Efficient information coding and degeneracy in the nervous system

Efficient information coding (EIC) is a universal biological framework rooted in the fundamental principle that system responses should match their natural stimulus statistics for maximizing environmental information. Quantitatively assessed through information theory, such adaptation to the environment occurs at all biological levels and timescales. The context dependence of environmental stimuli and the need for stable adaptations make EIC a daunting task. We argue that biological complexity is the principal architect that subserves deft execution of stable EIC. Complexity in a system is characterized by several functionally segregated subsystems that show a high degree of functional integration when they interact with each other. Complex biological systems manifest heterogeneities and degeneracy, wherein structurally different subsystems could interact to yield the same functional outcome. We argue that complex systems offer several choices that effectively implement EIC and homeostasis for each of the different contexts encountered by the system.     

Systems analysis of RNA trafficking in neural cells

In neural cells, certain RNAs are targeted to dendrites by a specific RNA trafficking pathway, termed the A2 pathway, mediated by the trans-acting trafficking factor, heterogeneous nuclear ribonucleoprotein (hnRNP) A2, which binds to an 11 nucleotide cis-acting trafficking sequence, termed the hnRNP A2 response element (A2RE). RNAs containing A2RE-like sequences are recognized by hnRNP A2 in the nucleus and exported to the cytoplasm where they assemble into trafficking intermediates, termed granules, which also contain components of the translation machinery and molecular motors (cytoplasmic dynein and conventional kinesin). RNA granules move along microtubules to the cell periphery where they become localized and where the encoded protein is translated. Intracellular trafficking of RNA molecules by the A2 pathway is mediated by a complex system consisting of five different subsystems, approximately 35 different molecules and approximately 45 different molecular interactions. Specificity in the A2 pathway is provided by specific interactions of hnRNP A2 with different molecular partners in different subsystems. Polarity of RNA trafficking is controlled by transitions of trafficking intermediates between different subsystems. Comprehensive understanding of the A2 RNA trafficking pathway will require quantitative analysis of concentrations and diffusion constants for each of the different molecules, on rates and off rates for each of the different interactions, relevant conditional operators controlling specific interactions, and interactions of different subsystems. Once the necessary quantitative data are available, mathematical models for the different RNA trafficking subsystems can be developed using computational platforms such as the 'Virtual Cell'. Here we describe how each of the subsystems in the A2 system functions and how the different subsystems interact to regulate RNA trafficking.     

京郊农业生物循环系统生态经济能值评估——以密云尖岩村为例

国内外学术界和决策者对于循环农业给予了相当关注,但关于循环农业研究,从产业经济角度进行定量分析目前仍处于相对匮乏状态.以京郊典型的尖岩村农业生物循环农业范式为案例,采用能值方法,以翔实的数据描述了从种植、养殖到食用菌生产的各个阶段能量输入与输出,通过能值评估指标体系判断在整个循环产业链条中,各生产环节对环境经济产生的影响,结果显示:(1)农业生物循环系统的能值投资率(2.57)较养殖(116.23)、食用菌子系统(158.73)低;环境负荷率(1.40)也较养殖子系统(7.24)、食用菌子系统(13)低,表明,该循环模式可减少对自然资源和外来经济投入的依赖,能够获得自身的资源补偿.(2)农业生物循环系统的净能值产出率和可持续发展指数较高,说明,该模式有较强的获利性,是较理想的产业系统,在北京郊区推广价值较高.     

The system of the epidemic process

An original social-ecological concept of the epidemic process has been constructed on the basis of using social ecology, systemic approach and the basic principles of cybernetics. According to this concept, the epidemic process is regarded as a biosocial, hierarchic, integral system providing for the reproduction of the species of human parasites. At a higher level of organization, the epidemic process is an epidemiological social-ecological system consisting of two interacting subsystems: the biological (epidemiological ecosystem) and the social (social and economic conditions of life of the society) subsystems where the biological subsystem plays the role of the governed object and the social acts as the internal regulator of these interactions. On the basis of this concept a rational structure of the system of epidemiological surveillance over infectious diseases has been proposed according to which each level of the structure of the epidemic process should be subject to adequate monitoring.     

