Husimi coordinates of multipartite separable states

NASA Astrophysics Data System (ADS)

Parfionov, Georges; Zapatrin, Romàn R.

2010-12-01

A parametrization of multipartite separable states in a finite-dimensional Hilbert space is suggested. It is proved to be a diffeomorphism between the set of zero-trace operators and the interior of the set of separable density operators. The result is applicable to any tensor product decomposition of the state space. An analytical criterion for separability of density operators is established in terms of the boundedness of a sequence of operators.

Lyapunov Exponents of Minimizing Measures for Globally Positive Diffeomorphisms in All Dimensions

NASA Astrophysics Data System (ADS)

Arnaud, M.-C.

2016-05-01

The globally positive diffeomorphisms of the 2 n-dimensional annulus are important because they represent what happens close to a completely elliptic periodic point of a symplectic diffeomorphism where the torsion is positive definite. For these globally positive diffeomorphisms, an Aubry-Mather theory was developed by Garibaldi and Thieullen that provides the existence of some minimizing measures. Using the two Green bundles {G_-} and {G_+} that can be defined along the support of these minimizing measures, we will prove that there is a deep link between: the angle between {G_-} and {G_+} along the support of the considered measure {μ};

Unique equilibrium states for Bonatti–Viana diffeomorphisms

NASA Astrophysics Data System (ADS)

Climenhaga, Vaughn; Fisher, Todd; Thompson, Daniel J.

2018-06-01

We show that the robustly transitive diffeomorphisms constructed by Bonatti and Viana have unique equilibrium states for natural classes of potentials. In particular, we characterize the SRB measure as the unique equilibrium state for a suitable geometric potential. The techniques developed are applicable to a wide class of DA diffeomorphisms, and persist under C 1 perturbations of the map. These results are an application of general machinery developed by the first and last named authors.

Diffeomorphic demons: efficient non-parametric image registration.

PubMed

Vercauteren, Tom; Pennec, Xavier; Perchant, Aymeric; Ayache, Nicholas

2009-03-01

We propose an efficient non-parametric diffeomorphic image registration algorithm based on Thirion's demons algorithm. In the first part of this paper, we show that Thirion's demons algorithm can be seen as an optimization procedure on the entire space of displacement fields. We provide strong theoretical roots to the different variants of Thirion's demons algorithm. This analysis predicts a theoretical advantage for the symmetric forces variant of the demons algorithm. We show on controlled experiments that this advantage is confirmed in practice and yields a faster convergence. In the second part of this paper, we adapt the optimization procedure underlying the demons algorithm to a space of diffeomorphic transformations. In contrast to many diffeomorphic registration algorithms, our solution is computationally efficient since in practice it only replaces an addition of displacement fields by a few compositions. Our experiments show that in addition to being diffeomorphic, our algorithm provides results that are similar to the ones from the demons algorithm but with transformations that are much smoother and closer to the gold standard, available in controlled experiments, in terms of Jacobians.

Diffeomorphism invariance and black hole entropy

NASA Astrophysics Data System (ADS)

Huang, Chao-Guang; Guo, Han-Ying; Wu, Xiaoning

2003-11-01

The Noether-charge and the Hamiltonian realizations for the diff(M) algebra in diffeomorphism-invariant gravitational theories without a cosmological constant in any dimension are studied in a covariant formalism. We analyze how the Hamiltonian functionals form the diff(M) algebra under the Poisson brackets and show how the Noether charges with respect to the diffeomorphism generated by the vector fields and their variations in n-dimensional general relativity form this algebra. The asymptotic behaviors of vector fields generating diffeomorphism of the manifold with boundaries are discussed. It is shown that the “central extension” for a large class of vector fields is always zero on the Killing horizon. We also check whether choosing the vector fields near the horizon may pick up the Virasoro algebra. The conclusion is unfortunately negative in any dimension.

Black hole entropy and Lorentz-diffeomorphism Noether charge

NASA Astrophysics Data System (ADS)

Jacobson, Ted; Mohd, Arif

2015-12-01

We show that, in the first or second order orthonormal frame formalism, black hole entropy is the horizon Noether charge for a combination of diffeomorphism and local Lorentz symmetry involving the Lie derivative of the frame. The Noether charge for diffeomorphisms alone is unsuitable, since a regular frame cannot be invariant under the flow of the Killing field at the bifurcation surface. We apply this formalism to Lagrangians polynomial in wedge products of the frame field 1-form and curvature 2-form, including general relativity, Lovelock gravity, and "topological" terms in four dimensions.

A hybrid multimodal non-rigid registration of MR images based on diffeomorphic demons.

PubMed

Lu, Huanxiang; Cattin, Philippe C; Reyes, Mauricio

2010-01-01

In this paper we present a novel hybrid approach for multimodal medical image registration based on diffeomorphic demons. Diffeomorphic demons have proven to be a robust and efficient way for intensity-based image registration. A very recent extension even allows to use mutual information (MI) as a similarity measure to registration multimodal images. However, due to the intensity correspondence uncertainty existing in some anatomical parts, it is difficult for a purely intensity-based algorithm to solve the registration problem. Therefore, we propose to combine the resulting transformations from both intensity-based and landmark-based methods for multimodal non-rigid registration based on diffeomorphic demons. Several experiments on different types of MR images were conducted, for which we show that a better anatomical correspondence between the images can be obtained using the hybrid approach than using either intensity information or landmarks alone.

Sobolev metrics on diffeomorphism groups and the derived geometry of spaces of submanifolds

NASA Astrophysics Data System (ADS)

Micheli, Mario; Michor, Peter W.; Mumford, David

2013-06-01

Given a finite-dimensional manifold N, the group \\operatorname{Diff}_{ S}(N) of diffeomorphisms diffeomorphism of N which decrease suitably rapidly to the identity, acts on the manifold B(M,N) of submanifolds of N of diffeomorphism-type M, where M is a compact manifold with \\operatorname{dim} M<\\operatorname{dim} N. Given the right-invariant weak Riemannian metric on \\operatorname{Diff}_{ S}(N) induced by a quite general operator L\\colon \\mathfrak{X}_{ S}(N)\\to \\Gamma(T^*N\\otimes\\operatorname{vol}(N)), we consider the induced weak Riemannian metric on B(M,N) and compute its geodesics and sectional curvature. To do this, we derive a covariant formula for the curvature in finite and infinite dimensions, we show how it makes O'Neill's formula very transparent, and we finally use it to compute the sectional curvature on B(M,N).

The quantum holonomy-diffeomorphism algebra and quantum gravity

NASA Astrophysics Data System (ADS)

Aastrup, Johannes; Grimstrup, Jesper Møller

2016-03-01

We introduce the quantum holonomy-diffeomorphism ∗-algebra, which is generated by holonomy-diffeomorphisms on a three-dimensional manifold and translations on a space of SU(2)-connections. We show that this algebra encodes the canonical commutation relations of canonical quantum gravity formulated in terms of Ashtekar variables. Furthermore, we show that semiclassical states exist on the holonomy-diffeomorphism part of the algebra but that these states cannot be extended to the full algebra. Via a Dirac-type operator we derive a certain class of unbounded operators that act in the GNS construction of the semiclassical states. These unbounded operators are the type of operators, which we have previously shown to entail the spatial three-dimensional Dirac operator and Dirac-Hamiltonian in a semiclassical limit. Finally, we show that the structure of the Hamilton constraint emerges from a Yang-Mills-type operator over the space of SU(2)-connections.

Effective field theory of broken spatial diffeomorphisms

DOE PAGES

Lin, Chunshan; Labun, Lance Z.

2016-03-17

We study the low energy effective theory describing gravity with broken spatial diffeomorphism invariance. In the unitary gauge, the Goldstone bosons associated with broken diffeomorphisms are eaten and the graviton becomes a massive spin-2 particle with 5 well-behaved degrees of freedom. In this gauge, the most general theory is built with the lowest dimension operators invariant under only temporal diffeomorphisms. Imposing the additional shift and SO(3) internal symmetries, we analyze the perturbations on a FRW background. At linear perturbation level, the observables of this theory are characterized by five parameters, including the usual cosmological parameters and one additional coupling constantmore » for the symmetry-breaking scalars. In the de Sitter and Minkowski limit, the three Goldstone bosons are supermassive and can be integrated out, leaving two massive tensor modes as the only propagating degrees of freedom. In conclusion, we discuss several examples relevant to theories of massive gravity.« less

Adaptive Diffeomorphic Multiresolution Demons and Their Application to Same Modality Medical Image Registration with Large Deformation

PubMed Central

Wang, Chang; Ren, Qiongqiong; Qin, Xin

2018-01-01

Diffeomorphic demons can guarantee smooth and reversible deformation and avoid unreasonable deformation. However, the number of iterations needs to be set manually, and this greatly influences the registration result. In order to solve this problem, we proposed adaptive diffeomorphic multiresolution demons in this paper. We used an optimized framework with nonrigid registration and diffeomorphism strategy, designed a similarity energy function based on grey value, and stopped iterations adaptively. This method was tested by synthetic image and same modality medical image. Large deformation was simulated by rotational distortion and extrusion transform, medical image registration with large deformation was performed, and quantitative analyses were conducted using the registration evaluation indexes, and the influence of different driving forces and parameters on the registration result was analyzed. The registration results of same modality medical images were compared with those obtained using active demons, additive demons, and diffeomorphic demons. Quantitative analyses showed that the proposed method's normalized cross-correlation coefficient and structural similarity were the highest and mean square error was the lowest. Medical image registration with large deformation could be performed successfully; evaluation indexes remained stable with an increase in deformation strength. The proposed method is effective and robust, and it can be applied to nonrigid registration of same modality medical images with large deformation.

Adaptive Diffeomorphic Multiresolution Demons and Their Application to Same Modality Medical Image Registration with Large Deformation.

PubMed

Wang, Chang; Ren, Qiongqiong; Qin, Xin; Yu, Yi

2018-01-01

Diffeomorphic demons can guarantee smooth and reversible deformation and avoid unreasonable deformation. However, the number of iterations needs to be set manually, and this greatly influences the registration result. In order to solve this problem, we proposed adaptive diffeomorphic multiresolution demons in this paper. We used an optimized framework with nonrigid registration and diffeomorphism strategy, designed a similarity energy function based on grey value, and stopped iterations adaptively. This method was tested by synthetic image and same modality medical image. Large deformation was simulated by rotational distortion and extrusion transform, medical image registration with large deformation was performed, and quantitative analyses were conducted using the registration evaluation indexes, and the influence of different driving forces and parameters on the registration result was analyzed. The registration results of same modality medical images were compared with those obtained using active demons, additive demons, and diffeomorphic demons. Quantitative analyses showed that the proposed method's normalized cross-correlation coefficient and structural similarity were the highest and mean square error was the lowest. Medical image registration with large deformation could be performed successfully; evaluation indexes remained stable with an increase in deformation strength. The proposed method is effective and robust, and it can be applied to nonrigid registration of same modality medical images with large deformation.

Right ventricular strain analysis from three-dimensional echocardiography by using temporally diffeomorphic motion estimation.

PubMed

Zhang, Zhijun; Zhu, Meihua; Ashraf, Muhammad; Broberg, Craig S; Sahn, David J; Song, Xubo

2014-12-01

Quantitative analysis of right ventricle (RV) motion is important for study of the mechanism of congenital and acquired diseases. Unlike left ventricle (LV), motion estimation of RV is more difficult because of its complex shape and thin myocardium. Although attempts of finite element models on MR images and speckle tracking on echocardiography have shown promising results on RV strain analysis, these methods can be improved since the temporal smoothness of the motion is not considered. The authors have proposed a temporally diffeomorphic motion estimation method in which a spatiotemporal transformation is estimated by optimization of a registration energy functional of the velocity field in their earlier work. The proposed motion estimation method is a fully automatic process for general image sequences. The authors apply the method by combining with a semiautomatic myocardium segmentation method to the RV strain analysis of three-dimensional (3D) echocardiographic sequences of five open-chest pigs under different steady states. The authors compare the peak two-point strains derived by their method with those estimated from the sonomicrometry, the results show that they have high correlation. The motion of the right ventricular free wall is studied by using segmental strains. The baseline sequence results show that the segmental strains in their methods are consistent with results obtained by other image modalities such as MRI. The image sequences of pacing steady states show that segments with the largest strain variation coincide with the pacing sites. The high correlation of the peak two-point strains of their method and sonomicrometry under different steady states demonstrates that their RV motion estimation has high accuracy. The closeness of the segmental strain of their method to those from MRI shows the feasibility of their method in the study of RV function by using 3D echocardiography. The strain analysis of the pacing steady states shows the potential utility of their method in study on RV diseases.

Evaluation of GMI and PMI diffeomorphic-based demons algorithms for aligning PET and CT Images.

PubMed

Yang, Juan; Wang, Hongjun; Zhang, You; Yin, Yong

2015-07-08

Fusion of anatomic information in computed tomography (CT) and functional information in 18F-FDG positron emission tomography (PET) is crucial for accurate differentiation of tumor from benign masses, designing radiotherapy treatment plan and staging of cancer. Although current PET and CT images can be acquired from combined 18F-FDG PET/CT scanner, the two acquisitions are scanned separately and take a long time, which may induce potential positional errors in global and local caused by respiratory motion or organ peristalsis. So registration (alignment) of whole-body PET and CT images is a prerequisite for their meaningful fusion. The purpose of this study was to assess the performance of two multimodal registration algorithms for aligning PET and CT images. The proposed gradient of mutual information (GMI)-based demons algorithm, which incorporated the GMI between two images as an external force to facilitate the alignment, was compared with the point-wise mutual information (PMI) diffeomorphic-based demons algorithm whose external force was modified by replacing the image intensity difference in diffeomorphic demons algorithm with the PMI to make it appropriate for multimodal image registration. Eight patients with esophageal cancer(s) were enrolled in this IRB-approved study. Whole-body PET and CT images were acquired from a combined 18F-FDG PET/CT scanner for each patient. The modified Hausdorff distance (d(MH)) was used to evaluate the registration accuracy of the two algorithms. Of all patients, the mean values and standard deviations (SDs) of d(MH) were 6.65 (± 1.90) voxels and 6.01 (± 1.90) after the GMI-based demons and the PMI diffeomorphic-based demons registration algorithms respectively. Preliminary results on oncological patients showed that the respiratory motion and organ peristalsis in PET/CT esophageal images could not be neglected, although a combined 18F-FDG PET/CT scanner was used for image acquisition. The PMI diffeomorphic-based demons algorithm was more accurate than the GMI-based demons algorithm in registering PET/CT esophageal images.

Fourier dimension of random images

NASA Astrophysics Data System (ADS)

Ekström, Fredrik

2016-10-01

Given a compact set of real numbers, a random C^{m + α}-diffeomorphism is constructed such that the image of any measure concentrated on the set and satisfying a certain condition involving a real number s, almost surely has Fourier dimension greater than or equal to s / (m + α). This is used to show that every Borel subset of the real numbers of Hausdorff dimension s is C^{m + α}-equivalent to a set of Fourier dimension greater than or equal to s / (m + α ). In particular every Borel set is diffeomorphic to a Salem set, and the Fourier dimension is not invariant under Cm-diffeomorphisms for any m.

Lorentz and diffeomorphism violations in linearized gravity

NASA Astrophysics Data System (ADS)

Kostelecký, V. Alan; Mewes, Matthew

2018-04-01

Lorentz and diffeomorphism violations are studied in linearized gravity using effective field theory. A classification of all gauge-invariant and gauge-violating terms is given. The exact covariant dispersion relation for gravitational modes involving operators of arbitrary mass dimension is constructed, and various special limits are discussed.

A maximum likelihood approach to diffeomorphic speckle tracking for 3D strain estimation in echocardiography.

PubMed

Curiale, Ariel H; Vegas-Sánchez-Ferrero, Gonzalo; Bosch, Johan G; Aja-Fernández, Santiago

2015-08-01

The strain and strain-rate measures are commonly used for the analysis and assessment of regional myocardial function. In echocardiography (EC), the strain analysis became possible using Tissue Doppler Imaging (TDI). Unfortunately, this modality shows an important limitation: the angle between the myocardial movement and the ultrasound beam should be small to provide reliable measures. This constraint makes it difficult to provide strain measures of the entire myocardium. Alternative non-Doppler techniques such as Speckle Tracking (ST) can provide strain measures without angle constraints. However, the spatial resolution and the noisy appearance of speckle still make the strain estimation a challenging task in EC. Several maximum likelihood approaches have been proposed to statistically characterize the behavior of speckle, which results in a better performance of speckle tracking. However, those models do not consider common transformations to achieve the final B-mode image (e.g. interpolation). This paper proposes a new maximum likelihood approach for speckle tracking which effectively characterizes speckle of the final B-mode image. Its formulation provides a diffeomorphic scheme than can be efficiently optimized with a second-order method. The novelty of the method is threefold: First, the statistical characterization of speckle generalizes conventional speckle models (Rayleigh, Nakagami and Gamma) to a more versatile model for real data. Second, the formulation includes local correlation to increase the efficiency of frame-to-frame speckle tracking. Third, a probabilistic myocardial tissue characterization is used to automatically identify more reliable myocardial motions. The accuracy and agreement assessment was evaluated on a set of 16 synthetic image sequences for three different scenarios: normal, acute ischemia and acute dyssynchrony. The proposed method was compared to six speckle tracking methods. Results revealed that the proposed method is the most accurate method to measure the motion and strain with an average median motion error of 0.42 mm and a median strain error of 2.0 ± 0.9%, 2.1 ± 1.3% and 7.1 ± 4.9% for circumferential, longitudinal and radial strain respectively. It also showed its capability to identify abnormal segments with reduced cardiac function and timing differences for the dyssynchrony cases. These results indicate that the proposed diffeomorphic speckle tracking method provides robust and accurate motion and strain estimation. Copyright © 2015. Published by Elsevier B.V.

Current algebras, measures quasi-invariant under diffeomorphism groups, and infinite quantum systems with accumulation points

NASA Astrophysics Data System (ADS)

Sakuraba, Takao

The approach to quantum physics via current algebra and unitary representations of the diffeomorphism group is established. This thesis studies possible infinite Bose gas systems using this approach. Systems of locally finite configurations and systems of configurations with accumulation points are considered, with the main emphasis on the latter. In Chapter 2, canonical quantization, quantization via current algebra and unitary representations of the diffeomorphism group are reviewed. In Chapter 3, a new definition of the space of configurations is proposed and an axiom for general configuration spaces is abstracted. Various subsets of the configuration space, including those specifying the number of points in a Borel set and those specifying the number of accumulation points in a Borel set are proved to be measurable using this axiom. In Chapter 4, known results on the space of locally finite configurations and Poisson measure are reviewed in the light of the approach developed in Chapter 3, including the approach to current algebra in the Poisson space by Albeverio, Kondratiev, and Rockner. Goldin and Moschella considered unitary representations of the group of diffeomorphisms of the line based on self-similar random processes, which may describe infinite quantum gas systems with clusters. In Chapter 5, the Goldin-Moschella theory is developed further. Their construction of measures quasi-invariant under diffeomorphisms is reviewed, and a rigorous proof of their conjectures is given. It is proved that their measures with distinct correlation parameters are mutually singular. A quasi-invariant measure constructed by Ismagilov on the space of configurations with accumulation points on the circle is proved to be singular with respect to the Goldin-Moschella measures. Finally a generalization of the Goldin-Moschella measures to the higher-dimensional case is studied, where the notion of covariance matrix and the notion of condition number play important roles. A rigorous construction of measures quasi-invariant under the group of diffeomorphisms of d-dimensional space stabilizing a point is given.

Cosmic time and reduced phase space of general relativity

NASA Astrophysics Data System (ADS)

Ita, Eyo Eyo; Soo, Chopin; Yu, Hoi-Lai

2018-05-01

In an ever-expanding spatially closed universe, the fractional change of the volume is the preeminent intrinsic time interval to describe evolution in general relativity. The expansion of the universe serves as a subsidiary condition which transforms Einstein's theory from a first class to a second class constrained system when the physical degrees of freedom (d.o.f.) are identified with transverse traceless excitations. The super-Hamiltonian constraint is solved by eliminating the trace of the momentum in terms of the other variables, and spatial diffeomorphism symmetry is tackled explicitly by imposing transversality. The theorems of Maskawa-Nishijima appositely relate the reduced phase space to the physical variables in canonical functional integral and Dirac's criterion for second class constraints to nonvanishing Faddeev-Popov determinants in the phase space measures. A reduced physical Hamiltonian for intrinsic time evolution of the two physical d.o.f. emerges. Freed from the first class Dirac algebra, deformation of the Hamiltonian constraint is permitted, and natural extension of the Hamiltonian while maintaining spatial diffeomorphism invariance leads to a theory with Cotton-York term as the ultraviolet completion of Einstein's theory.

p-Forms and diffeomorphisms: Hamiltonian formulation

NASA Astrophysics Data System (ADS)

Baulieu, Laurent; Henneaux, Marc

1987-07-01

The BRST charges corresponding to various (equivalent) ways of writing the action of the diffeomorphism group on p-form gauge fields are canonically related by a canonical transformation in the extended phase space which is explicitly constructed. The occurrence of higher order structure functions is pointed out. Also at: Centro de Estudios Cientificos de Santiago, Casilla 16443, Santiago 9, Chile.

Robust Criterion for the Existence of Nonhyperbolic Ergodic Measures

NASA Astrophysics Data System (ADS)

Bochi, Jairo; Bonatti, Christian; Díaz, Lorenzo J.

2016-06-01

We give explicit C 1-open conditions that ensure that a diffeomorphism possesses a nonhyperbolic ergodic measure with positive entropy. Actually, our criterion provides the existence of a partially hyperbolic compact set with one-dimensional center and positive topological entropy on which the center Lyapunov exponent vanishes uniformly. The conditions of the criterion are met on a C 1-dense and open subset of the set of diffeomorphisms having a robust cycle. As a corollary, there exists a C 1-open and dense subset of the set of non-Anosov robustly transitive diffeomorphisms consisting of systems with nonhyperbolic ergodic measures with positive entropy. The criterion is based on a notion of a blender defined dynamically in terms of strict invariance of a family of discs.

Change detection in the dynamics of an intracellular protein synthesis model using nonlinear Kalman filtering.

PubMed

Rigatos, Gerasimos G; Rigatou, Efthymia G; Djida, Jean Daniel

2015-10-01

A method for early diagnosis of parametric changes in intracellular protein synthesis models (e.g. the p53 protein - mdm2 inhibitor model) is developed with the use of a nonlinear Kalman Filtering approach (Derivative-free nonlinear Kalman Filter) and of statistical change detection methods. The intracellular protein synthesis dynamic model is described by a set of coupled nonlinear differential equations. It is shown that such a dynamical system satisfies differential flatness properties and this allows to transform it, through a change of variables (diffeomorphism), to the so-called linear canonical form. For the linearized equivalent of the dynamical system, state estimation can be performed using the Kalman Filter recursion. Moreover, by applying an inverse transformation based on the previous diffeomorphism it becomes also possible to obtain estimates of the state variables of the initial nonlinear model. By comparing the output of the Kalman Filter (which is assumed to correspond to the undistorted dynamical model) with measurements obtained from the monitored protein synthesis system, a sequence of differences (residuals) is obtained. The statistical processing of the residuals with the use of x2 change detection tests, can provide indication within specific confidence intervals about parametric changes in the considered biological system and consequently indications about the appearance of specific diseases (e.g. malignancies).

The Camassa-Holm equation as an incompressible Euler equation: A geometric point of view

NASA Astrophysics Data System (ADS)

Gallouët, Thomas; Vialard, François-Xavier

2018-04-01

The group of diffeomorphisms of a compact manifold endowed with the L2 metric acting on the space of probability densities gives a unifying framework for the incompressible Euler equation and the theory of optimal mass transport. Recently, several authors have extended optimal transport to the space of positive Radon measures where the Wasserstein-Fisher-Rao distance is a natural extension of the classical L2-Wasserstein distance. In this paper, we show a similar relation between this unbalanced optimal transport problem and the Hdiv right-invariant metric on the group of diffeomorphisms, which corresponds to the Camassa-Holm (CH) equation in one dimension. Geometrically, we present an isometric embedding of the group of diffeomorphisms endowed with this right-invariant metric in the automorphisms group of the fiber bundle of half densities endowed with an L2 type of cone metric. This leads to a new formulation of the (generalized) CH equation as a geodesic equation on an isotropy subgroup of this automorphisms group; On S1, solutions to the standard CH thus give radially 1-homogeneous solutions of the incompressible Euler equation on R2 which preserves a radial density that has a singularity at 0. An other application consists in proving that smooth solutions of the Euler-Arnold equation for the Hdiv right-invariant metric are length minimizing geodesics for sufficiently short times.

Spherical Demons: Fast Diffeomorphic Landmark-Free Surface Registration

PubMed Central

Yeo, B.T. Thomas; Sabuncu, Mert R.; Vercauteren, Tom; Ayache, Nicholas; Fischl, Bruce; Golland, Polina

2010-01-01

We present the Spherical Demons algorithm for registering two spherical images. By exploiting spherical vector spline interpolation theory, we show that a large class of regularizors for the modified Demons objective function can be efficiently approximated on the sphere using iterative smoothing. Based on one parameter subgroups of diffeomorphisms, the resulting registration is diffeomorphic and fast. The Spherical Demons algorithm can also be modified to register a given spherical image to a probabilistic atlas. We demonstrate two variants of the algorithm corresponding to warping the atlas or warping the subject. Registration of a cortical surface mesh to an atlas mesh, both with more than 160k nodes requires less than 5 minutes when warping the atlas and less than 3 minutes when warping the subject on a Xeon 3.2GHz single processor machine. This is comparable to the fastest non-diffeomorphic landmark-free surface registration algorithms. Furthermore, the accuracy of our method compares favorably to the popular FreeSurfer registration algorithm. We validate the technique in two different applications that use registration to transfer segmentation labels onto a new image: (1) parcellation of in-vivo cortical surfaces and (2) Brodmann area localization in ex-vivo cortical surfaces. PMID:19709963

Representations of spacetime diffeomorphisms. I. Canonical parametrized field theories

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

Isham, C.J.; Kuchar, K.V.

The super-Hamiltonian and supermomentum in canonical geometrodynamics or in a parametried field theory on a given Riemannian background have Poisson brackets which obey the Dirac relations. By smearing the supermomentum with vector fields VepsilonL Diff..sigma.. on the space manifold ..sigma.., the Lie algebra L Diff ..sigma.. of the spatial diffeomorphism group Diff ..sigma.. can be mapped antihomomorphically into the Poisson bracket algebra on the phase space of the system. The explicit dependence of the Poisson brackets between two super-Hamiltonians on canonical coordinates (spatial metrics in geometrodynamics and embedding variables in parametrized theories) is usually regarded as an indication that themore » Dirac relations cannot be connected with a representation of the complete Lie algebra L Diff M of spacetime diffeomorphisms.« less

Hamiltonian Systems and Optimal Control in Computational Anatomy: 100 Years Since D'Arcy Thompson.

PubMed

Miller, Michael I; Trouvé, Alain; Younes, Laurent

2015-01-01

The Computational Anatomy project is the morphome-scale study of shape and form, which we model as an orbit under diffeomorphic group action. Metric comparison calculates the geodesic length of the diffeomorphic flow connecting one form to another. Geodesic connection provides a positioning system for coordinatizing the forms and positioning their associated functional information. This article reviews progress since the Euler-Lagrange characterization of the geodesics a decade ago. Geodesic positioning is posed as a series of problems in Hamiltonian control, which emphasize the key reduction from the Eulerian momentum with dimension of the flow of the group, to the parametric coordinates appropriate to the dimension of the submanifolds being positioned. The Hamiltonian viewpoint provides important extensions of the core setting to new, object-informed positioning systems. Several submanifold mapping problems are discussed as they apply to metamorphosis, multiple shape spaces, and longitudinal time series studies of growth and atrophy via shape splines.

Dirac operator on spinors and diffeomorphisms

NASA Astrophysics Data System (ADS)

Dąbrowski, Ludwik; Dossena, Giacomo

2013-01-01

The issue of general covariance of spinors and related objects is reconsidered. Given an oriented manifold M, to each spin structure σ and Riemannian metric g there is associated a space Sσ, g of spinor fields on M and a Hilbert space {H}_{σ, g}= L^2(S_{σ, g}, vol_{g}(M)) of L2-spinors of Sσ, g. The group Diff+(M) of orientation-preserving diffeomorphisms of M acts both on g (by pullback) and on [σ] (by a suitably defined pullback f*σ). Any f ∈ Diff+(M) lifts in exactly two ways to a unitary operator U from {H}_{σ, g} to {H}_{f^*σ ,f^*g}. The canonically defined Dirac operator is shown to be equivariant with respect to the action of U, so in particular its spectrum is invariant under the diffeomorphisms.

New phases of D ge 2 current and diffeomorphism algebras in particle physics

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

Tze, Chia-Hsiung.

We survey some global results and open issues of current algebras and their canonical field theoretical realization in D {ge} 2 dimensional spacetime. We assess the status of the representation theory of their generalized Kac-Moody and diffeomorphism algebras. Particular emphasis is put on higher dimensional analogs of fermi-bose correspondence, complex analyticity and the phase entanglements of anyonic solitons with exotic spin and statistics. 101 refs.

Quasi-local conserved charges in Lorenz-diffeomorphism covariant theory of gravity

NASA Astrophysics Data System (ADS)

Adami, H.; Setare, M. R.

2016-04-01

In this paper, using the combined Lorenz-diffeomorphism symmetry, we find a general formula for the quasi-local conserved charge of the covariant gravity theories in a first order formalism of gravity. We simplify the general formula for the Lovelock theory of gravity. Afterwards, we apply the obtained formula on BHT gravity to obtain the energy and angular momentum of the rotating OTT black hole solution in the context of this theory.

Schwarzschild solution from Weyl transverse gravity

NASA Astrophysics Data System (ADS)

Oda, Ichiro

2017-01-01

We study classical solutions in the Weyl-transverse (WTDiff) gravity. The WTDiff gravity is invariant under both the local Weyl (conformal) transformation and the volume preserving diffeomorphisms (Diff) (transverse diffeomorphisms (TDiff)) and is known to be equivalent to general relativity at least at the classical level. In particular, we find that in a general spacetime dimension, the Schwarzschild metric is a classical solution in the WTDiff gravity when it is expressed in the Cartesian coordinate system.

FreeSurfer-initiated fully-automated subcortical brain segmentation in MRI using Large Deformation Diffeomorphic Metric Mapping.

PubMed

Khan, Ali R; Wang, Lei; Beg, Mirza Faisal

2008-07-01

Fully-automated brain segmentation methods have not been widely adopted for clinical use because of issues related to reliability, accuracy, and limitations of delineation protocol. By combining the probabilistic-based FreeSurfer (FS) method with the Large Deformation Diffeomorphic Metric Mapping (LDDMM)-based label-propagation method, we are able to increase reliability and accuracy, and allow for flexibility in template choice. Our method uses the automated FreeSurfer subcortical labeling to provide a coarse-to-fine introduction of information in the LDDMM template-based segmentation resulting in a fully-automated subcortical brain segmentation method (FS+LDDMM). One major advantage of the FS+LDDMM-based approach is that the automatically generated segmentations generated are inherently smooth, thus subsequent steps in shape analysis can directly follow without manual post-processing or loss of detail. We have evaluated our new FS+LDDMM method on several databases containing a total of 50 subjects with different pathologies, scan sequences and manual delineation protocols for labeling the basal ganglia, thalamus, and hippocampus. In healthy controls we report Dice overlap measures of 0.81, 0.83, 0.74, 0.86 and 0.75 for the right caudate nucleus, putamen, pallidum, thalamus and hippocampus respectively. We also find statistically significant improvement of accuracy in FS+LDDMM over FreeSurfer for the caudate nucleus and putamen of Huntington's disease and Tourette's syndrome subjects, and the right hippocampus of Schizophrenia subjects.

Chaotic attractors of relaxation oscillators

NASA Astrophysics Data System (ADS)

Guckenheimer, John; Wechselberger, Martin; Young, Lai-Sang

2006-03-01

We develop a general technique for proving the existence of chaotic attractors for three-dimensional vector fields with two time scales. Our results connect two important areas of dynamical systems: the theory of chaotic attractors for discrete two-dimensional Henon-like maps and geometric singular perturbation theory. Two-dimensional Henon-like maps are diffeomorphisms that limit on non-invertible one-dimensional maps. Wang and Young formulated hypotheses that suffice to prove the existence of chaotic attractors in these families. Three-dimensional singularly perturbed vector fields have return maps that are also two-dimensional diffeomorphisms limiting on one-dimensional maps. We describe a generic mechanism that produces folds in these return maps and demonstrate that the Wang-Young hypotheses are satisfied. Our analysis requires a careful study of the convergence of the return maps to their singular limits in the Ck topology for k >= 3. The theoretical results are illustrated with a numerical study of a variant of the forced van der Pol oscillator.

Resolving the issue of branched Hamiltonian in modified Lanczos-Lovelock gravity

NASA Astrophysics Data System (ADS)

Ruz, Soumendranath; Mandal, Ranajit; Debnath, Subhra; Sanyal, Abhik Kumar

2016-07-01

The Hamiltonian constraint H_c = N{H} = 0, defines a diffeomorphic structure on spatial manifolds by the lapse function N in general theory of relativity. However, it is not manifest in Lanczos-Lovelock gravity, since the expression for velocity in terms of the momentum is multivalued. Thus the Hamiltonian is a branch function of momentum. Here we propose an extended theory of Lanczos-Lovelock gravity to construct a unique Hamiltonian in its minisuperspace version, which results in manifest diffeomorphic invariance and canonical quantization.

DR-TAMAS: Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures

PubMed Central

Irfanoglu, M. Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B.; Sadeghi, Neda; Thomas, Cibu P.; Pierpaoli, Carlo

2016-01-01

In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. PMID:26931817

A LAGRANGIAN GAUSS-NEWTON-KRYLOV SOLVER FOR MASS- AND INTENSITY-PRESERVING DIFFEOMORPHIC IMAGE REGISTRATION.

PubMed

Mang, Andreas; Ruthotto, Lars

2017-01-01

We present an efficient solver for diffeomorphic image registration problems in the framework of Large Deformations Diffeomorphic Metric Mappings (LDDMM). We use an optimal control formulation, in which the velocity field of a hyperbolic PDE needs to be found such that the distance between the final state of the system (the transformed/transported template image) and the observation (the reference image) is minimized. Our solver supports both stationary and non-stationary (i.e., transient or time-dependent) velocity fields. As transformation models, we consider both the transport equation (assuming intensities are preserved during the deformation) and the continuity equation (assuming mass-preservation). We consider the reduced form of the optimal control problem and solve the resulting unconstrained optimization problem using a discretize-then-optimize approach. A key contribution is the elimination of the PDE constraint using a Lagrangian hyperbolic PDE solver. Lagrangian methods rely on the concept of characteristic curves. We approximate these curves using a fourth-order Runge-Kutta method. We also present an efficient algorithm for computing the derivatives of the final state of the system with respect to the velocity field. This allows us to use fast Gauss-Newton based methods. We present quickly converging iterative linear solvers using spectral preconditioners that render the overall optimization efficient and scalable. Our method is embedded into the image registration framework FAIR and, thus, supports the most commonly used similarity measures and regularization functionals. We demonstrate the potential of our new approach using several synthetic and real world test problems with up to 14.7 million degrees of freedom.

DR-TAMAS: Diffeomorphic Registration for Tensor Accurate Alignment of Anatomical Structures.

PubMed

Irfanoglu, M Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B; Sadeghi, Neda; Thomas, Cibu P; Pierpaoli, Carlo

2016-05-15

In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantum gravity in the Eddington purely affine picture

NASA Astrophysics Data System (ADS)

Martellini, M.

1984-06-01

It was shown by Kijowski and Tulczjew that pure gravity with a cosmological constant can be obtained by a covariant Legendre transformation of a purely affine Lagrangian "in the manner of Eddington" constructed from a symmetric linear connection. In this paper I prove by explicit calculations that the Eddington Lagrangian is equivalent, in the sense which gives the same field equations, to a polynomial effective Lagrangian which turns out to be power-counting renormalizable. Then a formal proof of the unitarity of this theory is stated in the Kugo-Ojima formalism on the basis of the existence of two local Becchi-Rouet-Stora symmetries. These supertransformations are related to the algebra of the diffeomorphisms of the space-time, as well as to that of the volume-preserving space-time transformations which are not fixed by the gauge fixing used for the diffeomorphism group itself. Furthermore, I find that in the purely affine picture quantum gravity exhibits an infrared freedom. Since now the self-coupling constant is given by the cosmological constant, such a property could explain the observed almost zero value of the cosmological term at very large distances, i.e., to very low energies.

Nonlinear image registration with bidirectional metric and reciprocal regularization

PubMed Central

Ying, Shihui; Li, Dan; Xiao, Bin; Peng, Yaxin; Du, Shaoyi; Xu, Meifeng

2017-01-01

Nonlinear registration is an important technique to align two different images and widely applied in medical image analysis. In this paper, we develop a novel nonlinear registration framework based on the diffeomorphic demons, where a reciprocal regularizer is introduced to assume that the deformation between two images is an exact diffeomorphism. In detail, first, we adopt a bidirectional metric to improve the symmetry of the energy functional, whose variables are two reciprocal deformations. Secondly, we slack these two deformations into two independent variables and introduce a reciprocal regularizer to assure the deformations being the exact diffeomorphism. Then, we utilize an alternating iterative strategy to decouple the model into two minimizing subproblems, where a new closed form for the approximate velocity of deformation is calculated. Finally, we compare our proposed algorithm on two data sets of real brain MR images with two relative and conventional methods. The results validate that our proposed method improves accuracy and robustness of registration, as well as the gained bidirectional deformations are actually reciprocal. PMID:28231342

Hyperbolic Harmonic Mapping for Surface Registration

PubMed Central

Shi, Rui; Zeng, Wei; Su, Zhengyu; Jiang, Jian; Damasio, Hanna; Lu, Zhonglin; Wang, Yalin; Yau, Shing-Tung; Gu, Xianfeng

2016-01-01

Automatic computation of surface correspondence via harmonic map is an active research field in computer vision, computer graphics and computational geometry. It may help document and understand physical and biological phenomena and also has broad applications in biometrics, medical imaging and motion capture inducstries. Although numerous studies have been devoted to harmonic map research, limited progress has been made to compute a diffeomorphic harmonic map on general topology surfaces with landmark constraints. This work conquers this problem by changing the Riemannian metric on the target surface to a hyperbolic metric so that the harmonic mapping is guaranteed to be a diffeomorphism under landmark constraints. The computational algorithms are based on Ricci flow and nonlinear heat diffusion methods. The approach is general and robust. We employ our algorithm to study the constrained surface registration problem which applies to both computer vision and medical imaging applications. Experimental results demonstrate that, by changing the Riemannian metric, the registrations are always diffeomorphic and achieve relatively high performance when evaluated with some popular surface registration evaluation standards. PMID:27187948

Novel symmetries in Weyl-invariant gravity with massive gauge field

NASA Astrophysics Data System (ADS)

Abhinav, K.; Shukla, A.; Panigrahi, P. K.

2016-11-01

The background field method is used to linearize the Weyl-invariant scalar-tensor gravity, coupled with a Stückelberg field. For a generic background metric, this action is found not to be invariant, under both a diffeomorphism and generalized Weyl symmetry, the latter being a combination of gauge and Weyl transformations. Interestingly, the quadratic Lagrangian, emerging from a background of Minkowski metric, respects both transformations independently. The Becchi-Rouet-Stora-Tyutin symmetry of scalar-tensor gravity coupled with a Stückelberg-like massive gauge particle, possessing a diffeomorphism and generalized Weyl symmetry, reveals that in both cases negative-norm states with unphysical degrees of freedom do exist. We then show that, by combining diffeomorphism and generalized Weyl symmetries, all the ghost states decouple, thereby removing the unphysical redundancies of the theory. During this process, the scalar field does not represent any dynamic mode, yet modifies the usual harmonic gauge condition through non-minimal coupling with gravity.

Homogeneous Yang-Baxter deformations as generalized diffeomorphisms

NASA Astrophysics Data System (ADS)

Sakamoto, Jun-ichi; Sakatani, Yuho; Yoshida, Kentaroh

2017-10-01

Yang-Baxter (YB) deformations of string sigma model provide deformed target spaces. We propose that homogeneous YB deformations always lead to a certain class of β-twisted backgrounds and represent the bosonic part of the supergravity fields in terms of the classical r-matrix associated with the YB deformation. We then show that various β-twisted backgrounds can be realized by considering generalized diffeomorphisms in the undeformed background. Our result extends the notable relation between the YB deformations and (non-commuting) TsT transformations. We also discuss more general deformations beyond the YB deformations.

Interactions of a String Inspired Graviton Field

NASA Astrophysics Data System (ADS)

Branson, Thomas P.; Rodgers, V. G. J.; Yasuda, Takeshi

We continue to explore the possibility that the graviton in two dimensions is related to a quadratic differential that appears in the anomalous contribution of the gravitational effective action for chiral fermions. A higher dimensional analog of this field might exist as well. We improve the defining action for this diffeomorphism tensor field and establish a principle for how it interacts with other fields and with point particles in any dimension. All interactions are related to the action of the diffeomorphism group. We discuss possible interpretations of this field.

Area-Preserving Diffeomorphisms, W∞ and { U}q [sl(2)] in Chern-Simons Theory and the Quantum Hall System

NASA Astrophysics Data System (ADS)

Kogan, Ian I.

We discuss a quantum { U}q [sl(2)] symmetry in the Landau problem, which naturally arises due to the relation between { U}q [sl(2)] and the group of magnetic translations. The latter is connected with W∞ and area-preserving (symplectic) diffeomorphisms which are the canonical transformations in the two-dimensional phase space. We shall discuss the hidden quantum symmetry in a 2 + 1 gauge theory with the Chern-Simons term and in a quantum Hall system, which are both connected with the Landau problem.

The Supersymmetric Effective Field Theory of Inflation

DOE PAGES

Delacrétaz, Luca V.; Gorbenko, Victor; Senatore, Leonardo

2017-03-10

We construct the Supersymmetric Effective Field Theory of Inflation, that is the most general theory of inflationary fluctuations when time-translations and supersymmetry are spontaneously broken. The non-linear realization of these invariances allows us to define a complete SUGRA multiplet containing the graviton, the gravitino, the Goldstone of time translations and the Goldstino, with no auxiliary fields. Going to a unitary gauge where only the graviton and the gravitino are present, we write the most general Lagrangian built out of the fluctuations of these fields, invariant under time-dependent spatial diffeomorphisms, but softly-breaking time diffeomorphisms and gauged SUSY. With a suitable Stückelbergmore » transformation, we introduce the Goldstone boson of time translation and the Goldstino of SUSY. No additional dynamical light field is needed. In the high energy limit, larger than the inflationary Hubble scale for the Goldstino, these fields decouple from the graviton and the gravitino, greatly simplifying the analysis in this regime. We study the phenomenology of this Lagrangian. The Goldstino can have a non-relativistic dispersion relation. Gravitino and Goldstino affect the primordial curvature perturbations at loop level. The UV modes running in the loops generate three-point functions which are degenerate with the ones coming from operators already present in the absence of supersymmetry. Their size is potentially as large as corresponding to fNL equil.,orthog.~1 or, for particular operators, even >> 1. The non-degenerate contribution from modes of order H is estimated to be very small.« less

Time and a physical Hamiltonian for quantum gravity.

PubMed

Husain, Viqar; Pawłowski, Tomasz

2012-04-06

We present a nonperturbative quantization of general relativity coupled to dust and other matter fields. The dust provides a natural time variable, leading to a physical Hamiltonian with spatial diffeomorphism symmetry. The surprising feature is that the Hamiltonian is not a square root. This property, together with the kinematical structure of loop quantum gravity, provides a complete theory of quantum gravity, and puts applications to cosmology, quantum gravitational collapse, and Hawking radiation within technical reach. © 2012 American Physical Society

MIND Demons: Symmetric Diffeomorphic Deformable Registration of MR and CT for Image-Guided Spine Surgery.

PubMed

Reaungamornrat, Sureerat; De Silva, Tharindu; Uneri, Ali; Vogt, Sebastian; Kleinszig, Gerhard; Khanna, Akhil J; Wolinsky, Jean-Paul; Prince, Jerry L; Siewerdsen, Jeffrey H

2016-11-01

Intraoperative localization of target anatomy and critical structures defined in preoperative MR/CT images can be achieved through the use of multimodality deformable registration. We propose a symmetric diffeomorphic deformable registration algorithm incorporating a modality-independent neighborhood descriptor (MIND) and a robust Huber metric for MR-to-CT registration. The method, called MIND Demons, finds a deformation field between two images by optimizing an energy functional that incorporates both the forward and inverse deformations, smoothness on the integrated velocity fields, a modality-insensitive similarity function suitable to multimodality images, and smoothness on the diffeomorphisms themselves. Direct optimization without relying on the exponential map and stationary velocity field approximation used in conventional diffeomorphic Demons is carried out using a Gauss-Newton method for fast convergence. Registration performance and sensitivity to registration parameters were analyzed in simulation, phantom experiments, and clinical studies emulating application in image-guided spine surgery, and results were compared to mutual information (MI) free-form deformation (FFD), local MI (LMI) FFD, normalized MI (NMI) Demons, and MIND with a diffusion-based registration method (MIND-elastic). The method yielded sub-voxel invertibility (0.008 mm) and nonzero-positive Jacobian determinants. It also showed improved registration accuracy in comparison to the reference methods, with mean target registration error (TRE) of 1.7 mm compared to 11.3, 3.1, 5.6, and 2.4 mm for MI FFD, LMI FFD, NMI Demons, and MIND-elastic methods, respectively. Validation in clinical studies demonstrated realistic deformations with sub-voxel TRE in cases of cervical, thoracic, and lumbar spine.

MIND Demons: Symmetric Diffeomorphic Deformable Registration of MR and CT for Image-Guided Spine Surgery

PubMed Central

Reaungamornrat, Sureerat; De Silva, Tharindu; Uneri, Ali; Vogt, Sebastian; Kleinszig, Gerhard; Khanna, Akhil J; Wolinsky, Jean-Paul; Prince, Jerry L.

2016-01-01

Intraoperative localization of target anatomy and critical structures defined in preoperative MR/CT images can be achieved through the use of multimodality deformable registration. We propose a symmetric diffeomorphic deformable registration algorithm incorporating a modality-independent neighborhood descriptor (MIND) and a robust Huber metric for MR-to-CT registration. The method, called MIND Demons, finds a deformation field between two images by optimizing an energy functional that incorporates both the forward and inverse deformations, smoothness on the integrated velocity fields, a modality-insensitive similarity function suitable to multimodality images, and smoothness on the diffeomorphisms themselves. Direct optimization without relying on the exponential map and stationary velocity field approximation used in conventional diffeomorphic Demons is carried out using a Gauss-Newton method for fast convergence. Registration performance and sensitivity to registration parameters were analyzed in simulation, phantom experiments, and clinical studies emulating application in image-guided spine surgery, and results were compared to mutual information (MI) free-form deformation (FFD), local MI (LMI) FFD, normalized MI (NMI) Demons, and MIND with a diffusion-based registration method (MIND-elastic). The method yielded sub-voxel invertibility (0.008 mm) and nonzero-positive Jacobian determinants. It also showed improved registration accuracy in comparison to the reference methods, with mean target registration error (TRE) of 1.7 mm compared to 11.3, 3.1, 5.6, and 2.4 mm for MI FFD, LMI FFD, NMI Demons, and MIND-elastic methods, respectively. Validation in clinical studies demonstrated realistic deformations with sub-voxel TRE in cases of cervical, thoracic, and lumbar spine. PMID:27295656

Cohomological rigidity of manifolds defined by 3-dimensional polytopes

NASA Astrophysics Data System (ADS)

Buchstaber, V. M.; Erokhovets, N. Yu.; Masuda, M.; Panov, T. E.; Park, S.

2017-04-01

A family of closed manifolds is said to be cohomologically rigid if a cohomology ring isomorphism implies a diffeomorphism for any two manifolds in the family. Cohomological rigidity is established here for large families of 3-dimensional and 6-dimensional manifolds defined by 3-dimensional polytopes. The class \\mathscr{P} of 3-dimensional combinatorial simple polytopes P different from tetrahedra and without facets forming 3- and 4-belts is studied. This class includes mathematical fullerenes, that is, simple 3- polytopes with only 5-gonal and 6-gonal facets. By a theorem of Pogorelov, any polytope in \\mathscr{P} admits in Lobachevsky 3-space a right-angled realisation which is unique up to isometry. Our families of smooth manifolds are associated with polytopes in the class \\mathscr{P}. The first family consists of 3-dimensional small covers of polytopes in \\mathscr{P}, or equivalently, hyperbolic 3-manifolds of Löbell type. The second family consists of 6-dimensional quasitoric manifolds over polytopes in \\mathscr{P}. Our main result is that both families are cohomologically rigid, that is, two manifolds M and M' from either family are diffeomorphic if and only if their cohomology rings are isomorphic. It is also proved that if M and M' are diffeomorphic, then their corresponding polytopes P and P' are combinatorially equivalent. These results are intertwined with classical subjects in geometry and topology such as the combinatorics of 3-polytopes, the Four Colour Theorem, aspherical manifolds, a diffeomorphism classification of 6-manifolds, and invariance of Pontryagin classes. The proofs use techniques of toric topology. Bibliography: 69 titles.

Local and gauge invariant observables in gravity

NASA Astrophysics Data System (ADS)

Khavkine, Igor

2015-09-01

It is well known that general relativity (GR) does not possess any non-trivial local (in a precise standard sense) and diffeomorphism invariant observable. We propose a generalized notion of local observables, which retain the most important properties that follow from the standard definition of locality, yet is flexible enough to admit a large class of diffeomorphism invariant observables in GR. The generalization comes at a small price—that the domain of definition of a generalized local observable may not cover the entire phase space of GR and two such observables may have distinct domains. However, the subset of metrics on which generalized local observables can be defined is in a sense generic (its open interior is non-empty in the Whitney strong topology). Moreover, generalized local gauge invariant observables are sufficient to separate diffeomorphism orbits on this admissible subset of the phase space. Connecting the construction with the notion of differential invariants gives a general scheme for defining generalized local gauge invariant observables in arbitrary gauge theories, which happens to agree with well-known results for Maxwell and Yang-Mills theories.

Remarks on the "Non-canonicity Puzzle": Lagrangian Symmetries of the Einstein-Hilbert Action

NASA Astrophysics Data System (ADS)

Kiriushcheva, N.; Komorowski, P. G.; Kuzmin, S. V.

2012-07-01

Given the non-canonical relationship between variables used in the Hamiltonian formulations of the Einstein-Hilbert action (due to Pirani, Schild, Skinner (PSS) and Dirac) and the Arnowitt-Deser-Misner (ADM) action, and the consequent difference in the gauge transformations generated by the first-class constraints of these two formulations, the assumption that the Lagrangians from which they were derived are equivalent leads to an apparent contradiction that has been called "the non-canonicity puzzle". In this work we shall investigate the group properties of two symmetries derived for the Einstein-Hilbert action: diffeomorphism, which follows from the PSS and Dirac formulations, and the one that arises from the ADM formulation. We demonstrate that unlike the diffeomorphism transformations, the ADM transformations (as well as others, which can be constructed for the Einstein-Hilbert Lagrangian using Noether's identities) do not form a group. This makes diffeomorphism transformations unique (the term "canonical" symmetry might be suggested). If the two Lagrangians are to be called equivalent, canonical symmetry must be preserved. The interplay between general covariance and the canonicity of the variables used is discussed.

Diffeomorphism groups and nonlinear quantum mechanics

NASA Astrophysics Data System (ADS)

Goldin, Gerald A.

2012-02-01

This talk is dedicated to my friend and collaborator, Prof. Dr. Heinz-Dietrich Doebner, on the occasion of his 80th birthday. I shall review some highlights of the approach we have taken in deriving and interpreting an interesting class of nonlinear time-evolution equations for quantum-mechanical wave functions, with few equations; more detail may be found in the references. Then I shall comment on the corresponding hydrodynamical description.

A SEMI-LAGRANGIAN TWO-LEVEL PRECONDITIONED NEWTON-KRYLOV SOLVER FOR CONSTRAINED DIFFEOMORPHIC IMAGE REGISTRATION.

PubMed

Mang, Andreas; Biros, George

2017-01-01

We propose an efficient numerical algorithm for the solution of diffeomorphic image registration problems. We use a variational formulation constrained by a partial differential equation (PDE), where the constraints are a scalar transport equation. We use a pseudospectral discretization in space and second-order accurate semi-Lagrangian time stepping scheme for the transport equations. We solve for a stationary velocity field using a preconditioned, globalized, matrix-free Newton-Krylov scheme. We propose and test a two-level Hessian preconditioner. We consider two strategies for inverting the preconditioner on the coarse grid: a nested preconditioned conjugate gradient method (exact solve) and a nested Chebyshev iterative method (inexact solve) with a fixed number of iterations. We test the performance of our solver in different synthetic and real-world two-dimensional application scenarios. We study grid convergence and computational efficiency of our new scheme. We compare the performance of our solver against our initial implementation that uses the same spatial discretization but a standard, explicit, second-order Runge-Kutta scheme for the numerical time integration of the transport equations and a single-level preconditioner. Our improved scheme delivers significant speedups over our original implementation. As a highlight, we observe a 20 × speedup for a two dimensional, real world multi-subject medical image registration problem.

Spherical demons: fast diffeomorphic landmark-free surface registration.

PubMed

Yeo, B T Thomas; Sabuncu, Mert R; Vercauteren, Tom; Ayache, Nicholas; Fischl, Bruce; Golland, Polina

2010-03-01

We present the Spherical Demons algorithm for registering two spherical images. By exploiting spherical vector spline interpolation theory, we show that a large class of regularizors for the modified Demons objective function can be efficiently approximated on the sphere using iterative smoothing. Based on one parameter subgroups of diffeomorphisms, the resulting registration is diffeomorphic and fast. The Spherical Demons algorithm can also be modified to register a given spherical image to a probabilistic atlas. We demonstrate two variants of the algorithm corresponding to warping the atlas or warping the subject. Registration of a cortical surface mesh to an atlas mesh, both with more than 160 k nodes requires less than 5 min when warping the atlas and less than 3 min when warping the subject on a Xeon 3.2 GHz single processor machine. This is comparable to the fastest nondiffeomorphic landmark-free surface registration algorithms. Furthermore, the accuracy of our method compares favorably to the popular FreeSurfer registration algorithm. We validate the technique in two different applications that use registration to transfer segmentation labels onto a new image 1) parcellation of in vivo cortical surfaces and 2) Brodmann area localization in ex vivo cortical surfaces.

Validation of an improved 'diffeomorphic demons' algorithm for deformable image registration in image-guided radiation therapy.

PubMed

Zhou, Lu; Zhou, Linghong; Zhang, Shuxu; Zhen, Xin; Yu, Hui; Zhang, Guoqian; Wang, Ruihao

2014-01-01

Deformable image registration (DIR) was widely used in radiation therapy, such as in automatic contour generation, dose accumulation, tumor growth or regression analysis. To achieve higher registration accuracy and faster convergence, an improved 'diffeomorphic demons' registration algorithm was proposed and validated. Based on Brox et al.'s gradient constancy assumption and Malis's efficient second-order minimization (ESM) algorithm, a grey value gradient similarity term and a transformation error term were added into the demons energy function, and a formula was derived to calculate the update of transformation field. The limited Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm was used to optimize the energy function so that the iteration number could be determined automatically. The proposed algorithm was validated using mathematically deformed images and physically deformed phantom images. Compared with the original 'diffeomorphic demons' algorithm, the registration method proposed achieve a higher precision and a faster convergence speed. Due to the influence of different scanning conditions in fractionated radiation, the density range of the treatment image and the planning image may be different. In such a case, the improved demons algorithm can achieve faster and more accurate radiotherapy.

Symmetric log-domain diffeomorphic Registration: a demons-based approach.

PubMed

Vercauteren, Tom; Pennec, Xavier; Perchant, Aymeric; Ayache, Nicholas

2008-01-01

Modern morphometric studies use non-linear image registration to compare anatomies and perform group analysis. Recently, log-Euclidean approaches have contributed to promote the use of such computational anatomy tools by permitting simple computations of statistics on a rather large class of invertible spatial transformations. In this work, we propose a non-linear registration algorithm perfectly fit for log-Euclidean statistics on diffeomorphisms. Our algorithm works completely in the log-domain, i.e. it uses a stationary velocity field. This implies that we guarantee the invertibility of the deformation and have access to the true inverse transformation. This also means that our output can be directly used for log-Euclidean statistics without relying on the heavy computation of the log of the spatial transformation. As it is often desirable, our algorithm is symmetric with respect to the order of the input images. Furthermore, we use an alternate optimization approach related to Thirion's demons algorithm to provide a fast non-linear registration algorithm. First results show that our algorithm outperforms both the demons algorithm and the recently proposed diffeomorphic demons algorithm in terms of accuracy of the transformation while remaining computationally efficient.

First Law for fields with Internal Gauge Freedom

NASA Astrophysics Data System (ADS)

Prabhu, Kartik

2016-03-01

We extend the analysis of Iyer and Wald to derive the First Law of blackhole mechanics in the presence of fields charged under an `internal gauge group'. We treat diffeomorphisms and gauge transformations in a unified way by formulating the theory on a principal bundle. The first law then relates the energy and angular momentum at infinity to a potential times charge term at the horizon. The gravitational potential and charge give a notion of temperature and entropy respectively.

Classical Optimal Control for Energy Minimization Based On Diffeomorphic Modulation under Observable-Response-Preserving Homotopy.

PubMed

Soley, Micheline B; Markmann, Andreas; Batista, Victor S

2018-06-12

We introduce the so-called "Classical Optimal Control Optimization" (COCO) method for global energy minimization based on the implementation of the diffeomorphic modulation under observable-response-preserving homotopy (DMORPH) gradient algorithm. A probe particle with time-dependent mass m( t;β) and dipole μ( r, t;β) is evolved classically on the potential energy surface V( r) coupled to an electric field E( t;β), as described by the time-dependent density of states represented on a grid, or otherwise as a linear combination of Gaussians generated by the k-means clustering algorithm. Control parameters β defining m( t;β), μ( r, t;β), and E( t;β) are optimized by following the gradients of the energy with respect to β, adapting them to steer the particle toward the global minimum energy configuration. We find that the resulting COCO algorithm is capable of resolving near-degenerate states separated by large energy barriers and successfully locates the global minima of golf potentials on flat and rugged surfaces, previously explored for testing quantum annealing methodologies and the quantum optimal control optimization (QuOCO) method. Preliminary results show successful energy minimization of multidimensional Lennard-Jones clusters. Beyond the analysis of energy minimization in the specific model systems investigated, we anticipate COCO should be valuable for solving minimization problems in general, including optimization of parameters in applications to machine learning and molecular structure determination.

Higgs mechanism for gravity. II. Higher spin connections

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

Boulanger, Nicolas; Kirsch, Ingo; Jefferson Laboratory of Physics, Harvard University, Cambridge, Massachusetts 02138

We continue the work of [Phys. Rev. D 72, 024001 (2005)] in which gravity is considered as the Goldstone realization of a spontaneously broken diffeomorphism group. We complete the discussion of the coset space Diff (d,R)/SO(1,d-1) formed by the d-dimensional group of analytic diffeomorphisms and the Lorentz group. We find that this coset space is parametrized by coordinates, a metric, and an infinite tower of higher-spin or generalized connections. We then study effective actions for the corresponding symmetry breaking which gives mass to the higher spin connections. Our model predicts that gravity is modified at high energies by the exchangemore » of massive higher spin particles.« less

Prima facie questions in quantum gravity

NASA Astrophysics Data System (ADS)

Isham, C. J.

The long history of the study of quantum gravity has thrown up a complex web of ideas and approaches. The aim of this article is to unravel this web a little by analysing some of the {\\em prima facie\\/} questions that can be asked of almost any approach to quantum gravity and whose answers assist in classifying the different schemes. Particular emphasis is placed on (i) the role of background conceptual and technical structure; (ii) the role of spacetime diffeomorphisms; and (iii) the problem of time.

Evaluation of five diffeomorphic image registration algorithms for mouse brain magnetic resonance microscopy.

PubMed

Fu, Zhenrong; Lin, Lan; Tian, Miao; Wang, Jingxuan; Zhang, Baiwen; Chu, Pingping; Li, Shaowu; Pathan, Muhammad Mohsin; Deng, Yulin; Wu, Shuicai

2017-11-01

The development of genetically engineered mouse models for neuronal diseases and behavioural disorders have generated a growing need for small animal imaging. High-resolution magnetic resonance microscopy (MRM) provides powerful capabilities for noninvasive studies of mouse brains, while avoiding some limits associated with the histological procedures. Quantitative comparison of structural images is a critical step in brain imaging analysis, which highly relies on the performance of image registration techniques. Nowadays, there is a mushrooming growth of human brain registration algorithms, while fine-tuning of those algorithms for mouse brain MRMs is rarely addressed. Because of their topology preservation property and outstanding performance in human studies, diffeomorphic transformations have become popular in computational anatomy. In this study, we specially tuned five diffeomorphic image registration algorithms [DARTEL, geodesic shooting, diffeo-demons, SyN (Greedy-SyN and geodesic-SyN)] for mouse brain MRMs and evaluated their performance using three measures [volume overlap percentage (VOP), residual intensity error (RIE) and surface concordance ratio (SCR)]. Geodesic-SyN performed significantly better than the other methods according to all three different measures. These findings are important for the studies on structural brain changes that may occur in wild-type and transgenic mouse brains. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

MIND Demons for MR-to-CT Deformable Image Registration In Image-Guided Spine Surgery

PubMed Central

Reaungamornrat, S.; De Silva, T.; Uneri, A.; Wolinsky, J.-P.; Khanna, A. J.; Kleinszig, G.; Vogt, S.; Prince, J. L.; Siewerdsen, J. H.

2016-01-01

Purpose Localization of target anatomy and critical structures defined in preoperative MR images can be achieved by means of multi-modality deformable registration to intraoperative CT. We propose a symmetric diffeomorphic deformable registration algorithm incorporating a modality independent neighborhood descriptor (MIND) and a robust Huber metric for MR-to-CT registration. Method The method, called MIND Demons, solves for the deformation field between two images by optimizing an energy functional that incorporates both the forward and inverse deformations, smoothness on the velocity fields and the diffeomorphisms, a modality-insensitive similarity function suitable to multi-modality images, and constraints on geodesics in Lagrangian coordinates. Direct optimization (without relying on an exponential map of stationary velocity fields used in conventional diffeomorphic Demons) is carried out using a Gauss-Newton method for fast convergence. Registration performance and sensitivity to registration parameters were analyzed in simulation, in phantom experiments, and clinical studies emulating application in image-guided spine surgery, and results were compared to conventional mutual information (MI) free-form deformation (FFD), local MI (LMI) FFD, and normalized MI (NMI) Demons. Result The method yielded sub-voxel invertibility (0.006 mm) and nonsingular spatial Jacobians with capability to preserve local orientation and topology. It demonstrated improved registration accuracy in comparison to the reference methods, with mean target registration error (TRE) of 1.5 mm compared to 10.9, 2.3, and 4.6 mm for MI FFD, LMI FFD, and NMI Demons methods, respectively. Validation in clinical studies demonstrated realistic deformation with sub-voxel TRE in cases of cervical, thoracic, and lumbar spine. Conclusions A modality-independent deformable registration method has been developed to estimate a viscoelastic diffeomorphic map between preoperative MR and intraoperative CT. The method yields registration accuracy suitable to application in image-guided spine surgery across a broad range of anatomical sites and modes of deformation. PMID:27330239

MIND Demons for MR-to-CT deformable image registration in image-guided spine surgery

NASA Astrophysics Data System (ADS)

Reaungamornrat, S.; De Silva, T.; Uneri, A.; Wolinsky, J.-P.; Khanna, A. J.; Kleinszig, G.; Vogt, S.; Prince, J. L.; Siewerdsen, J. H.

2016-03-01

Purpose: Localization of target anatomy and critical structures defined in preoperative MR images can be achieved by means of multi-modality deformable registration to intraoperative CT. We propose a symmetric diffeomorphic deformable registration algorithm incorporating a modality independent neighborhood descriptor (MIND) and a robust Huber metric for MR-to-CT registration. Method: The method, called MIND Demons, solves for the deformation field between two images by optimizing an energy functional that incorporates both the forward and inverse deformations, smoothness on the velocity fields and the diffeomorphisms, a modality-insensitive similarity function suitable to multi-modality images, and constraints on geodesics in Lagrangian coordinates. Direct optimization (without relying on an exponential map of stationary velocity fields used in conventional diffeomorphic Demons) is carried out using a Gauss-Newton method for fast convergence. Registration performance and sensitivity to registration parameters were analyzed in simulation, in phantom experiments, and clinical studies emulating application in image-guided spine surgery, and results were compared to conventional mutual information (MI) free-form deformation (FFD), local MI (LMI) FFD, and normalized MI (NMI) Demons. Result: The method yielded sub-voxel invertibility (0.006 mm) and nonsingular spatial Jacobians with capability to preserve local orientation and topology. It demonstrated improved registration accuracy in comparison to the reference methods, with mean target registration error (TRE) of 1.5 mm compared to 10.9, 2.3, and 4.6 mm for MI FFD, LMI FFD, and NMI Demons methods, respectively. Validation in clinical studies demonstrated realistic deformation with sub-voxel TRE in cases of cervical, thoracic, and lumbar spine. Conclusions: A modality-independent deformable registration method has been developed to estimate a viscoelastic diffeomorphic map between preoperative MR and intraoperative CT. The method yields registration accuracy suitable to application in image-guided spine surgery across a broad range of anatomical sites and modes of deformation.

