Mean and oscillating plasma flows and turbulence interactions across the L-H confinement transition

A complex interaction between turbulence driven E × B zonal flow oscillations, i.e., geodesic acoustic modes (GAMs), the turbulence, and mean equilibrium flows is observed during the low to high (L-H) plasma confinement mode transition in the ASDEX Upgrade tokamak. Below the L-H threshold at low densities a limit-cycle oscillation forms with competition between the turbulence level and the GAM flow shearing. At higher densities the cycle is diminished, while in the H mode the cycle duration becomes too short to sustain the GAM, which is replaced by large amplitude broadband flow perturbations. Initially GAM amplitude increases as the H-mode transition is approached, but is then suppressed in the H mode by enhanced mean flow shear.     

Monte Carlo maximum likelihood circle fitting using circular density functions

Finding the “best-fitting” circle to describe a set of points in two dimensions is discussed in terms of maximum likelihood estimation. Several combinations of distributions are proposed to describe the stochastic nature of points in the plane, as the points are considered to have a common, typically unknown center, a random radius, and random angular orientation. A Monte Carlo search algorithm over part of the parameter space is suggested for finding the maximum likelihood parameter estimates. Examples are presented, and comparisons are drawn between circles fit by this proposed method, least squares, and other maximum likelihood methods found in the literature.     

Unexpected Acetylation of Endogenous Aliphatic Amines by Arylamine N-Acetyltransferase NAT2

N-Acetyltransferases play critical roles in the deactivation and clearance of xenobiotics, including clinical drugs. NAT2 has been classified as an arylamine N-acetyltransferase that mainly converts aromatic amines, hydroxylamines, and hydrazines. Herein, we demonstrate that the human arylamine N-acetyltransferase NAT2 also acetylates aliphatic endogenous amines. Metabolomic analysis and chemical synthesis revealed increased intracellular concentrations of mono- and diacetylated spermidine in human cell lines expressing the rapid compared to the slow acetylator NAT2 phenotype. The regioselective N⁸-acetylation of monoacetylated spermidine by NAT2 answers the long-standing question of the source of diacetylspermidine. We also identified selective acetylation of structurally diverse alkylamine-containing drugs by NAT2, which may contribute to variations in patient responses. The results demonstrate a previously unknown functionality and potential regulatory role for NAT2, and we suggest that this enzyme should be considered for re-classification.     

A Survey of Methods Available for the Numerical Optimization of Continuous Dynamic Systems

There has been significant progress in the development of numerical methods for the determination of optimal trajectories for continuous dynamic systems, especially in the last 20 years. In the 1980s, the principal contribution was new methods for discretizing the continuous system and converting the optimization problem into a nonlinear programming problem. This has been a successful approach that has yielded optimal trajectories for very sophisticated problems. In the last 15–20 years, researchers have applied a qualitatively different approach, using evolutionary algorithms or metaheuristics, to solve similar parameter optimization problems. Evolutionary algorithms use the principle of “survival of the fittest” applied to a population of individuals representing candidate solutions for the optimal trajectories. Metaheuristics optimize by iteratively acting to improve candidate solutions, often using stochastic methods. In this paper, the advantages and disadvantages of these recently developed methods are described and an attempt is made to answer the question of what is now the best extant numerical solution method.     

Indefinite integrals of special functions from hybrid equations

ABSTRACT

Elementary linear first and second order differential equations can always be constructed for twice differentiable functions by explicitly including the function's derivatives in the definition of these equations. If the function also obeys a conventional differential equation, information from this equation can be introduced into the elementary equations to give blended linear equations which are here called hybrid equations. Integration theorems are derived for these hybrid equations and several universal integrals are also derived. The paper presents integrals derived with these methods for cylinder functions, associated Legendre functions, and the Gegenbauer, Chebyshev, Hermite, Jacobi and Laguerre orthogonal polynomials. All the results presented have been checked using Mathematica.     

Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target Validation

Epigenetics is currently the focus of intense research interest across a broad range of disciplines due to its importance in a multitude of biological processes and disease states. Epigenetic functions result partly from modification of the nucleobases in DNA and RNA, and/or post‐translational modifications of histone proteins. These modifications are dynamic, with cellular machinery identified to modulate and interpret the marks. Our focus is on bromodomains, which bind to acetylated lysine residues. Progress in the study of bromodomains, and the development of bromodomain ligands, has been rapid. These advances have been underpinned by many disciplines, but chemistry and chemical biology have undoubtedly played a significant role. Herein, we review the key chemistry and chemical biology approaches that have furthered our study of bromodomains, enabled the development of bromodomain ligands, and played a critical role in the validation of bromodomains as therapeutic targets.     

Phase ripple correction: theory and application

Spectral phase ripple associated with novel dispersive devices can distort broadband optical signals. We present a digital postprocessing algorithm to correct for this distortion by exploiting the static deterministic nature of the ripple. This algorithm is demonstrated with empirical data for several systems employing chirped fiber Bragg gratings (CFBGs). We employ this technique in a photonic time-stretch system incorporating CFBGs, improving the signal fidelity by 9 dB. Simulations and experiments show that this algorithm, which can be reduced to a simple interpolation and matrix multiplication, also mitigates additive noise. We see that the act of distortion correction yields signal fidelity superior to that of an ideal dispersive element.     

Scattered-light determination of mode I stress-intensity factors by a fringe gradient independent technique

Integration of the scattered-light stress-optic law and established bending and singular crack-tip relationships yielded new experimental equations for calibration and for the determination of mode I stress-intensity factors which are independent of a stress-fringe gradient. Scattered-light stressoptic coefficients determined from four-point bending tests and an integrated scattered-light bending equation show good agreement with values based on stress-fringe gradients computed with polynomials. Excellent agreement was also shown between mode I stress-intensity factors predicted by the integrated stress-optic equation and analytical solutions available in the literature. Favorable comparisons were also made with predictions based on a polynomial-finite-difference method of determining a stress-fringe gradient. Analyses were limited to flaw geometries and locations where there was minimal rotation of the refraction tensor.     

The conditioning of the maximum entropy covariance matrix and its inverse

The maximum entropy covariance matrix is positive definite even when the number of variables p exceeds the sample size n. However, the inverse of this matrix can have stability problems when p is close to n, although these problems tend to disappear as p increases beyond n. We analyze such problems using the variance of the latent roots in a particular metric as a condition number.