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Sample records for random fields reveal

  1. Social patterns revealed through random matrix theory

    NASA Astrophysics Data System (ADS)

    Sarkar, Camellia; Jalan, Sarika

    2014-11-01

    Despite the tremendous advancements in the field of network theory, very few studies have taken weights in the interactions into consideration that emerge naturally in all real-world systems. Using random matrix analysis of a weighted social network, we demonstrate the profound impact of weights in interactions on emerging structural properties. The analysis reveals that randomness existing in particular time frame affects the decisions of individuals rendering them more freedom of choice in situations of financial security. While the structural organization of networks remains the same throughout all datasets, random matrix theory provides insight into the interaction pattern of individuals of the society in situations of crisis. It has also been contemplated that individual accountability in terms of weighted interactions remains as a key to success unless segregation of tasks comes into play.

  2. On Pfaffian Random Point Fields

    NASA Astrophysics Data System (ADS)

    Kargin, V.

    2014-02-01

    We study Pfaffian random point fields by using the Moore-Dyson quaternion determinants. First, we give sufficient conditions that ensure that a self-dual quaternion kernel defines a valid random point field, and then we prove a CLT for Pfaffian point fields. The proofs are based on a new quaternion extension of the Cauchy-Binet determinantal identity. In addition, we derive the Fredholm determinantal formulas for the Pfaffian point fields which use the quaternion determinant.

  3. Markov random fields reveal an N-terminal double beta-propeller motif as part of a bacterial hybrid two-component sensor system

    PubMed Central

    Menke, Matt; Berger, Bonnie; Cowen, Lenore

    2010-01-01

    The recent explosion in newly sequenced bacterial genomes is outpacing the capacity of researchers to try to assign functional annotation to all the new proteins. Hence, computational methods that can help predict structural motifs provide increasingly important clues in helping to determine how these proteins might function. We introduce a Markov Random Field approach tailored for recognizing proteins that fold into mainly β-structural motifs, and apply it to build recognizers for the β-propeller shapes. As an application, we identify a potential class of hybrid two-component sensor proteins, that we predict contain a double-propeller domain. PMID:20147619

  4. Efficient robust conditional random fields.

    PubMed

    Song, Dongjin; Liu, Wei; Zhou, Tianyi; Tao, Dacheng; Meyer, David A

    2015-10-01

    Conditional random fields (CRFs) are a flexible yet powerful probabilistic approach and have shown advantages for popular applications in various areas, including text analysis, bioinformatics, and computer vision. Traditional CRF models, however, are incapable of selecting relevant features as well as suppressing noise from noisy original features. Moreover, conventional optimization methods often converge slowly in solving the training procedure of CRFs, and will degrade significantly for tasks with a large number of samples and features. In this paper, we propose robust CRFs (RCRFs) to simultaneously select relevant features. An optimal gradient method (OGM) is further designed to train RCRFs efficiently. Specifically, the proposed RCRFs employ the l1 norm of the model parameters to regularize the objective used by traditional CRFs, therefore enabling discovery of the relevant unary features and pairwise features of CRFs. In each iteration of OGM, the gradient direction is determined jointly by the current gradient together with the historical gradients, and the Lipschitz constant is leveraged to specify the proper step size. We show that an OGM can tackle the RCRF model training very efficiently, achieving the optimal convergence rate [Formula: see text] (where k is the number of iterations). This convergence rate is theoretically superior to the convergence rate O(1/k) of previous first-order optimization methods. Extensive experiments performed on three practical image segmentation tasks demonstrate the efficacy of OGM in training our proposed RCRFs. PMID:26080050

  5. Summer School Effects in a Randomized Field Trial

    ERIC Educational Resources Information Center

    Zvoch, Keith; Stevens, Joseph J.

    2013-01-01

    This field-based randomized trial examined the effect of assignment to and participation in summer school for two moderately at-risk samples of struggling readers. Application of multiple regression models to difference scores capturing the change in summer reading fluency revealed that kindergarten students randomly assigned to summer school…

  6. Defect Detection Using Hidden Markov Random Fields

    NASA Astrophysics Data System (ADS)

    Dogandžić, Aleksandar; Eua-anant, Nawanat; Zhang, Benhong

    2005-04-01

    We derive an approximate maximum a posteriori (MAP) method for detecting NDE defect signals using hidden Markov random fields (HMRFs). In the proposed HMRF framework, a set of spatially distributed NDE measurements is assumed to form a noisy realization of an underlying random field that has a simple structure with Markovian dependence. Here, the random field describes the defect signals to be estimated or detected. The HMRF models incorporate measurement locations into the statistical analysis, which is important in scenarios where the same defect affects measurements at multiple locations. We also discuss initialization of the proposed HMRF detector and apply to simulated eddy-current data and experimental ultrasonic C-scan data from an inspection of a cylindrical Ti 6-4 billet.

  7. Relativistic diffusive motion in random electromagnetic fields

    NASA Astrophysics Data System (ADS)

    Haba, Z.

    2011-08-01

    We show that the relativistic dynamics in a Gaussian random electromagnetic field can be approximated by the relativistic diffusion of Schay and Dudley. Lorentz invariant dynamics in the proper time leads to the diffusion in the proper time. The dynamics in the laboratory time gives the diffusive transport equation corresponding to the Jüttner equilibrium at the inverse temperature β-1 = mc2. The diffusion constant is expressed by the field strength correlation function (Kubo's formula).

  8. Digital servo control of random sound fields

    NASA Technical Reports Server (NTRS)

    Nakich, R. B.

    1973-01-01

    It is necessary to place number of sensors at different positions in sound field to determine actual sound intensities to which test object is subjected. It is possible to determine whether specification is being met adequately or exceeded. Since excitation is of random nature, signals are essentially coherent and it is impossible to obtain true average.

  9. Interfaces in Random Field Ising Systems

    NASA Astrophysics Data System (ADS)

    Seppälä, Eira

    2001-03-01

    Domain walls are studied in random field Ising magnets at T=0 in two and three dimensions using exact ground state calculations. In 2D below the random field strength dependent length scale Lb the walls exhibit a super-rough behavior with a roughness exponent greater than unity ζ ~= 1.20 ± 0.05. The nearest-neighbor height difference probability distribution depends on the system size below L_b. Above Lb domains become fractal, ζ ~= 1.(E. T. Seppälä, V. Petäjä, and M. J. Alava, Phys. Rev. E 58), R5217 (1998). The energy fluctuation exponent has a value θ=1, contradicting the exponent relation θ = 2ζ -1 due to the broken scale-invariance, below Lb and vanishes for system sizes above L_b. The broken scale-invariance should be manifest also in Kardar-Parisi-Zhang problem with random-field noise.(E. Frey, U. C. Täuber, and H. K. Janssen, Europhys. Lett. 47), 14 (1999). In 3D there exists a transition between ferromagnetic and paramagnetic phases at the critical random field strength (Δ/J)_c. Below (Δ/J)c the roughness exponent is also greater ζ ~= 0.73 ± 0.03 than the functional-renormalization-group calculation result ζ = (5-d)/3.(D. Fisher, Phys. Rev. Lett. 56), 1964 (1986).(P. Chauve, P. Le Doussal, and K. Wiese, cond-mat/0006056.) The height differences are system size dependent in 3D, as well. The behavior of the domain walls in 2D below Lb with a constant external field, i.e., the random-bulk wetting, is demonstrated.(E. T. Seppälä, I. Sillanpää, and M. J. Alava, unpublished.)

  10. Random fields at a nonequilibrium phase transition.

    PubMed

    Barghathi, Hatem; Vojta, Thomas

    2012-10-26

    We study nonequilibrium phase transitions in the presence of disorder that locally breaks the symmetry between two equivalent macroscopic states. In low-dimensional equilibrium systems, such random-field disorder is known to have dramatic effects: it prevents spontaneous symmetry breaking and completely destroys the phase transition. In contrast, we show that the phase transition of the one-dimensional generalized contact process persists in the presence of random-field disorder. The ultraslow dynamics in the symmetry-broken phase is described by a Sinai walk of the domain walls between two different absorbing states. We discuss the generality and limitations of our theory, and we illustrate our results by large-scale Monte Carlo simulations. PMID:23215170

  11. Variational Infinite Hidden Conditional Random Fields.

    PubMed

    Bousmalis, Konstantinos; Zafeiriou, Stefanos; Morency, Louis-Philippe; Pantic, Maja; Ghahramani, Zoubin

    2015-09-01

    Hidden conditional random fields (HCRFs) are discriminative latent variable models which have been shown to successfully learn the hidden structure of a given classification problem. An Infinite hidden conditional random field is a hidden conditional random field with a countably infinite number of hidden states, which rids us not only of the necessity to specify a priori a fixed number of hidden states available but also of the problem of overfitting. Markov chain Monte Carlo (MCMC) sampling algorithms are often employed for inference in such models. However, convergence of such algorithms is rather difficult to verify, and as the complexity of the task at hand increases the computational cost of such algorithms often becomes prohibitive. These limitations can be overcome by variational techniques. In this paper, we present a generalized framework for infinite HCRF models, and a novel variational inference approach on a model based on coupled Dirichlet Process Mixtures, the HCRF-DPM. We show that the variational HCRF-DPM is able to converge to a correct number of represented hidden states, and performs as well as the best parametric HCRFs-chosen via cross-validation-for the difficult tasks of recognizing instances of agreement, disagreement, and pain in audiovisual sequences. PMID:26353136

  12. Role of random electric fields in relaxors

    PubMed Central

    Phelan, Daniel; Stock, Christopher; Rodriguez-Rivera, Jose A.; Chi, Songxue; Leão, Juscelino; Long, Xifa; Xie, Yujuan; Bokov, Alexei A.; Ye, Zuo-Guang; Ganesh, Panchapakesan; Gehring, Peter M.

    2014-01-01

    PbZr1–xTixO3 (PZT) and Pb(Mg1/3Nb2/3)1–xTixO3 (PMN-xPT) are complex lead-oxide perovskites that display exceptional piezoelectric properties for pseudorhombohedral compositions near a tetragonal phase boundary. In PZT these compositions are ferroelectrics, but in PMN-xPT they are relaxors because the dielectric permittivity is frequency dependent and exhibits non-Arrhenius behavior. We show that the nanoscale structure unique to PMN-xPT and other lead-oxide perovskite relaxors is absent in PZT and correlates with a greater than 100% enhancement of the longitudinal piezoelectric coefficient in PMN-xPT relative to that in PZT. By comparing dielectric, structural, lattice dynamical, and piezoelectric measurements on PZT and PMN-xPT, two nearly identical compounds that represent weak and strong random electric field limits, we show that quenched (static) random fields establish the relaxor phase and identify the order parameter. PMID:24449912

  13. Efficient prediction designs for random fields

    PubMed Central

    Müller, Werner G; Pronzato, Luc; Rendas, Joao; Waldl, Helmut

    2015-01-01

    For estimation and predictions of random fields, it is increasingly acknowledged that the kriging variance may be a poor representative of true uncertainty. Experimental designs based on more elaborate criteria that are appropriate for empirical kriging (EK) are then often non-space-filling and very costly to determine. In this paper, we investigate the possibility of using a compound criterion inspired by an equivalence theorem type relation to build designs quasi-optimal for the EK variance when space-filling designs become unsuitable. Two algorithms are proposed, one relying on stochastic optimization to explicitly identify the Pareto front, whereas the second uses the surrogate criteria as local heuristic to choose the points at which the (costly) true EK variance is effectively computed. We illustrate the performance of the algorithms presented on both a simple simulated example and a real oceanographic dataset. © 2014 The Authors. Applied Stochastic Models in Business and Industry published by John Wiley & Sons, Ltd. PMID:26300698

  14. Neutrino conversions in solar random magnetic fields

    NASA Astrophysics Data System (ADS)

    Semikoz, V. B.; Torrente-Lujan, E.

    1999-09-01

    We consider the effect of a random magnetic field in the convective zone of the Sun superimposed to a regular magnetic field on resonant neutrino spin-flavor oscillations. We argue for the existence of a field of strongly chaotic nature at the bottom of the convective zone. In contrast to previous attempts we employ a model motivated regular magnetic field profile: it is a static field solution to the solar equilibrium hydro-magnetic equations. These solutions have been known for a long time in the literature. We show for the first time that in addition they are twisting solutions. In this scenario electron antineutrinos are produced through cascades like νeL-->νμL-- >ν~eR, The detection of ν~eR at Earth would be a long-awaited signature of the Majorana nature of the neutrino. The expected signals in the different experiments (SK, GALLEX-SAGE, Homestake) are obtained as a function of the level of noise, regular magnetic field and neutrino mixing parameters. Previous results obtained for small mixing and ad-hoc regular magnetic profiles are reobtained. We confirm the strong suppression for a large part of the parameter space of the ν~eR-flux for high energy boron neutrinos in agreement with present data of the SK experiment. We find that MSW (Mikheyev-Smirnov-Wolfenstein) regions (Δm2~=10-5 eV2, both small and large mixing solutions) are stable up to very large levels of noise (P=0.7-0.8) but they are acceptable from the point of view of antineutrino production only for moderate levels of noise (P~=0.95). For strong noise and a reasonable regular magnetic field, any parameter region (Δm2, sin 2 2θ) is excluded. As a consequence, we are allowed to reverse the problem and to put limits on the r.m.s. field strength and transition magnetic moments by demanding a particle physics solution to the SNP in this scenario.

  15. Unmixing hyperspectral images using Markov random fields

    SciTech Connect

    Eches, Olivier; Dobigeon, Nicolas; Tourneret, Jean-Yves

    2011-03-14

    This paper proposes a new spectral unmixing strategy based on the normal compositional model that exploits the spatial correlations between the image pixels. The pure materials (referred to as endmembers) contained in the image are assumed to be available (they can be obtained by using an appropriate endmember extraction algorithm), while the corresponding fractions (referred to as abundances) are estimated by the proposed algorithm. Due to physical constraints, the abundances have to satisfy positivity and sum-to-one constraints. The image is divided into homogeneous distinct regions having the same statistical properties for the abundance coefficients. The spatial dependencies within each class are modeled thanks to Potts-Markov random fields. Within a Bayesian framework, prior distributions for the abundances and the associated hyperparameters are introduced. A reparametrization of the abundance coefficients is proposed to handle the physical constraints (positivity and sum-to-one) inherent to hyperspectral imagery. The parameters (abundances), hyperparameters (abundance mean and variance for each class) and the classification map indicating the classes of all pixels in the image are inferred from the resulting joint posterior distribution. To overcome the complexity of the joint posterior distribution, Markov chain Monte Carlo methods are used to generate samples asymptotically distributed according to the joint posterior of interest. Simulations conducted on synthetic and real data are presented to illustrate the performance of the proposed algorithm.

  16. Conrad: gene prediction using conditional random fields.

    PubMed

    DeCaprio, David; Vinson, Jade P; Pearson, Matthew D; Montgomery, Philip; Doherty, Matthew; Galagan, James E

    2007-09-01

    We present Conrad, the first comparative gene predictor based on semi-Markov conditional random fields (SMCRFs). Unlike the best standalone gene predictors, which are based on generalized hidden Markov models (GHMMs) and trained by maximum likelihood, Conrad is discriminatively trained to maximize annotation accuracy. In addition, unlike the best annotation pipelines, which rely on heuristic and ad hoc decision rules to combine standalone gene predictors with additional information such as ESTs and protein homology, Conrad encodes all sources of information as features and treats all features equally in the training and inference algorithms. Conrad outperforms the best standalone gene predictors in cross-validation and whole chromosome testing on two fungi with vastly different gene structures. The performance improvement arises from the SMCRF's discriminative training methods and their ability to easily incorporate diverse types of information by encoding them as feature functions. On Cryptococcus neoformans, configuring Conrad to reproduce the predictions of a two-species phylo-GHMM closely matches the performance of Twinscan. Enabling discriminative training increases performance, and adding new feature functions further increases performance, achieving a level of accuracy that is unprecedented for this organism. Similar results are obtained on Aspergillus nidulans comparing Conrad versus Fgenesh. SMCRFs are a promising framework for gene prediction because of their highly modular nature, simplifying the process of designing and testing potential indicators of gene structure. Conrad's implementation of SMCRFs advances the state of the art in gene prediction in fungi and provides a robust platform for both current application and future research. PMID:17690204

  17. Cluster Mass Inference via Random Field Theory

    PubMed Central

    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 method 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 extent inference, and good accuracy relative to a gold-standard permutation test. PMID:18805493

  18. Random Field effects in perpendicular-anisotropy multilayer films

    NASA Astrophysics Data System (ADS)

    Xu, Jian; Silevitch, Daniel; Rosenbaum, Thomas

    With the application of a magnetic field transverse to the magnetic easy axis, randomly-distributed 3D collections of dipole-coupled Ising spins form a realization of the Random-Field Ising Model. Tuning the strength of the site-specific random field, and hence the disorder, via the applied transverse field regulates the domain reversal energetics and hence the macroscopic hysteresis loop. We extend this approach to two dimensions, using sputtered Perpendicular Magnetic Anisotropy (PMA) Co/Pt multilayer thin films. We characterize the coercive fields and hysteresis loops at a series of temperatures and transverse fields.

  19. Simulation of 3D infrared scenes using random fields model

    NASA Astrophysics Data System (ADS)

    Shao, Xiaopeng; Zhang, Jianqi

    2001-09-01

    Analysis and simulation of smart munitions requires imagery for the munition's sensor to view. The traditional infrared background simulations are always limited in the plane scene studies. A new method is described to synthesize the images in 3D view and with various terrains texture. We develop the random fields model and temperature fields to simulate 3D infrared scenes. Generalized long-correlation (GLC) model, one of random field models, will generate both the 3D terrains skeleton data and the terrains texture in this work. To build the terrain mesh with the random fields, digital elevation models (DEM) are introduced in the paper. And texture mapping technology will perform the task of pasting the texture in the concavo-convex surfaces of the 3D scene. The simulation using random fields model is a very available method to produce 3D infrared scene with great randomicity and reality.

  20. Ordering and phase transitions in random-field Ising systems

    NASA Technical Reports Server (NTRS)

    Maritan, Amos; Swift, Michael R.; Cieplak, Marek; Chan, Moses H. W.; Cole, Milton W.; Banavar, Jayanth R.

    1991-01-01

    An exact analysis of the Ising model with infinite-range interactions in a random field and a local mean-field theory in three dimensions is carried out leading to a phase diagram with several coexistence surfaces and lines of critical points. The results show that the phase diagram depends crucially on whether the distribution of random fields is symmetric or not. Thus, Ising-like phase transitions in a porous medium (the asymmetric case) are in a different universality class from the conventional random-field model (symmetric case).

  1. Listening to the noise: random fluctuations reveal gene network parameters

    SciTech Connect

    Munsky, Brian; Khammash, Mustafa

    2009-01-01

    The cellular environment is abuzz with noise. The origin of this noise is attributed to the inherent random motion of reacting molecules that take part in gene expression and post expression interactions. In this noisy environment, clonal populations of cells exhibit cell-to-cell variability that frequently manifests as significant phenotypic differences within the cellular population. The stochastic fluctuations in cellular constituents induced by noise can be measured and their statistics quantified. We show that these random fluctuations carry within them valuable information about the underlying genetic network. Far from being a nuisance, the ever-present cellular noise acts as a rich source of excitation that, when processed through a gene network, carries its distinctive fingerprint that encodes a wealth of information about that network. We demonstrate that in some cases the analysis of these random fluctuations enables the full identification of network parameters, including those that may otherwise be difficult to measure. This establishes a potentially powerful approach for the identification of gene networks and offers a new window into the workings of these networks.

  2. Is the Non-Dipole Magnetic Field Random?

    NASA Technical Reports Server (NTRS)

    Walker, Andrew D.; Backus, George E.

    1996-01-01

    Statistical modelling of the Earth's magnetic field B has a long history. In particular, the spherical harmonic coefficients of scalar fields derived from B can be treated as Gaussian random variables. In this paper, we give examples of highly organized fields whose spherical harmonic coefficients pass tests for independent Gaussian random variables. The fact that coefficients at some depth may be usefully summarized as independent samples from a normal distribution need not imply that there really is some physical, random process at that depth. In fact, the field can be extremely structured and still be regarded for some purposes as random. In this paper, we examined the radial magnetic field B(sub r) produced by the core, but the results apply to any scalar field on the core-mantle boundary (CMB) which determines B outside the CMB.

  3. Creating order with the help of randomness: generating transversely random, longitudinally invariant vector optical fields.

    PubMed

    Khonina, Svetlana N; Golub, Ilya

    2015-09-01

    We show that it is possible to generate transversely random, diffraction-free/longitudinally invariant vector optical fields. The randomness in transverse polarization distribution complements a previously studied one in intensity of scalar Bessel-type beams, adding another degree of freedom to control these beams. Moreover, we show that the relative transversely random phase distribution is also conserved along the optical axis. Thus, intensity, phase, and polarization of Bessel-type beams can be transversely random/arbitrary while invariant upon propagation. Such fields may find applications in encryption/secure communications, optical trapping, etc. PMID:26368714

  4. Generating functionals for quantum field theories with random potentials

    NASA Astrophysics Data System (ADS)

    Jain, Mudit; Vanchurin, Vitaly

    2016-01-01

    We consider generating functionals for computing correlators in quantum field theories with random potentials. Examples of such theories include cosmological systems in context of the string theory landscape (e.g. cosmic inflation) or condensed matter systems with quenched disorder (e.g. spin glass). We use the so-called replica trick to define two different generating functionals for calculating correlators of the quantum fields averaged over a given distribution of random potentials. The first generating functional is appropriate for calculating averaged (in-out) amplitudes and involves a single replica of fields, but the replica limit is taken to an (unphysical) negative one number of fields outside of the path integral. When the number of replicas is doubled the generating functional can also be used for calculating averaged probabilities (squared amplitudes) using the in-in construction. The second generating functional involves an infinite number of replicas, but can be used for calculating both in-out and in-in correlators and the replica limits are taken to only a zero number of fields. We discuss the formalism in details for a single real scalar field, but the generalization to more fields or to different types of fields is straightforward. We work out three examples: one where the mass of scalar field is treated as a random variable and two where the functional form of interactions is random, one described by a Gaussian random field and the other by a Euclidean action in the field configuration space.

  5. Diffusion of charged particles in a random magnetic field

    NASA Technical Reports Server (NTRS)

    Earl, J. A.

    1972-01-01

    When charged particles move in a random magnetic field superimposed upon a relatively large constant field, their pitch angle distribution can be calculated to any desired precision by an iterative approximation procedure. Improved knowledge of the pitch angle distribution and of the characteristic time for relaxation of anisotropy leads to an accurate expression for the coefficient of diffusion parallel to the mean field.

  6. The space transformation in the simulation of multidimensional random fields

    USGS Publications Warehouse

    Christakos, G.

    1987-01-01

    Space transformations are proposed as a mathematically meaningful and practically comprehensive approach to simulate multidimensional random fields. Within this context the turning bands method of simulation is reconsidered and improved in both the space and frequency domains. ?? 1987.

  7. Statistical analysis of loopy belief propagation in random fields

    NASA Astrophysics Data System (ADS)

    Yasuda, Muneki; Kataoka, Shun; Tanaka, Kazuyuki

    2015-10-01

    Loopy belief propagation (LBP), which is equivalent to the Bethe approximation in statistical mechanics, is a message-passing-type inference method that is widely used to analyze systems based on Markov random fields (MRFs). In this paper, we propose a message-passing-type method to analytically evaluate the quenched average of LBP in random fields by using the replica cluster variation method. The proposed analytical method is applicable to general pairwise MRFs with random fields whose distributions differ from each other and can give the quenched averages of the Bethe free energies over random fields, which are consistent with numerical results. The order of its computational cost is equivalent to that of standard LBP. In the latter part of this paper, we describe the application of the proposed method to Bayesian image restoration, in which we observed that our theoretical results are in good agreement with the numerical results for natural images.

  8. Multilevel Compression of Random Walks on Networks Reveals Hierarchical Organization in Large Integrated Systems

    PubMed Central

    Rosvall, Martin; Bergstrom, Carl T.

    2011-01-01

    To comprehend the hierarchical organization of large integrated systems, we introduce the hierarchical map equation, which reveals multilevel structures in networks. In this information-theoretic approach, we exploit the duality between compression and pattern detection; by compressing a description of a random walker as a proxy for real flow on a network, we find regularities in the network that induce this system-wide flow. Finding the shortest multilevel description of the random walker therefore gives us the best hierarchical clustering of the network — the optimal number of levels and modular partition at each level — with respect to the dynamics on the network. With a novel search algorithm, we extract and illustrate the rich multilevel organization of several large social and biological networks. For example, from the global air traffic network we uncover countries and continents, and from the pattern of scientific communication we reveal more than 100 scientific fields organized in four major disciplines: life sciences, physical sciences, ecology and earth sciences, and social sciences. In general, we find shallow hierarchical structures in globally interconnected systems, such as neural networks, and rich multilevel organizations in systems with highly separated regions, such as road networks. PMID:21494658

  9. Subpixel translation-registration of random fields

    NASA Technical Reports Server (NTRS)

    Slud, Eric V.

    1988-01-01

    The author examines both theoretically and through a simulation study the feasibility of identifying the location within a large reference gray-level array of a smaller sensed array to an accuracy finer than one pixel. It is assumed that the sensed image before discretization into pixels consists of a translated, but not rotated, section of the reference image with some superposed noise. The theoretical and empirical results show that when the noise has standard deviation no larger than that of a realistic reference field, the upper quartile of the registration error is on the order of 0.25-0.5 pixels.

  10. A universal form of slow dynamics in zero-temperature random-field Ising model

    NASA Astrophysics Data System (ADS)

    Ohta, H.; Sasa, S.

    2010-04-01

    The zero-temperature Glauber dynamics of the random-field Ising model describes various ubiquitous phenomena such as avalanches, hysteresis, and related critical phenomena. Here, for a model on a random graph with a special initial condition, we derive exactly an evolution equation for an order parameter. Through a bifurcation analysis of the obtained equation, we reveal a new class of cooperative slow dynamics with the determination of critical exponents.

  11. Barkhausen noise in the random field Ising magnet Nd2Fe14B

    NASA Astrophysics Data System (ADS)

    Xu, J.; Silevitch, D. M.; Dahmen, K. A.; Rosenbaum, T. F.

    2015-07-01

    With sintered needles aligned and a magnetic field applied transverse to its easy axis, the rare-earth ferromagnet Nd2Fe14B becomes a room-temperature realization of the random field Ising model. The transverse field tunes the pinning potential of the magnetic domains in a continuous fashion. We study the magnetic domain reversal and avalanche dynamics between liquid helium and room temperatures at a series of transverse fields using a Barkhausen noise technique. The avalanche size and energy distributions follow power-law behavior with a cutoff dependent on the pinning strength dialed in by the transverse field, consistent with theoretical predictions for Barkhausen avalanches in disordered materials. A scaling analysis reveals two regimes of behavior: one at low temperature and high transverse field, where the dynamics are governed by the randomness, and the second at high temperature and low transverse field, where thermal fluctuations dominate the dynamics.

  12. Synchronization and Spin-Flop Transitions for a Mean-Field XY Model in Random Field

    NASA Astrophysics Data System (ADS)

    Collet, Francesca; Ruszel, Wioletta

    2016-08-01

    We characterize the phase space for the infinite volume limit of a ferromagnetic mean-field XY model in a random field pointing in one direction with two symmetric values. We determine the stationary solutions and detect possible phase transitions in the interaction strength for fixed random field intensity. We show that at low temperature magnetic ordering appears perpendicularly to the field. The latter situation corresponds to a spin-flop transition.

  13. The spectral expansion of the elasticity random field

    SciTech Connect

    Malyarenko, Anatoliy; Ostoja-Starzewski, Martin

    2014-12-10

    We consider a deformable body that occupies a region D in the plane. In our model, the body’s elasticity tensor H(x) is the restriction to D of a second-order mean-square continuous random field. Under translation, the expected value and the correlation tensor of the field H(x) do not change. Under action of an arbitrary element k of the orthogonal group O(2), they transform according to the reducible orthogonal representation k ⟼ S{sup 2}(S{sup 2}(k)) of the above group. We find the spectral expansion of the correlation tensor R(x) of the elasticity field as well as the expansion of the field itself in terms of stochastic integrals with respect to a family of orthogonal scattered random measures.

  14. MC Estimator Variance Reduction with Antithetic and Common Random Fields

    NASA Astrophysics Data System (ADS)

    Guthke, P.; Bardossy, A.

    2011-12-01

    Monte Carlo methods are widely used to estimate the outcome of complex physical models. For physical models with spatial parameter uncertainty, it is common to apply spatial random functions to the uncertain variables, which can then be used to interpolate between known values or to simulate a number of equally likely realizations .The price, that has to be paid for such a stochastic approach, are many simulations of the physical model instead of just running one model with one 'best' input parameter set. The number of simulations is often limited because of computational constraints, so that a modeller has to make a compromise between the benefit in terms of an increased accuracy of the results and the effort in terms of a massively increased computational time. Our objective is, to reduce the estimator variance of dependent variables in Monte Carlo frameworks. Therefore, we adapt two variance reduction techniques (antithetic variates and common random numbers) to a sequential random field simulation scheme that uses copulas as spatial dependence functions. The proposed methodology leads to pairs of spatial random fields with special structural properties, that are advantageous in MC frameworks. Antithetic Random fields (ARF) exhibit a reversed structure on the large scale, while the dependence on the local scale is preserved. Common random fields (CRF) show the same large scale structures, but different spatial dependence on the local scale. The performances of the proposed methods are examined with two typical applications of stochastic hydrogeology. It is shown, that ARF have the property to massively reduce the number of simulation runs required for convergence in Monte Carlo frameworks while keeping the same accuracy in terms of estimator variance. Furthermore, in multi-model frameworks like in sensitivity analysis of the spatial structure, where more than one spatial dependence model is used, the influence of different dependence structures becomes obvious

  15. Probability Statements Extraction with Constrained Conditional Random Fields.

    PubMed

    Deleris, Léa A; Jochim, Charles

    2016-01-01

    This paper investigates how to extract probability statements from academic medical papers. In previous work we have explored traditional classification methods which led to numerous false negatives. This current work focuses on constraining classification output obtained from a Conditional Random Field (CRF) model to allow for domain knowledge constraints. Our experimental results indicate constraining leads to a significant improvement in performance. PMID:27577439

  16. A Multisite Cluster Randomized Field Trial of Open Court Reading

    ERIC Educational Resources Information Center

    Borman, Geoffrey D.; Dowling, N. Maritza; Schneck, Carrie

    2008-01-01

    In this article, the authors report achievement outcomes of a multisite cluster randomized field trial of Open Court Reading 2005 (OCR), a K-6 literacy curriculum published by SRA/McGraw-Hill. The participants are 49 first-grade through fifth-grade classrooms from predominantly minority and poor contexts across the nation. Blocking by grade level…

  17. Can fluctuations of classical random field produce quantum averages?

    NASA Astrophysics Data System (ADS)

    Khrennikov, Andrei

    2009-08-01

    Albert Einstein did not believe in completeness of QM. He dreamed of creation of prequantum classical statistical mechanics such that QM will be reproduced as its approximation. He also dreamed of total exclusion of corpuscules from the future model. Reality of Einstein's dream was pure fields' reality. Recently I made his dream come true in the form of so called prequantum classical statistical field theory (PCSFT). In this approach quantum systems are described by classical random fields, e.g., electromagnetic field (instead of photon), electron field or neutron field. In this paper we generalize PCSFT to composite quantum system. It is well known that in QM, unlike classical mechanics, the state of a composite system is described by the tensor product of state spaces for its subsystems. In PCSFT one can still use Cartesian product, but state spaces are spaces of classical fields (not particles). In particular, entanglement is nothing else than correlation of classical random fields, cf. again Einstein. Thus entanglement was finally demystified.

  18. Three-dimensional extinction mapping using Gaussian random fields

    NASA Astrophysics Data System (ADS)

    Sale, S. E.; Magorrian, J.

    2014-11-01

    We present a scheme for using stellar catalogues to map the three-dimensional distributions of extinction and dust within our Galaxy. Extinction is modelled as a Gaussian random field, whose covariance function is set by a simple physical model of the interstellar medium that assumes a Kolmogorov-like power spectrum of turbulent fluctuations. As extinction is modelled as a random field, the spatial resolution of the resulting maps is set naturally by the data available; there is no need to impose any spatial binning. We verify the validity of our scheme by testing it on simulated extinction fields and show that its precision is significantly improved over previous dust-mapping efforts. The approach we describe here can make use of any photometric, spectroscopic or astrometric data; it is not limited to any particular survey. Consequently, it can be applied to a wide range of data from both existing and future surveys.

  19. Cosmological fluctuations of a random field and radiation fluid

    SciTech Connect

    Bastero-Gil, Mar; Berera, Arjun; Moss, Ian G.; Ramos, Rudnei O. E-mail: ab@ph.ed.ac.uk E-mail: rudnei@uerj.br

    2014-05-01

    A generalization of the random fluid hydrodynamic fluctuation theory due to Landau and Lifshitz is applied to describe cosmological fluctuations in systems with radiation and scalar fields. The viscous pressures, parametrized in terms of the bulk and shear viscosity coefficients, and the respective random fluctuations in the radiation fluid are combined with the stochastic and dissipative scalar evolution equation. This results in a complete set of equations describing the perturbations in both scalar and radiation fluids. These derived equations are then studied, as an example, in the context of warm inflation. Similar treatments can be done for other cosmological early universe scenarios involving thermal or statistical fluctuations.

  20. Transformation of phase transitions driven by an anisotropic random field

    NASA Astrophysics Data System (ADS)

    Popa-Nita, V.; Kralj, Samo

    2005-04-01

    We carry out a comparative study of the influence of a random anisotropy field on continuous and discontinuous phase transitions. The ordered phase, which is reached via a continuous symmetry breaking phase transition, is characterized by an order parameter and by a corresponding hydrodynamic continuum field. We assume that the response of the hydrodynamic field to the imposed disorder results in a domainlike pattern of the system. For a strong enough disorder both transitions become gradual. For weaker disorder strengths the disorder converts a second order transition into a discontinuous one.

  1. Disorder Identification in Hysteresis Data: Recognition Analysis of the Random-Bond-Random-Field Ising Model

    SciTech Connect

    Ovchinnikov, O. S.; Jesse, S.; Kalinin, S. V.; Bintacchit, P.; Trolier-McKinstry, S.

    2009-10-09

    An approach for the direct identification of disorder type and strength in physical systems based on recognition analysis of hysteresis loop shape is developed. A large number of theoretical examples uniformly distributed in the parameter space of the system is generated and is decorrelated using principal component analysis (PCA). The PCA components are used to train a feed-forward neural network using the model parameters as targets. The trained network is used to analyze hysteresis loops for the investigated system. The approach is demonstrated using a 2D random-bond-random-field Ising model, and polarization switching in polycrystalline ferroelectric capacitors.

  2. Simulation of Radar Rainfall Fields: A Random Error Model

    NASA Astrophysics Data System (ADS)

    Aghakouchak, A.; Habib, E.; Bardossy, A.

    2008-12-01

    Precipitation is a major input in hydrological and meteorological models. It is believed that uncertainties due to input data will propagate in modeling hydrologic processes. Stochastically generated rainfall data are used as input to hydrological and meteorological models to assess model uncertainties and climate variability in water resources systems. The superposition of random errors of different sources is one of the main factors in uncertainty of radar estimates. One way to express these uncertainties is to stochastically generate random error fields to impose them on radar measurements in order to obtain an ensemble of radar rainfall estimates. In the method introduced here, the random error consists of two components: purely random error and dependent error on the indicator variable. Model parameters of the error model are estimated using a heteroscedastic maximum likelihood model in order to account for variance heterogeneity in radar rainfall error estimates. When reflectivity values are considered, the exponent and multiplicative factor of the Z-R relationship are estimated simultaneously with the model parameters. The presented model performs better compared to the previous approaches that generally result in unaccounted heteroscedasticity in error fields and thus radar ensemble.

  3. Extreme value statistics of smooth Gaussian random fields

    NASA Astrophysics Data System (ADS)

    Colombi, Stéphane; Davis, Olaf; Devriendt, Julien; Prunet, Simon; Silk, Joe

    2011-07-01

    We consider the Gumbel or extreme value statistics describing the distribution function pG(νmax) of the maximum values of a random field ν within patches of fixed size. We present, for smooth Gaussian random fields in two and three dimensions, an analytical estimate of pG which is expected to hold in a regime where local maxima of the field are moderately high and weakly clustered. When the patch size becomes sufficiently large, the negative of the logarithm of the cumulative extreme value distribution is simply equal to the average of the Euler characteristic of the field in the excursion ν≥νmax inside the patches. The Gumbel statistics therefore represents an interesting alternative probe of the genus as a test of non-Gaussianity, e.g. in cosmic microwave background temperature maps or in 3D galaxy catalogues. It can be approximated, except in the remote positive tail, by a negative Weibull-type form, converging slowly to the expected Gumbel-type form for infinitely large patch size. Convergence is facilitated when large-scale correlations are weaker. We compare the analytic predictions to numerical experiments for the case of a scale-free Gaussian field in two dimensions, achieving impressive agreement between approximate theory and measurements. We also discuss the generalization of our formalism to non-Gaussian fields.

  4. Phase conjugation with random fields and with deterministic and random scatterers

    SciTech Connect

    Gbur, G.; Wolf, E.

    1999-01-01

    The theory of distortion correction by phase conjugation, developed since the discovery of this phenomenon many years ago, applies to situations when the field that is conjugated is monochromatic and the medium with which it interacts is deterministic. In this Letter a generalization of the theory is presented that applies to phase conjugation of partially coherent waves interacting with either deterministic or random weakly scattering nonabsorbing media. {copyright} {ital 1999} {ital Optical Society of America}

  5. Markov-random-field modeling for linear seismic tomography.

    PubMed

    Kuwatani, Tatsu; Nagata, Kenji; Okada, Masato; Toriumi, Mitsuhiro

    2014-10-01

    We apply the Markov-random-field model to linear seismic tomography and propose a method to estimate the hyperparameters for the smoothness and the magnitude of the noise. Optimal hyperparameters can be determined analytically by minimizing the free energy function, which is defined by marginalizing the evaluation function. In synthetic inversion tests under various settings, the assumed velocity structures are successfully reconstructed, which shows the effectiveness and robustness of the proposed method. The proposed mathematical framework can be applied to inversion problems in various fields in the natural sciences. PMID:25375468

  6. Synthetic aperture radar system design for random field classification

    NASA Technical Reports Server (NTRS)

    Harger, R. O.

    1973-01-01

    An optimum design study is carried out for synthetic aperture radar systems intended for classifying randomly reflecting areas (such as agricultural fields) characterized by a reflectivity density spectral density. The problem solution is obtained, neglecting interfield interference and assuming areas of known configuration and location, as well as a certain Gaussian signal field property. The optimum processor is nonlinear, but includes conventional matched filter processing. A set of summary design curves is plotted, and is applied to the design of a satellite synthetic aperture radar system.

  7. The excursion set approach in non-Gaussian random fields

    NASA Astrophysics Data System (ADS)

    Musso, Marcello; Sheth, Ravi K.

    2014-04-01

    Insight into a number of interesting questions in cosmology can be obtained by studying the first crossing distributions of physically motivated barriers by random walks with correlated steps: higher mass objects are associated with walks that cross the barrier in fewer steps. We write the first crossing distribution as a formal series, ordered by the number of times a walk upcrosses the barrier. Since the fraction of walks with many upcrossings is negligible if the walk has not taken many steps, the leading order term in this series is the most relevant for understanding the massive objects of most interest in cosmology. For walks associated with Gaussian random fields, this first term only requires knowledge of the bivariate distribution of the walk height and slope, and provides an excellent approximation to the first crossing distribution for all barriers and smoothing filters of current interest. We show that this simplicity survives when extending the approach to the case of non-Gaussian random fields. For non-Gaussian fields which are obtained by deterministic transformations of a Gaussian, the first crossing distribution is simply related to that for Gaussian walks crossing a suitably rescaled barrier. Our analysis shows that this is a useful way to think of the generic case as well. Although our study is motivated by the possibility that the primordial fluctuation field was non-Gaussian, our results are general. In particular, they do not assume the non-Gaussianity is small, so they may be viewed as the solution to an excursion set analysis of the late-time, non-linear fluctuation field rather than the initial one. They are also useful for models in which the barrier height is determined by quantities other than the initial density, since most other physically motivated variables (such as the shear) are usually stochastic and non-Gaussian. We use the Lognormal transformation to illustrate some of our arguments.

  8. Localization of disordered bosons and magnets in random fields

    SciTech Connect

    Yu, Xiaoquan; Müller, Markus

    2013-10-15

    We study localization properties of disordered bosons and spins in random fields at zero temperature. We focus on two representatives of different symmetry classes, hard-core bosons (XY magnets) and Ising magnets in random transverse fields, and contrast their physical properties. We describe localization properties using a locator expansion on general lattices. For 1d Ising chains, we find non-analytic behavior of the localization length as a function of energy at ω=0, ξ{sup −1}(ω)=ξ{sup −1}(0)+A|ω|{sup α}, with α vanishing at criticality. This contrasts with the much smoother behavior predicted for XY magnets. We use these results to approach the ordering transition on Bethe lattices of large connectivity K, which mimic the limit of high dimensionality. In both models, in the paramagnetic phase with uniform disorder, the localization length is found to have a local maximum at ω=0. For the Ising model, we find activated scaling at the phase transition, in agreement with infinite randomness studies. In the Ising model long range order is found to arise due to a delocalization and condensation initiated at ω=0, without a closing mobility gap. We find that Ising systems establish order on much sparser (fractal) subgraphs than XY models. Possible implications of these results for finite-dimensional systems are discussed. -- Highlights: •Study of localization properties of disordered bosons and spins in random fields. •Comparison between XY magnets (hard-core bosons) and Ising magnets. •Analysis of the nature of the magnetic transition in strong quenched disorder. •Ising magnets: activated scaling, no closing mobility gap at the transition. •Ising order emerges on sparser (fractal) support than XY order.

  9. Global diffusion of cosmic rays in random magnetic fields

    NASA Astrophysics Data System (ADS)

    Snodin, A. P.; Shukurov, A.; Sarson, G. R.; Bushby, P. J.; Rodrigues, L. F. S.

    2016-04-01

    The propagation of charged particles, including cosmic rays, in a partially ordered magnetic field is characterized by a diffusion tensor whose components depend on the particle's Larmor radius RL and the degree of order in the magnetic field. Most studies of the particle diffusion presuppose a scale separation between the mean and random magnetic fields (e.g. there being a pronounced minimum in the magnetic power spectrum at intermediate scales). Scale separation is often a good approximation in laboratory plasmas, but not in most astrophysical environments such as the interstellar medium (ISM). Modern simulations of the ISM have numerical resolution of the order of 1 pc, so the Larmor radius of the cosmic rays that dominate in energy density is at least 106 times smaller than the resolved scales. Large-scale simulations of cosmic ray propagation in the ISM thus rely on oversimplified forms of the diffusion tensor. We take the first steps towards a more realistic description of cosmic ray diffusion for such simulations, obtaining direct estimates of the diffusion tensor from test particle simulations in random magnetic fields (with the Larmor radius scale being fully resolved), for a range of particle energies corresponding to 10-2 ≲ RL/lc ≲ 103, where lc is the magnetic correlation length. We obtain explicit expressions for the cosmic ray diffusion tensor for RL/lc ≪ 1, that might be used in a sub-grid model of cosmic ray diffusion. The diffusion coefficients obtained are closely connected with existing transport theories that include the random walk of magnetic lines.

  10. Propagation of acoustic pulses in random gravity wave fields

    NASA Astrophysics Data System (ADS)

    Millet, Christophe; de La Camara, Alvaro; Lott, François

    2015-11-01

    A linear solution modeling the interaction between an incoming acoustic wave and a randomly perturbed atmosphere is developed, using the normal mode method. The wave mode structure is determined by a sound speed profile that is confining. The environmental uncertainty is described by a stochastic field obtained with a multiwave stochastic parameterization of gravity waves (GW). Using the propagating modes of the unperturbed atmosphere, the wave propagation problem is reduced to solving a system of ordinary differential equations. We focus on the asymptotic behavior of the transmitted waves in the weakly heterogeneous regime. In this regime, the coupling between the acoustic pulse and the randomly perturbed waveguides is weak and the propagation distance must be large enough for the wave to experience significant scattering. A general expression for the pressure far-field is derived in terms of saddle-point contributions. The saddle-points are obtained from a WKB approximation of the vertical eigenvalue problem. We present preliminary results that show how statistics of the transmitted signal are related to some eigenvalues and how an ``optimal'' GW field can trigger large deviations in the acoustic signals. The present model is used to explain the variability of infrasound signals.

  11. PREDICTION INTERVALS FOR INTEGRALS OF GAUSSIAN RANDOM FIELDS.

    PubMed

    De Oliveira, Victor; Kone, Bazoumana

    2015-03-01

    Methodology is proposed for the construction of prediction intervals for integrals of Gaussian random fields over bounded regions (called block averages in the geostatistical literature) based on observations at a finite set of sampling locations. Two bootstrap calibration algorithms are proposed, termed indirect and direct, aimed at improving upon plug-in prediction intervals in terms of coverage probability. A simulation study is carried out that illustrates the effectiveness of both procedures, and these procedures are applied to estimate block averages of chromium traces in a potentially contaminated region in Switzerland. PMID:25431507

  12. PREDICTION INTERVALS FOR INTEGRALS OF GAUSSIAN RANDOM FIELDS

    PubMed Central

    De Oliveira, Victor; Kone, Bazoumana

    2014-01-01

    Methodology is proposed for the construction of prediction intervals for integrals of Gaussian random fields over bounded regions (called block averages in the geostatistical literature) based on observations at a finite set of sampling locations. Two bootstrap calibration algorithms are proposed, termed indirect and direct, aimed at improving upon plug-in prediction intervals in terms of coverage probability. A simulation study is carried out that illustrates the effectiveness of both procedures, and these procedures are applied to estimate block averages of chromium traces in a potentially contaminated region in Switzerland. PMID:25431507

  13. Mean field theory for scale-free random networks

    NASA Astrophysics Data System (ADS)

    Barabási, Albert-László; Albert, Réka; Jeong, Hawoong

    1999-10-01

    Random networks with complex topology are common in Nature, describing systems as diverse as the world wide web or social and business networks. Recently, it has been demonstrated that most large networks for which topological information is available display scale-free features. Here we study the scaling properties of the recently introduced scale-free model, that can account for the observed power-law distribution of the connectivities. We develop a mean-field method to predict the growth dynamics of the individual vertices, and use this to calculate analytically the connectivity distribution and the scaling exponents. The mean-field method can be used to address the properties of two variants of the scale-free model, that do not display power-law scaling.

  14. Monte Carlo Integration Using Spatial Structure of Markov Random Field

    NASA Astrophysics Data System (ADS)

    Yasuda, Muneki

    2015-03-01

    Monte Carlo integration (MCI) techniques are important in various fields. In this study, a new MCI technique for Markov random fields (MRFs) is proposed. MCI consists of two successive parts: the first involves sampling using a technique such as the Markov chain Monte Carlo method, and the second involves an averaging operation using the obtained sample points. In the averaging operation, a simple sample averaging technique is often employed. The method proposed in this paper improves the averaging operation by addressing the spatial structure of the MRF and is mathematically guaranteed to statistically outperform standard MCI using the simple sample averaging operation. Moreover, the proposed method can be improved in a systematic manner and is numerically verified by numerical simulations using planar Ising models. In the latter part of this paper, the proposed method is applied to the inverse Ising problem and we observe that it outperforms the maximum pseudo-likelihood estimation.

  15. Critical Casimir forces in the presence of random surface fields

    NASA Astrophysics Data System (ADS)

    Maciołek, A.; Vasilyev, O.; Dotsenko, V.; Dietrich, S.

    2015-03-01

    We study critical Casimir forces (CCFs) fC for films of thickness L which in the three-dimensional bulk belong to the Ising universality class and which are exposed to random surface fields (RSFs) on both surfaces. We consider the case in which, in the absence of RSFs, the surfaces of the film belong to the surface universality class of the so-called ordinary transition. We carry out a finite-size scaling analysis and show that for weak disorder, CCFs still exhibit scaling, acquiring a random field scaling variable w that is zero for pure systems. We confirm these analytic predictions by Monte Carlo (MC) simulations. Moreover, our MC data show that fC varies as fC(w →0 ) -fC(w =0 ) ˜w2 . Asymptotically, for large L , w scales as w ˜L-0.26→0 , indicating that this type of disorder is an irrelevant perturbation of the ordinary surface universality class. However, for thin films such that w ≃1 , we find that the presence of RSFs with vanishing mean value increases significantly the strength of CCFs, as compared to systems without them, and it shifts the extremum of the scaling function of fC toward lower temperatures. But fC remains attractive.

  16. Distributed estimation of a parametric field with random sensor placements

    NASA Astrophysics Data System (ADS)

    Alkhweldi, Marwan; Cao, Zhicheng; Schmid, Natalia A.

    2015-05-01

    This paper considers a problem of distributed function estimation in the case when sensor locations are modeled as Gaussian random variables. We consider a scenario where sensors are deployed in clusters with cluster centers known a priori (or estimated by a high performance GPS) and the average quadratic spread of sensors around the cluster center also known. Distributed sensors make noisy observations about an unknown parametric field generated by a physical object of interest (for example, magnetic field generated by a ferrous object and sensed by a network of magnetometers). Each sensor then performs local signal processing of its noisy observation and sends it to a central processor (called fusion center) in the wireless sensor network over parallel channels corrupted by fading and additive noise. The central processor combines the set of received signals to form an estimate of the unknown parametric field. In our numerical analysis, we involve a field shaped as a Gaussian bell. We experiment with the size of sensor clusters and with their number. A mean square error between the estimated parameters of the field and the true parameters used in simulations is involved as a performance measure. It can be shown that a relatively good estimate of the field can be obtained with only a small number of clusters. As the number of clusters increases, the estimation performance steadily improves. The results also indicate that, on the average, the number of clusters has more impact on the performance than the number of sensors per cluster, given the same size of the total network.

  17. Collapse transition of randomly branched polymers: renormalized field theory.

    PubMed

    Janssen, Hans-Karl; Stenull, Olaf

    2011-05-01

    We present a minimal dynamical model for randomly branched isotropic polymers, and we study this model in the framework of renormalized field theory. For the swollen phase, we show that our model provides a route to understand the well-established dimensional-reduction results from a different angle. For the collapse θ transition, we uncover a hidden Becchi-Rouet-Stora supersymmetry, signaling the sole relevance of tree configurations. We correct the long-standing one-loop results for the critical exponents, and we push these results on to two-loop order. For the collapse θ' transition, we find a runaway of the renormalization group flow, which lends credence to the possibility that this transition is a fluctuation-induced first-order transition. Our dynamical model allows us to calculate for the first time the fractal dimension of the shortest path on randomly branched polymers in the swollen phase as well as at the collapse transition and related fractal dimensions. PMID:21728509

  18. New description of charged particle propagation in random magnetic fields

    NASA Technical Reports Server (NTRS)

    Earl, James A.

    1994-01-01

    When charged particles spiral along a large constant magnetic field, their trajectories are scattered by random components that are superposed on the guiding field. In the simplest analysis of this situation, scattering causes the particles to diffuse parallel to the guiding field. At the next level of approximation, moving pulses that correspond to a coherent mode of propagation are present, but they are represented by delta-functions whose infinitely narrow width makes no sense physically and is inconsistent with the finite duration of coherent pulses observed in solar energetic particle events. To derive a more realistic description, the transport problem is formulated in terms of 4 x 4 matrices, which derive from a representation of the particle distribution function in terms of eigenfunctions of the scattering operator, and which lead to useful approximations that give explicit predictions of the detailed evolution not only of the coherent pulses, but also of the diffusive wake. More specifically, the new description embodies a simple convolution of a narrow Gaussian with the solutions above that involve delta-functions, but with a slightly reduced coherent velocity. The validity of these approximations, which can easily be calculated on a desktop computer, has been exhaustively confirmed by comparison with results of Monte Carlo simulations which kept track of 50 million particles and which were carried out on the Maspar computer at Goddard Space Flight Center.

  19. Fuzzy Markov random fields versus chains for multispectral image segmentation.

    PubMed

    Salzenstein, Fabien; Collet, Christophe

    2006-11-01

    This paper deals with a comparison of recent statistical models based on fuzzy Markov random fields and chains for multispectral image segmentation. The fuzzy scheme takes into account discrete and continuous classes which model the imprecision of the hidden data. In this framework, we assume the dependence between bands and we express the general model for the covariance matrix. A fuzzy Markov chain model is developed in an unsupervised way. This method is compared with the fuzzy Markovian field model previously proposed by one of the authors. The segmentation task is processed with Bayesian tools, such as the well-known MPM (Mode of Posterior Marginals) criterion. Our goal is to compare the robustness and rapidity for both methods (fuzzy Markov fields versus fuzzy Markov chains). Indeed, such fuzzy-based procedures seem to be a good answer, e.g., for astronomical observations when the patterns present diffuse structures. Moreover, these approaches allow us to process missing data in one or several spectral bands which correspond to specific situations in astronomy. To validate both models, we perform and compare the segmentation on synthetic images and raw multispectral astronomical data. PMID:17063681

  20. CAUSAL MARKOV RANDOM FIELD FOR BRAIN MR IMAGE SEGMENTATION

    PubMed Central

    Razlighi, Qolamreza R.; Orekhov, Aleksey; Laine, Andrew; Stern, Yaakov

    2013-01-01

    We propose a new Bayesian classifier, based on the recently introduced causal Markov random field (MRF) model, Quadrilateral MRF (QMRF). We use a second order inhomogeneous anisotropic QMRF to model the prior and likelihood probabilities in the maximum a posteriori (MAP) classifier, named here as MAP-QMRF. The joint distribution of QMRF is given in terms of the product of two dimensional clique distributions existing in its neighboring structure. 20 manually labeled human brain MR images are used to train and assess the MAP-QMRF classifier using the jackknife validation method. Comparing the results of the proposed classifier and FreeSurfer on the Dice overlap measure shows an average gain of 1.8%. We have performed a power analysis to demonstrate that this increase in segmentation accuracy substantially reduces the number of samples required to detect a 5% change in volume of a brain region. PMID:23366607

  1. Renormalized field theory of collapsing directed randomly branched polymers.

    PubMed

    Janssen, Hans-Karl; Wevelsiep, Frank; Stenull, Olaf

    2009-10-01

    We present a dynamical field theory for directed randomly branched polymers and in particular their collapse transition. We develop a phenomenological model in the form of a stochastic response functional that allows us to address several interesting problems such as the scaling behavior of the swollen phase and the collapse transition. For the swollen phase, we find that by choosing model parameters appropriately, our stochastic functional reduces to the one describing the relaxation dynamics near the Yang-Lee singularity edge. This corroborates that the scaling behavior of swollen branched polymers is governed by the Yang-Lee universality class as has been known for a long time. The main focus of our paper lies on the collapse transition of directed branched polymers. We show to arbitrary order in renormalized perturbation theory with epsilon expansion that this transition belongs to the same universality class as directed percolation. PMID:19905335

  2. Multiple testing for neuroimaging via hidden Markov random field.

    PubMed

    Shu, Hai; Nan, Bin; Koeppe, Robert

    2015-09-01

    Traditional voxel-level multiple testing procedures in neuroimaging, mostly p-value based, often ignore the spatial correlations among neighboring voxels and thus suffer from substantial loss of power. We extend the local-significance-index based procedure originally developed for the hidden Markov chain models, which aims to minimize the false nondiscovery rate subject to a constraint on the false discovery rate, to three-dimensional neuroimaging data using a hidden Markov random field model. A generalized expectation-maximization algorithm for maximizing the penalized likelihood is proposed for estimating the model parameters. Extensive simulations show that the proposed approach is more powerful than conventional false discovery rate procedures. We apply the method to the comparison between mild cognitive impairment, a disease status with increased risk of developing Alzheimer's or another dementia, and normal controls in the FDG-PET imaging study of the Alzheimer's Disease Neuroimaging Initiative. PMID:26012881

  3. A Markov random field approach for microstructure synthesis

    NASA Astrophysics Data System (ADS)

    Kumar, A.; Nguyen, L.; DeGraef, M.; Sundararaghavan, V.

    2016-03-01

    We test the notion that many microstructures have an underlying stationary probability distribution. The stationary probability distribution is ubiquitous: we know that different windows taken from a polycrystalline microstructure are generally ‘statistically similar’. To enable computation of such a probability distribution, microstructures are represented in the form of undirected probabilistic graphs called Markov Random Fields (MRFs). In the model, pixels take up integer or vector states and interact with multiple neighbors over a window. Using this lattice structure, algorithms are developed to sample the conditional probability density for the state of each pixel given the known states of its neighboring pixels. The sampling is performed using reference experimental images. 2D microstructures are artificially synthesized using the sampled probabilities. Statistical features such as grain size distribution and autocorrelation functions closely match with those of the experimental images. The mechanical properties of the synthesized microstructures were computed using the finite element method and were also found to match the experimental values.

  4. Conditional Random Fields for Morphological Analysis of Wireless ECG Signals

    PubMed Central

    Natarajan, Annamalai; Gaiser, Edward; Angarita, Gustavo; Malison, Robert; Ganesan, Deepak; Marlin, Benjamin

    2015-01-01

    Thanks to advances in mobile sensing technologies, it has recently become practical to deploy wireless electrocardiograph sensors for continuous recording of ECG signals. This capability has diverse applications in the study of human health and behavior, but to realize its full potential, new computational tools are required to effectively deal with the uncertainty that results from the noisy and highly non-stationary signals collected using these devices. In this work, we present a novel approach to the problem of extracting the morphological structure of ECG signals based on the use of dynamically structured conditional random field (CRF) models. We apply this framework to the problem of extracting morphological structure from wireless ECG sensor data collected in a lab-based study of habituated cocaine users. Our results show that the proposed CRF-based approach significantly out-performs independent prediction models using the same features, as well as a widely cited open source toolkit. PMID:26726321

  5. Multi-illuminant estimation with conditional random fields.

    PubMed

    Beigpour, Shida; Riess, Christian; van de Weijer, Joost; Angelopoulou, Elli

    2014-01-01

    Most existing color constancy algorithms assume uniform illumination. However, in real-world scenes, this is not often the case. Thus, we propose a novel framework for estimating the colors of multiple illuminants and their spatial distribution in the scene. We formulate this problem as an energy minimization task within a conditional random field over a set of local illuminant estimates. In order to quantitatively evaluate the proposed method, we created a novel data set of two-dominant-illuminant images comprised of laboratory, indoor, and outdoor scenes. Unlike prior work, our database includes accurate pixel-wise ground truth illuminant information. The performance of our method is evaluated on multiple data sets. Experimental results show that our framework clearly outperforms single illuminant estimators as well as a recently proposed multi-illuminant estimation approach. PMID:24144663

  6. Mean-Field Theory is Exact for the Random-Field Model with Long-Range Interactions

    NASA Astrophysics Data System (ADS)

    Tsuda, Junichi; Nishimori, Hidetoshi

    2014-07-01

    We study the classical spin model in random fields with long-range interactions and show the exactness of the mean-field theory under certain mild conditions. This is a generalization of the result of Mori for the non-random and spin-glass cases. To treat random fields, we evoke the self-averaging property of a function of random fields, without recourse to the replica method. The result is that the mean-field theory gives the exact expression of the canonical free energy for systems with power-decaying interactions if the power is smaller than or equal to the spatial dimension.

  7. Random fields and the weakly first-order phase transition in superconductors

    SciTech Connect

    Busiello, G.; De Cesare, L.; Uzunov, D.I.

    1986-10-01

    We study the influence of random fields with short-range and long-range correlations on the weakly first-order phase transition in superconductors. Renormalization-group (RG) analysis near the upper critical dimensionality d/sub u/ = 6 (short-range correlations) reveals a new critical behavior which holds if the number of the order-parameter components is n>10. In the long-range case, the RG transformation is self-consistent only if the parameter theta of the long-range correlations is assumed of order epsilon, epsilon = 6-d.

  8. Condensation of helium in aerogel and athermal dynamics of the random-field Ising model.

    PubMed

    Aubry, Geoffroy J; Bonnet, Fabien; Melich, Mathieu; Guyon, Laurent; Spathis, Panayotis; Despetis, Florence; Wolf, Pierre-Etienne

    2014-08-22

    High resolution measurements reveal that condensation isotherms of (4)He in high porosity silica aerogel become discontinuous below a critical temperature. We show that this behavior does not correspond to an equilibrium phase transition modified by the disorder induced by the aerogel structure, but to the disorder-driven critical point predicted for the athermal out-of-equilibrium dynamics of the random-field Ising model. Our results evidence the key role of nonequilibrium effects in the phase transitions of disordered systems. PMID:25192103

  9. Adaptive Thouless-Anderson-Palmer approach to inverse Ising problems with quenched random fields.

    PubMed

    Huang, Haiping; Kabashima, Yoshiyuki

    2013-06-01

    The adaptive Thouless-Anderson-Palmer equation is derived for inverse Ising problems in the presence of quenched random fields. We test the proposed scheme on Sherrington-Kirkpatrick, Hopfield, and random orthogonal models and find that the adaptive Thouless-Anderson-Palmer approach allows accurate inference of quenched random fields whose distribution can be either Gaussian or bimodal. In particular, another competitive method for inferring external fields, namely, the naive mean field method with diagonal weights, is compared and discussed. PMID:23848649

  10. Gaussian conditional random fields for regression in remote sensing

    NASA Astrophysics Data System (ADS)

    Radosavljevic, Vladan

    In recent years many remote sensing instruments of various properties have been employed in an attempt to better characterize important geophysical phenomena. Satellite instruments provide an exceptional opportunity for global long-term observations of the land, the biosphere, the atmosphere, and the oceans. The collected data are used for estimation and better understanding of geophysical parameters such as land cover type, atmospheric properties, or ocean temperature. Achieving accurate estimations of such parameters is an important requirement for development of models able to predict global climate changes. One of the most challenging climate research problems is estimation of global composition, load, and variability of aerosols, small airborne particles that reflect and absorb incoming solar radiation. The existing algorithm for aerosol prediction from satellite observations is deterministic and manually tuned by domain scientist. In contrast to domain-driven method, we show that aerosol prediction is achievable by completely data-driven approaches. These statistical methods consist of learning of nonlinear regression models to predict aerosol load using the satellite observations as inputs. Measurements from unevenly distributed ground-based sites over the world are used as proxy to ground-truth outputs. Although statistical methods achieve better accuracy than deterministic method this setup is appropriate when data are independently and identically distributed (IID). The IID assumption is often violated in remote sensing where data exhibit temporal, spatial, or spatio-temporal dependencies. In such cases, the traditional supervised learning approaches could result in a model with degraded accuracy. Conditional random fields (CRF) are widely used for predicting output variables that have some internal structure. Most of the CRF research has been done on structured classification where the outputs are discrete. We propose a CRF model for continuous outputs

  11. Transverse Field and Random-Field Ising Ferromagnetism in Mn12-acetates

    NASA Astrophysics Data System (ADS)

    Subedi, Pradeep

    2013-03-01

    Single molecule magnets (SMMs) single crystals can exhibit long range ferromagnetic order associated with intermolecular interactions, principally magnetic dipole interactions. With their high spin (S ~ 10) and strong Ising-like magnetic anisotropy, they are model materials to the study of physics associated with Transverse-Field Ising Ferromagnet Model (TFIFM). We have measured magnetic susceptibility of single crystals of the prototype SMM, Mn12-acetate, and of a new high-symmetry variant, Mn12-ac-MeOH. At zero transverse field the inverse susceptibility of both SMMs is found to accurately follow a Curie-Weiss law with an intercept at a non-zero temperature Tcw ~ 0.9 K, indicating a transition to a ferromagnetic phase due to dipolar interactions. With increasing transverse field, the susceptibility and the Curie-Weiss temperature decreases due to increase in spin fluctuations but the nature of the decrease is very different in the two materials. We find that in Mn12-ac-MeOH, the suppression of ferromagnetism by the transverse field is consistent with TFIFM, while the suppression of ferromagnetism by the transverse field is considerably more rapid in Mn12-acetate. Previous studies show that due to solvent disorder Mn12-acetate has an intrinsic distribution of discrete tilts of the molecular magnetic easy axis from the global easy axis of the crystal. Thus with the application of transverse field, the molecules with tilted easy axis experience an additional field along their easy axis and give rise to a distribution of random-fields that further destroys the long-range order, suggesting that this prototypical molecular magnet is a realization of Random-Field Ising Ferromagnet (RFIFM). Work performed in collaboration with: A. D. Kent, Physics Dept., NYU, Bo Wen, M. P. Sarachik, Physics Dept., CCNY, CUNY, Y. Yeshurun, Physics Dept., Bar Ilan U, A. J. Millis, Physics Dept., Columbia U, and G. Christou, Chemistry Dept., U of Florida.

  12. A Markov Random Field Groupwise Registration Framework for Face Recognition

    PubMed Central

    Liao, Shu; Shen, Dinggang; Chung, Albert C.S.

    2014-01-01

    In this paper, we propose a new framework for tackling face recognition problem. The face recognition problem is formulated as groupwise deformable image registration and feature matching problem. The main contributions of the proposed method lie in the following aspects: (1) Each pixel in a facial image is represented by an anatomical signature obtained from its corresponding most salient scale local region determined by the survival exponential entropy (SEE) information theoretic measure. (2) Based on the anatomical signature calculated from each pixel, a novel Markov random field based groupwise registration framework is proposed to formulate the face recognition problem as a feature guided deformable image registration problem. The similarity between different facial images are measured on the nonlinear Riemannian manifold based on the deformable transformations. (3) The proposed method does not suffer from the generalizability problem which exists commonly in learning based algorithms. The proposed method has been extensively evaluated on four publicly available databases: FERET, CAS-PEAL-R1, FRGC ver 2.0, and the LFW. It is also compared with several state-of-the-art face recognition approaches, and experimental results demonstrate that the proposed method consistently achieves the highest recognition rates among all the methods under comparison. PMID:25506109

  13. Biomedical image analysis using Markov random fields & efficient linear programing.

    PubMed

    Komodakis, Nikos; Besbes, Ahmed; Glocker, Ben; Paragios, Nikos

    2009-01-01

    Computer-aided diagnosis through biomedical image analysis is increasingly considered in health sciences. This is due to the progress made on the acquisition side, as well as on the processing one. In vivo visualization of human tissues where one can determine both anatomical and functional information is now possible. The use of these images with efficient intelligent mathematical and processing tools allows the interpretation of the tissues state and facilitates the task of the physicians. Segmentation and registration are the two most fundamental tools in bioimaging. The first aims to provide automatic tools for organ delineation from images, while the second focuses on establishing correspondences between observations inter and intra subject and modalities. In this paper, we present some recent results towards a common formulation addressing these problems, called the Markov Random Fields. Such an approach is modular with respect to the application context, can be easily extended to deal with various modalities, provides guarantees on the optimality properties of the obtained solution and is computationally efficient. PMID:19963682

  14. Conditional random fields for pattern recognition applied to structured data

    SciTech Connect

    Burr, Tom; Skurikhin, Alexei

    2015-07-14

    Pattern recognition uses measurements from an input domain, X, to predict their labels from an output domain, Y. Image analysis is one setting where one might want to infer whether a pixel patch contains an object that is “manmade” (such as a building) or “natural” (such as a tree). Suppose the label for a pixel patch is “manmade”; if the label for a nearby pixel patch is then more likely to be “manmade” there is structure in the output domain that can be exploited to improve pattern recognition performance. Modeling P(X) is difficult because features between parts of the model are often correlated. Therefore, conditional random fields (CRFs) model structured data using the conditional distribution P(Y|X = x), without specifying a model for P(X), and are well suited for applications with dependent features. This paper has two parts. First, we overview CRFs and their application to pattern recognition in structured problems. Our primary examples are image analysis applications in which there is dependence among samples (pixel patches) in the output domain. Second, we identify research topics and present numerical examples.

  15. Conditional random fields for pattern recognition applied to structured data

    DOE PAGESBeta

    Burr, Tom; Skurikhin, Alexei

    2015-07-14

    Pattern recognition uses measurements from an input domain, X, to predict their labels from an output domain, Y. Image analysis is one setting where one might want to infer whether a pixel patch contains an object that is “manmade” (such as a building) or “natural” (such as a tree). Suppose the label for a pixel patch is “manmade”; if the label for a nearby pixel patch is then more likely to be “manmade” there is structure in the output domain that can be exploited to improve pattern recognition performance. Modeling P(X) is difficult because features between parts of the modelmore » are often correlated. Therefore, conditional random fields (CRFs) model structured data using the conditional distribution P(Y|X = x), without specifying a model for P(X), and are well suited for applications with dependent features. This paper has two parts. First, we overview CRFs and their application to pattern recognition in structured problems. Our primary examples are image analysis applications in which there is dependence among samples (pixel patches) in the output domain. Second, we identify research topics and present numerical examples.« less

  16. Infinite hidden conditional random fields for human behavior analysis.

    PubMed

    Bousmalis, Konstantinos; Zafeiriou, Stefanos; Morency, Louis-Philippe; Pantic, Maja

    2013-01-01

    Hidden conditional random fields (HCRFs) are discriminative latent variable models that have been shown to successfully learn the hidden structure of a given classification problem (provided an appropriate validation of the number of hidden states). In this brief, we present the infinite HCRF (iHCRF), which is a nonparametric model based on hierarchical Dirichlet processes and is capable of automatically learning the optimal number of hidden states for a classification task. We show how we learn the model hyperparameters with an effective Markov-chain Monte Carlo sampling technique, and we explain the process that underlines our iHCRF model with the Restaurant Franchise Rating Agencies analogy. We show that the iHCRF is able to converge to a correct number of represented hidden states, and outperforms the best finite HCRFs--chosen via cross-validation--for the difficult tasks of recognizing instances of agreement, disagreement, and pain. Moreover, the iHCRF manages to achieve this performance in significantly less total training, validation, and testing time. PMID:24808217

  17. GAUSSIAN RANDOM FIELD: PHYSICAL ORIGIN OF SERSIC PROFILES

    SciTech Connect

    Cen, Renyue

    2014-08-01

    While the Sersic profile family provides adequate fits for the surface brightness profiles of observed galaxies, its physical origin is unknown. We show that if the cosmological density field is seeded by random Gaussian fluctuations, as in the standard cold dark matter model, galaxies with steep central profiles have simultaneously extended envelopes of shallow profiles in the outskirts, whereas galaxies with shallow central profiles are accompanied by steep density profiles in the outskirts. These properties are in accord with those of the Sersic profile family. Moreover, galaxies with steep central profiles form their central regions in smaller denser subunits that possibly merge subsequently, which naturally leads to the formation of bulges. In contrast, galaxies with shallow central profiles form their central regions in a coherent fashion without significant substructure, a necessary condition for disk galaxy formation. Thus, the scenario is self-consistent with respect to the correlation between observed galaxy morphology and the Sersic index. We further predict that clusters of galaxies should display a similar trend, which should be verifiable observationally.