MIND Demons for MR-to-CT Deformable Image Registration In Image-Guided Spine Surgery.

PubMed

Reaungamornrat, S; De Silva, T; Uneri, A; Wolinsky, J-P; Khanna, A J; Kleinszig, G; Vogt, S; Prince, J L; Siewerdsen, J H

2016-02-27

Localization of target anatomy and critical structures defined in preoperative MR images can be achieved by means of multi-modality deformable registration to intraoperative CT. We propose a symmetric diffeomorphic deformable registration algorithm incorporating a modality independent neighborhood descriptor (MIND) and a robust Huber metric for MR-to-CT registration. The method, called MIND Demons, solves for the deformation field between two images by optimizing an energy functional that incorporates both the forward and inverse deformations, smoothness on the velocity fields and the diffeomorphisms, a modality-insensitive similarity function suitable to multi-modality images, and constraints on geodesics in Lagrangian coordinates. Direct optimization (without relying on an exponential map of stationary velocity fields used in conventional diffeomorphic Demons) is carried out using a Gauss-Newton method for fast convergence. Registration performance and sensitivity to registration parameters were analyzed in simulation, in phantom experiments, and clinical studies emulating application in image-guided spine surgery, and results were compared to conventional mutual information (MI) free-form deformation (FFD), local MI (LMI) FFD, and normalized MI (NMI) Demons. The method yielded sub-voxel invertibility (0.006 mm) and nonsingular spatial Jacobians with capability to preserve local orientation and topology. It demonstrated improved registration accuracy in comparison to the reference methods, with mean target registration error (TRE) of 1.5 mm compared to 10.9, 2.3, and 4.6 mm for MI FFD, LMI FFD, and NMI Demons methods, respectively. Validation in clinical studies demonstrated realistic deformation with sub-voxel TRE in cases of cervical, thoracic, and lumbar spine. A modality-independent deformable registration method has been developed to estimate a viscoelastic diffeomorphic map between preoperative MR and intraoperative CT. The method yields registration accuracy suitable to application in image-guided spine surgery across a broad range of anatomical sites and modes of deformation.

Spherical Demons: Fast Surface Registration

PubMed Central

Yeo, B.T. Thomas; Sabuncu, Mert; Vercauteren, Tom; Ayache, Nicholas; Fischl, Bruce; Golland, Polina

2009-01-01

We present the fast Spherical Demons algorithm for registering two spherical images. By exploiting spherical vector spline interpolation theory, we show that a large class of regularizers for the modified demons objective function can be efficiently implemented on the sphere using convolution. Based on the one parameter subgroups of diffeomorphisms, the resulting registration is diffeomorphic and fast – registration of two cortical mesh models with more than 100k nodes takes less than 5 minutes, comparable to the fastest surface registration algorithms. Moreover, the accuracy of our method compares favorably to the popular FreeSurfer registration algorithm. We validate the technique in two different settings: (1) parcellation in a set of in-vivo cortical surfaces and (2) Brodmann area localization in ex-vivo cortical surfaces. PMID:18979813

Spherical demons: fast surface registration.

PubMed

Yeo, B T Thomas; Sabuncu, Mert; Vercauteren, Tom; Ayache, Nicholas; Fischl, Bruce; Golland, Polina

2008-01-01

We present the fast Spherical Demons algorithm for registering two spherical images. By exploiting spherical vector spline interpolation theory, we show that a large class of regularizers for the modified demons objective function can be efficiently implemented on the sphere using convolution. Based on the one parameter subgroups of diffeomorphisms, the resulting registration is diffeomorphic and fast - registration of two cortical mesh models with more than 100k nodes takes less than 5 minutes, comparable to the fastest surface registration algorithms. Moreover, the accuracy of our method compares favorably to the popular FreeSurfer registration algorithm. We validate the technique in two different settings: (1) parcellation in a set of in-vivo cortical surfaces and (2) Brodmann area localization in ex-vivo cortical surfaces.

Quicksilver: Fast predictive image registration - A deep learning approach.

PubMed

Yang, Xiao; Kwitt, Roland; Styner, Martin; Niethammer, Marc

2017-09-01

This paper introduces Quicksilver, a fast deformable image registration method. Quicksilver registration for image-pairs works by patch-wise prediction of a deformation model based directly on image appearance. A deep encoder-decoder network is used as the prediction model. While the prediction strategy is general, we focus on predictions for the Large Deformation Diffeomorphic Metric Mapping (LDDMM) model. Specifically, we predict the momentum-parameterization of LDDMM, which facilitates a patch-wise prediction strategy while maintaining the theoretical properties of LDDMM, such as guaranteed diffeomorphic mappings for sufficiently strong regularization. We also provide a probabilistic version of our prediction network which can be sampled during the testing time to calculate uncertainties in the predicted deformations. Finally, we introduce a new correction network which greatly increases the prediction accuracy of an already existing prediction network. We show experimental results for uni-modal atlas-to-image as well as uni-/multi-modal image-to-image registrations. These experiments demonstrate that our method accurately predicts registrations obtained by numerical optimization, is very fast, achieves state-of-the-art registration results on four standard validation datasets, and can jointly learn an image similarity measure. Quicksilver is freely available as an open-source software. Copyright © 2017 Elsevier Inc. All rights reserved.

Asymptotic states and the definition of the S-matrix in quantum gravity

NASA Astrophysics Data System (ADS)

Wiesendanger, C.

2013-04-01

Viewing gravitational energy-momentum p_G^\\mu as equal by observation, but different in essence from inertial energy-momentum p_I^\\mu naturally leads to the gauge theory of volume-preserving diffeomorphisms of an inner Minkowski space M4. The generalized asymptotic free scalar, Dirac and gauge fields in that theory are canonically quantized, the Fock spaces of stationary states are constructed and the gravitational limit—mapping the gravitational energy-momentum onto the inertial energy-momentum to account for their observed equality—is introduced. Next the S-matrix in quantum gravity is defined as the gravitational limit of the transition amplitudes of asymptotic in- to out-states in the gauge theory of volume-preserving diffeomorphisms. The so-defined S-matrix relates in- and out-states of observable particles carrying gravitational equal to inertial energy-momentum. Finally, generalized Lehmann-Symanzik-Zimmermann reduction formulae for scalar, Dirac and gauge fields are established which allow us to express S-matrix elements as the gravitational limit of truncated Fourier-transformed vacuum expectation values of time-ordered products of field operators of the interacting theory. Together with the generating functional of the latter established in Wiesendanger (2011 arXiv:1103.1012) any transition amplitude can in principle be computed consistently to any order in perturbative quantum gravity.

Canonical quantization of general relativity in discrete space-times.

PubMed

Gambini, Rodolfo; Pullin, Jorge

2003-01-17

It has long been recognized that lattice gauge theory formulations, when applied to general relativity, conflict with the invariance of the theory under diffeomorphisms. We analyze discrete lattice general relativity and develop a canonical formalism that allows one to treat constrained theories in Lorentzian signature space-times. The presence of the lattice introduces a "dynamical gauge" fixing that makes the quantization of the theories conceptually clear, albeit computationally involved. The problem of a consistent algebra of constraints is automatically solved in our approach. The approach works successfully in other field theories as well, including topological theories. A simple cosmological application exhibits quantum elimination of the singularity at the big bang.

Medical image registration by combining global and local information: a chain-type diffeomorphic demons algorithm.

PubMed

Liu, Xiaozheng; Yuan, Zhenming; Zhu, Junming; Xu, Dongrong

2013-12-07

The demons algorithm is a popular algorithm for non-rigid image registration because of its computational efficiency and simple implementation. The deformation forces of the classic demons algorithm were derived from image gradients by considering the deformation to decrease the intensity dissimilarity between images. However, the methods using the difference of image intensity for medical image registration are easily affected by image artifacts, such as image noise, non-uniform imaging and partial volume effects. The gradient magnitude image is constructed from the local information of an image, so the difference in a gradient magnitude image can be regarded as more reliable and robust for these artifacts. Then, registering medical images by considering the differences in both image intensity and gradient magnitude is a straightforward selection. In this paper, based on a diffeomorphic demons algorithm, we propose a chain-type diffeomorphic demons algorithm by combining the differences in both image intensity and gradient magnitude for medical image registration. Previous work had shown that the classic demons algorithm can be considered as an approximation of a second order gradient descent on the sum of the squared intensity differences. By optimizing the new dissimilarity criteria, we also present a set of new demons forces which were derived from the gradients of the image and gradient magnitude image. We show that, in controlled experiments, this advantage is confirmed, and yields a fast convergence.

Constraining the break of spatial diffeomorphism invariance with Planck data

NASA Astrophysics Data System (ADS)

Graef, L. L.; Benetti, M.; Alcaniz, J. S.

2017-07-01

The current most accepted paradigm for the early universe cosmology, the inflationary scenario, shows a good agreement with the recent Cosmic Microwave Background (CMB) and polarization data. However, when the inflation consistency relation is relaxed, these observational data exclude a larger range of red tensor tilt values, prevailing the blue ones which are not predicted by the minimal inflationary models. Recently, it has been shown that the assumption of spatial diffeomorphism invariance breaking (SDB) in the context of an effective field theory of inflation leads to interesting observational consequences. Among them, the possibility of generating a blue tensor spectrum, which can recover the specific consistency relation of the String Gas Cosmology, for a certain choice of parameters. We use the most recent CMB data to constrain the SDB model and test its observational viability through a Bayesian analysis assuming as reference an extended ΛCDM+tensor perturbation model, which considers a power-law tensor spectrum parametrized in terms of the tensor-to-scalar ratio, r, and the tensor spectral index, nt. If the inflation consistency relation is imposed, r=-8 nt, we obtain a strong evidence in favor of the reference model whereas if such relation is relaxed, a weak evidence in favor of the model with diffeomorphism breaking is found. We also use the same CMB data set to make an observational comparison between the SDB model, standard inflation and String Gas Cosmology.

Spontaneous Lorentz and diffeomorphism violation, massive modes, and gravity

NASA Astrophysics Data System (ADS)

Bluhm, Robert; Fung, Shu-Hong; Kostelecký, V. Alan

2008-03-01

Theories with spontaneous local Lorentz and diffeomorphism violation contain massless Nambu-Goldstone modes, which arise as field excitations in the minimum of the symmetry-breaking potential. If the shape of the potential also allows excitations above the minimum, then an alternative gravitational Higgs mechanism can occur in which massive modes involving the metric appear. The origin and basic properties of the massive modes are addressed in the general context involving an arbitrary tensor vacuum value. Special attention is given to the case of bumblebee models, which are gravitationally coupled vector theories with spontaneous local Lorentz and diffeomorphism violation. Mode expansions are presented in both local and spacetime frames, revealing the Nambu-Goldstone and massive modes via decomposition of the metric and bumblebee fields, and the associated symmetry properties and gauge fixing are discussed. The class of bumblebee models with kinetic terms of the Maxwell form is used as a focus for more detailed study. The nature of the associated conservation laws and the interpretation as a candidate alternative to Einstein-Maxwell theory are investigated. Explicit examples involving smooth and Lagrange-multiplier potentials are studied to illustrate features of the massive modes, including their origin, nature, dispersion laws, and effects on gravitational interactions. In the weak static limit, the massive mode and Lagrange-multiplier fields are found to modify the Newton and Coulomb potentials. The nature and implications of these modifications are examined.

Local Operators in the Eternal Black Hole.

PubMed

Papadodimas, Kyriakos; Raju, Suvrat

2015-11-20

In the AdS/CFT correspondence, states obtained by Hamiltonian evolution of the thermofield doubled state are also dual to an eternal black-hole geometry, which is glued to the boundary with a time shift generated by a large diffeomorphism. We describe gauge-invariant relational observables that probe the black hole interior in these states and constrain their properties using effective field theory. By adapting recent versions of the information paradox we show that these observables are necessarily described by state-dependent bulk-boundary maps, which we construct explicitly.

BF actions for the Husain-Kuchař model

NASA Astrophysics Data System (ADS)

Barbero G., J. Fernando; Villaseñor, Eduardo J.

2001-04-01

We show that the Husain-Kuchař model can be described in the framework of BF theories. This is a first step towards its quantization by standard perturbative quantum field theory techniques or the spin-foam formalism introduced in the space-time description of general relativity and other diff-invariant theories. The actions that we will consider are similar to the ones describing the BF-Yang-Mills model and some mass generating mechanisms for gauge fields. We will also discuss the role of diffeomorphisms in the new formulations that we propose.

Gauge-transformation properties of cosmological observables and its application to the light-cone average

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

Yoo, Jaiyul; Durrer, Ruth, E-mail: jyoo@physik.uzh.ch, E-mail: ruth.durrer@unige.ch

Theoretical descriptions of observable quantities in cosmological perturbation theory should be independent of coordinate systems. This statement is often referred to as gauge-invariance of observable quantities, and the sanity of their theoretical description is verified by checking its gauge-invariance. We argue that cosmological observables are invariant scalars under diffeomorphisms and their theoretical description is gauge-invariant, only at linear order in perturbations. Beyond linear order, they are usually not gauge-invariant, and we provide the general law for the gauge-transformation that the perturbation part of an observable does obey. We apply this finding to derive the second-order expression for the observational light-conemore » average in cosmology and demonstrate that our expression is indeed invariant under diffeomorphisms.« less

A Lesson from the LQG String: Diffeomorphism Covariance is Enough

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

Helling, Robert C.

2009-12-15

The importance of manifest diffeomorphism invariance is often cited as a major strength of the loop approach to the quantization of gravity. We study this in a simple example: The world-sheet theory of the bosonic string. The conventional treatment differs in the choice of vacuum state from the loop inspired one, the latter being invariant while the first being only covariant. We argue that physically only covariance is required and display the physical consequences of the invariant but discontinuous choice in the one dimensional example of the harmonic oscillator. Finally, we demonstrate that discretization of infinitesimally singular expressions as commonmore » in the loop approach is not unique but can be seen in analogy with the choice of higher derivative counter terms.« less

Asymptotic symmetries of colored gravity in three dimensions

NASA Astrophysics Data System (ADS)

Joung, Euihun; Kim, Jaewon; Kim, Jihun; Rey, Soo-Jong

2018-03-01

Three-dimensional colored gravity refers to nonabelian isospin extension of Einstein gravity. We investigate the asymptotic symmetry algebra of the SU( N)-colored gravity in (2+1)-dimensional anti-de Sitter spacetime. Formulated by the Chern-Simons theory with SU( N, N) × SU( N, N) gauge group, the theory contains graviton, SU( N) Chern-Simons gauge fields and massless spin-two multiplets in the SU( N) adjoint representation, thus extending diffeomorphism to colored, nonabelian counterpart. We identify the asymptotic symmetry as Poisson algebra of generators associated with the residual global symmetries of the nonabelian diffeomorphism set by appropriately chosen boundary conditions. The resulting asymptotic symmetry algebra is a nonlinear extension of \\widehat{su(N)} Kac-Moody algebra, supplemented by additional generators corresponding to the massless spin-two adjoint matter fields.

Relationship between aging and T1 relaxation time in deep gray matter: A voxel-based analysis.

PubMed

Okubo, Gosuke; Okada, Tomohisa; Yamamoto, Akira; Fushimi, Yasutaka; Okada, Tsutomu; Murata, Katsutoshi; Togashi, Kaori

2017-09-01

To investigate age-related changes in T 1 relaxation time in deep gray matter structures in healthy volunteers using magnetization-prepared 2 rapid acquisition gradient echoes (MP2RAGE). In all, 70 healthy volunteers (aged 20-76, mean age 42.6 years) were scanned at 3T magnetic resonance imaging (MRI). A MP2RAGE sequence was employed to quantify T 1 relaxation times. After the spatial normalization of T 1 maps with the diffeomorphic anatomical registration using the exponentiated Lie algebra algorithm, voxel-based regression analysis was conducted. In addition, linear and quadratic regression analyses of regions of interest (ROIs) were also performed. With aging, voxel-based analysis (VBA) revealed significant T 1 value decreases in the ventral-inferior putamen, nucleus accumbens, and amygdala, whereas T 1 values significantly increased in the thalamus and white matter as well (P < 0.05 at cluster level, false discovery rate). ROI analysis revealed that T 1 values in the nucleus accumbens linearly decreased with aging (P = 0.0016), supporting the VBA result. T 1 values in the thalamus (P < 0.0001), substantia nigra (P = 0.0003), and globus pallidus (P < 0.0001) had a best fit to quadratic curves, with the minimum T 1 values observed between 30 and 50 years of age. Age-related changes in T 1 relaxation time vary by location in deep gray matter. 2 Technical Efficacy: Stage 2 J. MAGN. RESON. IMAGING 2017;46:724-731. © 2017 International Society for Magnetic Resonance in Medicine.

Numerical Evidence for a Phase Transition in 4D Spin-Foam Quantum Gravity

NASA Astrophysics Data System (ADS)

Bahr, Benjamin; Steinhaus, Sebastian

2016-09-01

Building on recent advances in defining Wilsonian renormalization group (RG) flows, and the notion of scales in particular, for background-independent theories, we present a first investigation of the renormalization of the 4D spin-foam path integral for quantum gravity, both analytically and numerically. Focusing on a specific truncation of the model using a hypercubic lattice, we compute the RG flow and find strong indications for a phase transition, as well as an interesting interplay between the different observed phases and the (broken) diffeomorphism symmetry of the model. Most notably, it appears that the critical point between the phases, which is a fixed point of the RG flow, is precisely where broken diffeomorphism symmetry is restored, which suggests that it might allow us to define a continuum limit of the quantum gravity theory.

Numerical Evidence for a Phase Transition in 4D Spin-Foam Quantum Gravity.

PubMed

Bahr, Benjamin; Steinhaus, Sebastian

2016-09-30

Building on recent advances in defining Wilsonian renormalization group (RG) flows, and the notion of scales in particular, for background-independent theories, we present a first investigation of the renormalization of the 4D spin-foam path integral for quantum gravity, both analytically and numerically. Focusing on a specific truncation of the model using a hypercubic lattice, we compute the RG flow and find strong indications for a phase transition, as well as an interesting interplay between the different observed phases and the (broken) diffeomorphism symmetry of the model. Most notably, it appears that the critical point between the phases, which is a fixed point of the RG flow, is precisely where broken diffeomorphism symmetry is restored, which suggests that it might allow us to define a continuum limit of the quantum gravity theory.

A Tour Through Shape Dynamic Black Holes

NASA Astrophysics Data System (ADS)

Herczeg, Gabriel

Shape dynamics is a classical theory of gravity which agrees with general relativity in many important cases, but possesses different gauge symmetries and constraints. Rather than spacetime diffeomorphism invariance, shape dynamics takes spatial diffeomorphism invariance and spatial Weyl invariance as the fundamental gauge symmetries associated with the gravitational field. Despite these differences, shape dynamics and general relativity generically predict the same dynamics--there exist gauge-fixings of each theory that ensure agreement with the other. However, these gauge-fixing conditions are not necessarily globally well-defined and it is therefore possible to find solutions of the shape dynamics equations of motion that agree with general relativity on some open neighborhoods, but which have different global structures. In particular, the black hole solutions of the two theories disagree globally. Understanding these novel "shape dynamic black holes" is the primary goal of this thesis.

In vivo delineation of subdivisions of the human amygdaloid complex in a high-resolution group template

PubMed Central

Tyszka, J. Michael; Pauli, Wolfgang M.

2016-01-01

The nuclei of the human amygdala remain difficult to distinguish in individual subject structural magnetic resonance images. However, interpretation of the amygdala’s role in whole brain networks requires accurate localization of functional activity to a particular nucleus or subgroup of nuclei. To address this, we constructed high spatial resolution, three-dimensional templates, using joint high accuracy diffeomorphic registration of T1- and T2-weighted structural images from 168 typical adults between 22 and 35 years old released by the Human Connectome Project. Several internuclear boundaries are clearly visible in these templates, which would otherwise be impossible to delineate in individual subject data. A probabilistic atlas of major nuclei and nuclear groups was constructed in this template space and mapped back to individual spaces by inversion of the individual diffeomorphisms. Group level analyses revealed a slight (approximately 2%) bias towards larger total amygdala and nuclear volumes in the right hemisphere. No substantial sex or age differences were found in amygdala volumes normalized to total intracranial volume, or subdivision volumes normalized to amygdala volume. The current delineation provides a finer parcellation of the amygdala with more accurate external boundary definition than current histology-based atlases when used in conjunction with high accuracy registration methods, such as diffeomorphic warping. These templates and delineation are intended to be an open and evolving resource for future functional and structural imaging studies of the human amygdala. PMID:27354150

Constraining the break of spatial diffeomorphism invariance with Planck data

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

Graef, L.L.; Benetti, M.; Alcaniz, J.S., E-mail: leilagraef@on.br, E-mail: micolbenetti@on.br, E-mail: alcaniz@on.br

The current most accepted paradigm for the early universe cosmology, the inflationary scenario, shows a good agreement with the recent Cosmic Microwave Background (CMB) and polarization data. However, when the inflation consistency relation is relaxed, these observational data exclude a larger range of red tensor tilt values, prevailing the blue ones which are not predicted by the minimal inflationary models. Recently, it has been shown that the assumption of spatial diffeomorphism invariance breaking (SDB) in the context of an effective field theory of inflation leads to interesting observational consequences. Among them, the possibility of generating a blue tensor spectrum, whichmore » can recover the specific consistency relation of the String Gas Cosmology, for a certain choice of parameters. We use the most recent CMB data to constrain the SDB model and test its observational viability through a Bayesian analysis assuming as reference an extended ΛCDM+tensor perturbation model, which considers a power-law tensor spectrum parametrized in terms of the tensor-to-scalar ratio, r , and the tensor spectral index, n {sub t} . If the inflation consistency relation is imposed, r =−8 n {sub t} , we obtain a strong evidence in favor of the reference model whereas if such relation is relaxed, a weak evidence in favor of the model with diffeomorphism breaking is found. We also use the same CMB data set to make an observational comparison between the SDB model, standard inflation and String Gas Cosmology.« less

Observables, gravitational dressing, and obstructions to locality and subsystems

NASA Astrophysics Data System (ADS)

Donnelly, William; Giddings, Steven B.

2016-11-01

Quantum field theory—our basic framework for describing all nongravitational physics—conflicts with general relativity: the latter precludes the standard definition of the former's essential principle of locality, in terms of commuting local observables. We examine this conflict more carefully, by investigating implications of gauge (diffeomorphism) invariance for observables in gravity. We prove a dressing theorem, showing that any operator with nonzero Poincaré charges, and in particular any compactly supported operator, in flat-spacetime quantum field theory must be gravitationally dressed once coupled to gravity, i.e., it must depend on the metric at arbitrarily long distances, and we put lower bounds on this nonlocal dependence. This departure from standard locality occurs in the most severe way possible: in perturbation theory about flat spacetime, at leading order in Newton's constant. The physical observables in a gravitational theory therefore do not organize themselves into local commuting subalgebras: the principle of locality must apparently be reformulated or abandoned, and in fact we lack a clear definition of the coarser and more basic notion of a quantum subsystem of the Universe. We discuss relational approaches to locality based on diffeomorphism-invariant nonlocal operators, and reinforce arguments that any such locality is state-dependent and approximate. We also find limitations to the utility of bilocal diffeomorphism-invariant operators that are considered in cosmological contexts. An appendix provides a concise review of the canonical covariant formalism for gravity, instrumental in the discussion of Poincaré charges and their associated long-range fields.

Exploring the spectrum of regularized bosonic string theory

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

Ambjørn, J., E-mail: ambjorn@nbi.dk; Makeenko, Y., E-mail: makeenko@nbi.dk

2015-03-15

We implement a UV regularization of the bosonic string by truncating its mode expansion and keeping the regularized theory “as diffeomorphism invariant as possible.” We compute the regularized determinant of the 2d Laplacian for the closed string winding around a compact dimension, obtaining the effective action in this way. The minimization of the effective action reliably determines the energy of the string ground state for a long string and/or for a large number of space-time dimensions. We discuss the possibility of a scaling limit when the cutoff is taken to infinity.

Superrotation charge and supertranslation hair on black holes

DOE PAGES

Hawking, Stephen W.; Perry, Malcolm J.; Strominger, Andrew

2017-05-31

It is shown that black hole spacetimes in classical Einstein gravity are characterized by, in addition to their ADM mass M, momentummore » $$\\vec{P}$$, angular momentum $$\\vec{J}$$ and boost charge $$\\vec{/k}$$ , an infinite head of supertranslation hair. Furthermore, the distinct black holes are distinguished by classical superrotation charges measured at infinity. Solutions with supertranslation hair are diffeomorphic to the Schwarzschild spacetime, but the diffeomorphisms are part of the BMS subgroup and act nontrivially on the physical phase space. It is shown that a black hole can be supertranslated by throwing in an asymmetric shock wave. We derive a leading-order Bondi-gauge expression for the linearized horizon supertranslation charge and shown to generate, via the Dirac bracket, supertranslations on the linearized phase space of gravitational excitations of the horizon. The considerations of this paper are largely classical augmented by comments on their implications for the quantum theory.« less

Superrotation charge and supertranslation hair on black holes

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

Hawking, Stephen W.; Perry, Malcolm J.; Strominger, Andrew

It is shown that black hole spacetimes in classical Einstein gravity are characterized by, in addition to their ADM mass M, momentummore » $$\\vec{P}$$, angular momentum $$\\vec{J}$$ and boost charge $$\\vec{/k}$$ , an infinite head of supertranslation hair. Furthermore, the distinct black holes are distinguished by classical superrotation charges measured at infinity. Solutions with supertranslation hair are diffeomorphic to the Schwarzschild spacetime, but the diffeomorphisms are part of the BMS subgroup and act nontrivially on the physical phase space. It is shown that a black hole can be supertranslated by throwing in an asymmetric shock wave. We derive a leading-order Bondi-gauge expression for the linearized horizon supertranslation charge and shown to generate, via the Dirac bracket, supertranslations on the linearized phase space of gravitational excitations of the horizon. The considerations of this paper are largely classical augmented by comments on their implications for the quantum theory.« less

Diffeomorphic Sulcal Shape Analysis on the Cortex

PubMed Central

Joshi, Shantanu H.; Cabeen, Ryan P.; Joshi, Anand A.; Sun, Bo; Dinov, Ivo; Narr, Katherine L.; Toga, Arthur W.; Woods, Roger P.

2014-01-01

We present a diffeomorphic approach for constructing intrinsic shape atlases of sulci on the human cortex. Sulci are represented as square-root velocity functions of continuous open curves in ℝ3, and their shapes are studied as functional representations of an infinite-dimensional sphere. This spherical manifold has some advantageous properties – it is equipped with a Riemannian metric on the tangent space and facilitates computational analyses and correspondences between sulcal shapes. Sulcal shape mapping is achieved by computing geodesics in the quotient space of shapes modulo scales, translations, rigid rotations and reparameterizations. The resulting sulcal shape atlas preserves important local geometry inherently present in the sample population. The sulcal shape atlas is integrated in a cortical registration framework and exhibits better geometric matching compared to the conventional euclidean method. We demonstrate experimental results for sulcal shape mapping, cortical surface registration, and sulcal classification for two different surface extraction protocols for separate subject populations. PMID:22328177

Superrotation charge and supertranslation hair on black holes

NASA Astrophysics Data System (ADS)

Hawking, Stephen W.; Perry, Malcolm J.; Strominger, Andrew

2017-05-01

It is shown that black hole spacetimes in classical Einstein gravity are characterized by, in addition to their ADM mass M, momentum \\overrightarrow{P} , angular momentum \\overrightarrow{J} and boost charge \\overrightarrow{K} , an infinite head of supertranslation hair. The distinct black holes are distinguished by classical superrotation charges measured at infinity. Solutions with super-translation hair are diffeomorphic to the Schwarzschild spacetime, but the diffeomorphisms are part of the BMS subgroup and act nontrivially on the physical phase space. It is shown that a black hole can be supertranslated by throwing in an asymmetric shock wave. A leading-order Bondi-gauge expression is derived for the linearized horizon supertranslation charge and shown to generate, via the Dirac bracket, supertranslations on the linearized phase space of gravitational excitations of the horizon. The considerations of this paper are largely classical augmented by comments on their implications for the quantum theory.

dRGT theory of massive gravity from spontaneous symmetry breaking

NASA Astrophysics Data System (ADS)

Torabian, Mahdi

2018-05-01

In this note we propose a topological action for a Poincare times diffeomorphism invariant gauge theory. We show that there is Higgs phase where the gauge symmetry is spontaneous broken to a diagonal Lorentz subgroup and gives the Einstein-Hilbert action plus the dRGT potential terms. In this vacuum, there are five (three from Goldstone modes) propagating degrees of freedom which form polarizations of a massive spin 2 particle, an extra healthy heavy scalar (Higgs) mode and no Boulware-Deser ghost mode. We further show that the action can be derived in a limit from a topological de Sitter invariant gauge theory in 4 dimensions.

Depth from Optical Turbulence

DTIC Science & Technology

2012-01-01

Dagobert, and C. Franchis . Atmospheric tur- bulence restoration by diffeomorphic image registration and blind deconvolution. In ACIVS, 2008. 1 [4] S...20] V. Tatarskii. Wave Propagation in a Turbulent Medium. McGraw-Hill Books, 1961. 2 [21] Y. Tian and S. Narasimhan. A globally optimal data-driven

Unimodular Einstein-Cartan gravity: Dynamics and conservation laws

NASA Astrophysics Data System (ADS)

Bonder, Yuri; Corral, Cristóbal

2018-04-01

Unimodular gravity is an interesting approach to address the cosmological constant problem, since the vacuum energy density of quantum fields does not gravitate in this framework, and the cosmological constant appears as an integration constant. These features arise as a consequence of considering a constrained volume element 4-form that breaks the diffeomorphisms invariance down to volume preserving diffeomorphisms. In this work, the first-order formulation of unimodular gravity is presented by considering the spin density of matter fields as a source of spacetime torsion. Even though the most general matter Lagrangian allowed by the symmetries is considered, dynamical restrictions arise on their functional dependence. The field equations are obtained and the conservation laws associated with the symmetries are derived. It is found that, analogous to torsion-free unimodular gravity, the field equation for the vierbein is traceless; nevertheless, torsion is algebraically related to the spin density as in standard Einstein-Cartan theory. The particular example of massless Dirac spinors is studied, and comparisons with standard Einstein-Cartan theory are shown.

Shape-based diffeomorphic registration on hippocampal surfaces using Beltrami holomorphic flow.

PubMed

Lui, Lok Ming; Wong, Tsz Wai; Thompson, Paul; Chan, Tony; Gu, Xianfeng; Yau, Shing-Tung

2010-01-01

We develop a new algorithm to automatically register hippocampal (HP) surfaces with complete geometric matching, avoiding the need to manually label landmark features. A good registration depends on a reasonable choice of shape energy that measures the dissimilarity between surfaces. In our work, we first propose a complete shape index using the Beltrami coefficient and curvatures, which measures subtle local differences. The proposed shape energy is zero if and only if two shapes are identical up to a rigid motion. We then seek the best surface registration by minimizing the shape energy. We propose a simple representation of surface diffeomorphisms using Beltrami coefficients, which simplifies the optimization process. We then iteratively minimize the shape energy using the proposed Beltrami Holomorphic flow (BHF) method. Experimental results on 212 HP of normal and diseased (Alzheimer's disease) subjects show our proposed algorithm is effective in registering HP surfaces with complete geometric matching. The proposed shape energy can also capture local shape differences between HP for disease analysis.

Probabilistic modeling of anatomical variability using a low dimensional parameterization of diffeomorphisms.

PubMed

Zhang, Miaomiao; Wells, William M; Golland, Polina

2017-10-01

We present an efficient probabilistic model of anatomical variability in a linear space of initial velocities of diffeomorphic transformations and demonstrate its benefits in clinical studies of brain anatomy. To overcome the computational challenges of the high dimensional deformation-based descriptors, we develop a latent variable model for principal geodesic analysis (PGA) based on a low dimensional shape descriptor that effectively captures the intrinsic variability in a population. We define a novel shape prior that explicitly represents principal modes as a multivariate complex Gaussian distribution on the initial velocities in a bandlimited space. We demonstrate the performance of our model on a set of 3D brain MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Our model yields a more compact representation of group variation at substantially lower computational cost than the state-of-the-art method such as tangent space PCA (TPCA) and probabilistic principal geodesic analysis (PPGA) that operate in the high dimensional image space. Copyright © 2017 Elsevier B.V. All rights reserved.

Recent Developments Related To An Optically Controlled Microwave Phased Array Antenna.

NASA Astrophysics Data System (ADS)

Kittel, A.; Peinke, J.; Klein, M.; Baier, G.; Parisi, J.; Rössler, O. E.

1990-12-01

A generic 3-dimensional diffeomorphic map, with constant Jacobian determinant, is proposed and looked at numerically. It contains a lower-dimensional basin boundary along which a chaotic motion takes place. This boundary is nowhere differentiable in one direction. Therefore, nowhere differentiable limit sets exist generically in nature.

Weyl invariance with a nontrivial mass scale

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

Álvarez, Enrique; González-Martín, Sergio; Departamento de Física Teórica, Universidad Autónoma de Madrid,28049 Madrid

2016-09-07

A theory with a mass scale and yet Weyl invariant is presented. The theory is not invariant under all diffeomorphisms but only under transverse ones. This is the reason why Weyl invariance does not imply scale invariance in a free falling frame. Physical implications of this framework are discussed.

Loop Quantum Gravity and the Meaning of Diffeomorphism Invariance

NASA Astrophysics Data System (ADS)

Rovelli, Carlo; Gaul, Marcus

This series of lectures gives an introduction to the non-perturbative and background-independent formulation for a quantum theory of gravitation which is called loop quantum gravity . The Hilbert space of kinematical quantum states is constructed and a complete basis of spin network states is introduced. Afterwards an application of the formalism is provided by the spectral analysis of the area operator, which is the quantum analogue of the classical area function. This leads to one of the key results of loop quantum gravity obtained in the last few years: the derivation of the discreteness of the geometry and the computation of the quanta of area. Special importance is attached to the role played by the diffeomorphism group in order to clarify the notion of observability in general relativity - a concept far from being trivial. Finally an outlock onto a possible dynamical extension of the theory is given, leading to a "sum over histories" approach, namely a so-called spin foam model . Throughout the whole lecture great significance is attached to conceptual and interpretational issues.

Constraining the physical state by symmetries

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

Fatibene, L., E-mail: lorenzo.fatibene@unito.it; INFN - Sezione Torino - IS QGSKY; Ferraris, M.

After reviewing the hole argument and its relations with initial value problem and general covariance, we shall discuss how much freedom one has to define the physical state in a generally covariant field theory (with or without internal gauge symmetries). Our analysis relies on Cauchy problems, thus it is restricted to globally hyperbolic spacetimes. We shall show that in generally covariant theories on a compact space (as well as for internal gauge symmetries on any spacetime) one has no freedom and one is forced to declare as physically equivalent two configurations which differ by a global spacetime diffeomorphism (or bymore » an internal gauge transformation) as it is usually prescribed. On the contrary, when space is not compact, the result does not hold true and one may have different options to define physically equivalent configurations, still preserving determinism. - Highlights: • Investigate the relation between the hole argument, covariance, determinism and physical state. • Show that if space is compact then any diffeomorphism is a gauge symmetry. • Show that if space is not compact then there may be more freedom in choosing gauge group.« less

Transformations based on continuous piecewise-affine velocity fields

DOE PAGES

Freifeld, Oren; Hauberg, Soren; Batmanghelich, Kayhan; ...

2017-01-11

Here, we propose novel finite-dimensional spaces of well-behaved Rn → Rn transformations. The latter are obtained by (fast and highly-accurate) integration of continuous piecewise-affine velocity fields. The proposed method is simple yet highly expressive, effortlessly handles optional constraints (e.g., volume preservation and/or boundary conditions), and supports convenient modeling choices such as smoothing priors and coarse-to-fine analysis. Importantly, the proposed approach, partly due to its rapid likelihood evaluations and partly due to its other properties, facilitates tractable inference over rich transformation spaces, including using Markov-Chain Monte-Carlo methods. Its applications include, but are not limited to: monotonic regression (more generally, optimization overmore » monotonic functions); modeling cumulative distribution functions or histograms; time-warping; image warping; image registration; real-time diffeomorphic image editing; data augmentation for image classifiers. Our GPU-based code is publicly available.« less

Transformations Based on Continuous Piecewise-Affine Velocity Fields

PubMed Central

Freifeld, Oren; Hauberg, Søren; Batmanghelich, Kayhan; Fisher, Jonn W.

2018-01-01

We propose novel finite-dimensional spaces of well-behaved ℝn → ℝn transformations. The latter are obtained by (fast and highly-accurate) integration of continuous piecewise-affine velocity fields. The proposed method is simple yet highly expressive, effortlessly handles optional constraints (e.g., volume preservation and/or boundary conditions), and supports convenient modeling choices such as smoothing priors and coarse-to-fine analysis. Importantly, the proposed approach, partly due to its rapid likelihood evaluations and partly due to its other properties, facilitates tractable inference over rich transformation spaces, including using Markov-Chain Monte-Carlo methods. Its applications include, but are not limited to: monotonic regression (more generally, optimization over monotonic functions); modeling cumulative distribution functions or histograms; time-warping; image warping; image registration; real-time diffeomorphic image editing; data augmentation for image classifiers. Our GPU-based code is publicly available. PMID:28092517

Remarks on thermalization in 2D CFT

NASA Astrophysics Data System (ADS)

de Boer, Jan; Engelhardt, Dalit

2016-12-01

We revisit certain aspects of thermalization in 2D conformal field theory (CFT). In particular, we consider similarities and differences between the time dependence of correlation functions in various states in rational and non-rational CFTs. We also consider the distinction between global and local thermalization and explain how states obtained by acting with a diffeomorphism on the ground state can appear locally thermal, and we review why the time-dependent expectation value of the energy-momentum tensor is generally a poor diagnostic of global thermalization. Since all 2D CFTs have an infinite set of commuting conserved charges, generic initial states might be expected to give rise to a generalized Gibbs ensemble rather than a pure thermal ensemble at late times. We construct the holographic dual of the generalized Gibbs ensemble and show that, to leading order, it is still described by a Banados-Teitelboim-Zanelli black hole. The extra conserved charges, while rendering c <1 theories essentially integrable, therefore seem to have little effect on large-c conformal field theories.

Black Hole Entropy from Bondi-Metzner-Sachs Symmetry at the Horizon.

PubMed

Carlip, S

2018-03-09

Near the horizon, the obvious symmetries of a black hole spacetime-the horizon-preserving diffeomorphisms-are enhanced to a larger symmetry group with a three-dimensional Bondi-Metzner-Sachs algebra. Using dimensional reduction and covariant phase space techniques, I investigate this augmented symmetry and show that it is strong enough to determine the black hole entropy in any dimension.

FLOWS WITH CROSS SECTIONS

PubMed Central

Verjovsky, Alberto

1970-01-01

Let M be a compact connected C∞-manifold, of dimension n, without boundary. Let ft: M → M be a Cr-flow with cross section. Let Dr(M) be the topological group of diffeomorphisms of M with Cr-topology (1 ≤ r ≤ ∞) and let Dor(M) be its connected component of the identity. Let [unk](M) be the group of I-cobordism classes in Dr(M) generated by orientation-preserving diffeomorphisms. For fεDr(M) denote by [f] its I-cobordism class. Theorem 1 deals with the dependence of M(f) on [f]. Theorem 2: S6 × S1 has at least 28 distinct differentiable structures. Let xoεS1 and let [unk]r be the set of Cr-flows (r ≥ 1) in M × S1 with cross section M × {xo} and inducing in it the identity. Theorem 3: Intuitively to a loop in Dor based at the identity there corresponds a flow in [unk]r, and to homotopic loops correspond isotopic flows. COROLLARY. complete analysis of [unk]r/ [unk] for dim M = 2. Theorems 4 and 5 refer to Anosov flows for dim M > 3. PMID:16591849

Landmark-guided diffeomorphic demons algorithm and its application to automatic segmentation of the whole spine and pelvis in CT images.

PubMed

Hanaoka, Shouhei; Masutani, Yoshitaka; Nemoto, Mitsutaka; Nomura, Yukihiro; Miki, Soichiro; Yoshikawa, Takeharu; Hayashi, Naoto; Ohtomo, Kuni; Shimizu, Akinobu

2017-03-01

A fully automatic multiatlas-based method for segmentation of the spine and pelvis in a torso CT volume is proposed. A novel landmark-guided diffeomorphic demons algorithm is used to register a given CT image to multiple atlas volumes. This algorithm can utilize both grayscale image information and given landmark coordinate information optimally. The segmentation has four steps. Firstly, 170 bony landmarks are detected in the given volume. Using these landmark positions, an atlas selection procedure is performed to reduce the computational cost of the following registration. Then the chosen atlas volumes are registered to the given CT image. Finally, voxelwise label voting is performed to determine the final segmentation result. The proposed method was evaluated using 50 torso CT datasets as well as the public SpineWeb dataset. As a result, a mean distance error of [Formula: see text] and a mean Dice coefficient of [Formula: see text] were achieved for the whole spine and the pelvic bones, which are competitive with other state-of-the-art methods. From the experimental results, the usefulness of the proposed segmentation method was validated.

Deterioration of abstract reasoning ability in mild cognitive impairment and Alzheimer's disease: correlation with regional grey matter volume loss revealed by diffeomorphic anatomical registration through exponentiated lie algebra analysis.

PubMed

Yoshiura, Takashi; Hiwatashi, Akio; Yamashita, Koji; Ohyagi, Yasumasa; Monji, Akira; Takayama, Yukihisa; Kamano, Norihiro; Kawashima, Toshiro; Kira, Jun-Ichi; Honda, Hiroshi

2011-02-01

To determine which brain regions are relevant to deterioration in abstract reasoning as measured by Raven's Colored Progressive Matrices (CPM) in the context of dementia. MR images of 37 consecutive patients including 19 with Alzheimer's disease (AD) and 18 with amnestic mild cognitive impairment (aMCI) were retrospectively analyzed. All patients were administered the CPM. Regional grey matter (GM) volume was evaluated according to the regimens of voxel-based morphometry, during which a non-linear registration algorithm called Diffeomorphic Anatomical Registration Through Exponentiated Lie algebra was employed. Multiple regression analyses were used to map the regions where GM volumes were correlated with CPM scores. The strongest correlation with CPM scores was seen in the left middle frontal gyrus while a region with the largest volume was identified in the left superior temporal gyrus. Significant correlations were seen in 14 additional regions in the bilateral cerebral hemispheres and right cerebellum. Deterioration of abstract reasoning ability in AD and aMCI measured by CPM is related to GM loss in multiple regions, which is in close agreement with the results of previous activation studies.

Voxel-based morphometric analysis in hypothyroidism using diffeomorphic anatomic registration via an exponentiated lie algebra algorithm approach.

PubMed

Singh, S; Modi, S; Bagga, D; Kaur, P; Shankar, L R; Khushu, S

2013-03-01

The present study aimed to investigate whether brain morphological differences exist between adult hypothyroid subjects and age-matched controls using voxel-based morphometry (VBM) with diffeomorphic anatomic registration via an exponentiated lie algebra algorithm (DARTEL) approach. High-resolution structural magnetic resonance images were taken in ten healthy controls and ten hypothyroid subjects. The analysis was conducted using statistical parametric mapping. The VBM study revealed a reduction in grey matter volume in the left postcentral gyrus and cerebellum of hypothyroid subjects compared to controls. A significant reduction in white matter volume was also found in the cerebellum, right inferior and middle frontal gyrus, right precentral gyrus, right inferior occipital gyrus and right temporal gyrus of hypothyroid patients compared to healthy controls. Moreover, no meaningful cluster for greater grey or white matter volume was obtained in hypothyroid subjects compared to controls. Our study is the first VBM study of hypothyroidism in an adult population and suggests that, compared to controls, this disorder is associated with differences in brain morphology in areas corresponding to known functional deficits in attention, language, motor speed, visuospatial processing and memory in hypothyroidism. © 2012 British Society for Neuroendocrinology.

Strain map of the tongue in normal and ALS speech patterns from tagged and diffusion MRI

NASA Astrophysics Data System (ADS)

Xing, Fangxu; Prince, Jerry L.; Stone, Maureen; Reese, Timothy G.; Atassi, Nazem; Wedeen, Van J.; El Fakhri, Georges; Woo, Jonghye

2018-03-01

Amyotrophic Lateral Sclerosis (ALS) is a neurological disease that causes death of neurons controlling muscle movements. Loss of speech and swallowing functions is a major impact due to degeneration of the tongue muscles. In speech studies using magnetic resonance (MR) techniques, diffusion tensor imaging (DTI) is used to capture internal tongue muscle fiber structures in three-dimensions (3D) in a non-invasive manner. Tagged magnetic resonance images (tMRI) are used to record tongue motion during speech. In this work, we aim to combine information obtained with both MR imaging techniques to compare the functionality characteristics of the tongue between normal and ALS subjects. We first extracted 3D motion of the tongue using tMRI from fourteen normal subjects in speech. The estimated motion sequences were then warped using diffeomorphic registration into the b0 spaces of the DTI data of two normal subjects and an ALS patient. We then constructed motion atlases by averaging all warped motion fields in each b0 space, and computed strain in the line of action along the muscle fiber directions provided by tractography. Strain in line with the fiber directions provides a quantitative map of the potential active region of the tongue during speech. Comparison between normal and ALS subjects explores the changing volume of compressing tongue tissues in speech facing the situation of muscle degradation. The proposed framework provides for the first time a dynamic map of contracting fibers in ALS speech patterns, and has the potential to provide more insight into the detrimental effects of ALS on speech.

Strain Map of the Tongue in Normal and ALS Speech Patterns from Tagged and Diffusion MRI.

PubMed

Xing, Fangxu; Prince, Jerry L; Stone, Maureen; Reese, Timothy G; Atassi, Nazem; Wedeen, Van J; El Fakhri, Georges; Woo, Jonghye

2018-02-01

Amyotrophic Lateral Sclerosis (ALS) is a neurological disease that causes death of neurons controlling muscle movements. Loss of speech and swallowing functions is a major impact due to degeneration of the tongue muscles. In speech studies using magnetic resonance (MR) techniques, diffusion tensor imaging (DTI) is used to capture internal tongue muscle fiber structures in three-dimensions (3D) in a non-invasive manner. Tagged magnetic resonance images (tMRI) are used to record tongue motion during speech. In this work, we aim to combine information obtained with both MR imaging techniques to compare the functionality characteristics of the tongue between normal and ALS subjects. We first extracted 3D motion of the tongue using tMRI from fourteen normal subjects in speech. The estimated motion sequences were then warped using diffeomorphic registration into the b0 spaces of the DTI data of two normal subjects and an ALS patient. We then constructed motion atlases by averaging all warped motion fields in each b0 space, and computed strain in the line of action along the muscle fiber directions provided by tractography. Strain in line with the fiber directions provides a quantitative map of the potential active region of the tongue during speech. Comparison between normal and ALS subjects explores the changing volume of compressing tongue tissues in speech facing the situation of muscle degradation. The proposed framework provides for the first time a dynamic map of contracting fibers in ALS speech patterns, and has the potential to provide more insight into the detrimental effects of ALS on speech.

Histories approach to general relativity: I. The spacetime character of the canonical description

NASA Astrophysics Data System (ADS)

Savvidou, Ntina

2004-01-01

The problem of time in canonical quantum gravity is related to the fact that the canonical description is based on the prior choice of a spacelike foliation, hence making a reference to a spacetime metric. However, the metric is expected to be a dynamical, fluctuating quantity in quantum gravity. We show how this problem can be solved in the histories formulation of general relativity. We implement the 3 + 1 decomposition using metric-dependent foliations which remain spacelike with respect to all possible Lorentzian metrics. This allows us to find an explicit relation of covariant and canonical quantities which preserves the spacetime character of the canonical description. In this new construction, we also have the coexistence of the spacetime diffeomorphisms group, Diff(M), and the Dirac algebra of constraints.

Feature-based respiratory motion tracking in native fluoroscopic sequences for dynamic roadmaps during minimally invasive procedures in the thorax and abdomen

NASA Astrophysics Data System (ADS)

Wagner, Martin G.; Laeseke, Paul F.; Schubert, Tilman; Slagowski, Jordan M.; Speidel, Michael A.; Mistretta, Charles A.

2017-03-01

Fluoroscopic image guidance for minimally invasive procedures in the thorax and abdomen suffers from respiratory and cardiac motion, which can cause severe subtraction artifacts and inaccurate image guidance. This work proposes novel techniques for respiratory motion tracking in native fluoroscopic images as well as a model based estimation of vessel deformation. This would allow compensation for respiratory motion during the procedure and therefore simplify the workflow for minimally invasive procedures such as liver embolization. The method first establishes dynamic motion models for both the contrast-enhanced vasculature and curvilinear background features based on a native (non-contrast) and a contrast-enhanced image sequence acquired prior to device manipulation, under free breathing conditions. The model of vascular motion is generated by applying the diffeomorphic demons algorithm to an automatic segmentation of the subtraction sequence. The model of curvilinear background features is based on feature tracking in the native sequence. The two models establish the relationship between the respiratory state, which is inferred from curvilinear background features, and the vascular morphology during that same respiratory state. During subsequent fluoroscopy, curvilinear feature detection is applied to determine the appropriate vessel mask to display. The result is a dynamic motioncompensated vessel mask superimposed on the fluoroscopic image. Quantitative evaluation of the proposed methods was performed using a digital 4D CT-phantom (XCAT), which provides realistic human anatomy including sophisticated respiratory and cardiac motion models. Four groups of datasets were generated, where different parameters (cycle length, maximum diaphragm motion and maximum chest expansion) were modified within each image sequence. Each group contains 4 datasets consisting of the initial native and contrast enhanced sequences as well as a sequence, where the respiratory motion is tracked. The respiratory motion tracking error was between 1.00 % and 1.09 %. The estimated dynamic vessel masks yielded a Sørensen-Dice coefficient between 0.94 and 0.96. Finally, the accuracy of the vessel contours was measured in terms of the 99th percentile of the error, which ranged between 0.64 and 0.96 mm. The presented results show that the approach is feasible for respiratory motion tracking and compensation and could therefore considerably improve the workflow of minimally invasive procedures in the thorax and abdomen

Human pose tracking from monocular video by traversing an image motion mapped body pose manifold

NASA Astrophysics Data System (ADS)

Basu, Saurav; Poulin, Joshua; Acton, Scott T.

2010-01-01

Tracking human pose from monocular video sequences is a challenging problem due to the large number of independent parameters affecting image appearance and nonlinear relationships between generating parameters and the resultant images. Unlike the current practice of fitting interpolation functions to point correspondences between underlying pose parameters and image appearance, we exploit the relationship between pose parameters and image motion flow vectors in a physically meaningful way. Change in image appearance due to pose change is realized as navigating a low dimensional submanifold of the infinite dimensional Lie group of diffeomorphisms of the two dimensional sphere S2. For small changes in pose, image motion flow vectors lie on the tangent space of the submanifold. Any observed image motion flow vector field is decomposed into the basis motion vector flow fields on the tangent space and combination weights are used to update corresponding pose changes in the different dimensions of the pose parameter space. Image motion flow vectors are largely invariant to style changes in experiments with synthetic and real data where the subjects exhibit variation in appearance and clothing. The experiments demonstrate the robustness of our method (within +/-4° of ground truth) to style variance.

Overdetermined elliptic problems in topological disks

NASA Astrophysics Data System (ADS)

Mira, Pablo

2018-06-01

We introduce a method, based on the Poincaré-Hopf index theorem, to classify solutions to overdetermined problems for fully nonlinear elliptic equations in domains diffeomorphic to a closed disk. Applications to some well-known nonlinear elliptic PDEs are provided. Our result can be seen as the analogue of Hopf's uniqueness theorem for constant mean curvature spheres, but for the general analytic context of overdetermined elliptic problems.

Statistical modeling of 4D respiratory lung motion using diffeomorphic image registration.

PubMed

Ehrhardt, Jan; Werner, René; Schmidt-Richberg, Alexander; Handels, Heinz

2011-02-01

Modeling of respiratory motion has become increasingly important in various applications of medical imaging (e.g., radiation therapy of lung cancer). Current modeling approaches are usually confined to intra-patient registration of 3D image data representing the individual patient's anatomy at different breathing phases. We propose an approach to generate a mean motion model of the lung based on thoracic 4D computed tomography (CT) data of different patients to extend the motion modeling capabilities. Our modeling process consists of three steps: an intra-subject registration to generate subject-specific motion models, the generation of an average shape and intensity atlas of the lung as anatomical reference frame, and the registration of the subject-specific motion models to the atlas in order to build a statistical 4D mean motion model (4D-MMM). Furthermore, we present methods to adapt the 4D mean motion model to a patient-specific lung geometry. In all steps, a symmetric diffeomorphic nonlinear intensity-based registration method was employed. The Log-Euclidean framework was used to compute statistics on the diffeomorphic transformations. The presented methods are then used to build a mean motion model of respiratory lung motion using thoracic 4D CT data sets of 17 patients. We evaluate the model by applying it for estimating respiratory motion of ten lung cancer patients. The prediction is evaluated with respect to landmark and tumor motion, and the quantitative analysis results in a mean target registration error (TRE) of 3.3 ±1.6 mm if lung dynamics are not impaired by large lung tumors or other lung disorders (e.g., emphysema). With regard to lung tumor motion, we show that prediction accuracy is independent of tumor size and tumor motion amplitude in the considered data set. However, tumors adhering to non-lung structures degrade local lung dynamics significantly and the model-based prediction accuracy is lower in these cases. The statistical respiratory motion model is capable of providing valuable prior knowledge in many fields of applications. We present two examples of possible applications in radiation therapy and image guided diagnosis.

Covariant balance laws in continua with microstructure

NASA Astrophysics Data System (ADS)

Yavari, Arash; Marsden, Jerrold E.

2009-02-01

The purpose of this paper is to extend the Green-Naghdi-Rivlin balance of energy method to continua with microstructure. The key idea is to replace the group of Galilean transformations with the group of diffeomorphisms of the ambient space. A key advantage is that one obtains in a natural way all the needed balance laws on both the macro and micro levels along with two Doyle-Erickson formulas. We model a structured continuum as a triplet of Riemannian manifolds: a material manifold, the ambient space manifold of material particles and a director field manifold. The Green-Naghdi-Rivlin theorem and its extensions for structured continua are critically reviewed. We show that when the ambient space is Euclidean and when the microstructure manifold is the tangent space of the ambient space manifold, postulating a single balance of energy law and its invariance under time-dependent isometries of the ambient space, one obtains conservation of mass, balances of linear and angular momenta but not a separate balance of linear momentum. We develop a covariant elasticity theory for structured continua by postulating that energy balance is invariant under time-dependent spatial diffeomorphisms of the ambient space, which in this case is the product of two Riemannian manifolds. We then introduce two types of constrained continua in which microstructure manifold is linked to the reference and ambient space manifolds. In the case when at every material point, the microstructure manifold is the tangent space of the ambient space manifold at the image of the material point, we show that the assumption of covariance leads to balances of linear and angular momenta with contributions from both forces and micro-forces along with two Doyle-Ericksen formulas. We show that generalized covariance leads to two balances of linear momentum and a single coupled balance of angular momentum. Using this theory, we covariantly obtain the balance laws for two specific examples, namely elastic solids with distributed voids and mixtures. Finally, the Lagrangian field theory of structured elasticity is revisited and a connection is made between covariance and Noether's theorem.

Biot-Savart helicity versus physical helicity: A topological description of ideal flows

NASA Astrophysics Data System (ADS)

Sahihi, Taliya; Eshraghi, Homayoon

2014-08-01

For an isentropic (thus compressible) flow, fluid trajectories are considered as orbits of a family of one parameter, smooth, orientation-preserving, and nonsingular diffeomorphisms on a compact and smooth-boundary domain in the Euclidian 3-space which necessarily preserve a finite measure, later interpreted as the fluid mass. Under such diffeomorphisms the Biot-Savart helicity of the pushforward of a divergence-free and tangent to the boundary vector field is proved to be conserved and since these circumstances present an isentropic flow, the conservation of the "Biot-Savart helicity" is established for such flows. On the other hand, the well known helicity conservation in ideal flows which here we call it "physical helicity" is found to be an independent constant with respect to the Biot-Savart helicity. The difference between these two helicities reflects some topological features of the domain as well as the velocity and vorticity fields which is discussed and is shown for simply connected domains the two helicities coincide. The energy variation of the vorticity field is shown to be formally the same as for the incompressible flow obtained before. For fluid domains consisting of several disjoint solid tori, at each time, the harmonic knot subspace of smooth vector fields on the fluid domain is found to have two independent base sets with a special type of orthogonality between these two bases by which a topological description of the vortex and velocity fields depending on the helicity difference is achieved since this difference is shown to depend only on the harmonic knot parts of velocity, vorticity, and its Biot-Savart vector field. For an ideal magnetohydrodynamics (MHD) flow three independent constant helicities are reviewed while the helicity of magnetic potential is generalized for non-simply connected domains by inserting a special harmonic knot field in the dynamics of the magnetic potential. It is proved that the harmonic knot part of the vorticity in hydrodynamics and the magnetic field in MHD is presented by constant coefficients (fluxes) when expanded in terms of one of the time dependent base functions.

Constraining the physical state by symmetries

NASA Astrophysics Data System (ADS)

Fatibene, L.; Ferraris, M.; Magnano, G.

2017-03-01

After reviewing the hole argument and its relations with initial value problem and general covariance, we shall discuss how much freedom one has to define the physical state in a generally covariant field theory (with or without internal gauge symmetries). Our analysis relies on Cauchy problems, thus it is restricted to globally hyperbolic spacetimes. We shall show that in generally covariant theories on a compact space (as well as for internal gauge symmetries on any spacetime) one has no freedom and one is forced to declare as physically equivalent two configurations which differ by a global spacetime diffeomorphism (or by an internal gauge transformation) as it is usually prescribed. On the contrary, when space is not compact, the result does not hold true and one may have different options to define physically equivalent configurations, still preserving determinism. For this scenario to be effective, the group G of formal transformations needs to be a subgroup of dynamical symmetries (otherwise field equations, which are written in terms of configurations would not induce equations for the physical state classes) and it must contain the group D generated by Cauchy transformations (otherwise the equations induced on physical state classes would not be well posed, either). We argue that it is exactly because of this double inclusion that the hole argument in its initial problem formulation is more powerful than in its boundary formulation. In the boundary formulation of the hole argument one still has that the group G of formal transformations is a subgroup of dynamical symmetries, but there is no evidence for it to contain a particular non-trivial subgroup.In this paper we shall show that this scenario is exactly implemented in generally covariant theories. In the last section we shall show it to be implemented in gauge theories as well.Norton also argued (see [1]) that the definition of physical state is something to be discussed in physics and it is not something which can be settled by a purely mathematical argument. This position is certainly plausible and agreeable. However, we shall here argue that some constraints to the definition of physical state can be in fact put on a mathematical stance (the ones which go back to Einstein-Hilbert about well-posedness of Cauchy problems).A physical state is hence defined as an equivalence class of configurations, for which dynamics is well-posed, i.e. its evolution is deterministically singled out by initial conditions. It also defines what the physical observables are, i.e., by definition, the quantities which depend on the equivalence classes, but not on the specific representative configurations. Equivalently, physical observables are defined as quantities which are invariant with respect to formal transformations.A detailed analysis of these issues shows an unexpected structure of cases which is not clarified in general, yet. What is clear is that assuming, as usually done, that the physical state of a generally covariant theory is to be identified with equivalence classes of configurations modulo spacetime diffeomorphisms is a fair assumption, still a choice which is sometimes forced by mathematics (in particular by determinism in the form of Cauchy theorem on globally hyperbolic spacetimes with a compact space) but sometimes it is one of many possible choices which, in those cases, we agree should be addressed from a physical stance.We shall argue that sometimes one can find subclasses of diffeomorphisms (i.e. the group generated by Cauchy-compatible transformations, below denoted by D →) which play a distinctive role in the discussion and which, to the best of our knowledge, has not properly been taken into account in standard frameworks.Let us start, for the sake of simplicity, by restricting to generally covariant theories. Gauge theories will be briefly discussed in the conclusions since most of what we shall do easily applies to those cases, as well; see [20] for general framework and notation.In a generally covariant theory one has a huge group of symmetries S containing the (lift to the configuration bundle of the) spacetime diffeomorphisms. The group of spacetime diffeomorphisms will be denoted by Diff(M) . In particular, the subgroup of spacetime diffeomorphisms which can be connected by a flow with the identity idM will be denoted by Diffe(M) . Any element Φ ∈Diffe(M) can be obtained by evaluating a 1-parameter subgroup Φs at s = 1, i.e. Φ =Φ1. The 1-parameter subgroup Φs is also called a flow of diffeomorphisms.The standard attitude is to assume that in a generally covariant theory any two configurations of fields differing by any spacetime diffeomorphism represent the same physical state. In other words, if σ is a section of the configuration bundle and Φ∗ σ =σ‧ is its image through a diffeomorphism (in Diffe(M) or in Diff(M) depending on the case) then both σ and σ‧ represent the same physical state of the system.Let us call formal transformations the group G of transformations which fix the physical state, or, equivalently, define the physical states of the orbits of the group G. As a matter of fact defining the group of formal transformations is equivalent to defining the physical state. Either one defines the physical state as the orbits of the action of formal transformations or defines formal transformations as the transformations acting on configurations by mapping one representative of the physical state into another representative of the same physical state, i.e. fixing the physical states.In order for this to make sense one needs a formal transformation Φ to be a symmetry of the system (as it is in generally covariant theories) since if σ is a solution, of course also σ‧ must be a solution as well. In other words any formal transformation (acting on configurations but leaving the physical state unchanged) must be a symmetry and the symmetry group is an upper bound to the group of formal transformations, i.e. one must have G ⊂ S.We shall show that there is a lower bound (which will be denoted by D → and which is generated by Cauchy transformations) for the group G of formal transformations as well, i.e. one must have D → ⊂ G ⊂ S.We shall argue that when D → ⊊ S =Diffe(M) one has a certain freedom in setting G between its lower and upper bounds. In these cases one has different options to set the group D → ⊂ G ⊂ S and each different assumption about what G is, in fact defines a different theory with the same dynamics but different interpretation of what is the physical state and what can be in principle observed; see [21]. We shall also discuss topological conditions on M for which this freedom is nullified and one is forced to set G =Diffe(M) as usually done in the literature. On the other hand, we can discuss the motion of particles in spacetime on a physical stance and show that it is reasonable to assume that the physical state is described by worldline trajectories and parameterisations are irrelevant. The two viewpoints come (quite independently) to the same conclusion, which is a good thing. We shall also show a counter example, showing a globally hyperbolic spacetime M = R × R with a non-compact space Σ ≡ R in which the situation is different from the compact space case. As a consequence, the usual assumption of identifying configurations which differ by a diffeomorphism is a legitimate though in general unmotivated choice. When describing a system one should be aware of which assumptions come from mathematical constraints and which assumptions are done on a physical stance.When setting up a general covariant theory one should first study whether the group D → is a strict subgroup of Diffe(M) . If it is, one should characterise possible subgroups D → ⊂ G ⊂ S. Then one should declare which one of such groups G is elected as the group of formal transformations. Different choices lead to different theories with an equivalent dynamics but different observables.

Entropy of nonrotating isolated horizons in Lovelock theory from loop quantum gravity

NASA Astrophysics Data System (ADS)

Wang, Jing-Bo; Huang, Chao-Guang; Li, Lin

2016-08-01

In this paper, the BF theory method is applied to the nonrotating isolated horizons in Lovelock theory. The final entropy matches the Wald entropy formula for this theory. We also confirm the conclusion obtained by Bodendorfer et al. that the entropy is related to the flux operator rather than the area operator in general diffeomorphic-invariant theory. Supported by National Natural Science Foundation of China (11275207)

A three-colour graph as a complete topological invariant for gradient-like diffeomorphisms of surfaces

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

Grines, V Z; Pochinka, O V; Kapkaeva, S Kh

In a paper of Oshemkov and Sharko, three-colour graphs were used to make the topological equivalence of Morse-Smale flows on surfaces obtained by Peixoto more precise. In the present paper, in the language of three-colour graphs equipped with automorphisms, we obtain a complete (including realization) topological classification of gradient-like cascades on surfaces. Bibliography: 25 titles.

Zernike-like systems in polygons and polygonal facets.

