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.

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 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

A Space–Time Permutation Scan Statistic for Disease Outbreak Detection

PubMed Central

Kulldorff, Martin; Heffernan, Richard; Hartman, Jessica; Assunção, Renato; Mostashari, Farzad

2005-01-01

Background The ability to detect disease outbreaks early is important in order to minimize morbidity and mortality through timely implementation of disease prevention and control measures. Many national, state, and local health departments are launching disease surveillance systems with daily analyses of hospital emergency department visits, ambulance dispatch calls, or pharmacy sales for which population-at-risk information is unavailable or irrelevant. Methods and Findings We propose a prospective space–time permutation scan statistic for the early detection of disease outbreaks that uses only case numbers, with no need for population-at-risk data. It makes minimal assumptions about the time, geographical location, or size of the outbreak, and it adjusts for natural purely spatial and purely temporal variation. The new method was evaluated using daily analyses of hospital emergency department visits in New York City. Four of the five strongest signals were likely local precursors to citywide outbreaks due to rotavirus, norovirus, and influenza. The number of false signals was at most modest. Conclusion If such results hold up over longer study times and in other locations, the space–time permutation scan statistic will be an important tool for local and national health departments that are setting up early disease detection surveillance systems. PMID:15719066

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.

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.

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

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

A PSO-based hybrid metaheuristic for permutation flowshop scheduling problems.

PubMed

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.

Palmprint verification using Lagrangian decomposition and invariant interest points

NASA Astrophysics Data System (ADS)

Gupta, P.; Rattani, A.; Kisku, D. R.; Hwang, C. J.; Sing, J. K.

2011-06-01

This paper presents a palmprint based verification system using SIFT features and Lagrangian network graph technique. We employ SIFT for feature extraction from palmprint images whereas the region of interest (ROI) which has been extracted from wide palm texture at the preprocessing stage, is considered for invariant points extraction. Finally, identity is established by finding permutation matrix for a pair of reference and probe palm graphs drawn on extracted SIFT features. Permutation matrix is used to minimize the distance between two graphs. The propsed system has been tested on CASIA and IITK palmprint databases and experimental results reveal the effectiveness and robustness of the system.

Effectiveness of qPCR permutations, internal controls and dilution as means for minimizing the impact of inhibition while measuring Enterococcus in environmental waters.

PubMed

Cao, Y; Griffith, J F; Dorevitch, S; Weisberg, S B

2012-07-01

  Draft criteria for the optional use of qPCR for recreational water quality monitoring have been published in the United States. One concern is that inhibition of the qPCR assay can lead to false-negative results and potentially inadequate public health protection. We evaluate the effectiveness of strategies for minimizing the impact of inhibition.   Five qPCR method permutations for measuring Enterococcus were challenged with 133 potentially inhibitory fresh and marine water samples. Serial dilutions were conducted to assess Enterococcus target assay inhibition, to which inhibition identified using four internal controls (IC) was compared. The frequency and magnitude of inhibition varied considerably among qPCR methods, with the permutation using an environmental master mix performing substantially better. Fivefold dilution was also effective at reducing inhibition in most samples (>78%). ICs were variable and somewhat ineffective, with 54-85% agreement between ICs and serial dilution.   The current IC methods appear to not accurately predict Enterococcus inhibition and should be used with caution; fivefold dilution and the use of reagents designed for environmental sample analysis (i.e. more robust qPCR chemistry) may be preferable.   Suitable approaches for defining, detecting and reducing inhibition will improve implementation of qPCR for water monitoring. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

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.

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.

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

Ferré, Grégoire; Maillet, Jean-Bernard; Stoltz, Gabriel

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 frameworkmore » 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.« less

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

Automatic event detection in low SNR microseismic signals based on multi-scale permutation entropy and a support vector machine

NASA Astrophysics Data System (ADS)

Jia, Rui-Sheng; Sun, Hong-Mei; Peng, Yan-Jun; Liang, Yong-Quan; Lu, Xin-Ming

2017-07-01

Microseismic monitoring is an effective means for providing early warning of rock or coal dynamical disasters, and its first step is microseismic event detection, although low SNR microseismic signals often cannot effectively be detected by routine methods. To solve this problem, this paper presents permutation entropy and a support vector machine to detect low SNR microseismic events. First, an extraction method of signal features based on multi-scale permutation entropy is proposed by studying the influence of the scale factor on the signal permutation entropy. Second, the detection model of low SNR microseismic events based on the least squares support vector machine is built by performing a multi-scale permutation entropy calculation for the collected vibration signals, constructing a feature vector set of signals. Finally, a comparative analysis of the microseismic events and noise signals in the experiment proves that the different characteristics of the two can be fully expressed by using multi-scale permutation entropy. The detection model of microseismic events combined with the support vector machine, which has the features of high classification accuracy and fast real-time algorithms, can meet the requirements of online, real-time extractions of microseismic events.

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

Multi-target detection and positioning in crowds using multiple camera surveillance

NASA Astrophysics Data System (ADS)

Huang, Jiahu; Zhu, Qiuyu; Xing, Yufeng

2018-04-01

In this study, we propose a pixel correspondence algorithm for positioning in crowds based on constraints on the distance between lines of sight, grayscale differences, and height in a world coordinates system. First, a Gaussian mixture model is used to obtain the background and foreground from multi-camera videos. Second, the hair and skin regions are extracted as regions of interest. Finally, the correspondences between each pixel in the region of interest are found under multiple constraints and the targets are positioned by pixel clustering. The algorithm can provide appropriate redundancy information for each target, which decreases the risk of losing targets due to a large viewing angle and wide baseline. To address the correspondence problem for multiple pixels, we construct a pixel-based correspondence model based on a similar permutation matrix, which converts the correspondence problem into a linear programming problem where a similar permutation matrix is found by minimizing an objective function. The correct pixel correspondences can be obtained by determining the optimal solution of this linear programming problem and the three-dimensional position of the targets can also be obtained by pixel clustering. Finally, we verified the algorithm with multiple cameras in experiments, which showed that the algorithm has high accuracy and robustness.

The Poincaré Half-Plane for Informationally-Complete POVMs

NASA Astrophysics Data System (ADS)

Planat, Michel

2017-12-01

It has been shown that classes of (minimal asymmetric) informationally complete POVMs in dimension d can be built using the multiparticle Pauli group acting on appropriate fiducial states [M. Planat and Z. Gedik, R. Soc. open sci. 4, 170387 (2017)]. The latter states may also be derived starting from the Poincar\\'e upper half-plane model H. For doing this, one translates the congruence (or non-congruence) subgroups of index d of the modular group into groups of permutation gates whose some of the eigenstates are the seeked fiducials. The structure of some IC-POVMs is found to be intimately related to the Kochen-Specker theorem.

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.

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.

A Spectral Algorithm for Envelope Reduction of Sparse Matrices

NASA Technical Reports Server (NTRS)

Barnard, Stephen T.; Pothen, Alex; Simon, Horst D.

1993-01-01

The problem of reordering a sparse symmetric matrix to reduce its envelope size is considered. A new spectral algorithm for computing an envelope-reducing reordering is obtained by associating a Laplacian matrix with the given matrix and then sorting the components of a specified eigenvector of the Laplacian. This Laplacian eigenvector solves a continuous relaxation of a discrete problem related to envelope minimization called the minimum 2-sum problem. The permutation vector computed by the spectral algorithm is a closest permutation vector to the specified Laplacian eigenvector. Numerical results show that the new reordering algorithm usually computes smaller envelope sizes than those obtained from the current standard algorithms such as Gibbs-Poole-Stockmeyer (GPS) or SPARSPAK reverse Cuthill-McKee (RCM), in some cases reducing the envelope by more than a factor of two.

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.

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.

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.

Communication: Fitting potential energy surfaces with fundamental invariant neural network

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

Shao, Kejie; Chen, Jun; Zhao, Zhiqiang

A more flexible neural network (NN) method using the fundamental invariants (FIs) as the input vector is proposed in the construction of potential energy surfaces for molecular systems involving identical atoms. Mathematically, FIs finitely generate the permutation invariant polynomial (PIP) ring. In combination with NN, fundamental invariant neural network (FI-NN) can approximate any function to arbitrary accuracy. Because FI-NN minimizes the size of input permutation invariant polynomials, it can efficiently reduce the evaluation time of potential energy, in particular for polyatomic systems. In this work, we provide the FIs for all possible molecular systems up to five atoms. Potential energymore » surfaces for OH{sub 3} and CH{sub 4} were constructed with FI-NN, with the accuracy confirmed by full-dimensional quantum dynamic scattering and bound state calculations.« less

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…

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).

Weighted fractional permutation entropy and fractional sample entropy for nonlinear Potts financial dynamics

NASA Astrophysics Data System (ADS)

Xu, Kaixuan; Wang, Jun

2017-02-01

In this paper, recently introduced permutation entropy and sample entropy are further developed to the fractional cases, weighted fractional permutation entropy (WFPE) and fractional sample entropy (FSE). The fractional order generalization of information entropy is utilized in the above two complexity approaches, to detect the statistical characteristics of fractional order information in complex systems. The effectiveness analysis of proposed methods on the synthetic data and the real-world data reveals that tuning the fractional order allows a high sensitivity and more accurate characterization to the signal evolution, which is useful in describing the dynamics of complex systems. Moreover, the numerical research on nonlinear complexity behaviors is compared between the returns series of Potts financial model and the actual stock markets. And the empirical results confirm the feasibility of the proposed model.

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.

Anatomy of a Hotspot: Chain and Seroepidemiology of Ebola Virus Transmission, Sukudu, Sierra Leone, 2015-16.

PubMed

Kelly, J Daniel; Barrie, Mohamed Bailor; Mesman, Annelies W; Karku, Sahr; Quiwa, Komba; Drasher, Michael; Schlough, Gabriel Warren; Dierberg, Kerry; Koedoyoma, Songor; Lindan, Christina P; Jones, James Holland; Chamie, Gabriel; Worden, Lee; Greenhouse, Bryan; Weiser, Sheri D; Porco, Travis C; Rutherford, George W; Richardson, Eugene T

2018-03-28

Studies have yet to include minimally symptomatic Ebola virus (EBOV) infections and unrecognized Ebola virus disease (EVD) in Ebola-related transmission chains and epidemiologic risk estimates. We conducted a cross-sectional, sero-epidemiological survey from October 2015 to January 2016 among 221 individuals living in quarantined households from November 2014 to February 2015 during the Ebola outbreak in the village of Sukudu, Sierra Leone. Of 48 EBOV-infected persons, 25% (95% confidence interval [CI], 14%-40%) had minimally symptomatic EBOV infections and 4% (95% CI, 1%-14%) were unrecognized EVD cases. The pattern of minimally symptomatic EBOV infections in the transmission chain was nonrandom (P < .001, permutation test). Not having lived in the same house as an EVD case was significantly associated with minimally symptomatic infection. This is the first study to investigate a chain of EBOV transmission inclusive of minimally symptomatic EBOV infections and unrecognized EVD. Our findings provide new insights into Ebola transmission dynamics and quarantine practices.

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

Tensor models, Kronecker coefficients and permutation centralizer algebras

NASA Astrophysics Data System (ADS)

Geloun, Joseph Ben; Ramgoolam, Sanjaye

2017-11-01

We show that the counting of observables and correlators for a 3-index tensor model are organized by the structure of a family of permutation centralizer algebras. These algebras are shown to be semi-simple and their Wedderburn-Artin decompositions into matrix blocks are given in terms of Clebsch-Gordan coefficients of symmetric groups. The matrix basis for the algebras also gives an orthogonal basis for the tensor observables which diagonalizes the Gaussian two-point functions. The centres of the algebras are associated with correlators which are expressible in terms of Kronecker coefficients (Clebsch-Gordan multiplicities of symmetric groups). The color-exchange symmetry present in the Gaussian model, as well as a large class of interacting models, is used to refine the description of the permutation centralizer algebras. This discussion is extended to a general number of colors d: it is used to prove the integrality of an infinite family of number sequences related to color-symmetrizations of colored graphs, and expressible in terms of symmetric group representation theory data. Generalizing a connection between matrix models and Belyi maps, correlators in Gaussian tensor models are interpreted in terms of covers of singular 2-complexes. There is an intriguing difference, between matrix and higher rank tensor models, in the computational complexity of superficially comparable correlators of observables parametrized by Young diagrams.

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.

Improved Potential Energy Surface of Ozone Constructed Using the Fitting by Permutationally Invariant Polynomial Function

DOE PAGES

Ayouz, Mehdi; Babikov, Dmitri

2012-01-01

New global potential energy surface for the ground electronic state of ozone is constructed at the complete basis set level of the multireference configuration interaction theory. A method of fitting the data points by analytical permutationally invariant polynomial function is adopted. A small set of 500 points is preoptimized using the old surface of ozone. In this procedure the positions of points in the configuration space are chosen such that the RMS deviation of the fit is minimized. New ab initio calculations are carried out at these points and are used to build new surface. Additional points are added tomore » the vicinity of the minimum energy path in order to improve accuracy of the fit, particularly in the region where the surface of ozone exhibits a shallow van der Waals well. New surface can be used to study formation of ozone at thermal energies and its spectroscopy near the dissociation threshold.« less

Graph Matching: Relax at Your Own Risk.

PubMed

Lyzinski, Vince; Fishkind, Donniell E; Fiori, Marcelo; Vogelstein, Joshua T; Priebe, Carey E; Sapiro, Guillermo

2016-01-01

Graph matching-aligning a pair of graphs to minimize their edge disagreements-has received wide-spread attention from both theoretical and applied communities over the past several decades, including combinatorics, computer vision, and connectomics. Its attention can be partially attributed to its computational difficulty. Although many heuristics have previously been proposed in the literature to approximately solve graph matching, very few have any theoretical support for their performance. A common technique is to relax the discrete problem to a continuous problem, therefore enabling practitioners to bring gradient-descent-type algorithms to bear. We prove that an indefinite relaxation (when solved exactly) almost always discovers the optimal permutation, while a common convex relaxation almost always fails to discover the optimal permutation. These theoretical results suggest that initializing the indefinite algorithm with the convex optimum might yield improved practical performance. Indeed, experimental results illuminate and corroborate these theoretical findings, demonstrating that excellent results are achieved in both benchmark and real data problems by amalgamating the two approaches.

Design of a magnetic-tunnel-junction-oriented nonvolatile lookup table circuit with write-operation-minimized data shifting

NASA Astrophysics Data System (ADS)

Suzuki, Daisuke; Hanyu, Takahiro

2018-04-01

A magnetic-tunnel-junction (MTJ)-oriented nonvolatile lookup table (LUT) circuit, in which a low-power data-shift function is performed by minimizing the number of write operations in MTJ devices is proposed. The permutation of the configuration memory cell for read/write access is performed as opposed to conventional direct data shifting to minimize the number of write operations, which results in significant write energy savings in the data-shift function. Moreover, the hardware cost of the proposed LUT circuit is small since the selector is shared between read access and write access. In fact, the power consumption in the data-shift function and the transistor count are reduced by 82 and 52%, respectively, compared with those in a conventional static random-access memory-based implementation using a 90 nm CMOS technology.

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.

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.

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 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.

A Comparison of Multiscale Permutation Entropy Measures in On-Line Depth of Anesthesia Monitoring

PubMed Central

Li, Xiaoli; Li, Duan; Li, Yongwang; Ursino, Mauro

2016-01-01

Objective Multiscale permutation entropy (MSPE) is becoming an interesting tool to explore neurophysiological mechanisms in recent years. In this study, six MSPE measures were proposed for on-line depth of anesthesia (DoA) monitoring to quantify the anesthetic effect on the real-time EEG recordings. The performance of these measures in describing the transient characters of simulated neural populations and clinical anesthesia EEG were evaluated and compared. Methods Six MSPE algorithms—derived from Shannon permutation entropy (SPE), Renyi permutation entropy (RPE) and Tsallis permutation entropy (TPE) combined with the decomposition procedures of coarse-graining (CG) method and moving average (MA) analysis—were studied. A thalamo-cortical neural mass model (TCNMM) was used to generate noise-free EEG under anesthesia to quantitatively assess the robustness of each MSPE measure against noise. Then, the clinical anesthesia EEG recordings from 20 patients were analyzed with these measures. To validate their effectiveness, the ability of six measures were compared in terms of tracking the dynamical changes in EEG data and the performance in state discrimination. The Pearson correlation coefficient (R) was used to assess the relationship among MSPE measures. Results CG-based MSPEs failed in on-line DoA monitoring at multiscale analysis. In on-line EEG analysis, the MA-based MSPE measures at 5 decomposed scales could track the transient changes of EEG recordings and statistically distinguish the awake state, unconsciousness and recovery of consciousness (RoC) state significantly. Compared to single-scale SPE and RPE, MSPEs had better anti-noise ability and MA-RPE at scale 5 performed best in this aspect. MA-TPE outperformed other measures with faster tracking speed of the loss of unconsciousness. Conclusions MA-based multiscale permutation entropies have the potential for on-line anesthesia EEG analysis with its simple computation and sensitivity to drug effect changes. CG-based multiscale permutation entropies may fail to describe the characteristics of EEG at high decomposition scales. PMID:27723803

A Comparison of Multiscale Permutation Entropy Measures in On-Line Depth of Anesthesia Monitoring.

PubMed

Su, Cui; Liang, Zhenhu; Li, Xiaoli; Li, Duan; Li, Yongwang; Ursino, Mauro

2016-01-01

Multiscale permutation entropy (MSPE) is becoming an interesting tool to explore neurophysiological mechanisms in recent years. In this study, six MSPE measures were proposed for on-line depth of anesthesia (DoA) monitoring to quantify the anesthetic effect on the real-time EEG recordings. The performance of these measures in describing the transient characters of simulated neural populations and clinical anesthesia EEG were evaluated and compared. Six MSPE algorithms-derived from Shannon permutation entropy (SPE), Renyi permutation entropy (RPE) and Tsallis permutation entropy (TPE) combined with the decomposition procedures of coarse-graining (CG) method and moving average (MA) analysis-were studied. A thalamo-cortical neural mass model (TCNMM) was used to generate noise-free EEG under anesthesia to quantitatively assess the robustness of each MSPE measure against noise. Then, the clinical anesthesia EEG recordings from 20 patients were analyzed with these measures. To validate their effectiveness, the ability of six measures were compared in terms of tracking the dynamical changes in EEG data and the performance in state discrimination. The Pearson correlation coefficient (R) was used to assess the relationship among MSPE measures. CG-based MSPEs failed in on-line DoA monitoring at multiscale analysis. In on-line EEG analysis, the MA-based MSPE measures at 5 decomposed scales could track the transient changes of EEG recordings and statistically distinguish the awake state, unconsciousness and recovery of consciousness (RoC) state significantly. Compared to single-scale SPE and RPE, MSPEs had better anti-noise ability and MA-RPE at scale 5 performed best in this aspect. MA-TPE outperformed other measures with faster tracking speed of the loss of unconsciousness. MA-based multiscale permutation entropies have the potential for on-line anesthesia EEG analysis with its simple computation and sensitivity to drug effect changes. CG-based multiscale permutation entropies may fail to describe the characteristics of EEG at high decomposition scales.

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.

A New Model for Solving Time-Cost-Quality Trade-Off Problems in Construction

PubMed Central

Fu, Fang; Zhang, Tao

2016-01-01

A poor quality affects project makespan and its total costs negatively, but it can be recovered by repair works during construction. We construct a new non-linear programming model based on the classic multi-mode resource constrained project scheduling problem considering repair works. In order to obtain satisfactory quality without a high increase of project cost, the objective is to minimize total quality cost which consists of the prevention cost and failure cost according to Quality-Cost Analysis. A binary dependent normal distribution function is adopted to describe the activity quality; Cumulative quality is defined to determine whether to initiate repair works, according to the different relationships among activity qualities, namely, the coordinative and precedence relationship. Furthermore, a shuffled frog-leaping algorithm is developed to solve this discrete trade-off problem based on an adaptive serial schedule generation scheme and adjusted activity list. In the program of the algorithm, the frog-leaping progress combines the crossover operator of genetic algorithm and a permutation-based local search. Finally, an example of a construction project for a framed railway overpass is provided to examine the algorithm performance, and it assist in decision making to search for the appropriate makespan and quality threshold with minimal cost. PMID:27911939

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.

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.

Assessing Discriminative Performance at External Validation of Clinical Prediction Models

PubMed Central

Nieboer, Daan; van der Ploeg, Tjeerd; Steyerberg, Ewout W.

2016-01-01

Introduction External validation studies are essential to study the generalizability of prediction models. Recently a permutation test, focusing on discrimination as quantified by the c-statistic, was proposed to judge whether a prediction model is transportable to a new setting. We aimed to evaluate this test and compare it to previously proposed procedures to judge any changes in c-statistic from development to external validation setting. Methods We compared the use of the permutation test to the use of benchmark values of the c-statistic following from a previously proposed framework to judge transportability of a prediction model. In a simulation study we developed a prediction model with logistic regression on a development set and validated them in the validation set. We concentrated on two scenarios: 1) the case-mix was more heterogeneous and predictor effects were weaker in the validation set compared to the development set, and 2) the case-mix was less heterogeneous in the validation set and predictor effects were identical in the validation and development set. Furthermore we illustrated the methods in a case study using 15 datasets of patients suffering from traumatic brain injury. Results The permutation test indicated that the validation and development set were homogenous in scenario 1 (in almost all simulated samples) and heterogeneous in scenario 2 (in 17%-39% of simulated samples). Previously proposed benchmark values of the c-statistic and the standard deviation of the linear predictors correctly pointed at the more heterogeneous case-mix in scenario 1 and the less heterogeneous case-mix in scenario 2. Conclusion The recently proposed permutation test may provide misleading results when externally validating prediction models in the presence of case-mix differences between the development and validation population. To correctly interpret the c-statistic found at external validation it is crucial to disentangle case-mix differences from incorrect regression coefficients. PMID:26881753

Assessing Discriminative Performance at External Validation of Clinical Prediction Models.

PubMed

Nieboer, Daan; van der Ploeg, Tjeerd; Steyerberg, Ewout W

2016-01-01

External validation studies are essential to study the generalizability of prediction models. Recently a permutation test, focusing on discrimination as quantified by the c-statistic, was proposed to judge whether a prediction model is transportable to a new setting. We aimed to evaluate this test and compare it to previously proposed procedures to judge any changes in c-statistic from development to external validation setting. We compared the use of the permutation test to the use of benchmark values of the c-statistic following from a previously proposed framework to judge transportability of a prediction model. In a simulation study we developed a prediction model with logistic regression on a development set and validated them in the validation set. We concentrated on two scenarios: 1) the case-mix was more heterogeneous and predictor effects were weaker in the validation set compared to the development set, and 2) the case-mix was less heterogeneous in the validation set and predictor effects were identical in the validation and development set. Furthermore we illustrated the methods in a case study using 15 datasets of patients suffering from traumatic brain injury. The permutation test indicated that the validation and development set were homogenous in scenario 1 (in almost all simulated samples) and heterogeneous in scenario 2 (in 17%-39% of simulated samples). Previously proposed benchmark values of the c-statistic and the standard deviation of the linear predictors correctly pointed at the more heterogeneous case-mix in scenario 1 and the less heterogeneous case-mix in scenario 2. The recently proposed permutation test may provide misleading results when externally validating prediction models in the presence of case-mix differences between the development and validation population. To correctly interpret the c-statistic found at external validation it is crucial to disentangle case-mix differences from incorrect regression coefficients.

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.

Detecting the influence of rare stressors on rare species in Yosemite National Park using a novel stratified permutation test

USGS Publications Warehouse

Matchett, John R.; Stark, Philip B.; Ostoja, Steven M.; Knapp, Roland A.; McKenny, Heather C.; Brooks, Matthew L.; Langford, William T.; Joppa, Lucas N.; Berlow, Eric L.

2015-01-01

Statistical models often use observational data to predict phenomena; however, interpreting model terms to understand their influence can be problematic. This issue poses a challenge in species conservation where setting priorities requires estimating influences of potential stressors using observational data. We present a novel approach for inferring influence of a rare stressor on a rare species by blending predictive models with nonparametric permutation tests. We illustrate the approach with two case studies involving rare amphibians in Yosemite National Park, USA. The endangered frog, Rana sierrae, is known to be negatively impacted by non-native fish, while the threatened toad, Anaxyrus canorus, is potentially affected by packstock. Both stressors and amphibians are rare, occurring in ~10% of potential habitat patches. We first predict amphibian occupancy with a statistical model that includes all predictors but the stressor to stratify potential habitat by predicted suitability. A stratified permutation test then evaluates the association between stressor and amphibian, all else equal. Our approach confirms the known negative relationship between fish and R. sierrae, but finds no evidence of a negative relationship between current packstock use and A. canorus breeding. Our statistical approach has potential broad application for deriving understanding (not just prediction) from observational data.

Detecting the influence of rare stressors on rare species in Yosemite National Park using a novel stratified permutation test

PubMed Central

Matchett, J. R.; Stark, Philip B.; Ostoja, Steven M.; Knapp, Roland A.; McKenny, Heather C.; Brooks, Matthew L.; Langford, William T.; Joppa, Lucas N.; Berlow, Eric L.

2015-01-01

Statistical models often use observational data to predict phenomena; however, interpreting model terms to understand their influence can be problematic. This issue poses a challenge in species conservation where setting priorities requires estimating influences of potential stressors using observational data. We present a novel approach for inferring influence of a rare stressor on a rare species by blending predictive models with nonparametric permutation tests. We illustrate the approach with two case studies involving rare amphibians in Yosemite National Park, USA. The endangered frog, Rana sierrae, is known to be negatively impacted by non-native fish, while the threatened toad, Anaxyrus canorus, is potentially affected by packstock. Both stressors and amphibians are rare, occurring in ~10% of potential habitat patches. We first predict amphibian occupancy with a statistical model that includes all predictors but the stressor to stratify potential habitat by predicted suitability. A stratified permutation test then evaluates the association between stressor and amphibian, all else equal. Our approach confirms the known negative relationship between fish and R. sierrae, but finds no evidence of a negative relationship between current packstock use and A. canorus breeding. Our statistical approach has potential broad application for deriving understanding (not just prediction) from observational data. PMID:26031755

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.

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.

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.

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.

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

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.

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.

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.

Estimating times of surgeries with two component procedures: comparison of the lognormal and normal models.

PubMed

Strum, David P; May, Jerrold H; Sampson, Allan R; Vargas, Luis G; Spangler, William E

2003-01-01

Variability inherent in the duration of surgical procedures complicates surgical scheduling. Modeling the duration and variability of surgeries might improve time estimates. Accurate time estimates are important operationally to improve utilization, reduce costs, and identify surgeries that might be considered outliers. Surgeries with multiple procedures are difficult to model because they are difficult to segment into homogenous groups and because they are performed less frequently than single-procedure surgeries. The authors studied, retrospectively, 10,740 surgeries each with exactly two CPTs and 46,322 surgical cases with only one CPT from a large teaching hospital to determine if the distribution of dual-procedure surgery times fit more closely a lognormal or a normal model. The authors tested model goodness of fit to their data using Shapiro-Wilk tests, studied factors affecting the variability of time estimates, and examined the impact of coding permutations (ordered combinations) on modeling. The Shapiro-Wilk tests indicated that the lognormal model is statistically superior to the normal model for modeling dual-procedure surgeries. Permutations of component codes did not appear to differ significantly with respect to total procedure time and surgical time. To improve individual models for infrequent dual-procedure surgeries, permutations may be reduced and estimates may be based on the longest component procedure and type of anesthesia. The authors recommend use of the lognormal model for estimating surgical times for surgeries with two component procedures. Their results help legitimize the use of log transforms to normalize surgical procedure times prior to hypothesis testing using linear statistical models. Multiple-procedure surgeries may be modeled using the longest (statistically most important) component procedure and type of anesthesia.

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.

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.

The traveling salesman problem in surgery: economy of motion for the FLS Peg Transfer task.

PubMed

Falcone, John L; Chen, Xiaotian; Hamad, Giselle G

2013-05-01

In the Peg Transfer task in the Fundamentals of Laparoscopic Surgery (FLS) curriculum, six peg objects are sequentially transferred in a bimanual fashion using laparoscopic instruments across a pegboard and back. There are over 268 trillion ways of completing this task. In the setting of many possibilities, the traveling salesman problem is one where the objective is to solve for the shortest distance traveled through a fixed number of points. The goal of this study is to apply the traveling salesman problem to find the shortest two-dimensional path length for this task. A database platform was used with permutation application output to generate all of the single-direction solutions of the FLS Peg Transfer task. A brute-force search was performed using nested Boolean operators and database equations to calculate the overall two-dimensional distances for the efficient and inefficient solutions. The solutions were found by evaluating peg object transfer distances and distances between transfers for the nondominant and dominant hands. For the 518,400 unique single-direction permutations, the mean total two-dimensional peg object travel distance was 33.3 ± 1.4 cm. The range in distances was from 30.3 to 36.5 cm. There were 1,440 (0.28 %) of 518,400 efficient solutions with the minimized peg object travel distance of 30.3 cm. There were 8 (0.0015 %) of 518,400 solutions in the final solution set that minimized the distance of peg object transfer and minimized the distance traveled between peg transfers. Peg objects moved 12.7 cm (17.4 %) less in the efficient solutions compared to the inefficient solutions. The traveling salesman problem can be applied to find efficient solutions for surgical tasks. The eight solutions to the FLS Peg Transfer task are important for any examinee taking the FLS curriculum and for certification by the American Board of Surgery.

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.

Symmetry-Adapted Machine Learning for Tensorial Properties of Atomistic Systems.

PubMed

Grisafi, Andrea; Wilkins, David M; Csányi, Gábor; Ceriotti, Michele

2018-01-19

Statistical learning methods show great promise in providing an accurate prediction of materials and molecular properties, while minimizing the need for computationally demanding electronic structure calculations. The accuracy and transferability of these models are increased significantly by encoding into the learning procedure the fundamental symmetries of rotational and permutational invariance of scalar properties. However, the prediction of tensorial properties requires that the model respects the appropriate geometric transformations, rather than invariance, when the reference frame is rotated. We introduce a formalism that extends existing schemes and makes it possible to perform machine learning of tensorial properties of arbitrary rank, and for general molecular geometries. To demonstrate it, we derive a tensor kernel adapted to rotational symmetry, which is the natural generalization of the smooth overlap of atomic positions kernel commonly used for the prediction of scalar properties at the atomic scale. The performance and generality of the approach is demonstrated by learning the instantaneous response to an external electric field of water oligomers of increasing complexity, from the isolated molecule to the condensed phase.

AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra

PubMed Central

Tian, Ye; Schwieters, Charles D.; Opella, Stanley J.; Marassi, Francesca M.

2011-01-01

AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes. PMID:22036904

Symmetry-Adapted Machine Learning for Tensorial Properties of Atomistic Systems

NASA Astrophysics Data System (ADS)

Grisafi, Andrea; Wilkins, David M.; Csányi, Gábor; Ceriotti, Michele

2018-01-01

Statistical learning methods show great promise in providing an accurate prediction of materials and molecular properties, while minimizing the need for computationally demanding electronic structure calculations. The accuracy and transferability of these models are increased significantly by encoding into the learning procedure the fundamental symmetries of rotational and permutational invariance of scalar properties. However, the prediction of tensorial properties requires that the model respects the appropriate geometric transformations, rather than invariance, when the reference frame is rotated. We introduce a formalism that extends existing schemes and makes it possible to perform machine learning of tensorial properties of arbitrary rank, and for general molecular geometries. To demonstrate it, we derive a tensor kernel adapted to rotational symmetry, which is the natural generalization of the smooth overlap of atomic positions kernel commonly used for the prediction of scalar properties at the atomic scale. The performance and generality of the approach is demonstrated by learning the instantaneous response to an external electric field of water oligomers of increasing complexity, from the isolated molecule to the condensed phase.

Permutation importance: a corrected feature importance measure.

PubMed

Altmann, André; Toloşi, Laura; Sander, Oliver; Lengauer, Thomas

2010-05-15

In life sciences, interpretability of machine learning models is as important as their prediction accuracy. Linear models are probably the most frequently used methods for assessing feature relevance, despite their relative inflexibility. However, in the past years effective estimators of feature relevance have been derived for highly complex or non-parametric models such as support vector machines and RandomForest (RF) models. Recently, it has been observed that RF models are biased in such a way that categorical variables with a large number of categories are preferred. In this work, we introduce a heuristic for normalizing feature importance measures that can correct the feature importance bias. The method is based on repeated permutations of the outcome vector for estimating the distribution of measured importance for each variable in a non-informative setting. The P-value of the observed importance provides a corrected measure of feature importance. We apply our method to simulated data and demonstrate that (i) non-informative predictors do not receive significant P-values, (ii) informative variables can successfully be recovered among non-informative variables and (iii) P-values computed with permutation importance (PIMP) are very helpful for deciding the significance of variables, and therefore improve model interpretability. Furthermore, PIMP was used to correct RF-based importance measures for two real-world case studies. We propose an improved RF model that uses the significant variables with respect to the PIMP measure and show that its prediction accuracy is superior to that of other existing models. R code for the method presented in this article is available at http://www.mpi-inf.mpg.de/ approximately altmann/download/PIMP.R CONTACT: altmann@mpi-inf.mpg.de, laura.tolosi@mpi-inf.mpg.de Supplementary data are available at Bioinformatics online.

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.

Permutation entropy and statistical complexity analysis of turbulence in laboratory plasmas and the solar wind.

PubMed

Weck, P J; Schaffner, D A; Brown, M R; Wicks, R T

2015-02-01

The Bandt-Pompe permutation entropy and the Jensen-Shannon statistical complexity are used to analyze fluctuating time series of three different turbulent plasmas: the magnetohydrodynamic (MHD) turbulence in the plasma wind tunnel of the Swarthmore Spheromak Experiment (SSX), drift-wave turbulence of ion saturation current fluctuations in the edge of the Large Plasma Device (LAPD), and fully developed turbulent magnetic fluctuations of the solar wind taken from the Wind spacecraft. The entropy and complexity values are presented as coordinates on the CH plane for comparison among the different plasma environments and other fluctuation models. The solar wind is found to have the highest permutation entropy and lowest statistical complexity of the three data sets analyzed. Both laboratory data sets have larger values of statistical complexity, suggesting that these systems have fewer degrees of freedom in their fluctuations, with SSX magnetic fluctuations having slightly less complexity than the LAPD edge I(sat). The CH plane coordinates are compared to the shape and distribution of a spectral decomposition of the wave forms. These results suggest that fully developed turbulence (solar wind) occupies the lower-right region of the CH plane, and that other plasma systems considered to be turbulent have less permutation entropy and more statistical complexity. This paper presents use of this statistical analysis tool on solar wind plasma, as well as on an MHD turbulent experimental plasma.

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

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…

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

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.

N=2 Minimal Conformal Field Theories and Matrix Bifactorisations of x d

NASA Astrophysics Data System (ADS)

Davydov, Alexei; Camacho, Ana Ros; Runkel, Ingo

2018-01-01

We establish an action of the representations of N = 2-superconformal symmetry on the category of matrix factorisations of the potentials x d and x d - y d , for d odd. More precisely we prove a tensor equivalence between (a) the category of Neveu-Schwarz-type representations of the N = 2 minimal super vertex operator algebra at central charge 3-6/d, and (b) a full subcategory of graded matrix factorisations of the potential x d - y d . The subcategory in (b) is given by permutation-type matrix factorisations with consecutive index sets. The physical motivation for this result is the Landau-Ginzburg/conformal field theory correspondence, where it amounts to the equivalence of a subset of defects on both sides of the correspondence. Our work builds on results by Brunner and Roggenkamp [BR], where an isomorphism of fusion rules was established.

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.

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.

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.

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

Linear algebra of the permutation invariant Crow-Kimura model of prebiotic evolution.

PubMed

Bratus, Alexander S; Novozhilov, Artem S; Semenov, Yuri S

2014-10-01

A particular case of the famous quasispecies model - the Crow-Kimura model with a permutation invariant fitness landscape - is investigated. Using the fact that the mutation matrix in the case of a permutation invariant fitness landscape has a special tridiagonal form, a change of the basis is suggested such that in the new coordinates a number of analytical results can be obtained. In particular, using the eigenvectors of the mutation matrix as the new basis, we show that the quasispecies distribution approaches a binomial one and give simple estimates for the speed of convergence. Another consequence of the suggested approach is a parametric solution to the system of equations determining the quasispecies. Using this parametric solution we show that our approach leads to exact asymptotic results in some cases, which are not covered by the existing methods. In particular, we are able to present not only the limit behavior of the leading eigenvalue (mean population fitness), but also the exact formulas for the limit quasispecies eigenvector for special cases. For instance, this eigenvector has a geometric distribution in the case of the classical single peaked fitness landscape. On the biological side, we propose a mathematical definition, based on the closeness of the quasispecies to the binomial distribution, which can be used as an operational definition of the notorious error threshold. Using this definition, we suggest two approximate formulas to estimate the critical mutation rate after which the quasispecies delocalization occurs. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

Approximate strip exchanging.

PubMed

Roy, Swapnoneel; Thakur, Ashok Kumar

2008-01-01

Genome rearrangements have been modelled by a variety of primitives such as reversals, transpositions, block moves and block interchanges. We consider such a genome rearrangement primitive Strip Exchanges. Given a permutation, the challenge is to sort it by using minimum number of strip exchanges. A strip exchanging move interchanges the positions of two chosen strips so that they merge with other strips. The strip exchange problem is to sort a permutation using minimum number of strip exchanges. We present here the first non-trivial 2-approximation algorithm to this problem. We also observe that sorting by strip-exchanges is fixed-parameter-tractable. Lastly we discuss the application of strip exchanges in a different area Optical Character Recognition (OCR) with an example.

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.

The bilinear-biquadratic model on the complete graph

NASA Astrophysics Data System (ADS)

Jakab, Dávid; Szirmai, Gergely; Zimborás, Zoltán

2018-03-01

We study the spin-1 bilinear-biquadratic model on the complete graph of N sites, i.e. when each spin is interacting with every other spin with the same strength. Because of its complete permutation invariance, this Hamiltonian can be rewritten as the linear combination of the quadratic Casimir operators of \

A bootstrap based space-time surveillance model with an application to crime occurrences

NASA Astrophysics Data System (ADS)

Kim, Youngho; O'Kelly, Morton

2008-06-01

This study proposes a bootstrap-based space-time surveillance model. Designed to find emerging hotspots in near-real time, the bootstrap based model is characterized by its use of past occurrence information and bootstrap permutations. Many existing space-time surveillance methods, using population at risk data to generate expected values, have resulting hotspots bounded by administrative area units and are of limited use for near-real time applications because of the population data needed. However, this study generates expected values for local hotspots from past occurrences rather than population at risk. Also, bootstrap permutations of previous occurrences are used for significant tests. Consequently, the bootstrap-based model, without the requirement of population at risk data, (1) is free from administrative area restriction, (2) enables more frequent surveillance for continuously updated registry database, and (3) is readily applicable to criminology and epidemiology surveillance. The bootstrap-based model performs better for space-time surveillance than the space-time scan statistic. This is shown by means of simulations and an application to residential crime occurrences in Columbus, OH, year 2000.

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.

Learning molecular energies using localized graph kernels.

PubMed

Ferré, Grégoire; Haut, Terry; Barros, Kipton

2017-03-21

Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.

Learning molecular energies using localized graph kernels

NASA Astrophysics Data System (ADS)

Ferré, Grégoire; Haut, Terry; Barros, Kipton

2017-03-01

Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturally incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. We benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.

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.

Is different better?: models of teaching and their influence on the net financial outcome for general practice teaching posts.

