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| 2. |
- 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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| 3. |
- Abbafati, Cristiana, et al.
(författare)
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- 2020
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Cai, Simin, et al.
(författare)
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A Formal Approach for Flexible Modeling and Analysis of Transaction Timeliness and Isolation
- 2016
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Ingår i: Proceedings of the 24th International Conference on Real-Time Networks and Systems. - Brest, France : ACM.
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Konferensbidrag (refereegranskat)abstract
- Traditional Concurrency Control (CC) mechanisms ensure absence of undesired interference in transaction-based systems and enforce isolation. However, CC may introduce unpredictable delays that could lead to breached timeliness, which is unwanted for real-time transactions. To avoid deadline misses, some CC algorithms relax isolation in favor of timeliness, whereas others limit possible interleavings by leveraging real-time constraints and preserve isolation. Selecting an appropriate CC algorithm that can guarantee timeliness at an acceptable level of isolation thus becomes an essential concern for system designers. However, trading-off isolation for timeliness is not easy with existing analysis techniques in database and real-time communities. In this paper, we propose to use model checking of a timed automata model of the transaction system, in order to check the traded-off timeliness and isolation. Our solution provides modularization for the basic transactional constituents, which enables flexible modeling and composition of various candidate CC algorithms, and thus reduces the effort of selecting the appropriate CC algorithm.
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| 5. |
- Cai, Simin, et al.
(författare)
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Customized Real-Time Data Management for Automotive Systems : A Case Study
- 2017
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Ingår i: IECON 2017 - 43RD ANNUAL CONFERENCE OF THE IEEE INDUSTRIAL ELECTRONICS SOCIETY. - 9781538611272 ; , s. 8397-8404
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Konferensbidrag (refereegranskat)abstract
- Real-time DataBase Management Systems (RTDBMS) have been considered as a promising means to manage data for data-centric automotive systems. During the design of an RTDBMS, one must carefully trade off data consistency and timeliness, in order to achieve an acceptable level of both properties. Previously, we have proposed a design process called DAGGERS to facilitate a systematic customization of transaction models and decision on the run-time mechanisms. In this paper, we evaluate the applicability of DAGGERS via an industrially relevant case study that aims to design the transaction management for an on-board diagnostic system, which should guarantee both timeliness and data consistency under concurrent access. To achieve this, we apply the pattern-based approach of DAGGERS to formalize the transactions, and derive the appropriate isolation level and concurrency control algorithm guided by model checking. We show by simulation that the implementation of our designed system satisfies the desired timeliness and derived isolation, and demonstrate that DAGGERS helps to customize desired real-time transaction management prior to implementation.
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| 6. |
- Cai, Simin, et al.
(författare)
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DAGGTAX : A Taxonomy of Data Aggregation Processes
- 2017
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Data aggregation processes are essential constituents in many data management applications. Due to their complexity, designing data aggregation processes often demands considerable efforts. A study on the features of data aggregation processes will provide a comprehensive view for the designers and ease the design process. Existing works either propose application-specific aggregation solutions, or focus on particular aspects of aggregation processes such as aggregate functions, hence they do not offer a high-level, generic description. In this paper, we propose a taxonomy of data aggregation processes called DAGGTAX, which builds on the results of an extensive survey within various application domains. Our work focuses on the features of aggregation processes and their implications, especially on the temporal data consistency and the process timeliness. We present our taxonomy as a feature diagram, which is a visual notation with formal semantics. The taxonomy can then serve as the foundation of a design tool that enables designers to build an aggregation process by selecting and composing desired features. Based on the implications of the features, we formulate three design rules that eliminate infeasible feature combinations. We also provide a set of design heuristics that could help designers to decide the appropriate mechanisms for achieving the selected features.
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| 7. |
- Cai, Simin, et al.
