We also revealed this mechanism of the stability as follows: TYR2 and TRP9 side chains cover the hydrogen bonds that form a β-hairpin structure. The hydrogen bonds are protected from the water molecules that approach the protein as the pressure increases.

Dispersion entropy for the analysis of resting-state MEG regularity in Alzheimer's disease.

PubMed

Azami, Hamed; Rostaghi, Mostafa; Fernandez, Alberto; Escudero, Javier

2016-08-01

Alzheimer's disease (AD) is a progressive degenerative brain disorder affecting memory, thinking, behaviour and emotion. It is the most common form of dementia and a big social problem in western societies. The analysis of brain activity may help to diagnose this disease. Changes in entropy methods have been reported useful in research studies to characterize AD. We have recently proposed dispersion entropy (DisEn) as a very fast and powerful tool to quantify the irregularity of time series. The aim of this paper is to evaluate the ability of DisEn, in comparison with fuzzy entropy (FuzEn), sample entropy (SampEn), and permutation entropy (PerEn), to discriminate 36 AD patients from 26 elderly control subjects using resting-state magnetoencephalogram (MEG) signals. The results obtained by DisEn, FuzEn, and SampEn, unlike PerEn, show that the AD patients' signals are more regular than controls' time series. The p-values obtained by DisEn, FuzEn, SampEn, and PerEn based methods demonstrate the superiority of DisEn over PerEn, SampEn, and PerEn. Moreover, the computation time for the newly proposed DisEn-based method is noticeably less than for the FuzEn, SampEn, and PerEn based approaches.

Comparison of background EEG activity of different groups of patients with idiopathic epilepsy using Shannon spectral entropy and cluster-based permutation statistical testing

PubMed Central

Artieda, Julio; Iriarte, Jorge

2017-01-01

Idiopathic epilepsy is characterized by generalized seizures with no apparent cause. One of its main problems is the lack of biomarkers to monitor the evolution of patients. The only tools they can use are limited to inspecting the amount of seizures during previous periods of time and assessing the existence of interictal discharges. As a result, there is a need for improving the tools to assist the diagnosis and follow up of these patients. The goal of the present study is to compare and find a way to differentiate between two groups of patients suffering from idiopathic epilepsy, one group that could be followed-up by means of specific electroencephalographic (EEG) signatures (intercritical activity present), and another one that could not due to the absence of these markers. To do that, we analyzed the background EEG activity of each in the absence of seizures and epileptic intercritical activity. We used the Shannon spectral entropy (SSE) as a metric to discriminate between the two groups and performed permutation-based statistical tests to detect the set of frequencies that show significant differences. By constraining the spectral entropy estimation to the [6.25–12.89) Hz range, we detect statistical differences (at below 0.05 alpha-level) between both types of epileptic patients at all available recording channels. Interestingly, entropy values follow a trend that is inversely related to the elapsed time from the last seizure. Indeed, this trend shows asymptotical convergence to the SSE values measured in a group of healthy subjects, which present SSE values lower than any of the two groups of patients. All these results suggest that the SSE, measured in a specific range of frequencies, could serve to follow up the evolution of patients suffering from idiopathic epilepsy. Future studies remain to be conducted in order to assess the predictive value of this approach for the anticipation of seizures. PMID:28922360

Complexity analysis of the turbulent environmental fluid flow time series

NASA Astrophysics Data System (ADS)

Mihailović, D. T.; Nikolić-Đorić, E.; Drešković, N.; Mimić, G.

2014-02-01

We have used the Kolmogorov complexities, sample and permutation entropies to quantify the randomness degree in river flow time series of two mountain rivers in Bosnia and Herzegovina, representing the turbulent environmental fluid, for the period 1926-1990. In particular, we have examined the monthly river flow time series from two rivers (the Miljacka and the Bosnia) in the mountain part of their flow and then calculated the Kolmogorov complexity (KL) based on the Lempel-Ziv Algorithm (LZA) (lower-KLL and upper-KLU), sample entropy (SE) and permutation entropy (PE) values for each time series. The results indicate that the KLL, KLU, SE and PE values in two rivers are close to each other regardless of the amplitude differences in their monthly flow rates. We have illustrated the changes in mountain river flow complexity by experiments using (i) the data set for the Bosnia River and (ii) anticipated human activities and projected climate changes. We have explored the sensitivity of considered measures in dependence on the length of time series. In addition, we have divided the period 1926-1990 into three subintervals: (a) 1926-1945, (b) 1946-1965, (c) 1966-1990, and calculated the KLL, KLU, SE, PE values for the various time series in these subintervals. It is found that during the period 1946-1965, there is a decrease in their complexities, and corresponding changes in the SE and PE, in comparison to the period 1926-1990. This complexity loss may be primarily attributed to (i) human interventions, after the Second World War, on these two rivers because of their use for water consumption and (ii) climate change in recent times.

A secure image encryption method based on dynamic harmony search (DHS) combined with chaotic map

NASA Astrophysics Data System (ADS)

Mirzaei Talarposhti, Khadijeh; Khaki Jamei, Mehrzad

2016-06-01

In recent years, there has been increasing interest in the security of digital images. This study focuses on the gray scale image encryption using dynamic harmony search (DHS). In this research, first, a chaotic map is used to create cipher images, and then the maximum entropy and minimum correlation coefficient is obtained by applying a harmony search algorithm on them. This process is divided into two steps. In the first step, the diffusion of a plain image using DHS to maximize the entropy as a fitness function will be performed. However, in the second step, a horizontal and vertical permutation will be applied on the best cipher image, which is obtained in the previous step. Additionally, DHS has been used to minimize the correlation coefficient as a fitness function in the second step. The simulation results have shown that by using the proposed method, the maximum entropy and the minimum correlation coefficient, which are approximately 7.9998 and 0.0001, respectively, have been obtained.

Shortening a loop can increase protein native state entropy.

PubMed

Gavrilov, Yulian; Dagan, Shlomi; Levy, Yaakov

2015-12-01

Protein loops are essential structural elements that influence not only function but also protein stability and folding rates. It was recently reported that shortening a loop in the AcP protein may increase its native state conformational entropy. This effect on the entropy of the folded state can be much larger than the lower entropic penalty of ordering a shorter loop upon folding, and can therefore result in a more pronounced stabilization than predicted by polymer model for loop closure entropy. In this study, which aims at generalizing the effect of loop length shortening on native state dynamics, we use all-atom molecular dynamics simulations to study how gradual shortening a very long or solvent-exposed loop region in four different proteins can affect their stability. For two proteins, AcP and Ubc7, we show an increase in native state entropy in addition to the known effect of the loop length on the unfolded state entropy. However, for two permutants of SH3 domain, shortening a loop results only with the expected change in the entropy of the unfolded state, which nicely reproduces the observed experimental stabilization. Here, we show that an increase in the native state entropy following loop shortening is not unique to the AcP protein, yet nor is it a general rule that applies to all proteins following the truncation of any loop. This modification of the loop length on the folded state and on the unfolded state may result with a greater effect on protein stability. © 2015 Wiley Periodicals, Inc.

Classification of Partial Discharge Signals by Combining Adaptive Local Iterative Filtering and Entropy Features

PubMed Central

Morison, Gordon; Boreham, Philip

2018-01-01

Electromagnetic Interference (EMI) is a technique for capturing Partial Discharge (PD) signals in High-Voltage (HV) power plant apparatus. EMI signals can be non-stationary which makes their analysis difficult, particularly for pattern recognition applications. This paper elaborates upon a previously developed software condition-monitoring model for improved EMI events classification based on time-frequency signal decomposition and entropy features. The idea of the proposed method is to map multiple discharge source signals captured by EMI and labelled by experts, including PD, from the time domain to a feature space, which aids in the interpretation of subsequent fault information. Here, instead of using only one permutation entropy measure, a more robust measure, called Dispersion Entropy (DE), is added to the feature vector. Multi-Class Support Vector Machine (MCSVM) methods are utilized for classification of the different discharge sources. Results show an improved classification accuracy compared to previously proposed methods. This yields to a successful development of an expert’s knowledge-based intelligent system. Since this method is demonstrated to be successful with real field data, it brings the benefit of possible real-world application for EMI condition monitoring. PMID:29385030

Non-extensive entropy of modified Gaussian quantum dot under polaron effects

NASA Astrophysics Data System (ADS)

Bahramiyan, H.; Khordad, R.; Sedehi, H. R. Rastegar

2018-01-01

The effect of electron-phonon (e-p) interaction on the non-extensive Tsallis entropy of a modified Gaussian quantum dot has been investigated. In this work, the LO-phonons, SO-phonons and LO + SO-phonons have been considered. It is found that the entropy increases with enhancing the confinement potential range and depth. The entropy decreases with considering the electron-phonon interaction. The electron-LO + SO-phonon interaction has the largest contribution to the entropy.

MEMD-enhanced multivariate fuzzy entropy for the evaluation of complexity in biomedical signals.

PubMed

Azami, Hamed; Smith, Keith; Escudero, Javier

2016-08-01

Multivariate multiscale entropy (mvMSE) has been proposed as a combination of the coarse-graining process and multivariate sample entropy (mvSE) to quantify the irregularity of multivariate signals. However, both the coarse-graining process and mvSE may not be reliable for short signals. Although the coarse-graining process can be replaced with multivariate empirical mode decomposition (MEMD), the relative instability of mvSE for short signals remains a problem. Here, we address this issue by proposing the multivariate fuzzy entropy (mvFE) with a new fuzzy membership function. The results using white Gaussian noise show that the mvFE leads to more reliable and stable results, especially for short signals, in comparison with mvSE. Accordingly, we propose MEMD-enhanced mvFE to quantify the complexity of signals. The characteristics of brain regions influenced by partial epilepsy are investigated by focal and non-focal electroencephalogram (EEG) time series. In this sense, the proposed MEMD-enhanced mvFE and mvSE are employed to discriminate focal EEG signals from non-focal ones. The results demonstrate the MEMD-enhanced mvFE values have a smaller coefficient of variation in comparison with those obtained by the MEMD-enhanced mvSE, even for long signals. The results also show that the MEMD-enhanced mvFE has better performance to quantify focal and non-focal signals compared with multivariate multiscale permutation entropy.

High Entropy Alloys: Criteria for Stable Structure

NASA Astrophysics Data System (ADS)

Tripathy, Snehashish; Gupta, Gaurav; Chowdhury, Sandip Ghosh

2018-01-01

An effort has been made to reassess the phase predicting capability of various thermodynamic and topological parameters across a wide range of HEA systems. These parameters are valence electron concentration, atomic mismatch ( δ), electronegativity difference (Δ χ), mixing entropy (Δ S mix), entropy of fusion (Δ S f), and mismatch entropy ( S σ ). In continuation of that, two new parameters (a) Modified Darken-Gurry parameter ( A = Sσ * χ) and (b) Modified Mismatch Entropy parameter ( B = δ* Sσ) have been designed to predict the stable crystal structure that would form in the HEA systems considered for assessment.

On the efficiency of sovereign bond markets

NASA Astrophysics Data System (ADS)

Zunino, Luciano; Fernández Bariviera, Aurelio; Guercio, M. Belén; Martinez, Lisana B.; Rosso, Osvaldo A.

2012-09-01

The existence of memory in financial time series has been extensively studied for several stock markets around the world by means of different approaches. However, fixed income markets, i.e. those where corporate and sovereign bonds are traded, have been much less studied. We believe that, given the relevance of these markets, not only from the investors', but also from the issuers' point of view (government and firms), it is necessary to fill this gap in the literature. In this paper, we study the sovereign market efficiency of thirty bond indices of both developed and emerging countries, using an innovative statistical tool in the financial literature: the complexity-entropy causality plane. This representation space allows us to establish an efficiency ranking of different markets and distinguish different bond market dynamics. We conclude that the classification derived from the complexity-entropy causality plane is consistent with the qualifications assigned by major rating companies to the sovereign instruments. Additionally, we find a correlation between permutation entropy, economic development and market size that could be of interest for policy makers and investors.

Scale-specific effects: A report on multiscale analysis of acupunctured EEG in entropy and power

NASA Astrophysics Data System (ADS)

Song, Zhenxi; Deng, Bin; Wei, Xile; Cai, Lihui; Yu, Haitao; Wang, Jiang; Wang, Ruofan; Chen, Yingyuan

2018-02-01

Investigating acupuncture effects contributes to improving clinical application and understanding neuronal dynamics under external stimulation. In this report, we recorded electroencephalography (EEG) signals evoked by acupuncture at ST36 acupoint with three stimulus frequencies of 50, 100 and 200 times per minutes, and selected non-acupuncture EEGs as the control group. Multiscale analyses were introduced to investigate the possible acupuncture effects on complexity and power in multiscale level. Using multiscale weighted-permutation entropy, we found the significant effects on increased complexity degree in EEG signals induced by acupuncture. The comparison of three stimulation manipulations showed that 100 times/min generated most obvious effects, and affected most cortical regions. By estimating average power spectral density, we found decreased power induced by acupuncture. The joint distribution of entropy and power indicated an inverse correlation, and this relationship was weakened by acupuncture effects, especially under the manipulation of 100 times/min frequency. Above findings are more evident and stable in large scales than small scales, which suggests that multiscale analysis allows evaluating significant effects in specific scale and enables to probe the inherent characteristics underlying physiological signals.

Classification enhancement for post-stroke dementia using fuzzy neighborhood preserving analysis with QR-decomposition.

PubMed

Al-Qazzaz, Noor Kamal; Ali, Sawal; Ahmad, Siti Anom; Escudero, Javier

2017-07-01

The aim of the present study was to discriminate the electroencephalogram (EEG) of 5 patients with vascular dementia (VaD), 15 patients with stroke-related mild cognitive impairment (MCI), and 15 control normal subjects during a working memory (WM) task. We used independent component analysis (ICA) and wavelet transform (WT) as a hybrid preprocessing approach for EEG artifact removal. Three different features were extracted from the cleaned EEG signals: spectral entropy (SpecEn), permutation entropy (PerEn) and Tsallis entropy (TsEn). Two classification schemes were applied - support vector machine (SVM) and k-nearest neighbors (kNN) - with fuzzy neighborhood preserving analysis with QR-decomposition (FNPAQR) as a dimensionality reduction technique. The FNPAQR dimensionality reduction technique increased the SVM classification accuracy from 82.22% to 90.37% and from 82.6% to 86.67% for kNN. These results suggest that FNPAQR consistently improves the discrimination of VaD, MCI patients and control normal subjects and it could be a useful feature selection to help the identification of patients with VaD and MCI.

Efficiency and credit ratings: a permutation-information-theory analysis

NASA Astrophysics Data System (ADS)

Fernandez Bariviera, Aurelio; Zunino, Luciano; Belén Guercio, M.; Martinez, Lisana B.; Rosso, Osvaldo A.

2013-08-01

The role of credit rating agencies has been under severe scrutiny after the subprime crisis. In this paper we explore the relationship between credit ratings and informational efficiency of a sample of thirty nine corporate bonds of US oil and energy companies from April 2008 to November 2012. For this purpose we use a powerful statistical tool, relatively new in the financial literature: the complexity-entropy causality plane. This representation space allows us to graphically classify the different bonds according to their degree of informational efficiency. We find that this classification agrees with the credit ratings assigned by Moody’s. In particular, we detect the formation of two clusters, which correspond to the global categories of investment and speculative grades. Regarding the latter cluster, two subgroups reflect distinct levels of efficiency. Additionally, we also find an intriguing absence of correlation between informational efficiency and firm characteristics. This allows us to conclude that the proposed permutation-information-theory approach provides an alternative practical way to justify bond classification.

Design of an image encryption scheme based on a multiple chaotic map

NASA Astrophysics Data System (ADS)

Tong, Xiao-Jun

2013-07-01

In order to solve the problem that chaos is degenerated in limited computer precision and Cat map is the small key space, this paper presents a chaotic map based on topological conjugacy and the chaotic characteristics are proved by Devaney definition. In order to produce a large key space, a Cat map named block Cat map is also designed for permutation process based on multiple-dimensional chaotic maps. The image encryption algorithm is based on permutation-substitution, and each key is controlled by different chaotic maps. The entropy analysis, differential analysis, weak-keys analysis, statistical analysis, cipher random analysis, and cipher sensibility analysis depending on key and plaintext are introduced to test the security of the new image encryption scheme. Through the comparison to the proposed scheme with AES, DES and Logistic encryption methods, we come to the conclusion that the image encryption method solves the problem of low precision of one dimensional chaotic function and has higher speed and higher security.

Toward a general theory of conical intersections in systems of identical nuclei

NASA Astrophysics Data System (ADS)

Keating, Sean P.; Mead, C. Alden

1987-02-01

It has been shown previously that the Herzberg-Longuet-Higgins sign change produced in Born-Oppenheimer electronic wave functions when the nuclei traverse a closed path around a conical intersection has implications for the symmetry of wave functions under permutations of identical nuclei. For systems of three or four identical nuclei, there are special features present which have facilitated the detailed analysis. The present paper reports progress toward a general theory for systems of n nuclei. For n=3 or 4, the two key functions which locate conical intersections and define compensating phase factors can conveniently be defined so as to transform under permutations according to a two-dimensional irreducible representation of the permutation group. Since such representations do not exist for n>4, we have chosen to develop a formalism in terms of lab-fixed electronic basis functions, and we show how to define the two key functions in principle. The functions so defined both turn out to be totally symmetric under permutations. We show how they can be used to define compensating phase factors so that all modified electronic wave functions are either totally symmetric or totally antisymmetric under permutations. A detailed analysis is made to cyclic permutations in the neighborhood of Dnh symmetry, which can be extended by continuity arguments to more general configurations, and criteria are obtained for sign changes. There is a qualitative discussion of the treatment of more general permutations.

Correction of Cardy–Verlinde formula for Fermions and Bosons with modified dispersion relation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadatian, S. Davood, E-mail: sd-sadatian@um.ac.ir; Dareyni, H.

Cardy–Verlinde formula links the entropy of conformal symmetry field to the total energy and its Casimir energy in a D-dimensional space. To correct black hole thermodynamics, modified dispersion relation can be used which is proposed as a general feature of quantum gravity approaches. In this paper, the thermodynamics of Schwarzschild four-dimensional black hole is corrected using the modified dispersion relation for Fermions and Bosons. Finally, using modified thermodynamics of Schwarzschild four-dimensional black hole, generalization for Cardy–Verlinde formula is obtained. - Highlights: • The modified Cardy–Verlinde formula obtained using MDR for Fermions and Bosons. • The modified entropy of the blackmore » hole used to correct the Cardy–Verlinde formula. • The modified entropy of the CFT has been obtained.« less

Novel Image Encryption Scheme Based on Chebyshev Polynomial and Duffing Map

PubMed Central

2014-01-01

We present a novel image encryption algorithm using Chebyshev polynomial based on permutation and substitution and Duffing map based on substitution. Comprehensive security analysis has been performed on the designed scheme using key space analysis, visual testing, histogram analysis, information entropy calculation, correlation coefficient analysis, differential analysis, key sensitivity test, and speed test. The study demonstrates that the proposed image encryption algorithm shows advantages of more than 10113 key space and desirable level of security based on the good statistical results and theoretical arguments. PMID:25143970

Characterization of complexities in combustion instability in a lean premixed gas-turbine model combustor.

PubMed

Gotoda, Hiroshi; Amano, Masahito; Miyano, Takaya; Ikawa, Takuya; Maki, Koshiro; Tachibana, Shigeru

2012-12-01

We characterize complexities in combustion instability in a lean premixed gas-turbine model combustor by nonlinear time series analysis to evaluate permutation entropy, fractal dimensions, and short-term predictability. The dynamic behavior in combustion instability near lean blowout exhibits a self-affine structure and is ascribed to fractional Brownian motion. It undergoes chaos by the onset of combustion oscillations with slow amplitude modulation. Our results indicate that nonlinear time series analysis is capable of characterizing complexities in combustion instability close to lean blowout.

Distribution entropy analysis of epileptic EEG signals.

PubMed

Li, Peng; Yan, Chang; Karmakar, Chandan; Liu, Changchun

2015-01-01

It is an open-ended challenge to accurately detect the epileptic seizures through electroencephalogram (EEG) signals. Recently published studies have made elaborate attempts to distinguish between the normal and epileptic EEG signals by advanced nonlinear entropy methods, such as the approximate entropy, sample entropy, fuzzy entropy, and permutation entropy, etc. Most recently, a novel distribution entropy (DistEn) has been reported to have superior performance compared with the conventional entropy methods for especially short length data. We thus aimed, in the present study, to show the potential of DistEn in the analysis of epileptic EEG signals. The publicly-accessible Bonn database which consisted of normal, interictal, and ictal EEG signals was used in this study. Three different measurement protocols were set for better understanding the performance of DistEn, which are: i) calculate the DistEn of a specific EEG signal using the full recording; ii) calculate the DistEn by averaging the results for all its possible non-overlapped 5 second segments; and iii) calculate it by averaging the DistEn values for all the possible non-overlapped segments of 1 second length, respectively. Results for all three protocols indicated a statistically significantly increased DistEn for the ictal class compared with both the normal and interictal classes. Besides, the results obtained under the third protocol, which only used very short segments (1 s) of EEG recordings showed a significantly (p <; 0.05) increased DistEn for the interictal class in compassion with the normal class, whereas both analyses using relatively long EEG signals failed in tracking this difference between them, which may be due to a nonstationarity effect on entropy algorithm. The capability of discriminating between the normal and interictal EEG signals is of great clinical relevance since it may provide helpful tools for the detection of a seizure onset. Therefore, our study suggests that the DistEn analysis of EEG signals is very promising for clinical and even portable EEG monitoring.

Generalized Entanglement Entropy and Holography

NASA Astrophysics Data System (ADS)

Obregón, O.

2018-04-01

A nonextensive statistical mechanics entropy that depends only on the probability distribution is proposed in the framework of superstatistics. It is based on a Γ(χ 2) distribution that depends on β and also on pl . The corresponding modified von Neumann entropy is constructed; it is shown that it can also be obtained from a generalized Replica trick. We address the question whether the generalized entanglement entropy can play a role in the gauge/gravity duality. We pay attention to 2dCFT and their gravity duals. The correction terms to the von Neumann entropy result more relevant than the usual UV (for c = 1) ones and also than those due to the area dependent AdS 3 entropy which result comparable to the UV ones. Then the correction terms due to the new entropy would modify the Ryu-Takayanagi identification between the CFT entanglement entropy and the AdS entropy in a different manner than the UV ones or than the corrections to the AdS 3 area dependent entropy.

Forbidden patterns in financial time series

NASA Astrophysics Data System (ADS)

Zanin, Massimiliano

2008-03-01

The existence of forbidden patterns, i.e., certain missing sequences in a given time series, is a recently proposed instrument of potential application in the study of time series. Forbidden patterns are related to the permutation entropy, which has the basic properties of classic chaos indicators, such as Lyapunov exponent or Kolmogorov entropy, thus allowing to separate deterministic (usually chaotic) from random series; however, it requires fewer values of the series to be calculated, and it is suitable for using with small datasets. In this paper, the appearance of forbidden patterns is studied in different economical indicators such as stock indices (Dow Jones Industrial Average and Nasdaq Composite), NYSE stocks (IBM and Boeing), and others (ten year Bond interest rate), to find evidence of deterministic behavior in their evolutions. Moreover, the rate of appearance of the forbidden patterns is calculated, and some considerations about the underlying dynamics are suggested.

Permutation entropy analysis of heart rate variability for the assessment of cardiovascular autonomic neuropathy in type 1 diabetes mellitus.

PubMed

Carricarte Naranjo, Claudia; Sanchez-Rodriguez, Lazaro M; Brown Martínez, Marta; Estévez Báez, Mario; Machado García, Andrés

2017-07-01

Heart rate variability (HRV) analysis is a relevant tool for the diagnosis of cardiovascular autonomic neuropathy (CAN). To our knowledge, no previous investigation on CAN has assessed the complexity of HRV from an ordinal perspective. Therefore, the aim of this work is to explore the potential of permutation entropy (PE) analysis of HRV complexity for the assessment of CAN. For this purpose, we performed a short-term PE analysis of HRV in healthy subjects and type 1 diabetes mellitus patients, including patients with CAN. Standard HRV indicators were also calculated in the control group. A discriminant analysis was used to select the variables combination with best discriminative power between control and CAN patients groups, as well as for classifying cases. We found that for some specific temporal scales, PE indicators were significantly lower in CAN patients than those calculated for controls. In such cases, there were ordinal patterns with high probabilities of occurrence, while others were hardly found. We posit this behavior occurs due to a decrease of HRV complexity in the diseased system. Discriminant functions based on PE measures or probabilities of occurrence of ordinal patterns provided an average of 75% and 96% classification accuracy. Correlations of PE and HRV measures showed to depend only on temporal scale, regardless of pattern length. PE analysis at some specific temporal scales, seem to provide additional information to that obtained with traditional HRV methods. We concluded that PE analysis of HRV is a promising method for the assessment of CAN. Copyright © 2017 Elsevier Ltd. All rights reserved.

Complexity of cardiovascular rhythms during head-up tilt test by entropy of patterns.

PubMed

Wejer, Dorota; Graff, Beata; Makowiec, Danuta; Budrejko, Szymon; Struzik, Zbigniew R

2017-05-01

The head-up tilt (HUT) test, which provokes transient dynamical alterations in the regulation of cardiovascular system, provides insights into complex organization of this system. Based on signals with heart period intervals (RR-intervals) and/or systolic blood pressure (SBP), differences in the cardiovascular regulation between vasovagal patients (VVS) and the healthy people group (CG) are investigated. Short-term relations among signal data represented symbolically by three-beat patterns allow to qualify and quantify the complexity of the cardiovascular regulation by Shannon entropy. Four types of patterns: permutation, ordinal, deterministic and dynamical, are used, and different resolutions of signal values in the the symbolization are applied in order to verify how entropy of patterns depends on a way in which values of signals are preprocessed. At rest, in the physiologically important signal resolution ranges, independently of the type of patterns used in estimates, the complexity of SBP signals in VVS is different from the complexity found in CG. Entropy of VVS is higher than CG what could be interpreted as substantial presence of noisy ingredients in SBP of VVS. After tilting this relation switches. Entropy of CG occurs significantly higher than VVS for SBP signals. In the case of RR-intervals and large resolutions, the complexity after the tilt becomes reduced when compared to the complexity of RR-intervals at rest for both groups. However, in the case of VVS patients this reduction is significantly stronger than in CG. Our observations about opposite switches in entropy between CG and VVS might support a hypothesis that baroreflex in VVS affects stronger the heart rate because of the inefficient regulation (possibly impaired local vascular tone alternations) of the blood pressure.

A Novel Bit-level Image Encryption Method Based on Chaotic Map and Dynamic Grouping

NASA Astrophysics Data System (ADS)

Zhang, Guo-Ji; Shen, Yan

2012-10-01

In this paper, a novel bit-level image encryption method based on dynamic grouping is proposed. In the proposed method, the plain-image is divided into several groups randomly, then permutation-diffusion process on bit level is carried out. The keystream generated by logistic map is related to the plain-image, which confuses the relationship between the plain-image and the cipher-image. The computer simulation results of statistical analysis, information entropy analysis and sensitivity analysis show that the proposed encryption method is secure and reliable enough to be used for communication application.

Multiscale sample entropy and cross-sample entropy based on symbolic representation and similarity of stock markets

NASA Astrophysics Data System (ADS)

Wu, Yue; Shang, Pengjian; Li, Yilong

2018-03-01

A modified multiscale sample entropy measure based on symbolic representation and similarity (MSEBSS) is proposed in this paper to research the complexity of stock markets. The modified algorithm reduces the probability of inducing undefined entropies and is confirmed to be robust to strong noise. Considering the validity and accuracy, MSEBSS is more reliable than Multiscale entropy (MSE) for time series mingled with much noise like financial time series. We apply MSEBSS to financial markets and results show American stock markets have the lowest complexity compared with European and Asian markets. There are exceptions to the regularity that stock markets show a decreasing complexity over the time scale, indicating a periodicity at certain scales. Based on MSEBSS, we introduce the modified multiscale cross-sample entropy measure based on symbolic representation and similarity (MCSEBSS) to consider the degree of the asynchrony between distinct time series. Stock markets from the same area have higher synchrony than those from different areas. And for stock markets having relative high synchrony, the entropy values will decrease with the increasing scale factor. While for stock markets having high asynchrony, the entropy values will not decrease with the increasing scale factor sometimes they tend to increase. So both MSEBSS and MCSEBSS are able to distinguish stock markets of different areas, and they are more helpful if used together for studying other features of financial time series.

Electromyographic Permutation Entropy Quantifies Diaphragmatic Denervation and Reinnervation

PubMed Central

Kretschmer, Alexander; Lehmeyer, Veronika; Kellermann, Kristine; Schaller, Stephan J.; Blobner, Manfred; Kochs, Eberhard F.; Fink, Heidrun

2014-01-01

Spontaneous reinnervation after diaphragmatic paralysis due to trauma, surgery, tumors and spinal cord injuries is frequently observed. A possible explanation could be collateral reinnervation, since the diaphragm is commonly double-innervated by the (accessory) phrenic nerve. Permutation entropy (PeEn), a complexity measure for time series, may reflect a functional state of neuromuscular transmission by quantifying the complexity of interactions across neural and muscular networks. In an established rat model, electromyographic signals of the diaphragm after phrenicotomy were analyzed using PeEn quantifying denervation and reinnervation. Thirty-three anesthetized rats were unilaterally phrenicotomized. After 1, 3, 9, 27 and 81 days, diaphragmatic electromyographic PeEn was analyzed in vivo from sternal, mid-costal and crural areas of both hemidiaphragms. After euthanasia of the animals, both hemidiaphragms were dissected for fiber type evaluation. The electromyographic incidence of an accessory phrenic nerve was 76%. At day 1 after phrenicotomy, PeEn (normalized values) was significantly diminished in the sternal (median: 0.69; interquartile range: 0.66–0.75) and mid-costal area (0.68; 0.66–0.72) compared to the non-denervated side (0.84; 0.78–0.90) at threshold p<0.05. In the crural area, innervated by the accessory phrenic nerve, PeEn remained unchanged (0.79; 0.72–0.86). During reinnervation over 81 days, PeEn normalized in the mid-costal area (0.84; 0.77–0.86), whereas it remained reduced in the sternal area (0.77; 0.70–0.81). Fiber type grouping, a histological sign for reinnervation, was found in the mid-costal area in 20% after 27 days and in 80% after 81 days. Collateral reinnervation can restore diaphragm activity after phrenicotomy. Electromyographic PeEn represents a new, distinctive assessment characterizing intramuscular function following denervation and reinnervation. PMID:25532023

Spectral Dynamics of Resting State fMRI Within the Ventral Tegmental Area and Dorsal Raphe Nuclei in Medication-Free Major Depressive Disorder in Young Adults.

PubMed

Wohlschläger, Afra; Karne, Harish; Jordan, Denis; Lowe, Mark J; Jones, Stephen E; Anand, Amit

2018-01-01

Background: Dorsal raphe nucleus (DRN) and ventral tegmental area (VTA) are major brainstem monamine nuclei consisting of serotonin and dopamine neurons respectively. Animal studies show that firing patterns in both nuclei are altered when animals exhibit depression like behaviors. Functional MRI studies in humans have shown reduced VTA activation and DRN connectivity in depression. This study for the first time aims at investigating the functional integrity of local neuronal firing concurrently in both the VTA and DRN in vivo in humans using spectral analysis of resting state low frequency fluctuation fMRI. Method: A total of 97 medication-free subjects-67 medication-free young patients (ages 18-30) with major depressive disorder and 30 closely matched healthy controls were included in the study to detect aberrant dynamics in DRN and VTA. For the investigation of altered localized dynamics we conducted power spectral analysis and above this spectral cross correlation between the two groups. Complementary to this, spectral dependence of permutation entropy, an information theoretical measure, was compared between groups. Results: Patients displayed significant spectral slowing in VTA vs. controls ( p = 0.035, corrected). In DRN, spectral slowing was less pronounced, but the amount of slowing significantly correlated with 17-item Hamilton Depression Rating scores of depression severity ( p = 0.038). Signal complexity as assessed via permutation entropy showed spectral alterations inline with the results on spectral slowing. Conclusion: Our results indicate that altered functional dynamics of VTA and DRN in depression can be detected from regional fMRI signal. On this basis, impact of antidepressant treatment and treatment response can be assessed using these markers in future studies.

OmpF, a nucleotide-sensing nanoprobe, computational evaluation of single channel activities

NASA Astrophysics Data System (ADS)

Abdolvahab, R. H.; Mobasheri, H.; Nikouee, A.; Ejtehadi, M. R.

2016-09-01

The results of highthroughput practical single channel experiments should be formulated and validated by signal analysis approaches to increase the recognition precision of translocating molecules. For this purpose, the activities of the single nano-pore forming protein, OmpF, in the presence of nucleotides were recorded in real time by the voltage clamp technique and used as a means for nucleotide recognition. The results were analyzed based on the permutation entropy of current Time Series (TS), fractality, autocorrelation, structure function, spectral density, and peak fraction to recognize each nucleotide, based on its signature effect on the conductance, gating frequency and voltage sensitivity of channel at different concentrations and membrane potentials. The amplitude and frequency of ion current fluctuation increased in the presence of Adenine more than Cytosine and Thymine in milli-molar (0.5 mM) concentrations. The variance of the current TS at various applied voltages showed a non-monotonic trend whose initial increasing slope in the presence of Thymine changed to a decreasing one in the second phase and was different from that of Adenine and Cytosine; e.g., by increasing the voltage from 40 to 140 mV in the 0.5 mM concentration of Adenine or Cytosine, the variance decreased by one third while for the case of Thymine it was doubled. Moreover, according to the structure function of TS, the fractality of current TS differed as a function of varying membrane potentials (pd) and nucleotide concentrations. Accordingly, the calculated permutation entropy of the TS, validated the biophysical approach defined for the recognition of different nucleotides at various concentrations, pd's and polarities. Thus, the promising outcomes of the combined experimental and theoretical methodologies presented here can be implemented as a complementary means in pore-based nucleotide recognition approaches.

Complexity-Entropy Causality Plane as a Complexity Measure for Two-Dimensional Patterns

PubMed Central

Ribeiro, Haroldo V.; Zunino, Luciano; Lenzi, Ervin K.; Santoro, Perseu A.; Mendes, Renio S.

2012-01-01

Complexity measures are essential to understand complex systems and there are numerous definitions to analyze one-dimensional data. However, extensions of these approaches to two or higher-dimensional data, such as images, are much less common. Here, we reduce this gap by applying the ideas of the permutation entropy combined with a relative entropic index. We build up a numerical procedure that can be easily implemented to evaluate the complexity of two or higher-dimensional patterns. We work out this method in different scenarios where numerical experiments and empirical data were taken into account. Specifically, we have applied the method to fractal landscapes generated numerically where we compare our measures with the Hurst exponent; liquid crystal textures where nematic-isotropic-nematic phase transitions were properly identified; 12 characteristic textures of liquid crystals where the different values show that the method can distinguish different phases; and Ising surfaces where our method identified the critical temperature and also proved to be stable. PMID:22916097

Analysis of spontaneous EEG activity in Alzheimer's disease using cross-sample entropy and graph theory.

PubMed

Gomez, Carlos; Poza, Jesus; Gomez-Pilar, Javier; Bachiller, Alejandro; Juan-Cruz, Celia; Tola-Arribas, Miguel A; Carreres, Alicia; Cano, Monica; Hornero, Roberto

2016-08-01

The aim of this pilot study was to analyze spontaneous electroencephalography (EEG) activity in Alzheimer's disease (AD) by means of Cross-Sample Entropy (Cross-SampEn) and two local measures derived from graph theory: clustering coefficient (CC) and characteristic path length (PL). Five minutes of EEG activity were recorded from 37 patients with dementia due to AD and 29 elderly controls. Our results showed that Cross-SampEn values were lower in the AD group than in the control one for all the interactions among EEG channels. This finding indicates that EEG activity in AD is characterized by a lower statistical dissimilarity among channels. Significant differences were found mainly for fronto-central interactions (p <; 0.01, permutation test). Additionally, the application of graph theory measures revealed diverse neural network changes, i.e. lower CC and higher PL values in AD group, leading to a less efficient brain organization. This study suggests the usefulness of our approach to provide further insights into the underlying brain dynamics associated with AD.

A faster 1.375-approximation algorithm for sorting by transpositions.

PubMed

Cunha, Luís Felipe I; Kowada, Luis Antonio B; Hausen, Rodrigo de A; de Figueiredo, Celina M H

2015-11-01

Sorting by Transpositions is an NP-hard problem for which several polynomial-time approximation algorithms have been developed. Hartman and Shamir (2006) developed a 1.5-approximation [Formula: see text] algorithm, whose running time was improved to O(nlogn) by Feng and Zhu (2007) with a data structure they defined, the permutation tree. Elias and Hartman (2006) developed a 1.375-approximation O(n(2)) algorithm, and Firoz et al. (2011) claimed an improvement to the running time, from O(n(2)) to O(nlogn), by using the permutation tree. We provide counter-examples to the correctness of Firoz et al.'s strategy, showing that it is not possible to reach a component by sufficient extensions using the method proposed by them. In addition, we propose a 1.375-approximation algorithm, modifying Elias and Hartman's approach with the use of permutation trees and achieving O(nlogn) time.

Diffusivity anomaly in modified Stillinger-Weber liquids

NASA Astrophysics Data System (ADS)

Sengupta, Shiladitya; Vasisht, Vishwas V.; Sastry, Srikanth

2014-01-01

By modifying the tetrahedrality (the strength of the three body interactions) in the well-known Stillinger-Weber model for silicon, we study the diffusivity of a series of model liquids as a function of tetrahedrality and temperature at fixed pressure. Previous work has shown that at constant temperature, the diffusivity exhibits a maximum as a function of tetrahedrality, which we refer to as the diffusivity anomaly, in analogy with the well-known anomaly in water upon variation of pressure at constant temperature. We explore to what extent the structural and thermodynamic changes accompanying changes in the interaction potential can help rationalize the diffusivity anomaly, by employing the Rosenfeld relation between diffusivity and the excess entropy (over the ideal gas reference value), and the pair correlation entropy, which provides an approximation to the excess entropy in terms of the pair correlation function. We find that in the modified Stillinger-Weber liquids, the Rosenfeld relation works well above the melting temperatures but exhibits deviations below, with the deviations becoming smaller for smaller tetrahedrality. Further we find that both the excess entropy and the pair correlation entropy at constant temperature go through maxima as a function of the tetrahedrality, thus demonstrating the close relationship between structural, thermodynamic, and dynamical anomalies in the modified Stillinger-Weber liquids.

Assessing the Implications of Modified Nanomaterials in Bioassay Testing

EPA Science Inventory

As nanotechnology advances to product development, filling environmental health and safety knowledge gaps is critical. Nanotoxicology is over-generalized, provided the permutations of nanomaterial variants created by the classes of nanomaterials (carbonaceous, metals, quantum dot...

Eigensolutions, Shannon entropy and information energy for modified Tietz-Hua potential

NASA Astrophysics Data System (ADS)

Onate, C. A.; Onyeaju, M. C.; Ituen, E. E.; Ikot, A. N.; Ebomwonyi, O.; Okoro, J. O.; Dopamu, K. O.

2018-04-01

The Tietz-Hua potential is modified by the inclusion of De ( {{Ch - 1}/{1 - C_{h e^{{ - bh ( {r - re } )}} }}} )be^{{ - bh ( {r - re } )}} term to the Tietz-Hua potential model since a potential of such type is very good in the description and vibrational energy levels for diatomic molecules. The energy eigenvalues and the corresponding eigenfunctions are explicitly obtained using the methodology of parametric Nikiforov-Uvarov. By putting the potential parameter b = 0, in the modified Tietz-Hua potential quickly reduces to the Tietz-Hua potential. To show more applications of our work, we have computed the Shannon entropy and Information energy under the modified Tietz-Hua potential. However, the computation of the Shannon entropy and Information energy is an extension of the work of Falaye et al., who computed only the Fisher information under Tietz-Hua potential.

Generalized sample entropy analysis for traffic signals based on similarity measure

NASA Astrophysics Data System (ADS)

Shang, Du; Xu, Mengjia; Shang, Pengjian

2017-05-01

Sample entropy is a prevailing method used to quantify the complexity of a time series. In this paper a modified method of generalized sample entropy and surrogate data analysis is proposed as a new measure to assess the complexity of a complex dynamical system such as traffic signals. The method based on similarity distance presents a different way of signals patterns match showing distinct behaviors of complexity. Simulations are conducted over synthetic data and traffic signals for providing the comparative study, which is provided to show the power of the new method. Compared with previous sample entropy and surrogate data analysis, the new method has two main advantages. The first one is that it overcomes the limitation about the relationship between the dimension parameter and the length of series. The second one is that the modified sample entropy functions can be used to quantitatively distinguish time series from different complex systems by the similar measure.

The Contribution of the Activation Entropy to the Gas-Phase Stability of Modified Nucleic Acid Duplexes

NASA Astrophysics Data System (ADS)

Hari, Yvonne; Dugovič, Branislav; Istrate, Alena; Fignolé, Annabel; Leumann, Christian J.; Schürch, Stefan

2016-07-01

Tricyclo-DNA (tcDNA) is a sugar-modified analogue of DNA currently tested for the treatment of Duchenne muscular dystrophy in an antisense approach. Tandem mass spectrometry plays a key role in modern medical diagnostics and has become a widespread technique for the structure elucidation and quantification of antisense oligonucleotides. Herein, mechanistic aspects of the fragmentation of tcDNA are discussed, which lay the basis for reliable sequencing and quantification of the antisense oligonucleotide. Excellent selectivity of tcDNA for complementary RNA is demonstrated in direct competition experiments. Moreover, the kinetic stability and fragmentation pattern of matched and mismatched tcDNA heteroduplexes were investigated and compared with non-modified DNA and RNA duplexes. Although the separation of the constituting strands is the entropy-favored fragmentation pathway of all nucleic acid duplexes, it was found to be only a minor pathway of tcDNA duplexes. The modified hybrid duplexes preferentially undergo neutral base loss and backbone cleavage. This difference is due to the low activation entropy for the strand dissociation of modified duplexes that arises from the conformational constraint of the tc-sugar-moiety. The low activation entropy results in a relatively high free activation enthalpy for the dissociation comparable to the free activation enthalpy of the alternative reaction pathway, the release of a nucleobase. The gas-phase behavior of tcDNA duplexes illustrates the impact of the activation entropy on the fragmentation kinetics and suggests that tandem mass spectrometric experiments are not suited to determine the relative stability of different types of nucleic acid duplexes.

Permutation coding technique for image recognition systems.

PubMed

Kussul, Ernst M; Baidyk, Tatiana N; Wunsch, Donald C; Makeyev, Oleksandr; Martín, Anabel

2006-11-01

A feature extractor and neural classifier for image recognition systems are proposed. The proposed feature extractor is based on the concept of random local descriptors (RLDs). It is followed by the encoder that is based on the permutation coding technique that allows to take into account not only detected features but also the position of each feature on the image and to make the recognition process invariant to small displacements. The combination of RLDs and permutation coding permits us to obtain a sufficiently general description of the image to be recognized. The code generated by the encoder is used as an input data for the neural classifier. Different types of images were used to test the proposed image recognition system. It was tested in the handwritten digit recognition problem, the face recognition problem, and the microobject shape recognition problem. The results of testing are very promising. The error rate for the Modified National Institute of Standards and Technology (MNIST) database is 0.44% and for the Olivetti Research Laboratory (ORL) database it is 0.1%.

Comment on "Route from discreteness to the continuum for the Tsallis q -entropy"

NASA Astrophysics Data System (ADS)

Ou, Congjie; Abe, Sumiyoshi

2018-06-01

Several years ago, it had been discussed that nonlogarithmic entropies, such as the Tsallis q -entropy cannot be applied to systems with continuous variables. Now, in their recent paper [Phys. Rev. E 97, 012104 (2018), 10.1103/PhysRevE.97.012104], Oikonomou and Bagci have modified the form of the q -entropy for discrete variables in such a way that its continuum limit exists. Here, it is shown that this modification violates the expandability property of entropy, and their work is actually supporting evidence for the absence of the q -entropy for systems with continuous variables.

Complexity of heart rate fluctuations in near-term sheep and human fetuses during sleep.

PubMed

Frank, Birgit; Frasch, Martin G; Schneider, Uwe; Roedel, Marcus; Schwab, Matthias; Hoyer, Dirk

2006-10-01

We investigated how the complexity of fetal heart rate fluctuations (fHRF) is related to the sleep states in sheep and human fetuses. The complexity as a function of time scale for fetal heart rate data for 7 sheep and 27 human fetuses was estimated in rapid eye movement (REM) and non-REM sleep by means of permutation entropy and the associated Kullback-Leibler entropy. We found that in humans, fHRF complexity is higher in non-REM than REM sleep, whereas in sheep this relationship is reversed. To show this relation, choice of the appropriate time scale is crucial. In sheep fetuses, we found differences in the complexity of fHRF between REM and non-REM sleep only for larger time scales (above 2.5 s), whereas in human fetuses the complexity was clearly different between REM and non-REM sleep over the whole range of time scales. This may be due to inherent time scales of complexity, which reflect species-specific functions of the autonomic nervous system. Such differences have to be considered when animal data are translated to the human situation.

A modified belief entropy in Dempster-Shafer framework.

PubMed

Zhou, Deyun; Tang, Yongchuan; Jiang, Wen

2017-01-01

How to quantify the uncertain information in the framework of Dempster-Shafer evidence theory is still an open issue. Quite a few uncertainty measures have been proposed in Dempster-Shafer framework, however, the existing studies mainly focus on the mass function itself, the available information represented by the scale of the frame of discernment (FOD) in the body of evidence is ignored. Without taking full advantage of the information in the body of evidence, the existing methods are somehow not that efficient. In this paper, a modified belief entropy is proposed by considering the scale of FOD and the relative scale of a focal element with respect to FOD. Inspired by Deng entropy, the new belief entropy is consistent with Shannon entropy in the sense of probability consistency. What's more, with less information loss, the new measure can overcome the shortage of some other uncertainty measures. A few numerical examples and a case study are presented to show the efficiency and superiority of the proposed method.

A modified belief entropy in Dempster-Shafer framework

PubMed Central

Zhou, Deyun; Jiang, Wen

2017-01-01

How to quantify the uncertain information in the framework of Dempster-Shafer evidence theory is still an open issue. Quite a few uncertainty measures have been proposed in Dempster-Shafer framework, however, the existing studies mainly focus on the mass function itself, the available information represented by the scale of the frame of discernment (FOD) in the body of evidence is ignored. Without taking full advantage of the information in the body of evidence, the existing methods are somehow not that efficient. In this paper, a modified belief entropy is proposed by considering the scale of FOD and the relative scale of a focal element with respect to FOD. Inspired by Deng entropy, the new belief entropy is consistent with Shannon entropy in the sense of probability consistency. What’s more, with less information loss, the new measure can overcome the shortage of some other uncertainty measures. A few numerical examples and a case study are presented to show the efficiency and superiority of the proposed method. PMID:28481914

Firefly algorithm for cardinality constrained mean-variance portfolio optimization problem with entropy diversity constraint.

PubMed

Bacanin, Nebojsa; Tuba, Milan

2014-01-01

Portfolio optimization (selection) problem is an important and hard optimization problem that, with the addition of necessary realistic constraints, becomes computationally intractable. Nature-inspired metaheuristics are appropriate for solving such problems; however, literature review shows that there are very few applications of nature-inspired metaheuristics to portfolio optimization problem. This is especially true for swarm intelligence algorithms which represent the newer branch of nature-inspired algorithms. No application of any swarm intelligence metaheuristics to cardinality constrained mean-variance (CCMV) portfolio problem with entropy constraint was found in the literature. This paper introduces modified firefly algorithm (FA) for the CCMV portfolio model with entropy constraint. Firefly algorithm is one of the latest, very successful swarm intelligence algorithm; however, it exhibits some deficiencies when applied to constrained problems. To overcome lack of exploration power during early iterations, we modified the algorithm and tested it on standard portfolio benchmark data sets used in the literature. Our proposed modified firefly algorithm proved to be better than other state-of-the-art algorithms, while introduction of entropy diversity constraint further improved results.

Firefly Algorithm for Cardinality Constrained Mean-Variance Portfolio Optimization Problem with Entropy Diversity Constraint

PubMed Central

2014-01-01

Portfolio optimization (selection) problem is an important and hard optimization problem that, with the addition of necessary realistic constraints, becomes computationally intractable. Nature-inspired metaheuristics are appropriate for solving such problems; however, literature review shows that there are very few applications of nature-inspired metaheuristics to portfolio optimization problem. This is especially true for swarm intelligence algorithms which represent the newer branch of nature-inspired algorithms. No application of any swarm intelligence metaheuristics to cardinality constrained mean-variance (CCMV) portfolio problem with entropy constraint was found in the literature. This paper introduces modified firefly algorithm (FA) for the CCMV portfolio model with entropy constraint. Firefly algorithm is one of the latest, very successful swarm intelligence algorithm; however, it exhibits some deficiencies when applied to constrained problems. To overcome lack of exploration power during early iterations, we modified the algorithm and tested it on standard portfolio benchmark data sets used in the literature. Our proposed modified firefly algorithm proved to be better than other state-of-the-art algorithms, while introduction of entropy diversity constraint further improved results. PMID:24991645

From atomic structure to excess entropy: a neutron diffraction and density functional theory study of CaO-Al2O3-SiO2 melts

NASA Astrophysics Data System (ADS)

Liu, Maoyuan; Jacob, Aurélie; Schmetterer, Clemens; Masset, Patrick J.; Hennet, Louis; Fischer, Henry E.; Kozaily, Jad; Jahn, Sandro; Gray-Weale, Angus

2016-04-01

Calcium aluminosilicate \\text{CaO}-\\text{A}{{\\text{l}}2}{{\\text{O}}3}-\\text{Si}{{\\text{O}}2} (CAS) melts with compositions {{≤ft(\\text{CaO}-\\text{Si}{{\\text{O}}2}\\right)}x}{{≤ft(\\text{A}{{\\text{l}}2}{{\\text{O}}3}\\right)}1-x} for x  <  0.5 and {{≤ft(\\text{A}{{\\text{l}}2}{{\\text{O}}3}\\right)}x}{{≤ft(\\text{Si}{{\\text{O}}2}\\right)}1-x} for x≥slant 0.5 are studied using neutron diffraction with aerodynamic levitation and density functional theory molecular dynamics modelling. Simulated structure factors are found to be in good agreement with experimental structure factors. Local atomic structures from simulations reveal the role of calcium cations as a network modifier, and aluminium cations as a non-tetrahedral network former. Distributions of tetrahedral order show that an increasing concentration of the network former Al increases entropy, while an increasing concentration of the network modifier Ca decreases entropy. This trend is opposite to the conventional understanding that increasing amounts of network former should increase order in the network liquid, and so decrease entropy. The two-body correlation entropy S 2 is found to not correlate with the excess entropy values obtained from thermochemical databases, while entropies including higher-order correlations such as tetrahedral order, O-M-O or M-O-M bond angles and Q N environments show a clear linear correlation between computed entropy and database excess entropy. The possible relationship between atomic structures and excess entropy is discussed.

Statistical Entropy of Dirac Field Outside RN Black Hole and Modified Density Equation

NASA Astrophysics Data System (ADS)

Cao, Fei; He, Feng

2012-02-01

Statistical entropy of Dirac field in Reissner-Nordstrom black hole space-time is computed by state density equation corrected by the generalized uncertainty principle to all orders in Planck length and WKB approximation. The result shows that the statistical entropy is proportional to the horizon area but the present result is convergent without any artificial cutoff.

An entropy correction method for unsteady full potential flows with strong shocks

NASA Technical Reports Server (NTRS)

Whitlow, W., Jr.; Hafez, M. M.; Osher, S. J.

1986-01-01

An entropy correction method for the unsteady full potential equation is presented. The unsteady potential equation is modified to account for entropy jumps across shock waves. The conservative form of the modified equation is solved in generalized coordinates using an implicit, approximate factorization method. A flux-biasing differencing method, which generates the proper amounts of artificial viscosity in supersonic regions, is used to discretize the flow equations in space. Comparisons between the present method and solutions of the Euler equations and between the present method and experimental data are presented. The comparisons show that the present method more accurately models solutions of the Euler equations and experiment than does the isentropic potential formulation.

Possible signatures of dissipation from time-series analysis techniques using a turbulent laboratory magnetohydrodynamic plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaffner, D. A.; Brown, M. R.; Rock, A. B.

The frequency spectrum of magnetic fluctuations as measured on the Swarthmore Spheromak Experiment is broadband and exhibits a nearly Kolmogorov 5/3 scaling. It features a steepening region which is indicative of dissipation of magnetic fluctuation energy similar to that observed in fluid and magnetohydrodynamic turbulence systems. Two non-spectrum based time-series analysis techniques are implemented on this data set in order to seek other possible signatures of turbulent dissipation beyond just the steepening of fluctuation spectra. Presented here are results for the flatness, permutation entropy, and statistical complexity, each of which exhibits a particular character at spectral steepening scales which canmore » then be compared to the behavior of the frequency spectrum.« less

An entropy-based nonparametric test for the validation of surrogate endpoints.

PubMed

Miao, Xiaopeng; Wang, Yong-Cheng; Gangopadhyay, Ashis

2012-06-30

We present a nonparametric test to validate surrogate endpoints based on measure of divergence and random permutation. This test is a proposal to directly verify the Prentice statistical definition of surrogacy. The test does not impose distributional assumptions on the endpoints, and it is robust to model misspecification. Our simulation study shows that the proposed nonparametric test outperforms the practical test of the Prentice criterion in terms of both robustness of size and power. We also evaluate the performance of three leading methods that attempt to quantify the effect of surrogate endpoints. The proposed method is applied to validate magnetic resonance imaging lesions as the surrogate endpoint for clinical relapses in a multiple sclerosis trial. Copyright © 2012 John Wiley & Sons, Ltd.

Computer program for calculation of real gas turbulent boundary layers with variable edge entropy

NASA Technical Reports Server (NTRS)

Boney, L. R.

1974-01-01

A user's manual for a computer program which calculates real gas turbulent boundary layers with variable edge entropy on a blunt cone or flat plate at zero angle of attack is presented. An integral method is used. The method includes the effect of real gas in thermodynamic equilibrium and variable edge entropy. A modified Crocco enthalpy velocity relationship is used for the enthalpy profiles and an empirical correlation of the N-power law profile is used for the velocity profile. The skin-friction-coefficient expressions of Spalding and Chi and Van Driest are used in the solution of the momentum equation and in the heat-transfer predictions that use several modified forms of Reynolds analogy.

Full spinal cord regeneration after total transection is not possible due to entropy change.

PubMed

Zielinski, P; Sokal, P

2016-09-01

Transected spinal cord regeneration is a main challenge of regenerative medicine. The mainstream of research is focused on the promotion of spinal axons growth, which is strongly inhibited in mammals. Assuming that the inhibition of the axonal growth may be ever overcome, the complexity of neural reconnections may be the second serious stand to overcome. Peripheral nerve axons regeneration seem to form a random pattern of their targets reconnections. The hypothesis is that due to the laws of entropy or irreversible information loss the full spinal cord restoration after the transection is not possible. The hypothesis is discussed based on several assumptions. Simplifying the dissertation spinal cord is represented by 2millions of pyramidal axons. After the transection each of these axons has to make a growth and reconnect with exactly matching targets below the transection, in the same number. Axons are guided by neurotrophic factors and afterwards reconnected with neuroplasticity mechanisms. Assuming random reconnections, there are 2,000,000! permutations [Formula: see text] , therefore the chance of ideally random but correct reconnection of pyramidal axons with adequate targets is 1/2,000,000!. Apart from pyramidal axons, there are other axons, like extrapyramidal, sensory and associative. Empirical data and analysis of neurotrophic factors and organogenesis mechanisms may seem to slightly contradict the hypothesis, but strictly adhering to the second law of thermodynamics and entropy laws the full restoration of the transected cord may never be possible. Copyright © 2016 Elsevier Ltd. All rights reserved.

On holographic Rényi entropy in some modified theories of gravity

NASA Astrophysics Data System (ADS)

Dey, Anshuman; Roy, Pratim; Sarkar, Tapobrata

2018-04-01

We perform a detailed analysis of holographic entanglement Rényi entropy in some modified theories of gravity with four dimensional conformal field theory duals. First, we construct perturbative black hole solutions in a recently proposed model of Einsteinian cubic gravity in five dimensions, and compute the Rényi entropy as well as the scaling dimension of the twist operators in the dual field theory. Consistency of these results are verified from the AdS/CFT correspondence, via a corresponding computation of the Weyl anomaly on the gravity side. Similar analyses are then carried out for three other examples of modified gravity in five dimensions that include a chemical potential, namely Born-Infeld gravity, charged quasi-topological gravity and a class of Weyl corrected gravity theories with a gauge field, with the last example being treated perturbatively. Some interesting bounds in the dual conformal field theory parameters in quasi-topological gravity are pointed out. We also provide arguments on the validity of our perturbative analysis, whenever applicable.

Entropy corrected holographic dark energy models in modified gravity

NASA Astrophysics Data System (ADS)

Jawad, Abdul; Azhar, Nadeem; Rani, Shamaila

We consider the power law and the entropy corrected holographic dark energy (HDE) models with Hubble horizon in the dynamical Chern-Simons modified gravity. We explore various cosmological parameters and planes in this framework. The Hubble parameter lies within the consistent range at the present and later epoch for both entropy corrected models. The deceleration parameter explains the accelerated expansion of the universe. The equation of state (EoS) parameter corresponds to quintessence and cold dark matter (ΛCDM) limit. The ωΛ-ωΛ‧ approaches to ΛCDM limit and freezing region in both entropy corrected models. The statefinder parameters are consistent with ΛCDM limit and dark energy (DE) models. The generalized second law of thermodynamics remain valid in all cases of interacting parameter. It is interesting to mention here that our results of Hubble, EoS parameter and ωΛ-ωΛ‧ plane show consistency with the present observations like Planck, WP, BAO, H0, SNLS and nine-year WMAP.

Time-delay signature of chaos in 1550 nm VCSELs with variable-polarization FBG feedback.

PubMed

Li, Yan; Wu, Zheng-Mao; Zhong, Zhu-Qiang; Yang, Xian-Jie; Mao, Song; Xia, Guang-Qiong

2014-08-11

Based on the framework of spin-flip model (SFM), the output characteristics of a 1550 nm vertical-cavity surface-emitting laser (VCSEL) subject to variable-polarization fiber Bragg grating (FBG) feedback (VPFBGF) have been investigated. With the aid of the self-correlation function (SF) and the permutation entropy (PE) function, the time-delay signature (TDS) of chaos in the VPFBGF-VCSEL is evaluated, and then the influences of the operation parameters on the TDS of chaos are analyzed. The results show that the TDS of chaos can be suppressed efficiently through selecting suitable coupling coefficient and feedback rate of the FBG, and is weaker than that of chaos generated by traditional variable-polarization mirror feedback VCSELs (VPMF-VCSELs) or polarization-preserved FBG feedback VCSELs (PPFBGF-VCSELs).

