A Brief Review: The Z-curve Theory and its Application in Genome Analysis

In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.     

Game Theory of Mind

This paper introduces a model of ‘theory of mind’, namely, how we represent the intentions and goals of others to optimise our mutual interactions. We draw on ideas from optimum control and game theory to provide a ‘game theory of mind’. First, we consider the representations of goals in terms of value functions that are prescribed by utility or rewards. Critically, the joint value functions and ensuing behaviour are optimised recursively, under the assumption that I represent your value function, your representation of mine, your representation of my representation of yours, and so on ad infinitum. However, if we assume that the degree of recursion is bounded, then players need to estimate the opponent's degree of recursion (i.e., sophistication) to respond optimally. This induces a problem of inferring the opponent's sophistication, given behavioural exchanges. We show it is possible to deduce whether players make inferences about each other and quantify their sophistication on the basis of choices in sequential games. This rests on comparing generative models of choices with, and without, inference. Model comparison is demonstrated using simulated and real data from a ‘stag-hunt’. Finally, we note that exactly the same sophisticated behaviour can be achieved by optimising the utility function itself (through prosocial utility), producing unsophisticated but apparently altruistic agents. This may be relevant ethologically in hierarchal game theory and coevolution.     

一个具有年龄结构的博弈理论模型的研究

考虑一个鹰-鸽博弈的模型.在这个模型里,动物只知道自己的年龄,而不知道对方的年龄.对于这一个博弈模型,将会证明,在进化的平衡点上,存在两个不同的年龄临界点x1和x2(不妨设x1小于x2),并且年龄在这两个临界点之间的动物将会选择鹰策略;而年龄小于x1和年龄大于x2的动物将会选择鸽子策略.在这里,战争发生的可能性大小定义为:当两个个体相遇时,双方都选择鹰策略的概率.进一步,即使动物仅知道自己的年龄,那么在进化稳定性上战争发生的可能性大小也要比标准的鹰-鸽博弈中战争发生的可能性大小要低.     

Location of Pathogenic Bacteria during Persistent Infections: Insights from an Analysis Using Game Theory

Bacterial persistent infections are responsible for a significant amount of the human morbidity and mortality. Unlike acute bacterial infections, it is very difficult to treat persistent bacterial infections (e.g. tuberculosis). Knowledge about the location of pathogenic bacteria during persistent infection will help to treat such conditions by designing novel drugs which can reach such locations. In this study, events of bacterial persistent infections were analyzed using game theory. A game was defined where the pathogen and the host are the two players with a conflict of interest. Criteria for the establishment of Nash equilibrium were calculated for this game. This theoretical model, which is very simple and heuristic, predicts that during persistent infections pathogenic bacteria stay in both intracellular and extracellular compartments of the host. The result of this study implies that a bacterium should be able to survive in both intracellular and extracellular compartments of the host in order to cause persistent infections. This explains why persistent infections are more often caused by intracellular pathogens like Mycobacterium and Salmonella. Moreover, this prediction is in consistence with the results of previous experimental studies.     

Human Sensorimotor Communication: A Theory of Signaling in Online Social Interactions

Although the importance of communication is recognized in several disciplines, it is rarely studied in the context of online social interactions and joint actions. During online joint actions, language and gesture are often insufficient and humans typically use non-verbal, sensorimotor forms of communication to send coordination signals. For example, when playing volleyball, an athlete can exaggerate her movements to signal her intentions to her teammates (say, a pass to the right) or to feint an adversary. Similarly, a person who is transporting a table together with a co-actor can push the table in a certain direction to signal where and when he intends to place it. Other examples of “signaling” are over-articulating in noisy environments and over-emphasizing vowels in child-directed speech. In all these examples, humans intentionally modify their action kinematics to make their goals easier to disambiguate. At the moment no formal theory exists of these forms of sensorimotor communication and signaling. We present one such theory that describes signaling as a combination of a pragmatic and a communicative action, and explains how it simplifies coordination in online social interactions. We cast signaling within a “joint action optimization” framework in which co-actors optimize the success of their interaction and joint goals rather than only their part of the joint action. The decision of whether and how much to signal requires solving a trade-off between the costs of modifying one’s behavior and the benefits in terms of interaction success. Signaling is thus an intentional strategy that supports social interactions; it acts in concert with automatic mechanisms of resonance, prediction, and imitation, especially when the context makes actions and intentions ambiguous and difficult to read. Our theory suggests that communication dynamics should be studied within theories of coordination and interaction rather than only in terms of the maximization of information transmission.     