PubMed

Ferreira, Chelo; López, José L; Navarro, Rafael; Sinusía, Ester Pérez

2015-07-20

Zernike polynomials are commonly used to represent the wavefront phase on circular optical apertures, since they form a complete and orthonormal basis on the unit disk. In [Opt. Lett.32, 74 (2007)10.1364/OL.32.000074OPLEDP0146-9592] we introduced a new Zernike basis for elliptic and annular optical apertures based on an appropriate diffeomorphism between the unit disk and the ellipse and the annulus. Here, we present a generalization of this Zernike basis for a variety of important optical apertures, paying special attention to polygons and the polygonal facets present in segmented mirror telescopes. On the contrary to ad hoc solutions, most of them based on the Gram-Smith orthonormalization method, here we consider a piecewise diffeomorphism that transforms the unit disk into the polygon under consideration. We use this mapping to define a Zernike-like orthonormal system over the polygon. We also consider ensembles of polygonal facets that are essential in the design of segmented mirror telescopes. This generalization, based on in-plane warping of the basis functions, provides a unique solution, and what is more important, it guarantees a reasonable level of invariance of the mathematical properties and the physical meaning of the initial basis functions. Both the general form and the explicit expressions for a typical example of telescope optical aperture are provided.

On actions for (entangling) surfaces and DCFTs

NASA Astrophysics Data System (ADS)

Armas, Jay; Tarrío, Javier

2018-04-01

The dynamics of surfaces and interfaces describe many physical systems, including fluid membranes, entanglement entropy and the coupling of defects to quantum field theories. Based on the formulation of submanifold calculus developed by Carter, we introduce a new variational principle for (entangling) surfaces. This principle captures all diffeomorphism constraints on surface/interface actions and their associated spacetime stress tensor. The different couplings to the geometric tensors appearing in the surface action are interpreted in terms of response coefficients within elasticity theory. An example of a surface action with edges at the two-derivative level is studied, including both the parity-even and parity-odd sectors. Its conformally invariant counterpart restricts the type of conformal anomalies that can appear in two-dimensional submanifolds with boundaries. Analogously to hydrodynamics, it is shown that classification methods can be used to constrain the stress tensor of (entangling) surfaces at a given order in derivatives. This analysis reveals a purely geometric parity-odd contribution to the Young modulus of a thin elastic membrane. Extending this novel variational principle to BCFTs and DCFTs in curved spacetimes allows to obtain the Ward identities for diffeomorphism and Weyl transformations. In this context, we provide a formal derivation of the contact terms in the stress tensor and of the displacement operator for a broad class of actions.

Conservation laws and stress-energy-momentum tensors for systems with background fields

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

Gratus, Jonathan, E-mail: j.gratus@lancaster.ac.uk; The Cockcroft Institute, Daresbury Laboratory, Warrington WA4 4AD; Obukhov, Yuri N., E-mail: yo@thp.uni-koeln.de

2012-10-15

This article attempts to delineate the roles played by non-dynamical background structures and Killing symmetries in the construction of stress-energy-momentum tensors generated from a diffeomorphism invariant action density. An intrinsic coordinate independent approach puts into perspective a number of spurious arguments that have historically lead to the main contenders, viz the Belinfante-Rosenfeld stress-energy-momentum tensor derived from a Noether current and the Einstein-Hilbert stress-energy-momentum tensor derived in the context of Einstein's theory of general relativity. Emphasis is placed on the role played by non-dynamical background (phenomenological) structures that discriminate between properties of these tensors particularly in the context of electrodynamics inmore » media. These tensors are used to construct conservation laws in the presence of Killing Lie-symmetric background fields. - Highlights: Black-Right-Pointing-Pointer The role of background fields in diffeomorphism invariant actions is demonstrated. Black-Right-Pointing-Pointer Interrelations between different stress-energy-momentum tensors are emphasised. Black-Right-Pointing-Pointer The Abraham and Minkowski electromagnetic tensors are discussed in this context. Black-Right-Pointing-Pointer Conservation laws in the presence of nondynamic background fields are formulated. Black-Right-Pointing-Pointer The discussion is facilitated by the development of a new variational calculus.« less

Morphometric brain characterization of refractory obsessive-compulsive disorder: diffeomorphic anatomic registration using exponentiated Lie algebra.

PubMed

Tang, Wanjie; Li, Bin; Huang, Xiaoqi; Jiang, Xiaoyu; Li, Fei; Wang, Lijuan; Chen, Taolin; Wang, Jinhui; Gong, Qiyong; Yang, Yanchun

2013-10-01

Few studies have used neuroimaging to characterize treatment-refractory obsessive-compulsive disorder (OCD). This study sought to explore gray matter structure in patients with treatment-refractory OCD and compare it with that of healthy controls. A total of 18 subjects with treatment-refractory OCD and 26 healthy volunteers were analyzed by MRI using a 3.0-T scanner and voxel-based morphometry (VBM). Diffeomorphic anatomical registration using exponentiated Lie algebra (DARTEL) was used to identify structural changes in gray matter associated with treatment-refractory OCD. A partial correlation model was used to analyze whether morphometric changes were associated with Yale-Brown Obsessive-Compulsive Scale scores and illness duration. Gray matter volume did not differ significantly between the two groups. Treatment-refractory OCD patients showed significantly lower gray matter density than healthy subjects in the left posterior cingulate cortex (PCC) and mediodorsal thalamus (MD) and significantly higher gray matter density in the left dorsal striatum (putamen). These changes did not correlate with symptom severity or illness duration. Our findings provide new evidence of deficits in gray matter density in treatment-refractory OCD patients. These patients may show characteristic density abnormalities in the left PCC, MD and dorsal striatum (putamen), which should be verified in longitudinal studies. © 2013. Published by Elsevier Inc. All rights reserved.

Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra provides reduced effect of scanner for cortex volumetry with atlas-based method in healthy subjects.

PubMed

Goto, Masami; Abe, Osamu; Aoki, Shigeki; Hayashi, Naoto; Miyati, Tosiaki; Takao, Hidemasa; Iwatsubo, Takeshi; Yamashita, Fumio; Matsuda, Hiroshi; Mori, Harushi; Kunimatsu, Akira; Ino, Kenji; Yano, Keiichi; Ohtomo, Kuni

2013-07-01

This study aimed to investigate whether the effect of scanner for cortex volumetry with atlas-based method is reduced using Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra (DARTEL) normalization compared with standard normalization. Three-dimensional T1-weighted magnetic resonance images (3D-T1WIs) of 21 healthy subjects were obtained and evaluated for effect of scanner in cortex volumetry. 3D-T1WIs of the 21 subjects were obtained with five MRI systems. Imaging of each subject was performed on each of five different MRI scanners. We used the Voxel-Based Morphometry 8 tool implemented in Statistical Parametric Mapping 8 and WFU PickAtlas software (Talairach brain atlas theory). The following software default settings were used as bilateral region-of-interest labels: "Frontal Lobe," "Hippocampus," "Occipital Lobe," "Orbital Gyrus," "Parietal Lobe," "Putamen," and "Temporal Lobe." Effect of scanner for cortex volumetry using the atlas-based method was reduced with DARTEL normalization compared with standard normalization in Frontal Lobe, Occipital Lobe, Orbital Gyrus, Putamen, and Temporal Lobe; was the same in Hippocampus and Parietal Lobe; and showed no increase with DARTEL normalization for any region of interest (ROI). DARTEL normalization reduces the effect of scanner, which is a major problem in multicenter studies.

General Relativity without paradigm of space-time covariance, and resolution of the problem of time

NASA Astrophysics Data System (ADS)

Soo, Chopin; Yu, Hoi-Lai

2014-01-01

The framework of a theory of gravity from the quantum to the classical regime is presented. The paradigm shift from full space-time covariance to spatial diffeomorphism invariance, together with clean decomposition of the canonical structure, yield transparent physical dynamics and a resolution of the problem of time. The deep divide between quantum mechanics and conventional canonical formulations of quantum gravity is overcome with a Schrödinger equation for quantum geometrodynamics that describes evolution in intrinsic time. Unitary time development with gauge-invariant temporal ordering is also viable. All Kuchar observables become physical; and classical space-time, with direct correlation between its proper times and intrinsic time intervals, emerges from constructive interference. The framework not only yields a physical Hamiltonian for Einstein's theory, but also prompts natural extensions and improvements towards a well behaved quantum theory of gravity. It is a consistent canonical scheme to discuss Horava-Lifshitz theories with intrinsic time evolution, and of the many possible alternatives that respect 3-covariance (rather than the more restrictive 4-covariance of Einstein's theory), Horava's "detailed balance" form of the Hamiltonian constraint is essentially pinned down by this framework. Issues in quantum gravity that depend on radiative corrections and the rigorous definition and regularization of the Hamiltonian operator are not addressed in this work.

A 4D biomechanical lung phantom for joint segmentation/registration evaluation

NASA Astrophysics Data System (ADS)

Markel, Daniel; Levesque, Ives; Larkin, Joe; Léger, Pierre; El Naqa, Issam

2016-10-01

At present, there exists few openly available methods for evaluation of simultaneous segmentation and registration algorithms. These methods allow for a combination of both techniques to track the tumor in complex settings such as adaptive radiotherapy. We have produced a quality assurance platform for evaluating this specific subset of algorithms using a preserved porcine lung in such that it is multi-modality compatible: positron emission tomography (PET), computer tomography (CT) and magnetic resonance imaging (MRI). A computer controlled respirator was constructed to pneumatically manipulate the lungs in order to replicate human breathing traces. A registration ground truth was provided using an in-house bifurcation tracking pipeline. Segmentation ground truth was provided by synthetic multi-compartment lesions to simulate biologically active tumor, background tissue and a necrotic core. The bifurcation tracking pipeline results were compared to digital deformations and used to evaluate three registration algorithms, Diffeomorphic demons, fast-symmetric forces demons and MiMVista’s deformable registration tool. Three segmentation algorithms the Chan Vese level sets method, a Hybrid technique and the multi-valued level sets algorithm. The respirator was able to replicate three seperate breathing traces with a mean accuracy of 2-2.2%. Bifurcation tracking error was found to be sub-voxel when using human CT data for displacements up to 6.5 cm and approximately 1.5 voxel widths for displacements up to 3.5 cm for the porcine lungs. For the fast-symmetric, diffeomorphic and MiMvista registration algorithms, mean geometric errors were found to be 0.430+/- 0.001 , 0.416+/- 0.001 and 0.605+/- 0.002 voxels widths respectively using the vector field differences and 0.4+/- 0.2 , 0.4+/- 0.2 and 0.6+/- 0.2 voxel widths using the bifurcation tracking pipeline. The proposed phantom was found sufficient for accurate evaluation of registration and segmentation algorithms. The use of automatically generated anatomical landmarks proposed can eliminate the time and potential innacuracy of manual landmark selection using expert observers.

The first law of black hole mechanics for fields with internal gauge freedom

NASA Astrophysics Data System (ADS)

Prabhu, Kartik

2017-02-01

We derive the first law of black hole mechanics for physical theories based on a local, covariant and gauge-invariant Lagrangian where the dynamical fields transform non-trivially under the action of some internal gauge transformations. The theories of interest include General Relativity formulated in terms of tetrads, Einstein-Yang-Mills theory and Einstein-Dirac theory. Since the dynamical fields of these theories have some internal gauge freedom, we argue that there is no natural group action of diffeomorphisms of spacetime on such dynamical fields. In general, such fields cannot even be represented as smooth, globally well-defined tensor fields on spacetime. Consequently the derivation of the first law by Iyer and Wald cannot be used directly. Nevertheless, we show how such theories can be formulated on a principal bundle and that there is a natural action of automorphisms of the bundle on the fields. These bundle automorphisms encode both spacetime diffeomorphisms and internal gauge transformations. Using this reformulation we define the Noether charge associated to an infinitesimal automorphism and the corresponding notion of stationarity and axisymmetry of the dynamical fields. We first show that we can define certain potentials and charges at the horizon of a black hole so that the potentials are constant on the bifurcate Killing horizon, giving a generalised zeroth law for bifurcate Killing horizons. We further identify the gravitational potential and perturbed charge as the temperature and perturbed entropy of the black hole which gives an explicit formula for the perturbed entropy analogous to the Wald entropy formula. We then obtain a general first law of black hole mechanics for such theories. The first law relates the perturbed Hamiltonians at spatial infinity and the horizon, and the horizon contributions take the form of a ‘potential times perturbed charge’ term. We also comment on the ambiguities in defining a prescription for the total entropy for black holes.

Helicity is the only integral invariant of volume-preserving transformations

PubMed Central

Enciso, Alberto; Peralta-Salas, Daniel; de Lizaur, Francisco Torres

2016-01-01

We prove that any regular integral invariant of volume-preserving transformations is equivalent to the helicity. Specifically, given a functional ℐ defined on exact divergence-free vector fields of class C1 on a compact 3-manifold that is associated with a well-behaved integral kernel, we prove that ℐ is invariant under arbitrary volume-preserving diffeomorphisms if and only if it is a function of the helicity. PMID:26864201

Infinite Set of Soft Theorems in Gauge-Gravity Theories as Ward-Takahashi Identities

NASA Astrophysics Data System (ADS)

Hamada, Yuta; Shiu, Gary

2018-05-01

We show that the soft photon, gluon, and graviton theorems can be understood as the Ward-Takahashi identities of large gauge transformation, i.e., diffeomorphism that does not fall off at spatial infinity. We found infinitely many new identities which constrain the higher order soft behavior of the gauge bosons and gravitons in scattering amplitudes of gauge and gravity theories. Diagrammatic representations of these soft theorems are presented.

Symmetries and conservation laws of a nonlinear sigma model with gravitino

NASA Astrophysics Data System (ADS)

Jost, Jürgen; Keßler, Enno; Tolksdorf, Jürgen; Wu, Ruijun; Zhu, Miaomiao

2018-06-01

We study the symmetries and invariances of a version of the action functional of the nonlinear sigma model with gravitino, as considered in Jost et al. (2017). The action is invariant under rescaled conformal transformations, super Weyl transformations, and diffeomorphisms. In particular cases the functional possesses a degenerate supersymmetry. The corresponding conservation laws lead to a geometric interpretation of the energy-momentum tensor and supercurrent as holomorphic sections of appropriate bundles.

On Light-Like Extremal Surfaces in Curved Spacetimes

NASA Astrophysics Data System (ADS)

Huang, Shou-Jun; He, Chun-Lei

2014-01-01

In this paper, we are concerned with light-like extremal surfaces in curved spacetimes. It is interesting to find that under a diffeomorphic transformation of variables, the light-like extremal surfaces can be described by a system of nonlinear geodesic equations. Particularly, we investigate the light-like extremal surfaces in Schwarzschild spacetime in detail and some new special solutions are derived systematically with aim to compare with the known results and to illustrate the method.

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

Berezhiani, Lasha; Khoury, Justin; Wang, Junpu, E-mail: lashaber@gmail.com, E-mail: jkhoury@sas.upenn.edu, E-mail: jwang217@jhu.edu

Single-field perturbations satisfy an infinite number of consistency relations constraining the squeezed limit of correlation functions at each order in the soft momentum. These can be understood as Ward identities for an infinite set of residual global symmetries, or equivalently as Slavnov-Taylor identities for spatial diffeomorphisms. In this paper, we perform a number of novel, non-trivial checks of the identities in the context of single field inflationary models with arbitrary sound speed. We focus for concreteness on identities involving 3-point functions with a soft external mode, and consider all possible scalar and tensor combinations for the hard-momentum modes. In allmore » these cases, we check the consistency relations up to and including cubic order in the soft momentum. For this purpose, we compute for the first time the 3-point functions involving 2 scalars and 1 tensor, as well as 2 tensors and 1 scalar, for arbitrary sound speed.« less

Anisotropic tensor power spectrum at interferometer scales induced by tensor squeezed non-Gaussianity

NASA Astrophysics Data System (ADS)

Ricciardone, Angelo; Tasinato, Gianmassimo

2018-02-01

We develop a scenario of inflation with spontaneously broken time and space diffeomorphisms, with distinctive features for the primordial tensor modes. Inflationary tensor fluctuations are not conserved outside the horizon, and can acquire a mass during the inflationary epoch. They can evade the Higuchi bound around de Sitter space, thanks to interactions with the fields driving expansion. Correspondingly, the primordial stochastic gravitational wave background (SGWB) is characterised by a tuneable scale dependence, and can be detectable at interferometer scales. In this set-up, tensor non-Gaussianity can be parametrically enhanced in the squeezed limit. This induces a coupling between long and short tensor modes, leading to a specific quadrupolar anisotropy in the primordial SGWB spectrum, which can be used to build estimators for tensor non-Gaussianity. We analyse how our inflationary system can be tested with interferometers, also discussing how an interferometer can be sensitive to a primordial anisotropic SGWB.

Differential calculus and gauge transformations on a deformed space

NASA Astrophysics Data System (ADS)

Wess, Julius

2007-08-01

We consider a formalism by which gauge theories can be constructed on noncommutative space time structures. The coordinates are supposed to form an algebra, restricted by certain requirements that allow us to realise the algebra in terms of star products. In this formulation it is useful to define derivatives and to extend the algebra of coordinates by these derivatives. The elements of this extended algebra are deformed differential operators. We then show that there is a morphism between these deformed differential operators and the usual higher order differential operators acting on functions of commuting coordinates. In this way we obtain deformed gauge transformations and a deformed version of the algebra of diffeomorphisms. The deformation of these algebras can be clearly seen in the category of Hopf algebras. The comultiplication will be twisted. These twisted algebras can be realised on noncommutative spaces and allow the construction of deformed gauge theories and deformed gravity theory.

Flatness-based control and Kalman filtering for a continuous-time macroeconomic model

NASA Astrophysics Data System (ADS)

Rigatos, G.; Siano, P.; Ghosh, T.; Busawon, K.; Binns, R.

2017-11-01

The article proposes flatness-based control for a nonlinear macro-economic model of the UK economy. The differential flatness properties of the model are proven. This enables to introduce a transformation (diffeomorphism) of the system's state variables and to express the state-space description of the model in the linear canonical (Brunowsky) form in which both the feedback control and the state estimation problem can be solved. For the linearized equivalent model of the macroeconomic system, stabilizing feedback control can be achieved using pole placement methods. Moreover, to implement stabilizing feedback control of the system by measuring only a subset of its state vector elements the Derivative-free nonlinear Kalman Filter is used. This consists of the Kalman Filter recursion applied on the linearized equivalent model of the financial system and of an inverse transformation that is based again on differential flatness theory. The asymptotic stability properties of the control scheme are confirmed.

Prediction of CT Substitutes from MR Images Based on Local Diffeomorphic Mapping for Brain PET Attenuation Correction.

PubMed

Wu, Yao; Yang, Wei; Lu, Lijun; Lu, Zhentai; Zhong, Liming; Huang, Meiyan; Feng, Yanqiu; Feng, Qianjin; Chen, Wufan

2016-10-01

Attenuation correction is important for PET reconstruction. In PET/MR, MR intensities are not directly related to attenuation coefficients that are needed in PET imaging. The attenuation coefficient map can be derived from CT images. Therefore, prediction of CT substitutes from MR images is desired for attenuation correction in PET/MR. This study presents a patch-based method for CT prediction from MR images, generating attenuation maps for PET reconstruction. Because no global relation exists between MR and CT intensities, we propose local diffeomorphic mapping (LDM) for CT prediction. In LDM, we assume that MR and CT patches are located on 2 nonlinear manifolds, and the mapping from the MR manifold to the CT manifold approximates a diffeomorphism under a local constraint. Locality is important in LDM and is constrained by the following techniques. The first is local dictionary construction, wherein, for each patch in the testing MR image, a local search window is used to extract patches from training MR/CT pairs to construct MR and CT dictionaries. The k-nearest neighbors and an outlier detection strategy are then used to constrain the locality in MR and CT dictionaries. Second is local linear representation, wherein, local anchor embedding is used to solve MR dictionary coefficients when representing the MR testing sample. Under these local constraints, dictionary coefficients are linearly transferred from the MR manifold to the CT manifold and used to combine CT training samples to generate CT predictions. Our dataset contains 13 healthy subjects, each with T1- and T2-weighted MR and CT brain images. This method provides CT predictions with a mean absolute error of 110.1 Hounsfield units, Pearson linear correlation of 0.82, peak signal-to-noise ratio of 24.81 dB, and Dice in bone regions of 0.84 as compared with real CTs. CT substitute-based PET reconstruction has a regression slope of 1.0084 and R 2 of 0.9903 compared with real CT-based PET. In this method, no image segmentation or accurate registration is required. Our method demonstrates superior performance in CT prediction and PET reconstruction compared with competing methods. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Black holes, information, and the universal coefficient theorem

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

Patrascu, Andrei T.

2016-07-15

General relativity is based on the diffeomorphism covariant formulation of the laws of physics while quantum mechanics is based on the principle of unitary evolution. In this article, I provide a possible answer to the black hole information paradox by means of homological algebra and pairings generated by the universal coefficient theorem. The unitarity of processes involving black holes is restored by the demanding invariance of the laws of physics to the change of coefficient structures in cohomology.

Quantum mechanics from an equivalence principle

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

Faraggi, A.E.; Matone, M.

1997-05-15

The authors show that requiring diffeomorphic equivalence for one-dimensional stationary states implies that the reduced action S{sub 0} satisfies the quantum Hamilton-Jacobi equation with the Planck constant playing the role of a covariantizing parameter. The construction shows the existence of a fundamental initial condition which is strictly related to the Moebius symmetry of the Legendre transform and to its involutive character. The universal nature of the initial condition implies the Schroedinger equation in any dimension.

A general theory of linear cosmological perturbations: bimetric theories

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

Lagos, Macarena; Ferreira, Pedro G., E-mail: m.lagos13@imperial.ac.uk, E-mail: p.ferreira1@physics.ox.ac.uk

2017-01-01

We implement the method developed in [1] to construct the most general parametrised action for linear cosmological perturbations of bimetric theories of gravity. Specifically, we consider perturbations around a homogeneous and isotropic background, and identify the complete form of the action invariant under diffeomorphism transformations, as well as the number of free parameters characterising this cosmological class of theories. We discuss, in detail, the case without derivative interactions, and compare our results with those found in massive bigravity.

Galileons as the scalar analogue of general relativity

NASA Astrophysics Data System (ADS)

Klein, Remko; Ozkan, Mehmet; Roest, Diederik

2016-02-01

We establish a correspondence between general relativity with diffeomorphism invariance and scalar field theories with Galilean invariance: notions such as the Levi-Civita connection and the Riemann tensor have a Galilean counterpart. This suggests Galilean theories as the unique nontrivial alternative to gauge theories (including general relativity). Moreover, it is shown that the requirement of first-order Palatini formalism uniquely determines the Galileon models with second-order field equations, similar to the Lovelock gravity theories. Possible extensions are discussed.

LCC-Demons: a robust and accurate symmetric diffeomorphic registration algorithm.

PubMed

Lorenzi, M; Ayache, N; Frisoni, G B; Pennec, X

2013-11-01

Non-linear registration is a key instrument for computational anatomy to study the morphology of organs and tissues. However, in order to be an effective instrument for the clinical practice, registration algorithms must be computationally efficient, accurate and most importantly robust to the multiple biases affecting medical images. In this work we propose a fast and robust registration framework based on the log-Demons diffeomorphic registration algorithm. The transformation is parameterized by stationary velocity fields (SVFs), and the similarity metric implements a symmetric local correlation coefficient (LCC). Moreover, we show how the SVF setting provides a stable and consistent numerical scheme for the computation of the Jacobian determinant and the flux of the deformation across the boundaries of a given region. Thus, it provides a robust evaluation of spatial changes. We tested the LCC-Demons in the inter-subject registration setting, by comparing with state-of-the-art registration algorithms on public available datasets, and in the intra-subject longitudinal registration problem, for the statistically powered measurements of the longitudinal atrophy in Alzheimer's disease. Experimental results show that LCC-Demons is a generic, flexible, efficient and robust algorithm for the accurate non-linear registration of images, which can find several applications in the field of medical imaging. Without any additional optimization, it solves equally well intra & inter-subject registration problems, and compares favorably to state-of-the-art methods. Copyright © 2013 Elsevier Inc. All rights reserved.

Investigation of the spinfoam path integral with quantum cuboid intertwiners

NASA Astrophysics Data System (ADS)

Bahr, Benjamin; Steinhaus, Sebastian

2016-05-01

In this work, we investigate the 4d path integral for Euclidean quantum gravity on a hypercubic lattice, as given by the spinfoam model by Engle, Pereira, Rovelli, Livine, Freidel and Krasnov. To tackle the problem, we restrict to a set of quantum geometries that reflects the large amount of lattice symmetries. In particular, the sum over intertwiners is restricted to quantum cuboids, i.e. coherent intertwiners which describe a cuboidal geometry in the large-j limit. Using asymptotic expressions for the vertex amplitude, we find several interesting properties of the state sum. First of all, the value of coupling constants in the amplitude functions determines whether geometric or nongeometric configurations dominate the path integral. Secondly, there is a critical value of the coupling constant α , which separates two phases. In both phases, the diffeomorphism symmetry appears to be broken. In one, the dominant contribution comes from highly irregular, in the other from highly regular configurations, both describing flat Euclidean space with small quantum fluctuations around them, viewed in different coordinate systems. On the critical point diffeomorphism symmetry is nearly restored, however. Thirdly, we use the state sum to compute the physical norm of kinematical states, i.e. their norm in the physical Hilbert space. We find that states which describe boundary geometry with high torsion have an exponentially suppressed physical norm. We argue that this allows one to exclude them from the state sum in calculations.

Reformulation of the symmetries of first-order general relativity

NASA Astrophysics Data System (ADS)

Montesinos, Merced; González, Diego; Celada, Mariano; Díaz, Bogar

2017-10-01

We report a new internal gauge symmetry of the n-dimensional Palatini action with cosmological term (n>3 ) that is the generalization of three-dimensional local translations. This symmetry is obtained through the direct application of the converse of Noether’s second theorem on the theory under consideration. We show that diffeomorphisms can be expressed as linear combinations of it and local Lorentz transformations with field-dependent parameters up to terms involving the variational derivatives of the action. As a result, the new internal symmetry together with local Lorentz transformations can be adopted as the fundamental gauge symmetries of general relativity. Although their gauge algebra is open in general, it allows us to recover, without resorting to the equations of motion, the very well-known Lie algebra satisfied by translations and Lorentz transformations in three dimensions. We also report the analog of the new gauge symmetry for the Holst action with cosmological term, finding that it explicitly depends on the Immirzi parameter. The same result concerning its relation to diffeomorphisms and the open character of the gauge algebra also hold in this case. Finally, we consider the non-minimal coupling of a scalar field to gravity in n dimensions and establish that the new gauge symmetry is affected by this matter field. Our results indicate that general relativity in dimension greater than three can be thought of as a gauge theory.

On the approximation of Lyapunov exponents and a question suggested by Anatole Katok

NASA Astrophysics Data System (ADS)

Dai, Xiongping

2010-03-01

Let \\mathcal {F}\\colon X\\times\\mathbb{Z}_+\\rightarrow \\rm{GL}(n,\\mathbb{R}) be a Hölder-continuous linear cocycle whose driving semiflow f\\colon X\\times\\mathbb{Z}_+\\rightarrow X preserves a probability μ on a compact metric space X. Using the concept of two-sided quasi-Pesin orbits introduced in this paper, we show that the Lyapunov characteristic spectrum of μ can be approached arbitrarily by that of periodic points of f. So, if all periodic points of f have only positive Lyapunov exponents and such exponents are uniformly bounded away from zero, then μ also has only positive exponents. In our arguments, the exponential closing property of the driving semiflow is a basic condition, and it is easy to check that every C1-expanding map of a closed manifold obeys this closing property. Consequently, if f is a C1+Hölder local diffeomorphism of a closed manifold and if it is Hölder conjugated to some C1-expanding map, then f is itself expanding. This gives a positive answer to a question suggested by Anatole Katok.

Making classical and quantum canonical general relativity computable through a power series expansion in the inverse cosmological constant.

PubMed

Gambini, R; Pullin, J

2000-12-18

We consider general relativity with a cosmological constant as a perturbative expansion around a completely solvable diffeomorphism invariant field theory. This theory is the lambda --> infinity limit of general relativity. This allows an explicit perturbative computational setup in which the quantum states of the theory and the classical observables can be explicitly computed. An unexpected relationship arises at a quantum level between the discrete spectrum of the volume operator and the allowed values of the cosmological constant.

On the measure of conformal difference between Euclidean and Lobachevsky spaces

NASA Astrophysics Data System (ADS)

Zorich, Vladimir A.

2011-12-01

Euclidean space R^n and Lobachevsky space H^n are known to be not equivalent either conformally or quasiconformally. In this work we give exact asymptotics of the critical order of growth at infinity for the quasiconformality coefficient of a diffeomorphism f\\colon R^n\\to H^n for which such a mapping f is possible. We also consider the general case of immersions f\\colon M^n\\to N^n of conformally parabolic Riemannian manifolds. Bibliography: 17 titles.

Lagrangian averaging with geodesic mean

NASA Astrophysics Data System (ADS)

Oliver, Marcel

2017-11-01

This paper revisits the derivation of the Lagrangian averaged Euler (LAE), or Euler-α equations in the light of an intrinsic definition of the averaged flow map as the geodesic mean on the volume-preserving diffeomorphism group. Under the additional assumption that first-order fluctuations are statistically isotropic and transported by the mean flow as a vector field, averaging of the kinetic energy Lagrangian of an ideal fluid yields the LAE Lagrangian. The derivation presented here assumes a Euclidean spatial domain without boundaries.

Lagrangian averaging with geodesic mean.

PubMed

Oliver, Marcel

2017-11-01

This paper revisits the derivation of the Lagrangian averaged Euler (LAE), or Euler- α equations in the light of an intrinsic definition of the averaged flow map as the geodesic mean on the volume-preserving diffeomorphism group. Under the additional assumption that first-order fluctuations are statistically isotropic and transported by the mean flow as a vector field, averaging of the kinetic energy Lagrangian of an ideal fluid yields the LAE Lagrangian. The derivation presented here assumes a Euclidean spatial domain without boundaries.

O(2) Hopf bifurcation of viscous shock waves in a channel

NASA Astrophysics Data System (ADS)

Pogan, Alin; Yao, Jinghua; Zumbrun, Kevin

2015-07-01

Extending work of Texier and Zumbrun in the semilinear non-reflection symmetric case, we study O(2) transverse Hopf bifurcation, or "cellular instability", of viscous shock waves in a channel, for a class of quasilinear hyperbolic-parabolic systems including the equations of thermoviscoelasticity. The main difficulties are to (i) obtain Fréchet differentiability of the time- T solution operator by appropriate hyperbolic-parabolic energy estimates, and (ii) handle O(2) symmetry in the absence of either center manifold reduction (due to lack of spectral gap) or (due to nonstandard quasilinear hyperbolic-parabolic form) the requisite framework for treatment by spatial dynamics on the space of time-periodic functions, the two standard treatments for this problem. The latter issue is resolved by Lyapunov-Schmidt reduction of the time- T map, yielding a four-dimensional problem with O(2) plus approximate S1 symmetry, which we treat "by hand" using direct Implicit Function Theorem arguments. The former is treated by balancing information obtained in Lagrangian coordinates with that from associated constraints. Interestingly, this argument does not apply to gas dynamics or magnetohydrodynamics (MHD), due to the infinite-dimensional family of Lagrangian symmetries corresponding to invariance under arbitrary volume-preserving diffeomorphisms.

A Fully-Automated Subcortical and Ventricular Shape Generation Pipeline Preserving Smoothness and Anatomical Topology

PubMed Central

Tang, Xiaoying; Luo, Yuan; Chen, Zhibin; Huang, Nianwei; Johnson, Hans J.; Paulsen, Jane S.; Miller, Michael I.

2018-01-01

In this paper, we present a fully-automated subcortical and ventricular shape generation pipeline that acts on structural magnetic resonance images (MRIs) of the human brain. Principally, the proposed pipeline consists of three steps: (1) automated structure segmentation using the diffeomorphic multi-atlas likelihood-fusion algorithm; (2) study-specific shape template creation based on the Delaunay triangulation; (3) deformation-based shape filtering using the large deformation diffeomorphic metric mapping for surfaces. The proposed pipeline is shown to provide high accuracy, sufficient smoothness, and accurate anatomical topology. Two datasets focused upon Huntington's disease (HD) were used for evaluating the performance of the proposed pipeline. The first of these contains a total of 16 MRI scans, each with a gold standard available, on which the proposed pipeline's outputs were observed to be highly accurate and smooth when compared with the gold standard. Visual examinations and outlier analyses on the second dataset, which contains a total of 1,445 MRI scans, revealed 100% success rates for the putamen, the thalamus, the globus pallidus, the amygdala, and the lateral ventricle in both hemispheres and rates no smaller than 97% for the bilateral hippocampus and caudate. Another independent dataset, consisting of 15 atlas images and 20 testing images, was also used to quantitatively evaluate the proposed pipeline, with high accuracy having been obtained. In short, the proposed pipeline is herein demonstrated to be effective, both quantitatively and qualitatively, using a large collection of MRI scans. PMID:29867332

Diffeomorphic functional brain surface alignment: Functional demons.

PubMed

Nenning, Karl-Heinz; Liu, Hesheng; Ghosh, Satrajit S; Sabuncu, Mert R; Schwartz, Ernst; Langs, Georg

2017-08-01

Aligning brain structures across individuals is a central prerequisite for comparative neuroimaging studies. Typically, registration approaches assume a strong association between the features used for alignment, such as macro-anatomy, and the variable observed, such as functional activation or connectivity. Here, we propose to use the structure of intrinsic resting state fMRI signal correlation patterns as a basis for alignment of the cortex in functional studies. Rather than assuming the spatial correspondence of functional structures between subjects, we have identified locations with similar connectivity profiles across subjects. We mapped functional connectivity relationships within the brain into an embedding space, and aligned the resulting maps of multiple subjects. We then performed a diffeomorphic alignment of the cortical surfaces, driven by the corresponding features in the joint embedding space. Results show that functional alignment based on resting state fMRI identifies functionally homologous regions across individuals with higher accuracy than alignment based on the spatial correspondence of anatomy. Further, functional alignment enables measurement of the strength of the anatomo-functional link across the cortex, and reveals the uneven distribution of this link. Stronger anatomo-functional dissociation was found in higher association areas compared to primary sensory- and motor areas. Functional alignment based on resting state features improves group analysis of task based functional MRI data, increasing statistical power and improving the delineation of task-specific core regions. Finally, a comparison of the anatomo-functional dissociation between cohorts is demonstrated with a group of left and right handed subjects. Copyright © 2017 Elsevier Inc. All rights reserved.

Weyl and transverse diffeomorphism invariant spin-2 models in D=2+1

NASA Astrophysics Data System (ADS)

Dalmazi, Denis; dos Santos, A. L. R.; Ghosh, Subir; Mendonça, E. L.

2017-09-01

There are two covariant descriptions of massless spin-2 particles in D=3+1 via a symmetric rank-2 tensor: the linearized Einstein-Hilbert (LEH) theory and the Weyl plus transverse diffeomorphism (WTDIFF) invariant model. From the LEH theory one can obtain the linearized new massive gravity (NMG) in D=2+1 via Kaluza-Klein dimensional reduction followed by a dual master action. Here we show that a similar route takes us from the WTDIFF model to a linearized scalar-tensor NMG which belongs to a larger class of consistent spin-0 modifications of NMG. We also show that a traceless master action applied to a parity singlet furnishes two new spin-2 self-dual models. Moreover, we examine the singular replacement h_{μ ν } → h_{μ ν } - η _{μ ν }h/D and prove that it leads to consistent massive spin-2 models in D=2+1. They include linearized versions of unimodular topologically massive gravity (TMG) and unimodular NMG. Although the free part of those unimodular theories are Weyl invariant, we do not expect any improvement in the renormalizability. Both the linearized K-term (in NMG) and the linearized gravitational Chern-Simons term (in TMG) are invariant under longitudinal reparametrizations δ h_{μ ν } = partial _{μ }partial _{ν }ζ , which is not a symmetry of the WTDIFF Einstein-Hilbert term. Therefore, we still have one degree of freedom whose propagator behaves like 1/p^2 for large momentum.

A spline-based non-linear diffeomorphism for multimodal prostate registration.

PubMed

Mitra, Jhimli; Kato, Zoltan; Martí, Robert; Oliver, Arnau; Lladó, Xavier; Sidibé, Désiré; Ghose, Soumya; Vilanova, Joan C; Comet, Josep; Meriaudeau, Fabrice

2012-08-01

This paper presents a novel method for non-rigid registration of transrectal ultrasound and magnetic resonance prostate images based on a non-linear regularized framework of point correspondences obtained from a statistical measure of shape-contexts. The segmented prostate shapes are represented by shape-contexts and the Bhattacharyya distance between the shape representations is used to find the point correspondences between the 2D fixed and moving images. The registration method involves parametric estimation of the non-linear diffeomorphism between the multimodal images and has its basis in solving a set of non-linear equations of thin-plate splines. The solution is obtained as the least-squares solution of an over-determined system of non-linear equations constructed by integrating a set of non-linear functions over the fixed and moving images. However, this may not result in clinically acceptable transformations of the anatomical targets. Therefore, the regularized bending energy of the thin-plate splines along with the localization error of established correspondences should be included in the system of equations. The registration accuracies of the proposed method are evaluated in 20 pairs of prostate mid-gland ultrasound and magnetic resonance images. The results obtained in terms of Dice similarity coefficient show an average of 0.980±0.004, average 95% Hausdorff distance of 1.63±0.48 mm and mean target registration and target localization errors of 1.60±1.17 mm and 0.15±0.12 mm respectively. Copyright © 2012 Elsevier B.V. All rights reserved.

A Fully-Automated Subcortical and Ventricular Shape Generation Pipeline Preserving Smoothness and Anatomical Topology.

PubMed

Tang, Xiaoying; Luo, Yuan; Chen, Zhibin; Huang, Nianwei; Johnson, Hans J; Paulsen, Jane S; Miller, Michael I

2018-01-01

In this paper, we present a fully-automated subcortical and ventricular shape generation pipeline that acts on structural magnetic resonance images (MRIs) of the human brain. Principally, the proposed pipeline consists of three steps: (1) automated structure segmentation using the diffeomorphic multi-atlas likelihood-fusion algorithm; (2) study-specific shape template creation based on the Delaunay triangulation; (3) deformation-based shape filtering using the large deformation diffeomorphic metric mapping for surfaces. The proposed pipeline is shown to provide high accuracy, sufficient smoothness, and accurate anatomical topology. Two datasets focused upon Huntington's disease (HD) were used for evaluating the performance of the proposed pipeline. The first of these contains a total of 16 MRI scans, each with a gold standard available, on which the proposed pipeline's outputs were observed to be highly accurate and smooth when compared with the gold standard. Visual examinations and outlier analyses on the second dataset, which contains a total of 1,445 MRI scans, revealed 100% success rates for the putamen, the thalamus, the globus pallidus, the amygdala, and the lateral ventricle in both hemispheres and rates no smaller than 97% for the bilateral hippocampus and caudate. Another independent dataset, consisting of 15 atlas images and 20 testing images, was also used to quantitatively evaluate the proposed pipeline, with high accuracy having been obtained. In short, the proposed pipeline is herein demonstrated to be effective, both quantitatively and qualitatively, using a large collection of MRI scans.

Comparison of time-series registration methods in breast dynamic infrared imaging

NASA Astrophysics Data System (ADS)

Riyahi-Alam, S.; Agostini, V.; Molinari, F.; Knaflitz, M.

2015-03-01

Automated motion reduction in dynamic infrared imaging is on demand in clinical applications, since movement disarranges time-temperature series of each pixel, thus originating thermal artifacts that might bias the clinical decision. All previously proposed registration methods are feature based algorithms requiring manual intervention. The aim of this work is to optimize the registration strategy specifically for Breast Dynamic Infrared Imaging and to make it user-independent. We implemented and evaluated 3 different 3D time-series registration methods: 1. Linear affine, 2. Non-linear Bspline, 3. Demons applied to 12 datasets of healthy breast thermal images. The results are evaluated through normalized mutual information with average values of 0.70 ±0.03, 0.74 ±0.03 and 0.81 ±0.09 (out of 1) for Affine, Bspline and Demons registration, respectively, as well as breast boundary overlap and Jacobian determinant of the deformation field. The statistical analysis of the results showed that symmetric diffeomorphic Demons' registration method outperforms also with the best breast alignment and non-negative Jacobian values which guarantee image similarity and anatomical consistency of the transformation, due to homologous forces enforcing the pixel geometric disparities to be shortened on all the frames. We propose Demons' registration as an effective technique for time-series dynamic infrared registration, to stabilize the local temperature oscillation.

Diffeomorphism Group Representations in Relativistic Quantum Field Theory

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

Goldin, Gerald A.; Sharp, David H.

We explore the role played by the di eomorphism group and its unitary representations in relativistic quantum eld theory. From the quantum kinematics of particles described by representations of the di eomorphism group of a space-like surface in an inertial reference frame, we reconstruct the local relativistic neutral scalar eld in the Fock representation. An explicit expression for the free Hamiltonian is obtained in terms of the Lie algebra generators (mass and momentum densities). We suggest that this approach can be generalized to elds whose quanta are spatially extended objects.

Stability of marginally outer trapped surfaces and symmetries

NASA Astrophysics Data System (ADS)

Carrasco, Alberto; Mars, Marc

2009-09-01

We study the properties of stable, strictly stable and locally outermost marginally outer trapped surfaces in spacelike hypersurfaces of spacetimes possessing certain symmetries such as isometries, homotheties and conformal Killings. We first obtain results for general diffeomorphisms in terms of the so-called metric deformation tensor and then particularize to different types of symmetries. In particular, we find restrictions at the surfaces on the vector field generating the symmetry. Some consequences are discussed. As an application, we present a result on non-existence of stable marginally outer trapped surfaces in slices of FLRW.

Parent formulation at the Lagrangian level

NASA Astrophysics Data System (ADS)

Grigoriev, Maxim

2011-07-01

The recently proposed first-order parent formalism at the level of equations of motion is specialized to the case of Lagrangian systems. It is shown that for diffeomorphism-invariant theories the parent formulation takes the form of an AKSZ-type sigma model. The proposed formulation can be also seen as a Lagrangian version of the BV-BRST extension of the Vasiliev unfolded approach. We also discuss its possible interpretation as a multidimensional generalization of the Hamiltonian BFV-BRST formalism. The general construction is illustrated by examples of (parametrized) mechanics, relativistic particle, Yang-Mills theory, and gravity.

Sub-subleading soft gravitons and large diffeomorphisms

NASA Astrophysics Data System (ADS)

Campiglia, Miguel; Laddha, Alok

2017-01-01

We present strong evidence that the sub-subleading soft theorem in semiclassical (tree level) gravity discovered by Cachazo and Strominger is equivalent to the conservation of asymptotic charges associated to a new class of vector fields not contained within the previous extensions of BMS algebra. Our analysis crucially relies on analyzing the hitherto established equivalences between soft theorems and Ward identities from a new perspective. In this process we naturally (re)discover a class of `magnetic' charges at null infinity that are associated to the dual of the Weyl tensor.

Nonrelativistic trace and diffeomorphism anomalies in particle number background

NASA Astrophysics Data System (ADS)

Auzzi, Roberto; Baiguera, Stefano; Nardelli, Giuseppe

2018-04-01

Using the heat kernel method, we compute nonrelativistic trace anomalies for Schrödinger theories in flat spacetime, with a generic background gauge field for the particle number symmetry, both for a free scalar and a free fermion. The result is genuinely nonrelativistic, and it has no counterpart in the relativistic case. Contrary to naive expectations, the anomaly is not gauge invariant; this is similar to the nongauge covariance of the non-Abelian relativistic anomaly. We also show that, in the same background, the gravitational anomaly for a nonrelativistic scalar vanishes.

Perfect discretization of path integrals

NASA Astrophysics Data System (ADS)

Steinhaus, Sebastian

2012-05-01

In order to obtain a well-defined path integral one often employs discretizations. In the case of General Relativity these generically break diffeomorphism symmetry, which has severe consequences since these symmetries determine the dynamics of the corresponding system. In this article we consider the path integral of reparametrization invariant systems as a toy example and present an improvement procedure for the discretized propagator. Fixed points and convergence of the procedure are discussed. Furthermore we show that a reparametrization invariant path integral implies discretization independence and acts as a projector onto physical states.

Loop corrections in double field theory: non-trivial dilaton potentials

NASA Astrophysics Data System (ADS)

Lv, Songlin; Wu, Houwen; Yang, Haitang

2014-10-01

It is believed that the invariance of the generalised diffeomorphisms prevents any non-trivial dilaton potential from double field theory. It is therefore difficult to include loop corrections in the formalism. We show that by redefining a non-local dilaton field, under strong constraint which is necessary to preserve the gauge invariance of double field theory, the theory does permit non-constant dilaton potentials and loop corrections. If the fields have dependence on only one single coordinate, the non-local dilaton is identical to the ordinary one with an additive constant.

Exotica and the status of the strong cosmic censor conjecture in four dimensions

NASA Astrophysics Data System (ADS)

Etesi, Gábor

2017-12-01

An immense class of physical counterexamples to the four dimensional strong cosmic censor conjecture—in its usual broad formulation—is exhibited. More precisely, out of any closed and simply connected 4-manifold an open Ricci-flat Lorentzian 4-manifold is constructed which is not globally hyperbolic, and no perturbation of which, in any sense, can be globally hyperbolic. This very stable non-global-hyperbolicity is the consequence of our open spaces having a ‘creased end’—i.e. an end diffeomorphic to an exotic \

A high-resolution probabilistic in vivo atlas of human subcortical brain nuclei

PubMed Central

Pauli, Wolfgang M.; Nili, Amanda N.; Tyszka, J. Michael

2018-01-01

Recent advances in magnetic resonance imaging methods, including data acquisition, pre-processing and analysis, have benefited research on the contributions of subcortical brain nuclei to human cognition and behavior. At the same time, these developments have led to an increasing need for a high-resolution probabilistic in vivo anatomical atlas of subcortical nuclei. In order to address this need, we constructed high spatial resolution, three-dimensional templates, using high-accuracy diffeomorphic registration of T1- and T2- weighted structural images from 168 typical adults between 22 and 35 years old. In these templates, many tissue boundaries are clearly visible, which would otherwise be impossible to delineate in data from individual studies. The resulting delineations of subcortical nuclei complement current histology-based atlases. We further created a companion library of software tools for atlas development, to offer an open and evolving resource for the creation of a crowd-sourced in vivo probabilistic anatomical atlas of the human brain. PMID:29664465

Constraining dark sector perturbations I: cosmic shear and CMB lensing

NASA Astrophysics Data System (ADS)

Battye, Richard A.; Moss, Adam; Pearson, Jonathan A.

2015-04-01

We present current and future constraints on equations of state for dark sector perturbations. The equations of state considered are those corresponding to a generalized scalar field model and time-diffeomorphism invariant Script L(g) theories that are equivalent to models of a relativistic elastic medium and also Lorentz violating massive gravity. We develop a theoretical understanding of the observable impact of these models. In order to constrain these models we use CMB temperature data from Planck, BAO measurements, CMB lensing data from Planck and the South Pole Telescope, and weak galaxy lensing data from CFHTLenS. We find non-trivial exclusions on the range of parameters, although the data remains compatible with w=-1. We gauge how future experiments will help to constrain the parameters. This is done via a likelihood analysis for CMB experiments such as CoRE and PRISM, and tomographic galaxy weak lensing surveys, focussing in on the potential discriminatory power of Euclid on mildly non-linear scales.

Generative diffeomorphic modelling of large MRI data sets for probabilistic template construction.

PubMed

Blaiotta, Claudia; Freund, Patrick; Cardoso, M Jorge; Ashburner, John

2018-02-01

In this paper we present a hierarchical generative model of medical image data, which can capture simultaneously the variability of both signal intensity and anatomical shapes across large populations. Such a model has a direct application for learning average-shaped probabilistic tissue templates in a fully automated manner. While in principle the generality of the proposed Bayesian approach makes it suitable to address a wide range of medical image computing problems, our work focuses primarily on neuroimaging applications. In particular we validate the proposed method on both real and synthetic brain MR scans including the cervical cord and demonstrate that it yields accurate alignment of brain and spinal cord structures, as compared to state-of-the-art tools for medical image registration. At the same time we illustrate how the resulting tissue probability maps can readily be used to segment, bias correct and spatially normalise unseen data, which are all crucial pre-processing steps for MR imaging studies. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Hamiltonian General Relativity in Finite Space and Cosmological Potential Perturbations

NASA Astrophysics Data System (ADS)

Barbashov, B. M.; Pervushin, V. N.; Zakharov, A. F.; Zinchuk, V. A.

The Hamiltonian formulation of general relativity is considered in finite space-time and a specific reference frame given by the diffeo-invariant components of the Fock simplex in terms of the Dirac-ADM variables. The evolution parameter and energy invariant with respect to the time-coordinate transformations are constructed by the separation of the cosmological scale factor a(x0) and its identification with the spatial averaging of the metric determinant, so that the dimension of the kinemetric group of diffeomorphisms coincides with the dimension of a set of variables whose velocities are removed by the Gauss-type constraints in accordance with the second Nöther theorem. This coincidence allows us to solve the energy constraint, fulfil Dirac's Hamiltonian reduction, and to describe the potential perturbations in terms of the Lichnerowicz scale-invariant variables distinguished by the absence of the time derivatives of the spatial metric determinant. It was shown that the Hamiltonian version of the cosmological perturbation theory acquires attributes of the theory of superfluid liquid, and it leads to a generalization of the Schwarzschild solution. The astrophysical application of this approach to general relativity is considered under supposition that the Dirac-ADM Hamiltonian frame is identified with that of the Cosmic Microwave Background radiation distinguished by its dipole component in the frame of an Earth observer.

A New MRI-Based Model of Heart Function with Coupled Hemodynamics and Application to Normal and Diseased Canine Left Ventricles

PubMed Central

Choi, Young Joon; Constantino, Jason; Vedula, Vijay; Trayanova, Natalia; Mittal, Rajat

2015-01-01

A methodology for the simulation of heart function that combines an MRI-based model of cardiac electromechanics (CE) with a Navier–Stokes-based hemodynamics model is presented. The CE model consists of two coupled components that simulate the electrical and the mechanical functions of the heart. Accurate representations of ventricular geometry and fiber orientations are constructed from the structural magnetic resonance and the diffusion tensor MR images, respectively. The deformation of the ventricle obtained from the electromechanical model serves as input to the hemodynamics model in this one-way coupled approach via imposed kinematic wall velocity boundary conditions and at the same time, governs the blood flow into and out of the ventricular volume. The time-dependent endocardial surfaces are registered using a diffeomorphic mapping algorithm, while the intraventricular blood flow patterns are simulated using a sharp-interface immersed boundary method-based flow solver. The utility of the combined heart-function model is demonstrated by comparing the hemodynamic characteristics of a normal canine heart beating in sinus rhythm against that of the dyssynchronously beating failing heart. We also discuss the potential of coupled CE and hemodynamics models for various clinical applications. PMID:26442254

Optimal Fault-Tolerant Control for Discrete-Time Nonlinear Strict-Feedback Systems Based on Adaptive Critic Design.

PubMed

Wang, Zhanshan; Liu, Lei; Wu, Yanming; Zhang, Huaguang

2018-06-01

This paper investigates the problem of optimal fault-tolerant control (FTC) for a class of unknown nonlinear discrete-time systems with actuator fault in the framework of adaptive critic design (ACD). A pivotal highlight is the adaptive auxiliary signal of the actuator fault, which is designed to offset the effect of the fault. The considered systems are in strict-feedback forms and involve unknown nonlinear functions, which will result in the causal problem. To solve this problem, the original nonlinear systems are transformed into a novel system by employing the diffeomorphism theory. Besides, the action neural networks (ANNs) are utilized to approximate a predefined unknown function in the backstepping design procedure. Combined the strategic utility function and the ACD technique, a reinforcement learning algorithm is proposed to set up an optimal FTC, in which the critic neural networks (CNNs) provide an approximate structure of the cost function. In this case, it not only guarantees the stability of the systems, but also achieves the optimal control performance as well. In the end, two simulation examples are used to show the effectiveness of the proposed optimal FTC strategy.

Simulation of range imaging-based estimation of respiratory lung motion. Influence of noise, signal dimensionality and sampling patterns.

PubMed

Wilms, M; Werner, R; Blendowski, M; Ortmüller, J; Handels, H

2014-01-01

A major problem associated with the irradiation of thoracic and abdominal tumors is respiratory motion. In clinical practice, motion compensation approaches are frequently steered by low-dimensional breathing signals (e.g., spirometry) and patient-specific correspondence models, which are used to estimate the sought internal motion given a signal measurement. Recently, the use of multidimensional signals derived from range images of the moving skin surface has been proposed to better account for complex motion patterns. In this work, a simulation study is carried out to investigate the motion estimation accuracy of such multidimensional signals and the influence of noise, the signal dimensionality, and different sampling patterns (points, lines, regions). A diffeomorphic correspondence modeling framework is employed to relate multidimensional breathing signals derived from simulated range images to internal motion patterns represented by diffeomorphic non-linear transformations. Furthermore, an automatic approach for the selection of optimal signal combinations/patterns within this framework is presented. This simulation study focuses on lung motion estimation and is based on 28 4D CT data sets. The results show that the use of multidimensional signals instead of one-dimensional signals significantly improves the motion estimation accuracy, which is, however, highly affected by noise. Only small differences exist between different multidimensional sampling patterns (lines and regions). Automatically determined optimal combinations of points and lines do not lead to accuracy improvements compared to results obtained by using all points or lines. Our results show the potential of multidimensional breathing signals derived from range images for the model-based estimation of respiratory motion in radiation therapy.

IR-safe and UV-safe integrands in the EFTofLSS with exact time dependence

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

Lewandowski, Matthew; Senatore, Leonardo, E-mail: matthew.lewandowski@ipht.fr, E-mail: senatore@stanford.edu

Because large-scale structure surveys may very well be the next leading sources of cosmological information, it is important to have a precise understanding of the cosmological observables; for this reason, the Effective Field Theory of Large-Scale Structure (EFTofLSS) was developed. So far, most results in the EFTofLSS have used the so-called Einstein-de Sitter approximation, an approximation of the time dependence which is known to be accurate to better than one percent. However, in order to reach even higher accuracy, the full time dependence must be used. The computation with exact time dependence is sensitive to both infrared (IR) and ultravioletmore » (UV) effects in the loop integrands, and while these effects must cancel because of diffeomorphism invariance, they make numerical computation much less efficient. We provide a formulation of the one-loop, equal-time exact-time-dependence power spectrum of density perturbations which is manifestly free of these spurious IR and UV divergences at the level of the integrand. We extend our results to the total matter mode with clustering quintessence, show that IR and UV divergences cancel, and provide the associated IR- and UV-safe integrand. This also establishes that the consistency conditions are satisfied in this system. We then use our one-loop result to do an improved precision comparison of the two-loop dark-matter power spectrum with the Dark Sky N -body simulation.« less

IR-safe and UV-safe integrands in the EFTofLSS with exact time dependence

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

Lewandowski, Matthew; Senatore, Leonardo

Because large-scale structure surveys may very well be the next leading sources of cosmological information, it is important to have a precise understanding of the cosmological observables; for this reason, the Effective Field Theory of Large-Scale Structure (EFTofLSS) was developed. So far, most results in the EFTofLSS have used the so-called Einstein-de Sitter approximation, an approximation of the time dependence which is known to be accurate to better than one percent. However, in order to reach even higher accuracy, the full time dependence must be used. The computation with exact time dependence is sensitive to both infrared (IR) and ultravioletmore » (UV) effects in the loop integrands, and while these effects must cancel because of diffeomorphism invariance, they make numerical computation much less efficient. We provide a formulation of the one-loop, equal-time exact-time-dependence power spectrum of density perturbations which is manifestly free of these spurious IR and UV divergences at the level of the integrand. We extend our results to the total matter mode with clustering quintessence, show that IR and UV divergences cancel, and provide the associated IR- and UV-safe integrand. This also establishes that the consistency conditions are satisfied in this system. In conclusion, we then use our one-loop result to do an improved precision comparison of the two-loop dark-matter power spectrum with the Dark Sky N-body simulation.« less

IR-safe and UV-safe integrands in the EFTofLSS with exact time dependence

DOE PAGES

Lewandowski, Matthew; Senatore, Leonardo

2017-08-31

Because large-scale structure surveys may very well be the next leading sources of cosmological information, it is important to have a precise understanding of the cosmological observables; for this reason, the Effective Field Theory of Large-Scale Structure (EFTofLSS) was developed. So far, most results in the EFTofLSS have used the so-called Einstein-de Sitter approximation, an approximation of the time dependence which is known to be accurate to better than one percent. However, in order to reach even higher accuracy, the full time dependence must be used. The computation with exact time dependence is sensitive to both infrared (IR) and ultravioletmore » (UV) effects in the loop integrands, and while these effects must cancel because of diffeomorphism invariance, they make numerical computation much less efficient. We provide a formulation of the one-loop, equal-time exact-time-dependence power spectrum of density perturbations which is manifestly free of these spurious IR and UV divergences at the level of the integrand. We extend our results to the total matter mode with clustering quintessence, show that IR and UV divergences cancel, and provide the associated IR- and UV-safe integrand. This also establishes that the consistency conditions are satisfied in this system. In conclusion, we then use our one-loop result to do an improved precision comparison of the two-loop dark-matter power spectrum with the Dark Sky N-body simulation.« less

The cosmological Slavnov-Taylor identity from BRST symmetry in single-field inflation

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

Binosi, D.; Quadri, A., E-mail: binosi@ectstar.eu, E-mail: andrea.quadri@mi.infn.it

The cosmological Slavnov-Taylor (ST) identity of the Einstein-Hilbert action coupled to a single inflaton field is obtained from the Becchi-Rouet-Stora-Tyutin (BRST) symmetry associated with diffeomorphism invariance in the Arnowitt-Deser-Misner (ADM) formalism. The consistency conditions between the correlators of the scalar and tensor modes in the squeezed limit are then derived from the ST identity, together with the softly broken conformal symmetry. Maldacena's original relations connecting the 2- and 3-point correlators at horizon crossing are recovered, as well as the next-to-leading corrections, controlled by the special conformal transformations.

Exact solutions of the Wheeler–DeWitt equation and the Yamabe construction

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

Ita III, Eyo Eyo, E-mail: ita@usna.edu; Soo, Chopin, E-mail: cpsoo@mail.ncku.edu.tw

Exact solutions of the Wheeler–DeWitt equation of the full theory of four dimensional gravity of Lorentzian signature are obtained. They are characterized by Schrödinger wavefunctionals having support on 3-metrics of constant spatial scalar curvature, and thus contain two full physical field degrees of freedom in accordance with the Yamabe construction. These solutions are moreover Gaussians of minimum uncertainty and they are naturally associated with a rigged Hilbert space. In addition, in the limit the regulator is removed, exact 3-dimensional diffeomorphism and local gauge invariance of the solutions are recovered.

Soft theorems for shift-symmetric cosmologies

NASA Astrophysics Data System (ADS)

Finelli, Bernardo; Goon, Garrett; Pajer, Enrico; Santoni, Luca

2018-03-01

We derive soft theorems for single-clock cosmologies that enjoy a shift symmetry. These so-called consistency conditions arise from a combination of a large diffeomorphism and the internal shift symmetry and fix the squeezed limit of all correlators with a soft scalar mode. As an application, we show that our results reproduce the squeezed bispectrum for ultra-slow-roll inflation, a particular shift-symmetric, nonattractor model which is known to violate Maldacena's consistency relation. Similar results have been previously obtained by Mooij and Palma using background-wave methods. Our results shed new light on the infrared structure of single-clock cosmological spacetimes.

The Geometric Nature of the Flaschka Transformation

NASA Astrophysics Data System (ADS)

Bloch, Anthony M.; Gay-Balmaz, François; Ratiu, Tudor S.

2017-06-01

We show that the Flaschka map, originally introduced to analyze the dynamics of the integrable Toda lattice system, is the inverse of a momentum map. We discuss the geometrical setting of the map and apply it to the generalized Toda lattice systems on semisimple Lie algebras, the rigid body system on Toda orbits, and to coadjoint orbits of semidirect products groups. In addition, we develop an infinite-dimensional generalization for the group of area preserving diffeomorphisms of the annulus and apply it to the analysis of the dispersionless Toda lattice PDE and the solvable rigid body PDE.

Analytic integrable systems: Analytic normalization and embedding flows

NASA Astrophysics Data System (ADS)

Zhang, Xiang

In this paper we mainly study the existence of analytic normalization and the normal form of finite dimensional complete analytic integrable dynamical systems. More details, we will prove that any complete analytic integrable diffeomorphism F(x)=Bx+f(x) in (Cn,0) with B having eigenvalues not modulus 1 and f(x)=O(|) is locally analytically conjugate to its normal form. Meanwhile, we also prove that any complete analytic integrable differential system x˙=Ax+f(x) in (Cn,0) with A having nonzero eigenvalues and f(x)=O(|) is locally analytically conjugate to its normal form. Furthermore we will prove that any complete analytic integrable diffeomorphism defined on an analytic manifold can be embedded in a complete analytic integrable flow. We note that parts of our results are the improvement of Moser's one in J. Moser, The analytic invariants of an area-preserving mapping near a hyperbolic fixed point, Comm. Pure Appl. Math. 9 (1956) 673-692 and of Poincaré's one in H. Poincaré, Sur l'intégration des équations différentielles du premier order et du premier degré, II, Rend. Circ. Mat. Palermo 11 (1897) 193-239. These results also improve the ones in Xiang Zhang, Analytic normalization of analytic integrable systems and the embedding flows, J. Differential Equations 244 (2008) 1080-1092 in the sense that the linear part of the systems can be nonhyperbolic, and the one in N.T. Zung, Convergence versus integrability in Poincaré-Dulac normal form, Math. Res. Lett. 9 (2002) 217-228 in the way that our paper presents the concrete expression of the normal form in a restricted case.

Conserved charge of a gravity theory with p -form gauge fields and its property under Kaluza-Klein reduction

NASA Astrophysics Data System (ADS)

Peng, Jun-Jin

2017-05-01

In this paper, we investigate the conserved charges of generally diffeomorphism invariant gravity theories with a wide variety of matter fields, particularly of the theories with multiple scalar fields and p -form potentials, in the context of the off-shell generalized Abbott-Deser-Tekin (ADT) formalism. We first construct a new off-shell ADT current that consists of the terms for the variation of a Killing vector and expressions of the field equations as well as the Lie derivative of a surface term with respect to the Killing vector within the framework of generally diffeomorphism invariant gravity theories involving various matter fields. After deriving the off-shell ADT potential corresponding to this current, we propose a formula of conserved charges for these theories. Next, we derive the off-shell ADT potential associated with the generic Lagrangian that describes a large range of gravity theories with a number of scalar fields and p -form potentials. Finally, the properties of the off-shell generalized ADT charges for the theory of Einstein gravity and the gravity theories with a single p -form potential are investigated by performing Kaluza-Klein dimensional reduction along a compactified direction. The results indicate that the charge contributed by all the fields in the lower-dimensional theory is equal to that of the higher-dimensional one at mathematical level with the hypothesis that the higher-dimensional spacetime allows for the existence of the compactified dimension. In order to illustrate our calculations, the mass and angular momentum for the five-dimensional rotating Kaluza-Klein black holes are explicitly evaluated as an example.

Discrimination of dementia with Lewy bodies from Alzheimer's disease using voxel-based morphometry of white matter by statistical parametric mapping 8 plus diffeomorphic anatomic registration through exponentiated Lie algebra.

PubMed

Nakatsuka, Tomoya; Imabayashi, Etsuko; Matsuda, Hiroshi; Sakakibara, Ryuji; Inaoka, Tsutomu; Terada, Hitoshi

2013-05-01

The purpose of this study was to identify brain atrophy specific for dementia with Lewy bodies (DLB) and to evaluate the discriminatory performance of this specific atrophy between DLB and Alzheimer's disease (AD). We retrospectively reviewed 60 DLB and 30 AD patients who had undergone 3D T1-weighted MRI. We randomly divided the DLB patients into two equal groups (A and B). First, we obtained a target volume of interest (VOI) for DLB-specific atrophy using correlation analysis of the percentage rate of significant whole white matter (WM) atrophy calculated using the Voxel-based Specific Regional Analysis System for Alzheimer's Disease (VSRAD) based on statistical parametric mapping 8 (SPM8) plus diffeomorphic anatomic registration through exponentiated Lie algebra, with segmented WM images in group A. We then evaluated the usefulness of this target VOI for discriminating the remaining 30 DLB patients in group B from the 30 AD patients. Z score values in this target VOI obtained from VSRAD were used as the determinant in receiver operating characteristic (ROC) analysis. Specific target VOIs for DLB were determined in the right-side dominant dorsal midbrain, right-side dominant dorsal pons, and bilateral cerebellum. ROC analysis revealed that the target VOI limited to the midbrain exhibited the highest area under the ROC curves of 0.75. DLB patients showed specific atrophy in the midbrain, pons, and cerebellum. Midbrain atrophy demonstrated the highest power for discriminating DLB and AD. This approach may be useful for determining the contributions of DLB and AD pathologies to the dementia syndrome.