  18. Revealing giant internal magnetic fields due to spin fluctuations in magnetically doped colloidal nanocrystals.

    PubMed

    Rice, William D; Liu, Wenyong; Baker, Thomas A; Sinitsyn, Nikolai A; Klimov, Victor I; Crooker, Scott A

    2016-02-01

    Strong quantum confinement in semiconductors can compress the wavefunctions of band electrons and holes to nanometre-scale volumes, significantly enhancing interactions between themselves and individual dopants. In magnetically doped semiconductors, where paramagnetic dopants (such as Mn(2+), Co(2+) and so on) couple to band carriers via strong sp-d spin exchange, giant magneto-optical effects can therefore be realized in confined geometries using few or even single impurity spins. Importantly, however, thermodynamic spin fluctuations become increasingly relevant in this few-spin limit. In nanoscale volumes, the statistical fluctuations of N spins are expected to generate giant effective magnetic fields Beff, which should dramatically impact carrier spin dynamics, even in the absence of any applied field. Here we directly and unambiguously reveal the large Beff that exist in Mn(2+)-doped CdSe colloidal nanocrystals using ultrafast optical spectroscopy. At zero applied magnetic field, extremely rapid (300-600 GHz) spin precession of photoinjected electrons is observed, indicating Beff ∼ 15 -30 T for electrons. Precession frequencies exceed 2 THz in applied magnetic fields. These signals arise from electron precession about the random fields due to statistically incomplete cancellation of the embedded Mn(2+) moments, thereby revealing the initial coherent dynamics of magnetic polaron formation, and highlighting the importance of magnetization fluctuations on carrier spin dynamics in nanomaterials. PMID:26595331

  19. Theory and generation of conditional, scalable sub-Gaussian random fields

    NASA Astrophysics Data System (ADS)

    Panzeri, M.; Riva, M.; Guadagnini, A.; Neuman, S. P.

    2016-03-01

    Many earth and environmental (as well as a host of other) variables, Y, and their spatial (or temporal) increments, ΔY, exhibit non-Gaussian statistical scaling. Previously we were able to capture key aspects of such non-Gaussian scaling by treating Y and/or ΔY as sub-Gaussian random fields (or processes). This however left unaddressed the empirical finding that whereas sample frequency distributions of Y tend to display relatively mild non-Gaussian peaks and tails, those of ΔY often reveal peaks that grow sharper and tails that become heavier with decreasing separation distance or lag. Recently we proposed a generalized sub-Gaussian model (GSG) which resolves this apparent inconsistency between the statistical scaling behaviors of observed variables and their increments. We presented an algorithm to generate unconditional random realizations of statistically isotropic or anisotropic GSG functions and illustrated it in two dimensions. Most importantly, we demonstrated the feasibility of estimating all parameters of a GSG model underlying a single realization of Y by analyzing jointly spatial moments of Y data and corresponding increments, ΔY. Here, we extend our GSG model to account for noisy measurements of Y at a discrete set of points in space (or time), present an algorithm to generate conditional realizations of corresponding isotropic or anisotropic random fields, introduce two approximate versions of this algorithm to reduce CPU time, and explore them on one and two-dimensional synthetic test cases.

  20. MRFalign: protein homology detection through alignment of Markov random fields.

    PubMed

    Ma, Jianzhu; Wang, Sheng; Wang, Zhiyong; Xu, Jinbo

    2014-03-01

    Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2-5. PMID:24675572

  1. Understanding earthquake source processes with spatial random field models

    NASA Astrophysics Data System (ADS)

    Song, S.

    2011-12-01

    Earthquake rupture is a complex mechanical process that can be formulated as a dynamically running shear crack on a frictional interface embedded in an elastic continuum. This type of dynamic description of earthquake rupture is often preferred among researchers because they believe the kinematic description is likely to miss physical constraints introduced by dynamic approaches and to lead to arbitrary and nonphysical kinematic fault motions. However, dynamic rupture modeling, although they produce physically consistent models, often uses arbitrary input parameters, e.g., stress and fracture energy, partially because they are more difficult to constrain with data compared to kinematic ones. I propose to describe earthquake rupture as a stochastic model with a set of random variables (e.g., random field) that represent the spatial distribution of kinematic source parameters such as slip, rupture velocity, slip duration and velocity. This is a kinematic description of earthquake rupture in the sense that a model is formulated with kinematic parameters, but since the model can be constrained by both rupture dynamics and data, it may have both physical and observational constraints inside. The stochastic model is formulated by quantifying the 1-point and 2-point statistics of the kinematic parameters. 1-point statistics define a marginal probability density function for a certain source parameter at a given point on a fault. For example, a probability distribution for earthquake slip at a given point can control a possible range of values taken by earthquake slip and their likelihood. In the same way, we can control the existence of supershear rupture with a 1-point variability of the rupture velocity. Two point statistics, i.e. auto- and cross-coherence between source parameters, control the heterogeneity of each source parameter and their coupling, respectively. Several interesting features of earthquake rupture have been found by investigating cross

  2. MAGNETIC FIELD LINE RANDOM WALK IN ISOTROPIC TURBULENCE WITH ZERO MEAN FIELD

    SciTech Connect

    Sonsrettee, W.; Ruffolo, D.; Snodin, A. P.; Wongpan, P.; Subedi, P.; Matthaeus, W. H.; Chuychai, P. E-mail: david.ruf@mahidol.ac.th E-mail: pat.wongpan@postgrad.otago.ac.nz E-mail: prasub@udel.edu

    2015-01-01

    In astrophysical plasmas, magnetic field lines often guide the motions of thermal and non-thermal particles. The field line random walk (FLRW) is typically considered to depend on the Kubo number R = (b/B {sub 0})(ℓ{sub ∥}/ℓ ) for rms magnetic fluctuation b, large-scale mean field B {sub 0}, and parallel and perpendicular coherence scales ℓ{sub ∥} and ℓ , respectively. Here we examine the FLRW when R → ∞ by taking B {sub 0} → 0 for finite b{sub z} (fluctuation component along B {sub 0}), which differs from the well-studied route with b{sub z} = 0 or b{sub z} << B {sub 0} as the turbulence becomes quasi-two-dimensional (quasi-2D). Fluctuations with B {sub 0} = 0 are typically isotropic, which serves as a reasonable model of interstellar turbulence. We use a non-perturbative analytic framework based on Corrsin's hypothesis to determine closed-form solutions for the asymptotic field line diffusion coefficient for three versions of the theory, which are directly related to the k {sup –1} or k {sup –2} moment of the power spectrum. We test these theories by performing computer simulations of the FLRW, obtaining the ratio of diffusion coefficients for two different parameterizations of a field line. Comparing this with theoretical ratios, the random ballistic decorrelation version of the theory agrees well with the simulations. All results exhibit an analog to Bohm diffusion. In the quasi-2D limit, previous works have shown that Corrsin-based theories deviate substantially from simulation results, but here we find that as B {sub 0} → 0, they remain in reasonable agreement. We conclude that their applicability is limited not by large R, but rather by quasi-two-dimensionality.

  3. Magnetic Field Line Random Walk in Isotropic Turbulence with Zero Mean Field

    NASA Astrophysics Data System (ADS)

    Sonsrettee, W.; Subedi, P.; Ruffolo, D.; Matthaeus, W. H.; Snodin, A. P.; Wongpan, P.; Chuychai, P.

    2015-01-01

    In astrophysical plasmas, magnetic field lines often guide the motions of thermal and non-thermal particles. The field line random walk (FLRW) is typically considered to depend on the Kubo number R = (b/B 0)(l∥/l) for rms magnetic fluctuation b, large-scale mean field B 0, and parallel and perpendicular coherence scales l∥ and l, respectively. Here we examine the FLRW when R → ∞ by taking B 0 → 0 for finite bz (fluctuation component along B 0), which differs from the well-studied route with bz = 0 or bz Lt B 0 as the turbulence becomes quasi-two-dimensional (quasi-2D). Fluctuations with B 0 = 0 are typically isotropic, which serves as a reasonable model of interstellar turbulence. We use a non-perturbative analytic framework based on Corrsin's hypothesis to determine closed-form solutions for the asymptotic field line diffusion coefficient for three versions of the theory, which are directly related to the k -1 or k -2 moment of the power spectrum. We test these theories by performing computer simulations of the FLRW, obtaining the ratio of diffusion coefficients for two different parameterizations of a field line. Comparing this with theoretical ratios, the random ballistic decorrelation version of the theory agrees well with the simulations. All results exhibit an analog to Bohm diffusion. In the quasi-2D limit, previous works have shown that Corrsin-based theories deviate substantially from simulation results, but here we find that as B 0 → 0, they remain in reasonable agreement. We conclude that their applicability is limited not by large R, but rather by quasi-two-dimensionality.

  4. Functional Redundancy Patterns Reveal Non-Random Assembly Rules in a Species-Rich Marine Assemblage

    PubMed Central

    Guillemot, Nicolas; Kulbicki, Michel; Chabanet, Pascale; Vigliola, Laurent

    2011-01-01

    The relationship between species and the functional diversity of assemblages is fundamental in ecology because it contains key information on functional redundancy, and functionally redundant ecosystems are thought to be more resilient, resistant and stable. However, this relationship is poorly understood and undocumented for species-rich coastal marine ecosystems. Here, we used underwater visual censuses to examine the patterns of functional redundancy for one of the most diverse vertebrate assemblages, the coral reef fishes of New Caledonia, South Pacific. First, we found that the relationship between functional and species diversity displayed a non-asymptotic power-shaped curve, implying that rare functions and species mainly occur in highly diverse assemblages. Second, we showed that the distribution of species amongst possible functions was significantly different from a random distribution up to a threshold of ∼90 species/transect. Redundancy patterns for each function further revealed that some functions displayed fast rates of increase in redundancy at low species diversity, whereas others were only becoming redundant past a certain threshold. This suggested non-random assembly rules and the existence of some primordial functions that would need to be fulfilled in priority so that coral reef fish assemblages can gain a basic ecological structure. Last, we found little effect of habitat on the shape of the functional-species diversity relationship and on the redundancy of functions, although habitat is known to largely determine assemblage characteristics such as species composition, biomass, and abundance. Our study shows that low functional redundancy is characteristic of this highly diverse fish assemblage, and, therefore, that even species-rich ecosystems such as coral reefs may be vulnerable to the removal of a few keystone species. PMID:22039543

  5. Magnetic nanoparticle imaging by random and maximum length sequences of inhomogeneous activation fields.

    PubMed

    Baumgarten, Daniel; Eichardt, Roland; Crevecoeur, Guillaume; Supriyanto, Eko; Haueisen, Jens

    2013-01-01

    Biomedical applications of magnetic nanoparticles require a precise knowledge of their biodistribution. From multi-channel magnetorelaxometry measurements, this distribution can be determined by means of inverse methods. It was recently shown that the combination of sequential inhomogeneous excitation fields in these measurements is favorable regarding the reconstruction accuracy when compared to homogeneous activation . In this paper, approaches for the determination of activation sequences for these measurements are investigated. Therefor, consecutive activation of single coils, random activation patterns and families of m-sequences are examined in computer simulations involving a sample measurement setup and compared with respect to the relative condition number of the system matrix. We obtain that the values of this condition number decrease with larger number of measurement samples for all approaches. Random sequences and m-sequences reveal similar results with a significant reduction of the required number of samples. We conclude that the application of pseudo-random sequences for sequential activation in the magnetorelaxometry imaging of magnetic nanoparticles considerably reduces the number of required sequences while preserving the relevant measurement information. PMID:24110423

  6. The mean field theory in EM procedures for blind Markov random field image restoration.

    PubMed

    Zhang, J

    1993-01-01

    A Markov random field (MRF) model-based EM (expectation-maximization) procedure for simultaneously estimating the degradation model and restoring the image is described. The MRF is a coupled one which provides continuity (inside regions of smooth gray tones) and discontinuity (at region boundaries) constraints for the restoration problem which is, in general, ill posed. The computational difficulty associated with the EM procedure for MRFs is resolved by using the mean field theory from statistical mechanics. An orthonormal blur decomposition is used to reduce the chances of undesirable locally optimal estimates. Experimental results on synthetic and real-world images show that this approach provides good blur estimates and restored images. The restored images are comparable to those obtained by a Wiener filter in mean-square error, but are most visually pleasing. PMID:18296192

  7. One-dimensional random field Ising model and discrete stochastic mappings

    SciTech Connect

    Behn, U.; Zagrebnov, V.A.

    1987-06-01

    Previous results relating the one-dimensional random field Ising model to a discrete stochastic mapping are generalized to a two-valued correlated random (Markovian) field and to the case of zero temperature. The fractal dimension of the support of the invariant measure is calculated in a simple approximation and its dependence on the physical parameters is discussed.

  8. Compliant random fields in gels formed from side-chain liquid crystalline polymers

    NASA Astrophysics Data System (ADS)

    Goldbart, Paul; Ye, Fangfu; Lu, Bing; Xing, Xiangjun

    2013-03-01

    Localized polymer-chain backbones in gels formed from side-chain liquid crystalline polymers serve to create random fields that induce local orientational order of the nematogenic pendants of the side chains. These random fields differ, however, from conventional ones, in that they are compliant, and thus themselves undergo thermal fluctuations. We develop a free energy that describes local nematic ordering in presence of such compliant random fields. In particular, we show that, as a result of this compliance, the free energy has a qualitatively new structure, unattainable via truly static random fields. We discuss the physical implications this free energy, focusing on the consequences of the compliant nature of the random fields.

  9. Random field disorder and charge order driven quantum oscillations in cuprates

    NASA Astrophysics Data System (ADS)

    Russo, Antonio; Chakravarty, Sudip

    In the pseudogap regime of the cuprates, charge order breaks a ℤ2 symmetry. Therefore, the interaction of charge order and quenched disorder due to potential scattering, can, in principle, be treated as a random field Ising model. A numerical analysis of the ground state of such a random field Ising model reveals local, glassy dynamics in both 2 D and 3 D . The glassy dynamics are treated as a heat bath which couple to the itinerant electrons, leading to an unusual electronic non-Fermi liquid. If the dynamics are strong enough, the electron spectral function has no quasiparticle peak and the effective mass diverges at the Fermi surface, precluding quantum oscillations. In contrast to charge density, d-density wave order (reflecting staggered circulating currents) does not directly couple to potential disorder, allowing it to support quantum oscillations. At fourth order in Landau theory, there is a term consisting of the square of the d-density wave order parameter, and the square of the charge order. This coupling could induce parasitic charge order, which may be weak enough for the Fermi liquid behavior to remain uncorrupted. Here, we argue that this distinction must be made clear, as one interprets quantum oscillations in cuprates.

  10. Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models.

    PubMed

    Wang, Hongyan; Zhou, Xiaobo

    2013-04-01

    By altering the electrostatic charge of histones or providing binding sites to protein recognition molecules, Chromatin marks have been proposed to regulate gene expression, a property that has motivated researchers to link these marks to cis-regulatory elements. With the help of next generation sequencing technologies, we can now correlate one specific chromatin mark with regulatory elements (e.g. enhancers or promoters) and also build tools, such as hidden Markov models, to gain insight into mark combinations. However, hidden Markov models have limitation for their character of generative models and assume that a current observation depends only on a current hidden state in the chain. Here, we employed two graphical probabilistic models, namely the linear conditional random field model and multivariate hidden Markov model, to mark gene regions with different states based on recurrent and spatially coherent character of these eight marks. Both models revealed chromatin states that may correspond to enhancers and promoters, transcribed regions, transcriptional elongation, and low-signal regions. We also found that the linear conditional random field model was more effective than the hidden Markov model in recognizing regulatory elements, such as promoter-, enhancer-, and transcriptional elongation-associated regions, which gives us a better choice. PMID:23237214

  11. Random field disorder and charge order driven quantum oscillations in cuprates

    NASA Astrophysics Data System (ADS)

    Russo, Antonio; Chakravarty, Sudip

    2016-03-01

    In the pseudogap regime of the cuprates, a period-2 charge order breaks a Z2 symmetry, reflecting a broken translational symmetry. Therefore, the interaction of charge order and quenched disorder due to potential scattering, can, in principle, be treated as a random field Ising model. A numerical analysis of the ground state of such a random field Ising model reveals local, glassy dynamics in both two and three dimensions. The dynamics are treated in the glassy limit as a heat bath which couples to the itinerant electrons, leading to an unusual electronic non-Fermi-liquid. If the dynamics are strong enough, the electron spectral function has no quasiparticle peak and the effective mass diverges at the Fermi surface, precluding quantum oscillations. In contrast to charge density, d -density wave order (reflecting staggered circulating currents) does not directly couple to potential disorder, allowing it to support quantum oscillations. At fourth order in Landau theory, there is a term consisting of the square of the d -density wave order parameter, and the square of the charge order. This coupling could induce parasitic charge order, which may be weak enough for the Fermi liquid behavior to remain uncorrupted. Here, we argue that this distinction must be made clear, as one interprets quantum oscillations in cuprates.

  12. Magnetic Field Line Random Walk in Isotropic Turbulence with Varying Mean Field

    NASA Astrophysics Data System (ADS)

    Sonsrettee, W.; Subedi, P.; Ruffolo, D.; Matthaeus, W. H.; Snodin, A. P.; Wongpan, P.; Chuychai, P.; Rowlands, G.; Vyas, S.

    2016-08-01

    In astrophysical plasmas, the magnetic field line random walk (FLRW) plays an important role in guiding particle transport. The FLRW behavior is scaled by the Kubo number R=(b/{B}0)({{\\ell }}\\parallel /{{\\ell }}\\perp ) for rms magnetic fluctuation b, large-scale mean field {{\\boldsymbol{B}}}0, and coherence scales parallel ({{\\ell }}\\parallel ) and perpendicular ({{\\ell }}\\perp ) to {{\\boldsymbol{B}}}0. Here we use a nonperturbative analytic framework based on Corrsin’s hypothesis, together with direct computer simulations, to examine the R-scaling of the FLRW for varying B 0 with finite b and isotropic fluctuations with {{\\ell }}\\parallel /{{\\ell }}\\perp =1, instead of the well-studied route of varying {{\\ell }}\\parallel /{{\\ell }}\\perp for b \\ll {B}0. The FLRW for isotropic magnetic fluctuations is also of astrophysical interest regarding transport processes in the interstellar medium. With a mean field, fluctuations may have variance anisotropy, so we consider limiting cases of isotropic variance and transverse variance (with b z = 0). We obtain analytic theories, and closed-form solutions for extreme cases. Padé approximants are provided to interpolate all versions of theory and simulations to any B 0. We demonstrate that, for isotropic turbulence, Corrsin-based theories generally work well, and with increasing R there is a transition from quasilinear to Bohm diffusion. This holds even with b z = 0, when different routes to R\\to ∞ are mathematically equivalent; in contrast with previous studies, we find that a Corrsin-based theory with random ballistic decorrelation works well even up to R = 400, where the effects of trapping are barely perceptible in simulation results.

  13. Field assisted spin switching in magnetic random access memory

    NASA Astrophysics Data System (ADS)

    Jeong, W. C.; Park, J. H.; Oh, J. H.; Koh, G. H.; Jeong, G. T.; Jeong, H. S.; Kim, Kinam

    2006-04-01

    A switching method called by field assisted spin switching has been investigated. A field assisted spin switching consists of a metal line induced magnetic field and a spin switching through a magnetic tunnel junction. It is a variation of a current induced switching and assisted by the magnetic field induced by the current-carrying metal line. Various current paths have been tested to investigate how and how much the spin switching contributes to the overall switching and the results will be explained. A computer simulation has been complemented to measure the degree of the thermal effect in the switching.

  14. Spectral expansions of homogeneous and isotropic tensor-valued random fields

    NASA Astrophysics Data System (ADS)

    Malyarenko, Anatoliy; Ostoja-Starzewski, Martin

    2016-06-01

    We establish spectral expansions of tensor-valued homogeneous and isotropic random fields in terms of stochastic integrals with respect to orthogonal scattered random measures previously known only for the case of tensor rank 0. The fields under consideration take values in the 3-dimensional Euclidean space {E^3} and in the space {S^2(E^3)} of symmetric rank 2 tensors over {E^3}. We find a link between the theory of random fields and the theory of finite-dimensional convex compact sets. These random fields furnish stepping-stone for models of rank 1 and rank 2 tensor-valued fields in continuum physics, such as displacement, velocity, stress, strain, providing appropriate conditions (such as the governing equation or positive-definiteness) are imposed.

  15. Development of a Random Field Model for Gas Plume Detection in Multiple LWIR Images.

    SciTech Connect

    Heasler, Patrick G.

    2008-09-30

    This report develops a random field model that describes gas plumes in LWIR remote sensing images. The random field model serves as a prior distribution that can be combined with LWIR data to produce a posterior that determines the probability that a gas plume exists in the scene and also maps the most probable location of any plume. The random field model is intended to work with a single pixel regression estimator--a regression model that estimates gas concentration on an individual pixel basis.

  16. Modulation of electromagnetic fields by a depolarizer of random polarizer array.

    PubMed

    Ma, Ning; Hanson, Steen G; Wang, Wei

    2016-05-01

    The statistical properties of the electric fields with random changes of the polarization state in space generated by a depolarizer are investigated on the basis of the coherence matrix. The depolarizer is a polarizer array composed of a multitude of contiguous square cells of polarizers with randomly distributed polarization angles, where the incident fields experience a random polarization modulation after passing through the depolarizer. The propagation of the modulated electric fields through any quadratic optical system is examined within the framework of the complex ABCD matrix to show how the degree of coherence and the degree of polarization change on propagation. PMID:27128058

  17. Charged Particle Diffusion in Isotropic Random Static Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Subedi, P.; Sonsrettee, W.; Matthaeus, W. H.; Ruffolo, D. J.; Wan, M.; Montgomery, D.

    2013-12-01

    Study of the transport and diffusion of charged particles in a turbulent magnetic field remains a subject of considerable interest. Research has most frequently concentrated on determining the diffusion coefficient in the presence of a mean magnetic field. Here we consider Diffusion of charged particles in fully three dimensional statistically isotropic magnetic field turbulence with no mean field which is pertinent to many astrophysical situations. We classify different regions of particle energy depending upon the ratio of Larmor radius of the charged particle to the characteristic outer length scale of turbulence. We propose three different theoretical models to calculate the diffusion coefficient each applicable to a distinct range of particle energies. The theoretical results are compared with those from computer simulations, showing very good agreement.

  18. Detection and inpainting of facial wrinkles using texture orientation fields and Markov random field modeling.

    PubMed

    Batool, Nazre; Chellappa, Rama

    2014-09-01

    Facial retouching is widely used in media and entertainment industry. Professional software usually require a minimum level of user expertise to achieve the desirable results. In this paper, we present an algorithm to detect facial wrinkles/imperfection. We believe that any such algorithm would be amenable to facial retouching applications. The detection of wrinkles/imperfections can allow these skin features to be processed differently than the surrounding skin without much user interaction. For detection, Gabor filter responses along with texture orientation field are used as image features. A bimodal Gaussian mixture model (GMM) represents distributions of Gabor features of normal skin versus skin imperfections. Then, a Markov random field model is used to incorporate the spatial relationships among neighboring pixels for their GMM distributions and texture orientations. An expectation-maximization algorithm then classifies skin versus skin wrinkles/imperfections. Once detected automatically, wrinkles/imperfections are removed completely instead of being blended or blurred. We propose an exemplar-based constrained texture synthesis algorithm to inpaint irregularly shaped gaps left by the removal of detected wrinkles/imperfections. We present results conducted on images downloaded from the Internet to show the efficacy of our algorithms. PMID:24968171

  19. Nonstationary elementary-field light randomly triggered by Poisson impulses.

    PubMed

    Fernández-Pousa, Carlos R

    2013-05-01

    A stochastic theory of nonstationary light describing the random emission of elementary pulses is presented. The emission is governed by a nonhomogeneous Poisson point process determined by a time-varying emission rate. The model describes, in the appropriate limits, stationary, cyclostationary, locally stationary, and pulsed radiation, and reduces to a Gaussian theory in the limit of dense emission rate. The first- and second-order coherence theories are solved after the computation of second- and fourth-order correlation functions by use of the characteristic function. The ergodicity of second-order correlations under various types of detectors is explored and a number of observables, including optical spectrum, amplitude, and intensity correlations, are analyzed. PMID:23695325

  20. Mean-field magnetohydrodynamics associated with random Alfven waves in a plasma with weak magnetic diffusion

    NASA Astrophysics Data System (ADS)

    Hamabata, Hiromitsu; Namikawa, Tomikazu

    1988-02-01

    Using first-order smoothing theory, Fourier analysis and perturbation methods, a new equation is derived governing the evolution of the spectrum tensor (including the energy and helicity spectrum functions) of the random velocity field as well as the ponderomotive and mean electromotive forces generated by random Alfven waves in a plasma with weak magnetic diffusion. The ponderomotive and mean electromotive forces are expressed as series involving spatial derivatives of mean magnetic and velocity fields whose coefficients are associated with the helicity spectrum function of the random velocity field. The effect of microscale random Alfven waves, through ponderomotive and mean electromotive forces generated by them, on the propagation of large-scale Alfven waves is also investigated by solving the mean-field equations, including the transport equation of the helicity spectrum function.

  1. Phase diagram of the random-field Ising system Fe{sub 0.60}Zn{sub 0.40}F{sub 2} at intense fields

    SciTech Connect

    Montenegro, F.C.; Lima, K.A.; Torikachvili, M.S.; Lacerda, A.H.

    1997-10-01

    The critical and irreversibility phase boundaries of the d = 3 diluted uniaxial antiferromagnet Fe{sub 0.60}Zn{sub 0.40}F{sub 2} have been determined under strong external magnetic fields by means of magnetization measurements. The data reveal that the random-field-induced glassy phase, previously observed in the upper part of the (H,T) phase diagram for highly diluted samples (x {approx_equal} 0.3), is extended to higher values of x.

  2. Long term field evaluation reveals HLB resistance in Citrus relatives

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Citrus huanglongbing (HLB) is a destructive disease with no known cure. To identify sources of HLB resistance in the subfamily Aurantioideae to which citrus belongs, we conducted a six-year field trial under natural disease challenge conditions in an HLB endemic region. The study included 65 Citrus ...

  3. Binary 3-D Markov Chain Random Fields: Finite-size Scaling Analysis of Percolation Properties

    NASA Astrophysics Data System (ADS)

    Harter, T.

    2004-12-01

    Percolation phenomena in random media have been extensively studied in a wide variety of fields in physics, chemistry, engineering, bio-, earth-, and environmental sciences. Most work has focused on uncorrelated random fields. The critical behavior in media with short-range correlations is thought to be identical to that in uncorrelated systems. However, the percolation threshold, pc, which is 0.3116 in uncorrelated media, has been observed to vary with the correlation scale and also with the random field type. Here, we present percolation properties and finite-size scaling effects in three-dimensional binary cubic lattices represented by correlated Markov-chain random fields and compare them to those in sequential Gaussian and sequential indicator random fields. We find that the computed percolation threshold in correlated random fields is significantly lower than in the uncorrelated lattice and decreases with increasing correlation scale. The rate of decrease rapidly flattens out for correlation lengths larger than 2-3 grid-blocks. At correlation scales of 5-6 grid blocks, pc is found to be 0.126 for the Markov chain random fields and slightly higher for sequential Gaussian and indicator random fields. The universal scaling constants for mean cluster size, backbone fraction, and connectivity are found to be consistent with results on uncorrelated lattices. For numerical studies, it is critical to understand finite-size effects on the percolation and associated phase connectivity properties of lattices. We present detailed statistical results on the percolation properties in finite sized lattice and their dependence on correlation scale. We show that appropriate grid resolution and choice of simulation boundaries is critical to properly simulate correlated natural geologic systems, which may display significant finite-size effects.

  4. Cauchy-Laguerre Two-Matrix Model and the Meijer-G Random Point Field

    NASA Astrophysics Data System (ADS)

    Bertola, M.; Gekhtman, M.; Szmigielski, J.

    2014-02-01

    We apply the general theory of Cauchy biorthogonal polynomials developed in Bertola et al. (Commun Math Phys 287(3):983-1014, 2009) and Bertola et al. (J Approx Th 162(4):832-867, 2010) to the case associated with Laguerre measures. In particular, we obtain explicit formulae in terms of Meijer-G functions for all key objects relevant to the study of the corresponding biorthogonal polynomials and the Cauchy two-matrix model associated with them. The central theorem we prove is that a scaling limit of the correlation functions for eigenvalues near the origin exists, and is given by a new determinantal two-level random point field, the Meijer-G random field. We conjecture that this random point field leads to a novel universality class of random fields parametrized by exponents of Laguerre weights. We express the joint distributions of the smallest eigenvalues in terms of suitable Fredholm determinants and evaluate them numerically. We also show that in a suitable limit, the Meijer-G random field converges to the Bessel random field and hence the behavior of the eigenvalues of one of the two matrices converges to the one of the Laguerre ensemble.

  5. Effect of random field disorder on the first order transition in p-spin interaction model

    NASA Astrophysics Data System (ADS)

    Sumedha; Singh, Sushant K.

    2016-01-01

    We study the random field p-spin model with Ising spins on a fully connected graph using the theory of large deviations in this paper. This is a good model to study the effect of quenched random field on systems which have a sharp first order transition in the pure state. For p = 2, the phase-diagram of the model, for bimodal distribution of the random field, has been well studied and is known to undergo a continuous transition for lower values of the random field (h) and a first order transition beyond a threshold, htp(≈ 0.439) . We find the phase diagram of the model, for all p ≥ 2, with bimodal random field distribution, using large deviation techniques. We also look at the fluctuations in the system by calculating the magnetic susceptibility. For p = 2, beyond the tricritical point in the regime of first order transition, we find that for htp < h < 0.447, magnetic susceptibility increases rapidly (even though it never diverges) as one approaches the transition from the high temperature side. On the other hand, for 0.447 < h ≤ 0.5, the high temperature behaviour is well described by the Curie-Weiss law. For all p ≥ 2, we find that for larger magnitudes of the random field (h >ho = 1 / p!), the system does not show ferromagnetic order even at zero temperature. We find that the magnetic susceptibility for p ≥ 3 is discontinuous at the transition point for h

  6. Synchronization in the random-field Kuramoto model on complex networks

    NASA Astrophysics Data System (ADS)

    Lopes, M. A.; Lopes, E. M.; Yoon, S.; Mendes, J. F. F.; Goltsev, A. V.

    2016-07-01

    We study the impact of random pinning fields on the emergence of synchrony in the Kuramoto model on complete graphs and uncorrelated random complex networks. We consider random fields with uniformly distributed directions and homogeneous and heterogeneous (Gaussian) field magnitude distribution. In our analysis, we apply the Ott-Antonsen method and the annealed-network approximation to find the critical behavior of the order parameter. In the case of homogeneous fields, we find a tricritical point above which a second-order phase transition gives place to a first-order phase transition when the network is either fully connected or scale-free with the degree exponent γ >5 . Interestingly, for scale-free networks with 2 <γ ≤5 , the phase transition is of second-order at any field magnitude, except for degree distributions with γ =3 when the transition is of infinite order at Kc=0 independent of the random fields. Contrary to the Ising model, even strong Gaussian random fields do not suppress the second-order phase transition in both complete graphs and scale-free networks, although the fields increase the critical coupling for γ >3 . Our simulations support these analytical results.

  7. Synchronization in the random-field Kuramoto model on complex networks.

    PubMed

    Lopes, M A; Lopes, E M; Yoon, S; Mendes, J F F; Goltsev, A V

    2016-07-01

    We study the impact of random pinning fields on the emergence of synchrony in the Kuramoto model on complete graphs and uncorrelated random complex networks. We consider random fields with uniformly distributed directions and homogeneous and heterogeneous (Gaussian) field magnitude distribution. In our analysis, we apply the Ott-Antonsen method and the annealed-network approximation to find the critical behavior of the order parameter. In the case of homogeneous fields, we find a tricritical point above which a second-order phase transition gives place to a first-order phase transition when the network is either fully connected or scale-free with the degree exponent γ>5. Interestingly, for scale-free networks with 2<γ≤5, the phase transition is of second-order at any field magnitude, except for degree distributions with γ=3 when the transition is of infinite order at K_{c}=0 independent of the random fields. Contrary to the Ising model, even strong Gaussian random fields do not suppress the second-order phase transition in both complete graphs and scale-free networks, although the fields increase the critical coupling for γ>3. Our simulations support these analytical results. PMID:27575149

  8. [Randomized field study of the etiology of strabismus concomitans].

    PubMed

    Aichmair, H; Grossmann, W; Aichmair, M; Bomze, I; Fröschl, K; Futschik, A; Theyer, I; Hirmann, E; Kautzky, I; Hafner, J

    1992-01-01

    After an introduction to the problems of binocular vision and an overview of the literature, the authors report on the reasons for undertaking this study and on its practical implications. Up to now, no other randomized study has been undertaken to our knowledge on children of this age group in such a large city as Vienna. All children in primary 3 classes in 20 out of the 256 elementary schools were examined ophthalmologically and orthoptically. It was found that hereditary factors are of statistically significant importance. Especially important for the ophthalmologist is also the statistically significant relation between the diagnosis poor range of fusion, poor fixation, incorrect Worth test for distance and/or proximity, and poor or lacking stereoscopic vision with the occurrence of strabism. The authors were astonished to find a remarkably high percentage of exophoria (58%), in contrast to esophoria (16%). It is interesting for prophylaxis and therapy that children originating from families where spectacles are worn, acted more cooperatively and tended to take the orders of the physician more seriously than those coming from families without eye problems. The promotion of genetic research related to squint and more counselling for couples wishing to have children or confronted with risk factor problems would be desirable, as well as the inclusion of more obligatory ophthalmological examinations in the mother-child medical "passport". PMID:1441555

  9. Structural aspects of antibody-antigen interaction revealed through small random peptide libraries.

    PubMed

    Slootstra, J W; Puijk, W C; Ligtvoet, G J; Langeveld, J P; Meloen, R H

    1996-02-01

    Two small random peptide libraries, one composed of 4550 dodecapeptides and one of 8000 tripeptides, were synthesized in newly developed credit-card format miniPEPSCAN cards (miniPEPSCAN libraries). Each peptide was synthesized in a discrete well (455 peptides/card). The two miniPEPSCAN libraries were screened with three different monoclonal antibodies (Mabs). Two other random peptide libraries, expressed on the wall of bacteria (recombinant libraries) and composed of 10(7) hexa- and octapeptides, were screened with the same three Mabs. The aim of this study was to compare the amino acid sequence of peptides selected from small and large pools of random peptides and, in this way, investigate the potential of small random peptide libraries. The screening of the two miniPEPSCAN libraries resulted in the identification of a surprisingly large number of antibody-binding peptides, while the screening of the large recombinant libraries, using the same Mabs, resulted in the identification of only a small number of peptides. The large number of peptides derived from the small random peptide libraries allowed the determination of consensus sequences. These consensus sequences could be related to small linear and nonlinear parts of the respective epitopes. The small number of peptides derived from the large random peptide libraries could only be related to linear epitopes that were previously mapped using small libraries of overlapping peptides covering the antigenic protein. Thus, with respect to the cost and speed of identifying peptides that resemble linear and nonlinear parts of epitopes, small diversity libraries based on synthetic peptides appear to be superior to large diversity libraries based on expression systems. PMID:9237197

  10. Random walk study of electron motion in helium in crossed electromagnetic fields

    NASA Technical Reports Server (NTRS)

    Englert, G. W.

    1972-01-01

    Random walk theory, previously adapted to electron motion in the presence of an electric field, is extended to include a transverse magnetic field. In principle, the random walk approach avoids mathematical complexity and concomitant simplifying assumptions and permits determination of energy distributions and transport coefficients within the accuracy of available collisional cross section data. Application is made to a weakly ionized helium gas. Time of relaxation of electron energy distribution, determined by the random walk, is described by simple expressions based on energy exchange between the electron and an effective electric field. The restrictive effect of the magnetic field on electron motion, which increases the required number of collisions per walk to reach a terminal steady state condition, as well as the effect of the magnetic field on electron transport coefficients and mean energy can be quite adequately described by expressions involving only the Hall parameter.

  11. Tuning of random lasers by means of external magnetic fields based on the Voigt effect

    NASA Astrophysics Data System (ADS)

    Ghasempour Ardakani, Abbas; Mahdavi, Seyed Mohammad; Bahrampour, Ali Reza

    2013-04-01

    It has been proposed that emission spectrum of random lasers with magnetically active semiconductor constituents can be made tunable by external magnetic fields. By employing the FDTD method, the spectral intensity and spatial distribution of electric field are calculated in the presence of an external magnetic field. It is numerically shown that due to the magneto-optical Voigt effect, the emission spectrum of a semiconductor-based random laser can be made tunable by adjusting the external magnetic field. The effect of magnetic field on the localization length of the laser modes is investigated. It is also shown that the spatial distribution of electric field exhibited remarkable modification with variation of magnetic field.

  12. Magnetite reveals ambient field strength at low temperatures

    NASA Astrophysics Data System (ADS)

    Smirnov, Alexei V.; Tarduno, John A.

    Magnetite (Fe3O4) is the most important and oldest known magnetic mineral on Earth (Figure l). We have come a long way from the magnetite loadstone compasses of ancient China; magnetite and titanomagnetite have been established as the principal carriers of geologically important remanent magnetizations in rocks, the study of which led to the plate tectonic paradigm. We now recognize that magnetite plays an important role in the biosphere. Some organisms contain intra-cellular particles of Fe3O4 that they use for spatial orientation and navigation. When preserved in rocks, these particles—called "magnetofossils"— can provide important insight into the origin and development of life here, and perhaps, on other planets [e.g., Thomas-Keprta et al., 2000]. Magnetite is now used in the medical field and in nanotechnology research. Nanoparticles of magnetite are used as a contrasting agent in magnetic resonance imaging and are being developed to deliver site-specific drugs for the treatment of cancer [Alexiou et al., 2000]. Such applications add to a long list of industrial uses of magnetite that range from magnetic ink to magnetic recording media.

  13. Solution NMR of MPS-1 reveals a random coil cytosolic domain structure.

    PubMed

    Li, Pan; Shi, Pan; Lai, Chaohua; Li, Juan; Zheng, Yuanyuan; Xiong, Ying; Zhang, Longhua; Tian, Changlin

    2014-01-01

    Caenorhabditis elegans MPS1 is a single transmembrane helical auxiliary subunit that co-localizes with the voltage-gated potassium channel KVS1 in the nematode nervous system. MPS-1 shares high homology with KCNE (potassium voltage-gated channel subfamily E member) auxiliary subunits, and its cytosolic domain was reported to have a serine/threonine kinase activity that modulates KVS1 channel function via phosphorylation. In this study, NMR spectroscopy indicated that the full length and truncated MPS-1 cytosolic domain (134-256) in the presence or absence of n-dodecylphosphocholine detergent micelles adopted a highly flexible random coil secondary structure. In contrast, protein kinases usually adopt a stable folded conformation in order to implement substrate recognition and phosphoryl transfer. The highly flexible random coil secondary structure suggests that MPS-1 in the free state is unstructured but may require a substrate or binding partner to adopt stable structure required for serine/threonine kinase activity. PMID:25347290

  14. Solution NMR of MPS-1 Reveals a Random Coil Cytosolic Domain Structure

    PubMed Central

    Lai, Chaohua; Li, Juan; Zheng, Yuanyuan; Xiong, Ying; Zhang, Longhua; Tian, Changlin

    2014-01-01

    Caenorhabditis elegans MPS1 is a single transmembrane helical auxiliary subunit that co-localizes with the voltage-gated potassium channel KVS1 in the nematode nervous system. MPS-1 shares high homology with KCNE (potassium voltage-gated channel subfamily E member) auxiliary subunits, and its cytosolic domain was reported to have a serine/threonine kinase activity that modulates KVS1 channel function via phosphorylation. In this study, NMR spectroscopy indicated that the full length and truncated MPS-1 cytosolic domain (134–256) in the presence or absence of n-dodecylphosphocholine detergent micelles adopted a highly flexible random coil secondary structure. In contrast, protein kinases usually adopt a stable folded conformation in order to implement substrate recognition and phosphoryl transfer. The highly flexible random coil secondary structure suggests that MPS-1 in the free state is unstructured but may require a substrate or binding partner to adopt stable structure required for serine/threonine kinase activity. PMID:25347290

  15. Identifying protein interaction subnetworks by a bagging Markov random field-based method

    PubMed Central

    Chen, Li; Xuan, Jianhua; Riggins, Rebecca B.; Wang, Yue; Clarke, Robert

    2013-01-01

    Identification of differentially expressed subnetworks from protein–protein interaction (PPI) networks has become increasingly important to our global understanding of the molecular mechanisms that drive cancer. Several methods have been proposed for PPI subnetwork identification, but the dependency among network member genes is not explicitly considered, leaving many important hub genes largely unidentified. We present a new method, based on a bagging Markov random field (BMRF) framework, to improve subnetwork identification for mechanistic studies of breast cancer. The method follows a maximum a posteriori principle to form a novel network score that explicitly considers pairwise gene interactions in PPI networks, and it searches for subnetworks with maximal network scores. To improve their robustness across data sets, a bagging scheme based on bootstrapping samples is implemented to statistically select high confidence subnetworks. We first compared the BMRF-based method with existing methods on simulation data to demonstrate its improved performance. We then applied our method to breast cancer data to identify PPI subnetworks associated with breast cancer progression and/or tamoxifen resistance. The experimental results show that not only an improved prediction performance can be achieved by the BMRF approach when tested on independent data sets, but biologically meaningful subnetworks can also be revealed that are relevant to breast cancer and tamoxifen resistance. PMID:23161673

  16. Markov random field restoration of point correspondences for active shape modeling

    NASA Astrophysics Data System (ADS)

    Hilger, Klaus B.; Paulsen, Rasmus R.; Larsen, Rasmus

    2004-05-01

    In this paper it is described how to build a statistical shape model using a training set with a sparse of landmarks. A well defined model mesh is selected and fitted to all shapes in the training set using thin plate spline warping. This is followed by a projection of the points of the warped model mesh to the target shapes. When this is done by a nearest neighbour projection it can result in folds and inhomogeneities in the correspondence vector field. The novelty in this paper is the use and extension of a Markov random field regularisation of the correspondence field. The correspondence field is regarded as a collection of random variables, and using the Hammersley-Clifford theorem it is proved that it can be treated as a Markov Random Field. The problem of finding the optimal correspondence field is cast into a Bayesian framework for Markov Random Field restoration, where the prior distribution is a smoothness term and the observation model is the curvature of the shapes. The Markov Random Field is optimised using a combination of Gibbs sampling and the Metropolis-Hasting algorithm. The parameters of the model are found using a leave-one-out approach. The method leads to a generative model that produces highly homogeneous polygonised shapes with improved reconstruction capabilities of the training data. Furthermore, the method leads to an overall reduction in the total variance of the resulting point distribution model. The method is demonstrated on a set of human ear canals extracted from 3D-laser scans.

  17. Dynamics of Crowd Behaviors: From Complex Plane to Quantum Random Fields

    NASA Astrophysics Data System (ADS)

    Ivancevic, Vladimir G.; Reid, Darryn J.

    2015-11-01

    The following sections are included: * Complex Plane Dynamics of Crowds and Groups * Introduction * Complex-Valued Dynamics of Crowd and Group Behaviors * Kähler Geometry of Crowd and Group Dynamics * Computer Simulations of Crowds and Croups Dynamics * Braids of Agents' Behaviors in the Complex Plane * Hilbert-Space Control of Crowds and Groups Dynamics * Quantum Random Fields: A Unique Framework for Simulation, Optimization, Control and Learning * Introduction * Adaptive Quantum Oscillator * Optimization and Learning on Banach and Hilbert Spaces * Appendix * Complex-Valued Image Processing * Linear Integral Equations * Riemann-Liouville Fractional Calculus * Rigorous Geometric Quantization * Supervised Machine-Learning Methods * First-Order Logic and Quantum Random Fields

  18. Object-based Conditional Random Fields for Road Extraction from Remote Sensing Image

    NASA Astrophysics Data System (ADS)

    Huang, Zhijian; Xu, Fanjiang; Lu, Lei; Nie, Hongshan

    2014-03-01

    To make full use of spatially contextual information and topological information in the procedure of Object-based Image Analysis (OBIA), an object-based conditional random field is proposed and used for road extraction. Objects are produced with an initial segmentation, then their neighbours are constructed. Each object is represented by three kinds of features, including the colour, the gradient of histogram and the texture. Formulating the road extraction as a binary classification problem, a Conditional Random Fields model learns and is used for inference. The experimental results demonstrate that the proposed method is effective.

  19. Thermal Non-equilibrium Revealed by Periodic Pulses of Random Amplitudes in Solar Coronal Loops

    NASA Astrophysics Data System (ADS)

    Auchère, F.; Froment, C.; Bocchialini, K.; Buchlin, E.; Solomon, J.

    2016-08-01

    We recently detected variations in extreme ultraviolet intensity in coronal loops repeating with periods of several hours. Models of loops including stratified and quasi-steady heating predict the development of a state of thermal non-equilibrium (TNE): cycles of evaporative upflows at the footpoints followed by falling condensations at the apex. Based on Fourier and wavelet analysis, we demonstrate that the observed periodic signals are indeed not signatures of vibrational modes. Instead, superimposed on the power law expected from the stochastic background emission, the power spectra of the time series exhibit the discrete harmonics and continua expected from periodic trains of pulses of random amplitudes. These characteristics reinforce our earlier interpretation of these pulsations as being aborted TNE cycles.

  20. Field Studies Reveal Strong Postmating Isolation between Ecologically Divergent Butterfly Populations

    PubMed Central

    McBride, Carolyn S.; Singer, Michael C.

    2010-01-01

    Gene flow between populations that are adapting to distinct environments may be restricted if hybrids inherit maladaptive, intermediate phenotypes. This phenomenon, called extrinsic postzygotic isolation (EPI), is thought to play a critical role in the early stages of speciation. However, despite its intuitive appeal, we know surprisingly little about the strength and prevalence of EPI in nature, and even less about the specific phenotypes that tend to cause problems for hybrids. In this study, we searched for EPI among allopatric populations of the butterfly Euphydryas editha that have specialized on alternative host plants. These populations recall a situation thought typical of the very early stages of speciation. They lack consistent host-associated genetic differentiation at random nuclear loci and show no signs of reproductive incompatibility in the laboratory. However, they do differ consistently in diverse host-related traits. For each of these traits, we first asked whether hybrids between populations that use different hosts (different-host hybrids) were intermediate to parental populations and to hybrids between populations that use the same host (same-host hybrids). We then conducted field experiments to estimate the effects of intermediacy on fitness in nature. Our results revealed strong EPI under field conditions. Different-host hybrids exhibited an array of intermediate traits that were significantly maladaptive, including four behaviors. Intermediate foraging height slowed the growth of larvae, while intermediate oviposition preference, oviposition site height, and clutch size severely reduced the growth and survival of the offspring of adult females. We used our empirical data to construct a fitness surface on which different-host hybrids can be seen to fall in an adaptive valley between two peaks occupied by same-host hybrids. These findings demonstrate how ecological selection against hybrids can create a strong barrier to gene flow at the early

  1. Magnetic field line random walk in models and simulations of reduced magnetohydrodynamic turbulence

    SciTech Connect

    Snodin, A. P.; Ruffolo, D.; Oughton, S.; Servidio, S.; Matthaeus, W. H.

    2013-12-10

    The random walk of magnetic field lines is examined numerically and analytically in the context of reduced magnetohydrodynamic (RMHD) turbulence, which provides a useful description of plasmas dominated by a strong mean field, such as in the solar corona. A recently developed non-perturbative theory of magnetic field line diffusion is compared with the diffusion coefficients obtained by accurate numerical tracing of magnetic field lines for both synthetic models and direct numerical simulations of RMHD. Statistical analysis of an ensemble of trajectories confirms the applicability of the theory, which very closely matches the numerical field line diffusion coefficient as a function of distance z along the mean magnetic field for a wide range of the Kubo number R. This theory employs Corrsin's independence hypothesis, sometimes thought to be valid only at low R. However, the results demonstrate that it works well up to R = 10, both for a synthetic RMHD model and an RMHD simulation. The numerical results from the RMHD simulation are compared with and without phase randomization, demonstrating a clear effect of coherent structures on the field line random walk for a very low Kubo number.

  2. A first-order statistical smoothing approximation for the coherent wave field in random porous random media.

    PubMed

    Müller, Tobias M; Gurevich, Boris

    2005-04-01

    An important dissipation mechanism for waves in randomly inhomogeneous poroelastic media is the effect of wave-induced fluid flow. In the framework of Biot's theory of poroelasticity, this mechanism can be understood as scattering from fast into slow compressional waves. To describe this conversion scattering effect in poroelastic random media, the dynamic characteristics of the coherent wavefield using the theory of statistical wave propagation are analyzed. In particular, the method of statistical smoothing is applied to Biot's equations of poroelasticity. Within the accuracy of the first-order statistical smoothing an effective wave number of the coherent field, which accounts for the effect of wave-induced flow, is derived. This wave number is complex and involves an integral over the correlation function of the medium's fluctuations. It is shown that the known one-dimensional (1-D) result can be obtained as a special case of the present 3-D theory. The expression for the effective wave number allows to derive a model for elastic attenuation and dispersion due to wave-induced fluid flow. These wavefield attributes are analyzed in a companion paper. PMID:15898626

  3. Quantification of deterministic matched-field source localization error in the face of random model inputs

    NASA Astrophysics Data System (ADS)

    Daly, Peter M.; Hebenstreit, Gerald T.

    2003-04-01

    Deterministic source localization using matched-field processing (MFP) has yielded good results in propagation scenarios where the nonrandom model parameter input assumption is valid. In many shallow water environments, inputs to acoustic propagation models may be better represented using random distributions rather than fixed quantities. One can estimate the negative effect of random source inputs on deterministic MFP by (1) obtaining a realistic statistical representation of a signal model parameter, then (2) using the mean of the parameter as input to the MFP signal model (the so-called ``replica vector''), (3) synthesizing a source signal using multiple realizations of the random parameter, and (4) estimating the source localization error by correlating the synthesized signal vector with the replica vector over a three dimensional space. This approach allows one to quantify deterministic localization error introduced by random model parameters, including sound velocity profile, hydrophone locations, and sediment thickness and speed. [Work supported by DARPA Advanced Technology Office.

  4. Intraspecific differentiation of Hancornia speciosa revealed by simple sequence repeat and random amplified polymorphic DNA markers.

    PubMed

    Nogueira, C A; Stafuzza, N B; Ribeiro, T P; Prado, A D L; Menezes, I P P; Peixoto, N; Gonçalves, P J; Almeida, L M

    2015-01-01

    Hancornia speciosa, popularly known as mangabeira, is a fruit tree native to the Brazilian Cerrado that shows great economic potential, due to its multiple uses. Intraspecific classification of this species is difficult because it shows high morphological diversity. An early study of the species reported that there are six botanic varieties that differ morphologically mainly in the shapes of their leaves and flowers. Except to note the wide morphological variation and economic potential of this species, few studies have been published about the genetic diversity of mangabeira. Knowledge of the genetic variability of this species among populations would be useful for genetic conservation and breeding programs. Therefore, we tested the transferability of 12 simple sequence repeats from expressed sequence tags (EST-SSRs) from Catharanthus roseus to H. speciosa and used 10 random amplified polymorphic DNA markers to evaluate the genetic variability among botanical varieties of H. speciosa. We obtained a high transferability frequency of EST-SSR markers from C. roseus to H. speciosa (75%). However, EST-SSR markers showed low heterozygosity and locus variability (two or three alleles by locus), which suggest low genetic diversity in the mangabeira samples. The Jaccard dissimilarity index and an examination of geographic distances indicated a non-spatial structuring of the genetic variability. Our markers were unable to distinguish H. speciosa botanical varieties. PMID:26662392

  5. Experimental measurements of topological singularity screening in random paraxial scalar and vector optical fields.

    PubMed

    Egorov, Roman I; Soskin, Marat S; Kessler, David A; Freund, Isaac

    2008-03-14

    There exists a substantial body of theory that predicts mutual screening of signed topological singularities (topological charges) in random optical fields (speckle patterns). Such screening appears to be rather mysterious because there are neither energetic nor entropic reasons for its existence. We present the first experimental confirmation of mutual screening by the stationary points of the intensity, the canonical optical scalar field, and of mutual screening by C points in elliptically polarized light, the generic optical vector field. We also elucidate specific aspects of the geometry and topology of these fields that we argue give rise to screening. PMID:18352186

  6. Phase-space representation and polarization domains of random electromagnetic fields.

    PubMed

    Castaneda, Roman; Betancur, Rafael; Herrera, Jorge; Carrasquilla, Juan

    2008-08-01

    The phase-space representation of stationary random electromagnetic fields is developed by using electromagnetic spatial coherence wavelets. The propagation of the field's power and states of spatial coherence and polarization results from correlations between the components of the field vectors at pairs of points in space. Polarization domains are theoretically predicted as the structure of the field polarization at the observation plane. In addition, the phase-space representation provides a generalization of the Poynting theorem. Theoretical predictions are examined by numerically simulating the Young experiment with electromagnetic waves. The experimental implementation of these results is a current subject of research. PMID:18670539

  7. Theory of weak scattering of stochastic electromagnetic fields from deterministic and random media

    SciTech Connect

    Tong Zhisong; Korotkova, Olga

    2010-09-15

    The theory of scattering of scalar stochastic fields from deterministic and random media is generalized to the electromagnetic domain under the first-order Born approximation. The analysis allows for determining the changes in spectrum, coherence, and polarization of electromagnetic fields produced on their propagation from the source to the scattering volume, interaction with the scatterer, and propagation from the scatterer to the far field. An example of scattering of a field produced by a {delta}-correlated partially polarized source and scattered from a {delta}-correlated medium is provided.

  8. Anisotropic four-state clock model in the presence of random fields

    NASA Astrophysics Data System (ADS)

    Salmon, Octavio D. Rodriguez; Nobre, Fernando D.

    2016-02-01

    A four-state clock ferromagnetic model is studied in the presence of different configurations of anisotropies and random fields. The model is considered in the limit of infinite-range interactions, for which the mean-field approach becomes exact. Both representations of Cartesian spin components and two Ising variables are used, in terms of which the physical properties and phase diagrams are discussed. The random fields follow bimodal probability distributions and the richest criticality is found when the fields, applied in the two Ising systems, are not correlated. The phase diagrams present new interesting topologies, with a wide variety of critical points, which are expected to be useful in describing different complex phenomena.

  9. Sensitivity of Lagrangian coherent structure identification to flow field resolution and random errors

    NASA Astrophysics Data System (ADS)

    Olcay, Ali B.; Pottebaum, Tait S.; Krueger, Paul S.

    2010-03-01

    The effect of spatial and temporal resolutions and random errors on identification of Lagrangian coherent structures (LCSs) from Eulerian velocity fields is evaluated using two canonical flows: a two-dimensional vortex pair and a vortex ring formed by transient ejection of a jet from a tube. The flow field for the vortex pair case was steady and obtained analytically while the transient vortex ring flow was simulated using computational fluid dynamics. To evaluate resolution and random error effects, the flow fields were degraded by locally smoothing the flow and sampling it on a sparser grid to reduce spatial resolution, adding Gaussian distributed random noise to provide random errors, and/or subsampling the time series of vector fields to reduce the temporal resolution (the latter applying only for the vortex ring case). The degradation methods were meant to emulate distortions and errors introduced in common flow measurement methods such as digital particle image velocimetry. Comparing the LCS corresponding to the vortex boundary (separatrix) obtained from the degraded velocity fields with the true separatrix (obtained analytically for the vortex pair case or from high resolution, noise-free velocity fields for the vortex ring case) showed that noise levels as low as 5%-10% of the vortex velocity can cause the separatrix to significantly deviate from its true location in a random fashion, but the "mean" location still remained close to the true location. Temporal and spatial resolution degradations were found to primarily affect transient portions of the flow with strong spatial gradients. Significant deviations in the location of the separatrix were observed even for spatial resolutions as high as 2% of the jet diameter for the vortex ring case.

  10. Spin relaxation of a diffusively moving carrier in a random hyperfine field

    NASA Astrophysics Data System (ADS)

    Roundy, R. C.; Raikh, M. E.

    2014-11-01

    Relaxation, , of the average spin of a carrier in a course of hops over sites hosting random hyperfine fields is studied theoretically. In low dimensions, d =1 ,2 , the decay of average spin with time is nonexponential at all times. The origin of the effect is that for d =1 ,2 a typical random-walk trajectory exhibits numerous self-intersections. Multiple visits of the carrier to the same site accelerates the relaxation since the corresponding partial rotations of spin during these visits add up. Another consequence of self-intersections of the random-walk trajectories is that, in all dimensions, the average, , becomes sensitive to a weak magnetic field directed along z . Our analytical predictions are complemented by the numerical simulations of . The scenario of acceleration of spin relaxation due to returns applies also to the non-Markovian decoherence of a qubit surrounded by multiple fluctuators.

  11. On the unlikeliness of multi-field inflation: bounded random potentials and our vacuum

    SciTech Connect

    Battefeld, Diana; Battefeld, Thorsten; Schulz, Sebastian E-mail: tbattefe@astro.physik.uni-goettingen.de

    2012-06-01

    Based on random matrix theory, we compute the likelihood of saddles and minima in a class of random potentials that are softly bounded from above and below, as required for the validity of low energy effective theories. Imposing this bound leads to a random mass matrix with non-zero mean of its entries. If the dimensionality of field-space is large, inflation is rare, taking place near a saddle point (if at all), since saddles are more likely than minima or maxima for common values of the potential. Due to the boundedness of the potential, the latter become more ubiquitous for rare low/large values respectively. Based on the observation of a positive cosmological constant, we conclude that the dimensionality of field-space after (and most likely during) inflation has to be low if no anthropic arguments are invoked, since the alternative, encountering a metastable deSitter vacuum by chance, is extremely unlikely.

  12. Random Field Driven Spatial Complexity at the Mott Transition in VO2

    NASA Astrophysics Data System (ADS)

    Carlson, Erica; Liu, Shuo; Phillabaum, Benjamin; Dahmen, Karin; Vidhyadhiraja, Narsimhamurthy; Qazilbash, Mumtaz; Basov, Dimitri

    We report the first application of critical cluster techniques to the Mott metal-insulator transition in vanadium dioxide. We show that the geometric properties of the metallic and insulating puddles observed by scanning near-field infrared microscopy are consistent with the system passing near criticality of the random field Ising model as temperature is varied. The resulting large barriers to equilibrium may be the source of the unusually robust hysteresis phenomena associated with the metal-insulator transition in this system.

  13. Application of operator-scaling anisotropic random fields to binary mixtures

    NASA Astrophysics Data System (ADS)

    Anders, Denis; Hoffmann, Alexander; Scheffler, Hans-Peter; Weinberg, Kerstin

    2011-10-01

    In modern technical applications various multiphase mixtures are used to meet demanding mechanical, chemical and electrical requirements. To understand their structural properties as continuous macroscopic materials, it is important to capture the microstructure of these mixtures. Due to their vast range of applications multicomponent systems are subjected to microstructural changes such as phase separation and coarsening. Therefore the ultimate microstructural arrangement depends on the system's configuration and on exterior driving forces. In addition to this, random physical imperfections within the material and random noise in the exterior thermodynamic fields influence in essence the microstructural evolution. Since all physical processes are subjected to a certain degree of random inhomogeneity under realistic conditions, the influence of random phenomena cannot be neglected in modern physical models. An advanced mathematical description and an implementation of these stochastic processes are required to adapt simulation results based on deterministic mathematical models to experimental observations. In our contribution we will present an operator-scaling anisotropic random field embedded in the Cahn-Hilliard phase-field model to describe the phase evolution in a binary mixture. The arising nonlinear diffusion equation will be solved numerically in the innovative framework of the isogeometric finite element method. To illustrate the flexibility and versatility of our approach, numerical and experimental results for a eutectic Sn-Pb alloy are contraposed. This is the first time that the microstructural evolution in a multicomponent system has been associated with operator-scaling anisotropic random fields. Due to its enormous potential as an essential ingredient in stochastic mathematical and physical modeling it is only a matter of time until these processes will become prevalent in engineering applications.

  14. The Role of Treatment Fidelity on Outcomes during a Randomized Field Trial of an Autism Intervention

    ERIC Educational Resources Information Center

    Mandell, David S; Stahmer, Aubyn C; Shin, Sujie; Xie, Ming; Reisinger, Erica; Marcus, Steven C

    2013-01-01

    This randomized field trial comparing Strategies for Teaching based on Autism Research and Structured Teaching enrolled educators in 33 kindergarten-through-second-grade autism support classrooms and 119 students, aged 5-8 years in the School District of Philadelphia. Students were assessed at the beginning and end of the academic year using the…

  15. What Works Clearinghouse Quick Review: "Information and College Access: Evidence from a Randomized Field Experiment"

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2013

    2013-01-01

    "Information and College Access: Evidence From a Randomized Field Experiment" examined the impact of offering an online informational video and financial aid materials to high school students on: (1) their postsecondary aspirations, (2) the accuracy of their understanding of financial aid availability, and (3) the accuracy of their estimates of…

  16. Directed random walks and constraint programming reveal active pathways in hepatocyte growth factor signaling.

    PubMed

    Kittas, Aristotelis; Delobelle, Aurélien; Schmitt, Sabrina; Breuhahn, Kai; Guziolowski, Carito; Grabe, Niels

    2016-01-01

    An effective means to analyze mRNA expression data is to take advantage of established knowledge from pathway databases, using methods such as pathway-enrichment analyses. However, pathway databases are not case-specific and expression data could be used to infer gene-regulation patterns in the context of specific pathways. In addition, canonical pathways may not always describe the signaling mechanisms properly, because interactions can frequently occur between genes in different pathways. Relatively few methods have been proposed to date for generating and analyzing such networks, preserving the causality between gene interactions and reasoning over the qualitative logic of regulatory effects. We present an algorithm (MCWalk) integrated with a logic programming approach, to discover subgraphs in large-scale signaling networks by random walks in a fully automated pipeline. As an exemplary application, we uncover the signal transduction mechanisms in a gene interaction network describing hepatocyte growth factor-stimulated cell migration and proliferation from gene-expression measured with microarray and RT-qPCR using in-house perturbation experiments in a keratinocyte-fibroblast co-culture. The resulting subgraphs illustrate possible associations of hepatocyte growth factor receptor c-Met nodes, differentially expressed genes and cellular states. Using perturbation experiments and Answer Set programming, we are able to select those which are more consistent with the experimental data. We discover key regulator nodes by measuring the frequency with which they are traversed when connecting signaling between receptors and significantly regulated genes and predict their expression-shift consistently with the measured data. The Java implementation of MCWalk is publicly available under the MIT license at: https://bitbucket.org/akittas/biosubg. PMID:26518250

  17. New constraints on modelling the random magnetic field of the MW

    NASA Astrophysics Data System (ADS)

    Beck, Marcus C.; Beck, Alexander M.; Beck, Rainer; Dolag, Klaus; Strong, Andrew W.; Nielaba, Peter

    2016-05-01

    We extend the description of the isotropic and anisotropic random component of the small-scale magnetic field within the existing magnetic field model of the Milky Way from Jansson & Farrar, by including random realizations of the small-scale component. Using a magnetic-field power spectrum with Gaussian random fields, the NE2001 model for the thermal electrons and the Galactic cosmic-ray electron distribution from the current GALPROP model we derive full-sky maps for the total and polarized synchrotron intensity as well as the Faraday rotation-measure distribution. While previous work assumed that small-scale fluctuations average out along the line-of-sight or which only computed ensemble averages of random fields, we show that these fluctuations need to be carefully taken into account. Comparing with observational data we obtain not only good agreement with 408 MHz total and WMAP7 22 GHz polarized intensity emission maps, but also an improved agreement with Galactic foreground rotation-measure maps and power spectra, whose amplitude and shape strongly depend on the parameters of the random field. We demonstrate that a correlation length of 0≈22 pc (05 pc being a 5σ lower limit) is needed to match the slope of the observed power spectrum of Galactic foreground rotation-measure maps. Using multiple realizations allows us also to infer errors on individual observables. We find that previously-used amplitudes for random and anisotropic random magnetic field components need to be rescaled by factors of ≈0.3 and 0.6 to account for the new small-scale contributions. Our model predicts a rotation measure of ‑2.8±7.1 rad/m2 and 04.4±11. rad/m2 for the north and south Galactic poles respectively, in good agreement with observations. Applying our model to deflections of ultra-high-energy cosmic rays we infer a mean deflection of ≈3.5±1.1 degree for 60 EeV protons arriving from CenA.

  18. Multitemporal Crop Type Classification Using Conditional Random Fields and Rapideye Data

    NASA Astrophysics Data System (ADS)

    Hoberg, T.; Müller, S.

    2011-09-01

    The task of crop type classification with multitemporal imagery is nowadays often done applying classifiers that are originally developed for single images like support vector machines (SVM). These approaches do not model temporal dependencies in an explicit way. Existing approaches that make use of temporal dependencies are in most cases quite simple and based on rules. Approaches that integrate temporal dependencies to statistical models are very rare and at an early stage of development. Here our approach CRFmulti, based on conditional random fields (CRF), should make a contribution. Conditional random fields consider context knowledge among neighboring primitives in the same way as Markov random fields (MRF) do. Furthermore conditional random fields handle the feature vectors of the neighboring primitives and not only the class labels. Additional to taking spatial context into account, we present an approach for multitemporal data processing where a temporal association potential has been integrated to the common CRF approach to model temporal dependencies. The classification works on pixel -level using spectral image features, whereas all available single images are taken separately. For our experiments a high resolution RapidEye satellite data set of 2010 consisting of 4 images made during the whole vegetation period from April to October is taken. Six crop type categories are distinguished, namely grassland, corn, winter crop, rapeseed, root crops and other crops. To evaluate the potential of the new conditional random field approach the classification result is compared to a manual reference on pixel- and on object-level. Additional a SVM approach is applied under the same conditions and should serve as a benchmark.

  19. A model of gene expression based on random dynamical systems reveals modularity properties of gene regulatory networks.

    PubMed

    Antoneli, Fernando; Ferreira, Renata C; Briones, Marcelo R S

    2016-06-01

    Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node is modeled by a RDS. The main virtues of this approach are the following: (i) it provides a natural way to obtain arbitrarily large networks by coupling together simple basic pieces, thus revealing the modularity of regulatory networks; (ii) the assumptions about the stochastic processes used in the modeling are fairly general, in the sense that the only requirement is stationarity; (iii) there is a well developed mathematical theory, which is a blend of smooth dynamical systems theory, ergodic theory and stochastic analysis that allows one to extract relevant dynamical and statistical information without solving the system; (iv) one may obtain the classical rate equations form the corresponding stochastic version by averaging the dynamic random variables (small noise limit). It is important to emphasize that unlike the deterministic case, where coupling two equations is a trivial matter, coupling two RDS is non-trivial, specially in our case, where the coupling is performed between a state variable of one gene and the switching stochastic process of another gene and, hence, it is not a priori true that the resulting coupled system will satisfy the definition of a random dynamical system. We shall provide the necessary arguments that ensure that our coupling prescription does indeed furnish a coupled regulatory network of random dynamical systems. Finally, the fact that classical rate equations are the small noise limit of our stochastic model ensures that any validation or prediction made on the basis of the classical theory is also a validation or prediction of our model. We illustrate our framework with some simple examples of single-gene system and network motifs. PMID:27036626

  20. Planetary science. Low-altitude magnetic field measurements by MESSENGER reveal Mercury's ancient crustal field.

    PubMed

    Johnson, Catherine L; Phillips, Roger J; Purucker, Michael E; Anderson, Brian J; Byrne, Paul K; Denevi, Brett W; Feinberg, Joshua M; Hauck, Steven A; Head, James W; Korth, Haje; James, Peter B; Mazarico, Erwan; Neumann, Gregory A; Philpott, Lydia C; Siegler, Matthew A; Tsyganenko, Nikolai A; Solomon, Sean C

    2015-05-22

    Magnetized rocks can record the history of the magnetic field of a planet, a key constraint for understanding its evolution. From orbital vector magnetic field measurements of Mercury taken by the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft at altitudes below 150 kilometers, we have detected remanent magnetization in Mercury's crust. We infer a lower bound on the average age of magnetization of 3.7 to 3.9 billion years. Our findings indicate that a global magnetic field driven by dynamo processes in the fluid outer core operated early in Mercury's history. Ancient field strengths that range from those similar to Mercury's present dipole field to Earth-like values are consistent with the magnetic field observations and with the low iron content of Mercury's crust inferred from MESSENGER elemental composition data. PMID:25953822

  1. Controlling dispersion forces between small particles with artificially created random light fields

    NASA Astrophysics Data System (ADS)

    Brügger, Georges; Froufe-Pérez, Luis S.; Scheffold, Frank; José Sáenz, Juan

    2015-06-01

    Appropriate combinations of laser beams can be used to trap and manipulate small particles with optical tweezers as well as to induce significant optical binding forces between particles. These interaction forces are usually strongly anisotropic depending on the interference landscape of the external fields. This is in contrast with the familiar isotropic, translationally invariant, van der Waals and, in general, Casimir-Lifshitz interactions between neutral bodies arising from random electromagnetic waves generated by equilibrium quantum and thermal fluctuations. Here we show, both theoretically and experimentally, that dispersion forces between small colloidal particles can also be induced and controlled using artificially created fluctuating light fields. Using optical tweezers as a gauge, we present experimental evidence for the predicted isotropic attractive interactions between dielectric microspheres induced by laser-generated, random light fields. These light-induced interactions open a path towards the control of translationally invariant interactions with tuneable strength and range in colloidal systems.

  2. Characterization of a random anisotropic conductivity field with Karhunen-Loeve methods

    SciTech Connect

    Cherry, Matthew R.; Sabbagh, Harold S.; Pilchak, Adam L.; Knopp, Jeremy S.

    2014-02-18

    While parametric uncertainty quantification for NDE models has been addressed in recent years, the problem of stochastic field parameters such as spatially distributed electrical conductivity has only been investigated minimally in the last year. In that work, the authors treated the field as a one-dimensional random process and Karhunen-Loeve methods were used to discretize this process to make it amenable to UQ methods such as ANOVA expansions. In the present work, we will treat the field as a two dimensional random process, and the eigenvalues and eigenfunctions of the integral operator will be determined via Galerkin methods. The Karhunen-Loeve methods is extended to two dimensions and implemented to represent this process. Several different choices for basis functions will be discussed, as well as convergence criteria for each. The methods are applied to correlation functions collected over electron backscatter data from highly micro textured Ti-7Al.

