| 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. |
- Rong, Zhi-Hai, et al.
(author)
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Emergence of cooperation through coevolving time scale in spatial prisoner's dilemma
- 2010
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In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - : American Physical Society. - 1063-651X .- 1095-3787. ; 82:2, s. 026101-
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Journal article (peer-reviewed)abstract
- We study evolutionary prisoner’s dilemma game by considering adaptive strategy-selection time scale among individuals according to a “win-slower, lose-faster” rule: if an individual successfully resists the invasion of an opponent, she is prone to hold her strategy for longer time through decreasing her strategy-selection time scale; otherwise, she increases the time scale because of losing. We find that the greater the losers increase their strategy-selection time scales, the better for cooperation. Interestingly, optimal cooperation can be induced by proper adaptive rate in the strategy-selection time scale. Our results may have potential implications in the design of consensus protocol in multiagent systems.
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| 3. |
- Feng, Cun-Feng, et al.
(author)
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Effects of average degree of network on an order-disorder transition in opinion dynamics
- 2010
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In: Chinese Physics B. - : IOPScience. - 1674-1056. ; 19:6, s. 060203-
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Journal article (peer-reviewed)abstract
- We have investigated the influence of the average degree (k) of network on the location of an order-disorder transition in opinion dynamics. For this purpose, a variant of majority rule (VMR) model is applied to Watts–Strogatz (WS) small-world networks and Barabási–Albert (BA) scale-free networks which may describe some non-trivial properties of social systems. Using Monte Carlo simulations, we find that the order–disorder transition point of the VMR model is greatly affected by the average degree (k) of the networks; a larger value of (k) results in a more ordered state of the system. Comparing WS networks with BA networks, we find WS networks have better orderliness than BA networks when the average degree (k) is small. With the increase of (k), BA networks have a more ordered state. By implementing finite-size scaling analysis, we also obtain critical exponents β/ν, γ/ν and 1/ν for several values of average degree (k). Our results may be helpful to understand structural effects on order–disorder phase transition in the context of the majority rule model.
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| 4. |
- Guan, Jian-Yue, et al.
(author)
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Cooperation influenced by the correlation degree of two-layered complex networks in evolutionary prisoner's dilemma games
- 2010
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In: Chinese Physics B. - : Institute of Physics (IOP). - 1674-1056. ; 19:2
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Journal article (peer-reviewed)abstract
- An evolutionary prisoner's dilemma game is investigated on two-layered complex networks respectively representing interaction and learning networks in one and two dimensions. A parameter q is introduced to denote the correlation degree between the two-layered networks. Using Monte Carlo simulations we studied the effects of the correlation degree on cooperative behaviour and found that the cooperator density nontrivially changes with q for different payoff parameter values depending on the detailed strategy updating and network dimension. An explanation for the obtained results is provided.
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| 5. |
- Lee, Sungmin, et al.
(author)
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Cooperation, structure, and hierarchy in multiadaptive games
- 2011
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In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - Melville, N. Y. : American Physical Society. - 1539-3755 .- 1550-2376. ; 84:6, s. 61148-
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Journal article (peer-reviewed)abstract
- Game-theoretical models where the rules of the game and the interaction structure both coevolve with the game dynamics-multiadaptive games-capture very flexible situations where cooperation among selfish agents can emerge. In this work, we will discuss a multiadaptive model presented in a recent Letter [Phys. Rev. Lett. 106, 028702 (2011)] as well as generalizations of it. The model captures a nonequilibrium situation where social unrest increases the incentive to cooperate and, simultaneously, agents are partly free to influence with whom they interact. First, we investigate the details of how feedback from the behavior of agents determines the emergence of cooperation and hierarchical contact structures. We also study the stability of the system to different types of noise, and find that different regions of parameter space show very different response. Some types of noise can destroy an all-cooperator (C) state. If, on the other hand, hubs are stable, then so is the all-C state. Finally, we investigate the dependence of the ratio between the time scales of strategy updates and the evolution of the interaction structure. We find that a comparatively fast strategy dynamics is a prerequisite for the emergence of cooperation.
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| 6. |
- Lee, Sungmin, et al.
(author)
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Emergent hierarchical structures in multiadaptive games
- 2011
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In: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 106:2, s. 028702-4
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Journal article (peer-reviewed)abstract
- We investigate a game-theoretic model of a social system where both the rules of the game and the interaction structure are shaped by the behavior of the agents. We call this type of model, with several types of feedback couplings from the behavior of the agents to their environment, a multiadaptive game. Our model has a complex behavior with several regimes of different dynamic behavior accompanied by different network topological properties. Some of these regimes are characterized by heterogeneous, hierarchical interaction networks, where cooperation and network topology coemerge from the dynamics.
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| 7. |
- Lin, Yin-Ting, et al.
(author)
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Promotion of cooperation by aspiration-induced migration
- 2011
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In: Physica A: Statistical Mechanics and its Applications. - : Elsevier. - 0378-4371. ; 390:1, s. 77-82
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Journal article (peer-reviewed)abstract
- In this paper, we study an aspiration-induced migration model, in which each individual plays the prisoner’s dilemma game with those being within a circle of radius r centered on himself/herself. An individual will migrate to a randomly chosen place with the velocity v if his/her payoff is below the aspiration level. We report that cooperative behavior is favored when the aspiration level and interaction radius are moderate, and the migration velocity is slow.
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| 8. |
- Sheng-Jun, Wang, et al.
(author)
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Undetermination of the relation between network synchronizability and betweenness centrality
- 2011
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In: Chinese Physics B. - : IOP Publishing. - 1674-1056. ; 20:4
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Journal article (peer-reviewed)abstract
- Betweenness centrality is taken as a sensible indicator of the synchronizability of complex networks. To test whether betweenness centrality is a proper measure of the synchronizability in specific realizations of random networks, this paper adds edges to the networks and then evaluates the changes of betweenness centrality and network synchronizability. It finds that the two quantities vary independently.
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| 9. |
- Wang, Sheng-Jun, et al.
(author)
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Enhancing the synchronizability of scale-free networks by adding edges
- 2010
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In: International Journal of Modern Physics C. - 0129-1831. ; 21:1, s. 67-77
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Journal article (peer-reviewed)abstract
- To efficiently enhance the synchronizability of a scale-free network by adding some edges, we numerically study the effect of edge-adding on the spectrum of the network Laplacian matrix. Based on the relation between the largest eigenvalue of the Laplacian matrix and the largest degree of the scale-free network, we show that adding a new edge to the node of largest degree will generally weaken the synchronizability of a scale-free network. We consequently propose a method to effectively enhance the network synchronizability by attaching the new edge to a node whose nearest-neighbors have small degrees. The effect of the new method is analyzed and demonstrated with comparisons.
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| 10. |
- Wu, Zhi-Xi, et al.
(author)
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Local interaction scale controls the existence of a non-trivial optimal critical mass in opinion spreading
- 2010
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In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1063-651X .- 1095-3787. ; 82:2, s. 022102-
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Journal article (peer-reviewed)abstract
- We study a model of opinion formation where the collective decision of a group is said to happen if the fraction of agents having the most common opinion exceeds a threshold value, a critical mass. We find that there exists a unique nontrivial critical mass giving the most efficient convergence to consensus. In addition, we observe that for small critical masses, the characteristic time scale for the relaxation to consensus splits into two. The shorter time scale corresponds to a direct relaxation and the longer one can be explained by the existence of intermediate metastable states similar to those found in [P. Chen and S. Redner, Phys. Rev. E 71, 036101 (2005)]. This longer time scale is dependent on the precise condition for consensus—with a modification of the condition it can go away.
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