Special ergodic theorems and dynamical large deviations

NASA Astrophysics Data System (ADS)

Kleptsyn, Victor; Ryzhov, Dmitry; Minkov, Stanislav

2012-11-01

Let f : M → M be a self-map of a compact Riemannian manifold M, admitting a global SRB measure μ. For a continuous test function \\varphi\\colon M\\to R and a constant α > 0, consider the set Kφ,α of the initial points for which the Birkhoff time averages of the function φ differ from its μ-space average by at least α. As the measure μ is a global SRB one, the set Kφ,α should have zero Lebesgue measure. The special ergodic theorem, whenever it holds, claims that, moreover, this set has a Hausdorff dimension less than the dimension of M. We prove that for Lipschitz maps, the special ergodic theorem follows from the dynamical large deviations principle. We also define and prove analogous result for flows. Applying the theorems of Young and of Araújo and Pacifico, we conclude that the special ergodic theorem holds for transitive hyperbolic attractors of C2-diffeomorphisms, as well as for some other known classes of maps (including the one of partially hyperbolic non-uniformly expanding maps) and flows.

Towards conformal loop quantum gravity

NASA Astrophysics Data System (ADS)

H-T Wang, Charles

2006-03-01

A discussion is given of recent developments in canonical gravity that assimilates the conformal analysis of gravitational degrees of freedom. The work is motivated by the problem of time in quantum gravity and is carried out at the metric and the triad levels. At the metric level, it is shown that by extending the Arnowitt-Deser-Misner (ADM) phase space of general relativity (GR), a conformal form of geometrodynamics can be constructed. In addition to the Hamiltonian and Diffeomorphism constraints, an extra first class constraint is introduced to generate conformal transformations. This phase space consists of York's mean extrinsic curvature time, conformal three-metric and their momenta. At the triad level, the phase space of GR is further enlarged by incorporating spin-gauge as well as conformal symmetries. This leads to a canonical formulation of GR using a new set of real spin connection variables. The resulting gravitational constraints are first class, consisting of the Hamiltonian constraint and the canonical generators for spin-gauge and conformorphism transformations. The formulation has a remarkable feature of being parameter-free. Indeed, it is shown that a conformal parameter of the Barbero-Immirzi type can be absorbed by the conformal symmetry of the extended phase space. This gives rise to an alternative approach to loop quantum gravity that addresses both the conceptual problem of time and the technical problem of functional calculus in quantum gravity.

New variables for classical and quantum gravity in all dimensions: I. Hamiltonian analysis

NASA Astrophysics Data System (ADS)

Bodendorfer, N.; Thiemann, T.; Thurn, A.

2013-02-01

Loop quantum gravity (LQG) relies heavily on a connection formulation of general relativity such that (1) the connection Poisson commutes with itself and (2) the corresponding gauge group is compact. This can be achieved starting from the Palatini or Holst action when imposing the time gauge. Unfortunately, this method is restricted to D + 1 = 4 spacetime dimensions. However, interesting string theories and supergravity theories require higher dimensions and it would therefore be desirable to have higher dimensional supergravity loop quantizations at one’s disposal in order to compare these approaches. In this series of papers we take first steps toward this goal. The present first paper develops a classical canonical platform for a higher dimensional connection formulation of the purely gravitational sector. The new ingredient is a different extension of the ADM phase space than the one used in LQG which does not require the time gauge and which generalizes to any dimension D > 1. The result is a Yang-Mills theory phase space subject to Gauß, spatial diffeomorphism and Hamiltonian constraint as well as one additional constraint, called the simplicity constraint. The structure group can be chosen to be SO(1, D) or SO(D + 1) and the latter choice is preferred for purposes of quantization.

Q-ball imaging with PROPELLER EPI acquisition.

PubMed

Chou, Ming-Chung; Huang, Teng-Yi; Chung, Hsiao-Wen; Hsieh, Tsyh-Jyi; Chang, Hing-Chiu; Chen, Cheng-Yu

2013-12-01

Q-ball imaging (QBI) is an imaging technique that is capable of resolving intravoxel fiber crossings; however, the signal readout based on echo-planar imaging (EPI) introduces geometric distortions in the presence of susceptibility gradients. This study proposes an imaging technique that reduces susceptibility distortions in QBI by short-axis PROPELLER EPI acquisition. Conventional QBI and PROPELLER QBI data were acquired from two 3T MR scans of the brains of five healthy subjects. Prior to the PROPELLER reconstruction, residual distortions in single-blade low-resolution b0 and diffusion-weighted images (DWIs) were minimized by linear affine and nonlinear diffeomorphic demon registrations. Subsequently, the PROPELLER keyhole reconstruction was applied to the corrected DWIs to obtain high-resolution PROPELLER DWIs. The generalized fractional anisotropy and orientation distribution function maps contained fewer distortions in PROPELLER QBI than in conventional QBI, and the fiber tracts more closely matched the brain anatomy depicted by turbo spin-echo (TSE) T2-weighted imaging (T2WI). Furthermore, for fixed T(E), PROPELLER QBI enabled a shorter scan time than conventional QBI. We conclude that PROPELLER QBI can reduce susceptibility distortions without lengthening the acquisition time and is suitable for tracing neuronal fiber tracts in the human brain. Copyright © 2013 John Wiley & Sons, Ltd.

Automated Bone Segmentation and Surface Evaluation of a Small Animal Model of Post-Traumatic Osteoarthritis.

PubMed

Ramme, Austin J; Voss, Kevin; Lesporis, Jurinus; Lendhey, Matin S; Coughlin, Thomas R; Strauss, Eric J; Kennedy, Oran D

2017-05-01

MicroCT imaging allows for noninvasive microstructural evaluation of mineralized bone tissue, and is essential in studies of small animal models of bone and joint diseases. Automatic segmentation and evaluation of articular surfaces is challenging. Here, we present a novel method to create knee joint surface models, for the evaluation of PTOA-related joint changes in the rat using an atlas-based diffeomorphic registration to automatically isolate bone from surrounding tissues. As validation, two independent raters manually segment datasets and the resulting segmentations were compared to our novel automatic segmentation process. Data were evaluated using label map volumes, overlap metrics, Euclidean distance mapping, and a time trial. Intraclass correlation coefficients were calculated to compare methods, and were greater than 0.90. Total overlap, union overlap, and mean overlap were calculated to compare the automatic and manual methods and ranged from 0.85 to 0.99. A Euclidean distance comparison was also performed and showed no measurable difference between manual and automatic segmentations. Furthermore, our new method was 18 times faster than manual segmentation. Overall, this study describes a reliable, accurate, and automatic segmentation method for mineralized knee structures from microCT images, and will allow for efficient assessment of bony changes in small animal models of PTOA.

Adaptive Control via Neural Output Feedback for a Class of Nonlinear Discrete-Time Systems in a Nested Interconnected Form.

PubMed

Li, Dong-Juan; Li, Da-Peng

2017-09-14

In this paper, an adaptive output feedback control is framed for uncertain nonlinear discrete-time systems. The considered systems are a class of multi-input multioutput nonaffine nonlinear systems, and they are in the nested lower triangular form. Furthermore, the unknown dead-zone inputs are nonlinearly embedded into the systems. These properties of the systems will make it very difficult and challenging to construct a stable controller. By introducing a new diffeomorphism coordinate transformation, the controlled system is first transformed into a state-output model. By introducing a group of new variables, an input-output model is finally obtained. Based on the transformed model, the implicit function theorem is used to determine the existence of the ideal controllers and the approximators are employed to approximate the ideal controllers. By using the mean value theorem, the nonaffine functions of systems can become an affine structure but nonaffine terms still exist. The adaptation auxiliary terms are skillfully designed to cancel the effect of the dead-zone input. Based on the Lyapunov difference theorem, the boundedness of all the signals in the closed-loop system can be ensured and the tracking errors are kept in a bounded compact set. The effectiveness of the proposed technique is checked by a simulation study.

Global anomalies and effective field theory

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

Golkar, Siavash; Sethi, Savdeep

2016-05-17

Here, we show that matching anomalies under large gauge transformations and large diffeomorphisms can explain the appearance and non-renormalization of couplings in effective field theory. We focus on thermal effective field theory, where we argue that the appearance of certain unusual Chern-Simons couplings is a consequence of global anomalies. As an example, we show that a mixed global anomaly in four dimensions fixes the chiral vortical effect coefficient (up to an overall additive factor). This is an experimentally measurable prediction from a global anomaly. For certain situations, we propose a simpler method for calculating global anomalies which uses correlation functionsmore » rather than eta invariants.« less

Regularity and Tresse's theorem for geometric structures

NASA Astrophysics Data System (ADS)

Sarkisyan, R. A.; Shandra, I. G.

2008-04-01

For any non-special bundle P\\to X of geometric structures we prove that the k-jet space J^k of this bundle with an appropriate k contains an open dense domain U_k on which Tresse's theorem holds. For every s\\geq k we prove that the pre-image \\pi^{-1}(k,s)(U_k) of U_k under the natural projection \\pi(k,s)\\colon J^s\\to J^k consists of regular points. (A point of J^s is said to be regular if the orbits of the group of diffeomorphisms induced from X have locally constant dimension in a neighbourhood of this point.)

Effective response theory for zero-energy Majorana bound states in three spatial dimensions

NASA Astrophysics Data System (ADS)

Lopes, Pedro L. e. S.; Teo, Jeffrey C. Y.; Ryu, Shinsei

2015-05-01

We propose a gravitational response theory for point defects (hedgehogs) binding Majorana zero modes in (3 + 1)-dimensional superconductors. Starting in 4 + 1 dimensions, where the point defect is extended into a line, a coupling of the bulk defect texture with the gravitational field is introduced. Diffeomorphism invariance then leads to an S U (2) 2 Kac-Moody current running along the defect line. The S U (2) 2 Kac-Moody algebra accounts for the non-Abelian nature of the zero modes in 3 + 1 dimensions. It is then shown to also encode the angular momentum density which permeates throughout the bulk between hedgehog-antihedgehog pairs.

Hamiltonian structure of three-dimensional gravity in Vielbein formalism

NASA Astrophysics Data System (ADS)

Hajihashemi, Mahdi; Shirzad, Ahmad

2018-01-01

Considering Chern-Simons like gravity theories in three dimensions as first order systems, we analyze the Hamiltonian structure of three theories Topological massive gravity, New massive gravity, and Zwei-Dreibein Gravity. We show that these systems demonstrate a new feature of the constrained systems in which a new kind of constraints emerge due to factorization of determinant of the matrix of Poisson brackets of constraints. We find the desired number of degrees of freedom as well as the generating functional of local Lorentz transformations and diffeomorphism through canonical structure of the system. We also compare the Hamiltonian structure of linearized version of the considered models with the original ones.

Using tensor-based morphometry to detect structural brain abnormalities in rats with adolescent intermittent alcohol exposure

NASA Astrophysics Data System (ADS)

Paniagua, Beatriz; Ehlers, Cindy; Crews, Fulton; Budin, Francois; Larson, Garrett; Styner, Martin; Oguz, Ipek

2011-03-01

Understanding the effects of adolescent binge drinking that persist into adulthood is a crucial public health issue. Adolescent intermittent ethanol exposure (AIE) is an animal model that can be used to investigate these effects in rodents. In this work, we investigate the application of a particular image analysis technique, tensor-based morphometry, for detecting anatomical differences between AIE and control rats using Diffusion Tensor Imaging (DTI). Deformation field analysis is a popular method for detecting volumetric changes analyzing Jacobian determinants calculated on deformation fields. Recent studies showed that computing deformation field metrics on the full deformation tensor, often referred to as tensor-based morphometry (TBM), increases the sensitivity to anatomical differences. In this paper we conduct a comprehensive TBM study for precisely locating differences between control and AIE rats. Using a DTI RARE sequence designed for minimal geometric distortion, 12-directional images were acquired postmortem for control and AIE rats (n=9). After preprocessing, average images for the two groups were constructed using an unbiased atlas building approach. We non-rigidly register the two atlases using Large Deformation Diffeomorphic Metric Mapping, and analyze the resulting deformation field using TBM. In particular, we evaluate the tensor determinant, geodesic anisotropy, and deformation direction vector (DDV) on the deformation field to detect structural differences. This yields data on the local amount of growth, shrinkage and the directionality of deformation between the groups. We show that TBM can thus be used to measure group morphological differences between rat populations, demonstrating the potential of the proposed framework.

Comparing fractional anisotropy in patients with childhood-onset schizophrenia, their healthy siblings, and normal volunteers through DTI.

PubMed

Moran, Marcel E; Luscher, Zoe I; McAdams, Harrison; Hsu, John T; Greenstein, Deanna; Clasen, Liv; Ludovici, Katharine; Lloyd, Jonae; Rapoport, Judith; Mori, Susumu; Gogtay, Nitin

2015-01-01

Diffusion tensor imaging is a neuroimaging method that quantifies white matter (WM) integrity and brain connectivity based on the diffusion of water in the brain. White matter has been hypothesized to be of great importance in the development of schizophrenia as part of the dysconnectivity model. Childhood-onset schizophrenia (COS), is a rare, severe form of the illness that resembles poor outcome adult-onset schizophrenia. We hypothesized that COS would be associated with WM abnormalities relative to a sample of controls. To evaluate WM integrity in this population 39 patients diagnosed with COS, 39 of their healthy (nonpsychotic) siblings, and 50 unrelated healthy volunteers were scanned using a diffusion tensor imaging (DTI) sequence during a 1.5 T MRI acquisition. Each DTI scan was processed via atlas-based analysis using a WM parcellation map, and diffeomorphic mapping that shapes a template atlas to each individual subject space. Fractional anisotropy (FA), a measure of WM integrity was averaged over each of the 46 regions of the atlas. Eleven WM regions were examined based on previous reports of WM growth abnormalities in COS. Of those regions, patients with COS, and their healthy siblings had significantly lower mean FA in the left and right cuneus as compared to the healthy volunteers (P < .005). Together, these findings represent the largest DTI study in COS to date, and provide evidence that WM integrity is significantly impaired in COS. Shared deficits in their healthy siblings might result from increased genetic risk. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center 2014.

Comparing Fractional Anisotropy in Patients With Childhood-Onset Schizophrenia, Their Healthy Siblings, and Normal Volunteers Through DTI

PubMed Central

Moran, Marcel E.; Luscher, Zoe I.; McAdams, Harrison; Hsu, John T.; Greenstein, Deanna; Clasen, Liv; Ludovici, Katharine; Lloyd, Jonae; Rapoport, Judith; Mori, Susumu; Gogtay, Nitin

2015-01-01

Background: Diffusion tensor imaging is a neuroimaging method that quantifies white matter (WM) integrity and brain connectivity based on the diffusion of water in the brain. White matter has been hypothesized to be of great importance in the development of schizophrenia as part of the dysconnectivity model. Childhood-onset schizophrenia (COS), is a rare, severe form of the illness that resembles poor outcome adult-onset schizophrenia. We hypothesized that COS would be associated with WM abnormalities relative to a sample of controls. Methods: To evaluate WM integrity in this population 39 patients diagnosed with COS, 39 of their healthy (nonpsychotic) siblings, and 50 unrelated healthy volunteers were scanned using a diffusion tensor imaging (DTI) sequence during a 1.5 T MRI acquisition. Each DTI scan was processed via atlas-based analysis using a WM parcellation map, and diffeomorphic mapping that shapes a template atlas to each individual subject space. Fractional anisotropy (FA), a measure of WM integrity was averaged over each of the 46 regions of the atlas. Eleven WM regions were examined based on previous reports of WM growth abnormalities in COS. Results: Of those regions, patients with COS, and their healthy siblings had significantly lower mean FA in the left and right cuneus as compared to the healthy volunteers (P < .005). Together, these findings represent the largest DTI study in COS to date, and provide evidence that WM integrity is significantly impaired in COS. Shared deficits in their healthy siblings might result from increased genetic risk. PMID:25217482

Wavefront sensing with a thin diffuser

NASA Astrophysics Data System (ADS)

Berto, Pascal; Rigneault, Hervé; Guillon, Marc

2017-12-01

We propose and implement a broadband, compact, and low-cost wavefront sensing scheme by simply placing a thin diffuser in the close vicinity of a camera. The local wavefront gradient is determined from the local translation of the speckle pattern. The translation vector map is computed thanks to a fast diffeomorphic image registration algorithm and integrated to reconstruct the wavefront profile. The simple translation of speckle grains under local wavefront tip/tilt is ensured by the so-called "memory effect" of the diffuser. Quantitative wavefront measurements are experimentally demonstrated both for the few first Zernike polynomials and for phase-imaging applications requiring high resolution. We finally provided a theoretical description of the resolution limit that is supported experimentally.

General theories of linear gravitational perturbations to a Schwarzschild black hole

NASA Astrophysics Data System (ADS)

Tattersall, Oliver J.; Ferreira, Pedro G.; Lagos, Macarena

2018-02-01

We use the covariant formulation proposed by Tattersall, Lagos, and Ferreira [Phys. Rev. D 96, 064011 (2017), 10.1103/PhysRevD.96.064011] to analyze the structure of linear perturbations about a spherically symmetric background in different families of gravity theories, and hence study how quasinormal modes of perturbed black holes may be affected by modifications to general relativity. We restrict ourselves to single-tensor, scalar-tensor and vector-tensor diffeomorphism-invariant gravity models in a Schwarzschild black hole background. We show explicitly the full covariant form of the quadratic actions in such cases, which allow us to then analyze odd parity (axial) and even parity (polar) perturbations simultaneously in a straightforward manner.

The canonical Lagrangian approach to three-space general relativity

NASA Astrophysics Data System (ADS)

Shyam, Vasudev; Venkatesh, Madhavan

2013-07-01

We study the action for the three-space formalism of general relativity, better known as the Barbour-Foster-Ó Murchadha action, which is a square-root Baierlein-Sharp-Wheeler action. In particular, we explore the (pre)symplectic structure by pulling it back via a Legendre map to the tangent bundle of the configuration space of this action. With it we attain the canonical Lagrangian vector field which generates the gauge transformations (3-diffeomorphisms) and the true physical evolution of the system. This vector field encapsulates all the dynamics of the system. We also discuss briefly the observables and perennials for this theory. We then present a symplectic reduction of the constrained phase space.

Inner mechanics of three-dimensional black holes.

PubMed

Detournay, Stéphane

2012-07-20

We investigate properties of the inner horizons of certain black holes in higher-derivative three-dimensional gravity theories. We focus on Bañados-Teitelboim-Zanelli and spacelike warped anti-de Sitter black holes, as well as on asymptotically warped de Sitter solutions exhibiting both a cosmological and a black hole horizon. We verify that a first law is satisfied at the inner horizon, in agreement with the proposal of Castro and Rodriguez [arXiv:1204.1284]. We then show that, in topologically massive gravity, the product of the areas of the inner and outer horizons fails to be independent on the mass, and we trace this to the diffeomorphism anomaly of the theory.

Stability of the matrix model in operator interpretation

NASA Astrophysics Data System (ADS)

Sakai, Katsuta

2017-12-01

The IIB matrix model is one of the candidates for nonperturbative formulation of string theory, and it is believed that the model contains gravitational degrees of freedom in some manner. In some preceding works, it was proposed that the matrix model describes the curved space where the matrices represent differential operators that are defined on a principal bundle. In this paper, we study the dynamics of the model in this interpretation, and point out the necessity of the principal bundle from the viewpoint of the stability and diffeomorphism invariance. We also compute the one-loop correction which yields a mass term for each field due to the principal bundle. We find that the stability is not violated.

Field theory of hyperfluid

NASA Astrophysics Data System (ADS)

Ariki, Taketo

2018-02-01

A hyperfluid model is constructed on the basis of its action entirely free from external constraints, regarding the hyperfluid as a self-consistent classical field. Intrinsic hypermomentum is no longer a supplemental variable given by external constraints, but arises purely from the diffeomorphism covariance of dynamical field. The field-theoretic approach allows natural classification of a hyperfluid on the basis of its symmetry group and corresponding homogeneous space; scalar, spinor, vector, and tensor fluids are introduced as simple examples. Apart from phenomenological constraints, the theory predicts the hypermomentum exchange of fluid via field-theoretic interactions of various classes; fluid–fluid interactions, minimal and non-minimal SU(n) -gauge couplings, and coupling with metric-affine gravity are all successfully formulated within the classical regime.

On the Hamiltonian formalism of the tetrad-gravity with fermions

NASA Astrophysics Data System (ADS)

Lagraa, M. H.; Lagraa, M.

2018-06-01

We extend the analysis of the Hamiltonian formalism of the d-dimensional tetrad-connection gravity to the fermionic field by fixing the non-dynamic part of the spatial connection to zero (Lagraa et al. in Class Quantum Gravity 34:115010, 2017). Although the reduced phase space is equipped with complicated Dirac brackets, the first-class constraints which generate the diffeomorphisms and the Lorentz transformations satisfy a closed algebra with structural constants analogous to that of the pure gravity. We also show the existence of a canonical transformation leading to a new reduced phase space equipped with Dirac brackets having a canonical form leading to the same algebra of the first-class constraints.

Conservation of ζ with radiative corrections from heavy field

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

Tanaka, Takahiro; Yukawa Institute for Theoretical Physics, Kyoto University,Kyoto, 606-8502; Urakawa, Yuko

2016-06-08

In this paper, we address a possible impact of radiative corrections from a heavy scalar field χ on the curvature perturbation ζ. Integrating out χ, we derive the effective action for ζ, which includes the loop corrections of the heavy field χ. When the mass of χ is much larger than the Hubble scale H, the loop corrections of χ only yield a local contribution to the effective action and hence the effective action simply gives an action for ζ in a single field model, where, as is widely known, ζ is conserved in time after the Hubble crossing time.more » Meanwhile, when the mass of χ is comparable to H, the loop corrections of χ can give a non-local contribution to the effective action. Because of the non-local contribution from χ, in general, ζ may not be conserved, even if the classical background trajectory is determined only by the evolution of the inflaton. In this paper, we derive the condition that ζ is conserved in time in the presence of the radiative corrections from χ. Namely, we show that when the dilatation invariance, which is a part of the diffeomorphism invariance, is preserved at the quantum level, the loop corrections of the massive field χ do not disturb the constant evolution of ζ at super Hubble scales. In this discussion, we show the Ward-Takahashi identity for the dilatation invariance, which yields a consistency relation for the correlation functions of the massive field χ.« less

A gauge-theoretic approach to gravity.

PubMed

Krasnov, Kirill

2012-08-08

Einstein's general relativity (GR) is a dynamical theory of the space-time metric. We describe an approach in which GR becomes an SU(2) gauge theory. We start at the linearized level and show how a gauge-theoretic Lagrangian for non-interacting massless spin two particles (gravitons) takes a much more simple and compact form than in the standard metric description. Moreover, in contrast to the GR situation, the gauge theory Lagrangian is convex. We then proceed with a formulation of the full nonlinear theory. The equivalence to the metric-based GR holds only at the level of solutions of the field equations, that is, on-shell. The gauge-theoretic approach also makes it clear that GR is not the only interacting theory of massless spin two particles, in spite of the GR uniqueness theorems available in the metric description. Thus, there is an infinite-parameter class of gravity theories all describing just two propagating polarizations of the graviton. We describe how matter can be coupled to gravity in this formulation and, in particular, how both the gravity and Yang-Mills arise as sectors of a general diffeomorphism-invariant gauge theory. We finish by outlining a possible scenario of the ultraviolet completion of quantum gravity within this approach.

Graviweak Unification, Invisible Universe and Dark Energy

NASA Astrophysics Data System (ADS)

Das, C. R.; Laperashvili, L. V.; Tureanu, A.

2013-07-01

We consider a graviweak unification model with the assumption of the existence of a hidden (invisible) sector of our Universe, parallel to the visible world. This Hidden World (HW) is assumed to be a Mirror World (MW) with broken mirror parity. We start with a diffeomorphism invariant theory of a gauge field valued in a Lie algebra g, which is broken spontaneously to the direct sum of the space-time Lorentz algebra and the Yang-Mills algebra: ˜ {g} = {{su}}(2) (grav)L ⊕ {{su}}(2)L — in the ordinary world, and ˜ {g}' = {{su}}(2){' (grav)}R ⊕ {{su}}(2)'R — in the hidden world. Using an extension of the Plebanski action for general relativity, we recover the actions for gravity, SU(2) Yang-Mills and Higgs fields in both (visible and invisible) sectors of the Universe, and also the total action. After symmetry breaking, all physical constants, including the Newton's constants, cosmological constants, Yang-Mills couplings, and other parameters, are determined by a single parameter g present in the initial action, and by the Higgs VEVs. The dark energy problem of this model predicts a too large supersymmetric breaking scale (MSUSY 1010GeV), which is not within the reach of the LHC experiments.

Constraints on primordial magnetic fields from inflation

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

Green, Daniel; Kobayashi, Takeshi, E-mail: drgreen@cita.utoronto.ca, E-mail: takeshi.kobayashi@sissa.it

2016-03-01

We present generic bounds on magnetic fields produced from cosmic inflation. By investigating field bounds on the vector potential, we constrain both the quantum mechanical production of magnetic fields and their classical growth in a model independent way. For classical growth, we show that only if the reheating temperature is as low as T{sub reh} ∼< 10{sup 2} MeV can magnetic fields of 10{sup −15} G be produced on Mpc scales in the present universe. For purely quantum mechanical scenarios, even stronger constraints are derived. Our bounds on classical and quantum mechanical scenarios apply to generic theories of inflationary magnetogenesis with a two-derivative timemore » kinetic term for the vector potential. In both cases, the magnetic field strength is limited by the gravitational back-reaction of the electric fields that are produced simultaneously. As an example of quantum mechanical scenarios, we construct vector field theories whose time diffeomorphisms are spontaneously broken, and explore magnetic field generation in theories with a variable speed of light. Transitions of quantum vector field fluctuations into classical fluctuations are also analyzed in the examples.« less

The Lyapunov dimension and its estimation via the Leonov method

NASA Astrophysics Data System (ADS)

Kuznetsov, N. V.

2016-06-01

Along with widely used numerical methods for estimating and computing the Lyapunov dimension there is an effective analytical approach, proposed by G.A. Leonov in 1991. The Leonov method is based on the direct Lyapunov method with special Lyapunov-like functions. The advantage of the method is that it allows one to estimate the Lyapunov dimension of invariant sets without localization of the set in the phase space and, in many cases, to get effectively an exact Lyapunov dimension formula. In this work the invariance of the Lyapunov dimension with respect to diffeomorphisms and its connection with the Leonov method are discussed. For discrete-time dynamical systems an analog of Leonov method is suggested. In a simple but rigorous way, here it is presented the connection between the Leonov method and the key related works: Kaplan and Yorke (the concept of the Lyapunov dimension, 1979), Douady and Oesterlé (upper bounds of the Hausdorff dimension via the Lyapunov dimension of maps, 1980), Constantin, Eden, Foiaş, and Temam (upper bounds of the Hausdorff dimension via the Lyapunov exponents and Lyapunov dimension of dynamical systems, 1985-90), and the numerical calculation of the Lyapunov exponents and dimension.

A new combined surface and volume registration

NASA Astrophysics Data System (ADS)

Lepore, Natasha; Joshi, Anand A.; Leahy, Richard M.; Brun, Caroline; Chou, Yi-Yu; Pennec, Xavier; Lee, Agatha D.; Barysheva, Marina; De Zubicaray, Greig I.; Wright, Margaret J.; McMahon, Katie L.; Toga, Arthur W.; Thompson, Paul M.

2010-03-01

3D registration of brain MRI data is vital for many medical imaging applications. However, purely intensitybased approaches for inter-subject matching of brain structure are generally inaccurate in cortical regions, due to the highly complex network of sulci and gyri, which vary widely across subjects. Here we combine a surfacebased cortical registration with a 3D fluid one for the first time, enabling precise matching of cortical folds, but allowing large deformations in the enclosed brain volume, which guarantee diffeomorphisms. This greatly improves the matching of anatomy in cortical areas. The cortices are segmented and registered with the software Freesurfer. The deformation field is initially extended to the full 3D brain volume using a 3D harmonic mapping that preserves the matching between cortical surfaces. Finally, these deformation fields are used to initialize a 3D Riemannian fluid registration algorithm, that improves the alignment of subcortical brain regions. We validate this method on an MRI dataset from 92 healthy adult twins. Results are compared to those based on volumetric registration without surface constraints; the resulting mean templates resolve consistent anatomical features both subcortically and at the cortex, suggesting that the approach is well-suited for cross-subject integration of functional and anatomic data.

Inverting dedevelopment: geometric singularity theory in embryology

NASA Astrophysics Data System (ADS)

Bookstein, Fred L.; Smith, Bradley R.

2000-10-01

The diffeomorphism model so useful in the biomathematics of normal morphological variability and disease is inappropriate for applications in embryogenesis, where whole coordinate patches are created out of single points. For this application we need a suitable algebra for the creation of something from nothing in a carefully organized geometry: a formalism for parameterizing discrete nondifferentiabilities of invertible functions on Rk, k $GTR 1. One easy way to begin is via the inverse of the development map - call it the dedevelopment map, the deformation backwards in time. Extrapolated, this map will inevitably have singularities at which its derivative is zero. When the dedevelopment map is inverted to face forward in time, the singularities become appropriately isolated infinities of derivative. We have recently introduced growth visualizations via extrapolations to the isolated singularities at which only one directional derivative is zero. Maps inverse to these create new coordinate patches directionally rather than radically. The most generic singularity that suits this purpose is the crease f(x,y) equals (x,x2y+y3), which has already been applied in morphometrics for the description of focal morphogenetic phenomena. We apply it to embryogenesis in the form of its analytic inverse, and demonstrate its power using a priceless new data set of mouse embryos imaged in 3D by micro-MR with voxels smaller than 100micrometers 3.

Non-rigid registration of serial dedicated breast CT, longitudinal dedicated breast CT and PET/CT images using the diffeomorphic demons method.

PubMed

Santos, Jonathan; Chaudhari, Abhijit J; Joshi, Anand A; Ferrero, Andrea; Yang, Kai; Boone, John M; Badawi, Ramsey D

2014-09-01

Dedicated breast CT and PET/CT scanners provide detailed 3D anatomical and functional imaging data sets and are currently being investigated for applications in breast cancer management such as diagnosis, monitoring response to therapy and radiation therapy planning. Our objective was to evaluate the performance of the diffeomorphic demons (DD) non-rigid image registration method to spatially align 3D serial (pre- and post-contrast) dedicated breast computed tomography (CT), and longitudinally-acquired dedicated 3D breast CT and positron emission tomography (PET)/CT images. The algorithmic parameters of the DD method were optimized for the alignment of dedicated breast CT images using training data and fixed. The performance of the method for image alignment was quantitatively evaluated using three separate data sets; (1) serial breast CT pre- and post-contrast images of 20 women, (2) breast CT images of 20 women acquired before and after repositioning the subject on the scanner, and (3) dedicated breast PET/CT images of 7 women undergoing neo-adjuvant chemotherapy acquired pre-treatment and after 1 cycle of therapy. The DD registration method outperformed no registration (p < 0.001) and conventional affine registration (p ≤ 0.002) for serial and longitudinal breast CT and PET/CT image alignment. In spite of the large size of the imaging data, the computational cost of the DD method was found to be reasonable (3-5 min). Co-registration of dedicated breast CT and PET/CT images can be performed rapidly and reliably using the DD method. This is the first study evaluating the DD registration method for the alignment of dedicated breast CT and PET/CT images. Copyright © 2014 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Evaluation of MRI and cannabinoid type 1 receptor PET templates constructed using DARTEL for spatial normalization of rat brains

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

Kronfeld, Andrea; Müller-Forell, Wibke; Buchholz, Hans-Georg

Purpose: Image registration is one prerequisite for the analysis of brain regions in magnetic-resonance-imaging (MRI) or positron-emission-tomography (PET) studies. Diffeomorphic anatomical registration through exponentiated Lie algebra (DARTEL) is a nonlinear, diffeomorphic algorithm for image registration and construction of image templates. The goal of this small animal study was (1) the evaluation of a MRI and calculation of several cannabinoid type 1 (CB1) receptor PET templates constructed using DARTEL and (2) the analysis of the image registration accuracy of MR and PET images to their DARTEL templates with reference to analytical and iterative PET reconstruction algorithms. Methods: Five male Sprague Dawleymore » rats were investigated for template construction using MRI and [{sup 18}F]MK-9470 PET for CB1 receptor representation. PET images were reconstructed using the algorithms filtered back-projection, ordered subset expectation maximization in 2D, and maximum a posteriori in 3D. Landmarks were defined on each MR image, and templates were constructed under different settings, i.e., based on different tissue class images [gray matter (GM), white matter (WM), and GM + WM] and regularization forms (“linear elastic energy,” “membrane energy,” and “bending energy”). Registration accuracy for MRI and PET templates was evaluated by means of the distance between landmark coordinates. Results: The best MRI template was constructed based on gray and white matter images and the regularization form linear elastic energy. In this case, most distances between landmark coordinates were <1 mm. Accordingly, MRI-based spatial normalization was most accurate, but results of the PET-based spatial normalization were quite comparable. Conclusions: Image registration using DARTEL provides a standardized and automatic framework for small animal brain data analysis. The authors were able to show that this method works with high reliability and validity. Using DARTEL templates together with nonlinear registration algorithms allows for accurate spatial normalization of combined MRI/PET or PET-only studies.« less

SU-F-J-80: Deformable Image Registration for Residual Organ Motion Estimation in Respiratory Gated Treatments with Scanned Carbon Ion Beams

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

Meschini, G; Seregni, M; Pella, A

Purpose: At the Centro Nazionale di Adroterapia Oncologica (CNAO, Pavia, Italy) C-ions respiratory gated treatments of patients with abdominal tumours started in 2014. In these cases, the therapeutic dose is delivered around end-exhale. We propose the use of a respiratory motion model to evaluate residual tumour motion. Such a model requires motion fields obtained from deformable image registration (DIR) between 4DCT phases, estimating anatomical motion through interpolation. The aim of this work is to identify the optimal DIR technique to be integrated in the modeling pipeline. Methods: We used 4DCT datasets from 4 patients to test 4 DIR algorithms: Bspline,more » demons, log-domain and symmetric log domain diffeomorphic demons. We evaluate DIR performance in terms of registration accuracy (RMSE between registered images) and anatomical consistency of the motion field (Jacobian) when registering end-inhale to end-exhale. We subsequently employed the model to estimate the tumour trajectory within the ideal gating window. Results: Within the liver contour, the RMSE is in the range 31–46 HU for the best performing algorithm (Bspline) and 43–145 HU for the worst one (demons). The Jacobians featured zero negative voxels (which indicate singularities in the motion field) for the Bspline fields in 3 of 4 patients, whereas diffeomorphic demons fields showed a non-null number of negative voxels in every case. GTV motion in the gating window measured less than 7 mm for every patient, displaying a predominant superior-inferior (SI) component. Conclusion: The Bspline algorithm allows for acceptable DIR results in the abdominal region, exhibiting the property of anatomical consistency of the computed field. Computed trajectories are in agreement with clinical expectations (small and prevalent SI displacements), since patients lie wearing semi-rigid immobilizing masks. In future, the model could be used for retrospective estimation of organ motion during treatment, as guided by the breathing surrogate signal.« less

On the geometry of mixed states and the Fisher information tensor

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

Contreras, I., E-mail: icontrer@illinois.edu; Ercolessi, E., E-mail: ercolessi@bo.infn.it; Schiavina, M., E-mail: michele.schiavina@math.uzh.ch

2016-06-15

In this paper, we will review the co-adjoint orbit formulation of finite dimensional quantum mechanics, and in this framework, we will interpret the notion of quantum Fisher information index (and metric). Following previous work of part of the authors, who introduced the definition of Fisher information tensor, we will show how its antisymmetric part is the pullback of the natural Kostant–Kirillov–Souriau symplectic form along some natural diffeomorphism. In order to do this, we will need to understand the symmetric logarithmic derivative as a proper 1-form, settling the issues about its very definition and explicit computation. Moreover, the fibration of co-adjointmore » orbits, seen as spaces of mixed states, is also discussed.« less

Applications of AdS-CFT to problems in black hole physics and hydrodynamics

NASA Astrophysics Data System (ADS)

Hansen, James Michael

The work contained in this thesis is divided naturally into two parts. In the first part we present a systematic treatment of angular momentum charges in asymptotically AdS spacetimes. This treatment, motivated by AdS-CFT, explains the puzzle of charges generated by coordinate transformations in a manifestly diffeomorphism invariant theory. In the second part we explore a promising connection between the dynamics of dyonic black holes and 2+1 dimensional conformal fluids in the presence of a strong magnetic field. We explicitly demonstrate that long-wavelength perturbations of the dyonic black hole satisfy the equations of motion of a conformal fluid and derive the stress tensor, currents, and transport properties of this fluid.

Current algebra, statistical mechanics and quantum models

NASA Astrophysics Data System (ADS)

Vilela Mendes, R.

2017-11-01

Results obtained in the past for free boson systems at zero and nonzero temperatures are revisited to clarify the physical meaning of current algebra reducible functionals which are associated to systems with density fluctuations, leading to observable effects on phase transitions. To use current algebra as a tool for the formulation of quantum statistical mechanics amounts to the construction of unitary representations of diffeomorphism groups. Two mathematical equivalent procedures exist for this purpose. One searches for quasi-invariant measures on configuration spaces, the other for a cyclic vector in Hilbert space. Here, one argues that the second approach is closer to the physical intuition when modelling complex systems. An example of application of the current algebra methodology to the pairing phenomenon in two-dimensional fermion systems is discussed.

Analytic proof of the existence of the Lorenz attractor in the extended Lorenz model

NASA Astrophysics Data System (ADS)

Ovsyannikov, I. I.; Turaev, D. V.

2017-01-01

We give an analytic (free of computer assistance) proof of the existence of a classical Lorenz attractor for an open set of parameter values of the Lorenz model in the form of Yudovich-Morioka-Shimizu. The proof is based on detection of a homoclinic butterfly with a zero saddle value and rigorous verification of one of the Shilnikov criteria for the birth of the Lorenz attractor; we also supply a proof for this criterion. The results are applied in order to give an analytic proof for the existence of a robust, pseudohyperbolic strange attractor (the so-called discrete Lorenz attractor) for an open set of parameter values in a 4-parameter family of 3D Henon-like diffeomorphisms.

Tensor Galileons and gravity

NASA Astrophysics Data System (ADS)

Chatzistavrakidis, Athanasios; Khoo, Fech Scen; Roest, Diederik; Schupp, Peter

2017-03-01

The particular structure of Galileon interactions allows for higher-derivative terms while retaining second order field equations for scalar fields and Abelian p-forms. In this work we introduce an index-free formulation of these interactions in terms of two sets of Grassmannian variables. We employ this to construct Galileon interactions for mixed-symmetry tensor fields and coupled systems thereof. We argue that these tensors are the natural generalization of scalars with Galileon symmetry, similar to p-forms and scalars with a shift-symmetry. The simplest case corresponds to linearised gravity with Lovelock invariants, relating the Galileon symmetry to diffeomorphisms. Finally, we examine the coupling of a mixed-symmetry tensor to gravity, and demonstrate in an explicit example that the inclusion of appropriate counterterms retains second order field equations.

Polymer-Fourier quantization of the scalar field revisited

NASA Astrophysics Data System (ADS)

Garcia-Chung, Angel; Vergara, J. David

2016-10-01

The polymer quantization of the Fourier modes of the real scalar field is studied within algebraic scheme. We replace the positive linear functional of the standard Poincaré invariant quantization by a singular one. This singular positive linear functional is constructed as mimicking the singular limit of the complex structure of the Poincaré invariant Fock quantization. The resulting symmetry group of such polymer quantization is the subgroup SDiff(ℝ4) which is a subgroup of Diff(ℝ4) formed by spatial volume preserving diffeomorphisms. In consequence, this yields an entirely different irreducible representation of the canonical commutation relations, nonunitary equivalent to the standard Fock representation. We also compared the Poincaré invariant Fock vacuum with the polymer Fourier vacuum.

It is hard to learn how gravity and electromagnetism couple

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

Chu Yizen; Jacobs, David M.; Ng Yifung

2010-09-15

We construct the most general effective Lagrangian coupling gravity and electromagnetism up to mass dimension 6 by enumerating all possible nonminimal coupling terms respecting both diffeomorphism and gauge invariance. In all, there are only two unique terms after field redefinitions: one is known to arise from loop effects in QED, while the other is a parity-violating term which may be generated by weak interactions within the standard model of particle physics. We show that neither the cosmological propagation of light nor, contrary to earlier claims, solar system tests of general relativity are useful probes of these terms. These nonminimal couplingsmore » of gravity and electromagnetism may remain a mystery for the foreseeable future.« less

[Voxel-Based Morphometry in Medicated-naive Boys with Attention-deficit/hyperactivity Disorder(ADHD)].

PubMed

Liu, Qi; Chen, Lizhou; Li, Fei; Chen, Ying; Guo, Lanting; Gong, Qiyong; Huang, Xiaoqi

2016-06-01

Attention-deficit/hyperactivity disorder(ADHD)is one of the most common neuro-developmental disorders occurring in childhood,characterized by symptoms of age-inappropriate inattention,hyperactivity/impulsivity,and the prevalence is higher in boys.Although gray matter volume deficits have been frequently reported for ADHD children via structural magnetic resonance imaging,few of them had specifically focused on male patients.The present study aimed to explore the alterations of gray matter volumes in medicated-naive boys with ADHD via a relatively new voxel-based morphometry technique.According to the criteria of DSM-IV-TR,43medicated-naive ADHD boys and 44age-matched healthy boys were recruited.The magnetic resonance image(MRI)scan was performed via a 3T MRI system with three-dimensional(3D)spoiled gradient recalled echo(SPGR)sequence.Voxel-based morphometry with diffeomorphic anatomical registration through exponentiated lie algebra in SPM8 was used to preprocess the3DT1-weighted images.To identify gray matter volume differences between the ADHD and the controls,voxelbased analysis of whole brain gray matter volumes between two groups were done via two sample t-test in SPM8 with age as covariate,threshold at P<0.001.Finally,compared to the controls,significantly reduced gray matter volumes were identified in the right orbitofrontal cortex(peak coordinates[-2,52,-25],t=4.01),and bilateral hippocampus(Left:peak coordinates[14,0,-18],t=3.61;Right:peak coordinates[-14,15,-28],t=3.64)of ADHD boys.Our results demonstrated obvious reduction of whole brain gray matter volumes in right orbitofrontal cortex and bilateral hippocampus in boys with ADHD.This suggests that the abnormalities of prefrontal-hippocampus circuit may be the underlying cause of the cognitive dysfunction and abnormal behavioral inhibition in medicatednaive boys with ADHD.

Tensor hierarchy and generalized Cartan calculus in SL(3) × SL(2) exceptional field theory

NASA Astrophysics Data System (ADS)

Hohm, Olaf; Wang, Yi-Nan

2015-04-01

We construct exceptional field theory for the duality group SL(3) × SL(2). The theory is defined on a space with 8 `external' coordinates and 6 `internal' coordinates in the (3, 2) fundamental representation, leading to a 14-dimensional generalized spacetime. The bosonic theory is uniquely determined by gauge invariance under generalized external and internal diffeomorphisms. The latter invariance can be made manifest by introducing higher form gauge fields and a so-called tensor hierarchy, which we systematically develop to much higher degree than in previous studies. To this end we introduce a novel Cartan-like tensor calculus based on a covariant nil-potent differential, generalizing the exterior derivative of conventional differential geometry. The theory encodes the full D = 11 or type IIB supergravity, respectively.

Covariant Derivatives and the Renormalization Group Equation

NASA Astrophysics Data System (ADS)

Dolan, Brian P.

The renormalization group equation for N-point correlation functions can be interpreted in a geometrical manner as an equation for Lie transport of amplitudes in the space of couplings. The vector field generating the diffeomorphism has components given by the β functions of the theory. It is argued that this simple picture requires modification whenever any one of the points at which the amplitude is evaluated becomes close to any other. This modification necessitates the introduction of a connection on the space of couplings and new terms appear in the renormalization group equation involving covariant derivatives of the β function and the curvature associated with the connection. It is shown how the connection is related to the operator product expansion coefficients, but there remains an arbitrariness in its definition.

Ranking of stopping criteria for log domain diffeomorphic demons application in clinical radiation therapy.

PubMed

Peroni, M; Golland, P; Sharp, G C; Baroni, G

2011-01-01

Deformable Image Registration is a complex optimization algorithm with the goal of modeling a non-rigid transformation between two images. A crucial issue in this field is guaranteeing the user a robust but computationally reasonable algorithm. We rank the performances of four stopping criteria and six stopping value computation strategies for a log domain deformable registration. The stopping criteria we test are: (a) velocity field update magnitude, (b) vector field Jacobian, (c) mean squared error, and (d) harmonic energy. Experiments demonstrate that comparing the metric value over the last three iterations with the metric minimum of between four and six previous iterations is a robust and appropriate strategy. The harmonic energy and vector field update magnitude metrics give the best results in terms of robustness and speed of convergence.

Hamiltonian BFV-BRST theory of closed quantum cosmological models

NASA Astrophysics Data System (ADS)

Kamenshchik, A. Yu.; Lyakhovich, S. L.

1997-02-01

We introduce and study a new discrete basis of gravity constraints by making use of harmonic expansion for closed cosmological models. The full set of constraints is split into area-preserving spatial diffeomorphisms, forming closed subalgebra, and Virasoro-like generators. Operational Hamiltonian BFV-BRST quantization is performed in the framework of perturbative expansion in the dimensionless parameter, which is a positive power of the ratio of Planckian volume to the volume of the Universe. For the (N + 1)-dimensional generalization of stationary closed Bianchi-I cosmology the nilpotency condition for the BRST operator is examined in the first quantum approximation. It turns out that a certain relationship between the dimensionality of the space and the spectrum of matter fields emerges from the requirement of quantum consistency of the model.

Hamiltonian BFV-BRST theory of closed quantum cosmological models

NASA Astrophysics Data System (ADS)

Kamenshchik, A. Yu.; Lyakhovich, S. L.

1997-08-01

We introduce and study a new discrete basis of gravity constraints by making use of the harmonic expansion for closed cosmological models. The full set of constraints is split into area-preserving spatial diffeomorphisms, forming a closed subalgebra, and Virasoro-like generators. The operatorial Hamiltonian BFV-BRST quantization is performed in the framework of a perturbative expansion in the dimensionless parameter which is a positive power of the ratio of the Planck volume to the volume of the Universe. For the (N + 1) - dimensional generalization of a stationary closed Bianchi-I cosmology the nilpotency condition for the BRST operator is examined in the first quantum approximation. It turns out that a relationship between the dimensionality of the space and the spectrum of matter fields emerges from the requirement of quantum consistency of the model.

Exploring the Tomlin-Varadarajan quantum constraints in U (1 )3 loop quantum gravity: Solutions and the Minkowski theorem

NASA Astrophysics Data System (ADS)

Lewandowski, Jerzy; Lin, Chun-Yen

2017-03-01

We explicitly solved the anomaly-free quantum constraints proposed by Tomlin and Varadarajan for the weak Euclidean model of canonical loop quantum gravity, in a large subspace of the model's kinematic Hilbert space, which is the space of the charge network states. In doing so, we first identified the subspace on which each of the constraints acts convergingly, and then by explicitly evaluating such actions we found the complete set of the solutions in the identified subspace. We showed that the space of solutions consists of two classes of states, with the first class having a property that involves the condition known from the Minkowski theorem on polyhedra, and the second class satisfying a weaker form of the spatial diffeomorphism invariance.

Noether’s second theorem and Ward identities for gauge symmetries

DOE PAGES

Avery, Steven G.; Schwab, Burkhard U. W.

2016-02-04

Recently, a number of new Ward identities for large gauge transformations and large diffeomorphisms have been discovered. Some of the identities are reinterpretations of previously known statements, while some appear to be genuinely new. We present and use Noether’s second theorem with the path integral as a powerful way of generating these kinds of Ward identities. We reintroduce Noether’s second theorem and discuss how to work with the physical remnant of gauge symmetry in gauge fixed systems. We illustrate our mechanism in Maxwell theory, Yang-Mills theory, p-form field theory, and Einstein-Hilbert gravity. We comment on multiple connections between Noether’s secondmore » theorem and known results in the recent literature. Finally, our approach suggests a novel point of view with important physical consequences.« less

Positive signs in massive gravity

NASA Astrophysics Data System (ADS)

Cheung, Clifford; Remmen, Grant N.

2016-04-01

We derive new constraints on massive gravity from unitarity and analyticity of scattering amplitudes. Our results apply to a general effective theory defined by Einstein gravity plus the leading soft diffeomorphism-breaking corrections. We calculate scattering amplitudes for all combinations of tensor, vector, and scalar polarizations. The high-energy behavior of these amplitudes prescribes a specific choice of couplings that ameliorates the ultraviolet cutoff, in agreement with existing literature. We then derive consistency conditions from analytic dispersion relations, which dictate positivity of certain combinations of parameters appearing in the forward scattering amplitudes. These constraints exclude all but a small island in the parameter space of ghost-free massive gravity. While the theory of the "Galileon" scalar mode alone is known to be inconsistent with positivity constraints, this is remedied in the full massive gravity theory.

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

Cheung, Clifford; Remmen, Grant N.

Here, we derive new constraints on massive gravity from unitarity and analyticity of scattering amplitudes. Our results apply to a general effective theory defined by Einstein gravity plus the leading soft diffeomorphism-breaking corrections. We calculate scattering amplitudes for all combinations of tensor, vector, and scalar polarizations. Furthermore, the high-energy behavior of these amplitudes prescribes a specific choice of couplings that ameliorates the ultraviolet cutoff, in agreement with existing literature. We then derive consistency conditions from analytic dispersion relations, which dictate positivity of certain combinations of parameters appearing in the forward scattering amplitudes. These constraints exclude all but a small islandmore » in the parameter space of ghost-free massive gravity. And while the theory of the "Galileon" scalar mode alone is known to be inconsistent with positivity constraints, this is remedied in the full massive gravity theory.« less

Beyond Lovelock gravity: Higher derivative metric theories

NASA Astrophysics Data System (ADS)

Crisostomi, M.; Noui, K.; Charmousis, C.; Langlois, D.

2018-02-01

We consider theories describing the dynamics of a four-dimensional metric, whose Lagrangian is diffeomorphism invariant and depends at most on second derivatives of the metric. Imposing degeneracy conditions we find a set of Lagrangians that, apart form the Einstein-Hilbert one, are either trivial or contain more than 2 degrees of freedom. Among the partially degenerate theories, we recover Chern-Simons gravity, endowed with constraints whose structure suggests the presence of instabilities. Then, we enlarge the class of parity violating theories of gravity by introducing new "chiral scalar-tensor theories." Although they all raise the same concern as Chern-Simons gravity, they can nevertheless make sense as low energy effective field theories or, by restricting them to the unitary gauge (where the scalar field is uniform), as Lorentz breaking theories with a parity violating sector.

Estimating Dense Cardiac 3D Motion Using Sparse 2D Tagged MRI Cross-sections*

PubMed Central

Ardekani, Siamak; Gunter, Geoffrey; Jain, Saurabh; Weiss, Robert G.; Miller, Michael I.; Younes, Laurent

2015-01-01

In this work, we describe a new method, an extension of the Large Deformation Diffeomorphic Metric Mapping to estimate three-dimensional deformation of tagged Magnetic Resonance Imaging Data. Our approach relies on performing non-rigid registration of tag planes that were constructed from set of initial reference short axis tag grids to a set of deformed tag curves. We validated our algorithm using in-vivo tagged images of normal mice. The mapping allows us to compute root mean square distance error between simulated tag curves in a set of long axis image planes and the acquired tag curves in the same plane. Average RMS error was 0.31±0.36(SD) mm, which is approximately 2.5 voxels, indicating good matching accuracy. PMID:25571140

Covariance in self-dual inhomogeneous models of effective quantum geometry: Spherical symmetry and Gowdy systems

NASA Astrophysics Data System (ADS)

Ben Achour, Jibril; Brahma, Suddhasattwa

2018-06-01

When applying the techniques of loop quantum gravity (LQG) to symmetry-reduced gravitational systems, one first regularizes the scalar constraint using holonomy corrections, prior to quantization. In inhomogeneous system, where a residual spatial diffeomorphism symmetry survives, such modification of the gauge generator generating time reparametrization can potentially lead to deformations or anomalies in the modified algebra of first-class constraints. When working with self-dual variables, it has already been shown that, for spherically symmetric geometry coupled to a scalar field, the holonomy-modified constraints do not generate any modifications to general covariance, as one faces in the real variables formulation, and can thus accommodate local degrees of freedom in such inhomogeneous models. In this paper, we extend this result to Gowdy cosmologies in the self-dual Ashtekar formulation. Furthermore, we show that the introduction of a μ ¯-scheme in midisuperspace models, as is required in the "improved dynamics" of LQG, is possible in the self-dual formalism while being out of reach in the current effective models using real-valued Ashtekar-Barbero variables. Our results indicate the advantages of using the self-dual variables to obtain a covariant loop regularization prior to quantization in inhomogeneous symmetry-reduced polymer models, additionally implementing the crucial μ ¯-scheme, and thus a consistent semiclassical limit.

A gauge-theoretic approach to gravity

PubMed Central

Krasnov, Kirill

2012-01-01

Einstein's general relativity (GR) is a dynamical theory of the space–time metric. We describe an approach in which GR becomes an SU(2) gauge theory. We start at the linearized level and show how a gauge-theoretic Lagrangian for non-interacting massless spin two particles (gravitons) takes a much more simple and compact form than in the standard metric description. Moreover, in contrast to the GR situation, the gauge theory Lagrangian is convex. We then proceed with a formulation of the full nonlinear theory. The equivalence to the metric-based GR holds only at the level of solutions of the field equations, that is, on-shell. The gauge-theoretic approach also makes it clear that GR is not the only interacting theory of massless spin two particles, in spite of the GR uniqueness theorems available in the metric description. Thus, there is an infinite-parameter class of gravity theories all describing just two propagating polarizations of the graviton. We describe how matter can be coupled to gravity in this formulation and, in particular, how both the gravity and Yang–Mills arise as sectors of a general diffeomorphism-invariant gauge theory. We finish by outlining a possible scenario of the ultraviolet completion of quantum gravity within this approach. PMID:22792040

Highly accurate fast lung CT registration

NASA Astrophysics Data System (ADS)

Rühaak, Jan; Heldmann, Stefan; Kipshagen, Till; Fischer, Bernd

2013-03-01

Lung registration in thoracic CT scans has received much attention in the medical imaging community. Possible applications range from follow-up analysis, motion correction for radiation therapy, monitoring of air flow and pulmonary function to lung elasticity analysis. In a clinical environment, runtime is always a critical issue, ruling out quite a few excellent registration approaches. In this paper, a highly efficient variational lung registration method based on minimizing the normalized gradient fields distance measure with curvature regularization is presented. The method ensures diffeomorphic deformations by an additional volume regularization. Supplemental user knowledge, like a segmentation of the lungs, may be incorporated as well. The accuracy of our method was evaluated on 40 test cases from clinical routine. In the EMPIRE10 lung registration challenge, our scheme ranks third, with respect to various validation criteria, out of 28 algorithms with an average landmark distance of 0.72 mm. The average runtime is about 1:50 min on a standard PC, making it by far the fastest approach of the top-ranking algorithms. Additionally, the ten publicly available DIR-Lab inhale-exhale scan pairs were registered to subvoxel accuracy at computation times of only 20 seconds. Our method thus combines very attractive runtimes with state-of-the-art accuracy in a unique way.

(Small) Resonant non-Gaussianities: Signatures of a Discrete Shift Symmetry in the Effective Field Theory of Inflation

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

Behbahani, Siavosh R.; /SLAC /Stanford U., Phys. Dept. /Boston U.; Dymarsky, Anatoly

2012-06-06

We apply the Effective Field Theory of Inflation to study the case where the continuous shift symmetry of the Goldstone boson {pi} is softly broken to a discrete subgroup. This case includes and generalizes recently proposed String Theory inspired models of Inflation based on Axion Monodromy. The models we study have the property that the 2-point function oscillates as a function of the wavenumber, leading to oscillations in the CMB power spectrum. The non-linear realization of time diffeomorphisms induces some self-interactions for the Goldstone boson that lead to a peculiar non-Gaussianity whose shape oscillates as a function of the wavenumber.more » We find that in the regime of validity of the effective theory, the oscillatory signal contained in the n-point correlation functions, with n > 2, is smaller than the one contained in the 2-point function, implying that the signature of oscillations, if ever detected, will be easier to find first in the 2-point function, and only then in the higher order correlation functions. Still the signal contained in higher-order correlation functions, that we study here in generality, could be detected at a subleading level, providing a very compelling consistency check for an approximate discrete shift symmetry being realized during inflation.« less

Electrical impedance tomography in anisotropic media with known eigenvectors

NASA Astrophysics Data System (ADS)

Abascal, Juan-Felipe P. J.; Lionheart, William R. B.; Arridge, Simon R.; Schweiger, Martin; Atkinson, David; Holder, David S.

2011-06-01

Electrical impedance tomography is an imaging method, with which volumetric images of conductivity are produced by injecting electrical current and measuring boundary voltages. It has the potential to become a portable non-invasive medical imaging technique. Until now, most implementations have neglected anisotropy even though human tissues like bone, muscle and brain white matter are markedly anisotropic. The recovery of an anisotropic conductivity tensor is uniquely determined by boundary measurements only up to a diffeomorphism that fixes the boundary. Nevertheless, uniqueness can be restored by providing information about the diffeomorphism. There are uniqueness results for two constraints: one eigenvalue and a multiple scalar of a general tensor. A useable constraint for medical applications is when the eigenvectors of the underlying tissue are known, which can be approximated from MRI or estimated from DT-MRI, although the eigenvalues are unknown. However there is no known theoretical result guaranteeing uniqueness for this constraint. In fact, only a few previous inversion studies have attempted to recover one or more eigenvalues assuming certain symmetries while ignoring nonuniqueness. In this work, the aim was to undertake a numerical study of the feasibility of the recovery of a piecewise linear finite element conductivity tensor in anisotropic media with known eigenvectors from the complete boundary data. The work suggests that uniqueness holds for this constraint, in addition to proposing a methodology for the incorporation of this prior for general conductivity tensors. This was carried out by performing an analysis of the Jacobian rank and by reconstructing four conductivity distributions: two diagonal tensors whose eigenvalues were linear and sinusoidal functions, and two general tensors whose eigenvectors resembled physiological tissue, one with eigenvectors spherically orientated like a spherical layered structure, and a sample of DT-MRI data of brain white matter. The Jacobian with respect to three eigenvalues was full-rank and it was possible to recover three eigenvalues for the four simulated distributions. This encourages further theoretical study of the uniqueness for this constraint and supports the use of this as a relevant usable method for medical applications.

Integration of Temporal and Ordinal Information During Serial Interception Sequence Learning

PubMed Central

Gobel, Eric W.; Sanchez, Daniel J.; Reber, Paul J.

2011-01-01

The expression of expert motor skills typically involves learning to perform a precisely timed sequence of movements (e.g., language production, music performance, athletic skills). Research examining incidental sequence learning has previously relied on a perceptually-cued task that gives participants exposure to repeating motor sequences but does not require timing of responses for accuracy. Using a novel perceptual-motor sequence learning task, learning a precisely timed cued sequence of motor actions is shown to occur without explicit instruction. Participants learned a repeating sequence through practice and showed sequence-specific knowledge via a performance decrement when switched to an unfamiliar sequence. In a second experiment, the integration of representation of action order and timing sequence knowledge was examined. When either action order or timing sequence information was selectively disrupted, performance was reduced to levels similar to completely novel sequences. Unlike prior sequence-learning research that has found timing information to be secondary to learning action sequences, when the task demands require accurate action and timing information, an integrated representation of these types of information is acquired. These results provide the first evidence for incidental learning of fully integrated action and timing sequence information in the absence of an independent representation of action order, and suggest that this integrative mechanism may play a material role in the acquisition of complex motor skills. PMID:21417511

COMPARISON OF VOLUMETRIC REGISTRATION ALGORITHMS FOR TENSOR-BASED MORPHOMETRY

PubMed Central

Villalon, Julio; Joshi, Anand A.; Toga, Arthur W.; Thompson, Paul M.

2015-01-01

Nonlinear registration of brain MRI scans is often used to quantify morphological differences associated with disease or genetic factors. Recently, surface-guided fully 3D volumetric registrations have been developed that combine intensity-guided volume registrations with cortical surface constraints. In this paper, we compare one such algorithm to two popular high-dimensional volumetric registration methods: large-deformation viscous fluid registration, formulated in a Riemannian framework, and the diffeomorphic “Demons” algorithm. We performed an objective morphometric comparison, by using a large MRI dataset from 340 young adult twin subjects to examine 3D patterns of correlations in anatomical volumes. Surface-constrained volume registration gave greater effect sizes for detecting morphometric associations near the cortex, while the other two approaches gave greater effects sizes subcortically. These findings suggest novel ways to combine the advantages of multiple methods in the future. PMID:26925198

Positive signs in massive gravity

DOE PAGES

Cheung, Clifford; Remmen, Grant N.

2016-04-01

Here, we derive new constraints on massive gravity from unitarity and analyticity of scattering amplitudes. Our results apply to a general effective theory defined by Einstein gravity plus the leading soft diffeomorphism-breaking corrections. We calculate scattering amplitudes for all combinations of tensor, vector, and scalar polarizations. Furthermore, the high-energy behavior of these amplitudes prescribes a specific choice of couplings that ameliorates the ultraviolet cutoff, in agreement with existing literature. We then derive consistency conditions from analytic dispersion relations, which dictate positivity of certain combinations of parameters appearing in the forward scattering amplitudes. These constraints exclude all but a small islandmore » in the parameter space of ghost-free massive gravity. And while the theory of the "Galileon" scalar mode alone is known to be inconsistent with positivity constraints, this is remedied in the full massive gravity theory.« less

On the symplectic structure of harmonic superspace

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

Kachkachi, M.; Saidi, E.H.

In this paper, the symplectic properties of harmonic superspace are studied. It is shown that Diff(S[sup 2]) is isomorphic to Diff[sub 0](S[sup 3])/Ab(Diff[sub 0](S[sup 3])), where Diff[sub 0](S[sup 3]) is the group of the diffeomorphisms of S[sup 3] preserving the Cartan charge operator D[sup 0] and Ab(Diff[sub 0](S[sup 3])) is its Abelian subgroup generated by the Cartan vectors L[sub 0] = w[sup 0]D[sup 0]. The authors show also that the eigenvalue equation D[sup 0] [lambda](z) = 0 defines a symplectic structure in harmonic superspace, and the authors calculate the corresponding algebra. The general symplectic invariant coupling of the Maxwell prepotentialmore » is constructed in both flat and curved harmonic superspace. Other features are discussed.« less

General coordinate invariance in quantum many-body systems

NASA Astrophysics Data System (ADS)

Brauner, Tomáš; Endlich, Solomon; Monin, Alexander; Penco, Riccardo

2014-11-01

We extend the notion of general coordinate invariance to many-body, not necessarily relativistic, systems. As an application, we investigate nonrelativistic general covariance in Galilei-invariant systems. The peculiar transformation rules for the background metric and gauge fields, first introduced by Son and Wingate in 2005 and refined in subsequent works, follow naturally from our framework. Our approach makes it clear that Galilei or Poincaré symmetry is by no means a necessary prerequisite for making the theory invariant under coordinate diffeomorphisms. General covariance merely expresses the freedom to choose spacetime coordinates at will, whereas the true, physical symmetries of the system can be separately implemented as "internal" symmetries within the vielbein formalism. A systematic way to implement such symmetries is provided by the coset construction. We illustrate this point by applying our formalism to nonrelativistic s -wave superfluids.

Immirzi parameter and Noether charges in first order gravity

NASA Astrophysics Data System (ADS)

Durka, Remigiusz

2012-02-01

The framework of SO(3,2) constrained BF theory applied to gravity makes it possible to generalize formulas for gravitational diffeomorphic Noether charges (mass, angular momentum, and entropy). It extends Wald's approach to the case of first order gravity with a negative cosmological constant, the Holst modification and the topological terms (Nieh-Yan, Euler, and Pontryagin). Topological invariants play essential role contributing to the boundary terms in the regularization scheme for the asymptotically AdS spacetimes, so that the differentiability of the action is automatically secured. Intriguingly, it turns out that the black hole thermodynamics does not depend on the Immirzi parameter for the AdS-Schwarzschild, AdS-Kerr, and topological black holes, whereas a nontrivial modification appears for the AdS-Taub-NUT spacetime, where it impacts not only the entropy, but also the total mass.

Computational Cardiac Anatomy Using MRI

PubMed Central

Beg, Mirza Faisal; Helm, Patrick A.; McVeigh, Elliot; Miller, Michael I.; Winslow, Raimond L.