PubMed

Laurence, Caroline O; Black, Linda E; Cheah, Carolyn; Karnon, Jonathan

2011-07-12

In Australia, training for general practice (GP) occurs within private practices and their involvement in teaching can have significant financial costs. At the same time there are growing demands for clinical places for all disciplines and for GP there is concern that there are insufficient teaching practices to meet the demand at the medical student, prevocational and vocational training levels. One option to address this may be to change how teaching occurs in the practice. A question that arises in posing such an option is whether different models of teaching change the costs for a teaching practice. The aim of this study is to determine the net financial outcome of teaching models in private GP. Modelling the financial implications for a range of teaching options using a costing framework developed from a survey of teaching practices in South Australia. Each option was compared with the traditional model of teaching where one GP supervisor is singularly responsible for one learner. The main outcome measure was net financial outcome per week. Decisions on the model cost parameters were made by the study's Steering Group which comprised of experienced GP supervisors. Four teaching models are presented. Model 1 investigates the gains from teaching multiple same level learners, Models 2 and 3, the benefits of vertically integrated teaching using different permutations, and Model 4 the concept of a GP teacher who undertakes all the teaching. There was a significant increase in net benefits of Aus$547 per week (95% confidence intervals $459, $668) to the practice when a GP taught two same level learners (Model 1) and when a senior registrar participated in teaching a prevocational doctor (Model 3, Aus$263, 95% confidence intervals $80, $570). For Model 2, a practice could significantly reduce the loss if a registrar was involved in vertically integrated teaching which included the training of a medical student (Aus$551, 95% confidence intervals $419, $718). The GP teacher model resulted in a net remuneration of Aus$207,335 per year, sourced predominantly from the GP teacher activities, with no loss to the practice. Our study costed teaching options that can maximise the financial outcomes from teaching. The inclusion of GP registrars in the teaching model or the supervisor teaching more than one same level learner results in a greater financial benefit. This gain was achieved through a reduction in supervisor teaching time and the sharing of administrative and teaching activities with GP registrars. We also show that a GP teacher who carries a minimal patient load can be a sustainable option for a practice. Further, the costing framework used for the teaching models presented in this study has the ability to be applied to any number of teaching model permutations.

Interpreting support vector machine models for multivariate group wise analysis in neuroimaging

PubMed Central

Gaonkar, Bilwaj; Shinohara, Russell T; Davatzikos, Christos

2015-01-01

Machine learning based classification algorithms like support vector machines (SVMs) have shown great promise for turning a high dimensional neuroimaging data into clinically useful decision criteria. However, tracing imaging based patterns that contribute significantly to classifier decisions remains an open problem. This is an issue of critical importance in imaging studies seeking to determine which anatomical or physiological imaging features contribute to the classifier’s decision, thereby allowing users to critically evaluate the findings of such machine learning methods and to understand disease mechanisms. The majority of published work addresses the question of statistical inference for support vector classification using permutation tests based on SVM weight vectors. Such permutation testing ignores the SVM margin, which is critical in SVM theory. In this work we emphasize the use of a statistic that explicitly accounts for the SVM margin and show that the null distributions associated with this statistic are asymptotically normal. Further, our experiments show that this statistic is a lot less conservative as compared to weight based permutation tests and yet specific enough to tease out multivariate patterns in the data. Thus, we can better understand the multivariate patterns that the SVM uses for neuroimaging based classification. PMID:26210913

cit: hypothesis testing software for mediation analysis in genomic applications.

PubMed

Millstein, Joshua; Chen, Gary K; Breton, Carrie V

2016-08-01

The challenges of successfully applying causal inference methods include: (i) satisfying underlying assumptions, (ii) limitations in data/models accommodated by the software and (iii) low power of common multiple testing approaches. The causal inference test (CIT) is based on hypothesis testing rather than estimation, allowing the testable assumptions to be evaluated in the determination of statistical significance. A user-friendly software package provides P-values and optionally permutation-based FDR estimates (q-values) for potential mediators. It can handle single and multiple binary and continuous instrumental variables, binary or continuous outcome variables and adjustment covariates. Also, the permutation-based FDR option provides a non-parametric implementation. Simulation studies demonstrate the validity of the cit package and show a substantial advantage of permutation-based FDR over other common multiple testing strategies. The cit open-source R package is freely available from the CRAN website (https://cran.r-project.org/web/packages/cit/index.html) with embedded C ++ code that utilizes the GNU Scientific Library, also freely available (http://www.gnu.org/software/gsl/). joshua.millstein@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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.

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.

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.

An analytical study of composite laminate lay-up using search algorithms for maximization of flexural stiffness and minimization of springback angle

NASA Astrophysics Data System (ADS)

Singh, Ranjan Kumar; Rinawa, Moti Lal

2018-04-01

The residual stresses arising in fiber-reinforced laminates during their curing in closed molds lead to changes in the composites after their removal from the molds and cooling. One of these dimensional changes of angle sections is called springback. The parameters such as lay-up, stacking sequence, material system, cure temperature, thickness etc play important role in it. In present work, it is attempted to optimize lay-up and stacking sequence for maximization of flexural stiffness and minimization of springback angle. The search algorithms are employed to obtain best sequence through repair strategy such as swap. A new search algorithm, termed as lay-up search algorithm (LSA) is also proposed, which is an extension of permutation search algorithm (PSA). The efficacy of PSA and LSA is tested on the laminates with a range of lay-ups. A computer code is developed on MATLAB implementing the above schemes. Also, the strategies for multi objective optimization using search algorithms are suggested and tested.

Relationship between systolic and diastolic function with improvements in forward stroke volume following reduction in mitral regurgitation

NASA Technical Reports Server (NTRS)

Firstenberg, M. S.; Greenberg, N. L.; Smedira, N. G.; McCarthy, P. M.; Garcia, M. J.; Thomas, J. D.

2001-01-01

Efforts to improve mitral regurgitation (MR) are often performed in conjunction with coronary revascularization. However, the independent effects of a reduced MR area (MRa) are difficult to quantify. Using a previously developed cardiovascular model, ventricular contractility (elastance 1-8 mmHg/ml) and relaxation (tau: 40-150 msec) were independently adjusted for four grades of MR orifice areas (0.0 to 0.8 cm2). Improvements in forward stroke volume (fSV) were determined for the permutations of reduced MRa. For all conditions, LV end-diastolic pressure and volumes ranged from 7.3-24.2 mmHg and 64.8-174.3 ml, respectively. Overall, fSV ranged from 36.0-89.4 (mean: 64.2 +/- 12.8) ml, improved between 6.4 and 35.3% (mean: 15.6 +/- 8.1%), and was best predicted by (r=0.97, p<0.01) %delta(fSV)[correction of fVS]=34[MRa initial] - 46[MRa final] -0.5[elastance]. Reduced MRa, independent of relaxation and minimally influence by contractility, yield improved fSVs.

Data-Science Analysis of the Macro-scale Features Governing the Corrosion to Crack Transition in AA7050-T7451

NASA Astrophysics Data System (ADS)

Co, Noelle Easter C.; Brown, Donald E.; Burns, James T.

2018-05-01

This study applies data science approaches (random forest and logistic regression) to determine the extent to which macro-scale corrosion damage features govern the crack formation behavior in AA7050-T7451. Each corrosion morphology has a set of corresponding predictor variables (pit depth, volume, area, diameter, pit density, total fissure length, surface roughness metrics, etc.) describing the shape of the corrosion damage. The values of the predictor variables are obtained from white light interferometry, x-ray tomography, and scanning electron microscope imaging of the corrosion damage. A permutation test is employed to assess the significance of the logistic and random forest model predictions. Results indicate minimal relationship between the macro-scale corrosion feature predictor variables and fatigue crack initiation. These findings suggest that the macro-scale corrosion features and their interactions do not solely govern the crack formation behavior. While these results do not imply that the macro-features have no impact, they do suggest that additional parameters must be considered to rigorously inform the crack formation location.

Confusing the heterotic string

NASA Astrophysics Data System (ADS)

Benett, D.; Brene, N.; Mizrachi, Leah; Nielsen, H. B.

1986-10-01

A confusion mechanism is proposed as a global modification of the heterotic string model. It envolves a confusion hypersurface across which the two E 8's of the heterotic string are permuted. A remarkable numerical coincidence is found which prevents an inconsistency in the model. The low energy limit of this theory (after compactification) is typically invariant under one E 8 only, thereby removing the shadow world from the original model.

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 coupling analysis between stock market indices based on permutation measures

NASA Astrophysics Data System (ADS)

Shi, Wenbin; Shang, Pengjian; Xia, Jianan; Yeh, Chien-Hung

2016-04-01

Many information-theoretic methods have been proposed for analyzing the coupling dependence between time series. And it is significant to quantify the correlation relationship between financial sequences since the financial market is a complex evolved dynamic system. Recently, we developed a new permutation-based entropy, called cross-permutation entropy (CPE), to detect the coupling structures between two synchronous time series. In this paper, we extend the CPE method to weighted cross-permutation entropy (WCPE), to address some of CPE's limitations, mainly its inability to differentiate between distinct patterns of a certain motif and the sensitivity of patterns close to the noise floor. It shows more stable and reliable results than CPE does when applied it to spiky data and AR(1) processes. Besides, we adapt the CPE method to infer the complexity of short-length time series by freely changing the time delay, and test it with Gaussian random series and random walks. The modified method shows the advantages in reducing deviations of entropy estimation compared with the conventional one. Finally, the weighted cross-permutation entropy of eight important stock indices from the world financial markets is investigated, and some useful and interesting empirical results are obtained.

Permutation entropy of fractional Brownian motion and fractional Gaussian noise

NASA Astrophysics Data System (ADS)

Zunino, L.; Pérez, D. G.; Martín, M. T.; Garavaglia, M.; Plastino, A.; Rosso, O. A.

2008-06-01

We have worked out theoretical curves for the permutation entropy of the fractional Brownian motion and fractional Gaussian noise by using the Bandt and Shiha [C. Bandt, F. Shiha, J. Time Ser. Anal. 28 (2007) 646] theoretical predictions for their corresponding relative frequencies. Comparisons with numerical simulations show an excellent agreement. Furthermore, the entropy-gap in the transition between these processes, observed previously via numerical results, has been here theoretically validated. Also, we have analyzed the behaviour of the permutation entropy of the fractional Gaussian noise for different time delays.

Learning molecular energies using localized graph kernels

DOE PAGES

Ferré, Grégoire; Haut, Terry Scot; Barros, Kipton Marcos

2017-03-21

We report that recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturallymore » incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. Finally, we benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.« less

Statistical physics of the symmetric group.

PubMed

Williams, Mobolaji

2017-04-01

Ordered chains (such as chains of amino acids) are ubiquitous in biological cells, and these chains perform specific functions contingent on the sequence of their components. Using the existence and general properties of such sequences as a theoretical motivation, we study the statistical physics of systems whose state space is defined by the possible permutations of an ordered list, i.e., the symmetric group, and whose energy is a function of how certain permutations deviate from some chosen correct ordering. Such a nonfactorizable state space is quite different from the state spaces typically considered in statistical physics systems and consequently has novel behavior in systems with interacting and even noninteracting Hamiltonians. Various parameter choices of a mean-field model reveal the system to contain five different physical regimes defined by two transition temperatures, a triple point, and a quadruple point. Finally, we conclude by discussing how the general analysis can be extended to state spaces with more complex combinatorial properties and to other standard questions of statistical mechanics models.

Learning molecular energies using localized graph kernels

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

Ferré, Grégoire; Haut, Terry Scot; Barros, Kipton Marcos

We report that recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab initio calculations) and at speeds suitable for molecular dynamics simulation. Best performance is achieved when the known physical constraints are encoded in the machine learning models. For example, the atomic energy is invariant under global translations and rotations; it is also invariant to permutations of same-species atoms. Although simple to state, these symmetries are complicated to encode into machine learning algorithms. In this paper, we present a machine learning approach based on graph theory that naturallymore » incorporates translation, rotation, and permutation symmetries. Specifically, we use a random walk graph kernel to measure the similarity of two adjacency matrices, each of which represents a local atomic environment. This Graph Approximated Energy (GRAPE) approach is flexible and admits many possible extensions. Finally, we benchmark a simple version of GRAPE by predicting atomization energies on a standard dataset of organic molecules.« less

Statistical physics of the symmetric group

NASA Astrophysics Data System (ADS)

Williams, Mobolaji

2017-04-01

Ordered chains (such as chains of amino acids) are ubiquitous in biological cells, and these chains perform specific functions contingent on the sequence of their components. Using the existence and general properties of such sequences as a theoretical motivation, we study the statistical physics of systems whose state space is defined by the possible permutations of an ordered list, i.e., the symmetric group, and whose energy is a function of how certain permutations deviate from some chosen correct ordering. Such a nonfactorizable state space is quite different from the state spaces typically considered in statistical physics systems and consequently has novel behavior in systems with interacting and even noninteracting Hamiltonians. Various parameter choices of a mean-field model reveal the system to contain five different physical regimes defined by two transition temperatures, a triple point, and a quadruple point. Finally, we conclude by discussing how the general analysis can be extended to state spaces with more complex combinatorial properties and to other standard questions of statistical mechanics models.

Development of estrogen receptor beta binding prediction model using large sets of chemicals.

PubMed

Sakkiah, Sugunadevi; Selvaraj, Chandrabose; Gong, Ping; Zhang, Chaoyang; Tong, Weida; Hong, Huixiao

2017-11-03

We developed an ER β binding prediction model to facilitate identification of chemicals specifically bind ER β or ER α together with our previously developed ER α binding model. Decision Forest was used to train ER β binding prediction model based on a large set of compounds obtained from EADB. Model performance was estimated through 1000 iterations of 5-fold cross validations. Prediction confidence was analyzed using predictions from the cross validations. Informative chemical features for ER β binding were identified through analysis of the frequency data of chemical descriptors used in the models in the 5-fold cross validations. 1000 permutations were conducted to assess the chance correlation. The average accuracy of 5-fold cross validations was 93.14% with a standard deviation of 0.64%. Prediction confidence analysis indicated that the higher the prediction confidence the more accurate the predictions. Permutation testing results revealed that the prediction model is unlikely generated by chance. Eighteen informative descriptors were identified to be important to ER β binding prediction. Application of the prediction model to the data from ToxCast project yielded very high sensitivity of 90-92%. Our results demonstrated ER β binding of chemicals could be accurately predicted using the developed model. Coupling with our previously developed ER α prediction model, this model could be expected to facilitate drug development through identification of chemicals that specifically bind ER β or ER α .

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.

Generalized permutation entropy analysis based on the two-index entropic form S q , δ

NASA Astrophysics Data System (ADS)

Xu, Mengjia; Shang, Pengjian

2015-05-01

Permutation entropy (PE) is a novel measure to quantify the complexity of nonlinear time series. In this paper, we propose a generalized permutation entropy ( P E q , δ ) based on the recently postulated entropic form, S q , δ , which was proposed as an unification of the well-known Sq of nonextensive-statistical mechanics and S δ , a possibly appropriate candidate for the black-hole entropy. We find that P E q , δ with appropriate parameters can amplify minor changes and trends of complexities in comparison to PE. Experiments with this generalized permutation entropy method are performed with both synthetic and stock data showing its power. Results show that P E q , δ is an exponential function of q and the power ( k ( δ ) ) is a constant if δ is determined. Some discussions about k ( δ ) are provided. Besides, we also find some interesting results about power law.

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.

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.

Biosurveillance in a Highly Mobile Population - Year 3

DTIC Science & Technology

2012-07-01

provides an opportunity- rich tested for the impact upon infectious disease modeling, biosurveillance, and public health. Kulldorf et al (2005) assessed...Secular Circles and Millenial Trends. URSS, Moscow 2006 Kulldorff M, Heffernan R, Hartman J, Assunção RM, Mostashari F. (2005). “Space-Time Permutation

Inference With Difference-in-Differences With a Small Number of Groups: A Review, Simulation Study, and Empirical Application Using SHARE Data.

PubMed

Rokicki, Slawa; Cohen, Jessica; Fink, Günther; Salomon, Joshua A; Landrum, Mary Beth

2018-01-01

Difference-in-differences (DID) estimation has become increasingly popular as an approach to evaluate the effect of a group-level policy on individual-level outcomes. Several statistical methodologies have been proposed to correct for the within-group correlation of model errors resulting from the clustering of data. Little is known about how well these corrections perform with the often small number of groups observed in health research using longitudinal data. First, we review the most commonly used modeling solutions in DID estimation for panel data, including generalized estimating equations (GEE), permutation tests, clustered standard errors (CSE), wild cluster bootstrapping, and aggregation. Second, we compare the empirical coverage rates and power of these methods using a Monte Carlo simulation study in scenarios in which we vary the degree of error correlation, the group size balance, and the proportion of treated groups. Third, we provide an empirical example using the Survey of Health, Ageing, and Retirement in Europe. When the number of groups is small, CSE are systematically biased downwards in scenarios when data are unbalanced or when there is a low proportion of treated groups. This can result in over-rejection of the null even when data are composed of up to 50 groups. Aggregation, permutation tests, bias-adjusted GEE, and wild cluster bootstrap produce coverage rates close to the nominal rate for almost all scenarios, though GEE may suffer from low power. In DID estimation with a small number of groups, analysis using aggregation, permutation tests, wild cluster bootstrap, or bias-adjusted GEE is recommended.

Is different better? Models of teaching and their influence on the net financial outcome for general practice teaching posts

PubMed Central

2011-01-01

Background In Australia, training for general practice (GP) occurs within private practices and their involvement in teaching can have significant financial costs. At the same time there are growing demands for clinical places for all disciplines and for GP there is concern that there are insufficient teaching practices to meet the demand at the medical student, prevocational and vocational training levels. One option to address this may be to change how teaching occurs in the practice. A question that arises in posing such an option is whether different models of teaching change the costs for a teaching practice. The aim of this study is to determine the net financial outcome of teaching models in private GP. Methods Modelling the financial implications for a range of teaching options using a costing framework developed from a survey of teaching practices in South Australia. Each option was compared with the traditional model of teaching where one GP supervisor is singularly responsible for one learner. The main outcome measure was net financial outcome per week. Decisions on the model cost parameters were made by the study's Steering Group which comprised of experienced GP supervisors. Four teaching models are presented. Model 1 investigates the gains from teaching multiple same level learners, Models 2 and 3, the benefits of vertically integrated teaching using different permutations, and Model 4 the concept of a GP teacher who undertakes all the teaching. Results There was a significant increase in net benefits of Aus$547 per week (95% confidence intervals $459, $668) to the practice when a GP taught two same level learners (Model 1) and when a senior registrar participated in teaching a prevocational doctor (Model 3, Aus$263, 95% confidence intervals $80, $570). For Model 2, a practice could significantly reduce the loss if a registrar was involved in vertically integrated teaching which included the training of a medical student (Aus$551, 95% confidence intervals $419, $718). The GP teacher model resulted in a net remuneration of Aus$207,335 per year, sourced predominantly from the GP teacher activities, with no loss to the practice. Conclusions Our study costed teaching options that can maximise the financial outcomes from teaching. The inclusion of GP registrars in the teaching model or the supervisor teaching more than one same level learner results in a greater financial benefit. This gain was achieved through a reduction in supervisor teaching time and the sharing of administrative and teaching activities with GP registrars. We also show that a GP teacher who carries a minimal patient load can be a sustainable option for a practice. Further, the costing framework used for the teaching models presented in this study has the ability to be applied to any number of teaching model permutations. PMID:21749692

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

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

Development of time-trend model for analysing and predicting case pattern of dog bite injury induced rabies-like-illness in Liberia, 2014-2017.

PubMed

Jomah, N D; Ojo, J F; Odigie, E A; Olugasa, B O

2014-12-01

The post-civil war records of dog bite injuries (DBI) and rabies-like-illness (RLI) among humans in Liberia is a vital epidemiological resource for developing a predictive model to guide the allocation of resources towards human rabies control. Whereas DBI and RLI are high, they are largely under-reported. The objective of this study was to develop a time model of the case-pattern and apply it to derive predictors of time-trend point distribution of DBI-RLI cases. A retrospective 6 years data of DBI distribution among humans countrywide were converted to quarterly series using a transformation technique of Minimizing Squared First Difference statistic. The generated dataset was used to train a time-trend model of the DBI-RLI syndrome in Liberia. An additive detenninistic time-trend model was selected due to its performance compared to multiplication model of trend and seasonal movement. Parameter predictors were run on least square method to predict DBI cases for a prospective 4 years period, covering 2014-2017. The two-stage predictive model of DBI case-pattern between 2014 and 2017 was characterised by a uniform upward trend within Liberia's coastal and hinterland Counties over the forecast period. This paper describes a translational application of the time-trend distribution pattern of DBI epidemics, 2008-2013 reported in Liberia, on which a predictive model was developed. A computationally feasible two-stage time-trend permutation approach is proposed to estimate the time-trend parameters and conduct predictive inference on DBI-RLI in Liberia.

User manual for Blossom statistical package for R

USGS Publications Warehouse

Talbert, Marian; Cade, Brian S.

2005-01-01

Blossom is an R package with functions for making statistical comparisons with distance-function based permutation tests developed by P.W. Mielke, Jr. and colleagues at Colorado State University (Mielke and Berry, 2001) and for testing parameters estimated in linear models with permutation procedures developed by B. S. Cade and colleagues at the Fort Collins Science Center, U.S. Geological Survey. This manual is intended to provide identical documentation of the statistical methods and interpretations as the manual by Cade and Richards (2005) does for the original Fortran program, but with changes made with respect to command inputs and outputs to reflect the new implementation as a package for R (R Development Core Team, 2012). This implementation in R has allowed for numerous improvements not supported by the Cade and Richards (2005) Fortran implementation, including use of categorical predictor variables in most routines.

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

Atypical nucleus accumbens morphology in psychopathy: another limbic piece in the puzzle.

PubMed

Boccardi, Marina; Bocchetta, Martina; Aronen, Hannu J; Repo-Tiihonen, Eila; Vaurio, Olli; Thompson, Paul M; Tiihonen, Jari; Frisoni, Giovanni B

2013-01-01

Psychopathy has been associated with increased putamen and striatum volumes. The nucleus accumbens - a key structure in reversal learning, less effective in psychopathy - has not yet received specific attention. Moreover, basal ganglia morphology has never been explored. We examined the morphology of the caudate, putamen and accumbens, manually segmented from magnetic resonance images of 26 offenders (age: 32.5 ± 8.4) with medium-high psychopathy (mean PCL-R=30 ± 5) and 25 healthy controls (age: 34.6 ± 10.8). Local differences were statistically modeled using a surface-based radial distance mapping method (p<0.05; multiple comparisons correction through permutation tests). In psychopathy, the caudate and putamen had normal global volume, but different morphology, significant after correction for multiple comparisons, for the right dorsal putamen (permutation test: p=0.02). The volume of the nucleus accumbens was 13% smaller in psychopathy (p corrected for multiple comparisons <0.006). The atypical morphology consisted of predominant anterior hypotrophy bilaterally (10-30%). Caudate and putamen local morphology displayed negative correlation with the lifestyle factor of the PCL-R (permutation test: p=0.05 and 0.03). From these data, psychopathy appears to be associated with an atypical striatal morphology, with highly significant global and local differences of the accumbens. This is consistent with the clinical syndrome and with theories of limbic involvement. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fostering Recursive Thinking in Combinatorics through the Use of Manipulatives and Computing Technology.

ERIC Educational Resources Information Center

Abramovich, Sergei; Pieper, Anne

1996-01-01

Describes the use of manipulatives for solving simple combinatorial problems which can lead to the discovery of recurrence relations for permutations and combinations. Numerical evidence and visual imagery generated by a computer spreadsheet through modeling these relations can enable students to experience the ease and power of combinatorial…

Group-theoretic models of the inversion process in bacterial genomes.

PubMed

Egri-Nagy, Attila; Gebhardt, Volker; Tanaka, Mark M; Francis, Andrew R

2014-07-01

The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent than longer, and those that move the terminus of replication are less probable than those that do not. Current methods for establishing the inversion distance between two bacterial genomes are unable to incorporate such information. In this paper we suggest a group-theoretic framework that in principle can take these constraints into account. In particular, we show that by lifting the problem from circular permutations to the affine symmetric group, the inversion distance can be found in polynomial time for a model in which inversions are restricted to acting on two regions. This requires the proof of new results in group theory, and suggests a vein of new combinatorial problems concerning permutation groups on which group theorists will be needed to collaborate with biologists. We apply the new method to inferring distances and phylogenies for published Yersinia pestis data.

A multipopulation PSO based memetic algorithm for permutation flow shop scheduling.

PubMed

Liu, Ruochen; Ma, Chenlin; Ma, Wenping; Li, Yangyang

2013-01-01

The permutation flow shop scheduling problem (PFSSP) is part of production scheduling, which belongs to the hardest combinatorial optimization problem. In this paper, a multipopulation particle swarm optimization (PSO) based memetic algorithm (MPSOMA) is proposed in this paper. In the proposed algorithm, the whole particle swarm population is divided into three subpopulations in which each particle evolves itself by the standard PSO and then updates each subpopulation by using different local search schemes such as variable neighborhood search (VNS) and individual improvement scheme (IIS). Then, the best particle of each subpopulation is selected to construct a probabilistic model by using estimation of distribution algorithm (EDA) and three particles are sampled from the probabilistic model to update the worst individual in each subpopulation. The best particle in the entire particle swarm is used to update the global optimal solution. The proposed MPSOMA is compared with two recently proposed algorithms, namely, PSO based memetic algorithm (PSOMA) and hybrid particle swarm optimization with estimation of distribution algorithm (PSOEDA), on 29 well-known PFFSPs taken from OR-library, and the experimental results show that it is an effective approach for the PFFSP.

A Comparison of Techniques for Scheduling Fleets of Earth-Observing Satellites

NASA Technical Reports Server (NTRS)

Globus, Al; Crawford, James; Lohn, Jason; Pryor, Anna

2003-01-01

Earth observing satellite (EOS) scheduling is a complex real-world domain representative of a broad class of over-subscription scheduling problems. Over-subscription problems are those where requests for a facility exceed its capacity. These problems arise in a wide variety of NASA and terrestrial domains and are .XI important class of scheduling problems because such facilities often represent large capital investments. We have run experiments comparing multiple variants of the genetic algorithm, hill climbing, simulated annealing, squeaky wheel optimization and iterated sampling on two variants of a realistically-sized model of the EOS scheduling problem. These are implemented as permutation-based methods; methods that search in the space of priority orderings of observation requests and evaluate each permutation by using it to drive a greedy scheduler. Simulated annealing performs best and random mutation operators outperform our squeaky (more intelligent) operator. Furthermore, taking smaller steps towards the end of the search improves performance.

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.

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.

PubMed

Gel, Bernat; Díez-Villanueva, Anna; Serra, Eduard; Buschbeck, Marcus; Peinado, Miguel A; Malinverni, Roberto

2016-01-15

Statistically assessing the relation between a set of genomic regions and other genomic features is a common challenging task in genomic and epigenomic analyses. Randomization based approaches implicitly take into account the complexity of the genome without the need of assuming an underlying statistical model. regioneR is an R package that implements a permutation test framework specifically designed to work with genomic regions. In addition to the predefined randomization and evaluation strategies, regioneR is fully customizable allowing the use of custom strategies to adapt it to specific questions. Finally, it also implements a novel function to evaluate the local specificity of the detected association. regioneR is an R package released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/regioneR). rmalinverni@carrerasresearch.org. © The Author 2015. Published by Oxford University Press.

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…

METABOLIC EFFECTS OF ANGULATION, COMPRESSION AND REDUCED MOBILITY ON ANNULUS FIBROSIS IN A MODEL OF ALTERED MECHANICAL ENVIRONMENT IN SCOLIOSIS

PubMed Central

Stokes, Ian A.F.; McBride, Carole; Aronsson, David D.; Roughley, Peter J.

2013-01-01

Study Design Comparison of disc tissue from rat tails in six groups having different mechanical conditions imposed. Objectives To identify disc annulus changes associated with the supposed altered biomechanical environment in a spine with scoliosis deformity using an immature rat model that produces disc narrowing and wedging. Background Intervertebral discs become wedged and narrowed in a scoliosis curve, probably due in part to altered biomechanical environment. Methods Tail discs of 5-week-old immature Sprague-Dawley rats were subjected to an altered mechanical environment using an external apparatus applying permutations of loading and deformity for 5 weeks. Four groups of rats (A) 15 degrees Angulation, (B) Angulation with 0.1 MPa Compression, (C) 0.1 MPa Compression, and (R) Reduced mobility, together with a sham and a control group were studied. Disc height changes and matrix composition (water, DNA, GAG and HA content) were measured after 5 weeks, and proline and sulphate incorporation and mRNA expression were measured at 5 days and 5 weeks. Results After 5 weeks, disc space was significantly narrowed relative to internal controls in all four intervention groups. Water content and cellularity (DNA content) were not different at interventional levels relative to internal controls and not different between the concave and convex sides of the angulated discs. There was increased GAG content in compressed tissue (in Groups B and C), as expected, and compression resulted in a decrease in hyaluronic acid size. Slightly increased incorporation of tritiated-proline into the concave side of angulated discs and compressed discs was observed. Asymmetries of gene expression in Groups A and B, and some group-wise differences, did not identify consistent patterns associating the discs’ responses to mechanical alterations. Conclusions Intervertebral discs in this model underwent substantial narrowing after 5 weeks, with minimal alteration in tissue composition and minimal evidence of metabolic changes. PMID:27927288

Overcoming the effects of false positives and threshold bias in graph theoretical analyses of neuroimaging data.

PubMed

Drakesmith, M; Caeyenberghs, K; Dutt, A; Lewis, G; David, A S; Jones, D K

2015-09-01

Graph theory (GT) is a powerful framework for quantifying topological features of neuroimaging-derived functional and structural networks. However, false positive (FP) connections arise frequently and influence the inferred topology of networks. Thresholding is often used to overcome this problem, but an appropriate threshold often relies on a priori assumptions, which will alter inferred network topologies. Four common network metrics (global efficiency, mean clustering coefficient, mean betweenness and smallworldness) were tested using a model tractography dataset. It was found that all four network metrics were significantly affected even by just one FP. Results also show that thresholding effectively dampens the impact of FPs, but at the expense of adding significant bias to network metrics. In a larger number (n=248) of tractography datasets, statistics were computed across random group permutations for a range of thresholds, revealing that statistics for network metrics varied significantly more than for non-network metrics (i.e., number of streamlines and number of edges). Varying degrees of network atrophy were introduced artificially to half the datasets, to test sensitivity to genuine group differences. For some network metrics, this atrophy was detected as significant (p<0.05, determined using permutation testing) only across a limited range of thresholds. We propose a multi-threshold permutation correction (MTPC) method, based on the cluster-enhanced permutation correction approach, to identify sustained significant effects across clusters of thresholds. This approach minimises requirements to determine a single threshold a priori. We demonstrate improved sensitivity of MTPC-corrected metrics to genuine group effects compared to an existing approach and demonstrate the use of MTPC on a previously published network analysis of tractography data derived from a clinical population. In conclusion, we show that there are large biases and instability induced by thresholding, making statistical comparisons of network metrics difficult. However, by testing for effects across multiple thresholds using MTPC, true group differences can be robustly identified. Copyright © 2015. Published by Elsevier Inc.

Proposed minimal panel of antibodies for cost-effectiveness and accuracy in acute leukemias immunophenotyping: Prospective study at a tertiary care center.

PubMed

Singh, Neha; Pati, Hara Prasad P; Tyagi, Seema; Deka, Roopam; Sharma, Rahul; Saxena, Renu

2016-07-01

Flowcytometry has an essential role in the diagnosis and classification of acute leukemias. However, there exists a great degree of inter-laboratory variability on issues like panel selection, antibody combinations, gating strategies, fluorochromes, and clonal selection. The primary aim of this study was to derive a minimal panel of antibodies and evaluate its diagnostic usefulness in acute leukemias by flowcytometry by using the detailed immune-phenotype of different lineage-specific or non-specific markers. This prospective observational study involved 400 newly diagnosed cases of acute leukemias. Bone marrow aspirate samples were subjected to morphological evaluation, cytogenetics and flow cytometric immunophenotyping. A minimal panel of eight antibodies comprising of CD45/CD34/CD19/MPO/cytoCD3/CD64/CD117/CD79a was derived by applying different permutations and combinations with a diagnostic yield of 97.5%. The minimal panel was further validated by testing in an independent cohort of patients with similar demographic characteristics, where it showed a high diagnostic yield of 98% in comparison with the screening panels proposed by other recently published studies. It may be concluded that the diagnostic performance of the eight antibody panel is better than most other panels used across the different laboratories in terms of yield, number of antibodies used and the scientific approach used to derive and validate the results and so henceforth may be applied in any setting with limited resources for better diagnostic accuracy.

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.

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…

Permutation Entropy and Signal Energy Increase the Accuracy of Neuropathic Change Detection in Needle EMG

PubMed Central

2018-01-01

Background and Objective. Needle electromyography can be used to detect the number of changes and morphological changes in motor unit potentials of patients with axonal neuropathy. General mathematical methods of pattern recognition and signal analysis were applied to recognize neuropathic changes. This study validates the possibility of extending and refining turns-amplitude analysis using permutation entropy and signal energy. Methods. In this study, we examined needle electromyography in 40 neuropathic individuals and 40 controls. The number of turns, amplitude between turns, signal energy, and “permutation entropy” were used as features for support vector machine classification. Results. The obtained results proved the superior classification performance of the combinations of all of the above-mentioned features compared to the combinations of fewer features. The lowest accuracy from the tested combinations of features had peak-ratio analysis. Conclusion. Using the combination of permutation entropy with signal energy, number of turns and mean amplitude in SVM classification can be used to refine the diagnosis of polyneuropathies examined by needle electromyography. PMID:29606959

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.

Multi-scale symbolic transfer entropy analysis of EEG

NASA Astrophysics Data System (ADS)

Yao, Wenpo; Wang, Jun

2017-10-01

From both global and local perspectives, we symbolize two kinds of EEG and analyze their dynamic and asymmetrical information using multi-scale transfer entropy. Multi-scale process with scale factor from 1 to 199 and step size of 2 is applied to EEG of healthy people and epileptic patients, and then the permutation with embedding dimension of 3 and global approach are used to symbolize the sequences. The forward and reverse symbol sequences are taken as the inputs of transfer entropy. Scale factor intervals of permutation and global way are (37, 57) and (65, 85) where the two kinds of EEG have satisfied entropy distinctions. When scale factor is 67, transfer entropy of the healthy and epileptic subjects of permutation, 0.1137 and 0.1028, have biggest difference. And the corresponding values of the global symbolization is 0.0641 and 0.0601 which lies in the scale factor of 165. Research results show that permutation which takes contribution of local information has better distinction and is more effectively applied to our multi-scale transfer entropy analysis of EEG.

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.

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.

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.

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

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 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

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

Permutation testing of orthogonal factorial effects in a language-processing experiment using fMRI.

PubMed

Suckling, John; Davis, Matthew H; Ooi, Cinly; Wink, Alle Meije; Fadili, Jalal; Salvador, Raymond; Welchew, David; Sendur, Levent; Maxim, Vochita; Bullmore, Edward T

2006-05-01

The block-paradigm of the Functional Image Analysis Contest (FIAC) dataset was analysed with the Brain Activation and Morphological Mapping software. Permutation methods in the wavelet domain were used for inference on cluster-based test statistics of orthogonal contrasts relevant to the factorial design of the study, namely: the average response across all active blocks, the main effect of speaker, the main effect of sentence, and the interaction between sentence and speaker. Extensive activation was seen with all these contrasts. In particular, different vs. same-speaker blocks produced elevated activation in bilateral regions of the superior temporal lobe and repetition suppression for linguistic materials (same vs. different-sentence blocks) in left inferior frontal regions. These are regions previously reported in the literature. Additional regions were detected in this study, perhaps due to the enhanced sensitivity of the methodology. Within-block sentence suppression was tested post-hoc by regression of an exponential decay model onto the extracted time series from the left inferior frontal gyrus, but no strong evidence of such an effect was found. The significance levels set for the activation maps are P-values at which we expect <1 false-positive cluster per image. Nominal type I error control was verified by empirical testing of a test statistic corresponding to a randomly ordered design matrix. The small size of the BOLD effect necessitates sensitive methods of detection of brain activation. Permutation methods permit the necessary flexibility to develop novel test statistics to meet this challenge.

Local and Regional Determinants of an Uncommon Functional Group in Freshwater Lakes and Ponds

PubMed Central

McCann, Michael James

2015-01-01

A combination of local and regional factors and stochastic forces is expected to determine the occurrence of species and the structure of communities. However, in most cases, our understanding is incomplete, with large amounts of unexplained variation. Using functional groups rather than individual species may help explain the relationship between community composition and conditions. In this study, I used survey data from freshwater lakes and ponds to understand factors that determine the presence of the floating plant functional group in the northeast United States. Of the 176 water bodies surveyed, 104 (59.1%) did not contain any floating plant species. The occurrence of this functional group was largely determined by local abiotic conditions, which were spatially autocorrelated across the region. A model predicting the presence of the floating plant functional group performed similarly to the best species-specific models. Using a permutation test, I also found that the observed prevalence of floating plants is no different than expected by random assembly from a species pool of its size. These results suggest that the size of the species pool interacts with local conditions in determining the presence of a functional group. Nevertheless, a large amount of unexplained variation remains, attributable to either stochastic species occurrence or incomplete predictive models. The simple permutation approach in this study can be extended to test alternative models of community assembly. PMID:26121636

Linkage analysis of alternative anxiety phenotypes in multiply affected panic disorder families

PubMed Central

Fyer, Abby J.; Costa, Ramiro; Haghighi, Fatemeh; Logue, Mark W.; Knowles, James A.; Weissman, Myrna M.; Hodge, Susan E.; Hamilton, Steven P.

2013-01-01

Background The choice of phenotype definitions for genetic studies of panic and phobic disorders is complicated by family, twin and neurobiological data indicating both distinct and shared risk factors as well as heterogeneity within categories. We previously reported a genome scan in 120 multiplex panic disorder (PD) families using a phenotype that closely adhered to the DSM IV PD definition. Here we extend this work by conducting exploratory linkage analyses in this same pedigree set using ten additional literature- based panic and phobia-related phenotypes that take into account aspects of these hypothesized complexities. Methods Multiply affected families (> 2 individuals with PD) were recruited from clinical and non-clinical sources, evaluated by clinician administered semi-structured interview and subsequent blind consensus best estimate procedure. Each phenotype was analyzed under dominant and recessive models using parametric 2-point (homogeneity and heterogeneity), multipoint, and non-parametric methods. Empirically based permutations were used to estimate model specific and global (across all phenotypes) p-values. Results The highest score was a 2-point lod (4.27, global p < 0.08) on chromosome 13 (D13S793, 76cM) for the phenotype “specific or social phobia” under a recessive model and conditions of homogeneity. There was minimal support for linkage to any of the remaining nine phenotypes. Conclusions Though interpretation of findings is limited by sample size and the large number of phenotypes and models analyzed these data suggest a region on chromosome 13 as a potential site for further exploration in relation to risk for specific and social phobias. PMID:22525237

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…

Weighted multiscale Rényi permutation entropy of nonlinear time series

NASA Astrophysics Data System (ADS)

Chen, Shijian; Shang, Pengjian; Wu, Yue

2018-04-01

In this paper, based on Rényi permutation entropy (RPE), which has been recently suggested as a relative measure of complexity in nonlinear systems, we propose multiscale Rényi permutation entropy (MRPE) and weighted multiscale Rényi permutation entropy (WMRPE) to quantify the complexity of nonlinear time series over multiple time scales. First, we apply MPRE and WMPRE to the synthetic data and make a comparison of modified methods and RPE. Meanwhile, the influence of the change of parameters is discussed. Besides, we interpret the necessity of considering not only multiscale but also weight by taking the amplitude into account. Then MRPE and WMRPE methods are employed to the closing prices of financial stock markets from different areas. By observing the curves of WMRPE and analyzing the common statistics, stock markets are divided into 4 groups: (1) DJI, S&P500, and HSI, (2) NASDAQ and FTSE100, (3) DAX40 and CAC40, and (4) ShangZheng and ShenCheng. Results show that the standard deviations of weighted methods are smaller, showing WMRPE is able to ensure the results more robust. Besides, WMPRE can provide abundant dynamical properties of complex systems, and demonstrate the intrinsic mechanism.

Confidence intervals and hypothesis testing for the Permutation Entropy with an application to epilepsy

NASA Astrophysics Data System (ADS)

Traversaro, Francisco; O. Redelico, Francisco

2018-04-01

In nonlinear dynamics, and to a lesser extent in other fields, a widely used measure of complexity is the Permutation Entropy. But there is still no known method to determine the accuracy of this measure. There has been little research on the statistical properties of this quantity that characterize time series. The literature describes some resampling methods of quantities used in nonlinear dynamics - as the largest Lyapunov exponent - but these seems to fail. In this contribution, we propose a parametric bootstrap methodology using a symbolic representation of the time series to obtain the distribution of the Permutation Entropy estimator. We perform several time series simulations given by well-known stochastic processes: the 1/fα noise family, and show in each case that the proposed accuracy measure is as efficient as the one obtained by the frequentist approach of repeating the experiment. The complexity of brain electrical activity, measured by the Permutation Entropy, has been extensively used in epilepsy research for detection in dynamical changes in electroencephalogram (EEG) signal with no consideration of the variability of this complexity measure. An application of the parametric bootstrap methodology is used to compare normal and pre-ictal EEG signals.