Tree tensor network approach to simulating Shor's algorithm

NASA Astrophysics Data System (ADS)

Dumitrescu, Eugene

2017-12-01

Constructively simulating quantum systems furthers our understanding of qualitative and quantitative features which may be analytically intractable. In this paper, we directly simulate and explore the entanglement structure present in the paradigmatic example for exponential quantum speedups: Shor's algorithm. To perform our simulation, we construct a dynamic tree tensor network which manifestly captures two salient circuit features for modular exponentiation. These are the natural two-register bipartition and the invariance of entanglement with respect to permutations of the top-register qubits. Our construction help identify the entanglement entropy properties, which we summarize by a scaling relation. Further, the tree network is efficiently projected onto a matrix product state from which we efficiently execute the quantum Fourier transform. Future simulation of quantum information states with tensor networks exploiting circuit symmetries is discussed.

Entanglement entropy in integrable field theories with line defects II. Non-topological defect

NASA Astrophysics Data System (ADS)

Jiang, Yunfeng

2017-08-01

This is the second part of two papers where we study the effect of integrable line defects on bipartite entanglement entropy in integrable field theories. In this paper, we consider non-topological line defects in Ising field theory. We derive an infinite series expression for the entanglement entropy and show that both the UV and IR limits of the bulk entanglement entropy are modified by the line defect. In the UV limit, we give an infinite series expression for the coefficient in front of the logarithmic divergence and the exact defect g-function. By tuning the defect to be purely transmissive and reflective, we recover correctly the entanglement entropy of the bulk and with integrable boundary respectively.

Repelling Point Bosons

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGuire, J. B.

2011-12-01

There is a body of conventional wisdom that holds that a solvable quantum problem, by virtue of its solvability, is pathological and thus irrelevant. It has been difficult to refute this view owing to the paucity of theoretical constructs and experimental results. Recent experiments involving equivalent ions trapped in a spatial conformation of extreme anisotropic confinement (longitudinal extension tens, hundreds or even thousands of times transverse extension) have modified the view of relevancy, and it is now possible to consider systems previously thought pathological, in particular point Bosons that repel in one dimension. It has been difficult for the experimentalistsmore » to utilize existing theory, mainly due to long-standing theoretical misunderstanding of the relevance of the permutation group, in particular the non-commutativity of translations (periodicity) and transpositions (permutation). This misunderstanding is most easily rectified in the case of repelling Bosons.« less

Tsallis and Kaniadakis statistics from a point of view of the holographic equipartition law

NASA Astrophysics Data System (ADS)

Abreu, Everton M. C.; Ananias Neto, Jorge; Mendes, Albert C. R.; Bonilla, Alexander

2018-02-01

In this work, we have illustrated the difference between both Tsallis and Kaniadakis entropies through cosmological models obtained from the formalism proposed by Padmanabhan, which is called holographic equipartition law. Similarly to the formalism proposed by Komatsu, we have obtained an extra driving constant term in the Friedmann equation if we deform the Tsallis entropy by Kaniadakis' formalism. We have considered initially Tsallis entropy as the black-hole (BH) area entropy. This constant term may lead the universe to be in an accelerated or decelerated mode. On the other hand, if we start with the Kaniadakis entropy as the BH area entropy and then by modifying the Kappa expression by Tsallis' formalism, the same absolute value but with opposite sign is obtained. In an opposite limit, no driving inflation term of the early universe was derived from both deformations.

Relative entropy of steering: on its definition and properties

NASA Astrophysics Data System (ADS)

Kaur, Eneet; Wilde, Mark M.

2017-11-01

In Gallego and Aolita (2015 Phys. Rev. X 5 041008), the authors proposed a definition for the relative entropy of steering and showed that the resulting quantity is a convex steering monotone. Here we advocate for a different definition for relative entropy of steering, based on well grounded concerns coming from quantum Shannon theory. We prove that this modified relative entropy of steering is a convex steering monotone. Furthermore, we establish that it is uniformly continuous and faithful, in both cases giving quantitative bounds that should be useful in applications. We also consider a restricted relative entropy of steering which is relevant for the case in which the free operations in the resource theory of steering have a more restricted form (the restricted operations could be more relevant in practical scenarios). The restricted relative entropy of steering is convex, monotone with respect to these restricted operations, uniformly continuous, and faithful.

Decreased Complexity in Alzheimer's Disease: Resting-State fMRI Evidence of Brain Entropy Mapping.

PubMed

Wang, Bin; Niu, Yan; Miao, Liwen; Cao, Rui; Yan, Pengfei; Guo, Hao; Li, Dandan; Guo, Yuxiang; Yan, Tianyi; Wu, Jinglong; Xiang, Jie; Zhang, Hui

2017-01-01

Alzheimer's disease (AD) is a frequently observed, irreversible brain function disorder among elderly individuals. Resting-state functional magnetic resonance imaging (rs-fMRI) has been introduced as an alternative approach to assessing brain functional abnormalities in AD patients. However, alterations in the brain rs-fMRI signal complexities in mild cognitive impairment (MCI) and AD patients remain unclear. Here, we described the novel application of permutation entropy (PE) to investigate the abnormal complexity of rs-fMRI signals in MCI and AD patients. The rs-fMRI signals of 30 normal controls (NCs), 33 early MCI (EMCI), 32 late MCI (LMCI), and 29 AD patients were obtained from the Alzheimer's disease Neuroimaging Initiative (ADNI) database. After preprocessing, whole-brain entropy maps of the four groups were extracted and subjected to Gaussian smoothing. We performed a one-way analysis of variance (ANOVA) on the brain entropy maps of the four groups. The results after adjusting for age and sex differences together revealed that the patients with AD exhibited lower complexity than did the MCI and NC controls. We found five clusters that exhibited significant differences and were distributed primarily in the occipital, frontal, and temporal lobes. The average PE of the five clusters exhibited a decreasing trend from MCI to AD. The AD group exhibited the least complexity. Additionally, the average PE of the five clusters was significantly positively correlated with the Mini-Mental State Examination (MMSE) scores and significantly negatively correlated with Functional Assessment Questionnaire (FAQ) scores and global Clinical Dementia Rating (CDR) scores in the patient groups. Significant correlations were also found between the PE and regional homogeneity (ReHo) in the patient groups. These results indicated that declines in PE might be related to changes in regional functional homogeneity in AD. These findings suggested that complexity analyses using PE in rs-fMRI signals can provide important information about the fMRI characteristics of cognitive impairments in MCI and AD.

Decreased Complexity in Alzheimer's Disease: Resting-State fMRI Evidence of Brain Entropy Mapping

PubMed Central

Wang, Bin; Niu, Yan; Miao, Liwen; Cao, Rui; Yan, Pengfei; Guo, Hao; Li, Dandan; Guo, Yuxiang; Yan, Tianyi; Wu, Jinglong; Xiang, Jie; Zhang, Hui

2017-01-01

Alzheimer's disease (AD) is a frequently observed, irreversible brain function disorder among elderly individuals. Resting-state functional magnetic resonance imaging (rs-fMRI) has been introduced as an alternative approach to assessing brain functional abnormalities in AD patients. However, alterations in the brain rs-fMRI signal complexities in mild cognitive impairment (MCI) and AD patients remain unclear. Here, we described the novel application of permutation entropy (PE) to investigate the abnormal complexity of rs-fMRI signals in MCI and AD patients. The rs-fMRI signals of 30 normal controls (NCs), 33 early MCI (EMCI), 32 late MCI (LMCI), and 29 AD patients were obtained from the Alzheimer's disease Neuroimaging Initiative (ADNI) database. After preprocessing, whole-brain entropy maps of the four groups were extracted and subjected to Gaussian smoothing. We performed a one-way analysis of variance (ANOVA) on the brain entropy maps of the four groups. The results after adjusting for age and sex differences together revealed that the patients with AD exhibited lower complexity than did the MCI and NC controls. We found five clusters that exhibited significant differences and were distributed primarily in the occipital, frontal, and temporal lobes. The average PE of the five clusters exhibited a decreasing trend from MCI to AD. The AD group exhibited the least complexity. Additionally, the average PE of the five clusters was significantly positively correlated with the Mini-Mental State Examination (MMSE) scores and significantly negatively correlated with Functional Assessment Questionnaire (FAQ) scores and global Clinical Dementia Rating (CDR) scores in the patient groups. Significant correlations were also found between the PE and regional homogeneity (ReHo) in the patient groups. These results indicated that declines in PE might be related to changes in regional functional homogeneity in AD. These findings suggested that complexity analyses using PE in rs-fMRI signals can provide important information about the fMRI characteristics of cognitive impairments in MCI and AD. PMID:29209199

Comparative analysis of electric field influence on the quantum wells with different boundary conditions.: I. Energy spectrum, quantum information entropy and polarization.

PubMed

Olendski, Oleg

2015-04-01

Analytical solutions of the Schrödinger equation for the one-dimensional quantum well with all possible permutations of the Dirichlet and Neumann boundary conditions (BCs) in perpendicular to the interfaces uniform electric field [Formula: see text] are used for the comparative investigation of their interaction and its influence on the properties of the system. Limiting cases of the weak and strong voltages allow an easy mathematical treatment and its clear physical explanation; in particular, for the small [Formula: see text], the perturbation theory derives for all geometries a linear dependence of the polarization on the field with the BC-dependent proportionality coefficient being positive (negative) for the ground (excited) states. Simple two-level approximation elementary explains the negative polarizations as a result of the field-induced destructive interference of the unperturbed modes and shows that in this case the admixture of only the neighboring states plays a dominant role. Different magnitudes of the polarization for different BCs in this regime are explained physically and confirmed numerically. Hellmann-Feynman theorem reveals a fundamental relation between the polarization and the speed of the energy change with the field. It is proved that zero-voltage position entropies [Formula: see text] are BC independent and for all states but the ground Neumann level (which has [Formula: see text]) are equal to [Formula: see text] while the momentum entropies [Formula: see text] depend on the edge requirements and the level. Varying electric field changes position and momentum entropies in the opposite directions such that the entropic uncertainty relation is satisfied. Other physical quantities such as the BC-dependent zero-energy and zero-polarization fields are also studied both numerically and analytically. Applications to different branches of physics, such as ocean fluid dynamics and atmospheric and metallic waveguide electrodynamics, are discussed.

Correntropy-based partial directed coherence for testing multivariate Granger causality in nonlinear processes

NASA Astrophysics Data System (ADS)

Kannan, Rohit; Tangirala, Arun K.

2014-06-01

Identification of directional influences in multivariate systems is of prime importance in several applications of engineering and sciences such as plant topology reconstruction, fault detection and diagnosis, and neurosciences. A spectrum of related directionality measures, ranging from linear measures such as partial directed coherence (PDC) to nonlinear measures such as transfer entropy, have emerged over the past two decades. The PDC-based technique is simple and effective, but being a linear directionality measure has limited applicability. On the other hand, transfer entropy, despite being a robust nonlinear measure, is computationally intensive and practically implementable only for bivariate processes. The objective of this work is to develop a nonlinear directionality measure, termed as KPDC, that possesses the simplicity of PDC but is still applicable to nonlinear processes. The technique is founded on a nonlinear measure called correntropy, a recently proposed generalized correlation measure. The proposed method is equivalent to constructing PDC in a kernel space where the PDC is estimated using a vector autoregressive model built on correntropy. A consistent estimator of the KPDC is developed and important theoretical results are established. A permutation scheme combined with the sequential Bonferroni procedure is proposed for testing hypothesis on absence of causality. It is demonstrated through several case studies that the proposed methodology effectively detects Granger causality in nonlinear processes.

Phase transitions between lower and higher level management learning in times of crisis: an experimental study based on synergetics.

PubMed

Liening, Andreas; Strunk, Guido; Mittelstadt, Ewald

2013-10-01

Much has been written about the differences between single- and double-loop learning, or more general between lower level and higher level learning. Especially in times of a fundamental crisis, a transition between lower and higher level learning would be an appropriate reaction to a challenge coming entirely out of the dark. However, so far there is no quantitative method to monitor such a transition. Therefore we introduce theory and methods of synergetics and present results from an experimental study based on the simulation of a crisis within a business simulation game. Hypothesized critical fluctuations - as a marker for so-called phase transitions - have been assessed with permutation entropy. Results show evidence for a phase transition during the crisis, which can be interpreted as a transition between lower and higher level learning.

Thermodynamic geometry for a non-extensive ideal gas

NASA Astrophysics Data System (ADS)

López, J. L.; Obregón, O.; Torres-Arenas, J.

2018-05-01

A generalized entropy arising in the context of superstatistics is applied to an ideal gas. The curvature scalar associated to the thermodynamic space generated by this modified entropy is calculated using two formalisms of the geometric approach to thermodynamics. By means of the curvature/interaction hypothesis of the geometric approach to thermodynamic geometry it is found that as a consequence of considering a generalized statistics, an effective interaction arises but the interaction is not enough to generate a phase transition. This generalized entropy seems to be relevant in confinement or in systems with not so many degrees of freedom, so it could be interesting to use such entropies to characterize the thermodynamics of small systems.

Novel permutation measures for image encryption algorithms

NASA Astrophysics Data System (ADS)

Abd-El-Hafiz, Salwa K.; AbdElHaleem, Sherif H.; Radwan, Ahmed G.

2016-10-01

This paper proposes two measures for the evaluation of permutation techniques used in image encryption. First, a general mathematical framework for describing the permutation phase used in image encryption is presented. Using this framework, six different permutation techniques, based on chaotic and non-chaotic generators, are described. The two new measures are, then, introduced to evaluate the effectiveness of permutation techniques. These measures are (1) Percentage of Adjacent Pixels Count (PAPC) and (2) Distance Between Adjacent Pixels (DBAP). The proposed measures are used to evaluate and compare the six permutation techniques in different scenarios. The permutation techniques are applied on several standard images and the resulting scrambled images are analyzed. Moreover, the new measures are used to compare the permutation algorithms on different matrix sizes irrespective of the actual parameters used in each algorithm. The analysis results show that the proposed measures are good indicators of the effectiveness of the permutation technique.

Blocks in cycles and k-commuting permutations.

PubMed

Moreno, Rutilo; Rivera, Luis Manuel

2016-01-01

We introduce and study k -commuting permutations. One of our main results is a characterization of permutations that k -commute with a given permutation. Using this characterization, we obtain formulas for the number of permutations that k -commute with a permutation [Formula: see text], for some cycle types of [Formula: see text]. Our enumerative results are related with integer sequences in "The On-line Encyclopedia of Integer Sequences", and in some cases provide new interpretations for such sequences.

Fast algorithms for transforming back and forth between a signed permutation and its equivalent simple permutation.

PubMed

Gog, Simon; Bader, Martin

2008-10-01

The problem of sorting signed permutations by reversals is a well-studied problem in computational biology. The first polynomial time algorithm was presented by Hannenhalli and Pevzner in 1995. The algorithm was improved several times, and nowadays the most efficient algorithm has a subquadratic running time. Simple permutations played an important role in the development of these algorithms. Although the latest result of Tannier et al. does not require simple permutations, the preliminary version of their algorithm as well as the first polynomial time algorithm of Hannenhalli and Pevzner use the structure of simple permutations. More precisely, the latter algorithms require a precomputation that transforms a permutation into an equivalent simple permutation. To the best of our knowledge, all published algorithms for this transformation have at least a quadratic running time. For further investigations on genome rearrangement problems, the existence of a fast algorithm for the transformation could be crucial. Another important task is the back transformation, i.e. if we have a sorting on the simple permutation, transform it into a sorting on the original permutation. Again, the naive approach results in an algorithm with quadratic running time. In this paper, we present a linear time algorithm for transforming a permutation into an equivalent simple permutation, and an O(n log n) algorithm for the back transformation of the sorting sequence.

A Random Variable Related to the Inversion Vector of a Partial Random Permutation

ERIC Educational Resources Information Center

Laghate, Kavita; Deshpande, M. N.

2005-01-01

In this article, we define the inversion vector of a permutation of the integers 1, 2,..., n. We set up a particular kind of permutation, called a partial random permutation. The sum of the elements of the inversion vector of such a permutation is a random variable of interest.

A transposase strategy for creating libraries of circularly permuted proteins.

PubMed

Mehta, Manan M; Liu, Shirley; Silberg, Jonathan J

2012-05-01

A simple approach for creating libraries of circularly permuted proteins is described that is called PERMutation Using Transposase Engineering (PERMUTE). In PERMUTE, the transposase MuA is used to randomly insert a minitransposon that can function as a protein expression vector into a plasmid that contains the open reading frame (ORF) being permuted. A library of vectors that express different permuted variants of the ORF-encoded protein is created by: (i) using bacteria to select for target vectors that acquire an integrated minitransposon; (ii) excising the ensemble of ORFs that contain an integrated minitransposon from the selected vectors; and (iii) circularizing the ensemble of ORFs containing integrated minitransposons using intramolecular ligation. Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods. In addition, selection of this library for variants that complement the growth of Escherichia coli with a temperature-sensitive AK identified functional proteins with novel architectures, suggesting that PERMUTE will be useful for the directed evolution of proteins with new functions.

A transposase strategy for creating libraries of circularly permuted proteins

PubMed Central

Mehta, Manan M.; Liu, Shirley; Silberg, Jonathan J.

2012-01-01

A simple approach for creating libraries of circularly permuted proteins is described that is called PERMutation Using Transposase Engineering (PERMUTE). In PERMUTE, the transposase MuA is used to randomly insert a minitransposon that can function as a protein expression vector into a plasmid that contains the open reading frame (ORF) being permuted. A library of vectors that express different permuted variants of the ORF-encoded protein is created by: (i) using bacteria to select for target vectors that acquire an integrated minitransposon; (ii) excising the ensemble of ORFs that contain an integrated minitransposon from the selected vectors; and (iii) circularizing the ensemble of ORFs containing integrated minitransposons using intramolecular ligation. Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods. In addition, selection of this library for variants that complement the growth of Escherichia coli with a temperature-sensitive AK identified functional proteins with novel architectures, suggesting that PERMUTE will be useful for the directed evolution of proteins with new functions. PMID:22319214

Bootstrapping on Undirected Binary Networks Via Statistical Mechanics

NASA Astrophysics Data System (ADS)

Fushing, Hsieh; Chen, Chen; Liu, Shan-Yu; Koehl, Patrice

2014-09-01

We propose a new method inspired from statistical mechanics for extracting geometric information from undirected binary networks and generating random networks that conform to this geometry. In this method an undirected binary network is perceived as a thermodynamic system with a collection of permuted adjacency matrices as its states. The task of extracting information from the network is then reformulated as a discrete combinatorial optimization problem of searching for its ground state. To solve this problem, we apply multiple ensembles of temperature regulated Markov chains to establish an ultrametric geometry on the network. This geometry is equipped with a tree hierarchy that captures the multiscale community structure of the network. We translate this geometry into a Parisi adjacency matrix, which has a relative low energy level and is in the vicinity of the ground state. The Parisi adjacency matrix is then further optimized by making block permutations subject to the ultrametric geometry. The optimal matrix corresponds to the macrostate of the original network. An ensemble of random networks is then generated such that each of these networks conforms to this macrostate; the corresponding algorithm also provides an estimate of the size of this ensemble. By repeating this procedure at different scales of the ultrametric geometry of the network, it is possible to compute its evolution entropy, i.e. to estimate the evolution of its complexity as we move from a coarse to a fine description of its geometric structure. We demonstrate the performance of this method on simulated as well as real data networks.

Entropy stable high order discontinuous Galerkin methods for ideal compressible MHD on structured meshes

NASA Astrophysics Data System (ADS)

Liu, Yong; Shu, Chi-Wang; Zhang, Mengping

2018-02-01

We present a discontinuous Galerkin (DG) scheme with suitable quadrature rules [15] for ideal compressible magnetohydrodynamic (MHD) equations on structural meshes. The semi-discrete scheme is analyzed to be entropy stable by using the symmetrizable version of the equations as introduced by Godunov [32], the entropy stable DG framework with suitable quadrature rules [15], the entropy conservative flux in [14] inside each cell and the entropy dissipative approximate Godunov type numerical flux at cell interfaces to make the scheme entropy stable. The main difficulty in the generalization of the results in [15] is the appearance of the non-conservative "source terms" added in the modified MHD model introduced by Godunov [32], which do not exist in the general hyperbolic system studied in [15]. Special care must be taken to discretize these "source terms" adequately so that the resulting DG scheme satisfies entropy stability. Total variation diminishing / bounded (TVD/TVB) limiters and bound-preserving limiters are applied to control spurious oscillations. We demonstrate the accuracy and robustness of this new scheme on standard MHD examples.

Examination of polymorphic glutathione S-transferase (GST) genes, tobacco smoking and prostate cancer risk among Men of African Descent: A case-control study

PubMed Central

2009-01-01

Background Polymorphisms in glutathione S-transferase (GST) genes may influence response to oxidative stress and modify prostate cancer (PCA) susceptibility. These enzymes generally detoxify endogenous and exogenous agents, but also participate in the activation and inactivation of oxidative metabolites that may contribute to PCA development. Genetic variations within selected GST genes may influence PCA risk following exposure to carcinogen compounds found in cigarette smoke and decreased the ability to detoxify them. Thus, we evaluated the effects of polymorphic GSTs (M1, T1, and P1) alone and combined with cigarette smoking on PCA susceptibility. Methods In order to evaluate the effects of GST polymorphisms in relation to PCA risk, we used TaqMan allelic discrimination assays along with a multi-faceted statistical strategy involving conventional and advanced statistical methodologies (e.g., Multifactor Dimensionality Reduction and Interaction Graphs). Genetic profiles collected from 873 men of African-descent (208 cases and 665 controls) were utilized to systematically evaluate the single and joint modifying effects of GSTM1 and GSTT1 gene deletions, GSTP1 105 Val and cigarette smoking on PCA risk. Results We observed a moderately significant association between risk among men possessing at least one variant GSTP1 105 Val allele (OR = 1.56; 95%CI = 0.95-2.58; p = 0.049), which was confirmed by MDR permutation testing (p = 0.001). We did not observe any significant single gene effects among GSTM1 (OR = 1.08; 95%CI = 0.65-1.82; p = 0.718) and GSTT1 (OR = 1.15; 95%CI = 0.66-2.02; p = 0.622) on PCA risk among all subjects. Although the GSTM1-GSTP1 pairwise combination was selected as the best two factor LR and MDR models (p = 0.01), assessment of the hierarchical entropy graph suggested that the observed synergistic effect was primarily driven by the GSTP1 Val marker. Notably, the GSTM1-GSTP1 axis did not provide additional information gain when compared to either loci alone based on a hierarchical entropy algorithm and graph. Smoking status did not significantly modify the relationship between the GST SNPs and PCA. Conclusion A moderately significant association was observed between PCA risk and men possessing at least one variant GSTP1 105 Val allele (p = 0.049) among men of African descent. We also observed a 2.1-fold increase in PCA risk associated with men possessing the GSTP1 (Val/Val) and GSTM1 (*1/*1 + *1/*0) alleles. MDR analysis validated these findings; detecting GSTP1 105 Val (p = 0.001) as the best single factor for predicting PCA risk. Our findings emphasize the importance of utilizing a combination of traditional and advanced statistical tools to identify and validate single gene and multi-locus interactions in relation to cancer susceptibility. PMID:19917083

Versatile platform for nanotechnology based on circular permutations of chaperonin protein

NASA Technical Reports Server (NTRS)

McMillan, R. Andrew (Inventor); Kagawa, Hiromi (Inventor); Paavola, Chad D. (Inventor); Chan, Suzanne L. (Inventor); Li, Yi-Fen (Inventor); Trent, Jonathan D. (Inventor)

2010-01-01

The present invention provides chaperonin polypeptides which are modified to include N-terminal and C-terminal ends that are relocated from the central pore region to various different positions in the polypeptide which are located on the exterior of the folded modified chaperonin polypeptide. In the modified chaperonin polypeptide, the naturally-occurring N-terminal and C-terminal ends are joined together directly or with an intervening linker peptide sequence. The relocated N-terminal or C-terminal ends can be covalently joined to, or bound with another molecule such as a nucleic acid molecule, a lipid, a carbohydrate, a second polypeptide, or a nanoparticle. The modified chaperonin polypeptides can assemble into double-ringed chaperonin structures. Further, the chaperonin structures can organize into higher order structures such as nanofilaments or nanoarrays which can be used to produce nanodevices and nanocoatings.

Encoding Sequential Information in Semantic Space Models: Comparing Holographic Reduced Representation and Random Permutation

PubMed Central

Recchia, Gabriel; Sahlgren, Magnus; Kanerva, Pentti; Jones, Michael N.

2015-01-01

Circular convolution and random permutation have each been proposed as neurally plausible binding operators capable of encoding sequential information in semantic memory. We perform several controlled comparisons of circular convolution and random permutation as means of encoding paired associates as well as encoding sequential information. Random permutations outperformed convolution with respect to the number of paired associates that can be reliably stored in a single memory trace. Performance was equal on semantic tasks when using a small corpus, but random permutations were ultimately capable of achieving superior performance due to their higher scalability to large corpora. Finally, “noisy” permutations in which units are mapped to other units arbitrarily (no one-to-one mapping) perform nearly as well as true permutations. These findings increase the neurological plausibility of random permutations and highlight their utility in vector space models of semantics. PMID:25954306

Finite state model and compatibility theory - New analysis tools for permutation networks

NASA Technical Reports Server (NTRS)

Huang, S.-T.; Tripathi, S. K.

1986-01-01

A simple model to describe the fundamental operation theory of shuffle-exchange-type permutation networks, the finite permutation machine (FPM), is described, and theorems which transform the control matrix result to a continuous compatible vector result are developed. It is found that only 2n-1 shuffle exchange passes are necessary, and that 3n-3 passes are sufficient, to realize all permutations, reducing the sufficient number of passes by two from previous results. The flexibility of the approach is demonstrated by the description of a stack permutation machine (SPM) which can realize all permutations, and by showing that the FPM corresponding to the Benes (1965) network belongs to the SPM. The FPM corresponding to the network with two cascaded reverse-exchange networks is found to realize all permutations, and a simple mechanism to verify several equivalence relationships of various permutation networks is discussed.

Sorting permutations by prefix and suffix rearrangements.

PubMed

Lintzmayer, Carla Negri; Fertin, Guillaume; Dias, Zanoni

2017-02-01

Some interesting combinatorial problems have been motivated by genome rearrangements, which are mutations that affect large portions of a genome. When we represent genomes as permutations, the goal is to transform a given permutation into the identity permutation with the minimum number of rearrangements. When they affect segments from the beginning (respectively end) of the permutation, they are called prefix (respectively suffix) rearrangements. This paper presents results for rearrangement problems that involve prefix and suffix versions of reversals and transpositions considering unsigned and signed permutations. We give 2-approximation and ([Formula: see text])-approximation algorithms for these problems, where [Formula: see text] is a constant divided by the number of breakpoints (pairs of consecutive elements that should not be consecutive in the identity permutation) in the input permutation. We also give bounds for the diameters concerning these problems and provide ways of improving the practical results of our algorithms.

Low-Complexity Discriminative Feature Selection From EEG Before and After Short-Term Memory Task.

PubMed

Behzadfar, Neda; Firoozabadi, S Mohammad P; Badie, Kambiz

2016-10-01

A reliable and unobtrusive quantification of changes in cortical activity during short-term memory task can be used to evaluate the efficacy of interfaces and to provide real-time user-state information. In this article, we investigate changes in electroencephalogram signals in short-term memory with respect to the baseline activity. The electroencephalogram signals have been analyzed using 9 linear and nonlinear/dynamic measures. We applied statistical Wilcoxon examination and Davis-Bouldian criterion to select optimal discriminative features. The results show that among the features, the permutation entropy significantly increased in frontal lobe and the occipital second lower alpha band activity decreased during memory task. These 2 features reflect the same mental task; however, their correlation with memory task varies in different intervals. In conclusion, it is suggested that the combination of the 2 features would improve the performance of memory based neurofeedback systems. © EEG and Clinical Neuroscience Society (ECNS) 2016.

Polarization-resolved time-delay signatures of chaos induced by FBG-feedback in VCSEL.

PubMed

Zhong, Zhu-Qiang; Li, Song-Sui; Chan, Sze-Chun; Xia, Guang-Qiong; Wu, Zheng-Mao

2015-06-15

Polarization-resolved chaotic emission intensities from a vertical-cavity surface-emitting laser (VCSEL) subject to feedback from a fiber Bragg grating (FBG) are numerically investigated. Time-delay (TD) signatures of the feedback are examined through various means including self-correlations of intensity time-series of individual polarizations, cross-correlation of intensities time-series between both polarizations, and permutation entropies calculated for the individual polarizations. The results show that the TD signatures can be clearly suppressed by selecting suitable operation parameters such as the feedback strength, FBG bandwidth, and Bragg frequency. Also, in the operational parameter space, numerical maps of TD signatures and effective bandwidths are obtained, which show regions of chaotic signals with both wide bandwidths and weak TD signatures. Finally, by comparing with a VCSEL subject to feedback from a mirror, the VCSEL subject to feedback from the FBG generally shows better concealment of the TD signatures with similar, or even wider, bandwidths.

A Reversible Logical Circuit Synthesis Algorithm Based on Decomposition of Cycle Representations of Permutations

NASA Astrophysics Data System (ADS)

Zhu, Wei; Li, Zhiqiang; Zhang, Gaoman; Pan, Suhan; Zhang, Wei

2018-05-01

A reversible function is isomorphic to a permutation and an arbitrary permutation can be represented by a series of cycles. A new synthesis algorithm for 3-qubit reversible circuits was presented. It consists of two parts, the first part used the Number of reversible function's Different Bits (NDBs) to decide whether the NOT gate should be added to decrease the Hamming distance of the input and output vectors; the second part was based on the idea of exploring properties of the cycle representation of permutations, decomposed the cycles to make the permutation closer to the identity permutation and finally turn into the identity permutation, it was realized by using totally controlled Toffoli gates with positive and negative controls.

Magnetic stirling cycles: A new application for magnetic materials

NASA Technical Reports Server (NTRS)

Brown, G. V.

1977-01-01

The elements of the cycle are summarized. The basic advantages include high entropy density in the magnetic material, completely reversible processes, convenient control of the entropy by the applied field, the feature that heat transfer is possible during all processes, and the ability of the ideal cycle to attain Carnot efficiency. The mean field theory is used to predict the entropy of a ferromagnet in an applied field and also the isothermal entropy change and isentropic temperature change caused by applying a field. The results for isentropic temperature change are compared with experimental data on Gd. Coarse mixtures of ferromagnetic materials with different Curie points are proposed to modify the path of the cycle in the T-S diagram in order to improve the efficiency or to increase the specific power.

Modified Dispersion Relations: from Black-Hole Entropy to the Cosmological Constant

NASA Astrophysics Data System (ADS)

Garattini, Remo

2012-07-01

Quantum Field Theory is plagued by divergences in the attempt to calculate physical quantities. Standard techniques of regularization and renormalization are used to keep under control such a problem. In this paper we would like to use a different scheme based on Modified Dispersion Relations (MDR) to remove infinities appearing in one loop approximation in contrast to what happens in conventional approaches. In particular, we apply the MDR regularization to the computation of the entropy of a Schwarzschild black hole from one side and the Zero Point Energy (ZPE) of the graviton from the other side. The graviton ZPE is connected to the cosmological constant by means of of the Wheeler-DeWitt equation.

Consciousness Indexing and Outcome Prediction with Resting-State EEG in Severe Disorders of Consciousness.

PubMed

Stefan, Sabina; Schorr, Barbara; Lopez-Rolon, Alex; Kolassa, Iris-Tatjana; Shock, Jonathan P; Rosenfelder, Martin; Heck, Suzette; Bender, Andreas

2018-04-17

We applied the following methods to resting-state EEG data from patients with disorders of consciousness (DOC) for consciousness indexing and outcome prediction: microstates, entropy (i.e. approximate, permutation), power in alpha and delta frequency bands, and connectivity (i.e. weighted symbolic mutual information, symbolic transfer entropy, complex network analysis). Patients with unresponsive wakefulness syndrome (UWS) and patients in a minimally conscious state (MCS) were classified into these two categories by fitting and testing a generalised linear model. We aimed subsequently to develop an automated system for outcome prediction in severe DOC by selecting an optimal subset of features using sequential floating forward selection (SFFS). The two outcome categories were defined as UWS or dead, and MCS or emerged from MCS. Percentage of time spent in microstate D in the alpha frequency band performed best at distinguishing MCS from UWS patients. The average clustering coefficient obtained from thresholding beta coherence performed best at predicting outcome. The optimal subset of features selected with SFFS consisted of the frequency of microstate A in the 2-20 Hz frequency band, path length obtained from thresholding alpha coherence, and average path length obtained from thresholding alpha coherence. Combining these features seemed to afford high prediction power. Python and MATLAB toolboxes for the above calculations are freely available under the GNU public license for non-commercial use ( https://qeeg.wordpress.com ).

Free energy of mixing of acetone and methanol: a computer simulation investigation.

PubMed

Idrissi, Abdenacer; Polok, Kamil; Barj, Mohammed; Marekha, Bogdan; Kiselev, Mikhail; Jedlovszky, Pál

2013-12-19

The change of the Helmholtz free energy, internal energy, and entropy accompanying the mixing of acetone and methanol is calculated in the entire composition range by the method of thermodynamic integration using three different potential model combinations of the two compounds. In the first system, both molecules are described by the OPLS, and in the second system, both molecules are described by the original TraPPE force field, whereas in the third system a modified version of the TraPPE potential is used for acetone in combination with the original TraPPE model of methanol. The results reveal that, in contrast with the acetone-water system, all of these three model combinations are able to reproduce the full miscibility of acetone and methanol, although the thermodynamic driving force of this mixing is very small. It is also seen, in accordance with the finding of former structural analyses, that the mixing of the two components is driven by the entropy term corresponding to the ideal mixing, which is large enough to overcompensate the effect of the energy increase and entropy loss due to the interaction of the unlike components in the mixtures. Among the three model combinations, the use of the original TraPPE model of methanol and modified TraPPE model of acetone turns out to be clearly the best in this respect, as it is able to reproduce the experimental free energy, internal energy, and entropy of mixing values within 0.15 kJ/mol, 0.2 kJ/mol, and 1 J/(mol K), respectively, in the entire composition range. The success of this model combination originates from the fact that the use of the modified TraPPE model of acetone instead of the original one in these mixtures improves the reproduction of the entropy of mixing, while it retains the ability of the original model of excellently reproducing the internal energy of mixing.

The cancer Warburg effect may be a testable example of the minimum entropy production rate principle

NASA Astrophysics Data System (ADS)

Marín, Dolores; Sabater, Bartolomé

2017-04-01

Cancer cells consume more glucose by glycolytic fermentation to lactate than by respiration, a characteristic known as the Warburg effect. In contrast with the 36 moles of ATP produced by respiration, fermentation produces two moles of ATP per mole of glucose consumed, which poses a puzzle with regard to the function of the Warburg effect. The production of free energy (ΔG), enthalpy (ΔH), and entropy (ΔS) per mole linearly varies with the fraction (x) of glucose consumed by fermentation that is frequently estimated around 0.9. Hence, calculation shows that, in respect to pure respiration, the predominant fermentative metabolism decreases around 10% the production of entropy per mole of glucose consumed in cancer cells. We hypothesize that increased fermentation could allow cancer cells to accomplish the Prigogine theorem of the trend to minimize the rate of production of entropy. According to the theorem, open cellular systems near the steady state could evolve to minimize the rates of entropy production that may be reached by modified replicating cells producing entropy at a low rate. Remarkably, at CO2 concentrations above 930 ppm, glucose respiration produces less entropy than fermentation, which suggests experimental tests to validate the hypothesis of minimization of the rate of entropy production through the Warburg effect.

The cancer Warburg effect may be a testable example of the minimum entropy production rate principle.

PubMed

Marín, Dolores; Sabater, Bartolomé

2017-04-28

Cancer cells consume more glucose by glycolytic fermentation to lactate than by respiration, a characteristic known as the Warburg effect. In contrast with the 36 moles of ATP produced by respiration, fermentation produces two moles of ATP per mole of glucose consumed, which poses a puzzle with regard to the function of the Warburg effect. The production of free energy (ΔG), enthalpy (ΔH), and entropy (ΔS) per mole linearly varies with the fraction (x) of glucose consumed by fermentation that is frequently estimated around 0.9. Hence, calculation shows that, in respect to pure respiration, the predominant fermentative metabolism decreases around 10% the production of entropy per mole of glucose consumed in cancer cells. We hypothesize that increased fermentation could allow cancer cells to accomplish the Prigogine theorem of the trend to minimize the rate of production of entropy. According to the theorem, open cellular systems near the steady state could evolve to minimize the rates of entropy production that may be reached by modified replicating cells producing entropy at a low rate. Remarkably, at CO 2 concentrations above 930 ppm, glucose respiration produces less entropy than fermentation, which suggests experimental tests to validate the hypothesis of minimization of the rate of entropy production through the Warburg effect.

Comparison of entropy and bispectral index during propofol and fentanyl sedation in monitored anaesthesia care.

PubMed

Balci, Canan; Karabekir, H S; Kahraman, F; Sivaci, R G

2009-01-01

Comparison of entropy (state entropy [SE] and response entropy [RE]) with the bispectral index (BIS) during propofol sedation in monitored anaesthesia care (MAC) was carried out in patients undergoing hand surgery. Thirty candidates for elective hand surgery were pre-medicated with midazolam 0.06 mg/kg and atropine 0.01 mg/kg. Sedation was induced with intravenous propofol and fentanyl was also administered. The Modified Observer's Assessment of Alertness/Sedation Scale (MOAA/S) was used to determine sedation level and pain was maintained at < 4 on a 0 - 10 verbal rating scale. The BIS, entropy, MOAA/S and pain values were recorded before initiation of sedation (control), during initiation of sedation, during surgery, and for 30 min after the end of surgery and anaesthesia. On initiation of sedation, entropy decreased more rapidly than BIS. At 10 min after initiation of sedation, the mean +/- SD values for MOAA/S, BIS, RE and SE were 3.00 +/- 0.36, 85.45 +/- 0.15, 74.00 +/- 0.60 and 72.02 +/- 0.12, respectively. During recovery, BIS and RE and SE increased in parallel with MOAA/S. It is concluded that entropy monitoring is as reliable as BIS monitoring in MAC.

Effective Iterated Greedy Algorithm for Flow-Shop Scheduling Problems with Time lags

NASA Astrophysics Data System (ADS)

ZHAO, Ning; YE, Song; LI, Kaidian; CHEN, Siyu

2017-05-01

Flow shop scheduling problem with time lags is a practical scheduling problem and attracts many studies. Permutation problem(PFSP with time lags) is concentrated but non-permutation problem(non-PFSP with time lags) seems to be neglected. With the aim to minimize the makespan and satisfy time lag constraints, efficient algorithms corresponding to PFSP and non-PFSP problems are proposed, which consist of iterated greedy algorithm for permutation(IGTLP) and iterated greedy algorithm for non-permutation (IGTLNP). The proposed algorithms are verified using well-known simple and complex instances of permutation and non-permutation problems with various time lag ranges. The permutation results indicate that the proposed IGTLP can reach near optimal solution within nearly 11% computational time of traditional GA approach. The non-permutation results indicate that the proposed IG can reach nearly same solution within less than 1% computational time compared with traditional GA approach. The proposed research combines PFSP and non-PFSP together with minimal and maximal time lag consideration, which provides an interesting viewpoint for industrial implementation.

An Extension to Deng's Entropy in the Open World Assumption with an Application in Sensor Data Fusion.

PubMed

Tang, Yongchuan; Zhou, Deyun; Chan, Felix T S

2018-06-11

Quantification of uncertain degree in the Dempster-Shafer evidence theory (DST) framework with belief entropy is still an open issue, even a blank field for the open world assumption. Currently, the existed uncertainty measures in the DST framework are limited to the closed world where the frame of discernment (FOD) is assumed to be complete. To address this issue, this paper focuses on extending a belief entropy to the open world by considering the uncertain information represented as the FOD and the nonzero mass function of the empty set simultaneously. An extension to Deng’s entropy in the open world assumption (EDEOW) is proposed as a generalization of the Deng’s entropy and it can be degenerated to the Deng entropy in the closed world wherever necessary. In order to test the reasonability and effectiveness of the extended belief entropy, an EDEOW-based information fusion approach is proposed and applied to sensor data fusion under uncertainty circumstance. The experimental results verify the usefulness and applicability of the extended measure as well as the modified sensor data fusion method. In addition, a few open issues still exist in the current work: the necessary properties for a belief entropy in the open world assumption, whether there exists a belief entropy that satisfies all the existed properties, and what is the most proper fusion frame for sensor data fusion under uncertainty.

Modified cross sample entropy and surrogate data analysis method for financial time series

NASA Astrophysics Data System (ADS)

Yin, Yi; Shang, Pengjian

2015-09-01

For researching multiscale behaviors from the angle of entropy, we propose a modified cross sample entropy (MCSE) and combine surrogate data analysis with it in order to compute entropy differences between original dynamics and surrogate series (MCSDiff). MCSDiff is applied to simulated signals to show accuracy and then employed to US and Chinese stock markets. We illustrate the presence of multiscale behavior in the MCSDiff results and reveal that there are synchrony containing in the original financial time series and they have some intrinsic relations, which are destroyed by surrogate data analysis. Furthermore, the multifractal behaviors of cross-correlations between these financial time series are investigated by multifractal detrended cross-correlation analysis (MF-DCCA) method, since multifractal analysis is a multiscale analysis. We explore the multifractal properties of cross-correlation between these US and Chinese markets and show the distinctiveness of NQCI and HSI among the markets in their own region. It can be concluded that the weaker cross-correlation between US markets gives the evidence for the better inner mechanism in the US stock markets than that of Chinese stock markets. To study the multiscale features and properties of financial time series can provide valuable information for understanding the inner mechanism of financial markets.

Decryption of pure-position permutation algorithms.

PubMed

Zhao, Xiao-Yu; Chen, Gang; Zhang, Dan; Wang, Xiao-Hong; Dong, Guang-Chang

2004-07-01

Pure position permutation image encryption algorithms, commonly used as image encryption investigated in this work are unfortunately frail under known-text attack. In view of the weakness of pure position permutation algorithm, we put forward an effective decryption algorithm for all pure-position permutation algorithms. First, a summary of the pure position permutation image encryption algorithms is given by introducing the concept of ergodic matrices. Then, by using probability theory and algebraic principles, the decryption probability of pure-position permutation algorithms is verified theoretically; and then, by defining the operation system of fuzzy ergodic matrices, we improve a specific decryption algorithm. Finally, some simulation results are shown.

Entropy Generation Minimization in Dimethyl Ether Synthesis: A Case Study

NASA Astrophysics Data System (ADS)

Kingston, Diego; Razzitte, Adrián César

2018-04-01

Entropy generation minimization is a method that helps improve the efficiency of real processes and devices. In this article, we study the entropy production (due to chemical reactions, heat exchange and friction) in a conventional reactor that synthesizes dimethyl ether and minimize it by modifying different operating variables of the reactor, such as composition, temperature and pressure, while aiming at a fixed production of dimethyl ether. Our results indicate that it is possible to reduce the entropy production rate by nearly 70 % and that, by changing only the inlet composition, it is possible to cut it by nearly 40 %, though this comes at the expense of greater dissipation due to heat transfer. We also study the alternative of coupling the reactor with another, where dehydrogenation of methylcyclohexane takes place. In that case, entropy generation can be reduced by 54 %, when pressure, temperature and inlet molar flows are varied. These examples show that entropy generation analysis can be a valuable tool in engineering design and applications aiming at process intensification and efficient operation of plant equipment.

Weight distributions for turbo codes using random and nonrandom permutations

NASA Technical Reports Server (NTRS)

Dolinar, S.; Divsalar, D.

1995-01-01

This article takes a preliminary look at the weight distributions achievable for turbo codes using random, nonrandom, and semirandom permutations. Due to the recursiveness of the encoders, it is important to distinguish between self-terminating and non-self-terminating input sequences. The non-self-terminating sequences have little effect on decoder performance, because they accumulate high encoded weight until they are artificially terminated at the end of the block. From probabilistic arguments based on selecting the permutations randomly, it is concluded that the self-terminating weight-2 data sequences are the most important consideration in the design of constituent codes; higher-weight self-terminating sequences have successively decreasing importance. Also, increasing the number of codes and, correspondingly, the number of permutations makes it more and more likely that the bad input sequences will be broken up by one or more of the permuters. It is possible to design nonrandom permutations that ensure that the minimum distance due to weight-2 input sequences grows roughly as the square root of (2N), where N is the block length. However, these nonrandom permutations amplify the bad effects of higher-weight inputs, and as a result they are inferior in performance to randomly selected permutations. But there are 'semirandom' permutations that perform nearly as well as the designed nonrandom permutations with respect to weight-2 input sequences and are not as susceptible to being foiled by higher-weight inputs.

PERMutation Using Transposase Engineering (PERMUTE): A Simple Approach for Constructing Circularly Permuted Protein Libraries.

PubMed

Jones, Alicia M; Atkinson, Joshua T; Silberg, Jonathan J

2017-01-01

Rearrangements that alter the order of a protein's sequence are used in the lab to study protein folding, improve activity, and build molecular switches. One of the simplest ways to rearrange a protein sequence is through random circular permutation, where native protein termini are linked together and new termini are created elsewhere through random backbone fission. Transposase mutagenesis has emerged as a simple way to generate libraries encoding different circularly permuted variants of proteins. With this approach, a synthetic transposon (called a permuteposon) is randomly inserted throughout a circularized gene to generate vectors that express different permuted variants of a protein. In this chapter, we outline the protocol for constructing combinatorial libraries of circularly permuted proteins using transposase mutagenesis, and we describe the different permuteposons that have been developed to facilitate library construction.

Ensembles of physical states and random quantum circuits on graphs

NASA Astrophysics Data System (ADS)

Hamma, Alioscia; Santra, Siddhartha; Zanardi, Paolo

2012-11-01

In this paper we continue and extend the investigations of the ensembles of random physical states introduced in Hamma [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.109.040502 109, 040502 (2012)]. These ensembles are constructed by finite-length random quantum circuits (RQC) acting on the (hyper)edges of an underlying (hyper)graph structure. The latter encodes for the locality structure associated with finite-time quantum evolutions generated by physical, i.e., local, Hamiltonians. Our goal is to analyze physical properties of typical states in these ensembles; in particular here we focus on proxies of quantum entanglement as purity and α-Renyi entropies. The problem is formulated in terms of matrix elements of superoperators which depend on the graph structure, choice of probability measure over the local unitaries, and circuit length. In the α=2 case these superoperators act on a restricted multiqubit space generated by permutation operators associated to the subsets of vertices of the graph. For permutationally invariant interactions the dynamics can be further restricted to an exponentially smaller subspace. We consider different families of RQCs and study their typical entanglement properties for finite time as well as their asymptotic behavior. We find that area law holds in average and that the volume law is a typical property (that is, it holds in average and the fluctuations around the average are vanishing for the large system) of physical states. The area law arises when the evolution time is O(1) with respect to the size L of the system, while the volume law arises as is typical when the evolution time scales like O(L).

Modulation of frustration in folding by sequence permutation.

PubMed

Nobrega, R Paul; Arora, Karunesh; Kathuria, Sagar V; Graceffa, Rita; Barrea, Raul A; Guo, Liang; Chakravarthy, Srinivas; Bilsel, Osman; Irving, Thomas C; Brooks, Charles L; Matthews, C Robert

2014-07-22

Folding of globular proteins can be envisioned as the contraction of a random coil unfolded state toward the native state on an energy surface rough with local minima trapping frustrated species. These substructures impede productive folding and can serve as nucleation sites for aggregation reactions. However, little is known about the relationship between frustration and its underlying sequence determinants. Chemotaxis response regulator Y (CheY), a 129-amino acid bacterial protein, has been shown previously to populate an off-pathway kinetic trap in the microsecond time range. The frustration has been ascribed to premature docking of the N- and C-terminal subdomains or, alternatively, to the formation of an unproductive local-in-sequence cluster of branched aliphatic side chains, isoleucine, leucine, and valine (ILV). The roles of the subdomains and ILV clusters in frustration were tested by altering the sequence connectivity using circular permutations. Surprisingly, the stability and buried surface area of the intermediate could be increased or decreased depending on the location of the termini. Comparison with the results of small-angle X-ray-scattering experiments and simulations points to the accelerated formation of a more compact, on-pathway species for the more stable intermediate. The effect of chain connectivity in modulating the structures and stabilities of the early kinetic traps in CheY is better understood in terms of the ILV cluster model. However, the subdomain model captures the requirement for an intact N-terminal domain to access the native conformation. Chain entropy and aliphatic-rich sequences play crucial roles in biasing the early events leading to frustration in the folding of CheY.

Logarithmic entropy of Kehagias-Sfetsos black hole with self-gravitation in asymptotically flat IR modified Hořava gravity

NASA Astrophysics Data System (ADS)

Liu, Molin; Lu, Junwang

2011-05-01

Motivated by recent logarithmic entropy of Hořava-Lifshitz gravity, we investigate Hawking radiation for Kehagias-Sfetsos black hole from tunneling perspective. After considering the effect of self-gravitation, we calculate the emission rate and entropy of quantum tunneling by using Kraus-Parikh-Wilczek method. Meanwhile, both massless and massive particles are considered in this Letter. Interestingly, two types tunneling particles have the same emission rate Γ and entropy Sb whose analytical formulae are Γ=exp[π(rin2-rout2)/2+π/αln rin/rout] and Sb=A/4+π/αln(A/4), respectively. Here, α is the Hořava-Lifshitz field parameter. The results show that the logarithmic entropy of Hořava-Lifshitz gravity could be explained well by the self-gravitation, which is totally different from other methods. The study of this semiclassical tunneling process may shed light on understanding the Hořava-Lifshitz gravity.

Opposition-Based Memetic Algorithm and Hybrid Approach for Sorting Permutations by Reversals.

PubMed

Soncco-Álvarez, José Luis; Muñoz, Daniel M; Ayala-Rincón, Mauricio

2018-02-21

Sorting unsigned permutations by reversals is a difficult problem; indeed, it was proved to be NP-hard by Caprara (1997). Because of its high complexity, many approximation algorithms to compute the minimal reversal distance were proposed until reaching the nowadays best-known theoretical ratio of 1.375. In this article, two memetic algorithms to compute the reversal distance are proposed. The first one uses the technique of opposition-based learning leading to an opposition-based memetic algorithm; the second one improves the previous algorithm by applying the heuristic of two breakpoint elimination leading to a hybrid approach. Several experiments were performed with one-hundred randomly generated permutations, single benchmark permutations, and biological permutations. Results of the experiments showed that the proposed OBMA and Hybrid-OBMA algorithms achieve the best results for practical cases, that is, for permutations of length up to 120. Also, Hybrid-OBMA showed to improve the results of OBMA for permutations greater than or equal to 60. The applicability of our proposed algorithms was checked processing permutations based on biological data, in which case OBMA gave the best average results for all instances.

Visual recognition of permuted words

NASA Astrophysics Data System (ADS)

Rashid, Sheikh Faisal; Shafait, Faisal; Breuel, Thomas M.

2010-02-01

In current study we examine how letter permutation affects in visual recognition of words for two orthographically dissimilar languages, Urdu and German. We present the hypothesis that recognition or reading of permuted and non-permuted words are two distinct mental level processes, and that people use different strategies in handling permuted words as compared to normal words. A comparison between reading behavior of people in these languages is also presented. We present our study in context of dual route theories of reading and it is observed that the dual-route theory is consistent with explanation of our hypothesis of distinction in underlying cognitive behavior for reading permuted and non-permuted words. We conducted three experiments in lexical decision tasks to analyze how reading is degraded or affected by letter permutation. We performed analysis of variance (ANOVA), distribution free rank test, and t-test to determine the significance differences in response time latencies for two classes of data. Results showed that the recognition accuracy for permuted words is decreased 31% in case of Urdu and 11% in case of German language. We also found a considerable difference in reading behavior for cursive and alphabetic languages and it is observed that reading of Urdu is comparatively slower than reading of German due to characteristics of cursive script.

Four applications of permutation methods to testing a single-mediator model.

PubMed

Taylor, Aaron B; MacKinnon, David P

2012-09-01

Four applications of permutation tests to the single-mediator model are described and evaluated in this study. Permutation tests work by rearranging data in many possible ways in order to estimate the sampling distribution for the test statistic. The four applications to mediation evaluated here are the permutation test of ab, the permutation joint significance test, and the noniterative and iterative permutation confidence intervals for ab. A Monte Carlo simulation study was used to compare these four tests with the four best available tests for mediation found in previous research: the joint significance test, the distribution of the product test, and the percentile and bias-corrected bootstrap tests. We compared the different methods on Type I error, power, and confidence interval coverage. The noniterative permutation confidence interval for ab was the best performer among the new methods. It successfully controlled Type I error, had power nearly as good as the most powerful existing methods, and had better coverage than any existing method. The iterative permutation confidence interval for ab had lower power than do some existing methods, but it performed better than any other method in terms of coverage. The permutation confidence interval methods are recommended when estimating a confidence interval is a primary concern. SPSS and SAS macros that estimate these confidence intervals are provided.

Circular Permutation of a Chaperonin Protein: Biophysics and Application to Nanotechnology

NASA Technical Reports Server (NTRS)

Paavola, Chad; Chan, Suzanne; Li, Yi-Fen; McMillan, R. Andrew; Trent, Jonathan

2004-01-01

We have designed five circular permutants of a chaperonin protein derived from the hyperthermophilic organism Sulfolobus shibatae. These permuted proteins were expressed in E. coli and are well-folded. Furthermore, all the permutants assemble into 18-mer double rings of the same form as the wild-type protein. We characterized the thermodynamics of folding for each permutant by both guanidine denaturation and differential scanning calorimetry. We also examined the assembly of chaperonin rings into higher order structures that may be used as nanoscale templates. The results show that circular permutation can be used to tune the thermodynamic properties of a protein template as well as facilitating the fusion of peptides, binding proteins or enzymes onto nanostructured templates.

The structure of a thermophilic kinase shapes fitness upon random circular permutation

PubMed Central

Jones, Alicia M.; Mehta, Manan M.; Thomas, Emily E.; Atkinson, Joshua T.; Segall-Shapiro, Thomas H.; Liu, Shirley; Silberg, Jonathan J.

2016-01-01

Proteins can be engineered for synthetic biology through circular permutation, a sequence rearrangement where native protein termini become linked and new termini are created elsewhere through backbone fission. However, it remains challenging to anticipate a protein’s functional tolerance to circular permutation. Here, we describe new transposons for creating libraries of randomly circularly permuted proteins that minimize peptide additions at their termini, and we use transposase mutagenesis to study the tolerance of a thermophilic adenylate kinase (AK) to circular permutation. We find that libraries expressing permuted AK with either short or long peptides amended to their N-terminus yield distinct sets of active variants and present evidence that this trend arises because permuted protein expression varies across libraries. Mapping all sites that tolerate backbone cleavage onto AK structure reveals that the largest contiguous regions of sequence that lack cleavage sites are proximal to the phosphotransfer site. A comparison of our results with a range of structure-derived parameters further showed that retention of function correlates to the strongest extent with the distance to the phosphotransfer site, amino acid variability in an AK family sequence alignment, and residue-level deviations in superimposed AK structures. Our work illustrates how permuted protein libraries can be created with minimal peptide additions using transposase mutagenesis, and they reveal a challenge of maintaining consistent expression across permuted variants in a library that minimizes peptide additions. Furthermore, these findings provide a basis for interpreting responses of thermophilic phosphotransferases to circular permutation by calibrating how different structure-derived parameters relate to retention of function in a cellular selection. PMID:26976658

The Structure of a Thermophilic Kinase Shapes Fitness upon Random Circular Permutation.

PubMed

Jones, Alicia M; Mehta, Manan M; Thomas, Emily E; Atkinson, Joshua T; Segall-Shapiro, Thomas H; Liu, Shirley; Silberg, Jonathan J

2016-05-20

Proteins can be engineered for synthetic biology through circular permutation, a sequence rearrangement in which native protein termini become linked and new termini are created elsewhere through backbone fission. However, it remains challenging to anticipate a protein's functional tolerance to circular permutation. Here, we describe new transposons for creating libraries of randomly circularly permuted proteins that minimize peptide additions at their termini, and we use transposase mutagenesis to study the tolerance of a thermophilic adenylate kinase (AK) to circular permutation. We find that libraries expressing permuted AKs with either short or long peptides amended to their N-terminus yield distinct sets of active variants and present evidence that this trend arises because permuted protein expression varies across libraries. Mapping all sites that tolerate backbone cleavage onto AK structure reveals that the largest contiguous regions of sequence that lack cleavage sites are proximal to the phosphotransfer site. A comparison of our results with a range of structure-derived parameters further showed that retention of function correlates to the strongest extent with the distance to the phosphotransfer site, amino acid variability in an AK family sequence alignment, and residue-level deviations in superimposed AK structures. Our work illustrates how permuted protein libraries can be created with minimal peptide additions using transposase mutagenesis, and it reveals a challenge of maintaining consistent expression across permuted variants in a library that minimizes peptide additions. Furthermore, these findings provide a basis for interpreting responses of thermophilic phosphotransferases to circular permutation by calibrating how different structure-derived parameters relate to retention of function in a cellular selection.

On the convergence of difference approximations to scalar conservation laws

NASA Technical Reports Server (NTRS)

Osher, Stanley; Tadmor, Eitan

1988-01-01

A unified treatment is given for time-explicit, two-level, second-order-resolution (SOR), total-variation-diminishing (TVD) approximations to scalar conservation laws. The schemes are assumed only to have conservation form and incremental form. A modified flux and a viscosity coefficient are introduced to obtain results in terms of the latter. The existence of a cell entropy inequality is discussed, and such an equality for all entropies is shown to imply that the scheme is an E scheme on monotone (actually more general) data, hence at most only first-order accurate in general. Convergence for TVD-SOR schemes approximating convex or concave conservation laws is shown by enforcing a single discrete entropy inequality.

Dynamics of entanglement entropy of interacting fermions in a 1D driven harmonic trap

NASA Astrophysics Data System (ADS)

McKenney, Joshua R.; Porter, William J.; Drut, Joaquín E.

2018-03-01

Following up on a recent analysis of two cold atoms in a time-dependent harmonic trap in one dimension, we explore the entanglement entropy of two and three fermions in the same situation when driven through a parametric resonance. We find that the presence of such a resonance in the two-particle system leaves a clear imprint on the entanglement entropy. We show how the signal is modified by attractive and repulsive contact interactions, and how it remains present for the three-particle system. Additionaly, we extend the work of recent experiments to demonstrate how restricting observation to a limited subsystem gives rise to locally thermal behavior.

Teaching Tip: When a Matrix and Its Inverse Are Stochastic

ERIC Educational Resources Information Center

Ding, J.; Rhee, N. H.

2013-01-01

A stochastic matrix is a square matrix with nonnegative entries and row sums 1. The simplest example is a permutation matrix, whose rows permute the rows of an identity matrix. A permutation matrix and its inverse are both stochastic. We prove the converse, that is, if a matrix and its inverse are both stochastic, then it is a permutation matrix.

A hybrid fault diagnosis approach based on mixed-domain state features for rotating machinery.