  3. Controlling dispersion forces between small particles with artificially created random light fields

    PubMed Central

    Brügger, Georges; Froufe-Pérez, Luis S.; Scheffold, Frank; José Sáenz, Juan

    2015-01-01

    Appropriate combinations of laser beams can be used to trap and manipulate small particles with optical tweezers as well as to induce significant optical binding forces between particles. These interaction forces are usually strongly anisotropic depending on the interference landscape of the external fields. This is in contrast with the familiar isotropic, translationally invariant, van der Waals and, in general, Casimir–Lifshitz interactions between neutral bodies arising from random electromagnetic waves generated by equilibrium quantum and thermal fluctuations. Here we show, both theoretically and experimentally, that dispersion forces between small colloidal particles can also be induced and controlled using artificially created fluctuating light fields. Using optical tweezers as a gauge, we present experimental evidence for the predicted isotropic attractive interactions between dielectric microspheres induced by laser-generated, random light fields. These light-induced interactions open a path towards the control of translationally invariant interactions with tuneable strength and range in colloidal systems. PMID:26096622

  4. Methods for testing theory and evaluating impact in randomized field trials

    PubMed Central

    Brown, C. Hendricks; Wang, Wei; Kellam, Sheppard G.; Muthén, Bengt O.; Petras, Hanno; Toyinbo, Peter; Poduska, Jeanne; Ialongo, Nicholas; Wyman, Peter A.; Chamberlain, Patricia; Sloboda, Zili; MacKinnon, David P.; Windham, Amy

    2008-01-01

    Randomized field trials provide unique opportunities to examine the effectiveness of an intervention in real world settings and to test and extend both theory of etiology and theory of intervention. These trials are designed not only to test for overall intervention impact but also to examine how impact varies as a function of individual level characteristics, context, and across time. Examination of such variation in impact requires analytical methods that take into account the trial’s multiple nested structure and the evolving changes in outcomes over time. The models that we describe here merge multilevel modeling with growth modeling, allowing for variation in impact to be represented through discrete mixtures—growth mixture models—and nonparametric smooth functions—generalized additive mixed models. These methods are part of an emerging class of multilevel growth mixture models, and we illustrate these with models that examine overall impact and variation in impact. In this paper, we define intent-to-treat analyses in group-randomized multilevel field trials and discuss appropriate ways to identify, examine, and test for variation in impact without inflating the Type I error rate. We describe how to make causal inferences more robust to misspecification of covariates in such analyses and how to summarize and present these interactive intervention effects clearly. Practical strategies for reducing model complexity, checking model fit, and handling missing data are discussed using six randomized field trials to show how these methods may be used across trials randomized at different levels. PMID:18215473

  5. MODEL OF THE FIELD LINE RANDOM WALK EVOLUTION AND APPROACH TO ASYMPTOTIC DIFFUSION IN MAGNETIC TURBULENCE

    SciTech Connect

    Snodin, A. P.; Ruffolo, D.; Matthaeus, W. H. E-mail: david.ruf@mahidol.ac.th

    2013-01-01

    The turbulent random walk of magnetic field lines plays an important role in the transport of plasmas and energetic particles in a wide variety of astrophysical situations, but most theoretical work has concentrated on determination of the asymptotic field line diffusion coefficient. Here we consider the evolution with distance of the field line random walk using a general ordinary differential equation (ODE), which for most cases of interest in astrophysics describes a transition from free streaming to asymptotic diffusion. By challenging theories of asymptotic diffusion to also describe the evolution, one gains insight on how accurately they describe the random walk process. Previous theoretical work has effectively involved closure of the ODE, often by assuming Corrsin's hypothesis and a Gaussian displacement distribution. Approaches that use quasilinear theory and prescribe the mean squared displacement ({Delta}x {sup 2}) according to free streaming (random ballistic decorrelation, RBD) or asymptotic diffusion (diffusive decorrelation, DD) can match computer simulation results, but only over specific parameter ranges, with no obvious 'marker' of the range of validity. Here we make use of a unified description in which the ODE determines ({Delta}x {sup 2}) self-consistently, providing a natural transition between the assumptions of RBD and DD. We find that the minimum kurtosis of the displacement distribution provides a good indicator of whether the self-consistent ODE is applicable, i.e., inaccuracy of the self-consistent ODE is associated with non-Gaussian displacement distributions.

  6. On Polynomial Lieb-Robinson Bounds for the XY Chain in a Decaying Random Field

    NASA Astrophysics Data System (ADS)

    Gebert, Martin; Lemm, Marius

    2016-06-01

    We consider the isotropic XY quantum spin chain in a random external field in the z direction, with single site distributions given by i.i.d. random variables times the critical decaying envelope j^{-1/2} . Our motivation is the study of many-body localization. We investigate transport properties in terms of polynomial Lieb-Robinson (PLR) bounds. We prove a zero-velocity PLR bound for large disorder strength λ and for small λ we show a partial converse, which suggests the existence of a transition to non-trivial transport in the model.

  7. On Polynomial Lieb-Robinson Bounds for the XY Chain in a Decaying Random Field

    NASA Astrophysics Data System (ADS)

    Gebert, Martin; Lemm, Marius

    2016-08-01

    We consider the isotropic XY quantum spin chain in a random external field in the z direction, with single site distributions given by i.i.d. random variables times the critical decaying envelope j^{-1/2}. Our motivation is the study of many-body localization. We investigate transport properties in terms of polynomial Lieb-Robinson (PLR) bounds. We prove a zero-velocity PLR bound for large disorder strength λ and for small λ we show a partial converse, which suggests the existence of a transition to non-trivial transport in the model.

  8. Analysis and Prediction of the Critical Regions of Antimicrobial Peptides Based on Conditional Random Fields

    PubMed Central

    Chang, Kuan Y.; Lin, Tung-pei; Shih, Ling-Yi; Wang, Chien-Kuo

    2015-01-01

    Antimicrobial peptides (AMPs) are potent drug candidates against microbes such as bacteria, fungi, parasites, and viruses. The size of AMPs ranges from less than ten to hundreds of amino acids. Often only a few amino acids or the critical regions of antimicrobial proteins matter the functionality. Accurately predicting the AMP critical regions could benefit the experimental designs. However, no extensive analyses have been done specifically on the AMP critical regions and computational modeling on them is either non-existent or settled to other problems. With a focus on the AMP critical regions, we thus develop a computational model AMPcore by introducing a state-of-the-art machine learning method, conditional random fields. We generate a comprehensive dataset of 798 AMPs cores and a low similarity dataset of 510 representative AMP cores. AMPcore could reach a maximal accuracy of 90% and 0.79 Matthew’s correlation coefficient on the comprehensive dataset and a maximal accuracy of 83% and 0.66 MCC on the low similarity dataset. Our analyses of AMP cores follow what we know about AMPs: High in glycine and lysine, but low in aspartic acid, glutamic acid, and methionine; the abundance of α-helical structures; the dominance of positive net charges; the peculiarity of amphipathicity. Two amphipathic sequence motifs within the AMP cores, an amphipathic α-helix and an amphipathic π-helix, are revealed. In addition, a short sequence motif at the N-terminal boundary of AMP cores is reported for the first time: arginine at the P(-1) coupling with glycine at the P1 of AMP cores occurs the most, which might link to microbial cell adhesion. PMID:25803302

  9. A new test statistic for climate models that includes field and spatial dependencies using Gaussian Markov random fields

    NASA Astrophysics Data System (ADS)

    Nosedal-Sanchez, Alvaro; Jackson, Charles S.; Huerta, Gabriel

    2016-07-01

    A new test statistic for climate model evaluation has been developed that potentially mitigates some of the limitations that exist for observing and representing field and space dependencies of climate phenomena. Traditionally such dependencies have been ignored when climate models have been evaluated against observational data, which makes it difficult to assess whether any given model is simulating observed climate for the right reasons. The new statistic uses Gaussian Markov random fields for estimating field and space dependencies within a first-order grid point neighborhood structure. We illustrate the ability of Gaussian Markov random fields to represent empirical estimates of field and space covariances using "witch hat" graphs. We further use the new statistic to evaluate the tropical response of a climate model (CAM3.1) to changes in two parameters important to its representation of cloud and precipitation physics. Overall, the inclusion of dependency information did not alter significantly the recognition of those regions of parameter space that best approximated observations. However, there were some qualitative differences in the shape of the response surface that suggest how such a measure could affect estimates of model uncertainty.

  10. Typical kernel size and number of sparse random matrices over Galois fields: A statistical physics approach

    NASA Astrophysics Data System (ADS)

    Alamino, R. C.; Saad, D.

    2008-06-01

    Using methods of statistical physics, we study the average number and kernel size of general sparse random matrices over Galois fields GF(q) , with a given connectivity profile, in the thermodynamical limit of large matrices. We introduce a mapping of GF(q) matrices onto spin systems using the representation of the cyclic group of order q as the q th complex roots of unity. This representation facilitates the derivation of the average kernel size of random matrices using the replica approach, under the replica-symmetric ansatz, resulting in saddle point equations for general connectivity distributions. Numerical solutions are then obtained for particular cases by population dynamics. Similar techniques also allow us to obtain an expression for the exact and average numbers of random matrices for any general connectivity profile. We present numerical results for particular distributions.

  11. Random fields generation on the GPU with the spectral turning bands method

    NASA Astrophysics Data System (ADS)

    Hunger, L.; Cosenza, B.; Kimeswenger, S.; Fahringer, T.

    2014-08-01

    Random field (RF) generation algorithms are of paramount importance for many scientific domains, such as astrophysics, geostatistics, computer graphics and many others. Some examples are the generation of initial conditions for cosmological simulations or hydrodynamical turbulence driving. In the latter a new random field is needed every time-step. Current approaches commonly make use of 3D FFT (Fast Fourier Transform) and require the whole generated field to be stored in memory. Moreover, they are limited to regular rectilinear meshes and need an extra processing step to support non-regular meshes. In this paper, we introduce TBARF (Turning BAnd Random Fields), a RF generation algorithm based on the turning band method that is optimized for massively parallel hardware such as GPUs. Our algorithm replaces the 3D FFT with a lower order, one-dimensional FFT followed by a projection step, and is further optimized with loop unrolling and blocking. We show that TBARF can easily generate RF on non-regular (non uniform) meshes and can afford mesh sizes bigger than the available GPU memory by using a streaming, out-of-core approach. TBARF is 2 to 5 times faster than the traditional methods when generating RFs with more than 16M cells. It can also generate RF on non-regular meshes, and has been successfully applied to two real case scenarios: planetary nebulae and cosmological simulations.

  12. Analytic Theory and Numerical Study of the Magnetic Field Line Random Walk in Reduced Magnetohydrodynamic Turbulence

    NASA Astrophysics Data System (ADS)

    Ruffolo, D. J.; Snodin, A. P.; Oughton, S.; Servidio, S.; Matthaeus, W. H.

    2013-12-01

    The random walk of magnetic field lines is examined analytically and numerically in the context of reduced magnetohydrodynamic (RMHD) turbulence, which provides a useful description of plasmas dominated by a strong mean field, such as in the solar corona. A nonperturbative theory of magnetic field line diffusion [1] is compared with the diffusion coefficients obtained by accurate numerical tracing of magnetic field lines for both synthetic models and direct numerical simulations of RMHD. Statistical analysis of an ensemble of trajectories confirms the applicability of the theory, which very closely matches the numerical field line diffusion coefficient as a function of distance z along the mean magnetic field for a wide range of the Kubo number R. The theory employs Corrsin's independence hypothesis, sometimes thought to be valid only at low R. However, the results demonstrate that it works well up to R=10, both for a synthetic RMHD model and an RMHD simulation. The numerical results from RMHD simulation are compared with and without phase randomization, demonstrating an effect of coherent structures on the field line random walk for low Kubo number. Partially supported by a postdoctoral fellowship from Mahidol University, the Thailand Research Fund, POR Calabria FSE-2007/2013, the US NSF (AGS-1063439 and SHINE AGS-1156094), NASA (Heliophysics Theory NNX08AI47G & NNX11AJ44G), by the Solar Probe Plus Project through the ISIS Theory team, by the MMS Theory and Modeling team, and by EU Marie Curie Project FP7 PIRSES-2010-269297 'Turboplasmas' at Università della Calabria. [1] D. Ruffolo and W. H. Matthaeus, Phys. Plasmas, 20, 012308 (2013).

  13. A new test statistic for climate models that includes field and spatial dependencies using Gaussian Markov random fields

    DOE PAGESBeta

    Nosedal-Sanchez, Alvaro; Jackson, Charles S.; Huerta, Gabriel

    2016-07-20

    A new test statistic for climate model evaluation has been developed that potentially mitigates some of the limitations that exist for observing and representing field and space dependencies of climate phenomena. Traditionally such dependencies have been ignored when climate models have been evaluated against observational data, which makes it difficult to assess whether any given model is simulating observed climate for the right reasons. The new statistic uses Gaussian Markov random fields for estimating field and space dependencies within a first-order grid point neighborhood structure. We illustrate the ability of Gaussian Markov random fields to represent empirical estimates of fieldmore » and space covariances using "witch hat" graphs. We further use the new statistic to evaluate the tropical response of a climate model (CAM3.1) to changes in two parameters important to its representation of cloud and precipitation physics. Overall, the inclusion of dependency information did not alter significantly the recognition of those regions of parameter space that best approximated observations. However, there were some qualitative differences in the shape of the response surface that suggest how such a measure could affect estimates of model uncertainty.« less

  14. Possible Statistics of Two Coupled Random Fields: Application to Passive Scalar

    NASA Technical Reports Server (NTRS)

    Dubrulle, B.; He, Guo-Wei; Bushnell, Dennis M. (Technical Monitor)

    2000-01-01

    We use the relativity postulate of scale invariance to derive the similarity transformations between two coupled scale-invariant random elds at different scales. We nd the equations leading to the scaling exponents. This formulation is applied to the case of passive scalars advected i) by a random Gaussian velocity field; and ii) by a turbulent velocity field. In the Gaussian case, we show that the passive scalar increments follow a log-Levy distribution generalizing Kraichnan's solution and, in an appropriate limit, a log-normal distribution. In the turbulent case, we show that when the velocity increments follow a log-Poisson statistics, the passive scalar increments follow a statistics close to log-Poisson. This result explains the experimental observations of Ruiz et al. about the temperature increments.

  15. Quantum correlations and dynamics from classical random fields valued in complex Hilbert spaces

    SciTech Connect

    Khrennikov, Andrei

    2010-08-15

    One of the crucial differences between mathematical models of classical and quantum mechanics (QM) is the use of the tensor product of the state spaces of subsystems as the state space of the corresponding composite system. (To describe an ensemble of classical composite systems, one uses random variables taking values in the Cartesian product of the state spaces of subsystems.) We show that, nevertheless, it is possible to establish a natural correspondence between the classical and the quantum probabilistic descriptions of composite systems. Quantum averages for composite systems (including entangled) can be represented as averages with respect to classical random fields. It is essentially what Albert Einstein dreamed of. QM is represented as classical statistical mechanics with infinite-dimensional phase space. While the mathematical construction is completely rigorous, its physical interpretation is a complicated problem. We present the basic physical interpretation of prequantum classical statistical field theory in Sec. II. However, this is only the first step toward real physical theory.

  16. Ordered vs. disordered states of the random-field model in three dimensions

    NASA Astrophysics Data System (ADS)

    Garanin, Dmitry A.; Chudnovsky, Eugene M.

    2015-04-01

    We report numerical investigation of the glassy behavior of random-field exchange models in three dimensions. Correlation of energy with the magnetization for different numbers of spin components has been studied. There is a profound difference between the models with two and three spin components with respect to the stability of the magnetized state due to the different kinds of singularities: vortex loops and hedgehogs, respectively. Memory effects pertinent to such states have been investigated. Insight into the mechanism of the large-scale disordering is provided by numerically implementing the Imry-Ma argument in which the spins follow the random field averaged over correlated volumes. Thermal stability of the magnetized states is investigated by the Monte Carlo method.

  17. Quantum correlations of three-qubit states driven by a classical random external field

    NASA Astrophysics Data System (ADS)

    Guo, Youneng; Fang, Maofa; Zhang, Shiyang; Liu, Xiang

    2015-03-01

    In this paper, we exploit the notions of tripartite quantum discord {{D}(3)}, tripartite negativity {{N}(3)}, and entanglement witnesses (EWs), respectively, as a measure of quantum correlations in a model of three noninteracting qubits subject to a classical random external field. We compare the dynamics of {{D}(3)} with that of entanglement for the initial entangled pure or mixed GHZ- and W-type states. We find that the quantum correlations dynamics depend on the input configuration of the purity of the initial states. The results show that {{D}(3)} may be more robust than entanglement and no sudden death of the {{D}(3)} occurs, whereas entanglement displays periodically sudden death and revivals in the regions for GHZ- and W-type states driven by a classical random external field. Furthermore, we also show that the survival partial entanglement can be detected by means of the suitable EWs.

  18. Fuzzy-based latent-dynamic conditional random fields for continuous gesture recognition

    NASA Astrophysics Data System (ADS)

    Zhang, Shengjun; He, Xiaohai; Teng, Qizhi

    2012-06-01

    We show an original method for automatic hand gesture recognition that makes use of fuzzified latent-dynamic conditional random fields (LDCRF). In this method, fuzzy linguistic variables are used to model the features of hand gestures and then to modify the potential function in LDCRFs. By combining LDCRFs and fuzzy sets, these fuzzy-based LDCRFs (FLDCRF) have the advantages of LDCRFs in sequence labeling along with the advantage of retaining the imprecise character of gestures. The efficiency of the proposed method was tested with unsegmented gesture sequences in three different hand gesture data sets. The experimental results demonstrate that FLDCRFs compare favorably with support vector machines, hidden conditional random fields, and LDCRFs on hand gesture recognition tasks.

  19. Planned Variations Study. Volume IV: Field Implementation Plan for a Field Randomized Experiment.

    ERIC Educational Resources Information Center

    Shiban, John R.

    System Development Corporation conducted an extensive project of conceptualization and planning of models for compensatory educational intervention for older disadvantaged youth, at the secondary and postsecondary levels. Two intervention strategies were developed, and this report details the development of a field implementation plan for a…

  20. A heuristic for the distribution of point counts for random curves over a finite field

    PubMed Central

    Achter, Jeffrey D.; Erman, Daniel; Kedlaya, Kiran S.; Wood, Melanie Matchett; Zureick-Brown, David

    2015-01-01

    How many rational points are there on a random algebraic curve of large genus g over a given finite field ? We propose a heuristic for this question motivated by a (now proven) conjecture of Mumford on the cohomology of moduli spaces of curves; this heuristic suggests a Poisson distribution with mean q+1+1/(q−1). We prove a weaker version of this statement in which g and q tend to infinity, with q much larger than g. PMID:25802415

  1. Classification of high resolution remote sensing image based on geo-ontology and conditional random fields

    NASA Astrophysics Data System (ADS)

    Hong, Liang

    2013-10-01

    The availability of high spatial resolution remote sensing data provides new opportunities for urban land-cover classification. More geometric details can be observed in the high resolution remote sensing image, Also Ground objects in the high resolution remote sensing image have displayed rich texture, structure, shape and hierarchical semantic characters. More landscape elements are represented by a small group of pixels. Recently years, the an object-based remote sensing analysis methodology is widely accepted and applied in high resolution remote sensing image processing. The classification method based on Geo-ontology and conditional random fields is presented in this paper. The proposed method is made up of four blocks: (1) the hierarchical ground objects semantic framework is constructed based on geoontology; (2) segmentation by mean-shift algorithm, which image objects are generated. And the mean-shift method is to get boundary preserved and spectrally homogeneous over-segmentation regions ;(3) the relations between the hierarchical ground objects semantic and over-segmentation regions are defined based on conditional random fields framework ;(4) the hierarchical classification results are obtained based on geo-ontology and conditional random fields. Finally, high-resolution remote sensed image data -GeoEye, is used to testify the performance of the presented method. And the experimental results have shown the superiority of this method to the eCognition method both on the effectively and accuracy, which implies it is suitable for the classification of high resolution remote sensing image.

  2. Fluorescence microscopy image noise reduction using a stochastically-connected random field model

    PubMed Central

    Haider, S. A.; Cameron, A.; Siva, P.; Lui, D.; Shafiee, M. J.; Boroomand, A.; Haider, N.; Wong, A.

    2016-01-01

    Fluorescence microscopy is an essential part of a biologist’s toolkit, allowing assaying of many parameters like subcellular localization of proteins, changes in cytoskeletal dynamics, protein-protein interactions, and the concentration of specific cellular ions. A fundamental challenge with using fluorescence microscopy is the presence of noise. This study introduces a novel approach to reducing noise in fluorescence microscopy images. The noise reduction problem is posed as a Maximum A Posteriori estimation problem, and solved using a novel random field model called stochastically-connected random field (SRF), which combines random graph and field theory. Experimental results using synthetic and real fluorescence microscopy data show the proposed approach achieving strong noise reduction performance when compared to several other noise reduction algorithms, using quantitative metrics. The proposed SRF approach was able to achieve strong performance in terms of signal-to-noise ratio in the synthetic results, high signal to noise ratio and contrast to noise ratio in the real fluorescence microscopy data results, and was able to maintain cell structure and subtle details while reducing background and intra-cellular noise. PMID:26884148

  3. Spectral turning bands for efficient Gaussian random fields generation on GPUs and accelerators

    NASA Astrophysics Data System (ADS)

    Hunger, L.; Cosenza, B.; Kimeswenger, S.; Fahringer, T.

    2015-11-01

    A random field (RF) is a set of correlated random variables associated with different spatial locations. RF generation algorithms are of crucial importance for many scientific areas, such as astrophysics, geostatistics, computer graphics, and many others. Current approaches commonly make use of 3D fast Fourier transform (FFT), which does not scale well for RF bigger than the available memory; they are also limited to regular rectilinear meshes. We introduce random field generation with the turning band method (RAFT), an RF generation algorithm based on the turning band method that is optimized for massively parallel hardware such as GPUs and accelerators. Our algorithm replaces the 3D FFT with a lower-order, one-dimensional FFT followed by a projection step and is further optimized with loop unrolling and blocking. RAFT can easily generate RF on non-regular (non-uniform) meshes and efficiently produce fields with mesh sizes bigger than the available device memory by using a streaming, out-of-core approach. Our algorithm generates RF with the correct statistical behavior and is tested on a variety of modern hardware, such as NVIDIA Tesla, AMD FirePro and Intel Phi. RAFT is faster than the traditional methods on regular meshes and has been successfully applied to two real case scenarios: planetary nebulae and cosmological simulations.

  4. Random field disorder at an absorbing state transition in one and two dimensions

    NASA Astrophysics Data System (ADS)

    Barghathi, Hatem; Vojta, Thomas

    2016-02-01

    We investigate the behavior of nonequilibrium phase transitions under the influence of disorder that locally breaks the symmetry between two symmetrical macroscopic absorbing states. In equilibrium systems such "random-field" disorder destroys the phase transition in low dimensions by preventing spontaneous symmetry breaking. In contrast, we show here that random-field disorder fails to destroy the nonequilibrium phase transition of the one- and two-dimensional generalized contact process. Instead, it modifies the dynamics in the symmetry-broken phase. Specifically, the dynamics in the one-dimensional case is described by a Sinai walk of the domain walls between two different absorbing states. In the two-dimensional case, we map the dynamics onto that of the well studied low-temperature random-field Ising model. We also study the critical behavior of the nonequilibrium phase transition and characterize its universality class in one dimension. We support our results by large-scale Monte Carlo simulations, and we discuss the applicability of our theory to other systems.

  5. Nonlinear amplification of Langmuir waves in a plasma with regular and random magnetic fields

    NASA Astrophysics Data System (ADS)

    Krivitskii, V. S.; Priadko, Iu. M.; Tsytovich, V. N.

    1990-07-01

    The nonlinear interaction of Langmuir waves in a turbulent plasma with random resonance magnetic fields in the presence of an external regular magnetic field is investigated analytically. In particular, attention is given to the possibility of Langmuir wave amplification using the plasma maser effect. The frequency and angle dependences of the amplification increment (attenuation decrement) of Langmuir waves are determined in the isotropic case and in the presence of anisotropy. For an anisotropic particle distribution function, the amplification increment of Langmuir waves may reach values of the order of the plasma frequency.

  6. Random Field Driven Spatial Complexity at the Mott Transition in VO2

    NASA Astrophysics Data System (ADS)

    Liu, Shuo; Phillabaum, B.; Carlson, E. W.; Dahmen, K. A.; Vidhyadhiraja, N. S.; Qazilbash, M. M.; Basov, D. N.

    2016-01-01

    We report the first application of critical cluster techniques to the Mott metal-insulator transition in vanadium dioxide. We show that the geometric universal properties of the metallic and insulating puddles observed by scanning near-field infrared microscopy are consistent with the system passing near criticality of the random field Ising model as temperature is varied. The resulting large barriers to equilibrium may be the source of the unusually robust hysteresis phenomena associated with the metal-insulator transition in this system.

  7. The diffusive idealization of charged-particle transport in random magnetic fields. [cosmic ray propagation

    NASA Technical Reports Server (NTRS)

    Earl, J. A.

    1974-01-01

    The uniqueness and accuracy of the equations which describe the transport of charged particles diffusing in a random magnetic field parallel to a relatively large guiding field is examined. With regard to uniqueness, it is found that the same coefficient of diffusion is obtained by three methods that have apparently led to discrepancies in previous work. With regard to accuracy, it is found that two corrections must be added to Fick's law in which the diffusive flux is proportional to the gradient of the density. Explicit expressions are given for a characteristic time and a characteristic length which describe the corrections.

  8. Random Field Driven Spatial Complexity at the Mott Transition in VO(2).

    PubMed

    Liu, Shuo; Phillabaum, B; Carlson, E W; Dahmen, K A; Vidhyadhiraja, N S; Qazilbash, M M; Basov, D N

    2016-01-22

    We report the first application of critical cluster techniques to the Mott metal-insulator transition in vanadium dioxide. We show that the geometric universal properties of the metallic and insulating puddles observed by scanning near-field infrared microscopy are consistent with the system passing near criticality of the random field Ising model as temperature is varied. The resulting large barriers to equilibrium may be the source of the unusually robust hysteresis phenomena associated with the metal-insulator transition in this system. PMID:26849604

  9. Proteomics Analysis with a Nano Random Forest Approach Reveals Novel Functional Interactions Regulated by SMC Complexes on Mitotic Chromosomes*

    PubMed Central

    Ohta, Shinya; Montaño-Gutierrez, Luis F.; de Lima Alves, Flavia; Ogawa, Hiromi; Toramoto, Iyo; Sato, Nobuko; Morrison, Ciaran G.; Takeda, Shunichi; Hudson, Damien F.; Earnshaw, William C.

    2016-01-01

    Packaging of DNA into condensed chromosomes during mitosis is essential for the faithful segregation of the genome into daughter nuclei. Although the structure and composition of mitotic chromosomes have been studied for over 30 years, these aspects are yet to be fully elucidated. Here, we used stable isotope labeling with amino acids in cell culture to compare the proteomes of mitotic chromosomes isolated from cell lines harboring conditional knockouts of members of the condensin (SMC2, CAP-H, CAP-D3), cohesin (Scc1/Rad21), and SMC5/6 (SMC5) complexes. Our analysis revealed that these complexes associate with chromosomes independently of each other, with the SMC5/6 complex showing no significant dependence on any other chromosomal proteins during mitosis. To identify subtle relationships between chromosomal proteins, we employed a nano Random Forest (nanoRF) approach to detect protein complexes and the relationships between them. Our nanoRF results suggested that as few as 113 of 5058 detected chromosomal proteins are functionally linked to chromosome structure and segregation. Furthermore, nanoRF data revealed 23 proteins that were not previously suspected to have functional interactions with complexes playing important roles in mitosis. Subsequent small-interfering-RNA-based validation and localization tracking by green fluorescent protein-tagging highlighted novel candidates that might play significant roles in mitotic progression. PMID:27231315

  10. Proteomics Analysis with a Nano Random Forest Approach Reveals Novel Functional Interactions Regulated by SMC Complexes on Mitotic Chromosomes.

    PubMed

    Ohta, Shinya; Montaño-Gutierrez, Luis F; de Lima Alves, Flavia; Ogawa, Hiromi; Toramoto, Iyo; Sato, Nobuko; Morrison, Ciaran G; Takeda, Shunichi; Hudson, Damien F; Rappsilber, Juri; Earnshaw, William C

    2016-08-01

    Packaging of DNA into condensed chromosomes during mitosis is essential for the faithful segregation of the genome into daughter nuclei. Although the structure and composition of mitotic chromosomes have been studied for over 30 years, these aspects are yet to be fully elucidated. Here, we used stable isotope labeling with amino acids in cell culture to compare the proteomes of mitotic chromosomes isolated from cell lines harboring conditional knockouts of members of the condensin (SMC2, CAP-H, CAP-D3), cohesin (Scc1/Rad21), and SMC5/6 (SMC5) complexes. Our analysis revealed that these complexes associate with chromosomes independently of each other, with the SMC5/6 complex showing no significant dependence on any other chromosomal proteins during mitosis. To identify subtle relationships between chromosomal proteins, we employed a nano Random Forest (nanoRF) approach to detect protein complexes and the relationships between them. Our nanoRF results suggested that as few as 113 of 5058 detected chromosomal proteins are functionally linked to chromosome structure and segregation. Furthermore, nanoRF data revealed 23 proteins that were not previously suspected to have functional interactions with complexes playing important roles in mitosis. Subsequent small-interfering-RNA-based validation and localization tracking by green fluorescent protein-tagging highlighted novel candidates that might play significant roles in mitotic progression. PMID:27231315

  11. Multi-fidelity modelling via recursive co-kriging and Gaussian–Markov random fields

    PubMed Central

    Perdikaris, P.; Venturi, D.; Royset, J. O.; Karniadakis, G. E.

    2015-01-01

    We propose a new framework for design under uncertainty based on stochastic computer simulations and multi-level recursive co-kriging. The proposed methodology simultaneously takes into account multi-fidelity in models, such as direct numerical simulations versus empirical formulae, as well as multi-fidelity in the probability space (e.g. sparse grids versus tensor product multi-element probabilistic collocation). We are able to construct response surfaces of complex dynamical systems by blending multiple information sources via auto-regressive stochastic modelling. A computationally efficient machine learning framework is developed based on multi-level recursive co-kriging with sparse precision matrices of Gaussian–Markov random fields. The effectiveness of the new algorithms is demonstrated in numerical examples involving a prototype problem in risk-averse design, regression of random functions, as well as uncertainty quantification in fluid mechanics involving the evolution of a Burgers equation from a random initial state, and random laminar wakes behind circular cylinders. PMID:26345079

  12. Modeling of nonlinear microscopy of localized field enhancements in random metal nanostructures

    NASA Astrophysics Data System (ADS)

    Beermann, Jonas; Bozhevolnyi, Sergey I.; Coello, Victor

    2006-03-01

    Nonlinear microscopy of localized field enhancements in random metal nanostructures with a tightly focused laser beam scanning over a sample surface is modeled by making use of analytic representations of the Green dyadic in the near- and far-field regions, with the latter being approximated by the part describing the scattering via excitation of surface plasmon polaritons. The developed approach is applied to scanning second-harmonic (SH) microscopy of small gold spheres placed randomly on a gold surface. We calculate self-consistent fundamental harmonic (FH) and SH field distributions at the illuminated sample surface and, thereby, FH and SH images for different polarization configurations of the illuminating and detected fields. The simulated images bear close resemblance to the images obtained experimentally, exhibiting similar sensitivity to the wavelength and polarization, as well as sensitivity to the scattering configuration. We verify directly our conjecture that very bright spots in the SH images occur due to the spatial overlap of properly polarized FH and SH eigenmodes. Applications and further improvements of the developed model are discussed.

  13. Critical and umbilical points of a non-Gaussian random field

    NASA Astrophysics Data System (ADS)

    Beuman, T. H.; Turner, A. M.; Vitelli, V.

    2013-07-01

    Random fields in nature often have, to a good approximation, Gaussian characteristics. For such fields, the number of maxima and minima are the same. Furthermore, the relative densities of umbilical points, topological defects which can be classified into three types, have certain fixed values. Phenomena described by nonlinear laws can, however, give rise to a non-Gaussian contribution, causing a deviation from these universal values. We consider a random surface, whose height is given by a nonlinear function of a Gaussian field. We find that, as a result of the non-Gaussianity, the density of maxima and minima no longer match and we calculate the relative imbalance between the two. We also calculate the change in the relative density of umbilics. This allows us not only to detect a perturbation, but to determine its size as well. This geometric approach offers an independent way of detecting non-Gaussianity, which even works in cases where the field itself can not be probed directly.

  14. Metastates in Mean-Field Models with Random External Fields Generated by Markov Chains

    NASA Astrophysics Data System (ADS)

    Formentin, M.; Külske, C.; Reichenbachs, A.

    2012-01-01

    We extend the construction by Külske and Iacobelli of metastates in finite-state mean-field models in independent disorder to situations where the local disorder terms are a sample of an external ergodic Markov chain in equilibrium. We show that for non-degenerate Markov chains, the structure of the theorems is analogous to the case of i.i.d. variables when the limiting weights in the metastate are expressed with the aid of a CLT for the occupation time measure of the chain. As a new phenomenon we also show in a Potts example that for a degenerate non-reversible chain this CLT approximation is not enough, and that the metastate can have less symmetry than the symmetry of the interaction and a Gaussian approximation of disorder fluctuations would suggest.

  15. Spatial-Temporal Conditional Random Fields Crop Classification from Terrasar-X Images

    NASA Astrophysics Data System (ADS)

    Kenduiywoa, B. K.; Bargiel, D.; Soergel, U.

    2015-03-01

    The rapid increase in population in the world has propelled pressure on arable land. Consequently, the food basket has continuously declined while global demand for food has grown twofold. There is need to monitor and update agriculture land-cover to support food security measures. This study develops a spatial-temporal approach using conditional random fields (CRF) to classify co-registered images acquired in two epochs. We adopt random forest (RF) as CRF association potential and introduce a temporal potential for mutual crop phenology information exchange between spatially corresponding sites in two epochs. An important component of temporal potential is a transitional matrix that bears intra- and inter-class changes between considered epochs. Conventionally, one matrix has been used in the entire image thereby enforcing stationary transition probabilities in all sites. We introduce a site dependent transition matrix to incorporate phenology information from images. In our study, images are acquired within a vegetation season, thus perceived spectral changes are due to crop phenology. To exploit this phenomena, we develop a novel approach to determine site-wise transition matrix using conditional probabilities computed from two corresponding temporal sites. Conditional probability determines transitions between classes in different epochs and thus we used it to propagate crop phenology information. Classification results show that our approach improved crop discrimination in all epochs compared to state-of-the-art mono-temporal approaches (RF and CRF monotemporal) and existing multi-temporal markov random fields approach by Liu et al. (2008).

  16. Mean-field behavior of the negative-weight percolation model on random regular graphs.

    PubMed

    Melchert, Oliver; Hartmann, Alexander K; Mézard, Marc

    2011-10-01

    We investigate both analytically and numerically the ensemble of minimum-weight loops in the negative-weight percolation model on random graphs with fixed connectivity and bimodal weight distribution. This allows us to study the mean-field behavior of this model. The analytical study is based on a conjectured equivalence with the problem of self-avoiding walks in a random medium. The numerical study is based on a mapping to a standard minimum-weight matching problem for which fast algorithms exist. Both approaches yield results that are in agreement on the location of the phase transition, on the value of critical exponents, and on the absence of any sizable indications of a glass phase. By these results, the previously conjectured upper critical dimension of d(u)=6 is confirmed. PMID:22181086

  17. Karhunen-Loève expansion revisited for vector-valued random fields: Scaling, errors and optimal basis.

    NASA Astrophysics Data System (ADS)

    Perrin, G.; Soize, C.; Duhamel, D.; Funfschilling, C.

    2013-06-01

    Due to scaling effects, when dealing with vector-valued random fields, the classical Karhunen-Loève expansion, which is optimal with respect to the total mean square error, tends to favorize the components of the random field that have the highest signal energy. When these random fields are to be used in mechanical systems, this phenomenon can introduce undesired biases for the results. This paper presents therefore an adaptation of the Karhunen-Loève expansion that allows us to control these biases and to minimize them. This original decomposition is first analyzed from a theoretical point of view, and is then illustrated on a numerical example.

  18. The spectrum of random magnetic fields in the mean field dynamo theory of the Galactic magnetic field

    NASA Technical Reports Server (NTRS)

    Kulsrud, Russell M.; Anderson, Stephen W.

    1992-01-01

    The fluctuation spectrum that must arise in a mean field dynamo generation of galactic fields if the initial field is weak is considered. A kinetic equation for its evolution is derived and solved. The spectrum evolves by transfer of energy from one magnetic mode to another by interaction with turbulent velocity modes. This kinetic equation is valid in the limit that the rate of evolution of the magnetic modes is slower than the reciprocal decorrelation time of the turbulent modes. This turns out to be the case by a factor greater than 3. Most of the fluctuation energy concentrates on small scales, shorter than the hydrodynamic turbulent scales. The fluctuation energy builds up to equipartition with the turbulent energy in times that are short compared to the e-folding time of the mean field. The turbulence becomes strongly modified before the dynamo amplification starts. Thus, the kinematic assumption of the mean dynamo theory is invalid. Thus, the galactic field must have a primordial origin, although it may subsequently be modified by dynamo action.

  19. Genetic profiling of Klebsiella pneumoniae: comparison of pulsed field gel electrophoresis and random amplified polymorphic DNA

    PubMed Central

    Ashayeri-Panah, Mitra; Eftekhar, Fereshteh; Ghamsari, Maryam Mobarak; Parvin, Mahmood; Feizabadi, Mohammad Mehdi

    2013-01-01

    In this study, the discriminatory power of pulsed field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) methods for subtyping of 54 clinical isolates of Klebsiella pneumoniae were compared. All isolates were typeable by RAPD, while 3.6% of them were not typeable by PFGE. The repeatability of both typing methods were 100% with satisfying reproducibility (≥ 95%). Although the discriminatory power of PFGE was greater than RAPD, both methods showed sufficient discriminatory power (DI > 0.95) which reflects the heterogeneity among the K. pneumoniae isolates. An optimized RAPD protocol is less technically demanding and time consuming that makes it a reliable typing method and competitive with PFGE. PMID:24516423

  20. Central Limit Theorems and Uniform Laws of Large Numbers for Arrays of Random Fields

    PubMed Central

    Jenish, Nazgul; Prucha, Ingmar R.

    2009-01-01

    Over the last decades, spatial-interaction models have been increasingly used in economics. However, the development of a sufficiently general asymptotic theory for nonlinear spatial models has been hampered by a lack of relevant central limit theorems (CLTs), uniform laws of large numbers (ULLNs) and pointwise laws of large numbers (LLNs). These limit theorems form the essential building blocks towards developing the asymptotic theory of M-estimators, including maximum likelihood and generalized method of moments estimators. The paper establishes a CLT, ULLN, and LLN for spatial processes or random fields that should be applicable to a broad range of data processes. PMID:20161289

  1. Conditional Random Field-Based Offline Map Matching for Indoor Environments.

    PubMed

    Bataineh, Safaa; Bahillo, Alfonso; Díez, Luis Enrique; Onieva, Enrique; Bataineh, Ikram

    2016-01-01

    In this paper, we present an offline map matching technique designed for indoor localization systems based on conditional random fields (CRF). The proposed algorithm can refine the results of existing indoor localization systems and match them with the map, using loose coupling between the existing localization system and the proposed map matching technique. The purpose of this research is to investigate the efficiency of using the CRF technique in offline map matching problems for different scenarios and parameters. The algorithm was applied to several real and simulated trajectories of different lengths. The results were then refined and matched with the map using the CRF algorithm. PMID:27537892

  2. Fusion of Hidden Markov Random Field models and its Bayesian estimation.

    PubMed

    Destrempes, François; Angers, Jean-François; Mignotte, Max

    2006-10-01

    In this paper, we present a Hidden Markov Random Field (HMRF) data-fusion model. The proposed model is applied to the segmentation of natural images based on the fusion of colors and textons into Julesz ensembles. The corresponding Exploration/ Selection/Estimation (ESE) procedure for the estimation of the parameters is presented. This method achieves the estimation of the parameters of the Gaussian kernels, the mixture proportions, the region labels, the number of regions, and the Markov hyper-parameter. Meanwhile, we present a new proof of the asymptotic convergence of the ESE procedure, based on original finite time bounds for the rate of convergence. PMID:17022259

  3. Hierarchical Markov random-field modeling for texture classification in chest radiographs

    NASA Astrophysics Data System (ADS)

    Vargas-Voracek, Rene; Floyd, Carey E., Jr.; Nolte, Loren W.; McAdams, Page

    1996-04-01

    A hierarchical Markov random field (MRF) modeling approach is presented for the classification of textures in selected regions of interest (ROIs) of chest radiographs. The procedure integrates possible texture classes and their spatial definition with other components present in an image such as noise and background trend. Classification is performed as a maximum a-posteriori (MAP) estimation of texture class and involves an iterative Gibbs- sampling technique. Two cases are studied: classification of lung parenchyma versus bone and classification of normal lung parenchyma versus miliary tuberculosis (MTB). Accurate classification was obtained for all examined cases showing the potential of the proposed modeling approach for texture analysis of radiographic images.

  4. Ensemble solute transport in two-dimensional operator-scaling random fields

    NASA Astrophysics Data System (ADS)

    Monnig, Nathan D.; Benson, David A.; Meerschaert, Mark M.

    2008-02-01

    Motivated by field measurements of aquifer hydraulic conductivity (K), recent techniques were developed to construct anisotropic fractal random fields in which the scaling, or self-similarity parameter, varies with direction and is defined by a matrix. Ensemble numerical results are analyzed for solute transport through these two-dimensional "operator-scaling" fractional Brownian motion ln(K) fields. Both the longitudinal and transverse Hurst coefficients, as well as the "radius of isotropy" are important to both plume growth rates and the timing and duration of breakthrough. It is possible to create operator-scaling fractional Brownian motion fields that have more "continuity" or stratification in the direction of transport. The effects on a conservative solute plume are continually faster-than-Fickian growth rates, highly non-Gaussian shapes, and a heavier tail early in the breakthrough curve. Contrary to some analytic stochastic theories for monofractal K fields, the plume growth rates never exceed A. Mercado's (1967) purely stratified aquifer growth rate of plume apparent dispersivity proportional to mean distance. Apparent superstratified growth must be the result of other demonstrable factors, such as initial plume size.

  5. An exact solution of solute transport by one-dimensional random velocity fields

    USGS Publications Warehouse

    Cvetkovic, V.D.; Dagan, G.; Shapiro, A.M.

    1991-01-01

    The problem of one-dimensional transport of passive solute by a random steady velocity field is investigated. This problem is representative of solute movement in porous media, for example, in vertical flow through a horizontally stratified formation of variable porosity with a constant flux at the soil surface. Relating moments of particle travel time and displacement, exact expressions for the advection and dispersion coefficients in the Focker-Planck equation are compared with the perturbation results for large distances. The first- and second-order approximations for the dispersion coefficient are robust for a lognormal velocity field. The mean Lagrangian velocity is the harmonic mean of the Eulerian velocity for large distances. This is an artifact of one-dimensional flow where the continuity equation provides for a divergence free fluid flux, rather than a divergence free fluid velocity. ?? 1991 Springer-Verlag.

  6. Glassy phases and driven response of the phase-field-crystal model with random pinning.

    PubMed

    Granato, E; Ramos, J A P; Achim, C V; Lehikoinen, J; Ying, S C; Ala-Nissila, T; Elder, K R

    2011-09-01

    We study the structural correlations and the nonlinear response to a driving force of a two-dimensional phase-field-crystal model with random pinning. The model provides an effective continuous description of lattice systems in the presence of disordered external pinning centers, allowing for both elastic and plastic deformations. We find that the phase-field crystal with disorder assumes an amorphous glassy ground state, with only short-ranged positional and orientational correlations, even in the limit of weak disorder. Under increasing driving force, the pinned amorphous-glass phase evolves into a moving plastic-flow phase and then, finally, a moving smectic phase. The transverse response of the moving smectic phase shows a vanishing transverse critical force for increasing system sizes. PMID:22060323

  7. Randomized field experiments for program planning, development, and evaluation: an illustrative bibliography.

    PubMed

    Boruch, R F; Mcsweeny, A J; Soderstrom, E J

    1978-11-01

    This bibliography lists references to over 300 field experiments undertaken in schools, hospitals, prisons, and other social settings, mainly in the U.S. The list is divided into 10 major categories corresponding to the type of program under examination. They include: criminal and civil justice programs, mental health, training and education, mass media, information collection, utilization, commerce and industry, welfare, health, and family planning. The main purpose of the bibliography is to provide evidence on feasibility and scope of randomized field tests, since despite their advantages, it is not always clear from managerial, political, and other constraints on research that they can be mounted. Dates of publications range from 1944 to 1978. PMID:12335777

  8. Efficient Semantic Segmentation of Man-Made Scenes Using Fully-Connected Conditional Random Field

    NASA Astrophysics Data System (ADS)

    Li, Weihao; Yang, Michael Ying

    2016-06-01

    In this paper we explore semantic segmentation of man-made scenes using fully connected conditional random field (CRF). Images of man-made scenes display strong contextual dependencies in the spatial structures. Fully connected CRFs can model long-range connections within the image of man-made scenes and make use of contextual information of scene structures. The pairwise edge potentials of fully connected CRF models are defined by a linear combination of Gaussian kernels. Using filter-based mean field algorithm, the inference is very efficient. Our experimental results demonstrate that fully connected CRF performs better than previous state-of-the-art approaches on both eTRIMS dataset and LabelMeFacade dataset.

  9. Deviations from the mean-field predictions for the phase behaviour of random copolymers melts

    NASA Astrophysics Data System (ADS)

    Houdayer, J.; Müller, M.

    2002-06-01

    We investigate the phase behaviour of random copolymers melts via large-scale Monte Carlo simulations. We observe macrophase separation into A- and B-rich phases as predicted by the mean-field theory only for systems with a very large correlation λ of blocks along the polymer chains, far away from the Lifshitz point. For smaller values of λ, we find that a locally segregated, disordered microemulsion-like structure gradually forms as the temperature decreases. As we increase the number of blocks in the polymers, the region of macrophase separation further shrinks. The results of our Monte Carlo simulation are in agreement with a Ginzburg criterium, which suggests that the mean-field theory becomes worse as the number of blocks in polymers increases.

  10. The effect of adiabatic focusing upon charged particle propagation in random magnetic fields

    NASA Technical Reports Server (NTRS)

    Earl, J. A.

    1975-01-01

    Charged particles propagating along the diverging lines of force of a spatially inhomogeneous guiding field were considered as they are scattered by random fields. Their longitudinal transport is described in terms of the eigenfunctions of a Sturm-Liouville operator incorporating the effect of adiabatic focussing along with that of scattering. The relaxation times and characteristic velocities are graphed and tabulated. The particle density is evaluated as a function of space and time for two different regimes. In the first regime (relatively weak focussing), a diffusive mode of propagation is dominant but coherent modes are also dominant. In the second regime (strong focussing), diffusion does not occur and the propagation is purely coherent. This supercoherent mode corresponds exactly to the so-called scatter-free propagation of kilovolt solar flare electrons. On a larger scale, focussed transport provides an interpretation of many observed characteristics of extragalactic radio sources.

  11. Prediction coefficient estimation in Markov random fields for iterative x-ray CT reconstruction

    NASA Astrophysics Data System (ADS)

    Wang, Jiao; Sauer, Ken; Thibault, Jean-Baptiste; Yu, Zhou; Bouman, Charles

    2012-02-01

    Bayesian estimation is a statistical approach for incorporating prior information through the choice of an a priori distribution for a random field. A priori image models in Bayesian image estimation are typically low-order Markov random fields (MRFs), effectively penalizing only differences among immediately neighboring voxels. This limits spectral description to a crude low-pass model. For applications where more flexibility in spectral response is desired, potential benefit exists in models which accord higher a priori probability to content in higher frequencies. Our research explores the potential of larger neighborhoods in MRFs to raise the number of degrees of freedom in spectral description. Similarly to classical filter design, the MRF coefficients may be chosen to yield a desired pass-band/stop-band characteristic shape in the a priori model of the images. In this paper, we present an alternative design method, where high-quality sample images are used to estimate the MRF coefficients by fitting them into the spatial correlation of the given ensemble. This method allows us to choose weights that increase the probability of occurrence of strong components at particular spatial frequencies. This allows direct adaptation of the MRFs for different tissue types based on sample images with different frequency content. In this paper, we consider particularly the preservation of detail in bone structure in X-ray CT. Our results show that MRF design can be used to obtain bone emphasis similar to that of conventional filtered back-projection (FBP) with a bone kernel.

  12. Risk Prediction Modeling of Sequencing Data Using a Forward Random Field Method

    PubMed Central

    Wen, Yalu; He, Zihuai; Li, Ming; Lu, Qing

    2016-01-01

    With the advance in high-throughput sequencing technology, it is feasible to investigate the role of common and rare variants in disease risk prediction. While the new technology holds great promise to improve disease prediction, the massive amount of data and low frequency of rare variants pose great analytical challenges on risk prediction modeling. In this paper, we develop a forward random field method (FRF) for risk prediction modeling using sequencing data. In FRF, subjects’ phenotypes are treated as stochastic realizations of a random field on a genetic space formed by subjects’ genotypes, and an individual’s phenotype can be predicted by adjacent subjects with similar genotypes. The FRF method allows for multiple similarity measures and candidate genes in the model, and adaptively chooses the optimal similarity measure and disease-associated genes to reflect the underlying disease model. It also avoids the specification of the threshold of rare variants and allows for different directions and magnitudes of genetic effects. Through simulations, we demonstrate the FRF method attains higher or comparable accuracy over commonly used support vector machine based methods under various disease models. We further illustrate the FRF method with an application to the sequencing data obtained from the Dallas Heart Study. PMID:26892725

  13. Does Encouragement Matter in Improving Gender Imbalances in Technical Fields? Evidence from a Randomized Controlled Trial.

    PubMed

    Unkovic, Cait; Sen, Maya; Quinn, Kevin M

    2016-01-01

    Does encouragement help address gender imbalances in technical fields? We present the results of one of the first and largest randomized controlled trials on the topic. Using an applied statistics conference in the social sciences as our context, we randomly assigned half of a pool of 3,945 graduate students to receive two personalized emails encouraging them to apply (n = 1,976) and the other half to receive nothing (n = 1,969). We find a robust, positive effect associated with this simple intervention and suggestive evidence that women responded more strongly than men. However, we find that women's conference acceptance rates are higher within the control group than in the treated group. This is not the case for men. The reason appears to be that female applicants in the treated group solicited supporting letters at lower rates. Our findings therefore suggest that "low dose" interventions may promote diversity in STEM fields but may also have the potential to expose underlying disparities when used alone or in a non-targeted way. PMID:27097315

  14. A Gaussian random field model for similarity-based smoothing in Bayesian disease mapping.

    PubMed

    Baptista, Helena; Mendes, Jorge M; MacNab, Ying C; Xavier, Miguel; Caldas-de-Almeida, José

    2016-08-01

    Conditionally specified Gaussian Markov random field (GMRF) models with adjacency-based neighbourhood weight matrix, commonly known as neighbourhood-based GMRF models, have been the mainstream approach to spatial smoothing in Bayesian disease mapping. In the present paper, we propose a conditionally specified Gaussian random field (GRF) model with a similarity-based non-spatial weight matrix to facilitate non-spatial smoothing in Bayesian disease mapping. The model, named similarity-based GRF, is motivated for modelling disease mapping data in situations where the underlying small area relative risks and the associated determinant factors do not vary systematically in space, and the similarity is defined by "similarity" with respect to the associated disease determinant factors. The neighbourhood-based GMRF and the similarity-based GRF are compared and accessed via a simulation study and by two case studies, using new data on alcohol abuse in Portugal collected by the World Mental Health Survey Initiative and the well-known lip cancer data in Scotland. In the presence of disease data with no evidence of positive spatial correlation, the simulation study showed a consistent gain in efficiency from the similarity-based GRF, compared with the adjacency-based GMRF with the determinant risk factors as covariate. This new approach broadens the scope of the existing conditional autocorrelation models. PMID:27566771

  15. Scene-Layout Compatible Conditional Random Field for Classifying Terrestrial Laser Point Clouds

    NASA Astrophysics Data System (ADS)

    Luo, C.; Sohn, G.

    2014-08-01

    Terrestrial Laser Scanning (TLS) rapidly becomes a primary surveying tool due to its fast acquisition of highly dense threedimensional point clouds. For fully utilizing its benefits, developing a robust method to classify many objects of interests from huge amounts of laser point clouds is urgently required. Conditional Random Field (CRF) is a well-known discriminative classifier, which integrates local appearance of the observation (laser point) with spatial interactions among its neighbouring points in classification process. Typical CRFs employ generic label consistency using short-range dependency only, which often causes locality problem. In this paper, we present a multi-range and asymmetric Conditional Random Field (CRF) (maCRF), which adopts a priori information of scene-layout compatibility addressing long-range dependency. The proposed CRF constructs two graphical models, one for enhancing a local labelling smoothness within short-range (srCRF) and the other for favouring a global and asymmetric regularity of spatial arrangement between different object classes within long-range (lrCRF). This maCRF classifier assumes two graphical models (srCRF and lrCRF) are independent of each other. Final labelling decision was accomplished by probabilistically combining prediction results obtained from two CRF models. We validated maCRF's performance with TLS point clouds acquired from RIEGL LMS-Z390i scanner using cross validation. Experiment results demonstrate that synergetic classification improvement can be achievable by incorporating two CRF models.

  16. Seeking mathematics success for college students: a randomized field trial of an adapted approach

    NASA Astrophysics Data System (ADS)

    Gula, Taras; Hoessler, Carolyn; Maciejewski, Wes

    2015-11-01

    Many students enter the Canadian college system with insufficient mathematical ability and leave the system with little improvement. Those students who enter with poor mathematics ability typically take a developmental mathematics course as their first and possibly only mathematics course. The educational experiences that comprise a developmental mathematics course vary widely and are, too often, ineffective at improving students' ability. This trend is concerning, since low mathematics ability is known to be related to lower rates of success in subsequent courses. To date, little attention has been paid to the selection of an instructional approach to consistently apply across developmental mathematics courses. Prior research suggests that an appropriate instructional method would involve explicit instruction and practising mathematical procedures linked to a mathematical concept. This study reports on a randomized field trial of a developmental mathematics approach at a college in Ontario, Canada. The new approach is an adaptation of the JUMP Math program, an explicit instruction method designed for primary and secondary school curriculae, to the college learning environment. In this study, a subset of courses was assigned to JUMP Math and the remainder was taught in the same style as in the previous years. We found consistent, modest improvement in the JUMP Math sections compared to the non-JUMP sections, after accounting for potential covariates. The findings from this randomized field trial, along with prior research on effective education for developmental mathematics students, suggest that JUMP Math is a promising way to improve college student outcomes.

  17. A recursive model-reduction method for approximate inference in Gaussian Markov random fields.

    PubMed

    Johnson, Jason K; Willsky, Alan S

    2008-01-01

    This paper presents recursive cavity modeling--a principled, tractable approach to approximate, near-optimal inference for large Gauss-Markov random fields. The main idea is to subdivide the random field into smaller subfields, constructing cavity models which approximate these subfields. Each cavity model is a concise, yet faithful, model for the surface of one subfield sufficient for near-optimal inference in adjacent subfields. This basic idea leads to a tree-structured algorithm which recursively builds a hierarchy of cavity models during an "upward pass" and then builds a complementary set of blanket models during a reverse "downward pass." The marginal statistics of individual variables can then be approximated using their blanket models. Model thinning plays an important role, allowing us to develop thinned cavity and blanket models thereby providing tractable approximate inference. We develop a maximum-entropy approach that exploits certain tractable representations of Fisher information on thin chordal graphs. Given the resulting set of thinned cavity models, we also develop a fast preconditioner, which provides a simple iterative method to compute optimal estimates. Thus, our overall approach combines recursive inference, variational learning and iterative estimation. We demonstrate the accuracy and scalability of this approach in several challenging, large-scale remote sensing problems. PMID:18229805

  18. Effects of dehydroepiandrosterone supplementation during stressful military training: a randomized, controlled, double-blind field study.

    PubMed

    Taylor, Marcus K; Padilla, Genieleah A; Stanfill, Katherine E; Markham, Amanda E; Khosravi, Jasmine Y; Ward, Michael D Dial; Koehler, Matthew M

    2012-01-01

    Dehydroepiandrosterone (DHEA) and DHEA sulfate (DHEAS) are anabolic prehormones involved in the synthesis of testosterone. Both have been shown to exert neuroprotective effects during stress. In this randomized, controlled, double-blind field study, we examined the effects of a 12-day DHEA regimen on stress indices in military men undergoing survival training. Forty-eight men were randomized to either a DHEA treatment group or placebo control group. The treatment group received 50 mg of oral DHEA supplementation daily for 5 days during classroom training followed by 7 days of 75 mg during stressful field operations. Control subjects received identical placebo pills. Salivary assays (DHEA[S], testosterone, and cortisol) were conducted at four time points: distal pre-stress (T1), proximal pre-stress (T2), mock-captivity stress (T3), and 24 h recovery (T4). Subjective distress was also assessed at T1, T3, and T4. As expected, DHEA treatment resulted in higher salivary concentrations of DHEA and DHEAS during daily living, mock-captivity stress, and recovery. Similar patterns were observed for salivary markers of anabolic balance: DHEA/cortisol, DHEAS/cortisol, and testosterone/cortisol concentration ratios. Despite notable time effects, no group differences emerged for subjective distress. A brief, low dose DHEA regimen yielded large increases in salivary DHEA(S) concentrations and enhanced anabolic balance throughout sustained military stress. These physiological changes did not extrapolate to subjective distress. PMID:21790446

  19. Does Encouragement Matter in Improving Gender Imbalances in Technical Fields? Evidence from a Randomized Controlled Trial

    PubMed Central

    Unkovic, Cait; Sen, Maya; Quinn, Kevin M.

    2016-01-01

    Does encouragement help address gender imbalances in technical fields? We present the results of one of the first and largest randomized controlled trials on the topic. Using an applied statistics conference in the social sciences as our context, we randomly assigned half of a pool of 3,945 graduate students to receive two personalized emails encouraging them to apply (n = 1,976) and the other half to receive nothing (n = 1,969). We find a robust, positive effect associated with this simple intervention and suggestive evidence that women responded more strongly than men. However, we find that women’s conference acceptance rates are higher within the control group than in the treated group. This is not the case for men. The reason appears to be that female applicants in the treated group solicited supporting letters at lower rates. Our findings therefore suggest that “low dose” interventions may promote diversity in STEM fields but may also have the potential to expose underlying disparities when used alone or in a non-targeted way. PMID:27097315

  20. Metabolomics reveals the metabolic shifts following an intervention with rye bread in postmenopausal women- a randomized control trial

    PubMed Central

    2012-01-01

    Background Epidemiological studies have consistently shown that whole grain (WG) cereals can protect against the development of chronic diseases, but the underlying mechanism is not fully understood. Among WG products, WG rye is considered even more potent because of its unique discrepancy in postprandial insulin and glucose responses known as the rye factor. In this study, an NMR-based metabolomics approach was applied to study the metabolic effects of WG rye as a tool to determine the beneficial effects of WG rye on human health. Methods Thirty-three postmenopausal Finnish women with elevated serum total cholesterol (5.0-8.5 mmol/L) and BMI of 20–33 kg/m2 consumed a minimum of 20% of their daily energy intake as high fiber WG rye bread (RB) or refined wheat bread (WB) in a randomized, controlled, crossover design with two 8-wk intervention periods separated by an 8-wk washout period. At the end of each intervention period, fasting serum was collected for NMR-based metabolomics and the analysis of cholesterol fractions. Multilevel partial least squares discriminant analysis was used for paired comparisons of multivariate data. Results The metabolomics analysis of serum showed lower leucine and isoleucine and higher betaine and N,N-dimethylglycine levels after RB than WB intake. To further investigate the metabolic effects of RB, the serum cholesterol fractions were measured. Total- and LDL-cholesterol levels were higher after RB intake than after WB (p<0.05). Conclusions This study revealed favorable shifts in branched amino acid and single carbon metabolism and an unfavorable shift in serum cholesterol levels after RB intake in postmenopausal women, which should be considered for evaluating health beneficial effects of rye products. PMID:23088297

  1. Local Autoencoding for Parameter Estimation in a Hidden Potts-Markov Random Field.

    PubMed

    Song, Sanming; Si, Bailu; Herrmann, J Michael; Feng, Xisheng

    2016-05-01

    A local-autoencoding (LAE) method is proposed for the parameter estimation in a Hidden Potts-Markov random field model. Due to sampling cost, Markov chain Monte Carlo methods are rarely used in real-time applications. Like other heuristic methods, LAE is based on a conditional independence assumption. It adapts, however, the parameters in a block-by-block style with a simple Hebbian learning rule. Experiments with given label fields show that the LAE is able to converge in far less time than required for a scan. It is also possible to derive an estimate for LAE based on a Cramer–Rao bound that is similar to the classical maximum pseudolikelihood method. As a general algorithm, LAE can be used to estimate the parameters in anisotropic label fields. Furthermore, LAE is not limited to the classical Potts model and can be applied to other types of Potts models by simple label field transformations and straightforward learning rule extensions. Experimental results on image segmentations demonstrate the efficiency and generality of the LAE algorithm. PMID:27019491

  2. Discharge simulation using downscaled spatial rainfall field by introducing correlation effect in random cascade method

    NASA Astrophysics Data System (ADS)

    Shrestha, R. K.; Tachikawa, Y.; Takara, K.

    2003-04-01

    The simulation of spatial rainfall field based on non-homogenous random cascade method disaggregates a regionally averaged rainfall such as the GCM output. The cascade-generators are used to disaggregate and produce spatial patterns across the region (Over and Gupta, 1996; Chatchai et al. 2000; Tachikawa et al. 2003). However, the disaggregated data is rarely used to produce discharge by using distributed hydrological model. The hesitation to use disaggregated GCM data in discharge simulation is mainly due to lower reliability to reproduce spatial pattern and higher chance of magnitude fluctuation in a few trials of disaggregation. Long term disaggregation results, which are expected to produce true spatial pattern, may not be convenient for practical discharge simulation. A modified method is tested by keeping the volume balanced and forcing the location of cascade generators on the basis of spatial correlation of rainfall field with respect to surround regions. In this method, a reference matrix is prepared, which is calculated for every target grid by summing the multiplication of rainfall magnitude and spatial correlation coefficient of the respective reference grids. The reference matrix is used to adjust the location of random generator in two ways -- hierarchically and statistically. So, this method is designated as Hierarchical and Statistical Adjustment (HSA) method. The HSA method preserves the magnitude of random cascade generators but modifies the location. Unlike the previous non-homogenous random cascade method, this method produced similar spatial patterns as that of ground truth in every realization, which is a clear indication of improved reliability of the disaggregation method from coarse GCM output to a finer resolution as demanded by the hydrological model. The forced volume balance may be justified from the engineering aspect to maintain the same input quantity of rainfall in a watershed for hydrologic simulation purpose. The downscaled data

  3. Ensemble Solute Transport in 2-D Operator-Stable Random Fields

    NASA Astrophysics Data System (ADS)

    Monnig, N. D.; Benson, D. A.

    2006-12-01

    The heterogeneous velocity field that exists at many scales in an aquifer will typically cause a dissolved solute plume to grow at a rate faster than Fick's Law predicts. Some statistical model must be adopted to account for the aquifer structure that engenders the velocity heterogeneity. A fractional Brownian motion (fBm) model has been shown to create the long-range correlation that can produce continually faster-than-Fickian plume growth. Previous fBm models have assumed isotropic scaling (defined here by a scalar Hurst coefficient). Motivated by field measurements of aquifer hydraulic conductivity, recent techniques were developed to construct random fields with anisotropic scaling with a self-similarity parameter that is defined by a matrix. The growth of ensemble plumes is analyzed for transport through 2-D "operator- stable" fBm hydraulic conductivity (K) fields. Both the longitudinal and transverse Hurst coefficients are important to both plume growth rates and the timing and duration of breakthrough. Smaller Hurst coefficients in the transverse direction lead to more "continuity" or stratification in the direction of transport. The result is continually faster-than-Fickian growth rates, highly non-Gaussian ensemble plumes, and a longer tail early in the breakthrough curve. Contrary to some analytic stochastic theories for monofractal K fields, the plume growth rate never exceeds Mercado's [1967] purely stratified aquifer growth rate of plume apparent dispersivity proportional to mean distance. Apparent super-Mercado growth must be the result of other factors, such as larger plumes corresponding to either a larger initial plume size or greater variance of the ln(K) field.

  4. A Markov random field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data.

    PubMed

    Lin, Zhixiang; Li, Mingfeng; Sestan, Nenad; Zhao, Hongyu

    2016-04-01

    The statistical methodology developed in this study was motivated by our interest in studying neurodevelopment using the mouse brain RNA-Seq data set, where gene expression levels were measured in multiple layers in the somatosensory cortex across time in both female and male samples. We aim to identify differentially expressed genes between adjacent time points, which may provide insights on the dynamics of brain development. Because of the extremely small sample size (one male and female at each time point), simple marginal analysis may be underpowered. We propose a Markov random field (MRF)-based approach to capitalizing on the between layers similarity, temporal dependency and the similarity between sex. The model parameters are estimated by an efficient EM algorithm with mean field-like approximation. Simulation results and real data analysis suggest that the proposed model improves the power to detect differentially expressed genes than simple marginal analysis. Our method also reveals biologically interesting results in the mouse brain RNA-Seq data set. PMID:26926866

  5. A Poisson Random Field Framework Bridges Micro- To Macroscopic Scales In Microbial Transport

    NASA Astrophysics Data System (ADS)

    Yeghiazarian, L.; Safwat, A.; Shuster, W.; Samorodnitsky, G.; Whiteaker, T. L.; Maidment, D. R.

    2014-12-01

    Understanding microbial fate and transport in surface water and making accurate predictions is a formidable task. Evidence from experimental and observational studies unequivocally points to temporal and spatial variability in microbial distributions with significant correlation structure; and to the critical role of processes at the microscopic level. The temporal and spatial variability in microbial distributions arises from inherently random environmental factors and processes. Many cannot be described accurately using deterministic methods, necessitating a stochastic approach to microbial modeling. At the same time, microbial tracking studies identified significant spatial and temporal correlations in microbial distributions in streams, and highlighted the necessity of including microbial interactions with sediments, settling and re-suspension in models of microbial transport. Such understanding must be gained from microscopic, particle-scale research, because microdynamic interactions ultimately give rise to phenomena on higher scales. The challenge then is to be able to describe microbial behavior in probabilistic terms to take care of random drivers, while incorporating processes on microscopic scale and bridging the gap to macroscopic entities like concentrations that are used in watershed management. We have derived a stochastic modeling paradigm that bridges microscopic processes to macroscopic manifestation of microbial behavior in time and space, where the Markov behavior of individual microbes collectively translates into a non-homogeneous Poisson random field that describes microbial population dynamics. The Poisson framework is applied to a mixed-use watershed and implemented within ArcGIS, which makes a wealth of geographic, topologic, soil and other information, as well as data from national and regional datasets, instantly available. Probabilities of exceeding microbial safety thresholds are then obtained at any point in time and space in the

  6. Hyperspectral image clustering method based on artificial bee colony algorithm and Markov random fields

    NASA Astrophysics Data System (ADS)

    Sun, Xu; Yang, Lina; Gao, Lianru; Zhang, Bing; Li, Shanshan; Li, Jun

    2015-01-01

    Center-oriented hyperspectral image clustering methods have been widely applied to hyperspectral remote sensing image processing; however, the drawbacks are obvious, including the over-simplicity of computing models and underutilized spatial information. In recent years, some studies have been conducted trying to improve this situation. We introduce the artificial bee colony (ABC) and Markov random field (MRF) algorithms to propose an ABC-MRF-cluster model to solve the problems mentioned above. In this model, a typical ABC algorithm framework is adopted in which cluster centers and iteration conditional model algorithm's results are considered as feasible solutions and objective functions separately, and MRF is modified to be capable of dealing with the clustering problem. Finally, four datasets and two indices are used to show that the application of ABC-cluster and ABC-MRF-cluster methods could help to obtain better image accuracy than conventional methods. Specifically, the ABC-cluster method is superior when used for a higher power of spectral discrimination, whereas the ABC-MRF-cluster method can provide better results when used for an adjusted random index. In experiments on simulated images with different signal-to-noise ratios, ABC-cluster and ABC-MRF-cluster showed good stability.

  7. Automatic white matter lesion segmentation using contrast enhanced FLAIR intensity and Markov Random Field.

    PubMed

    Roy, Pallab Kanti; Bhuiyan, Alauddin; Janke, Andrew; Desmond, Patricia M; Wong, Tien Yin; Abhayaratna, Walter P; Storey, Elsdon; Ramamohanarao, Kotagiri

    2015-10-01

    White matter lesions (WMLs) are small groups of dead cells that clump together in the white matter of brain. In this paper, we propose a reliable method to automatically segment WMLs. Our method uses a novel filter to enhance the intensity of WMLs. Then a feature set containing enhanced intensity, anatomical and spatial information is used to train a random forest classifier for the initial segmentation of WMLs. Following that a reliable and robust edge potential function based Markov Random Field (MRF) is proposed to obtain the final segmentation by removing false positive WMLs. Quantitative evaluation of the proposed method is performed on 24 subjects of ENVISion study. The segmentation results are validated against the manual segmentation, performed under the supervision of an expert neuroradiologist. The results show a dice similarity index of 0.76 for severe lesion load, 0.73 for moderate lesion load and 0.61 for mild lesion load. In addition to that we have compared our method with three state of the art methods on 20 subjects of Medical Image Computing and Computer Aided Intervention Society's (MICCAI's) MS lesion challenge dataset, where our method shows better segmentation accuracy compare to the state of the art methods. These results indicate that the proposed method can assist the neuroradiologists in assessing the WMLs in clinical practice. PMID:26398564

  8. Distribution of the Height of Local Maxima of Gaussian Random Fields*

    PubMed Central

    Cheng, Dan; Schwartzman, Armin

    2015-01-01

    Let {f(t) : t ∈ T} be a smooth Gaussian random field over a parameter space T, where T may be a subset of Euclidean space or, more generally, a Riemannian manifold. We provide a general formula for the distribution of the height of a local maximum P{f(t0)>u∣t0 is a local maximum of f(t)} when f is non-stationary. Moreover, we establish asymptotic approximations for the overshoot distribution of a local maximum P{f(t0)>u+v∣t0 is a local maximum of f(t) and f(t0) > v} as v → ∞. Assuming further that f is isotropic, we apply techniques from random matrix theory related to the Gaussian orthogonal ensemble to compute such conditional probabilities explicitly when T is Euclidean or a sphere of arbitrary dimension. Such calculations are motivated by the statistical problem of detecting peaks in the presence of smooth Gaussian noise. PMID:26478714

  9. T-->0 mean-field population dynamics approach for the random 3-satisfiability problem.

    PubMed

    Zhou, Haijun

    2008-06-01

    During the past decade, phase-transition phenomena in the random 3-satisfiability ( 3 -SAT) problem has been intensively studied by statistical physics methods. In this work, we study the random 3 -SAT problem by the mean-field first-step replica-symmetry-broken cavity theory at the limit of temperature T-->0 . The reweighting parameter y of the cavity theory is allowed to approach infinity together with the inverse temperature beta with fixed ratio r=ybeta . Focusing on the system's space of satisfiable configurations, we carry out extensive population dynamics simulations using the technique of importance sampling, and we obtain the entropy density s(r) and complexity Sigma(r) of zero-energy clusters at different r values. We demonstrate that the population dynamics may reach different fixed points with different types of initial conditions. By knowing the trends of s(r) and Sigma(r) with r , we can judge whether a certain type of initial condition is appropriate at a given r value. This work complements and confirms the results of several other very recent theoretical studies. PMID:18643331

  10. Polarization dynamics and polarization time of random three-dimensional electromagnetic fields

    SciTech Connect

    Voipio, Timo; Setaelae, Tero; Shevchenko, Andriy; Friberg, Ari T.