An Analysis of Document Category Prediction Responses to Classifier Model Parameter Treatment Permutations within the Software Design Patterns Subject Domain

ERIC Educational Resources Information Center

Pankau, Brian L.

2009-01-01

This empirical study evaluates the document category prediction effectiveness of Naive Bayes (NB) and K-Nearest Neighbor (KNN) classifier treatments built from different feature selection and machine learning settings and trained and tested against textual corpora of 2300 Gang-Of-Four (GOF) design pattern documents. Analysis of the experiment's…

A power analysis for multivariate tests of temporal trend in species composition.

PubMed

Irvine, Kathryn M; Dinger, Eric C; Sarr, Daniel

2011-10-01

Long-term monitoring programs emphasize power analysis as a tool to determine the sampling effort necessary to effectively document ecologically significant changes in ecosystems. Programs that monitor entire multispecies assemblages require a method for determining the power of multivariate statistical models to detect trend. We provide a method to simulate presence-absence species assemblage data that are consistent with increasing or decreasing directional change in species composition within multiple sites. This step is the foundation for using Monte Carlo methods to approximate the power of any multivariate method for detecting temporal trends. We focus on comparing the power of the Mantel test, permutational multivariate analysis of variance, and constrained analysis of principal coordinates. We find that the power of the various methods we investigate is sensitive to the number of species in the community, univariate species patterns, and the number of sites sampled over time. For increasing directional change scenarios, constrained analysis of principal coordinates was as or more powerful than permutational multivariate analysis of variance, the Mantel test was the least powerful. However, in our investigation of decreasing directional change, the Mantel test was typically as or more powerful than the other models.

A ripple-spreading genetic algorithm for the aircraft sequencing problem.

PubMed

Hu, Xiao-Bing; Di Paolo, Ezequiel A

2011-01-01

When genetic algorithms (GAs) are applied to combinatorial problems, permutation representations are usually adopted. As a result, such GAs are often confronted with feasibility and memory-efficiency problems. With the aircraft sequencing problem (ASP) as a study case, this paper reports on a novel binary-representation-based GA scheme for combinatorial problems. Unlike existing GAs for the ASP, which typically use permutation representations based on aircraft landing order, the new GA introduces a novel ripple-spreading model which transforms the original landing-order-based ASP solutions into value-based ones. In the new scheme, arriving aircraft are projected as points into an artificial space. A deterministic method inspired by the natural phenomenon of ripple-spreading on liquid surfaces is developed, which uses a few parameters as input to connect points on this space to form a landing sequence. A traditional GA, free of feasibility and memory-efficiency problems, can then be used to evolve the ripple-spreading related parameters in order to find an optimal sequence. Since the ripple-spreading model is the centerpiece of the new algorithm, it is called the ripple-spreading GA (RSGA). The advantages of the proposed RSGA are illustrated by extensive comparative studies for the case of the ASP.

A Multipopulation PSO Based Memetic Algorithm for Permutation Flow Shop Scheduling

PubMed Central

Liu, Ruochen; Ma, Chenlin; Ma, Wenping; Li, Yangyang

2013-01-01

The permutation flow shop scheduling problem (PFSSP) is part of production scheduling, which belongs to the hardest combinatorial optimization problem. In this paper, a multipopulation particle swarm optimization (PSO) based memetic algorithm (MPSOMA) is proposed in this paper. In the proposed algorithm, the whole particle swarm population is divided into three subpopulations in which each particle evolves itself by the standard PSO and then updates each subpopulation by using different local search schemes such as variable neighborhood search (VNS) and individual improvement scheme (IIS). Then, the best particle of each subpopulation is selected to construct a probabilistic model by using estimation of distribution algorithm (EDA) and three particles are sampled from the probabilistic model to update the worst individual in each subpopulation. The best particle in the entire particle swarm is used to update the global optimal solution. The proposed MPSOMA is compared with two recently proposed algorithms, namely, PSO based memetic algorithm (PSOMA) and hybrid particle swarm optimization with estimation of distribution algorithm (PSOEDA), on 29 well-known PFFSPs taken from OR-library, and the experimental results show that it is an effective approach for the PFFSP. PMID:24453841

Time series segmentation: a new approach based on Genetic Algorithm and Hidden Markov Model

NASA Astrophysics Data System (ADS)

Toreti, A.; Kuglitsch, F. G.; Xoplaki, E.; Luterbacher, J.

2009-04-01

The subdivision of a time series into homogeneous segments has been performed using various methods applied to different disciplines. In climatology, for example, it is accompanied by the well-known homogenization problem and the detection of artificial change points. In this context, we present a new method (GAMM) based on Hidden Markov Model (HMM) and Genetic Algorithm (GA), applicable to series of independent observations (and easily adaptable to autoregressive processes). A left-to-right hidden Markov model, estimating the parameters and the best-state sequence, respectively, with the Baum-Welch and Viterbi algorithms, was applied. In order to avoid the well-known dependence of the Baum-Welch algorithm on the initial condition, a Genetic Algorithm was developed. This algorithm is characterized by mutation, elitism and a crossover procedure implemented with some restrictive rules. Moreover the function to be minimized was derived following the approach of Kehagias (2004), i.e. it is the so-called complete log-likelihood. The number of states was determined applying a two-fold cross-validation procedure (Celeux and Durand, 2008). Being aware that the last issue is complex, and it influences all the analysis, a Multi Response Permutation Procedure (MRPP; Mielke et al., 1981) was inserted. It tests the model with K+1 states (where K is the state number of the best model) if its likelihood is close to K-state model. Finally, an evaluation of the GAMM performances, applied as a break detection method in the field of climate time series homogenization, is shown. 1. G. Celeux and J.B. Durand, Comput Stat 2008. 2. A. Kehagias, Stoch Envir Res 2004. 3. P.W. Mielke, K.J. Berry, G.W. Brier, Monthly Wea Rev 1981.

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.

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).

Information transmission and signal permutation in active flow networks

NASA Astrophysics Data System (ADS)

Woodhouse, Francis G.; Fawcett, Joanna B.; Dunkel, Jörn

2018-03-01

Recent experiments show that both natural and artificial microswimmers in narrow channel-like geometries will self-organise to form steady, directed flows. This suggests that networks of flowing active matter could function as novel autonomous microfluidic devices. However, little is known about how information propagates through these far-from-equilibrium systems. Through a mathematical analogy with spin-ice vertex models, we investigate here the input–output characteristics of generic incompressible active flow networks (AFNs). Our analysis shows that information transport through an AFN is inherently different from conventional pressure or voltage driven networks. Active flows on hexagonal arrays preserve input information over longer distances than their passive counterparts and are highly sensitive to bulk topological defects, whose presence can be inferred from marginal input–output distributions alone. This sensitivity further allows controlled permutations on parallel inputs, revealing an unexpected link between active matter and group theory that can guide new microfluidic mixing strategies facilitated by active matter and aid the design of generic autonomous information transport networks.

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

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.

Boundary perimeter Bethe ansatz

NASA Astrophysics Data System (ADS)

Frassek, Rouven

2017-06-01

We study the partition function of the six-vertex model in the rational limit on arbitrary Baxter lattices with reflecting boundary. Every such lattice is interpreted as an invariant of the twisted Yangian. This identification allows us to relate the partition function of the vertex model to the Bethe wave function of an open spin chain. We obtain the partition function in terms of creation operators on a reference state from the algebraic Bethe ansatz and as a sum of permutations and reflections from the coordinate Bethe ansatz.

Optimization of the temporal pattern of radiation: An IMRT based study

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

Altman, Michael B.; Chmura, Steven J.; Deasy, Joseph O.

Purpose: To investigate how the temporal pattern of dose applied during a single-intensity modulated radiation therapy (IMRT) fraction can be arranged to maximize or minimize cell kill. Methods and Materials: Using the linear-quadratic repair-time model and a simplified IMRT delivery pattern model, the surviving fraction of cells for a single fraction was calculated for all permutations of the dose delivery pattern for an array of clinically based IMRT cases. Maximization of cell kill was achieved by concentrating the highest doses in the middle of a fraction, while minimization was achieved by spreading the highest doses between the beginning and end.more » The percent difference between maximum and minimum cell kill (%Diff{sub min/max}) and the difference between maximum and minimum total doses normalized to 2 Gy/fx ({delta}NTD{sub 2Gy}) was calculated for varying fraction durations (T), {alpha}/{beta} ratios, and doses/fx. Results: %Diff{sub min/max} and {delta}NTD{sub 2Gy} both increased with increasing T and with decreasing {alpha}/{beta}. The largest increases occurred with dose/fx. With {alpha}/{beta} = 3 Gy and 30 min/fx, %Diff{sub min/max} ranged from 2.7-5.3% for 2 Gy/fx to 48.6-74.1% for 10 Gy/fx, whereas {delta}NTD{sub 2Gy} ranged from 1.2 Gy-2.4 Gy for 30 fractions of 2 Gy/fx to 2.3-4.8 Gy for 2 fractions of 10.84 Gy/fx. Using {alpha}/{beta} = 1.5 Gy, an analysis of prostate hypofractionation schemes yielded differences in clinical outcome based on the pattern of applied dose ranging from 3.2%-6.1% of the treated population. Conclusions: Rearrangement of the temporal pattern of dose for a single IMRT fraction could be used to optimize cell kill and to directly, though modestly, affect treatment outcome.« less

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.

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.

An Affine Invariant Bivariate Version of the Sign Test.

DTIC Science & Technology

1987-06-01

words: affine invariance, bivariate quantile, bivariate symmetry, model,. generalized median, influence function , permutation test, normal efficiency...calculate a bivariate version of the influence function , and the resulting form is bounded, as is the case for the univartate sign test, and shows the...terms of a blvariate analogue of IHmpel’s (1974) influence function . The latter, though usually defined as a von-Mises derivative of certain

DEEP ATTRACTOR NETWORK FOR SINGLE-MICROPHONE SPEAKER SEPARATION.

PubMed

Chen, Zhuo; Luo, Yi; Mesgarani, Nima

2017-03-01

Despite the overwhelming success of deep learning in various speech processing tasks, the problem of separating simultaneous speakers in a mixture remains challenging. Two major difficulties in such systems are the arbitrary source permutation and unknown number of sources in the mixture. We propose a novel deep learning framework for single channel speech separation by creating attractor points in high dimensional embedding space of the acoustic signals which pull together the time-frequency bins corresponding to each source. Attractor points in this study are created by finding the centroids of the sources in the embedding space, which are subsequently used to determine the similarity of each bin in the mixture to each source. The network is then trained to minimize the reconstruction error of each source by optimizing the embeddings. The proposed model is different from prior works in that it implements an end-to-end training, and it does not depend on the number of sources in the mixture. Two strategies are explored in the test time, K-means and fixed attractor points, where the latter requires no post-processing and can be implemented in real-time. We evaluated our system on Wall Street Journal dataset and show 5.49% improvement over the previous state-of-the-art methods.

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

Research of Planetary Gear Fault Diagnosis Based on Permutation Entropy of CEEMDAN and ANFIS

PubMed Central

Kuai, Moshen; Cheng, Gang; Li, Yong

2018-01-01

For planetary gear has the characteristics of small volume, light weight and large transmission ratio, it is widely used in high speed and high power mechanical system. Poor working conditions result in frequent failures of planetary gear. A method is proposed for diagnosing faults in planetary gear based on permutation entropy of Complete Ensemble Empirical Mode Decomposition with Adaptive Noise (CEEMDAN) Adaptive Neuro-fuzzy Inference System (ANFIS) in this paper. The original signal is decomposed into 6 intrinsic mode functions (IMF) and residual components by CEEMDAN. Since the IMF contains the main characteristic information of planetary gear faults, time complexity of IMFs are reflected by permutation entropies to quantify the fault features. The permutation entropies of each IMF component are defined as the input of ANFIS, and its parameters and membership functions are adaptively adjusted according to training samples. Finally, the fuzzy inference rules are determined, and the optimal ANFIS is obtained. The overall recognition rate of the test sample used for ANFIS is 90%, and the recognition rate of gear with one missing tooth is relatively high. The recognition rates of different fault gears based on the method can also achieve better results. Therefore, the proposed method can be applied to planetary gear fault diagnosis effectively. PMID:29510569

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

Research of Planetary Gear Fault Diagnosis Based on Permutation Entropy of CEEMDAN and ANFIS.

PubMed

Kuai, Moshen; Cheng, Gang; Pang, Yusong; Li, Yong

2018-03-05

For planetary gear has the characteristics of small volume, light weight and large transmission ratio, it is widely used in high speed and high power mechanical system. Poor working conditions result in frequent failures of planetary gear. A method is proposed for diagnosing faults in planetary gear based on permutation entropy of Complete Ensemble Empirical Mode Decomposition with Adaptive Noise (CEEMDAN) Adaptive Neuro-fuzzy Inference System (ANFIS) in this paper. The original signal is decomposed into 6 intrinsic mode functions (IMF) and residual components by CEEMDAN. Since the IMF contains the main characteristic information of planetary gear faults, time complexity of IMFs are reflected by permutation entropies to quantify the fault features. The permutation entropies of each IMF component are defined as the input of ANFIS, and its parameters and membership functions are adaptively adjusted according to training samples. Finally, the fuzzy inference rules are determined, and the optimal ANFIS is obtained. The overall recognition rate of the test sample used for ANFIS is 90%, and the recognition rate of gear with one missing tooth is relatively high. The recognition rates of different fault gears based on the method can also achieve better results. Therefore, the proposed method can be applied to planetary gear fault diagnosis effectively.

Cut and join operator ring in tensor models

NASA Astrophysics Data System (ADS)

Itoyama, H.; Mironov, A.; Morozov, A.

2018-07-01

Recent advancement of rainbow tensor models based on their superintegrability (manifesting itself as the existence of an explicit expression for a generic Gaussian correlator) has allowed us to bypass the long-standing problem seen as the lack of eigenvalue/determinant representation needed to establish the KP/Toda integrability. As the mandatory next step, we discuss in this paper how to provide an adequate designation to each of the connected gauge-invariant operators that form a double coset, which is required to cleverly formulate a tree-algebra generalization of the Virasoro constraints. This problem goes beyond the enumeration problem per se tied to the permutation group, forcing us to introduce a few gauge fixing procedures to the coset. We point out that the permutation-based labeling, which has proven to be relevant for the Gaussian averages is, via interesting complexity, related to the one based on the keystone trees, whose algebra will provide the tensor counterpart of the Virasoro algebra for matrix models. Moreover, our simple analysis reveals the existence of nontrivial kernels and co-kernels for the cut operation and for the join operation respectively that prevent a straightforward construction of the non-perturbative RG-complete partition function and the identification of truly independent time variables. We demonstrate these problems by the simplest non-trivial Aristotelian RGB model with one complex rank-3 tensor, studying its ring of gauge-invariant operators, generated by the keystone triple with the help of four operations: addition, multiplication, cut and join.

Testing the significance of a correlation with nonnormal data: comparison of Pearson, Spearman, transformation, and resampling approaches.

PubMed

Bishara, Anthony J; Hittner, James B

2012-09-01

It is well known that when data are nonnormally distributed, a test of the significance of Pearson's r may inflate Type I error rates and reduce power. Statistics textbooks and the simulation literature provide several alternatives to Pearson's correlation. However, the relative performance of these alternatives has been unclear. Two simulation studies were conducted to compare 12 methods, including Pearson, Spearman's rank-order, transformation, and resampling approaches. With most sample sizes (n ≥ 20), Type I and Type II error rates were minimized by transforming the data to a normal shape prior to assessing the Pearson correlation. Among transformation approaches, a general purpose rank-based inverse normal transformation (i.e., transformation to rankit scores) was most beneficial. However, when samples were both small (n ≤ 10) and extremely nonnormal, the permutation test often outperformed other alternatives, including various bootstrap tests.

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.

An effective PSO-based memetic algorithm for flow shop scheduling.

PubMed

Liu, Bo; Wang, Ling; Jin, Yi-Hui

2007-02-01

This paper proposes an effective particle swarm optimization (PSO)-based memetic algorithm (MA) for the permutation flow shop scheduling problem (PFSSP) with the objective to minimize the maximum completion time, which is a typical non-deterministic polynomial-time (NP) hard combinatorial optimization problem. In the proposed PSO-based MA (PSOMA), both PSO-based searching operators and some special local searching operators are designed to balance the exploration and exploitation abilities. In particular, the PSOMA applies the evolutionary searching mechanism of PSO, which is characterized by individual improvement, population cooperation, and competition to effectively perform exploration. On the other hand, the PSOMA utilizes several adaptive local searches to perform exploitation. First, to make PSO suitable for solving PFSSP, a ranked-order value rule based on random key representation is presented to convert the continuous position values of particles to job permutations. Second, to generate an initial swarm with certain quality and diversity, the famous Nawaz-Enscore-Ham (NEH) heuristic is incorporated into the initialization of population. Third, to balance the exploration and exploitation abilities, after the standard PSO-based searching operation, a new local search technique named NEH_1 insertion is probabilistically applied to some good particles selected by using a roulette wheel mechanism with a specified probability. Fourth, to enrich the searching behaviors and to avoid premature convergence, a simulated annealing (SA)-based local search with multiple different neighborhoods is designed and incorporated into the PSOMA. Meanwhile, an effective adaptive meta-Lamarckian learning strategy is employed to decide which neighborhood to be used in SA-based local search. Finally, to further enhance the exploitation ability, a pairwise-based local search is applied after the SA-based search. Simulation results based on benchmarks demonstrate the effectiveness of the PSOMA. Additionally, the effects of some parameters on optimization performances are also discussed.

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

Data Decomposition Techniques with Multi-Scale Permutation Entropy Calculations for Bearing Fault Diagnosis

PubMed Central

Yasir, Muhammad Naveed; Koh, Bong-Hwan

2018-01-01

This paper presents the local mean decomposition (LMD) integrated with multi-scale permutation entropy (MPE), also known as LMD-MPE, to investigate the rolling element bearing (REB) fault diagnosis from measured vibration signals. First, the LMD decomposed the vibration data or acceleration measurement into separate product functions that are composed of both amplitude and frequency modulation. MPE then calculated the statistical permutation entropy from the product functions to extract the nonlinear features to assess and classify the condition of the healthy and damaged REB system. The comparative experimental results of the conventional LMD-based multi-scale entropy and MPE were presented to verify the authenticity of the proposed technique. The study found that LMD-MPE’s integrated approach provides reliable, damage-sensitive features when analyzing the bearing condition. The results of REB experimental datasets show that the proposed approach yields more vigorous outcomes than existing methods. PMID:29690526

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 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.

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.

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.

Data Decomposition Techniques with Multi-Scale Permutation Entropy Calculations for Bearing Fault Diagnosis.

PubMed

Yasir, Muhammad Naveed; Koh, Bong-Hwan

2018-04-21

This paper presents the local mean decomposition (LMD) integrated with multi-scale permutation entropy (MPE), also known as LMD-MPE, to investigate the rolling element bearing (REB) fault diagnosis from measured vibration signals. First, the LMD decomposed the vibration data or acceleration measurement into separate product functions that are composed of both amplitude and frequency modulation. MPE then calculated the statistical permutation entropy from the product functions to extract the nonlinear features to assess and classify the condition of the healthy and damaged REB system. The comparative experimental results of the conventional LMD-based multi-scale entropy and MPE were presented to verify the authenticity of the proposed technique. The study found that LMD-MPE’s integrated approach provides reliable, damage-sensitive features when analyzing the bearing condition. The results of REB experimental datasets show that the proposed approach yields more vigorous outcomes than existing methods.

Thresholding functional connectomes by means of mixture modeling.

PubMed

Bielczyk, Natalia Z; Walocha, Fabian; Ebel, Patrick W; Haak, Koen V; Llera, Alberto; Buitelaar, Jan K; Glennon, Jeffrey C; Beckmann, Christian F

2018-05-01

Functional connectivity has been shown to be a very promising tool for studying the large-scale functional architecture of the human brain. In network research in fMRI, functional connectivity is considered as a set of pair-wise interactions between the nodes of the network. These interactions are typically operationalized through the full or partial correlation between all pairs of regional time series. Estimating the structure of the latent underlying functional connectome from the set of pair-wise partial correlations remains an open research problem though. Typically, this thresholding problem is approached by proportional thresholding, or by means of parametric or non-parametric permutation testing across a cohort of subjects at each possible connection. As an alternative, we propose a data-driven thresholding approach for network matrices on the basis of mixture modeling. This approach allows for creating subject-specific sparse connectomes by modeling the full set of partial correlations as a mixture of low correlation values associated with weak or unreliable edges in the connectome and a sparse set of reliable connections. Consequently, we propose to use alternative thresholding strategy based on the model fit using pseudo-False Discovery Rates derived on the basis of the empirical null estimated as part of the mixture distribution. We evaluate the method on synthetic benchmark fMRI datasets where the underlying network structure is known, and demonstrate that it gives improved performance with respect to the alternative methods for thresholding connectomes, given the canonical thresholding levels. We also demonstrate that mixture modeling gives highly reproducible results when applied to the functional connectomes of the visual system derived from the n-back Working Memory task in the Human Connectome Project. The sparse connectomes obtained from mixture modeling are further discussed in the light of the previous knowledge of the functional architecture of the visual system in humans. We also demonstrate that with use of our method, we are able to extract similar information on the group level as can be achieved with permutation testing even though these two methods are not equivalent. We demonstrate that with both of these methods, we obtain functional decoupling between the two hemispheres in the higher order areas of the visual cortex during visual stimulation as compared to the resting state, which is in line with previous studies suggesting lateralization in the visual processing. However, as opposed to permutation testing, our approach does not require inference at the cohort level and can be used for creating sparse connectomes at the level of a single subject. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

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

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

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.

MCMC genome rearrangement.

PubMed

Miklós, István

2003-10-01

As more and more genomes have been sequenced, genomic data is rapidly accumulating. Genome-wide mutations are believed more neutral than local mutations such as substitutions, insertions and deletions, therefore phylogenetic investigations based on inversions, transpositions and inverted transpositions are less biased by the hypothesis on neutral evolution. Although efficient algorithms exist for obtaining the inversion distance of two signed permutations, there is no reliable algorithm when both inversions and transpositions are considered. Moreover, different type of mutations happen with different rates, and it is not clear how to weight them in a distance based approach. We introduce a Markov Chain Monte Carlo method to genome rearrangement based on a stochastic model of evolution, which can estimate the number of different evolutionary events needed to sort a signed permutation. The performance of the method was tested on simulated data, and the estimated numbers of different types of mutations were reliable. Human and Drosophila mitochondrial data were also analysed with the new method. The mixing time of the Markov Chain is short both in terms of CPU times and number of proposals. The source code in C is available on request from the author.

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

A novel iterative mixed model to remap three complex orthopedic traits in dogs

PubMed Central

Huang, Meng; Hayward, Jessica J.; Corey, Elizabeth; Garrison, Susan J.; Wagner, Gabriela R.; Krotscheck, Ursula; Hayashi, Kei; Schweitzer, Peter A.; Lust, George; Boyko, Adam R.; Todhunter, Rory J.

2017-01-01

Hip dysplasia (HD), elbow dysplasia (ED), and rupture of the cranial (anterior) cruciate ligament (RCCL) are the most common complex orthopedic traits of dogs and all result in debilitating osteoarthritis. We reanalyzed previously reported data: the Norberg angle (a quantitative measure of HD) in 921 dogs, ED in 113 cases and 633 controls, and RCCL in 271 cases and 399 controls and their genotypes at ~185,000 single nucleotide polymorphisms. A novel fixed and random model with a circulating probability unification (FarmCPU) function, with marker-based principal components and a kinship matrix to correct for population stratification, was used. A Bonferroni correction at p<0.01 resulted in a P< 6.96 ×10−8. Six loci were identified; three for HD and three for RCCL. An associated locus at CFA28:34,369,342 for HD was described previously in the same dogs using a conventional mixed model. No loci were identified for RCCL in the previous report but the two loci for ED in the previous report did not reach genome-wide significance using the FarmCPU model. These results were supported by simulation which demonstrated that the FarmCPU held no power advantage over the linear mixed model for the ED sample but provided additional power for the HD and RCCL samples. Candidate genes for HD and RCCL are discussed. When using FarmCPU software, we recommend a resampling test, that a positive control be used to determine the optimum pseudo quantitative trait nucleotide-based covariate structure of the model, and a negative control be used consisting of permutation testing and the identical resampling test as for the non-permuted phenotypes. PMID:28614352

Autocalibration of a one-dimensional hydrodynamic-ecological model (DYRESM 4.0-CAEDYM 3.1) using a Monte Carlo approach: simulations of hypoxic events in a polymictic lake

NASA Astrophysics Data System (ADS)

Luo, Liancong; Hamilton, David; Lan, Jia; McBride, Chris; Trolle, Dennis

2018-03-01

Automated calibration of complex deterministic water quality models with a large number of biogeochemical parameters can reduce time-consuming iterative simulations involving empirical judgements of model fit. We undertook autocalibration of the one-dimensional hydrodynamic-ecological lake model DYRESM-CAEDYM, using a Monte Carlo sampling (MCS) method, in order to test the applicability of this procedure for shallow, polymictic Lake Rotorua (New Zealand). The calibration procedure involved independently minimizing the root-mean-square error (RMSE), maximizing the Pearson correlation coefficient (r) and Nash-Sutcliffe efficient coefficient (Nr) for comparisons of model state variables against measured data. An assigned number of parameter permutations was used for 10 000 simulation iterations. The "optimal" temperature calibration produced a RMSE of 0.54 °C, Nr value of 0.99, and r value of 0.98 through the whole water column based on comparisons with 540 observed water temperatures collected between 13 July 2007 and 13 January 2009. The modeled bottom dissolved oxygen concentration (20.5 m below surface) was compared with 467 available observations. The calculated RMSE of the simulations compared with the measurements was 1.78 mg L-1, the Nr value was 0.75, and the r value was 0.87. The autocalibrated model was further tested for an independent data set by simulating bottom-water hypoxia events from 15 January 2009 to 8 June 2011 (875 days). This verification produced an accurate simulation of five hypoxic events corresponding to DO < 2 mg L-1 during summer of 2009-2011. The RMSE was 2.07 mg L-1, Nr value 0.62, and r value of 0.81, based on the available data set of 738 days. The autocalibration software of DYRESM-CAEDYM developed here is substantially less time-consuming and more efficient in parameter optimization than traditional manual calibration which has been the standard tool practiced for similar complex water quality models.

A MULTIPLE TESTING OF THE ABC METHOD AND THE DEVELOPMENT OF A SECOND GENERATION MODEL. PART I, PRELIMINARY DISCUSSIONS OF METHODOLOGY. SUPPLEMENT, COMPUTER PROGRAMS OF THE HDL INFORMATION SYSTEMS.

ERIC Educational Resources Information Center

ALTMANN, BERTHOLD; BROWN, WILLIAM G.

THE FIRST-GENERATION APPROACH BY CONCEPT (ABC) STORAGE AND RETRIEVAL METHOD, A METHOD WHICH UTILIZES AS A SUBJECT APPROACH APPROPRIATE STANDARDIZED ENGLISH-LANGUAGE STATEMENTS PROCESSED AND PRINTED IN A PERMUTED INDEX FORMAT, UNDERWENT A PERFORMANCE TEST, THE PRIMARY OBJECTIVE OF WHICH WAS TO SPOT DEFICIENCIES AND TO DEVELOP A SECOND-GENERATION…

Reducible boundary conditions in coupled channels

NASA Astrophysics Data System (ADS)

Pankrashkin, Konstantin

2005-10-01

We study Hamiltonians with point interactions in spaces of vector-valued functions. Using some information from the theory of quantum graphs, we describe a class of the operators which can be reduced to the direct sum of several one-dimensional problems. It shown that such a reduction is closely connected with the invariance under channel permutations. Examples are provided by some 'model' interactions, in particular, the so-called δ, δ' and the Kirchhoff couplings.

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.

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.

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.

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.

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%.

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.

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

A power comparison of generalized additive models and the spatial scan statistic in a case-control setting.

PubMed

Young, Robin L; Weinberg, Janice; Vieira, Verónica; Ozonoff, Al; Webster, Thomas F

2010-07-19

A common, important problem in spatial epidemiology is measuring and identifying variation in disease risk across a study region. In application of statistical methods, the problem has two parts. First, spatial variation in risk must be detected across the study region and, second, areas of increased or decreased risk must be correctly identified. The location of such areas may give clues to environmental sources of exposure and disease etiology. One statistical method applicable in spatial epidemiologic settings is a generalized additive model (GAM) which can be applied with a bivariate LOESS smoother to account for geographic location as a possible predictor of disease status. A natural hypothesis when applying this method is whether residential location of subjects is associated with the outcome, i.e. is the smoothing term necessary? Permutation tests are a reasonable hypothesis testing method and provide adequate power under a simple alternative hypothesis. These tests have yet to be compared to other spatial statistics. This research uses simulated point data generated under three alternative hypotheses to evaluate the properties of the permutation methods and compare them to the popular spatial scan statistic in a case-control setting. Case 1 was a single circular cluster centered in a circular study region. The spatial scan statistic had the highest power though the GAM method estimates did not fall far behind. Case 2 was a single point source located at the center of a circular cluster and Case 3 was a line source at the center of the horizontal axis of a square study region. Each had linearly decreasing logodds with distance from the point. The GAM methods outperformed the scan statistic in Cases 2 and 3. Comparing sensitivity, measured as the proportion of the exposure source correctly identified as high or low risk, the GAM methods outperformed the scan statistic in all three Cases. The GAM permutation testing methods provide a regression-based alternative to the spatial scan statistic. Across all hypotheses examined in this research, the GAM methods had competing or greater power estimates and sensitivities exceeding that of the spatial scan statistic.

A power comparison of generalized additive models and the spatial scan statistic in a case-control setting

PubMed Central

2010-01-01

Background A common, important problem in spatial epidemiology is measuring and identifying variation in disease risk across a study region. In application of statistical methods, the problem has two parts. First, spatial variation in risk must be detected across the study region and, second, areas of increased or decreased risk must be correctly identified. The location of such areas may give clues to environmental sources of exposure and disease etiology. One statistical method applicable in spatial epidemiologic settings is a generalized additive model (GAM) which can be applied with a bivariate LOESS smoother to account for geographic location as a possible predictor of disease status. A natural hypothesis when applying this method is whether residential location of subjects is associated with the outcome, i.e. is the smoothing term necessary? Permutation tests are a reasonable hypothesis testing method and provide adequate power under a simple alternative hypothesis. These tests have yet to be compared to other spatial statistics. Results This research uses simulated point data generated under three alternative hypotheses to evaluate the properties of the permutation methods and compare them to the popular spatial scan statistic in a case-control setting. Case 1 was a single circular cluster centered in a circular study region. The spatial scan statistic had the highest power though the GAM method estimates did not fall far behind. Case 2 was a single point source located at the center of a circular cluster and Case 3 was a line source at the center of the horizontal axis of a square study region. Each had linearly decreasing logodds with distance from the point. The GAM methods outperformed the scan statistic in Cases 2 and 3. Comparing sensitivity, measured as the proportion of the exposure source correctly identified as high or low risk, the GAM methods outperformed the scan statistic in all three Cases. Conclusions The GAM permutation testing methods provide a regression-based alternative to the spatial scan statistic. Across all hypotheses examined in this research, the GAM methods had competing or greater power estimates and sensitivities exceeding that of the spatial scan statistic. PMID:20642827

Classification of California streams using combined deductive and inductive approaches: Setting the foundation for analysis of hydrologic alteration

USGS Publications Warehouse

Pyne, Matthew I.; Carlisle, Daren M.; Konrad, Christopher P.; Stein, Eric D.

2017-01-01

Regional classification of streams is an early step in the Ecological Limits of Hydrologic Alteration framework. Many stream classifications are based on an inductive approach using hydrologic data from minimally disturbed basins, but this approach may underrepresent streams from heavily disturbed basins or sparsely gaged arid regions. An alternative is a deductive approach, using watershed climate, land use, and geomorphology to classify streams, but this approach may miss important hydrological characteristics of streams. We classified all stream reaches in California using both approaches. First, we used Bayesian and hierarchical clustering to classify reaches according to watershed characteristics. Streams were clustered into seven classes according to elevation, sedimentary rock, and winter precipitation. Permutation-based analysis of variance and random forest analyses were used to determine which hydrologic variables best separate streams into their respective classes. Stream typology (i.e., the class that a stream reach is assigned to) is shaped mainly by patterns of high and mean flow behavior within the stream's landscape context. Additionally, random forest was used to determine which hydrologic variables best separate minimally disturbed reference streams from non-reference streams in each of the seven classes. In contrast to stream typology, deviation from reference conditions is more difficult to detect and is largely defined by changes in low-flow variables, average daily flow, and duration of flow. Our combined deductive/inductive approach allows us to estimate flow under minimally disturbed conditions based on the deductive analysis and compare to measured flow based on the inductive analysis in order to estimate hydrologic change.

Predication-based semantic indexing: permutations as a means to encode predications in semantic space.

PubMed

Cohen, Trevor; Schvaneveldt, Roger W; Rindflesch, Thomas C

2009-11-14

Corpus-derived distributional models of semantic distance between terms have proved useful in a number of applications. For both theoretical and practical reasons, it is desirable to extend these models to encode discrete concepts and the ways in which they are related to one another. In this paper, we present a novel vector space model that encodes semantic predications derived from MEDLINE by the SemRep system into a compact spatial representation. The associations captured by this method are of a different and complementary nature to those derived by traditional vector space models, and the encoding of predication types presents new possibilities for knowledge discovery and information retrieval.

Integrative eQTL analysis of tumor and host omics data in individuals with bladder cancer.

PubMed

Pineda, Silvia; Van Steen, Kristel; Malats, Núria

2017-09-01

Integrative analyses of several omics data are emerging. The data are usually generated from the same source material (i.e., tumor sample) representing one level of regulation. However, integrating different regulatory levels (i.e., blood) with those from tumor may also reveal important knowledge about the human genetic architecture. To model this multilevel structure, an integrative-expression quantitative trait loci (eQTL) analysis applying two-stage regression (2SR) was proposed. This approach first regressed tumor gene expression levels with tumor markers and the adjusted residuals from the previous model were then regressed with the germline genotypes measured in blood. Previously, we demonstrated that penalized regression methods in combination with a permutation-based MaxT method (Global-LASSO) is a promising tool to fix some of the challenges that high-throughput omics data analysis imposes. Here, we assessed whether Global-LASSO can also be applied when tumor and blood omics data are integrated. We further compared our strategy with two 2SR-approaches, one using multiple linear regression (2SR-MLR) and other using LASSO (2SR-LASSO). We applied the three models to integrate genomic, epigenomic, and transcriptomic data from tumor tissue with blood germline genotypes from 181 individuals with bladder cancer included in the TCGA Consortium. Global-LASSO provided a larger list of eQTLs than the 2SR methods, identified a previously reported eQTLs in prostate stem cell antigen (PSCA), and provided further clues on the complexity of APBEC3B loci, with a minimal false-positive rate not achieved by 2SR-MLR. It also represents an important contribution for omics integrative analysis because it is easy to apply and adaptable to any type of data. © 2017 WILEY PERIODICALS, INC.

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 ).

Diffusion on an Ising chain with kinks

NASA Astrophysics Data System (ADS)

Hamma, Alioscia; Mansour, Toufik; Severini, Simone

2009-07-01

We count the number of histories between the two degenerate minimum energy configurations of the Ising model on a chain, as a function of the length n and the number d of kinks that appear above the critical temperature. This is equivalent to count permutations of length n avoiding certain subsequences depending on d. We give explicit generating functions and compute the asymptotics. The setting considered has a role when describing dynamics induced by quantum Hamiltonians with deconfined quasi-particles.

The Minnesota Innovation Research Program.

DTIC Science & Technology

1984-04-01

Stuart Albert has developed a TRACE relations framework for the study of innovation. T R A C E is an acronym for a set of hypothetical relations between...TRACE model by considering the relationships in a different order, A, E , R , C , T. An innovation can link the future with the past or present state of...of addition and complimentary relations). Furthermore, across temporal events, the innovation may consist of different permutations of T R A C E -- it

Direction of Coupling from Phases of Interacting Oscillators: A Permutation Information Approach

NASA Astrophysics Data System (ADS)

Bahraminasab, A.; Ghasemi, F.; Stefanovska, A.; McClintock, P. V. E.; Kantz, H.

2008-02-01

We introduce a directionality index for a time series based on a comparison of neighboring values. It can distinguish unidirectional from bidirectional coupling, as well as reveal and quantify asymmetry in bidirectional coupling. It is tested on a numerical model of coupled van der Pol oscillators, and applied to cardiorespiratory data from healthy subjects. There is no need for preprocessing and fine-tuning the parameters, which makes the method very simple, computationally fast and robust.

Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules

PubMed Central

Valach, Matus; Burger, Gertraud; Gray, Michael W.; Lang, B. Franz

2014-01-01

5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs (rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella. Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator. PMID:25429974

Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules.

PubMed

Valach, Matus; Burger, Gertraud; Gray, Michael W; Lang, B Franz

2014-12-16

5S Ribosomal RNA (5S rRNA) is a universal component of ribosomes, and the corresponding gene is easily identified in archaeal, bacterial and nuclear genome sequences. However, organelle gene homologs (rrn5) appear to be absent from most mitochondrial and several chloroplast genomes. Here, we re-examine the distribution of organelle rrn5 by building mitochondrion- and plastid-specific covariance models (CMs) with which we screened organelle genome sequences. We not only recover all organelle rrn5 genes annotated in GenBank records, but also identify more than 50 previously unrecognized homologs in mitochondrial genomes of various stramenopiles, red algae, cryptomonads, malawimonads and apusozoans, and surprisingly, in the apicoplast (highly derived plastid) genomes of the coccidian pathogens Toxoplasma gondii and Eimeria tenella. Comparative modeling of RNA secondary structure reveals that mitochondrial 5S rRNAs from brown algae adopt a permuted triskelion shape that has not been seen elsewhere. Expression of the newly predicted rrn5 genes is confirmed experimentally in 10 instances, based on our own and published RNA-Seq data. This study establishes that particularly mitochondrial 5S rRNA has a much broader taxonomic distribution and a much larger structural variability than previously thought. The newly developed CMs will be made available via the Rfam database and the MFannot organelle genome annotator. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Evaluation of variable selection methods for random forests and omics data sets.

PubMed

Degenhardt, Frauke; Seifert, Stephan; Szymczak, Silke

2017-10-16

Machine learning methods and in particular random forests are promising approaches for prediction based on high dimensional omics data sets. They provide variable importance measures to rank predictors according to their predictive power. If building a prediction model is the main goal of a study, often a minimal set of variables with good prediction performance is selected. However, if the objective is the identification of involved variables to find active networks and pathways, approaches that aim to select all relevant variables should be preferred. We evaluated several variable selection procedures based on simulated data as well as publicly available experimental methylation and gene expression data. Our comparison included the Boruta algorithm, the Vita method, recurrent relative variable importance, a permutation approach and its parametric variant (Altmann) as well as recursive feature elimination (RFE). In our simulation studies, Boruta was the most powerful approach, followed closely by the Vita method. Both approaches demonstrated similar stability in variable selection, while Vita was the most robust approach under a pure null model without any predictor variables related to the outcome. In the analysis of the different experimental data sets, Vita demonstrated slightly better stability in variable selection and was less computationally intensive than Boruta.In conclusion, we recommend the Boruta and Vita approaches for the analysis of high-dimensional data sets. Vita is considerably faster than Boruta and thus more suitable for large data sets, but only Boruta can also be applied in low-dimensional settings. © The Author 2017. Published by Oxford University Press.

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.

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.

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

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

Rigged String Configurations, Bethe Ansatz Qubits, and Conservation of Parity

NASA Astrophysics Data System (ADS)

Lulek, T.

Bethe Ansatz solutions for the Heisenberg Hamiltonian of a one - dimensional magnetic ring of N nodes, each with the spin 1/2, within the XXX model, have been presented as some composite systems, in a spirit of quantum information theory. The constituents are single - node spin states, which organize into strings of various length, and "seas of holes". The former are responsible for dynamics, whereas the latter determine the range of riggings for strings. Another aim was to demonstrate a unification of Bethe Ansatz eigenstates by means of Galois symmetries of finite field extensions. The key observation is that the original eigenproblem is expressible in integers, and thus, for a finite fixed N, the splitting field of the characteristic polynom of the Heisenberg Hamiltonian is also finite. The Galois group of the latter field permutes, by definition, roots of this polynom, which implies permutation of eigenstates. General considerations are demonstrated on the example of heptagon (N = 7), which admits an implementation of a collection of arithmetic qubits, and also demonstrates a special case of degeneration of the spectrum of the Hamiltonian, resulting from conservation of parity, within the realm of rigged string configurations.

