Guidelines for the use and interpretation of assays for monitoring autophagy

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field. © 2012 Landes Bioscience

Predictors of Response to Endobronchial Coil Therapy in Patients With Advanced Emphysema

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The upgraded JET toroidal Alfvén eigenmode diagnostic system

The main characteristics of toroidal Alfven eigenmodes (TAEs) have been successfully investigated in JET (Joint European Torus) using the scheme of sweeping-frequency external excitation with tracking of the synchronously-detected resonances. However, due to technical limitations, only modes with low values of the toroidal mode number n ≤7 could be effectively excited and unambiguously identified by the Alfven Eigenmode Active Diagnostic (AEAD) system. This represents a serious restriction because theoretical models indicate that medium-n Alfven eigenmodes (AEs) are the most prone to be destabilized by energetic particles in ignited plasmas and, therefore, reliable measurement of their damping rates remains a relevant issue to properly access their effect in ignited plasmas. For this reason, a major upgrade of the AEAD system has been carried out aiming at providing a state-of-the-art excitation and real-time detection system for the planned DT campaign in JET. This required the development of a new type of radio frequency amplifier and filter, not commercially available, and also a control system. In this paper, details of the concepts that are relevant to understand the operation of the new system in the next experimental campaigns are presented, as are the results of numerical simulations to model its performance

Benchmarking the GENE and GYRO codes through the relative roles of electromagnetic and e × B stabilization in JET high-performance discharges

Nonlinear gyrokinetic simulations using the GENE code have previously predicted a significant nonlinear enhanced electromagnetic stabilization in certain JET discharges with high neutral-beam power and low core magnetic shear (Citrin et al 2013 Phys. Rev. Lett. 111 155001, 2015 Plasma Phys. Control. Fusion 57 014032). This dominates over the impact of E × B flow shear in these discharges. Furthermore, fast ions were shown to be a major contributor to the electromagnetic stabilization. These conclusions were based on results from the GENE gyrokinetic turbulence code. In this work we verify these results using the GYRO code. Comparing results (linear frequencies, eigenfunctions, and nonlinear fluxes) from different gyrokinetic codes as a means of verification (benchmarking) is only convincing if the codes agree for more than one discharge. Otherwise, agreement may simply be fortuitous. Therefore, we analyze three discharges, all with a carbon wall: a simplified, two-species, circular geometry case based on an actual JET discharge; an L-mode discharge with a significant fast-ion pressure fraction; and a low-triangularity high-β hybrid discharge. All discharges were analyzed at normalized toroidal flux coordinate ρ = 0.33 where significant ion temperature peaking is observed. The GYRO simulations support the conclusion that electromagnetic stabilization is strong, and dominates E × B shear stabilization

ITER-like antenna capacitors voltage probes: Circuit/electromagnetic calculations and calibrations

The analyses illustrated in this manuscript have been performed in order to provide the required data for the amplitude-and-phase calibration of the D-dot voltage probes used in the ITER-like antenna at the Joint European Torus tokamak. Their equivalent electrical circuit has been extracted and analyzed, and it has been compared to the one of voltage probes installed in simple transmission lines. A radio-frequency calibration technique has been formulated and exact mathematical relations have been derived. This technique mixes in an elegant fashion data extracted from measurements and numerical calculations to retrieve the calibration factors. The latter have been compared to previous calibration data with excellent agreement proving the robustness of the proposed radio-frequency calibration technique. In particular, it has been stressed that it is crucial to take into account environmental parasitic effects. A low-frequency calibration technique has been in addition formulated and analyzed in depth. The equivalence between the radio-frequency and low-frequency techniques has been rigorously demonstrated. The radio-frequency calibration technique is preferable in the case of the ITER-like antenna due to uncertainties on the characteristics of the cables connected at the inputs of the voltage probes. A method to extract the effect of a mismatched data acquisition system has been derived for both calibration techniques. Finally it has been outlined that in the case of the ITER-like antenna voltage probes can be in addition used to monitor the currents at the inputs of the antenna