Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

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. For example, 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 versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost 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 fi eld 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. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. 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. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. 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

Efficient large-scale power grid analysis based on preconditioned krylov-subspace iterative methods

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INDUCTWISE: Inductance-Wise Interconnect Simulator and Extractor

A robust, efficient, and accurate inductance extraction and simulation tool, INDUCTWISE, is developed and described in this paper. This work advances the state-of-the-art inductance extraction and simulation techniques, and has several major contributions. First, albeit the great benefits of efficiency, the recently proposed inductance matrix sparsification algorithm, the-method (Ji et al. 2001), has a flaw in the stability proof for general geometry. We provide a theoretical analysis as well as a provable stable algorithm for it. Second, a robust window-selection algorithm is presented for general geometry. Third, integrated with the nodal analysis formulation, INDUCTWISE achieves exceptional performance without frequency-dependent complex operations and directly gives time-domain responses. Experimental results show that INDUCTWISE extractor and simulator have dramatic speedup compared to FastHenry and SPICE3, respectively. It has been well tested and released on the web for public usage (Available: http://vlsi.ece.wisc.edu/Inductwise.htm)

ConvexFit: An optimal minimum-error convex fitting and smoothing algorithm with application to gate-sizing

Convex optimization has gained popularity due to its capability to reach global optimum in a reasonable amount of time. Convexity is often ensured by fitting the table data into analytically convex forms such as posynomials. However, fitting the look-up tables into the posynomial forms with minimum error itself may not be a convex optimization problem and hence excessive fitting errors may be introduced. In this paper, we propose to directly adjust the look-up table values into a numerically convex look-up table without explicit analytical form. We show that numerically ”convexifying” the table data with minimum perturbation can be formulated as a convex semidefinite optimization problem and hence optimality can be reached in polynomial time. Without an explicit form limitation, we find that the fitting error is significantly reduced while the convexity is still ensured. As a result, convex optimization algorithms can still be applied. Furthermore, we also develop a ”smoothing ” algorithm to make the table data smooth and convex to facilitate the optimization process. Results from extensive experiments on industrial cell libraries demonstrate that our method reduces 30X fitting error over a well-developed posynomial fitting algorithm. Its application to circuit tuning is also presented. 1