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.

Towards topological quantum computer

NASA Astrophysics Data System (ADS)

Melnikov, D.; Mironov, A.; Mironov, S.; Morozov, A.; Morozov, An.

2018-01-01

Quantum R-matrices, the entangling deformations of non-entangling (classical) permutations, provide a distinguished basis in the space of unitary evolutions and, consequently, a natural choice for a minimal set of basic operations (universal gates) for quantum computation. Yet they play a special role in group theory, integrable systems and modern theory of non-perturbative calculations in quantum field and string theory. Despite recent developments in those fields the idea of topological quantum computing and use of R-matrices, in particular, practically reduce to reinterpretation of standard sets of quantum gates, and subsequently algorithms, in terms of available topological ones. In this paper we summarize a modern view on quantum R-matrix calculus and propose to look at the R-matrices acting in the space of irreducible representations, which are unitary for the real-valued couplings in Chern-Simons theory, as the fundamental set of universal gates for topological quantum computer. Such an approach calls for a more thorough investigation of the relation between topological invariants of knots and quantum algorithms.

A novel hybrid genetic algorithm to solve the make-to-order sequence-dependent flow-shop scheduling problem

NASA Astrophysics Data System (ADS)

Mirabi, Mohammad; Fatemi Ghomi, S. M. T.; Jolai, F.

2014-04-01

Flow-shop scheduling problem (FSP) deals with the scheduling of a set of n jobs that visit a set of m machines in the same order. As the FSP is NP-hard, there is no efficient algorithm to reach the optimal solution of the problem. To minimize the holding, delay and setup costs of large permutation flow-shop scheduling problems with sequence-dependent setup times on each machine, this paper develops a novel hybrid genetic algorithm (HGA) with three genetic operators. Proposed HGA applies a modified approach to generate a pool of initial solutions, and also uses an improved heuristic called the iterated swap procedure to improve the initial solutions. We consider the make-to-order production approach that some sequences between jobs are assumed as tabu based on maximum allowable setup cost. In addition, the results are compared to some recently developed heuristics and computational experimental results show that the proposed HGA performs very competitively with respect to accuracy and efficiency of solution.

Why We Should Not Be Indifferent to Specification Choices for Difference-in-Differences.

PubMed

Ryan, Andrew M; Burgess, James F; Dimick, Justin B

2015-08-01

To evaluate the effects of specification choices on the accuracy of estimates in difference-in-differences (DID) models. Process-of-care quality data from Hospital Compare between 2003 and 2009. We performed a Monte Carlo simulation experiment to estimate the effect of an imaginary policy on quality. The experiment was performed for three different scenarios in which the probability of treatment was (1) unrelated to pre-intervention performance; (2) positively correlated with pre-intervention levels of performance; and (3) positively correlated with pre-intervention trends in performance. We estimated alternative DID models that varied with respect to the choice of data intervals, the comparison group, and the method of obtaining inference. We assessed estimator bias as the mean absolute deviation between estimated program effects and their true value. We evaluated the accuracy of inferences through statistical power and rates of false rejection of the null hypothesis. Performance of alternative specifications varied dramatically when the probability of treatment was correlated with pre-intervention levels or trends. In these cases, propensity score matching resulted in much more accurate point estimates. The use of permutation tests resulted in lower false rejection rates for the highly biased estimators, but the use of clustered standard errors resulted in slightly lower false rejection rates for the matching estimators. When treatment and comparison groups differed on pre-intervention levels or trends, our results supported specifications for DID models that include matching for more accurate point estimates and models using clustered standard errors or permutation tests for better inference. Based on our findings, we propose a checklist for DID analysis. © Health Research and Educational Trust.

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.

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.

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.

Diagnostic index of 3D osteoarthritic changes in TMJ condylar morphology

NASA Astrophysics Data System (ADS)

Gomes, Liliane R.; Gomes, Marcelo; Jung, Bryan; Paniagua, Beatriz; Ruellas, Antonio C.; Gonçalves, João. Roberto; Styner, Martin A.; Wolford, Larry; Cevidanes, Lucia

2015-03-01

The aim of this study was to investigate imaging statistical approaches for classifying 3D osteoarthritic morphological variations among 169 Temporomandibular Joint (TMJ) condyles. Cone beam Computed Tomography (CBCT) scans were acquired from 69 patients with long-term TMJ Osteoarthritis (OA) (39.1 ± 15.7 years), 15 patients at initial diagnosis of OA (44.9 ± 14.8 years) and 7 healthy controls (43 ± 12.4 years). 3D surface models of the condyles were constructed and Shape Correspondence was used to establish correspondent points on each model. The statistical framework included a multivariate analysis of covariance (MANCOVA) and Direction-Projection- Permutation (DiProPerm) for testing statistical significance of the differences between healthy control and the OA group determined by clinical and radiographic diagnoses. Unsupervised classification using hierarchical agglomerative clustering (HAC) was then conducted. Condylar morphology in OA and healthy subjects varied widely. Compared with healthy controls, OA average condyle was statistically significantly smaller in all dimensions except its anterior surface. Significant flattening of the lateral pole was noticed at initial diagnosis (p < 0.05). It was observed areas of 3.88 mm bone resorption at the superior surface and 3.10 mm bone apposition at the anterior aspect of the long-term OA average model. 1000 permutation statistics of DiProPerm supported a significant difference between the healthy control group and OA group (t = 6.7, empirical p-value = 0.001). Clinically meaningful unsupervised classification of TMJ condylar morphology determined a preliminary diagnostic index of 3D osteoarthritic changes, which may be the first step towards a more targeted diagnosis of this condition.

Permutation on hybrid natural inflation

NASA Astrophysics Data System (ADS)

Carone, Christopher D.; Erlich, Joshua; Ramos, Raymundo; Sher, Marc

2014-09-01

We analyze a model of hybrid natural inflation based on the smallest non-Abelian discrete group S3. Leading invariant terms in the scalar potential have an accidental global symmetry that is spontaneously broken, providing a pseudo-Goldstone boson that is identified as the inflaton. The S3 symmetry restricts both the form of the inflaton potential and the couplings of the inflaton field to the waterfall fields responsible for the end of inflation. We identify viable points in the model parameter space. Although the power in tensor modes is small in most of the parameter space of the model, we identify parameter choices that yield potentially observable values of r without super-Planckian initial values of the inflaton field.

Generation, Analysis and Characterization of Anisotropic Engineered Meta Materials

NASA Astrophysics Data System (ADS)

Trifale, Ninad T.

A methodology for a systematic generation of highly anisotropic micro-lattice structures was investigated. Multiple algorithms for generation and validation of engineered structures are developed and evaluated. Set of all possible permutations of structures for an 8-node cubic unit cell were considered and the degree of anisotropy of meta-properties in heat transport and mechanical elasticity were evaluated. Feasibility checks were performed to ensure that the generated unit cell network was repeatable and a continuous lattice structure. Four different strategies for generating permutations of the structures are discussed. Analytical models were developed to predict effective thermal, mechanical and permeability characteristics of these cellular structures.Experimentation and numerical modeling techniques were used to validate the models that are developed. A self-consistent mechanical elasticity model was developed which connects the meso-scale properties to stiffness of individual struts. A three dimensional thermal resistance network analogy was used to evaluate the effective thermal conductivity of the structures. The struts were modeled as a network of one dimensional thermal resistive elements and effective conductivity evaluated. Models were validated against numerical simulations and experimental measurements on 3D printed samples. Model was developed to predict effective permeability of these engineered structures based on Darcy's law. Drag coefficients were evaluated for individual connections in transverse and longitudinal directions and an interaction term was calibrated from the experimental data in literature in order to predict permeability. Generic optimization framework coupled to finite element solver is developed for analyzing any application involving use of porous structures. An objective functions were generated structure to address frequently observed trade-off between the stiffness, thermal conductivity, permeability and porosity. Three application were analyzed for potential use of engineered materials. Heat spreader application involving thermal and mechanical constraints, artificial bone grafts application involving mechanical and permeability constraints and structural materials applications involving mechanical, thermal and porosity constraints is analyzed. Recommendations for optimum topologies for specific operating conditions are provided.

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.

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.

Genome Scan Meta-Analysis of Schizophrenia and Bipolar Disorder, Part II: Schizophrenia

PubMed Central

Lewis, Cathryn M.; Levinson, Douglas F.; Wise, Lesley H.; DeLisi, Lynn E.; Straub, Richard E.; Hovatta, Iiris; Williams, Nigel M.; Schwab, Sibylle G.; Pulver, Ann E.; Faraone, Stephen V.; Brzustowicz, Linda M.; Kaufmann, Charles A.; Garver, David L.; Gurling, Hugh M. D.; Lindholm, Eva; Coon, Hilary; Moises, Hans W.; Byerley, William; Shaw, Sarah H.; Mesen, Andrea; Sherrington, Robin; O’Neill, F. Anthony; Walsh, Dermot; Kendler, Kenneth S.; Ekelund, Jesper; Paunio, Tiina; Lönnqvist, Jouko; Peltonen, Leena; O’Donovan, Michael C.; Owen, Michael J.; Wildenauer, Dieter B.; Maier, Wolfgang; Nestadt, Gerald; Blouin, Jean-Louis; Antonarakis, Stylianos E.; Mowry, Bryan J.; Silverman, Jeremy M.; Crowe, Raymond R.; Cloninger, C. Robert; Tsuang, Ming T.; Malaspina, Dolores; Harkavy-Friedman, Jill M.; Svrakic, Dragan M.; Bassett, Anne S.; Holcomb, Jennifer; Kalsi, Gursharan; McQuillin, Andrew; Brynjolfson, Jon; Sigmundsson, Thordur; Petursson, Hannes; Jazin, Elena; Zoëga, Tomas; Helgason, Tomas

2003-01-01

Schizophrenia is a common disorder with high heritability and a 10-fold increase in risk to siblings of probands. Replication has been inconsistent for reports of significant genetic linkage. To assess evidence for linkage across studies, rank-based genome scan meta-analysis (GSMA) was applied to data from 20 schizophrenia genome scans. Each marker for each scan was assigned to 1 of 120 30-cM bins, with the bins ranked by linkage scores (1 = most significant) and the ranks averaged across studies (Ravg) and then weighted for sample size (\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} \\begin{equation*}\\sqrt{N[affected cases]}\\end{equation*}\\end{document}). A permutation test was used to compute the probability of observing, by chance, each bin’s average rank (PAvgRnk) or of observing it for a bin with the same place (first, second, etc.) in the order of average ranks in each permutation (Pord). The GSMA produced significant genomewide evidence for linkage on chromosome 2q (PAvgRnk<.000417). Two aggregate criteria for linkage were also met (clusters of nominally significant P values that did not occur in 1,000 replicates of the entire data set with no linkage present): 12 consecutive bins with both PAvgRnk and Pord<.05, including regions of chromosomes 5q, 3p, 11q, 6p, 1q, 22q, 8p, 20q, and 14p, and 19 consecutive bins with Pord<.05, additionally including regions of chromosomes 16q, 18q, 10p, 15q, 6q, and 17q. There is greater consistency of linkage results across studies than has been previously recognized. The results suggest that some or all of these regions contain loci that increase susceptibility to schizophrenia in diverse populations. PMID:12802786

3D PATTERN OF BRAIN ABNORMALITIES IN FRAGILE X SYNDROME VISUALIZED USING TENSOR-BASED MORPHOMETRY

PubMed Central

Lee, Agatha D.; Leow, Alex D.; Lu, Allen; Reiss, Allan L.; Hall, Scott; Chiang, Ming-Chang; Toga, Arthur W.; Thompson, Paul M.

2007-01-01

Fragile X syndrome (FraX), a genetic neurodevelopmental disorder, results in impaired cognition with particular deficits in executive function and visuo-spatial skills. Here we report the first detailed 3D maps of the effects of the Fragile X mutation on brain structure, using tensor-based morphometry. TBM visualizes structural brain deficits automatically, without time-consuming specification of regions-of-interest. We compared 36 subjects with FraX (age: 14.66+/−1.58SD, 18 females/18 males), and 33 age-matched healthy controls (age: 14.67+/−2.2SD, 17 females/16 males), using high-dimensional elastic image registration. All 69 subjects' 3D T1-weighted brain MRIs were spatially deformed to match a high-resolution single-subject average MRI scan in ICBM space, whose geometry was optimized to produce a minimal deformation target. Maps of the local Jacobian determinant (expansion factor) were computed from the deformation fields. Statistical maps showed increased caudate (10% higher; p=0.001) and lateral ventricle volumes (19% higher; p=0.003), and trend-level parietal and temporal white matter excesses (10% higher locally; p=0.04). In affected females, volume abnormalities correlated with reduction in systemically measured levels of the fragile X mental retardation protein (FMRP; Spearman's r<−0.5 locally). Decreased FMRP correlated with ventricular expansion (p=0.042; permutation test), and anterior cingulate tissue reductions (p=0.0026; permutation test) supporting theories that FMRP is required for normal dendritic pruning in fronto-striatal-limbic pathways. No sex differences were found; findings were confirmed using traditional volumetric measures in regions of interest. Deficit patterns were replicated using Lie group statistics optimized for tensor-valued data. Investigation of how these anomalies emerge over time will accelerate our understanding of FraX and its treatment. PMID:17161622

Time needed to board an airplane: a power law and the structure behind it.

PubMed

Frette, Vidar; Hemmer, Per C

2012-01-01

A simple model for the boarding of an airplane is studied. Passengers have reserved seats but enter the airplane in arbitrary order. Queues are formed along the aisle, as some passengers have to wait to reach the seats for which they have reservation. We label a passenger by the number of his or her reserved seat. In most cases the boarding process is much slower than for the optimal situation, where passenger and seat orders are identical. We study this dynamical system by calculating the average boarding time when all permutations of N passengers are given equal weight. To first order, the boarding time for a given permutation (ordering) of the passengers is given by the number s of sequences of monotonically increasing values in the permutation. We show that the distribution of s is symmetric on [1,N], which leads to an average boarding time (N+1)/2. We have found an exact expression for s and have shown that the full distribution of s approaches a normal distribution as N increases. However, there are significant corrections to the first-order results, due to certain correlations between passenger ordering and the substrate (seat ordering). This occurs for some cases in which the sequence of the seats is partially mirrored in the passenger ordering. These cases with correlations have a boarding time that is lower than predicted by the first-order results. The large number of cases with reduced boarding times have been classified. We also give some indicative results on the geometry of the correlations, with sorting into geometry groups. With increasing N, both the number of correlation types and the number of cases belonging to each type increase rapidly. Using enumeration we find that as a result of these correlations the average boarding time behaves like N(α), with α≃0.69, as compared with α=1.0 for the first-order approximation. © 2012 American Physical Society

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.

DGCA: A comprehensive R package for Differential Gene Correlation Analysis.

PubMed

McKenzie, Andrew T; Katsyv, Igor; Song, Won-Min; Wang, Minghui; Zhang, Bin

2016-11-15

Dissecting the regulatory relationships between genes is a critical step towards building accurate predictive models of biological systems. A powerful approach towards this end is to systematically study the differences in correlation between gene pairs in more than one distinct condition. In this study we develop an R package, DGCA (for Differential Gene Correlation Analysis), which offers a suite of tools for computing and analyzing differential correlations between gene pairs across multiple conditions. To minimize parametric assumptions, DGCA computes empirical p-values via permutation testing. To understand differential correlations at a systems level, DGCA performs higher-order analyses such as measuring the average difference in correlation and multiscale clustering analysis of differential correlation networks. Through a simulation study, we show that the straightforward z-score based method that DGCA employs significantly outperforms the existing alternative methods for calculating differential correlation. Application of DGCA to the TCGA RNA-seq data in breast cancer not only identifies key changes in the regulatory relationships between TP53 and PTEN and their target genes in the presence of inactivating mutations, but also reveals an immune-related differential correlation module that is specific to triple negative breast cancer (TNBC). DGCA is an R package for systematically assessing the difference in gene-gene regulatory relationships under different conditions. This user-friendly, effective, and comprehensive software tool will greatly facilitate the application of differential correlation analysis in many biological studies and thus will help identification of novel signaling pathways, biomarkers, and targets in complex biological systems and diseases.

Index to Nuclear Safety: a technical progress review by chronology, permuted title, and author, Volume 18 (1) through Volume 22 (6)

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

Cottrell, W.B.; Passiakos, M.

This index to Nuclear Safety covers articles published in Nuclear Safety, Volume 18, Number 1 (January-February 1977) through Volume 22, Number 6 (November-December 1981). The index is divided into three section: a chronological list of articles (including abstracts), a permuted-title (KWIC) index, and an author index. Nuclear Safety, a bimonthly technical progress review prepared by the Nuclear Safety Information Center, covers all safety aspects of nuclear power reactors and associated facilities. Over 300 technical articles published in Nuclear Safety in the last 5 years are listed in this index.

Non-Weyl asymptotics for quantum graphs with general coupling conditions

NASA Astrophysics Data System (ADS)

Davies, E. Brian; Exner, Pavel; Lipovský, Jiří

2010-11-01

Inspired by a recent result of Davies and Pushnitski, we study resonance asymptotics of quantum graphs with general coupling conditions at the vertices. We derive a criterion for the asymptotics to be of a non-Weyl character. We show that for balanced vertices with permutation-invariant couplings the asymptotics is non-Weyl only in the case of Kirchhoff or anti-Kirchhoff conditions. While for graphs without permutation symmetry numerous examples of non-Weyl behaviour can be constructed. Furthermore, we present an insight into what makes the Kirchhoff/anti-Kirchhoff coupling particular from the resonance point of view. Finally, we demonstrate a generalization to quantum graphs with unequal edge weights.

[Local fractal analysis of noise-like time series by all permutations method for 1-115 min periods].

PubMed

Panchelyuga, V A; Panchelyuga, M S

2015-01-01

Results of local fractal analysis of 329-per-day time series of 239Pu alpha-decay rate fluctuations by means of all permutations method (APM) are presented. The APM-analysis reveals in the time series some steady frequency set. The coincidence of the frequency set with the Earth natural oscillations was demonstrated. A short review of works by different authors who analyzed the time series of fluctuations in processes of different nature is given. We have shown that the periods observed in those works correspond to the periods revealed in our study. It points to a common mechanism of the phenomenon observed.

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.

Chaotic Image Encryption Algorithm Based on Bit Permutation and Dynamic DNA Encoding.

PubMed

Zhang, Xuncai; Han, Feng; Niu, Ying

2017-01-01

With the help of the fact that chaos is sensitive to initial conditions and pseudorandomness, combined with the spatial configurations in the DNA molecule's inherent and unique information processing ability, a novel image encryption algorithm based on bit permutation and dynamic DNA encoding is proposed here. The algorithm first uses Keccak to calculate the hash value for a given DNA sequence as the initial value of a chaotic map; second, it uses a chaotic sequence to scramble the image pixel locations, and the butterfly network is used to implement the bit permutation. Then, the image is coded into a DNA matrix dynamic, and an algebraic operation is performed with the DNA sequence to realize the substitution of the pixels, which further improves the security of the encryption. Finally, the confusion and diffusion properties of the algorithm are further enhanced by the operation of the DNA sequence and the ciphertext feedback. The results of the experiment and security analysis show that the algorithm not only has a large key space and strong sensitivity to the key but can also effectively resist attack operations such as statistical analysis and exhaustive analysis.

Chaotic Image Encryption Algorithm Based on Bit Permutation and Dynamic DNA Encoding

PubMed Central

2017-01-01

With the help of the fact that chaos is sensitive to initial conditions and pseudorandomness, combined with the spatial configurations in the DNA molecule's inherent and unique information processing ability, a novel image encryption algorithm based on bit permutation and dynamic DNA encoding is proposed here. The algorithm first uses Keccak to calculate the hash value for a given DNA sequence as the initial value of a chaotic map; second, it uses a chaotic sequence to scramble the image pixel locations, and the butterfly network is used to implement the bit permutation. Then, the image is coded into a DNA matrix dynamic, and an algebraic operation is performed with the DNA sequence to realize the substitution of the pixels, which further improves the security of the encryption. Finally, the confusion and diffusion properties of the algorithm are further enhanced by the operation of the DNA sequence and the ciphertext feedback. The results of the experiment and security analysis show that the algorithm not only has a large key space and strong sensitivity to the key but can also effectively resist attack operations such as statistical analysis and exhaustive analysis. PMID:28912802

Analysis of crude oil markets with improved multiscale weighted permutation entropy

NASA Astrophysics Data System (ADS)

Niu, Hongli; Wang, Jun; Liu, Cheng

2018-03-01

Entropy measures are recently extensively used to study the complexity property in nonlinear systems. Weighted permutation entropy (WPE) can overcome the ignorance of the amplitude information of time series compared with PE and shows a distinctive ability to extract complexity information from data having abrupt changes in magnitude. Improved (or sometimes called composite) multi-scale (MS) method possesses the advantage of reducing errors and improving the accuracy when applied to evaluate multiscale entropy values of not enough long time series. In this paper, we combine the merits of WPE and improved MS to propose the improved multiscale weighted permutation entropy (IMWPE) method for complexity investigation of a time series. Then it is validated effective through artificial data: white noise and 1 / f noise, and real market data of Brent and Daqing crude oil. Meanwhile, the complexity properties of crude oil markets are explored respectively of return series, volatility series with multiple exponents and EEMD-produced intrinsic mode functions (IMFs) which represent different frequency components of return series. Moreover, the instantaneous amplitude and frequency of Brent and Daqing crude oil are analyzed by the Hilbert transform utilized to each IMF.

Diversification of Protein Cage Structure Using Circularly Permuted Subunits.

PubMed

Azuma, Yusuke; Herger, Michael; Hilvert, Donald

2018-01-17

Self-assembling protein cages are useful as nanoscale molecular containers for diverse applications in biotechnology and medicine. To expand the utility of such systems, there is considerable interest in customizing the structures of natural cage-forming proteins and designing new ones. Here we report that a circularly permuted variant of lumazine synthase, a cage-forming enzyme from Aquifex aeolicus (AaLS) affords versatile building blocks for the construction of nanocompartments that can be easily produced, tailored, and diversified. The topologically altered protein, cpAaLS, self-assembles into spherical and tubular cage structures with morphologies that can be controlled by the length of the linker connecting the native termini. Moreover, cpAaLS proteins integrate into wild-type and other engineered AaLS assemblies by coproduction in Escherichia coli to form patchwork cages. This coassembly strategy enables encapsulation of guest proteins in the lumen, modification of the exterior through genetic fusion, and tuning of the size and electrostatics of the compartments. This addition to the family of AaLS cages broadens the scope of this system for further applications and highlights the utility of circular permutation as a potentially general strategy for tailoring the properties of cage-forming proteins.

Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation.

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

Qian, Zhen; Horton, John R.; Cheng, Xiadong

2009-11-02

Circular permutation of Candida antarctica lipase B yields several enzyme variants with substantially increased catalytic activity. To better understand the structural and functional consequences of protein termini reorganization, we have applied protein engineering and x-ray crystallography to cp283, one of the most active hydrolase variants. Our initial investigation has focused on the role of an extended surface loop, created by linking the native N- and C-termini, on protein integrity. Incremental truncation of the loop partially compensates for observed losses in secondary structure and the permutants temperature of unfolding. Unexpectedly, the improvements are accompanied by quaternary-structure changes from monomer to dimer.more » The crystal structures of one truncated variant (cp283{Delta}7) in the apo-form determined at 1.49 {angstrom} resolution and with a bound phosphonate inhibitor at 1.69 {angstrom} resolution confirmed the formation of a homodimer by swapping of the enzyme's 35-residue N-terminal region. Separately, the new protein termini at amino acid positions 282/283 convert the narrow access tunnel to the catalytic triad into a broad crevice for accelerated substrate entry and product exit while preserving the native active-site topology for optimal catalytic turnover.« less

Conditional Bounds on Polarization Transfer

NASA Astrophysics Data System (ADS)

Nielsen, N. C.; Sorensen, O. W.

The implications of constraints on unitary transformations of spin operators with respect to the accessible regions of Liouville space are analyzed. Specifically, the effects of spin-permutation symmetry on the unitary propagators are investigated. The influence of S2 and S3 propagator symmetry on two-dimensional bounds for F z = Σ Ni=1 I iz ↔ G z = Σ Mj=1 S jz polarization transfer in IS and I 2S spin- {1}/{2} systems is examined in detail. One result is that the maximum achievable F z ↔ G z polarization transfer is not reduced by permutation symmetry among the spins. For I 2S spin systems, S3 symmetry in the unitary propagator is shown to significantly reduce the accessible region in the 2D F z-S z Liouville subspace compared to the case restricted by unitarity alone. That result is compared with transformations under symmetric dipolar and scalar J coupling as well as shift and RF interactions. An important practical implication is that the refined spin thermodynamic theory of Levitt, Suter, and Ernst ( J. Chem. Phys.84, 4243, 1986) for cross polarization in solid-state NMR does not predict experimental outcomes incompatible with constraints of unitarity and spin-permutation symmetry.

A hybrid quantum-inspired genetic algorithm for multiobjective flow shop scheduling.

PubMed

Li, Bin-Bin; Wang, Ling

2007-06-01

This paper proposes a hybrid quantum-inspired genetic algorithm (HQGA) for the multiobjective flow shop scheduling problem (FSSP), which is a typical NP-hard combinatorial optimization problem with strong engineering backgrounds. On the one hand, a quantum-inspired GA (QGA) based on Q-bit representation is applied for exploration in the discrete 0-1 hyperspace by using the updating operator of quantum gate and genetic operators of Q-bit. Moreover, random-key representation is used to convert the Q-bit representation to job permutation for evaluating the objective values of the schedule solution. On the other hand, permutation-based GA (PGA) is applied for both performing exploration in permutation-based scheduling space and stressing exploitation for good schedule solutions. To evaluate solutions in multiobjective sense, a randomly weighted linear-sum function is used in QGA, and a nondominated sorting technique including classification of Pareto fronts and fitness assignment is applied in PGA with regard to both proximity and diversity of solutions. To maintain the diversity of the population, two trimming techniques for population are proposed. The proposed HQGA is tested based on some multiobjective FSSPs. Simulation results and comparisons based on several performance metrics demonstrate the effectiveness of the proposed HQGA.

SO(4) algebraic approach to the three-body bound state problem in two dimensions

NASA Astrophysics Data System (ADS)

Dmitrašinović, V.; Salom, Igor

2014-08-01

We use the permutation symmetric hyperspherical three-body variables to cast the non-relativistic three-body Schrödinger equation in two dimensions into a set of (possibly decoupled) differential equations that define an eigenvalue problem for the hyper-radial wave function depending on an SO(4) hyper-angular matrix element. We express this hyper-angular matrix element in terms of SO(3) group Clebsch-Gordan coefficients and use the latter's properties to derive selection rules for potentials with different dynamical/permutation symmetries. Three-body potentials acting on three identical particles may have different dynamical symmetries, in order of increasing symmetry, as follows: (1) S3 ⊗ OL(2), the permutation times rotational symmetry, that holds in sums of pairwise potentials, (2) O(2) ⊗ OL(2), the so-called "kinematic rotations" or "democracy symmetry" times rotational symmetry, that holds in area-dependent potentials, and (3) O(4) dynamical hyper-angular symmetry, that holds in hyper-radial three-body potentials. We show how the different residual dynamical symmetries of the non-relativistic three-body Hamiltonian lead to different degeneracies of certain states within O(4) multiplets.

A novel image encryption algorithm based on the chaotic system and DNA computing

NASA Astrophysics Data System (ADS)

Chai, Xiuli; Gan, Zhihua; Lu, Yang; Chen, Yiran; Han, Daojun

A novel image encryption algorithm using the chaotic system and deoxyribonucleic acid (DNA) computing is presented. Different from the traditional encryption methods, the permutation and diffusion of our method are manipulated on the 3D DNA matrix. Firstly, a 3D DNA matrix is obtained through bit plane splitting, bit plane recombination, DNA encoding of the plain image. Secondly, 3D DNA level permutation based on position sequence group (3DDNALPBPSG) is introduced, and chaotic sequences generated from the chaotic system are employed to permutate the positions of the elements of the 3D DNA matrix. Thirdly, 3D DNA level diffusion (3DDNALD) is given, the confused 3D DNA matrix is split into sub-blocks, and XOR operation by block is manipulated to the sub-DNA matrix and the key DNA matrix from the chaotic system. At last, by decoding the diffused DNA matrix, we get the cipher image. SHA 256 hash of the plain image is employed to calculate the initial values of the chaotic system to avoid chosen plaintext attack. Experimental results and security analyses show that our scheme is secure against several known attacks, and it can effectively protect the security of the images.

A novel chaos-based image encryption algorithm using DNA sequence operations

NASA Astrophysics Data System (ADS)

Chai, Xiuli; Chen, Yiran; Broyde, Lucie

2017-01-01

An image encryption algorithm based on chaotic system and deoxyribonucleic acid (DNA) sequence operations is proposed in this paper. First, the plain image is encoded into a DNA matrix, and then a new wave-based permutation scheme is performed on it. The chaotic sequences produced by 2D Logistic chaotic map are employed for row circular permutation (RCP) and column circular permutation (CCP). Initial values and parameters of the chaotic system are calculated by the SHA 256 hash of the plain image and the given values. Then, a row-by-row image diffusion method at DNA level is applied. A key matrix generated from the chaotic map is used to fuse the confused DNA matrix; also the initial values and system parameters of the chaotic system are renewed by the hamming distance of the plain image. Finally, after decoding the diffused DNA matrix, we obtain the cipher image. The DNA encoding/decoding rules of the plain image and the key matrix are determined by the plain image. Experimental results and security analyses both confirm that the proposed algorithm has not only an excellent encryption result but also resists various typical attacks.

Searching for the fastest dynamo: laminar ABC flows.

PubMed

Alexakis, Alexandros

2011-08-01

The growth rate of the dynamo instability as a function of the magnetic Reynolds number R(M) is investigated by means of numerical simulations for the family of the Arnold-Beltrami-Childress (ABC) flows and for two different forcing scales. For the ABC flows that are driven at the largest available length scale, it is found that, as the magnetic Reynolds number is increased: (a) The flow that results first in a dynamo is the 2 1/2-dimensional flow for which A=B and C=0 (and all permutations). (b) The second type of flow that results in a dynamo is the one for which A=B≃2C/5 (and permutations). (c) The most symmetric flow, A=B=C, is the third type of flow that results in a dynamo. (d) As R(M) is increased, the A=B=C flow stops being a dynamo and transitions from a local maximum to a third-order saddle point. (e) At larger R(M), the A=B=C flow reestablishes itself as a dynamo but remains a saddle point. (f) At the largest examined R(M), the growth rate of the 2 1/2-dimensional flows starts to decay, the A=B=C flow comes close to a local maximum again, and the flow A=B≃2C/5 (and permutations) results in the fastest dynamo with growth rate γ≃0.12 at the largest examined R(M). For the ABC flows that are driven at the second largest available length scale, it is found that (a) the 2 1/2-dimensional flows A=B,C=0 (and permutations) are again the first flows that result in a dynamo with a decreased onset. (b) The most symmetric flow, A=B=C, is the second type of flow that results in a dynamo. It is, and it remains, a local maximum. (c) At larger R(M), the flow A=B≃2C/5 (and permutations) appears as the third type of flow that results in a dynamo. As R(M) is increased, it becomes the flow with the largest growth rate. The growth rates appear to have some correlation with the Lyapunov exponents, but constructive refolding of the field lines appears equally important in determining the fastest dynamo flow.

Inflammatory gene polymorphisms and risk of postoperative myocardial infarction after cardiac surgery.

PubMed

Podgoreanu, M V; White, W D; Morris, R W; Mathew, J P; Stafford-Smith, M; Welsby, I J; Grocott, H P; Milano, C A; Newman, M F; Schwinn, D A

2006-07-04

The inflammatory response triggered by cardiac surgery with cardiopulmonary bypass (CPB) is a primary mechanism in the pathogenesis of postoperative myocardial infarction (PMI), a multifactorial disorder with significant inter-patient variability poorly predicted by clinical and procedural factors. We tested the hypothesis that candidate gene polymorphisms in inflammatory pathways contribute to risk of PMI after cardiac surgery. We genotyped 48 polymorphisms from 23 candidate genes in a prospective cohort of 434 patients undergoing elective cardiac surgery with CPB. PMI was defined as creatine kinase-MB isoenzyme level > or = 10x upper limit of normal at 24 hours postoperatively. A 2-step analysis strategy was used: marker selection, followed by model building. To minimize false-positive associations, we adjusted for multiple testing by permutation analysis, Bonferroni correction, and controlling the false discovery rate; 52 patients (12%) experienced PMI. After adjusting for multiple comparisons and clinical risk factors, 3 polymorphisms were found to be independent predictors of PMI (adjusted P<0.05; false discovery rate <10%). These gene variants encode the proinflammatory cytokine interleukin 6 (IL6 -572G>C; odds ratio [OR], 2.47), and 2 adhesion molecules: intercellular adhesion molecule-1 (ICAM1 Lys469Glu; OR, 1.88), and E-selectin (SELE 98G>T; OR, 0.16). The inclusion of genotypic information from these polymorphisms improved prediction models for PMI based on traditional risk factors alone (C-statistic 0.764 versus 0.703). Functional genetic variants in cytokine and leukocyte-endothelial interaction pathways are independently associated with severity of myonecrosis after cardiac surgery. This may aid in preoperative identification of high-risk cardiac surgical patients and development of novel cardioprotective strategies.

Permutation tests for goodness-of-fit testing of mathematical models to experimental data.

PubMed

Fişek, M Hamit; Barlas, Zeynep

2013-03-01

This paper presents statistical procedures for improving the goodness-of-fit testing of theoretical models to data obtained from laboratory experiments. We use an experimental study in the expectation states research tradition which has been carried out in the "standardized experimental situation" associated with the program to illustrate the application of our procedures. We briefly review the expectation states research program and the fundamentals of resampling statistics as we develop our procedures in the resampling context. The first procedure we develop is a modification of the chi-square test which has been the primary statistical tool for assessing goodness of fit in the EST research program, but has problems associated with its use. We discuss these problems and suggest a procedure to overcome them. The second procedure we present, the "Average Absolute Deviation" test, is a new test and is proposed as an alternative to the chi square test, as being simpler and more informative. The third and fourth procedures are permutation versions of Jonckheere's test for ordered alternatives, and Kendall's tau(b), a rank order correlation coefficient. The fifth procedure is a new rank order goodness-of-fit test, which we call the "Deviation from Ideal Ranking" index, which we believe may be more useful than other rank order tests for assessing goodness-of-fit of models to experimental data. The application of these procedures to the sample data is illustrated in detail. We then present another laboratory study from an experimental paradigm different from the expectation states paradigm - the "network exchange" paradigm, and describe how our procedures may be applied to this data set. Copyright © 2012 Elsevier Inc. All rights reserved.

On Correlated-noise Analyses Applied to Exoplanet Light Curves

NASA Astrophysics Data System (ADS)

Cubillos, Patricio; Harrington, Joseph; Loredo, Thomas J.; Lust, Nate B.; Blecic, Jasmina; Stemm, Madison

2017-01-01

Time-correlated noise is a significant source of uncertainty when modeling exoplanet light-curve data. A correct assessment of correlated noise is fundamental to determine the true statistical significance of our findings. Here, we review three of the most widely used correlated-noise estimators in the exoplanet field, the time-averaging, residual-permutation, and wavelet-likelihood methods. We argue that the residual-permutation method is unsound in estimating the uncertainty of parameter estimates. We thus recommend to refrain from this method altogether. We characterize the behavior of the time averaging’s rms-versus-bin-size curves at bin sizes similar to the total observation duration, which may lead to underestimated uncertainties. For the wavelet-likelihood method, we note errors in the published equations and provide a list of corrections. We further assess the performance of these techniques by injecting and retrieving eclipse signals into synthetic and real Spitzer light curves, analyzing the results in terms of the relative-accuracy and coverage-fraction statistics. Both the time-averaging and wavelet-likelihood methods significantly improve the estimate of the eclipse depth over a white-noise analysis (a Markov-chain Monte Carlo exploration assuming uncorrelated noise). However, the corrections are not perfect when retrieving the eclipse depth from Spitzer data sets, these methods covered the true (injected) depth within the 68% credible region in only ˜45%-65% of the trials. Lastly, we present our open-source model-fitting tool, Multi-Core Markov-Chain Monte Carlo (MC3). This package uses Bayesian statistics to estimate the best-fitting values and the credible regions for the parameters for a (user-provided) model. MC3 is a Python/C code, available at https://github.com/pcubillos/MCcubed.

Multidimensional scaling analysis of financial time series based on modified cross-sample entropy methods

NASA Astrophysics Data System (ADS)

He, Jiayi; Shang, Pengjian; Xiong, Hui

2018-06-01

Stocks, as the concrete manifestation of financial time series with plenty of potential information, are often used in the study of financial time series. In this paper, we utilize the stock data to recognize their patterns through out the dissimilarity matrix based on modified cross-sample entropy, then three-dimensional perceptual maps of the results are provided through multidimensional scaling method. Two modified multidimensional scaling methods are proposed in this paper, that is, multidimensional scaling based on Kronecker-delta cross-sample entropy (MDS-KCSE) and multidimensional scaling based on permutation cross-sample entropy (MDS-PCSE). These two methods use Kronecker-delta based cross-sample entropy and permutation based cross-sample entropy to replace the distance or dissimilarity measurement in classical multidimensional scaling (MDS). Multidimensional scaling based on Chebyshev distance (MDSC) is employed to provide a reference for comparisons. Our analysis reveals a clear clustering both in synthetic data and 18 indices from diverse stock markets. It implies that time series generated by the same model are easier to have similar irregularity than others, and the difference in the stock index, which is caused by the country or region and the different financial policies, can reflect the irregularity in the data. In the synthetic data experiments, not only the time series generated by different models can be distinguished, the one generated under different parameters of the same model can also be detected. In the financial data experiment, the stock indices are clearly divided into five groups. Through analysis, we find that they correspond to five regions, respectively, that is, Europe, North America, South America, Asian-Pacific (with the exception of mainland China), mainland China and Russia. The results also demonstrate that MDS-KCSE and MDS-PCSE provide more effective divisions in experiments than MDSC.

Targeting Carcinoma-Associated Fibroblasts Within the Tumor Stroma With a Fibroblast Activation Protein-Activated Prodrug

PubMed Central

2012-01-01

Background Fibroblasts undergo a morphological transformation to a reactive phenotype in the tumor microenvironment characterized by the expression of proteins such as fibroblast activation protein (FAP), a post-prolyl endopeptidase with expression largely restricted to carcinoma-associated fibroblasts. Thapsigargin (TG) is a highly toxic natural plant product that triggers a rise in intracellular calcium levels and apoptosis. FAP is therefore a provocative target for the activation of prodrugs consisting of a FAP-specific peptide coupled to a potent cytotoxic analog of TG. Methods The efficacy of FAP-activated peptidyl-TG prodrugs was tested in vitro in cell proliferation assays and effects on intracellular calcium in human cancer cell lines. The effects of FAP-activated prodrugs on tumor growth and host toxicity were tested in Balb-C nude MCF-7 and LNCaP xenograft mice (n = 9–11 per group). P values were calculated using permutation tests based on 50 000 permutations. Mixed effects models were used to account for correlations among replicate measures. All statistical tests were two-sided. Results FAP-activated prodrugs killed human cancer cells at low nanomolar concentrations (MCF-7 cells: IC50 = 3.5nM). Amino acid-12ADT analogs from FAP-cleaved prodrugs, but not uncleaved prodrugs, produced a rapid rise in intracellular calcium within minutes of exposure. Immunohistochemical analysis of xenografts exposed to FAP-prodrugs documented stromal-selective cell death of fibroblasts, pericytes, and endothelial cells of sufficient magnitude to inhibit growth of MCF-7 and LNCaP xenografts with minimal systemic toxicity, whereas non-FAP cleavable prodrugs were inactive. MCF-7 and LNCaP xenografts treated with a FAP-activated prodrug had maximal treated-to-control tumor volume ratios of 0.36 (treated: mean = 0.206mm3, 95% CI = 0.068 to 0.344mm3; control: mean = 0.580mm3, 95% CI = 0.267 to 0.893mm3) and 0.24 (treated: mean = 0.131mm3, 95% CI = 0.09 to 0.180mm3; control: mean = 0.543mm3, 95% CI = 0.173 to 0.913mm3), respectively, on day 21 after therapy. Conclusions This study validates the proteolytic activity of FAP as a target for the activation of a systemically delivered cytotoxic prodrug and demonstrates that targeted killing of cells within the stromal compartment of the tumor microenvironment can produce a therapeutic response. PMID:22911669

Some applications of the Kronecker product in Hubbard representation

NASA Astrophysics Data System (ADS)

Enríquez, Marco; Rosas-Ortiz, Oscar

2014-10-01

The properties of the Kronecker product are revisited in terms of Hubbard operators. The simplest representation of a Hubbard operator Xi,jn is a square matrix of size n with an entry equal to 1 and zero elsewhere. This framework simplifies the calculation of the Kronecker product of arbitrary matrices no matter the size or the number of the involved factors. Some applications are presented, these include the algebra of permutation matrices, the Hadamard matrix, the XXX Heisenberg model and the interaction of an atom with radiation fields.

