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| 3. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 4. |
- 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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| 5. |
- Jiang, Wei, et al.
(författare)
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Energy Aware Real-Time Scheduling Policy with Guaranteed Security Protection
- 2014
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Ingår i: <em>2014 19TH ASIA AND SOUTH PACIFIC DESIGN AUTOMATION CONFERENCE (ASP-DAC)</em>. - : IEEE conference proceedings. - 9781479928163 ; , s. 317-322
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Konferensbidrag (refereegranskat)abstract
- In this work, we address the emerging scheduling problem existed in the design of secure and energy-efficient real-time embedded systems. The objective is to minimize the energy consumption subject to security and schedulability constraints. Due to the complexity of the problem, we propose a dynamic programming based approximation approach to find the near-optimal solutions with respect to predefined security constraint. The proposed technique has polynomial time complexity which is about half of traditional approximation approaches. The efficiency of our algorithm is validated by extensive experiments.
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| 6. |
- Jiang, Wei, et al.
(författare)
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Energy Optimization of Security-Critical Real-Time Applications with Guaranteed Security Protection
- 2015
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Ingår i: Journal of systems architecture. - : Elsevier. - 1383-7621 .- 1873-6165. ; 61:7, s. 282-292
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Tidskriftsartikel (refereegranskat)abstract
- Designing energy-efficient applications has become of critical importance for embedded systems, especially for battery-powered systems. Additionally, the emerging requirements on both security and real-time make it much more difficult to produce ideal solutions. In this work, we address the emerging scheduling problem existed in the design of secure and energy-efficient real-time embedded systems. The objective is to minimize the system energy consumption subject to security and schedulability constraints. Due to the complexity of the problem, we propose a dynamic programming based approximation approach to find efficient solutions under given constraints. The proposed technique has polynomial time complexity which is half of existing approximation approaches. The efficiency of our algorithm is validated by extensive experiments and a real-life case study. Comparing with other approaches, the proposed approach achieves energy-saving up to 37.6% without violating the real-time and security constraints of the system.
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| 7. |
- Jiang, Wei, et al.
(författare)
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Resource Allocation of Security-Critical Tasks with Statistically Guaranteed Energy Constraint
- 2012
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Ingår i: <em>International Conference on Embedded and Real-Time Computing Systems and Applications (RTCSA 2012), Seoul, Korea, August 19-22, 2012.</em>. - : IEEE. - 9780769548241 - 9781467330176 ; , s. 330-339
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- In this paper, we are interested in resourceallocation for energy constrained and security-criticalembedded systems. Tasks in such systems need to besuccessfully executed under certain energy budget and berobust against serious security threatens. Different to formerenergy minimal scheduling problem, we introduce a newoptimization problem for a set of tasks with energyconstraint and multiple security choices. We present adynamic programming based approximation algorithm tominimize the security risk of the system while statisticallyguaranteeing energy consumption constraints for givenenergy slack ratio. The proposed algorithm is very efficientin both time and space dimensions, and achieves goodsolutions. Extensive simulations demonstrate the superiorityof our algorithm over other approaches.
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| 8. |
- Zhan, Jinyu, et al.
(författare)
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Energy optimization of security-sensitive mixed-criticality applications for distributed real-time systems
- 2018
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Ingår i: Journal of Parallel and Distributed Computing. - : ACADEMIC PRESS INC ELSEVIER SCIENCE. - 0743-7315 .- 1096-0848. ; 117, s. 115-126
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Tidskriftsartikel (refereegranskat)abstract
- Existing studies on mixed-criticality systems are usually safety-oriented, which seriously ignore the security and energy related requirements. In this paper we are interested in the design of security-sensitive mixed-criticality real-time systems. We first establish the system model to capture security-critical applications in mixed-criticality systems. Higher security-criticality protection always results in significant time and energy overhead in mixed-criticality systems. Thus, this paper proposes a system-level design framework for energy optimization of security-sensitive mixed-criticality system with hard real-time constraints. Since the time complexity of finding optimal solutions grows exponentially as problem size grows, a GA (Genetic Algorithm) based on efficient heuristic algorithm is devised to address the system-level optimization problem. Extensive experiments and a real-life case study have been conducted to show the efficiency of the proposed technique, which can obtain balanced minimal energy consumption while satisfying strict security and timing constraints. The proposed approach can save up to 28.9% energy consumption compared with other three candidates. (C) 2018 Elsevier Inc. All rights reserved.
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| 9. |
- Zhang, Xia, et al.
(författare)
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Design Optimization of Energy- and Security-Critical Distributed Real-Time Embedded Systems
- 2013
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Ingår i: <em>15th Workshop on Advances in Parallel and Distributed Computational Models (APDCM 2013), Boston, USA, May 20, 2013.</em>. - : IEEE Press. - 9780769549798 ; , s. 741-750
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Konferensbidrag (refereegranskat)abstract
- In this paper, we approach the design of energy- and security-critical distributed real-time embedded systems from the early mapping and scheduling phases. Modern Distributed Embedded Systems (DESs) are common to be connected to external networks, which is beneficial for various purposes, but also opens up the gate for potential security attacks. However, security protections in DESs result in significant time and energy overhead. In this work, we focus on the problem of providing the best confidentiality protection of internal communication in DESs under time and energy constraints. The complexity of finding the optimal solution grows exponentially as problem size grows. Therefore, we propose an efficient genetic algorithm based heuristic for solving the problem. Extensive experiments demonstrate the efficiency of the proposed technique.
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| 10. |
- Zhang, Xia, et al.
(författare)
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Design Optimization of Security-Sensitive Mixed-Criticality Real-Time Embedded Systems
- 2013
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Konferensbidrag (refereegranskat)abstract
- In this paper we are interested in securitysensitive mixed-criticality real-time systems. Existing researches on mixed-criticality systems usually are safety-oriented, which seriously ignore the security requirements. We firstly establish the system model to capture security-critical applications in mixed-criticality systems. Higher security-criticality protection always results in significant time and energy overhead in mixedcriticality systems. Thus, this paper proposes a system-level design framework for energy optimization of security-sensitive mixed-criticality system. Since the time complexity of finding optimal solutions grows exponentially as problem size grows, a GA based efficient heuristic algorithm is devised to address the system-level optimization problem. Extensive experiments demonstrate the efficiency of the proposed technique, which can obtain balanced minimal energy consumption while satisfying strict security and timing constraints.
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