| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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. |
- Ma, Tao, et al.
(author)
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Genomic insights into salt adaptation in a desert poplar
- 2013
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2797-
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Journal article (peer-reviewed)abstract
- Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited. Here we report the genome sequence of the desert poplar, Populus euphratica, which exhibits high tolerance to salt stress. Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa. However, we find that several gene families likely to be involved in tolerance to salt stress contain significantly more gene copies within the P. euphratica lineage. Furthermore, genes showing evidence of positive selection are significantly enriched in functional categories related to salt stress. Some of these genes, and others within the same categories, are significantly upregulated under salt stress relative to their expression in another salt-sensitive poplar. Our results provide an important background for understanding tree adaptation to salt stress and facilitating the genetic improvement of cultivated poplars for saline soils.
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| 3. |
- Ai, Yue-Jie, 1982-, et al.
(author)
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Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase
- 2011
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 115:37, s. 10976-10982
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Journal article (peer-reviewed)abstract
- Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.
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| 4. |
- Lu, Gaimin, et al.
(author)
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Fully nonlinear electrostatic waves in electron-positron plasmas
- 2010
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In: JOURNAL OF PLASMA PHYSICS. - : Cambridge University Press. - 0022-3778 .- 1469-7807. ; 76, s. 267-275
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Journal article (peer-reviewed)abstract
- Fully nonlinear electrostatic waves in a plasma containing electrons, positrons, and ions are investigated by solving the governing equations exactly. It is found that both smooth and spiky quasistationary waves exist, and large-amplitude waves necessarily have large-phase velocities, but small-amplitude waves can be both fast and slow.
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| 5. |
- Lu, Yue, et al.
(author)
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A New Way about using Statistical Analysis of Worst-Case Execution Times
- 2011
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In: ACM SIGBED Review. - : Association for Computing Machinery (ACM). - 1551-3688. ; 8:3, s. 11-14
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Journal article (peer-reviewed)abstract
- In this paper, we revisit the problem of using Extreme Value Theory (EVT) in the Worst-Case Execution Time (WCET) analysis of the programs running on a single processor. Our proposed statistical WCET analysis method consists of a novel sampling mechanism tackling with some problems that hindered the application of using EVT in the context, and a statistical inference about computation of a WCET estimate of the target program. To be specific, the presented sampling mechanism takes analysis samples from the target program based around end-to-end measurements. Next, the statistical inference using EVT together with other statistical techniques, analyzes such timing traces which contain the execution time data of the program, to compute a WCET estimate with a certain predictable probability of being exceeded.
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| 7. |
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| 8. |
- Lu, Yue, et al.
(author)
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A Statistical Approach to Response-Time Analysis of Complex Real-Time Embedded Systems
- 2010
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In: Proceedings of the 16th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (RTCSA 2010). ; , s. 153-160
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Conference paper (peer-reviewed)abstract
- This paper presents RapidRT, a novel statistical approach to Worst-Case Response-Time (WCRT) analysis targeting complex embedded real-time systems. The proposed algorithm combines Extreme Value Theory (EVT) and other statistical methods in order to produce a probabilistic WCRT estimate. This estimate is calculated using response time data from either Monte Carlo simulations of a detailed model of the system, or from response-time measurements of the real system. The method could be considered as a pragmatic approach intended for complex industrial systems with real-time requirements. The target systems contain tasks with many intricate dependencies in theirtemporal behavior, which violates the assumptions of traditional analytical methods for response time analysis and thereby makes them overly pessimistic. An evaluation ispresented using two simulation models, inspired by an industrial robotic control system, and five other methods as reference.
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| 9. |
- Lu, Yue, et al.
(author)
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A statistical approach to simulation model validation in response-time analysis of complex real-time embedded systems
- 2011
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In: Proceedings of the ACM Symposium on Applied Computing 2011. - New York, NY, USA : ACM. - 9781450301138 ; , s. 711-716
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Conference paper (peer-reviewed)abstract
- As simulation-based analysis methods make few restrictions on the system design and scale to very large and complex systems, they are widely used in, e.g., timing analysis of complex real-time embedded systems (CRTES) in industrial circles. However, before such methods are used, the analysis simulation models have to be validated in order to assess if they represent the actual system or not, which also matters to the confidence in the simulation results. This paper presents a statistical approach to validation of temporal simulation models extracted from CRTES, by introducing existing mature statistical hypothesis tests to the context. Moreover, our evaluation using simulation models depicting a fictive but representative industrial robotic control system indicates that the proposed method can successfully identify temporal differences between different simulation models, hence it has the potential to be considered as an effective simulation model validation technique. © 2011 ACM.
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| 10. |
- Lu, Yue, et al.
(author)
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A Statistical Approach to Simulation Model Validation in Timing Analysis of Complex Real-Time Embedded Systems
- 2010. - 5
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In: Proceedings - 16th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications, RTCSA 2010. - Brussels. ; , s. -160
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Conference paper (peer-reviewed)abstract
- Simulation-based analysis methods make few restrictions on the system design and scale to very large and complex systems, therefore they are widely used in timing analysis of complex industrial embedded systems. This paper presents a statistical approach to validation of temporal simulation models extracted from complex embedded systems, by introducing existing mature statistical methods to the context. The proposed approach firstly collects sampling distributions of response time and execution time data of tasks in both the modeled system and the model, based on simple random samples (SRS). The second step of the approach is to compare the sampling distributions, regarding interesting timing properties, by using the non-parametric two-sample Kolmogorov-Smirnov test. The evaluation using a fictive system model inspired by a real robotic control system with a set of change scenarios, shows a promising result. The proposed algorithm can identify temporal differences between the target system and its extracted model, i.e., the algorithm can assess whether the extracted model is a sufficiently accurate approximation of the target system.
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