2005-01-01

Ventricular geometry and fiber orientation may undergo global or local remodeling in cardiac disease. However, there are as yet no mathematical and computational methods for quantifying variation of geometry and fiber orientation or the nature of their remodeling in disease. Toward this goal, a landmark and image intensity-based large deformation diffeomorphic metric mapping (LDDMM) method to transform heart geometry into common coordinates for quantification of shape and form was developed. Two automated landmark placement methods for modeling tissue deformations expected in different cardiac pathologies are presented. The transformations, computed using the combined use of landmarks and image intensities, yields high-registration accuracy of heart anatomies even in the presence of significant variation of cardiac shape and form. Once heart anatomies have been registered, properties of tissue geometry and cardiac fiber orientation in corresponding regions of different hearts may be quantified. PMID:15508155

On the background independence of two-dimensional topological gravity

NASA Astrophysics Data System (ADS)

Imbimbo, Camillo

1995-04-01

We formulate two-dimensional topological gravity in a background covariant Lagrangian framework. We derive the Ward identities which characterize the dependence of physical correlators on the background world-sheet metric defining the gauge-slice. We point out the existence of an "anomaly" in Ward identitites involving correlators of observables with higher ghost number. This "anomaly" represents an obstruction for physical correlators to be globally defined forms on moduli space which could be integrated in a background independent way. Starting from the anomalous Ward identities, we derive "descent" equations whose solutions are cocycles of the Lie algebra of the diffeomorphism group with values in the space of local forms on the moduli space. We solve the descent equations and provide explicit formulas for the cocycles, which allow for the definition of background independent integrals of physical correlators on the moduli space.

Joint T1 and brain fiber log-demons registration using currents to model geometry.

PubMed

Siless, Viviana; Glaunès, Joan; Guevara, Pamela; Mangin, Jean-François; Poupon, Cyril; Le Bihan, Denis; Thirion, Bertrand; Fillard, Pierre

2012-01-01

We present an extension of the diffeomorphic Geometric Demons algorithm which combines the iconic registration with geometric constraints. Our algorithm works in the log-domain space, so that one can efficiently compute the deformation field of the geometry. We represent the shape of objects of interest in the space of currents which is sensitive to both location and geometric structure of objects. Currents provides a distance between geometric structures that can be defined without specifying explicit point-to-point correspondences. We demonstrate this framework by registering simultaneously T1 images and 65 fiber bundles consistently extracted in 12 subjects and compare it against non-linear T1, tensor, and multi-modal T1 + Fractional Anisotropy (FA) registration algorithms. Results show the superiority of the Log-domain Geometric Demons over their purely iconic counterparts.

Membrane paradigm and RG flows for anomalous holographic theories

NASA Astrophysics Data System (ADS)

Copetti, Christian; Fernández-Pendás, Jorge

2018-04-01

Holographic RG flows can be better understood with the help of radially conserved charges. It was shown by various authors that the bulk gauge and diffeomorphism symmetries lead to the conservation of the zero mode of the holographic U(1) current and, if the spacetime is stationary, to that of the holographic heat current. In describing dual theories with 't Hooft anomalies the bulk gauge invariance is broken by Chern-Simons terms. We show that conservation laws can still be derived and used to characterize the anomalous transport in terms of membrane currents at the horizon. We devote particular attention to systems with gravitational anomalies. These are known to be problematic due to their higher derivative content. We show that this feature alters the construction of the membrane currents in a way which is deeply tied with the anomalous gravitational transport.

A lattice approach to spinorial quantum gravity

NASA Technical Reports Server (NTRS)

Renteln, Paul; Smolin, Lee

1989-01-01

A new lattice regularization of quantum general relativity based on Ashtekar's reformulation of Hamiltonian general relativity is presented. In this form, quantum states of the gravitational field are represented within the physical Hilbert space of a Kogut-Susskind lattice gauge theory. The gauge field of the theory is a complexified SU(2) connection which is the gravitational connection for left-handed spinor fields. The physical states of the gravitational field are those which are annihilated by additional constraints which correspond to the four constraints of general relativity. Lattice versions of these constraints are constructed. Those corresponding to the three-dimensional diffeomorphism generators move states associated with Wilson loops around on the lattice. The lattice Hamiltonian constraint has a simple form, and a correspondingly simple interpretation: it is an operator which cuts and joins Wilson loops at points of intersection.

Freesurfer-initialized large deformation diffeomorphic metric mapping with application to Parkinson's disease

NASA Astrophysics Data System (ADS)

Chen, Jingyun; Palmer, Samantha J.; Khan, Ali R.; Mckeown, Martin J.; Beg, Mirza Faial

2009-02-01

We apply a recently developed automated brain segmentation method, FS+LDDMM, to brain MRI scans from Parkinson's Disease (PD) subjects, and normal age-matched controls and compare the results to manual segmentation done by trained neuroscientists. The data set consisted of 14 PD subjects and 12 age-matched control subjects without neurologic disease and comparison was done on six subcortical brain structures (left and right caudate, putamen and thalamus). Comparison between automatic and manual segmentation was based on Dice Similarity Coefficient (Overlap Percentage), L1 Error, Symmetrized Hausdorff Distance and Symmetrized Mean Surface Distance. Results suggest that FS+LDDMM is well-suited for subcortical structure segmentation and further shape analysis in Parkinson's Disease. The asymmetry of the Dice Similarity Coefficient over shape change is also discussed based on the observation and measurement of FS+LDDMM segmentation results.

Near-horizon BMS symmetries as fluid symmetries

NASA Astrophysics Data System (ADS)

Penna, Robert F.

2017-10-01

The Bondi-van der Burg-Metzner-Sachs (BMS) group is the asymptotic symmetry group of asymptotically flat gravity. Recently, Donnay et al. have derived an analogous symmetry group acting on black hole event horizons. For a certain choice of boundary conditions, it is a semidirect product of Diff( S 2), the smooth diffeomorphisms of the twosphere, acting on C ∞( S 2), the smooth functions on the two-sphere. We observe that the same group appears in fluid dynamics as symmetries of the compressible Euler equations. We relate these two realizations of Diff( S 2) ⋉ C ∞( S 2) using the black hole membrane paradigm. We show that the Lie-Poisson brackets of membrane paradigm fluid charges reproduce the near-horizon BMS algebra. The perspective presented here may be useful for understanding the BMS algebra at null infinity.

Quantization of the nonlinear sigma model revisited

NASA Astrophysics Data System (ADS)

Nguyen, Timothy

2016-08-01

We revisit the subject of perturbatively quantizing the nonlinear sigma model in two dimensions from a rigorous, mathematical point of view. Our main contribution is to make precise the cohomological problem of eliminating potential anomalies that may arise when trying to preserve symmetries under quantization. The symmetries we consider are twofold: (i) diffeomorphism covariance for a general target manifold; (ii) a transitive group of isometries when the target manifold is a homogeneous space. We show that there are no anomalies in case (i) and that (ii) is also anomaly-free under additional assumptions on the target homogeneous space, in agreement with the work of Friedan. We carry out some explicit computations for the O(N)-model. Finally, we show how a suitable notion of the renormalization group establishes the Ricci flow as the one loop renormalization group flow of the nonlinear sigma model.

Structure theorems for game trees

PubMed Central

Govindan, Srihari; Wilson, Robert

2002-01-01

Kohlberg and Mertens [Kohlberg, E. & Mertens, J. (1986) Econometrica 54, 1003–1039] proved that the graph of the Nash equilibrium correspondence is homeomorphic to its domain when the domain is the space of payoffs in normal-form games. A counterexample disproves the analog for the equilibrium outcome correspondence over the space of payoffs in extensive-form games, but we prove an analog when the space of behavior strategies is perturbed so that every path in the game tree has nonzero probability. Without such perturbations, the graph is the closure of the union of a finite collection of its subsets, each diffeomorphic to a corresponding path-connected open subset of the space of payoffs. As an application, we construct an algorithm for computing equilibria of an extensive-form game with a perturbed strategy space, and thus approximate equilibria of the unperturbed game. PMID:12060702

Structure theorems for game trees.

PubMed

Govindan, Srihari; Wilson, Robert

2002-06-25

Kohlberg and Mertens [Kohlberg, E. & Mertens, J. (1986) Econometrica 54, 1003-1039] proved that the graph of the Nash equilibrium correspondence is homeomorphic to its domain when the domain is the space of payoffs in normal-form games. A counterexample disproves the analog for the equilibrium outcome correspondence over the space of payoffs in extensive-form games, but we prove an analog when the space of behavior strategies is perturbed so that every path in the game tree has nonzero probability. Without such perturbations, the graph is the closure of the union of a finite collection of its subsets, each diffeomorphic to a corresponding path-connected open subset of the space of payoffs. As an application, we construct an algorithm for computing equilibria of an extensive-form game with a perturbed strategy space, and thus approximate equilibria of the unperturbed game.

Association mining of dependency between time series

NASA Astrophysics Data System (ADS)

Hafez, Alaaeldin

2001-03-01

Time series analysis is considered as a crucial component of strategic control over a broad variety of disciplines in business, science and engineering. Time series data is a sequence of observations collected over intervals of time. Each time series describes a phenomenon as a function of time. Analysis on time series data includes discovering trends (or patterns) in a time series sequence. In the last few years, data mining has emerged and been recognized as a new technology for data analysis. Data Mining is the process of discovering potentially valuable patterns, associations, trends, sequences and dependencies in data. Data mining techniques can discover information that many traditional business analysis and statistical techniques fail to deliver. In this paper, we adapt and innovate data mining techniques to analyze time series data. By using data mining techniques, maximal frequent patterns are discovered and used in predicting future sequences or trends, where trends describe the behavior of a sequence. In order to include different types of time series (e.g. irregular and non- systematic), we consider past frequent patterns of the same time sequences (local patterns) and of other dependent time sequences (global patterns). We use the word 'dependent' instead of the word 'similar' for emphasis on real life time series where two time series sequences could be completely different (in values, shapes, etc.), but they still react to the same conditions in a dependent way. In this paper, we propose the Dependence Mining Technique that could be used in predicting time series sequences. The proposed technique consists of three phases: (a) for all time series sequences, generate their trend sequences, (b) discover maximal frequent trend patterns, generate pattern vectors (to keep information of frequent trend patterns), use trend pattern vectors to predict future time series sequences.

Spectral asymptotics of Euclidean quantum gravity with diff-invariant boundary conditions

NASA Astrophysics Data System (ADS)

Esposito, Giampiero; Fucci, Guglielmo; Kamenshchik, Alexander Yu; Kirsten, Klaus

2005-03-01

A general method is known to exist for studying Abelian and non-Abelian gauge theories, as well as Euclidean quantum gravity, at 1-loop level on manifolds with boundary. In the latter case, boundary conditions on metric perturbations h can be chosen to be completely invariant under infinitesimal diffeomorphisms, to preserve the invariance group of the theory and BRST symmetry. In the de Donder gauge, however, the resulting boundary-value problem for the Laplace-type operator acting on h is known to be self-adjoint but not strongly elliptic. The latter is a technical condition ensuring that a unique smooth solution of the boundary-value problem exists, which implies, in turn, that the global heat-kernel asymptotics yielding 1-loop divergences and 1-loop effective action actually exists. The present paper shows that, on the Euclidean 4-ball, only the scalar part of perturbative modes for quantum gravity is affected by the lack of strong ellipticity. Further evidence for lack of strong ellipticity, from an analytic point of view, is therefore obtained. Interestingly, three sectors of the scalar-perturbation problem remain elliptic, while lack of strong ellipticity is 'confined' to the remaining fourth sector. The integral representation of the resulting ζ-function asymptotics on the Euclidean 4-ball is also obtained; this remains regular at the origin by virtue of a spectral identity here obtained for the first time.

Diffeomorphometry and geodesic positioning systems for human anatomy.

PubMed

Miller, Michael I; Younes, Laurent; Trouvé, Alain

2014-03-01

The Computational Anatomy project has largely been a study of large deformations within a Riemannian framework as an efficient point of view for generating metrics between anatomical configurations. This approach turns D'Arcy Thompson's comparative morphology of human biological shape and form into a metrizable space. Since the metric is constructed based on the geodesic length of the flows of diffeomorphisms connecting the forms, we call it diffeomorphometry . Just as importantly, since the flows describe algebraic group action on anatomical submanifolds and associated functional measurements, they become the basis for positioning information, which we term geodesic positioning . As well the geodesic connections provide Riemannian coordinates for locating forms in the anatomical orbit, which we call geodesic coordinates . These three components taken together - the metric, geodesic positioning of information, and geodesic coordinates - we term the geodesic positioning system . We illustrate via several examples in human and biological coordinate systems and machine learning of the statistical representation of shape and form.

Quasi-local conserved charges in the Einstein-Maxwell theory

NASA Astrophysics Data System (ADS)

Setare, M. R.; Adami, H.

2017-05-01

In this paper we consider the Einstein-Maxwell theory and define a combined transformation composed of diffeomorphism and U(1) gauge transformation. For generality, we assume that the generator χ of such transformation is field-dependent. We define the extended off-shell ADT current and then off-shell ADT charge such that they are conserved off-shell for the asymptotically field-dependent symmetry generator χ. Then, we define the conserved charge corresponding to the asymptotically field-dependent symmetry generator χ. We apply the presented method to find the conserved charges of the asymptotically AdS3 spacetimes in the context of the Einstein-Maxwell theory in three dimensions. Although the usual proposal for the quasi local charges provides divergent global charges for the Einstein-Maxwell theory with negative cosmological constant in three dimensions, here we avoid this problem by introducing proposed combined transformation χ

G-Strands on symmetric spaces

PubMed Central

2017-01-01

We study the G-strand equations that are extensions of the classical chiral model of particle physics in the particular setting of broken symmetries described by symmetric spaces. These equations are simple field theory models whose configuration space is a Lie group, or in this case a symmetric space. In this class of systems, we derive several models that are completely integrable on finite dimensional Lie group G, and we treat in more detail examples with symmetric space SU(2)/S1 and SO(4)/SO(3). The latter model simplifies to an apparently new integrable nine-dimensional system. We also study the G-strands on the infinite dimensional group of diffeomorphisms, which gives, together with the Sobolev norm, systems of 1+2 Camassa–Holm equations. The solutions of these equations on the complementary space related to the Witt algebra decomposition are the odd function solutions. PMID:28413343

Near horizon symmetry and entropy formula for Kerr-Newman (A)dS black holes

NASA Astrophysics Data System (ADS)

Setare, Mohammad Reza; Adami, Hamed

2018-04-01

In this paper we provide the first non-trivial evidence for universality of the entropy formula 4 πJ 0 + J 0 - beyond pure Einstein gravity in 4-dimensions. We consider the Einstein-Maxwell theory in the presence of cosmological constant, then write near horizon metric of the Kerr-Newman (A)dS black hole in the Gaussian null coordinate system. We consider near horizon fall-off conditions for metric and U(1) gauge field. We find asymptotic combined symmetry generator, consists of diffeomorphism and U(1) gauge transformation, so that it preserves fall-off conditions. Consequently, we find supertranslation, supperrotation and multiple-charge modes and then we show that the entropy formula is held for the Kerr-Newman (A)dS black hole. Supperrotation modes suffer from a problem. By introducing new combined symmetry generator, we cure that problem.

Soft collinear effective theory for gravity

NASA Astrophysics Data System (ADS)

Okui, Takemichi; Yunesi, Arash

2018-03-01

We present how to construct a soft collinear effective theory (SCET) for gravity at the leading and next-to-leading powers from the ground up. The soft graviton theorem and decoupling of collinear gravitons at the leading power are manifest from the outset in the effective symmetries of the theory. At the next-to-leading power, certain simple structures of amplitudes, which are completely obscure in Feynman diagrams of the full theory, are also revealed, which greatly simplifies calculations. The effective Lagrangian is highly constrained by effectively multiple copies of diffeomorphism invariance that are inevitably present in gravity SCET due to mode separation, an essential ingredient of any SCET. Further explorations of effective theories of gravity with mode separation may shed light on Lagrangian-level understandings of some of the surprising properties of gravitational scattering amplitudes. A gravity SCET with an appropriate inclusion of Glauber modes may serve as a powerful tool for studying gravitational scattering in the Regge limit.

More on Weinberg's no-go theorem in quantum gravity

NASA Astrophysics Data System (ADS)

Nagahama, Munehiro; Oda, Ichiro

2018-05-01

We complement Weinberg's no-go theorem on the cosmological constant problem in quantum gravity by generalizing it to the case of a scale-invariant theory. Our analysis makes use of the effective action and the BRST symmetry in a manifestly covariant quantum gravity instead of the classical Lagrangian density and the G L (4 ) symmetry in classical gravity. In this sense, our proof is very general since it does not depend on details of quantum gravity and holds true for general gravitational theories which are invariant under diffeomorphisms. As an application of our theorem, we comment on an idea that in the asymptotic safety scenario the functional renormalization flow drives a cosmological constant to zero, solving the cosmological constant problem without reference to fine tuning of parameters. Finally, we also comment on the possibility of extending the Weinberg theorem in quantum gravity to the case where the translational invariance is spontaneously broken.

Low-Dimensional Statistics of Anatomical Variability via Compact Representation of Image Deformations.

PubMed

Zhang, Miaomiao; Wells, William M; Golland, Polina

2016-10-01

Using image-based descriptors to investigate clinical hypotheses and therapeutic implications is challenging due to the notorious "curse of dimensionality" coupled with a small sample size. In this paper, we present a low-dimensional analysis of anatomical shape variability in the space of diffeomorphisms and demonstrate its benefits for clinical studies. To combat the high dimensionality of the deformation descriptors, we develop a probabilistic model of principal geodesic analysis in a bandlimited low-dimensional space that still captures the underlying variability of image data. We demonstrate the performance of our model on a set of 3D brain MRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Our model yields a more compact representation of group variation at substantially lower computational cost than models based on the high-dimensional state-of-the-art approaches such as tangent space PCA (TPCA) and probabilistic principal geodesic analysis (PPGA).

Momentum-based morphometric analysis with application to Parkinson's disease

NASA Astrophysics Data System (ADS)

Chen, Jingyun; Khan, Ali R.; McKeown, Martin J.; Beg, Mirza F.

2011-03-01

We apply the initial momentum shape representation of diffeomorphic metric mapping from a template region of interest (ROI) to a given ROI as a morphometic marker in Parkinson's disease. We used a three-step segmentation-registrationmomentum process to derive feature vectors from ROIs in a group of 42 subjects consisting of 19 Parkinson's Disease (PD) subjects and 23 normal control (NC) subjects. Significant group differences between PD and NC subjects were detected in four basal ganglia structures including the caudate, putamen, thalamus and globus pallidus. The magnitude of regionally significant between-group differences detected ranged between 34-75%. Visualization of the different structural deformation pattern between-groups revealed that some parts of basal ganglia structure actually hypertrophy, presumably as a compensatory response to more widespread atrophy. Our results of both hypertrophy and atrophy in the same structures further demonstrate the importance of morphological measures as opposed to overall volume in the assessment of neurodegenerative disease.

Double metric, generalized metric, and α' -deformed double field theory

NASA Astrophysics Data System (ADS)

Hohm, Olaf; Zwiebach, Barton

2016-03-01

We relate the unconstrained "double metric" of the "α' -geometry" formulation of double field theory to the constrained generalized metric encoding the spacetime metric and b -field. This is achieved by integrating out auxiliary field components of the double metric in an iterative procedure that induces an infinite number of higher-derivative corrections. As an application, we prove that, to first order in α' and to all orders in fields, the deformed gauge transformations are Green-Schwarz-deformed diffeomorphisms. We also prove that to first order in α' the spacetime action encodes precisely the Green-Schwarz deformation with Chern-Simons forms based on the torsionless gravitational connection. This seems to be in tension with suggestions in the literature that T-duality requires a torsionful connection, but we explain that these assertions are ambiguous since actions that use different connections are related by field redefinitions.

A generalized non-Gaussian consistency relation for single field inflation

NASA Astrophysics Data System (ADS)

Bravo, Rafael; Mooij, Sander; Palma, Gonzalo A.; Pradenas, Bastián

2018-05-01

We show that a perturbed inflationary spacetime, driven by a canonical single scalar field, is invariant under a special class of coordinate transformations together with a field reparametrization of the curvature perturbation in co-moving gauge. This transformation may be used to derive the squeezed limit of the 3-point correlation function of the co-moving curvature perturbations valid in the case that these do not freeze after horizon crossing. This leads to a generalized version of Maldacena's non-Gaussian consistency relation in the sense that the bispectrum squeezed limit is completely determined by spacetime diffeomorphisms. Just as in the case of the standard consistency relation, this result may be understood as the consequence of how long-wavelength modes modulate those of shorter wavelengths. This relation allows one to derive the well known violation to the consistency relation encountered in ultra slow-roll, where curvature perturbations grow exponentially after horizon crossing.

z -Weyl gravity in higher dimensions

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

Moon, Taeyoon; Oh, Phillial, E-mail: dpproject@skku.edu, E-mail: ploh@skku.edu

We consider higher dimensional gravity in which the four dimensional spacetime and extra dimensions are not treated on an equal footing. The anisotropy is implemented in the ADM decomposition of higher dimensional metric by requiring the foliation preserving diffeomorphism invariance adapted to the extra dimensions, thus keeping the general covariance only for the four dimensional spacetime. The conformally invariant gravity can be constructed with an extra (Weyl) scalar field and a real parameter z which describes the degree of anisotropy of conformal transformation between the spacetime and extra dimensional metrics. In the zero mode effective 4D action, it reduces tomore » four-dimensional scalar-tensor theory coupled with nonlinear sigma model described by extra dimensional metrics. There are no restrictions on the value of z at the classical level and possible applications to the cosmological constant problem with a specific choice of z are discussed.« less

The Stabilizing Effect of Spacetime Expansion on Relativistic Fluids With Sharp Results for the Radiation Equation of State

NASA Astrophysics Data System (ADS)

Speck, Jared

2013-07-01

In this article, we study the 1 + 3-dimensional relativistic Euler equations on a pre-specified conformally flat expanding spacetime background with spatial slices that are diffeomorphic to {R}^3. We assume that the fluid verifies the equation of state {p = c2s ρ,} where {0 ≤ cs ≤ √{1/3}} is the speed of sound. We also assume that the reciprocal of the scale factor associated with the expanding spacetime metric verifies a c s -dependent time-integrability condition. Under these assumptions, we use the vector field energy method to prove that an explicit family of physically motivated, spatially homogeneous, and spatially isotropic fluid solutions are globally future-stable under small perturbations of their initial conditions. The explicit solutions corresponding to each scale factor are analogs of the well-known spatially flat Friedmann-Lemaître-Robertson-Walker family. Our nonlinear analysis, which exploits dissipative terms generated by the expansion, shows that the perturbed solutions exist for all future times and remain close to the explicit solutions. This work is an extension of previous results, which showed that an analogous stability result holds when the spacetime is exponentially expanding. In the case of the radiation equation of state p = (1/3)ρ, we also show that if the time-integrability condition for the reciprocal of the scale factor fails to hold, then the explicit fluid solutions are unstable. More precisely, we show the existence of an open family of initial data such that (i) it contains arbitrarily small smooth perturbations of the explicit solutions' data and (ii) the corresponding perturbed solutions necessarily form shocks in finite time. The shock formation proof is based on the conformal invariance of the relativistic Euler equations when {c2s = 1/3,} which allows for a reduction to a well-known result of Christodoulou.

Uncovering Neuronal Networks Defined by Consistent Between-Neuron Spike Timing from Neuronal Spike Recordings

PubMed Central

2018-01-01

Abstract It is widely assumed that distributed neuronal networks are fundamental to the functioning of the brain. Consistent spike timing between neurons is thought to be one of the key principles for the formation of these networks. This can involve synchronous spiking or spiking with time delays, forming spike sequences when the order of spiking is consistent. Finding networks defined by their sequence of time-shifted spikes, denoted here as spike timing networks, is a tremendous challenge. As neurons can participate in multiple spike sequences at multiple between-spike time delays, the possible complexity of networks is prohibitively large. We present a novel approach that is capable of (1) extracting spike timing networks regardless of their sequence complexity, and (2) that describes their spiking sequences with high temporal precision. We achieve this by decomposing frequency-transformed neuronal spiking into separate networks, characterizing each network’s spike sequence by a time delay per neuron, forming a spike sequence timeline. These networks provide a detailed template for an investigation of the experimental relevance of their spike sequences. Using simulated spike timing networks, we show network extraction is robust to spiking noise, spike timing jitter, and partial occurrences of the involved spike sequences. Using rat multineuron recordings, we demonstrate the approach is capable of revealing real spike timing networks with sub-millisecond temporal precision. By uncovering spike timing networks, the prevalence, structure, and function of complex spike sequences can be investigated in greater detail, allowing us to gain a better understanding of their role in neuronal functioning. PMID:29789811

Effects of quantum noise in 4D-CT on deformable image registration and derived ventilation data

NASA Astrophysics Data System (ADS)

Latifi, Kujtim; Huang, Tzung-Chi; Feygelman, Vladimir; Budzevich, Mikalai M.; Moros, Eduardo G.; Dilling, Thomas J.; Stevens, Craig W.; van Elmpt, Wouter; Dekker, Andre; Zhang, Geoffrey G.

2013-11-01

Quantum noise is common in CT images and is a persistent problem in accurate ventilation imaging using 4D-CT and deformable image registration (DIR). This study focuses on the effects of noise in 4D-CT on DIR and thereby derived ventilation data. A total of six sets of 4D-CT data with landmarks delineated in different phases, called point-validated pixel-based breathing thorax models (POPI), were used in this study. The DIR algorithms, including diffeomorphic morphons (DM), diffeomorphic demons (DD), optical flow and B-spline, were used to register the inspiration phase to the expiration phase. The DIR deformation matrices (DIRDM) were used to map the landmarks. Target registration errors (TRE) were calculated as the distance errors between the delineated and the mapped landmarks. Noise of Gaussian distribution with different standard deviations (SD), from 0 to 200 Hounsfield Units (HU) in amplitude, was added to the POPI models to simulate different levels of quantum noise. Ventilation data were calculated using the ΔV algorithm which calculates the volume change geometrically based on the DIRDM. The ventilation images with different added noise levels were compared using Dice similarity coefficient (DSC). The root mean square (RMS) values of the landmark TRE over the six POPI models for the four DIR algorithms were stable when the noise level was low (SD <150 HU) and increased with added noise when the level is higher. The most accurate DIR was DD with a mean RMS of 1.5 ± 0.5 mm with no added noise and 1.8 ± 0.5 mm with noise (SD = 200 HU). The DSC values between the ventilation images with and without added noise decreased with the noise level, even when the noise level was relatively low. The DIR algorithm most robust with respect to noise was DM, with mean DSC = 0.89 ± 0.01 and 0.66 ± 0.02 for the top 50% ventilation volumes, as compared between 0 added noise and SD = 30 and 200 HU, respectively. Although the landmark TRE were stable with low noise, the differences between ventilation images increased with noise level, even when the noise was low, indicating ventilation imaging from 4D-CT was sensitive to image noise. Therefore, high quality 4D-CT is essential for accurate ventilation images.

Non-Cartesian Balanced SSFP Pulse Sequences for Real-Time Cardiac MRI

PubMed Central

Feng, Xue; Salerno, Michael; Kramer, Christopher M.; Meyer, Craig H.

2015-01-01

Purpose To develop a new spiral-in/out balanced steady-state free precession (bSSFP) pulse sequence for real-time cardiac MRI and compare it with radial and spiral-out techniques. Methods Non-Cartesian sampling strategies are efficient and robust to motion and thus have important advantages for real-time bSSFP cine imaging. This study describes a new symmetric spiral-in/out sequence with intrinsic gradient moment compensation and SSFP refocusing at TE=TR/2. In-vivo real-time cardiac imaging studies were performed to compare radial, spiral-out, and spiral-in/out bSSFP pulse sequences. Furthermore, phase-based fat-water separation taking advantage of the refocusing mechanism of the spiral-in/out bSSFP sequence was also studied. Results The image quality of the spiral-out and spiral-in/out bSSFP sequences was improved with off-resonance and k-space trajectory correction. The spiral-in/out bSSFP sequence had the highest SNR, CNR, and image quality ratings, with spiral-out bSSFP sequence second in each category and the radial bSSFP sequence third. The spiral-in/out bSSFP sequence provides separated fat and water images with no additional scan time. Conclusions In this work a new spiral-in/out bSSFP sequence was developed and tested. The superiority of spiral bSSFP sequences over the radial bSSFP sequence in terms of SNR and reduced artifacts was demonstrated in real-time MRI of cardiac function without image acceleration. PMID:25960254

Continuous- and discrete-time stimulus sequences for high stimulus rate paradigm in evoked potential studies.

PubMed

Wang, Tao; Huang, Jiang-hua; Lin, Lin; Zhan, Chang'an A

2013-01-01

To obtain reliable transient auditory evoked potentials (AEPs) from EEGs recorded using high stimulus rate (HSR) paradigm, it is critical to design the stimulus sequences of appropriate frequency properties. Traditionally, the individual stimulus events in a stimulus sequence occur only at discrete time points dependent on the sampling frequency of the recording system and the duration of stimulus sequence. This dependency likely causes the implementation of suboptimal stimulus sequences, sacrificing the reliability of resulting AEPs. In this paper, we explicate the use of continuous-time stimulus sequence for HSR paradigm, which is independent of the discrete electroencephalogram (EEG) recording system. We employ simulation studies to examine the applicability of the continuous-time stimulus sequences and the impacts of sampling frequency on AEPs in traditional studies using discrete-time design. Results from these studies show that the continuous-time sequences can offer better frequency properties and improve the reliability of recovered AEPs. Furthermore, we find that the errors in the recovered AEPs depend critically on the sampling frequencies of experimental systems, and their relationship can be fitted using a reciprocal function. As such, our study contributes to the literature by demonstrating the applicability and advantages of continuous-time stimulus sequences for HSR paradigm and by revealing the relationship between the reliability of AEPs and sampling frequencies of the experimental systems when discrete-time stimulus sequences are used in traditional manner for the HSR paradigm.

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

PubMed

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-08-01

RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of [Formula: see text]. Subsequently, numerous faster 'Sankoff-style' approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity ([Formula: see text] quartic time). Breaking this barrier, we introduce the novel Sankoff-style algorithm 'sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)', which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff's original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. © The Author 2015. Published by Oxford University Press.

Timing, sequencing, and executive control in repetitive movement production.

PubMed

Krampe, Ralf Th; Mayr, Ulrich; Kliegl, Reinhold

2005-06-01

The authors demonstrate that the timing and sequencing of target durations require low-level timing and executive control. Sixteen young (M-sub(age) = 19 years) and 16 older (M-sub(age) = 70 years) adults participated in 2 experiments. In Experiment 1, individual mean-variance functions for low-level timing (isochronous tapping) and the sequencing of multiple targets (rhythm production) revealed (a) a dissociation of low-level timing and sequencing in both age groups, (b) negligible age differences for low-level timing, and (c) large age differences for sequencing. Experiment 2 supported the distinction between low-level timing and executive functions: Selection against a dominant rhythm and switching between rhythms impaired performances in both age groups and induced pronounced perseveration of the dominant pattern in older adults. ((c) 2005 APA, all rights reserved).

Serial Reaction Time Learning in Preschool- and School-Age Children.

ERIC Educational Resources Information Center

Thomas, Kathleen M.; Nelson, Charles A.

2001-01-01

Two experiments assessed visuomotor sequence learning in 4- to 10-year-olds using a serial reaction time (SRT) task with random and sequenced trials. Found that children demonstrated sequence-specific decreases in RT. Participants with explicit awareness of the sequence at the session's end showed larger sequence-specific RT decrements than…

On a canonical quantization of 3D Anti de Sitter pure gravity

NASA Astrophysics Data System (ADS)

Kim, Jihun; Porrati, Massimo

2015-10-01

We perform a canonical quantization of pure gravity on AdS 3 using as a technical tool its equivalence at the classical level with a Chern-Simons theory with gauge group SL(2,{R})× SL(2,{R}) . We first quantize the theory canonically on an asymptotically AdS space -which is topologically the real line times a Riemann surface with one connected boundary. Using the "constrain first" approach we reduce canonical quantization to quantization of orbits of the Virasoro group and Kähler quantization of Teichmüller space. After explicitly computing the Kähler form for the torus with one boundary component and after extending that result to higher genus, we recover known results, such as that wave functions of SL(2,{R}) Chern-Simons theory are conformal blocks. We find new restrictions on the Hilbert space of pure gravity by imposing invariance under large diffeomorphisms and normalizability of the wave function. The Hilbert space of pure gravity is shown to be the target space of Conformal Field Theories with continuous spectrum and a lower bound on operator dimensions. A projection defined by topology changing amplitudes in Euclidean gravity is proposed. It defines an invariant subspace that allows for a dual interpretation in terms of a Liouville CFT. Problems and features of the CFT dual are assessed and a new definition of the Hilbert space, exempt from those problems, is proposed in the case of highly-curved AdS 3.

Asynchronous, Decentralized DS-CDMA Using Feedback-Controlled Spreading Sequences for Time-Dispersive Channels

NASA Astrophysics Data System (ADS)

Miyatake, Teruhiko; Chiba, Kazuki; Hamamura, Masanori; Tachikawa, Shin'ichi

We propose a novel asynchronous direct-sequence codedivision multiple access (DS-CDMA) using feedback-controlled spreading sequences (FCSSs) (FCSS/DS-CDMA). At the receiver of FCSS/DS-CDMA, the code-orthogonalizing filter (COF) produces a spreading sequence, and the receiver returns the spreading sequence to the transmitter. Then the transmitter uses the spreading sequence as its updated version. The performance of FCSS/DS-CDMA is evaluated over time-dispersive channels. The results indicate that FCSS/DS-CDMA greatly suppresses both the intersymbol interference (ISI) and multiple access interference (MAI) over time-invariant channels. FCSS/DS-CDMA is applicable to the decentralized multiple access.

Fluid Registration of Diffusion Tensor Images Using Information Theory

PubMed Central

Chiang, Ming-Chang; Leow, Alex D.; Klunder, Andrea D.; Dutton, Rebecca A.; Barysheva, Marina; Rose, Stephen E.; McMahon, Katie L.; de Zubicaray, Greig I.; Toga, Arthur W.; Thompson, Paul M.

2008-01-01

We apply an information-theoretic cost metric, the symmetrized Kullback-Leibler (sKL) divergence, or J-divergence, to fluid registration of diffusion tensor images. The difference between diffusion tensors is quantified based on the sKL-divergence of their associated probability density functions (PDFs). Three-dimensional DTI data from 34 subjects were fluidly registered to an optimized target image. To allow large image deformations but preserve image topology, we regularized the flow with a large-deformation diffeomorphic mapping based on the kinematics of a Navier-Stokes fluid. A driving force was developed to minimize the J-divergence between the deforming source and target diffusion functions, while reorienting the flowing tensors to preserve fiber topography. In initial experiments, we showed that the sKL-divergence based on full diffusion PDFs is adaptable to higher-order diffusion models, such as high angular resolution diffusion imaging (HARDI). The sKL-divergence was sensitive to subtle differences between two diffusivity profiles, showing promise for nonlinear registration applications and multisubject statistical analysis of HARDI data. PMID:18390342

Quantum Gravity, Information Theory and the CMB

NASA Astrophysics Data System (ADS)

Kempf, Achim

2018-04-01

We review connections between the metric of spacetime and the quantum fluctuations of fields. We start with the finding that the spacetime metric can be expressed entirely in terms of the 2-point correlator of the fluctuations of quantum fields. We then discuss the open question whether the knowledge of only the spectra of the quantum fluctuations of fields also suffices to determine the spacetime metric. This question is of interest because spectra are geometric invariants and their quantization would, therefore, have the benefit of not requiring the modding out of diffeomorphisms. Further, we discuss the fact that spacetime at the Planck scale need not necessarily be either discrete or continuous. Instead, results from information theory show that spacetime may be simultaneously discrete and continuous in the same way that information can. Finally, we review the recent finding that a covariant natural ultraviolet cutoff at the Planck scale implies a signature in the cosmic microwave background (CMB) that may become observable.

Automatic categorization of anatomical landmark-local appearances based on diffeomorphic demons and spectral clustering for constructing detector ensembles.

PubMed

Hanaoka, Shouhei; Masutani, Yoshitaka; Nemoto, Mitsutaka; Nomura, Yukihiro; Yoshikawa, Takeharu; Hayashi, Naoto; Ohtomo, Kuni

2012-01-01

A method for categorizing landmark-local appearances extracted from computed tomography (CT) datasets is presented. Anatomical landmarks in the human body inevitably have inter-individual variations that cause difficulty in automatic landmark detection processes. The goal of this study is to categorize subjects (i.e., training datasets) according to local shape variations of such a landmark so that each subgroup has less shape variation and thus the machine learning of each landmark detector is much easier. The similarity between each subject pair is measured based on the non-rigid registration result between them. These similarities are used by the spectral clustering process. After the clustering, all training datasets in each cluster, as well as synthesized intermediate images calculated from all subject-pairs in the cluster, are used to train the corresponding subgroup detector. All of these trained detectors compose a detector ensemble to detect the target landmark. Evaluation with clinical CT datasets showed great improvement in the detection performance.

Groupwise shape analysis of the hippocampus using spectral matching

NASA Astrophysics Data System (ADS)

Shakeri, Mahsa; Lombaert, Hervé; Lippé, Sarah; Kadoury, Samuel

2014-03-01

The hippocampus is a prominent subcortical feature of interest in many neuroscience studies. Its subtle morphological changes often predicate illnesses, including Alzheimer's, schizophrenia or epilepsy. The precise location of structural differences requires a reliable correspondence between shapes across a population. In this paper, we propose an automated method for groupwise hippocampal shape analysis based on a spectral decomposition of a group of shapes to solve the correspondence problem between sets of meshes. The framework generates diffeomorphic correspondence maps across a population, which enables us to create a mean shape. Morphological changes are then located between two groups of subjects. The performance of the proposed method was evaluated on a dataset of 42 hippocampus shapes and compared with a state-of-the-art structural shape analysis approach, using spherical harmonics. Difference maps between mean shapes of two test groups demonstrates that the two approaches showed results with insignificant differences, while Gaussian curvature measures calculated between matched vertices showed a better fit and reduced variability with spectral matching.

Perfect discretization of reparametrization invariant path integrals

NASA Astrophysics Data System (ADS)

Bahr, Benjamin; Dittrich, Bianca; Steinhaus, Sebastian

2011-05-01

To obtain a well-defined path integral one often employs discretizations. In the case of gravity and reparametrization-invariant systems, the latter of which we consider here as a toy example, discretizations generically break diffeomorphism and reparametrization symmetry, respectively. This has severe implications, as these symmetries determine the dynamics of the corresponding system. Indeed we will show that a discretized path integral with reparametrization-invariance is necessarily also discretization independent and therefore uniquely determined by the corresponding continuum quantum mechanical propagator. We use this insight to develop an iterative method for constructing such a discretized path integral, akin to a Wilsonian RG flow. This allows us to address the problem of discretization ambiguities and of an anomaly-free path integral measure for such systems. The latter is needed to obtain a path integral, that can act as a projector onto the physical states, satisfying the quantum constraints. We will comment on implications for discrete quantum gravity models, such as spin foams.

Lie-Hamilton systems on the plane: Properties, classification and applications

NASA Astrophysics Data System (ADS)

Ballesteros, A.; Blasco, A.; Herranz, F. J.; de Lucas, J.; Sardón, C.

2015-04-01

We study Lie-Hamilton systems on the plane, i.e. systems of first-order differential equations describing the integral curves of a t-dependent vector field taking values in a finite-dimensional real Lie algebra of planar Hamiltonian vector fields with respect to a Poisson structure. We start with the local classification of finite-dimensional real Lie algebras of vector fields on the plane obtained in González-López, Kamran, and Olver (1992) [23] and we interpret their results as a local classification of Lie systems. By determining which of these real Lie algebras consist of Hamiltonian vector fields relative to a Poisson structure, we provide the complete local classification of Lie-Hamilton systems on the plane. We present and study through our results new Lie-Hamilton systems of interest which are used to investigate relevant non-autonomous differential equations, e.g. we get explicit local diffeomorphisms between such systems. We also analyse biomathematical models, the Milne-Pinney equations, second-order Kummer-Schwarz equations, complex Riccati equations and Buchdahl equations.

Kinematic space for conical defects

NASA Astrophysics Data System (ADS)

Cresswell, Jesse C.; Peet, Amanda W.

2017-11-01

Kinematic space can be used as an intermediate step in the AdS/CFT dictionary and lends itself naturally to the description of diffeomorphism invariant quantities. From the bulk it has been defined as the space of boundary anchored geodesics, and from the boundary as the space of pairs of CFT points. When the bulk is not globally AdS3 the appearance of non-minimal geodesics leads to ambiguities in these definitions. In this work conical defect spacetimes are considered as an example where non-minimal geodesics are common. From the bulk it is found that the conical defect kinematic space can be obtained from the AdS3 kinematic space by the same quotient under which one obtains the defect from AdS3. The resulting kinematic space is one of many equivalent fundamental regions. From the boundary the conical defect kinematic space can be determined by breaking up OPE blocks into contributions from individual bulk geodesics. A duality is established between partial OPE blocks and bulk fields integrated over individual geodesics, minimal or non-minimal.

Exotic differentiable structures and general relativity

NASA Astrophysics Data System (ADS)

Brans, Carl H.; Randall, Duane

1993-02-01

We review recent developments in differential topology with special concern for their possible significance to physical theories, especially general relativity. In particular we are concerned here with the discovery of the existence of non-standard (“fake” or “exotic”) differentiable structures on topologically simple manifolds such asS 7, ℝ4 andS 3 X ℝ1. Because of the technical difficulties involved in the smooth case, we begin with an easily understood toy example looking at the role which the choice of complex structures plays in the formulation of two-dimensional vacuum electrostatics. We then briefly review the mathematical formalisms involved with differentiable structures on topological manifolds, diffeomorphisms and their significance for physics. We summarize the important work of Milnor, Freedman, Donaldson, and others in developing exotic differentiable structures on well known topological manifolds. Finally, we discuss some of the geometric implications of these results and propose some conjectures on possible physical implications of these new manifolds which have never before been considered as physical models.

Observational constraints on transverse gravity: A generalization of unimodular gravity

NASA Astrophysics Data System (ADS)

Lopez-Villarejo, J. J.

2010-04-01

We explore the hypothesis that the set of symmetries enjoyed by the theory that describes gravity is not the full group of diffeomorphisms (Diff(M)), as in General Relativity, but a maximal subgroup of it (TransverseDiff(M)), with its elements having a jacobian equal to unity; at the infinitesimal level, the parameter describing the coordinate change xμ → xμ + ξμ(x) is transverse, i.e., δμξμ = 0. Incidentally, this is the smaller symmetry one needs to propagate consistently a graviton, which is a great theoretical motivation for considering these theories. Also, the determinant of the metric, g, behaves as a "transverse scalar", so that these theories can be seen as a generalization of the better-known unimodular gravity. We present our results on the observational constraints on transverse gravity, in close relation with the claim of equivalence with general scalar-tensor theory. We also comment on the structure of the divergences of the quantum theory to the one-loop order.

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

PubMed Central

Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

2015-01-01

Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time). Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25838465

Evaluation of 2-point, 3-point, and 6-point Dixon magnetic resonance imaging with flexible echo timing for muscle fat quantification.

PubMed

Grimm, Alexandra; Meyer, Heiko; Nickel, Marcel D; Nittka, Mathias; Raithel, Esther; Chaudry, Oliver; Friedberger, Andreas; Uder, Michael; Kemmler, Wolfgang; Quick, Harald H; Engelke, Klaus

2018-06-01

The purpose of this study is to evaluate and compare 2-point (2pt), 3-point (3pt), and 6-point (6pt) Dixon magnetic resonance imaging (MRI) sequences with flexible echo times (TE) to measure proton density fat fraction (PDFF) within muscles. Two subject groups were recruited (G1: 23 young and healthy men, 31 ± 6 years; G2: 50 elderly men, sarcopenic, 77 ± 5 years). A 3-T MRI system was used to perform Dixon imaging on the left thigh. PDFF was measured with six Dixon prototype sequences: 2pt, 3pt, and 6pt sequences once with optimal TEs (in- and opposed-phase echo times), lower resolution, and higher bandwidth (optTE sequences) and once with higher image resolution (highRes sequences) and shortest possible TE, respectively. Intra-fascia PDFF content was determined. To evaluate the comparability among the sequences, Bland-Altman analysis was performed. The highRes 6pt Dixon sequences served as reference as a high correlation of this sequence to magnetic resonance spectroscopy has been shown before. The PDFF difference between the highRes 6pt Dixon sequence and the optTE 6pt, both 3pt, and the optTE 2pt was low (between 2.2% and 4.4%), however, not to the highRes 2pt Dixon sequence (33%). For the optTE sequences, difference decreased with the number of echoes used. In conclusion, for Dixon sequences with more than two echoes, the fat fraction measurement was reliable with arbitrary echo times, while for 2pt Dixon sequences, it was reliable with dedicated in- and opposed-phase echo timing. Copyright © 2018 Elsevier B.V. All rights reserved.

SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

PubMed

Korpar, Matija; Šošić, Martin; Blažeka, Dino; Šikić, Mile

2015-01-01

In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases.

Streaming fragment assignment for real-time analysis of sequencing experiments

PubMed Central

Roberts, Adam; Pachter, Lior

2013-01-01

We present eXpress, a software package for highly efficient probabilistic assignment of ambiguously mapping sequenced fragments. eXpress uses a streaming algorithm with linear run time and constant memory use. It can determine abundances of sequenced molecules in real time, and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data. We demonstrate its use on RNA-seq data, showing greater efficiency than other quantification methods. PMID:23160280

Musical Scales in Tone Sequences Improve Temporal Accuracy.

PubMed

Li, Min S; Di Luca, Massimiliano

2018-01-01

Predicting the time of stimulus onset is a key component in perception. Previous investigations of perceived timing have focused on the effect of stimulus properties such as rhythm and temporal irregularity, but the influence of non-temporal properties and their role in predicting stimulus timing has not been exhaustively considered. The present study aims to understand how a non-temporal pattern in a sequence of regularly timed stimuli could improve or bias the detection of temporal deviations. We presented interspersed sequences of 3, 4, 5, and 6 auditory tones where only the timing of the last stimulus could slightly deviate from isochrony. Participants reported whether the last tone was 'earlier' or 'later' relative to the expected regular timing. In two conditions, the tones composing the sequence were either organized into musical scales or they were random tones. In one experiment, all sequences ended with the same tone; in the other experiment, each sequence ended with a different tone. Results indicate higher discriminability of anisochrony with musical scales and with longer sequences, irrespective of the knowledge of the final tone. Such an outcome suggests that the predictability of non-temporal properties, as enabled by the musical scale pattern, can be a factor in determining the sensitivity of time judgments.

Time-of-flight radio location system

DOEpatents

McEwan, T.E.

1996-04-23

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence. 7 figs.

Time-of-flight radio location system

DOEpatents

McEwan, Thomas E.

1996-01-01

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence.

Effects of Sequences of Cognitions on Group Performance Over Time

PubMed Central

Molenaar, Inge; Chiu, Ming Ming

2017-01-01

Extending past research showing that sequences of low cognitions (low-level processing of information) and high cognitions (high-level processing of information through questions and elaborations) influence the likelihoods of subsequent high and low cognitions, this study examines whether sequences of cognitions are related to group performance over time; 54 primary school students (18 triads) discussed and wrote an essay about living in another country (32,375 turns of talk). Content analysis and statistical discourse analysis showed that within each lesson, groups with more low cognitions or more sequences of low cognition followed by high cognition added more essay words. Groups with more high cognitions, sequences of low cognition followed by low cognition, or sequences of high cognition followed by an action followed by low cognition, showed different words and sequences, suggestive of new ideas. The links between cognition sequences and group performance over time can inform facilitation and assessment of student discussions. PMID:28490854

Effects of Sequences of Cognitions on Group Performance Over Time.

PubMed

Molenaar, Inge; Chiu, Ming Ming

2017-04-01

Extending past research showing that sequences of low cognitions (low-level processing of information) and high cognitions (high-level processing of information through questions and elaborations) influence the likelihoods of subsequent high and low cognitions, this study examines whether sequences of cognitions are related to group performance over time; 54 primary school students (18 triads) discussed and wrote an essay about living in another country (32,375 turns of talk). Content analysis and statistical discourse analysis showed that within each lesson, groups with more low cognitions or more sequences of low cognition followed by high cognition added more essay words. Groups with more high cognitions, sequences of low cognition followed by low cognition, or sequences of high cognition followed by an action followed by low cognition, showed different words and sequences, suggestive of new ideas. The links between cognition sequences and group performance over time can inform facilitation and assessment of student discussions.

Cell assembly sequences arising from spike threshold adaptation keep track of time in the hippocampus

PubMed Central

Itskov, Vladimir; Curto, Carina; Pastalkova, Eva; Buzsáki, György

2011-01-01

Hippocampal neurons can display reliable and long-lasting sequences of transient firing patterns, even in the absence of changing external stimuli. We suggest that time-keeping is an important function of these sequences, and propose a network mechanism for their generation. We show that sequences of neuronal assemblies recorded from rat hippocampal CA1 pyramidal cells can reliably predict elapsed time (15-20 sec) during wheel running with a precision of 0.5sec. In addition, we demonstrate the generation of multiple reliable, long-lasting sequences in a recurrent network model. These sequences are generated in the presence of noisy, unstructured inputs to the network, mimicking stationary sensory input. Identical initial conditions generate similar sequences, whereas different initial conditions give rise to distinct sequences. The key ingredients responsible for sequence generation in the model are threshold-adaptation and a Mexican-hat-like pattern of connectivity among pyramidal cells. This pattern may arise from recurrent systems such as the hippocampal CA3 region or the entorhinal cortex. We hypothesize that mechanisms that evolved for spatial navigation also support tracking of elapsed time in behaviorally relevant contexts. PMID:21414904

Augmented brain function by coordinated reset stimulation with slowly varying sequences.

PubMed

Zeitler, Magteld; Tass, Peter A

2015-01-01

Several brain disorders are characterized by abnormally strong neuronal synchrony. Coordinated Reset (CR) stimulation was developed to selectively counteract abnormal neuronal synchrony by desynchronization. For this, phase resetting stimuli are delivered to different subpopulations in a timely coordinated way. In neural networks with spike timing-dependent plasticity CR stimulation may eventually lead to an anti-kindling, i.e., an unlearning of abnormal synaptic connectivity and abnormal synchrony. The spatiotemporal sequence by which all stimulation sites are stimulated exactly once is called the stimulation site sequence, or briefly sequence. So far, in simulations, pre-clinical and clinical applications CR was applied either with fixed sequences or rapidly varying sequences (RVS). In this computational study we show that appropriate repetition of the sequence with occasional random switching to the next sequence may significantly improve the anti-kindling effect of CR. To this end, a sequence is applied many times before randomly switching to the next sequence. This new method is called SVS CR stimulation, i.e., CR with slowly varying sequences. In a neuronal network with strong short-range excitatory and weak long-range inhibitory dynamic couplings SVS CR stimulation turns out to be superior to CR stimulation with fixed sequences or RVS.

Augmented brain function by coordinated reset stimulation with slowly varying sequences

PubMed Central

Zeitler, Magteld; Tass, Peter A.

2015-01-01

Several brain disorders are characterized by abnormally strong neuronal synchrony. Coordinated Reset (CR) stimulation was developed to selectively counteract abnormal neuronal synchrony by desynchronization. For this, phase resetting stimuli are delivered to different subpopulations in a timely coordinated way. In neural networks with spike timing-dependent plasticity CR stimulation may eventually lead to an anti-kindling, i.e., an unlearning of abnormal synaptic connectivity and abnormal synchrony. The spatiotemporal sequence by which all stimulation sites are stimulated exactly once is called the stimulation site sequence, or briefly sequence. So far, in simulations, pre-clinical and clinical applications CR was applied either with fixed sequences or rapidly varying sequences (RVS). In this computational study we show that appropriate repetition of the sequence with occasional random switching to the next sequence may significantly improve the anti-kindling effect of CR. To this end, a sequence is applied many times before randomly switching to the next sequence. This new method is called SVS CR stimulation, i.e., CR with slowly varying sequences. In a neuronal network with strong short-range excitatory and weak long-range inhibitory dynamic couplings SVS CR stimulation turns out to be superior to CR stimulation with fixed sequences or RVS. PMID:25873867

Sequence learning in Parkinson's disease: Focusing on action dynamics and the role of dopaminergic medication.

PubMed

Ruitenberg, Marit F L; Duthoo, Wout; Santens, Patrick; Seidler, Rachael D; Notebaert, Wim; Abrahamse, Elger L

2016-12-01

Previous studies on movement sequence learning in Parkinson's disease (PD) have produced mixed results. A possible explanation for the inconsistent findings is that some studies have taken dopaminergic medication into account while others have not. Additionally, in previous studies the response modalities did not allow for an investigation of the action dynamics of sequential movements as they unfold over time. In the current study we investigated sequence learning in PD by specifically considering the role of medication status in a sequence learning task where mouse movements were performed. The focus on mouse movements allowed us to examine the action dynamics of sequential movement in terms of initiation time, movement time, movement accuracy, and velocity. PD patients performed the sequence learning task once on their regular medication, and once after overnight withdrawal from their medication. Results showed that sequence learning as reflected in initiation times was impaired when PD patients performed the task ON medication compared to OFF medication. In contrast, sequence learning as reflected in the accuracy of movement trajectories was enhanced when performing the task ON compared to OFF medication. Our findings suggest that while medication enhances execution processes of movement sequence learning, it may at the same time impair planning processes that precede actual execution. Overall, the current study extends earlier findings on movement sequence learning in PD by differentiating between various components of performance, and further refines previous dopamine overdose effects in sequence learning. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cluster-Based Multipolling Sequencing Algorithm for Collecting RFID Data in Wireless LANs

NASA Astrophysics Data System (ADS)

Choi, Woo-Yong; Chatterjee, Mainak

2015-03-01

With the growing use of RFID (Radio Frequency Identification), it is becoming important to devise ways to read RFID tags in real time. Access points (APs) of IEEE 802.11-based wireless Local Area Networks (LANs) are being integrated with RFID networks that can efficiently collect real-time RFID data. Several schemes, such as multipolling methods based on the dynamic search algorithm and random sequencing, have been proposed. However, as the number of RFID readers associated with an AP increases, it becomes difficult for the dynamic search algorithm to derive the multipolling sequence in real time. Though multipolling methods can eliminate the polling overhead, we still need to enhance the performance of the multipolling methods based on random sequencing. To that extent, we propose a real-time cluster-based multipolling sequencing algorithm that drastically eliminates more than 90% of the polling overhead, particularly so when the dynamic search algorithm fails to derive the multipolling sequence in real time.

Development of a real-time PCR for detection of Staphylococcus pseudintermedius using a novel automated comparison of whole-genome sequences.

PubMed

Verstappen, Koen M; Huijbregts, Loes; Spaninks, Mirlin; Wagenaar, Jaap A; Fluit, Ad C; Duim, Birgitta

2017-01-01

Staphylococcus pseudintermedius is an opportunistic pathogen in dogs and cats and occasionally causes infections in humans. S. pseudintermedius is often resistant to multiple classes of antimicrobials. It requires a reliable detection so that it is not misidentified as S. aureus. Phenotypic and currently-used molecular-based diagnostic assays lack specificity or are labour-intensive using multiplex PCR or nucleic acid sequencing. The aim of this study was to identify a specific target for real-time PCR by comparing whole genome sequences of S. pseudintermedius and non-pseudintermedius.Genome sequences were downloaded from public repositories and supplemented by isolates that were sequenced in this study. A Perl-script was written that analysed 300-nt fragments from a reference genome sequence of S. pseudintermedius and checked if this sequence was present in other S. pseudintermedius genomes (n = 74) and non-pseudintermedius genomes (n = 138). Six sequences specific for S. pseudintermedius were identified (sequence length between 300-500 nt). One sequence, which was located in the spsJ gene, was used to develop primers and a probe. The real-time PCR showed 100% specificity when testing for S. pseudintermedius isolates (n = 54), and eight other staphylococcal species (n = 43). In conclusion, a novel approach by comparing whole genome sequences identified a sequence that is specific for S. pseudintermedius and provided a real-time PCR target for rapid and reliable detection of S. pseudintermedius.

SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets.

PubMed

Yu, Qiang; Wei, Dingbang; Huo, Hongwei

2018-06-18

Given a set of t n-length DNA sequences, q satisfying 0 < q ≤ 1, and l and d satisfying 0 ≤ d < l < n, the quorum planted motif search (qPMS) finds l-length strings that occur in at least qt input sequences with up to d mismatches and is mainly used to locate transcription factor binding sites in DNA sequences. Existing qPMS algorithms have been able to efficiently process small standard datasets (e.g., t = 20 and n = 600), but they are too time consuming to process large DNA datasets, such as ChIP-seq datasets that contain thousands of sequences or more. We analyze the effects of t and q on the time performance of qPMS algorithms and find that a large t or a small q causes a longer computation time. Based on this information, we improve the time performance of existing qPMS algorithms by selecting a sample sequence set D' with a small t and a large q from the large input dataset D and then executing qPMS algorithms on D'. A sample sequence selection algorithm named SamSelect is proposed. The experimental results on both simulated and real data show (1) that SamSelect can select D' efficiently and (2) that the qPMS algorithms executed on D' can find implanted or real motifs in a significantly shorter time than when executed on D. We improve the ability of existing qPMS algorithms to process large DNA datasets from the perspective of selecting high-quality sample sequence sets so that the qPMS algorithms can find motifs in a short time in the selected sample sequence set D', rather than take an unfeasibly long time to search the original sequence set D. Our motif discovery method is an approximate algorithm.

Neural correlates of skill acquisition: decreased cortical activity during a serial interception sequence learning task.

PubMed

Gobel, Eric W; Parrish, Todd B; Reber, Paul J

2011-10-15

Learning of complex motor skills requires learning of component movements as well as the sequential structure of their order and timing. Using a Serial Interception Sequence Learning (SISL) task, participants learned a sequence of precisely timed interception responses through training with a repeating sequence. Following initial implicit learning of the repeating sequence, functional MRI data were collected during performance of that known sequence and compared with activity evoked during novel sequences of actions, novel timing patterns, or both. Reduced activity was observed during the practiced sequence in a distributed bilateral network including extrastriate occipital, parietal, and premotor cortical regions. These reductions in evoked activity likely reflect improved efficiency in visuospatial processing, spatio-motor integration, motor planning, and motor execution for the trained sequence, which is likely supported by nondeclarative skill learning. In addition, the practiced sequence evoked increased activity in the left ventral striatum and medial prefrontal cortex, while the posterior cingulate was more active during periods of better performance. Many prior studies of perceptual-motor skill learning have found increased activity in motor areas of the frontal cortex (e.g., motor and premotor cortex, SMA) and striatal areas (e.g., the putamen). The change in activity observed here (i.e., decreased activity across a cortical network) may reflect skill learning that is predominantly expressed through more accurate performance rather than decreased reaction time. Copyright © 2011 Elsevier Inc. All rights reserved.

Neural Correlates of Skill Acquisition: Decreased Cortical Activity During a Serial Interception Sequence Learning Task

PubMed Central

Gobel, Eric W.; Parrish, Todd B.; Reber, Paul J.

2011-01-01

Learning of complex motor skills requires learning of component movements as well as the sequential structure of their order and timing. Using a Serial Interception Sequence Learning (SISL) task, participants learned a sequence of precisely timed interception responses through training with a repeating sequence. Following initial implicit learning of the repeating sequence, functional MRI data were collected during performance of that known sequence and compared with activity evoked during novel sequences of actions, novel timing patterns, or both. Reduced activity was observed during the practiced sequence in a distributed bilateral network including extrastriate occipital, parietal, and premotor cortical regions. These reductions in evoked activity likely reflect improved efficiency in visuospatial processing, spatio-motor integration, motor planning, and motor execution for the trained sequence, which is likely supported by nondeclarative skill learning. In addition, the practiced sequence evoked increased activity in the left ventral striatum and medial prefrontal cortex, while the posterior cingulate was more active during periods of better performance. Many prior studies of perceptual-motor skill learning have found increased activity in motor areas of frontal cortex (e.g., motor and premotor cortex, SMA) and striatal areas (e.g., the putamen). The change in activity observed here (i.e., decreased activity across a cortical network) may reflect skill learning that is predominantly expressed through more accurate performance rather than decreased reaction time. PMID:21771663

An ultra-sparse code underliesthe generation of neural sequences in a songbird

NASA Astrophysics Data System (ADS)

Hahnloser, Richard H. R.; Kozhevnikov, Alexay A.; Fee, Michale S.

2002-09-01

Sequences of motor activity are encoded in many vertebrate brains by complex spatio-temporal patterns of neural activity; however, the neural circuit mechanisms underlying the generation of these pre-motor patterns are poorly understood. In songbirds, one prominent site of pre-motor activity is the forebrain robust nucleus of the archistriatum (RA), which generates stereotyped sequences of spike bursts during song and recapitulates these sequences during sleep. We show that the stereotyped sequences in RA are driven from nucleus HVC (high vocal centre), the principal pre-motor input to RA. Recordings of identified HVC neurons in sleeping and singing birds show that individual HVC neurons projecting onto RA neurons produce bursts sparsely, at a single, precise time during the RA sequence. These HVC neurons burst sequentially with respect to one another. We suggest that at each time in the RA sequence, the ensemble of active RA neurons is driven by a subpopulation of RA-projecting HVC neurons that is active only at that time. As a population, these HVC neurons may form an explicit representation of time in the sequence. Such a sparse representation, a temporal analogue of the `grandmother cell' concept for object recognition, eliminates the problem of temporal interference during sequence generation and learning attributed to more distributed representations.

Automated landmarking and geometric characterization of the carotid siphon.

PubMed

Bogunović, Hrvoje; Pozo, José María; Cárdenes, Rubén; Villa-Uriol, María Cruz; Blanc, Raphaël; Piotin, Michel; Frangi, Alejandro F

2012-05-01

The geometry of the carotid siphon has a large variability between subjects, which has prompted its study as a potential geometric risk factor for the onset of vascular pathologies on and off the internal carotid artery (ICA). In this work, we present a methodology for an objective and extensive geometric characterization of carotid siphon parameterized by a set of anatomical landmarks. We introduce a complete and automated characterization pipeline. Starting from the segmentation of vasculature from angiographic image and its centerline extraction, we first identify ICA by characterizing vessel tree bifurcations and training a support vector machine classifier to detect ICA terminal bifurcation. On ICA centerline curve, we detect anatomical landmarks of carotid siphon by modeling it as a sequence of four bends and selecting their centers and interfaces between them. Bends are detected from the trajectory of the curvature vector expressed in the parallel transport frame of the curve. Finally, using the detected landmarks, we characterize the geometry in two complementary ways. First, with a set of local and global geometric features, known to affect hemodynamics. Second, using large deformation diffeomorphic metric curve mapping (LDDMCM) to quantify pairwise shape similarity. We processed 96 images acquired with 3D rotational angiography. ICA identification had a cross-validation success rate of 99%. Automated landmarking was validated by computing limits of agreement with the reference taken to be the locations of the manually placed landmarks averaged across multiple observers. For all but one landmark, either the bias was not statistically significant or the variability was within 50% of the inter-observer one. The subsequently computed values of geometric features and LDDMCM were commensurate to the ones obtained with manual landmarking. The characterization based on pair-wise LDDMCM proved better in classifying the carotid siphon shape classes than the one based on geometric features. The proposed characterization provides a rich description of geometry and is ready to be applied in the search for geometric risk factors of the carotid siphon. Copyright © 2012 Elsevier B.V. All rights reserved.

Glutenite bodies sequence division of the upper Es4 in northern Minfeng zone of Dongying Sag, Bohai Bay Basin, China

NASA Astrophysics Data System (ADS)

Shao, Xupeng

2017-04-01

Glutenite bodies are widely developed in northern Minfeng zone of Dongying Sag. Their litho-electric relationship is not clear. In addition, as the conventional sequence stratigraphic research method drawbacks of involving too many subjective human factors, it has limited deepening of the regional sequence stratigraphic research. The wavelet transform technique based on logging data and the time-frequency analysis technique based on seismic data have advantages of dividing sequence stratigraphy quantitatively comparing with the conventional methods. Under the basis of the conventional sequence research method, this paper used the above techniques to divide the fourth-order sequence of the upper Es4 in northern Minfeng zone of Dongying Sag. The research shows that the wavelet transform technique based on logging data and the time-frequency analysis technique based on seismic data are essentially consistent, both of which divide sequence stratigraphy quantitatively in the frequency domain; wavelet transform technique has high resolutions. It is suitable for areas with wells. The seismic time-frequency analysis technique has wide applicability, but a low resolution. Both of the techniques should be combined; the upper Es4 in northern Minfeng zone of Dongying Sag is a complete set of third-order sequence, which can be further subdivided into 5 fourth-order sequences that has the depositional characteristics of fine-upward sequence in granularity. Key words: Dongying sag, northern Minfeng zone, wavelet transform technique, time-frequency analysis technique ,the upper Es4, sequence stratigraphy

Sequence search on a supercomputer.