基于博弈论的护理管理道德风险控制分析

护理管理过程中的委托代理关系及信息不对称性可能导致道德风险的存在,由此可能引发护患冲突,影响医院的品牌信誉和经济效益。以博弈论为研究方法,对护理管理过程中护理管理部门与护理人员之间和患者与护理人员之间存在的道德风险进行了博弈分析,找出了两种关系下博弈双方的混合战略纳什均衡。护理部与护理人员之间的混合战略纳什均衡是α=D/E与β=（E－B）/E,患者与护理人员之间的混合战略纳什均衡是γ=T/U与δ=（U＋R）/U。为持续维持护理管理中稳定均衡的博弈关系,医院应该采取措施加强道德风险的管理与防范,并开展延续护理服务,政府主导人力资源的配置改革并进行干预。     

基于博弈论的我国分级医疗服务体系构建策略分析

医疗服务体系是一个由多个利益相关集团组成的复杂系统,分级医疗模式即是要建立在不同层级、不同类别医疗机构之间有效分工协作的前提下。文章运用博弈论,在我国医疗行业各个利益集团纵向战略互动模型的理论基础上,基于激励相容理论,对上级医院与基层医疗机构垂直战略互动博弈行为进行分析,从理论层面探讨分级医疗服务体系中各利益相关方的博弈关系及行为选择。     

Microelectrode Experiments with Potato Cells: A Reinterpretation of the Experimental Findings

The conclusions of Macklon and Macdonald (1967) concerning theuptake of chloride at low temperatures by potato cells havebeen reinterpreted. It is believed that the lack of agreementbetween their experimental result and what is expected fromconventional electrochemical theory of the passive movementof ions into plant cells is due to the fact that electrodesinserted into potato cells only detect the potential acrossthe plasmalemma.     

Local Replicator Dynamics: A Simple Link Between Deterministic and Stochastic Models of Evolutionary Game Theory

Classical replicator dynamics assumes that individuals play their games and adopt new strategies on a global level: Each player interacts with a representative sample of the population and if a strategy yields a payoff above the average, then it is expected to spread. In this article, we connect evolutionary models for infinite and finite populations: While the population itself is infinite, interactions and reproduction occurs in random groups of size N. Surprisingly, the resulting dynamics simplifies to the traditional replicator system with a slightly modified payoff matrix. The qualitative results, however, mirror the findings for finite populations, in which strategies are selected according to a probabilistic Moran process. In particular, we derive a one-third law that holds for any population size. In this way, we show that the deterministic replicator equation in an infinite population can be used to study the Moran process in a finite population and vice versa. We apply the results to three examples to shed light on the evolution of cooperation in the iterated prisoner’s dilemma, on risk aversion in coordination games and on the maintenance of dominated strategies.     

Brief Communication: Stability and Catalytic Activity of Novel Circular DNAzymes

DNAzymes represent a new generation of catalytic nucleic acids for specific RNA targeting in order to inhibit protein translation from the specifically cleaved mRNA. The 10–23 DNAzyme was found to hydrolyze RNA in a sequence-specific manner both in vitro and in vivo. Although single-stranded DNAzymes may represent the most effective nucleic acid drug to date, they are nevertheless sensitive to nuclease degradation and require modifications for in vivo application. However, previously used stabilization of DNAzymes by site-specific phosphorothioate (PT) modifications reduces the catalytic activity, and the PTO displays toxic side effects when applied in vivo. Thus, improving the stability of DNAzymes without reducing their catalytic activity is essential if the potential of these compounds should be realized in vivo. Results: The Circozyme was tested targeting the mRNA of the most common genetic rearrangement in pediatric acute lymphoblastic leukemia TEL/AML1 (ETV6/RUNX1). The Circozyme exhibits a stability comparable to PTO-modified DNAzymes without reduction of catalytic activity and specificity and may represent a promising tool for DNAzyme in vivo applications. Conclusion: The inclusion of the catalytic site and the specific mRNA binding sequence of the DNAzyme into a circular loop-stem-loop structure (Circozyme) of approximately 70 bases presented here represents a new effective possibility of DNAzyme stabilization.     