    2010-12-15

    We investigate the polarization dynamics of random, stationary three-dimensional (3D) electromagnetic fields. For analyzing the time evolution of the instantaneous polarization state, two intensity-normalized polarization autocorrelation functions are introduced, one based on a geometric approach with the Poincare vectors and the other on energy considerations with the Jones vectors. Both approaches lead to the same conclusions on the rate and strength of the polarization dynamics and enable the definition of a polarization time over which the state of polarization remains essentially unchanged. For fields obeying Gaussian statistics, the two correlation functions are shown to be expressible in terms of quantities characterizing partial 3D polarization and electromagnetic coherence. The 3D degree of polarization is found to have the same meaning in the 3D polarization dynamics as the usual two-dimensional (2D) degree of polarization does with planar fields. The formalism is demonstrated with several examples, and it is expected to be useful in applications dealing with polarization fluctuations of 3D light.

  11. Stochastic generation of explicit pore structures by thresholding Gaussian random fields

    NASA Astrophysics Data System (ADS)

    Hyman, Jeffrey D.; Winter, C. Larrabee

    2014-11-01

    We provide a description and computational investigation of an efficient method to stochastically generate realistic pore structures. Smolarkiewicz and Winter introduced this specific method in pores resolving simulation of Darcy flows (Smolarkiewicz and Winter, 2010 [1]) without giving a complete formal description or analysis of the method, or indicating how to control the parameterization of the ensemble. We address both issues in this paper. The method consists of two steps. First, a realization of a correlated Gaussian field, or topography, is produced by convolving a prescribed kernel with an initial field of independent, identically distributed random variables. The intrinsic length scales of the kernel determine the correlation structure of the topography. Next, a sample pore space is generated by applying a level threshold to the Gaussian field realization: points are assigned to the void phase or the solid phase depending on whether the topography over them is above or below the threshold. Hence, the topology and geometry of the pore space depend on the form of the kernel and the level threshold. Manipulating these two user prescribed quantities allows good control of pore space observables, in particular the Minkowski functionals. Extensions of the method to generate media with multiple pore structures and preferential flow directions are also discussed. To demonstrate its usefulness, the method is used to generate a pore space with physical and hydrological properties similar to a sample of Berea sandstone.

  12. A NOVEL EMISSION SPECTRUM FROM A RELATIVISTIC ELECTRON MOVING IN A RANDOM MAGNETIC FIELD

    SciTech Connect

    Teraki, Yuto; Takahara, Fumio

    2011-07-10

    We numerically calculate the radiation spectrum from relativistic electrons moving in small-scale turbulent magnetic fields expected in high-energy astrophysical sources. Such a radiation spectrum is characterized by the strength parameter a = {lambda}{sub B} e|B|/mc {sup 2}, where {lambda}{sub B} is the length scale of the turbulent field. When a is much larger than the Lorentz factor of a radiating electron {gamma}, synchrotron radiation is realized, while a << 1 corresponds to the so-called jitter radiation regime. Because for 1 < a < {gamma} we cannot use either approximations, we should have recourse to the Lienard-Wiechert potential to evaluate the radiation spectrum, which is performed in this Letter. We generate random magnetic fields assuming Kolmogorov turbulence, inject monoenergetic electrons, solve the equation of motion, and calculate the radiation spectrum. We perform numerical calculations for several values of a with {gamma} = 10. We obtain various types of spectra ranging between jitter radiation and synchrotron radiation. For a {approx} 7, the spectrum takes a novel shape which had not been noticed up to now. It is like a synchrotron spectrum in the middle energy region, but in the low frequency region it is a broken power law and in the high frequency region an extra power-law component appears beyond the synchrotron cutoff. We give a physical explanation of these features.

  13. Spin-glass phase transition and behavior of nonlinear susceptibility in the Sherrington-Kirkpatrick model with random fields

    NASA Astrophysics Data System (ADS)

    Morais, C. V.; Zimmer, F. M.; Lazo, M. J.; Magalhães, S. G.; Nobre, F. D.

    2016-06-01

    The behavior of the nonlinear susceptibility χ3 and its relation to the spin-glass transition temperature Tf in the presence of random fields are investigated. To accomplish this task, the Sherrington-Kirkpatrick model is studied through the replica formalism, within a one-step replica-symmetry-breaking procedure. In addition, the dependence of the Almeida-Thouless eigenvalue λAT (replicon) on the random fields is analyzed. Particularly, in the absence of random fields, the temperature Tf can be traced by a divergence in the spin-glass susceptibility χSG, which presents a term inversely proportional to the replicon λAT. As a result of a relation between χSG and χ3, the latter also presents a divergence at Tf, which comes as a direct consequence of λAT=0 at Tf. However, our results show that, in the presence of random fields, χ3 presents a rounded maximum at a temperature T* which does not coincide with the spin-glass transition temperature Tf (i.e., T*>Tf for a given applied random field). Thus, the maximum value of χ3 at T* reflects the effects of the random fields in the paramagnetic phase instead of the nontrivial ergodicity breaking associated with the spin-glass phase transition. It is also shown that χ3 still maintains a dependence on the replicon λAT, although in a more complicated way as compared with the case without random fields. These results are discussed in view of recent observations in the LiHoxY1 -xF4 compound.

  14. RANDOM AND SYSTEMATIC FIELD ERRORS IN THE SNS RING: A STUDY OF THEIR EFFECTS AND COMPENSATION

    SciTech Connect

    GARDNER,C.J.; LEE,Y.Y.; WENG,W.T.

    1998-06-22

    The Accumulator Ring for the proposed Spallation Neutron Source (SNS) [l] is to accept a 1 ms beam pulse from a 1 GeV Proton Linac at a repetition rate of 60 Hz. For each beam pulse, 10{sup 14} protons (some 1,000 turns) are to be accumulated via charge-exchange injection and then promptly extracted to an external target for the production of neutrons by spallation. At this very high intensity, stringent limits (less than two parts in 10,000 per pulse) on beam loss during accumulation must be imposed in order to keep activation of ring components at an acceptable level. To stay within the desired limit, the effects of random and systematic field errors in the ring require careful attention. This paper describes the authors studies of these effects and the magnetic corrector schemes for their compensation.

  15. Specifications and Martin boundaries for P(Φ)2-random fields

    NASA Astrophysics Data System (ADS)

    Röckner, Michael

    1986-03-01

    It is shown that P(Φ)2-Gibbs states in the sense of Guerra, Rosen and Simon are given by a specification. The construction of the specification is based on finding a proper version of the interaction density given by the polynomial P. The existence of this version follows from the fact that all powers of the solution of a Dirichlet problem for an open bounded set U with boundary data given by a distribution are integrable on U. As a consequence the Martin boundary theory for specifications can be applied to P(Φ)2-random fields. It follows that any P(Φ)2-Gibbs state can be represented in terms of extreme Gibbs states. In certain cases the extreme Gibbs states are characterized in terms of harmonic functions. It follows, in particular, that for any given boundary condition introduced so far the associated cutoff P(Φ)2-measure has a representation as an integral over harmonic functions.

  16. Evaluating Consumer m-Health Services for Promoting Healthy Eating: A Randomized Field Experiment

    PubMed Central

    Kato-Lin, Yi-Chin; Padman, Rema; Downs, Julie; Abhishek, Vibhanshu

    2015-01-01

    Mobile apps have great potential to deliver promising interventions to engage consumers and change their health-related behaviors, such as healthy eating. Currently, the interventions for promoting healthy eating are either too onerous to keep consumers engaged or too restrictive to keep consumers connected with healthcare professionals. In addition, while social media allows individuals to receive information from many sources, it is unclear how peer support interacts with professional support in the context of such interventions. This study proposes and evaluates three mobile-enabled interventions to address these challenges. We examine their effects on user engagement and food choices via a 4-month randomized field experiment. Mixed models provide strong evidence of the positive effect of image-based dietitian support and negative effects of peer support, and moderate evidence of the positive effects of mobile-based visual diary, highlighting the value of mobile apps for delivering advanced interventions to engage users and facilitate behavior change. PMID:26958294

  17. Hysteresis in random-field Ising model on a Bethe lattice with a mixed coordination number

    NASA Astrophysics Data System (ADS)

    Shukla, Prabodh; Thongjaomayum, Diana

    2016-06-01

    We study zero-temperature hysteresis in the random-field Ising model on a Bethe lattice where a fraction c of the sites have coordination number z = 4 while the remaining fraction 1-c have z = 3. Numerical simulations as well as probabilistic methods are used to show the existence of critical hysteresis for all values of c\\gt 0. This extends earlier results for c = 0 and c = 1 to the entire range 0≤slant c≤slant 1, and provides new insight in non-equilibrium critical phenomena. Our analysis shows that a spanning avalanche can occur on a lattice even in the absence of a spanning cluster of z = 4 sites.

  18. Kinetic equations for hopping transport and spin relaxation in a random magnetic field

    NASA Astrophysics Data System (ADS)

    Shumilin, A. V.; Kabanov, V. V.

    2015-07-01

    We derive the kinetic equations for a hopping transport that take into account an electron spin and the possibility of double occupation. In the Ohmic regime, the equations are reduced to the generalized Miller-Abrahams resistor network. We apply these equations to the problem of the magnetic moment relaxation due to the interaction with the random hyperfine fields. It is shown that in a wide range of parameters the relaxation rate is governed by the hops with the similar rates as spin precession frequency. It is demonstrated that at the large time scale spin relaxation is nonexponential. We argue that the nonexponential relaxation of the magnetic moment is related to the spin of electrons in the slow-relaxing traps. Interestingly, the traps can significantly influence the spin relaxation in the infinite conducting cluster at large times.

  19. Long-range random transverse-field Ising model in three dimensions

    NASA Astrophysics Data System (ADS)

    Kovács, István A.; Juhász, Róbert; Iglói, Ferenc

    2016-05-01

    We consider the random transverse-field Ising model in d =3 dimensions with long-range ferromagnetic interactions which decay as a power α >d with the distance. Using a variant of the strong-disorder renormalization group method we study numerically the phase-transition point from the paramagnetic side. We find that the fixed point controlling the transition is of the strong-disorder type, and based on experience with other similar systems, we expect the results to be qualitatively correct, but probably not asymptotically exact. The distribution of the (sample dependent) pseudocritical points is found to scale with 1 /lnL , L being the linear size of the sample. Similarly, the critical magnetization scales with (lnL) χ/Ld and the excitation energy behaves as L-α. Using extreme-value statistics we argue that extrapolating from the ferromagnetic side the magnetization approaches a finite limiting value and thus the transition is of mixed order.

  20. High energy X-ray phase and dark-field imaging using a random absorption mask

    NASA Astrophysics Data System (ADS)

    Wang, Hongchang; Kashyap, Yogesh; Cai, Biao; Sawhney, Kawal

    2016-07-01

    High energy X-ray imaging has unique advantage over conventional X-ray imaging, since it enables higher penetration into materials with significantly reduced radiation damage. However, the absorption contrast in high energy region is considerably low due to the reduced X-ray absorption cross section for most materials. Even though the X-ray phase and dark-field imaging techniques can provide substantially increased contrast and complementary information, fabricating dedicated optics for high energies still remain a challenge. To address this issue, we present an alternative X-ray imaging approach to produce transmission, phase and scattering signals at high X-ray energies by using a random absorption mask. Importantly, in addition to the synchrotron radiation source, this approach has been demonstrated for practical imaging application with a laboratory-based microfocus X-ray source. This new imaging method could be potentially useful for studying thick samples or heavy materials for advanced research in materials science.

  1. Face Association for Videos Using Conditional Random Fields and Max-Margin Markov Networks.

    PubMed

    Du, Ming; Chellappa, Rama

    2016-09-01

    We address the video-based face association problem, in which one attempts to extract the face tracks of multiple subjects while maintaining label consistency. Traditional tracking algorithms have difficulty in handling this task, especially when challenging nuisance factors like motion blur, low resolution or significant camera motions are present. We demonstrate that contextual features, in addition to face appearance itself, play an important role in this case. We propose principled methods to combine multiple features using Conditional Random Fields and Max-Margin Markov networks to infer labels for the detected faces. Different from many existing approaches, our algorithms work in online mode and hence have a wider range of applications. We address issues such as parameter learning, inference and handling false positves/negatives that arise in the proposed approach. Finally, we evaluate our approach on several public databases. PMID:26552075

  2. Bayesian Clustering Using Hidden Markov Random Fields in Spatial Population Genetics

    PubMed Central

    François, Olivier; Ancelet, Sophie; Guillot, Gilles

    2006-01-01

    We introduce a new Bayesian clustering algorithm for studying population structure using individually geo-referenced multilocus data sets. The algorithm is based on the concept of hidden Markov random field, which models the spatial dependencies at the cluster membership level. We argue that (i) a Markov chain Monte Carlo procedure can implement the algorithm efficiently, (ii) it can detect significant geographical discontinuities in allele frequencies and regulate the number of clusters, (iii) it can check whether the clusters obtained without the use of spatial priors are robust to the hypothesis of discontinuous geographical variation in allele frequencies, and (iv) it can reduce the number of loci required to obtain accurate assignments. We illustrate and discuss the implementation issues with the Scandinavian brown bear and the human CEPH diversity panel data set. PMID:16888334

  3. Theory of Distribution Estimation of Hyperparameters in Markov Random Field Models

    NASA Astrophysics Data System (ADS)

    Sakamoto, Hirotaka; Nakanishi-Ohno, Yoshinori; Okada, Masato

    2016-06-01

    We investigated the performance of distribution estimation of hyperparameters in Markov random field models proposed by Nakanishi-Ohno et al., J. Phys. A 47, 045001 (2014) when used to evaluate the confidence of data. We analytically calculated the configurational average, with respect to data, of the negative logarithm of the posterior distribution, which is called free energy based on an analogy with statistical mechanics. This configurational average of free energy shrinks as the amount of data increases. Our results theoretically confirm the numerical results from that previous study.

  4. Adaptation of the projection-slice theorem for stock valuation estimation using random Markov fields

    NASA Astrophysics Data System (ADS)

    Riasati, Vahid R.

    2009-04-01

    The Projection-Slice Synthetic Discriminant function filter is utilized with Random Markov Fields, RMF to estimate trends that may be used as prediction for stock valuation through the representation of the market behavior as a hidden Markov Model, HMM. In this work, we utilize a set of progressive and contiguous time segments of a given stock, and treat the set as a two dimensional object that has been represented by its one-d projections. The abstract two-D object is thus an incarnation of N-temporal projections. The HMM is then utilized to generate N+1 projections that maximizes the two-dimensional correlation peak between the data and the HMM-generated stochastic processes. This application of the PSDF provides a method of stock valuation prediction via the market stochastic behavior utilized in the filter.

  5. Mean-field dynamics of a random neural network with noise

    NASA Astrophysics Data System (ADS)

    Klinshov, Vladimir; Franović, Igor

    2015-12-01

    We consider a network of randomly coupled rate-based neurons influenced by external and internal noise. We derive a second-order stochastic mean-field model for the network dynamics and use it to analyze the stability and bifurcations in the thermodynamic limit, as well as to study the fluctuations due to the finite-size effect. It is demonstrated that the two types of noise have substantially different impact on the network dynamics. While both sources of noise give rise to stochastic fluctuations in the case of the finite-size network, only the external noise affects the stationary activity levels of the network in the thermodynamic limit. We compare the theoretical predictions with the direct simulation results and show that they agree for large enough network sizes and for parameter domains sufficiently away from bifurcations.

  6. Object-oriented image coding scheme based on DWT and Markov random field

    NASA Astrophysics Data System (ADS)

    Zheng, Lei; Wu, Hsien-Hsun S.; Liu, Jyh-Charn S.; Chan, Andrew K.

    1998-12-01

    In this paper, we introduce an object-oriented image coding algorithm to differentiate regions of interest (ROI) in visual communications. Our scheme is motivated by the fact that in visual communications, image contents (objects) are not equally important. For a given network bandwidth budget, one should give the highest transmission priority to the most interesting object, and serve the remaining ones at lower priorities. We propose a DWT based Multiresolution Markov Random Field technique to segment image objects according to their textures. We show that this technique can effectively distinguish visual objects and assign them different priorities. This scheme can be integrated with our ROI compression coder, the Generalized Self-Similarity Tress codex, for networking applications.

  7. Extended power-law scaling of heavy-tailed random fields or processes

    NASA Astrophysics Data System (ADS)

    Guadagnini, A.; Riva, M.; Neuman, S. P.

    2012-06-01

    We analyze the scaling behaviors of two log permeability data sets showing heavy-tailed frequency distributions in three and two spatial dimensions, respectively. One set consists of 1-m scale pneumatic packer test data from six vertical and inclined boreholes spanning a decameters scale block of unsaturated fractured tuffs near Superior, Arizona, the other of pneumatic minipermeameter data measured at a spacing of 15 cm along two horizontal transects on a 21 m long outcrop of lower-shoreface bioturbated sandstone near Escalante, Utah. Order q sample structure functions of each data set scale as a power ξ (q) of separation scale or lag, s, over limited ranges of s. A procedure known as Extended Self-Similarity (ESS) extends this range to all lags and yields a nonlinear (concave) functional relationship between ξ (q) and q. Whereas the literature tends to associate extended and nonlinear power-law scaling with multifractals or fractional Laplace motions, we have shown elsewhere that (a) ESS of data having a normal frequency distribution is theoretically consistent with (Gaussian) truncated (additive, self-affine, monofractal) fractional Brownian motion (tfBm), the latter being unique in predicting a breakdown in power-law scaling at small and large lags, and (b) nonlinear power-law scaling of data having either normal or heavy-tailed frequency distributions is consistent with samples from sub-Gaussian random fields or processes subordinated to tfBm, stemming from lack of ergodicity which causes sample moments to scale differently than do their ensemble counterparts. Here we (i) demonstrate that the above two data sets are consistent with sub-Gaussian random fields subordinated to tfBm and (ii) provide maximum likelihood estimates of parameters characterizing the corresponding Lévy stable subordinators and tfBm functions.

  8. Crop Type Mapping from a Sequence of Terrasar-X Images with Dynamic Conditional Random Fields

    NASA Astrophysics Data System (ADS)

    Kenduiywo, B. K.; Bargiel, D.; Soergel, U.

    2016-06-01

    Crop phenology is dynamic as it changes with times of the year. Such biophysical processes also look spectrally different to remote sensing satellites. Some crops may depict similar spectral properties if their phenology coincide, but differ later when their phenology diverge. Thus, conventional approaches that select only images from phenological stages where crops are distinguishable for classification, have low discrimination. In contrast, stacking images within a cropping season limits discrimination to a single feature space that can suffer from overlapping classes. Since crop backscatter varies with time, it can aid discrimination. Therefore, our main objective is to develop a crop sequence classification method using multitemporal TerraSAR-X images. We adopt first order markov assumption in undirected temporal graph sequence. This property is exploited to implement Dynamic Conditional Random Fields (DCRFs). Our DCRFs model has a repeated structure of temporally connected Conditional Random Fields (CRFs). Each node in the sequence is connected to its predecessor via conditional probability matrix. The matrix is computed using posterior class probabilities from association potential. This way, there is a mutual temporal exchange of phenological information observed in TerraSAR-X images. When compared to independent epoch classification, the designed DCRF model improved crop discrimination at each epoch in the sequence. However, government, insurers, agricultural market traders and other stakeholders are interested in the quantity of a certain crop in a season. Therefore, we further develop a DCRF ensemble classifier. The ensemble produces an optimal crop map by maximizing over posterior class probabilities selected from the sequence based on maximum F1-score and weighted by correctness. Our ensemble technique is compared to standard approach of stacking all images as bands for classification using Maximum Likelihood Classifier (MLC) and standard CRFs. It

  9. A Randomized, Controlled Field Trial for the Prevention of Jellyfish Stings With a Topical Sting Inhibitor

    PubMed Central

    Boulware, David R.

    2007-01-01

    Background Jellyfish stings are a common occurrence among ocean goers worldwide with an estimated 150 million envenomations annually. Fatalities and hospitalizations occur annually, particularly in the Indo-Pacific regions. A new topical jellyfish sting inhibitor based on the mucous coating of the clown fish prevents 85% of jellyfish stings in laboratory settings. The field effectiveness is unknown. The objective is to evaluate the field efficacy of the jellyfish sting inhibitor, Safe Sea™. Methods A double-blind, randomized, placebo-controlled trial occurred at the Dry Tortugas National Park, FL, USA and Sapodilla Cayes, Belize. Participants were healthy volunteers planning to snorkel for 30 to 45 minutes. Ten minutes prior to swimming, each participant was directly observed applying a blinded sample of Safe Sea (Nidaria Technology Ltd, Jordan Valley, Israel) to one side of their body and a blinded sample of Coppertone® (Schering-Plough, Kenilworth, NJ, USA) to the contralateral side as placebo control. Masked 26 g samples of both Safe Sea SPF15 and Coppertone® SPF15 were provided in identical containers to achieve 2 mg/cm2 coverage. Sides were randomly chosen by participants. The incidence of jellyfish stings was the main outcome measure. This was assessed by participant interview and examination as subjects exited the water. Results A total of 82 observed water exposures occurred. Thirteen jellyfish stings occurred during the study period for a 16% incidence. Eleven jellyfish stings occurred with placebo, two with the sting inhibitor, resulting in a relative risk reduction of 82% (95% confidence interval: 21%–96%; p = 0.02). No seabather’s eruption or side effects occurred. Conclusions Safe Sea is a topical barrier cream effective at preventing >80% jellyfish stings under real-world conditions. PMID:16706948

  10. Classifying Urban Land cover using Spatial Weights: A Comparison of Discriminant Analysis and Markov Random Fields

    NASA Astrophysics Data System (ADS)

    Wentz, E.; Song, Y.

    2011-12-01

    Classifying urban area images is challenging because of the heterogeneous nature of the urban landscape. This means that each pixel represents a mixture of classes with potentially highly variable various spectral values. Land cover classification approaches using ancillary data, such as knowledge based or expert systems, have shown to improve the classification accuracy in urban areas, particularly with medium or low-resolution imagery. This is because information other than the spectral signatures is used to assign pixels to classes. Defining rules is challenging and acquiring appropriate ancillary data may not always be possible. The goal of this study is to compare the results of three approaches to classify urban land cover with medium resolution data with and without ancillary information. We compare discriminant analysis, Markov random fields, and an expert system. Furthermore, we explore whether including spatial weights improves classification accuracy of the discriminant model. Discriminant analysis is a statistical technique used to predict group membership for a pixel based on the linear combination of independent variables. Adding spatial weights to this includes a weighted value for neighboring pixels. Markov random fields represent spatial dependencies through conditional relationships defined using Markov principles. In comparison to using spatial dependencies in neighbouring pixels, strict per pixel statistical analysis, however, does not consider the spatial dependencies among neighbouring pixels. Our study showed that approaches using ancillary data continued to outperform strict spectral classifiers but that using a spatial weight improved the results. Furthermore, results demonstrate that when the discriminant analysis technique works well then the spatially weighted approach works better. However, when the discriminant analysis performs ineffectively, those poor results are magnified. This study suggests that spatial weights improve the

  11. The effect of random field errors on the radiation spectra of selected APS (Advanced Photon Source) undulators

    SciTech Connect

    Alp, E.E.; Viccaro, P.J.

    1987-08-01

    The effect of random magnetic field errors are introduced into the calculations of spectral characteristics of tunable undulators for the proposed 7 GeV Advanced Photon Source (APS). Single electron calculations are made for an undulator with a first harmonic radiation tunable between 3.5 and 13 keV. Using the universal curves developed by Kincaid, the effect of randomly distributed field errors on the first and third harmonics of two proposed typical undulators are calculated. It is found that the lower limit of 0.5% in field errors is more than sufficient for the successful operation of the undulators planned for the APS.

  12. Class-specific weighting for Markov random field estimation: application to medical image segmentation.

    PubMed

    Monaco, James P; Madabhushi, Anant

    2012-12-01

    Many estimation tasks require Bayesian classifiers capable of adjusting their performance (e.g. sensitivity/specificity). In situations where the optimal classification decision can be identified by an exhaustive search over all possible classes, means for adjusting classifier performance, such as probability thresholding or weighting the a posteriori probabilities, are well established. Unfortunately, analogous methods compatible with Markov random fields (i.e. large collections of dependent random variables) are noticeably absent from the literature. Consequently, most Markov random field (MRF) based classification systems typically restrict their performance to a single, static operating point (i.e. a paired sensitivity/specificity). To address this deficiency, we previously introduced an extension of maximum posterior marginals (MPM) estimation that allows certain classes to be weighted more heavily than others, thus providing a means for varying classifier performance. However, this extension is not appropriate for the more popular maximum a posteriori (MAP) estimation. Thus, a strategy for varying the performance of MAP estimators is still needed. Such a strategy is essential for several reasons: (1) the MAP cost function may be more appropriate in certain classification tasks than the MPM cost function, (2) the literature provides a surfeit of MAP estimation implementations, several of which are considerably faster than the typical Markov Chain Monte Carlo methods used for MPM, and (3) MAP estimation is used far more often than MPM. Consequently, in this paper we introduce multiplicative weighted MAP (MWMAP) estimation-achieved via the incorporation of multiplicative weights into the MAP cost function-which allows certain classes to be preferred over others. This creates a natural bias for specific classes, and consequently a means for adjusting classifier performance. Similarly, we show how this multiplicative weighting strategy can be applied to the MPM

  13. Stochastic generation of explicit pore structures by thresholding Gaussian random fields

    SciTech Connect

    Hyman, Jeffrey D.; Winter, C. Larrabee

    2014-11-15

    We provide a description and computational investigation of an efficient method to stochastically generate realistic pore structures. Smolarkiewicz and Winter introduced this specific method in pores resolving simulation of Darcy flows (Smolarkiewicz and Winter, 2010 [1]) without giving a complete formal description or analysis of the method, or indicating how to control the parameterization of the ensemble. We address both issues in this paper. The method consists of two steps. First, a realization of a correlated Gaussian field, or topography, is produced by convolving a prescribed kernel with an initial field of independent, identically distributed random variables. The intrinsic length scales of the kernel determine the correlation structure of the topography. Next, a sample pore space is generated by applying a level threshold to the Gaussian field realization: points are assigned to the void phase or the solid phase depending on whether the topography over them is above or below the threshold. Hence, the topology and geometry of the pore space depend on the form of the kernel and the level threshold. Manipulating these two user prescribed quantities allows good control of pore space observables, in particular the Minkowski functionals. Extensions of the method to generate media with multiple pore structures and preferential flow directions are also discussed. To demonstrate its usefulness, the method is used to generate a pore space with physical and hydrological properties similar to a sample of Berea sandstone. -- Graphical abstract: -- Highlights: •An efficient method to stochastically generate realistic pore structures is provided. •Samples are generated by applying a level threshold to a Gaussian field realization. •Two user prescribed quantities determine the topology and geometry of the pore space. •Multiple pore structures and preferential flow directions can be produced. •A pore space based on Berea sandstone is generated.

  14. Sub-pixel porosity revealed by x-ray scatter dark field imaging

    NASA Astrophysics Data System (ADS)

    Revol, V.; Jerjen, I.; Kottler, C.; Schütz, P.; Kaufmann, R.; Lüthi, T.; Sennhauser, U.; Straumann, U.; Urban, C.

    2011-08-01

    X-ray scatter dark field imaging based on the Talbot-Lau interferometer allows for the measurement of ultra-small angle x-ray scattering. The latter is related to the variations in the electron density in the sample at the sub- and micron-scale. Therefore, information on features of the object below the detector resolution can be revealed. In this article, it is demonstrated that scatter dark field imaging is particularly adapted to the study of a material's porosity. An interferometer, optimized for x-ray energies around 50 keV, enables the investigation of aluminum welding with conventional laboratory x-ray tubes. The results show an unprecedented contrast between the pool and the aluminum workpiece. Our conclusions are confirmed due to micro-tomographic three-dimensional reconstructions of the same object with a microscopic resolution.

  15. Temporal coherence of the acoustic field forward propagated through a continental shelf with random internal waves.

    PubMed

    Gong, Zheng; Chen, Tianrun; Ratilal, Purnima; Makris, Nicholas C

    2013-11-01

    An analytical model derived from normal mode theory for the accumulated effects of range-dependent multiple forward scattering is applied to estimate the temporal coherence of the acoustic field forward propagated through a continental-shelf waveguide containing random three-dimensional internal waves. The modeled coherence time scale of narrow band low-frequency acoustic field fluctuations after propagating through a continental-shelf waveguide is shown to decay with a power-law of range to the -1/2 beyond roughly 1 km, decrease with increasing internal wave energy, to be consistent with measured acoustic coherence time scales. The model should provide a useful prediction of the acoustic coherence time scale as a function of internal wave energy in continental-shelf environments. The acoustic coherence time scale is an important parameter in remote sensing applications because it determines (i) the time window within which standard coherent processing such as matched filtering may be conducted, and (ii) the number of statistically independent fluctuations in a given measurement period that determines the variance reduction possible by stationary averaging. PMID:24180758

  16. Compensated Row-Column Ultrasound Imaging System Using Fisher Tippett Multilayered Conditional Random Field Model

    PubMed Central

    Ben Daya, Ibrahim; Chen, Albert I. H.; Shafiee, Mohammad Javad; Wong, Alexander; Yeow, John T. W.

    2015-01-01

    3-D ultrasound imaging offers unique opportunities in the field of non destructive testing that cannot be easily found in A-mode and B-mode images. To acquire a 3-D ultrasound image without a mechanically moving transducer, a 2-D array can be used. The row column technique is preferred over a fully addressed 2-D array as it requires a significantly lower number of interconnections. Recent advances in 3-D row-column ultrasound imaging systems were largely focused on sensor design. However, these imaging systems face three intrinsic challenges that cannot be addressed by improving sensor design alone: speckle noise, sparsity of data in the imaged volume, and the spatially dependent point spread function of the imaging system. In this paper, we propose a compensated row-column ultrasound image reconstruction system using Fisher-Tippett multilayered conditional random field model. Tests carried out on both simulated and real row-column ultrasound images show the effectiveness of our proposed system as opposed to other published systems. Visual assessment of the results show our proposed system’s potential at preserving detail and reducing speckle. Quantitative analysis shows that our proposed system outperforms previously published systems when evaluated with metrics such as Peak Signal to Noise Ratio, Coefficient of Correlation, and Effective Number of Looks. These results show the potential of our proposed system as an effective tool for enhancing 3-D row-column imaging. PMID:26658577

  17. Multilayer Markov Random Field models for change detection in optical remote sensing images

    NASA Astrophysics Data System (ADS)

    Benedek, Csaba; Shadaydeh, Maha; Kato, Zoltan; Szirányi, Tamás; Zerubia, Josiane

    2015-09-01

    In this paper, we give a comparative study on three Multilayer Markov Random Field (MRF) based solutions proposed for change detection in optical remote sensing images, called Multicue MRF, Conditional Mixed Markov model, and Fusion MRF. Our purposes are twofold. On one hand, we highlight the significance of the focused model family and we set them against various state-of-the-art approaches through a thematic analysis and quantitative tests. We discuss the advantages and drawbacks of class comparison vs. direct approaches, usage of training data, various targeted application fields and different ways of Ground Truth generation, meantime informing the Reader in which roles the Multilayer MRFs can be efficiently applied. On the other hand we also emphasize the differences between the three focused models at various levels, considering the model structures, feature extraction, layer interpretation, change concept definition, parameter tuning and performance. We provide qualitative and quantitative comparison results using principally a publicly available change detection database which contains aerial image pairs and Ground Truth change masks. We conclude that the discussed models are competitive against alternative state-of-the-art solutions, if one uses them as pre-processing filters in multitemporal optical image analysis. In addition, they cover together a large range of applications, considering the different usage options of the three approaches.

  18. Diffuse scattered field of elastic waves from randomly rough surfaces using an analytical Kirchhoff theory

    NASA Astrophysics Data System (ADS)

    Shi, F.; Lowe, M. J. S.; Xi, X.; Craster, R. V.

    2016-07-01

    We develop an elastodynamic theory to predict the diffuse scattered field of elastic waves by randomly rough surfaces, for the first time, with the aid of the Kirchhoff approximation (KA). Analytical expressions are derived incorporating surface statistics, to represent the expectation of the angular distribution of the diffuse intensity for different modes. The analytical solutions are successfully verified with numerical Monte Carlo simulations, and also validated by comparison with experiments. We then apply the theory to quantitatively investigate the effects of the roughness and the shear-to-compressional wave speed ratio on the mode conversion and the scattering intensity, from low to high roughness within the valid region of KA. Both the direct and the mode converted intensities are significantly affected by the roughness, which leads to distinct scattering patterns for different wave modes. The mode conversion effect is very strong around the specular angle and it is found to increase as the surface appears to be more rough. In addition, the 3D roughness induced coupling between the out-of-plane shear horizontal (SH) mode and the in-plane modes is studied. The intensity of the SH mode is shown to be very sensitive to the out-of-plane correlation length, being influenced more by this than by the RMS value of the roughness. However, it is found that the depolarization pattern for the diffuse field is independent of the actual value of the roughness.

  19. A Novel Microaneurysms Detection Method Based on Local Applying of Markov Random Field.

    PubMed

    Ganjee, Razieh; Azmi, Reza; Moghadam, Mohsen Ebrahimi

    2016-03-01

    Diabetic Retinopathy (DR) is one of the most common complications of long-term diabetes. It is a progressive disease and by damaging retina, it finally results in blindness of patients. Since Microaneurysms (MAs) appear as a first sign of DR in retina, early detection of this lesion is an essential step in automatic detection of DR. In this paper, a new MAs detection method is presented. The proposed approach consists of two main steps. In the first step, the MA candidates are detected based on local applying of Markov random field model (MRF). In the second step, these candidate regions are categorized to identify the correct MAs using 23 features based on shape, intensity and Gaussian distribution of MAs intensity. The proposed method is evaluated on DIARETDB1 which is a standard and publicly available database in this field. Evaluation of the proposed method on this database resulted in the average sensitivity of 0.82 for a confidence level of 75 as a ground truth. The results show that our method is able to detect the low contrast MAs with the background while its performance is still comparable to other state of the art approaches. PMID:26779642

  20. A random field approach to the Lagrangian modeling of turbulent transport in vegetated canopies

    NASA Astrophysics Data System (ADS)

    Cesari, Rita; Paradisi, Paolo

    2015-09-01

    We present an application of a Lagrangian Stochastic Model (LSM) to turbulent dispersion over complex terrain, where turbulent coherent structures are known to play a crucial role. We investigate the case of a vegetated canopy by using semi-empirical parameterizations of turbulence profiles in the region inside and above a canopy layer. The LSM is based on a 4-dimensional Fokker-Planck (4DFP) equation, which extends the standard Thomson87 Lagrangian approach. The 4DFP model is derived by means of a Random Field description of the turbulent velocity field. The main advantage of this approach is that not only the experimental Eulerian one-point statistics, but also the Eulerian two-point two-time covariance structure can be included explicitly in the LSM. At variance with the standard Thomson87 approach, the 4DFP model allows to consider explicit parameterizations of the turbulent coherent structures as it explicitly includes both spatial and temporal correlation functions. In order to investigate the effect of the turbulent geometrical structure on a scalar concentration profile, we performed numerical simulations with two different covariance parameterizations, the first one isotropic and the second anisotropic. We show that the accumulation of scalars near the ground is due to the anisotropic geometrical properties of the turbulent boundary layer.

  1. Metabolic properties in stroked rats revealed by relaxation-enhanced magnetic resonance spectroscopy at ultrahigh fields.

    PubMed

    Shemesh, Noam; Rosenberg, Jens T; Dumez, Jean-Nicolas; Muniz, Jose A; Grant, Samuel C; Frydman, Lucio

    2014-01-01

    (1)H magnetic resonance spectroscopy (MRS) yields site-specific signatures that directly report metabolic concentrations, biochemistry and kinetics-provided spectral sensitivity and quality are sufficient. Here, an enabling relaxation-enhanced (RE) MRS approach is demonstrated that by combining highly selective spectral excitations with operation at very high magnetic fields, delivers spectra exhibiting signal-to-noise ratios >50:1 in under 6 s for ~5 × 5 × 5 (mm)(3) voxels, with flat baselines and no interference from water. With this spectral quality, MRS was used to interrogate a number of metabolic properties in stroked rat models. Metabolic confinements imposed by randomly oriented micro-architectures were detected and found to change upon ischaemia; intensities of downfield resonances were found to be selectively altered in stroked hemispheres; and longitudinal relaxation time of lactic acid was found to increase by over 50% its control value as early as 3-h post ischaemia, paralleling the onset of cytotoxic oedema. These results demonstrate potential of (1)H MRS at ultrahigh fields. PMID:25229942

  2. Analysis and Validation of Grid dem Generation Based on Gaussian Markov Random Field

    NASA Astrophysics Data System (ADS)

    Aguilar, F. J.; Aguilar, M. A.; Blanco, J. L.; Nemmaoui, A.; García Lorca, A. M.

    2016-06-01

    Digital Elevation Models (DEMs) are considered as one of the most relevant geospatial data to carry out land-cover and land-use classification. This work deals with the application of a mathematical framework based on a Gaussian Markov Random Field (GMRF) to interpolate grid DEMs from scattered elevation data. The performance of the GMRF interpolation model was tested on a set of LiDAR data (0.87 points/m2) provided by the Spanish Government (PNOA Programme) over a complex working area mainly covered by greenhouses in Almería, Spain. The original LiDAR data was decimated by randomly removing different fractions of the original points (from 10% to up to 99% of points removed). In every case, the remaining points (scattered observed points) were used to obtain a 1 m grid spacing GMRF-interpolated Digital Surface Model (DSM) whose accuracy was assessed by means of the set of previously extracted checkpoints. The GMRF accuracy results were compared with those provided by the widely known Triangulation with Linear Interpolation (TLI). Finally, the GMRF method was applied to a real-world case consisting of filling the LiDAR-derived DSM gaps after manually filtering out non-ground points to obtain a Digital Terrain Model (DTM). Regarding accuracy, both GMRF and TLI produced visually pleasing and similar results in terms of vertical accuracy. As an added bonus, the GMRF mathematical framework makes possible to both retrieve the estimated uncertainty for every interpolated elevation point (the DEM uncertainty) and include break lines or terrain discontinuities between adjacent cells to produce higher quality DTMs.

  3. Pulsed electromagnetic fields in knee osteoarthritis: a double blind, placebo-controlled, randomized clinical trial

    PubMed Central

    Miceli, Giovanni; Marino, Natale; Sciortino, Davide; Bagnato, Gian Filippo

    2016-01-01

    Objectives. This trial aimed to test the effectiveness of a wearable pulsed electromagnetic fields (PEMF) device in the management of pain in knee OA patients. Methods. In this randomized [with equal randomization (1:1)], double-blind, placebo-controlled clinical trial, patients with radiographic evidence of knee OA and persistent pain higher than 40 mm on the visual analog scale (VAS) were recruited. The trial consisted of 12 h daily treatment for 1 month in 60 knee OA patients. The primary outcome measure was the reduction in pain intensity, assessed through VAS and WOMAC scores. Secondary outcomes included quality of life assessment through the 36-item Medical Outcomes Study Short-Form version 2 (SF-36 v2), pressure pain threshold (PPT) and changes in intake of NSAIDs/analgesics. Results. Sixty-six patients were included, and 60 completed the study. After 1 month, PEMF induced a significant reduction in VAS pain and WOMAC scores compared with placebo. Additionally, pain tolerance, as expressed by PPT changes, and physical health improved in PEMF-treated patients. A mean treatment effect of −0.73 (95% CI − 1.24 to − 0.19) was seen in VAS score, while the effect size was −0.34 (95% CI − 0.85 to 0.17) for WOMAC score. Twenty-six per cent of patients in the PEMF group stopped NSAID/analgesic therapy. No adverse events were detected. Conclusion. These results suggest that PEMF therapy is effective for pain management in knee OA patients and also affects pain threshold and physical functioning. Future larger studies, including head-to-head studies comparing PEMF therapy with standard pharmacological approaches in OA, are warranted. Trial registration: ClinicalTrials.gov, http://www.clinicaltrials.gov, NCT01877278 PMID:26705327

  4. Image Enhancement and Speckle Reduction of Full Polarimetric SAR Data by Gaussian Markov Random Field

    NASA Astrophysics Data System (ADS)

    Mahdian, M.; Motagh, M.; Akbari, V.

    2013-09-01

    In recent years, the use of Polarimetric Synthetic Aperture Radar (PolSAR) data in different applications dramatically has been increased. In SAR imagery an interference phenomenon with random behavior exists which is called speckle noise. The interpretation of data encounters some troubles due to the presence of speckle which can be considered as a multiplicative noise affecting all coherent imaging systems. Indeed, speckle degrade radiometric resolution of PolSAR images, therefore it is needful to perform speckle filtering on the SAR data type. Markov Random Field (MRF) has proven to be a powerful method for drawing out eliciting contextual information from remotely sensed images. In the present paper, a probability density function (PDF), which is fitted well with the PolSAR data based on the goodness-of-fit test, is first obtained for the pixel-wise analysis. Then the contextual smoothing is achieved with the MRF method. This novel speckle reduction method combines an advanced statistical distribution with spatial contextual information for PolSAR data. These two parts of information are combined based on weighted summation of pixel-wise and contextual models. This approach not only preserves edge information in the images, but also improves signal-to-noise ratio of the results. The method maintains the mean value of original signal in the homogenous areas and preserves the edges of features in the heterogeneous regions. Experiments on real medium resolution ALOS data from Tehran, and also high resolution full polarimetric SAR data over the Oberpfaffenhofen test-site in Germany, demonstrate the effectiveness of the algorithm compared with well-known despeckling methods.

  5. A biorthogonal decomposition for the identification and simulation of non-stationary and non-Gaussian random fields

    NASA Astrophysics Data System (ADS)

    Zentner, I.; Ferré, G.; Poirion, F.; Benoit, M.

    2016-06-01

    In this paper, a new method for the identification and simulation of non-Gaussian and non-stationary stochastic fields given a database is proposed. It is based on two successive biorthogonal decompositions aiming at representing spatio-temporal stochastic fields. The proposed double expansion allows to build the model even in the case of large-size problems by separating the time, space and random parts of the field. A Gaussian kernel estimator is used to simulate the high dimensional set of random variables appearing in the decomposition. The capability of the method to reproduce the non-stationary and non-Gaussian features of random phenomena is illustrated by applications to earthquakes (seismic ground motion) and sea states (wave heights).

  6. A multiarm randomized field trial evaluating strategies for udder health improvement in Swiss dairy herds.

    PubMed

    Tschopp, A; Reist, M; Kaufmann, T; Bodmer, M; Kretzschmar, L; Heiniger, D; Berchtold, B; Wohlfender, F; Harisberger, M; Boss, R; Strabel, D; Cousin, M-E; Graber, H U; Steiner, A; van den Borne, B H P

    2015-02-01

    The aims of this study were to quantify the effectiveness of specialist advice about udder health in Swiss dairy herds and to compare 3 different udder health improvement strategies against a negative control group. In 2010, 100 Swiss dairy herds with a high (between 200,000 and 300,000 cells/mL) yield-corrected bulk milk somatic cell count (YCBMSCC) were recruited for a 1-yr multiarm randomized field trial. The herds were visited between September and December 2011 to evaluate udder health-management practices and then randomly allocated into 1 of 4 study arms containing 25 herds each. The negative control study arm received neither recommendations for improving udder health nor any active support. The remaining 75 farmers received a herd-specific report with recommendations to improve udder health management. The positive control study arm received no further active support during 2012. The veterinarian study arm received additional support in the form of monthly visits by their herd veterinarian. Finally, the study group study arm received support in the form of bimonthly study group meetings where different topics concerning udder health were discussed. One year later, implementation of recommendations and changes in udder health were assessed. Of the recommendations given, 44.3% were completely implemented, 23.1% partially, and 32.6% were not implemented. No differences in implementation of recommendations were noted between the 3 study arms. At study enrollment, farmers were asked for the study arm of their preference but were subsequently randomly assigned to 1 of the 4 study arms. Farmers that were assigned to the study arm of their preference implemented more recommendations than farmers assigned to a study arm not of their preference. No decrease in the within-herd prevalence of cows that had a high (≥200,000 cells/mL) composite somatic cell count was observed in herds that had a YCBMSCC ≥200,000 cells/mL at the start of intervention. However, the 3

  7. Reverse random amplified microsatellite polymorphism reveals enhanced polymorphisms in the 3' end of simple sequence repeats in the pepper genome.

    PubMed

    Min, Woong-Ki; Han, Jung-Heon; Kang, Won-Hee; Lee, Heung-Ryul; Kim, Byung-Dong

    2008-09-30

    Microsatellites or simple sequence repeats (SSR) are widely distributed in eukaryotic genomes and are informative genetic markers. Despite many advantages of SSR markers such as a high degree of allelic polymorphisms, co-dominant inheritance, multi-allelism, and genome-wide coverage in various plant species, they also have shortcomings such as low polymorphic rates between genetically close lines, especially in Capsicum annuum. We developed an alternative technique to SSR by normalizing and alternating anchored primers in random amplified microsatellite polymorphisms (RAMP). This technique, designated reverse random amplified microsatellite polymorphism (rRAMP), allows the detection of nucleotide variation in the 3' region flanking an SSR using normalized anchored and random primer combinations. The reproducibility and frequency of polymorphic loci in rRAMP was vigorously enhanced by translocation of the 5' anchor of repeat sequences to the 3' end position and selective use of moderate arbitrary primers. In our study, the PCR banding pattern of rRAMP was highly dependent on the frequency of repeat motifs and primer combinations with random primers. Linkage analysis showed that rRAMP markers were well scattered on an intra-specific pepper map. Based on these results, we suggest that this technique is useful for studying genetic diversity, molecular fingerprinting, and rapidly constructing molecular maps for diverse plant species. PMID:18483466

  8. Phase Transitions in Disordered Systems: The Example of the Random-Field Ising Model in Four Dimensions

    NASA Astrophysics Data System (ADS)

    Fytas, Nikolaos G.; Martín-Mayor, Víctor; Picco, Marco; Sourlas, Nicolas

    2016-06-01

    By performing a high-statistics simulation of the D =4 random-field Ising model at zero temperature for different shapes of the random-field distribution, we show that the model is ruled by a single universality class. We compute to a high accuracy the complete set of critical exponents for this class, including the correction-to-scaling exponent. Our results indicate that in four dimensions (i) dimensional reduction as predicted by the perturbative renormalization group does not hold and (ii) three independent critical exponents are needed to describe the transition.

  9. Nonpoint source solute transport normal to aquifer bedding in heterogeneous, Markov chain random fields

    NASA Astrophysics Data System (ADS)

    Zhang, Hua; Harter, Thomas; Sivakumar, Bellie

    2006-06-01

    examined, the third moment of the traveltime pdf varies from negatively skewed to strongly positively skewed. We also show that the Markov chain approach may give significantly different traveltime distributions when compared to the more commonly used Gaussian random field approach, even when the first- and second-order moments in the geostatistical distribution of the lnK field are identical. The choice of the appropriate geostatistical model is therefore critical in the assessment of nonpoint source transport, and uncertainty about that choice must be considered in evaluating the results.

  10. A Hypergraph-Based Reduction for Higher-Order Binary Markov Random Fields.

    PubMed

    Fix, Alexander; Gruber, Aritanan; Boros, Endre; Zabih, Ramin

    2015-07-01

    Higher-order Markov Random Fields, which can capture important properties of natural images, have become increasingly important in computer vision. While graph cuts work well for first-order MRF's, until recently they have rarely been effective for higher-order MRF's. Ishikawa's graph cut technique [1], [2] shows great promise for many higher-order MRF's. His method transforms an arbitrary higher-order MRF with binary labels into a first-order one with the same minima. If all the terms are submodular the exact solution can be easily found; otherwise, pseudoboolean optimization techniques can produce an optimal labeling for a subset of the variables. We present a new transformation with better performance than [1], [2], both theoretically and experimentally. While [1], [2] transforms each higher-order term independently, we use the underlying hypergraph structure of the MRF to transform a group of terms at once. For n binary variables, each of which appears in terms with k other variables, at worst we produce n non-submodular terms, while [1], [2] produces O(nk). We identify a local completeness property under which our method perform even better, and show that under certain assumptions several important vision problems (including common variants of fusion moves) have this property. We show experimentally that our method produces smaller weight of non-submodular edges, and that this metric is directly related to the effectiveness of QPBO [3]. Running on the same field of experts dataset used in [1], [2] we optimally label significantly more variables (96 versus 80 percent) and converge more rapidly to a lower energy. Preliminary experiments suggest that some other higher-order MRF's used in stereo [4] and segmentation [5] are also locally complete and would thus benefit from our work. PMID:26352447

  11. Action unit classification using active appearance models and conditional random fields.

    PubMed

    van der Maaten, Laurens; Hendriks, Emile

    2012-10-01

    In this paper, we investigate to what extent modern computer vision and machine learning techniques can assist social psychology research by automatically recognizing facial expressions. To this end, we develop a system that automatically recognizes the action units defined in the facial action coding system (FACS). The system uses a sophisticated deformable template, which is known as the active appearance model, to model the appearance of faces. The model is used to identify the location of facial feature points, as well as to extract features from the face that are indicative of the action unit states. The detection of the presence of action units is performed by a time series classification model, the linear-chain conditional random field. We evaluate the performance of our system in experiments on a large data set of videos with posed and natural facial expressions. In the experiments, we compare the action units detected by our approach with annotations made by human FACS annotators. Our results show that the agreement between the system and human FACS annotators is higher than 90% and underlines the potential of modern computer vision and machine learning techniques to social psychology research. We conclude with some suggestions on how systems like ours can play an important role in research on social signals. PMID:21989609

  12. a Method to Estimate Temporal Interaction in a Conditional Random Field Based Approach for Crop Recognition

    NASA Astrophysics Data System (ADS)

    Diaz, P. M. A.; Feitosa, R. Q.; Sanches, I. D.; Costa, G. A. O. P.

    2016-06-01

    This paper presents a method to estimate the temporal interaction in a Conditional Random Field (CRF) based approach for crop recognition from multitemporal remote sensing image sequences. This approach models the phenology of different crop types as a CRF. Interaction potentials are assumed to depend only on the class labels of an image site at two consecutive epochs. In the proposed method, the estimation of temporal interaction parameters is considered as an optimization problem, whose goal is to find the transition matrix that maximizes the CRF performance, upon a set of labelled data. The objective functions underlying the optimization procedure can be formulated in terms of different accuracy metrics, such as overall and average class accuracy per crop or phenological stages. To validate the proposed approach, experiments were carried out upon a dataset consisting of 12 co-registered LANDSAT images of a region in southeast of Brazil. Pattern Search was used as the optimization algorithm. The experimental results demonstrated that the proposed method was able to substantially outperform estimates related to joint or conditional class transition probabilities, which rely on training samples.

  13. High energy X-ray phase and dark-field imaging using a random absorption mask

    PubMed Central

    Wang, Hongchang; Kashyap, Yogesh; Cai, Biao; Sawhney, Kawal

    2016-01-01

    High energy X-ray imaging has unique advantage over conventional X-ray imaging, since it enables higher penetration into materials with significantly reduced radiation damage. However, the absorption contrast in high energy region is considerably low due to the reduced X-ray absorption cross section for most materials. Even though the X-ray phase and dark-field imaging techniques can provide substantially increased contrast and complementary information, fabricating dedicated optics for high energies still remain a challenge. To address this issue, we present an alternative X-ray imaging approach to produce transmission, phase and scattering signals at high X-ray energies by using a random absorption mask. Importantly, in addition to the synchrotron radiation source, this approach has been demonstrated for practical imaging application with a laboratory-based microfocus X-ray source. This new imaging method could be potentially useful for studying thick samples or heavy materials for advanced research in materials science. PMID:27466217

  14. High energy X-ray phase and dark-field imaging using a random absorption mask.

    PubMed

    Wang, Hongchang; Kashyap, Yogesh; Cai, Biao; Sawhney, Kawal

    2016-01-01

    High energy X-ray imaging has unique advantage over conventional X-ray imaging, since it enables higher penetration into materials with significantly reduced radiation damage. However, the absorption contrast in high energy region is considerably low due to the reduced X-ray absorption cross section for most materials. Even though the X-ray phase and dark-field imaging techniques can provide substantially increased contrast and complementary information, fabricating dedicated optics for high energies still remain a challenge. To address this issue, we present an alternative X-ray imaging approach to produce transmission, phase and scattering signals at high X-ray energies by using a random absorption mask. Importantly, in addition to the synchrotron radiation source, this approach has been demonstrated for practical imaging application with a laboratory-based microfocus X-ray source. This new imaging method could be potentially useful for studying thick samples or heavy materials for advanced research in materials science. PMID:27466217

  15. Colloids in light fields: Particle dynamics in random and periodic energy landscapes

    NASA Astrophysics Data System (ADS)

    Evers, F.; Hanes, R. D. L.; Zunke, C.; Capellmann, R. F.; Bewerunge, J.; Dalle-Ferrier, C.; Jenkins, M. C.; Ladadwa, I.; Heuer, A.; Castañeda-Priego, R.; Egelhaaf, S. U.

    2013-11-01

    The dynamics of colloidal particles in potential energy landscapes have mainly been investigated theoretically. In contrast, here we discuss the experimental realization of potential energy landscapes with the help of laser light fields and the observation of the particle dynamics by video microscopy. The experimentally observed dynamics in periodic and random potentials are compared to simulation and theoretical results in terms of, e.g. the mean-squared displacement, the time-dependent diffusion coefficient or the non-Gaussian parameter. The dynamics are initially diffusive followed by intermediate subdiffusive behaviour which again becomes diffusive at long times. How pronounced and extended the different regimes are, depends on the specific conditions, in particular the shape of the potential as well as its roughness or amplitude but also the particle concentration. Here we focus on dilute systems, but the dynamics of interacting systems in external potentials, and thus the interplay between particle-particle and particle-potential interactions, are also mentioned briefly. Furthermore, the observed dynamics of dilute systems resemble the dynamics of concentrated systems close to their glass transition, with which it is compared. The effect of certain potential energy landscapes on the dynamics of individual particles appears similar to the effect of interparticle interactions in the absence of an external potential.

  16. Random-field Ising model on isometric lattices: Ground states and non-Porod scattering

    NASA Astrophysics Data System (ADS)

    Bupathy, Arunkumar; Banerjee, Varsha; Puri, Sanjay

    2016-01-01

    We use a computationally efficient graph cut method to obtain ground state morphologies of the random-field Ising model (RFIM) on (i) simple cubic (SC), (ii) body-centered cubic (BCC), and (iii) face-centered cubic (FCC) lattices. We determine the critical disorder strength Δc at zero temperature with high accuracy. For the SC lattice, our estimate (Δc=2.278 ±0.002 ) is consistent with earlier reports. For the BCC and FCC lattices, Δc=3.316 ±0.002 and 5.160 ±0.002 , respectively, which are the most accurate estimates in the literature to date. The small-r behavior of the correlation function exhibits a cusp regime characterized by a cusp exponent α signifying fractal interfaces. In the paramagnetic phase, α =0.5 ±0.01 for all three lattices. In the ferromagnetic phase, the cusp exponent shows small variations due to the lattice structure. Consequently, the interfacial energy Ei(L ) for an interface of size L is significantly different for the three lattices. This has important implications for nonequilibrium properties.

  17. CHEMDNER system with mixed conditional random fields and multi-scale word clustering

    PubMed Central

    2015-01-01

    Background The chemical compound and drug name recognition plays an important role in chemical text mining, and it is the basis for automatic relation extraction and event identification in chemical information processing. So a high-performance named entity recognition system for chemical compound and drug names is necessary. Methods We developed a CHEMDNER system based on mixed conditional random fields (CRF) with word clustering for chemical compound and drug name recognition. For the word clustering, we used Brown's hierarchical algorithm and Skip-gram model based on deep learning with massive PubMed articles including titles and abstracts. Results This system achieved the highest F-score of 88.20% for the CDI task and the second highest F-score of 87.11% for the CEM task in BioCreative IV. The performance was further improved by multi-scale clustering based on deep learning, achieving the F-score of 88.71% for CDI and 88.06% for CEM. Conclusions The mixed CRF model represents both the internal complexity and external contexts of the entities, and the model is integrated with word clustering to capture domain knowledge with PubMed articles including titles and abstracts. The domain knowledge helps to ensure the performance of the entity recognition, even without fine-grained linguistic features and manually designed rules. PMID:25810775

  18. Context-aware patch-based image inpainting using Markov random field modeling.

    PubMed

    Ružić, Tijana; Pižurica, Aleksandra

    2015-01-01

    In this paper, we first introduce a general approach for context-aware patch-based image inpainting, where textural descriptors are used to guide and accelerate the search for well-matching (candidate) patches. A novel top-down splitting procedure divides the image into variable size blocks according to their context, constraining thereby the search for candidate patches to nonlocal image regions with matching context. This approach can be employed to improve the speed and performance of virtually any (patch-based) inpainting method. We apply this approach to the so-called global image inpainting with the Markov random field (MRF) prior, where MRF encodes a priori knowledge about consistency of neighboring image patches. We solve the resulting optimization problem with an efficient low-complexity inference method. Experimental results demonstrate the potential of the proposed approach in inpainting applications like scratch, text, and object removal. Improvement and significant acceleration of a related global MRF-based inpainting method is also evident. PMID:25420260

  19. Interplay between pair density waves and random field disorders in the pseudogap regime of cuprate superconductors

    NASA Astrophysics Data System (ADS)

    Chan, Cheung

    2016-05-01

    To capture various experimental results in the pseudogap regime of the underdoped cuprate superconductors for temperature T random field disorders (RFD), only one of the PDW components survives. If the RFD is included, this state could become phase separated and consist of short range PDW stripes, in which two PDW components coexist but differ in magnitudes, resulting in charge density waves (CDW) and a time-reversal symmetry breaking order, in the form of loop current, as secondary composite orders. We call this phase-separated pair nematic (PSPN) state, which could be responsible for the pseudogap. Using a phenomenological Ginzburg-Landau approach and Monte Carlo simulations, we found that in this state, RFD induces short range static CDW with phase-separated patterns in the directional components, and the static CDW is destroyed by thermal phase fluctuations at a crossover temperature TC O

  20. Statistical Inference of Selection and Divergence from a Time-Dependent Poisson Random Field Model

    PubMed Central

    Amei, Amei; Sawyer, Stanley

    2012-01-01

    We apply a recently developed time-dependent Poisson random field model to aligned DNA sequences from two related biological species to estimate selection coefficients and divergence time. We use Markov chain Monte Carlo methods to estimate species divergence time and selection coefficients for each locus. The model assumes that the selective effects of non-synonymous mutations are normally distributed across genetic loci but constant within loci, and synonymous mutations are selectively neutral. In contrast with previous models, we do not assume that the individual species are at population equilibrium after divergence. Using a data set of 91 genes in two Drosophila species, D. melanogaster and D. simulans, we estimate the species divergence time (or 1.68 million years, assuming the haploid effective population size years) and a mean selection coefficient per generation . Although the average selection coefficient is positive, the magnitude of the selection is quite small. Results from numerical simulations are also presented as an accuracy check for the time-dependent model. PMID:22509300

  1. A Markov Random Field Model-Based Approach To Image Interpretation

    NASA Astrophysics Data System (ADS)

    Zhang, Jun; Modestino, James W.

    1989-11-01

    In this paper, a Markov random field (MRF) model-based approach to automated image interpretation is described and demonstrated as a region-based scheme. In this approach, an image is first segmented into a collection of disjoint regions which form the nodes of an adjacency graph. Image interpretation is then achieved through assigning object labels, or interpretations, to the segmented regions, or nodes, using domain knowledge, extracted feature measurements and spatial relationships between the various regions. The interpretation labels are modeled as a MRF on the corresponding adjacency graph and the image interpretation problem is formulated as a maximum a posteriori (MAP) estimation rule. Simulated annealing is used to find the best realization, or optimal MAP interpretation. Through the MRF model, this approach also provides a systematic method for organizing and representing domain knowledge through the clique functions of the pdf of the underlying MRF. Results of image interpretation experiments performed on synthetic and real-world images using this approach are described and appear promising.

  2. An efficient conditional random field approach for automatic and interactive neuron segmentation.

    PubMed

    Uzunbas, Mustafa Gokhan; Chen, Chao; Metaxas, Dimitris

    2016-01-01

    We present a new graphical-model-based method for automatic and interactive segmentation of neuron structures from electron microscopy (EM) images. For automated reconstruction, our learning based model selects a collection of nodes from a hierarchical merging tree as the proposed segmentation. More specifically, this is achieved by training a conditional random field (CRF) whose underlying graph is the watershed merging tree. The maximum a posteriori (MAP) prediction of the CRF is the output segmentation. Our results are comparable to the results of state-of-the-art methods. Furthermore, both the inference and the training are very efficient as the graph is tree-structured. The problem of neuron segmentation requires extremely high segmentation quality. Therefore, proofreading, namely, interactively correcting mistakes of the automatic method, is a necessary module in the pipeline. Based on our efficient tree-structured inference algorithm, we develop an interactive segmentation framework which only selects locations where the model is uncertain for a user to proofread. The uncertainty is measured by the marginals of the graphical model. Only giving a limited number of choices makes the user interaction very efficient. Based on user corrections, our framework modifies the merging tree and thus improves the segmentation globally. PMID:26210001

  3. Transport of Dirac electrons in a random magnetic field in topological heterostructures

    NASA Astrophysics Data System (ADS)

    Hurst, Hilary M.; Efimkin, Dmitry K.; Galitski, Victor

    2016-06-01

    We consider the proximity effect between Dirac states at the surface of a topological insulator and a ferromagnet with easy plane anisotropy, which is described by the XY model and undergoes a Berezinskii-Kosterlitz-Thouless (BKT) phase transition. The surface states of the topological insulator interacting with classical magnetic fluctuations of the ferromagnet can be mapped onto the problem of Dirac fermions in a random magnetic field. However, this analogy is only partial in the presence of electron-hole asymmetry or warping of the Dirac dispersion, which results in screening of magnetic fluctuations. Scattering at magnetic fluctuations influences the behavior of the surface resistivity as a function of temperature. Near the BKT phase transition temperature we find that the resistivity of surface states scales linearly with temperature and has a clear maximum which becomes more pronounced as the Fermi energy decreases. Additionally, at low temperatures we find linear resistivity, usually associated with non-Fermi-liquid behavior; however, here it appears entirely within the Fermi-liquid picture.

  4. Heterogeneous Memorized Continuous Time Random Walks in an External Force Fields

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Zhou, Ji; Lv, Long-Jin; Qiu, Wei-Yuan; Ren, Fu-Yao

    2014-09-01

    In this paper, we study the anomalous diffusion of a particle in an external force field whose motion is governed by nonrenewal continuous time random walks with correlated memorized waiting times, which involves Reimann-Liouville fractional derivative or Reimann-Liouville fractional integral. We show that the mean squared displacement of the test particle which is dependent on its location of the form (El-Wakil and Zahran, Chaos Solitons Fractals, 12, 1929-1935, 2001) where is the anomalous exponent, the diffusion exponent is dependent on the model parameters. We obtain the Fokker-Planck-type dynamic equations, and their stationary solutions are of the Boltzmann-Gibbs form. These processes obey a generalized Einstein-Stokes-Smoluchowski relation and the second Einstein relation. We observe that the asymptotic behavior of waiting times and subordinations are of stretched Gaussian distributions. We also discuss the time averaged in the case of an harmonic potential, and show that the process exhibits aging and ergodicity breaking.

  5. Financial versus Health Motivation to Quit Smoking: A Randomized Field Study

    PubMed Central

    Sindelar, Jody L.; O’Malley, Stephanie S.

    2016-01-01

    Objective Smoking is the most preventable cause of death, thus justifying efforts to effectively motivate quitting. We compared the effectiveness of financial versus health messages to motivate smoking cessation. Low-income individuals disproportionately smoke and, given their greater income constraints, we hypothesized that making financial costs of smoking more salient would encourage more smokers to try quitting. Further, we predicted financial messages would be stronger in financial settings where pecuniary constraints are most salient. Methods We conducted a field study in low-income areas of New Haven, Connecticut using brochures with separate health vs. financial messages to motivate smoking cessation. Displays were rotated among community settings—check-cashing, health clinics, and grocery stores. We randomized brochure displays with gain-framed cessation messages across locations. Results Our predictions were confirmed. Financial messages attracted significantly more attention than health messages, especially in financial settings. Conclusions These findings suggest greater emphasis on the financial gains to quitting and use of financial settings to provide cessation messages may be more effective in motivating quitting. Importantly, use of financial settings could open new, non-medical venues for encouraging cessation. Encouraging quitting could improve health, enhance spending power of low-income smokers, and reduce health disparities in both health and purchasing power. PMID:24139975

  6. Segmentation of anatomical branching structures based on texture features and conditional random field

    NASA Astrophysics Data System (ADS)

    Nuzhnaya, Tatyana; Bakic, Predrag; Kontos, Despina; Megalooikonomou, Vasileios; Ling, Haibin

    2012-02-01

    This work is a part of our ongoing study aimed at understanding a relation between the topology of anatomical branching structures with the underlying image texture. Morphological variability of the breast ductal network is associated with subsequent development of abnormalities in patients with nipple discharge such as papilloma, breast cancer and atypia. In this work, we investigate complex dependence among ductal components to perform segmentation, the first step for analyzing topology of ductal lobes. Our automated framework is based on incorporating a conditional random field with texture descriptors of skewness, coarseness, contrast, energy and fractal dimension. These features are selected to capture the architectural variability of the enhanced ducts by encoding spatial variations between pixel patches in galactographic image. The segmentation algorithm was applied to a dataset of 20 x-ray galactograms obtained at the Hospital of the University of Pennsylvania. We compared the performance of the proposed approach with fully and semi automated segmentation algorithms based on neural network classification, fuzzy-connectedness, vesselness filter and graph cuts. Global consistency error and confusion matrix analysis were used as accuracy measurements. For the proposed approach, the true positive rate was higher and the false negative rate was significantly lower compared to other fully automated methods. This indicates that segmentation based on CRF incorporated with texture descriptors has potential to efficiently support the analysis of complex topology of the ducts and aid in development of realistic breast anatomy phantoms.

  7. A novel genome-wide polyadenylation sites recognition system based on condition random field.

    PubMed

    Han, Jiuqiang; Zhang, Shanxin; Liu, Jun; Liu, Ruiling

    2014-01-01

    Polyadenylation including the cleavage of pre-mRNA and addition of a stretch of adenosines to the 3'-end is an essential step of pre-mRNA processing in eukayotes. The known regulatory role of polyadenylation in mRNA localization, stability, and translation and the emerging link between poly(A) and disease states underline the necessary to fully characterize polyadenylation sites. Several artificial intelligence methods have been proposed for poly(A) sites recognition. However, these methods are suitable to small subsets of genome sequences. It is necessary to propose a method for genome-wide recognition of poly(A) sites. Recent efforts have found a lot of poly(A) related factors on DNA level. Here, we proposed a novel genome-wide poly(A) recognition method based on the Condition Random Field (CRF) by integrating multiple features. Compared with the polya_svm (the most accurate program for prediction of poly(A) sites till date), our method had a higher performance with the area under ROC curve(0.8621 versus 0.6796). The result suggests that our method is an effective method in genome wide poly(A) sites recognition. PMID:25571055

  8. Beyond-mean-field corrections within the second random-phase approximation

    NASA Astrophysics Data System (ADS)

    Grasso, M.; Gambacurta, D.; Engel, J.

    2016-06-01

    A subtraction procedure, introduced to overcome double-counting problems in beyond-mean-field theories, is used in the second random-phase approximation (SRPA). Doublecounting problems arise in the energy-density functional framework in all cases where effective interactions tailored at leading order are used for higher-order calculations, such as those done in the SRPA model. It was recently shown that this subtraction procedure also guarantees that the stability condition related to the Thouless theorem is verified in extended RPA models. We discuss applications of the subtraction procedure, introduced within the SRPA model, to the nucleus 16O. The application of the subtraction procedure leads to: (i) stable results that are weakly cutoff dependent; (ii) a considerable upwards correction of the SRPA spectra (which were systematically shifted downwards by several MeV with respect to RPA spectra, in all previous calculations). With this important implementation of the model, many applications may be foreseen to analyze the genuine impact of 2 particle-2 hole configurations (without any cutoff dependences and anomalous shifts) on the excitation spectra of medium-mass and heavy nuclei.

  9. Increasing the maximally random jammed density with electric field to reduce the fat level in chocolate

    NASA Astrophysics Data System (ADS)

    Tao, R.; Tang, H.

    Chocolate is one of the most popular food types and flavors in the world. Unfortunately, at present, chocolate products contain too much fat, leading to obesity. For example, a typical molding chocolate has various fat up to 40% in total and chocolate for covering ice cream has fat 50 -60%. Especially, as children are the leading chocolate consumers, reducing the fat level in chocolate products to make them healthier is important and urgent. While this issue was called into attention and elaborated in articles and books decades ago and led to some patent applications, no actual solution was found unfortunately. Why is reducing fat in chocolate so difficult? What is the underlying physical mechanism? We have found that this issue is deeply related to the basic science of soft matters, especially to their viscosity and maximally random jammed (MRJ) density φx. All chocolate productions are handling liquid chocolate, a suspension with cocoa solid particles in melted fat, mainly cocoa butter. The fat level cannot be lower than 1-φxin order to have liquid chocolate to flow. Here we show that that with application of an electric field to liquid chocolate, we can aggregate the suspended particles into prolate spheroids. This microstructure change reduces liquid chocolate's viscosity along the flow direction and increases its MRJ density significantly. Hence the fat level in chocolate can be effectively reduced. We are looking forward to a new class of healthier and tasteful chocolate coming to the market soon. Dept. of Physics, Temple Univ, Philadelphia, PA 19122.

  10. Medical image retrieval and analysis by Markov random fields and multi-scale fractal dimension.

    PubMed

    Backes, André Ricardo; Gerhardinger, Leandro Cavaleri; Batista Neto, João do Espírito Santo; Bruno, Odemir Martinez

    2015-02-01

    Many Content-based Image Retrieval (CBIR) systems and image analysis tools employ color, shape and texture (in a combined fashion or not) as attributes, or signatures, to retrieve images from databases or to perform image analysis in general. Among these attributes, texture has turned out to be the most relevant, as it allows the identification of a larger number of images of a different nature. This paper introduces a novel signature which can be used for image analysis and retrieval. It combines texture with complexity extracted from objects within the images. The approach consists of a texture segmentation step, modeled as a Markov Random Field process, followed by the estimation of the complexity of each computed region. The complexity is given by a Multi-scale Fractal Dimension. Experiments have been conducted using an MRI database in both pattern recognition and image retrieval contexts. The results show the accuracy of the proposed method in comparison with other traditional texture descriptors and also indicate how the performance changes as the level of complexity is altered. PMID:25586375

  11. Medical image retrieval and analysis by Markov random fields and multi-scale fractal dimension

    NASA Astrophysics Data System (ADS)

    Backes, André Ricardo; Cavaleri Gerhardinger, Leandro; do Espírito Santo Batista Neto, João; Martinez Bruno, Odemir

    2015-02-01

    Many Content-based Image Retrieval (CBIR) systems and image analysis tools employ color, shape and texture (in a combined fashion or not) as attributes, or signatures, to retrieve images from databases or to perform image analysis in general. Among these attributes, texture has turned out to be the most relevant, as it allows the identification of a larger number of images of a different nature. This paper introduces a novel signature which can be used for image analysis and retrieval. It combines texture with complexity extracted from objects within the images. The approach consists of a texture segmentation step, modeled as a Markov Random Field process, followed by the estimation of the complexity of each computed region. The complexity is given by a Multi-scale Fractal Dimension. Experiments have been conducted using an MRI database in both pattern recognition and image retrieval contexts. The results show the accuracy of the proposed method in comparison with other traditional texture descriptors and also indicate how the performance changes as the level of complexity is altered.