基于BP神经网络的京津冀城市群可持续发展综合评价

在综合分析了京津冀城市群各城市功能定位的基础上,构建了包含经济发展、社会发展、科技创新和生态环境4个子系统的城市可持续发展评价指标体系,运用2006—2015年的数据,采用熵值法和BP神经网络对京津冀城市群可持续发展能力进行非线性测度与分类,结果较为理想。结果表明:(1)北京和天津处于高可持续发展水平,可持续发展能力在空间上呈现出以京、津为中心随距离递减的趋势,最南端的邯郸和邢台处于低可持续发展水平;(2)北京可持续发展能力呈现下滑趋势,其他城市可持续发展能力逐年稳步上升,大城市可持续发展压力较大;(3)城市在不同子系统中存在各自的优劣势。各个子系统在可持续发展中均起到重要作用,城市宜结合各自子系统的优、劣势制定具有针对性的发展对策。     

基于NLPCA-GSO可持续发展评价——以环渤海区域为例

区域可持续发展水平、发展的持续性和系统的协调性是区域可持续发展定量评价研究的三角构架,而在传统上基于各子系统主成分分析结果直接进行形色各异的加权计算对可持续发展评价而言是有待商榷的。提出了非线性主成分分析和施密特正交化(NLPCA-GSO)相耦合的方法评价区域的可持续发展水平来弥补传统方法的不足,并由此建立区域发展持续性模型和可持续发展系统协调度模型,再以环渤海区域为实证分析其2001—2010年的可持续发展状况。结果表明:基于NLPCA-GSO的可持续发展水平模型可以很好地弥补传统主成分分析及对各子系统结果的综合评价的不足;区域发展持续性模型、协调性模型和区域可持续系统变化的滤波分析形象地揭示区域可持续发展的实质和内涵;实证研究表明环渤海区域在研究时段内可持续发展水平有所上升,而环境子系统持续性的下降是引起区域发展持续性和系统协调度的变化的主要原因。研究结果可丰富区域可持续发展评价的方法学,也可为环渤海区域的可持续发展研究奠定基础。     

Some notes on complexity in vegetation

Abstract. Vegetation is considered as a complex system with many subsystems. The system functions by using solar radiation as energy source and producing biomass and biodiversity. The different subsystems are connected by feedback loops and interact in a process of self-organisation. It appears impossible to characterize this system with mathematical expressions, because most of the basic processes are non-linear. Instead, vegetation can be described with dynamical models. Selection, competition as well as positive interactions can occur. The model accounts for the general dynamics, particularly fluctuations (when the system is in a steady state) and the climax situation. Many problems remain open: e.g. arbitrary limits of the system and its subsystems, macrostate/microstate relationships, thresholds and attractors. Single aspects of the subsystems can be linearized, but not the system as a whole and consequently its behaviour remains unpredictable.     

Model of two noise source dependent Ornstein-Uhlenbeck processes applied to postural sway

In this study the postural control system is modeled in terms of two counteracting bio-subsystems. Their activities are described by two Ornstein-Uhlenbeck processes with different-in-magnitude noise sources. The model is constructed as a sum of these processes, where in each of them the same noise source with opposite sign of the noise coefficients was introduced. Since the friction coefficients are also different for these processes, the delay of a crossover from ballistic to diffusive motion for one of the subsystems is greater than for its counterpart. It turns out that for smaller time intervals a superdiffusive behavior is observed, whereas, counteraction of subsystems is called into play for a larger time intervals, what for investigated range of data, is exhibited as a slow, subdiffusive behavior.     

我国农业系统可持续发展协调度分析

农业系统可持续协调发展作为一种发展理念已成为共识,受到我国政府高度重视。采用2004—2015年我国农业生产面板数据,运用熵值法、探索性空间数据分析等方法分析我国农业系统可持续发展协调度情况。研究结果表明:(1)2004—2015年我国各省(市、自治区)农业各子系统可持续能力之间协调度处于不稳定变动态势,且其协调度值较低。(2)从协调度分布来看,协调度处于"比较协调"和"协调"的省(市、自治区)主要分布在我国的东部和东南部地区,其余大多数省(市、自治区)农业各子系统可持续能力之间的协调度处于"不协调"。(3)从空间自相关性来看,各省(市、自治区)农业各子系统可持续能力之间协调度呈正的全局自相关性且相关程度逐渐增大,而大多数省(市、自治区)农业各子系统可持续能力之间协调度的局部自相关性不显著,且其农业各子系统可持续能力之间协调度空间极化不明显,处于较低水平均衡状态。从时空维度、空间相关性方面分析农业各子系统可持续能力之间协调度,为提高我国农业系统可持续发展水平提供政策建议。     

Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering

Large, naturally evolved biomolecular networks typically fulfil multiple functions. When modelling or redesigning such systems, functional subsystems are often analysed independently first, before subsequent integration into larger-scale computational models. In the design and analysis process, it is therefore important to quantitatively analyse and predict the dynamics of the interactions between integrated subsystems; in particular, how the incremental effect of integrating a subsystem into a network depends on the existing dynamics of that network. In this paper we present a framework for simulating the contribution of any given functional subsystem when integrated together with one or more other subsystems. This is achieved through a cascaded layering of a network into functional subsystems, where each layer is defined by an appropriate subset of the reactions. We exploit symmetries in our formulation to exhaustively quantify each subsystem’s incremental effects with minimal computational effort. When combining subsystems, their isolated behaviour may be amplified, attenuated, or be subject to more complicated effects. We propose the concept of mutual dynamics to quantify such nonlinear phenomena, thereby defining the incompatibility and cooperativity between all pairs of subsystems when integrated into any larger network. We exemplify our theoretical framework by analysing diverse behaviours in three dynamic models of signalling and metabolic pathways: the effect of crosstalk mechanisms on the dynamics of parallel signal transduction pathways; reciprocal side-effects between several integral feedback mechanisms and the subsystems they stabilise; and consequences of nonlinear interactions between elementary flux modes in glycolysis for metabolic engineering strategies. Our analysis shows that it is not sufficient to just specify subsystems and analyse their pairwise interactions; the environment in which the interaction takes place must also be explicitly defined. Our framework provides a natural representation of nonlinear interaction phenomena, and will therefore be an important tool for modelling large-scale evolved or synthetic biomolecular networks.     

Coupling cellular oscillators--circadian and cell division cycles in cyanobacteria

Understanding how different cellular subsystems are coupled to each other is a fundamental question in the quest for reliably predicting the dynamic state of a cell. Coupling of oscillatory subsystems is especially interesting as dynamic interactions play an important role in cell physiology. Here we review recent efforts that investigate and quantify the coupling between the circadian and cell cycle clocks in cyanobacteria as a model system. We discuss studies that quantify the coupling from a systems point of view in which the oscillators are described in abstract terms. We also emphasize recent developments aimed at uncovering the molecular details underlying the coupling between these systems. Finally we review recent studies that describe a potentially more overarching regulation scheme through global circadian regulation of DNA packing and gene expression.     

基于能值分析评估现代农牧循环系统的构建与优化

发展现代循环农业有助于推动农业生产方式高质量转型,是实现农业可持续发展的重要路径之一。但生产经营者在构建循环农业系统的过程中,因缺乏精确的参数测算,常存在投入产出不明、循环效率偏低、整体评估缺乏等问题,导致现代循环农业系统的物能高效运转面临阻碍。以江苏省太仓市东林村的现代农牧循环系统为对象,在四维时空尺度上界定系统边界并绘制能流图,全面梳理了案例系统全年运转过程中的投入与产出项目。现代“草-羊-田”农牧循环全系统由粮食种植、饲料加工、湖羊养殖与羊粪堆肥4个亚系统构成。通过模拟亚系统逐步结合、系统循环与优化调控的演进过程,采用能值分析方法对农牧系统不同构建阶段的亚系统与全系统的能值投入产出和结构进行定量评估与对比研究。结果表明,在农牧系统产业链逐步构建直至循环生产的过程中,全系统的总能值投入随各亚系统的扩增而有明显增加,系统的物能内部流通率逐渐升高。随后,以废弃物的系统内部消纳为目标,通过强化亚系统间的耦合对现状循环进行优化调控,系统所需的总能值投入有大幅减少,且各亚系统对本地资源的利用程度有明显提升。实证研究定量评估了现代农牧循环系统构建与优化过程中的能值投入与资源利用状况,为系统的高...     

矿区可持续发展系统动力学模拟与调控

矿区是由资源、环境、经济和社会等子系统构成的复杂系统。矿区的可持续发展依赖于矿各子系统的合理结构和发展模式以及人们对系统的有效调控,将可持续发展思想 模拟方法相结合,在系统地分析矿区ＲＥＥＳ系统结构的基础上,构建了矿区ＲＥＥＳ系统动力学模型,并以铁法矿为例论述了矿区ＲＥＥＳ系统的模拟和调控等有关问题。     