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

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

Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul

2015-01-21

The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, whichmore » is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.« less

A model of urban rational growth based on grey prediction

NASA Astrophysics Data System (ADS)

Xiao, Wenjing

2017-04-01

Smart growth focuses on building sustainable cities, using compact development to prevent urban sprawl. This paper establishes a series of models to implement smart growth theories into city design. Besides two specific city design cases are shown. Firstly, We establishes Smart Growth Measure Model to measure the success of smart growth of a city. And we use Full Permutation Polygon Synthetic Indicator Method to calculate the Comprehensive Indicator (CI) which is used to measure the success of smart growth. Secondly, this paper uses the principle of smart growth to develop a new growth plan for two cities. We establish an optimization model to maximum CI value. The Particle Swarm Optimization (PSO) algorithm is used to solve the model. Combined with the calculation results and the specific circumstances of cities, we make their the smart growth plan respectively.

Detection of frequency-mode-shift during thermoacoustic combustion oscillations in a staged aircraft engine model combustor

NASA Astrophysics Data System (ADS)

Kobayashi, Hiroaki; Gotoda, Hiroshi; Tachibana, Shigeru; Yoshida, Seiji

2017-12-01

We conduct an experimental study using time series analysis based on symbolic dynamics to detect a precursor of frequency-mode-shift during thermoacoustic combustion oscillations in a staged aircraft engine model combustor. With increasing amount of the main fuel, a significant shift in the dominant frequency-mode occurs in noisy periodic dynamics, leading to a notable increase in oscillation amplitudes. The sustainment of noisy periodic dynamics during thermoacoustic combustion oscillations is clearly shown by the multiscale complexity-entropy causality plane in terms of statistical complexity. A modified version of the permutation entropy allows us to detect a precursor of the frequency-mode-shift before the amplification of pressure fluctuations.

Quantile regression models of animal habitat relationships

USGS Publications Warehouse

Cade, Brian S.

2003-01-01

Typically, all factors that limit an organism are not measured and included in statistical models used to investigate relationships with their environment. If important unmeasured variables interact multiplicatively with the measured variables, the statistical models often will have heterogeneous response distributions with unequal variances. Quantile regression is an approach for estimating the conditional quantiles of a response variable distribution in the linear model, providing a more complete view of possible causal relationships between variables in ecological processes. Chapter 1 introduces quantile regression and discusses the ordering characteristics, interval nature, sampling variation, weighting, and interpretation of estimates for homogeneous and heterogeneous regression models. Chapter 2 evaluates performance of quantile rankscore tests used for hypothesis testing and constructing confidence intervals for linear quantile regression estimates (0 ≤ τ ≤ 1). A permutation F test maintained better Type I errors than the Chi-square T test for models with smaller n, greater number of parameters p, and more extreme quantiles τ. Both versions of the test required weighting to maintain correct Type I errors when there was heterogeneity under the alternative model. An example application related trout densities to stream channel width:depth. Chapter 3 evaluates a drop in dispersion, F-ratio like permutation test for hypothesis testing and constructing confidence intervals for linear quantile regression estimates (0 ≤ τ ≤ 1). Chapter 4 simulates from a large (N = 10,000) finite population representing grid areas on a landscape to demonstrate various forms of hidden bias that might occur when the effect of a measured habitat variable on some animal was confounded with the effect of another unmeasured variable (spatially and not spatially structured). Depending on whether interactions of the measured habitat and unmeasured variable were negative (interference interactions) or positive (facilitation interactions), either upper (τ > 0.5) or lower (τ < 0.5) quantile regression parameters were less biased than mean rate parameters. Sampling (n = 20 - 300) simulations demonstrated that confidence intervals constructed by inverting rankscore tests provided valid coverage of these biased parameters. Quantile regression was used to estimate effects of physical habitat resources on a bivalve mussel (Macomona liliana) in a New Zealand harbor by modeling the spatial trend surface as a cubic polynomial of location coordinates.

ON THE NUMBER OF SOLUTIONS OF THE EQUATION x^k = a IN THE SYMMETRIC GROUP S_n

NASA Astrophysics Data System (ADS)

Pavlov, A. I.

1981-04-01

This paper consists of three sections. In the first a formula is given for the number N_n^{(k)}(a) of solutions of the equation x^k = a in S_n depending on the cyclic structure of the permutation a. In the second an asymptotic formula is given for the quantity M_n^{(k)} = \\max_{a \\in S_n} N_n^{(k)}(a) for a fixed k \\geq 2 as n \\to \\infty. In the third an asymptotic formula is found for the cardinality of the set of permutations a such that the equation x^k = a has a unique solution. Bibliography: 5 titles.

EXTENDING MULTIVARIATE DISTANCE MATRIX REGRESSION WITH AN EFFECT SIZE MEASURE AND THE ASYMPTOTIC NULL DISTRIBUTION OF THE TEST STATISTIC

PubMed Central

McArtor, Daniel B.; Lubke, Gitta H.; Bergeman, C. S.

2017-01-01

Person-centered methods are useful for studying individual differences in terms of (dis)similarities between response profiles on multivariate outcomes. Multivariate distance matrix regression (MDMR) tests the significance of associations of response profile (dis)similarities and a set of predictors using permutation tests. This paper extends MDMR by deriving and empirically validating the asymptotic null distribution of its test statistic, and by proposing an effect size for individual outcome variables, which is shown to recover true associations. These extensions alleviate the computational burden of permutation tests currently used in MDMR and render more informative results, thus making MDMR accessible to new research domains. PMID:27738957

Extending multivariate distance matrix regression with an effect size measure and the asymptotic null distribution of the test statistic.

PubMed

McArtor, Daniel B; Lubke, Gitta H; Bergeman, C S

2017-12-01

Person-centered methods are useful for studying individual differences in terms of (dis)similarities between response profiles on multivariate outcomes. Multivariate distance matrix regression (MDMR) tests the significance of associations of response profile (dis)similarities and a set of predictors using permutation tests. This paper extends MDMR by deriving and empirically validating the asymptotic null distribution of its test statistic, and by proposing an effect size for individual outcome variables, which is shown to recover true associations. These extensions alleviate the computational burden of permutation tests currently used in MDMR and render more informative results, thus making MDMR accessible to new research domains.

On the representation matrices of the spin permutation group. [for atomic and molecular electronic structures

NASA Technical Reports Server (NTRS)

Wilson, S.

1977-01-01

A method is presented for the determination of the representation matrices of the spin permutation group (symmetric group), a detailed knowledge of these matrices being required in the study of the electronic structure of atoms and molecules. The method is characterized by the use of two different coupling schemes. Unlike the Yamanouchi spin algebraic scheme, the method is not recursive. The matrices for the fundamental transpositions can be written down directly in one of the two bases. The method results in a computationally significant reduction in the number of matrix elements that have to be stored when compared with, say, the standard Young tableaux group theoretical approach.

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.

Using model order tests to determine sensory inputs in a motion study

NASA Technical Reports Server (NTRS)

Repperger, D. W.; Junker, A. M.

1977-01-01

In the study of motion effects on tracking performance, a problem of interest is the determination of what sensory inputs a human uses in controlling his tracking task. In the approach presented here a simple canonical model (FID or a proportional, integral, derivative structure) is used to model the human's input-output time series. A study of significant changes in reduction of the output error loss functional is conducted as different permutations of parameters are considered. Since this canonical model includes parameters which are related to inputs to the human (such as the error signal, its derivatives and integration), the study of model order is equivalent to the study of which sensory inputs are being used by the tracker. The parameters are obtained which have the greatest effect on reducing the loss function significantly. In this manner the identification procedure converts the problem of testing for model order into the problem of determining sensory inputs.

Wildland Arson as Clandestine Resource Management: A Space-Time Permutation Analysis and Classification of Informal Fire Management Regimes in Georgia, USA

NASA Astrophysics Data System (ADS)

Coughlan, Michael R.

2016-05-01

Forest managers are increasingly recognizing the value of disturbance-based land management techniques such as prescribed burning. Unauthorized, "arson" fires are common in the southeastern United States where a legacy of agrarian cultural heritage persists amidst an increasingly forest-dominated landscape. This paper reexamines unauthorized fire-setting in the state of Georgia, USA from a historical ecology perspective that aims to contribute to historically informed, disturbance-based land management. A space-time permutation analysis is employed to discriminate systematic, management-oriented unauthorized fires from more arbitrary or socially deviant fire-setting behaviors. This paper argues that statistically significant space-time clusters of unauthorized fire occurrence represent informal management regimes linked to the legacy of traditional land management practices. Recent scholarship has pointed out that traditional management has actively promoted sustainable resource use and, in some cases, enhanced biodiversity often through the use of fire. Despite broad-scale displacement of traditional management during the 20th century, informal management practices may locally circumvent more formal and regionally dominant management regimes. Space-time permutation analysis identified 29 statistically significant fire regimes for the state of Georgia. The identified regimes are classified by region and land cover type and their implications for historically informed disturbance-based resource management are discussed.

Permuting input for more effective sampling of 3D conformer space

NASA Astrophysics Data System (ADS)

Carta, Giorgio; Onnis, Valeria; Knox, Andrew J. S.; Fayne, Darren; Lloyd, David G.

2006-03-01

SMILES strings and other classic 2D structural formats offer a convenient way to represent molecules as a simplistic connection table, with the inherent advantages of ease of handling and storage. In the context of virtual screening, chemical databases to be screened are often initially represented by canonicalised SMILES strings that can be filtered and pre-processed in a number of ways, resulting in molecules that occupy similar regions of chemical space to active compounds of a therapeutic target. A wide variety of software exists to convert molecules into SMILES format, namely, Mol2smi (Daylight Inc.), MOE (Chemical Computing Group) and Babel (Openeye Scientific Software). Depending on the algorithm employed, the atoms of a SMILES string defining a molecule can be ordered differently. Upon conversion to 3D coordinates they result in the production of ostensibly the same molecule. In this work we show how different permutations of a SMILES string can affect conformer generation, affecting reliability and repeatability of the results. Furthermore, we propose a novel procedure for the generation of conformers, taking advantage of the permutation of the input strings—both SMILES and other 2D formats, leading to more effective sampling of conformation space in output, and also implementing fingerprint and principal component analyses step to post process and visualise the results.

A simplified formalism of the algebra of partially transposed permutation operators with applications

NASA Astrophysics Data System (ADS)

Mozrzymas, Marek; Studziński, Michał; Horodecki, Michał

2018-03-01

Herein we continue the study of the representation theory of the algebra of permutation operators acting on the n -fold tensor product space, partially transposed on the last subsystem. We develop the concept of partially reduced irreducible representations, which allows us to significantly simplify previously proved theorems and, most importantly, derive new results for irreducible representations of the mentioned algebra. In our analysis we are able to reduce the complexity of the central expressions by getting rid of sums over all permutations from the symmetric group, obtaining equations which are much more handy in practical applications. We also find relatively simple matrix representations for the generators of the underlying algebra. The obtained simplifications and developments are applied to derive the characteristics of a deterministic port-based teleportation scheme written purely in terms of irreducible representations of the studied algebra. We solve an eigenproblem for the generators of the algebra, which is the first step towards a hybrid port-based teleportation scheme and gives us new proofs of the asymptotic behaviour of teleportation fidelity. We also show a connection between the density operator characterising port-based teleportation and a particular matrix composed of an irreducible representation of the symmetric group, which encodes properties of the investigated algebra.

Unequal homologous recombination between tandemly arranged sequences stably incorporated into cultured rat cells.

PubMed Central

Stringer, J R; Kuhn, R M; Newman, J L; Meade, J C

1985-01-01

Cultured rat cells deficient in endogenous thymidine kinase activity (tk) were stably transformed with a recombination-indicator DNA substrate constructed in vitro by rearrangement of the herpes simplex virus tk gene sequences into a partially redundant permutation of the functional gene. The recombination-indicator DNA did not express tk, but was designed to allow formation of a functional tk gene via homologous recombination. A clonal cell line (519) was isolated that harbored several permuted herpes simplex virus tk genes. 519 cells spontaneously produced progeny that survived in medium containing hypoxanthine, aminopterin, and thymidine. Acquisition of resistance to hypoxanthine, aminopterin, and thymidine was accompanied by the rearrangement of the defective tk gene to functional configuration. The rearrangement apparently occurred by unequal exchange between one permuted tk gene and a replicated copy of itself. Recombination was between 500-base-pair tracts of DNA sequence homology that were separated by 3.4 kilobases. Exchanges occurred spontaneously at a frequency of approximately 5 X 10(-6) events per cell per generation. Recombination also mediated reversion to the tk- phenotype; however, the predominant mechanism by which cells escaped death in the presence of drugs rendered toxic by thymidine kinase was not recombination, but rather inactivation of the intact tk gene. Images PMID:3016511

Limited Rationality and Its Quantification Through the Interval Number Judgments With Permutations.

PubMed

Liu, Fang; Pedrycz, Witold; Zhang, Wei-Guo

2017-12-01

The relative importance of alternatives expressed in terms of interval numbers in the fuzzy analytic hierarchy process aims to capture the uncertainty experienced by decision makers (DMs) when making a series of comparisons. Under the assumption of full rationality, the judgements of DMs in the typical analytic hierarchy process could be consistent. However, since the uncertainty in articulating the opinions of DMs is unavoidable, the interval number judgements are associated with the limited rationality. In this paper, we investigate the concept of limited rationality by introducing interval multiplicative reciprocal comparison matrices. By analyzing the consistency of interval multiplicative reciprocal comparison matrices, it is observed that the interval number judgements are inconsistent. By considering the permutations of alternatives, the concepts of approximation-consistency and acceptable approximation-consistency of interval multiplicative reciprocal comparison matrices are proposed. The exchange method is designed to generate all the permutations. A novel method of determining the interval weight vector is proposed under the consideration of randomness in comparing alternatives, and a vector of interval weights is determined. A new algorithm of solving decision making problems with interval multiplicative reciprocal preference relations is provided. Two numerical examples are carried out to illustrate the proposed approach and offer a comparison with the methods available in the literature.

Combining p-values in replicated single-case experiments with multivariate outcome.

PubMed

Solmi, Francesca; Onghena, Patrick

2014-01-01

Interest in combining probabilities has a long history in the global statistical community. The first steps in this direction were taken by Ronald Fisher, who introduced the idea of combining p-values of independent tests to provide a global decision rule when multiple aspects of a given problem were of interest. An interesting approach to this idea of combining p-values is the one based on permutation theory. The methods belonging to this particular approach exploit the permutation distributions of the tests to be combined, and use a simple function to combine probabilities. Combining p-values finds a very interesting application in the analysis of replicated single-case experiments. In this field the focus, while comparing different treatments effects, is more articulated than when just looking at the means of the different populations. Moreover, it is often of interest to combine the results obtained on the single patients in order to get more global information about the phenomenon under study. This paper gives an overview of how the concept of combining p-values was conceived, and how it can be easily handled via permutation techniques. Finally, the method of combining p-values is applied to a simulated replicated single-case experiment, and a numerical illustration is presented.

A permutation-based non-parametric analysis of CRISPR screen data.

PubMed

Jia, Gaoxiang; Wang, Xinlei; Xiao, Guanghua

2017-07-19

Clustered regularly-interspaced short palindromic repeats (CRISPR) screens are usually implemented in cultured cells to identify genes with critical functions. Although several methods have been developed or adapted to analyze CRISPR screening data, no single specific algorithm has gained popularity. Thus, rigorous procedures are needed to overcome the shortcomings of existing algorithms. We developed a Permutation-Based Non-Parametric Analysis (PBNPA) algorithm, which computes p-values at the gene level by permuting sgRNA labels, and thus it avoids restrictive distributional assumptions. Although PBNPA is designed to analyze CRISPR data, it can also be applied to analyze genetic screens implemented with siRNAs or shRNAs and drug screens. We compared the performance of PBNPA with competing methods on simulated data as well as on real data. PBNPA outperformed recent methods designed for CRISPR screen analysis, as well as methods used for analyzing other functional genomics screens, in terms of Receiver Operating Characteristics (ROC) curves and False Discovery Rate (FDR) control for simulated data under various settings. Remarkably, the PBNPA algorithm showed better consistency and FDR control on published real data as well. PBNPA yields more consistent and reliable results than its competitors, especially when the data quality is low. R package of PBNPA is available at: https://cran.r-project.org/web/packages/PBNPA/ .

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.

Wildland Arson as Clandestine Resource Management: A Space-Time Permutation Analysis and Classification of Informal Fire Management Regimes in Georgia, USA.

PubMed

Coughlan, Michael R

2016-05-01

Forest managers are increasingly recognizing the value of disturbance-based land management techniques such as prescribed burning. Unauthorized, "arson" fires are common in the southeastern United States where a legacy of agrarian cultural heritage persists amidst an increasingly forest-dominated landscape. This paper reexamines unauthorized fire-setting in the state of Georgia, USA from a historical ecology perspective that aims to contribute to historically informed, disturbance-based land management. A space-time permutation analysis is employed to discriminate systematic, management-oriented unauthorized fires from more arbitrary or socially deviant fire-setting behaviors. This paper argues that statistically significant space-time clusters of unauthorized fire occurrence represent informal management regimes linked to the legacy of traditional land management practices. Recent scholarship has pointed out that traditional management has actively promoted sustainable resource use and, in some cases, enhanced biodiversity often through the use of fire. Despite broad-scale displacement of traditional management during the 20th century, informal management practices may locally circumvent more formal and regionally dominant management regimes. Space-time permutation analysis identified 29 statistically significant fire regimes for the state of Georgia. The identified regimes are classified by region and land cover type and their implications for historically informed disturbance-based resource management are discussed.

Artificial Neural Identification and LMI Transformation for Model Reduction-Based Control of the Buck Switch-Mode Regulator

NASA Astrophysics Data System (ADS)

Al-Rabadi, Anas N.

2009-10-01

This research introduces a new method of intelligent control for the control of the Buck converter using newly developed small signal model of the pulse width modulation (PWM) switch. The new method uses supervised neural network to estimate certain parameters of the transformed system matrix [Ã]. Then, a numerical algorithm used in robust control called linear matrix inequality (LMI) optimization technique is used to determine the permutation matrix [P] so that a complete system transformation {[B˜], [C˜], [Ẽ]} is possible. The transformed model is then reduced using the method of singular perturbation, and state feedback control is applied to enhance system performance. The experimental results show that the new control methodology simplifies the model in the Buck converter and thus uses a simpler controller that produces the desired system response for performance enhancement.

Untangling the Relatedness among Correlations, Part II: Inter-Subject Correlation Group Analysis through Linear Mixed-Effects Modeling

PubMed Central

Chen, Gang; Taylor, Paul A.; Shin, Yong-Wook; Reynolds, Richard C.; Cox, Robert W.

2016-01-01

It has been argued that naturalistic conditions in FMRI studies provide a useful paradigm for investigating perception and cognition through a synchronization measure, inter-subject correlation (ISC). However, one analytical stumbling block has been the fact that the ISC values associated with each single subject are not independent, and our previous paper (Chen et al., 2016) used simulations and analyses of real data to show that the methodologies adopted in the literature do not have the proper control for false positives. In the same paper, we proposed nonparametric subject-wise bootstrapping and permutation testing techniques for one and two groups, respectively, which account for the correlation structure, and these greatly outperformed the prior methods in controlling the false positive rate (FPR); that is, subject-wise bootstrapping (SWB) worked relatively well for both cases with one and two groups, and subject-wise permutation (SWP) testing was virtually ideal for group comparisons. Here we seek to explicate and adopt a parametric approach through linear mixed-effects (LME) modeling for studying the ISC values, building on the previous correlation framework, with the benefit that the LME platform offers wider adaptability, more powerful interpretations, and quality control checking capability than nonparametric methods. We describe both theoretical and practical issues involved in the modeling and the manner in which LME with crossed random effects (CRE) modeling is applied. A data-doubling step further allows us to conveniently track the subject index, and achieve easy implementations. We pit the LME approach against the best nonparametric methods, and find that the LME framework achieves proper control for false positives. The new LME methodologies are shown to be both efficient and robust, and they will be added as an additional option and settings in an existing open source program, 3dLME, in AFNI (http://afni.nimh.nih.gov). PMID:27751943

Revealing kinetics and state-dependent binding properties of IKur-targeting drugs that maximize atrial fibrillation selectivity

NASA Astrophysics Data System (ADS)

Ellinwood, Nicholas; Dobrev, Dobromir; Morotti, Stefano; Grandi, Eleonora

2017-09-01

The KV1.5 potassium channel, which underlies the ultra-rapid delayed-rectifier current (IKur) and is predominantly expressed in atria vs. ventricles, has emerged as a promising target to treat atrial fibrillation (AF). However, while numerous KV1.5-selective compounds have been screened, characterized, and tested in various animal models of AF, evidence of antiarrhythmic efficacy in humans is still lacking. Moreover, current guidelines for pre-clinical assessment of candidate drugs heavily rely on steady-state concentration-response curves or IC50 values, which can overlook adverse cardiotoxic effects. We sought to investigate the effects of kinetics and state-dependent binding of IKur-targeting drugs on atrial electrophysiology in silico and reveal the ideal properties of IKur blockers that maximize anti-AF efficacy and minimize pro-arrhythmic risk. To this aim, we developed a new Markov model of IKur that describes KV1.5 gating based on experimental voltage-clamp data in atrial myocytes from patient right-atrial samples in normal sinus rhythm. We extended the IKur formulation to account for state-specificity and kinetics of KV1.5-drug interactions and incorporated it into our human atrial cell model. We simulated 1- and 3-Hz pacing protocols in drug-free conditions and with a [drug] equal to the IC50 value. The effects of binding and unbinding kinetics were determined by examining permutations of the forward (kon) and reverse (koff) binding rates to the closed, open, and inactivated states of the KV1.5 channel. We identified a subset of ideal drugs exhibiting anti-AF electrophysiological parameter changes at fast pacing rates (effective refractory period prolongation), while having little effect on normal sinus rhythm (limited action potential prolongation). Our results highlight that accurately accounting for channel interactions with drugs, including kinetics and state-dependent binding, is critical for developing safer and more effective pharmacological anti-AF options.

STRUCTURAL AND FUNCTIONAL CONSEQUENCES OF CIRCULAR PERMUTATION ON THE ACTIVE SITE OF OLD YELLOW ENZYME.

PubMed

Daugherty, Ashley B; Horton, John R; Cheng, Xiaodong; Lutz, Stefan

2015-02-06

Circular permutation of the NADPH-dependent oxidoreductase Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme's catalytic performance. Termini relocation into four regions of the protein (sectors I-IV) near the active site has proven effective in altering enzyme function. To better understand the structural consequences and rationalize the observed functional gains in these OYE1 variants, we selected representatives from sectors I-III for further characterization by biophysical methods and X-ray crystallography. These investigations not only show trends in enzyme stability and quaternary structure as a function of termini location, but also provide a possible explanation for the catalytic gains in our top-performing OYE variant (new N-terminus at residue 303; sector III). Crystallographic analysis indicates that termini relocation into sector III affects the loop β6 region (amino acid positions: 290-310) of OYE1 which forms a lid over the active site. Peptide backbone cleavage greatly enhances local flexibility, effectively converting the loop into a tether and consequently increasing the environmental exposure of the active site. Interestingly, such active site remodeling does not negatively impact the enzyme's activity and stereoselectivity, nor does it perturb the conformation of other key active site residues with the exception of Y375. These observations were confirmed in truncation experiments, deleting all residues of the loop β6 region in our OYE variant. Intrigued by the finding that circular permutation leaves most of the key catalytic residues unchanged, we also tested OYE permutants for possible additive or synergistic effects of amino acid substitutions. Distinct functional changes in these OYE variants were detected upon mutations at W116, known in native OYE1 to cause inversion of diastereo-selectivity for ( S )-carvone reduction. Our findings demonstrate the contribution of loop β6 toward determining the stereoselectivity of OYE1, an important insight for future OYE engineering efforts.

Structural and Functional Consequences of Circular Permutation on the Active Site of Old Yellow Enzyme

DOE PAGES

Daugherty, Ashley B.; Horton, John R.; Cheng, Xiaodong; ...

2014-12-09

Circular permutation of the NADPH-dependent oxidoreductase Old Yellow Enzyme from Saccharomyces pastorianus (OYE1) can significantly enhance the enzyme’s catalytic performance. Termini relocation into four regions of the protein (sectors I–IV) near the active site has proven effective in altering enzyme function. To better understand the structural consequences and rationalize the observed functional gains in these OYE1 variants, we selected representatives from sectors I–III for further characterization by biophysical methods and X-ray crystallography. These investigations not only show trends in enzyme stability and quaternary structure as a function of termini location but also provide a possible explanation for the catalytic gainsmore » in our top-performing OYE variant (new N-terminus at residue 303; sector III). Crystallographic analysis indicates that termini relocation into sector III affects the loop β6 region (amino acid positions: 290–310) of OYE1, which forms a lid over the active site. Peptide backbone cleavage greatly enhances local flexibility, effectively converting the loop into a tether and consequently increasing the environmental exposure of the active site. Interestingly, such an active site remodeling does not negatively impact the enzyme’s activity and stereoselectivity; neither does it perturb the conformation of other key active site residues with the exception of Y375. These observations were confirmed in truncation experiments, deleting all residues of the loop β6 region in our OYE variant. Intrigued by the finding that circular permutation leaves most of the key catalytic residues unchanged, we also tested OYE permutants for possible additive or synergistic effects of amino acid substitutions. Distinct functional changes in these OYE variants were detected upon mutations at W116, known in native OYE1 to cause inversion of diastereoselectivity for (S)-carvone reduction. In conclusion, our findings demonstrate the contribution of loop β6 toward determining the stereoselectivity of OYE1, an important insight for future OYE engineering efforts.« less

Deciphering the Preference and Predicting the Viability of Circular Permutations in Proteins

PubMed Central

Liu, Yen-Yi; Wang, Li-Fen; Hwang, Jenn-Kang; Lyu, Ping-Chiang

2012-01-01

Circular permutation (CP) refers to situations in which the termini of a protein are relocated to other positions in the structure. CP occurs naturally and has been artificially created to study protein function, stability and folding. Recently CP is increasingly applied to engineer enzyme structure and function, and to create bifunctional fusion proteins unachievable by tandem fusion. CP is a complicated and expensive technique. An intrinsic difficulty in its application lies in the fact that not every position in a protein is amenable for creating a viable permutant. To examine the preferences of CP and develop CP viability prediction methods, we carried out comprehensive analyses of the sequence, structural, and dynamical properties of known CP sites using a variety of statistics and simulation methods, such as the bootstrap aggregating, permutation test and molecular dynamics simulations. CP particularly favors Gly, Pro, Asp and Asn. Positions preferred by CP lie within coils, loops, turns, and at residues that are exposed to solvent, weakly hydrogen-bonded, environmentally unpacked, or flexible. Disfavored positions include Cys, bulky hydrophobic residues, and residues located within helices or near the protein's core. These results fostered the development of an effective viable CP site prediction system, which combined four machine learning methods, e.g., artificial neural networks, the support vector machine, a random forest, and a hierarchical feature integration procedure developed in this work. As assessed by using the hydrofolate reductase dataset as the independent evaluation dataset, this prediction system achieved an AUC of 0.9. Large-scale predictions have been performed for nine thousand representative protein structures; several new potential applications of CP were thus identified. Many unreported preferences of CP are revealed in this study. The developed system is the best CP viability prediction method currently available. This work will facilitate the application of CP in research and biotechnology. PMID:22359629

On the rank-distance median of 3 permutations.

PubMed

Chindelevitch, Leonid; Pereira Zanetti, João Paulo; Meidanis, João

2018-05-08

Recently, Pereira Zanetti, Biller and Meidanis have proposed a new definition of a rearrangement distance between genomes. In this formulation, each genome is represented as a matrix, and the distance d is the rank distance between these matrices. Although defined in terms of matrices, the rank distance is equal to the minimum total weight of a series of weighted operations that leads from one genome to the other, including inversions, translocations, transpositions, and others. The computational complexity of the median-of-three problem according to this distance is currently unknown. The genome matrices are a special kind of permutation matrices, which we study in this paper. In their paper, the authors provide an [Formula: see text] algorithm for determining three candidate medians, prove the tight approximation ratio [Formula: see text], and provide a sufficient condition for their candidates to be true medians. They also conduct some experiments that suggest that their method is accurate on simulated and real data. In this paper, we extend their results and provide the following: Three invariants characterizing the problem of finding the median of 3 matrices A sufficient condition for uniqueness of medians that can be checked in O(n) A faster, [Formula: see text] algorithm for determining the median under this condition A new heuristic algorithm for this problem based on compressed sensing A [Formula: see text] algorithm that exactly solves the problem when the inputs are orthogonal matrices, a class that includes both permutations and genomes as special cases. Our work provides the first proof that, with respect to the rank distance, the problem of finding the median of 3 genomes, as well as the median of 3 permutations, is exactly solvable in polynomial time, a result which should be contrasted with its NP-hardness for the DCJ (double cut-and-join) distance and most other families of genome rearrangement operations. This result, backed by our experimental tests, indicates that the rank distance is a viable alternative to the DCJ distance widely used in genome comparisons.

Identification of IL-7 as a candidate disease mediator in osteoarthritis in Chinese Han population: a case-control study.

PubMed

Zhang, Hong-Xin; Wang, Yan-Gui; Lu, Shun-Yuan; Lu, Xiong-Xiong; Liu, Jie

2016-09-01

Little is known about the biochemical mediators IL-7 that correlate with the initiation and progression of OA. We performed this study to assess the role of variants of IL-7 in OA susceptibility in the Chinese Han population. We performed a retrospective, case-control study in the Chinese Han population from 2013 to 2015. Four single nucleotide polymorphisms were genotyped (using a ligase detection reaction) in 602 patients and 454 controls. Differences between groups were analysed, and association was assessed by the odds ratio (OR) and 95% CI. Among these polymorphisms, rs2583764, rs2583760 and rs6993386 showed no significant association with OA in the Chinese Han population {rs2583764 [P-allele = 0.98651, P-genotype = 0.40392, OR (95% CI): 1.00162 (0.83066, 1.20775)]; rs2583760 [P-allele = 0.384500, P-genotype = 0.58752, OR (95% CI): 0.69859 (0.30996, 1.57449)]; rs6993386 [P-allele = 0.69525, P-genotype = 0.50712, OR (95% CI): 0.96432 (0.80406, 1.15653)]}. However, the results showed that the rs2583759 polymorphism was significantly associated with OA [P-allele = 0.00 P-genotype = 3.86 × 10(-30), OR (95% CI): 0.27794 (0.22407, 0.34476)], even when the 10 000 times permutation was performed (P-allele-permutation < 0.00010, P-genotype-permutation = 0.00010). Haplotype analyses showed A-G-A-C, A-G-A-T and G-G-G-C of rs2583764-rs2583760-rs6993386-rs2583759 were risk factors for OA, both before or after the 10 000 times permutation, indicating IL-7 to be associated with OA. There was a significant association between IL-7, especially rs2583759, and OA in the Chinese Han population. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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.

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

Orlenko, E. V., E-mail: eorlenko@mail.ru; Evstafev, A. V.; Orlenko, F. E.

A formalism of exchange perturbation theory (EPT) is developed for the case of interactions that explicitly depend on time. Corrections to the wave function obtained in any order of perturbation theory and represented in an invariant form include exchange contributions due to intercenter electron permutations in complex multicenter systems. For collisions of atomic systems with an arbitrary type of interaction, general expressions are obtained for the transfer (T) and scattering (S) matrices in which intercenter electron permutations between overlapping nonorthogonal states belonging to different centers (atoms) are consistently taken into account. The problem of collision of alpha particles with lithiummore » atoms accompanied by the redistribution of electrons between centers is considered. The differential and total charge-exchange cross sections of lithium are calculated.« less

Security Analysis of Some Diffusion Mechanisms Used in Chaotic Ciphers

NASA Astrophysics Data System (ADS)

Zhang, Leo Yu; Zhang, Yushu; Liu, Yuansheng; Yang, Anjia; Chen, Guanrong

As a variant of the substitution-permutation network, the permutation-diffusion structure has received extensive attention in the field of chaotic cryptography over the last three decades. Because of the high implementation speed and nonlinearity over GF(2), the Galois field of two elements, mixing modulo addition/multiplication and Exclusive OR becomes very popular in various designs to achieve the desired diffusion effect. This paper reports that some diffusion mechanisms based on modulo addition/multiplication and Exclusive OR are not resistant to plaintext attacks as claimed. By cracking several recently proposed chaotic ciphers as examples, it is demonstrated that a good understanding of the strength and weakness of these crypto-primitives is crucial for designing more practical chaotic encryption algorithms in the future.

Optimal recombination in genetic algorithms for flowshop scheduling problems

NASA Astrophysics Data System (ADS)

Kovalenko, Julia

2016-10-01

The optimal recombination problem consists in finding the best possible offspring as a result of a recombination operator in a genetic algorithm, given two parent solutions. We prove NP-hardness of the optimal recombination for various variants of the flowshop scheduling problem with makespan criterion and criterion of maximum lateness. An algorithm for solving the optimal recombination problem for permutation flowshop problems is built, using enumeration of prefect matchings in a special bipartite graph. The algorithm is adopted for the classical flowshop scheduling problem and for the no-wait flowshop problem. It is shown that the optimal recombination problem for the permutation flowshop scheduling problem is solvable in polynomial time for almost all pairs of parent solutions as the number of jobs tends to infinity.

On testing for spatial correspondence between maps of human brain structure and function.

PubMed

Alexander-Bloch, Aaron F; Shou, Haochang; Liu, Siyuan; Satterthwaite, Theodore D; Glahn, David C; Shinohara, Russell T; Vandekar, Simon N; Raznahan, Armin

2018-06-01

A critical issue in many neuroimaging studies is the comparison between brain maps. Nonetheless, it remains unclear how one should test hypotheses focused on the overlap or spatial correspondence between two or more brain maps. This "correspondence problem" affects, for example, the interpretation of comparisons between task-based patterns of functional activation, resting-state networks or modules, and neuroanatomical landmarks. To date, this problem has been addressed with remarkable variability in terms of methodological approaches and statistical rigor. In this paper, we address the correspondence problem using a spatial permutation framework to generate null models of overlap by applying random rotations to spherical representations of the cortical surface, an approach for which we also provide a theoretical statistical foundation. We use this method to derive clusters of cognitive functions that are correlated in terms of their functional neuroatomical substrates. In addition, using publicly available data, we formally demonstrate the correspondence between maps of task-based functional activity, resting-state fMRI networks and gyral-based anatomical landmarks. We provide open-access code to implement the methods presented for two commonly-used tools for surface based cortical analysis (https://www.github.com/spin-test). This spatial permutation approach constitutes a useful advance over widely-used methods for the comparison of cortical maps, thereby opening new possibilities for the integration of diverse neuroimaging data. Copyright © 2018 Elsevier Inc. All rights reserved.

Altered resting-state connectivity within default mode network associated with late chronotype.

PubMed

Horne, Charlotte Mary; Norbury, Ray

2018-04-20

Current evidence suggests late chronotype individuals have an increased risk of developing depression. However, the underlying neural mechanisms of this association are not fully understood. Forty-six healthy, right-handed individuals free of current or previous diagnosis of depression, family history of depression or sleep disorder underwent resting-state functional Magnetic Resonance Imaging (rsFMRI). Using an Independent Component Analysis (ICA) approach, the Default Mode Network (DMN) was identified based on a well validated template. Linear effects of chronotype on DMN connectivity were tested for significance using non-parametric permutation tests (applying 5000 permutations). Sleep quality, age, gender, measures of mood and anxiety, time of scan and cortical grey matter volume were included as covariates in the regression model. A significant positive correlation between chronotype and functional connectivity within nodes of the DMN was observed, including; bilateral PCC and precuneus, such that later chronotype (participants with lower rMEQ scores) was associated with decreased connectivity within these regions. The current results appear consistent with altered DMN connectivity in depressed patients and weighted evidence towards reduced DMN connectivity in other at-risk populations which may, in part, explain the increased vulnerability for depression in late chronotype individuals. The effect may be driven by self-critical thoughts associated with late chronotype although future studies are needed to directly investigate this. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Moderating Role of Close Friends in the Relationship Between Conduct Problems and Adolescent Substance Use

PubMed Central

Glaser, Beate; Shelton, Katherine H.; van den Bree, Marianne B.M.

2010-01-01

Purpose Conduct problems and peer effects are among the strongest risk factors for adolescent substance use and problem use. However, it is unclear to what extent the effects of conduct problems and peer behavior interact, and whether adolescents' capacity to refuse the offer of substances may moderate such links. This study was conducted to examine relationships between conduct problems, close friends' substance use, and refusal assertiveness with adolescents' alcohol use problems, tobacco, and marijuana use. Methods We studied a population-based sample of 1,237 individuals from the Cardiff Study of All Wales and North West of England Twins aged 11–18 years. Adolescent and mother-reported information was obtained. Statistical analyses included cross-sectional and prospective logistic regression models and family-based permutations. Results Conduct problems and close friends' substance use were associated with increased adolescents' substance use, whereas refusal assertiveness was associated with lower use of cigarettes, alcohol, and marijuana. Peer substance use moderated the relationship between conduct problems and alcohol use problems, such that conduct problems were only related to increased risk for alcohol use problems in the presence of substance-using friends. This effect was found in both cross-sectional and prospective analyses and confirmed using the permutation approach. Conclusions Reduced opportunities for interaction with alcohol-using peers may lower the risk of alcohol use problems in adolescents with conduct problems. PMID:20547290

Functional linear models to test for differences in prairie wetland hydraulic gradients

USGS Publications Warehouse

Greenwood, Mark C.; Sojda, Richard S.; Preston, Todd M.; Swayne, David A.; Yang, Wanhong; Voinov, A.A.; Rizzoli, A.; Filatova, T.

2010-01-01

Functional data analysis provides a framework for analyzing multiple time series measured frequently in time, treating each series as a continuous function of time. Functional linear models are used to test for effects on hydraulic gradient functional responses collected from three types of land use in Northeastern Montana at fourteen locations. Penalized regression-splines are used to estimate the underlying continuous functions based on the discretely recorded (over time) gradient measurements. Permutation methods are used to assess the statistical significance of effects. A method for accommodating missing observations in each time series is described. Hydraulic gradients may be an initial and fundamental ecosystem process that responds to climate change. We suggest other potential uses of these methods for detecting evidence of climate change.

Successful Manipulation in Stable Marriage Model with Complete Preference Lists

NASA Astrophysics Data System (ADS)

Kobayashi, Hirotatsu; Matsui, Tomomi

This paper deals with a strategic issue in the stable marriage model with complete preference lists (i.e., a preference list of an agent is a permutation of all the members of the opposite sex). Given complete preference lists of n men over n women, and a marriage µ, we consider the problem for finding preference lists of n women over n men such that the men-proposing deferred acceptance algorithm (Gale-Shapley algorithm) adopted to the lists produces µ. We show a simple necessary and sufficient condition for the existence of a set of preference lists of women over men. Our condition directly gives an O(n2) time algorithm for finding a set of preference lists, if it exists.

Composition in the Quantum World

NASA Astrophysics Data System (ADS)

Hall, Edward Jonathan

This thesis presents a problem for the foundations of quantum mechanics. It arises from the way that theory describes the composition of larger systems in terms of smaller ones, and renders untenable a wide range of interpretations of quantum mechanics. That quantum mechanics is difficult to interpret is old news, given the well-known Measurement Problem. But the problem I raise is quite different, and in important respects more fundamental. In brief: The physical world exhibits mereological structure: physical objects have parts, which in turn have parts, and so on. A natural way to try to represent this structure is by means of a particle theory, according to which the physical world consists entirely enduring physical objects which themselves have no proper parts, but aggregates of which are, or compose, all physical objects. Elementary, non-relativistic quantum mechanics can be cast in this mold--at least, according to the usual expositions of that theory. But herein lies the problem: the standard attempt to give a systematic particle interpretation to elementary quantum mechanics results in nonsense, thanks to the well-established principle of Permutation Invariance, which constrains the quantum -mechanical description of systems containing identical particles. Specifically, it follows from the most minimal principles of a particle interpretation (much weaker than those needed to generate the Measurement Problem), together with Permutation Invariance, that systems identical in composition must have the same physical state. In other words, systems which merely have the same numbers of the same types of particles are therefore, at all times, perfect physical duplicates. This conclusion is absurd: e.g., it is quite plausible that some of those particles which compose my body make up a system identical in composition to some pepperoni pizza. Yet no part of me is a qualitative physical duplicate of any pepperoni pizza. Perhaps "you are what you eat" --but not in this sense! In what follows I develop the principles needed to explore this problem, contrast it with the Measurement Problem, and consider, finally, how it should influence our judgments of the relative merits of the many extant interpretations of quantum mechanics.

