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Current nucleic acid amplification methods to detect Mycobacterium tuberculosis are complex, labor-intensive, and technically challenging. We developed and performed the first analysis of the Cepheid Gene Xpert System's MTB/RIF assay, an integrated hands-free sputum-processing and real-time PCR system with rapid on-demand, near-patient technology, to(More)
A global plasma turbulence simulation code, ORB5, is presented. It solves the gyrokinetic electrostatic equations including zonal flows in axisymmetric magnetic geometry. The present version of the code assumes a Boltzmann electron response on magnetic surfaces. It uses a Particle-In-Cell (PIC), δf scheme, 3D cubic B-splines finite elements for the field(More)
Several Seattle-area streams in Puget Sound were the focus of habitat restoration projects in the 1990s. Post-project effectiveness monitoring surveys revealed anomalous behaviors among adult coho salmon returning to spawn in restored reaches. These included erratic surface swimming, gaping, fin splaying, and loss of orientation and equilibrium. Affected(More)
In this work, a Fourier solver [McMillan et. in order to reduce the memory of the matrix associated with the field equation. This scheme is verified with linear and nonlinear simulations of turbulence. It is demonstrated that the straight-field-line angle is the coordinate that optimizes the Fourier solver, that both linear and nonlinear turbulent states(More)
In this paper, we present global nonlinear gyrokinetic simulations including finite β e effects and collisions in tokamak geometry. Global electromagnetic simulations using conventional δf particle in cell methods are very demanding, with respect to numerical resources, in order to correctly describe the evolution of the non-adiabatic part of the electron(More)
Linearized operators describing inter-species and like-species collisions have been discretized and implemented in the gyrokinetic Particle-In-Cell (PIC) code ORB5 [S. Jolliet, Comp. Phys. Comm. 177, 409 (2007)] based on the delta-f approach. Simulation results for neoclassical transport are compared with both analytical predictions as well as results from(More)
Highly variable flux surface averaged heat fluxes are resolved in gyrokinetic simulations of ion temperature gradient ͑ITG͒ turbulence, even in large systems. Radially propagating fronts or avalanches are also seen. Their propagation lengths in gyroradii and relative amplitude remain constant as simulation size is increased, so the avalanches appear to(More)
Turbulent transport dynamics and level are investigated with the 5D gyrokinetic global code GY-SELA, modelling the Ion Temperature Gradient instability with adiabatic electrons. The heat transport exhibits large scale events, propagating radially in both directions at velocities of the order of the diamag-netic velocity. The effective diffusivity is in(More)
The eigenmode spectrum is a fundamental starting point for the analysis of plasma stability and the onset of turbulence, but the characterization of the spectrum even for the simplest plasma model, ideal magnetohydrodynamics (MHD), is not fully understood. This is especially true in configurations with no continuous geometric symmetry, such as in a real(More)