PubMed

Xue, Xiaoming; Zhou, Jianzhong

2017-01-01

To make further improvement in the diagnosis accuracy and efficiency, a mixed-domain state features data based hybrid fault diagnosis approach, which systematically blends both the statistical analysis approach and the artificial intelligence technology, is proposed in this work for rolling element bearings. For simplifying the fault diagnosis problems, the execution of the proposed method is divided into three steps, i.e., fault preliminary detection, fault type recognition and fault degree identification. In the first step, a preliminary judgment about the health status of the equipment can be evaluated by the statistical analysis method based on the permutation entropy theory. If fault exists, the following two processes based on the artificial intelligence approach are performed to further recognize the fault type and then identify the fault degree. For the two subsequent steps, mixed-domain state features containing time-domain, frequency-domain and multi-scale features are extracted to represent the fault peculiarity under different working conditions. As a powerful time-frequency analysis method, the fast EEMD method was employed to obtain multi-scale features. Furthermore, due to the information redundancy and the submergence of original feature space, a novel manifold learning method (modified LGPCA) is introduced to realize the low-dimensional representations for high-dimensional feature space. Finally, two cases with 12 working conditions respectively have been employed to evaluate the performance of the proposed method, where vibration signals were measured from an experimental bench of rolling element bearing. The analysis results showed the effectiveness and the superiority of the proposed method of which the diagnosis thought is more suitable for practical application. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Permutation-based inference for the AUC: A unified approach for continuous and discontinuous data.

PubMed

Pauly, Markus; Asendorf, Thomas; Konietschke, Frank

2016-11-01

We investigate rank-based studentized permutation methods for the nonparametric Behrens-Fisher problem, that is, inference methods for the area under the ROC curve. We hereby prove that the studentized permutation distribution of the Brunner-Munzel rank statistic is asymptotically standard normal, even under the alternative. Thus, incidentally providing the hitherto missing theoretical foundation for the Neubert and Brunner studentized permutation test. In particular, we do not only show its consistency, but also that confidence intervals for the underlying treatment effects can be computed by inverting this permutation test. In addition, we derive permutation-based range-preserving confidence intervals. Extensive simulation studies show that the permutation-based confidence intervals appear to maintain the preassigned coverage probability quite accurately (even for rather small sample sizes). For a convenient application of the proposed methods, a freely available software package for the statistical software R has been developed. A real data example illustrates the application. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient Blockwise Permutation Tests Preserving Exchangeability

PubMed Central

Zhou, Chunxiao; Zwilling, Chris E.; Calhoun, Vince D.; Wang, Michelle Y.

2014-01-01

In this paper, we present a new blockwise permutation test approach based on the moments of the test statistic. The method is of importance to neuroimaging studies. In order to preserve the exchangeability condition required in permutation tests, we divide the entire set of data into certain exchangeability blocks. In addition, computationally efficient moments-based permutation tests are performed by approximating the permutation distribution of the test statistic with the Pearson distribution series. This involves the calculation of the first four moments of the permutation distribution within each block and then over the entire set of data. The accuracy and efficiency of the proposed method are demonstrated through simulated experiment on the magnetic resonance imaging (MRI) brain data, specifically the multi-site voxel-based morphometry analysis from structural MRI (sMRI). PMID:25289113

Large time behavior of entropy solutions to one-dimensional unipolar hydrodynamic model for semiconductor devices

NASA Astrophysics Data System (ADS)

Huang, Feimin; Li, Tianhong; Yu, Huimin; Yuan, Difan

2018-06-01

We are concerned with the global existence and large time behavior of entropy solutions to the one-dimensional unipolar hydrodynamic model for semiconductors in the form of Euler-Poisson equations in a bounded interval. In this paper, we first prove the global existence of entropy solution by vanishing viscosity and compensated compactness framework. In particular, the solutions are uniformly bounded with respect to space and time variables by introducing modified Riemann invariants and the theory of invariant region. Based on the uniform estimates of density, we further show that the entropy solution converges to the corresponding unique stationary solution exponentially in time. No any smallness condition is assumed on the initial data and doping profile. Moreover, the novelty in this paper is about the unform bound with respect to time for the weak solutions of the isentropic Euler-Poisson system.

On entropic uncertainty relations in the presence of a minimal length

NASA Astrophysics Data System (ADS)

Rastegin, Alexey E.

2017-07-01

Entropic uncertainty relations for the position and momentum within the generalized uncertainty principle are examined. Studies of this principle are motivated by the existence of a minimal observable length. Then the position and momentum operators satisfy the modified commutation relation, for which more than one algebraic representation is known. One of them is described by auxiliary momentum so that the momentum and coordinate wave functions are connected by the Fourier transform. However, the probability density functions of the physically true and auxiliary momenta are different. As the corresponding entropies differ, known entropic uncertainty relations are changed. Using differential Shannon entropies, we give a state-dependent formulation with correction term. State-independent uncertainty relations are obtained in terms of the Rényi entropies and the Tsallis entropies with binning. Such relations allow one to take into account a finiteness of measurement resolution.

Improved wavelet packet classification algorithm for vibrational intrusions in distributed fiber-optic monitoring systems

NASA Astrophysics Data System (ADS)

Wang, Bingjie; Pi, Shaohua; Sun, Qi; Jia, Bo

2015-05-01

An improved classification algorithm that considers multiscale wavelet packet Shannon entropy is proposed. Decomposition coefficients at all levels are obtained to build the initial Shannon entropy feature vector. After subtracting the Shannon entropy map of the background signal, components of the strongest discriminating power in the initial feature vector are picked out to rebuild the Shannon entropy feature vector, which is transferred to radial basis function (RBF) neural network for classification. Four types of man-made vibrational intrusion signals are recorded based on a modified Sagnac interferometer. The performance of the improved classification algorithm has been evaluated by the classification experiments via RBF neural network under different diffusion coefficients. An 85% classification accuracy rate is achieved, which is higher than the other common algorithms. The classification results show that this improved classification algorithm can be used to classify vibrational intrusion signals in an automatic real-time monitoring system.

An AUC-based permutation variable importance measure for random forests

PubMed Central

2013-01-01

Background The random forest (RF) method is a commonly used tool for classification with high dimensional data as well as for ranking candidate predictors based on the so-called random forest variable importance measures (VIMs). However the classification performance of RF is known to be suboptimal in case of strongly unbalanced data, i.e. data where response class sizes differ considerably. Suggestions were made to obtain better classification performance based either on sampling procedures or on cost sensitivity analyses. However to our knowledge the performance of the VIMs has not yet been examined in the case of unbalanced response classes. In this paper we explore the performance of the permutation VIM for unbalanced data settings and introduce an alternative permutation VIM based on the area under the curve (AUC) that is expected to be more robust towards class imbalance. Results We investigated the performance of the standard permutation VIM and of our novel AUC-based permutation VIM for different class imbalance levels using simulated data and real data. The results suggest that the new AUC-based permutation VIM outperforms the standard permutation VIM for unbalanced data settings while both permutation VIMs have equal performance for balanced data settings. Conclusions The standard permutation VIM loses its ability to discriminate between associated predictors and predictors not associated with the response for increasing class imbalance. It is outperformed by our new AUC-based permutation VIM for unbalanced data settings, while the performance of both VIMs is very similar in the case of balanced classes. The new AUC-based VIM is implemented in the R package party for the unbiased RF variant based on conditional inference trees. The codes implementing our study are available from the companion website: http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/070_drittmittel/janitza/index.html. PMID:23560875

An AUC-based permutation variable importance measure for random forests.

PubMed

Janitza, Silke; Strobl, Carolin; Boulesteix, Anne-Laure

2013-04-05

The random forest (RF) method is a commonly used tool for classification with high dimensional data as well as for ranking candidate predictors based on the so-called random forest variable importance measures (VIMs). However the classification performance of RF is known to be suboptimal in case of strongly unbalanced data, i.e. data where response class sizes differ considerably. Suggestions were made to obtain better classification performance based either on sampling procedures or on cost sensitivity analyses. However to our knowledge the performance of the VIMs has not yet been examined in the case of unbalanced response classes. In this paper we explore the performance of the permutation VIM for unbalanced data settings and introduce an alternative permutation VIM based on the area under the curve (AUC) that is expected to be more robust towards class imbalance. We investigated the performance of the standard permutation VIM and of our novel AUC-based permutation VIM for different class imbalance levels using simulated data and real data. The results suggest that the new AUC-based permutation VIM outperforms the standard permutation VIM for unbalanced data settings while both permutation VIMs have equal performance for balanced data settings. The standard permutation VIM loses its ability to discriminate between associated predictors and predictors not associated with the response for increasing class imbalance. It is outperformed by our new AUC-based permutation VIM for unbalanced data settings, while the performance of both VIMs is very similar in the case of balanced classes. The new AUC-based VIM is implemented in the R package party for the unbiased RF variant based on conditional inference trees. The codes implementing our study are available from the companion website: http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/070_drittmittel/janitza/index.html.

Circular permutant GFP insertion folding reporters

DOEpatents

Waldo, Geoffrey S [Santa Fe, NM; Cabantous, Stephanie [Los Alamos, NM

2008-06-24

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

Circular permutant GFP insertion folding reporters

DOEpatents

Waldo, Geoffrey S; Cabantous, Stephanie

2013-02-12

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

Circular permutant GFP insertion folding reporters

DOEpatents

Waldo, Geoffrey S [Santa Fe, NM; Cabantous, Stephanie [Los Alamos, NM

2011-06-14

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

Circular permutant GFP insertion folding reporters

DOEpatents

Waldo, Geoffrey S.; Cabantous, Stephanie

2013-04-16

Provided are methods of assaying and improving protein folding using circular permutants of fluorescent proteins, including circular permutants of GFP variants and combinations thereof. The invention further provides various nucleic acid molecules and vectors incorporating such nucleic acid molecules, comprising polynucleotides encoding fluorescent protein circular permutants derived from superfolder GFP, which polynucleotides include an internal cloning site into which a heterologous polynucleotide may be inserted in-frame with the circular permutant coding sequence, and which when expressed are capable of reporting on the degree to which a polypeptide encoded by such an inserted heterologous polynucleotide is correctly folded by correlation with the degree of fluorescence exhibited.

Calculation of heat transfer on shuttle type configurations including the effects of variable entropy at boundary layer edge

NASA Technical Reports Server (NTRS)

Dejarnette, F. R.

1972-01-01

A relatively simple method is presented for including the effect of variable entropy at the boundary-layer edge in a heat transfer method developed previously. For each inviscid surface streamline an approximate shockwave shape is calculated using a modified form of Maslen's method for inviscid axisymmetric flows. The entropy for the streamline at the edge of the boundary layer is determined by equating the mass flux through the shock wave to that inside the boundary layer. Approximations used in this technique allow the heating rates along each inviscid surface streamline to be calculated independent of the other streamlines. The shock standoff distances computed by the present method are found to compare well with those computed by Maslen's asymmetric method. Heating rates are presented for blunted circular and elliptical cones and a typical space shuttle orbiter at angles of attack. Variable entropy effects are found to increase heating rates downstream of the nose significantly higher than those computed using normal-shock entropy, and turbulent heating rates increased more than laminar rates. Effects of Reynolds number and angles of attack are also shown.

Entropy of dynamical social networks

NASA Astrophysics Data System (ADS)

Zhao, Kun; Karsai, Marton; Bianconi, Ginestra

2012-02-01

Dynamical social networks are evolving rapidly and are highly adaptive. Characterizing the information encoded in social networks is essential to gain insight into the structure, evolution, adaptability and dynamics. Recently entropy measures have been used to quantify the information in email correspondence, static networks and mobility patterns. Nevertheless, we still lack methods to quantify the information encoded in time-varying dynamical social networks. In this talk we present a model to quantify the entropy of dynamical social networks and use this model to analyze the data of phone-call communication. We show evidence that the entropy of the phone-call interaction network changes according to circadian rhythms. Moreover we show that social networks are extremely adaptive and are modified by the use of technologies such as mobile phone communication. Indeed the statistics of duration of phone-call is described by a Weibull distribution and is significantly different from the distribution of duration of face-to-face interactions in a conference. Finally we investigate how much the entropy of dynamical social networks changes in realistic models of phone-call or face-to face interactions characterizing in this way different type human social behavior.

Melting curves and entropy of fusion of body-centered cubic tungsten under pressure

NASA Astrophysics Data System (ADS)

Liu, Chun-Mei; Chen, Xiang-Rong; Xu, Chao; Cai, Ling-Cang; Jing, Fu-Qian

2012-07-01

The melting curves and entropy of fusion of body-centered cubic (bcc) tungsten (W) under pressure are investigated via molecular dynamics (MD) simulations with extended Finnis-Sinclair (EFS) potential. The zero pressure melting point obtained is better than other theoretical results by MD simulations with the embedded-atom-method (EAM), Finnis-Sinclair (FS) and modified EAM potentials, and by ab initio MD simulations. Our radial distribution function and running coordination number analyses indicate that apart from the expected increase in disorder, the main change on going from solid to liquid is thus a slight decrease in coordination number. Our entropy of fusion of W during melting, ΔS, at zero pressure, 7.619 J/mol.K, is in good agreement with the experimental and other theoretical data. We found that, with the increasing pressure, the entropy of fusion ΔS decreases fast first and then oscillates with pressure; when the pressure is higher than 100 GPa, the entropy of fusion ΔS is about 6.575 ± 0.086 J/mol.K, which shows less pressure effect.

Innovative techniques to analyze time series of geomagnetic activity indices

NASA Astrophysics Data System (ADS)

Balasis, Georgios; Papadimitriou, Constantinos; Daglis, Ioannis A.; Potirakis, Stelios M.; Eftaxias, Konstantinos

2016-04-01

Magnetic storms are undoubtedly among the most important phenomena in space physics and also a central subject of space weather. The non-extensive Tsallis entropy has been recently introduced, as an effective complexity measure for the analysis of the geomagnetic activity Dst index. The Tsallis entropy sensitively shows the complexity dissimilarity among different "physiological" (normal) and "pathological" states (intense magnetic storms). More precisely, the Tsallis entropy implies the emergence of two distinct patterns: (i) a pattern associated with the intense magnetic storms, which is characterized by a higher degree of organization, and (ii) a pattern associated with normal periods, which is characterized by a lower degree of organization. Other entropy measures such as Block Entropy, T-Complexity, Approximate Entropy, Sample Entropy and Fuzzy Entropy verify the above mentioned result. Importantly, the wavelet spectral analysis in terms of Hurst exponent, H, also shows the existence of two different patterns: (i) a pattern associated with the intense magnetic storms, which is characterized by a fractional Brownian persistent behavior (ii) a pattern associated with normal periods, which is characterized by a fractional Brownian anti-persistent behavior. Finally, we observe universality in the magnetic storm and earthquake dynamics, on a basis of a modified form of the Gutenberg-Richter law for the Tsallis statistics. This finding suggests a common approach to the interpretation of both phenomena in terms of the same driving physical mechanism. Signatures of discrete scale invariance in Dst time series further supports the aforementioned proposal.

Sample entropy analysis for the estimating depth of anaesthesia through human EEG signal at different levels of unconsciousness during surgeries.

PubMed

Liu, Quan; Ma, Li; Fan, Shou-Zen; Abbod, Maysam F; Shieh, Jiann-Shing

2018-01-01

Estimating the depth of anaesthesia (DoA) in operations has always been a challenging issue due to the underlying complexity of the brain mechanisms. Electroencephalogram (EEG) signals are undoubtedly the most widely used signals for measuring DoA. In this paper, a novel EEG-based index is proposed to evaluate DoA for 24 patients receiving general anaesthesia with different levels of unconsciousness. Sample Entropy (SampEn) algorithm was utilised in order to acquire the chaotic features of the signals. After calculating the SampEn from the EEG signals, Random Forest was utilised for developing learning regression models with Bispectral index (BIS) as the target. Correlation coefficient, mean absolute error, and area under the curve (AUC) were used to verify the perioperative performance of the proposed method. Validation comparisons with typical nonstationary signal analysis methods (i.e., recurrence analysis and permutation entropy) and regression methods (i.e., neural network and support vector machine) were conducted. To further verify the accuracy and validity of the proposed methodology, the data is divided into four unconsciousness-level groups on the basis of BIS levels. Subsequently, analysis of variance (ANOVA) was applied to the corresponding index (i.e., regression output). Results indicate that the correlation coefficient improved to 0.72 ± 0.09 after filtering and to 0.90 ± 0.05 after regression from the initial values of 0.51 ± 0.17. Similarly, the final mean absolute error dramatically declined to 5.22 ± 2.12. In addition, the ultimate AUC increased to 0.98 ± 0.02, and the ANOVA analysis indicates that each of the four groups of different anaesthetic levels demonstrated significant difference from the nearest levels. Furthermore, the Random Forest output was extensively linear in relation to BIS, thus with better DoA prediction accuracy. In conclusion, the proposed method provides a concrete basis for monitoring patients' anaesthetic level during surgeries.

On the convergence of difference approximations to scalar conservation laws

NASA Technical Reports Server (NTRS)

Osher, S.; Tadmor, E.

1985-01-01

A unified treatment of explicit in time, two level, second order resolution, total variation diminishing, approximations to scalar conservation laws are presented. The schemes are assumed only to have conservation form and incremental form. A modified flux and a viscosity coefficient are introduced and results in terms of the latter are obtained. The existence of a cell entropy inequality is discussed and such an equality for all entropies is shown to imply that the scheme is an E scheme on monotone (actually more general) data, hence at most only first order accurate in general. Convergence for total variation diminishing-second order resolution schemes approximating convex or concave conservation laws is shown by enforcing a single discrete entropy inequality.

Probing and exploiting the chaotic dynamics of a hydrodynamic photochemical oscillator to implement all the basic binary logic functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayashi, Kenta; Department of Chemistry, Biology, and Biotechnology, University of Perugia, 06123 Perugia; Gotoda, Hiroshi

2016-05-15

The convective motions within a solution of a photochromic spiro-oxazine being irradiated by UV only on the bottom part of its volume, give rise to aperiodic spectrophotometric dynamics. In this paper, we study three nonlinear properties of the aperiodic time series: permutation entropy, short-term predictability and long-term unpredictability, and degree distribution of the visibility graph networks. After ascertaining the extracted chaotic features, we show how the aperiodic time series can be exploited to implement all the fundamental two-inputs binary logic functions (AND, OR, NAND, NOR, XOR, and XNOR) and some basic arithmetic operations (half-adder, full-adder, half-subtractor). This is possible duemore » to the wide range of states a nonlinear system accesses in the course of its evolution. Therefore, the solution of the convective photochemical oscillator results in hardware for chaos-computing alternative to conventional complementary metal-oxide semiconductor-based integrated circuits.« less

Modelling the structure of Zr-rich Pb(Zr1-xTix)O3, x = 0.4 by a multiphase approach.

PubMed

Bogdanov, Alexander; Mysovsky, Andrey; Pickard, Chris J; Kimmel, Anna V

2016-10-12

Solid solution perovskite Pb(Zr 1-x Ti x )O 3 (PZT) is an industrially important material. Despite the long history of experimental and theoretical studies, the structure of this material is still under intensive discussion. In this work, we have applied structure searching coupled with density functional theory methods to provide a multiphase description of this material at x = 0.4. We demonstrate that the permutational freedom of B-site cations leads to the stabilisation of a variety of local phases reflecting a relatively flat energy landscape of PZT. Using a set of predicted local phases we reproduce the experimental pair distribution function (PDF) profile with high accuracy. We introduce a complex multiphase picture of the structure of PZT and show that additional monoclinic and rhombohedral phases account for a better description of the experimental PDF profile. We propose that such a multiphase picture reflects the entropy reached in the sample during the preparation process.

Fourier-Mellin moment-based intertwining map for image encryption

NASA Astrophysics Data System (ADS)

Kaur, Manjit; Kumar, Vijay

2018-03-01

In this paper, a robust image encryption technique that utilizes Fourier-Mellin moments and intertwining logistic map is proposed. Fourier-Mellin moment-based intertwining logistic map has been designed to overcome the issue of low sensitivity of an input image. Multi-objective Non-Dominated Sorting Genetic Algorithm (NSGA-II) based on Reinforcement Learning (MNSGA-RL) has been used to optimize the required parameters of intertwining logistic map. Fourier-Mellin moments are used to make the secret keys more secure. Thereafter, permutation and diffusion operations are carried out on input image using secret keys. The performance of proposed image encryption technique has been evaluated on five well-known benchmark images and also compared with seven well-known existing encryption techniques. The experimental results reveal that the proposed technique outperforms others in terms of entropy, correlation analysis, a unified average changing intensity and the number of changing pixel rate. The simulation results reveal that the proposed technique provides high level of security and robustness against various types of attacks.

[Portable Epileptic Seizure Monitoring Intelligent System Based on Android System].

PubMed

Liang, Zhenhu; Wu, Shufeng; Yang, Chunlin; Jiang, Zhenzhou; Yu, Tao; Lu, Chengbiao; Li, Xiaoli

2016-02-01

The clinical electroencephalogram (EEG) monitoring systems based on personal computer system can not meet the requirements of portability and home usage. The epilepsy patients have to be monitored in hospital for an extended period of time, which imposes a heavy burden on hospitals. In the present study, we designed a portable 16-lead networked monitoring system based on the Android smart phone. The system uses some technologies including the active electrode, the WiFi wireless transmission, the multi-scale permutation entropy (MPE) algorithm, the back-propagation (BP) neural network algorithm, etc. Moreover, the software of Android mobile application can realize the processing and analysis of EEG data, the display of EEG waveform and the alarm of epileptic seizure. The system has been tested on the mobile phones with Android 2. 3 operating system or higher version and the results showed that this software ran accurately and steadily in the detection of epileptic seizure. In conclusion, this paper provides a portable and reliable solution for epileptic seizure monitoring in clinical and home applications.

A new methodology for automated diagnosis of mild cognitive impairment (MCI) using magnetoencephalography (MEG).

PubMed

Amezquita-Sanchez, Juan P; Adeli, Anahita; Adeli, Hojjat

2016-05-15

Mild cognitive impairment (MCI) is a cognitive disorder characterized by memory impairment, greater than expected by age. A new methodology is presented to identify MCI patients during a working memory task using MEG signals. The methodology consists of four steps: In step 1, the complete ensemble empirical mode decomposition (CEEMD) is used to decompose the MEG signal into a set of adaptive sub-bands according to its contained frequency information. In step 2, a nonlinear dynamics measure based on permutation entropy (PE) analysis is employed to analyze the sub-bands and detect features to be used for MCI detection. In step 3, an analysis of variation (ANOVA) is used for feature selection. In step 4, the enhanced probabilistic neural network (EPNN) classifier is applied to the selected features to distinguish between MCI and healthy patients. The usefulness and effectiveness of the proposed methodology are validated using the sensed MEG data obtained experimentally from 18 MCI and 19 control patients. Copyright © 2016 Elsevier B.V. All rights reserved.

An improvement of the measurement of time series irreversibility with visibility graph approach

NASA Astrophysics Data System (ADS)

Wu, Zhenyu; Shang, Pengjian; Xiong, Hui

2018-07-01

We propose a method to improve the measure of real-valued time series irreversibility which contains two tools: the directed horizontal visibility graph and the Kullback-Leibler divergence. The degree of time irreversibility is estimated by the Kullback-Leibler divergence between the in and out degree distributions presented in the associated visibility graph. In our work, we reframe the in and out degree distributions by encoding them with different embedded dimensions used in calculating permutation entropy(PE). With this improved method, we can not only estimate time series irreversibility efficiently, but also detect time series irreversibility from multiple dimensions. We verify the validity of our method and then estimate the amount of time irreversibility of series generated by chaotic maps as well as global stock markets over the period 2005-2015. The result shows that the amount of time irreversibility reaches the peak with embedded dimension d = 3 under circumstances of experiment and financial markets.

Image encryption using a synchronous permutation-diffusion technique

NASA Astrophysics Data System (ADS)

Enayatifar, Rasul; Abdullah, Abdul Hanan; Isnin, Ismail Fauzi; Altameem, Ayman; Lee, Malrey

2017-03-01

In the past decade, the interest on digital images security has been increased among scientists. A synchronous permutation and diffusion technique is designed in order to protect gray-level image content while sending it through internet. To implement the proposed method, two-dimensional plain-image is converted to one dimension. Afterward, in order to reduce the sending process time, permutation and diffusion steps for any pixel are performed in the same time. The permutation step uses chaotic map and deoxyribonucleic acid (DNA) to permute a pixel, while diffusion employs DNA sequence and DNA operator to encrypt the pixel. Experimental results and extensive security analyses have been conducted to demonstrate the feasibility and validity of this proposed image encryption method.

Black hole radiation with modified dispersion relation in tunneling paradigm: Static frame

NASA Astrophysics Data System (ADS)

Tao, Jun; Wang, Peng; Yang, Haitang

2017-09-01

To study possible deviations from the Hawking's prediction, we assume that the dispersion relations of matter fields are modified at high energies and use the Hamilton-Jacobi method to investigate the corresponding effects on the Hawking radiation in this paper. The preferred frame is the static frame of the black hole. The dispersion relation adopted agrees with the relativistic one at low energies but is modified near the Planck mass mp. We calculate the corrections to the Hawking temperature for massive and charged particles to O (mp-2) and massless and neutral particles to all orders. Our results suggest that the thermal spectrum of radiations near horizon is robust, e.g. corrections to the Hawking temperature are suppressed by mp. After the spectrum of radiations near the horizon is obtained, we use the brick wall model to compute the thermal entropy of a massless scalar field near the horizon of a 4D spherically symmetric black hole. We find that the subleading logarithmic term of the entropy does not depend on how the dispersion relations of matter fields are modified. Finally, the luminosities of black holes are computed by using the geometric optics approximation.

A Permutation Approach for Selecting the Penalty Parameter in Penalized Model Selection

PubMed Central

Sabourin, Jeremy A; Valdar, William; Nobel, Andrew B

2015-01-01

Summary We describe a simple, computationally effcient, permutation-based procedure for selecting the penalty parameter in LASSO penalized regression. The procedure, permutation selection, is intended for applications where variable selection is the primary focus, and can be applied in a variety of structural settings, including that of generalized linear models. We briefly discuss connections between permutation selection and existing theory for the LASSO. In addition, we present a simulation study and an analysis of real biomedical data sets in which permutation selection is compared with selection based on the following: cross-validation (CV), the Bayesian information criterion (BIC), Scaled Sparse Linear Regression, and a selection method based on recently developed testing procedures for the LASSO. PMID:26243050

Modifications to holographic entanglement entropy in warped CFT

NASA Astrophysics Data System (ADS)

Song, Wei; Wen, Qiang; Xu, Jianfei

2017-02-01

In [1] it was observed that asymptotic boundary conditions play an important role in the study of holographic entanglement beyond AdS/CFT. In particular, the Ryu-Takayanagi proposal must be modified for warped AdS3 (WAdS3) with Dirichlet boundary conditions. In this paper, we consider AdS3 and WAdS3 with Dirichlet-Neumann boundary conditions. The conjectured holographic duals are warped conformal field theories (WCFTs), featuring a Virasoro-Kac-Moody algebra. We provide a holographic calculation of the entanglement entropy and Rényi entropy using AdS3/WCFT and WAdS3/WCFT dualities. Our bulk results are consistent with the WCFT results derived by Castro-Hofman-Iqbal using the Rindler method. Comparing with [1], we explicitly show that the holographic entanglement entropy is indeed affected by boundary conditions. Both results differ from the Ryu-Takayanagi proposal, indicating new relations between spacetime geometry and quantum entanglement for holographic dualities beyond AdS/CFT.

Demonstration and resolution of the Gibbs paradox of the first kind

NASA Astrophysics Data System (ADS)

Peters, Hjalmar

2014-01-01

The Gibbs paradox of the first kind (GP1) refers to the false increase in entropy which, in statistical mechanics, is calculated from the process of combining two gas systems S1 and S2 consisting of distinguishable particles. Presented in a somewhat modified form, the GP1 manifests as a contradiction to the second law of thermodynamics. Contrary to popular belief, this contradiction affects not only classical but also quantum statistical mechanics. This paper resolves the GP1 by considering two effects. (i) The uncertainty about which particles are located in S1 and which in S2 contributes to the entropies of S1 and S2. (ii) S1 and S2 are correlated by the fact that if a certain particle is located in one system, it cannot be located in the other. As a consequence, the entropy of the total system consisting of S1 and S2 is not the sum of the entropies of S1 and S2.

Particle swarm optimization-based local entropy weighted histogram equalization for infrared image enhancement

NASA Astrophysics Data System (ADS)

Wan, Minjie; Gu, Guohua; Qian, Weixian; Ren, Kan; Chen, Qian; Maldague, Xavier

2018-06-01

Infrared image enhancement plays a significant role in intelligent urban surveillance systems for smart city applications. Unlike existing methods only exaggerating the global contrast, we propose a particle swam optimization-based local entropy weighted histogram equalization which involves the enhancement of both local details and fore-and background contrast. First of all, a novel local entropy weighted histogram depicting the distribution of detail information is calculated based on a modified hyperbolic tangent function. Then, the histogram is divided into two parts via a threshold maximizing the inter-class variance in order to improve the contrasts of foreground and background, respectively. To avoid over-enhancement and noise amplification, double plateau thresholds of the presented histogram are formulated by means of particle swarm optimization algorithm. Lastly, each sub-image is equalized independently according to the constrained sub-local entropy weighted histogram. Comparative experiments implemented on real infrared images prove that our algorithm outperforms other state-of-the-art methods in terms of both visual and quantized evaluations.

Antenna entropy in plant photosystems does not reduce the free energy for primary charge separation.

PubMed

Jennings, Robert C; Zucchelli, Giuseppe

2014-12-01

We have investigated the concept of the so-called "antenna entropy" of higher plant photosystems. Several interesting points emerge: 1. In the case of a photosystemwhich harbours an excited state, the “antenna entropy” is equivalent to the configurational (mixing) entropy of a thermodynamic canonical ensemble. The energy associated with this parameter has been calculated for a hypothetical isoenergetic photosystem, photosystem I and photosystem II, and comes out in the range of 3.5 - 8% of the photon energy considering 680 nm. 2. The “antenna entropy” seems to be a rather unique thermodynamic phenomenon, in as much as it does not modify the free energy available for primary photochemistry, as has been previously suggested. 3. It is underlined that this configurational (mixing) entropy, unlike heat dispersal in a thermal system, does not involve energy dilution. This points out an important difference between thermal and electronic energy dispersal. Copyright © 2014 Elsevier B.V. All rights reserved.

Searching for a C-function on the three-dimensional sphere

NASA Astrophysics Data System (ADS)

Beneventano, C. G.; Cavero-Peláez, I.; D'Ascanio, D.; Santangelo, E. M.

2017-11-01

We present a detailed analytic study on the three-dimensional sphere of the most popular candidates for C-functions, both for Dirac and scalar free massive fields. We discuss to which extent the effective action, the Rényi entanglement entropy and the renormalized entanglement entropy fulfill the conditions expected from C-functions. In view of the absence of a good candidate in the case of the scalar field, we introduce a new candidate, which we call the modified effective action, and analyze its pros and cons.

Comparison of hemodynamic effects of intravenous etomidate versus propofol during induction and intubation using entropy guided hypnosis levels.

PubMed

Shah, Shagun Bhatia; Chowdhury, Itee; Bhargava, Ajay Kumar; Sabbharwal, Bhawnish

2015-01-01

This study aimed to compare the hemodynamic responses during induction and intubation between propofol and etomidate using entropy guided hypnosis. Sixty ASA I & II patients in the age group 20-60 yrs, scheduled for modified radical mastectomy were randomly allocated in two groups based on induction agent Etomidate or Propofol. Both groups received intravenous midazolam 0.03 mg kg(-1) and fentanyl 2 μg kg(-1) as premedication. After induction with the desired agent titrated to entropy 40, vecuronium 0.1 mg kg(-1) was administered for neuromuscular blockade. Heart rate, systolic, diastolic and mean arterial pressures, response entropy [RE] and state entropy [SE] were recorded at baseline, induction and upto three minutes post intubation. Data was subject to statistical analysis SPSS (version 12.0) the paired and the unpaired Student's T-tests for equality of means. Etomidate provided hemodynamic stability without the requirement of any rescue drug in 96.6% patients whereas rescue drug ephedrine was required in 36.6% patients in propofol group. Reduced induction doses 0.15mg kg(-1) for etomidate and 0.98 mg kg(-1) for propofol, sufficed to give an adequate anaesthetic depth based on entropy. Etomidate provides more hemodynamic stability than propofol during induction and intubation. Reduced induction doses of etomidate and propofol titrated to entropy translated into increased hemodynamic stability for both drugs and sufficed to give an adequate anaesthetic depth.

Comparison of hemodynamic effects of intravenous etomidate versus propofol during induction and intubation using entropy guided hypnosis levels

PubMed Central

Shah, Shagun Bhatia; Chowdhury, Itee; Bhargava, Ajay Kumar; Sabbharwal, Bhawnish

2015-01-01

Background and Aims: This study aimed to compare the hemodynamic responses during induction and intubation between propofol and etomidate using entropy guided hypnosis. Material and Methods: Sixty ASA I & II patients in the age group 20-60 yrs, scheduled for modified radical mastectomy were randomly allocated in two groups based on induction agent Etomidate or Propofol. Both groups received intravenous midazolam 0.03 mg kg-1 and fentanyl 2 μg kg-1 as premedication. After induction with the desired agent titrated to entropy 40, vecuronium 0.1 mg kg-1 was administered for neuromuscular blockade. Heart rate, systolic, diastolic and mean arterial pressures, response entropy [RE] and state entropy [SE] were recorded at baseline, induction and upto three minutes post intubation. Data was subject to statistical analysis SPSS (version 12.0) the paired and the unpaired Student's T-tests for equality of means. Results: Etomidate provided hemodynamic stability without the requirement of any rescue drug in 96.6% patients whereas rescue drug ephedrine was required in 36.6% patients in propofol group. Reduced induction doses 0.15mg kg-1 for etomidate and 0.98 mg kg-1 for propofol, sufficed to give an adequate anaesthetic depth based on entropy. Conclusion: Etomidate provides more hemodynamic stability than propofol during induction and intubation. Reduced induction doses of etomidate and propofol titrated to entropy translated into increased hemodynamic stability for both drugs and sufficed to give an adequate anaesthetic depth. PMID:25948897

Overlap Cycles for Permutations: Necessary and Sufficient Conditions

DTIC Science & Technology

2013-09-19

for Weak Orders, To appear in SIAM Journal of Discrete Math . [9] G. Hurlbert and G. Isaak, Equivalence class universal cycles for permutations, Discrete ... Math . 149 (1996), pp. 123–129. [10] J. R. Johnson, Universal cycles for permutations, Discrete Math . 309 (2009), pp. 5264– 5270. [11] E. A. Ragland

Multi-response permutation procedure as an alternative to the analysis of variance: an SPSS implementation.

PubMed

Cai, Li

2006-02-01

A permutation test typically requires fewer assumptions than does a comparable parametric counterpart. The multi-response permutation procedure (MRPP) is a class of multivariate permutation tests of group difference useful for the analysis of experimental data. However, psychologists seldom make use of the MRPP in data analysis, in part because the MRPP is not implemented in popular statistical packages that psychologists use. A set of SPSS macros implementing the MRPP test is provided in this article. The use of the macros is illustrated by analyzing example data sets.

A chaotic modified-DFT encryption scheme for physical layer security and PAPR reduction in OFDM-PON

NASA Astrophysics Data System (ADS)

Fu, Xiaosong; Bi, Meihua; Zhou, Xuefang; Yang, Guowei; Li, Qiliang; Zhou, Zhao; Yang, Xuelin

2018-05-01

This letter proposes a modified discrete Fourier transform (DFT) encryption scheme with multi-dimensional chaos for the physical layer security and peak-to-average power ratio (PAPR) reduction in orthogonal frequency division multiplexing passive optical network (OFDM-PON) system. This multiple-fold encryption algorithm is mainly composed by using the column vectors permutation and the random phase encryption in the standard DFT matrix, which can create ∼10551 key space. The transmission of ∼10 Gb/s encrypted OFDM signal is verified over 20-km standard single mode fiber (SMF). Moreover, experimental results show that, the proposed scheme can achieve ∼2.6-dB PAPR reduction and ∼1-dB improvement of receiver sensitivity if compared with the common OFDM-PON.

A fault diagnosis scheme for planetary gearboxes using modified multi-scale symbolic dynamic entropy and mRMR feature selection

NASA Astrophysics Data System (ADS)

Li, Yongbo; Yang, Yuantao; Li, Guoyan; Xu, Minqiang; Huang, Wenhu

2017-07-01

Health condition identification of planetary gearboxes is crucial to reduce the downtime and maximize productivity. This paper aims to develop a novel fault diagnosis method based on modified multi-scale symbolic dynamic entropy (MMSDE) and minimum redundancy maximum relevance (mRMR) to identify the different health conditions of planetary gearbox. MMSDE is proposed to quantify the regularity of time series, which can assess the dynamical characteristics over a range of scales. MMSDE has obvious advantages in the detection of dynamical changes and computation efficiency. Then, the mRMR approach is introduced to refine the fault features. Lastly, the obtained new features are fed into the least square support vector machine (LSSVM) to complete the fault pattern identification. The proposed method is numerically and experimentally demonstrated to be able to recognize the different fault types of planetary gearboxes.

Using R to Simulate Permutation Distributions for Some Elementary Experimental Designs

ERIC Educational Resources Information Center

Eudey, T. Lynn; Kerr, Joshua D.; Trumbo, Bruce E.

2010-01-01

Null distributions of permutation tests for two-sample, paired, and block designs are simulated using the R statistical programming language. For each design and type of data, permutation tests are compared with standard normal-theory and nonparametric tests. These examples (often using real data) provide for classroom discussion use of metrics…

Circular permutation of a WW domain: Folding still occurs after excising the turn of the folding-nucleating hairpin

PubMed Central

Kier, Brandon L.; Anderson, Jordan M.; Andersen, Niels H.

2014-01-01

A hyperstable Pin1 WW domain has been circularly permuted via excision of the fold-nucleating turn; it still folds to form the native three-strand sheet and hydrophobic core features. Multiprobe folding dynamics studies of the normal and circularly permuted sequences, as well as their constituent hairpin fragments and comparable-length β-strand-loop-β-strand models, indicate 2-state folding for all topologies. N-terminal hairpin formation is the fold nucleating event for the wild-type sequence; the slower folding circular permutant has a more distributed folding transition state. PMID:24350581

Physical Connectivity Mapping by Circular Permutation of Human Telomerase RNA Reveals New Regions Critical for Activity and Processivity.

PubMed

Mefford, Melissa A; Zappulla, David C

2016-01-15

Telomerase is a specialized ribonucleoprotein complex that extends the 3' ends of chromosomes to counteract telomere shortening. However, increased telomerase activity is associated with ∼90% of human cancers. The telomerase enzyme minimally requires an RNA (hTR) and a specialized reverse transcriptase protein (TERT) for activity in vitro. Understanding the structure-function relationships within hTR has important implications for human disease. For the first time, we have tested the physical-connectivity requirements in the 451-nucleotide hTR RNA using circular permutations, which reposition the 5' and 3' ends. Our extensive in vitro analysis identified three classes of hTR circular permutants with altered function. First, circularly permuting 3' of the template causes specific defects in repeat-addition processivity, revealing that the template recognition element found in ciliates is conserved in human telomerase RNA. Second, seven circular permutations residing within the catalytically important core and CR4/5 domains completely abolish telomerase activity, unveiling mechanistically critical portions of these domains. Third, several circular permutations between the core and CR4/5 significantly increase telomerase activity. Our extensive circular permutation results provide insights into the architecture and coordination of human telomerase RNA and highlight where the RNA could be targeted for the development of antiaging and anticancer therapeutics. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Physical Connectivity Mapping by Circular Permutation of Human Telomerase RNA Reveals New Regions Critical for Activity and Processivity

PubMed Central

Mefford, Melissa A.

2015-01-01

Telomerase is a specialized ribonucleoprotein complex that extends the 3′ ends of chromosomes to counteract telomere shortening. However, increased telomerase activity is associated with ∼90% of human cancers. The telomerase enzyme minimally requires an RNA (hTR) and a specialized reverse transcriptase protein (TERT) for activity in vitro. Understanding the structure-function relationships within hTR has important implications for human disease. For the first time, we have tested the physical-connectivity requirements in the 451-nucleotide hTR RNA using circular permutations, which reposition the 5′ and 3′ ends. Our extensive in vitro analysis identified three classes of hTR circular permutants with altered function. First, circularly permuting 3′ of the template causes specific defects in repeat-addition processivity, revealing that the template recognition element found in ciliates is conserved in human telomerase RNA. Second, seven circular permutations residing within the catalytically important core and CR4/5 domains completely abolish telomerase activity, unveiling mechanistically critical portions of these domains. Third, several circular permutations between the core and CR4/5 significantly increase telomerase activity. Our extensive circular permutation results provide insights into the architecture and coordination of human telomerase RNA and highlight where the RNA could be targeted for the development of antiaging and anticancer therapeutics. PMID:26503788

Set-Based Discrete Particle Swarm Optimization Based on Decomposition for Permutation-Based Multiobjective Combinatorial Optimization Problems.

PubMed

Yu, Xue; Chen, Wei-Neng; Gu, Tianlong; Zhang, Huaxiang; Yuan, Huaqiang; Kwong, Sam; Zhang, Jun

2018-07-01

This paper studies a specific class of multiobjective combinatorial optimization problems (MOCOPs), namely the permutation-based MOCOPs. Many commonly seen MOCOPs, e.g., multiobjective traveling salesman problem (MOTSP), multiobjective project scheduling problem (MOPSP), belong to this problem class and they can be very different. However, as the permutation-based MOCOPs share the inherent similarity that the structure of their search space is usually in the shape of a permutation tree, this paper proposes a generic multiobjective set-based particle swarm optimization methodology based on decomposition, termed MS-PSO/D. In order to coordinate with the property of permutation-based MOCOPs, MS-PSO/D utilizes an element-based representation and a constructive approach. Through this, feasible solutions under constraints can be generated step by step following the permutation-tree-shaped structure. And problem-related heuristic information is introduced in the constructive approach for efficiency. In order to address the multiobjective optimization issues, the decomposition strategy is employed, in which the problem is converted into multiple single-objective subproblems according to a set of weight vectors. Besides, a flexible mechanism for diversity control is provided in MS-PSO/D. Extensive experiments have been conducted to study MS-PSO/D on two permutation-based MOCOPs, namely the MOTSP and the MOPSP. Experimental results validate that the proposed methodology is promising.

Quadrantal multi-scale distribution entropy analysis of heartbeat interval series based on a modified Poincaré plot

NASA Astrophysics Data System (ADS)

Huo, Chengyu; Huang, Xiaolin; Zhuang, Jianjun; Hou, Fengzhen; Ni, Huangjing; Ning, Xinbao

2013-09-01

The Poincaré plot is one of the most important approaches in human cardiac rhythm analysis. However, further investigations are still needed to concentrate on techniques that can characterize the dispersion of the points displayed by a Poincaré plot. Based on a modified Poincaré plot, we provide a novel measurement named distribution entropy (DE) and propose a quadrantal multi-scale distribution entropy analysis (QMDE) for the quantitative descriptions of the scatter distribution patterns in various regions and temporal scales. We apply this method to the heartbeat interval series derived from healthy subjects and congestive heart failure (CHF) sufferers, respectively, and find that the discriminations between them are most significant in the first quadrant, which implies significant impacts on vagal regulation brought about by CHF. We also investigate the day-night differences of young healthy people, and it is shown that the results present a clearly circadian rhythm, especially in the first quadrant. In addition, the multi-scale analysis indicates that the results of healthy subjects and CHF sufferers fluctuate in different trends with variation of the scale factor. The same phenomenon also appears in circadian rhythm investigations of young healthy subjects, which implies that the cardiac dynamic system is affected differently in various temporal scales by physiological or pathological factors.

The Matter-Gravity Entanglement Hypothesis

NASA Astrophysics Data System (ADS)

Kay, Bernard S.

2018-03-01

I outline some of my work and results (some dating back to 1998, some more recent) on my matter-gravity entanglement hypothesis, according to which the entropy of a closed quantum gravitational system is equal to the system's matter-gravity entanglement entropy. The main arguments presented are: (1) that this hypothesis is capable of resolving what I call the second-law puzzle, i.e. the puzzle as to how the entropy increase of a closed system can be reconciled with the asssumption of unitary time-evolution; (2) that the black hole information loss puzzle may be regarded as a special case of this second law puzzle and that therefore the same resolution applies to it; (3) that the black hole thermal atmosphere puzzle (which I recall) can be resolved by adopting a radically different-from-usual description of quantum black hole equilibrium states, according to which they are total pure states, entangled between matter and gravity in such a way that the partial states of matter and gravity are each approximately thermal equilibrium states (at the Hawking temperature); (4) that the Susskind-Horowitz-Polchinski string-theoretic understanding of black hole entropy as the logarithm of the degeneracy of a long string (which is the weak string coupling limit of a black hole) cannot be quite correct but should be replaced by a modified understanding according to which it is the entanglement entropy between a long string and its stringy atmosphere, when in a total pure equilibrium state in a suitable box, which (in line with (3)) goes over, at strong-coupling, to a black hole in equilibrium with its thermal atmosphere. The modified understanding in (4) is based on a general result, which I also describe, which concerns the likely state of a quantum system when it is weakly coupled to an energy-bath and the total state is a random pure state with a given energy. This result generalizes Goldstein et al.'s `canonical typicality' result to systems which are not necessarily small.

The Matter-Gravity Entanglement Hypothesis

NASA Astrophysics Data System (ADS)

Kay, Bernard S.

2018-05-01

I outline some of my work and results (some dating back to 1998, some more recent) on my matter-gravity entanglement hypothesis, according to which the entropy of a closed quantum gravitational system is equal to the system's matter-gravity entanglement entropy. The main arguments presented are: (1) that this hypothesis is capable of resolving what I call the second-law puzzle, i.e. the puzzle as to how the entropy increase of a closed system can be reconciled with the asssumption of unitary time-evolution; (2) that the black hole information loss puzzle may be regarded as a special case of this second law puzzle and that therefore the same resolution applies to it; (3) that the black hole thermal atmosphere puzzle (which I recall) can be resolved by adopting a radically different-from-usual description of quantum black hole equilibrium states, according to which they are total pure states, entangled between matter and gravity in such a way that the partial states of matter and gravity are each approximately thermal equilibrium states (at the Hawking temperature); (4) that the Susskind-Horowitz-Polchinski string-theoretic understanding of black hole entropy as the logarithm of the degeneracy of a long string (which is the weak string coupling limit of a black hole) cannot be quite correct but should be replaced by a modified understanding according to which it is the entanglement entropy between a long string and its stringy atmosphere, when in a total pure equilibrium state in a suitable box, which (in line with (3)) goes over, at strong-coupling, to a black hole in equilibrium with its thermal atmosphere. The modified understanding in (4) is based on a general result, which I also describe, which concerns the likely state of a quantum system when it is weakly coupled to an energy-bath and the total state is a random pure state with a given energy. This result generalizes Goldstein et al.'s `canonical typicality' result to systems which are not necessarily small.

Altering the orientation of a fused protein to the RNA-binding ribosomal protein L7Ae and its derivatives through circular permutation.

PubMed

Ohuchi, Shoji J; Sagawa, Fumihiko; Sakamoto, Taiichi; Inoue, Tan

2015-10-23

RNA-protein complexes (RNPs) are useful for constructing functional nano-objects because a variety of functional proteins can be displayed on a designed RNA scaffold. Here, we report circular permutations of an RNA-binding protein L7Ae based on the three-dimensional structure information to alter the orientation of the displayed proteins on the RNA scaffold. An electrophoretic mobility shift assay and atomic force microscopy (AFM) analysis revealed that most of the designed circular permutants formed an RNP nano-object. Moreover, the alteration of the enhanced green fluorescent protein (EGFP) orientation was confirmed with AFM by employing EGFP on the L7Ae permutant on the RNA. The results demonstrate that targeted fine-tuning of the stereo-specific fixation of a protein on a protein-binding RNA is feasible by using the circular permutation technique. Copyright © 2015 Elsevier Inc. All rights reserved.

Linear models: permutation methods

USGS Publications Warehouse

Cade, B.S.; Everitt, B.S.; Howell, D.C.

2005-01-01

Permutation tests (see Permutation Based Inference) for the linear model have applications in behavioral studies when traditional parametric assumptions about the error term in a linear model are not tenable. Improved validity of Type I error rates can be achieved with properly constructed permutation tests. Perhaps more importantly, increased statistical power, improved robustness to effects of outliers, and detection of alternative distributional differences can be achieved by coupling permutation inference with alternative linear model estimators. For example, it is well-known that estimates of the mean in linear model are extremely sensitive to even a single outlying value of the dependent variable compared to estimates of the median [7, 19]. Traditionally, linear modeling focused on estimating changes in the center of distributions (means or medians). However, quantile regression allows distributional changes to be estimated in all or any selected part of a distribution or responses, providing a more complete statistical picture that has relevance to many biological questions [6]...

Altering the orientation of a fused protein to the RNA-binding ribosomal protein L7Ae and its derivatives through circular permutation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohuchi, Shoji J.; Sagawa, Fumihiko; Sakamoto, Taiichi

RNA-protein complexes (RNPs) are useful for constructing functional nano-objects because a variety of functional proteins can be displayed on a designed RNA scaffold. Here, we report circular permutations of an RNA-binding protein L7Ae based on the three-dimensional structure information to alter the orientation of the displayed proteins on the RNA scaffold. An electrophoretic mobility shift assay and atomic force microscopy (AFM) analysis revealed that most of the designed circular permutants formed an RNP nano-object. Moreover, the alteration of the enhanced green fluorescent protein (EGFP) orientation was confirmed with AFM by employing EGFP on the L7Ae permutant on the RNA. Themore » results demonstrate that targeted fine-tuning of the stereo-specific fixation of a protein on a protein-binding RNA is feasible by using the circular permutation technique.« less

Efficient identification of context dependent subgroups of risk from genome wide association studies

PubMed Central

Dyson, Greg; Sing, Charles F.

2014-01-01

We have developed a modified Patient Rule-Induction Method (PRIM) as an alternative strategy for analyzing representative samples of non-experimental human data to estimate and test the role of genomic variations as predictors of disease risk in etiologically heterogeneous sub-samples. A computational limit of the proposed strategy is encountered when the number of genomic variations (predictor variables) under study is large (> 500) because permutations are used to generate a null distribution to test the significance of a term (defined by values of particular variables) that characterizes a sub-sample of individuals through the peeling and pasting processes. As an alternative, in this paper we introduce a theoretical strategy that facilitates the quick calculation of Type I and Type II errors in the evaluation of terms in the peeling and pasting processes carried out in the execution of a PRIM analysis that are underestimated and non-existent, respectively, when a permutation-based hypothesis test is employed. The resultant savings in computational time makes possible the consideration of larger numbers of genomic variations (an example genome wide association study is given) in the selection of statistically significant terms in the formulation of PRIM prediction models. PMID:24570412

Conformational entropic maps of functional coupling domains in GPCR activation: A case study with beta2 adrenergic receptor

NASA Astrophysics Data System (ADS)

Liu, Fan; Abrol, Ravinder; Goddard, William, III; Dougherty, Dennis

2014-03-01

Entropic effect in GPCR activation is poorly understood. Based on the recent solved structures, researchers in the GPCR structural biology field have proposed several ``local activating switches'' that consisted of a few number of conserved residues, but have long ignored the collective dynamical effect (conformational entropy) of a domain comprised of an ensemble of residues. A new paradigm has been proposed recently that a GPCR can be viewed as a composition of several functional coupling domains, each of which undergoes order-to-disorder or disorder-to-order transitions upon activation. Here we identified and studied these functional coupling domains by comparing the local entropy changes of each residue between the inactive and active states of the β2 adrenergic receptor from computational simulation. We found that agonist and G-protein binding increases the heterogeneity of the entropy distribution in the receptor. This new activation paradigm and computational entropy analysis scheme provides novel ways to design functionally modified mutant and identify new allosteric sites for GPCRs. The authors thank NIH and Sanofi for funding this project.

Permutation inference for the general linear model

PubMed Central

Winkler, Anderson M.; Ridgway, Gerard R.; Webster, Matthew A.; Smith, Stephen M.; Nichols, Thomas E.

2014-01-01

Permutation methods can provide exact control of false positives and allow the use of non-standard statistics, making only weak assumptions about the data. With the availability of fast and inexpensive computing, their main limitation would be some lack of flexibility to work with arbitrary experimental designs. In this paper we report on results on approximate permutation methods that are more flexible with respect to the experimental design and nuisance variables, and conduct detailed simulations to identify the best method for settings that are typical for imaging research scenarios. We present a generic framework for permutation inference for complex general linear models (glms) when the errors are exchangeable and/or have a symmetric distribution, and show that, even in the presence of nuisance effects, these permutation inferences are powerful while providing excellent control of false positives in a wide range of common and relevant imaging research scenarios. We also demonstrate how the inference on glm parameters, originally intended for independent data, can be used in certain special but useful cases in which independence is violated. Detailed examples of common neuroimaging applications are provided, as well as a complete algorithm – the “randomise” algorithm – for permutation inference with the glm. PMID:24530839

Modulation of a protein free-energy landscape by circular permutation.

PubMed

Radou, Gaël; Enciso, Marta; Krivov, Sergei; Paci, Emanuele

2013-11-07

Circular permutations usually retain the native structure and function of a protein while inevitably perturbing its folding dynamics. By using simulations with a structure-based model and a rigorous methodology to determine free-energy surfaces from trajectories, we evaluate the effect of a circular permutation on the free-energy landscape of the protein T4 lysozyme. We observe changes which, although subtle, largely affect the cooperativity between the two subdomains. Such a change in cooperativity has been previously experimentally observed and recently also characterized using single molecule optical tweezers and the Crooks relation. The free-energy landscapes show that both the wild type and circular permutant have an on-pathway intermediate, previously experimentally characterized, in which one of the subdomains is completely formed. The landscapes, however, differ in the position of the rate-limiting step for folding, which occurs before the intermediate in the wild type and after in the circular permutant. This shift of transition state explains the observed change in the cooperativity. The underlying free-energy landscape thus provides a microscopic description of the folding dynamics and the connection between circular permutation and the loss of cooperativity experimentally observed.

Entropic nonadditivity, H theorem, and nonlinear Klein-Kramers equations.

PubMed

Dos Santos, M A F; Lenzi, E K

2017-11-01

We use the H theorem to establish the entropy and the entropic additivity law for a system composed of subsystems, with the dynamics governed by the Klein-Kramers equations, by considering relations among the dynamics of these subsystems and their entropies. We start considering the subsystems governed by linear Klein-Kramers equations and verify that the Boltzmann-Gibbs entropy is appropriated to this dynamics, leading us to the standard entropic additivity, S_{BG}^{(1∪2)}=S_{BG}^{1}+S_{BG}^{2}, consistent with the fact that the distributions of the subsystem are independent. We then extend the dynamics of these subsystems to independent nonlinear Klein-Kramers equations. For this case, the results show that the H theorem is verified for a generalized entropy, which does not preserve the standard entropic additivity for independent distributions. In this scenario, consistent results are obtained when a suitable coupling among the nonlinear Klein-Kramers equations is considered, in which each subsystem modifies the other until an equilibrium state is reached. This dynamics, for the subsystems, results in the Tsallis entropy for the system and, consequently, verifies the relation S_{q}^{(1∪2)}=S_{q}^{1}+S_{q}^{2}+(1-q)S_{q}^{1}S_{q}^{2}/k, which is a nonadditive entropic relation.

Statistical aspects of the Klein-Gordon oscillator in the frame work of GUP

NASA Astrophysics Data System (ADS)

Khosropour, B.

2018-01-01

Investigation in perturbative string theory and quantum gravity suggest that there is a measurable minimal length in nature. In this work, according to generalized uncertainty principle, we study the statistical characteristics of Klein-Gordon Oscillator (KLO). The modified energy spectrum of the KLO are obtained. The generalized thermodynamical quantities of the KLO such as partition function, mean energy and entropy are calculated by using the modified energy spectrum.

Hidden cross-correlation patterns in stock markets based on permutation cross-sample entropy and PCA

NASA Astrophysics Data System (ADS)

Lin, Aijing; Shang, Pengjian; Zhong, Bo

2014-12-01

In this article, we investigate the hidden cross-correlation structures in Chinese stock markets and US stock markets by performing PCSE combined with PCA approach. It is suggested that PCSE can provide a more faithful and more interpretable description of the dynamic mechanism between time series than cross-correlation matrix. We show that this new technique can be adapted to observe stock markets especially during financial crisis. In order to identify and compare the interactions and structures of stock markets during financial crisis, as well as in normal periods, all the samples are divided into four sub-periods. The results imply that the cross-correlations between Chinese group are stronger than the US group in the most sub-periods. In particular, it is likely that the US stock markets are more integrated with each other during global financial crisis than during Asian financial crisis. However, our results illustrate that Chinese stock markets are not immune from the global financial crisis, although less integrated with other markets if they are compared with US stock markets.

Permutation parity machines for neural cryptography.

PubMed

Reyes, Oscar Mauricio; Zimmermann, Karl-Heinz

2010-06-01

Recently, synchronization was proved for permutation parity machines, multilayer feed-forward neural networks proposed as a binary variant of the tree parity machines. This ability was already used in the case of tree parity machines to introduce a key-exchange protocol. In this paper, a protocol based on permutation parity machines is proposed and its performance against common attacks (simple, geometric, majority and genetic) is studied.

Inference for Distributions over the Permutation Group

DTIC Science & Technology

2008-05-01

world problems, such as voting , ranking, and data association. Representing uncertainty over permutations is challenging, since there are n...problems, such as voting , ranking, and data association. Representing uncertainty over permutations is challenging, since there are n! possibilities...the Krone ker (or Tensor ) Produ t Representation.In general, the Krone ker produ t representation is redu ible, and so it ande omposed into a dire t

Students' Errors in Solving the Permutation and Combination Problems Based on Problem Solving Steps of Polya

ERIC Educational Resources Information Center

Sukoriyanto; Nusantara, Toto; Subanji; Chandra, Tjang Daniel

2016-01-01

This article was written based on the results of a study evaluating students' errors in problem solving of permutation and combination in terms of problem solving steps according to Polya. Twenty-five students were asked to do four problems related to permutation and combination. The research results showed that the students still did a mistake in…

Permutation parity machines for neural cryptography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reyes, Oscar Mauricio; Escuela de Ingenieria Electrica, Electronica y Telecomunicaciones, Universidad Industrial de Santander, Bucaramanga; Zimmermann, Karl-Heinz

2010-06-15

Recently, synchronization was proved for permutation parity machines, multilayer feed-forward neural networks proposed as a binary variant of the tree parity machines. This ability was already used in the case of tree parity machines to introduce a key-exchange protocol. In this paper, a protocol based on permutation parity machines is proposed and its performance against common attacks (simple, geometric, majority and genetic) is studied.

Sorting signed permutations by short operations.