Visualization of Global Disease Burden for the Optimization of Patient Management and Treatment.

PubMed

Schlee, Winfried; Hall, Deborah A; Edvall, Niklas K; Langguth, Berthold; Canlon, Barbara; Cederroth, Christopher R

2017-01-01

The assessment and treatment of complex disorders is challenged by the multiple domains and instruments used to evaluate clinical outcome. With the large number of assessment tools typically used in complex disorders comes the challenge of obtaining an integrative view of disease status to further evaluate treatment outcome both at the individual level and at the group level. Radar plots appear as an attractive visual tool to display multivariate data on a two-dimensional graphical illustration. Here, we describe the use of radar plots for the visualization of disease characteristics applied in the context of tinnitus, a complex and heterogeneous condition, the treatment of which has shown mixed success. Data from two different cohorts, the Swedish Tinnitus Outreach Project (STOP) and the Tinnitus Research Initiative (TRI) database, were used. STOP is a population-based cohort where cross-sectional data from 1,223 non-tinnitus and 933 tinnitus subjects were analyzed. By contrast, the TRI contained data from 571 patients who underwent various treatments and whose Clinical Global Impression (CGI) score was accessible to infer treatment outcome. In the latter, 34,560 permutations were tested to evaluate whether a particular ordering of the instruments could reflect better the treatment outcome measured with the CGI. Radar plots confirmed that tinnitus subtypes such as occasional and chronic tinnitus from the STOP cohort could be strikingly different, and helped appreciate a gender bias in tinnitus severity. Radar plots with greater surface areas were consistent with greater burden, and enabled a rapid appreciation of the global distress associated with tinnitus in patients categorized according to tinnitus severity. Permutations in the arrangement of instruments allowed to identify a configuration with minimal variance and maximized surface difference between CGI groups from the TRI database, thus affording a means of optimally evaluating the outcomes in individual patients. We anticipate such a tool to become a starting point for more sophisticated measures in clinical outcomes, applicable not only in the context of tinnitus but also in other complex diseases where the integration of multiple variables is needed for a comprehensive evaluation of treatment response.

Isgur-Karl model revisited

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

Galeta, Leonardo; Pirjol, Dan; Schat, Carlos

2009-12-01

We show how to match the Isgur-Karl model to the spin-flavor quark operator expansion used in the 1/N{sub c} studies of the nonstrange negative parity L=1 excited baryons. Using the transformation properties of states and interactions under the permutation group S{sub 3} we are able to express the operator coefficients as overlap integrals, without making any assumption on the spatial dependence of the quark wave functions. The general mass operator leads to parameter free mass relations and constraints on the mixing angles that are valid beyond the usual harmonic oscillator approximation. The Isgur-Karl model with harmonic oscillator wave functions providesmore » a simple counterexample that demonstrates explicitly that the alternative operator basis for the 1/N{sub c} expansion for excited baryons recently proposed by Matagne and Stancu is incomplete.« less

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.

A secure transmission scheme of streaming media based on the encrypted control message

NASA Astrophysics Data System (ADS)

Li, Bing; Jin, Zhigang; Shu, Yantai; Yu, Li

2007-09-01

As the use of streaming media applications increased dramatically in recent years, streaming media security becomes an important presumption, protecting the privacy. This paper proposes a new encryption scheme in view of characteristics of streaming media and the disadvantage of the living method: encrypt the control message in the streaming media with the high security lever and permute and confuse the data which is non control message according to the corresponding control message. Here the so-called control message refers to the key data of the streaming media, including the streaming media header and the header of the video frame, and the seed key. We encrypt the control message using the public key encryption algorithm which can provide high security lever, such as RSA. At the same time we make use of the seed key to generate key stream, from which the permutation list P responding to GOP (group of picture) is derived. The plain text of the non-control message XORs the key stream and gets the middle cipher text. And then obtained one is permutated according to P. In contrast the decryption process is the inverse process of the above. We have set up a testbed for the above scheme and found our scheme is six to eight times faster than the conventional method. It can be applied not only between PCs but also between handheld devices.

Fecal Microbiota Characteristics of Patients with Colorectal Adenoma Detected by Screening: A Population-based Study

PubMed Central

Goedert, James J.; Gong, Yangming; Hua, Xing; Zhong, Huanzi; He, Yimin; Peng, Peng; Yu, Guoqin; Wang, Wenjing; Ravel, Jacques; Shi, Jianxin; Zheng, Ying

2015-01-01

Background Screening for colorectal cancer (CRC) and precancerous colorectal adenoma (CRA) can detect curable disease. However, participation in colonoscopy and sensitivity of fecal heme for CRA are low. Methods Microbiota metrics were determined by Illumina sequencing of 16S rRNA genes amplified from DNA extracted from feces self-collected in RNAlater. Among fecal immunochemical test-positive (FIT +) participants, colonoscopically-defined normal versus CRA patients were compared by regression, permutation, and random forest plus leave-one-out methods. Findings Of 95 FIT + participants, 61 had successful fecal microbiota profiling and colonoscopy, identifying 24 completely normal patients, 20 CRA patients, 2 CRC patients, and 15 with other conditions. Phylum-level fecal community composition differed significantly between CRA and normal patients (permutation P = 0.02). Rank phylum-level abundance distinguished CRA from normal patients (area under the curve = 0.767, permutation P = 0.006). CRA prevalence was 59% in phylum-level cluster B versus 20% in cluster A (exact P = 0.01). Most of the difference reflected 3-fold higher median relative abundance of Proteobacteria taxa (Wilcoxon signed-rank P = 0.03, positive predictive value = 67%). Antibiotic exposure and other potential confounders did not affect the associations. Interpretation If confirmed in larger, more diverse populations, fecal microbiota analysis might be employed to improve screening for CRA and ultimately to reduce mortality from CRC. PMID:26288821

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.

Adinkra (in)equivalence from Coxeter group representations: A case study

NASA Astrophysics Data System (ADS)

Chappell, Isaac; Gates, S. James; Hübsch, T.

2014-02-01

Using a MathematicaTM code, we present a straightforward numerical analysis of the 384-dimensional solution space of signed permutation 4×4 matrices, which in sets of four, provide representations of the 𝒢ℛ(4, 4) algebra, closely related to the 𝒩 = 1 (simple) supersymmetry algebra in four-dimensional space-time. Following after ideas discussed in previous papers about automorphisms and classification of adinkras and corresponding supermultiplets, we make a new and alternative proposal to use equivalence classes of the (unsigned) permutation group S4 to define distinct representations of higher-dimensional spin bundles within the context of adinkras. For this purpose, the definition of a dual operator akin to the well-known Hodge star is found to partition the space of these 𝒢ℛ(4, 4) representations into three suggestive classes.

Tag-KEM from Set Partial Domain One-Way Permutations

NASA Astrophysics Data System (ADS)

Abe, Masayuki; Cui, Yang; Imai, Hideki; Kurosawa, Kaoru

Recently a framework called Tag-KEM/DEM was introduced to construct efficient hybrid encryption schemes. Although it is known that generic encode-then-encrypt construction of chosen ciphertext secure public-key encryption also applies to secure Tag-KEM construction and some known encoding method like OAEP can be used for this purpose, it is worth pursuing more efficient encoding method dedicated for Tag-KEM construction. This paper proposes an encoding method that yields efficient Tag-KEM schemes when combined with set partial one-way permutations such as RSA and Rabin's encryption scheme. To our knowledge, this leads to the most practical hybrid encryption scheme of this type. We also present an efficient Tag-KEM which is CCA-secure under general factoring assumption rather than Blum factoring assumption.

Procuring load curtailment from local customers under uncertainty.

PubMed

Mijatović, Aleksandar; Moriarty, John; Vogrinc, Jure

2017-08-13

Demand side response (DSR) provides a flexible approach to managing constrained power network assets. This is valuable if future asset utilization is uncertain. However there may be uncertainty over the process of procurement of DSR from customers. In this context we combine probabilistic modelling, simulation and optimization to identify economically optimal procurement policies from heterogeneous customers local to the asset, under chance constraints on the adequacy of the procured DSR. Mathematically this gives rise to a search over permutations, and we provide an illustrative example implementation and case study.This article is part of the themed issue 'Energy management: flexibility, risk and optimization'. © 2017 The Author(s).

Point form relativistic quantum mechanics and relativistic SU(6)

NASA Technical Reports Server (NTRS)

Klink, W. H.

1993-01-01

The point form is used as a framework for formulating a relativistic quantum mechanics, with the mass operator carrying the interactions of underlying constituents. A symplectic Lie algebra of mass operators is introduced from which a relativistic harmonic oscillator mass operator is formed. Mass splittings within the degenerate harmonic oscillator levels arise from relativistically invariant spin-spin, spin-orbit, and tensor mass operators. Internal flavor (and color) symmetries are introduced which make it possible to formulate a relativistic SU(6) model of baryons (and mesons). Careful attention is paid to the permutation symmetry properties of the hadronic wave functions, which are written as polynomials in Bargmann spaces.

Generalized Heisenberg Algebras, SUSYQM and Degeneracies: Infinite Well and Morse Potential

NASA Astrophysics Data System (ADS)

Hussin, Véronique; Marquette, Ian

2011-03-01

We consider classical and quantum one and two-dimensional systems with ladder operators that satisfy generalized Heisenberg algebras. In the classical case, this construction is related to the existence of closed trajectories. In particular, we apply these results to the infinite well and Morse potentials. We discuss how the degeneracies of the permutation symmetry of quantum two-dimensional systems can be explained using products of ladder operators. These products satisfy interesting commutation relations. The two-dimensional Morse quantum system is also related to a generalized two-dimensional Morse supersymmetric model. Arithmetical or accidental degeneracies of such system are shown to be associated to additional supersymmetry.

Permutation-symmetric three-particle hyper-spherical harmonics based on the S3 ⊗ SO(3)rot ⊂ O(2)⊗SO(3)rot ⊂ U(3)⋊S2 ⊂ O(6) subgroup chain

NASA Astrophysics Data System (ADS)

Salom, Igor; Dmitrašinović, V.

2017-07-01

We construct the three-body permutation symmetric hyperspherical harmonics to be used in the non-relativistic three-body Schrödinger equation in three spatial dimensions (3D). We label the state vectors according to the S3 ⊗ SO(3)rot ⊂ O (2) ⊗ SO(3)rot ⊂ U (3) ⋊S2 ⊂ O (6) subgroup chain, where S3 is the three-body permutation group and S2 is its two element subgroup containing transposition of first two particles, O (2) is the ;democracy transformation;, or ;kinematic rotation; group for three particles; SO(3)rot is the 3D rotation group, and U (3) , O (6) are the usual Lie groups. We discuss the good quantum numbers implied by the above chain of algebras, as well as their relation to the S3 permutation properties of the harmonics, particularly in view of the SO(3)rot ⊂ SU (3) degeneracy. We provide a definite, practically implementable algorithm for the calculation of harmonics with arbitrary finite integer values of the hyper angular momentum K, and show an explicit example of this construction in a specific case with degeneracy, as well as tables of K ≤ 6 harmonics. All harmonics are expressed as homogeneous polynomials in the Jacobi vectors (λ , ρ) with coefficients given as algebraic numbers unless the ;operator method; is chosen for the lifting of the SO(3)rot ⊂ SU (3) multiplicity and the dimension of the degenerate subspace is greater than four - in which case one must resort to numerical diagonalization; the latter condition is not met by any K ≤ 15 harmonic, or by any L ≤ 7 harmonic with arbitrary K. We also calculate a certain type of matrix elements (the Gaunt integrals of products of three harmonics) in two ways: 1) by explicit evaluation of integrals and 2) by reduction to known SU (3) Clebsch-Gordan coefficients. In this way we complete the calculation of the ingredients sufficient for the solution to the quantum-mechanical three-body bound state problem.

A nine-dimensional ab initio global potential energy surface for the H2O+ + H2 → H3O+ + H reaction

NASA Astrophysics Data System (ADS)

Li, Anyang; Guo, Hua

2014-06-01

An accurate full-dimensional global potential energy surface (PES) is developed for the title reaction. While the long-range interactions in the reactant asymptote are represented by an analytical expression, the interaction region of the PES is fit to more than 81 000 of ab initio points at the UCCSD(T)-F12b/AVTZ level using the permutation invariant polynomial neural network approach. Fully symmetric with respect to permutation of all four hydrogen atoms, the PES provides a faithful representation of the ab initio points, with a root mean square error of 1.8 meV or 15 cm-1. The reaction path for this exoergic reaction features an attractive and barrierless entrance channel, a submerged saddle point, a shallow H4O+ well, and a barrierless exit channel. The rate coefficients for the title reaction and kinetic isotope effect have been determined on this PES using quasi-classical trajectories, and they are in good agreement with available experimental data. It is further shown that the H2O+ rotational enhancement of reactivity observed experimentally can be traced to the submerged saddle point. Using our recently proposed Sudden Vector Projection model, we demonstrate that a rotational degree of freedom of the H2O+ reactant is strongly coupled with the reaction coordinate at this saddle point, thus unraveling the origin of the pronounced mode specificity in this reaction.

The behaviour of random forest permutation-based variable importance measures under predictor correlation.

PubMed

Nicodemus, Kristin K; Malley, James D; Strobl, Carolin; Ziegler, Andreas

2010-02-27

Random forests (RF) have been increasingly used in applications such as genome-wide association and microarray studies where predictor correlation is frequently observed. Recent works on permutation-based variable importance measures (VIMs) used in RF have come to apparently contradictory conclusions. We present an extended simulation study to synthesize results. In the case when both predictor correlation was present and predictors were associated with the outcome (HA), the unconditional RF VIM attributed a higher share of importance to correlated predictors, while under the null hypothesis that no predictors are associated with the outcome (H0) the unconditional RF VIM was unbiased. Conditional VIMs showed a decrease in VIM values for correlated predictors versus the unconditional VIMs under HA and was unbiased under H0. Scaled VIMs were clearly biased under HA and H0. Unconditional unscaled VIMs are a computationally tractable choice for large datasets and are unbiased under the null hypothesis. Whether the observed increased VIMs for correlated predictors may be considered a "bias" - because they do not directly reflect the coefficients in the generating model - or if it is a beneficial attribute of these VIMs is dependent on the application. For example, in genetic association studies, where correlation between markers may help to localize the functionally relevant variant, the increased importance of correlated predictors may be an advantage. On the other hand, we show examples where this increased importance may result in spurious signals.

The moderating role of close friends in the relationship between conduct problems and adolescent substance use.

PubMed

Glaser, Beate; Shelton, Katherine H; van den Bree, Marianne B M

2010-07-01

Conduct problems and peer effects are among the strongest risk factors for adolescent substance use and problem use. However, it is unclear to what extent the effects of conduct problems and peer behavior interact, and whether adolescents' capacity to refuse the offer of substances may moderate such links. This study was conducted to examine relationships between conduct problems, close friends' substance use, and refusal assertiveness with adolescents' alcohol use problems, tobacco, and marijuana use. We studied a population-based sample of 1,237 individuals from the Cardiff Study of All Wales and North West of England Twins aged 11-18 years. Adolescent and mother-reported information was obtained. Statistical analyses included cross-sectional and prospective logistic regression models and family-based permutations. Conduct problems and close friends' substance use were associated with increased adolescents' substance use, whereas refusal assertiveness was associated with lower use of cigarettes, alcohol, and marijuana. Peer substance use moderated the relationship between conduct problems and alcohol use problems, such that conduct problems were only related to increased risk for alcohol use problems in the presence of substance-using friends. This effect was found in both cross-sectional and prospective analyses and confirmed using the permutation approach. Reduced opportunities for interaction with alcohol-using peers may lower the risk of alcohol use problems in adolescents with conduct problems. Copyright (c) 2010 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Capacity of the generalized PPM channel

NASA Technical Reports Server (NTRS)

Hamkins, Jon; Klimesh, Matt; McEliece, Bob; Moision, Bruce

2004-01-01

We show the capacity of a generalized pulse-position-modulation (PPM) channel, where the input vectors may be any set that allows a transitive group of coordinate permutations, is achieved by a uniform input distribution.

A space efficient flexible pivot selection approach to evaluate determinant and inverse of a matrix.

PubMed

Jafree, Hafsa Athar; Imtiaz, Muhammad; Inayatullah, Syed; Khan, Fozia Hanif; Nizami, Tajuddin

2014-01-01

This paper presents new simple approaches for evaluating determinant and inverse of a matrix. The choice of pivot selection has been kept arbitrary thus they reduce the error while solving an ill conditioned system. Computation of determinant of a matrix has been made more efficient by saving unnecessary data storage and also by reducing the order of the matrix at each iteration, while dictionary notation [1] has been incorporated for computing the matrix inverse thereby saving unnecessary calculations. These algorithms are highly class room oriented, easy to use and implemented by students. By taking the advantage of flexibility in pivot selection, one may easily avoid development of the fractions by most. Unlike the matrix inversion method [2] and [3], the presented algorithms obviate the use of permutations and inverse permutations.

Parallel approach on sorting of genes in search of optimal solution.

PubMed

Kumar, Pranav; Sahoo, G

2018-05-01

An important tool for comparing genome analysis is the rearrangement event that can transform one given genome into other. For finding minimum sequence of fission and fusion, we have proposed here an algorithm and have shown a transformation example for converting the source genome into the target genome. The proposed algorithm comprises of circular sequence i.e. "cycle graph" in place of mapping. The main concept of algorithm is based on optimal result of permutation. These sorting processes are performed in constant running time by showing permutation in the form of cycle. In biological instances it has been observed that transposition occurs half of the frequency as that of reversal. In this paper we are not dealing with reversal instead commencing with the rearrangement of fission, fusion as well as transposition. Copyright © 2017 Elsevier Inc. All rights reserved.

An authenticated image encryption scheme based on chaotic maps and memory cellular automata

NASA Astrophysics Data System (ADS)

Bakhshandeh, Atieh; Eslami, Ziba

2013-06-01

This paper introduces a new image encryption scheme based on chaotic maps, cellular automata and permutation-diffusion architecture. In the permutation phase, a piecewise linear chaotic map is utilized to confuse the plain-image and in the diffusion phase, we employ the Logistic map as well as a reversible memory cellular automata to obtain an efficient and secure cryptosystem. The proposed method admits advantages such as highly secure diffusion mechanism, computational efficiency and ease of implementation. A novel property of the proposed scheme is its authentication ability which can detect whether the image is tampered during the transmission or not. This is particularly important in applications where image data or part of it contains highly sensitive information. Results of various analyses manifest high security of this new method and its capability for practical image encryption.

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

Parallel solution of closely coupled systems

NASA Technical Reports Server (NTRS)

Utku, S.; Salama, M.

1986-01-01

The odd-even permutation and associated unitary transformations for reordering the matrix coefficient A are employed as means of breaking the strong seriality which is characteristic of closely coupled systems. The nested dissection technique is also reviewed, and the equivalence between reordering A and dissecting its network is established. The effect of transforming A with odd-even permutation on its topology and the topology of its Cholesky factors is discussed. This leads to the construction of directed graphs showing the computational steps required for factoring A, their precedence relationships and their sequential and concurrent assignment to the available processors. Expressions for the speed-up and efficiency of using N processors in parallel relative to the sequential use of a single processor are derived from the directed graph. Similar expressions are also derived when the number of available processors is fewer than required.

Simulating the component counts of combinatorial structures.

PubMed

Arratia, Richard; Barbour, A D; Ewens, W J; Tavaré, Simon

2018-02-09

This article describes and compares methods for simulating the component counts of random logarithmic combinatorial structures such as permutations and mappings. We exploit the Feller coupling for simulating permutations to provide a very fast method for simulating logarithmic assemblies more generally. For logarithmic multisets and selections, this approach is replaced by an acceptance/rejection method based on a particular conditioning relationship that represents the distribution of the combinatorial structure as that of independent random variables conditioned on a weighted sum. We show how to improve its acceptance rate. We illustrate the method by estimating the probability that a random mapping has no repeated component sizes, and establish the asymptotic distribution of the difference between the number of components and the number of distinct component sizes for a very general class of logarithmic structures. Copyright © 2018. Published by Elsevier Inc.

The structure of EAP-groups and self-autopermutable subgroups.

PubMed

Housieni, Shima; Moghaddam, Mohammad Reza Rajabzadeh

2014-01-01

A subgroup H of a given group G is said to be autopermutable, if HH(α) = H(α)H for all α ∈ Aut(G). We also call H a self-autopermutable subgroup of G, when HH(α) = H(α)H implies that H(α) = H. Moreover, G is said to be EAP-group, if every subgroup of G is autopermutable. One notes that if α runs over the inner automorphisms of the group, one obtains the notions of conjugate-permutability, self-conjugate-permutability, and ECP-groups, which were studied by Foguel in 1997, Li and Meng in 2007, and Xu and Zhang in 2005, respectively. In the present paper, we determine the structure of a finite EAP-group when its centre is of index 4 in G. We also show that self-autopermutability and characteristic properties are equivalent for nilpotent groups.

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.

Recursive boson system in the Cuntz algebra O{sub {infinity}}

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

Kawamura, Katsunori

2007-09-15

Bosons and fermions are often written by elements of other algebras. Abe (private communication) gave a realization of bosons by formal infinite sums of the canonical generators of the Cuntz algebra O{sub {infinity}}. We show that such formal infinite sum always makes sense on a certain dense subspace of any permutative representation of O{sub {infinity}}. In this meaning, we can regard as if the algebra B of bosons was a unital *-subalgebra of O{sub {infinity}} on a given permutative representation. According to this relation, we compute branching laws arising from restrictions of representations of O{sub {infinity}} on B. For example,more » it is shown that the Fock representation of B is given as the restriction of the standard representation of O{sub {infinity}} on B.« less

Intrinsically bent DNA in replication origins and gene promoters.

PubMed

Gimenes, F; Takeda, K I; Fiorini, A; Gouveia, F S; Fernandez, M A

2008-06-24

Intrinsically bent DNA is an alternative conformation of the DNA molecule caused by the presence of dA/dT tracts, 2 to 6 bp long, in a helical turn phase DNA or with multiple intervals of 10 to 11 bp. Other than flexibility, intrinsic bending sites induce DNA curvature in particular chromosome regions such as replication origins and promoters. Intrinsically bent DNA sites are important in initiating DNA replication, and are sometimes found near to regions associated with the nuclear matrix. Many methods have been developed to localize bent sites, for example, circular permutation, computational analysis, and atomic force microscopy. This review discusses intrinsically bent DNA sites associated with replication origins and gene promoter regions in prokaryote and eukaryote cells. We also describe methods for identifying bent DNA sites for circular permutation and computational analysis.

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.

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

Rouxelin, Pascal Nicolas; Strydom, Gerhard

Best-estimate plus uncertainty analysis of reactors is replacing the traditional conservative (stacked uncertainty) method for safety and licensing analysis. To facilitate uncertainty analysis applications, a comprehensive approach and methodology must be developed and applied. High temperature gas cooled reactors (HTGRs) have several features that require techniques not used in light-water reactor analysis (e.g., coated-particle design and large graphite quantities at high temperatures). The International Atomic Energy Agency has therefore launched the Coordinated Research Project on HTGR Uncertainty Analysis in Modeling to study uncertainty propagation in the HTGR analysis chain. The benchmark problem defined for the prismatic design is represented bymore » the General Atomics Modular HTGR 350. The main focus of this report is the compilation and discussion of the results obtained for various permutations of Exercise I 2c and the use of the cross section data in Exercise II 1a of the prismatic benchmark, which is defined as the last and first steps of the lattice and core simulation phases, respectively. The report summarizes the Idaho National Laboratory (INL) best estimate results obtained for Exercise I 2a (fresh single-fuel block), Exercise I 2b (depleted single-fuel block), and Exercise I 2c (super cell) in addition to the first results of an investigation into the cross section generation effects for the super-cell problem. The two dimensional deterministic code known as the New ESC based Weighting Transport (NEWT) included in the Standardized Computer Analyses for Licensing Evaluation (SCALE) 6.1.2 package was used for the cross section evaluation, and the results obtained were compared to the three dimensional stochastic SCALE module KENO VI. The NEWT cross section libraries were generated for several permutations of the current benchmark super-cell geometry and were then provided as input to the Phase II core calculation of the stand alone neutronics Exercise II 1a. The steady state core calculations were simulated with the INL coupled-code system known as the Parallel and Highly Innovative Simulation for INL Code System (PHISICS) and the system thermal-hydraulics code known as the Reactor Excursion and Leak Analysis Program (RELAP) 5 3D using the nuclear data libraries previously generated with NEWT. It was observed that significant differences in terms of multiplication factor and neutron flux exist between the various permutations of the Phase I super-cell lattice calculations. The use of these cross section libraries only leads to minor changes in the Phase II core simulation results for fresh fuel but shows significantly larger discrepancies for spent fuel cores. Furthermore, large incongruities were found between the SCALE NEWT and KENO VI results for the super cells, and while some trends could be identified, a final conclusion on this issue could not yet be reached. This report will be revised in mid 2016 with more detailed analyses of the super-cell problems and their effects on the core models, using the latest version of SCALE (6.2). The super-cell models seem to show substantial improvements in terms of neutron flux as compared to single-block models, particularly at thermal energies.« less

Keep it simple - A case study of model development in the context of the Dynamic Stocks and Flows (DSF) task

NASA Astrophysics Data System (ADS)

Halbrügge, Marc

2010-12-01

This paper describes the creation of a cognitive model submitted to the ‘Dynamic Stocks and Flows’ (DSF) modeling challenge. This challenge aims at comparing computational cognitive models for human behavior during an open ended control task. Participants in the modeling competition were provided with a simulation environment and training data for benchmarking their models while the actual specification of the competition task was withheld. To meet this challenge, the cognitive model described here was designed and optimized for generalizability. Only two simple assumptions about human problem solving were used to explain the empirical findings of the training data. In-depth analysis of the data set prior to the development of the model led to the dismissal of correlations or other parametric statistics as goodness-of-fit indicators. A new statistical measurement based on rank orders and sequence matching techniques is being proposed instead. This measurement, when being applied to the human sample, also identifies clusters of subjects that use different strategies for the task. The acceptability of the fits achieved by the model is verified using permutation tests.

Augmenting the logrank test in the design of clinical trials in which non-proportional hazards of the treatment effect may be anticipated.

PubMed

Royston, Patrick; Parmar, Mahesh K B

2016-02-11

Most randomized controlled trials with a time-to-event outcome are designed assuming proportional hazards (PH) of the treatment effect. The sample size calculation is based on a logrank test. However, non-proportional hazards are increasingly common. At analysis, the estimated hazards ratio with a confidence interval is usually presented. The estimate is often obtained from a Cox PH model with treatment as a covariate. If non-proportional hazards are present, the logrank and equivalent Cox tests may lose power. To safeguard power, we previously suggested a 'joint test' combining the Cox test with a test of non-proportional hazards. Unfortunately, a larger sample size is needed to preserve power under PH. Here, we describe a novel test that unites the Cox test with a permutation test based on restricted mean survival time. We propose a combined hypothesis test based on a permutation test of the difference in restricted mean survival time across time. The test involves the minimum of the Cox and permutation test P-values. We approximate its null distribution and correct it for correlation between the two P-values. Using extensive simulations, we assess the type 1 error and power of the combined test under several scenarios and compare with other tests. We investigate powering a trial using the combined test. The type 1 error of the combined test is close to nominal. Power under proportional hazards is slightly lower than for the Cox test. Enhanced power is available when the treatment difference shows an 'early effect', an initial separation of survival curves which diminishes over time. The power is reduced under a 'late effect', when little or no difference in survival curves is seen for an initial period and then a late separation occurs. We propose a method of powering a trial using the combined test. The 'insurance premium' offered by the combined test to safeguard power under non-PH represents about a single-digit percentage increase in sample size. The combined test increases trial power under an early treatment effect and protects power under other scenarios. Use of restricted mean survival time facilitates testing and displaying a generalized treatment effect.

Polyketide intermediate mimics as probes for revealing cryptic stereochemistry of ketoreductase domains.

PubMed

Li, Yang; Fiers, William D; Bernard, Steffen M; Smith, Janet L; Aldrich, Courtney C; Fecik, Robert A

2014-12-19

Among natural product families, polyketides have shown the most promise for combinatorial biosynthesis of natural product-like libraries. Though recent research in the area has provided many mechanistic revelations, a basic-level understanding of kinetic and substrate tolerability is still needed before the full potential of combinatorial biosynthesis can be realized. We have developed a novel set of chemical probes for the study of ketoreductase domains of polyketide synthases. This chemical tool-based approach was validated using the ketoreductase of pikromycin module 2 (PikKR2) as a model system. Triketide substrate mimics 12 and 13 were designed to increase stability (incorporating a nonhydrolyzable thioether linkage) and minimize nonessential functionality (truncating the phosphopantetheinyl arm). PikKR2 reduction product identities as well as steady-state kinetic parameters were determined by a combination of LC-MS/MS analysis of synthetic standards and a NADPH consumption assay. The d-hydroxyl product is consistent with bioinformatic analysis and results from a complementary biochemical and molecular biological approach. When compared to widely employed substrates in previous studies, diketide 63 and trans-decalone 64, substrates 12 and 13 showed 2-10 fold lower K(M) values (2.4 ± 0.8 and 7.8 ± 2.7 mM, respectively), indicating molecular recognition of intermediate-like substrates. Due to an abundance of the nonreducable enol-tautomer, the k(cat) values were attenuated by as much as 15-336 fold relative to known substrates. This study reveals the high stereoselectivity of PikKR2 in the face of gross substrate permutation, highlighting the utility of a chemical probe-based approach in the study of polyketide ketoreductases.

Mesoscale spatial variability of selected aquatic invertebrate community metrics from a minimally impaired stream segment

USGS Publications Warehouse

Gebler, J.B.

2004-01-01

The related topics of spatial variability of aquatic invertebrate community metrics, implications of spatial patterns of metric values to distributions of aquatic invertebrate communities, and ramifications of natural variability to the detection of human perturbations were investigated. Four metrics commonly used for stream assessment were computed for 9 stream reaches within a fairly homogeneous, minimally impaired stream segment of the San Pedro River, Arizona. Metric variability was assessed for differing sampling scenarios using simple permutation procedures. Spatial patterns of metric values suggest that aquatic invertebrate communities are patchily distributed on subsegment and segment scales, which causes metric variability. Wide ranges of metric values resulted in wide ranges of metric coefficients of variation (CVs) and minimum detectable differences (MDDs), and both CVs and MDDs often increased as sample size (number of reaches) increased, suggesting that any particular set of sampling reaches could yield misleading estimates of population parameters and effects that can be detected. Mean metric variabilities were substantial, with the result that only fairly large differences in metrics would be declared significant at ?? = 0.05 and ?? = 0.20. The number of reaches required to obtain MDDs of 10% and 20% varied with significance level and power, and differed for different metrics, but were generally large, ranging into tens and hundreds of reaches. Study results suggest that metric values from one or a small number of stream reach(es) may not be adequate to represent a stream segment, depending on effect sizes of interest, and that larger sample sizes are necessary to obtain reasonable estimates of metrics and sample statistics. For bioassessment to progress, spatial variability may need to be investigated in many systems and should be considered when designing studies and interpreting data.

Majorana fermion surface code for universal quantum computation

DOE PAGES

Vijay, Sagar; Hsieh, Timothy H.; Fu, Liang

2015-12-10

In this study, we introduce an exactly solvable model of interacting Majorana fermions realizing Z 2 topological order with a Z 2 fermion parity grading and lattice symmetries permuting the three fundamental anyon types. We propose a concrete physical realization by utilizing quantum phase slips in an array of Josephson-coupled mesoscopic topological superconductors, which can be implemented in a wide range of solid-state systems, including topological insulators, nanowires, or two-dimensional electron gases, proximitized by s-wave superconductors. Our model finds a natural application as a Majorana fermion surface code for universal quantum computation, with a single-step stabilizer measurement requiring no physicalmore » ancilla qubits, increased error tolerance, and simpler logical gates than a surface code with bosonic physical qubits. We thoroughly discuss protocols for stabilizer measurements, encoding and manipulating logical qubits, and gate implementations.« less

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

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...

Molecular symmetry: Why permutation-inversion (PI) groups don't render the point groups obsolete

NASA Astrophysics Data System (ADS)

Groner, Peter

2018-01-01

The analysis of spectra of molecules with internal large-amplitude motions (LAMs) requires molecular symmetry (MS) groups that are larger than and significantly different from the more familiar point groups. MS groups are described often by the permutation-inversion (PI) group method. It is shown that point groups still can and should play a significant role together with the PI groups for a class of molecules with internal rotors. In molecules of this class, several simple internal rotors are attached to a rigid molecular frame. The PI groups for this class are semidirect products like H ^ F, where the invariant subgroup H is a direct product of cyclic groups and F is a point group. This result is used to derive meaningful labels for MS groups, and to derive correlation tables between MS groups and point groups. MS groups of this class have many parallels to space groups of crystalline solids.

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.

A fault diagnosis scheme for planetary gearboxes using adaptive multi-scale morphology filter and modified hierarchical permutation entropy

NASA Astrophysics Data System (ADS)

Li, Yongbo; Li, Guoyan; Yang, Yuantao; Liang, Xihui; Xu, Minqiang

2018-05-01

The fault diagnosis of planetary gearboxes is crucial to reduce the maintenance costs and economic losses. This paper proposes a novel fault diagnosis method based on adaptive multi-scale morphological filter (AMMF) and modified hierarchical permutation entropy (MHPE) to identify the different health conditions of planetary gearboxes. In this method, AMMF is firstly adopted to remove the fault-unrelated components and enhance the fault characteristics. Second, MHPE is utilized to extract the fault features from the denoised vibration signals. Third, Laplacian score (LS) approach is employed to refine the fault features. In the end, the obtained features are fed into the binary tree support vector machine (BT-SVM) to accomplish the fault pattern identification. The proposed method is numerically and experimentally demonstrated to be able to recognize the different fault categories of planetary gearboxes.

An efficient genome-wide association test for mixed binary and continuous phenotypes with applications to substance abuse research.

PubMed

Buu, Anne; Williams, L Keoki; Yang, James J

2018-03-01

We propose a new genome-wide association test for mixed binary and continuous phenotypes that uses an efficient numerical method to estimate the empirical distribution of the Fisher's combination statistic under the null hypothesis. Our simulation study shows that the proposed method controls the type I error rate and also maintains its power at the level of the permutation method. More importantly, the computational efficiency of the proposed method is much higher than the one of the permutation method. The simulation results also indicate that the power of the test increases when the genetic effect increases, the minor allele frequency increases, and the correlation between responses decreases. The statistical analysis on the database of the Study of Addiction: Genetics and Environment demonstrates that the proposed method combining multiple phenotypes can increase the power of identifying markers that may not be, otherwise, chosen using marginal tests.

SAR processing on the MPP

NASA Technical Reports Server (NTRS)

Batcher, K. E.; Eddey, E. E.; Faiss, R. O.; Gilmore, P. A.

1981-01-01

The processing of synthetic aperture radar (SAR) signals using the massively parallel processor (MPP) is discussed. The fast Fourier transform convolution procedures employed in the algorithms are described. The MPP architecture comprises an array unit (ARU) which processes arrays of data; an array control unit which controls the operation of the ARU and performs scalar arithmetic; a program and data management unit which controls the flow of data; and a unique staging memory (SM) which buffers and permutes data. The ARU contains a 128 by 128 array of bit-serial processing elements (PE). Two-by-four surarrays of PE's are packaged in a custom VLSI HCMOS chip. The staging memory is a large multidimensional-access memory which buffers and permutes data flowing with the system. Efficient SAR processing is achieved via ARU communication paths and SM data manipulation. Real time processing capability can be realized via a multiple ARU, multiple SM configuration.

Demonstration of universal parametric entangling gates on a multi-qubit lattice

PubMed Central

Reagor, Matthew; Osborn, Christopher B.; Tezak, Nikolas; Staley, Alexa; Prawiroatmodjo, Guenevere; Scheer, Michael; Alidoust, Nasser; Sete, Eyob A.; Didier, Nicolas; da Silva, Marcus P.; Acala, Ezer; Angeles, Joel; Bestwick, Andrew; Block, Maxwell; Bloom, Benjamin; Bradley, Adam; Bui, Catvu; Caldwell, Shane; Capelluto, Lauren; Chilcott, Rick; Cordova, Jeff; Crossman, Genya; Curtis, Michael; Deshpande, Saniya; El Bouayadi, Tristan; Girshovich, Daniel; Hong, Sabrina; Hudson, Alex; Karalekas, Peter; Kuang, Kat; Lenihan, Michael; Manenti, Riccardo; Manning, Thomas; Marshall, Jayss; Mohan, Yuvraj; O’Brien, William; Otterbach, Johannes; Papageorge, Alexander; Paquette, Jean-Philip; Pelstring, Michael; Polloreno, Anthony; Rawat, Vijay; Ryan, Colm A.; Renzas, Russ; Rubin, Nick; Russel, Damon; Rust, Michael; Scarabelli, Diego; Selvanayagam, Michael; Sinclair, Rodney; Smith, Robert; Suska, Mark; To, Ting-Wai; Vahidpour, Mehrnoosh; Vodrahalli, Nagesh; Whyland, Tyler; Yadav, Kamal; Zeng, William; Rigetti, Chad T.

2018-01-01

We show that parametric coupling techniques can be used to generate selective entangling interactions for multi-qubit processors. By inducing coherent population exchange between adjacent qubits under frequency modulation, we implement a universal gate set for a linear array of four superconducting qubits. An average process fidelity of ℱ = 93% is estimated for three two-qubit gates via quantum process tomography. We establish the suitability of these techniques for computation by preparing a four-qubit maximally entangled state and comparing the estimated state fidelity with the expected performance of the individual entangling gates. In addition, we prepare an eight-qubit register in all possible bitstring permutations and monitor the fidelity of a two-qubit gate across one pair of these qubits. Across all these permutations, an average fidelity of ℱ = 91.6 ± 2.6% is observed. These results thus offer a path to a scalable architecture with high selectivity and low cross-talk. PMID:29423443

Chaotic reconfigurable ZCMT precoder for OFDM data encryption and PAPR reduction

NASA Astrophysics Data System (ADS)

Chen, Han; Yang, Xuelin; Hu, Weisheng

2017-12-01

A secure orthogonal frequency division multiplexing (OFDM) transmission scheme precoded by chaotic Zadoff-Chu matrix transform (ZCMT) is proposed and demonstrated. It is proved that the reconfigurable ZCMT matrices after row/column permutations can be applied as an alternative precoder for peak-to-average power ratio (PAPR) reduction. The permutations and the reconfigurable parameters in ZCMT matrix are generated by a hyper digital chaos, in which a huge key space of ∼ 10800 is created for physical-layer OFDM data encryption. An encrypted data transmission of 8.9 Gb/s optical OFDM signals is successfully demonstrated over 20 km standard single-mode fiber (SSMF) for 16-QAM. The BER performance of the encrypted signals is improved by ∼ 2 dB (BER@ 10-3), which is mainly attributed to the effective reduction of PAPR via chaotic ZCMT precoding. Moreover, the chaotic ZCMT precoding scheme requires no sideband information, thus the spectrum efficiency is enhanced during transmission.

Mass univariate analysis of event-related brain potentials/fields I: a critical tutorial review.

PubMed

Groppe, David M; Urbach, Thomas P; Kutas, Marta

2011-12-01

Event-related potentials (ERPs) and magnetic fields (ERFs) are typically analyzed via ANOVAs on mean activity in a priori windows. Advances in computing power and statistics have produced an alternative, mass univariate analyses consisting of thousands of statistical tests and powerful corrections for multiple comparisons. Such analyses are most useful when one has little a priori knowledge of effect locations or latencies, and for delineating effect boundaries. Mass univariate analyses complement and, at times, obviate traditional analyses. Here we review this approach as applied to ERP/ERF data and four methods for multiple comparison correction: strong control of the familywise error rate (FWER) via permutation tests, weak control of FWER via cluster-based permutation tests, false discovery rate control, and control of the generalized FWER. We end with recommendations for their use and introduce free MATLAB software for their implementation. Copyright © 2011 Society for Psychophysiological Research.