(författare)
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DAGGTAX : A taxonomy of data aggregation processes
- 2017
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Ingår i: Lecture Notes in Computer Science, vol. 10563. - Cham : Springer Verlag. - 9783319668536 ; , s. 324-339
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Konferensbidrag (refereegranskat)abstract
- Data aggregation processes are essential constituents for data management in modern computer systems, such as decision support systems and Internet of Things (IoT) systems. Due to the heterogeneity and real-time constraints in such systems, designing appropriate data aggregation processes often demands considerable effort. A study on the characteristics of data aggregation processes is then desirable, as it provides a comprehensive view of such processes, potentially facilitating their design, as well as the development of tool support to aid designers. In this paper, we propose a taxonomy called DAGGTAX, which is a feature diagram that models the common and variable characteristics of data aggregation processes, with a special focus on the real-time aspect. The taxonomy can serve as the foundation of a design tool, which we also introduce, enabling designers to build an aggregation process by selecting and composing desired features, and to reason about the feasibility of the design. We apply DAGGTAX on industrial case studies, showing that DAGGTAX not only strengthens the understanding, but also facilitates the model-driven design of data aggregation processes. © 2017, Springer International Publishing AG.
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| 8. |
- Cai, Simin, et al.
(författare)
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Data Aggregation Processes : A Survey, A Taxonomy, and Design Guidelines
- 2019
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Ingår i: Computing. - : Springer Science and Business Media LLC. - 0010-485X .- 1436-5057. ; 101:10, s. 1397-1429
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Tidskriftsartikel (refereegranskat)abstract
- Data aggregation processes are essential constituents for data management in modern computer systems, such as decision support systems and Internet of Things (IoT) systems, many with timing constraints. Understanding the common and variable features of data aggregation processes, especially their implications to the timerelated properties, is key to improving the quality of the designed system and reduce design effort. In this paper, we present a survey of data aggregation processes in a variety of application domains from literature.We investigate their common and variable features, which serves as the basis of our previously proposed taxonomy called DAGGTAX. By studying the implications of the DAGGTAX features, we formulate a set of constraints to be satisfied during design, which helps to check the correctness of the specifications and reduce the design space. We also provide a set of design heuristics that could help designers to decide the appropriate mechanisms for achieving the selected features. We apply DAGGTAX on industrial case studies, showing that DAGGTAX not only strengthens the understanding, but also serves as the foundation of a design tool which facilitates the model-driven design of data aggregation processes.
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| 9. |
- Cai, Simin, et al.
(författare)
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Design of Cloud Monitoring Systems via DAGGTAX : A Case Study
- 2017
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Ingår i: Procedia Computer Science. - : Elsevier BV. - 1877-0509. ; 109, s. 424-431
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Tidskriftsartikel (refereegranskat)abstract
- Efficient auto-scaling of cloud resources relies on the monitoring of the cloud, which involves multiple aggregation processes and large amounts of data with various and interdependent requirements. A systematic way of describing the data together with the possible aggregations is beneficial for designers to reason about the properties of these aspects as well as their implications on the design, thus improving quality and lowering development costs. In this paper, we propose to apply DAGGTAX, a feature-oriented taxonomy for organizing common and variable data and aggregation process properties, to the design of cloud monitoring systems. We demonstrate the effectiveness of DAGGTAX via a case study provided by industry, which aims to design a cloud monitoring system that serves auto-scaling for a video streaming system. We design the cloud monitoring system by selecting and composing DAGGTAX features, and reason about the feasibility of the selected features. The case study shows that the application of DAGGTAX can help designers to identify reusable features, analyze trade-offs between selected features, and derive crucial system parameters.
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| 10. |
- Cai, Simin, et al.
(författare)
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Effective Test Suite Design for Detecting Concurrency Control Faults in Distributed Transaction Systems
- 2018
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Ingår i: 8th International Symposium On Leveraging Applications of Formal Methods, Verification and Validation ISoLA 2018. - Cham : Springer International Publishing. - 9783030034245 ; , s. 355-374
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Konferensbidrag (refereegranskat)abstract
- Concurrency control faults may lead to unwanted interleavings, and breach data consistency in distributed transaction systems. However, due to the unpredictable delays between sites, detecting concurrency control faults in distributed transaction systems is difficult. In this paper, we propose a methodology, relying on model-based testing and mutation testing, for designing test cases in order to detect such faults. The generated test inputs are designated delays between distributed operations, while the outputs are the occurrence of unwanted interleavings that are consequences of the concurrency control faults. We mutate the distributed transaction specification with common concurrency control faults, and model them as UPPAAL timed automata, in which designated delays are encoded as stopwatches. Test cases are generated via reachability analysis using UPPAAL Model Checker, and are selected to form an effective test suite. Our methodology can reduce redundant test cases, and find the appropriate delays to detect concurrency control faults effectively.
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