PubMed

Galvão, Gustavo Rodrigues; Lee, Orlando; Dias, Zanoni

2015-01-01

During evolution, global mutations may alter the order and the orientation of the genes in a genome. Such mutations are referred to as rearrangement events, or simply operations. In unichromosomal genomes, the most common operations are reversals, which are responsible for reversing the order and orientation of a sequence of genes, and transpositions, which are responsible for switching the location of two contiguous portions of a genome. The problem of computing the minimum sequence of operations that transforms one genome into another - which is equivalent to the problem of sorting a permutation into the identity permutation - is a well-studied problem that finds application in comparative genomics. There are a number of works concerning this problem in the literature, but they generally do not take into account the length of the operations (i.e. the number of genes affected by the operations). Since it has been observed that short operations are prevalent in the evolution of some species, algorithms that efficiently solve this problem in the special case of short operations are of interest. In this paper, we investigate the problem of sorting a signed permutation by short operations. More precisely, we study four flavors of this problem: (i) the problem of sorting a signed permutation by reversals of length at most 2; (ii) the problem of sorting a signed permutation by reversals of length at most 3; (iii) the problem of sorting a signed permutation by reversals and transpositions of length at most 2; and (iv) the problem of sorting a signed permutation by reversals and transpositions of length at most 3. We present polynomial-time solutions for problems (i) and (iii), a 5-approximation for problem (ii), and a 3-approximation for problem (iv). Moreover, we show that the expected approximation ratio of the 5-approximation algorithm is not greater than 3 for random signed permutations with more than 12 elements. Finally, we present experimental results that show that the approximation ratios of the approximation algorithms cannot be smaller than 3. In particular, this means that the approximation ratio of the 3-approximation algorithm is tight.

Negative Entropy of Life

NASA Astrophysics Data System (ADS)

Goradia, Shantilal

2015-10-01

We modify Newtonian gravity to probabilistic quantum mechanical gravity to derive strong coupling. If this approach is valid, we should be able to extend it to the physical body (life) as follows. Using Boltzmann equation, we get the entropy of the universe (137) as if its reciprocal, the fine structure constant (ALPHA), is the hidden candidate representing the negative entropy of the universe which is indicative of the binary information as its basis (http://www.arXiv.org/pdf/physics0210040v5). Since ALPHA relates to cosmology, it must relate to molecular biology too, with the binary system as the fundamental source of information for the nucleotides of the DNA as implicit in the book by the author: ``Quantum Consciousness - The Road to Reality.'' We debate claims of anthropic principle based on the negligible variation of ALPHA and throw light on thermodynamics. We question constancy of G in multiple ways.

Measures of thermodynamic irreversibility in deterministic and stochastic dynamics

NASA Astrophysics Data System (ADS)

Ford, Ian J.

2015-07-01

It is generally observed that if a dynamical system is sufficiently complex, then as time progresses it will share out energy and other properties amongst its component parts to eliminate any initial imbalances, retaining only fluctuations. This is known as energy dissipation and it is closely associated with the concept of thermodynamic irreversibility, measured by the increase in entropy according to the second law. It is of interest to quantify such behaviour from a dynamical rather than a thermodynamic perspective and to this end stochastic entropy production and the time-integrated dissipation function have been introduced as analogous measures of irreversibility, principally for stochastic and deterministic dynamics, respectively. We seek to compare these measures. First we modify the dissipation function to allow it to measure irreversibility in situations where the initial probability density function (pdf) of the system is asymmetric as well as symmetric in velocity. We propose that it tests for failure of what we call the obversibility of the system, to be contrasted with reversibility, the failure of which is assessed by stochastic entropy production. We note that the essential difference between stochastic entropy production and the time-integrated modified dissipation function lies in the sequence of procedures undertaken in the associated tests of irreversibility. We argue that an assumed symmetry of the initial pdf with respect to velocity inversion (within a framework of deterministic dynamics) can be incompatible with the Past Hypothesis, according to which there should be a statistical distinction between the behaviour of certain properties of an isolated system as it evolves into the far future and the remote past. Imposing symmetry on a velocity distribution is acceptable for many applications of statistical physics, but can introduce difficulties when discussing irreversible behaviour.

Sample entropy analysis for the estimating depth of anaesthesia through human EEG signal at different levels of unconsciousness during surgeries

PubMed Central

Fan, Shou-Zen; Abbod, Maysam F.

2018-01-01

Estimating the depth of anaesthesia (DoA) in operations has always been a challenging issue due to the underlying complexity of the brain mechanisms. Electroencephalogram (EEG) signals are undoubtedly the most widely used signals for measuring DoA. In this paper, a novel EEG-based index is proposed to evaluate DoA for 24 patients receiving general anaesthesia with different levels of unconsciousness. Sample Entropy (SampEn) algorithm was utilised in order to acquire the chaotic features of the signals. After calculating the SampEn from the EEG signals, Random Forest was utilised for developing learning regression models with Bispectral index (BIS) as the target. Correlation coefficient, mean absolute error, and area under the curve (AUC) were used to verify the perioperative performance of the proposed method. Validation comparisons with typical nonstationary signal analysis methods (i.e., recurrence analysis and permutation entropy) and regression methods (i.e., neural network and support vector machine) were conducted. To further verify the accuracy and validity of the proposed methodology, the data is divided into four unconsciousness-level groups on the basis of BIS levels. Subsequently, analysis of variance (ANOVA) was applied to the corresponding index (i.e., regression output). Results indicate that the correlation coefficient improved to 0.72 ± 0.09 after filtering and to 0.90 ± 0.05 after regression from the initial values of 0.51 ± 0.17. Similarly, the final mean absolute error dramatically declined to 5.22 ± 2.12. In addition, the ultimate AUC increased to 0.98 ± 0.02, and the ANOVA analysis indicates that each of the four groups of different anaesthetic levels demonstrated significant difference from the nearest levels. Furthermore, the Random Forest output was extensively linear in relation to BIS, thus with better DoA prediction accuracy. In conclusion, the proposed method provides a concrete basis for monitoring patients’ anaesthetic level during surgeries. PMID:29844970

Hydration Differences Explain the Large Variations in the Complexation Thermodynamics of Modified γ-Cyclodextrins with Bile Salts.

PubMed

Køhler, Jonatan; Schönbeck, Christian; Westh, Peter; Holm, René

2016-01-28

The structure and thermodynamics of inclusion complexes of seven different γ-cyclodextrins (γCDs) and three biologically relevant bile salts (BS) were investigated in the present study. Natural γCD and six modified γCDs [two methyl-γCDs, one sulfobutyl ether-γCD (SBEγCD), and three 2-hydroxypropyl-γCDs (HPγCD)] and their complexes with BS were investigated by isothermal titration calorimetry, NMR, and molecular dynamics simulations. With the exception of the fully methylated γCD, which did not bind the BSs investigated, all of the γCDs formed 1:1 complexes with the BS, and the structures were similar to those with natural γCD; i.e., the modifications of the γCD had limited structural impact on the formation of complexes. Isothermal titration calorimetry was carried out over in the temperature interval 5-55 °C to enable the calculation of the stability constant (K) and the thermodynamic parameters enthalpy (ΔH°), entropy (ΔS°), and heat capacity (ΔCp°). The stability constants decreased with an increased degree of substitution (DS), with methyl substituents having a lower effect on the stability constant than the sulfobutyl ether and hydroxypropyl substituents on the stability constants. Enthalpy-entropy compensation was observed, since both enthalpy and entropy increased with the degree of substitution, which may reflect dehydration of the hydrophobic surface on both CD and BS. Calculations based on ΔCp° data suggested that each of the substituents dehydrated 10-20 (hydroxypropyl), 22-33 (sulfobutyl ether), and 10-15 Å(2) (methyl) of the BS surface area, in reasonable agreement with estimates from the molecular dynamics simulations. Combined with earlier investigations on modified βCDs, these results indicate general trends of the substituents on the thermodynamics of complex formation.

Determining distinct circuit in complete graphs using permutation

NASA Astrophysics Data System (ADS)

Karim, Sharmila; Ibrahim, Haslinda; Darus, Maizon Mohd

2017-11-01

A Half Butterfly Method (HBM) is a method introduced to construct the distinct circuits in complete graphs where used the concept of isomorphism. The Half Butterfly Method was applied in the field of combinatorics such as in listing permutations of n elements. However the method of determining distinct circuit using HBM for n > 4 is become tedious. Thus, in this paper, we present the method of generating distinct circuit using permutation.

An empirical study using permutation-based resampling in meta-regression

PubMed Central

2012-01-01

Background In meta-regression, as the number of trials in the analyses decreases, the risk of false positives or false negatives increases. This is partly due to the assumption of normality that may not hold in small samples. Creation of a distribution from the observed trials using permutation methods to calculate P values may allow for less spurious findings. Permutation has not been empirically tested in meta-regression. The objective of this study was to perform an empirical investigation to explore the differences in results for meta-analyses on a small number of trials using standard large sample approaches verses permutation-based methods for meta-regression. Methods We isolated a sample of randomized controlled clinical trials (RCTs) for interventions that have a small number of trials (herbal medicine trials). Trials were then grouped by herbal species and condition and assessed for methodological quality using the Jadad scale, and data were extracted for each outcome. Finally, we performed meta-analyses on the primary outcome of each group of trials and meta-regression for methodological quality subgroups within each meta-analysis. We used large sample methods and permutation methods in our meta-regression modeling. We then compared final models and final P values between methods. Results We collected 110 trials across 5 intervention/outcome pairings and 5 to 10 trials per covariate. When applying large sample methods and permutation-based methods in our backwards stepwise regression the covariates in the final models were identical in all cases. The P values for the covariates in the final model were larger in 78% (7/9) of the cases for permutation and identical for 22% (2/9) of the cases. Conclusions We present empirical evidence that permutation-based resampling may not change final models when using backwards stepwise regression, but may increase P values in meta-regression of multiple covariates for relatively small amount of trials. PMID:22587815

Rank score and permutation testing alternatives for regression quantile estimates

USGS Publications Warehouse

Cade, B.S.; Richards, J.D.; Mielke, P.W.

2006-01-01

Performance of quantile rank score tests used for hypothesis testing and constructing confidence intervals for linear quantile regression estimates (0 ≤ τ ≤ 1) were evaluated by simulation for models with p = 2 and 6 predictors, moderate collinearity among predictors, homogeneous and hetero-geneous errors, small to moderate samples (n = 20–300), and central to upper quantiles (0.50–0.99). Test statistics evaluated were the conventional quantile rank score T statistic distributed as χ2 random variable with q degrees of freedom (where q parameters are constrained by H 0:) and an F statistic with its sampling distribution approximated by permutation. The permutation F-test maintained better Type I errors than the T-test for homogeneous error models with smaller n and more extreme quantiles τ. An F distributional approximation of the F statistic provided some improvements in Type I errors over the T-test for models with > 2 parameters, smaller n, and more extreme quantiles but not as much improvement as the permutation approximation. Both rank score tests required weighting to maintain correct Type I errors when heterogeneity under the alternative model increased to 5 standard deviations across the domain of X. A double permutation procedure was developed to provide valid Type I errors for the permutation F-test when null models were forced through the origin. Power was similar for conditions where both T- and F-tests maintained correct Type I errors but the F-test provided some power at smaller n and extreme quantiles when the T-test had no power because of excessively conservative Type I errors. When the double permutation scheme was required for the permutation F-test to maintain valid Type I errors, power was less than for the T-test with decreasing sample size and increasing quantiles. Confidence intervals on parameters and tolerance intervals for future predictions were constructed based on test inversion for an example application relating trout densities to stream channel width:depth.

The right thalamus may play an important role in anesthesia-awakening regulation in frogs

PubMed Central

Fan, Yanzhu; Yue, Xizi; Xue, Fei; Brauth, Steven E.; Tang, Yezhong

2018-01-01

Background Previous studies have shown that the mammalian thalamus is a key structure for anesthesia-induced unconsciousness and anesthesia-awakening regulation. However, both the dynamic characteristics and probable lateralization of thalamic functioning during anesthesia-awakening regulation are not fully understood, and little is known of the evolutionary basis of the role of the thalamus in anesthesia-awakening regulation. Methods An amphibian species, the South African clawed frog (Xenopus laevis) was used in the present study. The frogs were immersed in triciane methanesulfonate (MS-222) for general anesthesia. Electroencephalogram (EEG) signals were recorded continuously from both sides of the telencephalon, diencephalon (thalamus) and mesencephalon during the pre-anesthesia stage, administration stage, recovery stage and post-anesthesia stage. EEG data was analyzed including calculation of approximate entropy (ApEn) and permutation entropy (PE). Results Both ApEn and PE values differed significantly between anesthesia stages, with the highest values occurring during the awakening period and the lowest values during the anesthesia period. There was a significant correlation between the stage durations and ApEn or PE values during anesthesia-awakening cycle primarily for the right diencephalon (right thalamus). ApEn and PE values for females were significantly higher than those for males. Discussion ApEn and PE measurements are suitable for estimating depth of anesthesia and complexity of amphibian brain activity. The right thalamus appears physiologically positioned to play an important role in anesthesia-awakening regulation in frogs indicating an early evolutionary origin of the role of the thalamus in arousal and consciousness in land vertebrates. Sex differences exist in the neural regulation of general anesthesia in frogs. PMID:29576980

Segment swapping aided the evolution of enzyme function: The case of uroporphyrinogen III synthase.

PubMed

Szilágyi, András; Györffy, Dániel; Závodszky, Péter

2017-01-01

In an earlier study, we showed that two-domain segment-swapped proteins can evolve by domain swapping and fusion, resulting in a protein with two linkers connecting its domains. We proposed that a potential evolutionary advantage of this topology may be the restriction of interdomain motions, which may facilitate domain closure by a hinge-like movement, crucial for the function of many enzymes. Here, we test this hypothesis computationally on uroporphyrinogen III synthase, a two-domain segment-swapped enzyme essential in porphyrin metabolism. To compare the interdomain flexibility between the wild-type, segment-swapped enzyme (having two interdomain linkers) and circular permutants of the same enzyme having only one interdomain linker, we performed geometric and molecular dynamics simulations for these species in their ligand-free and ligand-bound forms. We find that in the ligand-free form, interdomain motions in the wild-type enzyme are significantly more restricted than they would be with only one interdomain linker, while the flexibility difference is negligible in the ligand-bound form. We also estimated the entropy costs of ligand binding associated with the interdomain motions, and find that the change in domain connectivity due to segment swapping results in a reduction of this entropy cost, corresponding to ∼20% of the total ligand binding free energy. In addition, the restriction of interdomain motions may also help the functional domain-closure motion required for catalysis. This suggests that the evolution of the segment-swapped topology facilitated the evolution of enzyme function for this protein by influencing its dynamic properties. Proteins 2016; 85:46-53. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

An analog scrambler for speech based on sequential permutations in time and frequency

NASA Astrophysics Data System (ADS)

Cox, R. V.; Jayant, N. S.; McDermott, B. J.

Permutation of speech segments is an operation that is frequently used in the design of scramblers for analog speech privacy. In this paper, a sequential procedure for segment permutation is considered. This procedure can be extended to two dimensional permutation of time segments and frequency bands. By subjective testing it is shown that this combination gives a residual intelligibility for spoken digits of 20 percent with a delay of 256 ms. (A lower bound for this test would be 10 percent). The complexity of implementing such a system is considered and the issues of synchronization and channel equalization are addressed. The computer simulation results for the system using both real and simulated channels are examined.

A 1.375-approximation algorithm for sorting by transpositions.

PubMed

Elias, Isaac; Hartman, Tzvika

2006-01-01

Sorting permutations by transpositions is an important problem in genome rearrangements. A transposition is a rearrangement operation in which a segment is cut out of the permutation and pasted in a different location. The complexity of this problem is still open and it has been a 10-year-old open problem to improve the best known 1.5-approximation algorithm. In this paper, we provide a 1.375-approximation algorithm for sorting by transpositions. The algorithm is based on a new upper bound on the diameter of 3-permutations. In addition, we present some new results regarding the transposition diameter: we improve the lower bound for the transposition diameter of the symmetric group and determine the exact transposition diameter of simple permutations.

Permutational distribution of the log-rank statistic under random censorship with applications to carcinogenicity assays.

PubMed

Heimann, G; Neuhaus, G

1998-03-01

In the random censorship model, the log-rank test is often used for comparing a control group with different dose groups. If the number of tumors is small, so-called exact methods are often applied for computing critical values from a permutational distribution. Two of these exact methods are discussed and shown to be incorrect. The correct permutational distribution is derived and studied with respect to its behavior under unequal censoring in the light of recent results proving that the permutational version and the unconditional version of the log-rank test are asymptotically equivalent even under unequal censoring. The log-rank test is studied by simulations of a realistic scenario from a bioassay with small numbers of tumors.

Properties of permutation-based gene tests and controlling type 1 error using a summary statistic based gene test

PubMed Central

2013-01-01

Background The advent of genome-wide association studies has led to many novel disease-SNP associations, opening the door to focused study on their biological underpinnings. Because of the importance of analyzing these associations, numerous statistical methods have been devoted to them. However, fewer methods have attempted to associate entire genes or genomic regions with outcomes, which is potentially more useful knowledge from a biological perspective and those methods currently implemented are often permutation-based. Results One property of some permutation-based tests is that their power varies as a function of whether significant markers are in regions of linkage disequilibrium (LD) or not, which we show from a theoretical perspective. We therefore develop two methods for quantifying the degree of association between a genomic region and outcome, both of whose power does not vary as a function of LD structure. One method uses dimension reduction to “filter” redundant information when significant LD exists in the region, while the other, called the summary-statistic test, controls for LD by scaling marker Z-statistics using knowledge of the correlation matrix of markers. An advantage of this latter test is that it does not require the original data, but only their Z-statistics from univariate regressions and an estimate of the correlation structure of markers, and we show how to modify the test to protect the type 1 error rate when the correlation structure of markers is misspecified. We apply these methods to sequence data of oral cleft and compare our results to previously proposed gene tests, in particular permutation-based ones. We evaluate the versatility of the modification of the summary-statistic test since the specification of correlation structure between markers can be inaccurate. Conclusion We find a significant association in the sequence data between the 8q24 region and oral cleft using our dimension reduction approach and a borderline significant association using the summary-statistic based approach. We also implement the summary-statistic test using Z-statistics from an already-published GWAS of Chronic Obstructive Pulmonary Disorder (COPD) and correlation structure obtained from HapMap. We experiment with the modification of this test because the correlation structure is assumed imperfectly known. PMID:24199751

Properties of permutation-based gene tests and controlling type 1 error using a summary statistic based gene test.

PubMed

Swanson, David M; Blacker, Deborah; Alchawa, Taofik; Ludwig, Kerstin U; Mangold, Elisabeth; Lange, Christoph

2013-11-07

The advent of genome-wide association studies has led to many novel disease-SNP associations, opening the door to focused study on their biological underpinnings. Because of the importance of analyzing these associations, numerous statistical methods have been devoted to them. However, fewer methods have attempted to associate entire genes or genomic regions with outcomes, which is potentially more useful knowledge from a biological perspective and those methods currently implemented are often permutation-based. One property of some permutation-based tests is that their power varies as a function of whether significant markers are in regions of linkage disequilibrium (LD) or not, which we show from a theoretical perspective. We therefore develop two methods for quantifying the degree of association between a genomic region and outcome, both of whose power does not vary as a function of LD structure. One method uses dimension reduction to "filter" redundant information when significant LD exists in the region, while the other, called the summary-statistic test, controls for LD by scaling marker Z-statistics using knowledge of the correlation matrix of markers. An advantage of this latter test is that it does not require the original data, but only their Z-statistics from univariate regressions and an estimate of the correlation structure of markers, and we show how to modify the test to protect the type 1 error rate when the correlation structure of markers is misspecified. We apply these methods to sequence data of oral cleft and compare our results to previously proposed gene tests, in particular permutation-based ones. We evaluate the versatility of the modification of the summary-statistic test since the specification of correlation structure between markers can be inaccurate. We find a significant association in the sequence data between the 8q24 region and oral cleft using our dimension reduction approach and a borderline significant association using the summary-statistic based approach. We also implement the summary-statistic test using Z-statistics from an already-published GWAS of Chronic Obstructive Pulmonary Disorder (COPD) and correlation structure obtained from HapMap. We experiment with the modification of this test because the correlation structure is assumed imperfectly known.

Object-Based Land Use Classification of Agricultural Land by Coupling Multi-Temporal Spectral Characteristics and Phenological Events in Germany

NASA Astrophysics Data System (ADS)

Knoefel, Patrick; Loew, Fabian; Conrad, Christopher

2015-04-01

Crop maps based on classification of remotely sensed data are of increased attendance in agricultural management. This induces a more detailed knowledge about the reliability of such spatial information. However, classification of agricultural land use is often limited by high spectral similarities of the studied crop types. More, spatially and temporally varying agro-ecological conditions can introduce confusion in crop mapping. Classification errors in crop maps in turn may have influence on model outputs, like agricultural production monitoring. One major goal of the PhenoS project ("Phenological structuring to determine optimal acquisition dates for Sentinel-2 data for field crop classification"), is the detection of optimal phenological time windows for land cover classification purposes. Since many crop species are spectrally highly similar, accurate classification requires the right selection of satellite images for a certain classification task. In the course of one growing season, phenological phases exist where crops are separable with higher accuracies. For this purpose, coupling of multi-temporal spectral characteristics and phenological events is promising. The focus of this study is set on the separation of spectrally similar cereal crops like winter wheat, barley, and rye of two test sites in Germany called "Harz/Central German Lowland" and "Demmin". However, this study uses object based random forest (RF) classification to investigate the impact of image acquisition frequency and timing on crop classification uncertainty by permuting all possible combinations of available RapidEye time series recorded on the test sites between 2010 and 2014. The permutations were applied to different segmentation parameters. Then, classification uncertainty was assessed and analysed, based on the probabilistic soft-output from the RF algorithm at the per-field basis. From this soft output, entropy was calculated as a spatial measure of classification uncertainty. The results indicate that uncertainty estimates provide a valuable addition to traditional accuracy assessments and helps the user to allocate error in crop maps.

How unitary cosmology generalizes thermodynamics and solves the inflationary entropy problem

NASA Astrophysics Data System (ADS)

Tegmark, Max

2012-06-01

We analyze cosmology assuming unitary quantum mechanics, using a tripartite partition into system, observer, and environment degrees of freedom. This generalizes the second law of thermodynamics to “The system’s entropy cannot decrease unless it interacts with the observer, and it cannot increase unless it interacts with the environment.” The former follows from the quantum Bayes theorem we derive. We show that because of the long-range entanglement created by cosmological inflation, the cosmic entropy decreases exponentially rather than linearly with the number of bits of information observed, so that a given observer can reduce entropy by much more than the amount of information her brain can store. Indeed, we argue that as long as inflation has occurred in a non-negligible fraction of the volume, almost all sentient observers will find themselves in a post-inflationary low-entropy Hubble volume, and we humans have no reason to be surprised that we do so as well, which solves the so-called inflationary entropy problem. An arguably worse problem for unitary cosmology involves gamma-ray-burst constraints on the “big snap,” a fourth cosmic doomsday scenario alongside the “big crunch,” “big chill,” and “big rip,” where an increasingly granular nature of expanding space modifies our life-supporting laws of physics. Our tripartite framework also clarifies when the popular quantum gravity approximation Gμν≈8πG⟨Tμν⟩ is valid, and how problems with recent attempts to explain dark energy as gravitational backreaction from superhorizon scale fluctuations can be understood as a failure of this approximation.

Magnetic Stirling cycles - A new application for magnetic materials

NASA Technical Reports Server (NTRS)

Brown, G. V.

1977-01-01

There is the prospect of a fundamental new application for magnetic materials as the working substance in thermodynamic cycles. Recuperative cycles which use a rare-earth ferromagnetic material near its Curie point in the field of a superconducting magnet appear feasible for applications from below 20 K to above room temperature. The elements of the cycle, advanced in an earlier paper, are summarized. The basic advantages include high entropy density in the magnetic material, completely reversible processes, convenient control of the entropy by the applied field, the feature that heat transfer is possible during all processes, and the ability of the ideal cycle to attain Carnot efficiency. The mean field theory is used to predict the entropy of a ferromagnet in an applied field and also the isothermal entropy change and isentropic temperature change caused by applying a field. Results are presented for J = 7/2 and g = 2. The results for isentropic temperature change are compared with experimental data on Gd. Coarse mixtures of ferromagnetic materials with different Curie points are proposed to modify the path of the cycle in the T-S diagram in order to improve the efficiency or to increase the specific power.

A Computationally Efficient Hypothesis Testing Method for Epistasis Analysis using Multifactor Dimensionality Reduction

PubMed Central

Pattin, Kristine A.; White, Bill C.; Barney, Nate; Gui, Jiang; Nelson, Heather H.; Kelsey, Karl R.; Andrew, Angeline S.; Karagas, Margaret R.; Moore, Jason H.

2008-01-01

Multifactor dimensionality reduction (MDR) was developed as a nonparametric and model-free data mining method for detecting, characterizing, and interpreting epistasis in the absence of significant main effects in genetic and epidemiologic studies of complex traits such as disease susceptibility. The goal of MDR is to change the representation of the data using a constructive induction algorithm to make nonadditive interactions easier to detect using any classification method such as naïve Bayes or logistic regression. Traditionally, MDR constructed variables have been evaluated with a naïve Bayes classifier that is combined with 10-fold cross validation to obtain an estimate of predictive accuracy or generalizability of epistasis models. Traditionally, we have used permutation testing to statistically evaluate the significance of models obtained through MDR. The advantage of permutation testing is that it controls for false-positives due to multiple testing. The disadvantage is that permutation testing is computationally expensive. This is in an important issue that arises in the context of detecting epistasis on a genome-wide scale. The goal of the present study was to develop and evaluate several alternatives to large-scale permutation testing for assessing the statistical significance of MDR models. Using data simulated from 70 different epistasis models, we compared the power and type I error rate of MDR using a 1000-fold permutation test with hypothesis testing using an extreme value distribution (EVD). We find that this new hypothesis testing method provides a reasonable alternative to the computationally expensive 1000-fold permutation test and is 50 times faster. We then demonstrate this new method by applying it to a genetic epidemiology study of bladder cancer susceptibility that was previously analyzed using MDR and assessed using a 1000-fold permutation test. PMID:18671250

Estrogen pathway polymorphisms in relation to primary open angle glaucoma: An analysis accounting for gender from the United States

PubMed Central

Loomis, Stephanie J.; Weinreb, Robert N.; Kang, Jae H.; Yaspan, Brian L.; Bailey, Jessica Cooke; Gaasterland, Douglas; Gaasterland, Terry; Lee, Richard K.; Scott, William K.; Lichter, Paul R.; Budenz, Donald L.; Liu, Yutao; Realini, Tony; Friedman, David S.; McCarty, Catherine A.; Moroi, Sayoko E.; Olson, Lana; Schuman, Joel S.; Singh, Kuldev; Vollrath, Douglas; Wollstein, Gadi; Zack, Donald J.; Brilliant, Murray; Sit, Arthur J.; Christen, William G.; Fingert, John; Kraft, Peter; Zhang, Kang; Allingham, R. Rand; Pericak-Vance, Margaret A.; Richards, Julia E.; Hauser, Michael A.; Haines, Jonathan L.; Wiggs, Janey L.

2013-01-01

Purpose Circulating estrogen levels are relevant in glaucoma phenotypic traits. We assessed the association between an estrogen metabolism single nucleotide polymorphism (SNP) panel in relation to primary open angle glaucoma (POAG), accounting for gender. Methods We included 3,108 POAG cases and 3,430 controls of both genders from the Glaucoma Genes and Environment (GLAUGEN) study and the National Eye Institute Glaucoma Human Genetics Collaboration (NEIGHBOR) consortium genotyped on the Illumina 660W-Quad platform. We assessed the relation between the SNP panels representative of estrogen metabolism and POAG using pathway- and gene-based approaches with the Pathway Analysis by Randomization Incorporating Structure (PARIS) software. PARIS executes a permutation algorithm to assess statistical significance relative to the pathways and genes of comparable genetic architecture. These analyses were performed using the meta-analyzed results from the GLAUGEN and NEIGHBOR data sets. We evaluated POAG overall as well as two subtypes of POAG defined as intraocular pressure (IOP) ≥22 mmHg (high-pressure glaucoma [HPG]) or IOP <22 mmHg (normal pressure glaucoma [NPG]) at diagnosis. We conducted these analyses for each gender separately and then jointly in men and women. Results Among women, the estrogen SNP pathway was associated with POAG overall (permuted p=0.006) and HPG (permuted p<0.001) but not NPG (permuted p=0.09). Interestingly, there was no relation between the estrogen SNP pathway and POAG when men were considered alone (permuted p>0.99). Among women, gene-based analyses revealed that the catechol-O-methyltransferase gene showed strong associations with HTG (permuted gene p≤0.001) and NPG (permuted gene p=0.01). Conclusions The estrogen SNP pathway was associated with POAG among women. PMID:23869166

Error-free holographic frames encryption with CA pixel-permutation encoding algorithm

NASA Astrophysics Data System (ADS)

Li, Xiaowei; Xiao, Dan; Wang, Qiong-Hua

2018-01-01

The security of video data is necessary in network security transmission hence cryptography is technique to make video data secure and unreadable to unauthorized users. In this paper, we propose a holographic frames encryption technique based on the cellular automata (CA) pixel-permutation encoding algorithm. The concise pixel-permutation algorithm is used to address the drawbacks of the traditional CA encoding methods. The effectiveness of the proposed video encoding method is demonstrated by simulation examples.

A Flexible Computational Framework Using R and Map-Reduce for Permutation Tests of Massive Genetic Analysis of Complex Traits.

PubMed

Mahjani, Behrang; Toor, Salman; Nettelblad, Carl; Holmgren, Sverker

2017-01-01

In quantitative trait locus (QTL) mapping significance of putative QTL is often determined using permutation testing. The computational needs to calculate the significance level are immense, 10 4 up to 10 8 or even more permutations can be needed. We have previously introduced the PruneDIRECT algorithm for multiple QTL scan with epistatic interactions. This algorithm has specific strengths for permutation testing. Here, we present a flexible, parallel computing framework for identifying multiple interacting QTL using the PruneDIRECT algorithm which uses the map-reduce model as implemented in Hadoop. The framework is implemented in R, a widely used software tool among geneticists. This enables users to rearrange algorithmic steps to adapt genetic models, search algorithms, and parallelization steps to their needs in a flexible way. Our work underlines the maturity of accessing distributed parallel computing for computationally demanding bioinformatics applications through building workflows within existing scientific environments. We investigate the PruneDIRECT algorithm, comparing its performance to exhaustive search and DIRECT algorithm using our framework on a public cloud resource. We find that PruneDIRECT is vastly superior for permutation testing, and perform 2 ×10 5 permutations for a 2D QTL problem in 15 hours, using 100 cloud processes. We show that our framework scales out almost linearly for a 3D QTL search.

siRNAmod: A database of experimentally validated chemically modified siRNAs.

PubMed

Dar, Showkat Ahmad; Thakur, Anamika; Qureshi, Abid; Kumar, Manoj

2016-01-28

Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.

Photographs and Committees: Activities That Help Students Discover Permutations and Combinations.

ERIC Educational Resources Information Center

Szydlik, Jennifer Earles

2000-01-01

Presents problem situations that support students when discovering the multiplication principle, permutations, combinations, Pascal's triangle, and relationships among those objects in a concrete context. (ASK)

A permutation characterization of Sturm global attractors of Hamiltonian type

NASA Astrophysics Data System (ADS)

Fiedler, Bernold; Rocha, Carlos; Wolfrum, Matthias

We consider Neumann boundary value problems of the form u=u+f on the interval 0⩽x⩽π for dissipative nonlinearities f=f(u). A permutation characterization for the global attractors of the semiflows generated by these equations is well known, even in the much more general case f=f(x,u,u). We present a permutation characterization for the global attractors in the restrictive class of nonlinearities f=f(u). In this class the stationary solutions of the parabolic equation satisfy the second order ODE v+f(v)=0 and we obtain the permutation characterization from a characterization of the set of 2 π-periodic orbits of this planar Hamiltonian system. Our results are based on a diligent discussion of this mere pendulum equation.

A Novel Color Image Encryption Algorithm Based on Quantum Chaos Sequence

NASA Astrophysics Data System (ADS)

Liu, Hui; Jin, Cong

2017-03-01

In this paper, a novel algorithm of image encryption based on quantum chaotic is proposed. The keystreams are generated by the two-dimensional logistic map as initial conditions and parameters. And then general Arnold scrambling algorithm with keys is exploited to permute the pixels of color components. In diffusion process, a novel encryption algorithm, folding algorithm, is proposed to modify the value of diffused pixels. In order to get the high randomness and complexity, the two-dimensional logistic map and quantum chaotic map are coupled with nearest-neighboring coupled-map lattices. Theoretical analyses and computer simulations confirm that the proposed algorithm has high level of security.

PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies.

PubMed

Yang, Guangyuan; Jiang, Wei; Yang, Qiang; Yu, Weichuan

2015-05-01

The importance of testing associations allowing for interactions has been demonstrated by Marchini et al. (2005). A fast method detecting associations allowing for interactions has been proposed by Wan et al. (2010a). The method is based on likelihood ratio test with the assumption that the statistic follows the χ(2) distribution. Many single nucleotide polymorphism (SNP) pairs with significant associations allowing for interactions have been detected using their method. However, the assumption of χ(2) test requires the expected values in each cell of the contingency table to be at least five. This assumption is violated in some identified SNP pairs. In this case, likelihood ratio test may not be applicable any more. Permutation test is an ideal approach to checking the P-values calculated in likelihood ratio test because of its non-parametric nature. The P-values of SNP pairs having significant associations with disease are always extremely small. Thus, we need a huge number of permutations to achieve correspondingly high resolution for the P-values. In order to investigate whether the P-values from likelihood ratio tests are reliable, a fast permutation tool to accomplish large number of permutations is desirable. We developed a permutation tool named PBOOST. It is based on GPU with highly reliable P-value estimation. By using simulation data, we found that the P-values from likelihood ratio tests will have relative error of >100% when 50% cells in the contingency table have expected count less than five or when there is zero expected count in any of the contingency table cells. In terms of speed, PBOOST completed 10(7) permutations for a single SNP pair from the Wellcome Trust Case Control Consortium (WTCCC) genome data (Wellcome Trust Case Control Consortium, 2007) within 1 min on a single Nvidia Tesla M2090 device, while it took 60 min in a single CPU Intel Xeon E5-2650 to finish the same task. More importantly, when simultaneously testing 256 SNP pairs for 10(7) permutations, our tool took only 5 min, while the CPU program took 10 h. By permuting on a GPU cluster consisting of 40 nodes, we completed 10(12) permutations for all 280 SNP pairs reported with P-values smaller than 1.6 × 10⁻¹² in the WTCCC datasets in 1 week. The source code and sample data are available at http://bioinformatics.ust.hk/PBOOST.zip. gyang@ust.hk; eeyu@ust.hk Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Visual data mining for quantized spatial data

NASA Technical Reports Server (NTRS)

Braverman, Amy; Kahn, Brian

2004-01-01

In previous papers we've shown how a well known data compression algorithm called Entropy-constrained Vector Quantization ( can be modified to reduce the size and complexity of very large, satellite data sets. In this paper, we descuss how to visualize and understand the content of such reduced data sets.

Engineering calculations for solving the orbital allotment problem

NASA Technical Reports Server (NTRS)

Reilly, C.; Walton, E. K.; Mount-Campbell, C.; Caldecott, R.; Aebker, E.; Mata, F.

1988-01-01

Four approaches for calculating downlink interferences for shaped-beam antennas are described. An investigation of alternative mixed-integer programming models for satellite synthesis is summarized. Plans for coordinating the various programs developed under this grant are outlined. Two procedures for ordering satellites to initialize the k-permutation algorithm are proposed. Results are presented for the k-permutation algorithms. Feasible solutions are found for 5 of the 6 problems considered. Finally, it is demonstrated that the k-permutation algorithm can be used to solve arc allotment problems.

Competition between conceptual relations affects compound recognition: the role of entropy.

PubMed

Schmidtke, Daniel; Kuperman, Victor; Gagné, Christina L; Spalding, Thomas L

2016-04-01

Previous research has suggested that the conceptual representation of a compound is based on a relational structure linking the compound's constituents. Existing accounts of the visual recognition of modifier-head or noun-noun compounds posit that the process involves the selection of a relational structure out of a set of competing relational structures associated with the same compound. In this article, we employ the information-theoretic metric of entropy to gauge relational competition and investigate its effect on the visual identification of established English compounds. The data from two lexical decision megastudies indicates that greater entropy (i.e., increased competition) in a set of conceptual relations associated with a compound is associated with longer lexical decision latencies. This finding indicates that there exists competition between potential meanings associated with the same complex word form. We provide empirical support for conceptual composition during compound word processing in a model that incorporates the effect of the integration of co-activated and competing relational information.

Generalized entropy production fluctuation theorems for quantum systems

NASA Astrophysics Data System (ADS)

Rana, Shubhashis; Lahiri, Sourabh; Jayannavar, A. M.

2013-02-01

Based on trajectory dependent path probability formalism in state space, we derive generalized entropy production fluctuation relations for a quantum system in the presence of measurement and feedback. We have obtained these results for three different cases: (i) the system is evolving in isolation from its surroundings; (ii) the system being weakly coupled to a heat bath; and (iii) system in contact with reservoir using quantum Crooks fluctuation theorem. In case (iii), we build on the treatment carried out in [H. T. Quan and H. Dong, arxiv/cond-mat: 0812.4955], where a quantum trajectory has been defined as a sequence of alternating work and heat steps. The obtained entropy production fluctuation theorems retain the same form as in the classical case. The inequality of second law of thermodynamics gets modified in the presence of information. These fluctuation theorems are robust against intermediate measurements of any observable performed with respect to von Neumann projective measurements as well as weak or positive operator valued measurements.

Entropy production in photovoltaic-thermoelectric nanodevices from the non-equilibrium Green’s function formalism

NASA Astrophysics Data System (ADS)

Michelini, Fabienne; Crépieux, Adeline; Beltako, Katawoura

2017-05-01

We discuss some thermodynamic aspects of energy conversion in electronic nanosystems able to convert light energy into electrical or/and thermal energy using the non-equilibrium Green’s function formalism. In a first part, we derive the photon energy and particle currents inside a nanosystem interacting with light and in contact with two electron reservoirs at different temperatures. Energy conservation is verified, and radiation laws are discussed from electron non-equilibrium Green’s functions. We further use the photon currents to formulate the rate of entropy production for steady-state nanosystems, and we recast this rate in terms of efficiency for specific photovoltaic-thermoelectric nanodevices. In a second part, a quantum dot based nanojunction is closely examined using a two-level model. We show analytically that the rate of entropy production is always positive, but we find numerically that it can reach negative values when the derived particule and energy currents are empirically modified as it is usually done for modeling realistic photovoltaic systems.

Entropy production in photovoltaic-thermoelectric nanodevices from the non-equilibrium Green's function formalism.

PubMed

Michelini, Fabienne; Crépieux, Adeline; Beltako, Katawoura

2017-05-04

We discuss some thermodynamic aspects of energy conversion in electronic nanosystems able to convert light energy into electrical or/and thermal energy using the non-equilibrium Green's function formalism. In a first part, we derive the photon energy and particle currents inside a nanosystem interacting with light and in contact with two electron reservoirs at different temperatures. Energy conservation is verified, and radiation laws are discussed from electron non-equilibrium Green's functions. We further use the photon currents to formulate the rate of entropy production for steady-state nanosystems, and we recast this rate in terms of efficiency for specific photovoltaic-thermoelectric nanodevices. In a second part, a quantum dot based nanojunction is closely examined using a two-level model. We show analytically that the rate of entropy production is always positive, but we find numerically that it can reach negative values when the derived particule and energy currents are empirically modified as it is usually done for modeling realistic photovoltaic systems.

Local statistics adaptive entropy coding method for the improvement of H.26L VLC coding

NASA Astrophysics Data System (ADS)

Yoo, Kook-yeol; Kim, Jong D.; Choi, Byung-Sun; Lee, Yung Lyul

2000-05-01

In this paper, we propose an adaptive entropy coding method to improve the VLC coding efficiency of H.26L TML-1 codec. First of all, we will show that the VLC coding presented in TML-1 does not satisfy the sibling property of entropy coding. Then, we will modify the coding method into the local statistics adaptive one to satisfy the property. The proposed method based on the local symbol statistics dynamically changes the mapping relationship between symbol and bit pattern in the VLC table according to sibling property. Note that the codewords in the VLC table of TML-1 codec is not changed. Since this changed mapping relationship also derived in the decoder side by using the decoded symbols, the proposed VLC coding method does not require any overhead information. The simulation results show that the proposed method gives about 30% and 37% reduction in average bit rate for MB type and CBP information, respectively.

On the optimality of a universal noiseless coder

NASA Technical Reports Server (NTRS)

Yeh, Pen-Shu; Rice, Robert F.; Miller, Warner H.

1993-01-01

Rice developed a universal noiseless coding structure that provides efficient performance over an extremely broad range of source entropy. This is accomplished by adaptively selecting the best of several easily implemented variable length coding algorithms. Variations of such noiseless coders have been used in many NASA applications. Custom VLSI coder and decoder modules capable of processing over 50 million samples per second have been fabricated and tested. In this study, the first of the code options used in this module development is shown to be equivalent to a class of Huffman code under the Humblet condition, for source symbol sets having a Laplacian distribution. Except for the default option, other options are shown to be equivalent to the Huffman codes of a modified Laplacian symbol set, at specified symbol entropy values. Simulation results are obtained on actual aerial imagery over a wide entropy range, and they confirm the optimality of the scheme. Comparison with other known techniques are performed on several widely used images and the results further validate the coder's optimality.

Permutation invariant polynomial neural network approach to fitting potential energy surfaces. II. Four-atom systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jun; Jiang, Bin; Guo, Hua, E-mail: hguo@unm.edu

2013-11-28

A rigorous, general, and simple method to fit global and permutation invariant potential energy surfaces (PESs) using neural networks (NNs) is discussed. This so-called permutation invariant polynomial neural network (PIP-NN) method imposes permutation symmetry by using in its input a set of symmetry functions based on PIPs. For systems with more than three atoms, it is shown that the number of symmetry functions in the input vector needs to be larger than the number of internal coordinates in order to include both the primary and secondary invariant polynomials. This PIP-NN method is successfully demonstrated in three atom-triatomic reactive systems, resultingmore » in full-dimensional global PESs with average errors on the order of meV. These PESs are used in full-dimensional quantum dynamical calculations.« less

The dark-baryonic matter mass relation for observational verification in Verlinde's emergent gravity

NASA Astrophysics Data System (ADS)

Shen, Jian Qi

2018-06-01

Recently, a new interesting idea of origin of gravity has been developed by Verlinde. In this scheme of emergent gravity, where horizon entropy, microscopic de Sitter states and relevant contribution to gravity are involved, an entropy displacement resulting from matter behaves as a memory effect and can be exhibited at sub-Hubble scales, namely, the entropy displacement and its "elastic" response would lead to emergent gravity, which gives rise to an extra gravitational force. Then galactic dark matter effects may origin from such extra emergent gravity. We discuss some concepts in Verlinde's theory of emergent gravity and point out some possible problems or issues, e.g., the gravitational potential caused by Verlinde's emergent apparent dark matter may no longer be continuous in spatial distribution at ordinary matter boundary (such as a massive sphere surface). In order to avoid the unnatural discontinuity of the extra emergent gravity of Verlinde's apparent dark matter, we suggest a modified dark-baryonic mass relation (a formula relating Verlinde's apparent dark matter mass to ordinary baryonic matter mass) within this framework of emergent gravity. The modified mass relation is consistent with Verlinde's result at relatively small scales (e.g., R<3h_{70}^{-1} Mpc). However, it seems that, compared with Verlinde's relation, at large scales (e.g., gravitating systems with R>3h_{70}^{-1} Mpc), the modified dark-baryonic mass relation presented here might be in better agreement with the experimental curves of weak lensing analysis in the recent work of Brouwer et al. Galactic rotation curves are compared between Verlinde's emergent gravity and McGaugh's recent model of MOND (Modified Newtonian Dynamics established based on recent galaxy observations). It can be found that Verlinde rotational curves deviate far from those of McGaugh MOND model when the MOND effect (or emergent dark matter) dominates. Some applications of the modified dark-baryonic mass relation inspired by Verlinde's emergent gravity will be addressed for galactic and solar scales. Potential possibilities to test this dark-baryonic mass relation as well as apparent dark matter effects, e.g., planetary perihelion precession at Solar System scale, will be considered. This may enable to place some constraints on the magnitudes of the MOND characteristic acceleration at the small solar scale.

Critical behaviour and filed dependence of magnetic entropy change in K-doped manganites Pr0.8Na0.2-xKxMnO3 (x = 0.10 and 0.15)

NASA Astrophysics Data System (ADS)

Ben Khlifa, H.; M'nassri, R.; Tarhouni, S.; Regaieg, Y.; Cheikhrouhou-Koubaa, W.; Chniba-Boudjada, N.; Cheikhrouhou, A.

2018-01-01

The orthorhombic Pr0.8Na0.2-xKxMnO3 (x = 0.10 and 0.15) manganites are prepared by using the solid state reaction at high temperatures. The critical exponents (β, γ, δ) are investigated through various techniques such as modified Arrott plot, Kouvel-Fisher method and critical isotherm analysis based on the data of the magnetic measurements recorded around the Curie temperature. The critical exponents are derived from the magnetization data using the Kouvel-Fisher method, are found to be β = 0.32(4) and γ = 1.29(2) at TC 123 K for x = 0.10 and β = 0.31(1) and γ = 1.25(2) at TC 133 K for x = 0.15. The critical exponent values obtained for both samples are comparable to the values predicted by the 3D-Ising model, and have also been verified by the scaling equation of state. Such results demonstrate the existence of ferromagnetic short-range order in our materials. The magnetic entropy changes of polycrystalline samples with a second-order phase transition are investigated. A large magnetic entropy change deduced from isothermal magnetization curves, is observed in our samples with a peak centered on their respective Curie temperatures (TC). The field dependence of the magnetic entropy changes are analyzed, which show power law dependence ΔSmax ≈ a(μ0 H) n at transition temperature. The values of n obey to the Curie Weiss law above the transition temperature. It is shown that for the investigated materials, the magnetic entropy change follow a master curve behaviour. The rescaled magnetic entropy change curves for different applied fields collapse onto a single curve for both samples.

Thermodynamic Basis of Selectivity in the Interactions of Tissue Inhibitors of Metalloproteinases N-domains with Matrix Metalloproteinases-1, -3, and -14*

PubMed Central

Zou, Haiyin; Wu, Ying

2016-01-01

The four tissue inhibitors of metalloproteinases (TIMPs) are potent inhibitors of the many matrixins (MMPs), except that TIMP1 weakly inhibits some MMPs, including MMP14. The broad-spectrum inhibition of MMPs by TIMPs and their N-domains (NTIMPs) is consistent with the previous isothermal titration calorimetric finding that their interactions are entropy-driven but differ in contributions from solvent and conformational entropy (ΔSsolv, ΔSconf), estimated using heat capacity changes (ΔCp). Selective engineered NTIMPs have potential applications for treating MMP-related diseases, including cancer and cardiomyopathy. Here we report isothermal titration calorimetric studies of the effects of selectivity-modifying mutations in NTIMP1 and NTIMP2 on the thermodynamics of their interactions with MMP1, MMP3, and MMP14. The weak inhibition of MMP14 by NTIMP1 reflects a large conformational entropy penalty for binding. The T98L mutation, peripheral to the NTIMP1 reactive site, enhances binding by increasing ΔSsolv but also reduces ΔSconf. However, the same mutation increases NTIMP1 binding to MMP3 in an interaction that has an unusual positive ΔCp. This indicates a decrease in solvent entropy compensated by increased conformational entropy, possibly reflecting interactions involving alternative conformers. The NTIMP2 mutant, S2D/S4A is a selective MMP1 inhibitor through electrostatic effects of a unique MMP-1 arginine. Asp-2 increases reactive site polarity, reducing ΔCp, but increases conformational entropy to maintain strong binding to MMP1. There is a strong negative correlation between ΔSsolv and ΔSconf for all characterized interactions, but the data for each MMP have characteristic ranges, reflecting intrinsic differences in the structures and dynamics of their free and inhibitor-bound forms. PMID:27033700

Multiple comparisons permutation test for image based data mining in radiotherapy.

PubMed

Chen, Chun; Witte, Marnix; Heemsbergen, Wilma; van Herk, Marcel

2013-12-23

: Comparing incidental dose distributions (i.e. images) of patients with different outcomes is a straightforward way to explore dose-response hypotheses in radiotherapy. In this paper, we introduced a permutation test that compares images, such as dose distributions from radiotherapy, while tackling the multiple comparisons problem. A test statistic Tmax was proposed that summarizes the differences between the images into a single value and a permutation procedure was employed to compute the adjusted p-value. We demonstrated the method in two retrospective studies: a prostate study that relates 3D dose distributions to failure, and an esophagus study that relates 2D surface dose distributions of the esophagus to acute esophagus toxicity. As a result, we were able to identify suspicious regions that are significantly associated with failure (prostate study) or toxicity (esophagus study). Permutation testing allows direct comparison of images from different patient categories and is a useful tool for data mining in radiotherapy.

Permutational symmetries for coincidence rates in multimode multiphotonic interferometry

NASA Astrophysics Data System (ADS)

Khalid, Abdullah; Spivak, Dylan; Sanders, Barry C.; de Guise, Hubert

2018-06-01

We obtain coincidence rates for passive optical interferometry by exploiting the permutational symmetries of partially distinguishable input photons, and our approach elucidates qualitative features of multiphoton coincidence landscapes. We treat the interferometer input as a product state of any number of photons in each input mode with photons distinguished by their arrival time. Detectors at the output of the interferometer count photons from each output mode over a long integration time. We generalize and prove the claim of Tillmann et al. [Phys. Rev. X 5, 041015 (2015), 10.1103/PhysRevX.5.041015] that coincidence rates can be elegantly expressed in terms of immanants. Immanants are functions of matrices that exhibit permutational symmetries and the immanants appearing in our coincidence-rate expressions share permutational symmetries with the input state. Our results are obtained by employing representation theory of the symmetric group to analyze systems of an arbitrary number of photons in arbitrarily sized interferometers.

[The motive force of evolution based on the principle of organismal adjustment evolution.].

PubMed

Cao, Jia-Shu

2010-08-01

From the analysis of the existing problems of the prevalent theories of evolution, this paper discussed the motive force of evolution based on the knowledge of the principle of organismal adjustment evolution to get a new understanding of the evolution mechanism. In the guide of Schrodinger's theory - "life feeds on negative entropy", the author proposed that "negative entropy flow" actually includes material flow, energy flow and information flow, and the "negative entropy flow" is the motive force for living and development. By modifying my own theory of principle of organismal adjustment evolution (not adaptation evolution), a new theory of "regulation system of organismal adjustment evolution involved in DNA, RNA and protein interacting with environment" is proposed. According to the view that phylogenetic development is the "integral" of individual development, the difference of negative entropy flow between organisms and environment is considered to be a motive force for evolution, which is a new understanding of the mechanism of evolution. Based on such understanding, evolution is regarded as "a changing process that one subsystem passes all or part of its genetic information to the next generation in a larger system, and during the adaptation process produces some new elements, stops some old ones, and thereby lasts in the larger system". Some other controversial questions related to evolution are also discussed.

Complex-enhanced chaotic signals with time-delay signature suppression based on vertical-cavity surface-emitting lasers subject to chaotic optical injection

NASA Astrophysics Data System (ADS)

Chen, Jianjun; Duan, Yingni; Zhong, Zhuqiang

2018-06-01

A chaotic system is constructed on the basis of vertical-cavity surface-emitting lasers (VCSELs), where a slave VCSEL subject to chaotic optical injection (COI) from a master VCSEL with the external feedback. The complex degree (CD) and time-delay signature (TDS) of chaotic signals generated by this chaotic system are investigated numerically via permutation entropy (PE) and self-correlation function (SF) methods, respectively. The results show that, compared with master VCSEL subject to optical feedback, complex-enhanced chaotic signals with TDS suppression can be achieved for S-VCSEL subject to COI. Meanwhile, the influences of several controllable parameters on the evolution maps of CD of chaotic signals are carefully considered. It is shown that the CD of chaotic signals for S-VCSEL is always higher than that for M-VCSEL due to the CIO effect. The TDS of chaotic signals can be significantly suppressed by choosing the reasonable parameters in this system. Furthermore, TDS suppression and high CD chaos can be obtained simultaneously in the specific parameter ranges. The results confirm that this chaotic system may effectively improve the security of a chaos-based communication scheme.

Complex-enhanced chaotic signals with time-delay signature suppression based on vertical-cavity surface-emitting lasers subject to chaotic optical injection

NASA Astrophysics Data System (ADS)

Chen, Jianjun; Duan, Yingni; Zhong, Zhuqiang

2018-03-01

A chaotic system is constructed on the basis of vertical-cavity surface-emitting lasers (VCSELs), where a slave VCSEL subject to chaotic optical injection (COI) from a master VCSEL with the external feedback. The complex degree (CD) and time-delay signature (TDS) of chaotic signals generated by this chaotic system are investigated numerically via permutation entropy (PE) and self-correlation function (SF) methods, respectively. The results show that, compared with master VCSEL subject to optical feedback, complex-enhanced chaotic signals with TDS suppression can be achieved for S-VCSEL subject to COI. Meanwhile, the influences of several controllable parameters on the evolution maps of CD of chaotic signals are carefully considered. It is shown that the CD of chaotic signals for S-VCSEL is always higher than that for M-VCSEL due to the CIO effect. The TDS of chaotic signals can be significantly suppressed by choosing the reasonable parameters in this system. Furthermore, TDS suppression and high CD chaos can be obtained simultaneously in the specific parameter ranges. The results confirm that this chaotic system may effectively improve the security of a chaos-based communication scheme.

A novel algorithm for thermal image encryption.

PubMed

Hussain, Iqtadar; Anees, Amir; Algarni, Abdulmohsen

2018-04-16

Thermal images play a vital character at nuclear plants, Power stations, Forensic labs biological research, and petroleum products extraction. Safety of thermal images is very important. Image data has some unique features such as intensity, contrast, homogeneity, entropy and correlation among pixels that is why somehow image encryption is trickier as compare to other encryptions. With conventional image encryption schemes it is normally hard to handle these features. Therefore, cryptographers have paid attention to some attractive properties of the chaotic maps such as randomness and sensitivity to build up novel cryptosystems. That is why, recently proposed image encryption techniques progressively more depends on the application of chaotic maps. This paper proposed an image encryption algorithm based on Chebyshev chaotic map and S8 Symmetric group of permutation based substitution boxes. Primarily, parameters of chaotic Chebyshev map are chosen as a secret key to mystify the primary image. Then, the plaintext image is encrypted by the method generated from the substitution boxes and Chebyshev map. By this process, we can get a cipher text image that is perfectly twisted and dispersed. The outcomes of renowned experiments, key sensitivity tests and statistical analysis confirm that the proposed algorithm offers a safe and efficient approach for real-time image encryption.

A new feedback image encryption scheme based on perturbation with dynamical compound chaotic sequence cipher generator

NASA Astrophysics Data System (ADS)

Tong, Xiaojun; Cui, Minggen; Wang, Zhu

2009-07-01

The design of the new compound two-dimensional chaotic function is presented by exploiting two one-dimensional chaotic functions which switch randomly, and the design is used as a chaotic sequence generator which is proved by Devaney's definition proof of chaos. The properties of compound chaotic functions are also proved rigorously. In order to improve the robustness against difference cryptanalysis and produce avalanche effect, a new feedback image encryption scheme is proposed using the new compound chaos by selecting one of the two one-dimensional chaotic functions randomly and a new image pixels method of permutation and substitution is designed in detail by array row and column random controlling based on the compound chaos. The results from entropy analysis, difference analysis, statistical analysis, sequence randomness analysis, cipher sensitivity analysis depending on key and plaintext have proven that the compound chaotic sequence cipher can resist cryptanalytic, statistical and brute-force attacks, and especially it accelerates encryption speed, and achieves higher level of security. By the dynamical compound chaos and perturbation technology, the paper solves the problem of computer low precision of one-dimensional chaotic function.

Higher order explicit symmetric integrators for inseparable forms of coordinates and momenta

NASA Astrophysics Data System (ADS)

Liu, Lei; Wu, Xin; Huang, Guoqing; Liu, Fuyao

2016-06-01

Pihajoki proposed the extended phase-space second-order explicit symmetric leapfrog methods for inseparable Hamiltonian systems. On the basis of this work, we survey a critical problem on how to mix the variables in the extended phase space. Numerical tests show that sequent permutations of coordinates and momenta can make the leapfrog-like methods yield the most accurate results and the optimal long-term stabilized error behaviour. We also present a novel method to construct many fourth-order extended phase-space explicit symmetric integration schemes. Each scheme represents the symmetric production of six usual second-order leapfrogs without any permutations. This construction consists of four segments: the permuted coordinates, triple product of the usual second-order leapfrog without permutations, the permuted momenta and the triple product of the usual second-order leapfrog without permutations. Similarly, extended phase-space sixth, eighth and other higher order explicit symmetric algorithms are available. We used several inseparable Hamiltonian examples, such as the post-Newtonian approach of non-spinning compact binaries, to show that one of the proposed fourth-order methods is more efficient than the existing methods; examples include the fourth-order explicit symplectic integrators of Chin and the fourth-order explicit and implicit mixed symplectic integrators of Zhong et al. Given a moderate choice for the related mixing and projection maps, the extended phase-space explicit symplectic-like methods are well suited for various inseparable Hamiltonian problems. Samples of these problems involve the algorithmic regularization of gravitational systems with velocity-dependent perturbations in the Solar system and post-Newtonian Hamiltonian formulations of spinning compact objects.

Non-parametric combination and related permutation tests for neuroimaging.

PubMed

Winkler, Anderson M; Webster, Matthew A; Brooks, Jonathan C; Tracey, Irene; Smith, Stephen M; Nichols, Thomas E

2016-04-01

In this work, we show how permutation methods can be applied to combination analyses such as those that include multiple imaging modalities, multiple data acquisitions of the same modality, or simply multiple hypotheses on the same data. Using the well-known definition of union-intersection tests and closed testing procedures, we use synchronized permutations to correct for such multiplicity of tests, allowing flexibility to integrate imaging data with different spatial resolutions, surface and/or volume-based representations of the brain, including non-imaging data. For the problem of joint inference, we propose and evaluate a modification of the recently introduced non-parametric combination (NPC) methodology, such that instead of a two-phase algorithm and large data storage requirements, the inference can be performed in a single phase, with reasonable computational demands. The method compares favorably to classical multivariate tests (such as MANCOVA), even when the latter is assessed using permutations. We also evaluate, in the context of permutation tests, various combining methods that have been proposed in the past decades, and identify those that provide the best control over error rate and power across a range of situations. We show that one of these, the method of Tippett, provides a link between correction for the multiplicity of tests and their combination. Finally, we discuss how the correction can solve certain problems of multiple comparisons in one-way ANOVA designs, and how the combination is distinguished from conjunctions, even though both can be assessed using permutation tests. We also provide a common algorithm that accommodates combination and correction. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Thermodynamics of organic molecule adsorption on sorbents modified with 5-hydroxy-6-methyluracil by inverse gas chromatography.