Signal processing applications of massively parallel charge domain computing devices

NASA Technical Reports Server (NTRS)

Fijany, Amir (Inventor); Barhen, Jacob (Inventor); Toomarian, Nikzad (Inventor)

1999-01-01

The present invention is embodied in a charge coupled device (CCD)/charge injection device (CID) architecture capable of performing a Fourier transform by simultaneous matrix vector multiplication (MVM) operations in respective plural CCD/CID arrays in parallel in O(1) steps. For example, in one embodiment, a first CCD/CID array stores charge packets representing a first matrix operator based upon permutations of a Hartley transform and computes the Fourier transform of an incoming vector. A second CCD/CID array stores charge packets representing a second matrix operator based upon different permutations of a Hartley transform and computes the Fourier transform of an incoming vector. The incoming vector is applied to the inputs of the two CCD/CID arrays simultaneously, and the real and imaginary parts of the Fourier transform are produced simultaneously in the time required to perform a single MVM operation in a CCD/CID array.

Consultation sequencing of a hospital with multiple service points using genetic programming

NASA Astrophysics Data System (ADS)

Morikawa, Katsumi; Takahashi, Katsuhiko; Nagasawa, Keisuke

2018-07-01

A hospital with one consultation room operated by a physician and several examination rooms is investigated. Scheduled patients and walk-ins arrive at the hospital, each patient goes to the consultation room first, and some of them visit other service points before consulting the physician again. The objective function consists of the sum of three weighted average waiting times. The problem of sequencing patients for consultation is focused. To alleviate the stress of waiting, the consultation sequence is displayed. A dispatching rule is used to decide the sequence, and best rules are explored by genetic programming (GP). The simulation experiments indicate that the rules produced by GP can be reduced to simple permutations of queues, and the best permutation depends on the weight used in the objective function. This implies that a balanced allocation of waiting times can be achieved by ordering the priority among three queues.

Entanglement distillation protocols and number theory

NASA Astrophysics Data System (ADS)

Bombin, H.; Martin-Delgado, M. A.

2005-09-01

We show that the analysis of entanglement distillation protocols for qudits of arbitrary dimension D benefits from applying basic concepts from number theory, since the set ZDn associated with Bell diagonal states is a module rather than a vector space. We find that a partition of ZDn into divisor classes characterizes the invariant properties of mixed Bell diagonal states under local permutations. We construct a very general class of recursion protocols by means of unitary operations implementing these local permutations. We study these distillation protocols depending on whether we use twirling operations in the intermediate steps or not, and we study them both analytically and numerically with Monte Carlo methods. In the absence of twirling operations, we construct extensions of the quantum privacy algorithms valid for secure communications with qudits of any dimension D . When D is a prime number, we show that distillation protocols are optimal both qualitatively and quantitatively.

Permutation methods for the structured exploratory data analysis (SEDA) of familial trait values.

PubMed

Karlin, S; Williams, P T

1984-07-01

A collection of functions that contrast familial trait values between and across generations is proposed for studying transmission effects and other collateral influences in nuclear families. Two classes of structured exploratory data analysis (SEDA) statistics are derived from ratios of these functions. SEDA-functionals are the empirical cumulative distributions of the ratio of the two contrasts computed within each family. SEDA-indices are formed by first averaging the numerator and denominator contrasts separately over the population and then forming their ratio. The significance of SEDA results are determined by a spectrum of permutation techniques that selectively shuffle the trait values across families. The process systematically alters certain family structure relationships while keeping other familial relationships intact. The methodology is applied to five data examples of plasma total cholesterol concentrations, reported height values, dermatoglyphic pattern intensity index scores, measurements of dopamine-beta-hydroxylase activity, and psychometric cognitive test results.

Analysis of genome rearrangement by block-interchanges.

PubMed

Lu, Chin Lung; Lin, Ying Chih; Huang, Yen Lin; Tang, Chuan Yi

2007-01-01

Block-interchanges are a new kind of genome rearrangements that affect the gene order in a chromosome by swapping two nonintersecting blocks of genes of any length. More recently, the study of such rearrangements is becoming increasingly important because of its applications in molecular evolution. Usually, this kind of study requires to solve a combinatorial problem, called the block-interchange distance problem, which is to find a minimum number of block-interchanges between two given gene orders of linear/circular chromosomes to transform one gene order into another. In this chapter, we shall introduce the basics of block-interchange rearrangements and permutation groups in algebra that are useful in analyses of genome rearrangements. In addition, we shall present a simple algorithm on the basis of permutation groups to efficiently solve the block-interchange distance problem, as well as ROBIN, a web server for the online analyses of block-interchange rearrangements.

A New Efficient Algorithm for the All Sorting Reversals Problem with No Bad Components.

PubMed

Wang, Biing-Feng

2016-01-01

The problem of finding all reversals that take a permutation one step closer to a target permutation is called the all sorting reversals problem (the ASR problem). For this problem, Siepel had an O(n (3))-time algorithm. Most complications of his algorithm stem from some peculiar structures called bad components. Since bad components are very rare in both real and simulated data, it is practical to study the ASR problem with no bad components. For the ASR problem with no bad components, Swenson et al. gave an O (n(2))-time algorithm. Very recently, Swenson found that their algorithm does not always work. In this paper, a new algorithm is presented for the ASR problem with no bad components. The time complexity is O(n(2)) in the worst case and is linear in the size of input and output in practice.

A one-time pad color image cryptosystem based on SHA-3 and multiple chaotic systems

NASA Astrophysics Data System (ADS)

Wang, Xingyuan; Wang, Siwei; Zhang, Yingqian; Luo, Chao

2018-04-01

A novel image encryption algorithm is proposed that combines the SHA-3 hash function and two chaotic systems: the hyper-chaotic Lorenz and Chen systems. First, 384 bit keystream hash values are obtained by applying SHA-3 to plaintext. The sensitivity of the SHA-3 algorithm and chaotic systems ensures the effect of a one-time pad. Second, the color image is expanded into three-dimensional space. During permutation, it undergoes plane-plane displacements in the x, y and z dimensions. During diffusion, we use the adjacent pixel dataset and corresponding chaotic value to encrypt each pixel. Finally, the structure of alternating between permutation and diffusion is applied to enhance the level of security. Furthermore, we design techniques to improve the algorithm's encryption speed. Our experimental simulations show that the proposed cryptosystem achieves excellent encryption performance and can resist brute-force, statistical, and chosen-plaintext attacks.

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.

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.

A low speed wind tunnel test of a 0.050 scale model of shuttle orbiter (model 089B) to investigate the longitudinal and lateral directional effects of canard and tail configurational modifications in the LTV LSWT (MA14)

NASA Technical Reports Server (NTRS)

Chambliss, E. B.

1976-01-01

A low speed wind tunnel test was conducted to determine the effects of 6 canard configurations on the 0.050 scale model of shuttle orbiter 089B. In addition, two horizontal tail configurations were tested at two positions on the model as were two wing configurations. Since this test was restricted to 103 runs, only a limited number of permutations of the configurational changes could be tested. The testing was done in the 15 by 20 foot section of the LSWT and consisted of pitch polars, one yawed polar and several yaw runs. The pitch polars encompassed an alpha range from 0 to 28 deg; the yawed polar was run at beta = +2 degrees and the yaw runs covered a beta range from -6 to +6 deg at angles-of-attack of 0, 4, 10, 16, and 20 deg.

Low-rank factorization of electron integral tensors and its application in electronic structure theory

DOE PAGES

Peng, Bo; Kowalski, Karol

2017-01-25

In this paper, we apply reverse Cuthill-McKee (RCM) algorithm to transform two-electron integral tensors to their block diagonal forms. By further applying Cholesky decomposition (CD) on each of the diagonal blocks, we are able to represent the high-dimensional two-electron integral tensors in terms of permutation matrices and low-rank Cholesky vectors. This representation facilitates low-rank factorizations of high-dimensional tensor contractions in post-Hartree-Fock calculations. Finally, we discuss the second-order Møller-Plesset (MP2) method and the linear coupled-cluster model with doubles (L-CCD) as examples to demonstrate the efficiency of this technique in representing the two-electron integrals in a compact form.

Independent bases on the spatial wavefunction of four-identical-particle systems

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

Xiao, Shuyuan; Deng, Zhixuan; Chen, Hong

2013-12-15

We construct the independent bases on the spatial wavefunction of four-identical-particle systems classified under the rotational group SO(3) and the permutation group S{sub 4} with the usage of transformation coefficients that relate wavefunctions described in one set of internal coordinates with those in another. The basis functions for N⩽ 2 are presented in the explicit expressions based on the harmonic oscillator model. Such independent bases are supposed to play a key role in the construction of the wavefunctions of the five-quark states and the variation calculation of four-body systems. Our prescription avoids the spurious states and can be programmed formore » arbitrary N.« less

Low-rank factorization of electron integral tensors and its application in electronic structure theory

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

Peng, Bo; Kowalski, Karol

In this paper, we apply reverse Cuthill-McKee (RCM) algorithm to transform two-electron integral tensors to their block diagonal forms. By further applying Cholesky decomposition (CD) on each of the diagonal blocks, we are able to represent the high-dimensional two-electron integral tensors in terms of permutation matrices and low-rank Cholesky vectors. This representation facilitates low-rank factorizations of high-dimensional tensor contractions in post-Hartree-Fock calculations. Finally, we discuss the second-order Møller-Plesset (MP2) method and the linear coupled-cluster model with doubles (L-CCD) as examples to demonstrate the efficiency of this technique in representing the two-electron integrals in a compact form.

Color image encryption based on color blend and chaos permutation in the reality-preserving multiple-parameter fractional Fourier transform domain

NASA Astrophysics Data System (ADS)

Lang, Jun

2015-03-01

In this paper, we propose a novel color image encryption method by using Color Blend (CB) and Chaos Permutation (CP) operations in the reality-preserving multiple-parameter fractional Fourier transform (RPMPFRFT) domain. The original color image is first exchanged and mixed randomly from the standard red-green-blue (RGB) color space to R‧G‧B‧ color space by rotating the color cube with a random angle matrix. Then RPMPFRFT is employed for changing the pixel values of color image, three components of the scrambled RGB color space are converted by RPMPFRFT with three different transform pairs, respectively. Comparing to the complex output transform, the RPMPFRFT transform ensures that the output is real which can save storage space of image and convenient for transmission in practical applications. To further enhance the security of the encryption system, the output of the former steps is scrambled by juxtaposition of sections of the image in the reality-preserving multiple-parameter fractional Fourier domains and the alignment of sections is determined by two coupled chaotic logistic maps. The parameters in the Color Blend, Chaos Permutation and the RPMPFRFT transform are regarded as the key in the encryption algorithm. The proposed color image encryption can also be applied to encrypt three gray images by transforming the gray images into three RGB color components of a specially constructed color image. Numerical simulations are performed to demonstrate that the proposed algorithm is feasible, secure, sensitive to keys and robust to noise attack and data loss.

Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin

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

Le Trong, Isolde; University of Washington, Box 357742, Seattle, WA 98195-7742; Chu, Vano

2013-06-01

The crystal structures of two circularly permuted streptavidins probe the role of a flexible loop in the tight binding of biotin. Molecular-dynamics calculations for one of the mutants suggests that increased fluctuations in a hydrogen bond between the protein and biotin are associated with cleavage of the binding loop. Circular permutation of streptavidin was carried out in order to investigate the role of a main-chain amide in stabilizing the high-affinity complex of the protein and biotin. Mutant proteins CP49/48 and CP50/49 were constructed to place new N-termini at residues 49 and 50 in a flexible loop involved in stabilizing themore » biotin complex. Crystal structures of the two mutants show that half of each loop closes over the binding site, as observed in wild-type streptavidin, while the other half adopts the open conformation found in the unliganded state. The structures are consistent with kinetic and thermodynamic data and indicate that the loop plays a role in enthalpic stabilization of the bound state via the Asn49 amide–biotin hydrogen bond. In wild-type streptavidin, the entropic penalties of immobilizing a flexible portion of the protein to enhance binding are kept to a manageable level by using a contiguous loop of medium length (six residues) which is already constrained by its anchorage to strands of the β-barrel protein. A molecular-dynamics simulation for CP50/49 shows that cleavage of the binding loop results in increased structural fluctuations for Ser45 and that these fluctuations destabilize the streptavidin–biotin complex.« less

System for routing messages in a vertex symmetric network by using addresses formed from permutations of the transmission line indicees

DOEpatents

Faber, Vance; Moore, James W.

1992-01-01

A network of interconnected processors is formed from a vertex symmetric graph selected from graphs .GAMMA..sub.d (k) with degree d, diameter k, and (d+1)!/(d-k+1)! processors for each d.gtoreq.k and .GAMMA..sub.d (k,-1) with degree 3-1, diameter k+1, and (d+1)!/(d-k+1)! processors for each d.gtoreq.k.gtoreq.4. Each processor has an address formed by one of the permutations from a predetermined sequence of letters chosen a selected number of letters at a time, and an extended address formed by appending to the address the remaining ones of the predetermined sequence of letters. A plurality of transmission channels is provided from each of the processors, where each processor has one less channel than the selected number of letters forming the sequence. Where a network .GAMMA..sub.d (k,-1) is provided, no processor has a channel connected to form an edge in a direction .delta..sub.1. Each of the channels has an identification number selected from the sequence of letters and connected from a first processor having a first extended address to a second processor having a second address formed from a second extended address defined by moving to the front of the first extended address the letter found in the position within the first extended address defined by the channel identification number. The second address is then formed by selecting the first elements of the second extended address corresponding to the selected number used to form the address permutations.

Using permutation tests to enhance causal inference in interrupted time series analysis.

PubMed

Linden, Ariel

2018-06-01

Interrupted time series analysis (ITSA) is an evaluation methodology in which a single treatment unit's outcome is studied serially over time and the intervention is expected to "interrupt" the level and/or trend of that outcome. The internal validity is strengthened considerably when the treated unit is contrasted with a comparable control group. In this paper, we introduce a robustness check based on permutation tests to further improve causal inference. We evaluate the effect of California's Proposition 99 for reducing cigarette sales by iteratively casting each nontreated state into the role of "treated," creating a comparable control group using the ITSAMATCH package in Stata, and then evaluating treatment effects using ITSA regression. If statistically significant "treatment effects" are estimated for pseudotreated states, then any significant changes in the outcome of the actual treatment unit (California) cannot be attributed to the intervention. We perform these analyses setting the cutpoint significance level to P > .40 for identifying balanced matches (the highest threshold possible for which controls could still be found for California) and use the difference in differences of trends as the treatment effect estimator. Only California attained a statistically significant treatment effect, strengthening confidence in the conclusion that Proposition 99 reduced cigarette sales. The proposed permutation testing framework provides an additional robustness check to either support or refute a treatment effect identified in for the true treated unit in ITSA. Given its value and ease of implementation, this framework should be considered as a standard robustness test in all multiple group interrupted time series analyses. © 2018 John Wiley & Sons, Ltd.

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.

Event-based soil loss models for construction sites

NASA Astrophysics Data System (ADS)

Trenouth, William R.; Gharabaghi, Bahram

2015-05-01

The elevated rates of soil erosion stemming from land clearing and grading activities during urban development, can result in excessive amounts of eroded sediments entering waterways and causing harm to the biota living therein. However, construction site event-based soil loss simulations - required for reliable design of erosion and sediment controls - are one of the most uncertain types of hydrologic models. This study presents models with improved degree of accuracy to advance the design of erosion and sediment controls for construction sites. The new models are developed using multiple linear regression (MLR) on event-based permutations of the Universal Soil Loss Equation (USLE) and artificial neural networks (ANN). These models were developed using surface runoff monitoring datasets obtained from three sites - Greensborough, Cookstown, and Alcona - in Ontario and datasets mined from the literature for three additional sites - Treynor, Iowa, Coshocton, Ohio and Cordoba, Spain. The predictive MLR and ANN models can serve as both diagnostic and design tools for the effective sizing of erosion and sediment controls on active construction sites, and can be used for dynamic scenario forecasting when considering rapidly changing land use conditions during various phases of construction.

Conditional Monte Carlo randomization tests for regression models.

PubMed

Parhat, Parwen; Rosenberger, William F; Diao, Guoqing

2014-08-15

We discuss the computation of randomization tests for clinical trials of two treatments when the primary outcome is based on a regression model. We begin by revisiting the seminal paper of Gail, Tan, and Piantadosi (1988), and then describe a method based on Monte Carlo generation of randomization sequences. The tests based on this Monte Carlo procedure are design based, in that they incorporate the particular randomization procedure used. We discuss permuted block designs, complete randomization, and biased coin designs. We also use a new technique by Plamadeala and Rosenberger (2012) for simple computation of conditional randomization tests. Like Gail, Tan, and Piantadosi, we focus on residuals from generalized linear models and martingale residuals from survival models. Such techniques do not apply to longitudinal data analysis, and we introduce a method for computation of randomization tests based on the predicted rate of change from a generalized linear mixed model when outcomes are longitudinal. We show, by simulation, that these randomization tests preserve the size and power well under model misspecification. Copyright © 2014 John Wiley & Sons, Ltd.

Pharmaceutical patents and price controls.

PubMed

Vogel, Ronald J

2002-07-01

Since 1995, every member-country of the World Trade Organization (WTO) has agreed to honor a 20-year patent-life, from the date of a pharmaceutical company's application for the patent, in the country of application. Patent protection retards competitive imitation of an invented product. This kind of protection is particularly important for pharmaceuticals, because pharmaceuticals that are not derived from biotechnology can be imitated easily and inexpensively. The economic function of a patent is to allow a period of above-normal profits for a technically and commercially successful product; these profits stimulate further investment and invention. However, direct price controls, or permutations of direct price controls on pharmaceutical compounds, can fully or partially circumvent the economic intent of patent agreements. This paper formulates an economic model that takes into account demand and cost/supply dimensions of the output and pricing of a hypothetical pharmaceutical, extrapolating about the respective effects of direct price controls and lack of price controls, and describing permutations of direct price controls in different countries. The pharmaceutical industry depends on patents to fund the development and introduction of new products. A country can indirectly circumvent the economic logic of a patent by using price controls, but it cannot shift the economic costs of such a policy to another country that does not use price controls. Instead, less money is available for research and development (R&D). Pharmaceutical price controls allow some countries to avoid the constraints of patent agreements without breaking those agreements outright. This, in turn, reduces the amount of profit available for further R&D, which is a detriment to consumers worldwide.

Genetic variations in the dopamine system and facial expression recognition in healthy chinese college students.

PubMed

Zhu, Bi; Chen, Chuansheng; Moyzis, Robert K; Dong, Qi; Chen, Chunhui; He, Qinghua; Stern, Hal S; Li, He; Li, Jin; Li, Jun; Lessard, Jared; Lin, Chongde

2012-01-01

This study investigated the relation between genetic variations in the dopamine system and facial expression recognition. A sample of Chinese college students (n = 478) was given a facial expression recognition task. Subjects were genotyped for 98 loci [96 single-nucleotide polymorphisms (SNPs) and 2 variable number tandem repeats] in 16 genes involved in the dopamine neurotransmitter system, including its 4 subsystems: synthesis (TH, DDC, and DBH), degradation/transport (COMT,MAOA,MAOB, and SLC6A3), receptors (DRD1,DRD2,DRD3,DRD4, and DRD5), and modulation (NTS,NTSR1,NTSR2, and NLN). To quantify the total contributions of the dopamine system to emotion recognition, we used a series of multiple regression models. Permutation analyses were performed to assess the posterior probabilities of obtaining such results. Among the 78 loci that were included in the final analyses (after excluding 12 SNPs that were in high linkage disequilibrium and 8 that were not in Hardy-Weinberg equilibrium), 1 (for fear), 3 (for sadness), 5 (for anger), 13 (for surprise), and 15 (for disgust) loci exhibited main effects on the recognition of facial expressions. Genetic variations in the dopamine system accounted for 3% for fear, 6% for sadness, 7% for anger, 10% for surprise, and 18% for disgust, with the latter surviving a stringent permutation test. Genetic variations in the dopamine system (especially the dopamine synthesis and modulation subsystems) made significant contributions to individual differences in the recognition of disgust faces. Copyright © 2012 S. Karger AG, Basel.

Engineering bacteria to solve the Burnt Pancake Problem

PubMed Central

Haynes, Karmella A; Broderick, Marian L; Brown, Adam D; Butner, Trevor L; Dickson, James O; Harden, W Lance; Heard, Lane H; Jessen, Eric L; Malloy, Kelly J; Ogden, Brad J; Rosemond, Sabriya; Simpson, Samantha; Zwack, Erin; Campbell, A Malcolm; Eckdahl, Todd T; Heyer, Laurie J; Poet, Jeffrey L

2008-01-01

Background We investigated the possibility of executing DNA-based computation in living cells by engineering Escherichia coli to address a classic mathematical puzzle called the Burnt Pancake Problem (BPP). The BPP is solved by sorting a stack of distinct objects (pancakes) into proper order and orientation using the minimum number of manipulations. Each manipulation reverses the order and orientation of one or more adjacent objects in the stack. We have designed a system that uses site-specific DNA recombination to mediate inversions of genetic elements that represent pancakes within plasmid DNA. Results Inversions (or "flips") of the DNA fragment pancakes are driven by the Salmonella typhimurium Hin/hix DNA recombinase system that we reconstituted as a collection of modular genetic elements for use in E. coli. Our system sorts DNA segments by inversions to produce different permutations of a promoter and a tetracycline resistance coding region; E. coli cells become antibiotic resistant when the segments are properly sorted. Hin recombinase can mediate all possible inversion operations on adjacent flippable DNA fragments. Mathematical modeling predicts that the system reaches equilibrium after very few flips, where equal numbers of permutations are randomly sorted and unsorted. Semiquantitative PCR analysis of in vivo flipping suggests that inversion products accumulate on a time scale of hours or days rather than minutes. Conclusion The Hin/hix system is a proof-of-concept demonstration of in vivo computation with the potential to be scaled up to accommodate larger and more challenging problems. Hin/hix may provide a flexible new tool for manipulating transgenic DNA in vivo. PMID:18492232

Particle Filter with State Permutations for Solving Image Jigsaw Puzzles

PubMed Central

Yang, Xingwei; Adluru, Nagesh; Latecki, Longin Jan

2016-01-01

We deal with an image jigsaw puzzle problem, which is defined as reconstructing an image from a set of square and non-overlapping image patches. It is known that a general instance of this problem is NP-complete, and it is also challenging for humans, since in the considered setting the original image is not given. Recently a graphical model has been proposed to solve this and related problems. The target label probability function is then maximized using loopy belief propagation. We also formulate the problem as maximizing a label probability function and use exactly the same pairwise potentials. Our main contribution is a novel inference approach in the sampling framework of Particle Filter (PF). Usually in the PF framework it is assumed that the observations arrive sequentially, e.g., the observations are naturally ordered by their time stamps in the tracking scenario. Based on this assumption, the posterior density over the corresponding hidden states is estimated. In the jigsaw puzzle problem all observations (puzzle pieces) are given at once without any particular order. Therefore, we relax the assumption of having ordered observations and extend the PF framework to estimate the posterior density by exploring different orders of observations and selecting the most informative permutations of observations. This significantly broadens the scope of applications of the PF inference. Our experimental results demonstrate that the proposed inference framework significantly outperforms the loopy belief propagation in solving the image jigsaw puzzle problem. In particular, the extended PF inference triples the accuracy of the label assignment compared to that using loopy belief propagation. PMID:27795660

A Pilot Study of Contextual UMLS Indexing to Improve the Precision of Concept-based Representation in XML-structured Clinical Radiology Reports

PubMed Central

Huang, Yang; Lowe, Henry J.; Hersh, William R.

2003-01-01

Objective: Despite the advantages of structured data entry, much of the patient record is still stored as unstructured or semistructured narrative text. The issue of representing clinical document content remains problematic. The authors' prior work using an automated UMLS document indexing system has been encouraging but has been affected by the generally low indexing precision of such systems. In an effort to improve precision, the authors have developed a context-sensitive document indexing model to calculate the optimal subset of UMLS source vocabularies used to index each document section. This pilot study was performed to evaluate the utility of this indexing approach on a set of clinical radiology reports. Design: A set of clinical radiology reports that had been indexed manually using UMLS concept descriptors was indexed automatically by the SAPHIRE indexing engine. Using the data generated by this process the authors developed a system that simulated indexing, at the document section level, of the same document set using many permutations of a subset of the UMLS constituent vocabularies. Measurements: The precision and recall scores generated by simulated indexing for each permutation of two or three UMLS constituent vocabularies were determined. Results: While there was considerable variation in precision and recall values across the different subtypes of radiology reports, the overall effect of this indexing strategy using the best combination of two or three UMLS constituent vocabularies was an improvement in precision without significant impact of recall. Conclusion: In this pilot study a contextual indexing strategy improved overall precision in a set of clinical radiology reports. PMID:12925544

A pilot study of contextual UMLS indexing to improve the precision of concept-based representation in XML-structured clinical radiology reports.

PubMed

Huang, Yang; Lowe, Henry J; Hersh, William R

2003-01-01

Despite the advantages of structured data entry, much of the patient record is still stored as unstructured or semistructured narrative text. The issue of representing clinical document content remains problematic. The authors' prior work using an automated UMLS document indexing system has been encouraging but has been affected by the generally low indexing precision of such systems. In an effort to improve precision, the authors have developed a context-sensitive document indexing model to calculate the optimal subset of UMLS source vocabularies used to index each document section. This pilot study was performed to evaluate the utility of this indexing approach on a set of clinical radiology reports. A set of clinical radiology reports that had been indexed manually using UMLS concept descriptors was indexed automatically by the SAPHIRE indexing engine. Using the data generated by this process the authors developed a system that simulated indexing, at the document section level, of the same document set using many permutations of a subset of the UMLS constituent vocabularies. The precision and recall scores generated by simulated indexing for each permutation of two or three UMLS constituent vocabularies were determined. While there was considerable variation in precision and recall values across the different subtypes of radiology reports, the overall effect of this indexing strategy using the best combination of two or three UMLS constituent vocabularies was an improvement in precision without significant impact of recall. In this pilot study a contextual indexing strategy improved overall precision in a set of clinical radiology reports.

Past climate changes explain the phylogeography of Vitellaria paradoxa over Africa

PubMed Central

Allal, F; Sanou, H; Millet, L; Vaillant, A; Camus-Kulandaivelu, L; Logossa, Z A; Lefèvre, F; Bouvet, J-M

2011-01-01

The evolution of the savanna biome has been deeply marked by repeated contraction/expansion phases due to climate perturbations during the Quaternary period. In this study, we investigated the impact of the last glacial maximum (LGM) on the present genetic pattern of Vitellaria paradoxa (shea tree), a major African savanna tree. A range-wide sampling of the species enabled us to sample 374 individuals from 71 populations distributed throughout sub-Sahelian Africa. Trees were genotyped using 3 chloroplasts and 12 nuclear microsatellites, and were sequenced for 2 polymorphic chloroplast intergenic spacers. Analyses of genetic diversity and structure were based on frequency-based and Bayesian methods. Potential distributions of V. paradoxa at present, during the LGM and the last interglacial period, were examined using DIVA-GIS ecological niche modelling (ENM). Haplotypic and allelic richness varied significantly across the range according to chloroplast and nuclear microsatellites, which pointed to higher diversity in West Africa. A high but contrasted level of differentiation was revealed among populations with a clear phylogeographic signal, with both nuclear (FST=0.21; RST=0.28; RST>RST (permuted)) and chloroplast simple sequence repeats (SSRs) (GST=0.81; NST=0.90; NST>NST (permuted)). We identified a strong geographically related structure separating western and eastern populations, and a substructure in the eastern part of the area consistent with subspecies distinction. Using ENM, we deduced that perturbations during the LGM fragmented the potential eastern distribution of shea tree, but not its distribution in West Africa. Our main results suggest that climate variations are the major factor explaining the genetic pattern of V. paradoxa. PMID:21407253

Cobimaximal lepton mixing from soft symmetry breaking

NASA Astrophysics Data System (ADS)

Grimus, W.; Lavoura, L.

2017-11-01

Cobimaximal lepton mixing, i.e.θ23 = 45 ° and δ = ± 90 ° in the lepton mixing matrix V, arises as a consequence of SV =V* P, where S is the permutation matrix that interchanges the second and third rows of V and P is a diagonal matrix of phase factors. We prove that any such V may be written in the form V = URP, where U is any predefined unitary matrix satisfying SU =U*, R is an orthogonal, i.e. real, matrix, and P is a diagonal matrix satisfying P2 = P. Using this theorem, we demonstrate the equivalence of two ways of constructing models for cobimaximal mixing-one way that uses a standard CP symmetry and a different way that uses a CP symmetry including μ-τ interchange. We also present two simple seesaw models to illustrate this equivalence; those models have, in addition to the CP symmetry, flavour symmetries broken softly by the Majorana mass terms of the right-handed neutrino singlets. Since each of the two models needs four scalar doublets, we investigate how to accommodate the Standard Model Higgs particle in them.

Mathematical models of cell motility.

PubMed

Flaherty, Brendan; McGarry, J P; McHugh, P E

2007-01-01

Cell motility is an essential biological action in the creation, operation and maintenance of our bodies. Developing mathematical models elucidating cell motility will greatly advance our understanding of this fundamental biological process. With accurate models it is possible to explore many permutations of the same event and concisely investigate their outcome. While great advancements have been made in experimental studies of cell motility, it now has somewhat fallen on mathematical models to taking a leading role in future developments. The obvious reason for this is the complexity of cell motility. Employing the processing power of today's computers will give researches the ability to run complex biophysical and biochemical scenarios, without the inherent difficulty and time associated with in vitro investigations. Before any great advancement can be made, the basics of cell motility will have to be well-defined. Without this, complicated mathematical models will be hindered by their inherent conjecture. This review will look at current mathematical investigations of cell motility, explore the reasoning behind such work and conclude with how best to advance this interesting and challenging research area.

Learning to Predict Combinatorial Structures

NASA Astrophysics Data System (ADS)

Vembu, Shankar

2009-12-01

The major challenge in designing a discriminative learning algorithm for predicting structured data is to address the computational issues arising from the exponential size of the output space. Existing algorithms make different assumptions to ensure efficient, polynomial time estimation of model parameters. For several combinatorial structures, including cycles, partially ordered sets, permutations and other graph classes, these assumptions do not hold. In this thesis, we address the problem of designing learning algorithms for predicting combinatorial structures by introducing two new assumptions: (i) The first assumption is that a particular counting problem can be solved efficiently. The consequence is a generalisation of the classical ridge regression for structured prediction. (ii) The second assumption is that a particular sampling problem can be solved efficiently. The consequence is a new technique for designing and analysing probabilistic structured prediction models. These results can be applied to solve several complex learning problems including but not limited to multi-label classification, multi-category hierarchical classification, and label ranking.

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.

Origami rules for the construction of localized eigenstates of the Hubbard model in decorated lattices

NASA Astrophysics Data System (ADS)

Dias, R. G.; Gouveia, J. D.

2015-11-01

We present a method of construction of exact localized many-body eigenstates of the Hubbard model in decorated lattices, both for U = 0 and U → ∞. These states are localized in what concerns both hole and particle movement. The starting point of the method is the construction of a plaquette or a set of plaquettes with a higher symmetry than that of the whole lattice. Using a simple set of rules, the tight-binding localized state in such a plaquette can be divided, folded and unfolded to new plaquette geometries. This set of rules is also valid for the construction of a localized state for one hole in the U → ∞ limit of the same plaquette, assuming a spin configuration which is a uniform linear combination of all possible permutations of the set of spins in the plaquette.

Implications of the Daya Bay observation of θ13 on the leptonic flavor mixing structure and CP violation

NASA Astrophysics Data System (ADS)

Xing, Zhi-Zhong

2012-04-01

The Daya Bay collaboration has recently reported its first bar nue → bar nue oscillation result which points to θ13 simeq 8.8° +/- 0.8° (best-fit +/-1σ range) or θ13 ≠ 0° at the 5.2σ level. The fact that this smallest neutrino mixing angle is not strongly suppressed motivates us to look into the underlying structure of lepton flavor mixing and CP violation. Two phenomenological strategies are outlined: (1) the lepton flavor mixing matrix U consists of a constant leading term U0 and a small perturbation term ΔU and (2) the mixing angles of U are associated with the lepton mass ratios. Some typical patterns of U0 are reexamined by constraining their respective perturbations with current experimental data. We illustrate a few possible ways to minimally correct U0 in order to fit the observed values of three mixing angles. We point out that the structure of U may exhibit an approximate μ-τ permutation symmetry in modulus, and reiterate the geometrical description of CP violation in terms of the leptonic unitarity triangles. The salient features of nine distinct parametrizations of U are summarized, and its Wolfenstein-like expansion is presented by taking U0 to be the democratic mixing pattern.

INTERMITTENT AND PERENNIAL STREAM MACROINVERTEBRATE COMMUNITY RESPONSE TO IMPERVIOUS COVER: THRESHOLD INDICATOR TAXA ANALYSIS AND PERMUTATIONS

EPA Science Inventory

The urban stream syndrome and the impact of impervious cover on macroinvertebrate communities is well-documented, but many exclude intermittent streams despite their prevalence. This study investigated macroinvertebrate communities of intermittent and perennial streams separately...

Fast function-on-scalar regression with penalized basis expansions.

PubMed

Reiss, Philip T; Huang, Lei; Mennes, Maarten

2010-01-01

Regression models for functional responses and scalar predictors are often fitted by means of basis functions, with quadratic roughness penalties applied to avoid overfitting. The fitting approach described by Ramsay and Silverman in the 1990 s amounts to a penalized ordinary least squares (P-OLS) estimator of the coefficient functions. We recast this estimator as a generalized ridge regression estimator, and present a penalized generalized least squares (P-GLS) alternative. We describe algorithms by which both estimators can be implemented, with automatic selection of optimal smoothing parameters, in a more computationally efficient manner than has heretofore been available. We discuss pointwise confidence intervals for the coefficient functions, simultaneous inference by permutation tests, and model selection, including a novel notion of pointwise model selection. P-OLS and P-GLS are compared in a simulation study. Our methods are illustrated with an analysis of age effects in a functional magnetic resonance imaging data set, as well as a reanalysis of a now-classic Canadian weather data set. An R package implementing the methods is publicly available.

Vascular tone pathway polymorphisms in relation to primary open-angle glaucoma.

PubMed

Kang, J H; Loomis, S J; Yaspan, B L; Bailey, J C; Weinreb, R N; Lee, R K; Lichter, P R; Budenz, D L; Liu, Y; Realini, T; Gaasterland, D; Gaasterland, T; Friedman, D S; McCarty, C A; Moroi, S E; Olson, L; Schuman, J S; Singh, K; Vollrath, D; Wollstein, G; Zack, D J; Brilliant, M; Sit, A J; Christen, W G; Fingert, J; Forman, J P; Buys, E S; Kraft, P; Zhang, K; Allingham, R R; Pericak-Vance, M A; Richards, J E; Hauser, M A; Haines, J L; Wiggs, J L; Pasquale, L R

2014-06-01

Vascular perfusion may be impaired in primary open-angle glaucoma (POAG); thus, we evaluated a panel of markers in vascular tone-regulating genes in relation to POAG. We used Illumina 660W-Quad array genotype data and pooled P-values from 3108 POAG cases and 3430 controls from the combined National Eye Institute Glaucoma Human Genetics Collaboration consortium and Glaucoma Genes and Environment studies. Using information from previous literature and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, we compiled single-nucleotide polymorphisms (SNPs) in 186 vascular tone-regulating genes. We used the 'Pathway Analysis by Randomization Incorporating Structure' analysis software, which performed 1000 permutations to compare the overall pathway and selected genes with comparable randomly generated pathways and genes in their association with POAG. The vascular tone pathway was not associated with POAG overall or POAG subtypes, defined by the type of visual field loss (early paracentral loss (n=224 cases) or only peripheral loss (n=993 cases)) (permuted P≥0.20). In gene-based analyses, eight were associated with POAG overall at permuted P<0.001: PRKAA1, CAV1, ITPR3, EDNRB, GNB2, DNM2, HFE, and MYL9. Notably, six of these eight (the first six listed) code for factors involved in the endothelial nitric oxide synthase activity, and three of these six (CAV1, ITPR3, and EDNRB) were also associated with early paracentral loss at P<0.001, whereas none of the six genes reached P<0.001 for peripheral loss only. Although the assembled vascular tone SNP set was not associated with POAG, genes that code for local factors involved in setting vascular tone were associated with POAG.

Rapid and Accurate Multiple Testing Correction and Power Estimation for Millions of Correlated Markers

PubMed Central

Han, Buhm; Kang, Hyun Min; Eskin, Eleazar

2009-01-01

With the development of high-throughput sequencing and genotyping technologies, the number of markers collected in genetic association studies is growing rapidly, increasing the importance of methods for correcting for multiple hypothesis testing. The permutation test is widely considered the gold standard for accurate multiple testing correction, but it is often computationally impractical for these large datasets. Recently, several studies proposed efficient alternative approaches to the permutation test based on the multivariate normal distribution (MVN). However, they cannot accurately correct for multiple testing in genome-wide association studies for two reasons. First, these methods require partitioning of the genome into many disjoint blocks and ignore all correlations between markers from different blocks. Second, the true null distribution of the test statistic often fails to follow the asymptotic distribution at the tails of the distribution. We propose an accurate and efficient method for multiple testing correction in genome-wide association studies—SLIDE. Our method accounts for all correlation within a sliding window and corrects for the departure of the true null distribution of the statistic from the asymptotic distribution. In simulations using the Wellcome Trust Case Control Consortium data, the error rate of SLIDE's corrected p-values is more than 20 times smaller than the error rate of the previous MVN-based methods' corrected p-values, while SLIDE is orders of magnitude faster than the permutation test and other competing methods. We also extend the MVN framework to the problem of estimating the statistical power of an association study with correlated markers and propose an efficient and accurate power estimation method SLIP. SLIP and SLIDE are available at http://slide.cs.ucla.edu. PMID:19381255

CiPerGenesis, A Mutagenesis Approach that Produces Small Libraries of Circularly Permuted Proteins Randomly Opened at a Focused Region: Testing on the Green Fluorescent Protein.

PubMed

Gaytán, Paul; Roldán-Salgado, Abigail; Yáñez, Jorge A; Morales-Arrieta, Sandra; Juárez-González, Víctor R

2018-06-12

Circularly permuted proteins (cpPs) represent a novel type of mutant proteins with original termini that are covalently linked through a peptide connector and opened at any other place of the polypeptide backbone to create new ends. cpPs are finding wide applications in biotechnology because their properties may be quite different from those of the parental protein. However, the actual challenge for the creation of successful cpPs is to identify those peptide bonds that can be broken to create new termini and ensure functional and well-folded cpPs. Herein, we describe CiPerGenesis, a combinatorial mutagenesis approach that uses two oligonucleotide libraries to amplify a circularized gene by PCR, starting and ending from a focused target region. This approach creates small libraries of circularly permuted genes that are easily cloned in the correct direction and frame using two different restriction sites encoded in the oligonucleotides. Once expressed, the protein libraries exhibit a unique sequence diversity, comprising cpPs that exhibit ordinary breakpoints between adjacent amino acids localized at the target region as well as cpPs with new termini containing user-defined truncations and repeats of some amino acids. CiPerGenesis was tested at the lid region G134-H148 of green fluorescent protein (GFP), revealing that the most fluorescent variants were those starting at Leu141 and ending at amino acids Tyr145, Tyr143, Glu142, Leu141, Lys140, and H139. Purification and biochemical characterization of some variants suggested a differential expression, solubility and maturation extent of the mutant proteins as the likely cause for the variability in fluorescence intensity observed in colonies.