PubMed

Gotoh, O; Tagashira, Y

1986-01-10

A set of programs was developed for searching nucleic acid and protein sequence data bases for sequences similar to a given sequence. The programs, written in FORTRAN 77, were optimized for vector processing on a Hitachi S810-20 supercomputer. A search of a 500-residue protein sequence against the entire PIR data base Ver. 1.0 (1) (0.5 M residues) is carried out in a CPU time of 45 sec. About 4 min is required for an exhaustive search of a 1500-base nucleotide sequence against all mammalian sequences (1.2M bases) in Genbank Ver. 29.0. The CPU time is reduced to about a quarter with a faster version.

Chronology of Eocene-Miocene sequences on the New Jersey shallow shelf: implications for regional, interregional, and global correlations

USGS Publications Warehouse

Browning, James V.; Miller, Kenneth G.; Sugarman, Peter J.; Barron, John; McCarthy, Francine M.G.; Kulhanek, Denise K.; Katz, Miriam E.; Feigenson, Mark D.

2013-01-01

Integrated Ocean Drilling Program Expedition 313 continuously cored and logged latest Eocene to early-middle Miocene sequences at three sites (M27, M28, and M29) on the inner-middle continental shelf offshore New Jersey, providing an opportunity to evaluate the ages, global correlations, and significance of sequence boundaries. We provide a chronology for these sequences using integrated strontium isotopic stratigraphy and biostratigraphy (primarily calcareous nannoplankton, diatoms, and dinocysts [dinoflagellate cysts]). Despite challenges posed by shallow-water sediments, age resolution is typically ±0.5 m.y. and in many sequences is as good as ±0.25 m.y. Three Oligocene sequences were sampled at Site M27 on sequence bottomsets. Fifteen early to early-middle Miocene sequences were dated at Sites M27, M28, and M29 across clinothems in topsets, foresets (where the sequences are thickest), and bottomsets. A few sequences have coarse (∼1 m.y.) or little age constraint due to barren zones; we constrain the age estimates of these less well dated sequences by applying the principle of superposition, i.e., sediments above sequence boundaries in any site are younger than the sediments below the sequence boundaries at other sites. Our age control provides constraints on the timing of deposition in the clinothem; sequences on the topsets are generally the youngest in the clinothem, whereas the bottomsets generally are the oldest. The greatest amount of time is represented on foresets, although we have no evidence for a correlative conformity. Our chronology provides a baseline for regional and interregional correlations and sea-level reconstructions: (1) we correlate a major increase in sedimentation rate precisely with the timing of the middle Miocene climate changes associated with the development of a permanent East Antarctic Ice Sheet; and (2) the timing of sequence boundaries matches the deep-sea oxygen isotopic record, implicating glacioeustasy as a major driver for forming sequence boundaries.

The "Motor" in Implicit Motor Sequence Learning: A Foot-stepping Serial Reaction Time Task.

PubMed

Du, Yue; Clark, Jane E

2018-05-03

This protocol describes a modified serial reaction time (SRT) task used to study implicit motor sequence learning. Unlike the classic SRT task that involves finger-pressing movements while sitting, the modified SRT task requires participants to step with both feet while maintaining a standing posture. This stepping task necessitates whole body actions that impose postural challenges. The foot-stepping task complements the classic SRT task in several ways. The foot-stepping SRT task is a better proxy for the daily activities that require ongoing postural control, and thus may help us better understand sequence learning in real-life situations. In addition, response time serves as an indicator of sequence learning in the classic SRT task, but it is unclear whether response time, reaction time (RT) representing mental process, or movement time (MT) reflecting the movement itself, is a key player in motor sequence learning. The foot-stepping SRT task allows researchers to disentangle response time into RT and MT, which may clarify how motor planning and movement execution are involved in sequence learning. Lastly, postural control and cognition are interactively related, but little is known about how postural control interacts with learning motor sequences. With a motion capture system, the movement of the whole body (e.g., the center of mass (COM)) can be recorded. Such measures allow us to reveal the dynamic processes underlying discrete responses measured by RT and MT, and may aid in elucidating the relationship between postural control and the explicit and implicit processes involved in sequence learning. Details of the experimental set-up, procedure, and data processing are described. The representative data are adopted from one of our previous studies. Results are related to response time, RT, and MT, as well as the relationship between the anticipatory postural response and the explicit processes involved in implicit motor sequence learning.

DNA sequencing using polymerase substrate-binding kinetics

PubMed Central

Previte, Michael John Robert; Zhou, Chunhong; Kellinger, Matthew; Pantoja, Rigo; Chen, Cheng-Yao; Shi, Jin; Wang, BeiBei; Kia, Amirali; Etchin, Sergey; Vieceli, John; Nikoomanzar, Ali; Bomati, Erin; Gloeckner, Christian; Ronaghi, Mostafa; He, Molly Min

2015-01-01

Next-generation sequencing (NGS) has transformed genomic research by decreasing the cost of sequencing. However, whole-genome sequencing is still costly and complex for diagnostics purposes. In the clinical space, targeted sequencing has the advantage of allowing researchers to focus on specific genes of interest. Routine clinical use of targeted NGS mandates inexpensive instruments, fast turnaround time and an integrated and robust workflow. Here we demonstrate a version of the Sequencing by Synthesis (SBS) chemistry that potentially can become a preferred targeted sequencing method in the clinical space. This sequencing chemistry uses natural nucleotides and is based on real-time recording of the differential polymerase/DNA-binding kinetics in the presence of correct or mismatch nucleotides. This ensemble SBS chemistry has been implemented on an existing Illumina sequencing platform with integrated cluster amplification. We discuss the advantages of this sequencing chemistry for targeted sequencing as well as its limitations for other applications. PMID:25612848

Time-of-flight radio location system

DOEpatents

McEwan, T.E.

1997-08-26

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence. The sample signal in equivalent time is passed through an envelope detection circuit, formed of an absolute value circuit followed by a low pass filter, to convert the sample signal to a unipolar signal to eliminate effects of antenna misorientation. 8 figs.

Time-of-flight radio location system

DOEpatents

McEwan, Thomas E.

1997-01-01

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence. The sample signal in equivalent time is passed through an envelope detection circuit, formed of an absolute value circuit followed by a low pass filter, to convert the sample signal to a unipolar signal to eliminate effects of antenna misorientation.

tRNADB-CE: tRNA gene database well-timed in the era of big sequence data.

PubMed

Abe, Takashi; Inokuchi, Hachiro; Yamada, Yuko; Muto, Akira; Iwasaki, Yuki; Ikemura, Toshimichi

2014-01-01

The tRNA gene data base curated by experts "tRNADB-CE" (http://trna.ie.niigata-u.ac.jp) was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses', 121 chloroplasts', and 12 eukaryotes' genomes plus fragment sequences obtained by metagenome studies of environmental samples. 595,115 tRNA genes in total, and thus two times of genes compiled previously, have been registered, for which sequence, clover-leaf structure, and results of sequence-similarity and oligonucleotide-pattern searches can be browsed. To provide collective knowledge with help from experts in tRNA researches, we added a column for enregistering comments to each tRNA. By grouping bacterial tRNAs with an identical sequence, we have found high phylogenetic preservation of tRNA sequences, especially at the phylum level. Since many species-unknown tRNAs from metagenomic sequences have sequences identical to those found in species-known prokaryotes, the identical sequence group (ISG) can provide phylogenetic markers to investigate the microbial community in an environmental ecosystem. This strategy can be applied to a huge amount of short sequences obtained from next-generation sequencers, as showing that tRNADB-CE is a well-timed database in the era of big sequence data. It is also discussed that batch-learning self-organizing-map with oligonucleotide composition is useful for efficient knowledge discovery from big sequence data.

Renormalization in Quantum Field Theory and the Riemann-Hilbert Problem I: The Hopf Algebra Structure of Graphs and the Main Theorem

NASA Astrophysics Data System (ADS)

Connes, Alain; Kreimer, Dirk

This paper gives a complete selfcontained proof of our result announced in [6] showing that renormalization in quantum field theory is a special instance of a general mathematical procedure of extraction of finite values based on the Riemann-Hilbert problem. We shall first show that for any quantum field theory, the combinatorics of Feynman graphs gives rise to a Hopf algebra which is commutative as an algebra. It is the dual Hopf algebra of the enveloping algebra of a Lie algebra whose basis is labelled by the one particle irreducible Feynman graphs. The Lie bracket of two such graphs is computed from insertions of one graph in the other and vice versa. The corresponding Lie group G is the group of characters of . We shall then show that, using dimensional regularization, the bare (unrenormalized) theory gives rise to a loop where C is a small circle of complex dimensions around the integer dimension D of space-time. Our main result is that the renormalized theory is just the evaluation at z=D of the holomorphic part γ+ of the Birkhoff decomposition of γ. We begin to analyse the group G and show that it is a semi-direct product of an easily understood abelian group by a highly non-trivial group closely tied up with groups of diffeomorphisms. The analysis of this latter group as well as the interpretation of the renormalization group and of anomalous dimensions are the content of our second paper with the same overall title.

Spacetime completeness of non-singular black holes in conformal gravity

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

Bambi, Cosimo; Rachwał, Lesław; Modesto, Leonardo, E-mail: bambi@fudan.edu.cn, E-mail: lmodesto@sustc.edu.cn, E-mail: grzerach@gmail.com

We explicitly prove that the Weyl conformal symmetry solves the black hole singularity problem, otherwise unavoidable in a generally covariant local or non-local gravitational theory. Moreover, we yield explicit examples of local and non-local theories enjoying Weyl and diffeomorphism symmetry (in short co-covariant theories). Following the seminal paper by Narlikar and Kembhavi, we provide an explicit construction of singularity-free spherically symmetric and axi-symmetric exact solutions for black hole spacetimes conformally equivalent to the Schwarzschild or the Kerr spacetime. We first check the absence of divergences in the Kretschmann invariant for the rescaled metrics. Afterwords, we show that the new typesmore » of black holes are geodesically complete and linked by a Newman-Janis transformation just as in standard general relativity (based on Einstein-Hilbert action). Furthermore, we argue that no massive or massless particles can reach the former Schwarzschild singularity or touch the former Kerr ring singularity in a finite amount of their proper time or of their affine parameter. Finally, we discuss the Raychaudhuri equation in a co-covariant theory and we show that the expansion parameter for congruences of both types of geodesics (for massless and massive particles) never reaches minus infinity. Actually, the null geodesics become parallel at the r =0 point in the Schwarzschild spacetime (the origin) and the focusing of geodesics is avoided. The arguments of regularity of curvature invariants, geodesic completeness, and finiteness of geodesics' expansion parameter ensure us that we are dealing with singularity-free and geodesically-complete black hole spacetimes.« less

A DNA sequence element that advances replication origin activation time in Saccharomyces cerevisiae.

PubMed

Pohl, Thomas J; Kolor, Katherine; Fangman, Walton L; Brewer, Bonita J; Raghuraman, M K

2013-11-06

Eukaryotic origins of DNA replication undergo activation at various times in S-phase, allowing the genome to be duplicated in a temporally staggered fashion. In the budding yeast Saccharomyces cerevisiae, the activation times of individual origins are not intrinsic to those origins but are instead governed by surrounding sequences. Currently, there are two examples of DNA sequences that are known to advance origin activation time, centromeres and forkhead transcription factor binding sites. By combining deletion and linker scanning mutational analysis with two-dimensional gel electrophoresis to measure fork direction in the context of a two-origin plasmid, we have identified and characterized a 19- to 23-bp and a larger 584-bp DNA sequence that are capable of advancing origin activation time.

Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment

PubMed Central

2013-01-01

Background Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. Results In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Conclusion Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA. PMID:24564200

Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.

PubMed

Nagar, Anurag; Hahsler, Michael

2013-01-01

Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA.

Whole genome sequence analysis of unidentified genetically modified papaya for development of a specific detection method.

PubMed

Nakamura, Kosuke; Kondo, Kazunari; Akiyama, Hiroshi; Ishigaki, Takumi; Noguchi, Akio; Katsumata, Hiroshi; Takasaki, Kazuto; Futo, Satoshi; Sakata, Kozue; Fukuda, Nozomi; Mano, Junichi; Kitta, Kazumi; Tanaka, Hidenori; Akashi, Ryo; Nishimaki-Mogami, Tomoko

2016-08-15

Identification of transgenic sequences in an unknown genetically modified (GM) papaya (Carica papaya L.) by whole genome sequence analysis was demonstrated. Whole genome sequence data were generated for a GM-positive fresh papaya fruit commodity detected in monitoring using real-time polymerase chain reaction (PCR). The sequences obtained were mapped against an open database for papaya genome sequence. Transgenic construct- and event-specific sequences were identified as a GM papaya developed to resist infection from a Papaya ringspot virus. Based on the transgenic sequences, a specific real-time PCR detection method for GM papaya applicable to various food commodities was developed. Whole genome sequence analysis enabled identifying unknown transgenic construct- and event-specific sequences in GM papaya and development of a reliable method for detecting them in papaya food commodities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines.

PubMed

Oliveira, Francisco P M; Tavares, João Manuel R S

2013-03-01

This article presents an enhanced methodology to align plantar pressure image sequences simultaneously in time and space. The temporal alignment of the sequences is accomplished using B-splines in the time modeling, and the spatial alignment can be attained using several geometric transformation models. The methodology was tested on a dataset of 156 real plantar pressure image sequences (3 sequences for each foot of the 26 subjects) that was acquired using a common commercial plate during barefoot walking. In the alignment of image sequences that were synthetically deformed both in time and space, an outstanding accuracy was achieved with the cubic B-splines. This accuracy was significantly better (p < 0.001) than the one obtained using the best solution proposed in our previous work. When applied to align real image sequences with unknown transformation involved, the alignment based on cubic B-splines also achieved superior results than our previous methodology (p < 0.001). The consequences of the temporal alignment on the dynamic center of pressure (COP) displacement was also assessed by computing the intraclass correlation coefficients (ICC) before and after the temporal alignment of the three image sequence trials of each foot of the associated subject at six time instants. The results showed that, generally, the ICCs related to the medio-lateral COP displacement were greater when the sequences were temporally aligned than the ICCs of the original sequences. Based on the experimental findings, one can conclude that the cubic B-splines are a remarkable solution for the temporal alignment of plantar pressure image sequences. These findings also show that the temporal alignment can increase the consistency of the COP displacement on related acquired plantar pressure image sequences.

Demonstration of Nondeclarative Sequence Learning in Mice: Development of an Animal Analog of the Human Serial Reaction Time Task

ERIC Educational Resources Information Center

Christie, Michael A.; Hersch, Steven M.

2004-01-01

In this paper, we demonstrate nondeclarative sequence learning in mice using an animal analog of the human serial reaction time task (SRT) that uses a within-group comparison of behavior in response to a repeating sequence versus a random sequence. Ten female B6CBA mice performed eleven 96-trial sessions containing 24 repetitions of a 4-trial…

Analysis of delay reducing and fuel saving sequencing and spacing algorithms for arrival traffic

NASA Technical Reports Server (NTRS)

Neuman, Frank; Erzberger, Heinz

1991-01-01

The air traffic control subsystem that performs sequencing and spacing is discussed. The function of the sequencing and spacing algorithms is to automatically plan the most efficient landing order and to assign optimally spaced landing times to all arrivals. Several algorithms are described and their statistical performance is examined. Sequencing brings order to an arrival sequence for aircraft. First-come-first-served sequencing (FCFS) establishes a fair order, based on estimated times of arrival, and determines proper separations. Because of the randomness of the arriving traffic, gaps will remain in the sequence of aircraft. Delays are reduced by time-advancing the leading aircraft of each group while still preserving the FCFS order. Tightly spaced groups of aircraft remain with a mix of heavy and large aircraft. Spacing requirements differ for different types of aircraft trailing each other. Traffic is reordered slightly to take advantage of this spacing criterion, thus shortening the groups and reducing average delays. For heavy traffic, delays for different traffic samples vary widely, even when the same set of statistical parameters is used to produce each sample. This report supersedes NASA TM-102795 on the same subject. It includes a new method of time-advance as well as an efficient method of sequencing and spacing for two dependent runways.

A new molecular evolution model for limited insertion independent of substitution.

PubMed

Lèbre, Sophie; Michel, Christian J

2013-10-01

We recently introduced a new molecular evolution model called the IDIS model for Insertion Deletion Independent of Substitution [13,14]. In the IDIS model, the three independent processes of substitution, insertion and deletion of residues have constant rates. In order to control the genome expansion during evolution, we generalize here the IDIS model by introducing an insertion rate which decreases when the sequence grows and tends to 0 for a maximum sequence length nmax. This new model, called LIIS for Limited Insertion Independent of Substitution, defines a matrix differential equation satisfied by a vector P(t) describing the sequence content in each residue at evolution time t. An analytical solution is obtained for any diagonalizable substitution matrix M. Thus, the LIIS model gives an expression of the sequence content vector P(t) in each residue under evolution time t as a function of the eigenvalues and the eigenvectors of matrix M, the residue insertion rate vector R, the total insertion rate r, the initial and maximum sequence lengths n0 and nmax, respectively, and the sequence content vector P(t0) at initial time t0. The derivation of the analytical solution is much more technical, compared to the IDIS model, as it involves Gauss hypergeometric functions. Several propositions of the LIIS model are derived: proof that the IDIS model is a particular case of the LIIS model when the maximum sequence length nmax tends to infinity, fixed point, time scale, time step and time inversion. Using a relation between the sequence length l and the evolution time t, an expression of the LIIS model as a function of the sequence length l=n(t) is obtained. Formulas for 'insertion only', i.e. when the substitution rates are all equal to 0, are derived at evolution time t and sequence length l. Analytical solutions of the LIIS model are explicitly derived, as a function of either evolution time t or sequence length l, for two classical substitution matrices: the 3-parameter symmetric substitution matrix [12] (LIIS-SYM3) and the HKY asymmetric substitution matrix[9] (LIIS-HKY). An evaluation of the LIIS model (precisely, LIIS-HKY) based on four statistical analyses of the GC content in complete genomes of four prokaryotic taxonomic groups, namely Chlamydiae, Crenarchaeota, Spirochaetes and Thermotogae, shows the expected improvement from the theory of the LIIS model compared to the IDIS model. Copyright © 2013 Elsevier Inc. All rights reserved.

Periodic, On-Demand, and User-Specified Information Reconciliation

NASA Technical Reports Server (NTRS)

Kolano, Paul

2007-01-01

Automated sequence generation (autogen) signifies both a process and software used to automatically generate sequences of commands to operate various spacecraft. Autogen requires fewer workers than are needed for older manual sequence-generation processes and reduces sequence-generation times from weeks to minutes. The autogen software comprises the autogen script plus the Activity Plan Generator (APGEN) program. APGEN can be used for planning missions and command sequences. APGEN includes a graphical user interface that facilitates scheduling of activities on a time line and affords a capability to automatically expand, decompose, and schedule activities.

A DNA Sequence Element That Advances Replication Origin Activation Time in Saccharomyces cerevisiae

PubMed Central

Pohl, Thomas J.; Kolor, Katherine; Fangman, Walton L.; Brewer, Bonita J.; Raghuraman, M. K.

2013-01-01

Eukaryotic origins of DNA replication undergo activation at various times in S-phase, allowing the genome to be duplicated in a temporally staggered fashion. In the budding yeast Saccharomyces cerevisiae, the activation times of individual origins are not intrinsic to those origins but are instead governed by surrounding sequences. Currently, there are two examples of DNA sequences that are known to advance origin activation time, centromeres and forkhead transcription factor binding sites. By combining deletion and linker scanning mutational analysis with two-dimensional gel electrophoresis to measure fork direction in the context of a two-origin plasmid, we have identified and characterized a 19- to 23-bp and a larger 584-bp DNA sequence that are capable of advancing origin activation time. PMID:24022751

A space-efficient algorithm for local similarities.

PubMed

Huang, X Q; Hardison, R C; Miller, W

1990-10-01

Existing dynamic-programming algorithms for identifying similar regions of two sequences require time and space proportional to the product of the sequence lengths. Often this space requirement is more limiting than the time requirement. We describe a dynamic-programming local-similarity algorithm that needs only space proportional to the sum of the sequence lengths. The method can also find repeats within a single long sequence. To illustrate the algorithm's potential, we discuss comparison of a 73,360 nucleotide sequence containing the human beta-like globin gene cluster and a corresponding 44,594 nucleotide sequence for rabbit, a problem well beyond the capabilities of other dynamic-programming software.

[MRI of focal liver lesions using a 1.5 turbo-spin-echo technique compared with spin-echo technique].

PubMed

Steiner, S; Vogl, T J; Fischer, P; Steger, W; Neuhaus, P; Keck, H

1995-08-01

The aim of our study was to evaluate a T2-weighted turbo-spinecho sequence in comparison to a T2-weighted spinecho sequence in imaging focal liver lesions. In our study 35 patients with suspected focal liver lesions were examined. Standardised imaging protocol included a conventional T2-weighted SE sequence (TR/TE = 2000/90/45, acquisition time = 10.20) as well as a T2-weighted TSE sequence (TR/TE = 4700/90, acquisition time = 6.33). Calculation of S/N and C/N ratio as a basis of quantitative evaluation was done using standard methods. A diagnostic score was implemented to enable qualitative assessment. In 7% (n = 2) the TSE sequence enabled detection of further liver lesions showing a size of less than 1 cm in diameter. Comparing anatomical details the TSE sequence was superior. S/N and C/N ratio of anatomic and pathologic structures of the TSE sequence were higher compared to results of the SE sequence. Our results indicate that the T2-weighted turbo-spinecho sequence is well appropriate for imaging focal liver lesions, and leads to reduction of imaging time.

Analysis of noise-induced temporal correlations in neuronal spike sequences

NASA Astrophysics Data System (ADS)

Reinoso, José A.; Torrent, M. C.; Masoller, Cristina

2016-11-01

We investigate temporal correlations in sequences of noise-induced neuronal spikes, using a symbolic method of time-series analysis. We focus on the sequence of time-intervals between consecutive spikes (inter-spike-intervals, ISIs). The analysis method, known as ordinal analysis, transforms the ISI sequence into a sequence of ordinal patterns (OPs), which are defined in terms of the relative ordering of consecutive ISIs. The ISI sequences are obtained from extensive simulations of two neuron models (FitzHugh-Nagumo, FHN, and integrate-and-fire, IF), with correlated noise. We find that, as the noise strength increases, temporal order gradually emerges, revealed by the existence of more frequent ordinal patterns in the ISI sequence. While in the FHN model the most frequent OP depends on the noise strength, in the IF model it is independent of the noise strength. In both models, the correlation time of the noise affects the OP probabilities but does not modify the most probable pattern.

Influence of time and length size feature selections for human activity sequences recognition.

PubMed

Fang, Hongqing; Chen, Long; Srinivasan, Raghavendiran

2014-01-01

In this paper, Viterbi algorithm based on a hidden Markov model is applied to recognize activity sequences from observed sensors events. Alternative features selections of time feature values of sensors events and activity length size feature values are tested, respectively, and then the results of activity sequences recognition performances of Viterbi algorithm are evaluated. The results show that the selection of larger time feature values of sensor events and/or smaller activity length size feature values will generate relatively better results on the activity sequences recognition performances. © 2013 ISA Published by ISA All rights reserved.

Application of a time-dependent coalescence process for inferring the history of population size changes from DNA sequence data.

PubMed

Polanski, A; Kimmel, M; Chakraborty, R

1998-05-12

Distribution of pairwise differences of nucleotides from data on a sample of DNA sequences from a given segment of the genome has been used in the past to draw inferences about the past history of population size changes. However, all earlier methods assume a given model of population size changes (such as sudden expansion), parameters of which (e.g., time and amplitude of expansion) are fitted to the observed distributions of nucleotide differences among pairwise comparisons of all DNA sequences in the sample. Our theory indicates that for any time-dependent population size, N(tau) (in which time tau is counted backward from present), a time-dependent coalescence process yields the distribution, p(tau), of the time of coalescence between two DNA sequences randomly drawn from the population. Prediction of p(tau) and N(tau) requires the use of a reverse Laplace transform known to be unstable. Nevertheless, simulated data obtained from three models of monotone population change (stepwise, exponential, and logistic) indicate that the pattern of a past population size change leaves its signature on the pattern of DNA polymorphism. Application of the theory to the published mtDNA sequences indicates that the current mtDNA sequence variation is not inconsistent with a logistic growth of the human population.

The spatial alignment of time: Differences in alignment of deictic and sequence time along the sagittal and lateral axes.

PubMed

Walker, Esther J; Bergen, Benjamin K; Núñez, Rafael

2017-04-01

People use space in a variety of ways to structure their thoughts about time. The present report focuses on the different ways that space is employed when reasoning about deictic (past/future relationships) and sequence (earlier/later relationships) time. In the first study, we show that deictic and sequence time are aligned along the lateral axis in a manner consistent with previous work, with past and earlier events associated with left space and future and later events associated with right space. However, the alignment of time with space is different along the sagittal axis. Participants associated future events and earlier events-not later events-with the space in front of their body and past and later events with the space behind, consistent with the sagittal spatial terms (e.g., ahead, in front of) that we use to talk about deictic and sequence time. In the second study, we show that these associations between sequence time and sagittal space are sensitive to person-perspective. This suggests that the particular space-time associations observed in English speakers are influenced by a variety of different spatial properties, including spatial location and perspective. Copyright © 2016. Published by Elsevier B.V.

Quantum Structure of Space and Time

NASA Astrophysics Data System (ADS)

Duff, M. J.; Isham, C. J.

2012-07-01

Foreword Abdus Salam; Preface; List of participants; Part I. Quantum Gravity, Fields and Topology: 1. Some remarks on gravity and quantum mechanics Roger Penrose; 2. An experimental test of quantum gravity Don N. Page and C. D. Geilker; 3. Quantum mechanical origin of the sandwich theorem in classical gravitation theory Claudio Teitelboim; 4. θ-States induced by the diffeomorphism group in canonically quantized gravity C. J. Isham; 5. Strong coupling quantum gravity: an introduction Martin Pilati; 6. Quantizing fourth order gravity theories S. M. Christensen; 7. Green's functions, states and renormalisation M. R. Brown and A. C. Ottewill; 8. Introduction to quantum regge calculus Martin Roček and Ruth Williams; 9. Spontaneous symmetry breaking in curved space-time D. J. Toms; 10. Spontaneous symmetry breaking near a black hole M. S. Fawcett and B. F. Whiting; 11. Yang-Mills vacua in a general three-space G. Kunstatter; 12. Fermion fractionization in physics R. Jackiw; Part II. Supergravity: 13. The new minimal formulation of N=1 supergravity and its tensor calculus M. F. Sohnius and P. C. West; 14. A new deteriorated energy-momentum tensor M. J. Duff and P. K. Townsend; 15. Off-shell N=2 and N=4 supergravity in five dimensions P. Howe; 16. Supergravity in high dimensions P. van Niewenhuizen; 17. Building linearised extended supergravities J. G. Taylor; 18. (Super)gravity in the complex angular momentum plane M. T. Grisaru; 19. The multiplet structure of solitons in the O(2) supergravity theory G. W. Gibbons; 20. Ultra-violet properties of supersymmetric gauge theory S. Ferrara; 21. Extended supercurrents and the ultra-violet finiteness of N=4 supersymmetric Yang-Mills theories K. S. Stelle; 22. Duality rotations B. Zumino; Part III. Cosmology and the Early Universe: 23. Energy, stability and cosmological constant S. Deser; 24. Phase transitions in the early universe T. W. B. Kibble; 25. Complete cosmological theories L. P. Grishchuk and Ya. B. Zeldovich; 26. The cosmological constant and the weak anthropic principle S. W. Hawking.

Evaluation of Demons- and FEM-Based Registration Algorithms for Lung Cancer.

PubMed

Yang, Juan; Li, Dengwang; Yin, Yong; Zhao, Fen; Wang, Hongjun

2016-04-01

We evaluated and compared the accuracy of 2 deformable image registration algorithms in 4-dimensional computed tomography images for patients with lung cancer. Ten patients with non-small cell lung cancer or small cell lung cancer were enrolled in this institutional review board-approved study. The displacement vector fields relative to a specific reference image were calculated by using the diffeomorphic demons (DD) algorithm and the finite element method (FEM)-based algorithm. The registration accuracy was evaluated by using normalized mutual information (NMI), the sum of squared intensity difference (SSD), modified Hausdorff distance (dH_M), and ratio of gross tumor volume (rGTV) difference between reference image and deformed phase image. We also compared the registration speed of the 2 algorithms. Of all patients, the FEM-based algorithm showed stronger ability in aligning 2 images than the DD algorithm. The means (±standard deviation) of NMI were 0.86 (±0.05) and 0.90 (±0.05) using the DD algorithm and the FEM-based algorithm, respectively. The means of SSD were 0.006 (±0.003) and 0.003 (±0.002) using the DD algorithm and the FEM-based algorithm, respectively. The means of dH_M were 0.04 (±0.02) and 0.03 (±0.03) using the DD algorithm and the FEM-based algorithm, respectively. The means of rGTV were 3.9% (±1.01%) and 2.9% (±1.1%) using the DD algorithm and the FEM-based algorithm, respectively. However, the FEM-based algorithm costs a longer time than the DD algorithm, with the average running time of 31.4 minutes compared to 21.9 minutes for all patients. The preliminary results showed that the FEM-based algorithm was more accurate than the DD algorithm while compromised with the registration speed. © The Author(s) 2015.

Hippocampal atrophy and memory dysfunction associated with physical inactivity in community-dwelling elderly subjects: The Sefuri study.

PubMed

Hashimoto, Manabu; Araki, Yuko; Takashima, Yuki; Nogami, Kohjiro; Uchino, Akira; Yuzuriha, Takefumi; Yao, Hiroshi

2017-02-01

Physical inactivity is one of the modifiable risk factors for hippocampal atrophy and Alzheimer's disease. We investigated the relationship between physical activity, hippocampal atrophy, and memory using structural equation modeling (SEM). We examined 213 community-dwelling elderly subjects (99 men and 114 women with a mean age of 68.9 years) without dementia or clinically apparent depression. All participants underwent Mini-Mental State Examination (MMSE) and Rivermead Behavioral Memory Test (RBMT). Physical activities were assessed with a structured questionnaire. We evaluated the degree of hippocampal atrophy (z-score-referred to as ZAdvance hereafter), using a free software program-the voxel-based specific regional analysis system for Alzheimer's disease (VSRAD) based on statistical parametric mapping 8 plus Diffeomorphic Anatomical Registration Through an Exponentiated Lie algebra. Routine magnetic resonance imaging findings were as follows: silent brain infarction, n  = 24 (11.3%); deep white matter lesions, n  = 72 (33.8%); periventricular hyperintensities, n  = 35 (16.4%); and cerebral microbleeds, n  = 14 (6.6%). Path analysis based on SEM indicated that the direct paths from leisure-time activity to hippocampal atrophy (β = -.18, p  < .01) and from hippocampal atrophy to memory dysfunction (RBMT) (β = -.20, p  < .01) were significant. Direct paths from "hippocampus" gray matter volume to RBMT and MMSE were highly significant, while direct paths from "whole brain" gray matter volume to RBMT and MMSE were not significant. The presented SEM model fit the data reasonably well. Based on the present SEM analysis, we found that hippocampal atrophy was associated with age and leisure-time physical inactivity, and hippocampal atrophy appeared to cause memory dysfunction, although we are unable to infer a causal or temporal association between hippocampal atrophy and memory dysfunction from the present observational study.

Implications of Secondary Aftershocks for Failure Processes

NASA Astrophysics Data System (ADS)

Gross, S. J.

2001-12-01

When a seismic sequence with more than one mainshock or an unusually large aftershock occurs, there is a compound aftershock sequence. The secondary aftershocks need not have exactly the same decay as the primary sequence, with the differences having implications for the failure process. When the stress step from the secondary mainshock is positive but not large enough to cause immediate failure of all the remaining primary aftershocks, failure processes which involve accelerating slip will produce secondary aftershocks that decay more rapidly than primary aftershocks. This is because the primary aftershocks are an accelerated version of the background seismicity, and secondary aftershocks are an accelerated version of the primary aftershocks. Real stress perturbations may be negative, and heterogeneities in mainshock stress fields mean that the real world situation is quite complicated. I will first describe and verify my picture of secondary aftershock decay with reference to a simple numerical model of slipping faults which obeys rate and state dependent friction and lacks stress heterogeneity. With such a model, it is possible to generate secondary aftershock sequences with perturbed decay patterns, quantify those patterns, and develop an analysis technique capable of correcting for the effect in real data. The secondary aftershocks are defined in terms of frequency linearized time s(T), which is equal to the number of primary aftershocks expected by a time T, $ s ≡ ∫ t=0T n(t) dt, where the start time t=0 is the time of the primary aftershock, and the primary aftershock decay function n(t) is extrapolated forward to the times of the secondary aftershocks. In the absence of secondary sequences the function s(T)$ re-scales the time so that approximately one event occurs per new time unit; the aftershock sequence is gone. If this rescaling is applied in the presence of a secondary sequence, the secondary sequence is shaped like a primary aftershock sequence, and can be fit by the same modeling techniques applied to simple sequences. The later part of the presentation will concern the decay of Hector Mine aftershocks as influenced by the Landers aftershocks. Although attempts to predict the abundance of Hector aftershocks based on stress overlap analysis are not very successful, the analysis does do a good job fitting the decay of secondary sequences.

Retirement Sequences of Older Americans: Moderately Destandardized and Highly Stratified Across Gender, Class, and Race.

PubMed

Calvo, Esteban; Madero-Cabib, Ignacio; Staudinger, Ursula M

2017-06-06

A destandardization of labor-force patterns revolving around retirement has been observed in recent literature. It is unclear, however, to which degree and of which kind. This study looked at sequences rather than individual statuses or transitions and argued that differentiating older Americans' retirement sequences by type, order, and timing and considering gender, class, and race differences yields a less destandardized picture. Sequence analysis was employed to analyze panel data from the Health and Retirement Study (HRS) for 7,881 individuals observed 6 consecutive times between ages 60-61 and 70-71. As expected, types of retirement sequences were identified that cannot be subsumed under the conventional model of complete retirement from full-time employment around age 65. However, these retirement sequences were not entirely destandardized, as some irreversibility and age-grading persisted. Further, the degree of destandardization varied along gender, class, and race. Unconventional sequences were archetypal for middle-level educated individuals and Blacks. Also, sequences for women and individuals with lower education showed more unemployment and part-time jobs, and less age-grading. A sequence-analytic approach that models group differences uncovers misjudgments about the degree of destandardization of retirement sequences. When a continuous process is represented as individual transitions, the overall pattern of retirement sequences gets lost and appears destandardized. These patterns get further complicated by differences in social structures by gender, class, and race in ways that seem to reproduce advantages that men, more highly educated individuals, and Whites enjoy in numerous areas over the life course. © The Author 2017. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Anticipation measures of sequence learning: manual versus oculomotor versions of the serial reaction time task.

PubMed

Vakil, Eli; Bloch, Ayala; Cohen, Haggar

2017-03-01

The serial reaction time (SRT) task has generated a very large amount of research. Nevertheless the debate continues as to the exact cognitive processes underlying implicit sequence learning. Thus, the first goal of this study is to elucidate the underlying cognitive processes enabling sequence acquisition. We therefore compared reaction time (RT) in sequence learning in a standard manual activated (MA) to that in an ocular activated (OA) version of the task, within a single experimental setting. The second goal is to use eye movement measures to compare anticipation, as an additional indication of sequence learning, between the two versions of the SRT. Performance of the group given the MA version of the task (n = 29) was compared with that of the group given the OA version (n = 30). The results showed that although overall, RT was faster for the OA group, the rate of sequence learning was similar to that of the MA group performing the standard version of the SRT. Because the stimulus-response association is automatic and exists prior to training in the OA task, the decreased reaction time in this version of the task reflects a purer measure of the sequence learning that occurs in the SRT task. The results of this study show that eye tracking anticipation can be measured directly and can serve as a direct measure of sequence learning. Finally, using the OA version of the SRT to study sequence learning presents a significant methodological contribution by making sequence learning studies possible among populations that struggle to perform manual responses.

Expectation, information processing, and subjective duration.

PubMed

Simchy-Gross, Rhimmon; Margulis, Elizabeth Hellmuth

2018-01-01

In research on psychological time, it is important to examine the subjective duration of entire stimulus sequences, such as those produced by music (Teki, Frontiers in Neuroscience, 10, 2016). Yet research on the temporal oddball illusion (according to which oddball stimuli seem longer than standard stimuli of the same duration) has examined only the subjective duration of single events contained within sequences, not the subjective duration of sequences themselves. Does the finding that oddballs seem longer than standards translate to entire sequences, such that entire sequences that contain oddballs seem longer than those that do not? Is this potential translation influenced by the mode of information processing-whether people are engaged in direct or indirect temporal processing? Two experiments aimed to answer both questions using different manipulations of information processing. In both experiments, musical sequences either did or did not contain oddballs (auditory sliding tones). To manipulate information processing, we varied the task (Experiment 1), the sequence event structure (Experiments 1 and 2), and the sequence familiarity (Experiment 2) independently within subjects. Overall, in both experiments, the sequences that contained oddballs seemed shorter than those that did not when people were engaged in direct temporal processing, but longer when people were engaged in indirect temporal processing. These findings support the dual-process contingency model of time estimation (Zakay, Attention, Perception & Psychophysics, 54, 656-664, 1993). Theoretical implications for attention-based and memory-based models of time estimation, the pacemaker accumulator and coding efficiency hypotheses of time perception, and dynamic attending theory are discussed.

Effect of the sequence data deluge on the performance of methods for detecting protein functional residues.

PubMed

Garrido-Martín, Diego; Pazos, Florencio

2018-02-27

The exponential accumulation of new sequences in public databases is expected to improve the performance of all the approaches for predicting protein structural and functional features. Nevertheless, this was never assessed or quantified for some widely used methodologies, such as those aimed at detecting functional sites and functional subfamilies in protein multiple sequence alignments. Using raw protein sequences as only input, these approaches can detect fully conserved positions, as well as those with a family-dependent conservation pattern. Both types of residues are routinely used as predictors of functional sites and, consequently, understanding how the sequence content of the databases affects them is relevant and timely. In this work we evaluate how the growth and change with time in the content of sequence databases affect five sequence-based approaches for detecting functional sites and subfamilies. We do that by recreating historical versions of the multiple sequence alignments that would have been obtained in the past based on the database contents at different time points, covering a period of 20 years. Applying the methods to these historical alignments allows quantifying the temporal variation in their performance. Our results show that the number of families to which these methods can be applied sharply increases with time, while their ability to detect potentially functional residues remains almost constant. These results are informative for the methods' developers and final users, and may have implications in the design of new sequencing initiatives.

The proximal-to-distal sequence in upper-limb motions on multiple levels and time scales.

PubMed

Serrien, Ben; Baeyens, Jean-Pierre

2017-10-01

The proximal-to-distal sequence is a phenomenon that can be observed in a large variety of motions of the upper limbs in both humans and other mammals. The mechanisms behind this sequence are not completely understood and motor control theories able to explain this phenomenon are currently incomplete. The aim of this narrative review is to take a theoretical constraints-led approach to the proximal-to-distal sequence and provide a broad multidisciplinary overview of relevant literature. This sequence exists at multiple levels (brain, spine, muscles, kinetics and kinematics) and on multiple time scales (motion, motor learning and development, growth and possibly even evolution). We hypothesize that the proximodistal spatiotemporal direction on each time scale and level provides part of the organismic constraints that guide the dynamics at the other levels and time scales. The constraint-led approach in this review may serve as a first onset towards integration of evidence and a framework for further experimentation to reveal the dynamics of the proximal-to-distal sequence. Copyright © 2017 Elsevier B.V. All rights reserved.

[The principle and application of the single-molecule real-time sequencing technology].

PubMed

Yanhu, Liu; Lu, Wang; Li, Yu

2015-03-01

Last decade witnessed the explosive development of the third-generation sequencing strategy, including single-molecule real-time sequencing (SMRT), true single-molecule sequencing (tSMSTM) and the single-molecule nanopore DNA sequencing. In this review, we summarize the principle, performance and application of the SMRT sequencing technology. Compared with the traditional Sanger method and the next-generation sequencing (NGS) technologies, the SMRT approach has several advantages, including long read length, high speed, PCR-free and the capability of direct detection of epigenetic modifications. However, the disadvantage of its low accuracy, most of which resulted from insertions and deletions, is also notable. So, the raw sequence data need to be corrected before assembly. Up to now, the SMRT is a good fit for applications in the de novo genomic sequencing and the high-quality assemblies of small genomes. In the future, it is expected to play an important role in epigenetics, transcriptomic sequencing, and assemblies of large genomes.

Characterization of Hepatitis C Virus (HCV) Envelope Diversification from Acute to Chronic Infection within a Sexually Transmitted HCV Cluster by Using Single-Molecule, Real-Time Sequencing

PubMed Central

Ho, Cynthia K. Y.; Raghwani, Jayna; Koekkoek, Sylvie; Liang, Richard H.; Van der Meer, Jan T. M.; Van Der Valk, Marc; De Jong, Menno; Pybus, Oliver G.

2016-01-01

ABSTRACT In contrast to other available next-generation sequencing platforms, PacBio single-molecule, real-time (SMRT) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in unprocessed data. Using this platform, we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1,680 nucleotides [nt]) from individuals belonging to a cluster of sexually transmitted cases. All five subjects were coinfected with HIV-1 and a closely related strain of HCV genotype 4d. In total, 50 samples were analyzed by using SMRT sequencing. By using 7 passes of circular consensus sequencing, the error rate was reduced to 0.37%, and the median number of sequences was 612 per sample. A further reduction of insertions was achieved by alignment against a sample-specific reference sequence. However, in vitro recombination during PCR amplification could not be excluded. Phylogenetic analysis supported close relationships among HCV sequences from the four male subjects and subsequent transmission from one subject to his female partner. Transmission was characterized by a strong genetic bottleneck. Viral genetic diversity was low during acute infection and increased upon progression to chronicity but subsequently fluctuated during chronic infection, caused by the alternate detection of distinct coexisting lineages. SMRT sequencing combines long reads with sufficient depth for many phylogenetic analyses and can therefore provide insights into within-host HCV evolutionary dynamics without the need for haplotype reconstruction using statistical algorithms. IMPORTANCE Next-generation sequencing has revolutionized the study of genetically variable RNA virus populations, but for phylogenetic and evolutionary analyses, longer sequences than those generated by most available platforms, while minimizing the intrinsic error rate, are desired. Here, we demonstrate for the first time that PacBio SMRT sequencing technology can be used to generate full-length HCV envelope sequences at the single-molecule level, providing a data set with large sequencing depth for the characterization of intrahost viral dynamics. The selection of consensus reads derived from at least 7 full circular consensus sequencing rounds significantly reduced the intrinsic high error rate of this method. We used this method to genetically characterize a unique transmission cluster of sexually transmitted HCV infections, providing insight into the distinct evolutionary pathways in each patient over time and identifying the transmission-associated genetic bottleneck as well as fluctuations in viral genetic diversity over time, accompanied by dynamic shifts in viral subpopulations. PMID:28077634

Bidirectional holographic codes and sub-AdS locality

NASA Astrophysics Data System (ADS)

Yang, Zhao; Hayden, Patrick; Qi, Xiaoliang

Tensor networks implementing quantum error correcting codes have recently been used as toy models of the holographic duality which explicitly realize some of the more puzzling features of the AdS/CFT correspondence. These models reproduce the Ryu-Takayanagi entropy formula for boundary intervals, and allow bulk operators to be mapped to the boundary in a redundant fashion. These exactly solvable, explicit models have provided valuable insight but nonetheless suffer from many deficiencies, some of which we attempt to address in this talk. We propose a new class of tensor network models that subsume the earlier advances and, in addition, incorporate additional features of holographic duality, including: (1) a holographic interpretation of all boundary states, not just those in a ''code'' subspace, (2) a set of bulk states playing the role of ''classical geometries'' which reproduce the Ryu-Takayanagi formula for boundary intervals, (3) a bulk gauge symmetry analogous to diffeomorphism invariance in gravitational theories, (4) emergent bulk locality for sufficiently sparse excitations, and the ability to describe geometry at sub-AdS resolutions or even flat space. David and Lucile Packard Foundation.

Bidirectional holographic codes and sub-AdS locality

NASA Astrophysics Data System (ADS)

Yang, Zhao; Hayden, Patrick; Qi, Xiao-Liang

2016-01-01

Tensor networks implementing quantum error correcting codes have recently been used to construct toy models of holographic duality explicitly realizing some of the more puzzling features of the AdS/CFT correspondence. These models reproduce the Ryu-Takayanagi entropy formula for boundary intervals, and allow bulk operators to be mapped to the boundary in a redundant fashion. These exactly solvable, explicit models have provided valuable insight but nonetheless suffer from many deficiencies, some of which we attempt to address in this article. We propose a new class of tensor network models that subsume the earlier advances and, in addition, incorporate additional features of holographic duality, including: (1) a holographic interpretation of all boundary states, not just those in a "code" subspace, (2) a set of bulk states playing the role of "classical geometries" which reproduce the Ryu-Takayanagi formula for boundary intervals, (3) a bulk gauge symmetry analogous to diffeomorphism invariance in gravitational theories, (4) emergent bulk locality for sufficiently sparse excitations, and (5) the ability to describe geometry at sub-AdS resolutions or even flat space.

The Self-Liking Brain: A VBM Study on the Structural Substrate of Self-Esteem

PubMed Central

Agroskin, Dmitrij; Klackl, Johannes; Jonas, Eva

2014-01-01

Abundant evidence suggests that self-esteem is an important personality resource for emotion regulation in response to stressful experiences. It was thus hypothesized that the relative grey matter volume of brain regions involved in responding to and coping with stress is related to individual differences in trait self-esteem. Using structural magnetic resonance imaging of 48 healthy adults in conjunction with voxel-based morphometry and diffeomorphic anatomical registration using exponentiated lie algebra (VBM-DARTEL), positive associations between self-esteem and regional grey matter volume were indeed found in the anterior cingulate cortex (ACC), right lateral prefrontal cortex (LPFC), right hippocampus, and left hypothalamus. In addition, self-esteem positively covaried with grey matter volume in the right temporo-parietal junction (TPJ), which has been implicated in pride and theory of mind. The results suggest that persons with low self-esteem have reduced grey matter volume in brain regions that contribute to emotion/stress regulation, pride, and theory of mind. The findings provide novel neuroanatomical evidence for the view that self-esteem constitutes a vital coping resource. PMID:24489727

Conservation Laws and Symmetry Properties of a Class of Higher Order Theories of Gravity

NASA Astrophysics Data System (ADS)

Barraco, D.; Dominguez, E.; Guibert, R.; Hamity, V.

1998-04-01

We consider a class of fourth order theories of gravity with arbitrary matter fields arising from a diffeomorphism invariant Lagrangian density mathcal{L}_T = mathcal{L}_G + mathcal{L}_M, with mathcal{L}_G = sqrt { - g} left[ {R + hleft( R right)} right]and mathcal{L}_Mthe phenomenological representation of the nongravitational fields. We derive first the generalization of the Einstein pseudotensor and the von Freud superpotential. We then show, using the arbitrariness that is always present in the choice of pseudotensor and superpotential, that we can choose these superpotentials to have the same form as those for the Hilbert Lagrangian of general relativity (GR). In particular we may introduce the Moller superpotential of GR as associated with a double-index differential conservation law. Similarly, using the Moller superpotential we prove that we can choose the Komar vector of GR to construct a conserved quantity for isolated asymptotically flat systems. For the example R + R2theory we prove then, that the active mass is equal to the total energy (or inertial mass) of the system.

The self-liking brain: a VBM study on the structural substrate of self-esteem.

PubMed

Agroskin, Dmitrij; Klackl, Johannes; Jonas, Eva

2014-01-01

Abundant evidence suggests that self-esteem is an important personality resource for emotion regulation in response to stressful experiences. It was thus hypothesized that the relative grey matter volume of brain regions involved in responding to and coping with stress is related to individual differences in trait self-esteem. Using structural magnetic resonance imaging of 48 healthy adults in conjunction with voxel-based morphometry and diffeomorphic anatomical registration using exponentiated lie algebra (VBM-DARTEL), positive associations between self-esteem and regional grey matter volume were indeed found in the anterior cingulate cortex (ACC), right lateral prefrontal cortex (LPFC), right hippocampus, and left hypothalamus. In addition, self-esteem positively covaried with grey matter volume in the right temporo-parietal junction (TPJ), which has been implicated in pride and theory of mind. The results suggest that persons with low self-esteem have reduced grey matter volume in brain regions that contribute to emotion/stress regulation, pride, and theory of mind. The findings provide novel neuroanatomical evidence for the view that self-esteem constitutes a vital coping resource.

General covariant Horava-Lifshitz gravity without projectability condition and its applications to cosmology

NASA Astrophysics Data System (ADS)

Zhu, Tao; Shu, Fu-Wen; Wu, Qiang; Wang, Anzhong

2012-02-01

We consider an extended theory of Horava-Lifshitz gravity with the detailed balance condition softly breaking, but without the projectability condition. With the former, the number of independent coupling constants is significantly reduced. With the latter and by extending the original foliation-preserving diffeomorphism symmetry Diff(M,F) to include a local U(1) symmetry, the spin-0 gravitons are eliminated. Thus, all the problems related to them disappear, including the instability, strong coupling, and different speeds in the gravitational sector. When the theory couples to a scalar field, we find that the scalar field is not only stable in both the ultraviolet and infrared, but also free of the strong coupling problem, because of the presence of high-order spatial derivative terms of the scalar field. Furthermore, applying the theory to cosmology, we find that due to the additional U(1) symmetry, the Friedmann-Robertson-Walker (FRW) universe is necessarily flat. We also investigate the scalar, vector, and tensor perturbations of the flat FRW universe, and derive the general linearized field equations for each kind of the perturbations.

Improving Adaptive Learning Technology through the Use of Response Times

ERIC Educational Resources Information Center

Mettler, Everett; Massey, Christine M.; Kellman, Philip J.

2011-01-01

Adaptive learning techniques have typically scheduled practice using learners' accuracy and item presentation history. We describe an adaptive learning system (Adaptive Response Time Based Sequencing--ARTS) that uses both accuracy and response time (RT) as direct inputs into sequencing. Response times are used to assess learning strength and…

Noncontrast Peripheral MRA with Spiral Echo Train Imaging

PubMed Central

Fielden, Samuel W.; Mugler, John P.; Hagspiel, Klaus D.; Norton, Patrick T.; Kramer, Christopher M.; Meyer, Craig H.

2015-01-01

Purpose To develop a spin echo train sequence with spiral readout gradients with improved artery–vein contrast for noncontrast angiography. Theory Venous T2 becomes shorter as the echo spacing is increased in echo train sequences, improving contrast. Spiral acquisitions, due to their data collection efficiency, facilitate long echo spacings without increasing scan times. Methods Bloch equation simulations were performed to determine optimal sequence parameters, and the sequence was applied in five volunteers. In two volunteers, the sequence was performed with a range of echo times and echo spacings to compare with the theoretical contrast behavior. A Cartesian version of the sequence was used to compare contrast appearance with the spiral sequence. Additionally, spiral parallel imaging was optionally used to improve image resolution. Results In vivo, artery–vein contrast properties followed the general shape predicted by simulations, and good results were obtained in all stations. Compared with a Cartesian implementation, the spiral sequence had superior artery–vein contrast, better spatial resolution (1.2 mm2 versus 1.5 mm2), and was acquired in less time (1.4 min versus 7.5 min). Conclusion The spiral spin echo train sequence can be used for flow-independent angiography to generate threedimensional angiograms of the periphery quickly and without the use of contrast agents. PMID:24753164

Noncontrast peripheral MRA with spiral echo train imaging.

PubMed

Fielden, Samuel W; Mugler, John P; Hagspiel, Klaus D; Norton, Patrick T; Kramer, Christopher M; Meyer, Craig H

2015-03-01

To develop a spin echo train sequence with spiral readout gradients with improved artery-vein contrast for noncontrast angiography. Venous T2 becomes shorter as the echo spacing is increased in echo train sequences, improving contrast. Spiral acquisitions, due to their data collection efficiency, facilitate long echo spacings without increasing scan times. Bloch equation simulations were performed to determine optimal sequence parameters, and the sequence was applied in five volunteers. In two volunteers, the sequence was performed with a range of echo times and echo spacings to compare with the theoretical contrast behavior. A Cartesian version of the sequence was used to compare contrast appearance with the spiral sequence. Additionally, spiral parallel imaging was optionally used to improve image resolution. In vivo, artery-vein contrast properties followed the general shape predicted by simulations, and good results were obtained in all stations. Compared with a Cartesian implementation, the spiral sequence had superior artery-vein contrast, better spatial resolution (1.2 mm(2) versus 1.5 mm(2) ), and was acquired in less time (1.4 min versus 7.5 min). The spiral spin echo train sequence can be used for flow-independent angiography to generate three-dimensional angiograms of the periphery quickly and without the use of contrast agents. © 2014 Wiley Periodicals, Inc.

EventThread: Visual Summarization and Stage Analysis of Event Sequence Data.

PubMed

Guo, Shunan; Xu, Ke; Zhao, Rongwen; Gotz, David; Zha, Hongyuan; Cao, Nan

2018-01-01

Event sequence data such as electronic health records, a person's academic records, or car service records, are ordered series of events which have occurred over a period of time. Analyzing collections of event sequences can reveal common or semantically important sequential patterns. For example, event sequence analysis might reveal frequently used care plans for treating a disease, typical publishing patterns of professors, and the patterns of service that result in a well-maintained car. It is challenging, however, to visually explore large numbers of event sequences, or sequences with large numbers of event types. Existing methods focus on extracting explicitly matching patterns of events using statistical analysis to create stages of event progression over time. However, these methods fail to capture latent clusters of similar but not identical evolutions of event sequences. In this paper, we introduce a novel visualization system named EventThread which clusters event sequences into threads based on tensor analysis and visualizes the latent stage categories and evolution patterns by interactively grouping the threads by similarity into time-specific clusters. We demonstrate the effectiveness of EventThread through usage scenarios in three different application domains and via interviews with an expert user.

Composite Case Development for Weapons Applications and Testing

DTIC Science & Technology

2015-03-01

5 cm axial location for each layer. ............................................................... 68  Figure 52.  Hydra radiographic time sequence...increase by 6.7%. No significant change in hold time was observed for the model with reduced mass. Figure 52. Hydra radiographic time sequence of

Recurrence time statistics: versatile tools for genomic DNA sequence analysis.

PubMed

Cao, Yinhe; Tung, Wen-Wen; Gao, J B

2004-01-01

With the completion of the human and a few model organisms' genomes, and the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop faster computational tools which are capable of easily identifying the structures and extracting features from DNA sequences. One of the more important structures in a DNA sequence is repeat-related. Often they have to be masked before protein coding regions along a DNA sequence are to be identified or redundant expressed sequence tags (ESTs) are to be sequenced. Here we report a novel recurrence time based method for sequence analysis. The method can conveniently study all kinds of periodicity and exhaustively find all repeat-related features from a genomic DNA sequence. An efficient codon index is also derived from the recurrence time statistics, which has the salient features of being largely species-independent and working well on very short sequences. Efficient codon indices are key elements of successful gene finding algorithms, and are particularly useful for determining whether a suspected EST belongs to a coding or non-coding region. We illustrate the power of the method by studying the genomes of E. coli, the yeast S. cervisivae, the nematode worm C. elegans, and the human, Homo sapiens. Computationally, our method is very efficient. It allows us to carry out analysis of genomes on the whole genomic scale by a PC.

NCBI-compliant genome submissions: tips and tricks to save time and money.

PubMed

Pirovano, Walter; Boetzer, Marten; Derks, Martijn F L; Smit, Sandra

2017-03-01

Genome sequences nowadays play a central role in molecular biology and bioinformatics. These sequences are shared with the scientific community through sequence databases. The sequence repositories of the International Nucleotide Sequence Database Collaboration (INSDC, comprising GenBank, ENA and DDBJ) are the largest in the world. Preparing an annotated sequence in such a way that it will be accepted by the database is challenging because many validation criteria apply. In our opinion, it is an undesirable situation that researchers who want to submit their sequence need either a lot of experience or help from partners to get the job done. To save valuable time and money, we list a number of recommendations for people who want to submit an annotated genome to a sequence database, as well as for tool developers, who could help to ease the process. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

The Role of RT Carry-Over for Congruence Sequence Effects in Masked Priming

ERIC Educational Resources Information Center

Huber-Huber, Christoph; Ansorge, Ulrich

2017-01-01

The present study disentangles 2 sources of the congruence sequence effect with masked primes: congruence and response time of the previous trial (reaction time [RT] carry-over). Using arrows as primes and targets and a metacontrast masking procedure we found congruence as well as congruence sequence effects. In addition, congruence sequence…

454 next generation-sequencing outperforms allele-specific PCR, Sanger sequencing, and pyrosequencing for routine KRAS mutation analysis of formalin-fixed, paraffin-embedded samples

PubMed Central

Altimari, Annalisa; de Biase, Dario; De Maglio, Giovanna; Gruppioni, Elisa; Capizzi, Elisa; Degiovanni, Alessio; D’Errico, Antonia; Pession, Annalisa; Pizzolitto, Stefano; Fiorentino, Michelangelo; Tallini, Giovanni

2013-01-01

Detection of KRAS mutations in archival pathology samples is critical for therapeutic appropriateness of anti-EGFR monoclonal antibodies in colorectal cancer. We compared the sensitivity, specificity, and accuracy of Sanger sequencing, ARMS-Scorpion (TheraScreen®) real-time polymerase chain reaction (PCR), pyrosequencing, chip array hybridization, and 454 next-generation sequencing to assess KRAS codon 12 and 13 mutations in 60 nonconsecutive selected cases of colorectal cancer. Twenty of the 60 cases were detected as wild-type KRAS by all methods with 100% specificity. Among the 40 mutated cases, 13 were discrepant with at least one method. The sensitivity was 85%, 90%, 93%, and 92%, and the accuracy was 90%, 93%, 95%, and 95% for Sanger sequencing, TheraScreen real-time PCR, pyrosequencing, and chip array hybridization, respectively. The main limitation of Sanger sequencing was its low analytical sensitivity, whereas TheraScreen real-time PCR, pyrosequencing, and chip array hybridization showed higher sensitivity but suffered from the limitations of predesigned assays. Concordance between the methods was k = 0.79 for Sanger sequencing and k > 0.85 for the other techniques. Tumor cell enrichment correlated significantly with the abundance of KRAS-mutated deoxyribonucleic acid (DNA), evaluated as ΔCt for TheraScreen real-time PCR (P = 0.03), percentage of mutation for pyrosequencing (P = 0.001), ratio for chip array hybridization (P = 0.003), and percentage of mutation for 454 next-generation sequencing (P = 0.004). Also, 454 next-generation sequencing showed the best cross correlation for quantification of mutation abundance compared with all the other methods (P < 0.001). Our comparison showed the superiority of next-generation sequencing over the other techniques in terms of sensitivity and specificity. Next-generation sequencing will replace Sanger sequencing as the reference technique for diagnostic detection of KRAS mutation in archival tumor tissues. PMID:23950653

DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors.

PubMed

Schmollinger, Martin; Nieselt, Kay; Kaufmann, Michael; Morgenstern, Burkhard

2004-09-09

Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Herein, a parallel version of the multi-alignment program DIALIGN is introduced. We propose two ways of dividing the program into independent sub-routines that can be run on different processors: (a) pair-wise sequence alignments that are used as a first step to multiple alignment account for most of the CPU time in DIALIGN. Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments. (b) For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced anchored alignment procedure. For our test sequences, this combined approach reduces the program running time of DIALIGN by up to 97%. By distributing sub-routines to multiple processors, the running time of DIALIGN can be crucially improved. With these improvements, it is possible to apply the program in large-scale genomics and proteomics projects that were previously beyond its scope.

Impacts of visuomotor sequence learning methods on speed and accuracy: Starting over from the beginning or from the point of error.

PubMed

Tanaka, Kanji; Watanabe, Katsumi

2016-02-01

The present study examined whether sequence learning led to more accurate and shorter performance time if people who are learning a sequence start over from the beginning when they make an error (i.e., practice the whole sequence) or only from the point of error (i.e., practice a part of the sequence). We used a visuomotor sequence learning paradigm with a trial-and-error procedure. In Experiment 1, we found fewer errors, and shorter performance time for those who restarted their performance from the beginning of the sequence as compared to those who restarted from the point at which an error occurred, indicating better learning of spatial and motor representations of the sequence. This might be because the learned elements were repeated when the next performance started over from the beginning. In subsequent experiments, we increased the occasions for the repetitions of learned elements by modulating the number of fresh start points in the sequence after errors. The results showed that fewer fresh start points were likely to lead to fewer errors and shorter performance time, indicating that the repetitions of learned elements enabled participants to develop stronger spatial and motor representations of the sequence. Thus, a single or two fresh start points in the sequence (i.e., starting over only from the beginning or from the beginning or midpoint of the sequence after errors) is likely to lead to more accurate and faster performance. Copyright © 2016 Elsevier B.V. All rights reserved.

Compressing DNA sequence databases with coil.

PubMed

White, W Timothy J; Hendy, Michael D

2008-05-20

Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression - an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression - the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

Compressing DNA sequence databases with coil

PubMed Central

White, W Timothy J; Hendy, Michael D

2008-01-01

Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work. PMID:18489794

Optimization of parameter values for complex pulse sequences by simulated annealing: application to 3D MP-RAGE imaging of the brain.

PubMed

Epstein, F H; Mugler, J P; Brookeman, J R

1994-02-01

A number of pulse sequence techniques, including magnetization-prepared gradient echo (MP-GRE), segmented GRE, and hybrid RARE, employ a relatively large number of variable pulse sequence parameters and acquire the image data during a transient signal evolution. These sequences have recently been proposed and/or used for clinical applications in the brain, spine, liver, and coronary arteries. Thus, the need for a method of deriving optimal pulse sequence parameter values for this class of sequences now exists. Due to the complexity of these sequences, conventional optimization approaches, such as applying differential calculus to signal difference equations, are inadequate. We have developed a general framework for adapting the simulated annealing algorithm to pulse sequence parameter value optimization, and applied this framework to the specific case of optimizing the white matter-gray matter signal difference for a T1-weighted variable flip angle 3D MP-RAGE sequence. Using our algorithm, the values of 35 sequence parameters, including the magnetization-preparation RF pulse flip angle and delay time, 32 flip angles in the variable flip angle gradient-echo acquisition sequence, and the magnetization recovery time, were derived. Optimized 3D MP-RAGE achieved up to a 130% increase in white matter-gray matter signal difference compared with optimized 3D RF-spoiled FLASH with the same total acquisition time. The simulated annealing approach was effective at deriving optimal parameter values for a specific 3D MP-RAGE imaging objective, and may be useful for other imaging objectives and sequences in this general class.

Relative Suffix Trees.

PubMed

Farruggia, Andrea; Gagie, Travis; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

2018-05-01

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees.

Relative Suffix Trees

PubMed Central

Farruggia, Andrea; Gagie, Travis; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

2018-01-01

Abstract Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees. PMID:29795706

Random digital encryption secure communication system

NASA Technical Reports Server (NTRS)

Doland, G. D. (Inventor)

1982-01-01

The design of a secure communication system is described. A product code, formed from two pseudorandom sequences of digital bits, is used to encipher or scramble data prior to transmission. The two pseudorandom sequences are periodically changed at intervals before they have had time to repeat. One of the two sequences is transmitted continuously with the scrambled data for synchronization. In the receiver portion of the system, the incoming signal is compared with one of two locally generated pseudorandom sequences until correspondence between the sequences is obtained. At this time, the two locally generated sequences are formed into a product code which deciphers the data from the incoming signal. Provision is made to ensure synchronization of the transmitting and receiving portions of the system.