PubMed

Gus'kov, Vladimir Yu; Gainullina, Yulia Yu; Ivanov, Sergey P; Kudasheva, Florida Kh

2014-08-22

The thermodynamic features of organic molecule adsorption from the gaseous phase of sorbents modified with 5-hydroxy-6-methyluracil (HMU) were studied. Molar internal energy and entropy of adsorption variation analyses showed that with every type surface, except for silica gel, layers of supramolecular structure have cavities equal in size with the ones revealed in HMU crystals by X-ray diffraction. Adsorption thermodynamics on HMU-modified sorbents depended on the amount of impregnated HMU and on the polarity, but not the porosity, of the initial sorbent. Polarity of the modified surface increased as a function of HMU quantity and initial sorbent mean pore size, but become appreciably lower if the initial surface is capable of hydrogen bonding. Copyright © 2014 Elsevier B.V. All rights reserved.

Sylow p-groups of polynomial permutations on the integers mod pn☆

PubMed Central

Frisch, Sophie; Krenn, Daniel

2013-01-01

We enumerate and describe the Sylow p-groups of the groups of polynomial permutations of the integers mod pn for n⩾1 and of the pro-finite group which is the projective limit of these groups. PMID:26869732

Storage and computationally efficient permutations of factorized covariance and square-root information arrays

NASA Technical Reports Server (NTRS)

Muellerschoen, R. J.

1988-01-01

A unified method to permute vector stored Upper triangular Diagonal factorized covariance and vector stored upper triangular Square Root Information arrays is presented. The method involves cyclic permutation of the rows and columns of the arrays and retriangularization with fast (slow) Givens rotations (reflections). Minimal computation is performed, and a one dimensional scratch array is required. To make the method efficient for large arrays on a virtual memory machine, computations are arranged so as to avoid expensive paging faults. This method is potentially important for processing large volumes of radio metric data in the Deep Space Network.

Note on new KLT relations

NASA Astrophysics Data System (ADS)

Feng, Bo; He, Song; Huang, Rijun; Jia, Yin

2010-10-01

In this short note, we present two results about KLT relations discussed in recent several papers. Our first result is the re-derivation of Mason-Skinner MHV amplitude by applying the S n-3 permutation symmetric KLT relations directly to MHV amplitude. Our second result is the equivalence proof of the newly discovered S n-2 permutation symmetric KLT relations and the well-known S n-3 permutation symmetric KLT relations. Although both formulas have been shown to be correct by BCFW recursion relations, our result is the first direct check using the regularized definition of the new formula.

Combating HER2-overexpressing breast cancer through induction of calreticulin exposure by Tras-Permut CrossMab

PubMed Central

Zhang, Fan; Zhang, Jie; Liu, Moyan; Zhao, Lichao; LingHu, RuiXia; Feng, Fan; Gao, Xudong; Jiao, Shunchang; Zhao, Lei; Hu, Yi; Yang, Junlan

2015-01-01

Although trastuzumab has succeeded in breast cancer treatment, acquired resistance is one of the prime obstacles for breast cancer therapies. There is an urgent need to develop novel HER2 antibodies against trastuzumab resistance. Here, we first rational designed avidity-imporved trastuzumab and pertuzumab variants, and explored the correlation between the binding avidity improvement and their antitumor activities. After characterization of a pertuzumab variant L56TY with potent antitumor activities, a bispecific immunoglobulin G-like CrossMab (Tras-Permut CrossMab) was generated from trastuzumab and binding avidity-improved pertuzumab variant L56TY. Although, the antitumor efficacy of trastuzumab was not enhanced by improving its binding avidity, binding avidity improvement could significantly increase the anti-proliferative and antibody-dependent cellular cytotoxicity (ADCC) activities of pertuzumab. Further studies showed that Tras-Permut CrossMab exhibited exceptional high efficiency to inhibit the progression of trastuzumab-resistant breast cancer. Notably, we found that calreticulin (CRT) exposure induced by Tras-Permut CrossMab was essential for induction of tumor-specific T cell immunity against tumor recurrence. These data indicated that simultaneous blockade of HER2 protein by Tras-Permut CrossMab could trigger CRT exposure and subsequently induce potent tumor-specific T cell immunity, suggesting it could be a promising therapeutic strategy against trastuzumab resistance. PMID:25949918

Non-singular and cyclic universe from the modified GUP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salah, Maha; Hammad, Fayçal; Faizal, Mir

In this paper, we investigate the effects of a new version of the generalized uncertainty principle (modified GUP) on the dynamics of the Universe. As the modified GUP will modify the relation between the entropy and area of the apparent horizon, it will also deform the Friedmann equations within Jacobson's approach. We explicitly find these deformed Friedmann equations governing the modified GUP-corrected dynamics of such a Universe. It is shown that the modified GUP-deformed Jacobson's approach implies an upper bound for the density of such a Universe. The Big Bang singularity can therefore also be avoided using the modified GUP-correctionsmore » to horizons' thermodynamics. In fact, we are able to analyze the pre Big Bang state of the Universe. Furthermore, the equations imply that the expansion of the Universe will come to a halt and then will immediately be followed by a contracting phase. When the equations are extrapolated beyond the maximum rate of contraction, a cyclic Universe scenario emerges.« less

Non-singular and cyclic universe from the modified GUP

NASA Astrophysics Data System (ADS)

Salah, Maha; Hammad, Fayçal; Faizal, Mir; Farag Ali, Ahmed

2017-02-01

In this paper, we investigate the effects of a new version of the generalized uncertainty principle (modified GUP) on the dynamics of the Universe. As the modified GUP will modify the relation between the entropy and area of the apparent horizon, it will also deform the Friedmann equations within Jacobson's approach. We explicitly find these deformed Friedmann equations governing the modified GUP-corrected dynamics of such a Universe. It is shown that the modified GUP-deformed Jacobson's approach implies an upper bound for the density of such a Universe. The Big Bang singularity can therefore also be avoided using the modified GUP-corrections to horizons' thermodynamics. In fact, we are able to analyze the pre Big Bang state of the Universe. Furthermore, the equations imply that the expansion of the Universe will come to a halt and then will immediately be followed by a contracting phase. When the equations are extrapolated beyond the maximum rate of contraction, a cyclic Universe scenario emerges.

Automatic NEPHIS Coding of Descriptive Titles for Permuted Index Generation.

ERIC Educational Resources Information Center

Craven, Timothy C.

1982-01-01

Describes a system for the automatic coding of most descriptive titles which generates Nested Phrase Indexing System (NEPHIS) input strings of sufficient quality for permuted index production. A series of examples and an 11-item reference list accompany the text. (JL)

Non‐parametric combination and related permutation tests for neuroimaging

PubMed Central

Webster, Matthew A.; Brooks, Jonathan C.; Tracey, Irene; Smith, Stephen M.; Nichols, Thomas E.

2016-01-01

Abstract In this work, we show how permutation methods can be applied to combination analyses such as those that include multiple imaging modalities, multiple data acquisitions of the same modality, or simply multiple hypotheses on the same data. Using the well‐known definition of union‐intersection tests and closed testing procedures, we use synchronized permutations to correct for such multiplicity of tests, allowing flexibility to integrate imaging data with different spatial resolutions, surface and/or volume‐based representations of the brain, including non‐imaging data. For the problem of joint inference, we propose and evaluate a modification of the recently introduced non‐parametric combination (NPC) methodology, such that instead of a two‐phase algorithm and large data storage requirements, the inference can be performed in a single phase, with reasonable computational demands. The method compares favorably to classical multivariate tests (such as MANCOVA), even when the latter is assessed using permutations. We also evaluate, in the context of permutation tests, various combining methods that have been proposed in the past decades, and identify those that provide the best control over error rate and power across a range of situations. We show that one of these, the method of Tippett, provides a link between correction for the multiplicity of tests and their combination. Finally, we discuss how the correction can solve certain problems of multiple comparisons in one‐way ANOVA designs, and how the combination is distinguished from conjunctions, even though both can be assessed using permutation tests. We also provide a common algorithm that accommodates combination and correction. Hum Brain Mapp 37:1486‐1511, 2016. © 2016 Wiley Periodicals, Inc. PMID:26848101

Creation of a Ligand-Dependent Enzyme by Fusing Circularly Permuted Antibody Variable Region Domains.

PubMed

Iwai, Hiroto; Kojima-Misaizu, Miki; Dong, Jinhua; Ueda, Hiroshi

2016-04-20

Allosteric control of enzyme activity with exogenous substances has been hard to achieve, especially using antibody domains that potentially allow control by any antigens of choice. Here, in order to attain this goal, we developed a novel antibody variable region format introduced with circular permutations, called Clampbody. The two variable-region domains of the antibone Gla protein (BGP) antibody were each circularly permutated to have novel termini at the loops near their domain interface. Through their attachment to the N- and C-termini of a circularly permutated TEM-1 β-lactamase (cpBLA), we created a molecular switch that responds to the antigen peptide. The fusion protein specifically recognized the antigen, and in the presence of some detergent or denaturant, its catalytic activity was enhanced up to 4.7-fold in an antigen-dependent manner, due to increased resistance to these reagents. Hence, Clampbody will be a powerful tool for the allosteric regulation of enzyme and other protein activities and especially useful to design robust biosensors.

Multiple comparisons permutation test for image based data mining in radiotherapy

PubMed Central

2013-01-01

Comparing incidental dose distributions (i.e. images) of patients with different outcomes is a straightforward way to explore dose-response hypotheses in radiotherapy. In this paper, we introduced a permutation test that compares images, such as dose distributions from radiotherapy, while tackling the multiple comparisons problem. A test statistic Tmax was proposed that summarizes the differences between the images into a single value and a permutation procedure was employed to compute the adjusted p-value. We demonstrated the method in two retrospective studies: a prostate study that relates 3D dose distributions to failure, and an esophagus study that relates 2D surface dose distributions of the esophagus to acute esophagus toxicity. As a result, we were able to identify suspicious regions that are significantly associated with failure (prostate study) or toxicity (esophagus study). Permutation testing allows direct comparison of images from different patient categories and is a useful tool for data mining in radiotherapy. PMID:24365155

Quantum one-way permutation over the finite field of two elements

NASA Astrophysics Data System (ADS)

de Castro, Alexandre

2017-06-01

In quantum cryptography, a one-way permutation is a bounded unitary operator U:{H} → {H} on a Hilbert space {H} that is easy to compute on every input, but hard to invert given the image of a random input. Levin (Probl Inf Transm 39(1):92-103, 2003) has conjectured that the unitary transformation g(a,x)=(a,f(x)+ax), where f is any length-preserving function and a,x \\in {GF}_{{2}^{\\Vert x\\Vert }}, is an information-theoretically secure operator within a polynomial factor. Here, we show that Levin's one-way permutation is provably secure because its output values are four maximally entangled two-qubit states, and whose probability of factoring them approaches zero faster than the multiplicative inverse of any positive polynomial poly( x) over the Boolean ring of all subsets of x. Our results demonstrate through well-known theorems that existence of classical one-way functions implies existence of a universal quantum one-way permutation that cannot be inverted in subexponential time in the worst case.

Discrete Bat Algorithm for Optimal Problem of Permutation Flow Shop Scheduling

PubMed Central

Luo, Qifang; Zhou, Yongquan; Xie, Jian; Ma, Mingzhi; Li, Liangliang

2014-01-01

A discrete bat algorithm (DBA) is proposed for optimal permutation flow shop scheduling problem (PFSP). Firstly, the discrete bat algorithm is constructed based on the idea of basic bat algorithm, which divide whole scheduling problem into many subscheduling problems and then NEH heuristic be introduced to solve subscheduling problem. Secondly, some subsequences are operated with certain probability in the pulse emission and loudness phases. An intensive virtual population neighborhood search is integrated into the discrete bat algorithm to further improve the performance. Finally, the experimental results show the suitability and efficiency of the present discrete bat algorithm for optimal permutation flow shop scheduling problem. PMID:25243220

Discrete bat algorithm for optimal problem of permutation flow shop scheduling.

PubMed

Luo, Qifang; Zhou, Yongquan; Xie, Jian; Ma, Mingzhi; Li, Liangliang

2014-01-01

A discrete bat algorithm (DBA) is proposed for optimal permutation flow shop scheduling problem (PFSP). Firstly, the discrete bat algorithm is constructed based on the idea of basic bat algorithm, which divide whole scheduling problem into many subscheduling problems and then NEH heuristic be introduced to solve subscheduling problem. Secondly, some subsequences are operated with certain probability in the pulse emission and loudness phases. An intensive virtual population neighborhood search is integrated into the discrete bat algorithm to further improve the performance. Finally, the experimental results show the suitability and efficiency of the present discrete bat algorithm for optimal permutation flow shop scheduling problem.

Levels of Conceptual Development in Melodic Permutation Concepts Based on Piaget's Theory

ERIC Educational Resources Information Center

Larn, Ronald L.

1973-01-01

Article considered different ways in which subjects at different age levels solved a musical task involving melodic permutation. The differences in responses to the musical task between age groups were judged to be compatible with Piaget's theory of cognitive development. (Author/RK)

In Response to Rowland on "Realism and Debateability in Policy Advocacy."

ERIC Educational Resources Information Center

Herbeck, Dale A.; Katsulas, John P.

1986-01-01

Argues that Robert Rowland has overstated the case against the permutation process for assessing counterplan competitiveness. Claims that the permutation standard is a viable method for ascertaining counterplan competitiveness. Examines Rowland's alternative and argues that it is an unsatisfactory method for determining counterplan…

EPEPT: A web service for enhanced P-value estimation in permutation tests

PubMed Central

2011-01-01

Background In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations when small (and thus interesting) P-values are to be accurately estimated. This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values [1]. Results The proposed P-value estimator has been enriched with additional functionalities and is made available to the general community through a public website and web service, called EPEPT. This means that the EPEPT routines can be accessed not only via a website, but also programmatically using any programming language that can interact with the web. Examples of web service clients in multiple programming languages can be downloaded. Additionally, EPEPT accepts data of various common experiment types used in computational biology. For these experiment types EPEPT first computes the permutation values and then performs the P-value estimation. Finally, the source code of EPEPT can be downloaded. Conclusions Different types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way. Availability http://informatics.systemsbiology.net/EPEPT/ PMID:22024252

Radiation of quantum black holes and modified uncertainty relation

NASA Astrophysics Data System (ADS)

Kamali, A. D.; Pedram, P.

In this paper, using a deformed algebra [X,P] = iℏ/(1 ‑ λ2P2) which is originated from various theories of gravity, we study thermodynamical properties of quantum black holes (BHs) in canonical ensembles. We exactly calculate the modified internal energy, entropy and heat capacity. Moreover, we investigate a tunneling mechanism of massless particle in phase space. In this regard, the tunneling radiation of BH receives new corrections and the exact radiant spectrum is no longer precisely thermal. In addition, we show that our results are compatible with other quantum gravity (QG) approaches.

Deformations of the Almheiri-Polchinski model

NASA Astrophysics Data System (ADS)

Kyono, Hideki; Okumura, Suguru; Yoshida, Kentaroh

2017-03-01

We study deformations of the Almheiri-Polchinski (AP) model by employing the Yang-Baxter deformation technique. The general deformed AdS2 metric becomes a solution of a deformed AP model. In particular, the dilaton potential is deformed from a simple quadratic form to a hyperbolic function-type potential similarly to integrable deformations. A specific solution is a deformed black hole solution. Because the deformation makes the spacetime structure around the boundary change drastically and a new naked singularity appears, the holographic interpretation is far from trivial. The Hawking temperature is the same as the undeformed case but the Bekenstein-Hawking entropy is modified due to the deformation. This entropy can also be reproduced by evaluating the renormalized stress tensor with an appropriate counter-term on the regularized screen close to the singularity.

An Artificial Bee Colony Algorithm for Uncertain Portfolio Selection

PubMed Central

Chen, Wei

2014-01-01

Portfolio selection is an important issue for researchers and practitioners. In this paper, under the assumption that security returns are given by experts' evaluations rather than historical data, we discuss the portfolio adjusting problem which takes transaction costs and diversification degree of portfolio into consideration. Uncertain variables are employed to describe the security returns. In the proposed mean-variance-entropy model, the uncertain mean value of the return is used to measure investment return, the uncertain variance of the return is used to measure investment risk, and the entropy is used to measure diversification degree of portfolio. In order to solve the proposed model, a modified artificial bee colony (ABC) algorithm is designed. Finally, a numerical example is given to illustrate the modelling idea and the effectiveness of the proposed algorithm. PMID:25089292

Retention behavior of neutral solutes in pressurized flow-driven capillary electrochromatography using an ODS column.

PubMed

Nakagawa, Hiroyuki; Kitagawa, Shinya; Araki, Shuki; Ohtani, Hajime

2006-02-01

Several alkyl benzenes are separated by pressurized flow-driven capillary electrochromatography using a temperature-controlled capillary column packed with octadecyl siloxane-modified silica gel, and the effect of applied voltage on the retention is investigated. The van't Hoff plot shows good linearity at the column temperature between 305 and 330 K under applications from -6 to +6 kV. The applied voltage causes a relatively large variation in the enthalpy and the entropy of transfer of the solute from the mobile phase to the stationary phase (> 20%). However, the direction of variation in the enthalpy is almost opposite to that in the entropy, both of which might compensate each other. Therefore, the retention factor is not significantly varied (< 4%) by the application of voltage.

Access Selection Algorithm of Heterogeneous Wireless Networks for Smart Distribution Grid Based on Entropy-Weight and Rough Set

NASA Astrophysics Data System (ADS)

Xiang, Min; Qu, Qinqin; Chen, Cheng; Tian, Li; Zeng, Lingkang

2017-11-01

To improve the reliability of communication service in smart distribution grid (SDG), an access selection algorithm based on dynamic network status and different service types for heterogeneous wireless networks was proposed. The network performance index values were obtained in real time by multimode terminal and the variation trend of index values was analyzed by the growth matrix. The index weights were calculated by entropy-weight and then modified by rough set to get the final weights. Combining the grey relational analysis to sort the candidate networks, and the optimum communication network is selected. Simulation results show that the proposed algorithm can implement dynamically access selection in heterogeneous wireless networks of SDG effectively and reduce the network blocking probability.

An artificial bee colony algorithm for uncertain portfolio selection.

PubMed

Chen, Wei

2014-01-01

Portfolio selection is an important issue for researchers and practitioners. In this paper, under the assumption that security returns are given by experts' evaluations rather than historical data, we discuss the portfolio adjusting problem which takes transaction costs and diversification degree of portfolio into consideration. Uncertain variables are employed to describe the security returns. In the proposed mean-variance-entropy model, the uncertain mean value of the return is used to measure investment return, the uncertain variance of the return is used to measure investment risk, and the entropy is used to measure diversification degree of portfolio. In order to solve the proposed model, a modified artificial bee colony (ABC) algorithm is designed. Finally, a numerical example is given to illustrate the modelling idea and the effectiveness of the proposed algorithm.

A maximum entropy model for chromatin structure

NASA Astrophysics Data System (ADS)

Farre, Pau; Emberly, Eldon; Emberly Group Team

The DNA inside the nucleus of eukaryotic cells shows a variety of conserved structures at different length scales These structures are formed by interactions between protein complexes that bind to the DNA and regulate gene activity. Recent high throughput sequencing techniques allow for the measurement both of the genome wide contact map of the folded DNA within a cell (HiC) and where various proteins are bound to the DNA (ChIP-seq). In this talk I will present a maximum-entropy method capable of both predicting HiC contact maps from binding data, and binding data from HiC contact maps. This method results in an intuitive Ising-type model that is able to predict how altering the presence of binding factors can modify chromosome conformation, without the need of polymer simulations.

Introduction to Permutation and Resampling-Based Hypothesis Tests

ERIC Educational Resources Information Center

LaFleur, Bonnie J.; Greevy, Robert A.

2009-01-01

A resampling-based method of inference--permutation tests--is often used when distributional assumptions are questionable or unmet. Not only are these methods useful for obvious departures from parametric assumptions (e.g., normality) and small sample sizes, but they are also more robust than their parametric counterparts in the presences of…

Explorations in Statistics: Permutation Methods

ERIC Educational Resources Information Center

Curran-Everett, Douglas

2012-01-01

Learning about statistics is a lot like learning about science: the learning is more meaningful if you can actively explore. This eighth installment of "Explorations in Statistics" explores permutation methods, empiric procedures we can use to assess an experimental result--to test a null hypothesis--when we are reluctant to trust statistical…

Nonequilibrium thermodynamics and maximum entropy production in the Earth system: applications and implications.

PubMed

Kleidon, Axel

2009-06-01

The Earth system is maintained in a unique state far from thermodynamic equilibrium, as, for instance, reflected in the high concentration of reactive oxygen in the atmosphere. The myriad of processes that transform energy, that result in the motion of mass in the atmosphere, in oceans, and on land, processes that drive the global water, carbon, and other biogeochemical cycles, all have in common that they are irreversible in their nature. Entropy production is a general consequence of these processes and measures their degree of irreversibility. The proposed principle of maximum entropy production (MEP) states that systems are driven to steady states in which they produce entropy at the maximum possible rate given the prevailing constraints. In this review, the basics of nonequilibrium thermodynamics are described, as well as how these apply to Earth system processes. Applications of the MEP principle are discussed, ranging from the strength of the atmospheric circulation, the hydrological cycle, and biogeochemical cycles to the role that life plays in these processes. Nonequilibrium thermodynamics and the MEP principle have potentially wide-ranging implications for our understanding of Earth system functioning, how it has evolved in the past, and why it is habitable. Entropy production allows us to quantify an objective direction of Earth system change (closer to vs further away from thermodynamic equilibrium, or, equivalently, towards a state of MEP). When a maximum in entropy production is reached, MEP implies that the Earth system reacts to perturbations primarily with negative feedbacks. In conclusion, this nonequilibrium thermodynamic view of the Earth system shows great promise to establish a holistic description of the Earth as one system. This perspective is likely to allow us to better understand and predict its function as one entity, how it has evolved in the past, and how it is modified by human activities in the future.

Thermodynamic Basis of Selectivity in the Interactions of Tissue Inhibitors of Metalloproteinases N-domains with Matrix Metalloproteinases-1, -3, and -14.

PubMed

Zou, Haiyin; Wu, Ying; Brew, Keith

2016-05-20

The four tissue inhibitors of metalloproteinases (TIMPs) are potent inhibitors of the many matrixins (MMPs), except that TIMP1 weakly inhibits some MMPs, including MMP14. The broad-spectrum inhibition of MMPs by TIMPs and their N-domains (NTIMPs) is consistent with the previous isothermal titration calorimetric finding that their interactions are entropy-driven but differ in contributions from solvent and conformational entropy (ΔSsolv, ΔSconf), estimated using heat capacity changes (ΔCp). Selective engineered NTIMPs have potential applications for treating MMP-related diseases, including cancer and cardiomyopathy. Here we report isothermal titration calorimetric studies of the effects of selectivity-modifying mutations in NTIMP1 and NTIMP2 on the thermodynamics of their interactions with MMP1, MMP3, and MMP14. The weak inhibition of MMP14 by NTIMP1 reflects a large conformational entropy penalty for binding. The T98L mutation, peripheral to the NTIMP1 reactive site, enhances binding by increasing ΔSsolv but also reduces ΔSconf However, the same mutation increases NTIMP1 binding to MMP3 in an interaction that has an unusual positive ΔCp This indicates a decrease in solvent entropy compensated by increased conformational entropy, possibly reflecting interactions involving alternative conformers. The NTIMP2 mutant, S2D/S4A is a selective MMP1 inhibitor through electrostatic effects of a unique MMP-1 arginine. Asp-2 increases reactive site polarity, reducing ΔCp, but increases conformational entropy to maintain strong binding to MMP1. There is a strong negative correlation between ΔSsolv and ΔSconf for all characterized interactions, but the data for each MMP have characteristic ranges, reflecting intrinsic differences in the structures and dynamics of their free and inhibitor-bound forms. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models

PubMed Central

Grün, Sonja; Helias, Moritz

2017-01-01

Pairwise maximum-entropy models have been used in neuroscience to predict the activity of neuronal populations, given only the time-averaged correlations of the neuron activities. This paper provides evidence that the pairwise model, applied to experimental recordings, would produce a bimodal distribution for the population-averaged activity, and for some population sizes the second mode would peak at high activities, that experimentally would be equivalent to 90% of the neuron population active within time-windows of few milliseconds. Several problems are connected with this bimodality: 1. The presence of the high-activity mode is unrealistic in view of observed neuronal activity and on neurobiological grounds. 2. Boltzmann learning becomes non-ergodic, hence the pairwise maximum-entropy distribution cannot be found: in fact, Boltzmann learning would produce an incorrect distribution; similarly, common variants of mean-field approximations also produce an incorrect distribution. 3. The Glauber dynamics associated with the model is unrealistically bistable and cannot be used to generate realistic surrogate data. This bimodality problem is first demonstrated for an experimental dataset from 159 neurons in the motor cortex of macaque monkey. Evidence is then provided that this problem affects typical neural recordings of population sizes of a couple of hundreds or more neurons. The cause of the bimodality problem is identified as the inability of standard maximum-entropy distributions with a uniform reference measure to model neuronal inhibition. To eliminate this problem a modified maximum-entropy model is presented, which reflects a basic effect of inhibition in the form of a simple but non-uniform reference measure. This model does not lead to unrealistic bimodalities, can be found with Boltzmann learning, and has an associated Glauber dynamics which incorporates a minimal asymmetric inhibition. PMID:28968396

Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models.

PubMed

Rostami, Vahid; Porta Mana, PierGianLuca; Grün, Sonja; Helias, Moritz

2017-10-01

Pairwise maximum-entropy models have been used in neuroscience to predict the activity of neuronal populations, given only the time-averaged correlations of the neuron activities. This paper provides evidence that the pairwise model, applied to experimental recordings, would produce a bimodal distribution for the population-averaged activity, and for some population sizes the second mode would peak at high activities, that experimentally would be equivalent to 90% of the neuron population active within time-windows of few milliseconds. Several problems are connected with this bimodality: 1. The presence of the high-activity mode is unrealistic in view of observed neuronal activity and on neurobiological grounds. 2. Boltzmann learning becomes non-ergodic, hence the pairwise maximum-entropy distribution cannot be found: in fact, Boltzmann learning would produce an incorrect distribution; similarly, common variants of mean-field approximations also produce an incorrect distribution. 3. The Glauber dynamics associated with the model is unrealistically bistable and cannot be used to generate realistic surrogate data. This bimodality problem is first demonstrated for an experimental dataset from 159 neurons in the motor cortex of macaque monkey. Evidence is then provided that this problem affects typical neural recordings of population sizes of a couple of hundreds or more neurons. The cause of the bimodality problem is identified as the inability of standard maximum-entropy distributions with a uniform reference measure to model neuronal inhibition. To eliminate this problem a modified maximum-entropy model is presented, which reflects a basic effect of inhibition in the form of a simple but non-uniform reference measure. This model does not lead to unrealistic bimodalities, can be found with Boltzmann learning, and has an associated Glauber dynamics which incorporates a minimal asymmetric inhibition.

[Maximum entropy model versus remote sensing-based methods for extracting Oncomelania hupensis snail habitats].

PubMed

Cong-Cong, Xia; Cheng-Fang, Lu; Si, Li; Tie-Jun, Zhang; Sui-Heng, Lin; Yi, Hu; Ying, Liu; Zhi-Jie, Zhang

2016-12-02

To explore the technique of maximum entropy model for extracting Oncomelania hupensis snail habitats in Poyang Lake zone. The information of snail habitats and related environment factors collected in Poyang Lake zone were integrated to set up the maximum entropy based species model and generate snail habitats distribution map. Two Landsat 7 ETM+ remote sensing images of both wet and drought seasons in Poyang Lake zone were obtained, where the two indices of modified normalized difference water index (MNDWI) and normalized difference vegetation index (NDVI) were applied to extract snail habitats. The ROC curve, sensitivities and specificities were applied to assess their results. Furthermore, the importance of the variables for snail habitats was analyzed by using Jackknife approach. The evaluation results showed that the area under receiver operating characteristic curve (AUC) of testing data by the remote sensing-based method was only 0.56, and the sensitivity and specificity were 0.23 and 0.89 respectively. Nevertheless, those indices above-mentioned of maximum entropy model were 0.876, 0.89 and 0.74 respectively. The main concentration of snail habitats in Poyang Lake zone covered the northeast part of Yongxiu County, northwest of Yugan County, southwest of Poyang County and middle of Xinjian County, and the elevation was the most important environment variable affecting the distribution of snails, and the next was land surface temperature (LST). The maximum entropy model is more reliable and accurate than the remote sensing-based method for the sake of extracting snail habitats, which has certain guiding significance for the relevant departments to carry out measures to prevent and control high-risk snail habitats.

NASA Thesaurus. Volume 2: Access vocabulary

NASA Technical Reports Server (NTRS)

1976-01-01

The NASA Thesaurus -- Volume 2, Access Vocabulary -- contains an alphabetical listing of all Thesaurus terms (postable and nonpostable) and permutations of all multiword and pseudo-multiword terms. Also included are Other Words (non-Thesaurus terms) consisting of abbreviations, chemical symbols, etc. The permutations and Other Words provide 'access' to the appropriate postable entries in the Thesaurus.

A Permutation Test for Correlated Errors in Adjacent Questionnaire Items

ERIC Educational Resources Information Center

Hildreth, Laura A.; Genschel, Ulrike; Lorenz, Frederick O.; Lesser, Virginia M.

2013-01-01

Response patterns are of importance to survey researchers because of the insight they provide into the thought processes respondents use to answer survey questions. In this article we propose the use of structural equation modeling to examine response patterns and develop a permutation test to quantify the likelihood of observing a specific…

The Parity Theorem Shuffle

ERIC Educational Resources Information Center

Smith, Michael D.

2016-01-01

The Parity Theorem states that any permutation can be written as a product of transpositions, but no permutation can be written as a product of both an even number and an odd number of transpositions. Most proofs of the Parity Theorem take several pages of mathematical formalism to complete. This article presents an alternative but equivalent…

Heuristic Implementation of Dynamic Programming for Matrix Permutation Problems in Combinatorial Data Analysis

ERIC Educational Resources Information Center

Brusco, Michael J.; Kohn, Hans-Friedrich; Stahl, Stephanie

2008-01-01

Dynamic programming methods for matrix permutation problems in combinatorial data analysis can produce globally-optimal solutions for matrices up to size 30x30, but are computationally infeasible for larger matrices because of enormous computer memory requirements. Branch-and-bound methods also guarantee globally-optimal solutions, but computation…

Entropy and cosmology.

NASA Astrophysics Data System (ADS)

Zucker, M. H.

This paper is a critical analysis and reassessment of entropic functioning as it applies to the question of whether the ultimate fate of the universe will be determined in the future to be "open" (expanding forever to expire in a big chill), "closed" (collapsing to a big crunch), or "flat" (balanced forever between the two). The second law of thermodynamics declares that entropy can only increase and that this principle extends, inevitably, to the universe as a whole. This paper takes the position that this extension is an unwarranted projection based neither on experience nonfact - an extrapolation that ignores the powerful effect of a gravitational force acting within a closed system. Since it was originally presented by Clausius, the thermodynamic concept of entropy has been redefined in terms of "order" and "disorder" - order being equated with a low degree of entropy and disorder with a high degree. This revised terminology more subjective than precise, has generated considerable confusion in cosmology in several critical instances. For example - the chaotic fireball of the big bang, interpreted by Stephen Hawking as a state of disorder (high entropy), is infinitely hot and, thermally, represents zero entropy (order). Hawking, apparently focusing on the disorderly "chaotic" aspect, equated it with a high degree of entropy - overlooking the fact that the universe is a thermodynamic system and that the key factor in evaluating the big-bang phenomenon is the infinitely high temperature at the early universe, which can only be equated with zero entropy. This analysis resolves this confusion and reestablishes entropy as a cosmological function integrally linked to temperature. The paper goes on to show that, while all subsystems contained within the universe require external sources of energization to have their temperatures raised, this requirement does not apply to the universe as a whole. The universe is the only system that, by itself can raise its own temperature and thus, by itself; reverse entropy. The vast encompassing gravitational forces that the universe has at its disposal, forces that dominate the phase of contraction, provide the compacting, compressive mechanism that regenerates heat in an expanded, cooled universe and decreases entropy. And this phenomenon takes place without diminishing or depleting the finite amount of mass/energy with which the universe began. The fact that the universe can reverse the entropic process leads to possibilities previously ignored when assessing which of the three models (open, closed, of flat) most probably represents the future of the universe. After analyzing the models, the conclusion reached here is that the open model is only an expanded version of the closed model and therefore is not open, and the closed model will never collapse to a big crunch and, therefore, is not closed. Which leaves a modified model, oscillating forever between limited phases of expansion and contraction (a universe in "dynamic equilibrium") as the only feasible choice.

permGPU: Using graphics processing units in RNA microarray association studies.

PubMed

Shterev, Ivo D; Jung, Sin-Ho; George, Stephen L; Owzar, Kouros

2010-06-16

Many analyses of microarray association studies involve permutation, bootstrap resampling and cross-validation, that are ideally formulated as embarrassingly parallel computing problems. Given that these analyses are computationally intensive, scalable approaches that can take advantage of multi-core processor systems need to be developed. We have developed a CUDA based implementation, permGPU, that employs graphics processing units in microarray association studies. We illustrate the performance and applicability of permGPU within the context of permutation resampling for a number of test statistics. An extensive simulation study demonstrates a dramatic increase in performance when using permGPU on an NVIDIA GTX 280 card compared to an optimized C/C++ solution running on a conventional Linux server. permGPU is available as an open-source stand-alone application and as an extension package for the R statistical environment. It provides a dramatic increase in performance for permutation resampling analysis in the context of microarray association studies. The current version offers six test statistics for carrying out permutation resampling analyses for binary, quantitative and censored time-to-event traits.

Testing for the Presence of Correlation Changes in a Multivariate Time Series: A Permutation Based Approach.

PubMed

Cabrieto, Jedelyn; Tuerlinckx, Francis; Kuppens, Peter; Hunyadi, Borbála; Ceulemans, Eva

2018-01-15

Detecting abrupt correlation changes in multivariate time series is crucial in many application fields such as signal processing, functional neuroimaging, climate studies, and financial analysis. To detect such changes, several promising correlation change tests exist, but they may suffer from severe loss of power when there is actually more than one change point underlying the data. To deal with this drawback, we propose a permutation based significance test for Kernel Change Point (KCP) detection on the running correlations. Given a requested number of change points K, KCP divides the time series into K + 1 phases by minimizing the within-phase variance. The new permutation test looks at how the average within-phase variance decreases when K increases and compares this to the results for permuted data. The results of an extensive simulation study and applications to several real data sets show that, depending on the setting, the new test performs either at par or better than the state-of-the art significance tests for detecting the presence of correlation changes, implying that its use can be generally recommended.

A new EEG synchronization strength analysis method: S-estimator based normalized weighted-permutation mutual information.

PubMed

Cui, Dong; Pu, Weiting; Liu, Jing; Bian, Zhijie; Li, Qiuli; Wang, Lei; Gu, Guanghua

2016-10-01

Synchronization is an important mechanism for understanding information processing in normal or abnormal brains. In this paper, we propose a new method called normalized weighted-permutation mutual information (NWPMI) for double variable signal synchronization analysis and combine NWPMI with S-estimator measure to generate a new method named S-estimator based normalized weighted-permutation mutual information (SNWPMI) for analyzing multi-channel electroencephalographic (EEG) synchronization strength. The performances including the effects of time delay, embedding dimension, coupling coefficients, signal to noise ratios (SNRs) and data length of the NWPMI are evaluated by using Coupled Henon mapping model. The results show that the NWPMI is superior in describing the synchronization compared with the normalized permutation mutual information (NPMI). Furthermore, the proposed SNWPMI method is applied to analyze scalp EEG data from 26 amnestic mild cognitive impairment (aMCI) subjects and 20 age-matched controls with normal cognitive function, who both suffer from type 2 diabetes mellitus (T2DM). The proposed methods NWPMI and SNWPMI are suggested to be an effective index to estimate the synchronization strength. Copyright © 2016 Elsevier Ltd. All rights reserved.

Sorting signed permutations by inversions in O(nlogn) time.

PubMed

Swenson, Krister M; Rajan, Vaibhav; Lin, Yu; Moret, Bernard M E

2010-03-01

The study of genomic inversions (or reversals) has been a mainstay of computational genomics for nearly 20 years. After the initial breakthrough of Hannenhalli and Pevzner, who gave the first polynomial-time algorithm for sorting signed permutations by inversions, improved algorithms have been designed, culminating with an optimal linear-time algorithm for computing the inversion distance and a subquadratic algorithm for providing a shortest sequence of inversions--also known as sorting by inversions. Remaining open was the question of whether sorting by inversions could be done in O(nlogn) time. In this article, we present a qualified answer to this question, by providing two new sorting algorithms, a simple and fast randomized algorithm and a deterministic refinement. The deterministic algorithm runs in time O(nlogn + kn), where k is a data-dependent parameter. We provide the results of extensive experiments showing that both the average and the standard deviation for k are small constants, independent of the size of the permutation. We conclude (but do not prove) that almost all signed permutations can be sorted by inversions in O(nlogn) time.

Coexpression of Human α- and Circularly Permuted β-Globins Yields a Hemoglobin with Normal R State but Modified T State Properties†

PubMed Central

Asmundson, Anna L.; Taber, Alexandria M.; van der Walde, Adella; Lin, Danielle H.; Olson, John S.; Anthony-Cahill, Spencer J.

2009-01-01

For the first time, a circularly permuted human β-globin (cpβ) has been coexpressed with human α-globin in bacterial cells and shown to associate to form α-cpβ hemoglobin in solution. Flash photolysis studies of α-cpβ show markedly biphasic CO and O2 kinetics with the amplitudes for the fast association phases being dominant due the presence of large amounts of high-affinity liganded hemoglobin dimers. Extensive dimerization of liganded but not deoxygenated α-cpβ was observed by gel chromatography. The rate constants for O2 and CO binding to the R state forms of α-cpβ are almost identical to those of native HbA (k′R(CO) ≈ 5.0 μM−1 s−1; k′R(O2) ≈ 50 μM−1 s−1), and the rate of O2 dissociation from fully oxygenated α-cpβ is also very similar to that observed for HbA (kR(O2) ≈ 21–28 s−1). When the equilibrium deoxyHb form of α-cpβ is reacted with CO in rapid mixing experiments, the observed time courses are monophasic and the observed bimolecular association rate constant is ∼1.0 μM−1 s−1, which is intermediate between the R state rate measured in partial photolysis experiments (∼5 μM−1 s−1) and that observed for T state deoxyHbA (k′T(CO) ≈ 0.1 to 0.2 μM−1 s−1). Thus the deoxygenated permutated β subunits generate an intermediate, higher affinity, deoxyHb quaternary state. This conclusion is supported by equilibrium oxygen binding measurements in which α-cpβ exhibits a P50 of ∼1.5 mmHg and a low n-value (∼1.3) at pH 7, 20 °C, compared to 8.5 mmHg and n ≈ 2.8 for native HbA under identical, dilute conditions. PMID:19397368

EXPLICIT SYMPLECTIC-LIKE INTEGRATORS WITH MIDPOINT PERMUTATIONS FOR SPINNING COMPACT BINARIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Junjie; Wu, Xin; Huang, Guoqing

2017-01-01

We refine the recently developed fourth-order extended phase space explicit symplectic-like methods for inseparable Hamiltonians using Yoshida’s triple product combined with a midpoint permuted map. The midpoint between the original variables and their corresponding extended variables at every integration step is readjusted as the initial values of the original variables and their corresponding extended ones at the next step integration. The triple-product construction is apparently superior to the composition of two triple products in computational efficiency. Above all, the new midpoint permutations are more effective in restraining the equality of the original variables and their corresponding extended ones at each integration step thanmore » the existing sequent permutations of momenta and coordinates. As a result, our new construction shares the benefit of implicit symplectic integrators in the conservation of the second post-Newtonian Hamiltonian of spinning compact binaries. Especially for the chaotic case, it can work well, but the existing sequent permuted algorithm cannot. When dissipative effects from the gravitational radiation reaction are included, the new symplectic-like method has a secular drift in the energy error of the dissipative system for the orbits that are regular in the absence of radiation, as an implicit symplectic integrator does. In spite of this, it is superior to the same-order implicit symplectic integrator in accuracy and efficiency. The new method is particularly useful in discussing the long-term evolution of inseparable Hamiltonian problems.« less

A studentized permutation test for three-arm trials in the 'gold standard' design.

PubMed

Mütze, Tobias; Konietschke, Frank; Munk, Axel; Friede, Tim

2017-03-15

The 'gold standard' design for three-arm trials refers to trials with an active control and a placebo control in addition to the experimental treatment group. This trial design is recommended when being ethically justifiable and it allows the simultaneous comparison of experimental treatment, active control, and placebo. Parametric testing methods have been studied plentifully over the past years. However, these methods often tend to be liberal or conservative when distributional assumptions are not met particularly with small sample sizes. In this article, we introduce a studentized permutation test for testing non-inferiority and superiority of the experimental treatment compared with the active control in three-arm trials in the 'gold standard' design. The performance of the studentized permutation test for finite sample sizes is assessed in a Monte Carlo simulation study under various parameter constellations. Emphasis is put on whether the studentized permutation test meets the target significance level. For comparison purposes, commonly used Wald-type tests, which do not make any distributional assumptions, are included in the simulation study. The simulation study shows that the presented studentized permutation test for assessing non-inferiority in three-arm trials in the 'gold standard' design outperforms its competitors, for instance the test based on a quasi-Poisson model, for count data. The methods discussed in this paper are implemented in the R package ThreeArmedTrials which is available on the comprehensive R archive network (CRAN). Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

A Cellular Automata Model of Bone Formation

PubMed Central

Van Scoy, Gabrielle K.; George, Estee L.; Asantewaa, Flora Opoku; Kerns, Lucy; Saunders, Marnie M.; Prieto-Langarica, Alicia

2017-01-01

Bone remodeling is an elegantly orchestrated process by which osteocytes, osteoblasts and osteoclasts function as a syncytium to maintain or modify bone. On the microscopic level, bone consists of cells that create, destroy and monitor the bone matrix. These cells interact in a coordinated manner to maintain a tightly regulated homeostasis. It is this regulation that is responsible for the observed increase in bone gain in the dominant arm of a tennis player and the observed increase in bone loss associated with spaceflight and osteoporosis. The manner in which these cells interact to bring about a change in bone quality and quantity has yet to be fully elucidated. But efforts to understand the multicellular complexity can ultimately lead to eradication of metabolic bone diseases such as osteoporosis and improved implant longevity. Experimentally validated mathematical models that simulate functional activity and offer eventual predictive capabilities offer tremendous potential in understanding multicellular bone remodeling. Here we undertake the initial challenge to develop a mathematical model of bone formation validated with in vitro data obtained from osteoblastic bone cells induced to mineralize and quantified at 26 days of culture. A cellular automata model was constructed to simulate the in vitro characterization. Permutation tests were performed to compare the distribution of the mineralization in the cultures and the distribution of the mineralization in the mathematical models. The results of the permutation test show the distribution of mineralization from the characterization and mathematical model come from the same probability distribution, therefore validating the cellular automata model. PMID:28189632

Gene-environment interaction involving recently identified colorectal cancer susceptibility loci

PubMed Central

Kantor, Elizabeth D.; Hutter, Carolyn M.; Minnier, Jessica; Berndt, Sonja I.; Brenner, Hermann; Caan, Bette J.; Campbell, Peter T.; Carlson, Christopher S.; Casey, Graham; Chan, Andrew T.; Chang-Claude, Jenny; Chanock, Stephen J.; Cotterchio, Michelle; Du, Mengmeng; Duggan, David; Fuchs, Charles S.; Giovannucci, Edward L.; Gong, Jian; Harrison, Tabitha A.; Hayes, Richard B.; Henderson, Brian E.; Hoffmeister, Michael; Hopper, John L.; Jenkins, Mark A.; Jiao, Shuo; Kolonel, Laurence N.; Le Marchand, Loic; Lemire, Mathieu; Ma, Jing; Newcomb, Polly A.; Ochs-Balcom, Heather M.; Pflugeisen, Bethann M.; Potter, John D.; Rudolph, Anja; Schoen, Robert E.; Seminara, Daniela; Slattery, Martha L.; Stelling, Deanna L.; Thomas, Fridtjof; Thornquist, Mark; Ulrich, Cornelia M.; Warnick, Greg S.; Zanke, Brent W.; Peters, Ulrike; Hsu, Li; White, Emily

2014-01-01

BACKGROUND Genome-wide association studies have identified several single nucleotide polymorphisms (SNPs) that are associated with risk of colorectal cancer (CRC). Prior research has evaluated the presence of gene-environment interaction involving the first 10 identified susceptibility loci, but little work has been conducted on interaction involving SNPs at recently identified susceptibility loci, including: rs10911251, rs6691170, rs6687758, rs11903757, rs10936599, rs647161, rs1321311, rs719725, rs1665650, rs3824999, rs7136702, rs11169552, rs59336, rs3217810, rs4925386, and rs2423279. METHODS Data on 9160 cases and 9280 controls from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and Colon Cancer Family Registry (CCFR) were used to evaluate the presence of interaction involving the above-listed SNPs and sex, body mass index (BMI), alcohol consumption, smoking, aspirin use, post-menopausal hormone (PMH) use, as well as intake of dietary calcium, dietary fiber, dietary folate, red meat, processed meat, fruit, and vegetables. Interaction was evaluated using a fixed-effects meta-analysis of an efficient Empirical Bayes estimator, and permutation was used to account for multiple comparisons. RESULTS None of the permutation-adjusted p-values reached statistical significance. CONCLUSIONS The associations between recently identified genetic susceptibility loci and CRC are not strongly modified by sex, BMI, alcohol, smoking, aspirin, PMH use, and various dietary factors. IMPACT Results suggest no evidence of strong gene-environment interactions involving the recently identified 16 susceptibility loci for CRC taken one at a time. PMID:24994789

Time domain structures in a colliding magnetic flux rope experiment

NASA Astrophysics Data System (ADS)

Tang, Shawn Wenjie; Gekelman, Walter; Dehaas, Timothy; Vincena, Steve; Pribyl, Patrick

2017-10-01

Electron phase-space holes, regions of positive potential on the scale of the Debye length, have been observed in auroras as well as in laboratory experiments. These potential structures, also known as Time Domain Structures (TDS), are packets of intense electric field spikes that have significant components parallel to the local magnetic field. In an ongoing investigation at UCLA, TDS were observed on the surface of two magnetized flux ropes produced within the Large Plasma Device (LAPD). A barium oxide (BaO) cathode was used to produce an 18 m long magnetized plasma column and a lanthanum hexaboride (LaB6) source was used to create 11 m long kink unstable flux ropes. Using two probes capable of measuring the local electric and magnetic fields, correlation analysis was performed on tens of thousands of these structures and their propagation velocities, probability distribution function and spatial distribution were determined. The TDS became abundant as the flux ropes collided and appear to emanate from the reconnection region in between them. In addition, a preliminary analysis of the permutation entropy and statistical complexity of the data suggests that the TDS signals may be chaotic in nature. Work done at the Basic Plasma Science Facility (BaPSF) at UCLA which is supported by DOE and NSF.

A Hybrid Generalized Hidden Markov Model-Based Condition Monitoring Approach for Rolling Bearings

PubMed Central

Liu, Jie; Hu, Youmin; Wu, Bo; Wang, Yan; Xie, Fengyun

2017-01-01

The operating condition of rolling bearings affects productivity and quality in the rotating machine process. Developing an effective rolling bearing condition monitoring approach is critical to accurately identify the operating condition. In this paper, a hybrid generalized hidden Markov model-based condition monitoring approach for rolling bearings is proposed, where interval valued features are used to efficiently recognize and classify machine states in the machine process. In the proposed method, vibration signals are decomposed into multiple modes with variational mode decomposition (VMD). Parameters of the VMD, in the form of generalized intervals, provide a concise representation for aleatory and epistemic uncertainty and improve the robustness of identification. The multi-scale permutation entropy method is applied to extract state features from the decomposed signals in different operating conditions. Traditional principal component analysis is adopted to reduce feature size and computational cost. With the extracted features’ information, the generalized hidden Markov model, based on generalized interval probability, is used to recognize and classify the fault types and fault severity levels. Finally, the experiment results show that the proposed method is effective at recognizing and classifying the fault types and fault severity levels of rolling bearings. This monitoring method is also efficient enough to quantify the two uncertainty components. PMID:28524088

Analysis of EEG signals regularity in adults during video game play in 2D and 3D.

PubMed

Khairuddin, Hamizah R; Malik, Aamir S; Mumtaz, Wajid; Kamel, Nidal; Xia, Likun

2013-01-01

Video games have long been part of the entertainment industry. Nonetheless, it is not well known how video games can affect us with the advancement of 3D technology. The purpose of this study is to investigate the EEG signals regularity when playing video games in 2D and 3D modes. A total of 29 healthy subjects (24 male, 5 female) with mean age of 21.79 (1.63) years participated. Subjects were asked to play a car racing video game in three different modes (2D, 3D passive and 3D active). In 3D passive mode, subjects needed to wear a passive polarized glasses (cinema type) while for 3D active, an active shutter glasses was used. Scalp EEG data was recorded during game play using 19-channel EEG machine and linked ear was used as reference. After data were pre-processed, the signal irregularity for all conditions was computed. Two parameters were used to measure signal complexity for time series data: i) Hjorth-Complexity and ii) Composite Permutation Entropy Index (CPEI). Based on these two parameters, our results showed that the complexity level increased from eyes closed to eyes open condition; and further increased in the case of 3D as compared to 2D game play.

Optimized mixed Markov models for motif identification

PubMed Central

Huang, Weichun; Umbach, David M; Ohler, Uwe; Li, Leping

2006-01-01

Background Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challenging issue, largely due to limited availability of training samples. Results We introduce a novel and flexible model, the Optimized Mixture Markov model (OMiMa), and related methods to allow adjustment of model complexity for different motifs. In comparison with other leading methods, OMiMa can incorporate more than the NNSplice's pairwise dependencies; OMiMa avoids model over-fitting better than the Permuted Variable Length Markov Model (PVLMM); and OMiMa requires smaller training samples than the Maximum Entropy Model (MEM). Testing on both simulated and actual data (regulatory cis-elements and splice sites), we found OMiMa's performance superior to the other leading methods in terms of prediction accuracy, required size of training data or computational time. Our OMiMa system, to our knowledge, is the only motif finding tool that incorporates automatic selection of the best model. OMiMa is freely available at [1]. Conclusion Our optimized mixture of Markov models represents an alternative to the existing methods for modeling dependent structures within a biological motif. Our model is conceptually simple and effective, and can improve prediction accuracy and/or computational speed over other leading methods. PMID:16749929

Disposable, Autonomic, Energy-Converting Ion Channel Sensor Materials

DTIC Science & Technology

2018-07-02

variant forms well-defined pores _____________________________ 26 4.2. Another pore-forming peptide, Ceratotoxin A, displays alamethicin-like activity ...bilayer recordings to examine the activity of these compounds on the single-pore level. We plan to use modified CtxA for targeted cell killing...strongly dependent on entropy of activation . Tethering is one strategy towards achieving this goal. A manuscript regarding this work is currently in

Calculation of optical parameters for covalent binary alloys used in optical memories/solar cells: a modified approach

NASA Astrophysics Data System (ADS)

Bhatnagar, Promod K.; Gupta, Poonam; Singh, Laxman

2001-06-01

Chalcogenide based alloys find applications in a number of devices like optical memories, IR detectors, optical switches, photovoltaics, compound semiconductor heterosrtuctures etc. We have modified the Gurman's statistical thermodynamic model (STM) of binary covalent alloys. In the Gurman's model, entropy calculations are based on the number of structural units present. The need to modify this model arose due to the fact that it gives equal probability for all the tetrahedra present in the alloy. We have modified the Gurman's model by introducing the concept that the entropy is based on the bond arrangement rather than that on the structural units present. In the present work calculation based on this modification have been presented for optical properties, which find application in optical switching/memories, solar cells and other optical devices. It has been shown that the calculated optical parameters (for a typical case of GaxSe1-x) based on modified model are closer to the available experimental results. These parameters include refractive index, extinction coefficient, dielectric functions, optical band gap etc. GaxSe1-x has been found to be suitable for reversible optical memories also, where phase change (a yields c and vice versa) takes place at specified physical conditions. DTA/DSC studies also suggest the suitability of this material for optical switching/memory applications. We have also suggested possible use of GaxSe1-x (x = 0.4) in place of oxide layer in a Metal - Oxide - Semiconductor type solar cells. The new structure is Metal - Ga2Se3 - GaAs. The I-V characteristics and other parameters calculated for this structure are found to be much better than that for Si based solar cells. Maximum output power is obtained at the intermediate layer thickness approximately 40 angstroms for this typical solar cell.

On the optimality of code options for a universal noiseless coder

NASA Technical Reports Server (NTRS)

Yeh, Pen-Shu; Rice, Robert F.; Miller, Warner

1991-01-01

A universal noiseless coding structure was developed that provides efficient performance over an extremely broad range of source entropy. This is accomplished by adaptively selecting the best of several easily implemented variable length coding algorithms. Custom VLSI coder and decoder modules capable of processing over 20 million samples per second are currently under development. The first of the code options used in this module development is shown to be equivalent to a class of Huffman code under the Humblet condition, other options are shown to be equivalent to the Huffman codes of a modified Laplacian symbol set, at specified symbol entropy values. Simulation results are obtained on actual aerial imagery, and they confirm the optimality of the scheme. On sources having Gaussian or Poisson distributions, coder performance is also projected through analysis and simulation.

Quantum image encryption based on restricted geometric and color transformations

NASA Astrophysics Data System (ADS)

Song, Xian-Hua; Wang, Shen; Abd El-Latif, Ahmed A.; Niu, Xia-Mu

2014-08-01

A novel encryption scheme for quantum images based on restricted geometric and color transformations is proposed. The new strategy comprises efficient permutation and diffusion properties for quantum image encryption. The core idea of the permutation stage is to scramble the codes of the pixel positions through restricted geometric transformations. Then, a new quantum diffusion operation is implemented on the permutated quantum image based on restricted color transformations. The encryption keys of the two stages are generated by two sensitive chaotic maps, which can ensure the security of the scheme. The final step, measurement, is built by the probabilistic model. Experiments conducted on statistical analysis demonstrate that significant improvements in the results are in favor of the proposed approach.

Statistical validation of normal tissue complication probability models.

PubMed

Xu, Cheng-Jian; van der Schaaf, Arjen; Van't Veld, Aart A; Langendijk, Johannes A; Schilstra, Cornelis

2012-09-01

To investigate the applicability and value of double cross-validation and permutation tests as established statistical approaches in the validation of normal tissue complication probability (NTCP) models. A penalized regression method, LASSO (least absolute shrinkage and selection operator), was used to build NTCP models for xerostomia after radiation therapy treatment of head-and-neck cancer. Model assessment was based on the likelihood function and the area under the receiver operating characteristic curve. Repeated double cross-validation showed the uncertainty and instability of the NTCP models and indicated that the statistical significance of model performance can be obtained by permutation testing. Repeated double cross-validation and permutation tests are recommended to validate NTCP models before clinical use. Copyright © 2012 Elsevier Inc. All rights reserved.

Energetics of photosynthetic glow peaks

PubMed Central

DeVault, Don; Govindjee; Arnold, William

1983-01-01

By postulating temperature-dependent equilibria between two or more electron carriers acting as traps for electrons or holes, it is possible to modify the Randall-Wilkins theory of thermoluminescence so as to explain the abnormally large apparent activation energies and apparent frequency factors observed in photosynthetic glow curves when fitted by unmodified Randall-Wilkins theory. The equilibria serve to inhibit the formation of the light-emitting excited state by withholding the needed precursor state. When the inhibition is released at higher temperature by shift of equilibrium with temperature, the rise of the glow peak can be much faster than would result from Arrhenius behavior based on the true activation energy and so appears to correspond to a higher activation energy accompanied by a larger frequency factor. From another viewpoint, the enthalpy changes, ΔH, of the equilibria tend to add to the activation energy. Similarly the entropy changes, ΔS, of the equilibria tend to add to the entropy of activation, giving the large apparent frequency factors. The positive values of ΔS needed would correspond to entropy decreases in the forward early electron transport. A comparison of the glow peaks obtained by different workers is also presented. PMID:16593283

Age-related Multiscale Changes in Brain Signal Variability in Pre-task versus Post-task Resting-state EEG.

PubMed

Wang, Hongye; McIntosh, Anthony R; Kovacevic, Natasa; Karachalios, Maria; Protzner, Andrea B

2016-07-01

Recent empirical work suggests that, during healthy aging, the variability of network dynamics changes during task performance. Such variability appears to reflect the spontaneous formation and dissolution of different functional networks. We sought to extend these observations into resting-state dynamics. We recorded EEG in young, middle-aged, and older adults during a "rest-task-rest" design and investigated if aging modifies the interaction between resting-state activity and external stimulus-induced activity. Using multiscale entropy as our measure of variability, we found that, with increasing age, resting-state dynamics shifts from distributed to more local neural processing, especially at posterior sources. In the young group, resting-state dynamics also changed from pre- to post-task, where fine-scale entropy increased in task-positive regions and coarse-scale entropy increased in the posterior cingulate, a key region associated with the default mode network. Lastly, pre- and post-task resting-state dynamics were linked to performance on the intervening task for all age groups, but this relationship became weaker with increasing age. Our results suggest that age-related changes in resting-state dynamics occur across different spatial and temporal scales and have consequences for information processing capacity.

Flood control project selection using an interval type-2 entropy weight with interval type-2 fuzzy TOPSIS

NASA Astrophysics Data System (ADS)

Zamri, Nurnadiah; Abdullah, Lazim

2014-06-01

Flood control project is a complex issue which takes economic, social, environment and technical attributes into account. Selection of the best flood control project requires the consideration of conflicting quantitative and qualitative evaluation criteria. When decision-makers' judgment are under uncertainty, it is relatively difficult for them to provide exact numerical values. The interval type-2 fuzzy set (IT2FS) is a strong tool which can deal with the uncertainty case of subjective, incomplete, and vague information. Besides, it helps to solve for some situations where the information about criteria weights for alternatives is completely unknown. Therefore, this paper is adopted the information interval type-2 entropy concept into the weighting process of interval type-2 fuzzy TOPSIS. This entropy weight is believed can effectively balance the influence of uncertainty factors in evaluating attribute. Then, a modified ranking value is proposed in line with the interval type-2 entropy weight. Quantitative and qualitative factors that normally linked with flood control project are considered for ranking. Data in form of interval type-2 linguistic variables were collected from three authorised personnel of three Malaysian Government agencies. Study is considered for the whole of Malaysia. From the analysis, it shows that diversion scheme yielded the highest closeness coefficient at 0.4807. A ranking can be drawn using the magnitude of closeness coefficient. It was indicated that the diversion scheme recorded the first rank among five causes.

Chincup treatment modifies the mandibular shape in children with prognathism.

PubMed

Alarcón, José Antonio; Bastir, Markus; Rosas, Antonio; Molero, Julia

2011-07-01

Although chincups are the preferred treatment for growing children with mandibular prognathism, the mechanism by which chincups improve this condition remains unclear. The aim of this study was to use geometric morphometrics to evaluate changes in the shape of the mandible of prognathic children treated with a chincup. Geometric morphometrics were used to evaluate the short-term mandibular shape changes in 50 prognathic children treated with chincups compared with 40 untreated matched controls. Twenty-one 2-dimensional mandibular landmarks from cephalograms taken before and after 36 months of treatment or observation were analyzed by Procrustes superimposition and thin plate spline. Permutation tests of the treated patients showed highly significant differences in the mandibular shapes before and after treatment, and compared with the control group after the observation period. The thin plate spline grid deformations indicated more rectangular mandibular configuration, forward condyle orientation, condyle neck compression, gonial area compression, and symphysis narrowing. Early chincup treatment widely modifies the mandibular shape of prognathic children to improve Class III malocclusion. Copyright © 2011 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Strategy escalation: an emerging paradigm for safe clinical development of T cell gene therapies.