BROCCOLI: Software for fast fMRI analysis on many-core CPUs and GPUs

PubMed Central

Eklund, Anders; Dufort, Paul; Villani, Mattias; LaConte, Stephen

2014-01-01

Analysis of functional magnetic resonance imaging (fMRI) data is becoming ever more computationally demanding as temporal and spatial resolutions improve, and large, publicly available data sets proliferate. Moreover, methodological improvements in the neuroimaging pipeline, such as non-linear spatial normalization, non-parametric permutation tests and Bayesian Markov Chain Monte Carlo approaches, can dramatically increase the computational burden. Despite these challenges, there do not yet exist any fMRI software packages which leverage inexpensive and powerful graphics processing units (GPUs) to perform these analyses. Here, we therefore present BROCCOLI, a free software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. BROCCOLI has, for example, been tested with an Intel CPU, an Nvidia GPU, and an AMD GPU. These tests show that parallel processing of fMRI data can lead to significantly faster analysis pipelines. This speedup can be achieved on relatively standard hardware, but further, dramatic speed improvements require only a modest investment in GPU hardware. BROCCOLI (running on a GPU) can perform non-linear spatial normalization to a 1 mm3 brain template in 4–6 s, and run a second level permutation test with 10,000 permutations in about a minute. These non-parametric tests are generally more robust than their parametric counterparts, and can also enable more sophisticated analyses by estimating complicated null distributions. Additionally, BROCCOLI includes support for Bayesian first-level fMRI analysis using a Gibbs sampler. The new software is freely available under GNU GPL3 and can be downloaded from github (https://github.com/wanderine/BROCCOLI/). PMID:24672471

Visual field progression in glaucoma: estimating the overall significance of deterioration with permutation analyses of pointwise linear regression (PoPLR).

PubMed

O'Leary, Neil; Chauhan, Balwantray C; Artes, Paul H

2012-10-01

To establish a method for estimating the overall statistical significance of visual field deterioration from an individual patient's data, and to compare its performance to pointwise linear regression. The Truncated Product Method was used to calculate a statistic S that combines evidence of deterioration from individual test locations in the visual field. The overall statistical significance (P value) of visual field deterioration was inferred by comparing S with its permutation distribution, derived from repeated reordering of the visual field series. Permutation of pointwise linear regression (PoPLR) and pointwise linear regression were evaluated in data from patients with glaucoma (944 eyes, median mean deviation -2.9 dB, interquartile range: -6.3, -1.2 dB) followed for more than 4 years (median 10 examinations over 8 years). False-positive rates were estimated from randomly reordered series of this dataset, and hit rates (proportion of eyes with significant deterioration) were estimated from the original series. The false-positive rates of PoPLR were indistinguishable from the corresponding nominal significance levels and were independent of baseline visual field damage and length of follow-up. At P < 0.05, the hit rates of PoPLR were 12, 29, and 42%, at the fifth, eighth, and final examinations, respectively, and at matching specificities they were consistently higher than those of pointwise linear regression. In contrast to population-based progression analyses, PoPLR provides a continuous estimate of statistical significance for visual field deterioration individualized to a particular patient's data. This allows close control over specificity, essential for monitoring patients in clinical practice and in clinical trials.

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.

A chaotic cryptosystem for images based on Henon and Arnold cat map.

PubMed

Soleymani, Ali; Nordin, Md Jan; Sundararajan, Elankovan

2014-01-01

The rapid evolution of imaging and communication technologies has transformed images into a widespread data type. Different types of data, such as personal medical information, official correspondence, or governmental and military documents, are saved and transmitted in the form of images over public networks. Hence, a fast and secure cryptosystem is needed for high-resolution images. In this paper, a novel encryption scheme is presented for securing images based on Arnold cat and Henon chaotic maps. The scheme uses Arnold cat map for bit- and pixel-level permutations on plain and secret images, while Henon map creates secret images and specific parameters for the permutations. Both the encryption and decryption processes are explained, formulated, and graphically presented. The results of security analysis of five different images demonstrate the strength of the proposed cryptosystem against statistical, brute force and differential attacks. The evaluated running time for both encryption and decryption processes guarantee that the cryptosystem can work effectively in real-time applications.

A novel chaotic image encryption scheme using DNA sequence operations

NASA Astrophysics Data System (ADS)

Wang, Xing-Yuan; Zhang, Ying-Qian; Bao, Xue-Mei

2015-10-01

In this paper, we propose a novel image encryption scheme based on DNA (Deoxyribonucleic acid) sequence operations and chaotic system. Firstly, we perform bitwise exclusive OR operation on the pixels of the plain image using the pseudorandom sequences produced by the spatiotemporal chaos system, i.e., CML (coupled map lattice). Secondly, a DNA matrix is obtained by encoding the confused image using a kind of DNA encoding rule. Then we generate the new initial conditions of the CML according to this DNA matrix and the previous initial conditions, which can make the encryption result closely depend on every pixel of the plain image. Thirdly, the rows and columns of the DNA matrix are permuted. Then, the permuted DNA matrix is confused once again. At last, after decoding the confused DNA matrix using a kind of DNA decoding rule, we obtain the ciphered image. Experimental results and theoretical analysis show that the scheme is able to resist various attacks, so it has extraordinarily high security.

Four-point functions and the permutation group S4

NASA Astrophysics Data System (ADS)

Eichmann, Gernot; Fischer, Christian S.; Heupel, Walter

2015-09-01

Four-point functions are at the heart of many interesting physical processes. A prime example is the light-by-light scattering amplitude, which plays an important role in the calculation of hadronic contributions to the anomalous magnetic moment of the muon. In the calculation of such quantities one faces the challenge of finding a suitable and well-behaved basis of tensor structures in coordinate and/or momentum space. Provided all (or many) of the external legs represent similar particle content, a powerful tool to construct and organize such bases is the permutation group S4. We introduce an efficient notation for dealing with the irreducible multiplets of S4, and we highlight the merits of this treatment by exemplifying four-point functions with gauge-boson legs such as the four-gluon vertex and the light-by-light scattering amplitude. The multiplet analysis is also useful for isolating the important kinematic regions and the dynamical singularity content of such amplitudes. Our analysis serves as a basis for future efficient calculations of these and similar objects.

Evolution of a protein folding nucleus.

PubMed

Xia, Xue; Longo, Liam M; Sutherland, Mason A; Blaber, Michael

2016-07-01

The folding nucleus (FN) is a cryptic element within protein primary structure that enables an efficient folding pathway and is the postulated heritable element in the evolution of protein architecture; however, almost nothing is known regarding how the FN structurally changes as complex protein architecture evolves from simpler peptide motifs. We report characterization of the FN of a designed purely symmetric β-trefoil protein by ϕ-value analysis. We compare the structure and folding properties of key foldable intermediates along the evolutionary trajectory of the β-trefoil. The results show structural acquisition of the FN during gene fusion events, incorporating novel turn structure created by gene fusion. Furthermore, the FN is adjusted by circular permutation in response to destabilizing functional mutation. FN plasticity by way of circular permutation is made possible by the intrinsic C3 cyclic symmetry of the β-trefoil architecture, identifying a possible selective advantage that helps explain the prevalence of cyclic structural symmetry in the proteome. © 2015 The Protein Society.

Security scheme in IMDD-OFDM-PON system with the chaotic pilot interval and scrambling

NASA Astrophysics Data System (ADS)

Chen, Qianghua; Bi, Meihua; Fu, Xiaosong; Lu, Yang; Zeng, Ran; Yang, Guowei; Yang, Xuelin; Xiao, Shilin

2018-01-01

In this paper, a random chaotic pilot interval and permutations scheme without any requirement of redundant sideband information is firstly proposed for the physical layer security-enhanced intensity modulation direct detection orthogonal frequency division multiplexing passive optical network (IMDD-OFDM-PON) system. With the help of the position feature of inserting the pilot, a simple logistic chaos map is used to generate the random pilot interval and scramble the chaotic subcarrier allocation of each column pilot data for improving the physical layer confidentiality. Due to the dynamic chaotic permutations of pilot data, the enhanced key space of ∼103303 is achieved in OFDM-PON. Moreover, the transmission experiment of 10-Gb/s 16-QAM encrypted OFDM data is successfully demonstrated over 20-km single-mode fiber, which indicates that the proposed scheme not only improves the system security, but also can achieve the same performance as in the common IMDD-OFDM-PON system without encryption scheme.

A permutation testing framework to compare groups of brain networks.

PubMed

Simpson, Sean L; Lyday, Robert G; Hayasaka, Satoru; Marsh, Anthony P; Laurienti, Paul J

2013-01-01

Brain network analyses have moved to the forefront of neuroimaging research over the last decade. However, methods for statistically comparing groups of networks have lagged behind. These comparisons have great appeal for researchers interested in gaining further insight into complex brain function and how it changes across different mental states and disease conditions. Current comparison approaches generally either rely on a summary metric or on mass-univariate nodal or edge-based comparisons that ignore the inherent topological properties of the network, yielding little power and failing to make network level comparisons. Gleaning deeper insights into normal and abnormal changes in complex brain function demands methods that take advantage of the wealth of data present in an entire brain network. Here we propose a permutation testing framework that allows comparing groups of networks while incorporating topological features inherent in each individual network. We validate our approach using simulated data with known group differences. We then apply the method to functional brain networks derived from fMRI data.

Significance levels for studies with correlated test statistics.

PubMed

Shi, Jianxin; Levinson, Douglas F; Whittemore, Alice S

2008-07-01

When testing large numbers of null hypotheses, one needs to assess the evidence against the global null hypothesis that none of the hypotheses is false. Such evidence typically is based on the test statistic of the largest magnitude, whose statistical significance is evaluated by permuting the sample units to simulate its null distribution. Efron (2007) has noted that correlation among the test statistics can induce substantial interstudy variation in the shapes of their histograms, which may cause misleading tail counts. Here, we show that permutation-based estimates of the overall significance level also can be misleading when the test statistics are correlated. We propose that such estimates be conditioned on a simple measure of the spread of the observed histogram, and we provide a method for obtaining conditional significance levels. We justify this conditioning using the conditionality principle described by Cox and Hinkley (1974). Application of the method to gene expression data illustrates the circumstances when conditional significance levels are needed.

A single circularly permuted GFP sensor for inositol-1,3,4,5-tetrakisphosphate based on a split PH domain.

PubMed

Sakaguchi, Reiko; Endoh, Takashi; Yamamoto, Seigo; Tainaka, Kazuki; Sugimoto, Kenji; Fujieda, Nobutaka; Kiyonaka, Shigeki; Mori, Yasuo; Morii, Takashi

2009-10-15

A fluorescent sensor for the detection of inositol-1,3,4,5-tetrakisphosphate, Ins(1,3,4,5)P(4), was constructed from a split PH domain and a single circularly permuted GFP. A structure-based design was conducted to transduce a ligand-induced subtle structural perturbation of the split PH domain to an alteration in the population of the protonated and the deprotonated states of the GFP chromophore. Excitation of each distinct absorption band corresponding to the protonated or the deprotonated state of GFP resulted an increase and a decrease, respectively, in the intensity of emission spectra upon addition of Ins(1,3,4,5)P(4) to the split PH domain-based sensor. The Ins(1,3,4,5)P(4) sensor retained the ligand affinity and the selectivity of the parent PH domain, and realized the ratiometric fluorescence detection of Ins(1,3,4,5)P(4).

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.

On the Shapley Value of Unrooted Phylogenetic Trees.

PubMed

Wicke, Kristina; Fischer, Mareike

2018-01-17

The Shapley value, a solution concept from cooperative game theory, has recently been considered for both unrooted and rooted phylogenetic trees. Here, we focus on the Shapley value of unrooted trees and first revisit the so-called split counts of a phylogenetic tree and the Shapley transformation matrix that allows for the calculation of the Shapley value from the edge lengths of a tree. We show that non-isomorphic trees may have permutation-equivalent Shapley transformation matrices and permutation-equivalent null spaces. This implies that estimating the split counts associated with a tree or the Shapley values of its leaves does not suffice to reconstruct the correct tree topology. We then turn to the use of the Shapley value as a prioritization criterion in biodiversity conservation and compare it to a greedy solution concept. Here, we show that for certain phylogenetic trees, the Shapley value may fail as a prioritization criterion, meaning that the diversity spanned by the top k species (ranked by their Shapley values) cannot approximate the total diversity of all n species.

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.

A Comparison of Techniques for Scheduling Earth-Observing Satellites

NASA Technical Reports Server (NTRS)

Globus, Al; Crawford, James; Lohn, Jason; Pryor, Anna

2004-01-01

Scheduling observations by coordinated fleets of Earth Observing Satellites (EOS) involves large search spaces, complex constraints and poorly understood bottlenecks, conditions where evolutionary and related algorithms are often effective. However, there are many such algorithms and the best one to use is not clear. Here we compare multiple variants of the genetic algorithm: stochastic hill climbing, simulated annealing, squeaky wheel optimization and iterated sampling on ten realistically-sized EOS scheduling problems. Schedules are represented by a permutation (non-temperal ordering) of the observation requests. A simple deterministic scheduler assigns times and resources to each observation request in the order indicated by the permutation, discarding those that violate the constraints created by previously scheduled observations. Simulated annealing performs best. Random mutation outperform a more 'intelligent' mutator. Furthermore, the best mutator, by a small margin, was a novel approach we call temperature dependent random sampling that makes large changes in the early stages of evolution and smaller changes towards the end of search.

Thermodynamic properties of Fermi gases in states with defined many-body spins

NASA Astrophysics Data System (ADS)

Yurovsky, Vladimir

2016-05-01

Zero-range interactions in cold spin- 1 / 2 Fermi gases can be described by single interaction strength, since collisions of atoms in the same spin state are forbidden by the Pauli principle. In a spin-independent trap potential (even in the presence of a homogeneous spin-dependent external field), the gas can persist in a state with the given many-body spin, since the spin operator commutes with the Hamiltonian. Spin and spatial degrees of freedom in such systems are separated, and the spin and spatial wavefunctions form non-Abelian irreducible representations of the symmetric group, unless the total spin is S = N / 2 for N atoms (see). Although the total wavefunction, being a linear combination of products of the spin and spatial functions, is permutation-antisymmetric, the non-Abelian permutation symmetry is disclosed in the matrix elements and, as demonstrated here, in thermodynamic properties. The effects include modification of the specific heat and compressibility of the gas.

A Chaotic Cryptosystem for Images Based on Henon and Arnold Cat Map

PubMed Central

Sundararajan, Elankovan

2014-01-01

The rapid evolution of imaging and communication technologies has transformed images into a widespread data type. Different types of data, such as personal medical information, official correspondence, or governmental and military documents, are saved and transmitted in the form of images over public networks. Hence, a fast and secure cryptosystem is needed for high-resolution images. In this paper, a novel encryption scheme is presented for securing images based on Arnold cat and Henon chaotic maps. The scheme uses Arnold cat map for bit- and pixel-level permutations on plain and secret images, while Henon map creates secret images and specific parameters for the permutations. Both the encryption and decryption processes are explained, formulated, and graphically presented. The results of security analysis of five different images demonstrate the strength of the proposed cryptosystem against statistical, brute force and differential attacks. The evaluated running time for both encryption and decryption processes guarantee that the cryptosystem can work effectively in real-time applications. PMID:25258724

Integrated Analysis of Pharmacologic, Clinical, and SNP Microarray Data using Projection onto the Most Interesting Statistical Evidence with Adaptive Permutation Testing

PubMed Central

Pounds, Stan; Cao, Xueyuan; Cheng, Cheng; Yang, Jun; Campana, Dario; Evans, William E.; Pui, Ching-Hon; Relling, Mary V.

2010-01-01

Powerful methods for integrated analysis of multiple biological data sets are needed to maximize interpretation capacity and acquire meaningful knowledge. We recently developed Projection Onto the Most Interesting Statistical Evidence (PROMISE). PROMISE is a statistical procedure that incorporates prior knowledge about the biological relationships among endpoint variables into an integrated analysis of microarray gene expression data with multiple biological and clinical endpoints. Here, PROMISE is adapted to the integrated analysis of pharmacologic, clinical, and genome-wide genotype data that incorporating knowledge about the biological relationships among pharmacologic and clinical response data. An efficient permutation-testing algorithm is introduced so that statistical calculations are computationally feasible in this higher-dimension setting. The new method is applied to a pediatric leukemia data set. The results clearly indicate that PROMISE is a powerful statistical tool for identifying genomic features that exhibit a biologically meaningful pattern of association with multiple endpoint variables. PMID:21516175

Spatial Epidemiology and Risk Factor Analysis of White Spot Disease in the Shrimp Farming Industry of Sinaloa, Mexico, from 2005 to 2011.

PubMed

Muniesa, A; Mardones, F O; Chávez, M C; Montoya, L; Cabanillas, J A; de Blas, I; Martínez-López, B

2017-10-01

White spot disease (WSD), caused by the white spot syndrome virus, is currently one of the primary causes of mortality and economic losses in the shrimp farming industry worldwide. In Mexico, shrimp production is one of the most important primary activities generating an annual income of USD 711 million. However, WSD introduction in 1999 had a devastating impact for the Mexican shrimp industry. The aim of this study was to characterize the WSD spatio-temporal patterns and to identify the primary risk factors contributing to WSD occurrence from 2005 to 2011 in Sinaloa, Mexico. We used data collected by the 'Comité Estatal de Sanidad Acuícola de Sinaloa' from 2005 to 2011 regarding WSD outbreaks as well as environmental, production and husbandry factors at farm level. The spatio-temporal patterns of WSD were described using space-time scan statistics. The effect of 52 variables on the time to WSD outbreak occurrence was assessed using a multivariable Cox proportional hazards model. Results reveal that WSD risk and survival time were not homogeneously distributed as suggested by the significant clusters obtained using the space-time permutation model and the space-time exponential model, respectively. The Cox model revealed that the first production cycle [hazard ratio (HR) = 11.31], changes from 1 to 1.4°C of temperature oscillation caused by 'El Niño'/'La Niña' events (HR = 1.44) and high average daily growths (HR = 1.26) were significantly associated with lower survival (i.e. shorter time to WSD outbreak) on farm. Conversely, shrimp weight at the moment of the outbreak (HR = 0.159), changes from -0.9 to -0.5°C of temperature oscillation caused by 'El Niño'/'La Niña' events (HR = 0.540), high superficial water temperature during the pound stocking (HR = 0.823) and high (>100) number of days of culture (HR = 0.830) were factors associated with higher survival. Results are expected to inform the design of risk-based, intervention strategies to minimize the impact of WSD in Mexico. © 2016 Blackwell Verlag GmbH.

Simulations of Western North American Hydroclimate during the Little Ice Age and Medieval Climate Anomaly

NASA Astrophysics Data System (ADS)

Simon, S. M.; Mann, M. E.; Steinman, B. A.; Feng, S.; Zhang, Y.; Miller, S. K.

2013-12-01

Despite the immense impact that large, modern North American droughts, such as those of the 1930s and 1950s, have had on economic, social, aquacultural, and agricultural systems, they are smaller in duration and magnitude than the multidecadal megadroughts that affected North America, in particular the western United States, during the Medieval Climate Anomaly (MCA, ~ 900-1300 AD) and the Little Age (LIA, ~1450-1850 AD). Although various proxy records have been used to reconstruct the timing of these MCA and LIA megadroughts in the western United States, there still exists great uncertainty in the magnitude and spatial coherence of such droughts in the Pacific Northwest region, especially on decadal to centennial timescales. This uncertainty motivates the following study to establish a causal link between the climate forcing that induced these megadroughts and the spatiotemporal response of regional North American hydroclimates to this forcing. This study seeks to establish a better understanding of the influence of tropical Pacific and North Atlantic SSTs on North American drought during the MCA and LIA. We force NCAR's Community Atmospheric Model version 5.1.1 (CAM 5) with prescribed proxy-reconstructed tropical Pacific and North Atlantic SST anomalies from the MCA and LIA, in order to investigate the influence that these SST anomalies had on the spatiotemporal patterns of drought in North America. To isolate the effects of individual ocean basin SSTs on the North American climate system, the model experiments use a variety of SST permutations in the tropical Pacific and North Atlantic basin as external forcing. In order to quantify the spatiotemporal response of the North American climate system to these SST forcing permutations, temperature and precipitation data derived from the MCA and LIA model experiments are compared to lake sediment isotope and tree ring-based hydroclimate reconstructions from the Pacific Northwest. The spatiotemporal temperature and precipitation patterns from the model experiments indicate that in the Pacific Northwest, the MCA and LIA were anomalously wet and dry periods, respectively, a finding that is largely supported by the lake sediment records. This pattern contrasts with the dry MCA/wet LIA pattern diagnosed in model experiments for the U.S Southwest and indicated by tree ring-based proxy data. Thus, the CAM 5 model experiments confirm the wet/dry dipole pattern suggested by proxy data for the western U.S. during the MCA and LIA and highlights the role that the natural variability of tropical Pacific and North Atlantic SSTs played in driving this spatiotemporal climate pattern and its related teleconnections.

A bayesian approach for determining velocity and uncertainty estimates from seismic cone penetrometer testing or vertical seismic profiling data

USGS Publications Warehouse

Pidlisecky, Adam; Haines, S.S.

2011-01-01

Conventional processing methods for seismic cone penetrometer data present several shortcomings, most notably the absence of a robust velocity model uncertainty estimate. We propose a new seismic cone penetrometer testing (SCPT) data-processing approach that employs Bayesian methods to map measured data errors into quantitative estimates of model uncertainty. We first calculate travel-time differences for all permutations of seismic trace pairs. That is, we cross-correlate each trace at each measurement location with every trace at every other measurement location to determine travel-time differences that are not biased by the choice of any particular reference trace and to thoroughly characterize data error. We calculate a forward operator that accounts for the different ray paths for each measurement location, including refraction at layer boundaries. We then use a Bayesian inversion scheme to obtain the most likely slowness (the reciprocal of velocity) and a distribution of probable slowness values for each model layer. The result is a velocity model that is based on correct ray paths, with uncertainty bounds that are based on the data error. ?? NRC Research Press 2011.

Comparison of algorithms to generate event times conditional on time-dependent covariates.

PubMed

Sylvestre, Marie-Pierre; Abrahamowicz, Michal

2008-06-30

The Cox proportional hazards model with time-dependent covariates (TDC) is now a part of the standard statistical analysis toolbox in medical research. As new methods involving more complex modeling of time-dependent variables are developed, simulations could often be used to systematically assess the performance of these models. Yet, generating event times conditional on TDC requires well-designed and efficient algorithms. We compare two classes of such algorithms: permutational algorithms (PAs) and algorithms based on a binomial model. We also propose a modification of the PA to incorporate a rejection sampler. We performed a simulation study to assess the accuracy, stability, and speed of these algorithms in several scenarios. Both classes of algorithms generated data sets that, once analyzed, provided virtually unbiased estimates with comparable variances. In terms of computational efficiency, the PA with the rejection sampler reduced the time necessary to generate data by more than 50 per cent relative to alternative methods. The PAs also allowed more flexibility in the specification of the marginal distributions of event times and required less calibration.

Comparison of risk estimates using life-table methods.

PubMed

Sullivan, R E; Weng, P S

1987-08-01

Risk estimates promulgated by various radiation protection authorities in recent years have become increasingly more complex. Early "integral" estimates in the form of health effects per 0.01 person-Gy (per person-rad) or per 10(4) person-Gy (per 10(6) person-rad) have tended to be replaced by "differential" estimates which are age- and sex-dependent and specify both minimum induction (latency) and duration of risk expression (plateau) periods. These latter types of risk estimate must be used in conjunction with a life table in order to reduce them to integral form. In this paper, the life table has been used to effect a comparison of the organ and tissue risk estimates derived in several recent reports. In addition, a brief review of life-table methodology is presented and some features of the models used in deriving differential coefficients are discussed. While the great number of permutations possible with dose-response models, detailed risk estimates and proposed projection models precludes any unique result, the reduced integral coefficients are required to conform to the linear, absolute-risk model recommended for use with the integral risk estimates reviewed.

The Functionalist Tradition and Communication Theory.

ERIC Educational Resources Information Center

Burrowes, Carl Patrick

This paper traces the development of the functionalist position chronologically through its major permutations, from the defining contributions of Emile Durkheim, Bronislaw Malinowski, and A. R. Radcliffe-Brown in its anthropological phase through its development in American sociology by Talcott Parsons and Robert K. Merton to its explicit…

Four-qubit entanglement classification from string theory.

PubMed

Borsten, L; Dahanayake, D; Duff, M J; Marrani, A; Rubens, W

2010-09-03

We invoke the black-hole-qubit correspondence to derive the classification of four-qubit entanglement. The U-duality orbits resulting from timelike reduction of string theory from D=4 to D=3 yield 31 entanglement families, which reduce to nine up to permutation of the four qubits.

Summertime, and the Choosin' Ain't Easy: An Ice Cream Counting Problem.

ERIC Educational Resources Information Center

Kreith, Kurt

1992-01-01

Utilizes the problem of determining the number of different ice cream cones and cups that can be made from a choice of 31 flavors to investigate the concepts of combinations and permutations. Provides a set of six related problems with their answers. (MDH)

Frozen Scope and Grammatical Optimization

ERIC Educational Resources Information Center

Freedman, Michael

2014-01-01

The literature on quantifier scope has repeatedly observed that some otherwise expected permutations of scope taking elements are unavailable. Various methods have been proffered explaining these facts. This thesis aims to unify three disparate areas where the scope of operators seems to be frozen: the interaction of universal quantifiers with…

Glycerol acyl-transfer kinetics of a circular permutated Candida antarctica Lipase B

USDA-ARS?s Scientific Manuscript database

Triacylglycerols containing a high abundance of unusual fatty acids, such as y-linolenic acid, or novel arylaliphatic acids, such as ferulic acid, are useful in pharmaceutical and cosmeceutical applications. Candida antarctica lipase B (CALB) is quite often used for non-aqueous synthesis, although ...

A Preserved Context Indexing System for Microcomputers: PERMDEX.

ERIC Educational Resources Information Center

Yerkey, A. Neil

1983-01-01

Following a discussion of derivative versus assignment indexing, use of roles, and concept behind Preserved Concept Indexing System, features of PERMDEX (microcomputer program to assist in creation of permuted printed index) are described including indexer input and prompts, the shunting algorithm, and sorting and printing routines. Fourteen…

Teaching Determinants Using Rook Arrangements

ERIC Educational Resources Information Center

Hendrickson, Anders O. F.

2018-01-01

Teaching determinants poses significant challenges to the instructor of a proof-based undergraduate linear algebra course. The standard definition by cofactor expansion is ugly, lacks symmetry, and is hard for students to use in proofs. We introduce a visual definition of the determinant that interprets permutations as arrangements of…

Activities in Elementary Probability, Monograph No. 9.

ERIC Educational Resources Information Center

Fouch, Daniel J.

This monograph on elementary probability for middle school, junior high, or high school consumer mathematics students is divided into two parts. Part one emphasizes lessons which cover the fundamental counting principle, permutations, and combinations. The 5 lessons of part I indicate the objectives, examples, methods, application, and problems…

Substitution of stable isotopes in Chlorella

NASA Technical Reports Server (NTRS)

Flaumenhaft, E.; Katz, J. J.; Uphaus, R. A.

1969-01-01

Replacement of biologically important isotopes in the alga Chlorella by corresponding heavier stable isotopes produces increasingly greater deviations from the normal cell size and changes the quality and distribution of certain cellular components. The usefulness of isotopically altered organisms increases interest in the study of such permuted organisms.

Instant Insanity II

ERIC Educational Resources Information Center

Richmond, Tom; Young, Aaron

2013-01-01

"Instant Insanity II" is a sliding mechanical puzzle whose solution requires the special alignment of 16 colored tiles. We count the number of solutions of the puzzle's classic challenge and show that the more difficult ultimate challenge has, up to row permutation, exactly two solutions, and further show that no…

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

Physical and Biological Regulation of Carbon Sequestration in Tidal Marshes

NASA Astrophysics Data System (ADS)

Morris, J. T.; Callaway, J.

2017-12-01

The rate of carbon sequestration in tidal marshes is regulated by complex feedbacks among biological and physical factors including the rate of sea-level rise (SLR), biomass production, tidal amplitude, and the concentration of suspended sediment. We used the Marsh Equilibrium Model (MEM) to explore the effects on C-sequestration across a wide range of permutations of these variables. C-sequestration increased with the rate of SLR to a maximum, then down to a vanishing point at higher SLR when marshes convert to mudflats. An acceleration in SLR will increase C-sequestration in marshes that can keep pace, but at high rates of SLR this is only possible with high biomass and suspended sediment concentrations. We found that there were no feasible solutions at SLR >13 mm/yr for permutations of variables that characterize the great majority of tidal marshes, i.e., the equilibrium elevation exists below the lower vertical limit for survival of marsh vegetation. The rate of SLR resulting in maximum C-sequestration varies with biomass production. C-sequestration rates at SLR=1 mm/yr averaged only 36 g C m-2 yr-1, but at the highest maximum biomass tested (5000 g/m2) the mean C-sequestration reached 399 g C m-2 yr-1 at SLR = 14 mm/yr. The empirical estimate of C-sequestration in a core dated 50-years overestimates the theoretical long-term rate by 34% for realistic values of decomposition rate and belowground production. The overestimate of the empirical method arises from the live and decaying biomass contained within the carbon inventory above the marker horizon, and overestimates were even greater for shorter surface cores.

Mammographic breast density and breast cancer: evidence of a shared genetic basis.

PubMed

Varghese, Jajini S; Thompson, Deborah J; Michailidou, Kyriaki; Lindström, Sara; Turnbull, Clare; Brown, Judith; Leyland, Jean; Warren, Ruth M L; Luben, Robert N; Loos, Ruth J; Wareham, Nicholas J; Rommens, Johanna; Paterson, Andrew D; Martin, Lisa J; Vachon, Celine M; Scott, Christopher G; Atkinson, Elizabeth J; Couch, Fergus J; Apicella, Carmel; Southey, Melissa C; Stone, Jennifer; Li, Jingmei; Eriksson, Louise; Czene, Kamila; Boyd, Norman F; Hall, Per; Hopper, John L; Tamimi, Rulla M; Rahman, Nazneen; Easton, Douglas F

2012-03-15

Percent mammographic breast density (PMD) is a strong heritable risk factor for breast cancer. However, the pathways through which this risk is mediated are still unclear. To explore whether PMD and breast cancer have a shared genetic basis, we identified genetic variants most strongly associated with PMD in a published meta-analysis of five genome-wide association studies (GWAS) and used these to construct risk scores for 3,628 breast cancer cases and 5,190 controls from the UK2 GWAS of breast cancer. The signed per-allele effect estimates of single-nucleotide polymorphisms (SNP) were multiplied with the respective allele counts in the individual and summed over all SNPs to derive the risk score for an individual. These scores were included as the exposure variable in a logistic regression model with breast cancer case-control status as the outcome. This analysis was repeated using 10 different cutoff points for the most significant density SNPs (1%-10% representing 5,222-50,899 SNPs). Permutation analysis was also conducted across all 10 cutoff points. The association between risk score and breast cancer was significant for all cutoff points from 3% to 10% of top density SNPs, being most significant for the 6% (2-sided P = 0.002) to 10% (P = 0.001) cutoff points (overall permutation P = 0.003). Women in the top 10% of the risk score distribution had a 31% increased risk of breast cancer [OR = 1.31; 95% confidence interval (CI), 1.08-1.59] compared with women in the bottom 10%. Together, our results show that PMD and breast cancer have a shared genetic basis that is mediated through a large number of common variants.

Mammographic breast density and breast cancer: evidence of a shared genetic basis

PubMed Central

Varghese, Jajini S; Thompson, Deborah J; Michailidou, Kyriaki; Lindström, Sara; Turnbull, Clare; Brown, Judith; Leyland, Jean; Warren, Ruth ML; Luben, Robert N; Loos, Ruth J; Wareham, Nicholas J; Rommens, Johanna; Paterson, Andrew D; Martin, Lisa J; Vachon, Celine M; Scott, Christopher G; Atkinson, Elizabeth J; Couch, Fergus J; Apicella, Carmel; Southey, Melissa C; Stone, Jennifer; Li, Jingmei; Eriksson, Louise; Czene, Kamila; Boyd, Norman F; Hall, Per; Hopper, John L; Tamimi, Rulla M; Rahman, Nazneen; Easton, Douglas F

2012-01-01

Percent mammographic breast density (PMD) is a strong heritable risk factor for breast cancer. However, the pathways through which this risk is mediated are still unclear. To explore whether PMD and breast cancer have a shared genetic basis, we identified genetic variants most strongly associated with PMD in a published meta-analysis of five genome-wide association studies (GWAS) and used these to construct risk scores for 3628 breast cancer cases and 5190 controls from the UK2 GWAS of breast cancer. The signed per-allele effect estimates of SNPs were multiplied with the respective allele counts in the individual and summed over all SNPs to derive the risk score for an individual. These scores were included as the exposure variable in a logistic regression model with breast cancer case-control status as the outcome. This analysis was repeated using ten different cut-offs for the most significant density SNPs (1-10% representing 5,222-50,899 SNPs). Permutation analysis was also performed across all 10 cut-offs. The association between risk score and breast cancer was significant for all cut-offs from 3-10% of top density SNPs, being most significant for the 6% (2-sided P=0.002) to 10% (P=0.001) cut-offs (overall permutation P=0.003). Women in the top 10% of the risk score distribution had a 31% increased risk of breast cancer [OR= 1.31 (95%CI 1.08-1.59)] compared to women in the bottom 10%. Together, our results demonstrate that PMD and breast cancer have a shared genetic basis that is mediated through a large number of common variants. PMID:22266113

Minimizers with Bounded Action for the High-Dimensional Frenkel-Kontorova Model

NASA Astrophysics Data System (ADS)

Miao, Xue-Qing; Wang, Ya-Nan; Qin, Wen-Xin

In Aubry-Mather theory for monotone twist maps or for one-dimensional Frenkel-Kontorova (FK) model with nearest neighbor interactions, each global minimizer (minimal energy configuration) is naturally Birkhoff. However, this is not true for the one-dimensional FK model with non-nearest neighbor interactions or for the high-dimensional FK model. In this paper, we study the Birkhoff property of minimizers with bounded action for the high-dimensional FK model.

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

Development of a database-driven system for simulating water temperature in the lower Yakima River main stem, Washington, for various climate scenarios

USGS Publications Warehouse

Voss, Frank; Maule, Alec

2013-01-01

A model for simulating daily maximum and mean water temperatures was developed by linking two existing models: one developed by the U.S. Geological Survey and one developed by the Bureau of Reclamation. The study area included the lower Yakima River main stem between the Roza Dam and West Richland, Washington. To automate execution of the labor-intensive models, a database-driven model automation program was developed to decrease operation costs, to reduce user error, and to provide the capability to perform simulations quickly for multiple management and climate change scenarios. Microsoft© SQL Server 2008 R2 Integration Services packages were developed to (1) integrate climate, flow, and stream geometry data from diverse sources (such as weather stations, a hydrologic model, and field measurements) into a single relational database; (2) programmatically generate heavily formatted model input files; (3) iteratively run water temperature simulations; (4) process simulation results for export to other models; and (5) create a database-driven infrastructure that facilitated experimentation with a variety of scenarios, node permutations, weather data, and hydrologic conditions while minimizing costs of running the model with various model configurations. As a proof-of-concept exercise, water temperatures were simulated for a "Current Conditions" scenario, where local weather data from 1980 through 2005 were used as input, and for "Plus 1" and "Plus 2" climate warming scenarios, where the average annual air temperatures used in the Current Conditions scenario were increased by 1degree Celsius (°C) and by 2°C, respectively. Average monthly mean daily water temperatures simulated for the Current Conditions scenario were compared to measured values at the Bureau of Reclamation Hydromet gage at Kiona, Washington, for 2002-05. Differences ranged between 1.9° and 1.1°C for February, March, May, and June, and were less than 0.8°C for the remaining months of the year. The difference between current conditions and measured monthly values for the two warmest months (July and August) were 0.5°C and 0.2°C, respectively. The model predicted that water temperature generally becomes less sensitive to air temperature increases as the distance from the mouth of the river decreases. As a consequence, the difference between climate warming scenarios also decreased. The pattern of decreasing sensitivity is most pronounced from August to October. Interactive graphing tools were developed to explore the relative sensitivity of average monthly and mean daily water temperature to increases in air temperature for model output locations along the lower Yakima River main stem.

Simple model for multiple-choice collective decision making

NASA Astrophysics Data System (ADS)

Lee, Ching Hua; Lucas, Andrew

2014-11-01

We describe a simple model of heterogeneous, interacting agents making decisions between n ≥2 discrete choices. For a special class of interactions, our model is the mean field description of random field Potts-like models and is effectively solved by finding the extrema of the average energy E per agent. In these cases, by studying the propagation of decision changes via avalanches, we argue that macroscopic dynamics is well captured by a gradient flow along E . We focus on the permutation symmetric case, where all n choices are (on average) the same, and spontaneous symmetry breaking (SSB) arises purely from cooperative social interactions. As examples, we show that bimodal heterogeneity naturally provides a mechanism for the spontaneous formation of hierarchies between decisions and that SSB is a preferred instability to discontinuous phase transitions between two symmetric points. Beyond the mean field limit, exponentially many stable equilibria emerge when we place this model on a graph of finite mean degree. We conclude with speculation on decision making with persistent collective oscillations. Throughout the paper, we emphasize analogies between methods of solution to our model and common intuition from diverse areas of physics, including statistical physics and electromagnetism.

Pinochle Poker: An Activity for Counting and Probability

ERIC Educational Resources Information Center

Wroughton, Jacqueline; Nolan, Joseph

2012-01-01

Understanding counting rules is challenging for students; in particular, they struggle with determining when and how to implement combinations, permutations, and the multiplication rule as tools for counting large sets and computing probability. We present an activity--using ideas from the games of poker and pinochle--designed to help students…

Ordering Elements and Subsets: Examples for Student Understanding

ERIC Educational Resources Information Center

Mellinger, Keith E.

2004-01-01

Teaching the art of counting can be quite difficult. Many undergraduate students have difficulty separating the ideas of permutation, combination, repetition, etc. This article develops some examples to help explain some of the underlying theory while looking carefully at the selection of various subsets of objects from a larger collection. The…

Compilation of nuclear standards, 9th edition, 1972. Part I. United States activities. Final issue

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

None

Activities in nuclear standards preparation are presented in tables. Technical, industrial, and environmental organizations preparing standards are listed alphabetically and their activities are given. Approved standards, unapproved drafts, and tentative standards are listed. Standards are indexed by organization and permuted title. (FS)

75 FR 54656 - Notice of Intent To Grant Exclusive License

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-08

... States to practice the inventions described and claimed in U.S. Patent Applications corresponding to NASA Case Nos. ARC-14744-2 entitled ``A Versatile Platform for Nanotechnology Based on Circular Permutations... applications completed and received by NASA within fifteen (15) days of the date of this published notice will...

Using a Card Trick to Teach Discrete Mathematics

ERIC Educational Resources Information Center

Simonson, Shai; Holm, Tara S.

2003-01-01

We present a card trick that can be used to review or teach a variety of topics in discrete mathematics. We address many subjects, including permutations, combinations, functions, graphs, depth first search, the pigeonhole principle, greedy algorithms, and concepts from number theory. Moreover, the trick motivates the use of computers in…

Single Parent Families: Diversity, Myths and Realities.

ERIC Educational Resources Information Center

Hanson, Shirley M. H., Ed.; And Others

Major changes are taking place in western families which affect the way professionals interact with families. Drawing on a multidisciplinary team of scholars, this book presents a synthesis of the demographic, theoretical, and research data on the various permutations of the single parent family. Topics include economics, single custodial or…

The Lottery Is a Mathematics Powerball

ERIC Educational Resources Information Center

Lim, Vivian; Rubel, Laurie; Shookhoff, Lauren; Sullivan, Mathew; Williams, Sarah

2016-01-01

The lottery has rich potential for mathematical explorations. It serves as a real-world context to explore concepts of permutations, combinations, sample space, and probability in terms of making sense of the lottery games. The lottery offers additional possibilities in terms of scaling, data analysis, and spatial analysis. Finally, by readily…

Mathematical Methods of Communication Signal Design

DTIC Science & Technology

1990-09-30

Labelling of Annals of Discrete Math ., 1989-90. iv. T. Etzion, S.W. Golomb, and H. Taylor, "Polygonal Path Constructions for Tuscan-k Squares...the Special Issue on Graph Labellings of A,.nals of Discrete Math ., 1989-1990. vi. T. Etzion, "An Algorithm for Realization of Permutations in a

Heat pipe technology. A bibliography with abstracts

NASA Technical Reports Server (NTRS)

1978-01-01

This bibliography cites 55 publications on the theory, design, development, fabrication, and testing of heat pipes. Applications covered include solar, nuclear, and thermoelectric energy conversion. A book (in Russian) on low temperature heat pipes is included as well as abstracts when available. Indexes provided list authors, titles/keywords (permuted) and patents.

Variations on the Zilch Cycle

ERIC Educational Resources Information Center

Binder, P.-M.; Tanoue, C. K. S.

2013-01-01

Thermo dynamic cycles in introductory physics courses are usually made up from a small number of permutations of isothermal, adiabatic, and constant-pressure and volume quasistatic strokes, with the working fluid usually being an ideal gas. Among them we find the Carnot, Stirling, Otto, Diesel, and Joule-Brayton cycles; in more advanced courses,…