  12. Nonparametric Feature Matching Based Conditional Random Fields for Gesture Recognition from Multi-Modal Video.

    PubMed

    Chang, Ju Yong

    2016-08-01

    We present a new gesture recognition method that is based on the conditional random field (CRF) model using multiple feature matching. Our approach solves the labeling problem, determining gesture categories and their temporal ranges at the same time. A generative probabilistic model is formalized and probability densities are nonparametrically estimated by matching input features with a training dataset. In addition to the conventional skeletal joint-based features, the appearance information near the active hand in an RGB image is exploited to capture the detailed motion of fingers. The estimated likelihood function is then used as the unary term for our CRF model. The smoothness term is also incorporated to enforce the temporal coherence of our solution. Frame-wise recognition results can then be obtained by applying an efficient dynamic programming technique. To estimate the parameters of the proposed CRF model, we incorporate the structured support vector machine (SSVM) framework that can perform efficient structured learning by using large-scale datasets. Experimental results demonstrate that our method provides effective gesture recognition results for challenging real gesture datasets. By scoring 0.8563 in the mean Jaccard index, our method has obtained the state-of-the-art results for the gesture recognition track of the 2014 ChaLearn Looking at People (LAP) Challenge. PMID:26800528

  13. A new method for direction finding based on Markov random field model

    NASA Astrophysics Data System (ADS)

    Ota, Mamoru; Kasahara, Yoshiya; Goto, Yoshitaka

    2015-07-01

    Investigating the characteristics of plasma waves observed by scientific satellites in the Earth's plasmasphere/magnetosphere is effective for understanding the mechanisms for generating waves and the plasma environment that influences wave generation and propagation. In particular, finding the propagation directions of waves is important for understanding mechanisms of VLF/ELF waves. To find these directions, the wave distribution function (WDF) method has been proposed. This method is based on the idea that observed signals consist of a number of elementary plane waves that define wave energy density distribution. However, the resulting equations constitute an ill-posed problem in which a solution is not determined uniquely; hence, an adequate model must be assumed for a solution. Although many models have been proposed, we have to select the most optimum model for the given situation because each model has its own advantages and disadvantages. In the present study, we propose a new method for direction finding of the plasma waves measured by plasma wave receivers. Our method is based on the assumption that the WDF can be represented by a Markov random field model with inference of model parameters performed using a variational Bayesian learning algorithm. Using computer-generated spectral matrices, we evaluated the performance of the model and compared the results with those obtained from two conventional methods.

  14. Segmentation of complementary DNA microarray images by wavelet-based Markov random field model.

    PubMed

    Athanasiadis, Emmanouil I; Cavouras, Dionisis A; Glotsos, Dimitris Th; Georgiadis, Pantelis V; Kalatzis, Ioannis K; Nikiforidis, George C

    2009-11-01

    A wavelet-based modification of the Markov random field (WMRF) model is proposed for segmenting complementary DNA (cDNA) microarray images. For evaluation purposes, five simulated and a set of five real microarray images were used. The one-level stationary wavelet transform (SWT) of each microarray image was used to form two images, a denoised image, using hard thresholding filter, and a magnitude image, from the amplitudes of the horizontal and vertical components of SWT. Elements from these two images were suitably combined to form the WMRF model for segmenting spots from their background. The WMRF was compared against the conventional MRF and the Fuzzy C means (FCM) algorithms on simulated and real microarray images and their performances were evaluated by means of the segmentation matching factor (SMF) and the coefficient of determination (r2). Additionally, the WMRF was compared against the SPOT and SCANALYZE, and performances were evaluated by the mean absolute error (MAE) and the coefficient of variation (CV). The WMRF performed more accurately than the MRF and FCM (SMF: 92.66, 92.15, and 89.22, r2 : 0.92, 0.90, and 0.84, respectively) and achieved higher reproducibility than the MRF, SPOT, and SCANALYZE (MAE: 497, 1215, 1180, and 503, CV: 0.88, 1.15, 0.93, and 0.90, respectively). PMID:19783509

  15. A wavelet-based Markov random field segmentation model in segmenting microarray experiments.

    PubMed

    Athanasiadis, Emmanouil; Cavouras, Dionisis; Kostopoulos, Spyros; Glotsos, Dimitris; Kalatzis, Ioannis; Nikiforidis, George

    2011-12-01

    In the present study, an adaptation of the Markov Random Field (MRF) segmentation model, by means of the stationary wavelet transform (SWT), applied to complementary DNA (cDNA) microarray images is proposed (WMRF). A 3-level decomposition scheme of the initial microarray image was performed, followed by a soft thresholding filtering technique. With the inverse process, a Denoised image was created. In addition, by using the Amplitudes of the filtered wavelet Horizontal and Vertical images at each level, three different Magnitudes were formed. These images were combined with the Denoised one to create the proposed SMRF segmentation model. For numerical evaluation of the segmentation accuracy, the segmentation matching factor (SMF), the Coefficient of Determination (r(2)), and the concordance correlation (p(c)) were calculated on the simulated images. In addition, the SMRF performance was contrasted to the Fuzzy C Means (FCM), Gaussian Mixture Models (GMM), Fuzzy GMM (FGMM), and the conventional MRF techniques. Indirect accuracy performances were also tested on the experimental images by means of the Mean Absolute Error (MAE) and the Coefficient of Variation (CV). In the latter case, SPOT and SCANALYZE software results were also tested. In the former case, SMRF attained the best SMF, r(2), and p(c) (92.66%, 0.923, and 0.88, respectively) scores, whereas, in the latter case scored MAE and CV, 497 and 0.88, respectively. The results and support the performance superiority of the SMRF algorithm in segmenting cDNA images. PMID:21531035

  16. Semi-automatic medical image segmentation with adaptive local statistics in Conditional Random Fields framework.

    PubMed

    Hu, Yu-Chi J; Grossberg, Michael D; Mageras, Gikas S

    2008-01-01

    Planning radiotherapy and surgical procedures usually require onerous manual segmentation of anatomical structures from medical images. In this paper we present a semi-automatic and accurate segmentation method to dramatically reduce the time and effort required of expert users. This is accomplished by giving a user an intuitive graphical interface to indicate samples of target and non-target tissue by loosely drawing a few brush strokes on the image. We use these brush strokes to provide the statistical input for a Conditional Random Field (CRF) based segmentation. Since we extract purely statistical information from the user input, we eliminate the need of assumptions on boundary contrast previously used by many other methods, A new feature of our method is that the statistics on one image can be reused on related images without registration. To demonstrate this, we show that boundary statistics provided on a few 2D slices of volumetric medical data, can be propagated through the entire 3D stack of images without using the geometric correspondence between images. In addition, the image segmentation from the CRF can be formulated as a minimum s-t graph cut problem which has a solution that is both globally optimal and fast. The combination of a fast segmentation and minimal user input that is reusable, make this a powerful technique for the segmentation of medical images. PMID:19163362

  17. Segmentation of cone-beam CT using a hidden Markov random field with informative priors

    NASA Astrophysics Data System (ADS)

    Moores, M.; Hargrave, C.; Harden, F.; Mengersen, K.

    2014-03-01

    Cone-beam computed tomography (CBCT) has enormous potential to improve the accuracy of treatment delivery in image-guided radiotherapy (IGRT). To assist radiotherapists in interpreting these images, we use a Bayesian statistical model to label each voxel according to its tissue type. The rich sources of prior information in IGRT are incorporated into a hidden Markov random field model of the 3D image lattice. Tissue densities in the reference CT scan are estimated using inverse regression and then rescaled to approximate the corresponding CBCT intensity values. The treatment planning contours are combined with published studies of physiological variability to produce a spatial prior distribution for changes in the size, shape and position of the tumour volume and organs at risk. The voxel labels are estimated using iterated conditional modes. The accuracy of the method has been evaluated using 27 CBCT scans of an electron density phantom. The mean voxel-wise misclassification rate was 6.2%, with Dice similarity coefficient of 0.73 for liver, muscle, breast and adipose tissue. By incorporating prior information, we are able to successfully segment CBCT images. This could be a viable approach for automated, online image analysis in radiotherapy.

  18. D Classification of Crossroads from Multiple Aerial Images Using Markov Random Fields

    NASA Astrophysics Data System (ADS)

    Kosov, S.; Rottensteiner, F.; Heipke, C.; Leitloff, J.; Hinz, S.

    2012-08-01

    The precise classification and reconstruction of crossroads from multiple aerial images is a challenging problem in remote sensing. We apply the Markov Random Fields (MRF) approach to this problem, a probabilistic model that can be used to consider context in classification. A simple appearance-based model is combined with a probabilistic model of the co-occurrence of class label at neighbouring image sites to distinguish up to 14 different classes that are relevant for scenes containing crossroads. The parameters of these models are learnt from training data. We use multiple overlap aerial images to derive a digital surface model (DSM) and a true orthophoto without moving cars. From the DSM and the orthophoto we derive feature vectors that are used in the classification. One of the features is a car confidence value that is supposed to support the classification when the road surface is occluded by static cars. Our approach is evaluated on a dataset of airborne photos of an urban area by a comparison of the results to reference data. Whereas the method has problems in distinguishing classes having a similar appearance, it is shown to produce promising results if a reduced set of classes is considered, yielding an overall classification accuracy of 74.8%.

  19. Segmentation of 2D gel electrophoresis spots using a Markov random field

    NASA Astrophysics Data System (ADS)

    Hoeflich, Christopher S.; Corso, Jason J.

    2009-02-01

    We propose a statistical model-based approach for the segmentation of fragments of DNA as a first step in the automation of the primarily manual process of comparing two or more images resulting from the Restriction Landmark Genomic Scanning (RLGS) method. These 2D gel electrophoresis images are the product of the separation of DNA into fragments that appear as spots on X-ray films. The goal is to find instances where a spot appears in one image and not in another since a missing spot can be correlated with a region of DNA that has been affected by a disease such as cancer. The entire comparison process is typically done manually, which is tedious and very error prone. We pose the problem as the labeling of each image pixel as either a spot or non-spot and use a Markov Random Field (MRF) model and simulated annealing for inference. Neighboring spot labels are then connected to form spot regions. The MRF based model was tested on actual 2D gel electrophoresis images.

  20. Markov random field based automatic alignment for low SNR imagesfor cryo electron tomography

    SciTech Connect

    Amat, Fernando; Moussavi, Farshid; Comolli, Luis R.; Elidan, Gal; Horowitz, Mark

    2007-07-21

    We present a method for automatic full precision alignmentof the images in a tomographic tilt series. Full-precision automaticalignment of cryo electron microscopy images has remained a difficultchallenge to date, due to the limited electron dose and low imagecontrast. These facts lead to poor signal to noise ratio (SNR) in theimages, which causes automatic feature trackers to generate errors, evenwith high contrast gold particles as fiducial features. To enable fullyautomatic alignment for full-precision reconstructions, we frame theproblem probabilistically as finding the most likely particle tracksgiven a set of noisy images, using contextual information to make thesolution more robust to the noise in each image. To solve this maximumlikelihood problem, we use Markov Random Fields (MRF) to establish thecorrespondence of features in alignment and robust optimization forprojection model estimation. The resultingalgorithm, called RobustAlignment and Projection Estimation for Tomographic Reconstruction, orRAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as goodas the manual approach by an expert user. We are able to automaticallymap complete and partial marker trajectories and thus obtain highlyaccurate image alignment. Our method has been applied to challenging cryoelectron tomographic datasets with low SNR from intact bacterial cells,as well as several plastic section and x-ray datasets.

  1. Influence of a random field on particle fractionation and solidification in liquid-crystal colloid mixtures

    NASA Astrophysics Data System (ADS)

    Popa-Nita, V.; van der Schoot, P.; Kralj, S.

    2006-11-01

    The influence of a random-anisotropy (RA) type disorder on the phase separation of nematogen-colloid mixtures is studied theoretically by combining the phenomenological Landau-de Gennes, Carnahan-Starling, and hard-sphere crystal theories. We assume that the colloids enforce the RA disorder on the surrounding thermotropic liquid-crystal (LC) molecules. We adopt the Imry-Ma argument according to which the lower-temperature phase exhibits a domain-type pattern. The colloids impose a finite degree of orientational ordering even in the isotropic (paranematic) phase. In the ordered phase they give rise to a domain-type structure, resulting in the distorted nematic (speronematic) phase. The RA field opposes the phase separation tendency. With increasing disorder the difference between the paranematic and speronematic ordering decreases. Consequently there is a critical disorder, above which both phases become identical from the orientation point of view, but have different concentrations of colloids. We have also estimated another characteristic value of disorder above which the isotropic phase can exist only in a liquid state, the crystal phase being suppressed completely.

  2. Influence of memory in deterministic walks in random media: analytical calculation within a mean-field approximation.

    PubMed

    Terçariol, César Augusto Sangaletti; Martinez, Alexandre Souto

    2008-09-01

    Consider a random medium consisting of N points randomly distributed so that there is no correlation among the distances separating them. This is the random link model, which is the high dimensionality limit (mean-field approximation) for the Euclidean random point structure. In the random link model, at discrete time steps, a walker moves to the nearest point, which has not been visited in the last mu steps (memory), producing a deterministic partially self-avoiding walk (the tourist walk). We have analytically obtained the distribution of the number n of points explored by the walker with memory mu=2 , as well as the transient and period joint distribution. This result enables us to explain the abrupt change in the exploratory behavior between the cases mu=1 (memoryless walker, driven by extreme value statistics) and mu=2 (walker with memory, driven by combinatorial statistics). In the mu=1 case, the mean newly visited points in the thermodynamic limit (N1) is just n=e=2.72... while in the mu=2 case, the mean number n of visited points grows proportionally to N;{12} . Also, this result allows us to establish an equivalence between the random link model with mu=2 and random map (uncorrelated back and forth distances) with mu=0 and the abrupt change between the probabilities for null transient time and subsequent ones. PMID:18850997

  3. A Lagrangian description of nearshore hydrodynamics and rip currents forced by a random wave field

    NASA Astrophysics Data System (ADS)

    Leandro, S.; Cienfuegos, R.; Escauriaza, C. R.

    2011-12-01

    Nonlinear processes become important for waves propagating in the shoaling and surf zones. Wave shape changes when approaching the coast under the influence of bathymetry, becoming increasingly asymmetric until reaching the breaking limit. In the shoaling zone, non-linearities induce a net velocity in the direction of wave propagation, a phenomenon called Stokes drift, while in the surf zone, currents are mainly driven by spatio-temporal variations in energy dissipation gradients. In this work we aim at investigating and characterizing the nearshore circulation forced by a random wave field propagating over a variable bathymetry. We carry out numerical simulations over a laboratory experiment conducted in a wave basin over a realistic bathymetry [Michallet et al. 2010]. For the hydrodynamics, we use a 2D shock-capturing finite-volume model that solves the non-linear shallow water equations, taking into account energy dissipation by breaking, friction, bed-slope variations, and an accurate description for the moving shoreline in the swash zone [Marche et al. 2007;Guerra et al. 2010]. Model predictions are compared and validated against experimental data giving confidence for its use in the description of wave propagation in the surf/swash zone, together with mean eulerian velocities. The resulting wave propagation and circulation provided by the 2D model will then be used to describe drifter's patterns in the surf zone and construct Lagrangian particle tracking. The chosen experimental configuration is of great interest due to the random wave forcing (slowly modulated), the beach non-uniformities, and the existence of several bar-rip channels that enhance quasi-periodic rip instabilities. During the experiment, balloons filled with water, with a diameter between 5 and 10 cm, were placed in the surf zone in order to characterize circulation in a Lagrangian framework [Castelle et al. 2010]. The time-location of the balloons was continuously tracked by a shore

  4. Mindfulness Training and Reductions in Teacher Stress and Burnout: Results from Two Randomized, Waitlist-Control Field Trials

    ERIC Educational Resources Information Center

    Roeser, Robert W.; Schonert-Reichl, Kimberly A.; Jha, Amishi; Cullen, Margaret; Wallace, Linda; Wilensky, Rona; Oberle, Eva; Thomson, Kimberly; Taylor, Cynthia; Harrison, Jessica

    2013-01-01

    The effects of randomization to mindfulness training (MT) or to a waitlist-control condition on psychological and physiological indicators of teachers' occupational stress and burnout were examined in 2 field trials. The sample included 113 elementary and secondary school teachers (89% female) from Canada and the United States. Measures were…

  5. Assessment Data-Informed Guidance to Individualize Kindergarten Reading Instruction: Findings from a Cluster-Randomized Control Field Trial

    ERIC Educational Resources Information Center

    Al Otaiba, Stephanie; Connor, Carol M.; Folsom, Jessica S.; Greulich, Luana; Meadows, Jane; Li, Zhi

    2011-01-01

    The purpose of this cluster-randomized control field trial was to examine whether kindergarten teachers could learn to differentiate classroom reading instruction using Individualized Student Instruction for Kindergarten (ISI-K) and to test the efficacy of differentiation on reading outcomes. The study involved 14 schools, 23 ISI-K (n = 305…

  6. Final Reading Outcomes of the National Randomized Field Trial of Success for All

    ERIC Educational Resources Information Center

    Borman, Geoffrey D.; Slavin, Robert E.; Cheung, Alan C. K.; Chamberlain, Anne M.; Madden, Nancy A.; Chambers, Bette

    2007-01-01

    Using a cluster randomization design, schools were randomly assigned to implement Success for All, a comprehensive reading reform model, or control methods. This article reports final literacy outcomes for a 3-year longitudinal sample of children who participated in the treatment or control condition from kindergarten through second grade and a…

  7. Genotoxicity of Thermopsis turcica on Allium cepa L. roots revealed by alkaline comet and random amplified polymorphic DNA assays.

    PubMed

    Ciğerci, İbrahim Hakkı; Cenkci, Süleyman; Kargıoğlu, Mustafa; Konuk, Muhsin

    2016-08-01

    This study was undertaken to evaluate genotoxic potential of Thermopsis turcica aqueous extracts on the roots of onion bulb (Allium cepa L.) by comet assay and random amplified polymorphic DNA technique. The Allium root growth inhibition test indicated that the EC50 and 2×EC50 values were 8 and 16 mg/ml concentrations of T. turcica aqueous extracts, respectively. The negative control (distilled water), positive control (methyl methane sulfonate, 10 mg/l) and 8 and 16 mg/ml concentrations of T. turcica extracts were introduced to the roots of onion bulbs for 24 and 96 h. The root growth, DNA damage in root cells and randomly amplified polymorphic DNA (RAPD) profiles of root tissue were used as endpoints of the genotoxicity. The comet assay clearly indicated that dose-dependent single strand DNA breaks in the root nuclei of onions were determined for the treatment concentrations of T. turcica extracts. In comparison to RAPD profile of negative control group, RAPD polymorphisms became evident as disappearance and/or appearance of RAPD bands in treated roots. The diagnostic and phenetic numerical analyses of RAPD profiles obviously indicated dose-dependent genotoxicity induced by Thermopsis extracts. In conclusion, the results clearly indicated that water extract of T. turcica has genotoxic potential on the roots of onion bulbs as shown by comet assay and RAPD technique. PMID:25550040

  8. SAR-based change detection using hypothesis testing and Markov random field modelling

    NASA Astrophysics Data System (ADS)

    Cao, W.; Martinis, S.

    2015-04-01

    The objective of this study is to automatically detect changed areas caused by natural disasters from bi-temporal co-registered and calibrated TerraSAR-X data. The technique in this paper consists of two steps: Firstly, an automatic coarse detection step is applied based on a statistical hypothesis test for initializing the classification. The original analytical formula as proposed in the constant false alarm rate (CFAR) edge detector is reviewed and rewritten in a compact form of the incomplete beta function, which is a builtin routine in commercial scientific software such as MATLAB and IDL. Secondly, a post-classification step is introduced to optimize the noisy classification result in the previous step. Generally, an optimization problem can be formulated as a Markov random field (MRF) on which the quality of a classification is measured by an energy function. The optimal classification based on the MRF is related to the lowest energy value. Previous studies provide methods for the optimization problem using MRFs, such as the iterated conditional modes (ICM) algorithm. Recently, a novel algorithm was presented based on graph-cut theory. This method transforms a MRF to an equivalent graph and solves the optimization problem by a max-flow/min-cut algorithm on the graph. In this study this graph-cut algorithm is applied iteratively to improve the coarse classification. At each iteration the parameters of the energy function for the current classification are set by the logarithmic probability density function (PDF). The relevant parameters are estimated by the method of logarithmic cumulants (MoLC). Experiments are performed using two flood events in Germany and Australia in 2011 and a forest fire on La Palma in 2009 using pre- and post-event TerraSAR-X data. The results show convincing coarse classifications and considerable improvement by the graph-cut post-classification step.

  9. Adaptive multi-GPU Exchange Monte Carlo for the 3D Random Field Ising Model

    NASA Astrophysics Data System (ADS)

    Navarro, Cristóbal A.; Huang, Wei; Deng, Youjin

    2016-08-01

    This work presents an adaptive multi-GPU Exchange Monte Carlo approach for the simulation of the 3D Random Field Ising Model (RFIM). The design is based on a two-level parallelization. The first level, spin-level parallelism, maps the parallel computation as optimal 3D thread-blocks that simulate blocks of spins in shared memory with minimal halo surface, assuming a constant block volume. The second level, replica-level parallelism, uses multi-GPU computation to handle the simulation of an ensemble of replicas. CUDA's concurrent kernel execution feature is used in order to fill the occupancy of each GPU with many replicas, providing a performance boost that is more notorious at the smallest values of L. In addition to the two-level parallel design, the work proposes an adaptive multi-GPU approach that dynamically builds a proper temperature set free of exchange bottlenecks. The strategy is based on mid-point insertions at the temperature gaps where the exchange rate is most compromised. The extra work generated by the insertions is balanced across the GPUs independently of where the mid-point insertions were performed. Performance results show that spin-level performance is approximately two orders of magnitude faster than a single-core CPU version and one order of magnitude faster than a parallel multi-core CPU version running on 16-cores. Multi-GPU performance is highly convenient under a weak scaling setting, reaching up to 99 % efficiency as long as the number of GPUs and L increase together. The combination of the adaptive approach with the parallel multi-GPU design has extended our possibilities of simulation to sizes of L = 32 , 64 for a workstation with two GPUs. Sizes beyond L = 64 can eventually be studied using larger multi-GPU systems.

  10. Detecting Hedge Cues and their Scope in Biomedical Literature with Conditional Random Fields

    PubMed Central

    Agarwal, Shashank; Yu, Hong

    2010-01-01

    Objective Hedging is frequently used in both the biological literature and clinical notes to denote uncertainty or speculation. It is important for text-mining applications to detect hedge cues and their scope; otherwise, uncertain events are incorrectly identified as factual events. However, due to the complexity of language, identifying hedge cues and their scope in a sentence is not a trivial task. Our objective was to develop an algorithm that would automatically detect hedge cues and their scope in biomedical literature. Methodology We used conditional random fields (CRF), a supervised machine-learning algorithm, to train models to detect hedge cue phrases and their scope in biomedical literature. The models were trained on the publicly available BioScope corpus. We evaluated the performance of the CRF models in identifying hedge cue phrases and their scope by calculating recall, precision and F1-score. We compared our models with three competitive baseline systems. Results Our best CRF-based model performed statistically better than the baseline systems, achieving an F1-score of 88% and 86% in detecting hedge cue phrases and their scope in biological literature and an F1-score of 93% and 90% in detecting hedge cue phrases and their scope in clinical notes. Conclusions Our approach is robust, as it can identify hedge cues and their scope in both biological and clinical text. To benefit text-mining applications, our system is publicly available as a Java API and as an online application at http://hedgescope.askhermes.org. To our knowledge, this is the first publicly available system to detect hedge cues and their scope in biomedical literature. PMID:20709188

  11. A generalized genetic random field method for the genetic association analysis of sequencing data.

    PubMed

    Li, Ming; He, Zihuai; Zhang, Min; Zhan, Xiaowei; Wei, Changshuai; Elston, Robert C; Lu, Qing

    2014-04-01

    With the advance of high-throughput sequencing technologies, it has become feasible to investigate the influence of the entire spectrum of sequencing variations on complex human diseases. Although association studies utilizing the new sequencing technologies hold great promise to unravel novel genetic variants, especially rare genetic variants that contribute to human diseases, the statistical analysis of high-dimensional sequencing data remains a challenge. Advanced analytical methods are in great need to facilitate high-dimensional sequencing data analyses. In this article, we propose a generalized genetic random field (GGRF) method for association analyses of sequencing data. Like other similarity-based methods (e.g., SIMreg and SKAT), the new method has the advantages of avoiding the need to specify thresholds for rare variants and allowing for testing multiple variants acting in different directions and magnitude of effects. The method is built on the generalized estimating equation framework and thus accommodates a variety of disease phenotypes (e.g., quantitative and binary phenotypes). Moreover, it has a nice asymptotic property, and can be applied to small-scale sequencing data without need for small-sample adjustment. Through simulations, we demonstrate that the proposed GGRF attains an improved or comparable power over a commonly used method, SKAT, under various disease scenarios, especially when rare variants play a significant role in disease etiology. We further illustrate GGRF with an application to a real dataset from the Dallas Heart Study. By using GGRF, we were able to detect the association of two candidate genes, ANGPTL3 and ANGPTL4, with serum triglyceride. PMID:24482034

  12. Addressing the unmet need for visualizing conditional random fields in biological data

    PubMed Central

    2014-01-01

    Background The biological world is replete with phenomena that appear to be ideally modeled and analyzed by one archetypal statistical framework - the Graphical Probabilistic Model (GPM). The structure of GPMs is a uniquely good match for biological problems that range from aligning sequences to modeling the genome-to-phenome relationship. The fundamental questions that GPMs address involve making decisions based on a complex web of interacting factors. Unfortunately, while GPMs ideally fit many questions in biology, they are not an easy solution to apply. Building a GPM is not a simple task for an end user. Moreover, applying GPMs is also impeded by the insidious fact that the “complex web of interacting factors” inherent to a problem might be easy to define and also intractable to compute upon. Discussion We propose that the visualization sciences can contribute to many domains of the bio-sciences, by developing tools to address archetypal representation and user interaction issues in GPMs, and in particular a variety of GPM called a Conditional Random Field(CRF). CRFs bring additional power, and additional complexity, because the CRF dependency network can be conditioned on the query data. Conclusions In this manuscript we examine the shared features of several biological problems that are amenable to modeling with CRFs, highlight the challenges that existing visualization and visual analytics paradigms induce for these data, and document an experimental solution called StickWRLD which, while leaving room for improvement, has been successfully applied in several biological research projects. Software and tutorials are available at http://www.stickwrld.org/ PMID:25000815

  13. High-Resolution Image Classification Integrating Spectral-Spatial-Location Cues by Conditional Random Fields.

    PubMed

    Zhao, Ji; Zhong, Yanfei; Shu, Hong; Zhang, Liangpei

    2016-09-01

    With the increase in the availability of high-resolution remote sensing imagery, classification is becoming an increasingly useful technique for providing a large area of detailed land-cover information by the use of these high-resolution images. High-resolution images have the characteristics of abundant geometric and detail information, which are beneficial to detailed classification. In order to make full use of these characteristics, a classification algorithm based on conditional random fields (CRFs) is presented in this paper. The proposed algorithm integrates spectral, spatial contextual, and spatial location cues by modeling the probabilistic potentials. The spectral cues modeled by the unary potentials can provide basic information for discriminating the various land-cover classes. The pairwise potentials consider the spatial contextual information by establishing the neighboring interactions between pixels to favor spatial smoothing. The spatial location cues are explicitly encoded in the higher order potentials. The higher order potentials consider the nonlocal range of the spatial location interactions between the target pixel and its nearest training samples. This can provide useful information for the classes that are easily confused with other land-cover types in the spectral appearance. The proposed algorithm integrates spectral, spatial contextual, and spatial location cues within a CRF framework to provide complementary information from varying perspectives, so that it can address the common problem of spectral variability in remote sensing images, which is directly reflected in the accuracy of each class and the average accuracy. The experimental results with three high-resolution images show the validity of the algorithm, compared with the other state-of-the-art classification algorithms. PMID:27295673

  14. An automatic water body area monitoring algorithm for satellite images based on Markov Random Fields

    NASA Astrophysics Data System (ADS)

    Elmi, Omid; Tourian, Mohammad J.; Sneeuw, Nico

    2016-04-01

    Our knowledge about spatial and temporal variation of hydrological parameters are surprisingly poor, because most of it is based on in situ stations and the number of stations have reduced dramatically during the past decades. On the other hand, remote sensing techniques have proven their ability to measure different parameters of Earth phenomena. Optical and SAR satellite imagery provide the opportunity to monitor the spatial change in coastline, which can serve as a way to determine the water extent repeatedly in an appropriate time interval. An appropriate classification technique to separate water and land is the backbone of each automatic water body monitoring. Due to changes in the water level, river and lake extent, atmosphere, sunlight radiation and onboard calibration of the satellite over time, most of the pixel-based classification techniques fail to determine accurate water masks. Beyond pixel intensity, spatial correlation between neighboring pixels is another source of information that should be used to decide the label of pixels. Water bodies have strong spatial correlation in satellite images. Therefore including contextual information as additional constraint into the procedure of water body monitoring improves the accuracy of the derived water masks significantly. In this study, we present an automatic algorithm for water body area monitoring based on maximum a posteriori (MAP) estimation of Markov Random Fields (MRF). First we collect all available images from selected case studies during the monitoring period. Then for each image separately we apply a k-means clustering to derive a primary water mask. After that we develop a MRF using pixel values and the primary water mask for each image. Then among the different realizations of the field we select the one that maximizes the posterior estimation. We solve this optimization problem using graph cut techniques. A graph with two terminals is constructed, after which the best labelling structure for

  15. Differences between MyoD DNA binding and activation site requirements revealed by functional random sequence selection.

    PubMed Central

    Huang, J; Blackwell, T K; Kedes, L; Weintraub, H

    1996-01-01

    A method has been developed for selecting functional enhancer/promoter sites from random DNA sequences in higher eukaryotic cells. Of sequences that were thus selected for transcriptional activation by the muscle-specific basic helix-loop-helix protein MyoD, only a subset are similar to the preferred in vitro binding consensus, and in the same promoter context an optimal in vitro binding site was inactive. Other sequences with full transcriptional activity instead exhibit sequence preferences that, remarkably, are generally either identical or very similar to those found in naturally occurring muscle-specific promoters. This first systematic examination of the relation between DNA binding and transcriptional activation by basic helix-loop-helix proteins indicates that binding per se is necessary but not sufficient for transcriptional activation by MyoD and implies a requirement for other DNA sequence-dependent interactions or conformations at its binding site. PMID:8668207

  16. Random Addition Concatenation Analysis: A Novel Approach to the Exploration of Phylogenomic Signal Reveals Strong Agreement between Core and Shell Genomic Partitions in the Cyanobacteria

    PubMed Central

    Narechania, Apurva; Baker, Richard H.; Sit, Ryan; Kolokotronis, Sergios-Orestis; DeSalle, Rob; Planet, Paul J.

    2012-01-01

    Recent whole-genome approaches to microbial phylogeny have emphasized partitioning genes into functional classes, often focusing on differences between a stable core of genes and a variable shell. To rigorously address the effects of partitioning and combining genes in genome-level analyses, we developed a novel technique called Random Addition Concatenation Analysis (RADICAL). RADICAL operates by sequentially concatenating randomly chosen gene partitions starting with a single-gene partition and ending with the entire genomic data set. A phylogenetic tree is built for every successive addition, and the entire process is repeated creating multiple random concatenation paths. The result is a library of trees representing a large variety of differently sized random gene partitions. This library can then be mined to identify unique topologies, assess overall agreement, and measure support for different trees. To evaluate RADICAL, we used 682 orthologous genes across 13 cyanobacterial genomes. Despite previous assertions of substantial differences between a core and a shell set of genes for this data set, RADICAL reveals the two partitions contain congruent phylogenetic signal. Substantial disagreement within the data set is limited to a few nodes and genes involved in metabolism, a functional group that is distributed evenly between the core and the shell partitions. We highlight numerous examples where RADICAL reveals aspects of phylogenetic behavior not evident by examining individual gene trees or a “‘total evidence” tree. Our method also demonstrates that most emergent phylogenetic signal appears early in the concatenation process. The software is freely available at http://desalle.amnh.org. PMID:22094860

  17. Dynamic full field optical coherence tomography: subcellular metabolic contrast revealed in tissues by interferometric signals temporal analysis

    PubMed Central

    Apelian, Clement; Harms, Fabrice; Thouvenin, Olivier; Boccara, A. Claude

    2016-01-01

    We developed a new endogenous approach to reveal subcellular metabolic contrast in fresh ex vivo tissues taking advantage of the time dependence of the full field optical coherence tomography interferometric signals. This method reveals signals linked with local activity of the endogenous scattering elements which can reveal cells where other OCT-based techniques fail or need exogenous contrast agents. We benefit from the micrometric transverse resolution of full field OCT to image intracellular features. We used this time dependence to identify different dynamics at the millisecond scale on a wide range of organs in normal or pathological conditions. PMID:27446672

  18. Wide-field Ca2+ imaging reveals visually evoked activity in the retrosplenial area

    PubMed Central

    Murakami, Tomonari; Yoshida, Takashi; Matsui, Teppei; Ohki, Kenichi

    2015-01-01

    Due to recent advances of genetic manipulation, mouse brain has become a useful model for studying brain function, which demands whole brain functional mapping techniques in the mouse brain. In the present study, to finely map visual responsive areas in the mouse brain, we combined high-resolution wide-field optical imaging with transgenic mice containing the genetically encoded Ca2+ indicator, GCaMP3. With the high signal amplitude of GCaMP3 expressing in excitatory neurons, this system allowed neural activity to be observed with relatively fine spatial resolution and cell-type specificity. To evaluate this system, we examined whether non-visual areas exhibited a visual response over the entire surface of the mouse hemisphere. We found that two association areas, the retrosplenial area (RS) and secondary motor/anterior cingulate area (M2/AC), were significantly responsive to drifting gratings. Examination using gratings with distinct spatiotemporal frequency parameters revealed that the RS strongly responded to high-spatial and low-temporal frequency gratings. The M2/AC exhibited a response property similar to that of the RS, though it was not statistically significant. Finally, we performed cellular imaging using two-photon microscopy to examine orientation and direction selectivity of individual neurons, and found that a minority of neurons in the RS clearly showed visual responses sharply selective for orientation and direction. These results suggest that neurons in RS encode visual information of fine spatial details in images. Thus, the present study shows the usefulness of the functional mapping method using a combination of wide-field and two-photon Ca2+ imaging, which allows for whole brain mapping with high spatiotemporal resolution and cell-type specificity. PMID:26106292

  19. Irrational use of antimalarial drugs in rural areas of eastern Pakistan: a random field study

    PubMed Central

    2012-01-01

    Background Prescription of antimalarial drugs in the absence of malarial disease is a common practice in countries where malaria is endemic. However, unwarranted use of such drugs can cause side effects in some people and is a financial drain on local economies. In this study, we surveyed the prevalence of malaria parasites in humans, and the prevalence of the malaria transmitting mosquito vectors in the study area. We also investigated the use of antimalarial drugs in the local people. We focused on randomly selected rural areas of eastern Pakistan where no malaria cases had been reported since May 2004. Methods Mass blood surveys, active case detection, passive case detection, and vector density surveys were carried out in selected areas of Sargodha district from September 2008 to August 2009. Data pertaining to the quantities and types of antimalarial drugs used in these areas were collected from health centers, pharmacies, and the district CDC program of the Health Department of the Government of the Punjab. Results Seven hundred and forty four blood samples were examined, resulting in a Blood Examination Rate (BER) of 3.18; microscopic analysis of blood smears showed that none of the samples were positive for malaria parasites. Investigation of the mosquito vector density in 43 living rooms (bedrooms or rooms used for sleeping), 23 stores, and 32 animal sheds, revealed no vectors capable of transmitting malaria in these locations. In contrast, the density of Culex mosquitoes was high. Substantial consumption of a variety of antimalarial tablets, syrups, capsules and injections costing around 1000 US$, was documented for the region. Conclusion Use of antimalarial drugs in the absence of malarial infection or the vectors that transmit the disease was common in the study area. Continuous use of such drugs, not only in Pakistan, but in other parts of the world, may lead to drug-induced side effects amongst users. Better training of health care professionals is

  20. Some Trends in Radioactive Waste Form Behavior Revealed in Long-Term Field Tests

    SciTech Connect

    Ojovan, M. I.; Ojovan, N. V.; Startceva, I. V.; Barinov, A. S.

    2002-02-25

    Results from long-term field tests with borosilicate glass, cement and bitumen waste forms containing actual intermediate-level radioactive waste are summarized and discussed in the paper. Leaching behavior of the waste forms was evaluated by monitoring the contamination of contacting water. Measured leach rates of the three waste-form materials were in a narrow range in shallow subsurface repositories, but varied in a wide range at an open testing site owing to weathering of bitumen and cement materials. The repositories were opened after 12-year testing for visual examination, sampling and analysis. All retrieved waste forms were in good physical condition. The study has not revealed any negative changes in the waste glass. Some ageing processes were detected in cement and bitumen waste forms, which can positively (bitumen) or negatively (cement) affect physical and containment properties of these waste materials. It has been established that a significant proportion of the radioactive inventory in the bitumen waste form became associated with the bitumen phase. Phase separation of this radioactive bitumen has shown, than the asphaltene fraction is responsible for the major part of the radioactivity retained by the bitumen.

  1. Crustal Velocity Field from InSAR and GPS reveals Internal Deformation of Western Tibet

    NASA Astrophysics Data System (ADS)

    Wang, H.; Wright, T. J.

    2010-12-01

    a compromise between solution roughness and data misfit. The resultant velocity field satisfies the InSAR and GPS data with an rms misfit of ~1 mm/yr. It reveals a series of focused strain zones within the plateau and low slip rate on the Karakoram fault. Although focused strain zones are predicted by block models, those that we observe appear to occur away from the major faults, in the interior of the plateau. At least one is associated with a possible postseismic transient (1996 Mw6.8). This is incompatible with block models, but consistent with continuum models of continental deformation modified by the short-term influence of the earthquake cycle. Finally, we augmented the GPS velocity field using existing InSAR rate maps for the whole Tibetan plateau. It shows that a continental-scale velocity fields can be constructed without complete InSAR coverage using our method.

  2. Genetic diversity and phylogenetic relationship among Tunisian cactus species (Opuntia) as revealed by random amplified microsatellite polymorphism markers.

    PubMed

    Bendhifi Zarroug, M; Baraket, G; Zourgui, L; Souid, S; Salhi Hannachi, A

    2015-01-01

    Opuntia ficus indica is one of the most economically important species in the Cactaceae family. Increased interest in this crop stems from its potential contribution to agricultural diversification, application in the exploitation of marginal lands, and utility as additional income sources for farmers. In Tunisia, O. ficus indica has been affected by drastic genetic erosion resulting from biotic and abiotic stresses. Thus, it is imperative to identify and preserve this germplasm. In this study, we focused on the use of random amplified microsatellite polymorphisms to assess genetic diversity among 25 representatives of Tunisian Opuntia species maintained in the collection of the National Institute of Agronomic Research of Tunisia. Seventy-two DNA markers were screened to discriminate accessions using 16 successful primer combinations. The high percentage of polymorphic band (100%), the resolving power value (5.68), the polymorphic information content (0.94), and the marker index (7.2) demonstrated the efficiency of the primers tested. Therefore, appropriate cluster analysis used in this study illustrated a divergence among the cultivars studied and exhibited continuous variation that occurred independently of geographic origin. O. ficus indica accessions did not cluster separately from the other cactus pear species, indicating that their current taxonomical classifications are not well aligned with their genetic variability or locality of origin. PMID:25730081

  3. A modified hybrid uncertain analysis method for dynamic response field of the LSOAAC with random and interval parameters

    NASA Astrophysics Data System (ADS)

    Zi, Bin; Zhou, Bin

    2016-07-01

    For the prediction of dynamic response field of the luffing system of an automobile crane (LSOAAC) with random and interval parameters, a hybrid uncertain model is introduced. In the hybrid uncertain model, the parameters with certain probability distribution are modeled as random variables, whereas, the parameters with lower and upper bounds are modeled as interval variables instead of given precise values. Based on the hybrid uncertain model, the hybrid uncertain dynamic response equilibrium equation, in which different random and interval parameters are simultaneously included in input and output terms, is constructed. Then a modified hybrid uncertain analysis method (MHUAM) is proposed. In the MHUAM, based on random interval perturbation method, the first-order Taylor series expansion and the first-order Neumann series, the dynamic response expression of the LSOAAC is developed. Moreover, the mathematical characteristics of extrema of bounds of dynamic response are determined by random interval moment method and monotonic analysis technique. Compared with the hybrid Monte Carlo method (HMCM) and interval perturbation method (IPM), numerical results show the feasibility and efficiency of the MHUAM for solving the hybrid LSOAAC problems. The effects of different uncertain models and parameters on the LSOAAC response field are also investigated deeply, and numerical results indicate that the impact made by the randomness in the thrust of the luffing cylinder F is larger than that made by the gravity of the weight in suspension Q . In addition, the impact made by the uncertainty in the displacement between the lower end of the lifting arm and the luffing cylinder a is larger than that made by the length of the lifting arm L .

  4. A multiresolution random field model for estimating fossil-fuel CO2 emissions

    NASA Astrophysics Data System (ADS)

    Ray, J.; Yadav, V.; Michalak, A. M.; Lee, J.; Lefantzi, S.; VanBloemenWaanders, B.

    2013-12-01

    We present a multiscale random field model (MsRF) that can be used for representing fossil-fuel CO2 (ffCO2) emissions. It is low-dimensional and is meant to be used in atmospheric inversions. The MsRF is constructed using wavelets. In this work, we will demonstrate a synthetic-data inversion aimed at estimating ffCO2 emissions, with 1o x 1o resolution, in the lower 48 states of the US. Measurements from 35 towers will be used. The measurements are constructed using the Vulcan inventory. The MsRF consists of a subset of Haar wavelets that can be defined in a rectangle bounding the US. By subjecting the Vulcan database to wavelet-transforms with a wide choice, the Haar wavelet was found to offer the most compressible representation. The MsRF was constructed by subjecting an image of lights at night to Haar transforms and retaining those with large weights. The lights-at-night image is correlated with ffCO2 inversions and have been used to downscale national ffCO2 aggregates when constructing spatially resolved ffCO2 emission inventories. The MsRF is then used to solve the linear inverse problem that underlies ffCO2 emission estimation. The number of parameters in the MsRF is far too large to be constrained by the measurements and thus we enforce sparsity to regularize the inverse problem. Further, we show that the transport model is only somewhat incoherent with respect to the chosen Haar bases, indicating that sparsification will be insufficient and further regularization using a prior emission model is required. This model is obtained by scaling up the nightlights to match EDGAR emissions. Finally, we present the results of the inversion and show that the resulting inversion mechanism can extract information from the observation to update and improve upon the predictive accuracy of prior model. The density of measurements dominates the accuracy of the inversion. We find that sparsification plays an important role since it removes about 50% of the wavelets in the Ms

  5. A Monte Carlo study of the Blume-Capel thin film in the presence of a random crystal field

    NASA Astrophysics Data System (ADS)

    Boughrara, M.; Kerouad, M.; Zaim, A.

    2016-07-01

    A Monte Carlo simulation with heat bath algorithm is used to study the effect of random crystal field and surface exchange interactions on the critical behavior and the magnetic properties of a spin-1 Ising ferromagnetic thin film having the simple cubic symmetry. The phase diagram exhibits a rich variety of behaviors such as the double reentrant phenomena and the existence of tricritical points. Thermal magnetization behavior and phase diagrams have been discussed in detail.

  6. A randomized double-blind prospective study of the efficacy of pulsed electromagnetic fields for interbody lumbar fusions

    SciTech Connect

    Mooney, V. )

    1990-07-01

    A randomized double-blind prospective study of pulsed electromagnetic fields for lumbar interbody fusions was performed on 195 subjects. There were 98 subjects in the active group and 97 subjects in the placebo group. A brace containing equipment to induce an electromagnetic field was applied to patients undergoing interbody fusion in the active group, and a sham brace was used in the control group. In the active group there was a 92% success rate, while the control group had a 65% success rate (P greater than 0.005). The effectiveness of bone graft stimulation with the device is thus established.

  7. Explaining Feast or Famine in Randomized Field Trials: Medical Science and Criminology Compared.

    ERIC Educational Resources Information Center

    Shepherd, Jonathan P.

    2003-01-01

    Discusses the contrast between the frequency of randomized clinical trials in the health sciences and the relative famine of such studies in criminology. Attributes this difference to the contexts in which research is done and the difference in the status of situational research in the two disciplines. (SLD)

  8. Image segmentation for automatic particle identification in electron micrographs based on hidden Markov random field models and expectation maximization

    PubMed Central

    Singh, Vivek; Marinescu, Dan C.; Baker, Timothy S.

    2014-01-01

    Three-dimensional reconstruction of large macromolecules like viruses at resolutions below 10 ÅA requires a large set of projection images. Several automatic and semi-automatic particle detection algorithms have been developed along the years. Here we present a general technique designed to automatically identify the projection images of particles. The method is based on Markov random field modelling of the projected images and involves a pre-processing of electron micrographs followed by image segmentation and post-processing. The image is modelled as a coupling of two fields—a Markovian and a non-Markovian. The Markovian field represents the segmented image. The micrograph is the non-Markovian field. The image segmentation step involves an estimation of coupling parameters and the maximum áa posteriori estimate of the realization of the Markovian field i.e, segmented image. Unlike most current methods, no bootstrapping with an initial selection of particles is required. PMID:15065680

  9. A Markov Random Field Framework for Protein Side-Chain Resonance Assignment

    NASA Astrophysics Data System (ADS)

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    Nuclear magnetic resonance (NMR) spectroscopy plays a critical role in structural genomics, and serves as a primary tool for determining protein structures, dynamics and interactions in physiologically-relevant solution conditions. The current speed of protein structure determination via NMR is limited by the lengthy time required in resonance assignment, which maps spectral peaks to specific atoms and residues in the primary sequence. Although numerous algorithms have been developed to address the backbone resonance assignment problem [68,2,10,37,14,64,1,31,60], little work has been done to automate side-chain resonance assignment [43, 48, 5]. Most previous attempts in assigning side-chain resonances depend on a set of NMR experiments that record through-bond interactions with side-chain protons for each residue. Unfortunately, these NMR experiments have low sensitivity and limited performance on large proteins, which makes it difficult to obtain enough side-chain resonance assignments. On the other hand, it is essential to obtain almost all of the side-chain resonance assignments as a prerequisite for high-resolution structure determination. To overcome this deficiency, we present a novel side-chain resonance assignment algorithm based on alternative NMR experiments measuring through-space interactions between protons in the protein, which also provide crucial distance restraints and are normally required in high-resolution structure determination. We cast the side-chain resonance assignment problem into a Markov Random Field (MRF) framework, and extend and apply combinatorial protein design algorithms to compute the optimal solution that best interprets the NMR data. Our MRF framework captures the contact map information of the protein derived from NMR spectra, and exploits the structural information available from the backbone conformations determined by orientational restraints and a set of discretized side-chain conformations (i.e., rotamers). A Hausdorff

  10. Electric field dependence of charge carrier hopping transport within the random energy landscape in an organic field effect transistor

    NASA Astrophysics Data System (ADS)

    Fishchuk, I. I.; Kadashchuk, A.; Ullah, Mujeeb; Sitter, H.; Pivrikas, A.; Genoe, J.; Bässler, H.

    2012-07-01

    We extended our analytical effective medium theory [Phys. Rev. BPRBMDO0163-182910.1103/PhysRevB.81.045202 81, 045202 (2010)] to describe the temperature-dependent hopping charge carrier mobility at arbitrary electric fields in the large carrier density regime. Special emphasis was made to analyze the influence of the lateral electric field on the Meyer-Neldel (MN) phenomenon observed when studying the charge mobilities in thin-film organic field-effect transistors (OFET). Our calculations are based on the average hopping transition time approach, generalized for large carrier concentration limit finite fields, and taking into account also spatial energy correlations. The calculated electric field dependences of the hopping mobility at large carrier concentrations are in good agreement with previous computer simulations data. The shift of the MN temperature in an OFET upon applied electric field is shown to be a consequence of the spatial energy correlation in the organic semiconductor film. Our calculations show that the phenomenological Gill equation is clearly inappropriate for describing conventional charge carrier transport at low carrier concentrations. On the other hand a Gill-type behavior has been observed in a temperature range relevant for measurements of the charge carrier mobility in OFET structures. Since the present model is not limited to zero-field mobility, it allows a more accurate evaluation of important material parameters from experimental data measured at a given electric field. In particular, we showed that both the MN and Gill temperature can be used for estimating the width of the density of states distribution.

  11. Diffusion and stochastic island generation in the magnetic field line random walk

    SciTech Connect

    Vlad, M.; Spineanu, F.

    2014-08-10

    The cross-field diffusion of field lines in stochastic magnetic fields described by the 2D+slab model is studied using a semi-analytic statistical approach, the decorrelation trajectory method. We show that field line trapping and the associated stochastic magnetic islands strongly influence the diffusion coefficients, leading to dependences on the parameters that are different from the quasilinear and Bohm regimes. A strong amplification of the diffusion is produced by a small slab field in the presence of trapping. The diffusion regimes are determined and the corresponding physical processes are identified.

  12. Random Flips of Electric Field in Microwave-Induced States with Spontaneously Broken Symmetry

    NASA Astrophysics Data System (ADS)

    Dorozhkin, S. I.; Umansky, V.; Pfeiffer, L. N.; West, K. W.; Baldwin, K.; von Klitzing, K.; Smet, J. H.

    2015-05-01

    In a two-dimensional electron system subject to microwaves and a magnetic field, photovoltages emerge. They can be separated into two components originating from built-in electric fields and electric field domains arising from spontaneous symmetry breaking. The latter occurs in the zero resistance regime only and manifests itself in pulsed behavior, synchronous across the sample. The pulses show sign reversal. This implies a flip of the field in each domain, consistent with the existence of two equally probable electric field domain configurations due to the spontaneous symmetry breaking.

  13. The magnetic field of the Large Magellanic Cloud revealed through Faraday rotation.

    PubMed

    Gaensler, B M; Haverkorn, M; Staveley-Smith, L; Dickey, J M; McClure-Griffiths, N M; Dickel, J R; Wolleben, M

    2005-03-11

    We have measured the Faraday rotation toward a large sample of polarized radio sources behind the Large Magellanic Cloud (LMC) to determine the structure of this galaxy's magnetic field. The magnetic field of the LMC consists of a coherent axisymmetric spiral of field strength approximately 1 microgauss. Strong fluctuations in the magnetic field are also seen on small (<0.5 parsec) and large (approximately 100 parsecs) scales. The large bursts of recent star formation and supernova activity in the LMC argue against standard dynamo theory, adding to the growing evidence for rapid field amplification in galaxies. PMID:15761149

  14. Magnetic-field-induced ferroelectric polarization reversal in magnetoelectric composites revealed by piezoresponse force microscopy

    NASA Astrophysics Data System (ADS)

    Miao, Hongchen; Zhou, Xilong; Dong, Shuxiang; Luo, Haosu; Li, Faxin

    2014-07-01

    Controlling electric polarization (or magnetization) in multiferroic materials with external magnetic fields (or electric fields) is very important for fundamental physics and spintronic devices. Although there has been some progress on magnetic-field-induced polarization reversal in single-phase multiferroics, such behavior has so far never been realized in composites. Here we show that it is possible to reverse ferroelectric polarization using magnetic fields in a bilayer Terfenol-D/PMN-33%PT composite. We realized this by ferroelectric domain imaging using piezoresponse force microscopy (PFM) under applied magnetic field loading. The internal electric field caused by the magnetoelectric (ME) effect in the PMN-PT crystal is considered as the driving force for the 180° polarization switching, and its existence is verified by switching spectroscopy PFM testing under a series of external magnetic fields. A quantitative method is further suggested to estimate the local ME coefficient based on the switching spectroscopy PFM testing results.

  15. Magnetic-field-induced ferroelectric polarization reversal in magnetoelectric composites revealed by piezoresponse force microscopy.

    PubMed

    Miao, Hongchen; Zhou, Xilong; Dong, Shuxiang; Luo, Haosu; Li, Faxin

    2014-08-01

    Controlling electric polarization (or magnetization) in multiferroic materials with external magnetic fields (or electric fields) is very important for fundamental physics and spintronic devices. Although there has been some progress on magnetic-field-induced polarization reversal in single-phase multiferroics, such behavior has so far never been realized in composites. Here we show that it is possible to reverse ferroelectric polarization using magnetic fields in a bilayer Terfenol-D/PMN-33%PT composite. We realized this by ferroelectric domain imaging using piezoresponse force microscopy (PFM) under applied magnetic field loading. The internal electric field caused by the magnetoelectric (ME) effect in the PMN-PT crystal is considered as the driving force for the 180° polarization switching, and its existence is verified by switching spectroscopy PFM testing under a series of external magnetic fields. A quantitative method is further suggested to estimate the local ME coefficient based on the switching spectroscopy PFM testing results. PMID:24953042

  16. Electron random walk and collisional crossover in a gas in presence of electromagnetic waves and magnetostatic fields

    SciTech Connect

    Bhattacharjee, Sudeep; Paul, Samit; Dey, Indranuj

    2013-04-15

    This paper deals with random walk of electrons and collisional crossover in a gas evolving toward a plasma, in presence of electromagnetic (EM) waves and magnetostatic (B) fields, a fundamental subject of importance in areas requiring generation and confinement of wave assisted plasmas. In presence of EM waves and B fields, the number of collisions N suffered by an electron with neutral gas atoms while diffusing out of the volume during the walk is significantly modified when compared to the conventional field free square law diffusion; N=1.5({Lambda}/{lambda}){sup 2}, where {Lambda} is the characteristic diffusion length and {lambda} is the mean free path. There is a distinct crossover and a time scale associated with the transition from the elastic to inelastic collisions dominated regime, which can accurately predict the breakdown time ({tau}{sub c}) and the threshold electric field (E{sub BD}) for plasma initiation. The essential features of cyclotron resonance manifested as a sharp drop in {tau}{sub c}, lowering of E{sub BD} and enhanced electron energy gain is well reproduced in the constrained random walk.

  17. Towards phonon photonics: scattering-type near-field optical microscopy reveals phonon-enhanced near-field interaction.

    PubMed

    Hillenbrand, Rainer

    2004-08-01

    Diffraction limits the spatial resolution in classical microscopy or the dimensions of optical circuits to about half the illumination wavelength. Scanning near-field microscopy can overcome this limitation by exploiting the evanescent near fields existing close to any illuminated object. We use a scattering-type near-field optical microscope (s-SNOM) that uses the illuminated metal tip of an atomic force microscope (AFM) to act as scattering near-field probe. The presented images are direct evidence that the s-SNOM enables optical imaging at a spatial resolution on a 10nm scale, independent of the wavelength used (lambda=633 nm and 10 microm). Operating the microscope at specific mid-infrared frequencies we found a tip-induced phonon-polariton resonance on flat polar crystals such as SiC and Si3N4. Being a spectral fingerprint of any polar material such phonon-enhanced near-field interaction has enormous applicability in nondestructive, material-specific infrared microscopy at nanoscale resolution. The potential of s-SNOM to study eigenfields of surface polaritons in nanostructures opens the door to the development of phonon photonics-a proposed infrared nanotechnology that uses localized or propagating surface phonon polaritons for probing, manipulating and guiding infrared light in nanoscale devices, analogous to plasmon photonics. PMID:15231334

  18. Distinguishing between aligned and randomly oriented polar molecules by using a combination of strong laser field with a weak static field

    NASA Astrophysics Data System (ADS)

    Moiseyev, Nimrod; Gupta, Ashish Kumar

    2012-08-01

    The harmonic generation spectra (HGS) of two different ensembles of the same heteronuclear (polar) diatomic molecule are studied. In one ensemble the molecules are aligned (i.e. CO ↔ OC) whereas in the second ensemble the molecules are randomly distributed in different directions (and therefore not all molecules have the same orientation, e.g. CO or OC along one of the axes in the laboratory frame). Using the non-Hermitian formalism of quantum mechanics we prove that the HGS of the two ensembles consist of odd-order harmonics only, provided the photo-induced dynamics is controlled by a single resonance (metastable) state. As we show here by using the Friedrich and Herschbach approach [J. Phys. Chem. A 103, 10280 (1999); J. Chem. Phys. 111, 6157 (1999)], it is possible to distinguish between the ensemble of 'perfectly' aligned molecules and an ensemble of molecules with a random directional distribution, provided the dc-field is turned on adiabatically slow and all aligned molecules are in the same quantum state. As an illustrative numerical example the HGS of aligned and ensemble of random directional distributed CO molecules with and without dc field were computed by carrying out ab initio electronic structure calculations.

  19. Partial spatial coherence and partial polarization in random evanescent fields on lossless interfaces.

    PubMed

    Norrman, Andreas; Setälä, Tero; Friberg, Ari T

    2011-03-01

    We consider partial spatial coherence and partial polarization of purely evanescent optical fields generated in total internal reflection at an interface of two dielectric (lossless) media. Making use of the electromagnetic degree of coherence, we show that, in such fields, the coherence length can be notably shorter than the light's vacuum wavelength, especially at a high-index-contrast interface. Physical explanation for this behavior, analogous to the generation of incoherent light in a multimode laser, is provided. We also analyze the degree of polarization by using a recent three-dimensional formulation and show that the field may be partially polarized at a subwavelength distance from the surface even though it is fully polarized farther away. The degree of polarization can assume values unattainable by beamlike fields, indicating that electromagnetic evanescent waves generally are genuine three-dimensional fields. The results can find applications in near-field optics and nanophotonics. PMID:21383821

  20. Theory of magnetic field line random walk in noisy reduced magnetohydrodynamic turbulence

    SciTech Connect

    Ruffolo, D.; Matthaeus, W. H.

    2013-01-15

    When a magnetic field consists of a mean part and fluctuations, the stochastic wandering of its field lines is often treated as a diffusive process. Under suitable conditions, a stable value is found for the mean square transverse displacement per unit parallel displacement relative to the mean field. Here, we compute the associated field line diffusion coefficient for a highly anisotropic 'noisy' reduced magnetohydrodynamic model of the magnetic field, which is useful in describing low frequency turbulence in the presence of a strong applied DC mean magnetic field, as may be found, for example, in the solar corona, or in certain laboratory devices. Our approach is nonperturbative, based on Corrsin's independence hypothesis, and makes use of recent advances in understanding factors that control decorrelation over a range of parameters described by the Kubo number. Both Bohm and quasilinear regimes are identified.

  1. The rate of separation of magnetic lines of force in a random magnetic field.

    NASA Technical Reports Server (NTRS)

    Jokipii, J. R.

    1973-01-01

    The mixing of magnetic lines of force, as represented by their rate of separation, as a function of distance along the magnetic field, is considered with emphasis on neighboring lines of force. This effect is particularly important in understanding the transport of charged particles perpendicular to the average magnetic field. The calculation is carried out in the approximation that the separation changes by an amount small compared with the correlation scale normal to the field, in a distance along the field of a few correlation scales. It is found that the rate of separation is very sensitive to the precise form of the power spectrum. Application to the interplanetary and interstellar magnetic fields is discussed, and it is shown that in some cases field lines, much closer together than the correlation scale, separate at a rate which is effectively as rapid as if they were many correlation lengths apart.

  2. Spatial cross modulation method using a random diffuser and phase-only spatial light modulator for constructing arbitrary complex fields.

    PubMed

    Shibukawa, Atsushi; Okamoto, Atsushi; Takabayashi, Masanori; Tomita, Akihisa

    2014-02-24

    We propose a spatial cross modulation method using a random diffuser and a phase-only spatial light modulator (SLM), by which arbitrary complex-amplitude fields can be generated with higher spatial resolution and diffraction efficiency than off-axis and double-phase computer-generated holograms. Our method encodes the original complex object as a phase-only diffusion image by scattering the complex object using a random diffuser. In addition, all incoming light to the SLM is consumed for a single diffraction order, making a diffraction efficiency of more than 90% possible. This method can be applied for holographic data storage, three-dimensional displays, and other such applications. PMID:24663718

  3. The role of magnetic fields in starburst galaxies as revealed by OH megamasers

    SciTech Connect

    McBride, James; Quataert, Eliot; Heiles, Carl; Bauermeister, Amber E-mail: eliot@astro.berkeley.edu

    2014-01-10

    We present estimates of magnetic field strengths in the interstellar media of starburst galaxies derived from measurements of Zeeman splitting associated with OH megamasers. The results for eight galaxies with Zeeman detections suggest that the magnetic energy density in the interstellar medium of starburst galaxies is comparable to their hydrostatic gas pressure, as in the Milky Way. We discuss the significant uncertainties in this conclusion, and possible measurements that could reduce these uncertainties. We also compare the Zeeman splitting derived magnetic field estimates to magnetic field strengths estimated using synchrotron fluxes and assuming that the magnetic field and cosmic rays have comparable energy densities, known as the 'minimum energy' argument. We find that the minimum energy argument systematically underestimates magnetic fields in starburst galaxies, and that the conditions that would be required to produce agreement between the minimum energy estimate and the Zeeman derived estimate of interstellar medium magnetic fields are implausible. The conclusion that magnetic fields in starburst galaxies exceed the minimum energy magnetic fields is consistent with starburst galaxies adhering to the linearity of the far-infrared-radio correlation.

  4. Asteroseismology can reveal strong internal magnetic fields in red giant stars.

    PubMed

    Fuller, Jim; Cantiello, Matteo; Stello, Dennis; Garcia, Rafael A; Bildsten, Lars

    2015-10-23

    Internal stellar magnetic fields are inaccessible to direct observations, and little is known about their amplitude, geometry, and evolution. We demonstrate that strong magnetic fields in the cores of red giant stars can be identified with asteroseismology. The fields can manifest themselves via depressed dipole stellar oscillation modes, arising from a magnetic greenhouse effect that scatters and traps oscillation-mode energy within the core of the star. The Kepler satellite has observed a few dozen red giants with depressed dipole modes, which we interpret as stars with strongly magnetized cores. We find that field strengths larger than ~10(5) gauss may produce the observed depression, and in one case we infer a minimum core field strength of ≈10(7) gauss. PMID:26494754

  5. Ultrasonic propagation: a technique to reveal field induced structures in magnetic nanofluids.

    PubMed

    Parekh, Kinnari; Patel, Jaykumar; Upadhyay, R V

    2015-07-01

    The paper reports the study of magnetic field induced structures in magnetic nanofluid investigated through ultrasonic wave propagation. Modified Tarapov's theory is used to study variation in velocity anisotropy with magnetic field. The types of field induced structures depend upon the chemical structure of the carrier in which magnetic nanoparticles are dispersed. Our study indicates formation of fractals and chain respectively, in transformer oil and kerosene based fluid. This difference is explained on the basis of particle-particle interaction and particle-medium interaction. PMID:25791205

  6. Subthreshold-swing-adjustable tunneling-field-effect-transistor-based random-access memory for nonvolatile operation

    NASA Astrophysics Data System (ADS)

    Huh, In; Cheon, Woo Young; Choi, Woo Young

    2016-04-01

    A subthreshold-swing-adjustable tunneling-field-effect-transistor-based random-access memory (SAT RAM) has been proposed and fabricated for low-power nonvolatile memory applications. The proposed SAT RAM cell demonstrates adjustable subthreshold swing (SS) depending on stored information: small SS in the erase state ("1" state) and large SS in the program state ("0" state). Thus, SAT RAM cells can achieve low read voltage (Vread) with a large memory window in addition to the effective suppression of ambipolar behavior. These unique features of the SAT RAM are originated from the locally stored charge, which modulates the tunneling barrier width (Wtun) of the source-to-channel tunneling junction.

  7. A multiresolution wavelet analysis and Gaussian Markov random field algorithm for breast cancer screening of digital mammography

    SciTech Connect

    Lee, C.G.; Chen, C.H.

    1996-12-31

    In this paper a novel multiresolution wavelet analysis (MWA) and non-stationary Gaussian Markov random field (GMRF) technique is introduced for the identification of microcalcifications with high accuracy. The hierarchical multiresolution wavelet information in conjunction with the contextual information of the images extracted from GMRF provides a highly efficient technique for microcalcification detection. A Bayesian teaming paradigm realized via the expectation maximization (EM) algorithm was also introduced for edge detection or segmentation of larger lesions recorded on the mammograms. The effectiveness of the approach has been extensively tested with a number of mammographic images provided by a local hospital.

  8. Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction

    PubMed Central

    Müller, Knut; Krause, Florian F.; Béché, Armand; Schowalter, Marco; Galioit, Vincent; Löffler, Stefan; Verbeeck, Johan; Zweck, Josef; Schattschneider, Peter; Rosenauer, Andreas

    2014-01-01

    By focusing electrons on probes with a diameter of 50 pm, aberration-corrected scanning transmission electron microscopy (STEM) is currently crossing the border to probing subatomic details. A major challenge is the measurement of atomic electric fields using differential phase contrast (DPC) microscopy, traditionally exploiting the concept of a field-induced shift of diffraction patterns. Here we present a simplified quantum theoretical interpretation of DPC. This enables us to calculate the momentum transferred to the STEM probe from diffracted intensities recorded on a pixel array instead of conventional segmented bright-field detectors. The methodical development yielding atomic electric field, charge and electron density is performed using simulations for binary GaN as an ideal model system. We then present a detailed experimental study of SrTiO3 yielding atomic electric fields, validated by comprehensive simulations. With this interpretation and upgraded instrumentation, STEM is capable of quantifying atomic electric fields and high-contrast imaging of light atoms. PMID:25501385

  9. NEAR-INFRARED-IMAGING POLARIMETRY TOWARD SERPENS SOUTH: REVEALING THE IMPORTANCE OF THE MAGNETIC FIELD

    SciTech Connect

    Sugitani, K.; Nakamura, F.; Tamura, M.; Kandori, R.; Watanabe, M.; Nishiyama, S.; Nagata, T.; Nagayama, T.; Sato, S.; Gutermuth, R. A.; Wilson, G. W.; Kawabe, R.

    2011-06-10

    The Serpens South embedded cluster, which is located in the constricted part of a long, filamentary, infrared dark cloud, is believed to be in a very early stage of cluster formation. We present results of near-infrared (JHKs) polarization observations of the filamentary cloud. Our polarization measurements of near-infrared point sources indicate a well-ordered global magnetic field that is perpendicular to the main filament, implying that the magnetic field is likely to have controlled the formation of the main filament. On the other hand, the sub-filaments, which converge on the central part of the cluster, tend to run along the magnetic field. The global magnetic field appears to be curved in the southern part of the main filament. Such morphology is consistent with the idea that the global magnetic field is distorted by gravitational contraction along the main filament toward the northern part, which contains larger mass. Applying the Chandrasekhar-Fermi method, the magnetic field strength is roughly estimated to be a few x100 {mu}G, suggesting that the filamentary cloud is close to magnetically critical.

  10. The random field model of the spatial distribution of heavy vehicle loads on long-span bridges

    NASA Astrophysics Data System (ADS)

    Chen, Zhicheng; Bao, Yuequan; Li, Hui

    2016-04-01

    A stochastic model based on Markov random field is proposed to model the spatial distribution of vehicle loads on longspan bridges. The bridge deck is divided into a finite set of discrete grid cells, each cell has two states according to whether the cell is occupied by the heavy vehicle load or not, then a four-neighbor lattice-structured undirected graphical model with each node corresponding to a cell state variable is proposed to model the location distribution of heavy vehicle loads on the bridge deck. The node potential is defined to quantitatively describe the randomness of node state, and the edge potential is defined to quantitatively describe the correlation of the connected node pair. The junction tree algorithm is employed to obtain the systematic solutions of inference problems of the graphical model. A marked random variable is assigned to each node to represent the amplitude of the total weight of vehicle applied on the corresponding cell of the bridge deck. The rationality of the model is validated by a Monte Carlo simulation of a learned model based on monitored data of a cable-stayed bridge.

  11. Theory and implementation of a very high throughput true random number generator in field programmable gate array.

    PubMed

    Wang, Yonggang; Hui, Cong; Liu, Chong; Xu, Chao

    2016-04-01

    The contribution of this paper is proposing a new entropy extraction mechanism based on sampling phase jitter in ring oscillators to make a high throughput true random number generator in a field programmable gate array (FPGA) practical. Starting from experimental observation and analysis of the entropy source in FPGA, a multi-phase sampling method is exploited to harvest the clock jitter with a maximum entropy and fast sampling speed. This parametrized design is implemented in a Xilinx Artix-7 FPGA, where the carry chains in the FPGA are explored to realize the precise phase shifting. The generator circuit is simple and resource-saving, so that multiple generation channels can run in parallel to scale the output throughput for specific applications. The prototype integrates 64 circuit units in the FPGA to provide a total output throughput of 7.68 Gbps, which meets the requirement of current high-speed quantum key distribution systems. The randomness evaluation, as well as its robustness to ambient temperature, confirms that the new method in a purely digital fashion can provide high-speed high-quality random bit sequences for a variety of embedded applications. PMID:27131692

  12. Theory and implementation of a very high throughput true random number generator in field programmable gate array

    NASA Astrophysics Data System (ADS)

    Wang, Yonggang; Hui, Cong; Liu, Chong; Xu, Chao

    2016-04-01

    The contribution of this paper is proposing a new entropy extraction mechanism based on sampling phase jitter in ring oscillators to make a high throughput true random number generator in a field programmable gate array (FPGA) practical. Starting from experimental observation and analysis of the entropy source in FPGA, a multi-phase sampling method is exploited to harvest the clock jitter with a maximum entropy and fast sampling speed. This parametrized design is implemented in a Xilinx Artix-7 FPGA, where the carry chains in the FPGA are explored to realize the precise phase shifting. The generator circuit is simple and resource-saving, so that multiple generation channels can run in parallel to scale the output throughput for specific applications. The prototype integrates 64 circuit units in the FPGA to provide a total output throughput of 7.68 Gbps, which meets the requirement of current high-speed quantum key distribution systems. The randomness evaluation, as well as its robustness to ambient temperature, confirms that the new method in a purely digital fashion can provide high-speed high-quality random bit sequences for a variety of embedded applications.