Material Spiraling in Stream Corridors: A Telescoping Ecosystem Model

Stream ecosystems consist of several subsystems that are spatially distributed concentrically, analogous to the elements of a simple telescope. Subsystems include the central surface stream, vertically and laterally arrayed saturated sediments (hyporheic and parafluvial zones), and the most distal element, the riparian zone. These zones are hydrologically connected; thus water and its dissolved and suspended load move through all of these subsystems as it flows downstream. In any given subsystem, chemical transformations result in a change in the quantity of materials in transport. Processing length is the length of subsystem required to “process” an amount of substrate equal to advective input. Long processing lengths reflect low rates of material cycling. Processing length provides the length dimension of each cylindrical element of the telescope and is specific to subsystem (for example, the surface stream), substrate (for instance, nitrate), and process (denitrification, for example). Disturbance causes processing length to increase. Processing length decreases during succession following disturbance. The whole stream-corridor ecosystem consists of several nested cylindrical elements that extend and retract, much as would a telescope, in response to disturbance regime. This telescoping ecosystem model (TEM) can improve understanding of material retention in running water systems; that is, their “nutrient filtration” capacity. We hypothesize that disturbance by flooding alters this capacity in proportion to both intensity of disturbance and to the relative effect of disturbance on each subsystem. We would expect more distal subsystems (for example, the riparian zone) to show the highest resistance to floods. In contrast, we predict that postflood recovery of functions such as material processing (that is, resilience) will be highest in central elements and decrease laterally. Resistance and resilience of subsystems are thus both inversely correlated and spatially separated. We further hypothesize that cross-linkages between adjacent subsystems will enhance resilience of the system as a whole. Whole-ecosystem retention, transformation, and transport are thus viewed as a function of subsystem extent, lateral and vertical linkage, and disturbance regime. Received 15 April 1997; accepted 1 September 1997.     

Coordination of many oscillators and generation of locomotory patterns

This paper considers a synthesis approach to a decentralized autonomous system in which the functional order of the entire system is generated by cooperative interaction among its subsystems, each of which has the autonomy to control a part of the state of the system, and its application to pattern generators of animal locomotion. First, biological locomotory rhythms and their generators, swimming patterns of aquatic animals and gait patterns of quadrupeds, are reviewed briefly. Then, a design principle for autonomous coordination of many oscillators is proposed. Using these results, we synthesize a swimming pattern generator and a gait pattern generator. Finally, it is shown using computer simulations that the proposed systems generate desirable patterns.     

System-size resonance for intracellular and intercellular calcium signaling

Dynamical behaviors of unidirectionally, linearly coupled as well as isolated calcium subsystems are investigated by taking into account the internal noise resulting from finite system size and thus small numbers of interacting molecules. For an isolated calcium system, the internal noise can induce stochastic oscillations for a steady state close to the Hopf-bifurcation point, and the regularity of those stochastic oscillations depends resonantly on the system size, exhibiting system-size resonance. For the coupled system consisting of two subsystems, the system-size resonance effect observed in the subsystem subject to coupling is significantly amplified due to the nontrivial effects of coupling.     

医院信息系统整体柔性分析

医院信息系统是一项复杂的系统工程，要求在多变的环境下，与时俱进，作出改变。针对盲目强调柔性而可能导致的非柔性，提出医院信息系统需要适度柔性，以达到真正柔性的目的，并通过研究医院信息系统各分系统的运行关系并结合当前政策环境，确立电子病历系统以及医保系统应当具备相对高的柔性。     

When two become one: the limits of causality analysis of brain dynamics

Biological systems often consist of multiple interacting subsystems, the brain being a prominent example. To understand the functions of such systems it is important to analyze if and how the subsystems interact and to describe the effect of these interactions. In this work we investigate the extent to which the cause-and-effect framework is applicable to such interacting subsystems. We base our work on a standard notion of causal effects and define a new concept called natural causal effect. This new concept takes into account that when studying interactions in biological systems, one is often not interested in the effect of perturbations that alter the dynamics. The interest is instead in how the causal connections participate in the generation of the observed natural dynamics. We identify the constraints on the structure of the causal connections that determine the existence of natural causal effects. In particular, we show that the influence of the causal connections on the natural dynamics of the system often cannot be analyzed in terms of the causal effect of one subsystem on another. Only when the causing subsystem is autonomous with respect to the rest can this interpretation be made. We note that subsystems in the brain are often bidirectionally connected, which means that interactions rarely should be quantified in terms of cause-and-effect. We furthermore introduce a framework for how natural causal effects can be characterized when they exist. Our work also has important consequences for the interpretation of other approaches commonly applied to study causality in the brain. Specifically, we discuss how the notion of natural causal effects can be combined with Granger causality and Dynamic Causal Modeling (DCM). Our results are generic and the concept of natural causal effects is relevant in all areas where the effects of interactions between subsystems are of interest.