PubMed

Junghans, Richard Paul

2010-06-10

Gene therapy techniques are being applied to modify T cells with chimeric antigen receptors (CARs) for therapeutic ends. The versatility of this platform has spawned multiple options for their application with new permutations in strategies continually being invented, a testimony to the creative energies of many investigators. The field is rapidly expanding with immense potential for impact against diverse cancers. But this rapid expansion, like the Big Bang, comes with a somewhat chaotic evolution of its therapeutic universe that can also be dangerous, as seen by recently publicized deaths. Time-honored methods for new drug testing embodied in Dose Escalation that were suitable for traditional inert agents are now inadequate for these novel "living drugs". In the following, I propose an approach to escalating risk for patient exposures with these new immuno-gene therapy agents, termed Strategy Escalation, that accounts for the molecular and biological features of the modified cells and the methods of their administration. This proposal is offered not as a prescriptive but as a discussion framework that investigators may wish to consider in configuring their intended clinical applications.

NASA thesaurus. Volume 2: Access vocabulary

NASA Technical Reports Server (NTRS)

1985-01-01

The Access Vocabulary, which is essentially a permuted index, provides access to any word or number in authorized postable and nonpostable terms. Additional entries include postable and nonpostable terms, other word entries, and pseudo-multiword terms that are permutations of words that contain words within words. The Access Vocabulary contains 40,738 entries that give increased access to the hierarchies in Volume 1 - Hierarchical Listing.

NASA Thesaurus. Volume 2: Access vocabulary

NASA Technical Reports Server (NTRS)

1982-01-01

The Access Vocabulary, which is essentially a permuted index, provides access to any word or number in authorized postable and nonpostable terms. Additional entries include postable and nonpostable terms, other word entries, and pseudo-multiword terms that are permutations of words that contain words within words. The Access Vocabulary contains, 40,661 entries that give increased access to he hierarchies in Volume 1 - Hierarchical Listing.

Instability of Hierarchical Cluster Analysis Due to Input Order of the Data: The PermuCLUSTER Solution

ERIC Educational Resources Information Center

van der Kloot, Willem A.; Spaans, Alexander M. J.; Heiser, Willem J.

2005-01-01

Hierarchical agglomerative cluster analysis (HACA) may yield different solutions under permutations of the input order of the data. This instability is caused by ties, either in the initial proximity matrix or arising during agglomeration. The authors recommend to repeat the analysis on a large number of random permutations of the rows and columns…

Optimal control of hybrid qubits: Implementing the quantum permutation algorithm

NASA Astrophysics Data System (ADS)

Rivera-Ruiz, C. M.; de Lima, E. F.; Fanchini, F. F.; Lopez-Richard, V.; Castelano, L. K.

2018-03-01

The optimal quantum control theory is employed to determine electric pulses capable of producing quantum gates with a fidelity higher than 0.9997, when noise is not taken into account. Particularly, these quantum gates were chosen to perform the permutation algorithm in hybrid qubits in double quantum dots (DQDs). The permutation algorithm is an oracle based quantum algorithm that solves the problem of the permutation parity faster than a classical algorithm without the necessity of entanglement between particles. The only requirement for achieving the speedup is the use of a one-particle quantum system with at least three levels. The high fidelity found in our results is closely related to the quantum speed limit, which is a measure of how fast a quantum state can be manipulated. Furthermore, we model charge noise by considering an average over the optimal field centered at different values of the reference detuning, which follows a Gaussian distribution. When the Gaussian spread is of the order of 5 μ eV (10% of the correct value), the fidelity is still higher than 0.95. Our scheme also can be used for the practical realization of different quantum algorithms in DQDs.

PsiQuaSP-A library for efficient computation of symmetric open quantum systems.

PubMed

Gegg, Michael; Richter, Marten

2017-11-24

In a recent publication we showed that permutation symmetry reduces the numerical complexity of Lindblad quantum master equations for identical multi-level systems from exponential to polynomial scaling. This is important for open system dynamics including realistic system bath interactions and dephasing in, for instance, the Dicke model, multi-Λ system setups etc. Here we present an object-oriented C++ library that allows to setup and solve arbitrary quantum optical Lindblad master equations, especially those that are permutationally symmetric in the multi-level systems. PsiQuaSP (Permutation symmetry for identical Quantum Systems Package) uses the PETSc package for sparse linear algebra methods and differential equations as basis. The aim of PsiQuaSP is to provide flexible, storage efficient and scalable code while being as user friendly as possible. It is easily applied to many quantum optical or quantum information systems with more than one multi-level system. We first review the basics of the permutation symmetry for multi-level systems in quantum master equations. The application of PsiQuaSP to quantum dynamical problems is illustrated with several typical, simple examples of open quantum optical systems.

Connotations of pixel-based scale effect in remote sensing and the modified fractal-based analysis method

NASA Astrophysics Data System (ADS)

Feng, Guixiang; Ming, Dongping; Wang, Min; Yang, Jianyu

2017-06-01

Scale problems are a major source of concern in the field of remote sensing. Since the remote sensing is a complex technology system, there is a lack of enough cognition on the connotation of scale and scale effect in remote sensing. Thus, this paper first introduces the connotations of pixel-based scale and summarizes the general understanding of pixel-based scale effect. Pixel-based scale effect analysis is essentially important for choosing the appropriate remote sensing data and the proper processing parameters. Fractal dimension is a useful measurement to analysis pixel-based scale. However in traditional fractal dimension calculation, the impact of spatial resolution is not considered, which leads that the scale effect change with spatial resolution can't be clearly reflected. Therefore, this paper proposes to use spatial resolution as the modified scale parameter of two fractal methods to further analyze the pixel-based scale effect. To verify the results of two modified methods (MFBM (Modified Windowed Fractal Brownian Motion Based on the Surface Area) and MDBM (Modified Windowed Double Blanket Method)); the existing scale effect analysis method (information entropy method) is used to evaluate. And six sub-regions of building areas and farmland areas were cut out from QuickBird images to be used as the experimental data. The results of the experiment show that both the fractal dimension and information entropy present the same trend with the decrease of spatial resolution, and some inflection points appear at the same feature scales. Further analysis shows that these feature scales (corresponding to the inflection points) are related to the actual sizes of the geo-object, which results in fewer mixed pixels in the image, and these inflection points are significantly indicative of the observed features. Therefore, the experiment results indicate that the modified fractal methods are effective to reflect the pixel-based scale effect existing in remote sensing data and it is helpful to analyze the observation scale from different aspects. This research will ultimately benefit for remote sensing data selection and application.

Steganography Detection Using Entropy Measures

DTIC Science & Technology

2012-08-19

embedded steganography . For this research freely available software for embedding hidden messages will be used to create sample image files to... LSB ) is a simple approach to modify an image , while at the same time, making the change imperceptible to the human eye. By considering the redundant...to 00001110, we have applied the least significant bit technique. 2.4 Significant Bit Image Depiction Steganography fails to comply in its purpose, at

Finger Vein Segmentation from Infrared Images Based on a Modified Separable Mumford Shah Model and Local Entropy Thresholding

PubMed Central

Dermatas, Evangelos

2015-01-01

A novel method for finger vein pattern extraction from infrared images is presented. This method involves four steps: preprocessing which performs local normalization of the image intensity, image enhancement, image segmentation, and finally postprocessing for image cleaning. In the image enhancement step, an image which will be both smooth and similar to the original is sought. The enhanced image is obtained by minimizing the objective function of a modified separable Mumford Shah Model. Since, this minimization procedure is computationally intensive for large images, a local application of the Mumford Shah Model in small window neighborhoods is proposed. The finger veins are located in concave nonsmooth regions and, so, in order to distinct them from the other tissue parts, all the differences between the smooth neighborhoods, obtained by the local application of the model, and the corresponding windows of the original image are added. After that, veins in the enhanced image have been sufficiently emphasized. Thus, after image enhancement, an accurate segmentation can be obtained readily by a local entropy thresholding method. Finally, the resulted binary image may suffer from some misclassifications and, so, a postprocessing step is performed in order to extract a robust finger vein pattern. PMID:26120357

Controllability of symmetric spin networks

NASA Astrophysics Data System (ADS)

Albertini, Francesca; D'Alessandro, Domenico

2018-05-01

We consider a network of n spin 1/2 systems which are pairwise interacting via Ising interaction and are controlled by the same electro-magnetic control field. Such a system presents symmetries since the Hamiltonian is unchanged if we permute two spins. This prevents full (operator) controllability, in that not every unitary evolution can be obtained. We prove however that controllability is verified if we restrict ourselves to unitary evolutions which preserve the above permutation invariance. For low dimensional cases, n = 2 and n = 3, we provide an analysis of the Lie group of available evolutions and give explicit control laws to transfer between two arbitrary permutation invariant states. This class of states includes highly entangled states such as Greenberger-Horne-Zeilinger (GHZ) states and W states, which are of interest in quantum information.

Storage and computationally efficient permutations of factorized covariance and square-root information matrices

NASA Technical Reports Server (NTRS)

Muellerschoen, R. J.

1988-01-01

A unified method to permute vector-stored upper-triangular diagonal factorized covariance (UD) and vector stored upper-triangular square-root information filter (SRIF) arrays is presented. The method involves cyclical permutation of the rows and columns of the arrays and retriangularization with appropriate square-root-free fast Givens rotations or elementary slow Givens reflections. A minimal amount of computation is performed and only one scratch vector of size N is required, where N is the column dimension of the arrays. To make the method efficient for large SRIF arrays on a virtual memory machine, three additional scratch vectors each of size N are used to avoid expensive paging faults. The method discussed is compared with the methods and routines of Bierman's Estimation Subroutine Library (ESL).

Hawking radiation, the Stefan–Boltzmann law, and unitarization

DOE PAGES

Giddings, Steven B.

2016-01-06

Where does Hawking radiation originate? A common picture is that it arises from excitations very near or at the horizon, and this viewpoint has supported the “firewall” argument and arguments for a key role for the UV-dependent entanglement entropy in describing the quantum mechanics of black holes. Closer investigation of both the total emission rate and the stress tensor of Hawking radiation supports the statement that its source is a near-horizon quantum region, or “atmosphere,” whose radial extent is set by the horizon radius scale. Potentially important, since Hawking radiation needs to be modified to restore unitarity, and a naturalmore » assumption is that the scales relevant to such modifications are comparable to those governing the Hawking radiation. Moreover, related discussion suggests a resolution to questions regarding extra energy flux in “nonviolent” scenarios, that does not spoil black hole thermodynamics as governed by the Bekenstein–Hawking entropy.« less

Hawking radiation, the Stefan-Boltzmann law, and unitarization

NASA Astrophysics Data System (ADS)

Giddings, Steven B.

2016-03-01

Where does Hawking radiation originate? A common picture is that it arises from excitations very near or at the horizon, and this viewpoint has supported the ;firewall; argument and arguments for a key role for the UV-dependent entanglement entropy in describing the quantum mechanics of black holes. However, closer investigation of both the total emission rate and the stress tensor of Hawking radiation supports the statement that its source is a near-horizon quantum region, or ;atmosphere,; whose radial extent is set by the horizon radius scale. This is potentially important, since Hawking radiation needs to be modified to restore unitarity, and a natural assumption is that the scales relevant to such modifications are comparable to those governing the Hawking radiation. Moreover, related discussion suggests a resolution to questions regarding extra energy flux in ;nonviolent; scenarios, that does not spoil black hole thermodynamics as governed by the Bekenstein-Hawking entropy.

Ordering states with various coherence measures

NASA Astrophysics Data System (ADS)

Yang, Long-Mei; Chen, Bin; Fei, Shao-Ming; Wang, Zhi-Xi

2018-04-01

Quantum coherence is one of the most significant theories in quantum physics. Ordering states with various coherence measures is an intriguing task in quantification theory of coherence. In this paper, we study this problem by use of four important coherence measures—the l_1 norm of coherence, the relative entropy of coherence, the geometric measure of coherence and the modified trace distance measure of coherence. We show that each pair of these measures give a different ordering of qudit states when d≥3. However, for single-qubit states, the l_1 norm of coherence and the geometric coherence provide the same ordering. We also show that the relative entropy of coherence and the geometric coherence give a different ordering for single-qubit states. Then we partially answer the open question proposed in Liu et al. (Quantum Inf Process 15:4189, 2016) whether all the coherence measures give a different ordering of states.

Reaction of the Anticancer Organometallic Ruthenium Compound, [(η6-p-Cymene)Ru(ATSC)Cl]PF6 with Human Serum Albumin

PubMed Central

Beckford, Floyd A.

2010-01-01

The reaction of [(η6-p-cymene)Ru(ATSC)Cl]PF6 (ATSC = 9-anthraldehyde thiosemicarbazone) with human serum albumin was investigated at different temperatures using fluorescence and infrared spectrophotometry. The binding constant, K, for the reaction was determined using a number of different methods. Using a modified Stern-Volmer equation, K was determined to be 9.09 × 104, 12.1 × 104, and 13.1 × 104 M−1 at 293 K, 298 K, and 308 K, respectively. A thermodynamic analysis showed that the reaction is spontaneous with ΔG being negative. The enthalpy of reaction ΔH = 16.5kJ mol−1 and the entropy of reaction ΔS = 152 Jmol−1K−1. The values of ΔH and ΔS suggest that hydrophobic forces are dominant in the mode of interaction and that the process is mostly entropy driven. PMID:20671814

The generalized second law of thermodynamics in Hořava-Lifshitz cosmology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jamil, Mubasher; Saridakis, Emmanuel N.; Setare, M.R., E-mail: mjamil@camp.nust.edu.pk, E-mail: msaridak@phys.uoa.gr, E-mail: rezakord@ipm.ir

2010-11-01

We investigate the validity of the generalized second law of thermodynamics in a universe governed by Hořava-Lifshitz gravity. Under the equilibrium assumption, that is in the late-time cosmological regime, we calculate separately the entropy time-variation for the matter fluid and, using the modified entropy relation, that of the apparent horizon itself. We find that under detailed balance the generalized second law is generally valid for flat and closed geometry and it is conditionally valid for an open universe, while beyond detailed balance it is only conditionally valid for all curvatures. Furthermore, we also follow the effective approach showing that itmore » can lead to misleading results. The non-complete validity of the generalized second law could either provide a suggestion for its different application, or act as an additional problematic feature of Hořava-Lifshitz gravity.« less

Accelerated cosmos in a nonextensive setup

NASA Astrophysics Data System (ADS)

Moradpour, H.; Bonilla, Alexander; Abreu, Everton M. C.; Neto, Jorge Ananias

2017-12-01

Here we consider a flat FRW universe whose horizon entropy meets the Rényi entropy of nonextensive systems. In our model, the ordinary energy-momentum conservation law is not always valid. By applying the Clausius relation as well as the Cai-Kim temperature to the apparent horizon of a flat FRW universe, we obtain modified Friedmann equations. Fitting the model to the observational data on the current accelerated universe, some values for the model parameters are also addressed. Our study shows that the current accelerating phase of universe expansion may be described by a geometrical fluid, originated from the nonextensive aspects of geometry, which models a varying dark energy source interacting with the matter field in the Rastall way. Moreover, our results indicate that the probable nonextensive features of spacetime may also be used to model a varying dark energy source which does not interact with the matter field and is compatible with the current accelerated phase of the Universe.

NASA thesaurus. Volume 2: Access vocabulary

NASA Technical Reports Server (NTRS)

1988-01-01

The access vocabulary, which is essentially a permuted index, provides access to any word or number in authorized postable and nonpostable terms. Additional entries include postable and nonpostable terms, other word entries and pseudo-multiword terms that are permutations of words that contain words within words. The access vocabulary contains almost 42,000 entries that give increased access to the hierarchies in Volume 1 - Hierarchical Listing.

Genomic Analysis of Complex Microbial Communities in Wounds

DTIC Science & Technology

2012-01-01

thoroughly in the ecology literature. Permutation Multivariate Analysis of Variance ( PerMANOVA ). We used PerMANOVA to test the null-hypothesis of no...difference between the bacterial communities found within a single wound compared to those from different patients (α = 0.05). PerMANOVA is a...permutation-based version of the multivariate analysis of variance (MANOVA). PerMANOVA uses the distances between samples to partition variance and

Circular permutation of the starch-binding domain: inversion of ligand selectivity with increased affinity.

PubMed

Stephen, Preyesh; Tseng, Kai-Li; Liu, Yu-Nan; Lyu, Ping-Chiang

2012-03-07

Proteins containing starch-binding domains (SBDs) are used in a variety of scientific and technological applications. A circularly permutated SBD (CP90) with improved affinity and selectivity toward longer-chain carbohydrates was synthesized, suggesting that a new starch-binding protein may be developed for specific scientific and industrial applications. This journal is © The Royal Society of Chemistry 2012

Sampling solution traces for the problem of sorting permutations by signed reversals

PubMed Central

2012-01-01

Background Traditional algorithms to solve the problem of sorting by signed reversals output just one optimal solution while the space of all optimal solutions can be huge. A so-called trace represents a group of solutions which share the same set of reversals that must be applied to sort the original permutation following a partial ordering. By using traces, we therefore can represent the set of optimal solutions in a more compact way. Algorithms for enumerating the complete set of traces of solutions were developed. However, due to their exponential complexity, their practical use is limited to small permutations. A partial enumeration of traces is a sampling of the complete set of traces and can be an alternative for the study of distinct evolutionary scenarios of big permutations. Ideally, the sampling should be done uniformly from the space of all optimal solutions. This is however conjectured to be ♯P-complete. Results We propose and evaluate three algorithms for producing a sampling of the complete set of traces that instead can be shown in practice to preserve some of the characteristics of the space of all solutions. The first algorithm (RA) performs the construction of traces through a random selection of reversals on the list of optimal 1-sequences. The second algorithm (DFALT) consists in a slight modification of an algorithm that performs the complete enumeration of traces. Finally, the third algorithm (SWA) is based on a sliding window strategy to improve the enumeration of traces. All proposed algorithms were able to enumerate traces for permutations with up to 200 elements. Conclusions We analysed the distribution of the enumerated traces with respect to their height and average reversal length. Various works indicate that the reversal length can be an important aspect in genome rearrangements. The algorithms RA and SWA show a tendency to lose traces with high average reversal length. Such traces are however rare, and qualitatively our results show that, for testable-sized permutations, the algorithms DFALT and SWA produce distributions which approximate the reversal length distributions observed with a complete enumeration of the set of traces. PMID:22704580

Permutation glass.

PubMed

Williams, Mobolaji

2018-01-01

The field of disordered systems in statistical physics provides many simple models in which the competing influences of thermal and nonthermal disorder lead to new phases and nontrivial thermal behavior of order parameters. In this paper, we add a model to the subject by considering a disordered system where the state space consists of various orderings of a list. As in spin glasses, the disorder of such "permutation glasses" arises from a parameter in the Hamiltonian being drawn from a distribution of possible values, thus allowing nominally "incorrect orderings" to have lower energies than "correct orderings" in the space of permutations. We analyze a Gaussian, uniform, and symmetric Bernoulli distribution of energy costs, and, by employing Jensen's inequality, derive a simple condition requiring the permutation glass to always transition to the correctly ordered state at a temperature lower than that of the nondisordered system, provided that this correctly ordered state is accessible. We in turn find that in order for the correctly ordered state to be accessible, the probability that an incorrectly ordered component is energetically favored must be less than the inverse of the number of components in the system. We show that all of these results are consistent with a replica symmetric ansatz of the system. We conclude by arguing that there is no distinct permutation glass phase for the simplest model considered here and by discussing how to extend the analysis to more complex Hamiltonians capable of novel phase behavior and replica symmetry breaking. Finally, we outline an apparent correspondence between the presented system and a discrete-energy-level fermion gas. In all, the investigation introduces a class of exactly soluble models into statistical mechanics and provides a fertile ground to investigate statistical models of disorder.

Efficient computation of significance levels for multiple associations in large studies of correlated data, including genomewide association studies.

PubMed

Dudbridge, Frank; Koeleman, Bobby P C

2004-09-01

Large exploratory studies, including candidate-gene-association testing, genomewide linkage-disequilibrium scans, and array-expression experiments, are becoming increasingly common. A serious problem for such studies is that statistical power is compromised by the need to control the false-positive rate for a large family of tests. Because multiple true associations are anticipated, methods have been proposed that combine evidence from the most significant tests, as a more powerful alternative to individually adjusted tests. The practical application of these methods is currently limited by a reliance on permutation testing to account for the correlated nature of single-nucleotide polymorphism (SNP)-association data. On a genomewide scale, this is both very time-consuming and impractical for repeated explorations with standard marker panels. Here, we alleviate these problems by fitting analytic distributions to the empirical distribution of combined evidence. We fit extreme-value distributions for fixed lengths of combined evidence and a beta distribution for the most significant length. An initial phase of permutation sampling is required to fit these distributions, but it can be completed more quickly than a simple permutation test and need be done only once for each panel of tests, after which the fitted parameters give a reusable calibration of the panel. Our approach is also a more efficient alternative to a standard permutation test. We demonstrate the accuracy of our approach and compare its efficiency with that of permutation tests on genomewide SNP data released by the International HapMap Consortium. The estimation of analytic distributions for combined evidence will allow these powerful methods to be applied more widely in large exploratory studies.

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains.

PubMed

Xia, Li C; Ai, Dongmei; Cram, Jacob A; Liang, Xiaoyi; Fuhrman, Jed A; Sun, Fengzhu

2015-09-21

Local trend (i.e. shape) analysis of time series data reveals co-changing patterns in dynamics of biological systems. However, slow permutation procedures to evaluate the statistical significance of local trend scores have limited its applications to high-throughput time series data analysis, e.g., data from the next generation sequencing technology based studies. By extending the theories for the tail probability of the range of sum of Markovian random variables, we propose formulae for approximating the statistical significance of local trend scores. Using simulations and real data, we show that the approximate p-value is close to that obtained using a large number of permutations (starting at time points >20 with no delay and >30 with delay of at most three time steps) in that the non-zero decimals of the p-values obtained by the approximation and the permutations are mostly the same when the approximate p-value is less than 0.05. In addition, the approximate p-value is slightly larger than that based on permutations making hypothesis testing based on the approximate p-value conservative. The approximation enables efficient calculation of p-values for pairwise local trend analysis, making large scale all-versus-all comparisons possible. We also propose a hybrid approach by integrating the approximation and permutations to obtain accurate p-values for significantly associated pairs. We further demonstrate its use with the analysis of the Polymouth Marine Laboratory (PML) microbial community time series from high-throughput sequencing data and found interesting organism co-occurrence dynamic patterns. The software tool is integrated into the eLSA software package that now provides accelerated local trend and similarity analysis pipelines for time series data. The package is freely available from the eLSA website: http://bitbucket.org/charade/elsa.

Adsorption of organic molecules on a porous polymer surface modified with the supramolecular structure of melamine-cyanuric acid

NASA Astrophysics Data System (ADS)

Gainullina, Yu. Yu.; Guskov, V. Yu.

2017-10-01

The adsorption of organic molecules on the surface of a porous polymeric sorbent modified with a mixed cyanuric acid-melamine supramolecular structure is studied. The parameters of thermodynamic adsorption are considered and the contributions from intermolecular interactions to the Helmholtz energy of adsorption are assessed. Analysis of the molar changes in internal energy and adsorption entropy shows that the supramolecular structure formed on the surface could not exhibit dimension effects, indicating there were no cavities. The contributions from nonspecific interactions to the Helmholtz energy of adsorption generally fall, while those of specific interactions increase, indicating an increase in the polarity of the sorbent surface.

The Arrow of Time In a Universe with a Positive Cosmological Constant Λ

NASA Astrophysics Data System (ADS)

Mersini-Houghton, Laura

There is a mounting evidence that our universe is propelled into an accelerated expansion driven by Dark Energy. The simplest form of Dark Energy is a cosmological constant Λ, which is woven into the fabric of spacetime. For this reason it is often referred to as vacuum energy. It has the "strange" property of maintaining a constant energy density despite the expanding volume of the universe. Universes whose energy ismade of Λ posses an event horizon with and eternally finite constant temperature and entropy, and are known as DeSitter geometries. Since the entropy of DeSitter spaces remains a finite constant, then the meaning of a thermodynamic arrow of time becomes unclear. Here we explore the consequences of a fundamental cosmological constant Λ for our universe. We show that when the gravitational entropy of a pure DeSitter state ultimately dominates over the matter entropy, then the thermodynamic arrow of time in our universe may reverse in scales of order a Hubble time. We find that due to the dynamics of gravity and entanglement with other domain, a finite size system such as a DeSitter patch with horizon size H 0 -1 has a finite lifetime ∆t. This phenomenon arises from the dynamic gravitational instabilities that develop during a DeSitter epoch and turn catastrophic. A reversed arrow of time is in disagreementwith observations. Thus we explore the possibilities that: Nature may not favor a fundamental Λ, or else general relativity may be modified in the infrared regime when Λ dominates the expansion of the Universe.

An investigation of student thinking regarding calorimetry, entropy, and the second law of thermodynamics

NASA Astrophysics Data System (ADS)

Christensen, Warren Michael

This thesis constitutes an investigation into student understanding of concepts in thermal physics in an introductory calculus-based university physics course. Nearly 90% of students enrolled in the course had previous exposure to thermodynamics concepts in chemistry and/or high-school physics courses. The two major thrusts of this work are (1) an exploration of student approaches to solving calorimetry problems involving two substances with differing specific heats, and (2) a careful probing of student ideas regarding certain aspects of entropy and the second law of thermodynamics. We present extensive free-response, interview, and multiple-choice data regarding students' ideas, collected both before and after instruction from a diverse set of course semesters and instructors. For topics in calorimetry, we found via interviews that students frequently get confused by, or tend to overlook, the detailed proportional reasoning or algebraic procedures that could lead to correct solutions. Instead, students often proceed with semi-intuitive reasoning that at times may be productive, but more often leads to inconsistencies and non-uniform conceptual understanding. Our investigation of student thinking regarding entropy suggests that prior to instruction, students have consistent and distinct patterns of incorrect or incomplete responses that often persist despite deliberate and focused efforts by the instructor. With modified instruction based on research-based materials, significant learning gains were observed on certain key concepts, e.g., that the entropy of the universe increases for all non-ideal processes. The methodology for our work is described, the data are discussed and analyzed, and a description is given of goals for future work in this area.

Serotonergic Psychedelics Temporarily Modify Information Transfer in Humans

PubMed Central

Alonso, Joan Francesc; Romero, Sergio; Mañanas, Miquel Àngel

2015-01-01

Background: Psychedelics induce intense modifications in the sensorium, the sense of “self,” and the experience of reality. Despite advances in our understanding of the molecular and cellular level mechanisms of these drugs, knowledge of their actions on global brain dynamics is still incomplete. Recent imaging studies have found changes in functional coupling between frontal and parietal brain structures, suggesting a modification in information flow between brain regions during acute effects. Methods: Here we assessed the psychedelic-induced changes in directionality of information flow during the acute effects of a psychedelic in humans. We measured modifications in connectivity of brain oscillations using transfer entropy, a nonlinear measure of directed functional connectivity based on information theory. Ten healthy male volunteers with prior experience with psychedelics participated in 2 experimental sessions. They received a placebo or a dose of ayahuasca, a psychedelic preparation containing the serotonergic 5-HT2A agonist N,N-dimethyltryptamine. Results: The analysis showed significant changes in the coupling of brain oscillations between anterior and posterior recording sites. Transfer entropy analysis showed that frontal sources decreased their influence over central, parietal, and occipital sites. Conversely, sources in posterior locations increased their influence over signals measured at anterior locations. Exploratory correlations found that anterior-to-posterior transfer entropy decreases were correlated with the intensity of subjective effects, while the imbalance between anterior-to-posterior and posterior-to-anterior transfer entropy correlated with the degree of incapacitation experienced. Conclusions: These results suggest that psychedelics induce a temporary disruption of neural hierarchies by reducing top-down control and increasing bottom-up information transfer in the human brain. PMID:25820842

Heat dissipation guides activation in signaling proteins.

PubMed

Weber, Jeffrey K; Shukla, Diwakar; Pande, Vijay S

2015-08-18

Life is fundamentally a nonequilibrium phenomenon. At the expense of dissipated energy, living things perform irreversible processes that allow them to propagate and reproduce. Within cells, evolution has designed nanoscale machines to do meaningful work with energy harnessed from a continuous flux of heat and particles. As dictated by the Second Law of Thermodynamics and its fluctuation theorem corollaries, irreversibility in nonequilibrium processes can be quantified in terms of how much entropy such dynamics produce. In this work, we seek to address a fundamental question linking biology and nonequilibrium physics: can the evolved dissipative pathways that facilitate biomolecular function be identified by their extent of entropy production in general relaxation processes? We here synthesize massive molecular dynamics simulations, Markov state models (MSMs), and nonequilibrium statistical mechanical theory to probe dissipation in two key classes of signaling proteins: kinases and G-protein-coupled receptors (GPCRs). Applying machinery from large deviation theory, we use MSMs constructed from protein simulations to generate dynamics conforming to positive levels of entropy production. We note the emergence of an array of peaks in the dynamical response (transient analogs of phase transitions) that draw the proteins between distinct levels of dissipation, and we see that the binding of ATP and agonist molecules modifies the observed dissipative landscapes. Overall, we find that dissipation is tightly coupled to activation in these signaling systems: dominant entropy-producing trajectories become localized near important barriers along known biological activation pathways. We go on to classify an array of equilibrium and nonequilibrium molecular switches that harmonize to promote functional dynamics.

How to think about indiscernible particles

NASA Astrophysics Data System (ADS)

Giglio, Daniel Joseph

Permutation symmetries which arise in quantum mechanics pose an intriguing problem. It is not clear that particles which exhibit permutation symmetries (i.e. particles which are indiscernible, meaning that they can be swapped with each other without this yielding a new physical state) qualify as "objects" in any reasonable sense of the term. One solution to this puzzle, which I attribute to W.V. Quine, would have us eliminate such particles from our ontology altogether in order to circumvent the metaphysical vexations caused by permutation symmetries. In this essay I argue that Quine's solution is too rash, and in its place I suggest a novel solution based on altering some of the language of quantum mechanics. Before launching into the technical details of indiscernible particles, however, I begin this essay with some remarks on the methodology -- instrumentalism -- which motivates my arguments.

A cellular automata model of bone formation.

PubMed

Van Scoy, Gabrielle K; George, Estee L; Opoku Asantewaa, Flora; Kerns, Lucy; Saunders, Marnie M; Prieto-Langarica, Alicia

2017-04-01

Bone remodeling is an elegantly orchestrated process by which osteocytes, osteoblasts and osteoclasts function as a syncytium to maintain or modify bone. On the microscopic level, bone consists of cells that create, destroy and monitor the bone matrix. These cells interact in a coordinated manner to maintain a tightly regulated homeostasis. It is this regulation that is responsible for the observed increase in bone gain in the dominant arm of a tennis player and the observed increase in bone loss associated with spaceflight and osteoporosis. The manner in which these cells interact to bring about a change in bone quality and quantity has yet to be fully elucidated. But efforts to understand the multicellular complexity can ultimately lead to eradication of metabolic bone diseases such as osteoporosis and improved implant longevity. Experimentally validated mathematical models that simulate functional activity and offer eventual predictive capabilities offer tremendous potential in understanding multicellular bone remodeling. Here we undertake the initial challenge to develop a mathematical model of bone formation validated with in vitro data obtained from osteoblastic bone cells induced to mineralize and quantified at 26 days of culture. A cellular automata model was constructed to simulate the in vitro characterization. Permutation tests were performed to compare the distribution of the mineralization in the cultures and the distribution of the mineralization in the mathematical models. The results of the permutation test show the distribution of mineralization from the characterization and mathematical model come from the same probability distribution, therefore validating the cellular automata model. Copyright © 2017 Elsevier Inc. All rights reserved.

Griffiths-like phase, critical behavior near the paramagnetic-ferromagnetic phase transition and magnetic entropy change of nanocrystalline La0.75Ca0.25MnO3

NASA Astrophysics Data System (ADS)

Phong, P. T.; Ngan, L. T. T.; Dang, N. V.; Nguyen, L. H.; Nam, P. H.; Thuy, D. M.; Tuan, N. D.; Bau, L. V.; Lee, I. J.

2018-03-01

In this work, we report the structural and magnetic properties of La0.75Ca0.25MnO3 nanoparticles synthesized by the sol-gel route. Rietvield refinement of X-ray powder diffraction confirms that our sample is single phase and crystallizes in orthorhombic system with Pnma space group. The facts that effective magnetic moment is large and the inverse susceptibility deviates from the Curie Weiss lawn indicate the presence of Griffiths-like cluster phase. The critical exponents have been estimated using different techniques such as modified Arrott plot, Kouvel-Fisher plot and critical isotherm technique. The critical exponents values of La0.75Ca0.25MnO3 are very close to those found out by the mean-field model, and this can be explained by the existence of a long-range interactions between spins in this system. These results were in good agreement with those obtained using the critical exponents of magnetic entropy change. The self-consistency and reliability of the critical exponent was verified by the Widom scaling law and the universal scaling hypothesis. Using the Harris criterion, we deduced that the disorder is relevant in our case. The maximum magnetic entropy change (ΔSM) calculated from the M-H measurements is 3.47 J/kg K under an external field change of 5 T. The ΔSM-T curves collapsed onto a single master curve regardless of the composition and the applied field, confirming the magnetic ordering is of second order nature. The obtained result was compared to ones calculated based on the Arrott plot and a good concordance is observed. Moreover, the spontaneous magnetization obtained from the entropy change is in excellent agreement with that deduced by classically extrapolation the Arrott curves. This result confirms the validity of the estimation of the spontaneous magnetization using the magnetic entropy change.

Fermion systems in discrete space-time

NASA Astrophysics Data System (ADS)

Finster, Felix

2007-05-01

Fermion systems in discrete space-time are introduced as a model for physics on the Planck scale. We set up a variational principle which describes a non-local interaction of all fermions. This variational principle is symmetric under permutations of the discrete space-time points. We explain how for minimizers of the variational principle, the fermions spontaneously break this permutation symmetry and induce on space-time a discrete causal structure.

Dynamic Testing and Automatic Repair of Reconfigurable Wiring Harnesses

DTIC Science & Technology

2006-11-27

Switch An M ×N grid of switches configured to provide a M -input, N -output routing network. Permutation Network A permutation network performs an...wiring reduces the effective advantage of their reduced switch count, particularly when considering that regular grids (crossbar switches being a...are connected to. The outline circuit shown in Fig. 20 shows how a suitable ‘discovery probe’ might be implemented. The circuit shows a UART

Tolerance of a Knotted Near-Infrared Fluorescent Protein to Random Circular Permutation.

PubMed

Pandey, Naresh; Kuypers, Brianna E; Nassif, Barbara; Thomas, Emily E; Alnahhas, Razan N; Segatori, Laura; Silberg, Jonathan J

2016-07-12

Bacteriophytochrome photoreceptors (BphP) are knotted proteins that have been developed as near-infrared fluorescent protein (iRFP) reporters of gene expression. To explore how rearrangements in the peptides that interlace into the knot within the BphP photosensory core affect folding, we subjected iRFPs to random circular permutation using an improved transposase mutagenesis strategy and screened for variants that fluoresce. We identified 27 circularly permuted iRFPs that display biliverdin-dependent fluorescence in Escherichia coli. The variants with the brightest whole cell fluorescence initiated translation at residues near the domain linker and knot tails, although fluorescent variants that initiated translation within the PAS and GAF domains were discovered. Circularly permuted iRFPs retained sufficient cofactor affinity to fluoresce in tissue culture without the addition of biliverdin, and one variant displayed enhanced fluorescence when expressed in bacteria and tissue culture. This variant displayed a quantum yield similar to that of iRFPs but exhibited increased resistance to chemical denaturation, suggesting that the observed increase in the magnitude of the signal arose from more efficient protein maturation. These results show how the contact order of a knotted BphP can be altered without disrupting chromophore binding and fluorescence, an important step toward the creation of near-infrared biosensors with expanded chemical sensing functions for in vivo imaging.

Tolerance of a knotted near infrared fluorescent protein to random circular permutation

PubMed Central

Pandey, Naresh; Kuypers, Brianna E.; Nassif, Barbara; Thomas, Emily E.; Alnahhas, Razan N.; Segatori, Laura; Silberg, Jonathan J.

2016-01-01

Bacteriophytochrome photoreceptors (BphP) are knotted proteins that have been developed as near-infrared fluorescent protein (iRFP) reporters of gene expression. To explore how rearrangements in the peptides that interlace into the knot within the BphP photosensory core affect folding, we subjected iRFP to random circular permutation using an improved transposase mutagenesis strategy and screened for variants that fluoresce. We identified twenty seven circularly permuted iRFP that display biliverdin-dependent fluorescence in Escherichia coli. The variants with the brightest whole cell fluorescence initiated translation at residues near the domain linker and knot tails, although fluorescent variants were discovered that initiated translation within the PAS and GAF domains. Circularly permuted iRFP retained sufficient cofactor affinity to fluoresce in tissue culture without the addition of biliverdin, and one variant displayed enhanced fluorescence when expressed in bacteria and tissue culture. This variant displayed a similar quantum yield as iRFP, but exhibited increased resistance to chemical denaturation, suggesting that the observed signal increase arose from more efficient protein maturation. These results show how the contact order of a knotted BphP can be altered without disrupting chromophore binding and fluorescence, an important step towards the creation of near-infrared biosensors with expanded chemical-sensing functions for in vivo imaging. PMID:27304983

Parameter Estimation as a Problem in Statistical Thermodynamics.

PubMed

Earle, Keith A; Schneider, David J

2011-03-14

In this work, we explore the connections between parameter fitting and statistical thermodynamics using the maxent principle of Jaynes as a starting point. In particular, we show how signal averaging may be described by a suitable one particle partition function, modified for the case of a variable number of particles. These modifications lead to an entropy that is extensive in the number of measurements in the average. Systematic error may be interpreted as a departure from ideal gas behavior. In addition, we show how to combine measurements from different experiments in an unbiased way in order to maximize the entropy of simultaneous parameter fitting. We suggest that fit parameters may be interpreted as generalized coordinates and the forces conjugate to them may be derived from the system partition function. From this perspective, the parameter fitting problem may be interpreted as a process where the system (spectrum) does work against internal stresses (non-optimum model parameters) to achieve a state of minimum free energy/maximum entropy. Finally, we show how the distribution function allows us to define a geometry on parameter space, building on previous work[1, 2]. This geometry has implications for error estimation and we outline a program for incorporating these geometrical insights into an automated parameter fitting algorithm.

Convergence to equilibrium of renormalised solutions to nonlinear chemical reaction–diffusion systems

NASA Astrophysics Data System (ADS)

Fellner, Klemens; Tang, Bao Quoc

2018-06-01

The convergence to equilibrium for renormalised solutions to nonlinear reaction-diffusion systems is studied. The considered reaction-diffusion systems arise from chemical reaction networks with mass action kinetics and satisfy the complex balanced condition. By applying the so-called entropy method, we show that if the system does not have boundary equilibria, i.e. equilibrium states lying on the boundary of R_+^N, then any renormalised solution converges exponentially to the complex balanced equilibrium with a rate, which can be computed explicitly up to a finite-dimensional inequality. This inequality is proven via a contradiction argument and thus not explicitly. An explicit method of proof, however, is provided for a specific application modelling a reversible enzyme reaction by exploiting the specific structure of the conservation laws. Our approach is also useful to study the trend to equilibrium for systems possessing boundary equilibria. More precisely, to show the convergence to equilibrium for systems with boundary equilibria, we establish a sufficient condition in terms of a modified finite-dimensional inequality along trajectories of the system. By assuming this condition, which roughly means that the system produces too much entropy to stay close to a boundary equilibrium for infinite time, the entropy method shows exponential convergence to equilibrium for renormalised solutions to complex balanced systems with boundary equilibria.

Study of thermodynamic laws in f(R,T,R{sub μν}T{sup μν}) gravity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharif, M.; Zubair, M., E-mail: msharif.math@pu.edu.pk, E-mail: mzubairkk@gmail.com

2013-11-01

We study first and second laws of black hole thermodynamics at the apparent horizon of FRW spacetime in f(R,T,R{sub μν}T{sup μν}) gravity, where R, R{sub μν} are the Ricci scalar and Riemann tensor and T is the trace of the energy-momentum tensor T{sub μν}. We develop the Friedmann equations for any spatial curvature in this modified theory and show that these equations can be transformed to the form of Clausius relation T{sub h}S{sub eff} = δQ. Here T{sub h} is the horizon temperature, S{sub eff} is the entropy which contains contributions both from horizon entropy and additional entropy term introducedmore » due to the non-equilibrating description and δQ is the energy flux across the horizon. The generalized second law of thermodynamics is also established in a more comprehensive form and one can recover the corresponding results in Einstein, f(R) and f(R,T) gravities. We discuss GSLT in the locality of assumption that temperature of matter inside the horizon is similar to that of horizon. Finally, we consider particular models in this theory and generate constraints on the coupling parameter for the validity of GSLT.« less

An Improved Evidential-IOWA Sensor Data Fusion Approach in Fault Diagnosis

PubMed Central

Zhou, Deyun; Zhuang, Miaoyan; Fang, Xueyi; Xie, Chunhe

2017-01-01

As an important tool of information fusion, Dempster–Shafer evidence theory is widely applied in handling the uncertain information in fault diagnosis. However, an incorrect result may be obtained if the combined evidence is highly conflicting, which may leads to failure in locating the fault. To deal with the problem, an improved evidential-Induced Ordered Weighted Averaging (IOWA) sensor data fusion approach is proposed in the frame of Dempster–Shafer evidence theory. In the new method, the IOWA operator is used to determine the weight of different sensor data source, while determining the parameter of the IOWA, both the distance of evidence and the belief entropy are taken into consideration. First, based on the global distance of evidence and the global belief entropy, the α value of IOWA is obtained. Simultaneously, a weight vector is given based on the maximum entropy method model. Then, according to IOWA operator, the evidence are modified before applying the Dempster’s combination rule. The proposed method has a better performance in conflict management and fault diagnosis due to the fact that the information volume of each evidence is taken into consideration. A numerical example and a case study in fault diagnosis are presented to show the rationality and efficiency of the proposed method. PMID:28927017

Role of the heat capacity change in understanding and modeling melting thermodynamics of complementary duplexes containing standard and nucleobase-modified LNA.

PubMed

Hughesman, Curtis B; Turner, Robin F B; Haynes, Charles A

2011-06-14

Melting thermodynamic data obtained by differential scanning calorimetry (DSC) are reported for 43 duplexed oligonucleotides containing one or more locked nucleic acid (LNA) substitutions. The measured heat capacity change (ΔC(p)) for the helix-to-coil transition is used to compute the changes in enthalpy and entropy for melting of an LNA-bearing duplex at the T(m) of its corresponding isosequential unmodified DNA duplex to allow rigorous thermodynamic analysis of the stability enhancements provided by LNA substitutions. Contrary to previous studies, our analysis shows that the origin of the improved stability is almost exclusively a net reduction (ΔΔS° < 0) in the entropy gain accompanying the helix-to-coil transition, with the magnitude of the reduction dependent on the type of nucleobase and its base pairing properties. This knowledge and our average measured value for ΔC(p) of 42 ± 11 cal mol(-1) K(-1) bp(-1) are then used to derive a new model that accurately predicts melting thermodynamics and the increased melting temperature (ΔT(m)) of heteroduplexes formed between an unmodified DNA strand and a complementary strand containing any number and configuration of standard LNA nucleotides A, T, C, and G. This single-base thermodynamic (SBT) model requires only four entropy-related parameters in addition to ΔC(p). Finally, DSC data for 20 duplexes containing the nucleobase-modified LNAs 2-aminoadenine (D) and 2-thiothymine (H) are reported and used to determine SBT model parameters for D and H. The data and model suggest that along with the greater stability enhancement provided by D and H bases relative to their corresponding A and T analogues, the unique pseudocomplementary properties of D-H base pairs may make their use appealing for in vitro and in vivo applications.

Thermodynamic and hydration effects for the incorporation of a cationic 3-aminopropyl chain into DNA

PubMed Central

Soto, Ana Maria; Kankia, Besik I.; Dande, Prasad; Gold, Barry; Marky, Luis A.

2002-01-01

The introduction of cationic 5-(ω-aminoalkyl)-2′-deoxypyrimidines into duplex DNA has been shown to induce DNA bending. In order to understand the energetic and hydration contributions for the incorporation of a cationic side chain in DNA a combination of spectroscopy, calorimetry and density techniques were used. Specifically, the temperature unfolding and isothermal formation was studied for a pair of duplexes with sequence d(CGTAGUCG TGC)/d(GCACGACTACG), where U represents 2′-deoxyuridine (‘control’) or 5-(3-aminopropyl)-2′-deoxyuridine (‘modified’). Continuous variation experiments confirmed 1:1 stoichiometries for each duplex and the circular dichroism spectra show that both duplexes adopted the B conformation. UV and differential scanning calorimetry melting experiments reveal that each duplex unfolds in two-state transitions. In low salt buffer, the ‘modified’ duplex is more stable and unfolds with a lower endothermic heat and lower release of counterion and water. This electrostatic stabilization is entropy driven and disappears at higher salt concentrations. Complete thermodynamic profiles at 15°C show that the favorable formation of each duplex results from the compensation of a favorable exothermic heat with an unfavorable entropy contribution. However, the isothermal profiles yielded a differential enthalpy of 8.8 kcal/mol, which is 4.3 kcal/mol higher than the differential enthalpy observed in the unfolding profiles. This indicates that the presence of the aminopropyl chain induces an increase in base stacking interactions in the modified single strand and a decrease in base stacking interactions in the modified duplex. Furthermore, the formation of the ‘control’ duplex releases water while the ‘modified’ duplex takes up water. Relative to the control duplex, formation of the modified duplex at 15°C yielded a marginal differential ΔG° term, positive ΔΔHITC–Δ(TΔS) compensation, negative ΔΔV and a net release of counterions. The opposite signs of the differential enthalpy–entropy compensation and differential volume change terms show a net uptake of structural water around polar and non-polar groups. This indicates that incorporation of the aminopropyl chain induces a higher exposure of aromatic bases to the solvent, which may be consistent with a small and local bend in the ‘modified’ duplex. PMID:12136099

General Rotorcraft Aeromechanical Stability Program (GRASP) - Theory Manual

DTIC Science & Technology

1990-10-01

the A basis. Two symbols frequently encountered in vector operations that use index notation are the Kronecker delta eij and the Levi - Civita epsilon...Blade root cutout fijk Levi - Civita epsilon permutation symbol 0 pretwist angle 0’ pretwist per unit length (d;) Oi Tait-Bryan angles K~i moment strains...the components of the identity tensor in a Cartesian coordinate system, while the Levi Civita epsilon consists of components of the permutation

Using permutations to detect dependence between time series

NASA Astrophysics Data System (ADS)

Cánovas, Jose S.; Guillamón, Antonio; Ruíz, María del Carmen

2011-07-01

In this paper, we propose an independence test between two time series which is based on permutations. The proposed test can be carried out by means of different common statistics such as Pearson’s chi-square or the likelihood ratio. We also point out why an exact test is necessary. Simulated and real data (return exchange rates between several currencies) reveal the capacity of this test to detect linear and nonlinear dependences.

Testing of Error-Correcting Sparse Permutation Channel Codes

NASA Technical Reports Server (NTRS)

Shcheglov, Kirill, V.; Orlov, Sergei S.

2008-01-01

A computer program performs Monte Carlo direct numerical simulations for testing sparse permutation channel codes, which offer strong error-correction capabilities at high code rates and are considered especially suitable for storage of digital data in holographic and volume memories. A word in a code of this type is characterized by, among other things, a sparseness parameter (M) and a fixed number (K) of 1 or "on" bits in a channel block length of N.

Scrambled Sobol Sequences via Permutation

DTIC Science & Technology

2009-01-01

LCG LCG64 LFG MLFG PMLCG Sobol Scrambler PermutationScrambler LinearScrambler <<uses>> PermuationFactory StaticFactory DynamicFactory <<uses>> Figure 3...Phy., 19:252–256, 1979. [2] Emanouil I. Atanassov. A new efficient algorithm for generating the scrambled sobol ’ sequence. In NMA ’02: Revised Papers...Deidre W.Evan, and Micheal Mascagni. On the scrambled sobol sequence. In ICCS2005, pages 775–782, 2005. [7] Richard Durstenfeld. Algorithm 235: Random

Optimization and experimental realization of the quantum permutation algorithm

NASA Astrophysics Data System (ADS)

Yalçınkaya, I.; Gedik, Z.

2017-12-01

The quantum permutation algorithm provides computational speed-up over classical algorithms for determining the parity of a given cyclic permutation. For its n -qubit implementations, the number of required quantum gates scales quadratically with n due to the quantum Fourier transforms included. We show here for the n -qubit case that the algorithm can be simplified so that it requires only O (n ) quantum gates, which theoretically reduces the complexity of the implementation. To test our results experimentally, we utilize IBM's 5-qubit quantum processor to realize the algorithm by using the original and simplified recipes for the 2-qubit case. It turns out that the latter results in a significantly higher success probability which allows us to verify the algorithm more precisely than the previous experimental realizations. We also verify the algorithm for the first time for the 3-qubit case with a considerable success probability by taking the advantage of our simplified scheme.

A Weak Quantum Blind Signature with Entanglement Permutation

NASA Astrophysics Data System (ADS)

Lou, Xiaoping; Chen, Zhigang; Guo, Ying

2015-09-01

Motivated by the permutation encryption algorithm, a weak quantum blind signature (QBS) scheme is proposed. It involves three participants, including the sender Alice, the signatory Bob and the trusted entity Charlie, in four phases, i.e., initializing phase, blinding phase, signing phase and verifying phase. In a small-scale quantum computation network, Alice blinds the message based on a quantum entanglement permutation encryption algorithm that embraces the chaotic position string. Bob signs the blinded message with private parameters shared beforehand while Charlie verifies the signature's validity and recovers the original message. Analysis shows that the proposed scheme achieves the secure blindness for the signer and traceability for the message owner with the aid of the authentic arbitrator who plays a crucial role when a dispute arises. In addition, the signature can neither be forged nor disavowed by the malicious attackers. It has a wide application to E-voting and E-payment system, etc.

An extended continuous estimation of distribution algorithm for solving the permutation flow-shop scheduling problem

NASA Astrophysics Data System (ADS)

Shao, Zhongshi; Pi, Dechang; Shao, Weishi

2017-11-01

This article proposes an extended continuous estimation of distribution algorithm (ECEDA) to solve the permutation flow-shop scheduling problem (PFSP). In ECEDA, to make a continuous estimation of distribution algorithm (EDA) suitable for the PFSP, the largest order value rule is applied to convert continuous vectors to discrete job permutations. A probabilistic model based on a mixed Gaussian and Cauchy distribution is built to maintain the exploration ability of the EDA. Two effective local search methods, i.e. revolver-based variable neighbourhood search and Hénon chaotic-based local search, are designed and incorporated into the EDA to enhance the local exploitation. The parameters of the proposed ECEDA are calibrated by means of a design of experiments approach. Simulation results and comparisons based on some benchmark instances show the efficiency of the proposed algorithm for solving the PFSP.

Electrosorption of a modified electrode in the vicinity of phase transition: A Monte Carlo study

NASA Astrophysics Data System (ADS)

Gavilán Arriazu, E. M.; Pinto, O. A.

2018-03-01

We present a Monte Carlo study for the electrosorption of an electroactive species on a modified electrode. The surface of the electrode is modified by the irreversible adsorption of a non-electroactive species which is able to block a percentage of the adsorption sites. This generates an electrode with variable connectivity sites. A second species, electroactive in this case, is adsorbed in surface vacancies and can interact repulsively with itself. In particular, we are interested in the analysis of the effect of the non-electroactive species near of critical regime, where the c(2 × 2) structure is formed. Lattice-gas models and Monte Carlo simulations in the Gran Canonical Ensemble are used. The analysis conducted is based on the study of voltammograms, order parameters, isotherms, configurational entropy per site, at several values of energies and coverage degrees of the non-electroactive species.

Adsorption of arsenic(III) into modified lamellar Na-magadiite in aqueous medium—Thermodynamic of adsorption process

NASA Astrophysics Data System (ADS)

Guerra, Denis Lima; Pinto, Alane Azevedo; Airoldi, Claudio; Viana, Rúbia Ribeiro

2008-12-01

Synthetic Na-magadiite sample was used for organofunctionalization process with N-propyldiethylenetrimethoxysilane and bis[3-(triethoxysilyl)propyl]tetrasulfide, after expanding the interlayer distance with polar organic solvents such as dimethylsulfoxide (DMSO). The resulted materials were submitted to process of adsorption with arsenic solution at pH 2.0 and 298±1 K. The adsorption isotherms were adjusted using a modified Langmuir equation with regression nonlinear; the net thermal effects obtained from calorimetric titration measurements were adjusted to a modified Langmuir equation. The adsorption process was exothermic (Δ intH=-4.15-5.98 kJ mol -1) accompanied by increase in entropy (Δ intS=41.32-62.20 J k -1 mol -1) and Gibbs energy (Δ intG=-22.44-24.56 kJ mol -1). The favorable values corroborate with the arsenic (III)/basic reactive centers interaction at the solid-liquid interface in the spontaneous process.

A New Color Image Encryption Scheme Using CML and a Fractional-Order Chaotic System

PubMed Central

Wu, Xiangjun; Li, Yang; Kurths, Jürgen

2015-01-01

The chaos-based image cryptosystems have been widely investigated in recent years to provide real-time encryption and transmission. In this paper, a novel color image encryption algorithm by using coupled-map lattices (CML) and a fractional-order chaotic system is proposed to enhance the security and robustness of the encryption algorithms with a permutation-diffusion structure. To make the encryption procedure more confusing and complex, an image division-shuffling process is put forward, where the plain-image is first divided into four sub-images, and then the position of the pixels in the whole image is shuffled. In order to generate initial conditions and parameters of two chaotic systems, a 280-bit long external secret key is employed. The key space analysis, various statistical analysis, information entropy analysis, differential analysis and key sensitivity analysis are introduced to test the security of the new image encryption algorithm. The cryptosystem speed is analyzed and tested as well. Experimental results confirm that, in comparison to other image encryption schemes, the new algorithm has higher security and is fast for practical image encryption. Moreover, an extensive tolerance analysis of some common image processing operations such as noise adding, cropping, JPEG compression, rotation, brightening and darkening, has been performed on the proposed image encryption technique. Corresponding results reveal that the proposed image encryption method has good robustness against some image processing operations and geometric attacks. PMID:25826602

Classical mutual information in mean-field spin glass models

NASA Astrophysics Data System (ADS)

Alba, Vincenzo; Inglis, Stephen; Pollet, Lode

2016-03-01

We investigate the classical Rényi entropy Sn and the associated mutual information In in the Sherrington-Kirkpatrick (S-K) model, which is the paradigm model of mean-field spin glasses. Using classical Monte Carlo simulations and analytical tools we investigate the S-K model in the n -sheet booklet. This is achieved by gluing together n independent copies of the model, and it is the main ingredient for constructing the Rényi entanglement-related quantities. We find a glassy phase at low temperatures, whereas at high temperatures the model exhibits paramagnetic behavior, consistent with the regular S-K model. The temperature of the paramagnetic-glassy transition depends nontrivially on the geometry of the booklet. At high temperatures we provide the exact solution of the model by exploiting the replica symmetry. This is the permutation symmetry among the fictitious replicas that are used to perform disorder averages (via the replica trick). In the glassy phase the replica symmetry has to be broken. Using a generalization of the Parisi solution, we provide analytical results for Sn and In and for standard thermodynamic quantities. Both Sn and In exhibit a volume law in the whole phase diagram. We characterize the behavior of the corresponding densities, Sn/N and In/N , in the thermodynamic limit. Interestingly, at the critical point the mutual information does not exhibit any crossing for different system sizes, in contrast with local spin models.

Spatial EMG potential distribution pattern of vastus lateralis muscle during isometric knee extension in young and elderly men.

PubMed

Watanabe, Kohei; Kouzaki, Motoki; Merletti, Roberto; Fujibayashi, Mami; Moritani, Toshio

2012-02-01

The aim of the present study was to compare spatial electromyographic (EMG) potential distribution during force production between elderly and young individuals using multi-channel surface EMG (SEMG). Thirteen elderly (72-79years) and 13 young (21-27years) healthy male volunteers performed ramp submaximal contraction during isometric knee extension from 0% to 65% of maximal voluntary contraction. During contraction, multi-channel EMG was recorded from the vastus lateralis muscle. To evaluate alteration in heterogeneity and pattern in spatial EMG potential distribution, coefficient of variation (CoV), modified entropy and correlation coefficients with initial torque level were calculated from multi-channel SEMG at 5% force increment. Increase in CoV and decrease in modified entropy of RMS with increase of exerted torque were significantly smaller in elderly group (p<0.05) and correlation coefficients with initial torque level were significantly higher in elderly group than in young group at moderate torque levels (p<0.05). These data suggest that the increase of heterogeneity and the change in the activation pattern are smaller in elderly individuals than in young individuals. We speculated that multi-channel SEMG pattern in elderly individual reflects neuromuscular activation strategy regulated predominantly by clustering of similar type of muscle fibers in aged muscle. Copyright © 2011 Elsevier Ltd. All rights reserved.

Chaos in Magnetic Flux Ropes

NASA Astrophysics Data System (ADS)

Gekelman, W. N.; DeHaas, T.; Van Compernolle, B.

2013-12-01

Magnetic Flux Ropes Immersed in a uniform magnetoplasma are observed to twist about themselves, writhe about each other and rotate about a central axis. They are kink unstable and smash into one another as they move. Full three dimensional magnetic field and flows are measured at thousands of time steps. Each collision results in magnetic field line generation and the generation of a quasi-seperatrix layer and induced electric fields. Three dimensional magnetic field lines are computed by conditionally averaging the data using correlation techniques. The permutation entropy1 ,which is related to the Lyapunov exponent, can be calculated from the the time series of the magnetic field data (this is also done with flows) and used to calculate the positions of the data on a Jensen Shannon complexity map2. The location of data on this map indicates if the magnetic fields are stochastic, or fall into regions of minimal or maximal complexity. The complexity is a function of space and time. The complexity map, and analysis will be explained in the course of the talk. Other types of chaotic dynamical models such as the Lorentz, Gissinger and Henon process also fall on the map and can give a clue to the nature of the flux rope turbulence. The ropes fall in the region of the C-H plane where chaotic systems lie. The entropy and complexity change in space and time which reflects the change and possibly type of chaos associated with the ropes. The maps give insight as to the type of chaos (deterministic chaos, fractional diffusion , Levi flights..) and underlying dynamical process. The power spectra of much of the magnetic and flow data is exponential and Lorentzian structures in the time domain are embedded in them. Other quantities such as the Hurst exponent are evaluated for both magnetic fields and plasma flow. Work Supported by a UC-LANL Lab fund and the Basic Plasma Science Facility which is funded by DOE and NSF. 1) C. Bandt, B. Pompe, Phys. Rev. Lett., 88,174102 (2007) 2) O. Russo et al., Phys. Rev. Lett., 99, 154102 (2007), J. Maggs, G.Morales, 55, 085015 (2013)

Evaluation of Feature Extraction and Recognition for Activity Monitoring and Fall Detection Based on Wearable sEMG Sensors.

