| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
- 2008
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Ingår i: Autophagy. - : Landes Bioscience. - 1554-8627 .- 1554-8635. ; 4:2, s. 151-175
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Forskningsöversikt (refereegranskat)abstract
- Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.
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| 2. |
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| 3. |
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| 4. |
- de Foy, B., et al.
(författare)
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Modelling constraints on the emission inventory and on vertical dispersion for CO and SO2 in the Mexico City Metropolitan Area using Solar FTIR and zenith sky UV spectroscopy
- 2007
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 7, s. 781-801
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Tidskriftsartikel (refereegranskat)abstract
- Emissions of air pollutants in and around urban areas lead to negative health impacts on the population. To estimate these impacts, it is important to know the sources and transport mechanisms of the pollutants accurately. Mexico City has a large urban fleet in a topographically constrained basin leading to high levels of carbon monoxide ( CO). Large point sources of sulfur dioxide (SO2) surrounding the basin lead to episodes with high concentrations. An Eulerian grid model (CAMx) and a particle trajectory model ( FLEXPART) are used to evaluate the estimates of CO and SO2 in the current emission inventory using mesoscale meteorological simulations from MM5. Vertical column measurements of CO are used to constrain the total amount of emitted CO in the model and to identify the most appropriate vertical dispersion scheme. Zenith sky UV spectroscopy is used to estimate the emissions of SO2 from a large power plant and the Popocatepetl volcano. Results suggest that the models are able to identify correctly large point sources and that both the power plant and the volcano impact the MCMA. Modelled concentrations of CO based on the current emission inventory match observations suggesting that the current total emissions estimate is correct. Possible adjustments to the spatial and temporal distribution can be inferred from model results. Accurate source and dispersion modelling provides feedback for development of the emission inventory, verification of transport processes in air quality models and guidance for policy decisions.
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| 5. |
- Feng, Lei, et al.
(författare)
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A structural approach to the non-blocking supervisory control of discrete-event systems
- 2009
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Ingår i: The International Journal of Advanced Manufacturing Technology. - : Springer Science and Business Media LLC. - 0268-3768 .- 1433-3015. ; 41:11-12, s. 1152-1168
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Tidskriftsartikel (refereegranskat)abstract
- Many practical and important systemic properties of manufacturing systems, like deadlock freeness, liveness, and reversibility, can be formulated as the non-blocking property of discrete-event systems. It can be difficult, however, to verify non-blocking or design a supervisor to guarantee non-blocking control because of state size explosion in the concurrency model. In this paper, we present sufficient conditions for the computation of (small) model abstractions that preserve the non-blocking property. As a consequence, hierarchical and decentralized control structures can be flexibly integrated, and the proposed approach can synthesize maximally permissive and non-blocking control with reduced computational effort. The solution is a group of decentralized supervisors that transparently displays control logic and admits relatively simple implementation.
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| 6. |
- Feng, Lei, et al.
(författare)
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Designing communicating transaction processes by supervisory control theory
- 2007
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Ingår i: Formal methods in system design. - : Springer Science and Business Media LLC. - 0925-9856 .- 1572-8102. ; 30:2, s. 117-141
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Tidskriftsartikel (refereegranskat)abstract
- A Communicating Transaction Process (CTP) is a computational model that serves as a high level specification language for reactive embedded system components and their interactions. It consists of a network of communicating processes coordinating their behaviors via common actions and the common actions are refined as a set of guarded Message Sequence Charts (MSCs). There has been little work devoted to developing CTP models systematically. This paper takes the first step towards bridging this gap. In our work, communicating processes of embedded components are modeled and controlled as Discrete-Event Systems (DES). The control logic among communicating components is derived by Supervisory Control Theory (SCT), so as to guarantee that the communicating processes meet all predefined constraints and possess other desirable system behavioral properties. The control logic is then translated into propositional formulas for guarded MSCs which then results in a CTP model with guaranteed behavioral properties.
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| 7. |
- Feng, Lei, et al.
(författare)
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Supervisory control architecture for discrete-event systems
- 2008
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Ingår i: IEEE Transactions on Automatic Control. - 0018-9286 .- 1558-2523. ; 53:6, s. 1449-1461
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Tidskriftsartikel (refereegranskat)abstract
- A flexible decentralized and hierarchical architecture is presented to reduce computational effort in designing optimal nonblocking supervisors for discrete-event systems (DES). We organize a DES into modular subsystems that embody internal interacting dependencies. Verification of, and coordination among modular subsystems are achieved through their model abstractions. Sufficient conditions are presented to guarantee that coordinators and modular supervisors result in maximally permissive and nonblocking control. A medium-sized example demonstrates the computational effectiveness of our approach.
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| 8. |
- Gardino, Alexandra K, et al.
(författare)
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Transient Non-native Hydrogen Bonds Promote Activation of a Signaling Protein
- 2009
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 139:6, s. 1109-18
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Tidskriftsartikel (refereegranskat)abstract
- SummaryPhosphorylation is a common mechanism for activating proteins within signaling pathways. Yet, the molecular transitions between the inactive and active conformational states are poorly understood. Here we quantitatively characterize the free-energy landscape of activation of a signaling protein, nitrogen regulatory protein C (NtrC), by connecting functional protein dynamics of phosphorylation-dependent activation to protein folding and show that only a rarely populated, pre-existing active conformation is energetically stabilized by phosphorylation. Using nuclear magnetic resonance (NMR) dynamics, we test an atomic scale pathway for the complex conformational transition, inferred from molecular dynamics simulations (Lei et al., 2009). The data show that the loss of native stabilizing contacts during activation is compensated by non-native transient atomic interactions during the transition. The results unravel atomistic details of native-state protein energy landscapes by expanding the knowledge about ground states to transition landscapes.
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| 9. |
- Nascimento, V. B., et al.
(författare)
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Procedure for LEED I-V structural analysis of metal oxide surfaces : Ca1.5Sr0.5RuO4(001)
- 2007
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 75:3, s. 035408-
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Tidskriftsartikel (refereegranskat)abstract
- Transition metal oxides (TMOs) are famous for the intimate coupling between the lattice, electrons, and spin, creating exotic functionality. Creating a surface, breaking the symmetry, should result in lattice distortions that due to the close coupling could create different "surface phases." Historically it has been very difficult to use low energy electron diffraction I-V to quantitatively determine the surface structure of TMOs. A signature of this problem is the large values commonly reported in the literature of the Pendry reliability factor (R-P), which is used to quantify the agreement between experimental data and calculated diffraction. In this paper we describe a consistent procedure for determining the phase shifts using an optimized muffin-tin potential approach combined with an energy-dependent real and imaginary inner potential. This procedure is used to determine the surface structure of the layered TMO Ca1.5Sr0.5RuO4. An acceptable Pendry reliability factor is achieved (R-P=0.28).
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