  13. Neuromagnetic fields reveal cortical plasticity when learning an auditory discrimination task.

    PubMed

    Cansino, S; Williamson, S J

    1997-08-01

    Auditory evoked neuromagnetic fields of the primary and association auditory cortices were recorded while subjects learned to discriminate small differences in frequency and intensity between two consecutive tones. When discrimination was no better than chance, evoked field patterns across the scalp manifested no significant differences between correct and incorrect responses. However, when performance was correct on at least 75% of the trials, the spatial pattern of magnetic field differed significantly between correct and incorrect responses during the first 70 ms following the onset of the second tone. In this respect, the magnetic field pattern predicted when the subject would make an incorrect judgment more than 100 ms prior to indicating the judgment by a button press. One subject improved discrimination for much smaller differences between stimuli after 200 h of training. Evidence of cortical plasticity with improved discrimination is provided by an accompanying decrease of the relative magnetic field amplitude of the 100 ms response components in the primary and association auditory cortices. PMID:9295193

  14. High-field quantum calculation reveals time-dependent negative Kerr contribution.

    PubMed

    Béjot, P; Cormier, E; Hertz, E; Lavorel, B; Kasparian, J; Wolf, J-P; Faucher, O

    2013-01-25

    The exact quantum time-dependent optical response of hydrogen under strong-field near-infrared excitation is investigated and compared to the perturbative model widely used for describing the effective atomic polarization induced by intense laser fields. By solving the full 3D time-dependent Schrödinger equation, we exhibit a supplementary, quasi-instantaneous defocusing contribution missing in the weak-field model of polarization. We show that this effect is far from being negligible, in particular when closures of ionization channels occur and stems from the interaction of electrons with their parent ions. It provides an interpretation of the higher-order Kerr effect recently observed in various gases. PMID:25166165

  15. High-Field Quantum Calculation Reveals Time-Dependent Negative Kerr Contribution

    NASA Astrophysics Data System (ADS)

    Béjot, P.; Cormier, E.; Hertz, E.; Lavorel, B.; Kasparian, J.; Wolf, J.-P.; Faucher, O.

    2013-01-01

    The exact quantum time-dependent optical response of hydrogen under strong-field near-infrared excitation is investigated and compared to the perturbative model widely used for describing the effective atomic polarization induced by intense laser fields. By solving the full 3D time-dependent Schrödinger equation, we exhibit a supplementary, quasi-instantaneous defocusing contribution missing in the weak-field model of polarization. We show that this effect is far from being negligible, in particular when closures of ionization channels occur and stems from the interaction of electrons with their parent ions. It provides an interpretation of the higher-order Kerr effect recently observed in various gases.

  16. Magnetoelectric assisted 180° magnetization switching for electric field addressable writing in magnetoresistive random-access memory.

    PubMed

    Wang, Zhiguang; Zhang, Yue; Wang, Yaojin; Li, Yanxi; Luo, Haosu; Li, Jiefang; Viehland, Dwight

    2014-08-26

    Magnetization-based memories, e.g., hard drive and magnetoresistive random-access memory (MRAM), use bistable magnetic domains in patterned nanomagnets for information recording. Electric field (E) tunable magnetic anisotropy can lower the energy barrier between two distinct magnetic states, promising reduced power consumption and increased recording density. However, integration of magnetoelectric heterostructure into MRAM is a highly challenging task owing to the particular architecture requirements of each component. Here, we show an epitaxial growth of self-assembled CoFe2O4 nanostripes with bistable in-plane magnetizations on Pb(Mg,Nb)O3-PbTiO3 (PMN-PT) substrates, where the magnetic switching can be triggered by E-induced elastic strain effect. An unprecedented magnetic coercive field change of up to 600 Oe was observed with increasing E. A near 180° magnetization rotation can be activated by E in the vicinity of the magnetic coercive field. These findings might help to solve the 1/2-selection problem in traditional MRAM by providing reduced magnetic coercive field in E field selected memory cells. PMID:25093903

  17. Revisiting the Stark Broadening by fluctuating electric fields using the Continuous Time Random Walk Theory

    NASA Astrophysics Data System (ADS)

    Capes, H.; Christova, M.; Boland, D.; Catoire, F.; Godbert-Mouret, L.; Koubiti, M.; Mekkaoui, A.; Rosato, J.; Marandet, Y.; Stamm, R.

    2010-10-01

    Stark broadening of atomic lines in plasmas is calculated by modelling the plasma stochastic electric field using the CTRW approach [1,2]. This allows retaining non Markovian terms in the Schrödinger equation averaged over the electric field fluctuations. As an application we consider a special case of a non separable CTRW process, the so called Kangaroo process [3]. An analytic expression for the line profile is presented for arbitrary waiting time distribution functions. A preliminary application to the hydrogen Lyman α line is discussed.

  18. MAGNETIC FIELD LINE RANDOM WALK FOR DISTURBED FLUX SURFACES: TRAPPING EFFECTS AND MULTIPLE ROUTES TO BOHM DIFFUSION

    SciTech Connect

    Ghilea, M. C.; Ruffolo, D.; Sonsrettee, W.; Seripienlert, A.; Chuychai, P.; Matthaeus, W. H. E-mail: scdjr@mahidol.ac.th E-mail: achara.seri@gmail.com E-mail: yswhm@bartol.udel.edu

    2011-11-01

    The magnetic field line random walk (FLRW) is important for the transport of energetic particles in many astrophysical situations. While all authors agree on the quasilinear diffusion of field lines for fluctuations that mainly vary parallel to a large-scale field, for the opposite case of fluctuations that mainly vary in the perpendicular directions, there has been an apparent conflict between concepts of Bohm diffusion and percolation/trapping effects. Here computer simulation and non-perturbative analytic techniques are used to re-examine the FLRW in magnetic turbulence with slab and two-dimensional (2D) components, in which 2D flux surfaces are disturbed by the slab fluctuations. Previous non-perturbative theories for D{sub perpendicular}, based on Corrsin's hypothesis, have identified a slab contribution with quasilinear behavior and a 2D contribution due to Bohm diffusion with diffusive decorrelation (DD), combined in a quadratic formula. Here we present analytic theories for other routes to Bohm diffusion, with random ballistic decorrelation (RBD) either due to the 2D component itself (for a weak slab contribution) or the total fluctuation field (for a strong slab contribution), combined in a direct sum with the slab contribution. Computer simulations confirm the applicability of RBD routes for weak or strong slab contributions, while the DD route applies for a moderate slab contribution. For a very low slab contribution, interesting trapping effects are found, including a depressed diffusion coefficient and subdiffusive behavior. Thus quasilinear, Bohm, and trapping behaviors are all found in the same system, together with an overall viewpoint to explain these behaviors.

  19. THE RADIATIVE TRANSFER OF SYNCHROTRON RADIATION THROUGH A COMPRESSED RANDOM MAGNETIC FIELD

    SciTech Connect

    Cawthorne, T. V.; Hughes, P. A.

    2013-07-01

    This paper examines the radiative transfer of synchrotron radiation in the presence of a magnetic field configuration resulting from the compression of a highly disordered magnetic field. It is shown that, provided Faraday rotation and circular polarization can be neglected, the radiative transfer equations for synchrotron radiation separate for this configuration, and the intensities and polarization values for sources that are uniform on large scales can be found straightforwardly in the case where opacity is significant. Although the emission and absorption coefficients must, in general, be obtained numerically, the process is much simpler than a full numerical solution to the transfer equations. Some illustrative results are given and an interesting effect, whereby the polarization increases while the magnetic field distribution becomes less strongly confined to the plane of compression, is discussed. The results are of importance for the interpretation of polarization near the edges of lobes in radio galaxies and of bright features in the parsec-scale jets of active galactic nuclei, where such magnetic field configurations are believed to exist.

  20. Higher Order Cumulant Studies of Ocean Surface Random Fields from Satellite Altimeter Data

    NASA Technical Reports Server (NTRS)

    Cheng, B.

    1996-01-01

    Higher order statistics, especially 2nd order statistics, have been used to study ocean processes for many years in the past, and occupy an appreciable part of the research literature on physical oceanography. They in turn form part of a much larger field of study in statistical fluid mechanics.

  1. Detection of built-up area in optical and synthetic aperture radar images using conditional random fields

    NASA Astrophysics Data System (ADS)

    Kenduiywo, Benson Kipkemboi; Tolpekin, Valentyn A.; Stein, Alfred

    2014-01-01

    Classifying built-up areas from satellite images is a challenging task due to spatial and spectral heterogeneity of the classes. In this study, a contextual classification method based on conditional random fields (CRFs) has been used. Spatial and spectral information from blocks of pixels were employed to identify built-up areas. The CRF association potential was based on support vector machines (SVMs), whereas the CRF interaction potential included a data-dependent term using the inverse of the transformed Euclidean distance. In this way, accuracy was stable for a varying smoothness parameter, while preserving class boundaries and aggregating similar labels, and a discontinuity adaptive model was obtained and conditioned on data evidence. The classification was applied on satellite towns around the city of Nairobi, Kenya. The accuracy exceeded that of Markov random fields, SVM, and maximum likelihood classification by 1.13%, 2.22%, and 8.23%, respectively. The CRF method had the lowest fraction of false positives. The study concluded that CRFs can be used to better detect built-up areas. In this way, it provides accurate timely spatial information to urban planners and other professionals.

  2. Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles

    SciTech Connect

    Callister, S.J.; Wilkins, M.J.; Nicora, C.D.; Williams, K.H.; Banfield, J.F.; VerBerkmoes, N.C.; Hettich, R.L.; NGuessan, A.L.; Mouser, P.J.; Elifantz, H.; Smith, R.D.; Lovley, D.R.; Lipton, M.S.; Long, P.E.

    2010-07-15

    Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetate-amended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or “pseudo-metagenomes”, for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally, a shift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.

  3. Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles

    SciTech Connect

    Callister, Stephen J; Wilkins, Mike; Nicora, Carrie D.; Williams, Ken; Banfield, Jillian F.; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; N'Guessan, A. Lucie; Mouser, Paula J; Elifantz, Hila; Smith, Richard D.; Lovley, Derek; Lipton, Mary S; Long, Phil

    2010-01-01

    Stimulated by an acetate-amendment field experiment conducted in 2007, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this experiment, planktonic biomass was sampled at various time points to quantitatively evaluate proteomes. In 2008, an acetateamended field experiment was again conducted in a similar manner to the 2007 experiment. As there was no comprehensive metagenome sequence available for use in proteomics analysis, we systematically evaluated 12 different organism genome sequences to generate sets of aggregate genomes, or pseudo-metagenomes , for supplying relative quantitative peptide and protein identifications. Proteomics results support previous observations of the dominance of Geobacteraceae during biostimulation using acetate as sole electron donor, and revealed a shift from an early stage of iron reduction to a late stage of iron reduction. Additionally,ashift from iron reduction to sulfate reduction was indicated by changes in the contribution of proteome information contributed by different organism genome sequences within the aggregate set. In addition, the comparison of proteome measurements made between the 2007 field experiment and 2008 field experiment revealed differences in proteome profiles. These differences may be the result of alterations in abundance and population structure within the planktonic biomass samples collected for analysis.

  4. Field and laboratory studies reveal interacting effects of stream oxygenation and warming on aquatic ectotherms.

    PubMed

    Verberk, Wilco C E P; Durance, Isabelle; Vaughan, Ian P; Ormerod, Steve J

    2016-05-01

    Aquatic ecological responses to climatic warming are complicated by interactions between thermal effects and other environmental stressors such as organic pollution and hypoxia. Laboratory experiments have demonstrated how oxygen limitation can set heat tolerance for some aquatic ectotherms, but only at unrealistic lethal temperatures and without field data to assess whether oxygen shortages might also underlie sublethal warming effects. Here, we test whether oxygen availability affects both lethal and nonlethal impacts of warming on two widespread Eurasian mayflies, Ephemera danica, Müller 1764 and Serratella ignita (Poda 1761). Mayfly nymphs are often a dominant component of the invertebrate assemblage in streams, and play a vital role in aquatic and riparian food webs. In the laboratory, lethal impacts of warming were assessed under three oxygen conditions. In the field, effects of oxygen availability on nonlethal impacts of warming were assessed from mayfly occurrence in 42 293 UK stream samples where water temperature and biochemical oxygen demand were measured. Oxygen limitation affected both lethal and sublethal impacts of warming in each species. Hypoxia lowered lethal limits by 5.5 °C (±2.13) and 8.2 °C (±0.62) for E. danica and S. ignita respectively. Field data confirmed the importance of oxygen limitation in warmer waters; poor oxygenation drastically reduced site occupancy, and reductions were especially pronounced under warm water conditions. Consequently, poor oxygenation lowered optimal stream temperatures for both species. The broad concordance shown here between laboratory results and extensive field data suggests that oxygen limitation not only impairs survival at thermal extremes but also restricts species abundance in the field at temperatures well below upper lethal limits. Stream oxygenation could thus control the vulnerability of aquatic ectotherms to global warming. Improving water oxygenation and reducing pollution can provide

  5. The many assembly histories of massive void galaxies as revealed by integral field spectroscopy

    NASA Astrophysics Data System (ADS)

    Fraser-McKelvie, Amelia; Pimbblet, Kevin A.; Penny, Samantha J.; Brown, Michael J. I.

    2016-06-01

    We present the first detailed integral field spectroscopy study of nine central void galaxies with M⋆ > 1010 M⊙ using the Wide Field Spectrograph to determine how a range of assembly histories manifest themselves in the current day Universe. While the majority of these galaxies are evolving secularly, we find a range of morphologies, merger histories and stellar population distributions, though similarly low Hα-derived star formation rates (<1 M⊙ yr-1). Two of our nine galaxies host active galactic nuclei, and two have kinematic disruptions to their gas that are not seen in their stellar component. Most massive void galaxies are red and discy, which we attribute to a lack of major mergers. Some have disturbed morphologies and may be in the process of evolving to early-type thanks to ongoing minor mergers at present times, likely fed by tendrils leading off filaments. The diversity in our small galaxy sample, despite being of similar mass and environment means that these galaxies are still assembling at present day, with minor mergers playing an important role in their evolution. We compare our sample to a mass and magnitude-matched sample of field galaxies, using data from the Sydney-AAO Multi-object Integral field spectrograph galaxy survey. We find that despite environmental differences, galaxies of mass M⋆ > 1010 M⊙ have similarly low star formation rates (<3 M⊙ yr-1). The lack of distinction between the star formation rates of the void and field environments points to quenching of massive galaxies being a largely mass-related effect.

  6. Stochastic simulation for the propagation of high-frequency acoustic waves through a random velocity field

    NASA Astrophysics Data System (ADS)

    Lu, B.; Darmon, M.; Leymarie, N.; Chatillon, S.; Potel, C.

    2012-05-01

    In-service inspection of Sodium-Cooled Fast Reactors (SFR) requires the development of non-destructive techniques adapted to the harsh environment conditions and the examination complexity. From past experiences, ultrasonic techniques are considered as suitable candidates. The ultrasonic telemetry is a technique used to constantly insure the safe functioning of reactor inner components by determining their exact position: it consists in measuring the time of flight of the ultrasonic response obtained after propagation of a pulse emitted by a transducer and its interaction with the targets. While in-service the sodium flow creates turbulences that lead to temperature inhomogeneities, which translates into ultrasonic velocity inhomogeneities. These velocity variations could directly impact the accuracy of the target locating by introducing time of flight variations. A stochastic simulation model has been developed to calculate the propagation of ultrasonic waves in such an inhomogeneous medium. Using this approach, the travel time is randomly generated by a stochastic process whose inputs are the statistical moments of travel times known analytically. The stochastic model predicts beam deviations due to velocity inhomogeneities, which are similar to those provided by a determinist method, such as the ray method.

  7. Stochastic simulation for the propagation of high-frequency acoustic waves through a random velocity field

    SciTech Connect

    Lu, B.; Darmon, M.; Leymarie, N.; Chatillon, S.; Potel, C.

    2012-05-17

    In-service inspection of Sodium-Cooled Fast Reactors (SFR) requires the development of non-destructive techniques adapted to the harsh environment conditions and the examination complexity. From past experiences, ultrasonic techniques are considered as suitable candidates. The ultrasonic telemetry is a technique used to constantly insure the safe functioning of reactor inner components by determining their exact position: it consists in measuring the time of flight of the ultrasonic response obtained after propagation of a pulse emitted by a transducer and its interaction with the targets. While in-service the sodium flow creates turbulences that lead to temperature inhomogeneities, which translates into ultrasonic velocity inhomogeneities. These velocity variations could directly impact the accuracy of the target locating by introducing time of flight variations. A stochastic simulation model has been developed to calculate the propagation of ultrasonic waves in such an inhomogeneous medium. Using this approach, the travel time is randomly generated by a stochastic process whose inputs are the statistical moments of travel times known analytically. The stochastic model predicts beam deviations due to velocity inhomogeneities, which are similar to those provided by a determinist method, such as the ray method.

  8. Low-Energy Structures in Strong Field Ionization Revealed by Quantum Orbits

    SciTech Connect

    Yan, Tian-Min; Popruzhenko, S. V.; Vrakking, M. J. J.; Bauer, D.

    2010-12-17

    Experiments on atoms in intense laser pulses and the corresponding exact ab initio solutions of the time-dependent Schroedinger equation (TDSE) yield photoelectron spectra with low-energy features that are not reproduced by the otherwise successful work horse of strong field laser physics: the 'strong field approximation' (SFA). In the semiclassical limit, the SFA possesses an appealing interpretation in terms of interfering quantum trajectories. It is shown that a conceptually simple extension towards the inclusion of Coulomb effects yields very good agreement with exact TDSE results. Moreover, the Coulomb quantum orbits allow for a physically intuitive interpretation and detailed analysis of all low-energy features in the semiclassical regime, in particular, the recently discovered 'low-energy structure' [C. I. Blaga et al., Nature Phys. 5, 335 (2009) and W. Quan et al., Phys. Rev. Lett. 103, 093001 (2009)].

  9. Low-energy structures in strong field ionization revealed by quantum orbits.

    PubMed

    Yan, Tian-Min; Popruzhenko, S V; Vrakking, M J J; Bauer, D

    2010-12-17

    Experiments on atoms in intense laser pulses and the corresponding exact ab initio solutions of the time-dependent Schrödinger equation (TDSE) yield photoelectron spectra with low-energy features that are not reproduced by the otherwise successful work horse of strong field laser physics: the "strong field approximation" (SFA). In the semiclassical limit, the SFA possesses an appealing interpretation in terms of interfering quantum trajectories. It is shown that a conceptually simple extension towards the inclusion of Coulomb effects yields very good agreement with exact TDSE results. Moreover, the Coulomb quantum orbits allow for a physically intuitive interpretation and detailed analysis of all low-energy features in the semiclassical regime, in particular, the recently discovered "low-energy structure" [C. I. Blaga, Nature Phys. 5, 335 (2009) and W. Quan, Phys. Rev. Lett. 103, 093001 (2009). PMID:21231586

  10. Genetically engineered maize plants reveal distinct costs and benefits of constitutive volatile emissions in the field.

    PubMed

    Robert, Christelle Aurélie Maud; Erb, Matthias; Hiltpold, Ivan; Hibbard, Bruce Elliott; Gaillard, Mickaël David Philippe; Bilat, Julia; Degenhardt, Jörg; Cambet-Petit-Jean, Xavier; Turlings, Ted Christiaan Joannes; Zwahlen, Claudia

    2013-06-01

    Genetic manipulation of plant volatile emissions is a promising tool to enhance plant defences against herbivores. However, the potential costs associated with the manipulation of specific volatile synthase genes are unknown. Therefore, we investigated the physiological and ecological effects of transforming a maize line with a terpene synthase gene in field and laboratory assays, both above- and below ground. The transformation, which resulted in the constitutive emission of (E)-β-caryophyllene and α-humulene, was found to compromise seed germination, plant growth and yield. These physiological costs provide a possible explanation for the inducibility of an (E)-β-caryophyllene-synthase gene in wild and cultivated maize. The overexpression of the terpene synthase gene did not impair plant resistance nor volatile emission. However, constitutive terpenoid emission increased plant apparency to herbivores, including adults and larvae of the above ground pest Spodoptera frugiperda, resulting in an increase in leaf damage. Although terpenoid overproducing lines were also attractive to the specialist root herbivore Diabrotica virgifera virgifera below ground, they did not suffer more root damage in the field, possibly because of the enhanced attraction of entomopathogenic nematodes. Furthermore, fewer adults of the root herbivore Diabrotica undecimpunctata howardii were found to emerge near plants that emitted (E)-β-caryophyllene and α-humulene. Yet, overall, under the given field conditions, the costs of constitutive volatile production overshadowed its benefits. This study highlights the need for a thorough assessment of the physiological and ecological consequences of genetically engineering plant signals in the field to determine the potential of this approach for sustainable pest management strategies. PMID:23425633

  11. Two thousand years of geomagnetic field direction over central Europe revealed by indirect measurements

    NASA Astrophysics Data System (ADS)

    Márton, Péter

    2010-04-01

    Supplemented by 32 new directions, the Hungarian archaeomagnetic data set now consists of 217 archaeologically dated directions ranging in age from 300 BC to 1800 AD. From this data set, reference curves of secular variation of the geomagnetic field direction were computed using hierarchical modelling and curve estimation by moving average technique. Thanks to some of the new data, the gap in the earlier reference curves around 500 AD has now been filled up. For comparison's sake, directional records of comparable length from central Europe were also processed by the same curve building method. For this purpose, all dated directional data (declination and inclination with statistics) were drawn from the GEOMAGIA50 database for France, Germany, the Ukraine and Moldavia, Bulgaria and Italy and transferred via their virtual geomagnetic poles to a reference point of their respective countries. The resulting reference curves, including those for Hungary, show more or less similar temporal behaviour to the corresponding CALS7K.2 model curves (also available from the GEOMAGIA50 database), but significant deviations from the low-order CALS7K.2 predictions are also discernible owing to the likely presence of additional higher-order complications in the regional field. Therefore, the regional field and its secular variation are suggested to be approximated by the reference rather than the predicted curves. At any other location within the study area, the direction of the regional field can be obtained by spatial interpolation from the reference curves as illustrated by isogonic and isoclinic maps shown for selected times. Local time-series of interpolated directions for other central European countries lacking reference curves might serve as master curves for magnetic dating.

  12. Crustal Fracturing Field and Presence of Fluid as Revealed by Seismic Anisotropy

    NASA Astrophysics Data System (ADS)

    Pastori, M.; Piccinini, D.; de Gori, P.; Margheriti, L.; Barchi, M. R.; di Bucci, D.

    2010-12-01

    In the last three years, we developed, tested and improved an automatic analysis code (Anisomat+) to calculate the shear wave splitting parameters, fast polarization direction (φ) and delay time (∂t). The code is a set of MatLab scripts able to retrieve crustal anisotropy parameters from three-component seismic recording of local earthquakes using horizontal component cross-correlation method. The analysis procedure consists in choosing an appropriate frequency range, that better highlights the signal containing the shear waves, and a length of time window on the seismogram centered on the S arrival (the temporal window contains at least one cycle of S wave). The code was compared to other two automatic analysis code (SPY and SHEBA) and tested on three Italian areas (Val d’Agri, Tiber Valley and L’Aquila surrounding) along the Apennine mountains. For each region we used the anisotropic parameters resulting from the automatic computation as a tool to determine the fracture field geometries connected with the active stress field. We compare the temporal variations of anisotropic parameters to the evolution of vp/vs ratio for the same seismicity. The anisotropic fast directions are used to define the active stress field (EDA model), finding a general consistence between fast direction and main stress indicators (focal mechanism and borehole break-out). The magnitude of delay time is used to define the fracture field intensity finding higher value in the volume where micro-seismicity occurs. Furthermore we studied temporal variations of anisotropic parameters and vp/vs ratio in order to explain if fluids play an important role in the earthquake generation process. The close association of anisotropic and vp/vs parameters variations and seismicity rate changes supports the hypothesis that the background seismicity is influenced by the fluctuation of pore fluid pressure in the rocks.

  13. Space-time models based on random fields with local interactions

    NASA Astrophysics Data System (ADS)

    Hristopulos, Dionissios T.; Tsantili, Ivi C.

    2016-08-01

    The analysis of space-time data from complex, real-life phenomena requires the use of flexible and physically motivated covariance functions. In most cases, it is not possible to explicitly solve the equations of motion for the fields or the respective covariance functions. In the statistical literature, covariance functions are often based on mathematical constructions. In this paper, we propose deriving space-time covariance functions by solving “effective equations of motion”, which can be used as statistical representations of systems with diffusive behavior. In particular, we propose to formulate space-time covariance functions based on an equilibrium effective Hamiltonian using the linear response theory. The effective space-time dynamics is then generated by a stochastic perturbation around the equilibrium point of the classical field Hamiltonian leading to an associated Langevin equation. We employ a Hamiltonian which extends the classical Gaussian field theory by including a curvature term and leads to a diffusive Langevin equation. Finally, we derive new forms of space-time covariance functions.

  14. Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors

    PubMed Central

    2013-01-01

    Background Rice blast caused by the fungus Magnaporthe oryzae is an important disease in virtually every rice growing region of the world, which leads to significant annual decreases of grain quality and yield. To prevent disease, resistance genes in rice have been cloned and introduced into susceptible cultivars. However, introduced resistance can often be broken within few years of release, often due to mutation of cognate avirulence genes in fungal field populations. Results To better understand the pattern of mutation of M. oryzae field isolates under natural selection forces, we used a next generation sequencing approach to analyze the genomes of two field isolates FJ81278 and HN19311, as well as the transcriptome of FJ81278. By comparing the de novo genome assemblies of the two isolates against the finished reference strain 70–15, we identified extensive polymorphisms including unique genes, SNPs (single nucleotide polymorphism) and indels, structural variations, copy number variations, and loci under strong positive selection. The 1.75 MB of isolate-specific genome content carrying 118 novel genes from FJ81278, and 0.83 MB from HN19311 were also identified. By analyzing secreted proteins carrying polymorphisms, in total 256 candidate virulence effectors were found and 6 were chosen for functional characterization. Conclusions We provide results from genome comparison analysis showing extensive genome variation, and generated a list of M. oryzae candidate virulence effectors for functional characterization. PMID:24341723

  15. A Markov random field approach for topology-preserving registration: application to object-based tomographic image interpolation.

    PubMed

    Cordero-Grande, Lucilio; Vegas-Sánchez-Ferrero, Gonzalo; Casaseca-de-la-Higuera, Pablo; Alberola-López, Carlos

    2012-04-01

    This paper proposes a topology-preserving multiresolution elastic registration method based on a discrete Markov random field of deformations and a block-matching procedure. The method is applied to the object-based interpolation of tomographic slices. For that purpose, the fidelity of a given deformation to the data is established by a block-matching strategy based on intensity- and gradient-related features, the smoothness of the transformation is favored by an appropriate prior on the field, and the deformation is guaranteed to maintain the topology by imposing some hard constraints on the local configurations of the field. The resulting deformation is defined as the maximum a posteriori configuration. Additionally, the relative influence of the fidelity and smoothness terms is weighted by the unsupervised estimation of the field parameters. In order to obtain an unbiased interpolation result, the registration is performed both in the forward and backward directions, and the resulting transformations are combined by using the local information content of the deformation. The method is applied to magnetic resonance and computed tomography acquisitions of the brain and the torso. Quantitative comparisons offer an overall improvement in performance with respect to related works in the literature. Additionally, the application of the interpolation method to cardiac magnetic resonance images has shown that the removal of any of the main components of the algorithm results in a decrease in performance which has proven to be statistically significant. PMID:21997265

  16. Random crystal field effect on the kinetic spin-3/2 Blume-Capel model under a time-dependent oscillating field

    NASA Astrophysics Data System (ADS)

    El Hachimi, A. G.; Dakir, O.; Sidi Ahmed, S.; Zaari, H.; El Yadari, M.; Benyoussef, A.; El Kenz, A.

    2016-09-01

    The effect of random crystal-field on the stationary states of the kinetic spin-3/2 Blume-Capel model is investigated within the framework of the mean-field approach. The Glauber-type stochastic dynamics is used to describe the time evolution of the system which is subject to a time-dependent oscillating external magnetic field. In addition to the well-known phase transitions and the appearance of the partly ferromagnetic phase characterized by the magnetization m = 1 in equilibrium case, a new dynamical regions between the ferromagnetic phases F1/2, F1 and F3/2 are found where F3/2 +F 1 / 2 ,F3/2 +F1, F1 +F1/2 phases coexist for a weak value of the reduced magnetic field (h). Whereas for higher value of h both solutions ordered F and disordered P phases coexist. Hence we present six types topologies of phase diagrams which exhibit dynamical first-order, second-order transition lines, dynamical tricritical and isolated critical end points. Furthermore, the dynamical thermal behavior magnetizations, susceptibilities and phase space trajectories are given and discussed.

  17. Randomized Controlled Field Trial to Assess the Immunogenicity and Safety of Rift Valley Fever Clone 13 Vaccine in Livestock

    PubMed Central

    Njenga, M. Kariuki; Njagi, Leonard; Thumbi, S. Mwangi; Kahariri, Samuel; Githinji, Jane; Omondi, Eunice; Baden, Amy; Murithi, Mbabu; Paweska, Janusz; Ithondeka, Peter M.; Ngeiywa, Kisa J.; Dungu, Baptiste; Donadeu, Meritxell; Munyua, Peninah M.

    2015-01-01

    Background Although livestock vaccination is effective in preventing Rift Valley fever (RVF) epidemics, there are concerns about safety and effectiveness of the only commercially available RVF Smithburn vaccine. We conducted a randomized controlled field trial to evaluate the immunogenicity and safety of the new RVF Clone 13 vaccine, recently registered in South Africa. Methods In a blinded randomized controlled field trial, 404 animals (85 cattle, 168 sheep, and 151 goats) in three farms in Kenya were divided into three groups. Group A included males and non-pregnant females that were randomized and assigned to two groups; one vaccinated with RVF Clone 13 and the other given placebo. Groups B included animals in 1st half of pregnancy, and group C animals in 2nd half of pregnancy, which were also randomized and either vaccinated and given placebo. Animals were monitored for one year and virus antibodies titers assessed on days 14, 28, 56, 183 and 365. Results In vaccinated goats (N = 72), 72% developed anti-RVF virus IgM antibodies and 97% neutralizing IgG antibodies. In vaccinated sheep (N = 77), 84% developed IgM and 91% neutralizing IgG antibodies. Vaccinated cattle (N = 42) did not develop IgM antibodies but 67% developed neutralizing IgG antibodies. At day 14 post-vaccination, the odds of being seropositive for IgG in the vaccine group was 3.6 (95% CI, 1.5 – 9.2) in cattle, 90.0 (95% CI, 25.1 – 579.2) in goats, and 40.0 (95% CI, 16.5 – 110.5) in sheep. Abortion was observed in one vaccinated goat but histopathologic analysis did not indicate RVF virus infection. There was no evidence of teratogenicity in vaccinated or placebo animals. Conclusions The results suggest RVF Clone 13 vaccine is safe to use and has high (>90%) immunogenicity in sheep and goats but moderate (> 65%) immunogenicity in cattle. PMID:25756501

  18. Evaluating the impact of a school-based health intervention using a randomized field experiment.

    PubMed

    Greve, Jane; Heinesen, Eskil

    2015-07-01

    We conduct an econometric evaluation of a health-promoting programme in primary and lower secondary schools in Denmark. The programme includes health-related measurements of the students, communication of knowledge about health, and support of health-promoting projects for students. Half of the schools in the fourth largest municipality in Denmark were randomly selected into a treatment group implementing the programme, while the remainder served as a control group. We estimate both OLS models using only post-intervention observations and difference in differences (DID) models using also pre-intervention observations. We estimate effects of the initiative on BMI, waist/height ratio, overweight and obesity for the entire sample and by gender and grade. We find no consistent effect of the programme. When we use the entire sample, no estimates are statistically significant at conventional levels, although the point estimates for the effect on BMI, indicating an average reduction in the range of 0.10-0.15 kg/m(2), are consistent with the results in a recent Cochrane review evaluating 55 studies of diet and exercise interventions targeting children; and DID estimates which are marginally significant (at the 10% level) indicate that the intervention reduces the risk of obesity by 1% point. Running separate estimations by gender and grade we find a few statistically significant estimates: OLS estimates indicate that the intervention reduces BMI in females in grade 5 by 0.39 kg/m(2) and reduces the risk of obesity in females in grade 9 by 2.6% points; DID estimates indicate an increase in waist for females in preschool class by 1.2 cm and an increase in the risk of obesity in grade 9 males by 4% points. However, if we corrected for multiple hypotheses testing these estimates would be insignificant. There is no statistically significant correlation between participation in the programme and the number of other health-promoting projects at the schools. PMID:25898077

  19. Near-field deformation from the El Mayor-Cucapah earthquake revealed by differential LIDAR.

    PubMed

    Oskin, Michael E; Arrowsmith, J Ramon; Hinojosa Corona, Alejandro; Elliott, Austin J; Fletcher, John M; Fielding, Eric J; Gold, Peter O; Gonzalez Garcia, J Javier; Hudnut, Ken W; Liu-Zeng, Jing; Teran, Orlando J

    2012-02-10

    Large [moment magnitude (M(w)) ≥ 7] continental earthquakes often generate complex, multifault ruptures linked by enigmatic zones of distributed deformation. Here, we report the collection and results of a high-resolution (≥nine returns per square meter) airborne light detection and ranging (LIDAR) topographic survey of the 2010 M(w) 7.2 El Mayor-Cucapah earthquake that produced a 120-kilometer-long multifault rupture through northernmost Baja California, Mexico. This differential LIDAR survey completely captures an earthquake surface rupture in a sparsely vegetated region with pre-earthquake lower-resolution (5-meter-pixel) LIDAR data. The postevent survey reveals numerous surface ruptures, including previously undocumented blind faults within thick sediments of the Colorado River delta. Differential elevation changes show distributed, kilometer-scale bending strains as large as ~10(3) microstrains in response to slip along discontinuous faults cutting crystalline bedrock of the Sierra Cucapah. PMID:22323817

  20. Spectral shifts and switches in random fields upon interaction with negative-phase materials

    SciTech Connect

    Tong Zhisong; Korotkova, Olga

    2010-07-15

    Spectral shifts in stochastic beam-like fields on interaction with layers of positive- and negative-phase materials are examined on the basis of the ABCD-matrix approach and generalized Huygens-Fresnel principle. It is found that boundaries between such materials may cause spectral switches. Effect of absorption of negative-phase materials on the beam spectrum is discussed. Our results may find applications in connection with spectrum-selection optical interconnects, spectrally encoded information transfer, image formation in systems involving negative-phase materials, and geometrically tunable metamaterials.

  1. Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles

    SciTech Connect

    Callister, Stephen J.; Wilkins, Michael J.; Nicora, Carrie D.; Williams, Kenneth H.; Banfield, Jillian F.; VerBerkmoes, Nathan; Hettich, Robert L.; N'Guessan, A. Lucie; Mouser, Paula; Elifantz, H.; Smith, Richard D.; Lovley, Derek R.; Lipton, Mary S.; Long, Philip E.

    2010-12-01

    Stimulated by acetate-amendment field experiments conducted in 2007 and 2008, anaerobic microbial populations in the aquifer at the Rifle Integrated Field Research Challenge site in Colorado reduced mobile U(VI) to insoluble U(IV). During this period, planktonic biomass was sampled at various time points and used to quantitatively evaluate proteomes, both spatially and temporally to study the dynamics of the microbial community proteome dynamics in relationship to geochemical measurements. As there were no comprehensive genome sequence data available at the time, we systematically evaluated different organisms to generate a "pseudo-metagenome" for proteomics analyses. Proteomics results supported the dominance of Geobacteraceae during biostimulation and revealed a shift from iron reduction to sulfate reduction, evidenced by changes in community membership. Because U(VI) is reduced at a lower rate during sulfate reduction, detecting this shift is important to maintaining the maximum rate of U(VI) reduction. In addition, the comparison of proteome measurements made at the end of the 2007 field experiment to the 2008 field experiment revealed a modified community structure. Importantly, the failure of a community to rebound following the cessation of biostimulation needs to be included in long-term remediation strategies.

  2. Revealing the Exciton Fine Structure of PbSe Nanocrystal Quantum Dots Using Optical Spectroscopy in High Magnetic Fields

    SciTech Connect

    Schaller, Richard D.; Crooker, Scott A.; Bussian, David A.; Pietryga, Jeffrey M.; Joo, Jin; Klimov, Victor I.

    2010-08-04

    We measure the photoluminescence lifetime τ of excitons in colloidal PbSe nanocrystals (NCs) at low temperatures to 270 mK and in high magnetic fields to 15 T. For all NCs, τ increases sharply below 10 K but saturates by 500 mK. In contrast to the usual picture of well-separated “bright” and “dark” exciton states (found, e.g., in CdSe NCs), these dynamics fit remarkably well to a system having two exciton states with comparable—but small—oscillator strengths that are separated by only 300–900 μeV depending on NC size. Importantly, magnetic fields reduce τ below 10 K, consistent with field-induced mixing between the two states. Magnetic-circular dichroism studies reveal exciton g factors from 2–5, and magnetophotoluminescence shows >10% circularly polarized emission.

  3. The Topography of Visuospatial Attention as Revealed by a Novel Visual Field Mapping Technique

    PubMed Central

    Brefczynski-Lewis, Julie A.; Datta, Ritobrato; Lewis, James W.; DeYoe, Edgar A.

    2009-01-01

    Previously, we and others have shown that attention can enhance visual processing in a spatially specific manner that is retinotopically mapped in the occipital cortex. However, it is difficult to appreciate the functional significance of the spatial pattern of cortical activation just by examining the brain maps. In this study, we visualize the neural representation of the “spotlight” of attention using a back-projection of attention-related brain activation onto a diagram of the visual field. In the two main experiments, we examine the topography of attentional activation in the occipital and parietal cortices. In retinotopic areas, attentional enhancement is strongest at the locations of the attended target, but also spreads to nearby locations and even weakly to restricted locations in the opposite visual field. The dispersion of attentional effects around an attended site increases with the eccentricity of the target in a manner that roughly corresponds to a constant area of spread within the cortex. When averaged across multiple observers, these patterns appear consistent with a gradient model of spatial attention. However, individual observers exhibit complex variations that are unique but reproducible. Overall, these results suggest that the topography of visual attention for each individual is composed of a common theme plus a personal variation that may reflect their own unique “attentional style.” PMID:18752412

  4. Response bias reveals enhanced attention to inferior visual field in signers of American Sign Language.

    PubMed

    Dye, Matthew W G; Seymour, Jenessa L; Hauser, Peter C

    2016-04-01

    Deafness results in cross-modal plasticity, whereby visual functions are altered as a consequence of a lack of hearing. Here, we present a reanalysis of data originally reported by Dye et al. (PLoS One 4(5):e5640, 2009) with the aim of testing additional hypotheses concerning the spatial redistribution of visual attention due to deafness and the use of a visuogestural language (American Sign Language). By looking at the spatial distribution of errors made by deaf and hearing participants performing a visuospatial selective attention task, we sought to determine whether there was evidence for (1) a shift in the hemispheric lateralization of visual selective function as a result of deafness, and (2) a shift toward attending to the inferior visual field in users of a signed language. While no evidence was found for or against a shift in lateralization of visual selective attention as a result of deafness, a shift in the allocation of attention from the superior toward the inferior visual field was inferred in native signers of American Sign Language, possibly reflecting an adaptation to the perceptual demands imposed by a visuogestural language. PMID:26708522

  5. Imaging of action currents reveals the origin of biomagnetic fields in cardiac tissue

    NASA Astrophysics Data System (ADS)

    Holzer, Jenny R.; Sidorov, Veniamin; Fong, Luis; Baudenbacher, Franz

    2003-03-01

    The origin of the magnetocardiogram (MCG) and the relative information content between the MCG and the electrocardiogram (ECG) remain central questions in biomagnetism. To provide key insights to this question, we mapped excitation wave fronts in a thin layer of cardiac tissue of an isolated rabbit heart using high-resolution LTS-SQUID microscopy and epi-fluorescent imaging with sub-millimeter resolution. The combination of the two methods allows us to map the transmembrane potential (Vm) and the magnetic field over the same area. The leading edge of a propagating action potential can be defined as the wave front and can be identified by the difference in relative intensities of resting and depolarized tissue in the epi-fluorescence data. The corresponding magnetic field pattern was used to calculate the net action current, which shows a strong current component parallel to and overlying the Vm wave front. These electrically silent currents are a direct consequence of the cardiac bidomain with unequal anisotropies in the intra- and extracellular space and depend strongly on the angle of the wave front relative to the fiber orientation. We provide evidence that the MCG contains information not present in the ECG, and that it is necessary to reexamine the modeling and interpretation of the MCG.

  6. High-Throughput Genotyping of Green Algal Mutants Reveals Random Distribution of Mutagenic Insertion Sites and Endonucleolytic Cleavage of Transforming DNA[W][OPEN

    PubMed Central

    Zhang, Ru; Patena, Weronika; Armbruster, Ute; Gang, Spencer S.; Blum, Sean R.; Jonikas, Martin C.

    2014-01-01

    A high-throughput genetic screening platform in a single-celled photosynthetic eukaryote would be a transformative addition to the plant biology toolbox. Here, we present ChlaMmeSeq (Chlamydomonas MmeI-based insertion site Sequencing), a tool for simultaneous mapping of tens of thousands of mutagenic insertion sites in the eukaryotic unicellular green alga Chlamydomonas reinhardtii. We first validated ChlaMmeSeq by in-depth characterization of individual insertion sites. We then applied ChlaMmeSeq to a mutant pool and mapped 11,478 insertions, covering 39% of annotated protein coding genes. We observe that insertions are distributed in a manner largely indistinguishable from random, indicating that mutants in nearly all genes can be obtained efficiently. The data reveal that sequence-specific endonucleolytic activities cleave the transforming DNA and allow us to propose a simple model to explain the origin of the poorly understood exogenous sequences that sometimes surround insertion sites. ChlaMmeSeq is quantitatively reproducible, enabling its use for pooled enrichment screens and for the generation of indexed mutant libraries. Additionally, ChlaMmeSeq allows genotyping of hits from Chlamydomonas screens on an unprecedented scale, opening the door to comprehensive identification of genes with roles in photosynthesis, algal lipid metabolism, the algal carbon-concentrating mechanism, phototaxis, the biogenesis and function of cilia, and other processes for which C. reinhardtii is a leading model system. PMID:24706510

  7. Random Sampling of Squamate Reptiles in Spanish Natural Reserves Reveals the Presence of Novel Adenoviruses in Lacertids (Family Lacertidae) and Worm Lizards (Amphisbaenia)

    PubMed Central

    Szirovicza, Leonóra; López, Pilar; Kopena, Renáta; Benkő, Mária; Martín, José; Pénzes, Judit J.

    2016-01-01

    Here, we report the results of a large-scale PCR survey on the prevalence and diversity of adenoviruses (AdVs) in samples collected randomly from free-living reptiles. On the territories of the Guadarrama Mountains National Park in Central Spain and of the Chafarinas Islands in North Africa, cloacal swabs were taken from 318 specimens of eight native species representing five squamate reptilian families. The healthy-looking animals had been captured temporarily for physiological and ethological examinations, after which they were released. We found 22 AdV-positive samples in representatives of three species, all from Central Spain. Sequence analysis of the PCR products revealed the existence of three hitherto unknown AdVs in 11 Carpetane rock lizards (Iberolacerta cyreni), nine Iberian worm lizards (Blanus cinereus), and two Iberian green lizards (Lacerta schreiberi), respectively. Phylogeny inference showed every novel putative virus to be a member of the genus Atadenovirus. This is the very first description of the occurrence of AdVs in amphisbaenian and lacertid hosts. Unlike all squamate atadenoviruses examined previously, two of the novel putative AdVs had A+T rich DNA, a feature generally deemed to mirror previous host switch events. Our results shed new light on the diversity and evolution of atadenoviruses. PMID:27399970

  8. Random Sampling of Squamate Reptiles in Spanish Natural Reserves Reveals the Presence of Novel Adenoviruses in Lacertids (Family Lacertidae) and Worm Lizards (Amphisbaenia).

    PubMed

    Szirovicza, Leonóra; López, Pilar; Kopena, Renáta; Benkő, Mária; Martín, José; Pénzes, Judit J

    2016-01-01

    Here, we report the results of a large-scale PCR survey on the prevalence and diversity of adenoviruses (AdVs) in samples collected randomly from free-living reptiles. On the territories of the Guadarrama Mountains National Park in Central Spain and of the Chafarinas Islands in North Africa, cloacal swabs were taken from 318 specimens of eight native species representing five squamate reptilian families. The healthy-looking animals had been captured temporarily for physiological and ethological examinations, after which they were released. We found 22 AdV-positive samples in representatives of three species, all from Central Spain. Sequence analysis of the PCR products revealed the existence of three hitherto unknown AdVs in 11 Carpetane rock lizards (Iberolacerta cyreni), nine Iberian worm lizards (Blanus cinereus), and two Iberian green lizards (Lacerta schreiberi), respectively. Phylogeny inference showed every novel putative virus to be a member of the genus Atadenovirus. This is the very first description of the occurrence of AdVs in amphisbaenian and lacertid hosts. Unlike all squamate atadenoviruses examined previously, two of the novel putative AdVs had A+T rich DNA, a feature generally deemed to mirror previous host switch events. Our results shed new light on the diversity and evolution of atadenoviruses. PMID:27399970

  9. Exact Mapping of the Stochastic Field Theory for Manna Sandpiles to Interfaces in Random Media

    NASA Astrophysics Data System (ADS)

    Le Doussal, Pierre; Wiese, Kay Jörg

    2015-03-01

    We show that the stochastic field theory for directed percolation in the presence of an additional conservation law [the conserved directed-percolation (C-DP) class] can be mapped exactly to the continuum theory for the depinning of an elastic interface in short-range correlated quenched disorder. Along one line of the parameters commonly studied, this mapping leads to the simplest overdamped dynamics. Away from this line, an additional memory term arises in the interface dynamics; we argue that this does not change the universality class. Since C-DP is believed to describe the Manna class of self-organized criticality, this shows that Manna stochastic sandpiles and disordered elastic interfaces (i.e., the quenched Edwards-Wilkinson model) share the same universal large-scale behavior.

  10. Exact mapping of the stochastic field theory for Manna sandpiles to interfaces in random media.

    PubMed

    Le Doussal, Pierre; Wiese, Kay Jörg

    2015-03-20

    We show that the stochastic field theory for directed percolation in the presence of an additional conservation law [the conserved directed-percolation (C-DP) class] can be mapped exactly to the continuum theory for the depinning of an elastic interface in short-range correlated quenched disorder. Along one line of the parameters commonly studied, this mapping leads to the simplest overdamped dynamics. Away from this line, an additional memory term arises in the interface dynamics; we argue that this does not change the universality class. Since C-DP is believed to describe the Manna class of self-organized criticality, this shows that Manna stochastic sandpiles and disordered elastic interfaces (i.e., the quenched Edwards-Wilkinson model) share the same universal large-scale behavior. PMID:25839253

  11. Can stochastic, dissipative wave fields be treated as random walk generators

    NASA Technical Reports Server (NTRS)

    Weinstock, J.

    1986-01-01

    A suggestion by Meek et al. (1985) that the gravity wave field be viewed as stochastic, with significant nonlinearities, is applied to calculate diffusivities. The purpose here is to calculate the diffusivity for stochastic wave model and compare it with previous diffusivity estimates. The researchers do this for an idealized case in which the wind velocity changes but slowly, and for which saturation is the principal mechanism by which wave energy is lost. A related calculation was given in a very brief way (Weinstock, 1976), but the approximations were not fully justified, nor were the physical pre-suppositions clearly explained. The observations of Meek et al. (1985) have clarified the pre-suppositions for the researchers and provided a rationalization and improvement of the approximations employed.

  12. High-field proton magnetic resonance spectroscopy reveals metabolic effects of normal brain aging

    PubMed Central

    Harris, Janna L.; Yeh, Hung-Wen; Swerdlow, Russell H.; Choi, In-Young; Lee, Phil; Brooks, William M.

    2014-01-01

    Altered brain metabolism is likely to be an important contributor to normal cognitive decline and brain pathology in elderly individuals. To characterize the metabolic changes associated with normal brain aging, we used high-field proton magnetic resonance spectroscopy in vivo to quantify 20 neurochemicals in the hippocampus and sensorimotor cortex of young adult and aged rats. We found significant differences in the neurochemical profile of the aged brain when compared with younger adults, including lower aspartate, ascorbate, glutamate, and macromolecules, and higher glucose, myo-inositol, N-acetylaspartylglutamate, total choline, and glutamine. These neurochemical biomarkers point to specific cellular mechanisms that are altered in brain aging, such as bioenergetics, oxidative stress, inflammation, cell membrane turnover, and endogenous neuroprotection. Proton magnetic resonance spectroscopy may be a valuable translational approach for studying mechanisms of brain aging and pathology, and for investigating treatments to preserve or enhance cognitive function in aging. PMID:24559659

  13. Dark-field transmission electron microscopy of cortical bone reveals details of extrafibrillar crystals.

    PubMed

    Schwarcz, Henry P; McNally, Elizabeth A; Botton, Gianluigi A

    2014-12-01

    In a previous study we showed that most of the mineral in bone is present in the form of "mineral structures", 5-6nm-thick, elongated plates which surround and are oriented parallel to collagen fibrils. Using dark-field transmission electron microscopy, we viewed mineral structures in ion-milled sections of cortical human bone cut parallel to the collagen fibrils. Within the mineral structures we observe single crystals of apatite averaging 5.8±2.7nm in width and 28±19nm in length, their long axes oriented parallel to the fibril axis. Some appear to be composite, co-aligned crystals as thin as 2nm. From their similarity to TEM images of crystals liberated from deproteinated bone we infer that we are viewing sections through platy crystals of apatite that are assembled together to form the mineral structures. PMID:25449316

  14. A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate.

    PubMed

    Bataillon, Thomas; Galtier, Nicolas; Bernard, Aurelien; Cryer, Nicolai; Faivre, Nicolas; Santoni, Sylvain; Severac, Dany; Mikkelsen, Teis N; Larsen, Klaus S; Beier, Claus; Sørensen, Jesper G; Holmstrup, Martin; Ehlers, Bodil K

    2016-07-01

    Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short-time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response. PMID:27109012

  15. Remote Sensing of Desert Loess and Dune Fields Aids Revealing Proximal Loess Sources

    NASA Astrophysics Data System (ADS)

    Crouvi, O.; Gillespie, A.; Amit, R.; Enzel, Y.

    2008-12-01

    Loess is an eolian deposit composed mostly of silt-sized quartz, which serves as an important archive of Quaternary climate changes. Despite the long term support for the 'classical' glacial concept of loess formation, there have been challenges to this model focusing on the formation of silt grains in deserts, which is still controversial. The aim of this study is to trace the proximal dust sources of the Negev loess, Israel, using comprehensive remote-sensing mapping, field surveys, and laboratory analyses of hilltop, primary loess sequences. Based on field and spectral characterization of primary and secondary loess, we developed remote-sensing methodology to: 1) distinguish and classify loess types to better choose hilltop, un-reworked loess study sites; 2) map loess regionally and examine its spatial association with potential dust sources. The different loess types are spectrally distinguishable by using the difference in the magnitude of chlorophyll, ferric, Al-OH, and carbonate absorptions features that vary systematically by the relative abundance of clasts, loessial biogenic crust, and vegetation. We used band ratios and liner un-mixing techniques on ASTER and Landsat TM reflectance and thermal data to successfully map the different loess types and the regional loess distribution. We conclude that the border between the loess and the adjacent, upwind sand dunes exhibit gradual patterns of grain size, mineralogy, and spectral characteristics. These findings, together with detailed analyses of loess sequences show that the proximal dust source of the Negev loess is the adjacent sand dunes, and suggest that the silt grains were formed through eolian abrasion of sand grains. Applying the remote-sensing methodology on other desert loess (e.g. Tunisia) indicates similar pattern of gradual transition from sand dunes to loess, and suggests that this association is not unique to the Negev. Our findings imply that sand dunes are much more important proximal dust

  16. Trichoderma Biodiversity of Agricultural Fields in East China Reveals a Gradient Distribution of Species

    PubMed Central

    Chen, Jing; Mao, Li-Juan; Feng, Xiao-Xiao; Zhang, Chu-Long; Lin, Fu-Cheng

    2016-01-01

    We surveyed the Trichoderma (Hypocreales, Ascomycota) biodiversity in agricultural fields in four major agricultural provinces of East China. Trichoderma strains were identified based on molecular approaches and morphological characteristics. In three sampled seasons (spring, summer and autumn), 2078 strains were isolated and identified to 17 known species: T. harzianum (429 isolates), T. asperellum (425), T. hamatum (397), T. virens (340), T. koningiopsis (248), T. brevicompactum (73), T. atroviride (73), T. fertile (26), T. longibrachiatum (22), T. pleuroticola (16), T. erinaceum (16), T. oblongisporum (2), T. polysporum (2), T. spirale (2), T. capillare (2), T. velutinum (2), and T. saturnisporum (1). T. harzianum, T. asperellum, T. hamatum, and T. virens were identified as the dominant species with dominance (Y) values of 0.057, 0.052, 0.048, and 0.039, respectively. The species amount, isolate numbers and the dominant species of Trichoderma varied between provinces. Zhejiang Province has shown the highest diversity, which was reflected in the highest species amount (14) and the highest Shannon–Wiener diversity index of Trichoderma haplotypes (1.46). We observed that relative frequencies of T. hamatum and T. koningiopsis under rice soil were higher than those under wheat and maize soil, indicating the preference of Trichoderma to different crops. Remarkable seasonal variation was shown, with summer exhibiting the highest biodiversity of the studied seasons. These results show that Trichoderma biodiversity in agricultural fields varies by region, crop, and season. Zhejiang Province (the southernmost province in the investigated area) had more T. hamatum than Shandong Province (the northernmost province), not only in isolate amounts but also in haplotype amounts. Furthermore, at haplotype level, only T. hamatum showed a gradient distribution from south to north in correspondence analysis among the four dominant species. The above results would contribute to the

  17. Decades of field data reveal that turtles senesce in the wild.

    PubMed

    Warner, Daniel A; Miller, David A W; Bronikowski, Anne M; Janzen, Fredric J

    2016-06-01

    Lifespan and aging rates vary considerably across taxa; thus, understanding the factors that lead to this variation is a primary goal in biology and has ramifications for understanding constraints and flexibility in human aging. Theory predicts that senescence-declining reproduction and increasing mortality with advancing age-evolves when selection against harmful mutations is weaker at old ages relative to young ages or when selection favors pleiotropic alleles with beneficial effects early in life despite late-life costs. However, in many long-lived ectotherms, selection is expected to remain strong at old ages because reproductive output typically increases with age, which may lead to the evolution of slow or even negligible senescence. We show that, contrary to current thinking, both reproduction and survival decline with adult age in the painted turtle, Chrysemys picta, based on data spanning >20 y from a wild population. Older females, despite relatively high reproductive output, produced eggs with reduced hatching success. Additionally, age-specific mark-recapture analyses revealed increasing mortality with advancing adult age. These findings of reproductive and mortality senescence challenge the contention that chelonians do not age and more generally provide evidence of reduced fitness at old ages in nonmammalian species that exhibit long chronological lifespans. PMID:27140634

  18. Combat: Initial Experience with a Randomized Clinical Trial of Plasma-Based Resuscitation in the Field for Traumatic Hemorrhagic Shock.

    PubMed

    Chapman, Michael P; Moore, Ernest E; Chin, Theresa L; Ghasabyan, Arsen; Chandler, James; Stringham, John; Gonzalez, Eduardo; Moore, Hunter B; Banerjee, Anirban; Silliman, Christopher C; Sauaia, Angela

    2015-08-01

    The existing evidence shows great promise for plasma as the first resuscitation fluid in both civilian and military trauma. We embarked on the Control of Major Bleeding After Trauma (COMBAT) trial with the support of the Department of Defense to determine if plasma-first resuscitation yields hemostatic and survival benefits. The methodology of the COMBAT study represents not only 3 years of development work but also the integration of nearly two decades of technical experience with the design and implementation of other clinical trials and studies. Herein, we describe the key features of the study design, critical personnel and infrastructural elements, and key innovations. We will also briefly outline the systems engineering challenges entailed by this study. The COMBAT trial is a randomized, placebo-controlled, semiblinded, prospective, phase IIB clinical trial conducted in a ground ambulance fleet based at a level I trauma center and part of a multicenter collaboration. The primary objective of the COMBAT trial is to determine the efficacy of field resuscitation with plasma first compared with standard of care (normal saline). To date, we have enrolled 30 subjects in the COMBAT study. The ability to achieve intervention with a hemostatic resuscitation agent in the closest possible temporal proximity to injury is critical and represents an opportunity to forestall the evolution of the "bloody vicious cycle." Thus, the COMBAT model for deploying plasma in first-response units should serve as a model for randomized clinical trials of other hemostatic resuscitative agents. PMID:25784527

  19. Effects of pulsed electromagnetic fields on swelling and pain after implant surgery: a double-blind, randomized study.

    PubMed

    Menini, M; Bevilacqua, M; Setti, P; Tealdo, T; Pesce, P; Pera, P

    2016-03-01

    The aim of this split-mouth, double-blind, randomized study was to determine whether pulsed electromagnetic field therapy (PEMF) can improve swelling and the management of pain after full-arch immediate loading implant surgery. Eleven patients were selected for the study. Each patient received four distal tilted implants in the upper or lower jaw and underwent full-arch immediate loading rehabilitation. After surgery, two PEMF devices were applied to each patient, one on each cheek. In a random manner, one of these PEMF devices was switched on (test side); the other served as a placebo (control side). Forty-eight hours after surgery clinicians estimated postoperative swelling through photographic documentation, comparing the condition before and after surgery, while pain was assessed using a verbal rating scale. The patient's degree of comfort in relation to the PEMF devices was analyzed by questionnaire using a numerical rating scale. No statistically significant difference was observed between the test and control sides for swelling or pain (P>0.05). Most of the patients did not present swelling or pain at 48h after surgery, regardless of whether the PEMF device was activated or not. Various outcomes were found in the comfort evaluation. Within the limitations of this study, PEMF does not reduce postoperative swelling or pain after implant surgery. PMID:26586300

  20. Geographic Variation in Skull Morphology of the Large Japanese Field Mice, Apodemus speciosus (Rodentia: Muridae) Revealed by Geometric Morphometric Analysis.

    PubMed

    Shintaku, Yuta; Motokawa, Masaharu

    2016-04-01

    We analyzed geographic variation in skull morphology of the large Japanese field mouse (Apodemus speciosus) and determined changes in skull morphology that occurred during the evolutionary history of A. speciosus in relation to the estimated distribution range in the last glacial maximum (LGM). We analyzed 1,416 specimens from 78 localities using geometric morphometric techniques applied to the dorsal side of the cranium and mandible. While large variations within and among the populations in Honshu, Shikoku, and Kyushu were observed, geographic patterns were not observed. Hokkaido and peripheral island populations showed shared differentiation from the Honshu, Shikoku, and Kyushu populations with a larger skull and distinct mandible shape. In addition, these two groups also differed from each other in accumulated random shape variation. Common characteristics found in Hokkaido and peripheral island populations were considered to be the ancestral states, which were retained by geographic isolation from the main islands. Random variations in Hokkaido and the peripheral island populations were formed through stochastic processes in relation to their isolation. Characteristic morphologies widely found in the populations of Honshu, Shikoku, and Kyushu were considered to be derived states that expanded after separation from the peripheral islands. Complex geomorphology and a shift in distribution range related to climate change and altitudinal distribution are suggested to have formed the complex geographic variation in this species. PMID:27032678

  1. Exploring the Parameter Space of the Coarse-Grained UNRES Force Field by Random Search: Selecting a Transferable Medium-Resolution Force Field

    PubMed Central

    HE, YI; XIAO, YI; LIWO, ADAM; SCHERAGA, HAROLD A.

    2009-01-01

    We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal α-helical and a minimal β-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with α or α + β structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. PMID:19242966

  2. A Functional Networks Estimation Method of Resting-State fMRI Using a Hierarchical Markov Random Field

    PubMed Central

    Liu, Wei; Awate, Suyash P.; Anderson, Jeffrey S.; Fletcher, P. Thomas

    2014-01-01

    We propose a hierarchical Markov random field model that estimates both group and subject functional networks simultaneously. The model takes into account the within-subject spatial coherence as well as the between-subject consistency of the network label maps. The statistical dependency between group and subject networks acts as a regularization, which helps the network estimation on both layers. We use Gibbs sampling to approximate the posterior density of the network labels and Monte Carlo expectation maximization to estimate the model parameters. We compare our method with two alternative segmentation methods based on K-Means and normalized cuts, using synthetic and real fMRI data. The experimental results show our proposed model is able to identify both group and subject functional networks with higher accuracy, more robustness, and inter-session consistency. PMID:24954282

  3. An Investigation of Quasar Variability as a Damped Random Walk in the PanSTARRS-1 Medium Deep Fields

    NASA Astrophysics Data System (ADS)

    Cunningham, Virginia; Green, Paul J.; Morganson, Eric; Shen, Yue

    2015-01-01

    We model the lightcurves of 755 optically varying quasars from the Pan-STARRS Medium Deep Field 7 r band using a Damped Random Walk (DRW) model. The DRW describes quasar variability by its characteristic timescale, τ, and its variability at infinite time, V∞. We use Monte Carlo techniques to fit our data as a DRW. The model parameters are compared to physical properties of the quasars such as black hole mass, Eddington ratio, and bolometric luminosity. We find that bolometric luminosity, Eddington ratio, and black hole mass are positively correlated with V∞ and negatively correlated with τ. Quasars of greater luminosity, black hole mass, or Eddington ratio generally display smaller variations, and on longer timescales as estimated in the DRW model framework. This work was supported in part by the NSF REU and DoD ASSURE programs under NSF grant no. 1262851 and by the Smithsonian Institution.

  4. On the growth rate of bending induced edge cracks in panels excited by convected random pressure fields

    NASA Astrophysics Data System (ADS)

    Byrne, K. P.

    1980-01-01

    Parts of an aircraft structure may be made to vibrate as a result of acoustic waves generated by various aircraft noise sources impinging on the structure. The stresses associated with this acoustically induced vibration may be sufficiently large to result in fatigue failure of portions of the structure. If acoustically induced fatigue cracks occur in the stiffened skin structure widely used in aircraft construction they may initiate in the skin panels near the stiffener attachment points. The initiation and subsequent propagation of these cracks at the panel edges is primarily due to the bending stresses arising from the out-of-plane vibration of the individual skin panels. The emphasis of the work described in this paper is on devising a method of predicting the growth rate of an edge crack in a panel which is excited by a convected random pressure field.

  5. Remote Numerical Simulations of the Interaction of High Velocity Clouds with Random Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Santillan, Alfredo; Hernandez--Cervantes, Liliana; Gonzalez--Ponce, Alejandro; Kim, Jongsoo

    The numerical simulations associated with the interaction of High Velocity Clouds (HVC) with the Magnetized Galactic Interstellar Medium (ISM) are a powerful tool to describe the evolution of the interaction of these objects in our Galaxy. In this work we present a new project referred to as Theoretical Virtual i Observatories. It is oriented toward to perform numerical simulations in real time through a Web page. This is a powerful astrophysical computational tool that consists of an intuitive graphical user interface (GUI) and a database produced by numerical calculations. In this Website the user can make use of the existing numerical simulations from the database or run a new simulation introducing initial conditions such as temperatures, densities, velocities, and magnetic field intensities for both the ISM and HVC. The prototype is programmed using Linux, Apache, MySQL, and PHP (LAMP), based on the open source philosophy. All simulations were performed with the MHD code ZEUS-3D, which solves the ideal MHD equations by finite differences on a fixed Eulerian mesh. Finally, we present typical results that can be obtained with this tool.

  6. Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia

    PubMed Central

    Winter, David J.; Pacheco, M. Andreína; Vallejo, Andres F.; Schwartz, Rachel S.; Arevalo-Herrera, Myriam; Herrera, Socrates

    2015-01-01

    Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America. PMID:26709695

  7. Revealing backward rescattering photoelectron interference of molecules in strong infrared laser fields.

    PubMed

    Li, Min; Sun, Xufei; Xie, Xiguo; Shao, Yun; Deng, Yongkai; Wu, Chengyin; Gong, Qihuang; Liu, Yunquan

    2015-01-01

    Photoelectrons ionized from atoms and molecules in a strong laser field are either emitted directly or rescattered by the nucleus, both of which can serve as efficiently useful tools for molecular orbital imaging. We measure the photoelectron angular distributions of molecules (N2, O2 and CO2) ionized by infrared laser pulses (1320 nm, 0.2 ~ 1 × 10(14) W/cm(2)) from multiphoton to tunneling regime and observe an enhancement of interference stripes in the tunneling regime. Using a semiclassical rescattering model with implementing the interference effect, we show that the enhancement arises from the sub-laser-cycle holographic interference of the contributions of the back-rescattering and the non-rescattering electron trajectory. It is shown that the low-energy backscattering photoelectron interference patterns have encoded the structural information of the molecular initial orbitals and attosecond time-resolved dynamics of photoelectron, opening new paths in high-resolution imaging of sub-Ångström and sub-femtosecond structural dynamics in molecules. PMID:25687446

  8. Whole Genome Sequencing of Field Isolates Reveals Extensive Genetic Diversity in Plasmodium vivax from Colombia.

    PubMed

    Winter, David J; Pacheco, M Andreína; Vallejo, Andres F; Schwartz, Rachel S; Arevalo-Herrera, Myriam; Herrera, Socrates; Cartwright, Reed A; Escalante, Ananias A

    2015-12-01

    Plasmodium vivax is the most prevalent malarial species in South America and exerts a substantial burden on the populations it affects. The control and eventual elimination of P. vivax are global health priorities. Genomic research contributes to this objective by improving our understanding of the biology of P. vivax and through the development of new genetic markers that can be used to monitor efforts to reduce malaria transmission. Here we analyze whole-genome data from eight field samples from a region in Cordóba, Colombia where malaria is endemic. We find considerable genetic diversity within this population, a result that contrasts with earlier studies suggesting that P. vivax had limited diversity in the Americas. We also identify a selective sweep around a substitution known to confer resistance to sulphadoxine-pyrimethamine (SP). This is the first observation of a selective sweep for SP resistance in this species. These results indicate that P. vivax has been exposed to SP pressure even when the drug is not in use as a first line treatment for patients afflicted by this parasite. We identify multiple non-synonymous substitutions in three other genes known to be involved with drug resistance in Plasmodium species. Finally, we found extensive microsatellite polymorphisms. Using this information we developed 18 polymorphic and easy to score microsatellite loci that can be used in epidemiological investigations in South America. PMID:26709695

  9. Compartment shape anisotropy (CSA) revealed by double pulsed field gradient MR.

    PubMed

    Ozarslan, Evren

    2009-07-01

    The multiple scattering extensions of the pulsed field gradient (PFG) experiments can be used to characterize restriction-induced anisotropy at different length scales. In double-PFG acquisitions that involve two pairs of diffusion gradient pulses, the dependence of the MR signal attenuation on the angle between the two gradients is a signature of restriction that can be observed even at low gradient strengths. In this article, a comprehensive theoretical treatment of the double-PFG observation of restricted diffusion is presented. In the first part of the article, the problem is treated for arbitrarily shaped pores under idealized experimental conditions, comprising infinitesimally narrow gradient pulses with long separation times and long or vanishing mixing times. New insights are obtained when the treatment is applied to simple pore shapes of spheres, ellipsoids, and capped cylinders. The capped cylinder geometry is considered in the second part of the article where the solution for a double-PFG experiment with arbitrary experimental parameters is introduced. Although compartment shape anisotropy (CSA) is emphasized here, the findings of this article can be used in gleaning the volume, eccentricity, and orientation distribution function associated with ensembles of anisotropic compartments using double-PFG acquisitions with arbitrary experimental parameters. PMID:19398210

  10. Shipboard magnetic field "noise" reveals shallow heavy mineral sediment concentrations in Chesapeake Bay

    USGS Publications Warehouse

    Shah, Anjana K.; Vogt, Peter R.; Rosenbaum, Joseph G.; Newell, Wayne; Cronin, Thomas M.; Willard, Debra A.; Hagen, Rick A.; Brozena, John; Hofstra, Albert

    2012-01-01

    Shipboard magnetic field data collected over Chesapeake Bay exhibit low-amplitude, short-wavelength anomalies that most likely indicate shallow concentrations of heavy mineral sediments. Piston core layers and black sand beach samples exhibit enhanced magnetic susceptibilities and carry remanent magnetization, with mineralogical analyses indicating ilmenite and trace magnetite and/or maghemite and hematite. The anomalies are subtle and would be filtered as noise using traditional approaches, but can instead be highlighted using spectral methods, thus providing nearly continuous coverage along survey tracks. The distribution of the anomalies provides constraints on relevant sorting mechanisms. Comparisons to sonar data and previous grab samples show that two of three areas surveyed exhibit short-wavelength anomalies that are clustered over sand-covered areas, suggesting initial sorting through settling mechanisms. This is supported by a correlation between core magnetic susceptibility and grain size. Near the Choptank River, where sediment resuspension is wave-dominated, anomalies show a sharp decrease with seafloor depth that cannot be explained by signal attenuation alone. In Pocomoke Sound, where both tidal currents and wave-action impact sediment resuspension, anomalies show a more gradual decrease with depth. Near the mouth of the bay, where there is a higher influx of sediments from the continental shelf, short-wavelength anomalies are isolated and do not appear to represent heavy mineral sand concentrations. These combined observations suggest the importance of further sorting by erosional processes in certain parts of the bay. Additionally, comparisons of these data to cores sampling pre-Holocene sediments suggest that the sorting of heavy minerals in higher energy, shallow water environments provides a mechanism for correlations between core magnetic susceptibility and sea-level changes.

  11. Life table assay of field-caught Mediterranean fruit flies, Ceratitis capitata, reveals age bias

    PubMed Central

    Kouloussis, Nikos A.; Papadopoulos, Nikos T.; Müller, Hans-Georg; Wang, Jane-Ling; Mao, Meng; Katsoyannos, Byron I.; Duyck, Pierre-François; Carey, James R.

    2012-01-01

    Though traps are used widely to sample phytophagous insects for research or management purposes, and recently in aging research, possible bias stemming from differential response of individuals of various ages to traps has never been examined. In this paper, we tested the response of Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) males and females of four ages (spanning from 1 to 40 days) to McPhail-type traps baited with a synthetic food attractant in field cages and found that the probability of trapping was significantly influenced by age. The type of food on which flies were maintained before testing (sugar or protein) also had a strong effect and interacted with age. In another experiment, we collected wild C. capitata adults of unknown age using 1–3 methods and then reared them in the laboratory until death. The survival schedules of these flies were subsequently used in a life table assay to infer their age at the time of capture. Results showed that on a single sampling date, males captured in traps baited with a food attractant were younger compared with males aspirated from fruiting host trees, or males captured in traps baited with a sex attractant. Likewise, females captured in food-baited traps were younger compared with aspirated females. In addition to providing the first evidence of age-dependent sampling bias for a phytophagous insect species, this paper also provides a novel approach to estimate the differences in the age composition of samples collected with different techniques. These findings are of utmost importance for several categories of insects, medically important groups notwithstanding. PMID:22844133

  12. Change of translational-rotational coupling in liquids revealed by field-cycling 1H NMR

    NASA Astrophysics Data System (ADS)

    Meier, R.; Schneider, E.; Rössler, E. A.

