| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- 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.
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| 2. |
- Varga, Johannes, et al.
(författare)
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Interactive Job Scheduling with Partially Known Personnel Availabilities
- 2023
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Ingår i: Optimization and Learning. - : Springer. - 9783031340192 - 9783031340208
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Konferensbidrag (refereegranskat)abstract
- When solving a job scheduling problem that involves humans, the times in which they are available must be taken into account. For practical acceptance of a scheduling tool, it is further crucial that the interaction with the humans is kept simple and to a minimum. Requiring users to fully specify their availability times is typically not reasonable. We consider a scenario in which initially users only suggest single starting times for their jobs and an optimized schedule shall then be found within a small number of interaction rounds. In each round users may only be suggested a small set of alternative time intervals, which are accepted or rejected. To make the best out of these limited interaction possibilities, we propose an approach that utilizes integer linear programming and a theoretically derived probability calculation for the users’ availabilities based on a Markov model. Educated suggestions of alternative time intervals for performing jobs are determined from these acceptance probabilities as well as the optimization’s current state. The approach is experimentally evaluated and compared to diverse baselines. Results show that an initial schedule can be quickly improved over few interaction rounds, and the final schedule may come close to the solution of the full-knowledge case despite the limited interaction.
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| 3. |
- Varga, Johannes, et al.
(författare)
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Scheduling jobs using queries to interactively learn human availability times
- 2024
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Ingår i: Computers & Operations Research. - : Elsevier. - 0305-0548 .- 1873-765X. ; 167
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Tidskriftsartikel (refereegranskat)abstract
- The solution to a job scheduling problem that involves humans as well some other shared resource has to consider the humans’ availability times. For practical acceptance of a scheduling tool, it is crucial that the interaction with the humans is kept simple and to a minimum. It is rarely practical to ask users to fully specify their availability times or to let them enumerate all possible starting times for their jobs. In the scenario we are considering, users initially only propose a single starting time for each of their jobs and a feasible and optimized schedule shall then be found within a small number of interaction rounds. In each such interaction round, our scheduling approach may propose each user a small number of alternative time intervals for scheduling the user’s jobs, and then the user may accept or reject these. To make the best out of these limited interaction possibilities, we propose an approach that utilizes integer linear programming and an exact and computationally efficient probability calculation for the users’ availabilities assuming two different stochastic models. In this way, educated proposals of alternative time intervals for performing the jobs are determined based on the computed availability probabilities and the improvements these time intervals would enable. The approach is experimentally evaluated on a variety of artificial benchmark scenarios, and different variants are compared with each other and to diverse baselines. Results show that an initial schedule can usually be quickly improved over few interaction rounds even when assuming a quite simple stochastic model, and the final schedule may come close to the solution of the full-knowledge case despite the strongly limited interaction.
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| 4. |
- Varga, Johannes, et al.
(författare)
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Speeding Up Logic-Based Benders Decomposition by Strengthening Cuts with Graph Neural Networks
- 2023
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Ingår i: Machine Learning, Optimization, and Data Science. - Cham. - 9783031539688 - 9783031539695 ; , s. 24-38
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Konferensbidrag (refereegranskat)abstract
- Logic-based Benders decomposition is a technique to solve optimization problems to optimality. It works by splitting the problem into a master problem, which neglects some aspects of the problem, and a subproblem, which is used to iteratively produce cuts for the master problem to account for those aspects. It is critical for the computational performance that these cuts are strengthened, but the strengthening of cuts comes at the cost of solving additional subproblems. In this work we apply a graph neural network in an autoregressive fashion to approximate the compilation of an irreducible cut, which then only requires few postprocessing steps to ensure its validity. We test the approach on a job scheduling problem with a single machine and multiple time windows per job and compare to approaches from the literature. Results show that our approach is capable of considerably reducing the number of subproblems that need to be solved and hence the total computational effort.
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