Reinterpretation of crinoid-platyceratid interaction

The well-known association of platyceratid gastropods with crinoids has traditionally been considered an example of coprophagous commensalism. The Occurrence of several crinoid 'stands' ( Platycrinites sp.) from closely spaced bedding surfaces in the upper Mississippian Wymps Gap Limestone member of the Mauch Chunk Formation of southwestern Pennsylvania encourages reinterpretation of this relationship. Crinoid calyces were collected from five separate clusters, two of which contained associated platyceratids. 'Infested' crinoids either died prematurely or were stunted, compared to crinoids in the 'uninfested' clusters. Platyceratid attachment apparently had an adverse effect upon crinoid growth. Serial acetate peels show positioning of the gastropod on the crinoid tegmen over a highly developed anal tube, or chimney. However, the terminus of the anal tube abuts the gastropod's shell and is poorly situated for fecal ingestion by the snail. We suggest that the snail probably pursued another trophic strategy, perhaps taking advantage of aerosol filtration by the crinoid and elevation above the substrate.     

Presumed Behavior: Comments on Cara E. Richards' Brief Communication

Cara E. Richards recently pointed out that instead of the well-established dichotomy between ideal and real behavior, one should consider a trichotomy, with presumed behavior as a third term. The present note agrees with this, but (a) briefly examines some previous publications specifically dealing with this trichotomy, (b) suggests some points of view complementary to those of the Richards communication, and (c) attempts to place studies of presumed behavior in the context of anthropological theory.     

Brief Communication: Orphaned male Chimpanzees die young even after weaning

If a social‐living animal has a long life span, permitting different generations to co‐exist within a social group, as is the case in many primate species, it can be beneficial for a parent to continue to support its weaned offspring to increase the latter's survival and/or reproductive success. Chimpanzees have an even longer period of dependence on their mothers' milk than do humans, and consequently, offspring younger than 4.5–5 years old cannot survive if the mother dies. Most direct maternal investments, such as maternal transportation of infants and sharing of night shelters (beds or nests), end with nutritional weaning. Thus, it had been assumed that a mother's death was no longer critical to the survival of weaned offspring, in contrast to human children, who continue to depend on parental care long after weaning. However, in theory at least, maternal investment in a chimpanzee son after weaning could be beneficial because in chimpanzees' male‐philopatric society, mother and son co‐exist for a long time after the offspring's weaning. Using long‐term demographic data for a wild chimpanzee population in the Mahale Mountains, Tanzania, we show the first empirical evidence that orphaned chimpanzee sons die younger than expected even if they lose their mothers after weaning. This suggests that long‐lasting, but indirect, maternal investment in sons continues several years after weaning and is vital to the survival of the sons. The maternal influence on males in the male‐philopatric societies of hominids may be greater than previously believed. Am J Phys Anthropol, 153:139–143, 2014. © 2013 Wiley Periodicals, Inc.     

An Application of Evolutionary Game Theory to Social Dilemmas: The Traveler's Dilemma and the Minimum Effort Coordination Game

The Traveler''s Dilemma game and the Minimum Effort Coordination game are two social dilemmas that have attracted considerable attention due to the fact that the predictions of classical game theory are at odds with the results found when the games are studied experimentally. Moreover, a direct application of deterministic evolutionary game theory, as embodied in the replicator dynamics, to these games does not explain the observed behavior. In this work, we formulate natural variants of these two games as smoothed continuous-strategy games. We study the evolutionary dynamics of these continuous-strategy games, both analytically and through agent-based simulations, and show that the behavior predicted theoretically is in accord with that observed experimentally. Thus, these variants of the Traveler''s Dilemma and the Minimum Effort Coordination games provide a simple resolution of the paradoxical behavior associated with the original games.