    2015-01-01

    Applying the field-cycling nuclear magnetic resonance technique, the frequency dependence of the 1H spin-lattice relaxation rate, R 1 ω = T1 - 1 ω , is measured for propylene glycol (PG) which is increasingly diluted with deuterated chloroform. A frequency range of 10 kHz-20 MHz and a broad temperature interval from 220 to about 100 K are covered. The results are compared to those of experiments, where glycerol and o-terphenyl are diluted with their deuterated counter-part. Reflecting intra- as well as intermolecular relaxation, the dispersion curves R 1 ω , x (x denotes mole fraction PG) allow to extract the rotational time constant τrot(T, x) and the self-diffusion coefficient D(T, x) in a single experiment. The Stokes-Einstein-Debye (SED) relation is tested in terms of the quantity D(T, x) τrot(T, x) which provides a measure of an effective hydrodynamic radius or equivalently of the spectral separation of the translational and the rotational relaxation contribution. In contrast to o-terphenyl, glycerol and PG show a spectral separation much larger than suggested by the SED relation. In the case of PG/chloroform mixtures, not only an acceleration of the PG dynamics is observed with increasing dilution but also the spectral separation of rotational and translational relaxation contributions continuously decreases. Finally, following a behavior similar to that of o-terphenyl already at about x = 0.6; i.e., while D(T, x) τrot(T, x) in the mixture is essentially temperature independent, it strongly increases with x signaling thus a change of translational-rotational coupling. This directly reflects the dissolution of the hydrogen-bond network and thus a change of solution structure.

  13. Pulsed Electromagnetic Fields in the treatment of fresh scaphoid fractures. A multicenter, prospective, double blind, placebo controlled, randomized trial

    PubMed Central

    2011-01-01

    Background The scaphoid bone is the most commonly fractured of the carpal bones. In the Netherlands 90% of all carpal fractures is a fracture of the scaphoid bone. The scaphoid has an essential role in functionality of the wrist, acting as a pivot. Complications in healing can result in poor functional outcome. The scaphoid fracture is a troublesome fracture and failure of treatment can result in avascular necrosis (up to 40%), non-union (5-21%) and early osteo-arthritis (up to 32%) which may seriously impair wrist function. Impaired consolidation of scaphoid fractures results in longer immobilization and more days lost at work with significant psychosocial and financial consequences. Initially Pulsed Electromagnetic Fields was used in the treatment of tibial pseudoarthrosis and non-union. More recently there is evidence that physical forces can also be used in the treatment of fresh fractures, showing accelerated healing by 30% and 71% reduction in nonunion within 12 weeks after initiation of therapy. Until now no double blind randomized, placebo controlled trial has been conducted to investigate the effect of this treatment on the healing of fresh fractures of the scaphoid. Methods/Design This is a multi center, prospective, double blind, placebo controlled, randomized trial. Study population consists of all patients with unilateral acute scaphoid fracture. Pregnant women, patients having a life supporting implanted electronic device, patients with additional fractures of wrist, carpal or metacarpal bones and pre-existing impairment in wrist function are excluded. The scaphoid fracture is diagnosed by a combination of physical and radiographic examination (CT-scanning). Proven scaphoid fractures are treated with cast immobilization and a small Pulsed Electromagnetic Fields bone growth stimulating device placed on the cast. Half of the devices will be disabled at random in the factory. Study parameters are clinical consolidation, radiological consolidation

  14. Time resolved X-ray Dark-Field Tomography Revealing Water Transport in a Fresh Cement Sample.

    PubMed

    Prade, Friedrich; Fischer, Kai; Heinz, Detlef; Meyer, Pascal; Mohr, Jürgen; Pfeiffer, Franz

    2016-01-01

    Grating-based X-ray dark-field tomography is a promising technique for biomedical and materials research. Even if the resolution of conventional X-ray tomography does not suffice to resolve relevant structures, the dark-field signal provides valuable information about the sub-pixel microstructural properties of the sample. Here, we report on the potential of X-ray dark-field imaging to be used for time-resolved three-dimensional studies. By repeating consecutive tomography scans on a fresh cement sample, we were able to study the hardening dynamics of the cement paste in three dimensions over time. The hardening of the cement was accompanied by a strong decrease in the dark-field signal pointing to microstructural changes within the cement paste. Furthermore our results hint at the transport of water from certain limestone grains, which were embedded in the sample, to the cement paste during the process of hardening. This is indicated by an increasing scattering signal which was observed for two of the six tested limestone grains. Electron microscopy images revealed a distinct porous structure only for those two grains which supports the following interpretation of our results. When the water filled pores of the limestone grains empty during the experiment the scattering signal of the grains increases. PMID:27357449

  15. Time resolved X-ray Dark-Field Tomography Revealing Water Transport in a Fresh Cement Sample

    NASA Astrophysics Data System (ADS)

    Prade, Friedrich; Fischer, Kai; Heinz, Detlef; Meyer, Pascal; Mohr, Jürgen; Pfeiffer, Franz

    2016-06-01

    Grating-based X-ray dark-field tomography is a promising technique for biomedical and materials research. Even if the resolution of conventional X-ray tomography does not suffice to resolve relevant structures, the dark-field signal provides valuable information about the sub-pixel microstructural properties of the sample. Here, we report on the potential of X-ray dark-field imaging to be used for time-resolved three-dimensional studies. By repeating consecutive tomography scans on a fresh cement sample, we were able to study the hardening dynamics of the cement paste in three dimensions over time. The hardening of the cement was accompanied by a strong decrease in the dark-field signal pointing to microstructural changes within the cement paste. Furthermore our results hint at the transport of water from certain limestone grains, which were embedded in the sample, to the cement paste during the process of hardening. This is indicated by an increasing scattering signal which was observed for two of the six tested limestone grains. Electron microscopy images revealed a distinct porous structure only for those two grains which supports the following interpretation of our results. When the water filled pores of the limestone grains empty during the experiment the scattering signal of the grains increases.

  16. Time resolved X-ray Dark-Field Tomography Revealing Water Transport in a Fresh Cement Sample

    PubMed Central

    Prade, Friedrich; Fischer, Kai; Heinz, Detlef; Meyer, Pascal; Mohr, Jürgen; Pfeiffer, Franz

    2016-01-01

    Grating-based X-ray dark-field tomography is a promising technique for biomedical and materials research. Even if the resolution of conventional X-ray tomography does not suffice to resolve relevant structures, the dark-field signal provides valuable information about the sub-pixel microstructural properties of the sample. Here, we report on the potential of X-ray dark-field imaging to be used for time-resolved three-dimensional studies. By repeating consecutive tomography scans on a fresh cement sample, we were able to study the hardening dynamics of the cement paste in three dimensions over time. The hardening of the cement was accompanied by a strong decrease in the dark-field signal pointing to microstructural changes within the cement paste. Furthermore our results hint at the transport of water from certain limestone grains, which were embedded in the sample, to the cement paste during the process of hardening. This is indicated by an increasing scattering signal which was observed for two of the six tested limestone grains. Electron microscopy images revealed a distinct porous structure only for those two grains which supports the following interpretation of our results. When the water filled pores of the limestone grains empty during the experiment the scattering signal of the grains increases. PMID:27357449

  17. Extended power-law scaling of heavy-tailed random air-permeability fields in fractured and sedimentary rocks

    NASA Astrophysics Data System (ADS)

    Guadagnini, A.; Riva, M.; Neuman, S. P.

    2012-09-01

    We analyze the scaling behaviors of two field-scale log permeability data sets showing heavy-tailed frequency distributions in three and two spatial dimensions, respectively. One set consists of 1-m scale pneumatic packer test data from six vertical and inclined boreholes spanning a decameters scale block of unsaturated fractured tuffs near Superior, Arizona, the other of pneumatic minipermeameter data measured at a spacing of 15 cm along three horizontal transects on a 21 m long and 6 m high outcrop of the Upper Cretaceous Straight Cliffs Formation, including lower-shoreface bioturbated and cross-bedded sandstone near Escalante, Utah. Order q sample structure functions of each data set scale as a power ξ(q) of separation scale or lag, s, over limited ranges of s. A procedure known as extended self-similarity (ESS) extends this range to all lags and yields a nonlinear (concave) functional relationship between ξ(q) and q. Whereas the literature tends to associate extended and nonlinear power-law scaling with multifractals or fractional Laplace motions, we have shown elsewhere that (a) ESS of data having a normal frequency distribution is theoretically consistent with (Gaussian) truncated (additive, self-affine, monofractal) fractional Brownian motion (tfBm), the latter being unique in predicting a breakdown in power-law scaling at small and large lags, and (b) nonlinear power-law scaling of data having either normal or heavy-tailed frequency distributions is consistent with samples from sub-Gaussian random fields or processes subordinated to tfBm or truncated fractional Gaussian noise (tfGn), stemming from lack of ergodicity which causes sample moments to scale differently than do their ensemble counterparts. Here we (i) demonstrate that the above two data sets are consistent with sub-Gaussian random fields subordinated to tfBm or tfGn and (ii) provide maximum likelihood estimates of parameters characterizing the corresponding Lévy stable subordinators and tf

  18. Characterization of two Austrian porcine reproductive and respiratory syndrome virus (PRRSV) field isolates reveals relationship to East Asian strains.

    PubMed

    Sinn, Leonie J; Zieglowski, Leonie; Koinig, Hanna; Lamp, Benjamin; Jansko, Bettina; Mößlacher, Georg; Riedel, Christiane; Hennig-Pauka, Isabel; Rümenapf, Till

    2016-01-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) causes major problems for the swine industry worldwide. Due to Austria's central location in Europe, a large number of animals are transported through the country. However, little is known about current PRRSV strains and epidemiology. We determined full-length genome sequences of two Austrian field isolates (AUT13-883 and AUT14-440) from recent PRRSV outbreaks and of a related German isolate (GER09-613). Phylogenetic analysis revealed that the strains belong to European genotype 1 subtype 1 and form a cluster together with a South Korean strain. Remarkably, AUT14-440 infected the simian cell line MARC-145 without prior adaptation. In addition, this isolate showed exceptional deletions in nonstructural protein 2, in the overlapping region of glycoprotein 3 and 4 and in the 3' untranslated region. Both Austrian isolates caused similar lung lesions but only pigs infected with AUT14-440 developed clear clinical signs of infection. Taken together, the genetic and biological characterization of two novel Austrian PRRSV field isolates revealed similarities to East Asian strains. This stresses the necessity for a more detailed analysis of current PRRSV strains in Europe beyond the determination of short ORF5 and ORF7 sequences. PMID:26754154

  19. Pulsed electromagnetic fields after arthroscopic treatment for osteochondral defects of the talus: double-blind randomized controlled multicenter trial

    PubMed Central

    van Bergen, Christiaan JA; Blankevoort, Leendert; de Haan, Rob J; Sierevelt, Inger N; Meuffels, Duncan E; d'Hooghe, Pieter RN; Krips, Rover; van Damme, Geert; van Dijk, C Niek

    2009-01-01

    Background Osteochondral talar defects usually affect athletic patients. The primary surgical treatment consists of arthroscopic debridement and microfracturing. Although this is mostly successful, early sport resumption is difficult to achieve, and it can take up to one year to obtain clinical improvement. Pulsed electromagnetic fields (PEMFs) may be effective for talar defects after arthroscopic treatment by promoting tissue healing, suppressing inflammation, and relieving pain. We hypothesize that PEMF-treatment compared to sham-treatment after arthroscopy will lead to earlier resumption of sports, and aim at 25% increase in patients that resume sports. Methods/Design A prospective, double-blind, randomized, placebo-controlled trial (RCT) will be conducted in five centers throughout the Netherlands and Belgium. 68 patients will be randomized to either active PEMF-treatment or sham-treatment for 60 days, four hours daily. They will be followed-up for one year. The combined primary outcome measures are (a) the percentage of patients that resume and maintain sports, and (b) the time to resumption of sports, defined by the Ankle Activity Score. Secondary outcome measures include resumption of work, subjective and objective scoring systems (American Orthopaedic Foot and Ankle Society – Ankle-Hindfoot Scale, Foot Ankle Outcome Score, Numeric Rating Scales of pain and satisfaction, EuroQol-5D), and computed tomography. Time to resumption of sports will be analyzed using Kaplan-Meier curves and log-rank tests. Discussion This trial will provide level-1 evidence on the effectiveness of PEMFs in the management of osteochondral ankle lesions after arthroscopy. Trial registration Netherlands Trial Register (NTR1636) PMID:19591674

  20. Effects of resource-building group intervention on career management and mental health in work organizations: randomized controlled field trial.

    PubMed

    Vuori, Jukka; Toppinen-Tanner, Salla; Mutanen, Pertti

    2012-03-01

    A resource-building group intervention was developed to enhance career management, mental health, and job retention in work organizations. The in-company training program provided employees with better preparedness to manage their own careers. The program activities were universally implemented using an organization-level, 2-trainer model with trainers from the human resources management and occupational health services. The study was a within-organizations, randomly assigned field experimental study; it investigated the impacts of the intervention on immediate career management preparedness and later mental health and intentions to retire early. A total of 718 eligible individuals returned a questionnaire in 17 organizations and became voluntary participants. The respondents were randomly assigned to either an intervention (N = 369) or a comparison group (N = 349). Those in the intervention group were invited to group intervention workshops, whereas those in the comparison group received printed information about career and health-related issues. The 7-month follow-up results showed that the program significantly decreased depressive symptoms and intentions to retire early and increased mental resources among the group participants compared to the others. The mediation analyses demonstrated that the increase in career management preparedness as a proximal impact of the intervention mediated the longer term mental health effects. Those who benefited most from the intervention as regards their mental health were employees with elevated levels of depression or exhaustion and younger employees, implying additional benefits of a more targeted use of the intervention. The results demonstrated the benefits of the enhancement of individual-level career management and resilience resources as career and health promotion practice in work organizations. PMID:21942405

  1. Routine programs of health care systems as an opportunity toward communication skills training for family physicians: A randomized field trial

    PubMed Central

    Zamani, Ahmad Reza; Motamedi, Narges; Farajzadegan, Ziba

    2015-01-01

    Background: To have high-quality primary health care services, an adequate doctor–patient communication is necessary. Because of time restrictions and limited budget in health system, an effective, feasible, and continuous training approach is important. The aim of this study is to assess the appropriateness of a communication skills training program simultaneously with routine programs of health care system. Materials and Methods: It was a randomized field trial in two health network settings during 2013. Twenty-eight family physicians through simple random sampling and 140 patients through convenience sampling participated as intervention and control group. The physicians in the intervention group (n = 14) attended six educational sessions, simultaneous organization meeting, with case discussion and peer education method. In both the groups, physicians completed communication skills knowledge and attitude questionnaires, and patients completed patient satisfaction of medical interview questionnaire at baseline, immediately after intervention, and four months postintervention. Physicians and health network administrators (stakeholders), completed a set of program evaluation forms. Descriptive statistics and Chi-square test, t-test, and repeated measure analysis of variance were used to analyze the data. Results: Use of routine program as a strategy of training was rated by stakeholders highly on “feasibility” (80.5%), “acceptability” (93.5%), “educational content and method appropriateness” (80.75%), and “ability to integrating in the health system programs” (approximate 60%). Significant improvements were found in physicians’ knowledge (P < 0.001), attitude (P < 0.001), and patients’ satisfaction (P = 0.002) in intervention group. Conclusions: Communication skills training program, simultaneous organization meeting was successfully implemented and well received by stakeholders, without considering extra time and manpower. Therefore it can be

  2. Transcranial pulsed electromagnetic fields for multiple chemical sensitivity: study protocol for a randomized, double-blind, placebo-controlled trial

    PubMed Central

    2013-01-01

    Background Multiple chemical sensitivity (MCS) is a chronic condition of unknown etiology. MCS is characterized by recurrent nonspecific symptoms from multiple organ systems in response to chemical exposures in concentrations that are normally tolerated by the majority of the population. The symptoms may have severe impact on patients’ lives, but an evidence-based treatment for the condition is nonexisting. The pathophysiology is unclarified, but several indicators point towards abnormal processing of sensory signals in the central nervous system. Pulsed electromagnetic fields (PEMF) offer a promising new treatment for refractory depression and can be targeted at the brain, thereby activating biochemical cell processes. Methods/Design In a parallel, randomized, double-blind, placebo-controlled trial conducted at the Danish Research Centre for Chemical Sensitivities, the effects of PEMF in MCS patients will be assessed using the Re5 Independent System. Based on sample size estimation, 40 participants will be randomized to either PEMF therapy or placebo. The allocation sequence will be generated by computer. All involved parties (that is, participants, investigators, the research nurse, and the statistician) will be blinded to group allocation. The participants will receive PEMF therapy or placebo applied transcranially 30 minutes twice a day for 7 days a week over 6 consecutive weeks. Outcomes will be measured at baseline, once weekly during treatment, post treatment, and at 2.5-month and 4.5-month follow-up according to a predefined timetable. The primary outcome will be a measurement of the impact of MCS on everyday life. The secondary outcomes will be measurements of MCS symptoms, psychological distress (stress, anxiety or depressive symptoms), capsaicin-induced secondary punctate hyperalgesia, immunological markers in serum, and quality of life. Discussion This trial will assess the effects of PEMF therapy for MCS. Currently, there is no treatment with a

  3. Comparison of ribotyping, randomly amplified polymorphic DNA analysis, and pulsed-field gel electrophoresis in typing of Lactobacillus rhamnosus and L. casei strains.

    PubMed

    Tynkkynen, S; Satokari, R; Saarela, M; Mattila-Sandholm, T; Saxelin, M

    1999-09-01

    A total of 24 strains, biochemically identified as members of the Lactobacillus casei group, were identified by PCR with species-specific primers. The same set of strains was typed by randomly amplified polymorphic DNA (RAPD) analysis, ribotyping, and pulsed-field gel electrophoresis (PFGE) in order to compare the discriminatory power of the methods. Species-specific primers for L. rhamnosus and L. casei identified the type strain L. rhamnosus ATCC 7469 and the neotype strain L. casei ATCC 334, respectively, but did not give any signal with the recently revived species L. zeae, which contains the type strain ATCC 15820 and the strain ATCC 393, which was previously classified as L. casei. Our results are in accordance with the suggested new classification of the L. casei group. Altogether, 21 of the 24 strains studied were identified with the species-specific primers. In strain typing, PFGE was the most discriminatory method, revealing 17 genotypes for the 24 strains studied. Ribotyping and RAPD analysis yielded 15 and 12 genotypes, respectively. PMID:10473394

  4. a Comparative Study Between Pair-Point Clique and Multi-Point Clique Markov Random Field Models for Land Cover Classification

    NASA Astrophysics Data System (ADS)

    Hu, B.; Li, P.

    2013-07-01

    Markov random field (MRF) is an effective method for description of local spatial-temporal dependence of image and has been widely used in land cover classification and change detection. However, existing studies only use pair-point clique (PPC) to describe spatial dependence of neighbouring pixels, which may not fully quantify complex spatial relations, particularly in high spatial resolution images. In this study, multi-point clique (MPC) is adopted in MRF model to quantitatively express spatial dependence among pixels. A modified least squares fit (LSF) method based on robust estimation is proposed to calculate potential parameters for MRF models with different types. The proposed MPC-MRF method is evaluated and quantitatively compared with traditional PPCMRF in urban land cover classification using high resolution hyperspectral HYDICE data of Washington DC. The experimental results revealed that the proposed MPC-MRF method outperformed the traditional PPC-MRF method in terms of classification details. The MPC-MRF provides a sophisticated way of describing complex spatial dependence for relevant applications.

  5. Comparison of Ribotyping, Randomly Amplified Polymorphic DNA Analysis, and Pulsed-Field Gel Electrophoresis in Typing of Lactobacillus rhamnosus and L. casei Strains

    PubMed Central

    Tynkkynen, Soile; Satokari, Reetta; Saarela, Maria; Mattila-Sandholm, Tiina; Saxelin, Maija

    1999-01-01

    A total of 24 strains, biochemically identified as members of the Lactobacillus casei group, were identified by PCR with species-specific primers. The same set of strains was typed by randomly amplified polymorphic DNA (RAPD) analysis, ribotyping, and pulsed-field gel electrophoresis (PFGE) in order to compare the discriminatory power of the methods. Species-specific primers for L. rhamnosus and L. casei identified the type strain L. rhamnosus ATCC 7469 and the neotype strain L. casei ATCC 334, respectively, but did not give any signal with the recently revived species L. zeae, which contains the type strain ATCC 15820 and the strain ATCC 393, which was previously classified as L. casei. Our results are in accordance with the suggested new classification of the L. casei group. Altogether, 21 of the 24 strains studied were identified with the species-specific primers. In strain typing, PFGE was the most discriminatory method, revealing 17 genotypes for the 24 strains studied. Ribotyping and RAPD analysis yielded 15 and 12 genotypes, respectively. PMID:10473394

  6. Random amplified polymorphic DNA assay is less discriminant than pulsed-field gel electrophoresis for typing strains of methicillin-resistant Staphylococcus aureus.

    PubMed

    Saulnier, P; Bourneix, C; Prévost, G; Andremont, A

    1993-04-01

    Twenty-six strains of methicillin-resistant Staphylococcus aureus with different pulsed-field gel electrophoresis fingerprints were tested by random amplified polymorphic DNA assay with three primers, resulting in 15 to 20 different random amplified polymorphic DNA fingerprints. By summing the results for the three primers, the number of different fingerprints increased to 25, but two strains could not be differentiated. We conclude that pulsed-field gel electrophoresis remains the best method of typing methicillin-resistant S. aureus strains. PMID:8463406

  7. Random amplified polymorphic DNA assay is less discriminant than pulsed-field gel electrophoresis for typing strains of methicillin-resistant Staphylococcus aureus.

    PubMed Central

    Saulnier, P; Bourneix, C; Prévost, G; Andremont, A

    1993-01-01

    Twenty-six strains of methicillin-resistant Staphylococcus aureus with different pulsed-field gel electrophoresis fingerprints were tested by random amplified polymorphic DNA assay with three primers, resulting in 15 to 20 different random amplified polymorphic DNA fingerprints. By summing the results for the three primers, the number of different fingerprints increased to 25, but two strains could not be differentiated. We conclude that pulsed-field gel electrophoresis remains the best method of typing methicillin-resistant S. aureus strains. Images PMID:8463406

  8. RELAXATION OF MAGNETIC FIELD RELATIVE TO PLASMA DENSITY REVEALED FROM MICROWAVE ZEBRA PATTERNS ASSOCIATED WITH SOLAR FLARES

    SciTech Connect

    Yu Sijie; Yan Yihua; Tan Baolin E-mail: yyh@nao.cas.cn

    2012-12-20

    It is generally considered that the emission of microwave zebra pattern (ZP) structures requires high density and high temperature, which is similar to the situation of the flaring region where primary energy is released. Therefore, a parameter analysis of ZPs may reveal the physical conditions of the flaring source region. This work investigates the variations of 74 microwave ZP structures observed by the Chinese Solar Broadband Radio Spectrometer (SBRS/Huairou) at 2.6-3.8 GHz in nine solar flares, and we find that the ratio between the plasma density scale height L{sub N} and the magnetic field scale height L{sub B} in emission sources displays a tendency to decrease during the flaring processes. The ratio L{sub N} /L{sub B} is about 3-5 before the maximum of flares. It decreases to about 2 after the maximum. The detailed analysis of three typical X-class flares implies that the variation of L{sub N} /L{sub B} during the flaring process is most likely due to topological changes of the magnetic field in the flaring source region, and the stepwise decrease of L{sub N} /L{sub B} possibly reflects the magnetic field relaxation relative to the plasma density when the flaring energy is released. This result may also constrain solar flare modeling to some extent.

  9. Möbius-strip-like columnar functional connections are revealed in somato-sensory receptive field centroids

    PubMed Central

    Wright, James Joseph; Bourke, Paul David; Favorov, Oleg Vyachesslavovich

    2014-01-01

    Receptive fields of neurons in the forelimb region of areas 3b and 1 of primary somatosensory cortex, in cats and monkeys, were mapped using extracellular recordings obtained sequentially from nearly radial penetrations. Locations of the field centroids indicated the presence of a functional system in which cortical homotypic representations of the limb surfaces are entwined in three-dimensional Möbius-strip-like patterns of synaptic connections. Boundaries of somatosensory receptive field in nested groups irregularly overlie the centroid order, and are interpreted as arising from the superposition of learned connections upon the embryonic order. Since the theory of embryonic synaptic self-organization used to model these results was devised and earlier used to explain findings in primary visual cortex, the present findings suggest the theory may be of general application throughout cortex and may reveal a modular functional synaptic system, which, only in some parts of the cortex, and in some species, is manifest as anatomical ordering into columns. PMID:25400552

  10. Randomly Detected Genetically Modified (GM) Maize (Zea mays L.) near a Transport Route Revealed a Fragile 45S rDNA Phenotype

    PubMed Central

    Waminal, Nomar Espinosa; Ryu, Ki Hyun; Choi, Sun-Hee; Kim, Hyun Hee

    2013-01-01

    Monitoring of genetically modified (GM) crops has been emphasized to prevent their potential effects on the environment and human health. Monitoring of the inadvertent dispersal of transgenic maize in several fields and transport routes in Korea was carried out by qualitative multiplex PCR, and molecular analyses were conducted to identify the events of the collected GM maize. Cytogenetic investigations through fluorescence in situ hybridization (FISH) of the GM maize were performed to check for possible changes in the 45S rDNA cluster because this cluster was reported to be sensitive to replication and transcription stress. Three GM maize kernels were collected from a transport route near Incheon port, Korea, and each was found to contain NK603, stacked MON863 x NK603, and stacked NK603 x MON810 inserts, respectively. Cytogenetic analysis of the GM maize containing the stacked NK603 x MON810 insert revealed two normal compact 5S rDNA signals, but the 45S rDNA showed a fragile phenotype, demonstrating a “beads-on-a-string” fragmentation pattern, which seems to be a consequence of genetic modification. Implications of the 45S rDNA cluster fragility in GM maize are also discussed. PMID:24040165

  11. Sutureless Adult Voluntary Male Circumcision with Topical Anesthetic: A Randomized Field Trial of Unicirc, a Single-Use Surgical Instrument

    PubMed Central

    2016-01-01

    Introduction The World Health Organization has solicited rapid and minimally invasive techniques to facilitate scale-up of voluntary medical male circumcision (VMMC). Study design Non-blinded randomized controlled field trial with 2:1 allocation ratio. Participants 75 adult male volunteers. Setting Outpatient primary care clinic. Intervention Open surgical circumcision under local anesthetic with suturing vs. Unicirc disposable instrument under topical anesthetic and wound sealing with cyanoacrylate tissue adhesive. Primary Outcome Intraoperative duration. Secondary Outcomes Intraoperative and postoperative pain; adverse events; time to healing; patient satisfaction; cosmetic result. Results The intraoperative time was less with the Unicirc technique (median 12 vs. 25 min, p < 0.001). Wound healing and cosmetic results were superior in the Unicirc group. Adverse events were similar in both groups. Conclusions VMMC with Unicirc under topical anesthetic and wound sealing with cyanoacrylate tissue adhesive is rapid, heals by primary intention with superior cosmetic results, and is potentially safer and more cost-effective than open surgical VMMC. Trial Registration Clinicaltrials.gov NCT02443792 PMID:27299735

  12. A 0.5-V Six-Transistor Static Random Access Memory with Ferroelectric-Gate Field Effect Transistors

    NASA Astrophysics Data System (ADS)

    Tanakamaru, Shuhei; Hatanaka, Teruyoshi; Yajima, Ryoji; Miyaji, Kousuke; Takahashi, Mitsue; Sakai, Shigeki; Takeuchi, Ken

    2010-12-01

    A 0.5 V six-transistor static random access memory (6T-SRAM) with ferroelectric-gate field-effect-transistors (Fe-FETs) is proposed and experimentally demonstrated for the first time. During the read and the hold, the threshold voltage (VTH) of Fe-FETs automatically changes to increase the static noise margin (SNM) by 60%. During the stand-by, the VTH of the proposed SRAM cell increases to decrease the leakage current by 42%. In case of the read, the VTH of the read transistor decreases and increases the cell read current to achieve the fast read. During the write, the VTH of the SRAM cell dynamically changes and assist the cell data to flip, realizing a write assist function. The enlarged SNM realizes the VDD reduction by 0.11 V, which decreases the active power by 32%. The proposed SRAM layout is the same as the conventional 6T-SRAM and there is no area penalty.

  13. COMBAT: Initial experience with a randomized clinical trial of plasma-based resuscitation in the field for traumatic hemorrhagic shock

    PubMed Central

    Chapman, Michael P.; Moore, Ernest E.; Chin, Theresa L; Ghasabyan, Arsen; Chandler, James; Stringham, John; Gonzalez, Eduardo; Moore, Hunter B.; Banerjee, Anirban; Silliman, Christopher C; Sauaia, Angela

    2015-01-01

    The existing evidence shows great promise for plasma as the first resuscitation fluid in both civilian and military trauma. We embarked on the Control of Major Bleeding After Trauma (COMBAT) trial with the support of the Department of Defense, in order to determine if plasma-first resuscitation yields hemostatic and survival benefits. The methodology of the COMBAT study represents not only three years of development work, but the integration of nearly two-decades of technical experience with the design and implementation of other clinical trials and studies. Herein, we describe the key features of the study design, critical personnel and infrastructural elements, and key innovations. We will also briefly outline the systems engineering challenges entailed by this study. COMBAT is a randomized, placebo controlled, semi-blinded prospective Phase IIB clinical trial, conducted in a ground ambulance fleet based at a Level I trauma center, and part of a multicenter collaboration. The primary objective of COMBAT is to determine the efficacy of field resuscitation with plasma first, compared to standard of care (normal saline). To date we have enrolled 30 subjects in the COMBAT study. The ability to achieve intervention with a hemostatic resuscitation agent in the closest possible temporal proximity to injury is critical and represents an opportunity to forestall the evolution of the “bloody vicious cycle”. Thus, the COMBAT model for deploying plasma in first response units should serve as a model for RCTs of other hemostatic resuscitative agents. PMID:25784527

  14. Microbiological Evaluation of the Efficacy of Soapy Water to Clean Hands: A Randomized, Non-Inferiority Field Trial

    PubMed Central

    Amin, Nuhu; Pickering, Amy J.; Ram, Pavani K.; Unicomb, Leanne; Najnin, Nusrat; Homaira, Nusrat; Ashraf, Sania; Abedin, Jaynal; Islam, M. Sirajul; Luby, Stephen P.

    2014-01-01

    We conducted a randomized, non-inferiority field trial in urban Dhaka, Bangladesh among mothers to compare microbial efficacy of soapy water (30 g powdered detergent in 1.5 L water) with bar soap and water alone. Fieldworkers collected hand rinse samples before and after the following washing regimens: scrubbing with soapy water for 15 and 30 seconds; scrubbing with bar soap for 15 and 30 seconds; and scrubbing with water alone for 15 seconds. Soapy water and bar soap removed thermotolerant coliforms similarly after washing for 15 seconds (mean log10 reduction = 0.7 colony-forming units [CFU], P < 0.001 for soapy water; mean log10 reduction = 0.6 CFU, P = 0.001 for bar soap). Increasing scrubbing time to 30 seconds did not improve removal (P > 0.05). Scrubbing hands with water alone also reduced thermotolerant coliforms (mean log10 reduction = 0.3 CFU, P = 0.046) but was less efficacious than scrubbing hands with soapy water. Soapy water is an inexpensive and microbiologically effective cleansing agent to improve handwashing among households with vulnerable children. PMID:24914003

  15. Robust Foreground Detection: A Fusion of Masked Grey World, Probabilistic Gradient Information and Extended Conditional Random Field Approach

    PubMed Central

    Zulkifley, Mohd Asyraf; Moran, Bill; Rawlinson, David

    2012-01-01

    Foreground detection has been used extensively in many applications such as people counting, traffic monitoring and face recognition. However, most of the existing detectors can only work under limited conditions. This happens because of the inability of the detector to distinguish foreground and background pixels, especially in complex situations. Our aim is to improve the robustness of foreground detection under sudden and gradual illumination change, colour similarity issue, moving background and shadow noise. Since it is hard to achieve robustness using a single model, we have combined several methods into an integrated system. The masked grey world algorithm is introduced to handle sudden illumination change. Colour co-occurrence modelling is then fused with the probabilistic edge-based background modelling. Colour co-occurrence modelling is good in filtering moving background and robust to gradual illumination change, while an edge-based modelling is used for solving a colour similarity problem. Finally, an extended conditional random field approach is used to filter out shadow and afterimage noise. Simulation results show that our algorithm performs better compared to the existing methods, which makes it suitable for higher-level applications. PMID:22778605

  16. Automatic de-identification of electronic medical records using token-level and character-level conditional random fields.

    PubMed

    Liu, Zengjian; Chen, Yangxin; Tang, Buzhou; Wang, Xiaolong; Chen, Qingcai; Li, Haodi; Wang, Jingfeng; Deng, Qiwen; Zhu, Suisong

    2015-12-01

    De-identification, identifying and removing all protected health information (PHI) present in clinical data including electronic medical records (EMRs), is a critical step in making clinical data publicly available. The 2014 i2b2 (Center of Informatics for Integrating Biology and Bedside) clinical natural language processing (NLP) challenge sets up a track for de-identification (track 1). In this study, we propose a hybrid system based on both machine learning and rule approaches for the de-identification track. In our system, PHI instances are first identified by two (token-level and character-level) conditional random fields (CRFs) and a rule-based classifier, and then are merged by some rules. Experiments conducted on the i2b2 corpus show that our system submitted for the challenge achieves the highest micro F-scores of 94.64%, 91.24% and 91.63% under the "token", "strict" and "relaxed" criteria respectively, which is among top-ranked systems of the 2014 i2b2 challenge. After integrating some refined localization dictionaries, our system is further improved with F-scores of 94.83%, 91.57% and 91.95% under the "token", "strict" and "relaxed" criteria respectively. PMID:26122526

  17. Asynchronous decoding of finger movements from ECoG signals using long-range dependencies conditional random fields

    NASA Astrophysics Data System (ADS)

    Delgado Saa, Jaime F.; de Pesters, Adriana; Cetin, Mujdat

    2016-06-01

    Objective. In this work we propose the use of conditional random fields with long-range dependencies for the classification of finger movements from electrocorticographic recordings. Approach. The proposed method uses long-range dependencies taking into consideration time-lags between the brain activity and the execution of the motor task. In addition, the proposed method models the dynamics of the task executed by the subject and uses information about these dynamics as prior information during the classification stage. Main results. The results show that incorporating temporal information about the executed task as well as incorporating long-range dependencies between the brain signals and the labels effectively increases the system’s classification performance compared to methods in the state of art. Significance. The method proposed in this work makes use of probabilistic graphical models to incorporate temporal information in the classification of finger movements from electrocorticographic recordings. The proposed method highlights the importance of including prior information about the task that the subjects execute. As the results show, the combination of these two features effectively produce a significant improvement of the system’s classification performance.

  18. Detecting brain tumor in computed tomography images using Markov random fields and fuzzy C-means clustering techniques

    NASA Astrophysics Data System (ADS)

    Abdulbaqi, Hayder Saad; Jafri, Mohd Zubir Mat; Omar, Ahmad Fairuz; Mustafa, Iskandar Shahrim Bin; Abood, Loay Kadom

    2015-04-01

    Brain tumors, are an abnormal growth of tissues in the brain. They may arise in people of any age. They must be detected early, diagnosed accurately, monitored carefully, and treated effectively in order to optimize patient outcomes regarding both survival and quality of life. Manual segmentation of brain tumors from CT scan images is a challenging and time consuming task. Size and location accurate detection of brain tumor plays a vital role in the successful diagnosis and treatment of tumors. Brain tumor detection is considered a challenging mission in medical image processing. The aim of this paper is to introduce a scheme for tumor detection in CT scan images using two different techniques Hidden Markov Random Fields (HMRF) and Fuzzy C-means (FCM). The proposed method has been developed in this research in order to construct hybrid method between (HMRF) and threshold. These methods have been applied on 4 different patient data sets. The result of comparison among these methods shows that the proposed method gives good results for brain tissue detection, and is more robust and effective compared with (FCM) techniques.

  19. Effect of pulsed electromagnetic field therapy on experimental pain: A double-blind, randomized study in healthy young adults.

    PubMed

    Beaulieu, Karen; Beland, Patricia; Pinard, Marilee; Handfield, Guilène; Handfield, Nicole; Goffaux, Philippe; Corriveau, Hélène; Léonard, Guillaume

    2016-01-01

    Previous studies suggested that pulsed electromagnetic field (PEMF) therapy can decrease pain. To date, however, it remains difficult to determine whether the analgesic effect observed in patients are attributable to a direct effect of PEMF on pain or to an indirect effect of PEMF on inflammation and healing. In the present study, we used an experimental pain paradigm to evaluate the direct effect of PEMF on pain intensity, pain unpleasantness, and temporal summation of pain. Twenty-four healthy subjects (mean age 22 ± 2 years; 9 males) participated in the experiment. Both real and sham PEMF were administered to every participant using a randomized, double-blind, cross-over design. For each visit, PEMF was applied for 10 minutes on the right forearm using a portable device. Experimental pain was evoked before (baseline) and after PEMF with a 9 cm(2) Pelletier-type thermode, applied on the right forearm (120 s stimulation; temperature individually adjusted to produce moderate baseline pain). Pain intensity and unpleasantness were evaluated using a 0-100 numerical pain rating scale. Temporal summation was evaluated by comparing pain intensity ratings obtained at the end of tonic nociceptive stimulation (120 s) with pain intensity ratings obtained after 60 s of stimulation. When compared to baseline, there was no change in pain intensity and unpleasantness following the application of real or sham PEMF. PEMF did not affect temporal summation. The present observations suggest that PEMF does not directly influence heat pain perception in healthy individuals. PMID:27014804

  20. Spatio-contextual fuzzy clustering with Markov random field model for change detection in remotely sensed images

    NASA Astrophysics Data System (ADS)

    Subudhi, Badri Narayan; Bovolo, Francesca; Ghosh, Ashish; Bruzzone, Lorenzo

    2014-04-01

    This paper presents a novel spatio-contextual fuzzy clustering algorithm for unsupervised change detection from multispectral and multitemporal remote sensing images. The proposed technique uses fuzzy Gibbs Markov Random Field (GMRF) to model the spatial gray level attributes of the multispectral difference image. The change detection problem is solved using the maximum a posteriori probability (MAP) estimation principle. The MAP estimator of the fuzzy GMRF modeled difference image is found to be exponential in nature. Convergence of conventional fuzzy clustering based search criterion is more likely to lead the clustering solutions to be getting trapped in a local minimum. Hence we adhered to the variable neighborhood searching (VNS) based global convergence criterion for iterative estimation of the fuzzy GMRF parameters. Experiments are carried out on different multispectral and multitemporal remote sensing images. Results confirm the effectiveness of the proposed technique. It is also noticed that the proposed scheme provides better results with less misclassification error as compared to the existing techniques. The computational time taken by the proposed technique is comparable with that of the HTNN scheme.

  1. Recognition and Evaluation of Clinical Section Headings in Clinical Documents Using Token-Based Formulation with Conditional Random Fields.

    PubMed

    Dai, Hong-Jie; Syed-Abdul, Shabbir; Chen, Chih-Wei; Wu, Chieh-Chen

    2015-01-01

    Electronic health record (EHR) is a digital data format that collects electronic health information about an individual patient or population. To enhance the meaningful use of EHRs, information extraction techniques have been developed to recognize clinical concepts mentioned in EHRs. Nevertheless, the clinical judgment of an EHR cannot be known solely based on the recognized concepts without considering its contextual information. In order to improve the readability and accessibility of EHRs, this work developed a section heading recognition system for clinical documents. In contrast to formulating the section heading recognition task as a sentence classification problem, this work proposed a token-based formulation with the conditional random field (CRF) model. A standard section heading recognition corpus was compiled by annotators with clinical experience to evaluate the performance and compare it with sentence classification and dictionary-based approaches. The results of the experiments showed that the proposed method achieved a satisfactory F-score of 0.942, which outperformed the sentence-based approach and the best dictionary-based system by 0.087 and 0.096, respectively. One important advantage of our formulation over the sentence-based approach is that it presented an integrated solution without the need to develop additional heuristics rules for isolating the headings from the surrounding section contents. PMID:26380302

  2. Nonlinear scaling variable at the lower critical dimension: Scaling in the 2D random field Ising model

    NASA Astrophysics Data System (ADS)

    Hayden, Lorien; Sethna, James

    We systematically analyze the nonlinear invariant scaling variables at bifurcations in the renormalization-group flow, and apply our methods to the two-dimensional random-field Ising model (RFIM). At critical points, the universal scaling functions are usually written in terms of homogeneous invariant combinations of variables, like Ltν in the finite-size scaling form for the magnetization M (T | L) ~t-β M (Ltν) , where t ~Tc - T . The renormalization-group flow for the RFIM has a pitchfork bifurcation in two dimensions, where the correlation length has been argued to diverge exponentially, ξ ~ exp 1 / 2 At2 , leading to the invariant scaling combination L / ξ ~ L / exp 1 / 2 At2 . Our analysis, inspired by normal-form theory, suggests that this exponential divergence can take a richer, more general scaling form at a generic pitchfork bifurcation. We explore possible consequences for simulations. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. . DGE-1144153.

  3. Segmentation of Image Data from Complex Organotypic 3D Models of Cancer Tissues with Markov Random Fields

    PubMed Central

    Robinson, Sean; Guyon, Laurent; Nevalainen, Jaakko; Toriseva, Mervi

    2015-01-01

    Organotypic, three dimensional (3D) cell culture models of epithelial tumour types such as prostate cancer recapitulate key aspects of the architecture and histology of solid cancers. Morphometric analysis of multicellular 3D organoids is particularly important when additional components such as the extracellular matrix and tumour microenvironment are included in the model. The complexity of such models has so far limited their successful implementation. There is a great need for automatic, accurate and robust image segmentation tools to facilitate the analysis of such biologically relevant 3D cell culture models. We present a segmentation method based on Markov random fields (MRFs) and illustrate our method using 3D stack image data from an organotypic 3D model of prostate cancer cells co-cultured with cancer-associated fibroblasts (CAFs). The 3D segmentation output suggests that these cell types are in physical contact with each other within the model, which has important implications for tumour biology. Segmentation performance is quantified using ground truth labels and we show how each step of our method increases segmentation accuracy. We provide the ground truth labels along with the image data and code. Using independent image data we show that our segmentation method is also more generally applicable to other types of cellular microscopy and not only limited to fluorescence microscopy. PMID:26630674

  4. Testing Allele Transmission of an SNP Set Using a Family-Based Generalized Genetic Random Field Method.

    PubMed

    Li, Ming; Li, Jingyun; He, Zihuai; Lu, Qing; Witte, John S; Macleod, Stewart L; Hobbs, Charlotte A; Cleves, Mario A

    2016-05-01

    Family-based association studies are commonly used in genetic research because they can be robust to population stratification (PS). Recent advances in high-throughput genotyping technologies have produced a massive amount of genomic data in family-based studies. However, current family-based association tests are mainly focused on evaluating individual variants one at a time. In this article, we introduce a family-based generalized genetic random field (FB-GGRF) method to test the joint association between a set of autosomal SNPs (i.e., single-nucleotide polymorphisms) and disease phenotypes. The proposed method is a natural extension of a recently developed GGRF method for population-based case-control studies. It models offspring genotypes conditional on parental genotypes, and, thus, is robust to PS. Through simulations, we presented that under various disease scenarios the FB-GGRF has improved power over a commonly used family-based sequence kernel association test (FB-SKAT). Further, similar to GGRF, the proposed FB-GGRF method is asymptotically well-behaved, and does not require empirical adjustment of the type I error rates. We illustrate the proposed method using a study of congenital heart defects with family trios from the National Birth Defects Prevention Study (NBDPS). PMID:27061818

  5. Recognition and Evaluation of Clinical Section Headings in Clinical Documents Using Token-Based Formulation with Conditional Random Fields

    PubMed Central

    Dai, Hong-Jie; Syed-Abdul, Shabbir; Chen, Chih-Wei; Wu, Chieh-Chen

    2015-01-01

    Electronic health record (EHR) is a digital data format that collects electronic health information about an individual patient or population. To enhance the meaningful use of EHRs, information extraction techniques have been developed to recognize clinical concepts mentioned in EHRs. Nevertheless, the clinical judgment of an EHR cannot be known solely based on the recognized concepts without considering its contextual information. In order to improve the readability and accessibility of EHRs, this work developed a section heading recognition system for clinical documents. In contrast to formulating the section heading recognition task as a sentence classification problem, this work proposed a token-based formulation with the conditional random field (CRF) model. A standard section heading recognition corpus was compiled by annotators with clinical experience to evaluate the performance and compare it with sentence classification and dictionary-based approaches. The results of the experiments showed that the proposed method achieved a satisfactory F-score of 0.942, which outperformed the sentence-based approach and the best dictionary-based system by 0.087 and 0.096, respectively. One important advantage of our formulation over the sentence-based approach is that it presented an integrated solution without the need to develop additional heuristics rules for isolating the headings from the surrounding section contents. PMID:26380302

  6. Effects of pulsed electromagnetic fields on peripheral blood circulation in people with diabetes: A randomized controlled trial.

    PubMed

    Sun, Jiahui; Kwan, Rachel Lai-Chu; Zheng, Yongping; Cheing, Gladys Lai-Ying

    2016-07-01

    Cutaneous blood flow provides nourishment that plays an essential role in maintaining skin health. We examined the effects of pulsed electromagnetic fields (PEMFs) on cutaneous circulation of dorsal feet. Twenty-two patients with diabetes mellitus (DM) and 21 healthy control subjects were randomly allocated to receive either PEMFs or sham PEMFs (0.5 mT, 12 Hz, 30 min). Blood flow velocity and diameter of the small vein were examined by using ultrasound biomicroscopy; also, microcirculation at skin over the base of the 1st metatarsal bone (Flux1) and distal 1st phalange (Flux2) was measured by laser Doppler flowmetry before and after intervention. Results indicated that PEMFs produced significantly greater changes in blood flow velocity of the smallest observable vein than did sham PEMFs (both P < 0.05) in both types of subjects. However, no significant difference was found in changes of vein diameter, nor in Flux1 and Flux2, between PEMFs and sham PEMFs groups in subjects with or without DM. We hypothesized that PEMFs would increase blood flow velocity of the smallest observable vein in people with or without DM. Bioelectromagnetics. 37:290-297, 2016. © 2016 Wiley Periodicals, Inc. PMID:27227568

  7. Random amplified polymorphic DNA typing versus pulsed-field gel electrophoresis for epidemiological typing of vancomycin-resistant enterococci.

    PubMed Central

    Barbier, N; Saulnier, P; Chachaty, E; Dumontier, S; Andremont, A

    1996-01-01

    Sixty vancomycin-resistant vanA mutant Enterococcus faecium (VRE) isolates, collected during a 40-month period from 48 patients hospitalized in a French Cancer Referral Center, were typed by using random amplified polymorphic DNA (RAPD), and the results were compared with those previously obtained by typing with SmaI pulsed-field gel electrophoresis (PFGE), which is currently recognized as the "gold standard." The discriminating power of RAPD typing, with seven primers and 11 combinations of primers, was tested on 18 strains, and only the most discriminating combination was further tested on the whole collection. We compared the epidemiological usefulness of RAPD typing of 60 clinical VRE isolates with that of SmaI PFGE typing. With primers AP4 and ERIC1R, RAPD generated 30 patterns versus the 36 patterns generated by SmaI PFGE. However, this did not hamper the epidemiologically correct clustering of 15 related strains and the detection of multiple colonization in nine patients. We conclude that this simple RAPD technique is well suited to the epidemiological typing of VRE and the monitoring of its nosocomial spread. PMID:8727883

  8. Detecting brain tumor in computed tomography images using Markov random fields and fuzzy C-means clustering techniques

    SciTech Connect

    Abdulbaqi, Hayder Saad; Jafri, Mohd Zubir Mat; Omar, Ahmad Fairuz; Mustafa, Iskandar Shahrim Bin; Abood, Loay Kadom

    2015-04-24

    Brain tumors, are an abnormal growth of tissues in the brain. They may arise in people of any age. They must be detected early, diagnosed accurately, monitored carefully, and treated effectively in order to optimize patient outcomes regarding both survival and quality of life. Manual segmentation of brain tumors from CT scan images is a challenging and time consuming task. Size and location accurate detection of brain tumor plays a vital role in the successful diagnosis and treatment of tumors. Brain tumor detection is considered a challenging mission in medical image processing. The aim of this paper is to introduce a scheme for tumor detection in CT scan images using two different techniques Hidden Markov Random Fields (HMRF) and Fuzzy C-means (FCM). The proposed method has been developed in this research in order to construct hybrid method between (HMRF) and threshold. These methods have been applied on 4 different patient data sets. The result of comparison among these methods shows that the proposed method gives good results for brain tissue detection, and is more robust and effective compared with (FCM) techniques.

  9. The Application of a Car Confidence Feature for the Classification of Cross-Roads Using Conditional Random Fields

    NASA Astrophysics Data System (ADS)

    Kosov, S.; Rottensteiner, F.; Heipke, C.; Leitloff, J.; Hinz, S.

    2013-10-01

    The precise classification and reconstruction of crossroads from multiple aerial images is a challenging problem in remote sensing. We apply the Conditional Random Fields (CRF) approach to this problem, a probabilistic model that can be used to consider context in classification. A simple appearance-based model is combined with a probabilistic model of the co-occurrence of class label at neighbouring image sites to distinguish classes that are relevant for scenes containing crossroads. The parameters of these models are learnt from training data. We use multiple overlap aerial images to derive a digital surface model (DSM) and a true orthophoto without moving cars. From the DSM and the orthophoto we derive feature vectors that are used in the classification. Within our framework we make use of a car detector based on support vector machines (SVM), which delivers car probability values. These values are used as additional feature to support the classification when the road surface is occluded by static cars. Our approach is evaluated on a dataset of airborne photos of an urban area by a comparison of the results to reference data. The evaluation is performed for images of different resolution. The method is shown to produce promising results when using the car probability values and higher image resolution.

  10. Adaptive multi-level conditional random fields for detection and segmentation of small enhanced pathology in medical images.

    PubMed

    Karimaghaloo, Zahra; Arnold, Douglas L; Arbel, Tal

    2016-01-01

    Detection and segmentation of large structures in an image or within a region of interest have received great attention in the medical image processing domains. However, the problem of small pathology detection and segmentation still remains an unresolved challenge due to the small size of these pathologies, their low contrast and variable position, shape and texture. In many contexts, early detection of these pathologies is critical in diagnosis and assessing the outcome of treatment. In this paper, we propose a probabilistic Adaptive Multi-level Conditional Random Fields (AMCRF) with the incorporation of higher order cliques for detecting and segmenting such pathologies. In the first level of our graphical model, a voxel-based CRF is used to identify candidate lesions. In the second level, in order to further remove falsely detected regions, a new CRF is developed that incorporates higher order textural features, which are invariant to rotation and local intensity distortions. At this level, higher order textures are considered together with the voxel-wise cliques to refine boundaries and is therefore adaptive. The proposed algorithm is tested in the context of detecting enhancing Multiple Sclerosis (MS) lesions in brain MRI, where the problem is further complicated as many of the enhancing voxels are associated with normal structures (i.e. blood vessels) or noise in the MRI. The algorithm is trained and tested on large multi-center clinical trials from Relapsing-Remitting MS patients. The effect of several different parameter learning and inference techniques is further investigated. When tested on 120 cases, the proposed method reaches a lesion detection rate of 90%, with very few false positive lesion counts on average, ranging from 0.17 for very small (3-5 voxels) to 0 for very large (50+ voxels) regions. The proposed model is further tested on a very large clinical trial containing 2770 scans where a high sensitivity of 91% with an average false positive

  11. Effects of Adult Education Vouchers on the Labor Market: Evidence from a Randomized Field Experiment. Program on Education Policy and Governance Working Papers Series. PEPG 11-01

    ERIC Educational Resources Information Center

    Schwerdt, Guido; Messer, Dolores; Woessmann, Ludger; Wolter, Stefan C.

    2011-01-01

    Lifelong learning is often promoted in ageing societies, but little is known about its returns or governments' ability to advance it. This paper evaluates the effects of a large-scale randomized field experiment issuing vouchers for adult education in Switzerland. We find no significant average effects of voucher-induced adult education on…

  12. Invariant joint distribution of a stationary random field and its derivatives: Euler characteristic and critical point counts in 2 and 3D

    SciTech Connect

    Pogosyan, Dmitry; Gay, Christophe; Pichon, Christophe

    2009-10-15

    The full moments expansion of the joint probability distribution of an isotropic random field, its gradient, and invariants of the Hessian are presented in 2 and 3D. It allows for explicit expression for the Euler characteristic in ND and computation of extrema counts as functions of the excursion set threshold and the spectral parameter, as illustrated on model examples.

  13. Sequence polymorphism in an insect RNA virus field population: A snapshot from a single point in space and time reveals stochastic differences among and within individual hosts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects was examined. To minimize effects of different evolutionary histories and/or selection pressures, all glassy-winged sharpshooter (Homalodisca vitripennis; synonym H. coagulata) hosts were randomly...

  14. Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability.

    PubMed

    Henneberger, Ruth; Chiri, Eleonora; Bodelier, Paul E L; Frenzel, Peter; Lüke, Claudia; Schroth, Martin H

    2015-05-01

    Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4 ) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4 . Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body. PMID:25186436

  15. Preferential flow pathways revealed by field based stable isotope analysis of CO2 by mid-infrared laser spectroscopy

    NASA Astrophysics Data System (ADS)

    van Geldern, Robert; Nowak, Martin; Zimmer, Martin; Szizybalski, Alexandra; Myrttinen, Anssi; Barth, Johannes A. C.; Jost, Hj

    2016-04-01

    A newly developed and commercially available isotope ratio laser spectrometer for CO2 analyses has been tested during a 10-day field monitoring campaign at the Ketzin pilot site for CO2 storage in northern Germany. The laser instrument is based on tunable laser direct absorption in the mid-infrared. The instrument recorded a continuous 10-day carbon stable isotope data set with 30 minutes resolution directly on-site in a field-based laboratory container during a tracer experiment. To test the instruments performance and accuracy the monitoring campaign was accompanied by daily CO2 sampling for laboratory analyses with isotope ratio mass spectrometry (IRMS). The carbon stable isotope ratios measured by conventional IRMS technique and by the new mid-infrared laser spectrometer agree remarkably well within 2σ analytical precision (<0.3 ‰). This proves the capability of the new mid-infrared direct absorption technique to measure high precision and accurate real-time table isotope data directly in the field. The injected CO2 tracer had a distinct δ13C value that was largely different from the reservoir background value. The laser spectroscopy data revealed a prior to this study unknown, intensive dynamic with fast changing δ13C values. The arrival pattern of the tracer suggest that the observed fluctuations were probably caused by migration along separate and distinct preferential flow paths between injection well and observation well. The new technique might contribute to a better tracing of the migration of the underground CO2 plume and help to ensure the long-term integrity of the reservoir.

  16. Weighted maximum posterior marginals for random fields using an ensemble of conditional densities from multiple Markov chain Monte Carlo simulations.

    PubMed

    Monaco, James Peter; Madabhushi, Anant

    2011-07-01

    The ability of classification systems to adjust their performance (sensitivity/specificity) is essential for tasks in which certain errors are more significant than others. For example, mislabeling cancerous lesions as benign is typically more detrimental than mislabeling benign lesions as cancerous. Unfortunately, methods for modifying the performance of Markov random field (MRF) based classifiers are noticeably absent from the literature, and thus most such systems restrict their performance to a single, static operating point (a paired sensitivity/specificity). To address this deficiency we present weighted maximum posterior marginals (WMPM) estimation, an extension of maximum posterior marginals (MPM) estimation. Whereas the MPM cost function penalizes each error equally, the WMPM cost function allows misclassifications associated with certain classes to be weighted more heavily than others. This creates a preference for specific classes, and consequently a means for adjusting classifier performance. Realizing WMPM estimation (like MPM estimation) requires estimates of the posterior marginal distributions. The most prevalent means for estimating these--proposed by Marroquin--utilizes a Markov chain Monte Carlo (MCMC) method. Though Marroquin's method (M-MCMC) yields estimates that are sufficiently accurate for MPM estimation, they are inadequate for WMPM. To more accurately estimate the posterior marginals we present an equally simple, but more effective extension of the MCMC method (E-MCMC). Assuming an identical number of iterations, E-MCMC as compared to M-MCMC yields estimates with higher fidelity, thereby 1) allowing a far greater number and diversity of operating points and 2) improving overall classifier performance. To illustrate the utility of WMPM and compare the efficacies of M-MCMC and E-MCMC, we integrate them into our MRF-based classification system for detecting cancerous glands in (whole-mount or quarter) histological sections of the prostate

  17. Improved longitudinal gray and white matter atrophy assessment via application of a 4-dimensional hidden Markov random field model.

    PubMed

    Dwyer, Michael G; Bergsland, Niels; Zivadinov, Robert

    2014-04-15

    SIENA and similar techniques have demonstrated the utility of performing "direct" measurements as opposed to post-hoc comparison of cross-sectional data for the measurement of whole brain (WB) atrophy over time. However, gray matter (GM) and white matter (WM) atrophy are now widely recognized as important components of neurological disease progression, and are being actively evaluated as secondary endpoints in clinical trials. Direct measures of GM/WM change with advantages similar to SIENA have been lacking. We created a robust and easily-implemented method for direct longitudinal analysis of GM/WM atrophy, SIENAX multi-time-point (SIENAX-MTP). We built on the basic halfway-registration and mask composition components of SIENA to improve the raw output of FMRIB's FAST tissue segmentation tool. In addition, we created LFAST, a modified version of FAST incorporating a 4th dimension in its hidden Markov random field model in order to directly represent time. The method was validated by scan-rescan, simulation, comparison with SIENA, and two clinical effect size comparisons. All validation approaches demonstrated improved longitudinal precision with the proposed SIENAX-MTP method compared to SIENAX. For GM, simulation showed better correlation with experimental volume changes (r=0.992 vs. 0.941), scan-rescan showed lower standard deviations (3.8% vs. 8.4%), correlation with SIENA was more robust (r=0.70 vs. 0.53), and effect sizes were improved by up to 68%. Statistical power estimates indicated a potential drop of 55% in the number of subjects required to detect the same treatment effect with SIENAX-MTP vs. SIENAX. The proposed direct GM/WM method significantly improves on the standard SIENAX technique by trading a small amount of bias for a large reduction in variance, and may provide more precise data and additional statistical power in longitudinal studies. PMID:24333394

  18. Precise estimation of pressure-temperature paths from zoned minerals using Markov random field modeling: theory and synthetic inversion

    NASA Astrophysics Data System (ADS)

    Kuwatani, Tatsu; Nagata, Kenji; Okada, Masato; Toriumi, Mitsuhiro

    2012-03-01

    The chemical zoning profile in metamorphic minerals is often used to deduce the pressure-temperature ( P- T) history of rock. However, it remains difficult to restore detailed paths from zoned minerals because thermobarometric evaluation of metamorphic conditions involves several uncertainties, including measurement errors and geological noise. We propose a new stochastic framework for estimating precise P- T paths from a chemical zoning structure using the Markov random field (MRF) model, which is a type of Bayesian stochastic method that is often applied to image analysis. The continuity of pressure and temperature during mineral growth is incorporated by Gaussian Markov chains as prior probabilities in order to apply the MRF model to the P- T path inversion. The most probable P- T path can be obtained by maximizing the posterior probability of the sequential set of P and T given the observed compositions of zoned minerals. Synthetic P- T inversion tests were conducted in order to investigate the effectiveness and validity of the proposed model from zoned Mg-Fe-Ca garnet in the divariant KNCFMASH system. In the present study, the steepest descent method was implemented in order to maximize the posterior probability using the Markov chain Monte Carlo algorithm. The proposed method successfully reproduced the detailed shape of the synthetic P- T path by eliminating appropriately the statistical compositional noises without operator's subjectivity and prior knowledge. It was also used to simultaneously evaluate the uncertainty of pressure, temperature, and mineral compositions for all measurement points. The MRF method may have potential to deal with several geological uncertainties, which cause cumbersome systematic errors, by its Bayesian approach and flexible formalism, so that it comprises potentially powerful tools for various inverse problems in petrology.

  19. Methods for testing theory and evaluating impact in randomized field trials: intent-to-treat analyses for integrating the perspectives of person, place, and time.

    PubMed

    Brown, C Hendricks; Wang, Wei; Kellam, Sheppard G; Muthén, Bengt O; Petras, Hanno; Toyinbo, Peter; Poduska, Jeanne; Ialongo, Nicholas; Wyman, Peter A; Chamberlain, Patricia; Sloboda, Zili; MacKinnon, David P; Windham, Amy

    2008-06-01

    Randomized field trials provide unique opportunities to examine the effectiveness of an intervention in real world settings and to test and extend both theory of etiology and theory of intervention. These trials are designed not only to test for overall intervention impact but also to examine how impact varies as a function of individual level characteristics, context, and across time. Examination of such variation in impact requires analytical methods that take into account the trial's multiple nested structure and the evolving changes in outcomes over time. The models that we describe here merge multilevel modeling with growth modeling, allowing for variation in impact to be represented through discrete mixtures--growth mixture models--and nonparametric smooth functions--generalized additive mixed models. These methods are part of an emerging class of multilevel growth mixture models, and we illustrate these with models that examine overall impact and variation in impact. In this paper, we define intent-to-treat analyses in group-randomized multilevel field trials and discuss appropriate ways to identify, examine, and test for variation in impact without inflating the Type I error rate. We describe how to make causal inferences more robust to misspecification of covariates in such analyses and how to summarize and present these interactive intervention effects clearly. Practical strategies for reducing model complexity, checking model fit, and handling missing data are discussed using six randomized field trials to show how these methods may be used across trials randomized at different levels. PMID:18215473

  20. Multiple superhyperfine fields in a {DyFe2Dy} coordination cluster revealed using bulk susceptibility and (57)Fe Mössbauer studies.

    PubMed

    Peng, Yan; Mereacre, Valeriu; Anson, Christopher E; Powell, Annie K

    2016-08-01

    A [DyFeDy(μ3-OH)2(pmide)2(p-Me-PhCO2)6] coordination cluster, where pmideH2 = N-(2-pyridylmethyl)iminodiethanol, has been synthesized and the magnetic properties studied. The dc magnetic measurements reveal dominant antiferromagnetic interactions between the metal centres. The ac measurements reveal zero-field quantum tunnelling of the magnetisation (QTM) which can be understood, but not adequately modelled, in terms of at least three relaxation processes when appropriate static (dc) fields are applied. To investigate this further, (57)Fe Mössbauer spectroscopy was used and well-resolved nuclear hyperfine structures could be observed, showing that on the Mössbauer time scale, without applied field or else with very small applied fields, the iron nuclei experience three or more superhyperfine fields arising from the slow magnetisation reversal of the strongly polarized fields of the Dy(III) ions. PMID:27424877

  1. Time Series Measurements of Diffuse Hydrothermal Flow at the ASHES Vent Field Reveal Tidally Modulated Heat and Volume Flux

    NASA Astrophysics Data System (ADS)

    Mittelstaedt, E. L.; Fornari, D. J.; Crone, T. J.

    2015-12-01

    Existing time-series measurements of temperature and velocity of diffuse hydrothermal fluids exhibit variability over a range of periods from seconds to days. Frequency analysis of these measurements reveals differences between studies and field locations including nearly white spectra, as well as spectra with peaks at tidal and inertial periods. Based upon these results, previous authors have suggested several processes that may control diffuse flow rates, including tidally induced currents and 'tidal pumping', and have also suggested that there are no systematic controls. To further investigate the processes that control variability in diffuse flow, we use data from a new, deep-sea camera and temperature measurement system, the Diffuse Effluent Measurement System (DEMS), deployed during the July, 2014 cruise of the R/V Atlantis. The DEMS was deployed with DSV Alvin above a fracture network at the Phoenix vent within the ASHES vent field (Axial Seamount, 1541 mbsl). The system collected 20 seconds of imagery at 20 Hz and 24 seconds of temperature measurements at 1 Hz each hour over the period between July 22 and August 2nd. Velocities of the upwelling fluids were calculated using Diffuse Fluid Velocimetry (DFV; Mittelstaedt et al., 2010). DFV is a cross correlation technique that tracks moving index of refraction anomalies (i.e., hot parcels of fluid) through time. Over the ~12 day deployment, median flow rates ranged from 0.5 cm/s to 6 cm/s and mean fluid temperature anomalies from 0°C up to ~6.5°C, yielding an average heat flux density of 0.23 MW/m2. Spectral analysis of both the measured temperatures and calculated velocities yield a peak in normalized power at the semi-diurnal lunar period (M2, 12.4hrs), but no other spectral peaks above the 95% confidence level. Here, we present these results and discuss their implications for the tidal current and tidal pressure models of diffuse flow variability at the ASHES vent field.

  2. Cholinergic neurons and terminal fields revealed by immunohistochemistry for the vesicular acetylcholine transporter. II. The peripheral nervous system.

    PubMed

    Schäfer, M K; Eiden, L E; Weihe, E

    1998-05-01

    immunoreactivity was particularly useful for identification of parasympathetic intrinsic ganglia, and their terminal fields, in heart, uterus, and other peripheral organs receiving parasympathetic innervation. Extensive vesicular acetylcholine transporter-positive terminal fields were apparent in both atrial and ventricular tissues of the heart targeting cardiomyocytes as well as cardiac microvessels. Pericardiac brown adipose tissue was also supplied by vesicular acetylcholine transporter-positive varicose fibres. The enteric ganglia of the myenteric and submucous plexus, their synaptic junctions with circular and longitudinal smooth muscle, and terminal fields of the lamina propria of the stomach and intestine and of the local microvasculature were intensely vesicular acetylcholine transporter positive. Vesicular acetylcholine transporter-positive innervation was delivered to the exocrine and endocrine pancreas originating from vesicular acetylcholine transporter-positive intrapancreatic ganglia. Vesicular acetylcholine transporter immunoreactivity in urogenital organs revealed the patterns of terminal cholinergic fields arising from the sacral parasympathetic innervation of these structures. Components of the cholinergic nervous system in the periphery whose existence has been controversial have been confirmed, and the existence of new components of the cholinergic nervous system has been documented, with vesicular acetylcholine transporter immunohistochemistry. Visualization of vesicular acetylcholine transporter will allow documentation of changes in synaptic patency during development, in disease, and during changes in neurotransmission accompanying injury and dystrophy, in the peripheral nervous system. PMID:9539210

  3. Impact of model order and estimation window for indexing TerraSAR-X images using Gauss Markov random fields

    NASA Astrophysics Data System (ADS)

    Espinoza-Molina, Daniela; Datcu, Mihai

    2010-10-01

    TerraSAR-X is the Synthetic Aperture Radar (SAR) German satellite which provides a high diversity of information due to its high-resolution. TerraSAR-X acquires daily a volume of up to 100 GB of high complexity, multi-mode SAR images, i.e. SpotLight, StripMap, and ScanSAR data, with dual or quad-polarization, and with different look angles. The high and multiple resolutions of the instrument (1m, 3m or 10m) open perspectives for new applications, that were not possible with past lower resolution sensors (20-30m). Mainly the 1m and 3m modes we expect to support a broad range of new applications related to human activities with relevant structures and objects at the 1m scale. Thus, among the most interesting scenes are: urban, industrial, and rural data. In addition, the global coverage and the relatively frequent repeat pass will definitely help to acquire extremely relevant data sets. To analyze the available TerrrSAR-X data we rely on model based methods for feature extraction and despeckling. The image information content is extracted using model-based methods based on Gauss Markov Random Field (GMRF) and Bayesian inference approach. This approach enhances the local adaptation by using a prior model, which learns the image structure and enables to estimate the local description of the structures, acting as primitive feature extraction method. However, the GMRF model-based method uses as input parameters the Model Order (MO) and the size of Estimation Window (EW). The appropriated selection of these parameters allows us to improve the classification and indexing results due to the number of well separated classes could be determined by them. Our belief is that the selection of the MO depends on the kind of information that the image contains, explaining how well the model can recognize complex structures as objects, and according to the size of EW the accuracy of the estimation is determined. In the following, we present an evaluation of the impact of the model

  4. Evaluating coastal sea surface heights based on a novel sub-waveform approach using sparse representation and conditional random fields

    NASA Astrophysics Data System (ADS)

    Uebbing, Bernd; Roscher, Ribana; Kusche, Jürgen

    2016-04-01

    Satellite radar altimeters allow global monitoring of mean sea level changes over the last two decades. However, coastal regions are less well observed due to influences on the returned signal energy by land located inside the altimeter footprint. The altimeter emits a radar pulse, which is reflected at the nadir-surface and measures the two-way travel time, as well as the returned energy as a function of time, resulting in a return waveform. Over the open ocean the waveform shape corresponds to a theoretical model which can be used to infer information on range corrections, significant wave height or wind speed. However, in coastal areas the shape of the waveform is significantly influenced by return signals from land, located in the altimeter footprint, leading to peaks which tend to bias the estimated parameters. Recently, several approaches dealing with this problem have been published, including utilizing only parts of the waveform (sub-waveforms), estimating the parameters in two steps or estimating additional peak parameters. We present a new approach in estimating sub-waveforms using conditional random fields (CRF) based on spatio-temporal waveform information. The CRF piece-wise approximates the measured waveforms based on a pre-derived dictionary of theoretical waveforms for various combinations of the geophysical parameters; neighboring range gates are likely to be assigned to the same underlying sub-waveform model. Depending on the choice of hyperparameters in the CRF estimation, the classification into sub-waveforms can either be more fine or coarse resulting in multiple sub-waveform hypotheses. After the sub-waveforms have been detected, existing retracking algorithms can be applied to derive water heights or other desired geophysical parameters from particular sub-waveforms. To identify the optimal heights from the multiple hypotheses, instead of utilizing a known reference height, we apply a Dijkstra-algorithm to find the "shortest path" of all

  5. Micro-digitate Silica Structures on Earth and Mars: Potential Biosignatures Revealed in the Geyser Field of El Tatio, Chile

    NASA Astrophysics Data System (ADS)

    Ruff, S. W.; Farmer, J. D.

    2015-12-01

    Opaline silica outcrops and soil identified by the Spirit rover adjacent to "Home Plate" in Gusev crater are associated with a suite of geologic features that demonstrates that they are the products of a volcanic hydrothermal system, the first such example verified on Mars [1]. Fumarolic acid-sulfate leaching of basaltic precursor materials was suggested as the origin of the opaline silica, based largely on geochemical arguments. A more complete analysis by Ruff et al. [2] included stratigraphic and textural observations of the outcrops to advance the hypothesis of a hot spring and/or geyser-related origin under alkaline-neutral conditions; acid-sulfate leaching appears much less tenable. But the nodular expression of many of the outcrops and sub-cm-scale "digitate protrusions" they contain remained enigmatic, precluding a complete explanation for the silica. Now, new observations of silica deposits produced in small discharge channels from hot springs and geysers in a high elevation geothermal field known as El Tatio in the Atacama Desert of northern Chile reveal remarkably similar features, including infrared spectral characteristics and what we describe here as micro-digitate silica structures. We hypothesize that these structures at El Tatio arise through microbial mediation of silica precipitation, i.e., that they are microstromatolites and that they provide favorable environments for the capture and preservation of microbial biosignatures. Similar features have been identified among hot spring silica deposits in Yellowstone National Park, the Taupo Volcanic Zone of New Zealand, and Iceland [e.g., 3; 4; 5]. Our ongoing field and lab studies are intended provide a robust assessment of the biogenicity of the micro-digitate silica structures and other aspects of El Tatio silica sinter deposits and test their viability as direct analogs to similar features found among the Home Plate silica deposits on Mars. [1] Squyres, S. W., et al. (2008), Science, 320, 1063

  6. Endemism and diversification in freshwater insects of Madagascar revealed by coalescent and phylogenetic analysis of museum and field collections.