PubMed

Xi, Xugang; Tang, Minyan; Miran, Seyed M; Luo, Zhizeng

2017-05-27

As an essential subfield of context awareness, activity awareness, especially daily activity monitoring and fall detection, plays a significant role for elderly or frail people who need assistance in their daily activities. This study investigates the feature extraction and pattern recognition of surface electromyography (sEMG), with the purpose of determining the best features and classifiers of sEMG for daily living activities monitoring and fall detection. This is done by a serial of experiments. In the experiments, four channels of sEMG signal from wireless, wearable sensors located on lower limbs are recorded from three subjects while they perform seven activities of daily living (ADL). A simulated trip fall scenario is also considered with a custom-made device attached to the ankle. With this experimental setting, 15 feature extraction methods of sEMG, including time, frequency, time/frequency domain and entropy, are analyzed based on class separability and calculation complexity, and five classification methods, each with 15 features, are estimated with respect to the accuracy rate of recognition and calculation complexity for activity monitoring and fall detection. It is shown that a high accuracy rate of recognition and a minimal calculation time for daily activity monitoring and fall detection can be achieved in the current experimental setting. Specifically, the Wilson Amplitude (WAMP) feature performs the best, and the classifier Gaussian Kernel Support Vector Machine (GK-SVM) with Permutation Entropy (PE) or WAMP results in the highest accuracy for activity monitoring with recognition rates of 97.35% and 96.43%. For fall detection, the classifier Fuzzy Min-Max Neural Network (FMMNN) has the best sensitivity and specificity at the cost of the longest calculation time, while the classifier Gaussian Kernel Fisher Linear Discriminant Analysis (GK-FDA) with the feature WAMP guarantees a high sensitivity (98.70%) and specificity (98.59%) with a short calculation time (65.586 ms), making it a possible choice for pre-impact fall detection. The thorough quantitative comparison of the features and classifiers in this study supports the feasibility of a wireless, wearable sEMG sensor system for automatic activity monitoring and fall detection.

Evaluation of Feature Extraction and Recognition for Activity Monitoring and Fall Detection Based on Wearable sEMG Sensors

PubMed Central

Xi, Xugang; Tang, Minyan; Miran, Seyed M.; Luo, Zhizeng

2017-01-01

As an essential subfield of context awareness, activity awareness, especially daily activity monitoring and fall detection, plays a significant role for elderly or frail people who need assistance in their daily activities. This study investigates the feature extraction and pattern recognition of surface electromyography (sEMG), with the purpose of determining the best features and classifiers of sEMG for daily living activities monitoring and fall detection. This is done by a serial of experiments. In the experiments, four channels of sEMG signal from wireless, wearable sensors located on lower limbs are recorded from three subjects while they perform seven activities of daily living (ADL). A simulated trip fall scenario is also considered with a custom-made device attached to the ankle. With this experimental setting, 15 feature extraction methods of sEMG, including time, frequency, time/frequency domain and entropy, are analyzed based on class separability and calculation complexity, and five classification methods, each with 15 features, are estimated with respect to the accuracy rate of recognition and calculation complexity for activity monitoring and fall detection. It is shown that a high accuracy rate of recognition and a minimal calculation time for daily activity monitoring and fall detection can be achieved in the current experimental setting. Specifically, the Wilson Amplitude (WAMP) feature performs the best, and the classifier Gaussian Kernel Support Vector Machine (GK-SVM) with Permutation Entropy (PE) or WAMP results in the highest accuracy for activity monitoring with recognition rates of 97.35% and 96.43%. For fall detection, the classifier Fuzzy Min-Max Neural Network (FMMNN) has the best sensitivity and specificity at the cost of the longest calculation time, while the classifier Gaussian Kernel Fisher Linear Discriminant Analysis (GK-FDA) with the feature WAMP guarantees a high sensitivity (98.70%) and specificity (98.59%) with a short calculation time (65.586 ms), making it a possible choice for pre-impact fall detection. The thorough quantitative comparison of the features and classifiers in this study supports the feasibility of a wireless, wearable sEMG sensor system for automatic activity monitoring and fall detection. PMID:28555016

Visual information processing; Proceedings of the Meeting, Orlando, FL, Apr. 20-22, 1992

NASA Technical Reports Server (NTRS)

Huck, Friedrich O. (Editor); Juday, Richard D. (Editor)

1992-01-01

Topics discussed in these proceedings include nonlinear processing and communications; feature extraction and recognition; image gathering, interpolation, and restoration; image coding; and wavelet transform. Papers are presented on noise reduction for signals from nonlinear systems; driving nonlinear systems with chaotic signals; edge detection and image segmentation of space scenes using fractal analyses; a vision system for telerobotic operation; a fidelity analysis of image gathering, interpolation, and restoration; restoration of images degraded by motion; and information, entropy, and fidelity in visual communication. Attention is also given to image coding methods and their assessment, hybrid JPEG/recursive block coding of images, modified wavelets that accommodate causality, modified wavelet transform for unbiased frequency representation, and continuous wavelet transform of one-dimensional signals by Fourier filtering.

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insert].

PubMed

Kupriushkin, M S; Pyshnyĭ, D V

2012-01-01

Non-nucleotide phosporamidites were synthetized, having branched backbone with different position of functional groups. Obtained phosphoramidite monomers contain intercalator moiety--6-chloro-2-methoxyacridine, and additional hydroxyl residue protected with dimethoxytrityl group or with tert-butyldimethylsilyl group for post-synthetic modification. Synthesized oligothymidilates contain one or more modified units in different positions of sequence. Melting temperature and thermodynamic parameters of formation of complementary duplexes formed by modified oligonucleotides was defined (change in enthalpy and entropy). The introduction of intercalating residue causes a significant stabilization of DNA duplexes. It is shown that the efficiency of the fluorescence of acridine residue in the oligonucleotide conjugate significantly changes upon hybridization with DNA.

Unifying the rotational and permutation symmetry of nuclear spin states: Schur-Weyl duality in molecular physics.

PubMed

Schmiedt, Hanno; Jensen, Per; Schlemmer, Stephan

2016-08-21

In modern physics and chemistry concerned with many-body systems, one of the mainstays is identical-particle-permutation symmetry. In particular, both the intra-molecular dynamics of a single molecule and the inter-molecular dynamics associated, for example, with reactive molecular collisions are strongly affected by selection rules originating in nuclear-permutation symmetry operations being applied to the total internal wavefunctions, including nuclear spin, of the molecules involved. We propose here a general tool to determine coherently the permutation symmetry and the rotational symmetry (associated with the group of arbitrary rotations of the entire molecule in space) of molecular wavefunctions, in particular the nuclear-spin functions. Thus far, these two symmetries were believed to be mutually independent and it has even been argued that under certain circumstances, it is impossible to establish a one-to-one correspondence between them. However, using the Schur-Weyl duality theorem we show that the two types of symmetry are inherently coupled. In addition, we use the ingenious representation-theory technique of Young tableaus to represent the molecular nuclear-spin degrees of freedom in terms of well-defined mathematical objects. This simplifies the symmetry classification of the nuclear wavefunction even for large molecules. Also, the application to reactive collisions is very straightforward and provides a much simplified approach to obtaining selection rules.

Unifying the rotational and permutation symmetry of nuclear spin states: Schur-Weyl duality in molecular physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmiedt, Hanno; Schlemmer, Stephan; Jensen, Per, E-mail: jensen@uni-wuppertal.de

In modern physics and chemistry concerned with many-body systems, one of the mainstays is identical-particle-permutation symmetry. In particular, both the intra-molecular dynamics of a single molecule and the inter-molecular dynamics associated, for example, with reactive molecular collisions are strongly affected by selection rules originating in nuclear-permutation symmetry operations being applied to the total internal wavefunctions, including nuclear spin, of the molecules involved. We propose here a general tool to determine coherently the permutation symmetry and the rotational symmetry (associated with the group of arbitrary rotations of the entire molecule in space) of molecular wavefunctions, in particular the nuclear-spin functions. Thusmore » far, these two symmetries were believed to be mutually independent and it has even been argued that under certain circumstances, it is impossible to establish a one-to-one correspondence between them. However, using the Schur-Weyl duality theorem we show that the two types of symmetry are inherently coupled. In addition, we use the ingenious representation-theory technique of Young tableaus to represent the molecular nuclear-spin degrees of freedom in terms of well-defined mathematical objects. This simplifies the symmetry classification of the nuclear wavefunction even for large molecules. Also, the application to reactive collisions is very straightforward and provides a much simplified approach to obtaining selection rules.« less

Potential energy surface fitting by a statistically localized, permutationally invariant, local interpolating moving least squares method for the many-body potential: Method and application to N{sub 4}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bender, Jason D.; Doraiswamy, Sriram; Candler, Graham V., E-mail: truhlar@umn.edu, E-mail: candler@aem.umn.edu

2014-02-07

Fitting potential energy surfaces to analytic forms is an important first step for efficient molecular dynamics simulations. Here, we present an improved version of the local interpolating moving least squares method (L-IMLS) for such fitting. Our method has three key improvements. First, pairwise interactions are modeled separately from many-body interactions. Second, permutational invariance is incorporated in the basis functions, using permutationally invariant polynomials in Morse variables, and in the weight functions. Third, computational cost is reduced by statistical localization, in which we statistically correlate the cutoff radius with data point density. We motivate our discussion in this paper with amore » review of global and local least-squares-based fitting methods in one dimension. Then, we develop our method in six dimensions, and we note that it allows the analytic evaluation of gradients, a feature that is important for molecular dynamics. The approach, which we call statistically localized, permutationally invariant, local interpolating moving least squares fitting of the many-body potential (SL-PI-L-IMLS-MP, or, more simply, L-IMLS-G2), is used to fit a potential energy surface to an electronic structure dataset for N{sub 4}. We discuss its performance on the dataset and give directions for further research, including applications to trajectory calculations.« less

Effect of intravenous infusion of dexmedetomidine on perioperative haemodynamic changes and postoperative recovery: A study with entropy analysis

PubMed Central

Patel, Chirag Ramanlal; Engineer, Smita R; Shah, Bharat J; Madhu, S

2012-01-01

Background: Dexmedetomidine, an α2 agonist, when used as an adjuvant in general anaesthesia attenuates stress response to various noxious stimuli, maintains perioperative haemodynamic stability and provides sedation without significant respiratory depression postoperatively. Methods: Sixty patients were randomly divided into two groups of 30 each. In group A, fentanyl 2 μg/kg and in group B dexmedetomidine were given intravenously as loading dose of 1 μg/kg over 10 min prior to induction. After induction with thiopentone, in group B, dexmedetomidine was given as infusion at a dose of 0.2–0.8 μg/kg. Sevoflurane was used as inhalation agent in both groups. Haemodynamic variables and entropy (response entropy and state entropy) were recorded continuously. Postoperative sedation and recovery were assessed by sedation score and modified Aldrete's score, respectively. Results: Dexmedetomidine significantly attenuates stress response at intubation with lesser increase in heart rate (10% vs. 17%), systolic blood pressure (6% vs. 23%) and diastolic blood pressure (7% vs. 20%) as compared to the control group (P<0.05). Intraoperatively, an average of 8% fall in systolic blood pressure and 8.16% fall in diastolic pressure in the test group as compared to 3.6% rise in systolic and 3.3% in diastolic pressure of the control group was observed. Postoperatively, the test group showed significant sedation at 2 h as compared to the control group (P=0.00) and recovery was better in the control group for the first 2 h post extubation. Conclusion: Dexmedetomidine attenuates various stress responses during surgery and maintains the haemodynamic stability when used as an adjuvant in general anaesthesia. Also, the sedative action of dexmedetomidine delays recovery for the first few hours post extubation. PMID:23325938

Bi-spectral index, entropy and predicted plasma propofol concentrations with target controlled infusions in Indian patients.

PubMed

Puri, Goverdhan D; Mathew, Preethy J; Sethu Madhavan, J; Hegde, Harihar V; Fiehn, Andreas

2011-10-01

Many processed electroencephalographic signals are used now to help the anaesthesiologist titrate the depth of sedation. We investigated the relationship between target plasma propofol concentration and objective end-points of sedation- Bispectral Index (BIS), State Entropy (SE) and Response Entropy (RE)-at clinical end-points as assessed by Modified Observer Assessment of Alertness/sedation Scale (MOAAS) in Indian patients. Eighteen ASA 1 and 2 Indian adult patients scheduled to undergo elective surgery were included. The target control infusion (TCI) of propofol was administered using 'Diprifusor'. The level of sedation was assessed using MOAAS by the anaesthesiologist. BIS, SE, RE were recorded throughout. TCI was started at 0.5 μg/ml and increased by 0.5 μg/ml every 6 min till MOAAS scores reached 0 or there was sustained BIS value less than 30. The EC(50) and EC(95) of predicted plasma propofol concentration for loss of consciousness (assessed by loss of response to verbal command), were 2.3 and 2.8 μg/ml respectively and for loss of response to painful stimuli (trapezius squeeze) were 4.0 and 5.0 μg/ml respectively. The BIS and entropy values (EC(50) and EC(95)) for loss of consciousness and response to painful stimuli in Indian patients were estimated. The preliminary relation of target plasma propofol concentration with BIS was found to be BIS = 100.5-16.4 × (Target concentration). The target plasma propofol concentrations required to produce unconsciousness and loss of response to painful stimuli in Indian patients have been estimated. Also, the relations between target plasma concentration and objective measures of different levels of anaesthesia have been established.

Serotonergic psychedelics temporarily modify information transfer in humans.

PubMed

Alonso, Joan Francesc; Romero, Sergio; Mañanas, Miquel Àngel; Riba, Jordi

2015-03-28

Psychedelics induce intense modifications in the sensorium, the sense of "self," and the experience of reality. Despite advances in our understanding of the molecular and cellular level mechanisms of these drugs, knowledge of their actions on global brain dynamics is still incomplete. Recent imaging studies have found changes in functional coupling between frontal and parietal brain structures, suggesting a modification in information flow between brain regions during acute effects. Here we assessed the psychedelic-induced changes in directionality of information flow during the acute effects of a psychedelic in humans. We measured modifications in connectivity of brain oscillations using transfer entropy, a nonlinear measure of directed functional connectivity based on information theory. Ten healthy male volunteers with prior experience with psychedelics participated in 2 experimental sessions. They received a placebo or a dose of ayahuasca, a psychedelic preparation containing the serotonergic 5-HT2A agonist N,N-dimethyltryptamine. The analysis showed significant changes in the coupling of brain oscillations between anterior and posterior recording sites. Transfer entropy analysis showed that frontal sources decreased their influence over central, parietal, and occipital sites. Conversely, sources in posterior locations increased their influence over signals measured at anterior locations. Exploratory correlations found that anterior-to-posterior transfer entropy decreases were correlated with the intensity of subjective effects, while the imbalance between anterior-to-posterior and posterior-to-anterior transfer entropy correlated with the degree of incapacitation experienced. These results suggest that psychedelics induce a temporary disruption of neural hierarchies by reducing top-down control and increasing bottom-up information transfer in the human brain. © The Author 2015. Published by Oxford University Press on behalf of CINP.

Multiplicity and entropy scaling of medium-energy protons emitted in relativistic heavy-ion collisions

NASA Astrophysics Data System (ADS)

Abdelsalam, A.; Kamel, S.; Hafiz, M. E.

2015-10-01

The behavior and the properties of medium-energy protons with kinetic energies in the range 26 - 400 MeV is derived from measurements of the particle yields and spectra in the final state of relativistic heavy-ion collisions (16O-AgBr interactions at 60 A and 200 A GeV and 32S-AgBr interactions at 3.7 A and 200 A GeV) and their interpretation in terms of the higher order moments. The multiplicity distributions have been fitted well with the Gaussian distribution function. The data are also compared with the predictions of the modified FRITIOF model, showing that the FRITIOF model does not reproduce the trend and the magnitude of the data. Measurements of the ratio of the variance to the mean show that the production of target fragments at high energies cannot be considered as a statistically independent process. However, the deviation of each multiplicity distribution from a Poisson law provides evidence for correlations. The KNO scaling behavior of two types of scaling (Koba-Nielsen-Olesen (KNO) scaling and Hegyi scaling) functions in terms of the multiplicity distribution is investigated. A simplified universal function has been used in each scaling to display the experimental data. An examination of the relationship between the entropy, the average multiplicity, and the KNO function is performed. Entropy production and subsequent scaling in nucleus-nucleus collisions are carried out by analyzing the experimental data over a wide energy range (Dubna and SPS). Interestingly, the data points corresponding to various energies overlap and fall on a single curve, indicating the presence of a kind of entropy scaling.

Effect of intravenous infusion of dexmedetomidine on perioperative haemodynamic changes and postoperative recovery: A study with entropy analysis.

PubMed

Patel, Chirag Ramanlal; Engineer, Smita R; Shah, Bharat J; Madhu, S

2012-11-01

Dexmedetomidine, an α2 agonist, when used as an adjuvant in general anaesthesia attenuates stress response to various noxious stimuli, maintains perioperative haemodynamic stability and provides sedation without significant respiratory depression postoperatively. Sixty patients were randomly divided into two groups of 30 each. In group A, fentanyl 2 μg/kg and in group B dexmedetomidine were given intravenously as loading dose of 1 μg/kg over 10 min prior to induction. After induction with thiopentone, in group B, dexmedetomidine was given as infusion at a dose of 0.2-0.8 μg/kg. Sevoflurane was used as inhalation agent in both groups. Haemodynamic variables and entropy (response entropy and state entropy) were recorded continuously. Postoperative sedation and recovery were assessed by sedation score and modified Aldrete's score, respectively. Dexmedetomidine significantly attenuates stress response at intubation with lesser increase in heart rate (10% vs. 17%), systolic blood pressure (6% vs. 23%) and diastolic blood pressure (7% vs. 20%) as compared to the control group (P<0.05). Intraoperatively, an average of 8% fall in systolic blood pressure and 8.16% fall in diastolic pressure in the test group as compared to 3.6% rise in systolic and 3.3% in diastolic pressure of the control group was observed. Postoperatively, the test group showed significant sedation at 2 h as compared to the control group (P=0.00) and recovery was better in the control group for the first 2 h post extubation. Dexmedetomidine attenuates various stress responses during surgery and maintains the haemodynamic stability when used as an adjuvant in general anaesthesia. Also, the sedative action of dexmedetomidine delays recovery for the first few hours post extubation.

Ciliates learn to diagnose and correct classical error syndromes in mating strategies

PubMed Central

Clark, Kevin B.

2013-01-01

Preconjugal ciliates learn classical repetition error-correction codes to safeguard mating messages and replies from corruption by “rivals” and local ambient noise. Because individual cells behave as memory channels with Szilárd engine attributes, these coding schemes also might be used to limit, diagnose, and correct mating-signal errors due to noisy intracellular information processing. The present study, therefore, assessed whether heterotrich ciliates effect fault-tolerant signal planning and execution by modifying engine performance, and consequently entropy content of codes, during mock cell–cell communication. Socially meaningful serial vibrations emitted from an ambiguous artificial source initiated ciliate behavioral signaling performances known to advertise mating fitness with varying courtship strategies. Microbes, employing calcium-dependent Hebbian-like decision making, learned to diagnose then correct error syndromes by recursively matching Boltzmann entropies between signal planning and execution stages via “power” or “refrigeration” cycles. All eight serial contraction and reversal strategies incurred errors in entropy magnitude by the execution stage of processing. Absolute errors, however, subtended expected threshold values for single bit-flip errors in three-bit replies, indicating coding schemes protected information content throughout signal production. Ciliate preparedness for vibrations selectively and significantly affected the magnitude and valence of Szilárd engine performance during modal and non-modal strategy corrective cycles. But entropy fidelity for all replies mainly improved across learning trials as refinements in engine efficiency. Fidelity neared maximum levels for only modal signals coded in resilient three-bit repetition error-correction sequences. Together, these findings demonstrate microbes can elevate survival/reproductive success by learning to implement classical fault-tolerant information processing in social contexts. PMID:23966987

Dynamics of glass-forming liquids. XIX. Rise and decay of field induced anisotropy in the non-linear regime

NASA Astrophysics Data System (ADS)

Young-Gonzales, Amanda R.; Samanta, Subarna; Richert, Ranko

2015-09-01

For glycerol and three monohydroxy alcohols, we have measured the non-linear dielectric effects resulting from the application and removal of a high dc bias electric field. The field effects are detected by virtue of a small amplitude harmonic field, from which time resolved changes in the dielectric loss are derived. The changes in permittivity are dominated by modifications of the time constants (rather than amplitudes) which display two contributions: a heating-like decrease of relaxation times that originates from the time dependent field when the bias is switched on and off and a slowing down of the dynamics resulting from the field induced reduction of configurational entropy. As observed for the electro-optical Kerr effect, the rise of the entropy change is slower than its decay, a feature that we rationalize on the basis of the quadratic dependence of the entropy change on polarization. For glycerol, the observed steady state level of the field induced shift of the glass transition temperature (+84 mK) matches the expectation based on the entropy change and its impact on dynamics via the Adam-Gibbs relation (+88 mK). For the alcohols, these non-linear effects rise and decay on the time scales of the prominent dielectric Debye process, underscoring the relation of these features to polarization anisotropy, opposed to mechanical or enthalpy relaxation which are orders of magnitude faster in these systems. A model is discussed which captures the observed magnitudes as well as time dependences in a near quantitative fashion. It is demonstrated that the high bias field modifies the response of polarization to the ac field, including a temporary change in the low field susceptibility.

Brain Computation Is Organized via Power-of-Two-Based Permutation Logic.

PubMed

Xie, Kun; Fox, Grace E; Liu, Jun; Lyu, Cheng; Lee, Jason C; Kuang, Hui; Jacobs, Stephanie; Li, Meng; Liu, Tianming; Song, Sen; Tsien, Joe Z

2016-01-01

There is considerable scientific interest in understanding how cell assemblies-the long-presumed computational motif-are organized so that the brain can generate intelligent cognition and flexible behavior. The Theory of Connectivity proposes that the origin of intelligence is rooted in a power-of-two-based permutation logic ( N = 2 i -1), producing specific-to-general cell-assembly architecture capable of generating specific perceptions and memories, as well as generalized knowledge and flexible actions. We show that this power-of-two-based permutation logic is widely used in cortical and subcortical circuits across animal species and is conserved for the processing of a variety of cognitive modalities including appetitive, emotional and social information. However, modulatory neurons, such as dopaminergic (DA) neurons, use a simpler logic despite their distinct subtypes. Interestingly, this specific-to-general permutation logic remained largely intact although NMDA receptors-the synaptic switch for learning and memory-were deleted throughout adulthood, suggesting that the logic is developmentally pre-configured. Moreover, this computational logic is implemented in the cortex via combining a random-connectivity strategy in superficial layers 2/3 with nonrandom organizations in deep layers 5/6. This randomness of layers 2/3 cliques-which preferentially encode specific and low-combinatorial features and project inter-cortically-is ideal for maximizing cross-modality novel pattern-extraction, pattern-discrimination and pattern-categorization using sparse code, consequently explaining why it requires hippocampal offline-consolidation. In contrast, the nonrandomness in layers 5/6-which consists of few specific cliques but a higher portion of more general cliques projecting mostly to subcortical systems-is ideal for feedback-control of motivation, emotion, consciousness and behaviors. These observations suggest that the brain's basic computational algorithm is indeed organized by the power-of-two-based permutation logic. This simple mathematical logic can account for brain computation across the entire evolutionary spectrum, ranging from the simplest neural networks to the most complex.

Brain Computation Is Organized via Power-of-Two-Based Permutation Logic

PubMed Central

Xie, Kun; Fox, Grace E.; Liu, Jun; Lyu, Cheng; Lee, Jason C.; Kuang, Hui; Jacobs, Stephanie; Li, Meng; Liu, Tianming; Song, Sen; Tsien, Joe Z.

2016-01-01

There is considerable scientific interest in understanding how cell assemblies—the long-presumed computational motif—are organized so that the brain can generate intelligent cognition and flexible behavior. The Theory of Connectivity proposes that the origin of intelligence is rooted in a power-of-two-based permutation logic (N = 2i–1), producing specific-to-general cell-assembly architecture capable of generating specific perceptions and memories, as well as generalized knowledge and flexible actions. We show that this power-of-two-based permutation logic is widely used in cortical and subcortical circuits across animal species and is conserved for the processing of a variety of cognitive modalities including appetitive, emotional and social information. However, modulatory neurons, such as dopaminergic (DA) neurons, use a simpler logic despite their distinct subtypes. Interestingly, this specific-to-general permutation logic remained largely intact although NMDA receptors—the synaptic switch for learning and memory—were deleted throughout adulthood, suggesting that the logic is developmentally pre-configured. Moreover, this computational logic is implemented in the cortex via combining a random-connectivity strategy in superficial layers 2/3 with nonrandom organizations in deep layers 5/6. This randomness of layers 2/3 cliques—which preferentially encode specific and low-combinatorial features and project inter-cortically—is ideal for maximizing cross-modality novel pattern-extraction, pattern-discrimination and pattern-categorization using sparse code, consequently explaining why it requires hippocampal offline-consolidation. In contrast, the nonrandomness in layers 5/6—which consists of few specific cliques but a higher portion of more general cliques projecting mostly to subcortical systems—is ideal for feedback-control of motivation, emotion, consciousness and behaviors. These observations suggest that the brain’s basic computational algorithm is indeed organized by the power-of-two-based permutation logic. This simple mathematical logic can account for brain computation across the entire evolutionary spectrum, ranging from the simplest neural networks to the most complex. PMID:27895562

Successful attack on permutation-parity-machine-based neural cryptography.

PubMed

Seoane, Luís F; Ruttor, Andreas

2012-02-01

An algorithm is presented which implements a probabilistic attack on the key-exchange protocol based on permutation parity machines. Instead of imitating the synchronization of the communicating partners, the strategy consists of a Monte Carlo method to sample the space of possible weights during inner rounds and an analytic approach to convey the extracted information from one outer round to the next one. The results show that the protocol under attack fails to synchronize faster than an eavesdropper using this algorithm.

Crossbar Switches For Optical Data-Communication Networks

NASA Technical Reports Server (NTRS)

Monacos, Steve P.

1994-01-01

Optoelectronic and electro-optical crossbar switches called "permutation engines" (PE's) developed to route packets of data through fiber-optic communication networks. Basic network concept described in "High-Speed Optical Wide-Area Data-Communication Network" (NPO-18983). Nonblocking operation achieved by decentralized switching and control scheme. Each packet routed up or down in each column of this 5-input/5-output permutation engine. Routing algorithm ensures each packet arrives at its designated output port without blocking any other packet that does not contend for same output port.

Security of the Five-Round KASUMI Type Permutation

NASA Astrophysics Data System (ADS)

Iwata, Tetsu; Yagi, Tohru; Kurosawa, Kaoru

KASUMI is a blockcipher that forms the heart of the 3GPP confidentiality and integrity algorithms. In this paper, we study the security of the five-round KASUMI type permutations, and derive a highly non-trivial security bound against adversaries with adaptive chosen plaintext and chosen ciphertext attacks. To derive our security bound, we heavily use the tools from graph theory. However the result does not show its super-pseudorandomness, this gives us a strong evidence that the design of KASUMI is sound.

Salt dependence of compression normal forces of quenched polyelectrolyte brushes

NASA Astrophysics Data System (ADS)

Hernandez-Zapata, Ernesto; Tamashiro, Mario N.; Pincus, Philip A.

2001-03-01

We obtained mean-field expressions for the compression normal forces between two identical opposing quenched polyelectrolyte brushes in the presence of monovalent salt. The brush elasticity is modeled using the entropy of ideal Gaussian chains, while the entropy of the microions and the electrostatic contribution to the grand potential is obtained by solving the non-linear Poisson-Boltzmann equation for the system in contact with a salt reservoir. For the polyelectrolyte brush we considered both a uniformly charged slab as well as an inhomogeneous charge profile obtained using a self-consistent field theory. Using the Derjaguin approximation, we related the planar-geometry results to the realistic two-crossed cylinders experimental set up. Theoretical predictions are compared to experimental measurements(Marc Balastre's abstract, APS March 2001 Meeting.) of the salt dependence of the compression normal forces between two quenched polyelectrolyte brushes formed by the adsorption of diblock copolymers poly(tert-butyl styrene)-sodium poly(styrene sulfonate) [PtBs/NaPSS] onto an octadecyltriethoxysilane (OTE) hydrophobically modified mica, as well as onto bare mica.

Lattice thermal conductivity of multi-component alloys

DOE PAGES

Caro, Magdalena; Béland, Laurent K.; Samolyuk, German D.; ...

2015-06-12

High entropy alloys (HEA) have unique properties including the potential to be radiation tolerant. These materials with extreme disorder could resist damage because disorder, stabilized by entropy, is the equilibrium thermodynamic state. Disorder also reduces electron and phonon conductivity keeping the damage energy longer at the deposition locations, eventually favoring defect recombination. In the short time-scales related to thermal spikes induced by collision cascades, phonons become the relevant energy carrier. In this paper, we perform a systematic study of phonon thermal conductivity in multiple component solid solutions represented by Lennard-Jones (LJ) potentials. We explore the conditions that minimize phonon meanmore » free path via extreme alloy complexity, by varying the composition and the elements (differing in mass, atomic radii, and cohesive energy). We show that alloy complexity can be tailored to modify the scattering mechanisms that control energy transport in the phonon subsystem. Finally, our analysis provides a qualitative guidance for the selection criteria used in the design of HEA alloys with low phonon thermal conductivity.« less

Hydrodynamical simulations of the stream-core interaction in the slow merger of massive stars

NASA Astrophysics Data System (ADS)

Ivanova, N.; Podsiadlowski, Ph.; Spruit, H.

2002-08-01

We present detailed simulations of the interaction of a stream emanating from a mass-losing secondary with the core of a massive supergiant in the slow merger of two stars inside a common envelope. The dynamics of the stream can be divided into a ballistic phase, starting at the L1 point, and a hydrodynamical phase, where the stream interacts strongly with the core. Considering the merger of a 1- and 5-Msolar star with a 20-Msolar evolved supergiant, we present two-dimensional hydrodynamical simulations using the PROMETHEUS code to demonstrate how the penetration depth and post-impact conditions depend on the initial properties of the stream material (e.g. entropy, angular momentum, stream width) and the properties of the core (e.g. density structure and rotation rate). Using these results, we present a fitting formula for the entropy generated in the stream-core interaction and a recipe for the determination of the penetration depth based on a modified Bernoulli integral.

Second Law of Thermodynamics Applied to Metabolic Networks

NASA Technical Reports Server (NTRS)

Nigam, R.; Liang, S.

2003-01-01

We present a simple algorithm based on linear programming, that combines Kirchoff's flux and potential laws and applies them to metabolic networks to predict thermodynamically feasible reaction fluxes. These law's represent mass conservation and energy feasibility that are widely used in electrical circuit analysis. Formulating the Kirchoff's potential law around a reaction loop in terms of the null space of the stoichiometric matrix leads to a simple representation of the law of entropy that can be readily incorporated into the traditional flux balance analysis without resorting to non-linear optimization. Our technique is new as it can easily check the fluxes got by applying flux balance analysis for thermodynamic feasibility and modify them if they are infeasible so that they satisfy the law of entropy. We illustrate our method by applying it to the network dealing with the central metabolism of Escherichia coli. Due to its simplicity this algorithm will be useful in studying large scale complex metabolic networks in the cell of different organisms.

A surface acoustic wave response detection method for passive wireless torque sensor

NASA Astrophysics Data System (ADS)

Fan, Yanping; Kong, Ping; Qi, Hongli; Liu, Hongye; Ji, Xiaojun

2018-01-01

This paper presents an effective surface acoustic wave (SAW) response detection method for the passive wireless SAW torque sensor to improve the measurement accuracy. An analysis was conducted on the relationship between the response energy-entropy and the bandwidth of SAW resonator (SAWR). A self-correlation method was modified to suppress the blurred white noise and highlight the attenuation characteristic of wireless SAW response. The SAW response was detected according to both the variation and the duration of energy-entropy ascension of an acquired RF signal. Numerical simulation results showed that the SAW response can be detected even when the signal-to-noise ratio (SNR) is 6dB. The proposed SAW response detection method was evaluated with several experiments at different conditions. The SAW response can be well distinguished from the sinusoidal signal and the noise. The performance of the SAW torque measurement system incorporating the detection method was tested. The obtained repeatability error was 0.23% and the linearity was 0.9934, indicating the validity of the detection method.

Analysis of financial time series using multiscale entropy based on skewness and kurtosis

NASA Astrophysics Data System (ADS)

Xu, Meng; Shang, Pengjian

2018-01-01

There is a great interest in studying dynamic characteristics of the financial time series of the daily stock closing price in different regions. Multi-scale entropy (MSE) is effective, mainly in quantifying the complexity of time series on different time scales. This paper applies a new method for financial stability from the perspective of MSE based on skewness and kurtosis. To better understand the superior coarse-graining method for the different kinds of stock indexes, we take into account the developmental characteristics of the three continents of Asia, North America and European stock markets. We study the volatility of different financial time series in addition to analyze the similarities and differences of coarsening time series from the perspective of skewness and kurtosis. A kind of corresponding relationship between the entropy value of stock sequences and the degree of stability of financial markets, were observed. The three stocks which have particular characteristics in the eight piece of stock sequences were discussed, finding the fact that it matches the result of applying the MSE method to showing results on a graph. A comparative study is conducted to simulate over synthetic and real world data. Results show that the modified method is more effective to the change of dynamics and has more valuable information. The result is obtained at the same time, finding the results of skewness and kurtosis discrimination is obvious, but also more stable.

Hyperbolic heat conduction, effective temperature, and third law for nonequilibrium systems with heat flux

NASA Astrophysics Data System (ADS)

Sobolev, S. L.

2018-02-01

Some analogies between different nonequilibrium heat conduction models, particularly random walk, the discrete variable model, and the Boltzmann transport equation with the single relaxation time approximation, have been discussed. We show that, under an assumption of a finite value of the heat carrier velocity, these models lead to the hyperbolic heat conduction equation and the modified Fourier law with relaxation term. Corresponding effective temperature and entropy have been introduced and analyzed. It has been demonstrated that the effective temperature, defined as a geometric mean of the kinetic temperatures of the heat carriers moving in opposite directions, acts as a criterion for thermalization and is a nonlinear function of the kinetic temperature and heat flux. It is shown that, under highly nonequilibrium conditions when the heat flux tends to its maximum possible value, the effective temperature, heat capacity, and local entropy go to zero even at a nonzero equilibrium temperature. This provides a possible generalization of the third law to nonequilibrium situations. Analogies and differences between the proposed effective temperature and some other definitions of a temperature in nonequilibrium state, particularly for active systems, disordered semiconductors under electric field, and adiabatic gas flow, have been shown and discussed. Illustrative examples of the behavior of the effective temperature and entropy during nonequilibrium heat conduction in a monatomic gas and a strong shockwave have been analyzed.

Dietary Nutrient Intake, Ethnicity, and Epigenetic Silencing of Lung Cancer Genes Detected in Sputum in New Mexican Smokers.

PubMed

Leng, Shuguang; Picchi, Maria A; Kang, Huining; Wu, Guodong; Filipczak, Piotr T; Juri, Daniel E; Zhang, Xiequn; Gauderman, W James; Gilliland, Frank D; Belinsky, Steven A

2018-02-01

Lung cancer gene methylation detected in sputum assesses field cancerization and predicts lung cancer incidence. Hispanic smokers have higher lung cancer susceptibility compared with non-Hispanic whites (NHW). We aimed to identify novel dietary nutrients affecting lung cancer gene methylation and determine the degree of ethnic disparity in methylation explained by diet. Dietary intakes of 139 nutrients were assessed using a validated Harvard food frequency questionnaire in 327 Hispanics and 1,502 NHWs from the Lovelace Smokers Cohort. Promoter methylation of 12 lung cancer genes was assessed in sputum DNA. A global association was identified between dietary intake and gene methylation ( P permutation = 0.003). Seventeen nutrient measurements were identified with magnitude of association with methylation greater than that seen for folate. A stepwise approach identified B12, manganese, sodium, and saturated fat as the minimally correlated set of nutrients whose optimal intakes could reduce the methylation by 36% ( P permutation < 0.001). Six protective nutrients included vitamin D, B12, manganese, magnesium, niacin, and folate. Approximately 42% of ethnic disparity in methylation was explained by insufficient intake of protective nutrients in Hispanics compared with NHWs. Functional validation of protective nutrients showed an enhanced DNA repair capacity toward double-strand DNA breaks, a mechanistic biomarker strongly linked to acquisition of lung cancer gene methylation in smokers. Dietary intake is a major modifiable factor for preventing promoter methylation of lung cancer genes in smokers' lungs. Complex dietary supplements could be developed on the basis of these protective nutrients for lung cancer chemoprevention in smokers. Hispanic smokers may benefit the most from this complex for reducing their lung cancer susceptibility. Cancer Prev Res; 11(2); 93-102. ©2017 AACR . ©2017 American Association for Cancer Research.

Whole-Lesion Apparent Diffusion Coefficient-Based Entropy-Related Parameters for Characterizing Cervical Cancers: Initial Findings.

PubMed

Guan, Yue; Li, Weifeng; Jiang, Zhuoran; Chen, Ying; Liu, Song; He, Jian; Zhou, Zhengyang; Ge, Yun

2016-12-01

This study aimed to develop whole-lesion apparent diffusion coefficient (ADC)-based entropy-related parameters of cervical cancer to preliminarily assess intratumoral heterogeneity of this lesion in comparison to adjacent normal cervical tissues. A total of 51 women (mean age, 49 years) with cervical cancers confirmed by biopsy underwent 3-T pelvic diffusion-weighted magnetic resonance imaging with b values of 0 and 800 s/mm 2 prospectively. ADC-based entropy-related parameters including first-order entropy and second-order entropies were derived from the whole tumor volume as well as adjacent normal cervical tissues. Intraclass correlation coefficient, Wilcoxon test with Bonferroni correction, Kruskal-Wallis test, and receiver operating characteristic curve were used for statistical analysis. All the parameters showed excellent interobserver agreement (all intraclass correlation coefficients  > 0.900). Entropy, entropy(H) 0 , entropy(H) 45 , entropy(H) 90 , entropy(H) 135 , and entropy(H) mean were significantly higher, whereas entropy(H) range and entropy(H) std were significantly lower in cervical cancers compared to adjacent normal cervical tissues (all P <.0001). Kruskal-Wallis test showed that there were no significant differences among the values of various second-order entropies including entropy(H) 0, entropy(H) 45 , entropy(H) 90 , entropy(H) 135 , and entropy(H) mean. All second-order entropies had larger area under the receiver operating characteristic curve than first-order entropy in differentiating cervical cancers from adjacent normal cervical tissues. Further, entropy(H) 45 , entropy(H) 90 , entropy(H) 135 , and entropy(H) mean had the same largest area under the receiver operating characteristic curve of 0.867. Whole-lesion ADC-based entropy-related parameters of cervical cancers were developed successfully, which showed initial potential in characterizing intratumoral heterogeneity in comparison to adjacent normal cervical tissues. Copyright © 2016 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

A note on the estimation of the Pareto efficient set for multiobjective matrix permutation problems.

PubMed

Brusco, Michael J; Steinley, Douglas

2012-02-01

There are a number of important problems in quantitative psychology that require the identification of a permutation of the n rows and columns of an n × n proximity matrix. These problems encompass applications such as unidimensional scaling, paired-comparison ranking, and anti-Robinson forms. The importance of simultaneously incorporating multiple objective criteria in matrix permutation applications is well recognized in the literature; however, to date, there has been a reliance on weighted-sum approaches that transform the multiobjective problem into a single-objective optimization problem. Although exact solutions to these single-objective problems produce supported Pareto efficient solutions to the multiobjective problem, many interesting unsupported Pareto efficient solutions may be missed. We illustrate the limitation of the weighted-sum approach with an example from the psychological literature and devise an effective heuristic algorithm for estimating both the supported and unsupported solutions of the Pareto efficient set. © 2011 The British Psychological Society.

Automated matching of corresponding seed images of three simulator radiographs to allow 3D triangulation of implanted seeds.

PubMed

Altschuler, M D; Kassaee, A

1997-02-01

To match corresponding seed images in different radiographs so that the 3D seed locations can be triangulated automatically and without ambiguity requires (at least) three radiographs taken from different perspectives, and an algorithm that finds the proper permutations of the seed-image indices. Matching corresponding images in only two radiographs introduces inherent ambiguities which can be resolved only with the use of non-positional information obtained with intensive human effort. Matching images in three or more radiographs is an 'NP (Non-determinant in Polynomial time)-complete' problem. Although the matching problem is fundamental, current methods for three-radiograph seed-image matching use 'local' (seed-by-seed) methods that may lead to incorrect matchings. We describe a permutation-sampling method which not only gives good 'global' (full permutation) matches for the NP-complete three-radiograph seed-matching problem, but also determines the reliability of the radiographic data themselves, namely, whether the patient moved in the interval between radiographic perspectives.

Automated matching of corresponding seed images of three simulator radiographs to allow 3D triangulation of implanted seeds

NASA Astrophysics Data System (ADS)

Altschuler, Martin D.; Kassaee, Alireza

1997-02-01

To match corresponding seed images in different radiographs so that the 3D seed locations can be triangulated automatically and without ambiguity requires (at least) three radiographs taken from different perspectives, and an algorithm that finds the proper permutations of the seed-image indices. Matching corresponding images in only two radiographs introduces inherent ambiguities which can be resolved only with the use of non-positional information obtained with intensive human effort. Matching images in three or more radiographs is an `NP (Non-determinant in Polynomial time)-complete' problem. Although the matching problem is fundamental, current methods for three-radiograph seed-image matching use `local' (seed-by-seed) methods that may lead to incorrect matchings. We describe a permutation-sampling method which not only gives good `global' (full permutation) matches for the NP-complete three-radiograph seed-matching problem, but also determines the reliability of the radiographic data themselves, namely, whether the patient moved in the interval between radiographic perspectives.

Exploiting Lipid Permutation Symmetry to Compute Membrane Remodeling Free Energies.

PubMed

Bubnis, Greg; Risselada, Herre Jelger; Grubmüller, Helmut

2016-10-28

A complete physical description of membrane remodeling processes, such as fusion or fission, requires knowledge of the underlying free energy landscapes, particularly in barrier regions involving collective shape changes, topological transitions, and high curvature, where Canham-Helfrich (CH) continuum descriptions may fail. To calculate these free energies using atomistic simulations, one must address not only the sampling problem due to high free energy barriers, but also an orthogonal sampling problem of combinatorial complexity stemming from the permutation symmetry of identical lipids. Here, we solve the combinatorial problem with a permutation reduction scheme to map a structural ensemble into a compact, nondegenerate subregion of configuration space, thereby permitting straightforward free energy calculations via umbrella sampling. We applied this approach, using a coarse-grained lipid model, to test the CH description of bending and found sharp increases in the bending modulus for curvature radii below 10 nm. These deviations suggest that an anharmonic bending term may be required for CH models to give quantitative energetics of highly curved states.

A fast chaos-based image encryption scheme with a dynamic state variables selection mechanism

NASA Astrophysics Data System (ADS)

Chen, Jun-xin; Zhu, Zhi-liang; Fu, Chong; Yu, Hai; Zhang, Li-bo

2015-03-01

In recent years, a variety of chaos-based image cryptosystems have been investigated to meet the increasing demand for real-time secure image transmission. Most of them are based on permutation-diffusion architecture, in which permutation and diffusion are two independent procedures with fixed control parameters. This property results in two flaws. (1) At least two chaotic state variables are required for encrypting one plain pixel, in permutation and diffusion stages respectively. Chaotic state variables produced with high computation complexity are not sufficiently used. (2) The key stream solely depends on the secret key, and hence the cryptosystem is vulnerable against known/chosen-plaintext attacks. In this paper, a fast chaos-based image encryption scheme with a dynamic state variables selection mechanism is proposed to enhance the security and promote the efficiency of chaos-based image cryptosystems. Experimental simulations and extensive cryptanalysis have been carried out and the results prove the superior security and high efficiency of the scheme.

Simultaneous and Sequential MS/MS Scan Combinations and Permutations in a Linear Quadrupole Ion Trap.

PubMed

Snyder, Dalton T; Szalwinski, Lucas J; Cooks, R Graham

2017-10-17

Methods of performing precursor ion scans as well as neutral loss scans in a single linear quadrupole ion trap have recently been described. In this paper we report methodology for performing permutations of MS/MS scan modes, that is, ordered combinations of precursor, product, and neutral loss scans following a single ion injection event. Only particular permutations are allowed; the sequences demonstrated here are (1) multiple precursor ion scans, (2) precursor ion scans followed by a single neutral loss scan, (3) precursor ion scans followed by product ion scans, and (4) segmented neutral loss scans. (5) The common product ion scan can be performed earlier in these sequences, under certain conditions. Simultaneous scans can also be performed. These include multiple precursor ion scans, precursor ion scans with an accompanying neutral loss scan, and multiple neutral loss scans. We argue that the new capability to perform complex simultaneous and sequential MS n operations on single ion populations represents a significant step in increasing the selectivity of mass spectrometry.

A permutationally invariant full-dimensional ab initio potential energy surface for the abstraction and exchange channels of the H + CH{sub 4} system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jun, E-mail: jli15@cqu.edu.cn, E-mail: zhangdh@dicp.ac.cn; Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131; Chen, Jun

2015-05-28

We report a permutationally invariant global potential energy surface (PES) for the H + CH{sub 4} system based on ∼63 000 data points calculated at a high ab initio level (UCCSD(T)-F12a/AVTZ) using the recently proposed permutation invariant polynomial-neural network method. The small fitting error (5.1 meV) indicates a faithful representation of the ab initio points over a large configuration space. The rate coefficients calculated on the PES using tunneling corrected transition-state theory and quasi-classical trajectory are found to agree well with the available experimental and previous quantum dynamical results. The calculated total reaction probabilities (J{sub tot} = 0) including themore » abstraction and exchange channels using the new potential by a reduced dimensional quantum dynamic method are essentially the same as those on the Xu-Chen-Zhang PES [Chin. J. Chem. Phys. 27, 373 (2014)].« less

Rank-based permutation approaches for non-parametric factorial designs.

PubMed

Umlauft, Maria; Konietschke, Frank; Pauly, Markus

2017-11-01

Inference methods for null hypotheses formulated in terms of distribution functions in general non-parametric factorial designs are studied. The methods can be applied to continuous, ordinal or even ordered categorical data in a unified way, and are based only on ranks. In this set-up Wald-type statistics and ANOVA-type statistics are the current state of the art. The first method is asymptotically exact but a rather liberal statistical testing procedure for small to moderate sample size, while the latter is only an approximation which does not possess the correct asymptotic α level under the null. To bridge these gaps, a novel permutation approach is proposed which can be seen as a flexible generalization of the Kruskal-Wallis test to all kinds of factorial designs with independent observations. It is proven that the permutation principle is asymptotically correct while keeping its finite exactness property when data are exchangeable. The results of extensive simulation studies foster these theoretical findings. A real data set exemplifies its applicability. © 2017 The British Psychological Society.

On quantum Rényi entropies: A new generalization and some properties

NASA Astrophysics Data System (ADS)

Müller-Lennert, Martin; Dupuis, Frédéric; Szehr, Oleg; Fehr, Serge; Tomamichel, Marco

2013-12-01

The Rényi entropies constitute a family of information measures that generalizes the well-known Shannon entropy, inheriting many of its properties. They appear in the form of unconditional and conditional entropies, relative entropies, or mutual information, and have found many applications in information theory and beyond. Various generalizations of Rényi entropies to the quantum setting have been proposed, most prominently Petz's quasi-entropies and Renner's conditional min-, max-, and collision entropy. However, these quantum extensions are incompatible and thus unsatisfactory. We propose a new quantum generalization of the family of Rényi entropies that contains the von Neumann entropy, min-entropy, collision entropy, and the max-entropy as special cases, thus encompassing most quantum entropies in use today. We show several natural properties for this definition, including data-processing inequalities, a duality relation, and an entropic uncertainty relation.

Structure-based Design of Cyclically Permuted HIV-1 gp120 Trimers That Elicit Neutralizing Antibodies*

PubMed Central

Kesavardhana, Sannula; Das, Raksha; Citron, Michael; Datta, Rohini; Ecto, Linda; Srilatha, Nonavinakere Seetharam; DiStefano, Daniel; Swoyer, Ryan; Joyce, Joseph G.; Dutta, Somnath; LaBranche, Celia C.; Montefiori, David C.; Flynn, Jessica A.; Varadarajan, Raghavan

2017-01-01

A major goal for HIV-1 vaccine development is an ability to elicit strong and durable broadly neutralizing antibody (bNAb) responses. The trimeric envelope glycoprotein (Env) spikes on HIV-1 are known to contain multiple epitopes that are susceptible to bNAbs isolated from infected individuals. Nonetheless, all trimeric and monomeric Env immunogens designed to date have failed to elicit such antibodies. We report the structure-guided design of HIV-1 cyclically permuted gp120 that forms homogeneous, stable trimers, and displays enhanced binding to multiple bNAbs, including VRC01, VRC03, VRC-PG04, PGT128, and the quaternary epitope-specific bNAbs PGT145 and PGDM1400. Constructs that were cyclically permuted in the V1 loop region and contained an N-terminal trimerization domain to stabilize V1V2-mediated quaternary interactions, showed the highest homogeneity and the best antigenic characteristics. In guinea pigs, a DNA prime-protein boost regimen with these new gp120 trimer immunogens elicited potent neutralizing antibody responses against highly sensitive Tier 1A isolates and weaker neutralizing antibody responses with an average titer of about 115 against a panel of heterologous Tier 2 isolates. A modest fraction of the Tier 2 virus neutralizing activity appeared to target the CD4 binding site on gp120. These results suggest that cyclically permuted HIV-1 gp120 trimers represent a viable platform in which further modifications may be made to eventually achieve protective bNAb responses. PMID:27879316

Upper entropy axioms and lower entropy axioms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guo, Jin-Li, E-mail: phd5816@163.com; Suo, Qi

2015-04-15

The paper suggests the concepts of an upper entropy and a lower entropy. We propose a new axiomatic definition, namely, upper entropy axioms, inspired by axioms of metric spaces, and also formulate lower entropy axioms. We also develop weak upper entropy axioms and weak lower entropy axioms. Their conditions are weaker than those of Shannon–Khinchin axioms and Tsallis axioms, while these conditions are stronger than those of the axiomatics based on the first three Shannon–Khinchin axioms. The subadditivity and strong subadditivity of entropy are obtained in the new axiomatics. Tsallis statistics is a special case of satisfying our axioms. Moreover,more » different forms of information measures, such as Shannon entropy, Daroczy entropy, Tsallis entropy and other entropies, can be unified under the same axiomatics.« less

Two-level optimization of composite wing structures based on panel genetic optimization

NASA Astrophysics Data System (ADS)

Liu, Boyang

The design of complex composite structures used in aerospace or automotive vehicles presents a major challenge in terms of computational cost. Discrete choices for ply thicknesses and ply angles leads to a combinatorial optimization problem that is too expensive to solve with presently available computational resources. We developed the following methodology for handling this problem for wing structural design: we used a two-level optimization approach with response-surface approximations to optimize panel failure loads for the upper-level wing optimization. We tailored efficient permutation genetic algorithms to the panel stacking sequence design on the lower level. We also developed approach for improving continuity of ply stacking sequences among adjacent panels. The decomposition approach led to a lower-level optimization of stacking sequence with a given number of plies in each orientation. An efficient permutation genetic algorithm (GA) was developed for handling this problem. We demonstrated through examples that the permutation GAs are more efficient for stacking sequence optimization than a standard GA. Repair strategies for standard GA and the permutation GAs for dealing with constraints were also developed. The repair strategies can significantly reduce computation costs for both standard GA and permutation GA. A two-level optimization procedure for composite wing design subject to strength and buckling constraints is presented. At wing-level design, continuous optimization of ply thicknesses with orientations of 0°, 90°, and +/-45° is performed to minimize weight. At the panel level, the number of plies of each orientation (rounded to integers) and inplane loads are specified, and a permutation genetic algorithm is used to optimize the stacking sequence. The process begins with many panel genetic optimizations for a range of loads and numbers of plies of each orientation. Next, a cubic polynomial response surface is fitted to the optimum buckling load. The resulting response surface is used for wing-level optimization. In general, complex composite structures consist of several laminates. A common problem in the design of such structures is that some plies in the adjacent laminates terminate in the boundary between the laminates. These discontinuities may cause stress concentrations and may increase manufacturing difficulty and cost. We developed measures of continuity of two adjacent laminates. We studied tradeoffs between weight and continuity through a simple composite wing design. Finally, we compared the two-level optimization to a single-level optimization based on flexural lamination parameters. The single-level optimization is efficient and feasible for a wing consisting of unstiffened panels.

Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

NASA Astrophysics Data System (ADS)

Pietrucci, Fabio; Andreoni, Wanda

2011-08-01

Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

Finding fixed satellite service orbital allotments with a k-permutation algorithm

NASA Technical Reports Server (NTRS)

Reilly, Charles H.; Mount-Campbell, Clark A.; Gonsalvez, David J. A.

1990-01-01

A satellite system synthesis problem, the satellite location problem (SLP), is addressed. In SLP, orbital locations (longitudes) are allotted to geostationary satellites in the fixed satellite service. A linear mixed-integer programming model is presented that views SLP as a combination of two problems: the problem of ordering the satellites and the problem of locating the satellites given some ordering. A special-purpose heuristic procedure, a k-permutation algorithm, has been developed to find solutions to SLPs. Solutions to small sample problems are presented and analyzed on the basis of calculated interferences.

Permutation approach, high frequency trading and variety of micro patterns in financial time series

NASA Astrophysics Data System (ADS)

Aghamohammadi, Cina; Ebrahimian, Mehran; Tahmooresi, Hamed

2014-11-01

Permutation approach is suggested as a method to investigate financial time series in micro scales. The method is used to see how high frequency trading in recent years has affected the micro patterns which may be seen in financial time series. Tick to tick exchange rates are considered as examples. It is seen that variety of patterns evolve through time; and that the scale over which the target markets have no dominant patterns, have decreased steadily over time with the emergence of higher frequency trading.

Magic informationally complete POVMs with permutations

NASA Astrophysics Data System (ADS)

Planat, Michel; Gedik, Zafer

2017-09-01

Eigenstates of permutation gates are either stabilizer states (for gates in the Pauli group) or magic states, thus allowing universal quantum computation (Planat, Rukhsan-Ul-Haq 2017 Adv. Math. Phys. 2017, 5287862 (doi:10.1155/2017/5287862)). We show in this paper that a subset of such magic states, when acting on the generalized Pauli group, define (asymmetric) informationally complete POVMs. Such informationally complete POVMs, investigated in dimensions 2-12, exhibit simple finite geometries in their projector products and, for dimensions 4 and 8 and 9, relate to two-qubit, three-qubit and two-qutrit contextuality.

Thermodynamic phase transition in the rainbow Schwarzschild black hole

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gim, Yongwan; Kim, Wontae, E-mail: yongwan89@sogang.ac.kr, E-mail: wtkim@sogang.ac.kr

2014-10-01

We study the thermodynamic phase transition in the rainbow Schwarzschild black hole where the metric depends on the energy of the test particle. Identifying the black hole temperature with the energy from the modified dispersion relation, we obtain the modified entropy and thermodynamic energy along with the modified local temperature in the cavity to provide well defined black hole states. It is found that apart from the conventional critical temperature related to Hawking-Page phase transition there appears an additional critical temperature which is of relevance to the existence of a locally stable tiny black hole; however, the off-shell free energymore » tells us that this black hole should eventually tunnel into the stable large black hole. Finally, we discuss the reason why the temperature near the horizon is finite in the rainbow black hole by employing the running gravitational coupling constant, whereas it is divergent near the horizon in the ordinary Schwarzschild black hole.« less

Microcanonical entropy for classical systems

NASA Astrophysics Data System (ADS)

Franzosi, Roberto

2018-03-01

The entropy definition in the microcanonical ensemble is revisited. We propose a novel definition for the microcanonical entropy that resolve the debate on the correct definition of the microcanonical entropy. In particular we show that this entropy definition fixes the problem inherent the exact extensivity of the caloric equation. Furthermore, this entropy reproduces results which are in agreement with the ones predicted with standard Boltzmann entropy when applied to macroscopic systems. On the contrary, the predictions obtained with the standard Boltzmann entropy and with the entropy we propose, are different for small system sizes. Thus, we conclude that the Boltzmann entropy provides a correct description for macroscopic systems whereas extremely small systems should be better described with the entropy that we propose here.

On S-mixing entropy of quantum channels

NASA Astrophysics Data System (ADS)

Mukhamedov, Farrukh; Watanabe, Noboru

2018-06-01

In this paper, an S-mixing entropy of quantum channels is introduced as a generalization of Ohya's S-mixing entropy. We investigate several properties of the introduced entropy. Moreover, certain relations between the S-mixing entropy and the existing map and output entropies of quantum channels are investigated as well. These relations allowed us to find certain connections between separable states and the introduced entropy. Hence, there is a sufficient condition to detect entangled states. Moreover, several properties of the introduced entropy are investigated. Besides, entropies of qubit and phase-damping channels are calculated.

Development of the first georeferenced map of Rhipicephalus (Boophilus) spp. in Mexico from 1970 to date and prediction of its spatial distribution.

PubMed

Alcala-Canto, Yazmin; Figueroa-Castillo, Juan Antonio; Ibarra-Velarde, Froylán; Vera-Montenegro, Yolanda; Cervantes-Valencia, María Eugenia; Salem, Abdelfattah Z M; Cuéllar-Ordaz, Jorge Alfredo

2018-05-07

The tick genus Ripicephalus (Boophilus), particularly R. microplus, is one of the most important ectoparasites that affects livestock health and considered an epidemiological risk because it causes significant economic losses due, mainly, to restrictions in the export of infested animals to several countries. Its spatial distribution has been tied to environmental factors, mainly warm temperatures and high relative humidity. In this work, we integrated a dataset consisting of 5843 records of Rhipicephalus spp., in Mexico covering close to 50 years to know which environmental variables mostly influence this ticks' distribution. Occurrences were georeferenced using the software DIVA-GIS and the potential current distribution was modelled using the maximum entropy method (Maxent). The algorithm generated a map of high predictive capability (Area under the curve = 0.942), providing the various contribution and permutation importance of the tested variables. Precipitation seasonality, particularly in March, and isothermality were found to be the most significant climate variables in determining the probability of spatial distribution of Rhipicephalus spp. in Mexico (15.7%, 36.0% and 11.1%, respectively). Our findings demonstrate that Rhipicephalus has colonized Mexico widely, including areas characterized by different types of climate. We conclude that the Maxent distribution model using Rhipicephalus records and a set of environmental variables can predict the extent of the tick range in this country, information that should support the development of integrated control strategies.

Deep Learning Representation from Electroencephalography of Early-Stage Creutzfeldt-Jakob Disease and Features for Differentiation from Rapidly Progressive Dementia.

