MDRIP: A Hybrid Approach to Parallelisation of Discrete Event Simulation

The research project reported in this thesis considers Multiple Distributed Replications in Parallel (MDRIP), a hybrid approach to parallelisation of quantitative stochastic discrete-event simulation. Parallel Discrete-Event Simulation (PDES) generally covers distributed simulation or simulation with replicated trials. Distributed simulation requires model partitioning and synchronisation among submodels. Simulation with replicated trials can be executed on-line by applying Multiple Replications in Parallel (MRIP). MDRIP has been proposed for overcoming problems related to the large size of simulated models and their complexity, as well as with the problem of controlling the accuracy of the final simulation results. A survey of PDES investigates several primary issues which are directly related to the parallelisation of DES. A secondary issue related to implementation efficiency is also covered. Statistical analysis as a supporting issue is described. The AKAROA2 package is an implementation of making such supporting issue effortless. Existing solutions proposed for PDES have exclusively focused on collecting of output data during simulation and conducting analysis of these data when simulation is finished. Such off-line statistical analysis of output data offers no control of statistical errors of the final estimates. On-line control of statistical errors during simulation has been successfully implemented in AKAROA2, an automated controller of output data analysis during simulation executed in MRIP. However, AKAROA2 cannot be applied directly to distributed simulation. This thesis reports results of a research project aimed at employing AKAROA2 for launching multiple replications of distributed simulation models and for on-line sequential control of statistical errors associated with a distributed performance measure; i.e. with a performance measure which depends on output data being generated by a number of submodels of distributed simulation. We report changes required in the architecture of AKAROA2 to make MDRIP possible. A new MDRIP-related component of AKAROA2, a distributed simulation engine mdrip engine, is introduced. Stochastic simulation in its MDRIP version, as implemented in AKAROA2, has been tested in a number of simulation scenarios. We discuss two specific simulation models employed in our tests: (i) a model consisting of independent queues, and (ii) a queueing network consisting of tandem connection of queueing systems. In the first case, we look at the correctness of message orderings from the distributed messages. In the second case, we look at the correctness of output data analysis when the analysed performance measures require data from all submodels of a given (distributed) simulation model. Our tests confirm correctness of our mdrip engine design in the cases considered; i.e. in models in which causality errors do not occur. However, we argue that the same design principles should be applicable in the case of distributed simulation models with (potential) causality errors

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

Erratum to: Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) (Autophagy, 12, 1, 1-222, 10.1080/15548627.2015.1100356

non present