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

PubMed Central

Ardui, Simon; Ameur, Adam; Vermeesch, Joris R; Hestand, Matthew S

2018-01-01

Abstract Short read massive parallel sequencing has emerged as a standard diagnostic tool in the medical setting. However, short read technologies have inherent limitations such as GC bias, difficulties mapping to repetitive elements, trouble discriminating paralogous sequences, and difficulties in phasing alleles. Long read single molecule sequencers resolve these obstacles. Moreover, they offer higher consensus accuracies and can detect epigenetic modifications from native DNA. The first commercially available long read single molecule platform was the RS system based on PacBio's single molecule real-time (SMRT) sequencing technology, which has since evolved into their RSII and Sequel systems. Here we capsulize how SMRT sequencing is revolutionizing constitutional, reproductive, cancer, microbial and viral genetic testing. PMID:29401301

On the Landau-de Gennes Elastic Energy of a Q-Tensor Model for Soft Biaxial Nematics

NASA Astrophysics Data System (ADS)

Mucci, Domenico; Nicolodi, Lorenzo

2017-12-01

In the Landau-de Gennes theory of liquid crystals, the propensities for alignments of molecules are represented at each point of the fluid by an element Q of the vector space S_0 of 3× 3 real symmetric traceless matrices, or Q-tensors. According to Longa and Trebin (1989), a biaxial nematic system is called soft biaxial if the tensor order parameter Q satisfies the constraint tr(Q^2) = {const}. After the introduction of a Q-tensor model for soft biaxial nematic systems and the description of its geometric structure, we address the question of coercivity for the most common four-elastic-constant form of the Landau-de Gennes elastic free-energy (Iyer et al. 2015) in this model. For a soft biaxial nematic system, the tensor field Q takes values in a four-dimensional sphere S^4_ρ of radius ρ ≤ √{2/3} in the five-dimensional space S_0 with inner product < Q, P > = tr(QP). The rotation group it{SO}(3) acts orthogonally on S_0 by conjugation and hence induces an action on S^4_ρ \\subset {S}_0. This action has generic orbits of codimension one that are diffeomorphic to an eightfold quotient S^3/H of the unit three-sphere S^3, where H={± 1, ± i, ± j, ± k} is the quaternion group, and has two degenerate orbits of codimension two that are diffeomorphic to the projective plane RP^2. Each generic orbit can be interpreted as the order parameter space of a constrained biaxial nematic system and each singular orbit as the order parameter space of a constrained uniaxial nematic system. It turns out that S^4_ρ is a cohomogeneity one manifold, i.e., a manifold with a group action whose orbit space is one-dimensional. Another important geometric feature of the model is that the set Σ _ρ of diagonal Q-tensors of fixed norm ρ is a (geodesic) great circle in S^4_ρ which meets every orbit of S^4_ρ orthogonally and is then a section for S^4_ρ in the sense of the general theory of canonical forms. We compute necessary and sufficient coercivity conditions for the elastic energy by exploiting the it{SO}(3)-invariance of the elastic energy (frame-indifference), the existence of the section Σ _ρ for S^4_ρ , and the geometry of the model, which allow us to reduce to a suitable invariant problem on (an arc of) Σ _ρ . Our approach can ultimately be seen as an application of the general method of reduction of variables, or cohomogeneity method.

Influence of motion on face recognition.

PubMed

Bonfiglio, Natale S; Manfredi, Valentina; Pessa, Eliano

2012-02-01

The influence of motion information and temporal associations on recognition of non-familiar faces was investigated using two groups which performed a face recognition task. One group was presented with regular temporal sequences of face views designed to produce the impression of motion of the face rotating in depth, the other group with random sequences of the same views. In one condition, participants viewed the sequences of the views in rapid succession with a negligible interstimulus interval (ISI). This condition was characterized by three different presentation times. In another condition, participants were presented a sequence with a 1-sec. ISI among the views. That regular sequences of views with a negligible ISI and a shorter presentation time were hypothesized to give rise to better recognition, related to a stronger impression of face rotation. Analysis of data from 45 participants showed a shorter presentation time was associated with significantly better accuracy on the recognition task; however, differences between performances associated with regular and random sequences were not significant.

Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing.

PubMed

Euskirchen, Philipp; Bielle, Franck; Labreche, Karim; Kloosterman, Wigard P; Rosenberg, Shai; Daniau, Mailys; Schmitt, Charlotte; Masliah-Planchon, Julien; Bourdeaut, Franck; Dehais, Caroline; Marie, Yannick; Delattre, Jean-Yves; Idbaih, Ahmed

2017-11-01

Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making. Here, we explored the potential of a pocket-size nanopore sequencing device for multimodal and rapid molecular diagnostics of cancer. Low-pass whole genome sequencing was used to simultaneously generate copy number (CN) and methylation profiles from native tumor DNA in the same sequencing run. Single nucleotide variants in IDH1, IDH2, TP53, H3F3A, and the TERT promoter region were identified using deep amplicon sequencing. Nanopore sequencing yielded ~0.1X genome coverage within 6 h and resulting CN and epigenetic profiles correlated well with matched microarray data. Diagnostically relevant alterations, such as 1p/19q codeletion, and focal amplifications could be recapitulated. Using ad hoc random forests, we could perform supervised pan-cancer classification to distinguish gliomas, medulloblastomas, and brain metastases of different primary sites. Single nucleotide variants in IDH1, IDH2, and H3F3A were identified using deep amplicon sequencing within minutes of sequencing. Detection of TP53 and TERT promoter mutations shows that sequencing of entire genes and GC-rich regions is feasible. Nanopore sequencing allows same-day detection of structural variants, point mutations, and methylation profiling using a single device with negligible capital cost. It outperforms hybridization-based and current sequencing technologies with respect to time to diagnosis and required laboratory equipment and expertise, aiming to make precision medicine possible for every cancer patient, even in resource-restricted settings.

Small scale sequence automation pays big dividends

NASA Technical Reports Server (NTRS)

Nelson, Bill

1994-01-01

Galileo sequence design and integration are supported by a suite of formal software tools. Sequence review, however, is largely a manual process with reviewers scanning hundreds of pages of cryptic computer printouts to verify sequence correctness. Beginning in 1990, a series of small, PC based sequence review tools evolved. Each tool performs a specific task but all have a common 'look and feel'. The narrow focus of each tool means simpler operation, and easier creation, testing, and maintenance. Benefits from these tools are (1) decreased review time by factors of 5 to 20 or more with a concomitant reduction in staffing, (2) increased review accuracy, and (3) excellent returns on time invested.

A Paradox within the Time Value of Money: A Critical Thinking Exercise for Finance Students

ERIC Educational Resources Information Center

Delaney, Charles J.; Rich, Steven P.; Rose, John T.

2016-01-01

This study presents a paradox within the time value of money (TVM), namely, that the interest-principal sequence embedded in the payment stream of an amortized loan is exactly the opposite of the interest-principal sequence implicit in the present value of a matching annuity. We examine this inverse sequence, both mathematically and intuitively,…

Light beam range finder

DOEpatents

McEwan, Thomas E.

1998-01-01

A "laser tape measure" for measuring distance which includes a transmitter such as a laser diode which transmits a sequence of electromagnetic pulses in response to a transmit timing signal. A receiver samples reflections from objects within the field of the sequence of visible electromagnetic pulses with controlled timing, in response to a receive timing signal. The receiver generates a sample signal in response to the samples which indicates distance to the object causing the reflections. The timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the reflection such that the time between transmission of pulses in the sequence in sampling by the receiver sweeps over a range of delays. The transmit timing signal causes the transmitter to transmit the sequence of electromagnetic pulses at a pulse repetition rate, and the received timing signal sweeps over the range of delays in a sweep cycle such that reflections are sampled at the pulse repetition rate and with different delays in the range of delays, such that the sample signal represents received reflections in equivalent time. The receiver according to one aspect of the invention includes an avalanche photodiode and a sampling gate coupled to the photodiode which is responsive to the received timing signal. The transmitter includes a laser diode which supplies a sequence of visible electromagnetic pulses. A bright spot projected on to the target clearly indicates the point that is being measured, and the user can read the range to that point with precision of better than 0.1%.

Light beam range finder

DOEpatents

McEwan, T.E.

1998-06-16

A ``laser tape measure`` for measuring distance is disclosed which includes a transmitter such as a laser diode which transmits a sequence of electromagnetic pulses in response to a transmit timing signal. A receiver samples reflections from objects within the field of the sequence of visible electromagnetic pulses with controlled timing, in response to a receive timing signal. The receiver generates a sample signal in response to the samples which indicates distance to the object causing the reflections. The timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the reflection such that the time between transmission of pulses in the sequence in sampling by the receiver sweeps over a range of delays. The transmit timing signal causes the transmitter to transmit the sequence of electromagnetic pulses at a pulse repetition rate, and the received timing signal sweeps over the range of delays in a sweep cycle such that reflections are sampled at the pulse repetition rate and with different delays in the range of delays, such that the sample signal represents received reflections in equivalent time. The receiver according to one aspect of the invention includes an avalanche photodiode and a sampling gate coupled to the photodiode which is responsive to the received timing signal. The transmitter includes a laser diode which supplies a sequence of visible electromagnetic pulses. A bright spot projected on to the target clearly indicates the point that is being measured, and the user can read the range to that point with precision of better than 0.1%. 7 figs.

Structator: fast index-based search for RNA sequence-structure patterns

PubMed Central

2011-01-01

Background The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs. Results We present a novel method and readily applicable software for time efficient matching of RNA sequence-structure patterns in sequence databases. Our approach is based on affix arrays, a recently introduced index data structure, preprocessed from the target database. Affix arrays support bidirectional pattern search, which is required for efficiently handling the structural constraints of the pattern. Structural patterns like stem-loops can be matched inside out, such that the loop region is matched first and then the pairing bases on the boundaries are matched consecutively. This allows to exploit base pairing information for search space reduction and leads to an expected running time that is sublinear in the size of the sequence database. The incorporation of a new chaining approach in the search of RNA sequence-structure patterns enables the description of molecules folding into complex secondary structures with multiple ordered patterns. The chaining approach removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our method runs up to two orders of magnitude faster than previous methods. Conclusions The presented method's sublinear expected running time makes it well suited for RNA sequence-structure pattern matching in large sequence databases. RNA molecules containing several stem-loop substructures can be described by multiple sequence-structure patterns and their matches are efficiently handled by a novel chaining method. Beyond our algorithmic contributions, we provide with Structator a complete and robust open-source software solution for index-based search of RNA sequence-structure patterns. The Structator software is available at http://www.zbh.uni-hamburg.de/Structator. PMID:21619640

T1 weighted fat/water separated PROPELLER acquired with dual bandwidths.

PubMed

Rydén, Henric; Berglund, Johan; Norbeck, Ola; Avventi, Enrico; Skare, Stefan

2018-04-24

To describe a fat/water separated dual receiver bandwidth (rBW) spin echo PROPELLER sequence that eliminates the dead time associated with single rBW sequences. A nonuniform noise whitening by regularization of the fat/water inverse problem is proposed, to enable dual rBW reconstructions. Bipolar, flyback, and dual spin echo sequences were developed. All sequences acquire two echoes with different rBW without dead time. Chemical shift displacement was corrected by performing the fat/water separation in k-space, prior to gridding. The proposed sequences were compared to fat saturation, and single rBW sequences, in terms of SNR and CNR efficiency, using clinically relevant acquisition parameters. The impact of motion was investigated. Chemical shift correction greatly improved the image quality, especially at high resolution acquired with low rBW, and also improved motion estimates. SNR efficiency of the dual spin echo sequence was up to 20% higher than the single rBW acquisition, while CNR efficiency was 50% higher for the bipolar acquisition. Noise whitening was deemed necessary for all dual rBW acquisitions, rendering high image quality with strong and homogenous fat suppression. Dual rBW sequences eliminate the dead time present in single rBW sequences, which improves SNR efficiency. In combination with the proposed regularization, this enables highly efficient T1-weighted PROPELLER images without chemical shift displacement. © 2018 International Society for Magnetic Resonance in Medicine.

Evaluation of electrical test conditions in MIL-M-38510 slash sheets

NASA Astrophysics Data System (ADS)

Sandgren, K.

1980-08-01

Adequacy of MIL-M-38510 slash sheet requirements for electrical test conditions in an automated test environment were evaluated. Military temperature range commercial devices of 13 types from 6 manufacturers were purchased. Software for testing these devices and for varying the test conditions was written for the Tektronix S-3260 test system. The devices were tested to evaluate the effects of pin-condition settling time, measurement sequence of the same and different D-C parameters, temperature sequence, differently defined temperature ambients, variable measurement conditions, sequence of time measurements, pin-application sequence, and undesignated pin condition ambiguity. An alternative to current tri-state enable and disable time measurements is proposed; S-3260 'open' and 'ground' conditions are characterized; and suggestions for changes in MIL-M-38510 slash sheet specifications and MIL-STD-883 test methods are proposed, both to correct errors and ambiguities and to facilitate the gathering of repeatable data on automated test equipment. Data obtained showed no sensitivity to measurement or temperature sequence nor to temperature ambient, provided that test times were not excessive. V sub ICP tests and some low current measurements required allowance for a pin condition settling time because of the test system speed. Some pin condition application sequences yielded incorrect measurements. Undefined terminal conditions of output pins were found to affect I sub OS and propagation delay time measurements. Truth table test results varied with test frequency and V sub IL for low-power Schottky devices.

Improvements on a privacy-protection algorithm for DNA sequences with generalization lattices.

PubMed

Li, Guang; Wang, Yadong; Su, Xiaohong

2012-10-01

When developing personal DNA databases, there must be an appropriate guarantee of anonymity, which means that the data cannot be related back to individuals. DNA lattice anonymization (DNALA) is a successful method for making personal DNA sequences anonymous. However, it uses time-consuming multiple sequence alignment and a low-accuracy greedy clustering algorithm. Furthermore, DNALA is not an online algorithm, and so it cannot quickly return results when the database is updated. This study improves the DNALA method. Specifically, we replaced the multiple sequence alignment in DNALA with global pairwise sequence alignment to save time, and we designed a hybrid clustering algorithm comprised of a maximum weight matching (MWM)-based algorithm and an online algorithm. The MWM-based algorithm is more accurate than the greedy algorithm in DNALA and has the same time complexity. The online algorithm can process data quickly when the database is updated. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Ongoing behavior predicts perceptual report of interval duration

PubMed Central

Gouvêa, Thiago S.; Monteiro, Tiago; Soares, Sofia; Atallah, Bassam V.; Paton, Joseph J.

2014-01-01

The ability to estimate the passage of time is essential for adaptive behavior in complex environments. Yet, it is not known how the brain encodes time over the durations necessary to explain animal behavior. Under temporally structured reinforcement schedules, animals tend to develop temporally structured behavior, and interval timing has been suggested to be accomplished by learning sequences of behavioral states. If this is true, trial to trial fluctuations in behavioral sequences should be predictive of fluctuations in time estimation. We trained rodents in an duration categorization task while continuously monitoring their behavior with a high speed camera. Animals developed highly reproducible behavioral sequences during the interval being timed. Moreover, those sequences were often predictive of perceptual report from early in the trial, providing support to the idea that animals may use learned behavioral patterns to estimate the duration of time intervals. To better resolve the issue, we propose that continuous and simultaneous behavioral and neural monitoring will enable identification of neural activity related to time perception that is not explained by ongoing behavior. PMID:24672473

SNPServer: a real-time SNP discovery tool.

PubMed

Savage, David; Batley, Jacqueline; Erwin, Tim; Logan, Erica; Love, Christopher G; Lim, Geraldine A C; Mongin, Emmanuel; Barker, Gary; Spangenberg, German C; Edwards, David

2005-07-01

SNPServer is a real-time flexible tool for the discovery of SNPs (single nucleotide polymorphisms) within DNA sequence data. The program uses BLAST, to identify related sequences, and CAP3, to cluster and align these sequences. The alignments are parsed to the SNP discovery software autoSNP, a program that detects SNPs and insertion/deletion polymorphisms (indels). Alternatively, lists of related sequences or pre-assembled sequences may be entered for SNP discovery. SNPServer and autoSNP use redundancy to differentiate between candidate SNPs and sequence errors. For each candidate SNP, two measures of confidence are calculated, the redundancy of the polymorphism at a SNP locus and the co-segregation of the candidate SNP with other SNPs in the alignment. SNPServer is available at http://hornbill.cspp.latrobe.edu.au/snpdiscovery.html.

Implicit Sequence Learning in Dyslexia: A Within-Sequence Comparison of First- and Higher-Order Information

ERIC Educational Resources Information Center

Du, Wenchong; Kelly, Steve W.

2013-01-01

The present study examines implicit sequence learning in adult dyslexics with a focus on comparing sequence transitions with different statistical complexities. Learning of a 12-item deterministic sequence was assessed in 12 dyslexic and 12 non-dyslexic university students. Both groups showed equivalent standard reaction time increments when the…

Complete genome sequence of Southern tomato virus naturally infecting tomatoes in Bangladesh using small RNA deep sequencing

USDA-ARS?s Scientific Manuscript database

The complete genome sequence of a Southern tomato virus (STV) isolate on tomato plants in a seed production field in Bangladesh was obtained for the first time using next generation sequencing. The identified isolate STV_BD-13 shares high degree of sequence identity (99%) with several known STV isol...

Efficient methods for implementation of multi-level nonrigid mass-preserving image registration on GPUs and multi-threaded CPUs.

PubMed

Ellingwood, Nathan D; Yin, Youbing; Smith, Matthew; Lin, Ching-Long

2016-04-01

Faster and more accurate methods for registration of images are important for research involved in conducting population-based studies that utilize medical imaging, as well as improvements for use in clinical applications. We present a novel computation- and memory-efficient multi-level method on graphics processing units (GPU) for performing registration of two computed tomography (CT) volumetric lung images. We developed a computation- and memory-efficient Diffeomorphic Multi-level B-Spline Transform Composite (DMTC) method to implement nonrigid mass-preserving registration of two CT lung images on GPU. The framework consists of a hierarchy of B-Spline control grids of increasing resolution. A similarity criterion known as the sum of squared tissue volume difference (SSTVD) was adopted to preserve lung tissue mass. The use of SSTVD consists of the calculation of the tissue volume, the Jacobian, and their derivatives, which makes its implementation on GPU challenging due to memory constraints. The use of the DMTC method enabled reduced computation and memory storage of variables with minimal communication between GPU and Central Processing Unit (CPU) due to ability to pre-compute values. The method was assessed on six healthy human subjects. Resultant GPU-generated displacement fields were compared against the previously validated CPU counterpart fields, showing good agreement with an average normalized root mean square error (nRMS) of 0.044±0.015. Runtime and performance speedup are compared between single-threaded CPU, multi-threaded CPU, and GPU algorithms. Best performance speedup occurs at the highest resolution in the GPU implementation for the SSTVD cost and cost gradient computations, with a speedup of 112 times that of the single-threaded CPU version and 11 times over the twelve-threaded version when considering average time per iteration using a Nvidia Tesla K20X GPU. The proposed GPU-based DMTC method outperforms its multi-threaded CPU version in terms of runtime. Total registration time reduced runtime to 2.9min on the GPU version, compared to 12.8min on twelve-threaded CPU version and 112.5min on a single-threaded CPU. Furthermore, the GPU implementation discussed in this work can be adapted for use of other cost functions that require calculation of the first derivatives. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Free-breathing cardiac MR stress perfusion with real-time slice tracking.

PubMed

Basha, Tamer A; Roujol, Sébastien; Kissinger, Kraig V; Goddu, Beth; Berg, Sophie; Manning, Warren J; Nezafat, Reza

2014-09-01

To develop a free-breathing cardiac MR perfusion sequence with slice tracking for use after physical exercise. We propose to use a leading navigator, placed immediately before each 2D slice acquisition, for tracking the respiratory motion and updating the slice location in real-time. The proposed sequence was used to acquire CMR perfusion datasets in 12 healthy adult subjects and 8 patients. Images were compared with the conventional perfusion (i.e., without slice tracking) results from the same subjects. The location and geometry of the myocardium were quantitatively analyzed, and the perfusion signal curves were calculated from both sequences to show the efficacy of the proposed sequence. The proposed sequence was significantly better compared with the conventional perfusion sequence in terms of qualitative image scores. Changes in the myocardial location and geometry decreased by 50% in the slice tracking sequence. Furthermore, the proposed sequence had signal curves that are smoother and less noisy. The proposed sequence significantly reduces the effect of the respiratory motion on the image acquisition in both rest and stress perfusion scans. Copyright © 2013 Wiley Periodicals, Inc.

SSAW: A new sequence similarity analysis method based on the stationary discrete wavelet transform.

PubMed

Lin, Jie; Wei, Jing; Adjeroh, Donald; Jiang, Bing-Hua; Jiang, Yue

2018-05-02

Alignment-free sequence similarity analysis methods often lead to significant savings in computational time over alignment-based counterparts. A new alignment-free sequence similarity analysis method, called SSAW is proposed. SSAW stands for Sequence Similarity Analysis using the Stationary Discrete Wavelet Transform (SDWT). It extracts k-mers from a sequence, then maps each k-mer to a complex number field. Then, the series of complex numbers formed are transformed into feature vectors using the stationary discrete wavelet transform. After these steps, the original sequence is turned into a feature vector with numeric values, which can then be used for clustering and/or classification. Using two different types of applications, namely, clustering and classification, we compared SSAW against the the-state-of-the-art alignment free sequence analysis methods. SSAW demonstrates competitive or superior performance in terms of standard indicators, such as accuracy, F-score, precision, and recall. The running time was significantly better in most cases. These make SSAW a suitable method for sequence analysis, especially, given the rapidly increasing volumes of sequence data required by most modern applications.

Time-resolved fluorescence imaging of slab gels for lifetime base-calling in DNA sequencing applications.

PubMed

Lassiter, S J; Stryjewski, W; Legendre, B L; Erdmann, R; Wahl, M; Wurm, J; Peterson, R; Middendorf, L; Soper, S A

2000-11-01

A compact time-resolved near-IR fluorescence imager was constructed to obtain lifetime and intensity images of DNA sequencing slab gels. The scanner consisted of a microscope body with f/1.2 relay optics onto which was mounted a pulsed diode laser (repetition rate 80 MHz, lasing wavelength 680 nm, average power 5 mW), filtering optics, and a large photoactive area (diameter 500 microns) single-photon avalanche diode that was actively quenched to provide a large dynamic operating range. The time-resolved data were processed using electronics configured in a conventional time-correlated single-photon-counting format with all of the counting hardware situated on a PC card resident on the computer bus. The microscope head produced a timing response of 450 ps (fwhm) in a scanning mode, allowing the measurement of subnano-second lifetimes. The time-resolved microscope head was placed in an automated DNA sequencer and translated across a 21-cm-wide gel plate in approximately 6 s (scan rate 3.5 cm/s) with an accumulation time per pixel of 10 ms. The sampling frequency was 0.17 Hz (duty cycle 0.0017), sufficient to prevent signal aliasing during the electrophoresis separation. Software (written in Visual Basic) allowed acquisition of both the intensity image and lifetime analysis of DNA bands migrating through the gel in real time. Using a dual-labeling (IRD700 and Cy5.5 labeling dyes)/two-lane sequencing strategy, we successfully read 670 bases of a control M13mp18 ssDNA template using lifetime identification. Comparison of the reconstructed sequence with the known sequence of the phage indicated the number of miscalls was only 2, producing an error rate of approximately 0.3% (identification accuracy 99.7%). The lifetimes were calculated using maximum likelihood estimators and allowed on-line determinations with high precision, even when short integration times were used to construct the decay profiles. Comparison of the lifetime base calling to a single-dye/four-lane sequencing strategy indicated similar results in terms of miscalls, but reduced insertion and deletion errors using lifetime identification methods, improving the overall read accuracy.

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.

PubMed

White, Eric J; Emanuelsson, Olof; Scalzo, David; Royce, Thomas; Kosak, Steven; Oakeley, Edward J; Weissman, Sherman; Gerstein, Mark; Groudine, Mark; Snyder, Michael; Schübeler, Dirk

2004-12-21

Duplication of the genome during the S phase of the cell cycle does not occur simultaneously; rather, different sequences are replicated at different times. The replication timing of specific sequences can change during development; however, the determinants of this dynamic process are poorly understood. To gain insights into the contribution of developmental state, genomic sequence, and transcriptional activity to replication timing, we investigated the timing of DNA replication at high resolution along an entire human chromosome (chromosome 22) in two different cell types. The pattern of replication timing was correlated with respect to annotated genes, gene expression, novel transcribed regions of unknown function, sequence composition, and cytological features. We observed that chromosome 22 contains regions of early- and late-replicating domains of 100 kb to 2 Mb, many (but not all) of which are associated with previously described chromosomal bands. In both cell types, expressed sequences are replicated earlier than nontranscribed regions. However, several highly transcribed regions replicate late. Overall, the DNA replication-timing profiles of the two different cell types are remarkably similar, with only nine regions of difference observed. In one case, this difference reflects the differential expression of an annotated gene that resides in this region. Novel transcribed regions with low coding potential exhibit a strong propensity for early DNA replication. Although the cellular function of such transcripts is poorly understood, our results suggest that their activity is linked to the replication-timing program.

Adaptive efficient compression of genomes

PubMed Central

2012-01-01

Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. However, memory requirements of the current algorithms are high and run times often are slow. In this paper, we propose an adaptive, parallel and highly efficient referential sequence compression method which allows fine-tuning of the trade-off between required memory and compression speed. When using 12 MB of memory, our method is for human genomes on-par with the best previous algorithms in terms of compression ratio (400:1) and compression speed. In contrast, it compresses a complete human genome in just 11 seconds when provided with 9 GB of main memory, which is almost three times faster than the best competitor while using less main memory. PMID:23146997

Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data.

PubMed Central

Drummond, Alexei J; Nicholls, Geoff K; Rodrigo, Allen G; Solomon, Wiremu

2002-01-01

Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly available with modern sequencing technology. Here, we present a Bayesian statistical inference approach to the joint estimation of mutation rate and population size that incorporates the uncertainty in the genealogy of such temporally spaced sequences by using Markov chain Monte Carlo (MCMC) integration. The Kingman coalescent model is used to describe the time structure of the ancestral tree. We recover information about the unknown true ancestral coalescent tree, population size, and the overall mutation rate from temporally spaced data, that is, from nucleotide sequences gathered at different times, from different individuals, in an evolving haploid population. We briefly discuss the methodological implications and show what can be inferred, in various practically relevant states of prior knowledge. We develop extensions for exponentially growing population size and joint estimation of substitution model parameters. We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences. PMID:12136032

Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data.

PubMed

Drummond, Alexei J; Nicholls, Geoff K; Rodrigo, Allen G; Solomon, Wiremu

2002-07-01

Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly available with modern sequencing technology. Here, we present a Bayesian statistical inference approach to the joint estimation of mutation rate and population size that incorporates the uncertainty in the genealogy of such temporally spaced sequences by using Markov chain Monte Carlo (MCMC) integration. The Kingman coalescent model is used to describe the time structure of the ancestral tree. We recover information about the unknown true ancestral coalescent tree, population size, and the overall mutation rate from temporally spaced data, that is, from nucleotide sequences gathered at different times, from different individuals, in an evolving haploid population. We briefly discuss the methodological implications and show what can be inferred, in various practically relevant states of prior knowledge. We develop extensions for exponentially growing population size and joint estimation of substitution model parameters. We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences.

Beyond Reasonable Doubt: Evolution from DNA Sequences

PubMed Central

Penny, David

2013-01-01

We demonstrate quantitatively that, as predicted by evolutionary theory, sequences of homologous proteins from different species converge as we go further and further back in time. The converse, a non-evolutionary model can be expressed as probabilities, and the test works for chloroplast, nuclear and mitochondrial sequences, as well as for sequences that diverged at different time depths. Even on our conservative test, the probability that chance could produce the observed levels of ancestral convergence for just one of the eight datasets of 51 proteins is ≈1×10−19 and combined over 8 datasets is ≈1×10−132. By comparison, there are about 1080 protons in the universe, hence the probability that the sequences could have been produced by a process involving unrelated ancestral sequences is about 1050 lower than picking, among all protons, the same proton at random twice in a row. A non-evolutionary control model shows no convergence, and only a small number of parameters are required to account for the observations. It is time that that researchers insisted that doubters put up testable alternatives to evolution. PMID:23950906

Targeted Re-Sequencing Emulsion PCR Panel for Myopathies: Results in 94 Cases.

PubMed

Punetha, Jaya; Kesari, Akanchha; Uapinyoying, Prech; Giri, Mamta; Clarke, Nigel F; Waddell, Leigh B; North, Kathryn N; Ghaoui, Roula; O'Grady, Gina L; Oates, Emily C; Sandaradura, Sarah A; Bönnemann, Carsten G; Donkervoort, Sandra; Plotz, Paul H; Smith, Edward C; Tesi-Rocha, Carolina; Bertorini, Tulio E; Tarnopolsky, Mark A; Reitter, Bernd; Hausmanowa-Petrusewicz, Irena; Hoffman, Eric P

2016-05-27

Molecular diagnostics in the genetic myopathies often requires testing of the largest and most complex transcript units in the human genome (DMD, TTN, NEB). Iteratively targeting single genes for sequencing has traditionally entailed high costs and long turnaround times. Exome sequencing has begun to supplant single targeted genes, but there are concerns regarding coverage and needed depth of the very large and complex genes that frequently cause myopathies. To evaluate efficiency of next-generation sequencing technologies to provide molecular diagnostics for patients with previously undiagnosed myopathies. We tested a targeted re-sequencing approach, using a 45 gene emulsion PCR myopathy panel, with subsequent sequencing on the Illumina platform in 94 undiagnosed patients. We compared the targeted re-sequencing approach to exome sequencing for 10 of these patients studied. We detected likely pathogenic mutations in 33 out of 94 patients with a molecular diagnostic rate of approximately 35%. The remaining patients showed variants of unknown significance (35/94 patients) or no mutations detected in the 45 genes tested (26/94 patients). Mutation detection rates for targeted re-sequencing vs. whole exome were similar in both methods; however exome sequencing showed better distribution of reads and fewer exon dropouts. Given that costs of highly parallel re-sequencing and whole exome sequencing are similar, and that exome sequencing now takes considerably less laboratory processing time than targeted re-sequencing, we recommend exome sequencing as the standard approach for molecular diagnostics of myopathies.

Characterisation and Next-generation Sequencing Analysis of Unknown Arboviruses

DTIC Science & Technology

2012-09-01

on the development of real- time PCR detection assays for Vibrio cholerae, a water-borne bacterium responsible for severe enteric disease. From...specific sequence [22]. The length of time from harvesting virus to generating samples that are ready for sequencing takes about two weeks, which is a...two viruses, and on day 4 post infection significant and widespread cytopathic effect was observed. The viruses were harvested by ultracentrifugation

Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing.

PubMed

Nong, Rachel Yuan; Wu, Di; Yan, Junhong; Hammond, Maria; Gu, Gucci Jijuan; Kamali-Moghaddam, Masood; Landegren, Ulf; Darmanis, Spyros

2013-06-01

Solid-phase proximity ligation assays share properties with the classical sandwich immunoassays for protein detection. The proteins captured via antibodies on solid supports are, however, detected not by single antibodies with detectable functions, but by pairs of antibodies with attached DNA strands. Upon recognition by these sets of three antibodies, pairs of DNA strands brought in proximity are joined by ligation. The ligated reporter DNA strands are then detected via methods such as real-time PCR or next-generation sequencing (NGS). We describe how to construct assays that can offer improved detection specificity by virtue of recognition by three antibodies, as well as enhanced sensitivity owing to reduced background and amplified detection. Finally, we also illustrate how the assays can be applied for parallel detection of proteins, taking advantage of the oligonucleotide ligation step to avoid background problems that might arise with multiplexing. The protocol for the singleplex solid-phase proximity ligation assay takes ~5 h. The multiplex version of the assay takes 7-8 h depending on whether quantitative PCR (qPCR) or sequencing is used as the readout. The time for the sequencing-based protocol includes the library preparation but not the actual sequencing, as times may vary based on the choice of sequencing platform.

Detecting and Characterizing Repeating Earthquake Sequences During Volcanic Eruptions

NASA Astrophysics Data System (ADS)

Tepp, G.; Haney, M. M.; Wech, A.

2017-12-01

A major challenge in volcano seismology is forecasting eruptions. Repeating earthquake sequences often precede volcanic eruptions or lava dome activity, providing an opportunity for short-term eruption forecasting. Automatic detection of these sequences can lead to timely eruption notification and aid in continuous monitoring of volcanic systems. However, repeating earthquake sequences may also occur after eruptions or along with magma intrusions that do not immediately lead to an eruption. This additional challenge requires a better understanding of the processes involved in producing these sequences to distinguish those that are precursory. Calculation of the inverse moment rate and concepts from the material failure forecast method can lead to such insights. The temporal evolution of the inverse moment rate is observed to differ for precursory and non-precursory sequences, and multiple earthquake sequences may occur concurrently. These observations suggest that sequences may occur in different locations or through different processes. We developed an automated repeating earthquake sequence detector and near real-time alarm to send alerts when an in-progress sequence is identified. Near real-time inverse moment rate measurements can further improve our ability to forecast eruptions by allowing for characterization of sequences. We apply the detector to eruptions of two Alaskan volcanoes: Bogoslof in 2016-2017 and Redoubt Volcano in 2009. The Bogoslof eruption produced almost 40 repeating earthquake sequences between its start in mid-December 2016 and early June 2017, 21 of which preceded an explosive eruption, and 2 sequences in the months before eruptive activity. Three of the sequences occurred after the implementation of the alarm in late March 2017 and successfully triggered alerts. The nearest seismometers to Bogoslof are over 45 km away, requiring a detector that can work with few stations and a relatively low signal-to-noise ratio. During the Redoubt eruption, earthquake sequences were observed in the months leading up to the eruptive activity beginning in March 2009 as well as immediately preceding 7 of the 19 explosive events. In contrast to Bogoslof, Redoubt has a local monitoring network which allows for better detection and more detailed analysis of the repeating earthquake sequences.

Automated Sanger Analysis Pipeline (ASAP): A Tool for Rapidly Analyzing Sanger Sequencing Data with Minimum User Interference.

PubMed

Singh, Aditya; Bhatia, Prateek

2016-12-01

Sanger sequencing platforms, such as applied biosystems instruments, generate chromatogram files. Generally, for 1 region of a sequence, we use both forward and reverse primers to sequence that area, in that way, we have 2 sequences that need to be aligned and a consensus generated before mutation detection studies. This work is cumbersome and takes time, especially if the gene is large with many exons. Hence, we devised a rapid automated command system to filter, build, and align consensus sequences and also optionally extract exonic regions, translate them in all frames, and perform an amino acid alignment starting from raw sequence data within a very short time. In full capabilities of Automated Mutation Analysis Pipeline (ASAP), it is able to read "*.ab1" chromatogram files through command line interface, convert it to the FASTQ format, trim the low-quality regions, reverse-complement the reverse sequence, create a consensus sequence, extract the exonic regions using a reference exonic sequence, translate the sequence in all frames, and align the nucleic acid and amino acid sequences to reference nucleic acid and amino acid sequences, respectively. All files are created and can be used for further analysis. ASAP is available as Python 3.x executable at https://github.com/aditya-88/ASAP. The version described in this paper is 0.28.

Quantification of fetal heart rate regularity using symbolic dynamics

NASA Astrophysics Data System (ADS)

van Leeuwen, P.; Cysarz, D.; Lange, S.; Geue, D.; Groenemeyer, D.

2007-03-01

Fetal heart rate complexity was examined on the basis of RR interval time series obtained in the second and third trimester of pregnancy. In each fetal RR interval time series, short term beat-to-beat heart rate changes were coded in 8bit binary sequences. Redundancies of the 28 different binary patterns were reduced by two different procedures. The complexity of these sequences was quantified using the approximate entropy (ApEn), resulting in discrete ApEn values which were used for classifying the sequences into 17 pattern sets. Also, the sequences were grouped into 20 pattern classes with respect to identity after rotation or inversion of the binary value. There was a specific, nonuniform distribution of the sequences in the pattern sets and this differed from the distribution found in surrogate data. In the course of gestation, the number of sequences increased in seven pattern sets, decreased in four and remained unchanged in six. Sequences that occurred less often over time, both regular and irregular, were characterized by patterns reflecting frequent beat-to-beat reversals in heart rate. They were also predominant in the surrogate data, suggesting that these patterns are associated with stochastic heart beat trains. Sequences that occurred more frequently over time were relatively rare in the surrogate data. Some of these sequences had a high degree of regularity and corresponded to prolonged heart rate accelerations or decelerations which may be associated with directed fetal activity or movement or baroreflex activity. Application of the pattern classes revealed that those sequences with a high degree of irregularity correspond to heart rate patterns resulting from complex physiological activity such as fetal breathing movements. The results suggest that the development of the autonomic nervous system and the emergence of fetal behavioral states lead to increases in not only irregular but also regular heart rate patterns. Using symbolic dynamics to examine the cardiovascular system may thus lead to new insight with respect to fetal development.

A systematic evaluation of three different cardiac T2-mapping sequences at 1.5 and 3T in healthy volunteers.

PubMed

Baeßler, Bettina; Schaarschmidt, Frank; Stehning, Christian; Schnackenburg, Bernhard; Maintz, David; Bunck, Alexander C

2015-11-01

Previous studies showed that myocardial T2 relaxation times measured by cardiac T2-mapping vary significantly depending on sequence and field strength. Therefore, a systematic comparison of different T2-mapping sequences and the establishment of dedicated T2 reference values is mandatory for diagnostic decision-making. Phantom experiments using gel probes with a range of different T1 and T2 times were performed on a clinical 1.5T and 3T scanner. In addition, 30 healthy volunteers were examined at 1.5 and 3T in immediate succession. In each examination, three different T2-mapping sequences were performed at three short-axis slices: Multi Echo Spin Echo (MESE), T2-prepared balanced SSFP (T2prep), and Gradient Spin Echo with and without fat saturation (GraSEFS/GraSE). Segmented T2-Maps were generated according to the AHA 16-segment model and statistical analysis was performed. Significant intra-individual differences between mean T2 times were observed for all sequences. In general, T2prep resulted in lowest and GraSE in highest T2 times. A significant variation with field strength was observed for mean T2 in phantom as well as in vivo, with higher T2 values at 1.5T compared to 3T, regardless of the sequence used. Segmental T2 values for each sequence at 1.5 and 3T are presented. Despite a careful selection of sequence parameters and volunteers, significant variations of the measured T2 values were observed between field strengths, MR sequences and myocardial segments. Therefore, we present segmental T2 values for each sequence at 1.5 and 3T with the inherent potential to serve as reference values for future studies. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Use of the melting curve assay as a means for high-throughput quantification of Illumina sequencing libraries.

PubMed

Shinozuka, Hiroshi; Forster, John W

2016-01-01

Background. Multiplexed sequencing is commonly performed on massively parallel short-read sequencing platforms such as Illumina, and the efficiency of library normalisation can affect the quality of the output dataset. Although several library normalisation approaches have been established, none are ideal for highly multiplexed sequencing due to issues of cost and/or processing time. Methods. An inexpensive and high-throughput library quantification method has been developed, based on an adaptation of the melting curve assay. Sequencing libraries were subjected to the assay using the Bio-Rad Laboratories CFX Connect(TM) Real-Time PCR Detection System. The library quantity was calculated through summation of reduction of relative fluorescence units between 86 and 95 °C. Results.PCR-enriched sequencing libraries are suitable for this quantification without pre-purification of DNA. Short DNA molecules, which ideally should be eliminated from the library for subsequent processing, were differentiated from the target DNA in a mixture on the basis of differences in melting temperature. Quantification results for long sequences targeted using the melting curve assay were correlated with those from existing methods (R (2) > 0.77), and that observed from MiSeq sequencing (R (2) = 0.82). Discussion.The results of multiplexed sequencing suggested that the normalisation performance of the described method is equivalent to that of another recently reported high-throughput bead-based method, BeNUS. However, costs for the melting curve assay are considerably lower and processing times shorter than those of other existing methods, suggesting greater suitability for highly multiplexed sequencing applications.

SNaPshot and StripAssay as Valuable Alternatives to Direct Sequencing for KRAS Mutation Detection in Colon Cancer Routine Diagnostics

PubMed Central

Fariña Sarasqueta, Arantza; Moerland, Elna; de Bruyne, Hanneke; de Graaf, Henk; Vrancken, Tamara; van Lijnschoten, Gesina; van den Brule, Adriaan J.C.

2011-01-01

Although direct sequencing is the gold standard for KRAS mutation detection in routine diagnostics, it remains laborious, time consuming, and not very sensitive. Our objective was to evaluate SNaPshot and the KRAS StripAssay as alternatives to sequencing for KRAS mutation detection in daily practice. KRAS exon 2–specific PCR followed by sequencing or by a SNaPshot reaction was performed. For the StripAssay, a mutant-enriched PCR was followed by hybridization to KRAS-specific probes bound to a nitrocellulose strip. To test sensitivities, dilution series of mutated DNA in wild-type DNA were made. Additionally, direct sequencing and SNaPshot were evaluated in 296 colon cancer samples. Detection limits of direct sequencing, SNaPshot, and StripAssay were 20%, 10%, and 1% tumor cells, respectively. Direct sequencing and SNaPshot can detect all 12 mutations in KRAS codons 12 and 13, whereas the StripAssay detects 10 of the most frequent ones. Workload and time to results are comparable for SNaPshot and direct sequencing. SNaPshot is flexible and easy to multiplex. The StripAssay is less time consuming for daily laboratory practice. SNaPshot is more flexible and slightly more sensitive than direct sequencing. The clinical evaluation showed comparable performances between direct sequencing and SNaPshot. The StripAssay is rapid and an extremely sensitive assay that could be considered when few tumor cells are available. However, found mutants should be confirmed to avoid risk of false positives. PMID:21354055

Real-time, portable genome sequencing for Ebola surveillance.

PubMed

Quick, Joshua; Loman, Nicholas J; Duraffour, Sophie; Simpson, Jared T; Severi, Ettore; Cowley, Lauren; Bore, Joseph Akoi; Koundouno, Raymond; Dudas, Gytis; Mikhail, Amy; Ouédraogo, Nobila; Afrough, Babak; Bah, Amadou; Baum, Jonathan Hj; Becker-Ziaja, Beate; Boettcher, Jan-Peter; Cabeza-Cabrerizo, Mar; Camino-Sanchez, Alvaro; Carter, Lisa L; Doerrbecker, Juiliane; Enkirch, Theresa; Dorival, Isabel Graciela García; Hetzelt, Nicole; Hinzmann, Julia; Holm, Tobias; Kafetzopoulou, Liana Eleni; Koropogui, Michel; Kosgey, Abigail; Kuisma, Eeva; Logue, Christopher H; Mazzarelli, Antonio; Meisel, Sarah; Mertens, Marc; Michel, Janine; Ngabo, Didier; Nitzsche, Katja; Pallash, Elisa; Patrono, Livia Victoria; Portmann, Jasmine; Repits, Johanna Gabriella; Rickett, Natasha Yasmin; Sachse, Andrea; Singethan, Katrin; Vitoriano, Inês; Yemanaberhan, Rahel L; Zekeng, Elsa G; Trina, Racine; Bello, Alexander; Sall, Amadou Alpha; Faye, Ousmane; Faye, Oumar; Magassouba, N'Faly; Williams, Cecelia V; Amburgey, Victoria; Winona, Linda; Davis, Emily; Gerlach, Jon; Washington, Franck; Monteil, Vanessa; Jourdain, Marine; Bererd, Marion; Camara, Alimou; Somlare, Hermann; Camara, Abdoulaye; Gerard, Marianne; Bado, Guillaume; Baillet, Bernard; Delaune, Déborah; Nebie, Koumpingnin Yacouba; Diarra, Abdoulaye; Savane, Yacouba; Pallawo, Raymond Bernard; Gutierrez, Giovanna Jaramillo; Milhano, Natacha; Roger, Isabelle; Williams, Christopher J; Yattara, Facinet; Lewandowski, Kuiama; Taylor, Jamie; Rachwal, Philip; Turner, Daniel; Pollakis, Georgios; Hiscox, Julian A; Matthews, David A; O'Shea, Matthew K; Johnston, Andrew McD; Wilson, Duncan; Hutley, Emma; Smit, Erasmus; Di Caro, Antonino; Woelfel, Roman; Stoecker, Kilian; Fleischmann, Erna; Gabriel, Martin; Weller, Simon A; Koivogui, Lamine; Diallo, Boubacar; Keita, Sakoba; Rambaut, Andrew; Formenty, Pierre; Gunther, Stephan; Carroll, Miles W

2016-02-11

The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10(-3) and 1.42 × 10(-3) mutations per site per year. This is equivalent to 16-27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15-60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.

A Fast-Time Simulation Tool for Analysis of Airport Arrival Traffic

NASA Technical Reports Server (NTRS)

Erzberger, Heinz; Meyn, Larry A.; Neuman, Frank

2004-01-01

The basic objective of arrival sequencing in air traffic control automation is to match traffic demand and airport capacity while minimizing delays. The performance of an automated arrival scheduling system, such as the Traffic Management Advisor developed by NASA for the FAA, can be studied by a fast-time simulation that does not involve running expensive and time-consuming real-time simulations. The fast-time simulation models runway configurations, the characteristics of arrival traffic, deviations from predicted arrival times, as well as the arrival sequencing and scheduling algorithm. This report reviews the development of the fast-time simulation method used originally by NASA in the design of the sequencing and scheduling algorithm for the Traffic Management Advisor. The utility of this method of simulation is demonstrated by examining the effect on delays of altering arrival schedules at a hub airport.

Optimal MRI sequence for identifying occlusion location in acute stroke: which value of time-resolved contrast-enhanced MRA?

PubMed

Le Bras, A; Raoult, H; Ferré, J-C; Ronzière, T; Gauvrit, J-Y

2015-06-01

Identifying occlusion location is crucial for determining the optimal therapeutic strategy during the acute phase of ischemic stroke. The purpose of this study was to assess the diagnostic efficacy of MR imaging, including conventional sequences plus time-resolved contrast-enhanced MRA in comparison with DSA for identifying arterial occlusion location. Thirty-two patients with 34 occlusion levels referred for thrombectomy during acute cerebral stroke events were consecutively included from August 2010 to December 2012. Before thrombectomy, we performed 3T MR imaging, including conventional 3D-TOF and gradient-echo T2 sequences, along with time-resolved contrast-enhanced MRA of the extra- and intracranial arteries. The 3D-TOF, gradient-echo T2, and time-resolved contrast-enhanced MRA results were consensually assessed by 2 neuroradiologists and compared with prethrombectomy DSA results in terms of occlusion location. The Wilcoxon test was used for statistical analysis to compare MR imaging sequences with DSA, and the κ coefficient was used to determine intermodality agreement. The occlusion level on the 3D-TOF and gradient-echo T2 images differed significantly from that of DSA (P < .001 and P = .002, respectively), while no significant difference was observed between DSA and time-resolved contrast-enhanced MRA (P = .125). κ coefficients for intermodality agreement with DSA (95% CI, percentage agreement) were 0.43 (0.3%-0.6; 62%), 0.32 (0.2%-0.5; 56%), and 0.81 (0.6%-1.0; 88%) for 3D-TOF, gradient-echo T2, and time-resolved contrast-enhanced MRA, respectively. The time-resolved contrast-enhanced MRA sequence proved reliable for identifying occlusion location in acute stroke with performance superior to that of 3D-TOF and gradient-echo T2 sequences. © 2015 by American Journal of Neuroradiology.

Bi-exponential T2 analysis of healthy and diseased Achilles tendons: an in vivo preliminary magnetic resonance study and correlation with clinical score.

PubMed

Juras, Vladimir; Apprich, Sebastian; Szomolanyi, Pavol; Bieri, Oliver; Deligianni, Xeni; Trattnig, Siegfried

2013-10-01

To compare mono- and bi-exponential T2 analysis in healthy and degenerated Achilles tendons using a recently introduced magnetic resonance variable-echo-time sequence (vTE) for T2 mapping. Ten volunteers and ten patients were included in the study. A variable-echo-time sequence was used with 20 echo times. Images were post-processed with both techniques, mono- and bi-exponential [T2 m, short T2 component (T2 s) and long T2 component (T2 l)]. The number of mono- and bi-exponentially decaying pixels in each region of interest was expressed as a ratio (B/M). Patients were clinically assessed with the Achilles Tendon Rupture Score (ATRS), and these values were correlated with the T2 values. The means for both T2 m and T2 s were statistically significantly different between patients and volunteers; however, for T2 s, the P value was lower. In patients, the Pearson correlation coefficient between ATRS and T2 s was -0.816 (P = 0.007). The proposed variable-echo-time sequence can be successfully used as an alternative method to UTE sequences with some added benefits, such as a short imaging time along with relatively high resolution and minimised blurring artefacts, and minimised susceptibility artefacts and chemical shift artefacts. Bi-exponential T2 calculation is superior to mono-exponential in terms of statistical significance for the diagnosis of Achilles tendinopathy. • Magnetic resonance imaging offers new insight into healthy and diseased Achilles tendons • Bi-exponential T2 calculation in Achilles tendons is more beneficial than mono-exponential • A short T2 component correlates strongly with clinical score • Variable echo time sequences successfully used instead of ultrashort echo time sequences.

Bed II Sequence Stratigraphic context of EF-HR and HWK EE archaeological sites, and the Oldowan/Acheulean succession at Olduvai Gorge, Tanzania.

PubMed

Stanistreet, Ian G; McHenry, Lindsay J; Stollhofen, Harald; de la Torre, Ignacio

2018-04-20

Archaeological excavations at EF-HR and HWK EE allow reassessment of Bed II stratigraphy within the Junction Area and eastern Olduvai Gorge. Application of Sequence Stratigraphic methods provides a time-stratigraphic framework enabling correlation of sedimentary units across facies boundaries, applicable even in those areas where conventional timelines, such as tephrostratigraphic markers, are absent, eroded, or reworked. Sequence Stratigraphically, Bed II subdivides into five major Sequences 1 to 5, all floored by major disconformities that incise deeply into the underlying succession, proving that simple "layer cake" stratigraphy is inappropriate. Previous establishment of the Lemuta Member has invalidated the use of Tuff IIA as the boundary between Lower and Middle Bed II, now redefined at the disconformity between Sequences 2 and 3, a lithostratigraphic contact underlying the succession containing the Lower, Middle, and Upper Augitic Sandstones. HWK EE site records Oldowan technology in the Lower Augitic Sandstone at the base of Sequence 3, within Middle Bed II. We suggest placement of recently reported Acheulean levels at FLK W within the Middle Augitic Sandstone, thus emphasizing that handaxes are yet to be found in earlier stratigraphic units of the Olduvai sequence. This would place a boundary between the Oldowan and Acheulean technologies at Olduvai in the Tuff IIB zone or earliest Middle Augitic Sandstone. A major disconformity between Sequences 3 and 4 at and near EF-HR cuts through the level of Tuff IIC, placing the main Acheulean EF-HR assemblage at the base of Sequence 4, within Upper rather than Middle Bed II. Sequence stratigraphic methods also yield a more highly resolved Bed II stratigraphic framework. Backwall and sidewall surveying of archaeological trenches at EF-HR and HWK EE permits definition of "Lake-parasequences" nested within the major Sequences that record downcutting of disconformities associated with lake regression, then sedimentation associated with lake transgression, capped finally by another erosional disconformity or hiatal paraconformity caused by the next lake withdrawal. On a relative time-scale rather than a vertical metre scale, the resulting Wheeler diagram framework provides a basis for recognizing time-equivalent depositional episodes and the position of time gaps at various scales. Relative timing of archaeological assemblage levels can then be differentiated at a millennial scale within this framework. Copyright © 2018 Elsevier Ltd. All rights reserved.

Long-read sequencing and de novo assembly of a Chinese genome

USDA-ARS?s Scientific Manuscript database

Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arr...

Direct sequencing of hepatitis A virus and norovirus RT-PCR products from environmentally contaminated oyster using M13-tailed primers.

PubMed

Williams-Woods, Jacquelina; González-Escalona, Narjol; Burkhardt, William

2011-12-01

Human norovirus (HuNoV) and hepatitis A (HAV) are recognized as leading causes of non-bacterial foodborne associated illnesses in the United States. DNA sequencing is generally considered the standard for accurate viral genotyping in support of epidemiological investigations. Due to the genetic diversity of noroviruses (NoV), degenerate primer sets are often used in conventional reverse transcription (RT) PCR and real-time RT-quantitative PCR (RT-qPCR) for the detection of these viruses and cDNA fragments are generally cloned prior to sequencing. HAV detection methods that are sensitive and specific for real-time RT-qPCR yields small fragments sizes of 89-150bp, which can be difficult to sequence. In order to overcome these obstacles, norovirus and HAV primers were tailed with M13 forward and reverse primers. This modification increases the sequenced product size and allows for direct sequencing of the amplicons utilizing complementary M13 primers. HuNoV and HAV cDNA products from environmentally contaminated oysters were analyzed using this method. Alignments of the sequenced samples revealed ≥95% nucleotide identities. Tailing NoV and HAV primers with M13 sequence increases the cDNA product size, offers an alternative to cloning, and allows for rapid, accurate and direct sequencing of cDNA products produced by conventional or real time RT-qPCR assays. Published by Elsevier B.V.

Programming and Reprogramming Sequence Timing Following High and Low Contextual Interference Practice

ERIC Educational Resources Information Center

Wright, David L.; Magnuson, Curt E.; Black, Charles B.

2005-01-01

Individuals practiced two unique discrete sequence production tasks that differed in their relative time profile in either a blocked or random practice schedule. Each participant was subsequently administered a "precuing" protocol to examine the cost of initially compiling or modifying the plan for an upcoming movement's relative timing. The…

Single Machine Scheduling and Due Date Assignment with Past-Sequence-Dependent Setup Time and Position-Dependent Processing Time

PubMed Central

Zhao, Chuan-Li; Hsu, Hua-Feng

2014-01-01

This paper considers single machine scheduling and due date assignment with setup time. The setup time is proportional to the length of the already processed jobs; that is, the setup time is past-sequence-dependent (p-s-d). It is assumed that a job's processing time depends on its position in a sequence. The objective functions include total earliness, the weighted number of tardy jobs, and the cost of due date assignment. We analyze these problems with two different due date assignment methods. We first consider the model with job-dependent position effects. For each case, by converting the problem to a series of assignment problems, we proved that the problems can be solved in O(n 4) time. For the model with job-independent position effects, we proved that the problems can be solved in O(n 3) time by providing a dynamic programming algorithm. PMID:25258727

Single machine scheduling and due date assignment with past-sequence-dependent setup time and position-dependent processing time.

PubMed

Zhao, Chuan-Li; Hsu, Chou-Jung; Hsu, Hua-Feng

2014-01-01

This paper considers single machine scheduling and due date assignment with setup time. The setup time is proportional to the length of the already processed jobs; that is, the setup time is past-sequence-dependent (p-s-d). It is assumed that a job's processing time depends on its position in a sequence. The objective functions include total earliness, the weighted number of tardy jobs, and the cost of due date assignment. We analyze these problems with two different due date assignment methods. We first consider the model with job-dependent position effects. For each case, by converting the problem to a series of assignment problems, we proved that the problems can be solved in O(n(4)) time. For the model with job-independent position effects, we proved that the problems can be solved in O(n(3)) time by providing a dynamic programming algorithm.

Effects of learning duration on implicit transfer.

PubMed

Tanaka, Kanji; Watanabe, Katsumi

2015-10-01

Implicit learning and transfer in sequence acquisition play important roles in daily life. Several previous studies have found that even when participants are not aware that a transfer sequence has been transformed from the learning sequence, they are able to perform the transfer sequence faster and more accurately; this suggests implicit transfer of visuomotor sequences. Here, we investigated whether implicit transfer could be modulated by the number of trials completed in a learning session. Participants learned a sequence through trial and error, known as the m × n task (Hikosaka et al. in J Neurophysiol 74:1652-1661, 1995). In the learning session, participants were required to successfully perform the same sequence 4, 12, 16, or 20 times. In the transfer session, participants then learned one of two other sequences: one where the button configuration Vertically Mirrored the learning sequence, or a randomly generated sequence. Our results show that even when participants did not notice the alternation rule (i.e., vertical mirroring), their total working time was less and their total number of errors was lower in the transfer session compared with those who performed a Random sequence, irrespective of the number of trials completed in the learning session. This result suggests that implicit transfer likely occurs even over a shorter learning duration.

Dendrites, deep learning, and sequences in the hippocampus.

PubMed

Bhalla, Upinder S

2017-10-12

The hippocampus places us both in time and space. It does so over remarkably large spans: milliseconds to years, and centimeters to kilometers. This works for sensory representations, for memory, and for behavioral context. How does it fit in such wide ranges of time and space scales, and keep order among the many dimensions of stimulus context? A key organizing principle for a wide sweep of scales and stimulus dimensions is that of order in time, or sequences. Sequences of neuronal activity are ubiquitous in sensory processing, in motor control, in planning actions, and in memory. Against this strong evidence for the phenomenon, there are currently more models than definite experiments about how the brain generates ordered activity. The flip side of sequence generation is discrimination. Discrimination of sequences has been extensively studied at the behavioral, systems, and modeling level, but again physiological mechanisms are fewer. It is against this backdrop that I discuss two recent developments in neural sequence computation, that at face value share little beyond the label "neural." These are dendritic sequence discrimination, and deep learning. One derives from channel physiology and molecular signaling, the other from applied neural network theory - apparently extreme ends of the spectrum of neural circuit detail. I suggest that each of these topics has deep lessons about the possible mechanisms, scales, and capabilities of hippocampal sequence computation. © 2017 Wiley Periodicals, Inc.

In vivo Proton Electron Double Resonance Imaging of Mice with Fast Spin Echo Pulse Sequence

PubMed Central

Sun, Ziqi; Li, Haihong; Petryakov, Sergey; Samouilov, Alex; Zweier, Jay L.

2011-01-01

Purpose To develop and evaluate a 2D fast spin echo (FSE) pulse sequence for enhancing temporal resolution and reducing tissue heating for in vivo proton electron double resonance imaging (PEDRI) of mice. Materials and Methods A four-compartment phantom containing 2 mM TEMPONE was imaged at 20.1 mT using 2D FSE-PEDRI and regular gradient echo (GRE)-PEDRI pulse sequences. Control mice were infused with TEMPONE over ∼1 min followed by time-course imaging using the 2D FSE-PEDRI sequence at intervals of 10 – 30 s between image acquisitions. The average signal intensity from the time-course images was analyzed using a first-order kinetics model. Results Phantom experiments demonstrated that EPR power deposition can be greatly reduced using the FSE-PEDRI pulse sequence compared to the conventional gradient echo pulse sequence. High temporal resolution was achieved at ∼4 s per image acquisition using the FSE-PEDRI sequence with a good image SNR in the range of 233-266 in the phantom study. The TEMPONE half-life measured in vivo was ∼72 s. Conclusion Thus, the FSE-PEDRI pulse sequence enables fast in vivo functional imaging of free radical probes in small animals greatly reducing EPR irradiation time with decreased power deposition and provides increased temporal resolution. PMID:22147559

Short-term memory stores organized by information domain.

PubMed

Noyce, Abigail L; Cestero, Nishmar; Shinn-Cunningham, Barbara G; Somers, David C

2016-04-01

Vision and audition have complementary affinities, with vision excelling in spatial resolution and audition excelling in temporal resolution. Here, we investigated the relationships among the visual and auditory modalities and spatial and temporal short-term memory (STM) using change detection tasks. We created short sequences of visual or auditory items, such that each item within a sequence arose at a unique spatial location at a unique time. On each trial, two successive sequences were presented; subjects attended to either space (the sequence of locations) or time (the sequence of inter item intervals) and reported whether the patterns of locations or intervals were identical. Each subject completed blocks of unimodal trials (both sequences presented in the same modality) and crossmodal trials (Sequence 1 visual, Sequence 2 auditory, or vice versa) for both spatial and temporal tasks. We found a strong interaction between modality and task: Spatial performance was best on unimodal visual trials, whereas temporal performance was best on unimodal auditory trials. The order of modalities on crossmodal trials also mattered, suggesting that perceptual fidelity at encoding is critical to STM. Critically, no cost was attributable to crossmodal comparison: In both tasks, performance on crossmodal trials was as good as or better than on the weaker unimodal trials. STM representations of space and time can guide change detection in either the visual or the auditory modality, suggesting that the temporal or spatial organization of STM may supersede sensory-specific organization.

Multiplex, Rapid, and Sensitive Isothermal Detection of Nucleic-Acid Sequence by Endonuclease Restriction-Mediated Real-Time Multiple Cross Displacement Amplification.

PubMed

Wang, Yi; Wang, Yan; Zhang, Lu; Liu, Dongxin; Luo, Lijuan; Li, Hua; Cao, Xiaolong; Liu, Kai; Xu, Jianguo; Ye, Changyun

2016-01-01

We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA), which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5' end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labeled at the 5' end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 min, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here, we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

Are commercial providers a viable option for clinical bacterial sequencing?

PubMed

Raven, Kathy; Blane, Beth; Churcher, Carol; Parkhill, Julian; Peacock, Sharon J

2018-04-05

Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality. DNA was prepared from five methicillin-resistant Staphylococcus aureus (MRSA) isolates, four of which were investigated during a previously published outbreak in the UK together with a reference MRSA isolate (ST22 HO 5096 0412). Cost of sequencing per isolate ranged from £155 to £342 and turnaround times from DNA postage to arrival of sequence data ranged from 12 to 63 days. Comparison of commercially generated genomes against the original sequence data demonstrated very high concordance, with no more than one single nucleotide polymorphism (SNP) difference on core genome mapping between the original sequences and the new sequence for all four providers. Multilocus sequence type could not be assigned based on assembly for the two cheapest sequence providers due to fragmented assemblies probably caused by a lower output of sequence data per isolate. Our results indicate that external providers returned highly accurate genome data, but that improvements are required in turnaround time to make this a viable option for use in clinical practice.

High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences.

PubMed

Schönberg, Anna; Theunert, Christoph; Li, Mingkun; Stoneking, Mark; Nasidze, Ivan

2011-09-01

To investigate the demographic history of human populations from the Caucasus and surrounding regions, we used high-throughput sequencing to generate 147 complete mtDNA genome sequences from random samples of individuals from three groups from the Caucasus (Armenians, Azeri and Georgians), and one group each from Iran and Turkey. Overall diversity is very high, with 144 different sequences that fall into 97 different haplogroups found among the 147 individuals. Bayesian skyline plots (BSPs) of population size change through time show a population expansion around 40-50 kya, followed by a constant population size, and then another expansion around 15-18 kya for the groups from the Caucasus and Iran. The BSP for Turkey differs the most from the others, with an increase from 35 to 50 kya followed by a prolonged period of constant population size, and no indication of a second period of growth. An approximate Bayesian computation approach was used to estimate divergence times between each pair of populations; the oldest divergence times were between Turkey and the other four groups from the South Caucasus and Iran (~400-600 generations), while the divergence time of the three Caucasus groups from each other was comparable to their divergence time from Iran (average of ~360 generations). These results illustrate the value of random sampling of complete mtDNA genome sequences that can be obtained with high-throughput sequencing platforms.

Evolution dynamics of a model for gene duplication under adaptive conflict

NASA Astrophysics Data System (ADS)

Ancliff, Mark; Park, Jeong-Man

2014-06-01

We present and solve the dynamics of a model for gene duplication showing escape from adaptive conflict. We use a Crow-Kimura quasispecies model of evolution where the fitness landscape is a function of Hamming distances from two reference sequences, which are assumed to optimize two different gene functions, to describe the dynamics of a mixed population of individuals with single and double copies of a pleiotropic gene. The evolution equations are solved through a spin coherent state path integral, and we find two phases: one is an escape from an adaptive conflict phase, where each copy of a duplicated gene evolves toward subfunctionalization, and the other is a duplication loss of function phase, where one copy maintains its pleiotropic form and the other copy undergoes neutral mutation. The phase is determined by a competition between the fitness benefits of subfunctionalization and the greater mutational load associated with maintaining two gene copies. In the escape phase, we find a dynamics of an initial population of single gene sequences only which escape adaptive conflict through gene duplication and find that there are two time regimes: until a time t* single gene sequences dominate, and after t* double gene sequences outgrow single gene sequences. The time t* is identified as the time necessary for subfunctionalization to evolve and spread throughout the double gene sequences, and we show that there is an optimum mutation rate which minimizes this time scale.

Nanopore Technology: A Simple, Inexpensive, Futuristic Technology for DNA Sequencing.

PubMed

Gupta, P D

2016-10-01

In health care, importance of DNA sequencing has been fully established. Sanger's Capillary Electrophoresis DNA sequencing methodology is time consuming, cumbersome, hence become more expensive. Lately, because of its versatility DNA sequencing became house hold name, and therefore, there is an urgent need of simple, fast, inexpensive, DNA sequencing technology. In the beginning of this century efforts were made, and Nanopore DNA sequencing technology was developed; still it is infancy, nevertheless, it is the futuristic technology.

Method and Apparatus for Evaluating the Visual Quality of Processed Digital Video Sequences

NASA Technical Reports Server (NTRS)

Watson, Andrew B. (Inventor)

2002-01-01

A Digital Video Quality (DVQ) apparatus and method that incorporate a model of human visual sensitivity to predict the visibility of artifacts. The DVQ method and apparatus are used for the evaluation of the visual quality of processed digital video sequences and for adaptively controlling the bit rate of the processed digital video sequences without compromising the visual quality. The DVQ apparatus minimizes the required amount of memory and computation. The input to the DVQ apparatus is a pair of color image sequences: an original (R) non-compressed sequence, and a processed (T) sequence. Both sequences (R) and (T) are sampled, cropped, and subjected to color transformations. The sequences are then subjected to blocking and discrete cosine transformation, and the results are transformed to local contrast. The next step is a time filtering operation which implements the human sensitivity to different time frequencies. The results are converted to threshold units by dividing each discrete cosine transform coefficient by its respective visual threshold. At the next stage the two sequences are subtracted to produce an error sequence. The error sequence is subjected to a contrast masking operation, which also depends upon the reference sequence (R). The masked errors can be pooled in various ways to illustrate the perceptual error over various dimensions, and the pooled error can be converted to a visual quality measure.

Sequences of emotional distress expressed by clients and acknowledged by therapists: are they associated more with some therapists than others?