PubMed

Morabito, Francesco Carlo; Campolo, Maurizio; Mammone, Nadia; Versaci, Mario; Franceschetti, Silvana; Tagliavini, Fabrizio; Sofia, Vito; Fatuzzo, Daniela; Gambardella, Antonio; Labate, Angelo; Mumoli, Laura; Tripodi, Giovanbattista Gaspare; Gasparini, Sara; Cianci, Vittoria; Sueri, Chiara; Ferlazzo, Edoardo; Aguglia, Umberto

2017-03-01

A novel technique of quantitative EEG for differentiating patients with early-stage Creutzfeldt-Jakob disease (CJD) from other forms of rapidly progressive dementia (RPD) is proposed. The discrimination is based on the extraction of suitable features from the time-frequency representation of the EEG signals through continuous wavelet transform (CWT). An average measure of complexity of the EEG signal obtained by permutation entropy (PE) is also included. The dimensionality of the feature space is reduced through a multilayer processing system based on the recently emerged deep learning (DL) concept. The DL processor includes a stacked auto-encoder, trained by unsupervised learning techniques, and a classifier whose parameters are determined in a supervised way by associating the known category labels to the reduced vector of high-level features generated by the previous processing blocks. The supervised learning step is carried out by using either support vector machines (SVM) or multilayer neural networks (MLP-NN). A subset of EEG from patients suffering from Alzheimer's Disease (AD) and healthy controls (HC) is considered for differentiating CJD patients. When fine-tuning the parameters of the global processing system by a supervised learning procedure, the proposed system is able to achieve an average accuracy of 89%, an average sensitivity of 92%, and an average specificity of 89% in differentiating CJD from RPD. Similar results are obtained for CJD versus AD and CJD versus HC.

Entropy and equilibrium via games of complexity

NASA Astrophysics Data System (ADS)

Topsøe, Flemming

2004-09-01

It is suggested that thermodynamical equilibrium equals game theoretical equilibrium. Aspects of this thesis are discussed. The philosophy is consistent with maximum entropy thinking of Jaynes, but goes one step deeper by deriving the maximum entropy principle from an underlying game theoretical principle. The games introduced are based on measures of complexity. Entropy is viewed as minimal complexity. It is demonstrated that Tsallis entropy ( q-entropy) and Kaniadakis entropy ( κ-entropy) can be obtained in this way, based on suitable complexity measures. A certain unifying effect is obtained by embedding these measures in a two-parameter family of entropy functions.

Thermal isomerization of azobenzenes: on the performance of Eyring transition state theory.

PubMed

Rietze, Clemens; Titov, Evgenii; Lindner, Steven; Saalfrank, Peter

2017-08-09

The thermal [Formula: see text] (back-)isomerization of azobenzenes is a prototypical reaction occurring in molecular switches. It has been studied for decades, yet its kinetics is not fully understood. In this paper, quantum chemical calculations are performed to model the kinetics of an experimental benchmark system, where a modified azobenzene (AzoBiPyB) is embedded in a metal-organic framework (MOF). The molecule can be switched thermally from cis to trans, under solvent-free conditions. We critically test the validity of Eyring transition state theory for this reaction. As previously found for other azobenzenes (albeit in solution), good agreement between theory and experiment emerges for activation energies and activation free energies, already at a comparatively simple level of theory, B3LYP/6-31G * including dispersion corrections. However, theoretical Arrhenius prefactors and activation entropies are in qualitiative disagreement with experiment. Several factors are discussed that may have an influence on activation entropies, among them dynamical and geometric constraints (imposed by the MOF). For a simpler model-[Formula: see text] isomerization in azobenzene-a systematic test of quantum chemical methods from both density functional theory and wavefunction theory is carried out in the context of Eyring theory. Also, the effect of anharmonicities on activation entropies is discussed for this model system. Our work highlights capabilities and shortcomings of Eyring transition state theory and quantum chemical methods, when applied for the [Formula: see text] (back-)isomerization of azobenzenes under solvent-free conditions.

Thermal isomerization of azobenzenes: on the performance of Eyring transition state theory

NASA Astrophysics Data System (ADS)

Rietze, Clemens; Titov, Evgenii; Lindner, Steven; Saalfrank, Peter

2017-08-01

The thermal Z\\to E (back-)isomerization of azobenzenes is a prototypical reaction occurring in molecular switches. It has been studied for decades, yet its kinetics is not fully understood. In this paper, quantum chemical calculations are performed to model the kinetics of an experimental benchmark system, where a modified azobenzene (AzoBiPyB) is embedded in a metal-organic framework (MOF). The molecule can be switched thermally from cis to trans, under solvent-free conditions. We critically test the validity of Eyring transition state theory for this reaction. As previously found for other azobenzenes (albeit in solution), good agreement between theory and experiment emerges for activation energies and activation free energies, already at a comparatively simple level of theory, B3LYP/6-31G* including dispersion corrections. However, theoretical Arrhenius prefactors and activation entropies are in qualitiative disagreement with experiment. Several factors are discussed that may have an influence on activation entropies, among them dynamical and geometric constraints (imposed by the MOF). For a simpler model—Z\\to E isomerization in azobenzene—a systematic test of quantum chemical methods from both density functional theory and wavefunction theory is carried out in the context of Eyring theory. Also, the effect of anharmonicities on activation entropies is discussed for this model system. Our work highlights capabilities and shortcomings of Eyring transition state theory and quantum chemical methods, when applied for the Z\\to E (back-)isomerization of azobenzenes under solvent-free conditions.

Stochastic driven systems far from equilibrium

NASA Astrophysics Data System (ADS)

Kim, Kyung Hyuk

We study the dynamics and steady states of two systems far from equilibrium: a 1-D driven lattice gas and a driven Brownian particle with inertia. (1) We investigate the dynamical scaling behavior of a 1-D driven lattice gas model with two species of particles hopping in opposite directions. We confirm numerically that the dynamic exponent is equal to z = 1.5. We show analytically that a quasi-particle representation relates all phase points to a special phase line directly related to the single-species asymmetric simple exclusion process. Quasi-particle two-point correlations decay exponentially, and in such a manner that quasi-particles of opposite charge dynamically screen each other with a special balance. The balance encompasses all over the phase space. These results indicate that the model belongs to the Kardar-Parisi-Zhang (KPZ) universality class. (2) We investigate the non-equilibrium thermodynamics of a Brownian particle with inertia under feedback control of its inertia. We find such open systems can act as a molecular refrigerator due to an entropy pumping mechanism. We extend the fluctuation theorems to the refrigerator. The entropy pumping modifies both the Jarzynski equality and the fluctuation theorems. We discover that the entropy pumping has a dual role of work and heat. We also investigate the thermodynamics of the particle under a hydrodynamic interaction described by a Langevin equation with a multiplicative noise. The Stratonovich stochastic integration prescription involved in the definition of heat is shown to be the unique physical choice.

An information-theoretical perspective on weighted ensemble forecasts

NASA Astrophysics Data System (ADS)

Weijs, Steven V.; van de Giesen, Nick

2013-08-01

This paper presents an information-theoretical method for weighting ensemble forecasts with new information. Weighted ensemble forecasts can be used to adjust the distribution that an existing ensemble of time series represents, without modifying the values in the ensemble itself. The weighting can, for example, add new seasonal forecast information in an existing ensemble of historically measured time series that represents climatic uncertainty. A recent article in this journal compared several methods to determine the weights for the ensemble members and introduced the pdf-ratio method. In this article, a new method, the minimum relative entropy update (MRE-update), is presented. Based on the principle of minimum discrimination information, an extension of the principle of maximum entropy (POME), the method ensures that no more information is added to the ensemble than is present in the forecast. This is achieved by minimizing relative entropy, with the forecast information imposed as constraints. From this same perspective, an information-theoretical view on the various weighting methods is presented. The MRE-update is compared with the existing methods and the parallels with the pdf-ratio method are analysed. The paper provides a new, information-theoretical justification for one version of the pdf-ratio method that turns out to be equivalent to the MRE-update. All other methods result in sets of ensemble weights that, seen from the information-theoretical perspective, add either too little or too much (i.e. fictitious) information to the ensemble.

Minimal entropy reconstructions of thermal images for emissivity correction

NASA Astrophysics Data System (ADS)

Allred, Lloyd G.

1999-03-01

Low emissivity with corresponding low thermal emission is a problem which has long afflicted infrared thermography. The problem is aggravated by reflected thermal energy which increases as the emissivity decreases, thus reducing the net signal-to-noise ratio, which degrades the resulting temperature reconstructions. Additional errors are introduced from the traditional emissivity-correction approaches, wherein one attempts to correct for emissivity either using thermocouples or using one or more baseline images, collected at known temperatures. These corrections are numerically equivalent to image differencing. Errors in the baseline images are therefore additive, causing the resulting measurement error to either double or triple. The practical application of thermal imagery usually entails coating the objective surface to increase the emissivity to a uniform and repeatable value. While the author recommends that the thermographer still adhere to this practice, he has devised a minimal entropy reconstructions which not only correct for emissivity variations, but also corrects for variations in sensor response, using the baseline images at known temperatures to correct for these values. The minimal energy reconstruction is actually based on a modified Hopfield neural network which finds the resulting image which best explains the observed data and baseline data, having minimal entropy change between adjacent pixels. The autocorrelation of temperatures between adjacent pixels is a feature of most close-up thermal images. A surprising result from transient heating data indicates that the resulting corrected thermal images have less measurement error and are closer to the situational truth than the original data.

The modified gap excess ratio (GER*) and the stratigraphic congruence of dinosaur phylogenies.

PubMed

Wills, Matthew A; Barrett, Paul M; Heathcote, Julia F

2008-12-01

Palaeontologists routinely map their cladograms onto what is known of the fossil record. Where sister taxa first appear as fossils at different times, a ghost range is inferred to bridge the gap between these dates. Some measure of the total extent of ghost ranges across the tree underlies several indices of cladistic/stratigraphic congruence. We investigate this congruence for 19 independent, published cladograms of major dinosaur groups and report exceptional agreement between the phylogenetic and stratigraphic patterns, evidenced by sums of ghost ranges near the theoretical minima. This implies that both phylogenetic and stratigraphic data reflect faithfully the evolutionary history of dinosaurs, at least for the taxa included in this study. We formally propose modifications to an existing index of congruence (the gap excess ratio; GER), designed to remove a bias in the range of values possible with trees of different shapes. We also propose a more informative index of congruence--GER*--that takes account of the underlying distribution of sums of ghost ranges possible when permuting stratigraphic range data across the tree. Finally, we incorporate data on the range of possible first occurrence dates into our estimates of congruence, extending a procedure originally implemented with the modified Manhattan stratigraphic measure and GER to our new indices. Most dinosaur data sets maintain extremely high congruence despite such modifications.

Quantile based Tsallis entropy in residual lifetime

NASA Astrophysics Data System (ADS)

Khammar, A. H.; Jahanshahi, S. M. A.

2018-02-01

Tsallis entropy is a generalization of type α of the Shannon entropy, that is a nonadditive entropy unlike the Shannon entropy. Shannon entropy may be negative for some distributions, but Tsallis entropy can always be made nonnegative by choosing appropriate value of α. In this paper, we derive the quantile form of this nonadditive's entropy function in the residual lifetime, namely the residual quantile Tsallis entropy (RQTE) and get the bounds for it, depending on the Renyi's residual quantile entropy. Also, we obtain relationship between RQTE and concept of proportional hazards model in the quantile setup. Based on the new measure, we propose a stochastic order and aging classes, and study its properties. Finally, we prove characterizations theorems for some well known lifetime distributions. It is shown that RQTE uniquely determines the parent distribution unlike the residual Tsallis entropy.

Permutation-invariant distance between atomic configurations

NASA Astrophysics Data System (ADS)

Ferré, Grégoire; Maillet, Jean-Bernard; Stoltz, Gabriel

2015-09-01

We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables us to directly compare different atomic environments with an arbitrary number of particles, without going through a space of reduced dimensionality (i.e., fingerprints) as an intermediate step. Moreover, this distance is naturally invariant through permutations of atoms, avoiding the time consuming associated minimization required by other common criteria (like the root mean square distance). Finally, the invariance through global rotations is accounted for by a minimization procedure in the space of rotations solved by Monte Carlo simulated annealing. A formal framework is also introduced, showing that the distance we propose verifies the property of a metric on the space of atomic configurations. Two examples of applications are proposed. The first one consists in evaluating faithfulness of some fingerprints (or descriptors), i.e., their capacity to represent the structural information of a configuration. The second application concerns structural analysis, where our distance proves to be efficient in discriminating different local structures and even classifying their degree of similarity.

Hurdles and sorting by inversions: combinatorial, statistical, and experimental results.

PubMed

Swenson, Krister M; Lin, Yu; Rajan, Vaibhav; Moret, Bernard M E

2009-10-01

As data about genomic architecture accumulates, genomic rearrangements have attracted increasing attention. One of the main rearrangement mechanisms, inversions (also called reversals), was characterized by Hannenhalli and Pevzner and this characterization in turn extended by various authors. The characterization relies on the concepts of breakpoints, cycles, and obstructions colorfully named hurdles and fortresses. In this paper, we study the probability of generating a hurdle in the process of sorting a permutation if one does not take special precautions to avoid them (as in a randomized algorithm, for instance). To do this we revisit and extend the work of Caprara and of Bergeron by providing simple and exact characterizations of the probability of encountering a hurdle in a random permutation. Using similar methods we provide the first asymptotically tight analysis of the probability that a fortress exists in a random permutation. Finally, we study other aspects of hurdles, both analytically and through experiments: when are they created in a sequence of sorting inversions, how much later are they detected, and how much work may need to be undone to return to a sorting sequence.

SCOPES: steganography with compression using permutation search

NASA Astrophysics Data System (ADS)

Boorboor, Sahar; Zolfaghari, Behrouz; Mozafari, Saadat Pour

2011-10-01

LSB (Least Significant Bit) is a widely used method for image steganography, which hides the secret message as a bit stream in LSBs of pixel bytes in the cover image. This paper proposes a variant of LSB named SCOPES that encodes and compresses the secret message while being hidden through storing addresses instead of message bytes. Reducing the length of the stored message improves the storage capacity and makes the stego image visually less suspicious to the third party. The main idea behind the SCOPES approach is dividing the message into 3-character segments, seeking each segment in the cover image and storing the address of the position containing the segment instead of the segment itself. In this approach, every permutation of the 3 bytes (if found) can be stored along with some extra bits indicating the permutation. In some rare cases the segment may not be found in the image and this can cause the message to be expanded by some overhead bits2 instead of being compressed. But experimental results show that SCOPES performs overlay better than traditional LSB even in the worst cases.

An effective hybrid immune algorithm for solving the distributed permutation flow-shop scheduling problem

NASA Astrophysics Data System (ADS)

Xu, Ye; Wang, Ling; Wang, Shengyao; Liu, Min

2014-09-01

In this article, an effective hybrid immune algorithm (HIA) is presented to solve the distributed permutation flow-shop scheduling problem (DPFSP). First, a decoding method is proposed to transfer a job permutation sequence to a feasible schedule considering both factory dispatching and job sequencing. Secondly, a local search with four search operators is presented based on the characteristics of the problem. Thirdly, a special crossover operator is designed for the DPFSP, and mutation and vaccination operators are also applied within the framework of the HIA to perform an immune search. The influence of parameter setting on the HIA is investigated based on the Taguchi method of design of experiment. Extensive numerical testing results based on 420 small-sized instances and 720 large-sized instances are provided. The effectiveness of the HIA is demonstrated by comparison with some existing heuristic algorithms and the variable neighbourhood descent methods. New best known solutions are obtained by the HIA for 17 out of 420 small-sized instances and 585 out of 720 large-sized instances.

Cluster mass inference via random field theory.

PubMed

Zhang, Hui; Nichols, Thomas E; Johnson, Timothy D

2009-01-01

Cluster extent and voxel intensity are two widely used statistics in neuroimaging inference. Cluster extent is sensitive to spatially extended signals while voxel intensity is better for intense but focal signals. In order to leverage strength from both statistics, several nonparametric permutation methods have been proposed to combine the two methods. Simulation studies have shown that of the different cluster permutation methods, the cluster mass statistic is generally the best. However, to date, there is no parametric cluster mass inference available. In this paper, we propose a cluster mass inference method based on random field theory (RFT). We develop this method for Gaussian images, evaluate it on Gaussian and Gaussianized t-statistic images and investigate its statistical properties via simulation studies and real data. Simulation results show that the method is valid under the null hypothesis and demonstrate that it can be more powerful than the cluster extent inference method. Further, analyses with a single subject and a group fMRI dataset demonstrate better power than traditional cluster size inference, and good accuracy relative to a gold-standard permutation test.

Time-dependent entropy evolution in microscopic and macroscopic electromagnetic relaxation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baker-Jarvis, James

This paper is a study of entropy and its evolution in the time and frequency domains upon application of electromagnetic fields to materials. An understanding of entropy and its evolution in electromagnetic interactions bridges the boundaries between electromagnetism and thermodynamics. The approach used here is a Liouville-based statistical-mechanical theory. I show that the microscopic entropy is reversible and the macroscopic entropy satisfies an H theorem. The spectral entropy development can be very useful for studying the frequency response of materials. Using a projection-operator based nonequilibrium entropy, different equations are derived for the entropy and entropy production and are applied tomore » the polarization, magnetization, and macroscopic fields. I begin by proving an exact H theorem for the entropy, progress to application of time-dependent entropy in electromagnetics, and then apply the theory to relevant applications in electromagnetics. The paper concludes with a discussion of the relationship of the frequency-domain form of the entropy to the permittivity, permeability, and impedance.« less

Entropy flow and entropy production in the human body in basal conditions.

PubMed

Aoki, I

1989-11-08

Entropy inflow and outflow for the naked human body in basal conditions in the respiration calorimeter due to infrared radiation, convection, evaporation of water and mass-flow are calculated by use of the energetic data obtained by Hardy & Du Bois. Also, the change of entropy content in the body is estimated. The entropy production in the human body is obtained as the change of entropy content minus the net entropy flow into the body. The entropy production thus calculated becomes positive. The magnitude of entropy production per effective radiating surface area does not show any significant variation with subjects. The entropy production is nearly constant at the calorimeter temperatures of 26-32 degrees C; the average in this temperature range is 0.172 J m-2 sec-1 K-1. The forced air currents around the human body and also clothing have almost no effect in changing the entropy production. Thus, the entropy production of the naked human body in basal conditions does not depend on its environmental factors.

Brick walls and AdS/CFT

NASA Astrophysics Data System (ADS)

Kay, Bernard S.; Ortíz, L.

2014-05-01

We discuss the relationship between the bulk-boundary correspondence in Rehren's algebraic holography (and in other `fixed-background', QFT-based, approaches to holography) and in mainstream string-theoretic `Maldacena AdS/CFT'. Especially, we contrast the understanding of black-hole entropy from the point of view of QFT in curved spacetime—in the framework of 't Hooft's `brick wall' model—with the understanding based on Maldacena AdS/CFT. We show that the brick-wall modification of a Klein-Gordon field in the Hartle-Hawking-Israel state on dimensional Schwarzschild AdS has a well-defined boundary limit with the same temperature and entropy as the brick-wall-modified bulk theory. One of our main purposes is to point out a close connection, for general AdS/CFT situations, between the puzzle raised by Arnsdorf and Smolin regarding the relationship between Rehren's algebraic holography and mainstream AdS/CFT and the puzzle embodied in the `complementarity principle' proposed by Mukohyama and Israel in their work on the brick-wall approach to black hole entropy. Working on the assumption that similar results will hold for bulk QFT other than the Klein-Gordon field and for Schwarzschild AdS in other dimensions, and recalling the first author's proposed resolution to the Mukohyama-Israel puzzle based on his `matter-gravity entanglement hypothesis', we argue that, in Maldacena AdS/CFT, the algebra of the boundary CFT is isomorphic only to a proper subalgebra of the bulk algebra, albeit (at non-zero temperature) the (GNS) Hilbert spaces of bulk and boundary theories are still the `same'—the total bulk state being pure, while the boundary state is mixed (thermal). We also argue from the finiteness of its boundary (and hence, on our assumptions, also bulk) entropy at finite temperature, that the Rehren dual of the Maldacena boundary CFT cannot itself be a QFT and must, instead, presumably be something like a string theory.

SU-F-R-40: Robustness Test of Computed Tomography Textures of Lung Tissues to Varying Scanning Protocols Using a Realistic Phantom Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, S; Markel, D; Hegyi, G

2016-06-15

Purpose: The reliability of computed tomography (CT) textures is an important element of radiomics analysis. This study investigates the dependency of lung CT textures on different breathing phases and changes in CT image acquisition protocols in a realistic phantom setting. Methods: We investigated 11 CT texture features for radiation-induced lung disease from 3 categories (first-order, grey level co-ocurrence matrix (GLCM), and Law’s filter). A biomechanical swine lung phantom was scanned at two breathing phases (inhale/exhale) and two scanning protocols set for PET/CT and diagnostic CT scanning. Lung volumes acquired from the CT images were divided into 2-dimensional sub-regions with amore » grid spacing of 31 mm. The distribution of the evaluated texture features from these sub-regions were compared between the two scanning protocols and two breathing phases. The significance of each factor on feature values were tested at 95% significance level using analysis of covariance (ANCOVA) model with interaction terms included. Robustness of a feature to a scanning factor was defined as non-significant dependence on the factor. Results: Three GLCM textures (variance, sum entropy, difference entropy) were robust to breathing changes. Two GLCM (variance, sum entropy) and 3 Law’s filter textures (S5L5, E5L5, W5L5) were robust to scanner changes. Moreover, the two GLCM textures (variance, sum entropy) were consistent across all 4 scanning conditions. First-order features, especially Hounsfield unit intensity features, presented the most drastic variation up to 39%. Conclusion: Amongst the studied features, GLCM and Law’s filter texture features were more robust than first-order features. However, the majority of the features were modified by either breathing phase or scanner changes, suggesting a need for calibration when retrospectively comparing scans obtained at different conditions. Further investigation is necessary to identify the sensitivity of individual image acquisition parameters.« less

Three faces of entropy for complex systems: Information, thermodynamics, and the maximum entropy principle

NASA Astrophysics Data System (ADS)

Thurner, Stefan; Corominas-Murtra, Bernat; Hanel, Rudolf

2017-09-01

There are at least three distinct ways to conceptualize entropy: entropy as an extensive thermodynamic quantity of physical systems (Clausius, Boltzmann, Gibbs), entropy as a measure for information production of ergodic sources (Shannon), and entropy as a means for statistical inference on multinomial processes (Jaynes maximum entropy principle). Even though these notions represent fundamentally different concepts, the functional form of the entropy for thermodynamic systems in equilibrium, for ergodic sources in information theory, and for independent sampling processes in statistical systems, is degenerate, H (p ) =-∑ipilogpi . For many complex systems, which are typically history-dependent, nonergodic, and nonmultinomial, this is no longer the case. Here we show that for such processes, the three entropy concepts lead to different functional forms of entropy, which we will refer to as SEXT for extensive entropy, SIT for the source information rate in information theory, and SMEP for the entropy functional that appears in the so-called maximum entropy principle, which characterizes the most likely observable distribution functions of a system. We explicitly compute these three entropy functionals for three concrete examples: for Pólya urn processes, which are simple self-reinforcing processes, for sample-space-reducing (SSR) processes, which are simple history dependent processes that are associated with power-law statistics, and finally for multinomial mixture processes.

A k-permutation algorithm for Fixed Satellite Service orbital allotments

NASA Technical Reports Server (NTRS)

Reilly, Charles H.; Mount-Campbell, Clark A.; Gonsalvez, David J. A.

1988-01-01

A satellite system synthesis problem, the satellite location problem (SLP), is addressed in this paper. In SLP, orbital locations (longitudes) are allotted to geostationary satellites in the Fixed Satellite Service. A linear mixed-integer programming model is presented that views SLP as a combination of two problems: (1) the problem of ordering the satellites and (2) the problem of locating the satellites given some ordering. A special-purpose heuristic procedure, a k-permutation algorithm, that has been developed to find solutions to SLPs formulated in the manner suggested is described. Solutions to small example problems are presented and analyzed.

Convergence to equilibrium under a random Hamiltonian.

PubMed

Brandão, Fernando G S L; Ćwikliński, Piotr; Horodecki, Michał; Horodecki, Paweł; Korbicz, Jarosław K; Mozrzymas, Marek

2012-09-01

We analyze equilibration times of subsystems of a larger system under a random total Hamiltonian, in which the basis of the Hamiltonian is drawn from the Haar measure. We obtain that the time of equilibration is of the order of the inverse of the arithmetic average of the Bohr frequencies. To compute the average over a random basis, we compute the inverse of a matrix of overlaps of operators which permute four systems. We first obtain results on such a matrix for a representation of an arbitrary finite group and then apply it to the particular representation of the permutation group under consideration.

Convergence to equilibrium under a random Hamiltonian

NASA Astrophysics Data System (ADS)

Brandão, Fernando G. S. L.; Ćwikliński, Piotr; Horodecki, Michał; Horodecki, Paweł; Korbicz, Jarosław K.; Mozrzymas, Marek

2012-09-01

We analyze equilibration times of subsystems of a larger system under a random total Hamiltonian, in which the basis of the Hamiltonian is drawn from the Haar measure. We obtain that the time of equilibration is of the order of the inverse of the arithmetic average of the Bohr frequencies. To compute the average over a random basis, we compute the inverse of a matrix of overlaps of operators which permute four systems. We first obtain results on such a matrix for a representation of an arbitrary finite group and then apply it to the particular representation of the permutation group under consideration.

A new Nawaz-Enscore-Ham-based heuristic for permutation flow-shop problems with bicriteria of makespan and machine idle time

NASA Astrophysics Data System (ADS)

Liu, Weibo; Jin, Yan; Price, Mark

2016-10-01

A new heuristic based on the Nawaz-Enscore-Ham algorithm is proposed in this article for solving a permutation flow-shop scheduling problem. A new priority rule is proposed by accounting for the average, mean absolute deviation, skewness and kurtosis, in order to fully describe the distribution style of processing times. A new tie-breaking rule is also introduced for achieving effective job insertion with the objective of minimizing both makespan and machine idle time. Statistical tests illustrate better solution quality of the proposed algorithm compared to existing benchmark heuristics.

Neighbourhood generation mechanism applied in simulated annealing to job shop scheduling problems

NASA Astrophysics Data System (ADS)

Cruz-Chávez, Marco Antonio

2015-11-01

This paper presents a neighbourhood generation mechanism for the job shop scheduling problems (JSSPs). In order to obtain a feasible neighbour with the generation mechanism, it is only necessary to generate a permutation of an adjacent pair of operations in a scheduling of the JSSP. If there is no slack time between the adjacent pair of operations that is permuted, then it is proven, through theory and experimentation, that the new neighbour (schedule) generated is feasible. It is demonstrated that the neighbourhood generation mechanism is very efficient and effective in a simulated annealing.

New holographic dark energy model inspired by the DGP braneworld

NASA Astrophysics Data System (ADS)

Sheykhi, A.; Dehghani, M. H.; Ghaffari, S.

2016-11-01

The energy density of the holographic dark energy (HDE) is based on the area law of entropy, and thus any modification of the area law leads to a modified holographic energy density. Inspired by the entropy expression associated with the apparent horizon of a Friedmann-Robertson-Walker (FRW) universe in DGP braneworld, we propose a new model for the HDE in the framework of DGP brane cosmology. We investigate the cosmological consequences of this new model and calculate the equation of state (EoS) parameter by choosing the Hubble radius, L = H-1, as the system’s IR cutoff. Our study show that, due to the effects of the extra dimension (bulk), the identification of IR cutoff with Hubble radius, can reproduce the present acceleration of the universe expansion. This is in contrast to the ordinary HDE in standard cosmology which leads to the zero EoS parameter in the case of choosing the Hubble radius as system’s IR cutoff in the absence of interaction between dark matter (DM) and dark energy (DE).

Defying the activity-stability trade-off in enzymes: taking advantage of entropy to enhance activity and thermostability.

PubMed

Siddiqui, Khawar Sohail

2017-05-01

The biotechnological applications of enzymes are limited due to the activity-stability trade-off, which implies that an increase in activity is accompanied by a concomitant decrease in protein stability. This premise is based on thermally adapted homologous enzymes where cold-adapted enzymes show high intrinsic activity linked to enhanced thermolability. In contrast, thermophilic enzymes show low activity around ambient temperatures. Nevertheless, genetically and chemically modified enzymes are beginning to show that the activity-stability trade-off can be overcome. In this review, the origin of the activity-stability trade-off, the thermodynamic basis for enhanced activity and stability, and various approaches for escaping the activity-stability trade-off are discussed. The role of entropy in enhancing both the activity and the stability of enzymes is highlighted with a special emphasis placed on the involvement of solvent water molecules. This review is concluded with suggestions for further research, which underscores the implications of these findings in the context of productivity curves, the Daniel-Danson equilibrium model, catalytic antibodies, and life on cold planets.

Multiwavelet packet entropy and its application in transmission line fault recognition and classification.

PubMed

Liu, Zhigang; Han, Zhiwei; Zhang, Yang; Zhang, Qiaoge

2014-11-01

Multiwavelets possess better properties than traditional wavelets. Multiwavelet packet transformation has more high-frequency information. Spectral entropy can be applied as an analysis index to the complexity or uncertainty of a signal. This paper tries to define four multiwavelet packet entropies to extract the features of different transmission line faults, and uses a radial basis function (RBF) neural network to recognize and classify 10 fault types of power transmission lines. First, the preprocessing and postprocessing problems of multiwavelets are presented. Shannon entropy and Tsallis entropy are introduced, and their difference is discussed. Second, multiwavelet packet energy entropy, time entropy, Shannon singular entropy, and Tsallis singular entropy are defined as the feature extraction methods of transmission line fault signals. Third, the plan of transmission line fault recognition using multiwavelet packet entropies and an RBF neural network is proposed. Finally, the experimental results show that the plan with the four multiwavelet packet energy entropies defined in this paper achieves better performance in fault recognition. The performance with SA4 (symmetric antisymmetric) multiwavelet packet Tsallis singular entropy is the best among the combinations of different multiwavelet packets and the four multiwavelet packet entropies.

Uniqueness and characterization theorems for generalized entropies

NASA Astrophysics Data System (ADS)

Enciso, Alberto; Tempesta, Piergiulio

2017-12-01

The requirement that an entropy function be composable is key: it means that the entropy of a compound system can be calculated in terms of the entropy of its independent components. We prove that, under mild regularity assumptions, the only composable generalized entropy in trace form is the Tsallis one-parameter family (which contains Boltzmann-Gibbs as a particular case). This result leads to the use of generalized entropies that are not of trace form, such as Rényi’s entropy, in the study of complex systems. In this direction, we also present a characterization theorem for a large class of composable non-trace-form entropy functions with features akin to those of Rényi’s entropy.

Experimental heat capacities, excess entropies, and magnetic properties of bulk and nano Fe3O4-Co3O4 and Fe3O4-Mn3O4 spinel solid solutions

NASA Astrophysics Data System (ADS)

Schliesser, Jacob M.; Huang, Baiyu; Sahu, Sulata K.; Asplund, Megan; Navrotsky, Alexandra; Woodfield, Brian F.

2018-03-01

We have measured the heat capacities of several well-characterized bulk and nanophase Fe3O4-Co3O4 and Fe3O4-Mn3O4 spinel solid solution samples from which magnetic properties of transitions and third-law entropies have been determined. The magnetic transitions show several features common to effects of particle and magnetic domain sizes. From the standard molar entropies, excess entropies of mixing have been generated for these solid solutions and compared with configurational entropies determined previously by assuming appropriate cation and valence distributions. The vibrational and magnetic excess entropies for bulk materials are comparable in magnitude to the respective configurational entropies indicating that excess entropies of mixing must be included when analyzing entropies of mixing. The excess entropies for nanophase materials are even larger than the configurational entropies. Changes in valence, cation distribution, bonding and microstructure between the mixing ions are the likely sources of the positive excess entropies of mixing.

Stability of Tsallis entropy and instabilities of Rényi and normalized Tsallis entropies: a basis for q-exponential distributions.

PubMed

Abe, Sumiyoshi

2002-10-01

The q-exponential distributions, which are generalizations of the Zipf-Mandelbrot power-law distribution, are frequently encountered in complex systems at their stationary states. From the viewpoint of the principle of maximum entropy, they can apparently be derived from three different generalized entropies: the Rényi entropy, the Tsallis entropy, and the normalized Tsallis entropy. Accordingly, mere fittings of observed data by the q-exponential distributions do not lead to identification of the correct physical entropy. Here, stabilities of these entropies, i.e., their behaviors under arbitrary small deformation of a distribution, are examined. It is shown that, among the three, the Tsallis entropy is stable and can provide an entropic basis for the q-exponential distributions, whereas the others are unstable and cannot represent any experimentally observable quantities.

On the entropy variation in the scenario of entropic gravity

NASA Astrophysics Data System (ADS)

Xiao, Yong; Bai, Shi-Yang

2018-05-01

In the scenario of entropic gravity, entropy varies as a function of the location of the matter, while the tendency to increase entropy appears as gravity. We concentrate on studying the entropy variation of a typical gravitational system with different relative positions between the mass and the gravitational source. The result is that the entropy of the system doesn't increase when the mass is displaced closer to the gravitational source. In this way it disproves the proposal of entropic gravity from thermodynamic entropy. It doesn't exclude the possibility that gravity originates from non-thermodynamic entropy like entanglement entropy.

Entropy and climate. I - ERBE observations of the entropy production of the earth

NASA Technical Reports Server (NTRS)

Stephens, G. L.; O'Brien, D. M.

1993-01-01

An approximate method for estimating the global distributions of the entropy fluxes flowing through the upper boundary of the climate system is introduced, and an estimate of the entropy exchange between the earth and space and the entropy production of the planet is provided. Entropy fluxes calculated from the Earth Radiation Budget Experiment measurements show how the long-wave entropy flux densities dominate the total entropy fluxes at all latitudes compared with the entropy flux densities associated with reflected sunlight, although the short-wave flux densities are important in the context of clear sky-cloudy sky net entropy flux differences. It is suggested that the entropy production of the planet is both constant for the 36 months of data considered and very near its maximum possible value. The mean value of this production is 0.68 x 10 exp 15 W/K, and the amplitude of the annual cycle is approximately 1 to 2 percent of this value.

Logarithmic black hole entropy corrections and holographic Rényi entropy

NASA Astrophysics Data System (ADS)

Mahapatra, Subhash

2018-01-01

The entanglement and Rényi entropies for spherical entangling surfaces in CFTs with gravity duals can be explicitly calculated by mapping these entropies first to the thermal entropy on hyperbolic space and then, using the AdS/CFT correspondence, to the Wald entropy of topological black holes. Here we extend this idea by taking into account corrections to the Wald entropy. Using the method based on horizon symmetries and the asymptotic Cardy formula, we calculate corrections to the Wald entropy and find that these corrections are proportional to the logarithm of the area of the horizon. With the corrected expression for the entropy of the black hole, we then find corrections to the Rényi entropies. We calculate these corrections for both Einstein and Gauss-Bonnet gravity duals. Corrections with logarithmic dependence on the area of the entangling surface naturally occur at the order GD^0. The entropic c-function and the inequalities of the Rényi entropy are also satisfied even with the correction terms.

Maximum Relative Entropy of Coherence: An Operational Coherence Measure.

PubMed

Bu, Kaifeng; Singh, Uttam; Fei, Shao-Ming; Pati, Arun Kumar; Wu, Junde

2017-10-13

The operational characterization of quantum coherence is the cornerstone in the development of the resource theory of coherence. We introduce a new coherence quantifier based on maximum relative entropy. We prove that the maximum relative entropy of coherence is directly related to the maximum overlap with maximally coherent states under a particular class of operations, which provides an operational interpretation of the maximum relative entropy of coherence. Moreover, we show that, for any coherent state, there are examples of subchannel discrimination problems such that this coherent state allows for a higher probability of successfully discriminating subchannels than that of all incoherent states. This advantage of coherent states in subchannel discrimination can be exactly characterized by the maximum relative entropy of coherence. By introducing a suitable smooth maximum relative entropy of coherence, we prove that the smooth maximum relative entropy of coherence provides a lower bound of one-shot coherence cost, and the maximum relative entropy of coherence is equivalent to the relative entropy of coherence in the asymptotic limit. Similar to the maximum relative entropy of coherence, the minimum relative entropy of coherence has also been investigated. We show that the minimum relative entropy of coherence provides an upper bound of one-shot coherence distillation, and in the asymptotic limit the minimum relative entropy of coherence is equivalent to the relative entropy of coherence.

The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy across Protein Fold Space.

PubMed

Towse, Clare-Louise; Akke, Mikael; Daggett, Valerie

2017-04-27

Molecular dynamics (MD) simulations contain considerable information with regard to the motions and fluctuations of a protein, the magnitude of which can be used to estimate conformational entropy. Here we survey conformational entropy across protein fold space using the Dynameomics database, which represents the largest existing data set of protein MD simulations for representatives of essentially all known protein folds. We provide an overview of MD-derived entropies accounting for all possible degrees of dihedral freedom on an unprecedented scale. Although different side chains might be expected to impose varying restrictions on the conformational space that the backbone can sample, we found that the backbone entropy and side chain size are not strictly coupled. An outcome of these analyses is the Dynameomics Entropy Dictionary, the contents of which have been compared with entropies derived by other theoretical approaches and experiment. As might be expected, the conformational entropies scale linearly with the number of residues, demonstrating that conformational entropy is an extensive property of proteins. The calculated conformational entropies of folding agree well with previous estimates. Detailed analysis of specific cases identifies deviations in conformational entropy from the average values that highlight how conformational entropy varies with sequence, secondary structure, and tertiary fold. Notably, α-helices have lower entropy on average than do β-sheets, and both are lower than coil regions.

Endocannabinoids: Multi-scaled, Global Homeostatic Regulators of Cells and Society

NASA Astrophysics Data System (ADS)

Melamede, Robert

Living systems are far from equilibrium open systems that exhibit many scales of emergent behavior. They may be abstractly viewed as a complex weave of dissipative structures that maintain organization by passing electrons from reduced hydrocarbons to oxygen. Free radicals are unavoidable byproducts of biological electron flow. Due to their highly reactive chemical properties, free radicals modify all classes of biological molecules (carbohydrates, lipids, nucleic acids, and proteins). As a result, free radicals are destructive. The generally disruptive nature of free radicals makes them the "friction of life." As such, they are believed to be the etiological agents behind age related illnesses such as cardiovascular, immunological, and neurological diseases, cancer, and ageing itself. Free radicals also play a critical constructive role in living systems. From a thermodynamic perspective, life can only exist if a living system takes in sufficient negative entropy from its environment to overcome the obligatory increase in entropy that would result if the system could not appropriately exchange mass, energy and information with its environment. Free radicals are generated in response to perturbations in the relationship between a living system and its environment. However, evolution has selected for biological response systems to free radicals so that the cellular biochemistry can adapt to environmental perturbations by modifying cellular gene expression and biochemistry. Endocannabinoids are marijuana-like compounds that have their origins hundreds of millions of years in the evolutionary past. They serve as fundamental modulators of energy homeostasis in all vertebrates. Their widespread biological activities may often be attributed to their ability to minimize the negative consequences of free radicals.

Effect of entropy on anomalous transport in ITG-modes of magneto-plasma

NASA Astrophysics Data System (ADS)

Yaqub Khan, M.; Qaiser Manzoor, M.; Haq, A. ul; Iqbal, J.

2017-04-01

The ideal gas equation and S={{c}v}log ≤ft(P/ρ \\right) (where S is entropy, P is pressure and ρ is the mass density) define the interconnection of entropy with the temperature and density of plasma. Therefore, different phenomena relating to plasma and entropy need to be investigated. By employing the Braginskii transport equations for a nonuniform electron-ion magnetoplasma, two new parameters—the entropy distribution function and the entropy gradient drift—are defined, a new dispersion relation is obtained, and the dependence of anomalous transport on entropy is also proved. Some results, like monotonicity, the entropy principle and the second law of thermodynamics, are proved with a new definition of entropy. This work will open new horizons in fusion processes, not only by controlling entropy in tokamak plasmas—particularly in the pedestal regions of the H-mode and space plasmas—but also in engineering sciences.

Quantifying and minimizing entropy generation in AMTEC cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hendricks, T.J.; Huang, C.

1997-12-31

Entropy generation in an AMTEC cell represents inherent power loss to the AMTEC cell. Minimizing cell entropy generation directly maximizes cell power generation and efficiency. An internal project is on-going at AMPS to identify, quantify and minimize entropy generation mechanisms within an AMTEC cell, with the goal of determining cost-effective design approaches for maximizing AMTEC cell power generation. Various entropy generation mechanisms have been identified and quantified. The project has investigated several cell design techniques in a solar-driven AMTEC system to minimize cell entropy generation and produce maximum power cell designs. In many cases, various sources of entropy generation aremore » interrelated such that minimizing entropy generation requires cell and system design optimization. Some of the tradeoffs between various entropy generation mechanisms are quantified and explained and their implications on cell design are discussed. The relationship between AMTEC cell power and efficiency and entropy generation is presented and discussed.« less

Hemodynamic Response to Interictal Epileptiform Discharges Addressed by Personalized EEG-fNIRS Recordings

PubMed Central

Pellegrino, Giovanni; Machado, Alexis; von Ellenrieder, Nicolas; Watanabe, Satsuki; Hall, Jeffery A.; Lina, Jean-Marc; Kobayashi, Eliane; Grova, Christophe

2016-01-01

Objective: We aimed at studying the hemodynamic response (HR) to Interictal Epileptic Discharges (IEDs) using patient-specific and prolonged simultaneous ElectroEncephaloGraphy (EEG) and functional Near InfraRed Spectroscopy (fNIRS) recordings. Methods: The epileptic generator was localized using Magnetoencephalography source imaging. fNIRS montage was tailored for each patient, using an algorithm to optimize the sensitivity to the epileptic generator. Optodes were glued using collodion to achieve prolonged acquisition with high quality signal. fNIRS data analysis was handled with no a priori constraint on HR time course, averaging fNIRS signals to similar IEDs. Cluster-permutation analysis was performed on 3D reconstructed fNIRS data to identify significant spatio-temporal HR clusters. Standard (GLM with fixed HRF) and cluster-permutation EEG-fMRI analyses were performed for comparison purposes. Results: fNIRS detected HR to IEDs for 8/9 patients. It mainly consisted oxy-hemoglobin increases (seven patients), followed by oxy-hemoglobin decreases (six patients). HR was lateralized in six patients and lasted from 8.5 to 30 s. Standard EEG-fMRI analysis detected an HR in 4/9 patients (4/9 without enough IEDs, 1/9 unreliable result). The cluster-permutation EEG-fMRI analysis restricted to the region investigated by fNIRS showed additional strong and non-canonical BOLD responses starting earlier than the IEDs and lasting up to 30 s. Conclusions: (i) EEG-fNIRS is suitable to detect the HR to IEDs and can outperform EEG-fMRI because of prolonged recordings and greater chance to detect IEDs; (ii) cluster-permutation analysis unveils additional HR features underestimated when imposing a canonical HR function (iii) the HR is often bilateral and lasts up to 30 s. PMID:27047325

Quantile-based permutation thresholds for quantitative trait loci hotspots.

PubMed

Neto, Elias Chaibub; Keller, Mark P; Broman, Andrew F; Attie, Alan D; Jansen, Ritsert C; Broman, Karl W; Yandell, Brian S

2012-08-01

Quantitative trait loci (QTL) hotspots (genomic locations affecting many traits) are a common feature in genetical genomics studies and are biologically interesting since they may harbor critical regulators. Therefore, statistical procedures to assess the significance of hotspots are of key importance. One approach, randomly allocating observed QTL across the genomic locations separately by trait, implicitly assumes all traits are uncorrelated. Recently, an empirical test for QTL hotspots was proposed on the basis of the number of traits that exceed a predetermined LOD value, such as the standard permutation LOD threshold. The permutation null distribution of the maximum number of traits across all genomic locations preserves the correlation structure among the phenotypes, avoiding the detection of spurious hotspots due to nongenetic correlation induced by uncontrolled environmental factors and unmeasured variables. However, by considering only the number of traits above a threshold, without accounting for the magnitude of the LOD scores, relevant information is lost. In particular, biologically interesting hotspots composed of a moderate to small number of traits with strong LOD scores may be neglected as nonsignificant. In this article we propose a quantile-based permutation approach that simultaneously accounts for the number and the LOD scores of traits within the hotspots. By considering a sliding scale of mapping thresholds, our method can assess the statistical significance of both small and large hotspots. Although the proposed approach can be applied to any type of heritable high-volume "omic" data set, we restrict our attention to expression (e)QTL analysis. We assess and compare the performances of these three methods in simulations and we illustrate how our approach can effectively assess the significance of moderate and small hotspots with strong LOD scores in a yeast expression data set.

Thermodynamic and Differential Entropy under a Change of Variables

PubMed Central

Hnizdo, Vladimir; Gilson, Michael K.

2013-01-01

The differential Shannon entropy of information theory can change under a change of variables (coordinates), but the thermodynamic entropy of a physical system must be invariant under such a change. This difference is puzzling, because the Shannon and Gibbs entropies have the same functional form. We show that a canonical change of variables can, indeed, alter the spatial component of the thermodynamic entropy just as it alters the differential Shannon entropy. However, there is also a momentum part of the entropy, which turns out to undergo an equal and opposite change when the coordinates are transformed, so that the total thermodynamic entropy remains invariant. We furthermore show how one may correctly write the change in total entropy for an isothermal physical process in any set of spatial coordinates. PMID:24436633

Entropy for Mechanically Vibrating Systems

NASA Astrophysics Data System (ADS)

Tufano, Dante

The research contained within this thesis deals with the subject of entropy as defined for and applied to mechanically vibrating systems. This work begins with an overview of entropy as it is understood in the fields of classical thermodynamics, information theory, statistical mechanics, and statistical vibroacoustics. Khinchin's definition of entropy, which is the primary definition used for the work contained in this thesis, is introduced in the context of vibroacoustic systems. The main goal of this research is to to establish a mathematical framework for the application of Khinchin's entropy in the field of statistical vibroacoustics by examining the entropy context of mechanically vibrating systems. The introduction of this thesis provides an overview of statistical energy analysis (SEA), a modeling approach to vibroacoustics that motivates this work on entropy. The objective of this thesis is given, and followed by a discussion of the intellectual merit of this work as well as a literature review of relevant material. Following the introduction, an entropy analysis of systems of coupled oscillators is performed utilizing Khinchin's definition of entropy. This analysis develops upon the mathematical theory relating to mixing entropy, which is generated by the coupling of vibroacoustic systems. The mixing entropy is shown to provide insight into the qualitative behavior of such systems. Additionally, it is shown that the entropy inequality property of Khinchin's entropy can be reduced to an equality using the mixing entropy concept. This equality can be interpreted as a facet of the second law of thermodynamics for vibroacoustic systems. Following this analysis, an investigation of continuous systems is performed using Khinchin's entropy. It is shown that entropy analyses using Khinchin's entropy are valid for continuous systems that can be decomposed into a finite number of modes. The results are shown to be analogous to those obtained for simple oscillators, which demonstrates the applicability of entropy-based approaches to real-world systems. Three systems are considered to demonstrate these findings: 1) a rod end-coupled to a simple oscillator, 2) two end-coupled rods, and 3) two end-coupled beams. The aforementioned work utilizes the weak coupling assumption to determine the entropy of composite systems. Following this discussion, a direct method of finding entropy is developed which does not rely on this limiting assumption. The resulting entropy provides a useful benchmark for evaluating the accuracy of the weak coupling approach, and is validated using systems of coupled oscillators. The later chapters of this work discuss Khinchin's entropy as applied to nonlinear and nonconservative systems, respectively. The discussion of entropy for nonlinear systems is motivated by the desire to expand the applicability of SEA techniques beyond the linear regime. The discussion of nonconservative systems is also crucial, since real-world systems interact with their environment, and it is necessary to confirm the validity of an entropy approach for systems that are relevant in the context of SEA. Having developed a mathematical framework for determining entropy under a number of previously unexplored cases, the relationship between thermodynamics and statistical vibroacoustics can be better understood. Specifically, vibroacoustic temperatures can be obtained for systems that are not necessarily linear or weakly coupled. In this way, entropy provides insight into how the power flow proportionality of statistical energy analysis (SEA) can be applied to a broader class of vibroacoustic systems. As such, entropy is a useful tool for both justifying and expanding the foundational results of SEA.

Entropy is more resistant to artifacts than bispectral index in brain-dead organ donors.

PubMed

Wennervirta, Johanna; Salmi, Tapani; Hynynen, Markku; Yli-Hankala, Arvi; Koivusalo, Anna-Maria; Van Gils, Mark; Pöyhiä, Reino; Vakkuri, Anne

2007-01-01

To evaluate the usefulness of entropy and the bispectral index (BIS) in brain-dead subjects. A prospective, open, nonselective, observational study in the university hospital. 16 brain-dead organ donors. Time-domain electroencephalography (EEG), spectral entropy of the EEG, and BIS were recorded during solid organ harvest. State entropy differed significantly from 0 (isoelectric EEG) 28%, response entropy 29%, and BIS 68% of the total recorded time. The median values during the operation were state entropy 0.0, response entropy 0.0, and BIS 3.0. In four of 16 organ donors studied the EEG was not isoelectric, and nonreactive rhythmic activity was noted in time-domain EEG. After excluding the results from subjects with persistent residual EEG activity state entropy, response entropy, and BIS values differed from zero 17%, 18%, and 62% of the recorded time, respectively. Median values were 0.0, 0.0, and 2.0 for state entropy, response entropy, and BIS, respectively. The highest index values in entropy and BIS monitoring were recorded without neuromuscular blockade. The main sources of artifacts were electrocauterization, 50-Hz artifact, handling of the donor, ballistocardiography, electromyography, and electrocardiography. Both entropy and BIS showed nonzero values due to artifacts after brain death diagnosis. BIS was more liable to artifacts than entropy. Neither of these indices are diagnostic tools, and care should be taken when interpreting EEG and EEG-derived indices in the evaluation of brain death.

Mathematical investigations of branch length similarity entropy profiles of shapes for various resolutions

NASA Astrophysics Data System (ADS)

Jeon, Wonju; Lee, Sang-Hee

2012-12-01

In our previous study, we defined the branch length similarity (BLS) entropy for a simple network consisting of a single node and numerous branches. As the first application of this entropy to characterize shapes, the BLS entropy profiles of 20 battle tank shapes were calculated from simple networks created by connecting pixels in the boundary of the shape. The profiles successfully characterized the tank shapes through a comparison of their BLS entropy profiles. Following the application, this entropy was used to characterize human's emotional faces, such as happiness and sad, and to measure the degree of complexity for termite tunnel networks. These applications indirectly indicate that the BLS entropy profile can be a useful tool to characterize networks and shapes. However, the ability of the BLS entropy in the characterization depends on the image resolution because the entropy is determined by the number of nodes for the boundary of a shape. Higher resolution means more nodes. If the entropy is to be widely used in the scientific community, the effect of the resolution on the entropy profile should be understood. In the present study, we mathematically investigated the BLS entropy profile of a shape with infinite resolution and numerically investigated the variation in the pattern of the entropy profile caused by changes in the resolution change in the case of finite resolution.

A diameter-sensitive flow entropy method for reliability consideration in water distribution system design

NASA Astrophysics Data System (ADS)

Liu, Haixing; Savić, Dragan; Kapelan, Zoran; Zhao, Ming; Yuan, Yixing; Zhao, Hongbin

2014-07-01

Flow entropy is a measure of uniformity of pipe flows in water distribution systems. By maximizing flow entropy one can identify reliable layouts or connectivity in networks. In order to overcome the disadvantage of the common definition of flow entropy that does not consider the impact of pipe diameter on reliability, an extended definition of flow entropy, termed as diameter-sensitive flow entropy, is proposed. This new methodology is then assessed by using other reliability methods, including Monte Carlo Simulation, a pipe failure probability model, and a surrogate measure (resilience index) integrated with water demand and pipe failure uncertainty. The reliability assessment is based on a sample of WDS designs derived from an optimization process for each of the two benchmark networks. Correlation analysis is used to evaluate quantitatively the relationship between entropy and reliability. To ensure reliability, a comparative analysis between the flow entropy and the new method is conducted. The results demonstrate that the diameter-sensitive flow entropy shows consistently much stronger correlation with the three reliability measures than simple flow entropy. Therefore, the new flow entropy method can be taken as a better surrogate measure for reliability and could be potentially integrated into the optimal design problem of WDSs. Sensitivity analysis results show that the velocity parameters used in the new flow entropy has no significant impact on the relationship between diameter-sensitive flow entropy and reliability.

Entropy generation of nanofluid flow in a microchannel heat sink

NASA Astrophysics Data System (ADS)

Manay, Eyuphan; Akyürek, Eda Feyza; Sahin, Bayram

2018-06-01

Present study aims to investigate the effects of the presence of nano sized TiO2 particles in the base fluid on entropy generation rate in a microchannel heat sink. Pure water was chosen as base fluid, and TiO2 particles were suspended into the pure water in five different particle volume fractions of 0.25%, 0.5%, 1.0%, 1.5% and 2.0%. Under laminar, steady state flow and constant heat flux boundary conditions, thermal, frictional, total entropy generation rates and entropy generation number ratios of nanofluids were experimentally analyzed in microchannel flow for different channel heights of 200 μm, 300 μm, 400 μm and 500 μm. It was observed that frictional and total entropy generation rates increased as thermal entropy generation rate were decreasing with an increase in particle volume fraction. In microchannel flows, thermal entropy generation could be neglected due to its too low rate smaller than 1.10e-07 in total entropy generation. Higher channel heights caused higher thermal entropy generation rates, and increasing channel height yielded an increase from 30% to 52% in thermal entropy generation. When channel height decreased, an increase of 66%-98% in frictional entropy generation was obtained. Adding TiO2 nanoparticles into the base fluid caused thermal entropy generation to decrease about 1.8%-32.4%, frictional entropy generation to increase about 3.3%-21.6%.

Entropy and entropy production in Fokker–Plank equation under the generalized fluctuation–dissipation relation

NASA Astrophysics Data System (ADS)

Guo, Ran

2018-04-01

In this paper, we investigate the definition of the entropy in the Fokker–Planck equation under the generalized fluctuation–dissipation relation (FDR), which describes a Brownian particle moving in a complex medium with friction and multiplicative noise. The friction and the noise are related by the generalized FDR. The entropy for such a system is defined first. According to the definition of the entropy, we calculate the entropy production and the entropy flux. Lastly, we make a numerical calculation to display the results in figures.

Single water entropy: hydrophobic crossover and application to drug binding.

PubMed

Sasikala, Wilbee D; Mukherjee, Arnab

2014-09-11

Entropy of water plays an important role in both chemical and biological processes e.g. hydrophobic effect, molecular recognition etc. Here we use a new approach to calculate translational and rotational entropy of the individual water molecules around different hydrophobic and charged solutes. We show that for small hydrophobic solutes, the translational and rotational entropies of each water molecule increase as a function of its distance from the solute reaching finally to a constant bulk value. As the size of the solute increases (0.746 nm), the behavior of the translational entropy is opposite; water molecules closest to the solute have higher entropy that reduces with distance from the solute. This indicates that there is a crossover in translational entropy of water molecules around hydrophobic solutes from negative to positive values as the size of the solute is increased. Rotational entropy of water molecules around hydrophobic solutes for all sizes increases with distance from the solute, indicating the absence of crossover in rotational entropy. This makes the crossover in total entropy (translation + rotation) of water molecule happen at much larger size (>1.5 nm) for hydrophobic solutes. Translational entropy of single water molecule scales logarithmically (Str(QH) = C + kB ln V), with the volume V obtained from the ellipsoid of inertia. We further discuss the origin of higher entropy of water around water and show the possibility of recovering the entropy loss of some hypothetical solutes. The results obtained are helpful to understand water entropy behavior around various hydrophobic and charged environments within biomolecules. Finally, we show how our approach can be used to calculate the entropy of the individual water molecules in a protein cavity that may be replaced during ligand binding.

RNA Thermodynamic Structural Entropy

PubMed Central

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner’99 and Turner’04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs. PMID:26555444

RNA Thermodynamic Structural Entropy.

PubMed

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs.

Relating different quantum generalizations of the conditional Rényi entropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tomamichel, Marco; School of Physics, The University of Sydney, Sydney 2006; Berta, Mario

2014-08-15

Recently a new quantum generalization of the Rényi divergence and the corresponding conditional Rényi entropies was proposed. Here, we report on a surprising relation between conditional Rényi entropies based on this new generalization and conditional Rényi entropies based on the quantum relative Rényi entropy that was used in previous literature. Our result generalizes the well-known duality relation H(A|B) + H(A|C) = 0 of the conditional von Neumann entropy for tripartite pure states to Rényi entropies of two different kinds. As a direct application, we prove a collection of inequalities that relate different conditional Rényi entropies and derive a new entropicmore » uncertainty relation.« less

Exact analytical thermodynamic expressions for a Brownian heat engine

NASA Astrophysics Data System (ADS)

Taye, Mesfin Asfaw

2015-09-01

The nonequilibrium thermodynamics feature of a Brownian motor operating between two different heat baths is explored as a function of time t . Using the Gibbs entropy and Schnakenberg microscopic stochastic approach, we find exact closed form expressions for the free energy, the rate of entropy production, and the rate of entropy flow from the system to the outside. We show that when the system is out of equilibrium, it constantly produces entropy and at the same time extracts entropy out of the system. Its entropy production and extraction rates decrease in time and saturate to a constant value. In the long time limit, the rate of entropy production balances the rate of entropy extraction, and at equilibrium both entropy production and extraction rates become zero. Furthermore, via the present model, many thermodynamic theories can be checked.

Exact analytical thermodynamic expressions for a Brownian heat engine.

PubMed

Taye, Mesfin Asfaw

2015-09-01

The nonequilibrium thermodynamics feature of a Brownian motor operating between two different heat baths is explored as a function of time t. Using the Gibbs entropy and Schnakenberg microscopic stochastic approach, we find exact closed form expressions for the free energy, the rate of entropy production, and the rate of entropy flow from the system to the outside. We show that when the system is out of equilibrium, it constantly produces entropy and at the same time extracts entropy out of the system. Its entropy production and extraction rates decrease in time and saturate to a constant value. In the long time limit, the rate of entropy production balances the rate of entropy extraction, and at equilibrium both entropy production and extraction rates become zero. Furthermore, via the present model, many thermodynamic theories can be checked.

A PSO-Based Hybrid Metaheuristic for Permutation Flowshop Scheduling Problems

PubMed Central

Zhang, Le; Wu, Jinnan

2014-01-01

This paper investigates the permutation flowshop scheduling problem (PFSP) with the objectives of minimizing the makespan and the total flowtime and proposes a hybrid metaheuristic based on the particle swarm optimization (PSO). To enhance the exploration ability of the hybrid metaheuristic, a simulated annealing hybrid with a stochastic variable neighborhood search is incorporated. To improve the search diversification of the hybrid metaheuristic, a solution replacement strategy based on the pathrelinking is presented to replace the particles that have been trapped in local optimum. Computational results on benchmark instances show that the proposed PSO-based hybrid metaheuristic is competitive with other powerful metaheuristics in the literature. PMID:24672389