    PubMed

    Vuataz, Laurent; Sartori, Michel; Gattolliat, Jean-Luc; Monaghan, Michael T

    2013-03-01

    The biodiversity and endemism of Madagascar are among the most extraordinary and endangered in the world. This includes the island's freshwater biodiversity, although detailed knowledge of the diversity, endemism, and biogeographic origin of freshwater invertebrates is lacking. The aquatic immature stages of mayflies (Ephemeroptera) are widely used as bio-indicators and form an important component of Malagasy freshwater biodiversity. Many species are thought to be microendemics, restricted to single river basins in forested areas, making them particularly sensitive to habitat reduction and degradation. The Heptageniidae are a globally diverse family of mayflies (>500 species) but remain practically unknown in Madagascar except for two species described in 1996. The standard approach to understanding their diversity, endemism, and origin would require extensive field sampling on several continents and years of taxonomic work followed by phylogenetic analysis. Here we circumvent this using museum collections and freshly collected individuals in a combined approach of DNA taxonomy and phylogeny. The coalescent-based GMYC analysis of DNA barcode data (mitochondrial COI) revealed 14 putative species on Madagascar, 70% of which were microendemics. A phylogenetic analysis that included African and Asian species and data from two mitochondrial and four nuclear loci indicated the Malagasy Heptageniidae are monophyletic and sister to African species. The genus Compsoneuria is shown to be paraphyletic and the genus Notonurus is reinstalled for African and Malagasy species previously placed in Compsoneuria. A molecular clock excluded a Gondwanan vicariance origin and instead favoured a more recent overseas colonization of Madagascar. The observed monophyly and high microendemism highlight their conservation importance and suggest the DNA-based approach can rapidly provide information on the diversity, endemism, and origin of freshwater biodiversity. Our results underline the

  7. Yeast Three-Hybrid Screening of Rous Sarcoma Virus Mutants with Randomly Mutagenized Minimal Packaging Signals Reveals Regions Important for Gag Interactions

    PubMed Central

    Lee, Eun-Gyung; Linial, Maxine L.

    2000-01-01

    We previously showed that the yeast three-hybrid system provides a genetic assay of both RNA and protein components for avian retroviral RNA encapsidation. In the current study, we used this assay to precisely define cis-acting determinants involved in avian leukosis sarcoma virus packaging RNA binding to Gag protein. In vivo screening of Rous sarcoma virus mutants was performed with randomly mutated minimal packaging sequences (MΨ) made using PCR amplification after cotransformation with GagΔPR protein into yeast cells. Colonies with low β-galactosidase activity were analyzed to locate mutations in MΨ sequences affecting binding to Gag proteins. This genetic assay delineated secondary structural elements that are important for efficient RNA binding, including a single-stranded small bulge containing the initiation codon for uORF3, as well as adjacent stem structures. This implies a possible tertiary structure favoring the high-affinity binding sites for Gag. In most cases, results from the three-hybrid assay were well correlated with those from the viral RNA packaging assays. The results from random mutagenesis using the rapid three-hybrid binding assay are consistent with those from site-directed mutagenesis using in vivo packaging assays. PMID:10982363

  8. Hidden local symmetry of Eu{sup 3+} in xenotime-like crystals revealed by high magnetic fields

    SciTech Connect

    Han, Yibo; Ma, Zongwei; Zhang, Junpei; Wang, Junfeng; Du, Guihuan; Xia, Zhengcai; Han, Junbo Li, Liang; Yu, Xuefeng

    2015-02-07

    The excellent optical properties of europium-doped crystals in visible and near infrared wavelength regions enable them to have broad applications in optoelectronics, laser crystals and sensing devices. The local site crystal fields can affect the intensities and peak positions of the photo-emission lines strongly, but they are usually difficult to be clarified due to magnetically degenerate 4f electronic levels coupling with the crystal fields. Here, we provide an effective way to explore the hidden local symmetry of the Eu{sup 3+} sites in different hosts by taking photoluminescence measurements under pulsed high magnetic fields up to 46 T. The zero-field photoluminescence peaks split further at high magnetic fields when the Zeeman splitting energy is comparable to or larger than that of the crystal field induced zero-field splitting. In particular, a magnetic field induced crossover of the local crystal fields has been observed in the GdVO{sub 4}:Eu{sup 3+} crystal, which resulted from the alignment of Gd{sup 3+} magnetic moment in high magnetic fields; and a hexagonally symmetric local crystal fields was observed in the YPO{sub 4} nanocrystals at the Eu{sup 3+} sites characterized by the special axial and rhombic crystal field terms. These distinct Zeeman splitting behaviors uncover the crystal fields-related local symmetry of luminescent Eu{sup 3+} centers in different hosts or magnetic environments, which are significant for their applications in optics and optoelectronics.

  9. Enhancing superconducting critical current by randomness

    NASA Astrophysics Data System (ADS)

    Wang, Y. L.; Thoutam, L. R.; Xiao, Z. L.; Shen, B.; Pearson, J. E.; Divan, R.; Ocola, L. E.; Crabtree, G. W.; Kwok, W. K.

    2016-01-01

    The key ingredient of high critical currents in a type-II superconductor is defect sites that pin vortices. Contrary to earlier understanding on nanopatterned artificial pinning, here we show unequivocally the advantages of a random pinscape over an ordered array in a wide magnetic field range. We reveal that the better performance of a random pinscape is due to the variation of its local density of pinning sites (LDOPS), which mitigates the motion of vortices. This is confirmed by achieving even higher enhancement of the critical current through a conformally mapped random pinscape, where the distribution of the LDOPS is further enlarged. The demonstrated key role of LDOPS in enhancing superconducting critical currents gets at the heart of random versus commensurate pinning. Our findings highlight the importance of random pinscapes in enhancing the superconducting critical currents of applied superconductors.

  10. The influence of the directional energy distribution on the nonlinear dispersion relation in a random gravity wave field

    NASA Technical Reports Server (NTRS)

    Huang, N. E.; Tung, C.-C.

    1977-01-01

    The influence of the directional distribution of wave energy on the dispersion relation is calculated numerically using various directional wave spectrum models. The results indicate that the dispersion relation varies both as a function of the directional energy distribution and the direction of propagation of the wave component under consideration. Furthermore, both the mean deviation and the random scatter from the linear approximation increase as the energy spreading decreases. Limited observational data are compared with the theoretical results. The agreement is favorable.

  11. Radio polarization maps of shell-type supernova remnants - I. Effects of a random magnetic field component and thin-shell models

    NASA Astrophysics Data System (ADS)

    Bandiera, R.; Petruk, O.

    2016-06-01

    The maps of intensity and polarization of the radio synchrotron emission from shell-type supernova remnants (SNRs) contain a considerable amount of information, although of not easy interpretation. With the aim of deriving constraints on the 3D spatial distribution of the emissivity, as well as on the structure of both ordered and random magnetic fields (MFs), we present here a scheme to model maps of the emission and polarization in SNRs. We first generalize the classical treatment of the synchrotron emission to the case in which the MF is composed of an ordered MF plus an isotropic random component, with arbitrary relative strengths. For a power-law particle energy distribution, we derive analytic formulae that formally resemble those for the classical case. We also treat the shock compression of a fully random upstream field and we predict that the polarization fraction in this case should be higher than typically measured in SNRs. We implement the above treatment into a code, which simulates the observed polarized emission of an emitting shell, taking into account also the effect of the internal Faraday rotation. Finally, we show simulated maps for different orientations with respect to the observer, levels of the turbulent MF component, Faraday rotation levels, distributions of the emissivity (either barrel-shaped or limited to polar caps) and geometries for the ordered MF component (either tangential to the shell or radial). Their analysis allows us to outline properties useful for the interpretation of radio intensity and polarization maps.

  12. Improvement of Triglyceride Levels through the Intake of Enriched-β-Conglycinin Soybean (Nanahomare) Revealed in a Randomized, Double-Blind, Placebo-Controlled Study.

    PubMed

    Nishimura, Mie; Ohkawara, Tatsuya; Sato, Yuji; Satoh, Hiroki; Takahashi, Yoko; Hajika, Makita; Nishihira, Jun

    2016-01-01

    Soybean is recognized as a beneficial food with various functional components, such as β-conglycinin, which improves lipid metabolism. We evaluated the effects of the β-conglycinin-rich soybean Nanahomare on triglyceride (TG) levels. In this randomized, double-blind, placebo-controlled study, we divided 134 adult subjects into test and placebo groups that consumed processed food containing enriched-β-conglycinin soybean or low-β-conglycinin soybean. Hematological tests and body composition measurements were performed at weeks 0 (baseline), 4, 8, and 12 of the study period. TG levels significantly decreased in the test group compared with the placebo group at weeks 4 (change from baseline to week 4, placebo: 0.27 ± 44.13 mg/dL, test: -20.31 ± 43.74 mg/dL, p = 0.035) and 12 (change from baseline to week 12, placebo: -0.14 ± 65.83 mg/dL, test: -21.30 ± 46.21 mg/dL, p = 0.041). In addition, among subjects whose baseline TG levels were ≥100 mg/dL, the levels significantly improved in the test group at weeks 4 (p = 0.010) and 12 (p = 0.030), whereas the levels were not different between the test and placebo groups among those whose baseline levels were <100 mg/dL. These results suggest that the ingestion of enriched-β-conglycinin soybean improves serum TG levels. PMID:27529274

  13. Deep Sequencing of Random Mutant Libraries Reveals the Active Site of the Narrow Specificity CphA Metallo-β-Lactamase is Fragile to Mutations.

    PubMed

    Sun, Zhizeng; Mehta, Shrenik C; Adamski, Carolyn J; Gibbs, Richard A; Palzkill, Timothy

    2016-01-01

    CphA is a Zn(2+)-dependent metallo-β-lactamase that efficiently hydrolyzes only carbapenem antibiotics. To understand the sequence requirements for CphA function, single codon random mutant libraries were constructed for residues in and near the active site and mutants were selected for E. coli growth on increasing concentrations of imipenem, a carbapenem antibiotic. At high concentrations of imipenem that select for phenotypically wild-type mutants, the active-site residues exhibit stringent sequence requirements in that nearly all residues in positions that contact zinc, the substrate, or the catalytic water do not tolerate amino acid substitutions. In addition, at high imipenem concentrations a number of residues that do not directly contact zinc or substrate are also essential and do not tolerate substitutions. Biochemical analysis confirmed that amino acid substitutions at essential positions decreased the stability or catalytic activity of the CphA enzyme. Therefore, the CphA active - site is fragile to substitutions, suggesting active-site residues are optimized for imipenem hydrolysis. These results also suggest that resistance to inhibitors targeted to the CphA active site would be slow to develop because of the strong sequence constraints on function. PMID:27616327

  14. MAGNETIC FIELDS IN LARGE-DIAMETER H II REGIONS REVEALED BY THE FARADAY ROTATION OF COMPACT EXTRAGALACTIC RADIO SOURCES

    SciTech Connect

    Harvey-Smith, L.; Madsen, G. J.; Gaensler, B. M.

    2011-08-01

    We present a study of the line-of-sight magnetic fields in five large-diameter Galactic H II regions. Using the Faraday rotation of background polarized radio sources, as well as dust-corrected H{alpha} surface brightness as a probe of electron density, we estimated the strength and orientation of the magnetic field along 93 individual sight lines through the H II regions. Each of the H II regions displayed a coherent magnetic field. The magnetic field strength (line-of-sight component) in the regions ranges from 2 to 6 {mu}G, which is similar to the typical magnetic field strength in the diffuse interstellar medium. We investigated the relationship between magnetic field strength and electron density in the five H II regions. The slope of magnetic field versus density in the low-density regime (0.8 cm{sup -3} < n{sub e} <30 cm{sup -3}) is very slightly above zero. We also calculated the ratio of thermal to magnetic pressure, {beta}{sub th}, for each data point, which fell in the range 1.01 < {beta}{sub th} < 25. Finally, we studied the orientation of the magnetic field in the solar neighborhood (d < 1.1 kpc) using our data from five H II regions along with existing measurements of the line-of-sight magnetic field strength from polarized pulsars whose distances have been determined from their annual parallax. We identify a net direction for the magnetic field in the solar neighborhood, but find no evidence for a preferred vertical direction of the magnetic field above or below the Galactic plane.

  15. Improvement of Triglyceride Levels through the Intake of Enriched-β-Conglycinin Soybean (Nanahomare) Revealed in a Randomized, Double-Blind, Placebo-Controlled Study

    PubMed Central

    Nishimura, Mie; Ohkawara, Tatsuya; Sato, Yuji; Satoh, Hiroki; Takahashi, Yoko; Hajika, Makita; Nishihira, Jun

    2016-01-01

    Soybean is recognized as a beneficial food with various functional components, such as β-conglycinin, which improves lipid metabolism. We evaluated the effects of the β-conglycinin-rich soybean Nanahomare on triglyceride (TG) levels. In this randomized, double-blind, placebo-controlled study, we divided 134 adult subjects into test and placebo groups that consumed processed food containing enriched-β-conglycinin soybean or low-β-conglycinin soybean. Hematological tests and body composition measurements were performed at weeks 0 (baseline), 4, 8, and 12 of the study period. TG levels significantly decreased in the test group compared with the placebo group at weeks 4 (change from baseline to week 4, placebo: 0.27 ± 44.13 mg/dL, test: −20.31 ± 43.74 mg/dL, p = 0.035) and 12 (change from baseline to week 12, placebo: −0.14 ± 65.83 mg/dL, test: −21.30 ± 46.21 mg/dL, p = 0.041). In addition, among subjects whose baseline TG levels were ≥100 mg/dL, the levels significantly improved in the test group at weeks 4 (p = 0.010) and 12 (p = 0.030), whereas the levels were not different between the test and placebo groups among those whose baseline levels were <100 mg/dL. These results suggest that the ingestion of enriched-β-conglycinin soybean improves serum TG levels. PMID:27529274

  16. LD-Aminopterin in the Canine Homologue of Human Atopic Dermatitis: A Randomized, Controlled Trial Reveals Dosing Factors Affecting Optimal Therapy

    PubMed Central

    Zebala, John A.; Mundell, Alan; Messinger, Linda; Griffin, Craig E.; Schuler, Aaron D.; Kahn, Stuart J.

    2014-01-01

    Background Options are limited for patients with atopic dermatitis (AD) who do not respond to topical treatments. Antifolate therapy with systemic methotrexate improves the disease, but is associated with adverse effects. The investigational antifolate LD-aminopterin may offer improved safety. It is not known how antifolate dose and dosing frequency affect efficacy in AD, but a primary mechanism is thought to involve the antifolate-mediated accumulation of 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR). However, recent in vitro studies indicate that AICAR increases then decreases as a function of antifolate concentration. To address this issue and understand how dosing affects antifolate efficacy in AD, we examined the efficacy and safety of different oral doses and schedules of LD-aminopterin in the canine model of AD. Methods and Findings This was a multi-center, double-blind trial involving 75 subjects with canine AD randomized to receive up to 12 weeks of placebo, once-weekly (0.007, 0.014, 0.021 mg/kg) or twice-weekly (0.007 mg/kg) LD-aminopterin. The primary efficacy outcome was the Global Score (GS), a composite of validated measures of disease severity and itch. GS improved in all once-weekly cohorts, with 0.014 mg/kg being optimal and significant (43%, P<0.01). The majority of improvement was seen by 8 weeks. In contrast, GS in the twice-weekly cohort was similar to placebo and worse than all once-weekly cohorts. Adverse events were similar across all treated cohorts and placebo. Conclusions Once-weekly LD-aminopterin was safe and efficacious in canine AD. Twice-weekly dosing negated efficacy despite having the same daily and weekly dose as effective once-weekly regimens. Optimal dosing in this homologue of human AD correlated with the concentration-selective accumulation of AICAR in vitro, consistent with AICAR mediating LD-aminopterin efficacy in AD. PMID:25255447

  17. Magnetism and the atmosphere of Mars --- How polarimetric microwave observations may reveal magnetic properties of the southern crustal field

    NASA Astrophysics Data System (ADS)

    Larsson, R.; Ramstad, R.; Mendrok, J.; Buehler, S. A.; Kasai, Y.

    2013-12-01

    The southern crustal magnetic field of Mars has been mapped by satellite-borne magnetometers at 400 and 100 km above the surface. Between these heights, the magnetic field strength increases from around 100 nT to about 1000 nT in peak strength. The strong increase in field strength over a short distance indicates a surface source much stronger. Predictions by models put the surface magnetism at around 15,000 to 20,000 nT at its strongest. The close surface field strength has not been measured directly as no landers with magnetometers have reached the southern crust. Even if a landing was to take place and the near surface field could be mapped directly, a magnetometer will only gauge the magnetism locally so a moving platform is required to determine the overall field. A better map of the magnetic field of Mars would help support a multitude of efforts. The atmospheric escape rate, and therefore the evolution of atmospheric constituents, is coupled to the fields because it forces ionized particles to accelerate. The long-term evolution the crust can be better understood from the remaining magnetic field --- when and how did the global field disappear, and what was the cause? Answers to both questions strongly depend on the field today. In spirit of exploration, it has been suggested that the crustal fields can act as a protective dome for potential explorers; protecting the visitors against some of the charged cosmic particles that could otherwise be harmful to them. Our work suggests that a highly resolving spectropolarimeter in the microwave region observing an oxygen line on-board a satellite looking at the limb of Mars should be able to detect the magnetic field due to the polarized propagation caused by the Zeeman effect. The magnetic field of Mars is weak so the observation would not be of fully split lines. Instead, each perturbed line will contribute to a common polarized residual around the Doppler width of the central line. We present simulations from the

  18. Village sanitation and child health: Effects and external validity in a randomized field experiment in rural India.

    PubMed

    Hammer, Jeffrey; Spears, Dean

    2016-07-01

    Over a billion people worldwide defecate in the open, with important consequences for early-life health and human capital accumulation in developing countries. We report a cluster randomized controlled trial of a village sanitation intervention conducted in rural Maharashtra, India designed to identify an effect of village sanitation on average child height, an outcome of increasing importance to economists. We find an effect of approximately 0.3 height-for-age standard deviations, which is consistent with observations and hypotheses in economic and health literatures. We further exploit details of the planning and implementation of the experiment to study treatment heterogeneity and external validity. PMID:27179199

  19. Randomized, Double-Blind Clinical Trial to Assess the Acute Diuretic Effect of Equisetum arvense (Field Horsetail) in Healthy Volunteers.

    PubMed

    Carneiro, Danilo Maciel; Freire, Ramias Calixto; Honório, Tereza Cristina de Deus; Zoghaib, Iury; Cardoso, Fabiana Fernandes de S E Silva; Tresvenzol, Leonice Manrique F; de Paula, José Realino; Sousa, Ana Luiza Lima; Jardim, Paulo César Brandão Veiga; da Cunha, Luiz Carlos

    2014-01-01

    In this double-blind, randomized clinical trial, 36 healthy male volunteers were randomly distributed into three groups (n = 12) that underwent a three-step treatment. For four consecutive days, we alternately administered a standardized dried extract of Equisetum arvense (EADE, 900 mg/day), placebo (corn starch, 900 mg/day), or hydrochlorothiazide (25 mg/day), separated by a 10-day washout period. Each volunteer served as his own control, and the groups' results were compared. We repeated the same evaluation after each stage of treatment to evaluate the safety of the drug. The diuretic effect of EADE was assessed by monitoring the volunteers' water balance over a 24 h period. The E. arvense extract produced a diuretic effect that was stronger than that of the negative control and was equivalent to that of hydrochlorothiazide without causing significant changes in the elimination of electrolytes. There was no significant increase in the urinary elimination of catabolites. Rare minor adverse events were reported. The clinical examinations and laboratory tests showed no changes before or after the experiment, suggesting that the drug is safe for acute use. Further research is needed to better clarify the mechanism of diuretic action and the other possible pharmacological actions of this phytomedicine. PMID:24723963

  20. Device modeling of ferroelectric memory field-effect transistor for the application of ferroelectric random access memory.

    PubMed

    Lue, Hang-Ting; Wu, Chien-Jang; Tseng, Tseung-Yuen

    2003-01-01

    An improved theoretical analysis on the electrical characteristics of ferroelectric memory field-effect transistor (FeMFET) is given. First, we propose a new analytical expression for the polarization versus electric field (P-E) for the ferroelectric material. It is determined by one parameter and explicitly includes both the saturated and nonsaturated hysteresis loops. Using this expression, we then examine the operational properties for two practical devices such as the metal-ferroelectric-insulator-semiconductor field-effect transistor (MFIS-FET) and metal-ferroelectric-metal-insulator-semiconductor field-effect transistor (MFMIS-FET) as well. A double integral also has been used, in order to include the possible effects due to the nonuniform field and charge distribution along the channel of the device, to calculate the drain current of FeMFET. By using the relevant material parameters close to the (Bi, La)4Ti3O12 (BLT) system, accurate analyses on the capacitors and FeMFET's at various applied biases are made. We also address the issues of depolarization field and retention time about such a device. PMID:12578132

  1. High-Throughput miRNA Sequencing Reveals a Field Effect in Gastric Cancer and Suggests an Epigenetic Network Mechanism

    PubMed Central

    Assumpção, Monica B; Moreira, Fabiano C; Hamoy, Igor G; Magalhães, Leandro; Vidal, Amanda; Pereira, Adenilson; Burbano, Rommel; Khayat, André; Silva, Artur; Santos, Sidney; Demachki, Samia; Ribeiro-dos-Santos, Ândrea; Assumpção, Paulo

    2015-01-01

    Field effect in cancer, also called “field cancerization”, attempts to explain the development of multiple primary tumors and locally recurrent cancer. The concept of field effect in cancer has been reinforced, since molecular alterations were found in tumor-adjacent tissues with normal histopatho-logical appearances. With the aim of investigating field effects in gastric cancer (GC), we conducted a high-throughput sequencing of the miRnome of four GC samples and their respective tumor-adjacent tissues and compared them with the miRnome of a gastric antrum sample from patients without GC, assuming that tumor-adjacent tissues could not be considered as normal tissues. The global number of miRNAs and read counts was highest in tumor samples, followed by tumor-adjacent and normal samples. Analyzing the miRNA expression profile of tumor-adjacent miRNA, hsa-miR-3131, hsa-miR-664, hsa-miR-483, and hsa-miR-150 were significantly downregulated compared with the antrum without tumor tissue (P-value < 0.01; fold-change <5). Additionally, hsa-miR-3131, hsa-miR-664, and hsa-miR-150 were downregulated (P-value < 0.001) in all paired samples of tumor and tumor-adjacent tissues, compared with antrum without tumor mucosa. The field effect was clearly demonstrated in gastric carcinogenesis by an epigenetics-based approach, and potential biomarkers of the GC field effect were identified. The elevated expression of miRNAs in adjacent tissues and tumors tissues may indicate that a cascade of events takes place during gastric carcinogenesis, reinforcing the notion of field effects. This phenomenon seems to be linked to DNA methylation patterns in cancer and suggests the involvement of an epigenetic network mechanism. PMID:26244015

  2. High-Throughput miRNA Sequencing Reveals a Field Effect in Gastric Cancer and Suggests an Epigenetic Network Mechanism.

    PubMed

    Assumpção, Monica B; Moreira, Fabiano C; Hamoy, Igor G; Magalhães, Leandro; Vidal, Amanda; Pereira, Adenilson; Burbano, Rommel; Khayat, André; Silva, Artur; Santos, Sidney; Demachki, Samia; Ribeiro-Dos-Santos, Ândrea; Assumpção, Paulo

    2015-01-01

    Field effect in cancer, also called "field cancerization", attempts to explain the development of multiple primary tumors and locally recurrent cancer. The concept of field effect in cancer has been reinforced, since molecular alterations were found in tumor-adjacent tissues with normal histopatho-logical appearances. With the aim of investigating field effects in gastric cancer (GC), we conducted a high-throughput sequencing of the miRnome of four GC samples and their respective tumor-adjacent tissues and compared them with the miRnome of a gastric antrum sample from patients without GC, assuming that tumor-adjacent tissues could not be considered as normal tissues. The global number of miRNAs and read counts was highest in tumor samples, followed by tumor-adjacent and normal samples. Analyzing the miRNA expression profile of tumor-adjacent miRNA, hsa-miR-3131, hsa-miR-664, hsa-miR-483, and hsa-miR-150 were significantly downregulated compared with the antrum without tumor tissue (P-value < 0.01; fold-change <5). Additionally, hsa-miR-3131, hsa-miR-664, and hsa-miR-150 were downregulated (P-value < 0.001) in all paired samples of tumor and tumor-adjacent tissues, compared with antrum without tumor mucosa. The field effect was clearly demonstrated in gastric carcinogenesis by an epigenetics-based approach, and potential biomarkers of the GC field effect were identified. The elevated expression of miRNAs in adjacent tissues and tumors tissues may indicate that a cascade of events takes place during gastric carcinogenesis, reinforcing the notion of field effects. This phenomenon seems to be linked to DNA methylation patterns in cancer and suggests the involvement of an epigenetic network mechanism. PMID:26244015

  3. Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity

    PubMed Central

    Schwartz, Allison R.; Potnis, Neha; Timilsina, Sujan; Wilson, Mark; Patané, José; Martins, Joaquim; Minsavage, Gerald V.; Dahlbeck, Douglas; Akhunova, Alina; Almeida, Nalvo; Vallad, Gary E.; Barak, Jeri D.; White, Frank F.; Miller, Sally A.; Ritchie, David; Goss, Erica; Bart, Rebecca S.; Setubal, João C.; Jones, Jeffrey B.; Staskawicz, Brian J.

    2015-01-01

    Bacterial spot disease of pepper and tomato is caused by four distinct Xanthomonas species and is a severely limiting factor on fruit yield in these crops. The genetic diversity and the type III effector repertoires of a large sampling of field strains for this disease have yet to be explored on a genomic scale, limiting our understanding of pathogen evolution in an agricultural setting. Genomes of 67 Xanthomonas euvesicatoria (Xe), Xanthomonas perforans (Xp), and Xanthomonas gardneri (Xg) strains isolated from diseased pepper and tomato fields in the southeastern and midwestern United States were sequenced in order to determine the genetic diversity in field strains. Type III effector repertoires were computationally predicted for each strain, and multiple methods of constructing phylogenies were employed to understand better the genetic relationship of strains in the collection. A division in the Xp population was detected based on core genome phylogeny, supporting a model whereby the host-range expansion of Xp field strains on pepper is due, in part, to a loss of the effector AvrBsT. Xp-host compatibility was further studied with the observation that a double deletion of AvrBsT and XopQ allows a host range expansion for Nicotiana benthamiana. Extensive sampling of field strains and an improved understanding of effector content will aid in efforts to design disease resistance strategies targeted against highly conserved core effectors. PMID:26089818

  4. Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity.

    PubMed

    Schwartz, Allison R; Potnis, Neha; Timilsina, Sujan; Wilson, Mark; Patané, José; Martins, Joaquim; Minsavage, Gerald V; Dahlbeck, Douglas; Akhunova, Alina; Almeida, Nalvo; Vallad, Gary E; Barak, Jeri D; White, Frank F; Miller, Sally A; Ritchie, David; Goss, Erica; Bart, Rebecca S; Setubal, João C; Jones, Jeffrey B; Staskawicz, Brian J

    2015-01-01

    Bacterial spot disease of pepper and tomato is caused by four distinct Xanthomonas species and is a severely limiting factor on fruit yield in these crops. The genetic diversity and the type III effector repertoires of a large sampling of field strains for this disease have yet to be explored on a genomic scale, limiting our understanding of pathogen evolution in an agricultural setting. Genomes of 67 Xanthomonas euvesicatoria (Xe), Xanthomonas perforans (Xp), and Xanthomonas gardneri (Xg) strains isolated from diseased pepper and tomato fields in the southeastern and midwestern United States were sequenced in order to determine the genetic diversity in field strains. Type III effector repertoires were computationally predicted for each strain, and multiple methods of constructing phylogenies were employed to understand better the genetic relationship of strains in the collection. A division in the Xp population was detected based on core genome phylogeny, supporting a model whereby the host-range expansion of Xp field strains on pepper is due, in part, to a loss of the effector AvrBsT. Xp-host compatibility was further studied with the observation that a double deletion of AvrBsT and XopQ allows a host range expansion for Nicotiana benthamiana. Extensive sampling of field strains and an improved understanding of effector content will aid in efforts to design disease resistance strategies targeted against highly conserved core effectors. PMID:26089818

  5. Influence of the aspect ratio and boundary conditions on universal finite-size scaling functions in the athermal metastable two-dimensional random field Ising model.

    PubMed

    Navas-Portella, Víctor; Vives, Eduard

    2016-02-01

    This work studies universal finite size scaling functions for the number of one-dimensional spanning avalanches in a two-dimensional (2D) disordered system with boundary conditions of different nature and different aspect ratios. To this end, we will consider the 2D random field Ising model at T=0 driven by the external field H with athermal dynamics implemented with periodic and forced boundary conditions. We have chosen a convenient scaling variable z that accounts for the deformation of the distance to the critical point caused by the aspect ratio. In addition, assuming that the dependence of the finite size scaling functions on the aspect ratio can be accounted for by an additional multiplicative factor, we have been able to collapse data for different system sizes, different aspect ratios, and different types of the boundary conditions into a single scaling function Q̂. PMID:26986310

  6. Comparison of Haemophilus parasuis reference strains and field isolates by using random amplified polymorphic DNA and protein profiles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Haemophilus parasuis is the causative agent of Glässer’s disease and is a pathogen of swine in high-health status herds. Reports on serotyping of field strains from outbreaks describe that approximately 30% of them are nontypable and therefore cannot be traced. Molecular typing methods have been use...

  7. Lessons Learned from the Use of Randomized and Quasi-Experimental Field Designs for the Evaluation of Educational Programs

    ERIC Educational Resources Information Center

    Rudd, Andy; Johnson, R. Burke

    2008-01-01

    As a result of the federal No Child Left Behind Act (NCLB) of 2002, the field of education has seen a heavy emphasis on the use of "scientifically based research" for designing and testing the effectiveness of new and existing educational programs. According to NCLB, when addressing basic cause and effect questions scientifically based research…

  8. A Combined Motivation and Parent-Child Interaction Therapy Package Reduces Child Welfare Recidivism in a Randomized Dismantling Field Trial

    ERIC Educational Resources Information Center

    Chaffin, Mark; Funderburk, Beverly; Bard, David; Valle, Linda Anne; Gurwitch, Robin

    2011-01-01

    Objective: A package of parent-child interaction therapy (PCIT) combined with a self-motivational (SM) orientation previously was found in a laboratory trial to reduce child abuse recidivism compared with services as usual (SAU). Objectives of the present study were to test effectiveness in a field agency rather than in a laboratory setting and to…

  9. Small RNA deep sequencing revealed that mixed infection of known and unknown viruses were common in field collected vegetable samples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In an effort to characterize the causal agents for plant diseases in field collected samples using the small RNA deep sequencing technology, numerous known or novel viruses and viroids were identified. In many cases, a mixed infection with multiple pathogen species was common. Such situation compl...

  10. Quantum random number generation

    SciTech Connect

    Ma, Xiongfeng; Yuan, Xiao; Cao, Zhu; Zhang, Zhen; Qi, Bing

    2016-01-01

    Here, quantum physics can be exploited to generate true random numbers, which play important roles in many applications, especially in cryptography. Genuine randomness from the measurement of a quantum system reveals the inherent nature of quantumness — coherence, an important feature that differentiates quantum mechanics from classical physics. The generation of genuine randomness is generally considered impossible with only classical means. Based on the degree of trustworthiness on devices, quantum random number generators (QRNGs) can be grouped into three categories. The first category, practical QRNG, is built on fully trusted and calibrated devices and typically can generate randomness at a high speed by properly modeling the devices. The second category is self-testing QRNG, where verifiable randomness can be generated without trusting the actual implementation. The third category, semi-self-testing QRNG, is an intermediate category which provides a tradeoff between the trustworthiness on the device and the random number generation speed.

  11. Quantum random number generation

    DOE PAGESBeta

    Ma, Xiongfeng; Yuan, Xiao; Cao, Zhu; Zhang, Zhen; Qi, Bing

    2016-06-28

    Here, quantum physics can be exploited to generate true random numbers, which play important roles in many applications, especially in cryptography. Genuine randomness from the measurement of a quantum system reveals the inherent nature of quantumness -- coherence, an important feature that differentiates quantum mechanics from classical physics. The generation of genuine randomness is generally considered impossible with only classical means. Based on the degree of trustworthiness on devices, quantum random number generators (QRNGs) can be grouped into three categories. The first category, practical QRNG, is built on fully trusted and calibrated devices and typically can generate randomness at amore » high speed by properly modeling the devices. The second category is self-testing QRNG, where verifiable randomness can be generated without trusting the actual implementation. The third category, semi-self-testing QRNG, is an intermediate category which provides a tradeoff between the trustworthiness on the device and the random number generation speed.« less

  12. A cluster randomized control field trial of the ABRACADABRA web-based reading technology: replication and extension of basic findings

    PubMed Central

    Piquette, Noella A.; Savage, Robert S.; Abrami, Philip C.

    2014-01-01

    The present paper reports a cluster randomized control trial evaluation of teaching using ABRACADABRA (ABRA), an evidence-based and web-based literacy intervention (http://abralite.concordia.ca) with 107 kindergarten and 96 grade 1 children in 24 classes (12 intervention 12 control classes) from all 12 elementary schools in one school district in Canada. Children in the intervention condition received 10–12 h of whole class instruction using ABRA between pre- and post-test. Hierarchical linear modeling of post-test results showed significant gains in letter-sound knowledge for intervention classrooms over control classrooms. In addition, medium effect sizes were evident for three of five outcome measures favoring the intervention: letter-sound knowledge (d= +0.66), phonological blending (d = +0.52), and word reading (d = +0.52), over effect sizes for regular teaching. It is concluded that regular teaching with ABRA technology adds significantly to literacy in the early elementary years. PMID:25538663

  13. A cluster randomized control field trial of the ABRACADABRA web-based reading technology: replication and extension of basic findings.

    PubMed

    Piquette, Noella A; Savage, Robert S; Abrami, Philip C

    2014-01-01

    The present paper reports a cluster randomized control trial evaluation of teaching using ABRACADABRA (ABRA), an evidence-based and web-based literacy intervention (http://abralite.concordia.ca) with 107 kindergarten and 96 grade 1 children in 24 classes (12 intervention 12 control classes) from all 12 elementary schools in one school district in Canada. Children in the intervention condition received 10-12 h of whole class instruction using ABRA between pre- and post-test. Hierarchical linear modeling of post-test results showed significant gains in letter-sound knowledge for intervention classrooms over control classrooms. In addition, medium effect sizes were evident for three of five outcome measures favoring the intervention: letter-sound knowledge (d= +0.66), phonological blending (d = +0.52), and word reading (d = +0.52), over effect sizes for regular teaching. It is concluded that regular teaching with ABRA technology adds significantly to literacy in the early elementary years. PMID:25538663

  14. Mercury’s gravity field, tidal Love number k2, and spin axis orientation revealed with MESSENGER radio tracking data

    NASA Astrophysics Data System (ADS)

    Verma, Ashok Kumar; Margot, Jean-Luc

    2015-11-01

    We are conducting an independent analysis of two-way Doppler and two-way range radio tracking data from the MESSENGER spacecraft in orbit around Mercury from 2011 to 2015. Our goals are to estimate Mercury’s gravity field and to obtain independent estimates of the tidal Love number k2 and spin axis orientation. Our gravity field solution reproduces existing values with high fidelity, and prospects for recovery of the other quantities are excellent.The tidal Love number k2 provides powerful constraints on interior models of Mercury, including the mechanical properties of the mantle and the possibility of a solid FeS layer at the top of the core. Current gravity analyses cannot rule out a wide range of values (k2=43-0.50) and a variety of plausible interior models. We are seeking an independent estimate of tidal Love number k2 with improved errors to further constrain these models.Existing gravity-based solutions for Mercury's spin axis orientation differ from those of Earth-based radar and topography-based solutions. This difference may indicate an error in one of the determinations, or a real difference between the orientations about which the gravity field and the crust rotate, which can exist in a variety of plausible configuration. Securing an independent estimate of the spin axis orientation is vital because this quantity has a profound impact on the determination of the moment of inertia and interior models.We have derived a spherical harmonic solution of the gravity field to degree and order 40 as well as estimates of the tidal Love number k2 and spin axis orientation

  15. Intermittent criticality revealed in ULF magnetic fields prior to the 11 March 2011 Tohoku earthquake (MW = 9)

    NASA Astrophysics Data System (ADS)

    Contoyiannis, Y.; Potirakis, S. M.; Eftaxias, K.; Hayakawa, M.; Schekotov, A.

    2016-06-01

    The ultra-low-frequency (ULF) magnetic variations recorded prior to the 11 March 2011 Tohoku earthquake (EQ) are analyzed using the method of critical fluctuations (MCF). The first application of this specific method to ULF magnetic variations is performed on the unprocessed H- (horizontal) and Z- (vertical) components, as well as on the unprocessed total intensity, F, of the recorded magnetic field. The motivation for the present study was given by recent research results reporting criticality features in the ULF magnetic fields prior to the 2011 Tohoku EQ. These results call for a further analysis in order to verify the existence of criticality embedded in the specific ULF recordings using an independent method, as well as to investigate the type of the embedded criticality. The application of MCF indeed verifies the existence of criticality in the ULF magnetic fields a few days to one week before the occurrence of the main shock. Specifically, clear signatures of intermittent criticality are found in the recordings of 4 March 2011, while indications of critical behavior are also found in 3 and 6 March recordings, although not of the "stability" of those of 4 March. Moreover, it is found that only the ULF data of the nearest, to the epicenter of the EQ, geomagnetic observatory presented criticality. This finding further corroborates the view that the presented signal is indeed a precursor to the specific EQ.

  16. How random is a random vector?

    NASA Astrophysics Data System (ADS)

    Eliazar, Iddo

    2015-12-01

    Over 80 years ago Samuel Wilks proposed that the "generalized variance" of a random vector is the determinant of its covariance matrix. To date, the notion and use of the generalized variance is confined only to very specific niches in statistics. In this paper we establish that the "Wilks standard deviation" -the square root of the generalized variance-is indeed the standard deviation of a random vector. We further establish that the "uncorrelation index" -a derivative of the Wilks standard deviation-is a measure of the overall correlation between the components of a random vector. Both the Wilks standard deviation and the uncorrelation index are, respectively, special cases of two general notions that we introduce: "randomness measures" and "independence indices" of random vectors. In turn, these general notions give rise to "randomness diagrams"-tangible planar visualizations that answer the question: How random is a random vector? The notion of "independence indices" yields a novel measure of correlation for Lévy laws. In general, the concepts and results presented in this paper are applicable to any field of science and engineering with random-vectors empirical data.

  17. Te inclusion-induced electrical field perturbation in CdZnTe single crystals revealed by Kelvin probe force microscopy.

    PubMed

    Gu, Yaxu; Jie, Wanqi; Li, Linglong; Xu, Yadong; Yang, Yaodong; Ren, Jie; Zha, Gangqiang; Wang, Tao; Xu, Lingyan; He, Yihui; Xi, Shouzhi

    2016-09-01

    To understand the effects of tellurium (Te) inclusions on the device performance of CdZnTe radiation detectors, the perturbation of the electrical field in and around Te inclusions was studied in CdZnTe single crystals via Kelvin probe force microscopy (KPFM). Te inclusions were proved to act as lower potential centers with respect to surrounding CdZnTe matrix. Based on the KPFM results, the energy band diagram at the Te/CdZnTe interface was established, and the bias-dependent effects of Te inclusion on carrier transportation is discussed. PMID:27376976

  18. Ultrashort Single-Wall Carbon Nanotubes Reveal Field-Emission Coulomb Blockade and Highest Electron-Source Brightness

    NASA Astrophysics Data System (ADS)

    Pascale-Hamri, A.; Perisanu, S.; Derouet, A.; Journet, C.; Vincent, P.; Ayari, A.; Purcell, S. T.

    2014-03-01

    We present here well-defined Coulomb staircases using an original field-emission experiment on several individual in situ—grown single-wall carbon nanotubes. A unique in situ process was applied nine times to progressively shorten one single-wall carbon nanotube down to ≃10 nm, which increased the oscillations periods from 5.5 to 80 V, the temperature for observable Coulomb staircase to 1100 K and the currents to 1.8 μA. This process led to the brightest electron source ever reported [9×1011 A/(str m2 V)].

  19. Sun-induced chlorophyll fluorescence reveals strong representation of photosynthesis at ecosystem level in rice paddy field in Japan

    NASA Astrophysics Data System (ADS)

    Kato, T.; Tsujimoto, K.; Nasahara, K. N.; Akitsu, T.; Ono, K.; Miyata, A.

    2015-12-01

    Chlorophyll fluorescence emission from ecosystem induced by sunlight (Sun-Induced Fluorescence: SIF) is now a key factor to accurately estimate the ecosystem-level photosynthesis activity as suggested by satellite studies, and has been recently detected by satellites [Frankenberg et al., 2011; Guanter et al., 2012; Joiner et al., 2013] and measured at field stations [Daumard et al., 2010; Porcar-Castell, 2011]. However, the few example of field-based assessment on the representation ability reduces its value for the availability to better understand the dynamics in CO2uptake by land ecosystem. To elucidate the potential of SIF to estimate ecosystem GPP in typical Asian crop type, the canopy-top SIF was calculated from the spectrum data in Japanese rice paddy field in Mase in central Japan (36°03'N, 140°01'E, 11 m a.s.l.), and compared with eddy-tower measured GPP on half-hourly and daily bases during seven years from 2006 to 2012. The rice (Oriza sativa L.; cultivar Koshihikari) was transplanted in May and harvested in September normally. The SIF was estimated from the spectrums of downward Sun irradiance and upward canopy-reflected radiance measured at the height of 3m above ground by HemiSpherical Spectro-Radiometer (HSSR), consisting of the spectroradiometer (MS-700, Eko inc., Tokyo, Japan) with the full-width at half maximum (FWHM) of 10 nm and wavelength interval of 3.3 nm. The SIF around 760nm (O2-A band: Fs760) was calculated according to the Fraunhofer Line Depth principle [Maier et al., 2003] with several additional arrangements. The GPP increased almost linearly as both Fs760 and APAR (Absorbed Photosyntethically Active Radiation) increased based on monthly-averaged diurnal courses during the growing season in 2006. The slopes of their regression lines differed much among the months in APAR, but in Fs760. These nearly constant relationships among the months between GPP and Fs760 were kept for all the observation years. Daily averaged GPP and Fs760

  20. Broadband near-field enhancement in the macro-periodic and micro-random structure with a hybridized excitation of propagating Bloch-plasmonic and localized surface-plasmonic modes.

    PubMed

    Lu, Haifei; Ren, Xingang; Sha, Wei E I; Ho, Ho-Pui; Choy, Wallace C H

    2015-10-28

    We demonstrate that the silver nanoplate-based macroscopically periodic (macro-periodic) and microscopically random (micro-random) structure has a broadband near-field enhancement as compared to conventional silver gratings. The specific field enhancement in a wide spectral range (from UV to near-infrared) originates from the abundance of localized surface-plasmonic (LSP) modes in the microscopically random distributed silver nanoplates and propagating Bloch-plasmonic (PBP) modes from the macroscopically periodic pattern. The characterization of polarization dependent spectral absorption, surface-enhanced Raman spectroscopy (SERS), as well as theoretical simulation was conducted to comprehensively understand the features of the broadband spectrum and highly concentrated near-field. The reported macro-periodic and micro-random structure may offer a new route for the design of plasmonic systems for photonic and optoelectronic applications. PMID:26400003

  1. Novel Magnetic Phases Revealed by Ultra-High Magnetic Field in the Frustrated Magnet ZnCr2O4

    NASA Astrophysics Data System (ADS)

    Miyata, Atsuhiko; Ueda, Hiroaki; Ueda, Yutaka; Motome, Yukitoshi; Shannon, Nic; Penc, Karlo; Takeyama, Shojiro

    2011-07-01

    The Faraday rotation technique is used to map out the finite-temperature phase diagram of the prototypical frustrated magnet ZnCr2O4, in magnetic fields of up to 190 T generated by the single-turn coil method. We find evidence for a number of magnetic phase transitions, which are well-described by the theory based on spin--lattice coupling. In addition to the 1/2 plateau and a 3:1 canted phase, a 2:1:1 canted phase is found for the first time in chromium spinel oxides, which has been predicted by a theory of Penc et al. to realize in a small spin--lattice coupling limit. Both the new 2:1:1 and the 3:1 phases are regarded as the supersolid phases according to a magnetic analogy of Matsuda and Tsuneto, and Liu and Fisher.

  2. Auditory evoked fields measured noninvasively with small-animal MEG reveal rapid repetition suppression in the guinea pig

    PubMed Central

    Christianson, G. Björn; Chait, Maria; de Cheveigné, Alain

    2014-01-01

    In animal models, single-neuron response properties such as stimulus-specific adaptation have been described as possible precursors to mismatch negativity, a human brain response to stimulus change. In the present study, we attempted to bridge the gap between human and animal studies by characterising responses to changes in the frequency of repeated tone series in the anesthetised guinea pig using small-animal magnetoencephalography (MEG). We showed that 1) auditory evoked fields (AEFs) qualitatively similar to those observed in human MEG studies can be detected noninvasively in rodents using small-animal MEG; 2) guinea pig AEF amplitudes reduce rapidly with tone repetition, and this AEF reduction is largely complete by the second tone in a repeated series; and 3) differences between responses to the first (deviant) and later (standard) tones after a frequency transition resemble those previously observed in awake humans using a similar stimulus paradigm. PMID:25231619

  3. Field Evaluation of Picaridin Repellents Reveals Differences in Repellent Sensitivity between Southeast Asian Vectors of Malaria and Arboviruses

    PubMed Central

    Denis, Leen; Van den Broeck, Nick; Heng, Somony; Siv, Sovannaroth; Sluydts, Vincent; Sochantha, Tho; Coosemans, Marc; Durnez, Lies

    2014-01-01

    Scaling up of insecticide treated nets has contributed to a substantial malaria decline. However, some malaria vectors, and most arbovirus vectors, bite outdoors and in the early evening. Therefore, topically applied insect repellents may provide crucial additional protection against mosquito-borne pathogens. Among topical repellents, DEET is the most commonly used, followed by others such as picaridin. The protective efficacy of two formulated picaridin repellents against mosquito bites, including arbovirus and malaria vectors, was evaluated in a field study in Cambodia. Over a period of two years, human landing collections were performed on repellent treated persons, with rotation to account for the effect of collection place, time and individual collector. Based on a total of 4996 mosquitoes collected on negative control persons, the overall five hour protection rate was 97.4% [95%CI: 97.1–97.8%], not decreasing over time. Picaridin 20% performed equally well as DEET 20% and better than picaridin 10%. Repellents performed better against Mansonia and Culex spp. as compared to aedines and anophelines. A lower performance was observed against Aedes albopictus as compared to Aedes aegypti, and against Anopheles barbirostris as compared to several vector species. Parity rates were higher in vectors collected on repellent treated person as compared to control persons. As such, field evaluation shows that repellents can provide additional personal protection against early and outdoor biting malaria and arbovirus vectors, with excellent protection up to five hours after application. The heterogeneity in repellent sensitivity between mosquito genera and vector species could however impact the efficacy of repellents in public health programs. Considering its excellent performance and potential to protect against early and outdoor biting vectors, as well as its higher acceptability as compared to DEET, picaridin is an appropriate product to evaluate the epidemiological

  4. High-field fMRI reveals tonotopically-organized and core auditory cortex in the cat.

    PubMed

    Hall, Amee J; Lomber, Stephen G

    2015-07-01

    As frequency is one of the most basic elements of sound, it is not surprising that the earliest stages of auditory cortical processing are tonotopically organized. In cats, there are four known tonotopically organized cortical areas: the anterior (AAF), posterior (PAF), and ventral posterior (VPAF) auditory fields and primary auditory cortex (A1). Electrophysiological and anatomical evidence have suggested that AAF and A1 form core auditory cortex. The purpose of this investigation was to determine if high-field functional magnetic resonance imaging (fMRI) could be used to define the borders of all four tonotopically organized areas, identify core auditory cortex, and demonstrate tonotopy similar to that found using more invasive techniques. Five adult cats were examined. Eight different pure tones or one broad-band noise (BBN) stimuli were presented in a block paradigm during continuous fMRI scanning. Analysis was performed on each animal individually using conservative familywise error thresholds. Group analysis was performed by extracting data from fMRI analysis software and performing a battery of statistical tests. In auditory cortex, a reversal of the tonotopic gradient is known to occur at the borders between tonotopically organized areas. Therefore, high and low tones were used to delineate these borders. Activations in response to BBN as opposed to tonal stimulation demonstrated that core auditory cortex consists of both A1 and AAF. Finally, tonotopy was identified in each of the four known tonotopically organized areas. Therefore, we conclude that fMRI is effective at defining all four tonotopically organized cortical areas and delineating core auditory cortex. PMID:25776742

  5. An Extensive Field Survey Combined with a Phylogenetic Analysis Reveals Rapid and Widespread Invasion of Two Alien Whiteflies in China

    PubMed Central

    Hu, Jian; De Barro, Paul; Zhao, Hua; Wang, Jia; Nardi, Francesco; Liu, Shu-Sheng

    2011-01-01

    Background To understand the processes of invasions by alien insects is a pre-requisite for improving management. The whitefly Bemisia tabaci is a cryptic species complex that contains some of the most invasive pests worldwide. However, extensive field data to show the geographic distribution of the members of this species complex as well as the invasion by some of its members are scarce. Methodology/Principal Findings We used field surveys and published data to assess the current diversity and distribution of B. tabaci cryptic species in China and relate the indigenous members to other Asian and Australian members of the complex. The survey covered the 16 provinces where indigenous B. tabaci occur and extends this with published data for the whole of China. We used molecular markers to identify cryptic species. The evolutionary relationships between the different Asian B. tabaci were reconstructed using Bayesian methods. We show that whereas in the past the exotic invader Middle East-Asia Minor 1 was predominant across China, another newer invader Mediterranean is now the dominant species in the Yangtze River Valley and eastern coastal areas, and Middle East-Asia Minor 1 is now predominant only in the south and south eastern coastal areas. Based on mtCO1 we identified four new cryptic species, and in total we have recorded 13 indigenous and two invasive species from China. Diversity was highest in the southern and southeastern provinces and declined to north and west. Only the two invasive species were found in the northern part of the country where they occur primarily in protected cropping. By 2009, indigenous species were mainly found in remote mountainous areas and were mostly absent from extensive agricultural areas. Conclusions/Significance Invasions by some members of the whitefly B. tabaci species complex can be rapid and widespread, and indigenous species closely related to the invaders are replaced. PMID:21283707

  6. Receptive Field Vectors of Genetically-Identified Retinal Ganglion Cells Reveal Cell-Type-Dependent Visual Functions

    PubMed Central

    Katz, Matthew L.; Viney, Tim J.; Nikolic, Konstantin

    2016-01-01

    Sensory stimuli are encoded by diverse kinds of neurons but the identities of the recorded neurons that are studied are often unknown. We explored in detail the firing patterns of eight previously defined genetically-identified retinal ganglion cell (RGC) types from a single transgenic mouse line. We first introduce a new technique of deriving receptive field vectors (RFVs) which utilises a modified form of mutual information (“Quadratic Mutual Information”). We analysed the firing patterns of RGCs during presentation of short duration (~10 second) complex visual scenes (natural movies). We probed the high dimensional space formed by the visual input for a much smaller dimensional subspace of RFVs that give the most information about the response of each cell. The new technique is very efficient and fast and the derivation of novel types of RFVs formed by the natural scene visual input was possible even with limited numbers of spikes per cell. This approach enabled us to estimate the 'visual memory' of each cell type and the corresponding receptive field area by calculating Mutual Information as a function of the number of frames and radius. Finally, we made predictions of biologically relevant functions based on the RFVs of each cell type. RGC class analysis was complemented with results for the cells’ response to simple visual input in the form of black and white spot stimulation, and their classification on several key physiological metrics. Thus RFVs lead to predictions of biological roles based on limited data and facilitate analysis of sensory-evoked spiking data from defined cell types. PMID:26845435

  7. Receptive Field Vectors of Genetically-Identified Retinal Ganglion Cells Reveal Cell-Type-Dependent Visual Functions.

    PubMed

    Katz, Matthew L; Viney, Tim J; Nikolic, Konstantin

    2016-01-01

    Sensory stimuli are encoded by diverse kinds of neurons but the identities of the recorded neurons that are studied are often unknown. We explored in detail the firing patterns of eight previously defined genetically-identified retinal ganglion cell (RGC) types from a single transgenic mouse line. We first introduce a new technique of deriving receptive field vectors (RFVs) which utilises a modified form of mutual information ("Quadratic Mutual Information"). We analysed the firing patterns of RGCs during presentation of short duration (~10 second) complex visual scenes (natural movies). We probed the high dimensional space formed by the visual input for a much smaller dimensional subspace of RFVs that give the most information about the response of each cell. The new technique is very efficient and fast and the derivation of novel types of RFVs formed by the natural scene visual input was possible even with limited numbers of spikes per cell. This approach enabled us to estimate the 'visual memory' of each cell type and the corresponding receptive field area by calculating Mutual Information as a function of the number of frames and radius. Finally, we made predictions of biologically relevant functions based on the RFVs of each cell type. RGC class analysis was complemented with results for the cells' response to simple visual input in the form of black and white spot stimulation, and their classification on several key physiological metrics. Thus RFVs lead to predictions of biological roles based on limited data and facilitate analysis of sensory-evoked spiking data from defined cell types. PMID:26845435

  8. Impact Evaluation of Training Natural Leaders during a Community-Led Total Sanitation Intervention: A Cluster-Randomized Field Trial in Ghana

    PubMed Central

    2016-01-01

    We used a cluster-randomized field trial to evaluate training natural leaders (NLs) as an addition to a community-led total sanitation (CLTS) intervention in Ghana. NLs are motivated community members who influence their peers’ behaviors during CLTS. The outcomes were latrine use and quality, which were assessed from surveys and direct observation. From October 2012, Plan International Ghana (Plan) implemented CLTS in 60 villages in three regions in Ghana. After 5 months, Plan trained eight NLs from a randomly selected half of the villages, then continued implementing CLTS in all villages for 12 more months. The NL training led to increased time spent on CLTS by community members, increased latrine construction, and a 19.9 percentage point reduction in open defecation (p < 0.001). The training had the largest impact in small, remote villages with low exposure to prior water and sanitation projects, and may be most effective in socially cohesive villages. For both interventions, latrines built during CLTS were less likely to be constructed of durable materials than pre-existing latrines, but were equally clean, and more often had handwashing materials. CLTS with NL training contributes to three parts of Goal 6 of the Sustainable Development Goals: eliminating open defecation, expanding capacity-building, and strengthening community participation. PMID:27428399

  9. A randomized, double-blind, placebo-controlled clinical trial using a low-frequency magnetic field in the treatment of musculoskeletal chronic pain

    PubMed Central

    Thomas, Alex W; Graham, Karissa; Prato, Frank S; McKay, Julia; Forster, Patricia Morley; Moulin, Dwight E; Chari, Sesh

    2007-01-01

    Exposure to a specific pulsed electromagnetic field (PEMF) has been shown to produce analgesic (antinociceptive) effects in many organisms. In a randomized, double-blind, sham-controlled clinical trial, patients with either chronic generalized pain from fibromyalgia (FM) or chronic localized musculoskeletal or inflammatory pain were exposed to a PEMF (400 μT) through a portable device fitted to their head during twice-daily 40 min treatments over seven days. The effect of this PEMF on pain reduction was recorded using a visual analogue scale. A differential effect of PEMF over sham treatment was noticed in patients with FM, which approached statistical significance (P=0.06) despite low numbers (n=17); this effect was not evident in those without FM (P=0.93; n=15). PEMF may be a novel, safe and effective therapeutic tool for use in at least certain subsets of patients with chronic, nonmalignant pain. Clearly, however, a larger randomized, double-blind clinical trial with just FM patients is warranted. PMID:18080043

  10. Impact Evaluation of Training Natural Leaders during a Community-Led Total Sanitation Intervention: A Cluster-Randomized Field Trial in Ghana.

    PubMed

    Crocker, Jonny; Abodoo, Elvis; Asamani, Daniel; Domapielle, William; Gyapong, Benedict; Bartram, Jamie

    2016-08-16

    We used a cluster-randomized field trial to evaluate training natural leaders (NLs) as an addition to a community-led total sanitation (CLTS) intervention in Ghana. NLs are motivated community members who influence their peers' behaviors during CLTS. The outcomes were latrine use and quality, which were assessed from surveys and direct observation. From October 2012, Plan International Ghana (Plan) implemented CLTS in 60 villages in three regions in Ghana. After 5 months, Plan trained eight NLs from a randomly selected half of the villages, then continued implementing CLTS in all villages for 12 more months. The NL training led to increased time spent on CLTS by community members, increased latrine construction, and a 19.9 percentage point reduction in open defecation (p < 0.001). The training had the largest impact in small, remote villages with low exposure to prior water and sanitation projects, and may be most effective in socially cohesive villages. For both interventions, latrines built during CLTS were less likely to be constructed of durable materials than pre-existing latrines, but were equally clean, and more often had handwashing materials. CLTS with NL training contributes to three parts of Goal 6 of the Sustainable Development Goals: eliminating open defecation, expanding capacity-building, and strengthening community participation. PMID:27428399

  11. Near-field-assisted localization: effect of size and filling factor of randomly distributed zinc oxide nanoneedles on multiple scattering and localization of light

    NASA Astrophysics Data System (ADS)

    Silies, Martin; Mascheck, Manfred; Leipold, David; Kollmann, Heiko; Schmidt, Slawa; Sartor, Janos; Yatsui, Takashi; Kitamura, Kokoro; Ohtsu, Motoicho; Kalt, Heinz; Runge, Erich; Lienau, Christoph

    2016-07-01

    We investigate the influence of the diameter and the filling factor of randomly arranged ZnO nanoneedles on the multiple scattering and localization of light in disordered dielectrics. Coherent, ultra-broadband second-harmonic (SH) microscopy is used to probe the spatial localization of light in representative nm-sized ZnO arrays of needles. We observe strong fluctuations of the SH intensity inside different ZnO needle geometries. Comparison of the SH intensity distributions with predictions based on a one-parameter scaling model indicate that SH fluctuations can be taken as a quantitative measure for the degree of localization. Interestingly, the strongest localization signatures are found for densely packed arrays of thin needles with diameters in the range of only 30 nm range, despite the small scattering cross section of these needles. FDTD simulations indicate that in this case coupling of electric near-fields between neighbouring needles governs the localization.

  12. Fusing Markov random fields with anatomical knowledge and shape-based analysis to segment multiple sclerosis white matter lesions in magnetic resonance images of the brain

    NASA Astrophysics Data System (ADS)

    AlZubi, Stephan; Toennies, Klaus D.; Bodammer, N.; Hinrichs, Herman

    2002-05-01

    This paper proposes an image analysis system to segment multiple sclerosis lesions of magnetic resonance (MR) brain volumes consisting of 3 mm thick slices using three channels (images showing T1-, T2- and PD -weighted contrast). The method uses the statistical model of Markov Random Fields (MRF) both at low and high levels. The neighborhood system used in this MRF is defined in three types: (1) Voxel to voxel: a low-level heterogeneous neighborhood system is used to restore noisy images. (2) Voxel to segment: a fuzzy atlas, which indicates the probability distribution of each tissue type in the brain, is registered elastically with the MRF. It is used by the MRF as a-priori knowledge to correct miss-classified voxels. (3) Segment to segment: Remaining lesion candidates are processed by a feature based classifier that looks at unary and neighborhood information to eliminate more false positives. An expert's manual segmentation was compared with the algorithm.

  13. The understanding on the evolution of stress-induced gate leakage in high-k dielectric metal-oxide-field-effect transistor by random-telegraph-noise measurement

    NASA Astrophysics Data System (ADS)

    Hsieh, E. R.; Chung, Steve S.

    2015-12-01

    The evolution of gate-current leakage path has been observed and depicted by RTN signals on metal-oxide-silicon field effect transistor with high-k gate dielectric. An experimental method based on gate-current random telegraph noise (Ig-RTN) technique was developed to observe the formation of gate-leakage path for the device under certain electrical stress, such as Bias Temperature Instability. The results show that the evolution of gate-current path consists of three stages. In the beginning, only direct-tunnelling gate current and discrete traps inducing Ig-RTN are observed; in the middle stage, interaction between traps and the percolation paths presents a multi-level gate-current variation, and finally two different patterns of the hard or soft breakdown path can be identified. These observations provide us a better understanding of the gate-leakage and its impact on the device reliability.

  14. Prestack inversion based on anisotropic Markov random field-maximum posterior probability inversion and its application to identify shale gas sweet spots

    NASA Astrophysics Data System (ADS)

    Wang, Kang-Ning; Sun, Zan-Dong; Dong, Ning

    2015-12-01

    Economic shale gas production requires hydraulic fracture stimulation to increase the formation permeability. Hydraulic fracturing strongly depends on geomechanical parameters such as Young's modulus and Poisson's ratio. Fracture-prone sweet spots can be predicted by prestack inversion, which is an ill-posed problem; thus, regularization is needed to obtain unique and stable solutions. To characterize gas-bearing shale sedimentary bodies, elastic parameter variations are regarded as an anisotropic Markov random field. Bayesian statistics are adopted for transforming prestack inversion to the maximum posterior probability. Two energy functions for the lateral and vertical directions are used to describe the distribution, and the expectation-maximization algorithm is used to estimate the hyperparameters of the prior probability of elastic parameters. Finally, the inversion yields clear geological boundaries, high vertical resolution, and reasonable lateral continuity using the conjugate gradient method to minimize the objective function. Antinoise and imaging ability of the method were tested using synthetic and real data.

  15. Field surveys reveal the presence of anti-androgens in an effluent-receiving river using stickleback-specific biomarkers.

    PubMed

    Katsiadaki, Ioanna; Sanders, Matthew B; Henrys, Peter A; Scott, Alexander P; Matthiessen, Peter; Pottinger, Tom G

    2012-10-15

    This study was designed to assess whether the removal of endocrine disrupting chemicals (EDCs) and other substances from a Waste Water Treatment Works (WWTW) effluent (receiving water: R. Ray, Swindon, UK) by granular activated carbon (GAC) affected biomarkers of exposure to EDCs [vitellogenin (VTG) and spiggin] in male and female three-spined sticklebacks in the receiving water. A nearby river (R. Ock), with a negligible effluent loading, was used as a control. On each river fish were sampled from four sites on five occasions both before and after remediation of the WWTW effluent. The results show for the first time in a UK field study a clear seasonality of blood VTG concentrations in wild male fish, following closely the VTG profile in female fish from both rivers. VTG levels in male fish from the R. Ray were significantly reduced after the GAC installation. However, VTG levels in males from the control sites also varied significantly across the same period, reducing the significance of this finding. A laboratory exposure to oestradiol (using site-specific lower and upper levels of oestrogenic activity) failed to elevate VTG concentrations in male sticklebacks suggesting that concentrations in the effluent, even prior to remediation, may not have exceeded a critical sensitivity threshold. Most importantly, a significant increase in female kidney spiggin content (a highly specific biomarker of xeno-androgen exposure) occurred in fish in the R. Ray after the GAC installation to levels comparable with those in fish from the control river. The significance of this finding is strengthened by the fact that during the pre-remediation period in the R. Ray, female spiggin levels increased with increasing distance from the WWTW. Our results provide the first in vivo evidence of the presence of anti-androgens in a UK WWTW effluent. To our knowledge this is the first UK-based comprehensive field study on the effects of a WWTW upgrade on biomarkers of EDC exposure using a

  16. Long-Term Field Study Reveals Subtle Effects of the Invasive Alga Sargassum muticum upon the Epibiota of Zostera marina.

    PubMed

    DeAmicis, Stacey; Foggo, Andrew

    2015-01-01

    Invasive species can alter coastal ecosystems both directly, e.g. through competition for substratum and nutrients, and indirectly. Indirect effects may be mediated by creation of dissimilar or inimical habitats, changes in predator and/or prey assemblages, alterations in associated biota, and perturbations of water movement and thermal regimes. Previous studies have shown that invasive algae can modify native habitat architecture, disrupt intricately linked food webs and alter epibiotic assemblages. In the UK, the seagrass Zostera marina supports a diverse epibiotic assemblage, influencing key factors such as sediment dynamics, depositional regime and trophic linkages. Increasing encroachment of the invasive alga Sargassum muticum into seagrass meadows changes the physical and chemical characteristics of the local environment and creates the potential for changes in the epibionts associated with the seagrass blades, threatening the integrity of the seagrass ecosystem. We investigated the effects of S. muticum invasion upon the epibiota of Z. marina in a drowned river valley in SW England seasonally from spring to autumn over four years in an in-situ manipulative experiment, comparing permanent quadrats with and without artificially introduced S. muticum. Epibiota were weighed, identified to the most detailed operational taxonomic unit (OTU) possible, and unitary organisms were enumerated. Multivariate PERMANOVA+ analysis revealed significant differences in epibiont assemblages between Sargassum treatments. Linear mixed effects models indicated that differences in epibiota assemblage composition were not reflected as significant differences in mean biomass per sample, or number of epibiont OTUs per sample. We conclude that S. muticum invasion into Z. marina meadows may significantly alter the species composition and abundance distribution of epibiotic assemblages found on the blades of the seagrass. Thus S. muticum invasion could have more wide-reaching effects on

  17. Long-Term Field Study Reveals Subtle Effects of the Invasive Alga Sargassum muticum upon the Epibiota of Zostera marina

    PubMed Central

    2015-01-01

    Invasive species can alter coastal ecosystems both directly, e.g. through competition for substratum and nutrients, and indirectly. Indirect effects may be mediated by creation of dissimilar or inimical habitats, changes in predator and/or prey assemblages, alterations in associated biota, and perturbations of water movement and thermal regimes. Previous studies have shown that invasive algae can modify native habitat architecture, disrupt intricately linked food webs and alter epibiotic assemblages. In the UK, the seagrass Zostera marina supports a diverse epibiotic assemblage, influencing key factors such as sediment dynamics, depositional regime and trophic linkages. Increasing encroachment of the invasive alga Sargassum muticum into seagrass meadows changes the physical and chemical characteristics of the local environment and creates the potential for changes in the epibionts associated with the seagrass blades, threatening the integrity of the seagrass ecosystem. We investigated the effects of S. muticum invasion upon the epibiota of Z. marina in a drowned river valley in SW England seasonally from spring to autumn over four years in an in-situ manipulative experiment, comparing permanent quadrats with and without artificially introduced S. muticum. Epibiota were weighed, identified to the most detailed operational taxonomic unit (OTU) possible, and unitary organisms were enumerated. Multivariate PERMANOVA+ analysis revealed significant differences in epibiont assemblages between Sargassum treatments. Linear mixed effects models indicated that differences in epibiota assemblage composition were not reflected as significant differences in mean biomass per sample, or number of epibiont OTUs per sample. We conclude that S. muticum invasion into Z. marina meadows may significantly alter the species composition and abundance distribution of epibiotic assemblages found on the blades of the seagrass. Thus S. muticum invasion could have more wide-reaching effects on

  18. Reduction in Tension and Stiffening of Lipid Membranes in an Electric Field Revealed by X-Ray Scattering

    NASA Astrophysics Data System (ADS)

    Hemmerle, Arnaud; Fragneto, Giovanna; Daillant, Jean; Charitat, Thierry

    2016-06-01

    The effect of ac electric fields on the elasticity of supported lipid bilayers is investigated at the microscopic level using grazing incidence synchrotron x-ray scattering. A strong decrease in the membrane tension up to 1 mN /m and a dramatic increase of its effective rigidity up to 300 kBT are observed for local electric potentials seen by the membrane ≲1 V . The experimental results are analyzed using detailed electrokinetic modeling and nonlinear Poisson-Boltzmann theory. Based on a modeling of the electromagnetic stress, which provides an accurate description of the bilayer separation versus pressure curves, we show that the decrease in tension results from the amplification of charge fluctuations on the membrane surface whereas the increase in bending rigidity results from the direct interaction between charges in the electric double layer. These effects eventually lead to a destabilization of the bilayer and vesicle formation. Similar effects are expected at the tens of nanometers length scale in cell membranes with lower tension, and could explain a number of electrically driven processes.

  19. Field flume reveals aquatic vegetation's role in sediment and particulate phosphorus transport in a shallow aquatic ecosystem

    NASA Astrophysics Data System (ADS)

    Harvey, Judson W.; Noe, Gregory B.; Larsen, Laurel G.; Nowacki, Daniel J.; McPhillips, Lauren E.

    2011-03-01

    Flow interactions with aquatic vegetation and effects on sediment transport and nutrient redistribution are uncertain in shallow aquatic ecosystems. Here we quantified sediment transport in the Everglades by progressively increasing flow velocity in a field flume constructed around undisturbed bed sediment and emergent macrophytes. Suspended sediment < 100 μm was dominant in the lower range of laminar flow and was supplied by detachment from epiphyton. Sediment flux increased by a factor of four and coarse flocculent sediment > 100 μm became dominant at higher velocity steps after a threshold shear stress for bed floc entrainment was exceeded. Shedding of vortices that had formed downstream of plant stems also occurred on that velocity step which promoted additional sediment detachment from epiphyton. Modeling determined that the potentially entrainable sediment reservoir, 46 g m - 2 , was similar to the reservoir of epiphyton (66 g m - 2 ) but smaller than the reservoir of flocculent bed sediment (330 g m - 2 ). All suspended sediment was enriched in phosphorus (by approximately twenty times) compared with bulk sediment on the bed surface and on plant stems, indicating that the most easily entrainable sediment is also the most nutrient rich (and likely the most biologically active).

  20. Correlations between the Dielectric Properties and Exterior Morphology of Cells Revealed by Dielectrophoretic Field-Flow Fractionation

    PubMed Central

    Gascoyne, Peter R. C.; Shim, Sangjo; Noshari, Jamileh; Becker, Frederick F.; Stemke-Hale, Katherine

    2013-01-01

    Although dielectrophoresis (DEP) has great potential for addressing clinical cell isolation problems based on cell dielectric differences, a biological basis for predicting the DEP behavior of cells has been lacking. Here, the dielectric properties of the NCI-60 panel of tumor cell types have been measured by dielectrophoretic (DEP) field-flow fractionation, correlated with the exterior morphologies of the cells during growth, and compared with the dielectric and morphological characteristics of the subpopulations of peripheral blood. In agreement with earlier findings, cell total capacitance varied with both cell size and plasma membrane folding and the dielectric properties of the NCI-60 cell types in suspension reflected the plasma membrane area and volume of the cells at their growth sites. Therefore, the behavior of cells in DEP-based manipulations is largely determined by their exterior morphological characteristics prior to release into suspension. As a consequence, DEP is able to discriminate between cells of similar size having different morphological origins, offering a significant advantage over size-based filtering for isolating circulating tumor cells, for example. The findings provide a framework for anticipating cell dielectric behavior on the basis of structure-function relationships and suggest that DEP should be widely applicable as a surface marker-independent method for sorting cells. PMID:23172680