PubMed

Viney, L L

1994-11-01

When clients come to psychotherapy they are distressed, this distress usually being expressed in the form of anxiety, hostility, depression and helplessness. This study explored the sequences of emotional distress expressed by clients and acknowledged by therapists, and examined their associations with other factors. The transcripts of five therapists (two single sessions each) were content-analysed: they used personal construct, client centered, rational-emotive, Gestalt and transactional analysis therapy. Log-linear analyses of appropriate contingency table cell frequencies were conducted to test associations between identified sequences and the two variables of therapist and timing of completion of the sequence. Therapist-client sequences of Anxiety-Anxiety, Anxiety-Hostility and Helplessness-Hostility were found to be associated more with the personal construct and client centred therapists than with the rational-emotive therapist. Client-therapist sequences of Anxiety-Anxiety, Helplessness-Anxiety and Helplessness-Helplessness were more often found with the client centred therapist than the other therapists. For most of these sequences timing had an effect, yet timing rarely interacted with the therapist variable. The findings are discussed in terms of their relevance to the theoretical positions represented, the shortcomings of the research and the value of this methodology in studies linking therapy process with outcome.

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen).

PubMed

Rambaut, Andrew; Lam, Tommy T; Max Carvalho, Luiz; Pybus, Oliver G

2016-01-01

Gene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the sequences in question undergo measurable amounts of evolutionary change between sampling times. Data sets with this property are termed heterochronous and have become increasingly common in several fields of biology, most notably the molecular epidemiology of rapidly evolving viruses. Here we introduce the cross-platform software tool, TempEst (formerly known as Path-O-Gen), for the visualization and analysis of temporally sampled sequence data. Given a molecular phylogeny and the dates of sampling for each sequence, TempEst uses an interactive regression approach to explore the association between genetic divergence through time and sampling dates. TempEst can be used to (1) assess whether there is sufficient temporal signal in the data to proceed with phylogenetic molecular clock analysis, and (2) identify sequences whose genetic divergence and sampling date are incongruent. Examination of the latter can help identify data quality problems, including errors in data annotation, sample contamination, sequence recombination, or alignment error. We recommend that all users of the molecular clock models implemented in BEAST first check their data using TempEst prior to analysis.

Time sequence photography of Roosters Comb

USDA-ARS?s Scientific Manuscript database

The importance of understanding natural landscape changes is key in properly determining rangeland ecology. Time sequence photography allows a landscape snapshot to be documented and enables the ability to compare natural changes overtime. Photographs of Roosters Comb were taken from the same vantag...

Comparison of DNA Microarray, Loop-Mediated Isothermal Amplification (LAMP) and Real-Time PCR with DNA Sequencing for Identification of Fusarium spp. Obtained from Patients with Hematologic Malignancies.

PubMed

de Souza, Marcela; Matsuzawa, Tetsuhiro; Sakai, Kanae; Muraosa, Yasunori; Lyra, Luzia; Busso-Lopes, Ariane Fidelis; Levin, Anna Sara Shafferman; Schreiber, Angélica Zaninelli; Mikami, Yuzuru; Gonoi, Tohoru; Kamei, Katsuhiko; Moretti, Maria Luiza; Trabasso, Plínio

2017-08-01

The performance of three molecular biology techniques, i.e., DNA microarray, loop-mediated isothermal amplification (LAMP), and real-time PCR were compared with DNA sequencing for properly identification of 20 isolates of Fusarium spp. obtained from blood stream as etiologic agent of invasive infections in patients with hematologic malignancies. DNA microarray, LAMP and real-time PCR identified 16 (80%) out of 20 samples as Fusarium solani species complex (FSSC) and four (20%) as Fusarium spp. The agreement among the techniques was 100%. LAMP exhibited 100% specificity, while DNA microarray, LAMP and real-time PCR showed 100% sensitivity. The three techniques had 100% agreement with DNA sequencing. Sixteen isolates were identified as FSSC by sequencing, being five Fusarium keratoplasticum, nine Fusarium petroliphilum and two Fusarium solani. On the other hand, sequencing identified four isolates as Fusarium non-solani species complex (FNSSC), being three isolates as Fusarium napiforme and one isolate as Fusarium oxysporum. Finally, LAMP proved to be faster and more accessible than DNA microarray and real-time PCR, since it does not require a thermocycler. Therefore, LAMP signalizes as emerging and promising methodology to be used in routine identification of Fusarium spp. among cases of invasive fungal infections.

Multiple echo multi-shot diffusion sequence.

PubMed

Chabert, Steren; Galindo, César; Tejos, Cristian; Uribe, Sergio A

2014-04-01

To measure both transversal relaxation time (T2 ) and diffusion coefficients within a single scan using a multi-shot approach. Both measurements have drawn interest in many applications, especially in skeletal muscle studies, which have short T2 values. Multiple echo single-shot schemes have been proposed to obtain those variables simultaneously within a single scan, resulting in a reduction of the scanning time. However, one problem with those approaches is the associated long echo read-out. Consequently, the minimum achievable echo time tends to be long, limiting the application of these sequences to tissues with relatively long T2 . To address this problem, we propose to extend the multi-echo sequences using a multi-shot approach, so that to allow shorter echo times. A multi-shot dual-echo EPI sequence with diffusion gradients and echo navigators was modified to include independent diffusion gradients in any of the two echoes. The multi-shot approach allows us to drastically reduce echo times. Results showed a good agreement for the T2 and mean diffusivity measurements with gold standard sequences in phantoms and in vivo data of calf muscles from healthy volunteers. A fast and accurate method is proposed to measure T2 and diffusion coefficients simultaneously, tested in vitro and in healthy volunteers. Copyright © 2013 Wiley Periodicals, Inc.

Probabilistic Evaluation of Competing Climate Models

NASA Astrophysics Data System (ADS)

Braverman, A. J.; Chatterjee, S.; Heyman, M.; Cressie, N.

2017-12-01

A standard paradigm for assessing the quality of climate model simulations is to compare what these models produce for past and present time periods, to observations of the past and present. Many of these comparisons are based on simple summary statistics called metrics. Here, we propose an alternative: evaluation of competing climate models through probabilities derived from tests of the hypothesis that climate-model-simulated and observed time sequences share common climate-scale signals. The probabilities are based on the behavior of summary statistics of climate model output and observational data, over ensembles of pseudo-realizations. These are obtained by partitioning the original time sequences into signal and noise components, and using a parametric bootstrap to create pseudo-realizations of the noise sequences. The statistics we choose come from working in the space of decorrelated and dimension-reduced wavelet coefficients. We compare monthly sequences of CMIP5 model output of average global near-surface temperature anomalies to similar sequences obtained from the well-known HadCRUT4 data set, as an illustration.

Faster sequence homology searches by clustering subsequences.

PubMed

Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

2015-04-15

Sequence homology searches are used in various fields. New sequencing technologies produce huge amounts of sequence data, which continuously increase the size of sequence databases. As a result, homology searches require large amounts of computational time, especially for metagenomic analysis. We developed a fast homology search method based on database subsequence clustering, and implemented it as GHOSTZ. This method clusters similar subsequences from a database to perform an efficient seed search and ungapped extension by reducing alignment candidates based on triangle inequality. The database subsequence clustering technique achieved an ∼2-fold increase in speed without a large decrease in search sensitivity. When we measured with metagenomic data, GHOSTZ is ∼2.2-2.8 times faster than RAPSearch and is ∼185-261 times faster than BLASTX. The source code is freely available for download at http://www.bi.cs.titech.ac.jp/ghostz/ akiyama@cs.titech.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Predicting earthquakes by analyzing accelerating precursory seismic activity

USGS Publications Warehouse

Varnes, D.J.

1989-01-01

During 11 sequences of earthquakes that in retrospect can be classed as foreshocks, the accelerating rate at which seismic moment is released follows, at least in part, a simple equation. This equation (1) is {Mathematical expression},where {Mathematical expression} is the cumulative sum until time, t, of the square roots of seismic moments of individual foreshocks computed from reported magnitudes;C and n are constants; and tfis a limiting time at which the rate of seismic moment accumulation becomes infinite. The possible time of a major foreshock or main shock, tf,is found by the best fit of equation (1), or its integral, to step-like plots of {Mathematical expression} versus time using successive estimates of tfin linearized regressions until the maximum coefficient of determination, r2,is obtained. Analyzed examples include sequences preceding earthquakes at Cremasta, Greece, 2/5/66; Haicheng, China 2/4/75; Oaxaca, Mexico, 11/29/78; Petatlan, Mexico, 3/14/79; and Central Chile, 3/3/85. In 29 estimates of main-shock time, made as the sequences developed, the errors in 20 were less than one-half and in 9 less than one tenth the time remaining between the time of the last data used and the main shock. Some precursory sequences, or parts of them, yield no solution. Two sequences appear to include in their first parts the aftershocks of a previous event; plots using the integral of equation (1) show that the sequences are easily separable into aftershock and foreshock segments. Synthetic seismic sequences of shocks at equal time intervals were constructed to follow equation (1), using four values of n. In each series the resulting distributions of magnitudes closely follow the linear Gutenberg-Richter relation log N=a-bM, and the product n times b for each series is the same constant. In various forms and for decades, equation (1) has been used successfully to predict failure times of stressed metals and ceramics, landslides in soil and rock slopes, and volcanic eruptions. Results of more recent experiments and theoretical studies on crack propagation, fault mechanics, and acoustic emission can be closely reproduced by equation (1). Rate-process theory and continuum damage mechanics offer leads toward understanding the physical processes. ?? 1989 Birkha??user Verlag.

Elimination sequence optimization for SPAR

NASA Technical Reports Server (NTRS)

Hogan, Harry A.

1986-01-01

SPAR is a large-scale computer program for finite element structural analysis. The program allows user specification of the order in which the joints of a structure are to be eliminated since this order can have significant influence over solution performance, in terms of both storage requirements and computer time. An efficient elimination sequence can improve performance by over 50% for some problems. Obtaining such sequences, however, requires the expertise of an experienced user and can take hours of tedious effort to affect. Thus, an automatic elimination sequence optimizer would enhance productivity by reducing the analysts' problem definition time and by lowering computer costs. Two possible methods for automating the elimination sequence specifications were examined. Several algorithms based on the graph theory representations of sparse matrices were studied with mixed results. Significant improvement in the program performance was achieved, but sequencing by an experienced user still yields substantially better results. The initial results provide encouraging evidence that the potential benefits of such an automatic sequencer would be well worth the effort.

Complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1 using PacBio single-molecule real-time technology

USDA-ARS?s Scientific Manuscript database

We report the complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1 isolated in Minnesota, USA. The R1-1 genome, generated by de novo assembly of PacBio sequencing data, is the first complete genome sequence available for this subspecies....

Integrated and Independent Learning of Hand-Related Constituent Sequences

ERIC Educational Resources Information Center

Berner, Michael P.; Hoffmann, Joachim

2009-01-01

In almost all daily activities fingers of both hands are used in coordinated succession. The present experiments explored whether learning in such tasks pertains not only to the overall sequence spanning both hands but also to the constituent sequences of each hand. In a serial reaction time task, 2 repeating hand-related sequences were…

PLAN-IT: Knowledge-Based Mission Sequencing

NASA Astrophysics Data System (ADS)

Biefeld, Eric W.

1987-02-01

Mission sequencing consumes a large amount of time and manpower during a space exploration effort. Plan-It is a knowledge-based approach to assist in mission sequencing. Plan-It uses a combined frame and blackboard architecture. This paper reports on the approach implemented by Plan-It and the current applications of Plan-It for sequencing at NASA.

Is There a Time for Everything? Attitudes Related to Women's Sequencing of Career and Family.

ERIC Educational Resources Information Center

Sullivan, Sherry E.

1992-01-01

Examined business students' (n=203) attitudes relating to sequencing of career and family events for women. Results indicated gender, attitudes regarding women's timing of career and children, and women's ability to balance work and family demands were significantly related. There was a relationship between attitudes toward timing of marriage and…

HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing.

PubMed

Wan, Shixiang; Zou, Quan

2017-01-01

Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign.

Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.

PubMed

Zhu, Tianqi; Dos Reis, Mario; Yang, Ziheng

2015-03-01

Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating species divergences estimate times and rates by assigning priors on them. In particular, the prior on times (node ages on the phylogeny) incorporates information in the fossil record to calibrate the molecular tree. Because times and rates are confounded, our posterior time estimates will not approach point values even if an infinite amount of sequence data are used in the analysis. In a previous study we developed a finite-sites theory to characterize the uncertainty in Bayesian divergence time estimation in analysis of large but finite sequence data sets under a strict molecular clock. As most modern clock dating analyses use more than one locus and are conducted under relaxed clock models, here we extend the theory to the case of relaxed clock analysis of data from multiple loci (site partitions). Uncertainty in posterior time estimates is partitioned into three sources: Sampling errors in the estimates of branch lengths in the tree for each locus due to limited sequence length, variation of substitution rates among lineages and among loci, and uncertainty in fossil calibrations. Using a simple but analogous estimation problem involving the multivariate normal distribution, we predict that as the number of loci ([Formula: see text]) goes to infinity, the variance in posterior time estimates decreases and approaches the infinite-data limit at the rate of 1/[Formula: see text], and the limit is independent of the number of sites in the sequence alignment. We then confirmed the predictions by using computer simulation on phylogenies of two or three species, and by analyzing a real genomic data set for six primate species. Our results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way for improving the precision of posterior time estimation. However, even if a huge amount of sequence data is analyzed, considerable uncertainty will persist in time estimates. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

Aligner optimization increases accuracy and decreases compute times in multi-species sequence data.

PubMed

Robinson, Kelly M; Hawkins, Aziah S; Santana-Cruz, Ivette; Adkins, Ricky S; Shetty, Amol C; Nagaraj, Sushma; Sadzewicz, Lisa; Tallon, Luke J; Rasko, David A; Fraser, Claire M; Mahurkar, Anup; Silva, Joana C; Dunning Hotopp, Julie C

2017-09-01

As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows-Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for alignment of data from multi-species samples in order to reduce alignment time and increase the specificity of alignments. In the multi-species cases examined, there was one majority member (i.e. Plasmodium falciparum or Brugia malayi ) and one minority member (i.e. human or the Wolbachia endosymbiont w Bm) of the sequence data. Increasing bwa-mem seed length from the default value reduced the number of read pairs from the majority sequence member that incorrectly aligned to the reference genome of the minority sequence member. Combining both source genomes into a single reference genome increased the specificity of mapping, while also reducing the central processing unit (CPU) time. In Plasmodium , at a seed length of 18 nt, 24.1 % of reads mapped to the human genome using 1.7±0.1 CPU hours, while 83.6 % of reads mapped to the Plasmodium genome using 0.2±0.0 CPU hours (total: 107.7 % reads mapping; in 1.9±0.1 CPU hours). In contrast, 97.1 % of the reads mapped to a combined Plasmodium- human reference in only 0.7±0.0 CPU hours. Overall, the results suggest that combining all references into a single reference database and using a 23 nt seed length reduces the computational time, while maximizing specificity. Similar results were found for simulated sequence reads from a mock metagenomic data set. We found similar improvements to computation time in a publicly available human-only data set.

Parameterizing time in electronic health record studies.

PubMed

Hripcsak, George; Albers, David J; Perotte, Adler

2015-07-01

Fields like nonlinear physics offer methods for analyzing time series, but many methods require that the time series be stationary-no change in properties over time.Objective Medicine is far from stationary, but the challenge may be able to be ameliorated by reparameterizing time because clinicians tend to measure patients more frequently when they are ill and are more likely to vary. We compared time parameterizations, measuring variability of rate of change and magnitude of change, and looking for homogeneity of bins of temporal separation between pairs of time points. We studied four common laboratory tests drawn from 25 years of electronic health records on 4 million patients. We found that sequence time-that is, simply counting the number of measurements from some start-produced more stationary time series, better explained the variation in values, and had more homogeneous bins than either traditional clock time or a recently proposed intermediate parameterization. Sequence time produced more accurate predictions in a single Gaussian process model experiment. Of the three parameterizations, sequence time appeared to produce the most stationary series, possibly because clinicians adjust their sampling to the acuity of the patient. Parameterizing by sequence time may be applicable to association and clustering experiments on electronic health record data. A limitation of this study is that laboratory data were derived from only one institution. Sequence time appears to be an important potential parameterization. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work properly cited. For commercial re-use, please contact journals.permissions@oup.com.

Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

PubMed

Wang, Ji; Ke, Yue Hua; Zhang, Yong; Huang, Ke Qiang; Wang, Lei; Shen, Xin Xin; Dong, Xiao Ping; Xu, Wen Bo; Ma, Xue Jun

2017-10-01

Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Reprint of: Early Behavioural Facilitation by Temporal Expectations in Complex Visual-motor Sequences.

PubMed

Heideman, Simone G; van Ede, Freek; Nobre, Anna C

2018-05-24

In daily life, temporal expectations may derive from incidental learning of recurring patterns of intervals. We investigated the incidental acquisition and utilisation of combined temporal-ordinal (spatial/effector) structure in complex visual-motor sequences using a modified version of a serial reaction time (SRT) task. In this task, not only the series of targets/responses, but also the series of intervals between subsequent targets was repeated across multiple presentations of the same sequence. Each participant completed three sessions. In the first session, only the repeating sequence was presented. During the second and third session, occasional probe blocks were presented, where a new (unlearned) spatial-temporal sequence was introduced. We first confirm that participants not only got faster over time, but that they were slower and less accurate during probe blocks, indicating that they incidentally learned the sequence structure. Having established a robust behavioural benefit induced by the repeating spatial-temporal sequence, we next addressed our central hypothesis that implicit temporal orienting (evoked by the learned temporal structure) would have the largest influence on performance for targets following short (as opposed to longer) intervals between temporally structured sequence elements, paralleling classical observations in tasks using explicit temporal cues. We found that indeed, reaction time differences between new and repeated sequences were largest for the short interval, compared to the medium and long intervals, and that this was the case, even when comparing late blocks (where the repeated sequence had been incidentally learned), to early blocks (where this sequence was still unfamiliar). We conclude that incidentally acquired temporal expectations that follow a sequential structure can have a robust facilitatory influence on visually-guided behavioural responses and that, like more explicit forms of temporal orienting, this effect is most pronounced for sequence elements that are expected at short inter-element intervals. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

cyclostratigraphy, sequence stratigraphy and organic matter accumulation mechanism

NASA Astrophysics Data System (ADS)

Cong, F.; Li, J.

2016-12-01

The first member of Maokou Formation of Sichuan basin is composed of well preserved carbonate ramp couplets of limestone and marlstone/shale. It acts as one of the potential shale gas source rock, and is suitable for time-series analysis. We conducted time-series analysis to identify high-frequency sequences, reconstruct high-resolution sedimentation rate, estimate detailed primary productivity for the first time in the study intervals and discuss organic matter accumulation mechanism of source rock under sequence stratigraphic framework.Using the theory of cyclostratigraphy and sequence stratigraphy, the high-frequency sequences of one outcrop profile and one drilling well are identified. Two third-order sequences and eight fourth-order sequences are distinguished on outcrop profile based on the cycle stacking patterns. For drilling well, sequence boundary and four system tracts is distinguished by "integrated prediction error filter analysis" (INPEFA) of Gamma-ray logging data, and eight fourth-order sequences is identified by 405ka long eccentricity curve in depth domain which is quantified and filtered by integrated analysis of MTM spectral analysis, evolutive harmonic analysis (EHA), evolutive average spectral misfit (eASM) and band-pass filtering. It suggests that high-frequency sequences correlate well with Milankovitch orbital signals recorded in sediments, and it is applicable to use cyclostratigraphy theory in dividing high-frequency(4-6 orders) sequence stratigraphy.High-resolution sedimentation rate is reconstructed through the study interval by tracking the highly statistically significant short eccentricity component (123ka) revealed by EHA. Based on sedimentation rate, measured TOC and density data, the burial flux, delivery flux and primary productivity of organic carbon was estimated. By integrating redox proxies, we can discuss the controls on organic matter accumulation by primary production and preservation under the high-resolution sequence stratigraphic framework. Results show that high average organic carbon contents in the study interval are mainly attributed to high primary production. The results also show a good correlation between high organic carbon accumulation and intervals of transgression.

Breaking barriers and halting rupture: the 2016 Amatrice-Visso-Castelluccio earthquake sequence, central Italy

NASA Astrophysics Data System (ADS)

Gregory, L. C.; Walters, R. J.; Wedmore, L. N. J.; Craig, T. J.; McCaffrey, K. J. W.; Wilkinson, M. W.; Livio, F.; Michetti, A.; Goodall, H.; Li, Z.; Chen, J.; De Martini, P. M.

2017-12-01

In 2016 the Central Italian Apennines was struck by a sequence of normal faulting earthquakes that ruptured in three separate events on the 24th August (Mw 6.2), the 26th Oct (Mw 6.1), and the 30th Oct (Mw 6.6). We reveal the complex nature of the individual events and the time-evolution of the sequence using multiple datasets. We will present an overview of the results from field geology, satellite geodesy, GNSS (including low-cost short baseline installations), and terrestrial laser scanning (TLS). Sequences of earthquakes of mid to high magnitude 6 are common in historical and seismological records in Italy and other similar tectonic settings globally. Multi-fault rupture during these sequences can occur in seconds, as in the M 6.9 1980 Irpinia earthquake, or can span days, months, or years (e.g. the 1703 Norcia-L'Aquila sequence). It is critical to determine why the causative faults in the 2016 sequence did not rupture simultaneously, and how this relates to fault segmentation and structural barriers. This is the first sequence of this kind to be observed using modern geodetic techniques, and only with all of the datasets combined can we begin to understand how and why the sequence evolved in time and space. We show that earthquake rupture both broke through structural barriers that were thought to exist, but was also inhibited by a previously unknown structure. We will also discuss the logistical challenges in generating datasets on the time-evolving sequence, and show how rapid response and international collaboration within the Open EMERGEO Working Group was critical for gaining a complete picture of the ongoing activity.

Persistence Probabilities of Two-Sided (Integrated) Sums of Correlated Stationary Gaussian Sequences

NASA Astrophysics Data System (ADS)

Aurzada, Frank; Buck, Micha

2018-02-01

We study the persistence probability for some two-sided, discrete-time Gaussian sequences that are discrete-time analogues of fractional Brownian motion and integrated fractional Brownian motion, respectively. Our results extend the corresponding ones in continuous time in Molchan (Commun Math Phys 205(1):97-111, 1999) and Molchan (J Stat Phys 167(6):1546-1554, 2017) to a wide class of discrete-time processes.

Fast Algorithms for Mining Co-evolving Time Series

DTIC Science & Technology

2011-09-01

Keogh et al., 2001, 2004] and (b) forecasting, like an autoregressive integrated moving average model ( ARIMA ) and related meth- ods [Box et al., 1994...computing hardware? We develop models to mine time series with missing values, to extract compact representation from time sequences, to segment the...sequences, and to do forecasting. For large scale data, we propose algorithms for learning time series models , in particular, including Linear Dynamical

Assessment of cardiac time intervals using high temporal resolution real-time spiral phase contrast with UNFOLDed-SENSE.

PubMed

Kowalik, Grzegorz T; Knight, Daniel S; Steeden, Jennifer A; Tann, Oliver; Odille, Freddy; Atkinson, David; Taylor, Andrew; Muthurangu, Vivek

2015-02-01

To develop a real-time phase contrast MR sequence with high enough temporal resolution to assess cardiac time intervals. The sequence utilized spiral trajectories with an acquisition strategy that allowed a combination of temporal encoding (Unaliasing by fourier-encoding the overlaps using the temporal dimension; UNFOLD) and parallel imaging (Sensitivity encoding; SENSE) to be used (UNFOLDed-SENSE). An in silico experiment was performed to determine the optimum UNFOLD filter. In vitro experiments were carried out to validate the accuracy of time intervals calculation and peak mean velocity quantification. In addition, 15 healthy volunteers were imaged with the new sequence, and cardiac time intervals were compared to reference standard Doppler echocardiography measures. For comparison, in silico, in vitro, and in vivo experiments were also carried out using sliding window reconstructions. The in vitro experiments demonstrated good agreement between real-time spiral UNFOLDed-SENSE phase contrast MR and the reference standard measurements of velocity and time intervals. The protocol was successfully performed in all volunteers. Subsequent measurement of time intervals produced values in keeping with literature values and good agreement with the gold standard echocardiography. Importantly, the proposed UNFOLDed-SENSE sequence outperformed the sliding window reconstructions. Cardiac time intervals can be successfully assessed with UNFOLDed-SENSE real-time spiral phase contrast. Real-time MR assessment of cardiac time intervals may be beneficial in assessment of patients with cardiac conditions such as diastolic dysfunction. © 2014 Wiley Periodicals, Inc.

A stereoscopic look into the bulk

DOE PAGES

Czech, Bartlomiej; Lamprou, Lampros; McCandlish, Samuel; ...

2016-07-26

Here, we present the foundation for a holographic dictionary with depth perception. The dictionary consists of natural CFT operators whose duals are simple, diffeomorphism-invariant bulk operators. The CFT operators of interest are the “OPE blocks,” contributions to the OPE from a single conformal family. In holographic theories, we show that the OPE blocks are dual at leading order in 1/N to integrals of effective bulk fields along geodesics or homogeneous minimal surfaces in anti-de Sitter space. One widely studied example of an OPE block is the modular Hamiltonian, which is dual to the fluctuation in the area of a minimalmore » surface. Thus, our operators pave the way for generalizing the Ryu-Takayanagi relation to other bulk fields. Although the OPE blocks are non-local operators in the CFT, they admit a simple geometric description as fields in kinematic space — the space of pairs of CFT points. We develop the tools for constructing local bulk operators in terms of these non-local objects. The OPE blocks also allow for conceptually clean and technically simple derivations of many results known in the literature, including linearized Einstein’s equations and the relation between conformal blocks and geodesic Witten diagrams.« less

Black hole evaporation, quantum hair and supertranslations

NASA Astrophysics Data System (ADS)

Gómez, César; Zell, Sebastian

2018-04-01

In a black hole, hair and quantum information retrieval are interrelated phenomena. The existence of any new form of hair necessarily implies the existence of features in the quantum-mechanically evaporated radiation. Therefore, classical supertranslation hair can be only distinguished from global diffeomorphisms if we have access to the interior of the black hole. Indirect information on the interior can only be obtained from the features of the quantum evaporation. We demonstrate that supertranslations (T^-,T^+) \\in BMS-⊗ BMS+ can be used as bookkeepers of the probability distributions of the emitted quanta where the first element describes the classical injection of energy and the second one is associated to quantum-mechanical emission. However, the connection between T^- and T^+ is determined by the interior quantum dynamics of the black hole. We argue that restricting to the diagonal subgroup is only possible for decoupled modes, which do not bring any non-trivial information about the black hole interior and therefore do not constitute physical hair. It is shown that this is also true for gravitational systems without horizon, for which both injection and emission can be described classically. Moreover, we discuss and clarify the role of infrared physics in purification.

Some Properties of Generalized Connections in Quantum Gravity

NASA Astrophysics Data System (ADS)

Velhinho, J. M.

2002-12-01

Theories of connections play an important role in fundamental interactions, including Yang-Mills theories and gravity in the Ashtekar formulation. Typically in such cases, the classical configuration space {A}/ {G} of connections modulo gauge transformations is an infinite dimensional non-linear space of great complexity. Having in mind a rigorous quantization procedure, methods of functional calculus in an extension of {A}/ {G} have been developed. For a compact gauge group G, the compact space /line { {A}{ {/}} {G}} ( ⊃ {A}/ {G}) introduced by Ashtekar and Isham using C*-algebraic methods is a natural candidate to replace {A}/ {G} in the quantum context, 1 allowing the construction of diffeomorphism invariant measures. 2,3,4 Equally important is the space of generalized connections bar {A} introduced in a similar way by Baez. 5 bar {A} is particularly useful for the definition of vector fields in /line { {A}{ {/}} {G}} , fundamental in the construction of quantum observables. 6 These works crucially depend on the use of (generalized) Wilson variables associated to certain types of curves. We will consider the case of piecewise analytic curves, 1,2,5 althought most of the arguments apply equally to the piecewise smooth case. 7,8...

Cracks in Complex Bodies: Covariance of Tip Balances

NASA Astrophysics Data System (ADS)

Mariano, Paolo Maria

2008-04-01

In complex bodies, actions due to substructural changes alter (in some cases drastically) the force driving the tip of macroscopic cracks in quasi-static and dynamic growth, and must be represented directly. Here it is proven that tip balances of standard and substructural interactions are covariant. In fact, the former balance follows from the Lagrangian density’s requirement of invariance with respect to the action of the group of diffeomorphisms of the ambient space to itself, the latter balance accrues from an analogous invariance with respect to the action of a Lie group over the manifold of substructural shapes. The evolution equation of the crack tip can be obtained by exploiting invariance with respect to relabeling the material elements in the reference place. The analysis is developed by first focusing on general complex bodies that admit metastable states with substructural dissipation of viscous-like type inside each material element. Then we account for gradient dissipative effects that induce nonconservative stresses; the covariance of tip balances in simple bodies follows as a corollary. When body actions and boundary data of Dirichlet type are absent, the standard variational description of quasi-static crack growth is simply extended to the case of complex materials.

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

Donnelly, William; Freidel, Laurent

We consider the problem of defining localized subsystems in gauge theory and gravity. Such systems are associated to spacelike hypersurfaces with boundaries and provide the natural setting for studying entanglement entropy of regions of space. We present a general formalism to associate a gauge-invariant classical phase space to a spatial slice with boundary by introducing new degrees of freedom on the boundary. In Yang-Mills theory the new degrees of freedom are a choice of gauge on the boundary, transformations of which are generated by the normal component of the nonabelian electric field. In general relativity the new degrees of freedommore » are the location of a codimension-2 surface and a choice of conformal normal frame. These degrees of freedom transform under a group of surface symmetries, consisting of diffeomorphisms of the codimension-2 boundary, and position-dependent linear deformations of its normal plane. We find the observables which generate these symmetries, consisting of the conformal normal metric and curvature of the normal connection. We discuss the implications for the problem of defining entanglement entropy in quantum gravity. Finally, our work suggests that the Bekenstein-Hawking entropy may arise from the different ways of gluing together two partial Cauchy surfaces at a cross-section of the horizon.« less

Deep Adaptive Log-Demons: Diffeomorphic Image Registration with Very Large Deformations

PubMed Central

Jia, Kebin

2015-01-01

This paper proposes a new framework for capturing large and complex deformation in image registration. Traditionally, this challenging problem relies firstly on a preregistration, usually an affine matrix containing rotation, scale, and translation and afterwards on a nonrigid transformation. According to preregistration, the directly calculated affine matrix, which is obtained by limited pixel information, may misregistrate when large biases exist, thus misleading following registration subversively. To address this problem, for two-dimensional (2D) images, the two-layer deep adaptive registration framework proposed in this paper firstly accurately classifies the rotation parameter through multilayer convolutional neural networks (CNNs) and then identifies scale and translation parameters separately. For three-dimensional (3D) images, affine matrix is located through feature correspondences by a triplanar 2D CNNs. Then deformation removal is done iteratively through preregistration and demons registration. By comparison with the state-of-the-art registration framework, our method gains more accurate registration results on both synthetic and real datasets. Besides, principal component analysis (PCA) is combined with correlation like Pearson and Spearman to form new similarity standards in 2D and 3D registration. Experiment results also show faster convergence speed. PMID:26120356

Deep Adaptive Log-Demons: Diffeomorphic Image Registration with Very Large Deformations.

PubMed

Zhao, Liya; Jia, Kebin

2015-01-01

This paper proposes a new framework for capturing large and complex deformation in image registration. Traditionally, this challenging problem relies firstly on a preregistration, usually an affine matrix containing rotation, scale, and translation and afterwards on a nonrigid transformation. According to preregistration, the directly calculated affine matrix, which is obtained by limited pixel information, may misregistrate when large biases exist, thus misleading following registration subversively. To address this problem, for two-dimensional (2D) images, the two-layer deep adaptive registration framework proposed in this paper firstly accurately classifies the rotation parameter through multilayer convolutional neural networks (CNNs) and then identifies scale and translation parameters separately. For three-dimensional (3D) images, affine matrix is located through feature correspondences by a triplanar 2D CNNs. Then deformation removal is done iteratively through preregistration and demons registration. By comparison with the state-of-the-art registration framework, our method gains more accurate registration results on both synthetic and real datasets. Besides, principal component analysis (PCA) is combined with correlation like Pearson and Spearman to form new similarity standards in 2D and 3D registration. Experiment results also show faster convergence speed.

Voxel-based morphometry study of the insular cortex in bipolar depression.

PubMed

Tang, Li-Rong; Liu, Chun-Hong; Jing, Bin; Ma, Xin; Li, Hai-Yun; Zhang, Yu; Li, Feng; Wang, Yu-Ping; Yang, Zhi; Wang, Chuan-Yue

2014-11-30

Bipolar depression (BD) is a common psychiatric illness characterized by deficits in emotional and cognitive processing. Abnormalities in the subregions of the insula are common findings in neuroanatomical studies of patients with bipolar disorder. However, the specific relationships between morphometric changes in specific insular subregions and the pathogenesis of BD are not clear. In this study, structural magnetic resonance imaging (MRI) was used to investigate gray matter volume abnormalities in the insular subregion in 27 patients with BD and in 27 age and sex-matched controls. Using DARTEL (diffeomorphic anatomical registration through exponentiated lie algebra) for voxel-based morphometry (VBM), we examined changes in regional gray matter volumes of the insula in patients with BD. As compared with healthy controls, the BD patients showed decreased gray matter volumes in the right posterior insula and left ventral anterior insula and increased gray matter volumes in the left dorsal anterior insula. Consistent with the emerging theory of insular interference as a contributor to emotional-cognitive dysregulation, the current findings suggest that the insular cortex may be involved in the neural substrates of BD. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

An image registration pipeline for analysis of transsynaptic tracing in mice

NASA Astrophysics Data System (ADS)

Kutten, Kwame S.; Eacker, Stephen M.; Dawson, Valina L.; Dawson, Ted M.; Ratnanather, Tilak; Miller, Michael I.

2016-03-01

Parkinson's Disease (PD) is a movement disorder characterized by the loss of dopamine neurons in the substantia nigra pars compacta (SNpc) and norepinephrine neurons in the locus coeruleus (LC). To further understand the pathophysiology of PD, the input neurons of the SNpc and LC will be transsynapticly traced in mice using a fluorescent recombinant rabies virus (RbV) and imaged using serial two-photon tomography (STP). A mapping between these images and a brain atlas must be found to accurately determine the locations of input neurons in the brain. Therefore a registration pipeline to align the Allen Reference Atlas (ARA) to these types of images was developed. In the preprocessing step, a brain mask was generated from the transsynaptic tracing images using simple morphological operators. The masks were then registered to the ARA using Large Deformation Diffeomorphic Metric Mapping (LDDMM), an algorithm specialized for calculating anatomically realistic transforms between images. The pipeline was then tested on an STP scan of a mouse brain labeled by an adeno-associated virus (AAV). Based on qualitative evaluation of the registration results, the pipeline was found to be sufficient for use with transsynaptic RbV tracing.

Path integral measure and triangulation independence in discrete gravity

NASA Astrophysics Data System (ADS)

Dittrich, Bianca; Steinhaus, Sebastian

2012-02-01

A path integral measure for gravity should also preserve the fundamental symmetry of general relativity, which is diffeomorphism symmetry. In previous work, we argued that a successful implementation of this symmetry into discrete quantum gravity models would imply discretization independence. We therefore consider the requirement of triangulation independence for the measure in (linearized) Regge calculus, which is a discrete model for quantum gravity, appearing in the semi-classical limit of spin foam models. To this end we develop a technique to evaluate the linearized Regge action associated to Pachner moves in 3D and 4D and show that it has a simple, factorized structure. We succeed in finding a local measure for 3D (linearized) Regge calculus that leads to triangulation independence. This measure factor coincides with the asymptotics of the Ponzano Regge Model, a 3D spin foam model for gravity. We furthermore discuss to which extent one can find a triangulation independent measure for 4D Regge calculus and how such a measure would be related to a quantum model for 4D flat space. To this end, we also determine the dependence of classical Regge calculus on the choice of triangulation in 3D and 4D.

Metaplectic-c Quantomorphisms

NASA Astrophysics Data System (ADS)

Vaughan, Jennifer

2015-03-01

In the classical Kostant-Souriau prequantization procedure, the Poisson algebra of a symplectic manifold (M,ω) is realized as the space of infinitesimal quantomorphisms of the prequantization circle bundle. Robinson and Rawnsley developed an alternative to the Kostant-Souriau quantization process in which the prequantization circle bundle and metaplectic structure for (M,ω) are replaced by a metaplectic-c prequantization. They proved that metaplectic-c quantization can be applied to a larger class of manifolds than the classical recipe. This paper presents a definition for a metaplectic-c quantomorphism, which is a diffeomorphism of metaplectic-c prequantizations that preserves all of their structures. Since the structure of a metaplectic-c prequantization is more complicated than that of a circle bundle, we find that the definition must include an extra condition that does not have an analogue in the Kostant-Souriau case. We then define an infinitesimal quantomorphism to be a vector field whose flow consists of metaplectic-c quantomorphisms, and prove that the space of infinitesimal metaplectic-c quantomorphisms exhibits all of the same properties that are seen for the infinitesimal quantomorphisms of a prequantization circle bundle. In particular, this space is isomorphic to the Poisson algebra C^∞(M).

Alterations in white matter volume and its correlation with neuropsychological scales in patients with Alzheimer's disease: a DARTEL-based voxel-based morphometry study.

PubMed

Moon, Chung-Man; Shin, Il-Seon; Jeong, Gwang-Woo

2017-02-01

Background Non-invasive imaging markers can be used to diagnose Alzheimer's disease (AD) in its early stages, but an optimized quantification analysis to measure the brain integrity has been less studied. Purpose To evaluate white matter volume change and its correlation with neuropsychological scales in patients with AD using a diffeomorphic anatomical registration through exponentiated lie algebra (DARTEL)-based voxel-based morphometry (VBM). Material and Methods The 21 participants comprised 11 patients with AD and 10 age-matched healthy controls. High-resolution magnetic resonance imaging (MRI) data were processed by VBM analysis based on DARTEL algorithm. Results The patients showed significant white matter volume reductions in the posterior limb of the internal capsule, cerebral peduncle of the midbrain, and parahippocampal gyrus compared to healthy controls. In correlation analysis, the parahippocampal volume was positively correlated with the Korean-mini mental state examination score in AD. Conclusion This study provides an evidence for localized white matter volume deficits in conjunction with cognitive dysfunction in AD. These findings would be helpful to understand the neuroanatomical mechanisms in AD and to robust the diagnostic accuracy for AD.

Probing the string winding sector

NASA Astrophysics Data System (ADS)

Aldazabal, Gerardo; Mayo, Martín; Nuñez, Carmen

2017-03-01

We probe a slice of the massive winding sector of bosonic string theory from toroidal compactifications of Double Field Theory (DFT). This string subsector corresponds to states containing one left and one right moving oscillators. We perform a generalized Kaluza Klein compactification of DFT on generic 2 n-dimensional toroidal constant backgrounds and show that, up to third order in fluctuations, the theory coincides with the corresponding effective theory of the bosonic string compactified on n-dimensional toroidal constant backgrounds, obtained from three-point amplitudes. The comparison between both theories is facilitated by noticing that generalized diffeomorphisms in DFT allow to fix generalized harmonic gauge conditions that help in identifying the physical degrees of freedom. These conditions manifest as conformal anomaly cancellation requirements on the string theory side. The explicit expression for the gauge invariant effective action containing the physical massless sector (gravity+antisymmetric+gauge+ scalar fields) coupled to towers of generalized Kaluza Klein massive states (corresponding to compact momentum and winding modes) is found. The action acquires a very compact form when written in terms of fields carrying O( n, n) indices, and is explicitly T-duality invariant. The global algebra associated to the generalized Kaluza Klein compactification is discussed.

An early illness recognition framework using a temporal Smith Waterman algorithm and NLP.

PubMed

Hajihashemi, Zahra; Popescu, Mihail

2013-01-01

In this paper we propose a framework for detecting health patterns based on non-wearable sensor sequence similarity and natural language processing (NLP). In TigerPlace, an aging in place facility from Columbia, MO, we deployed 47 sensor networks together with a nursing electronic health record (EHR) system to provide early illness recognition. The proposed framework utilizes sensor sequence similarity and NLP on EHR nursing comments to automatically notify the physician when health problems are detected. The reported methodology is inspired by genomic sequence annotation using similarity algorithms such as Smith Waterman (SW). Similarly, for each sensor sequence, we associate health concepts extracted from the nursing notes using Metamap, a NLP tool provided by Unified Medical Language System (UMLS). Since sensor sequences, unlike genomics ones, have an associated time dimension we propose a temporal variant of SW (TSW) to account for time. The main challenges presented by our framework are finding the most suitable time sequence similarity and aggregation of the retrieved UMLS concepts. On a pilot dataset from three Tiger Place residents, with a total of 1685 sensor days and 626 nursing records, we obtained an average precision of 0.64 and a recall of 0.37.

The Swiss-Army-Knife Approach to the Nearly Automatic Analysis for Microearthquake Sequences.

NASA Astrophysics Data System (ADS)

Kraft, T.; Simon, V.; Tormann, T.; Diehl, T.; Herrmann, M.

2017-12-01

Many Swiss earthquake sequence have been studied using relative location techniques, which often allowed to constrain the active fault planes and shed light on the tectonic processes that drove the seismicity. Yet, in the majority of cases the number of located earthquakes was too small to infer the details of the space-time evolution of the sequences, or their statistical properties. Therefore, it has mostly been impossible to resolve clear patterns in the seismicity of individual sequences, which are needed to improve our understanding of the mechanisms behind them. Here we present a nearly automatic workflow that combines well-established seismological analysis techniques and allows to significantly improve the completeness of detected and located earthquakes of a sequence. We start from the manually timed routine catalog of the Swiss Seismological Service (SED), which contains the larger events of a sequence. From these well-analyzed earthquakes we dynamically assemble a template set and perform a matched filter analysis on the station with: the best SNR for the sequence; and a recording history of at least 10-15 years, our typical analysis period. This usually allows us to detect events several orders of magnitude below the SED catalog detection threshold. The waveform similarity of the events is then further exploited to derive accurate and consistent magnitudes. The enhanced catalog is then analyzed statistically to derive high-resolution time-lines of the a- and b-value and consequently the occurrence probability of larger events. Many of the detected events are strong enough to be located using double-differences. No further manual interaction is needed; we simply time-shift the arrival-time pattern of the detecting template to the associated detection. Waveform similarity assures a good approximation of the expected arrival-times, which we use to calculate event-pair arrival-time differences by cross correlation. After a SNR and cycle-skipping quality check these are directly fed into hypoDD. Using this procedure we usually improve the number of well-relocated events by a factor 2-5. We demonstrate the successful application of the workflow at the example of natural sequences in Switzerland and present first results of the advanced analysis the was possible with the enhanced catalogs.

Self-Exciting Point Process Modeling of Conversation Event Sequences

NASA Astrophysics Data System (ADS)

Masuda, Naoki; Takaguchi, Taro; Sato, Nobuo; Yano, Kazuo

Self-exciting processes of Hawkes type have been used to model various phenomena including earthquakes, neural activities, and views of online videos. Studies of temporal networks have revealed that sequences of social interevent times for individuals are highly bursty. We examine some basic properties of event sequences generated by the Hawkes self-exciting process to show that it generates bursty interevent times for a wide parameter range. Then, we fit the model to the data of conversation sequences recorded in company offices in Japan. In this way, we can estimate relative magnitudes of the self excitement, its temporal decay, and the base event rate independent of the self excitation. These variables highly depend on individuals. We also point out that the Hawkes model has an important limitation that the correlation in the interevent times and the burstiness cannot be independently modulated.

Pulseq: A rapid and hardware-independent pulse sequence prototyping framework.

PubMed

Layton, Kelvin J; Kroboth, Stefan; Jia, Feng; Littin, Sebastian; Yu, Huijun; Leupold, Jochen; Nielsen, Jon-Fredrik; Stöcker, Tony; Zaitsev, Maxim

2017-04-01

Implementing new magnetic resonance experiments, or sequences, often involves extensive programming on vendor-specific platforms, which can be time consuming and costly. This situation is exacerbated when research sequences need to be implemented on several platforms simultaneously, for example, at different field strengths. This work presents an alternative programming environment that is hardware-independent, open-source, and promotes rapid sequence prototyping. A novel file format is described to efficiently store the hardware events and timing information required for an MR pulse sequence. Platform-dependent interpreter modules convert the file to appropriate instructions to run the sequence on MR hardware. Sequences can be designed in high-level languages, such as MATLAB, or with a graphical interface. Spin physics simulation tools are incorporated into the framework, allowing for comparison between real and virtual experiments. Minimal effort is required to implement relatively advanced sequences using the tools provided. Sequences are executed on three different MR platforms, demonstrating the flexibility of the approach. A high-level, flexible and hardware-independent approach to sequence programming is ideal for the rapid development of new sequences. The framework is currently not suitable for large patient studies or routine scanning although this would be possible with deeper integration into existing workflows. Magn Reson Med 77:1544-1552, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

SOMKE: kernel density estimation over data streams by sequences of self-organizing maps.

PubMed

Cao, Yuan; He, Haibo; Man, Hong

2012-08-01

In this paper, we propose a novel method SOMKE, for kernel density estimation (KDE) over data streams based on sequences of self-organizing map (SOM). In many stream data mining applications, the traditional KDE methods are infeasible because of the high computational cost, processing time, and memory requirement. To reduce the time and space complexity, we propose a SOM structure in this paper to obtain well-defined data clusters to estimate the underlying probability distributions of incoming data streams. The main idea of this paper is to build a series of SOMs over the data streams via two operations, that is, creating and merging the SOM sequences. The creation phase produces the SOM sequence entries for windows of the data, which obtains clustering information of the incoming data streams. The size of the SOM sequences can be further reduced by combining the consecutive entries in the sequence based on the measure of Kullback-Leibler divergence. Finally, the probability density functions over arbitrary time periods along the data streams can be estimated using such SOM sequences. We compare SOMKE with two other KDE methods for data streams, the M-kernel approach and the cluster kernel approach, in terms of accuracy and processing time for various stationary data streams. Furthermore, we also investigate the use of SOMKE over nonstationary (evolving) data streams, including a synthetic nonstationary data stream, a real-world financial data stream and a group of network traffic data streams. The simulation results illustrate the effectiveness and efficiency of the proposed approach.

Development of a State Machine Sequencer for the Keck Interferometer: Evolution, Development and Lessons Learned using a CASE Tool Approach

NASA Technical Reports Server (NTRS)

Rede, Leonard J.; Booth, Andrew; Hsieh, Jonathon; Summer, Kellee

2004-01-01

This paper presents a discussion of the evolution of a sequencer from a simple EPICS (Experimental Physics and Industrial Control System) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a CASE (Computer Aided Software Engineering) tool approach. The main purpose of the sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Hare1 finite state machine, software program designed to orchestrate several lower-level hardware and software hard real time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORB A, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

Development of a state machine sequencer for the Keck Interferometer: evolution, development, and lessons learned using a CASE tool approach

NASA Astrophysics Data System (ADS)

Reder, Leonard J.; Booth, Andrew; Hsieh, Jonathan; Summers, Kellee R.

2004-09-01

This paper presents a discussion of the evolution of a sequencer from a simple Experimental Physics and Industrial Control System (EPICS) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a Computer Aided Software Engineering (CASE) tool approach. The main purpose of the Interferometer Sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations to be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Harel finite state machine software program designed to orchestrate several lower-level hardware and software hard real-time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORBA, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

Autogen Version 2.0

NASA Technical Reports Server (NTRS)

Gladden, Roy

2007-01-01

Version 2.0 of the autogen software has been released. "Autogen" (automated sequence generation) signifies both a process and software used to implement the process of automated generation of sequences of commands in a standard format for uplink to spacecraft. Autogen requires fewer workers than are needed for older manual sequence-generation processes and reduces sequence-generation times from weeks to minutes.

MAIZEGDB.ORG, the Maize Genetics Cooperation and the 2500 MB B73 Genome-Generated Tsunami

USDA-ARS?s Scientific Manuscript database

Advances in sequencing technology have made it possible to sequence the 2500 MB B73 maize genome, both cheaply and in a relatively short time. Nearly simultaneously, other sequencing-based data are on the leading edge of a data tsunami: sequenced differences (currently >300,000 SNP for >1000 inbre...

Complete Genome Sequence of Clavibacter michiganensis subsp. insidiosus R1-1 Using PacBio Single-Molecule Real-Time Technology

PubMed Central

Lu, You; Samac, Deborah A.; Glazebrook, Jane

2015-01-01

We report here the complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1, isolated in Minnesota, USA. The R1-1 genome, generated by a de novo assembly of PacBio sequencing data, is the first complete genome sequence available for this subspecies. PMID:25953184

Ground penetrating radar documents short-term near-surface hydrological changes around Old Faithful Geyser, Yellowstone National Park, USA

NASA Astrophysics Data System (ADS)

Lynne, Bridget Y.; Heasler, Henry; Jaworowski, Cheryl; Smith, Gary J.; Smith, Isaac J.; Foley, Duncan

2018-04-01

In April 2015, Ground Penetrating Radar (GPR) was used to characterize the shallow subsurface (< 5 m depth) of the western sinter slope immediately adjacent to Old Faithful Geyser and near the north side of an inferred geyser cavity. A series of time-sequence images were collected between two eruptions of Old Faithful Geyser. Each set of time-sequence GPR recordings consisted of four transects aligned to provide coverage near the potential location of the inferred 15 m deep geyser chamber. However, the deepest penetration we could achieve with a 200 MHz GPR antennae was 5 m. Seven time-sequence events were collected over a 48-minute interval to image changes in the near-surface, during pre- and post-eruptive cycles. Time-sequence GPR images revealed a series of possible micro-fractures in a highly porous siliceous sinter in the near-surface that fill and drain repetitively, immediately after an eruption and during the recharge period prior to the next main eruptive event.

A Time Sequence-Oriented Concept Map Approach to Developing Educational Computer Games for History Courses

ERIC Educational Resources Information Center

Chu, Hui-Chun; Yang, Kai-Hsiang; Chen, Jing-Hong

2015-01-01

Concept maps have been recognized as an effective tool for students to organize their knowledge; however, in history courses, it is important for students to learn and organize historical events according to the time of their occurrence. Therefore, in this study, a time sequence-oriented concept map approach is proposed for developing a game-based…

The sequence of sequencers: The history of sequencing DNA

PubMed Central

Heather, James M.; Chain, Benjamin

2016-01-01

Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

PubMed Central

Leonard, Guy; Stevens, Jamie R.; Richards, Thomas A.

2009-01-01

The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends. PMID:19812722

Method and apparatus for characterizing reflected ultrasonic pulses

NASA Technical Reports Server (NTRS)

Yost, William T. (Inventor); Cantrell, John H., Jr. (Inventor)

1991-01-01

The invention is a method of and apparatus for characterizing the amplitudes of a sequence of reflected pulses R1, R2, and R3 by converting them into corresponding electric signals E1, E2, and E3 to substantially the same value during each sequence thereby restoring the reflected pulses R1, R2, and R3 to their initial reflection values by timing means, an exponential generator, and a time gain compensator. Envelope and baseline reject circuits permit the display and accurate location of the time spaced sequence of electric signals having substantially the same amplitude on a measurement scale on a suitable video display or oscilloscope.

Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae

NASA Technical Reports Server (NTRS)

Springer, E.; Sachs, M. S.; Woese, C. R.; Boone, D. R.

1995-01-01

Representatives of the family Methanosarcinaceae were analyzed phylogenetically by comparing partial sequences of their methyl-coenzyme M reductase (mcrI) genes. A 490-bp fragment from the A subunit of the gene was selected, amplified by the PCR, cloned, and sequenced for each of 25 strains belonging to the Methanosarcinaceae. The sequences obtained were aligned with the corresponding portions of five previously published sequences, and all of the sequences were compared to determine phylogenetic distances by Fitch distance matrix methods. We prepared analogous trees based on 16S rRNA sequences; these trees corresponded closely to the mcrI trees, although the mcrI sequences of pairs of organisms had 3.01 +/- 0.541 times more changes than the respective pairs of 16S rRNA sequences, suggesting that the mcrI fragment evolved about three times more rapidly than the 16S rRNA gene. The qualitative similarity of the mcrI and 16S rRNA trees suggests that transfer of genetic information between dissimilar organisms has not significantly affected these sequences, although we found inconsistencies between some mcrI distances that we measured and and previously published DNA reassociation data. It is unlikely that multiple mcrI isogenes were present in the organisms that we examined, because we found no major discrepancies in multiple determinations of mcrI sequences from the same organism. Our primers for the PCR also match analogous sites in the previously published mcrII sequences, but all of the sequences that we obtained from members of the Methanosarcinaceae were more closely related to mcrI sequences than to mcrII sequences, suggesting that members of the Methanosarcinaceae do not have distinct mcrII genes.

Development and Evaluation of Novel Real-Time Reverse Transcription-PCR Assays with Locked Nucleic Acid Probes Targeting Leader Sequences of Human-Pathogenic Coronaviruses

PubMed Central

Chan, Jasper Fuk-Woo; Choi, Garnet Kwan-Yue; Tsang, Alan Ka-Lun; Tee, Kah-Meng; Lam, Ho-Yin; Yip, Cyril Chik-Yan; To, Kelvin Kai-Wang; Cheng, Vincent Chi-Chung; Yeung, Man-Lung; Lau, Susanna Kar-Pui; Woo, Patrick Chiu-Yat; Chan, Kwok-Hung; Tang, Bone Siu-Fai

2015-01-01

Based on findings in small RNA-sequencing (Seq) data analysis, we developed highly sensitive and specific real-time reverse transcription (RT)-PCR assays with locked nucleic acid probes targeting the abundantly expressed leader sequences of Middle East respiratory syndrome coronavirus (MERS-CoV) and other human coronaviruses. Analytical and clinical evaluations showed their noninferiority to a commercial multiplex PCR test for the detection of these coronaviruses. PMID:26019210

Directionality analysis on functional magnetic resonance imaging during motor task using Granger causality.

PubMed

Anwar, A R; Muthalib, M; Perrey, S; Galka, A; Granert, O; Wolff, S; Deuschl, G; Raethjen, J; Heute, U; Muthuraman, M

2012-01-01

Directionality analysis of signals originating from different parts of brain during motor tasks has gained a lot of interest. Since brain activity can be recorded over time, methods of time series analysis can be applied to medical time series as well. Granger Causality is a method to find a causal relationship between time series. Such causality can be referred to as a directional connection and is not necessarily bidirectional. The aim of this study is to differentiate between different motor tasks on the basis of activation maps and also to understand the nature of connections present between different parts of the brain. In this paper, three different motor tasks (finger tapping, simple finger sequencing, and complex finger sequencing) are analyzed. Time series for each task were extracted from functional magnetic resonance imaging (fMRI) data, which have a very good spatial resolution and can look into the sub-cortical regions of the brain. Activation maps based on fMRI images show that, in case of complex finger sequencing, most parts of the brain are active, unlike finger tapping during which only limited regions show activity. Directionality analysis on time series extracted from contralateral motor cortex (CMC), supplementary motor area (SMA), and cerebellum (CER) show bidirectional connections between these parts of the brain. In case of simple finger sequencing and complex finger sequencing, the strongest connections originate from SMA and CMC, while connections originating from CER in either direction are the weakest ones in magnitude during all paradigms.

A vision for ubiquitous sequencing

PubMed Central

Erlich, Yaniv

2015-01-01

Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors—miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors. PMID:26430149

Improving the time efficiency of the Fourier synthesis method for slice selection in magnetic resonance imaging.

PubMed

Tahayori, B; Khaneja, N; Johnston, L A; Farrell, P M; Mareels, I M Y

2016-01-01

The design of slice selective pulses for magnetic resonance imaging can be cast as an optimal control problem. The Fourier synthesis method is an existing approach to solve these optimal control problems. In this method the gradient field as well as the excitation field are switched rapidly and their amplitudes are calculated based on a Fourier series expansion. Here, we provide a novel insight into the Fourier synthesis method via representing the Bloch equation in spherical coordinates. Based on the spherical Bloch equation, we propose an alternative sequence of pulses that can be used for slice selection which is more time efficient compared to the original method. Simulation results demonstrate that while the performance of both methods is approximately the same, the required time for the proposed sequence of pulses is half of the original sequence of pulses. Furthermore, the slice selectivity of both sequences of pulses changes with radio frequency field inhomogeneities in a similar way. We also introduce a measure, referred to as gradient complexity, to compare the performance of both sequences of pulses. This measure indicates that for a desired level of uniformity in the excited slice, the gradient complexity for the proposed sequence of pulses is less than the original sequence. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Optical Processing Techniques For Pseudorandom Sequence Prediction

NASA Astrophysics Data System (ADS)

Gustafson, Steven C.

1983-11-01

Pseudorandom sequences are series of apparently random numbers generated, for example, by linear or nonlinear feedback shift registers. An important application of these sequences is in spread spectrum communication systems, in which, for example, the transmitted carrier phase is digitally modulated rapidly and pseudorandomly and in which the information to be transmitted is incorporated as a slow modulation in the pseudorandom sequence. In this case the transmitted information can be extracted only by a receiver that uses for demodulation the same pseudorandom sequence used by the transmitter, and thus this type of communication system has a very high immunity to third-party interference. However, if a third party can predict in real time the probable future course of the transmitted pseudorandom sequence given past samples of this sequence, then interference immunity can be significantly reduced.. In this application effective pseudorandom sequence prediction techniques should be (1) applicable in real time to rapid (e.g., megahertz) sequence generation rates, (2) applicable to both linear and nonlinear pseudorandom sequence generation processes, and (3) applicable to error-prone past sequence samples of limited number and continuity. Certain optical processing techniques that may meet these requirements are discussed in this paper. In particular, techniques based on incoherent optical processors that perform general linear transforms or (more specifically) matrix-vector multiplications are considered. Computer simulation examples are presented which indicate that significant prediction accuracy can be obtained using these transforms for simple pseudorandom sequences. However, the useful prediction of more complex pseudorandom sequences will probably require the application of more sophisticated optical processing techniques.

Finite State Models of Manned Systems: Validation, Simplification, and Extension.

DTIC Science & Technology

1979-11-01

model a time set is needed. A time set is some set T together with a binary relation defined on T which linearly orders the set. If "model time" is...discrete, so is T ; continuous time is represented by a set corresponding to a subset of the non-negative real numbers. In the following discussion time...defined as sequences, over time, of input and outIut values. The notion of sequences or trajectories is formalized as: AT = xx: T -- Al BT = tyIy: T -4BJ AT

Dissociable effects of practice variability on learning motor and timing skills.

PubMed

Caramiaux, Baptiste; Bevilacqua, Frédéric; Wanderley, Marcelo M; Palmer, Caroline

2018-01-01

Motor skill acquisition inherently depends on the way one practices the motor task. The amount of motor task variability during practice has been shown to foster transfer of the learned skill to other similar motor tasks. In addition, variability in a learning schedule, in which a task and its variations are interweaved during practice, has been shown to help the transfer of learning in motor skill acquisition. However, there is little evidence on how motor task variations and variability schedules during practice act on the acquisition of complex motor skills such as music performance, in which a performer learns both the right movements (motor skill) and the right time to perform them (timing skill). This study investigated the impact of rate (tempo) variability and the schedule of tempo change during practice on timing and motor skill acquisition. Complete novices, with no musical training, practiced a simple musical sequence on a piano keyboard at different rates. Each novice was assigned to one of four learning conditions designed to manipulate the amount of tempo variability across trials (large or small tempo set) and the schedule of tempo change (randomized or non-randomized order) during practice. At test, the novices performed the same musical sequence at a familiar tempo and at novel tempi (testing tempo transfer), as well as two novel (but related) sequences at a familiar tempo (testing spatial transfer). We found that practice conditions had little effect on learning and transfer performance of timing skill. Interestingly, practice conditions influenced motor skill learning (reduction of movement variability): lower temporal variability during practice facilitated transfer to new tempi and new sequences; non-randomized learning schedule improved transfer to new tempi and new sequences. Tempo (rate) and the sequence difficulty (spatial manipulation) affected performance variability in both timing and movement. These findings suggest that there is a dissociable effect of practice variability on learning complex skills that involve both motor and timing constraints.

How Does Sequence Structure Affect the Judgment of Time? Exploring a Weighted Sum of Segments Model

ERIC Educational Resources Information Center

Matthews, William J.

2013-01-01

This paper examines the judgment of segmented temporal intervals, using short tone sequences as a convenient test case. In four experiments, we investigate how the relative lengths, arrangement, and pitches of the tones in a sequence affect judgments of sequence duration, and ask whether the data can be described by a simple weighted sum of…

Complete Genome Sequence of Clavibacter michiganensis subsp. insidiosus R1-1 Using PacBio Single-Molecule Real-Time Technology.

PubMed

Lu, You; Samac, Deborah A; Glazebrook, Jane; Ishimaru, Carol A

2015-05-07

We report here the complete genome sequence of Clavibacter michiganensis subsp. insidiosus R1-1, isolated in Minnesota, USA. The R1-1 genome, generated by a de novo assembly of PacBio sequencing data, is the first complete genome sequence available for this subspecies. Copyright © 2015 Lu et al.

String Mining in Bioinformatics

NASA Astrophysics Data System (ADS)

Abouelhoda, Mohamed; Ghanem, Moustafa

Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word "data-mining" is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

String Mining in Bioinformatics

NASA Astrophysics Data System (ADS)

Abouelhoda, Mohamed; Ghanem, Moustafa

Sequence analysis is a major area in bioinformatics encompassing the methods and techniques for studying the biological sequences, DNA, RNA, and proteins, on the linear structure level. The focus of this area is generally on the identification of intra- and inter-molecular similarities. Identifying intra-molecular similarities boils down to detecting repeated segments within a given sequence, while identifying inter-molecular similarities amounts to spotting common segments among two or multiple sequences. From a data mining point of view, sequence analysis is nothing but string- or pattern mining specific to biological strings. For a long time, this point of view, however, has not been explicitly embraced neither in the data mining nor in the sequence analysis text books, which may be attributed to the co-evolution of the two apparently independent fields. In other words, although the word “data-mining” is almost missing in the sequence analysis literature, its basic concepts have been implicitly applied. Interestingly, recent research in biological sequence analysis introduced efficient solutions to many problems in data mining, such as querying and analyzing time series [49,53], extracting information from web pages [20], fighting spam mails [50], detecting plagiarism [22], and spotting duplications in software systems [14].

Abdominal MR imaging in children: motion compensation, sequence optimization, and protocol organization.

PubMed

Chavhan, Govind B; Babyn, Paul S; Vasanawala, Shreyas S

2013-05-01

Familiarity with basic sequence properties and their trade-offs is necessary for radiologists performing abdominal magnetic resonance (MR) imaging. Acquiring diagnostic-quality MR images in the pediatric abdomen is challenging due to motion, inability to breath hold, varying patient size, and artifacts. Motion-compensation techniques (eg, respiratory gating, signal averaging, suppression of signal from moving tissue, swapping phase- and frequency-encoding directions, use of faster sequences with breath holding, parallel imaging, and radial k-space filling) can improve image quality. Each of these techniques is more suitable for use with certain sequences and acquisition planes and in specific situations and age groups. Different T1- and T2-weighted sequences work better in different age groups and with differing acquisition planes and have specific advantages and disadvantages. Dynamic imaging should be performed differently in younger children than in older children. In younger children, the sequence and the timing of dynamic phases need to be adjusted. Different sequences work better in smaller children and in older children because of differing breath-holding ability, breathing patterns, field of view, and use of sedation. Hence, specific protocols should be maintained for younger children and older children. Combining longer-higher-resolution sequences and faster-lower-resolution sequences helps acquire diagnostic-quality images in a reasonable time. © RSNA, 2013.

Optimization of a double inversion recovery sequence for noninvasive synovium imaging of joint effusion in the knee.

PubMed

Jahng, Geon-Ho; Jin, Wook; Yang, Dal Mo; Ryu, Kyung Nam

2011-05-01

We wanted to optimize a double inversion recovery (DIR) sequence to image joint effusion regions of the knee, especially intracapsular or intrasynovial imaging in the suprapatellar bursa and patellofemoral joint space. Computer simulations were performed to determine the optimum inversion times (TI) for suppressing both fat and water signals, and a DIR sequence was optimized based on the simulations for distinguishing synovitis from fluid. In vivo studies were also performed on individuals who showed joint effusion on routine knee MR images to demonstrate the feasibility of using the DIR sequence with a 3T whole-body MR scanner. To compare intracapsular or intrasynovial signals on the DIR images, intermediate density-weighted images and/or post-enhanced T1-weighted images were acquired. The timings to enhance the synovial contrast from the fluid components were TI1 = 2830 ms and TI2 = 254 ms for suppressing the water and fat signals, respectively. Improved contrast for the intrasynovial area in the knees was observed with the DIR turbo spin-echo pulse sequence compared to the intermediate density-weighted sequence. Imaging contrast obtained noninvasively with the DIR sequence was similar to that of the post-enhanced T1-weighted sequence. The DIR sequence may be useful for delineating synovium without using contrast materials.