Modeling direct positive feedback between predators and prey

Predators can have positive impacts on their prey through such mechanisms as nutrient mineralization and prey transport. These positive feedbacks have the potential to change predictions based on food web theory, such as the assertion that enrichment is destabilizing. We present a model of a simple food web, consisting of a resource, a consumer, and its predator. We assume that the predator has a direct positive effect on the consumer, by increasing the rate at which the consumer acquires resources. We consider two cases: the feedback strength is a saturating function of predator density, or it is proportional to the encounter rate between predators and prey. In both cases, the positive feedback is stabilizing, delaying or preventing the onset of oscillations due to enrichment. Positive feedback can introduce an Allee effect for the predator population, yielding multiple stable equilibria. Strong positive feedback can yield counterintuitive results such as a transient increase in consumer density following the introduction of predators, and a decrease in the resource pool following enrichment.     

Simulation of deformable models with the Poisson equation

In this paper, we present a new methodology for the deformation of soft objects by drawing an analogy between the Poisson equation and elastic deformation from the viewpoint of energy propagation. The potential energy stored due to a deformation caused by an external force is calculated and treated as the source injected into the Poisson system, as described by the law of conservation of energy. An improved Poisson model is developed for propagating the energy generated by the external force in a natural manner. An autonomous cellular neural network (CNN) model is established by using the analogy between the Poisson equation and CNN to solve the Poisson model for the real-time requirement of soft object deformation. A method is presented to derive the internal forces from the potential energy distribution. The proposed methodology models non-linear materials with the non-linear Poisson equation and thus non-linear CNN, rather than geometric non-linearity. It not only deals with large-range deformations, but also accommodates isotropic, anisotropic and inhomogeneous materials by simply modifying constitutive coefficients. A haptic virtual reality system has been developed for deformation simulation with force feedback. Examples are presented to demonstrate the efficiency of the proposed methodology.     

Control of constraint forces and trajectories in a rich sensory and actuation environment

A simple control strategy is proposed and applied to a class of non-linear systems that have abundant sensory and actuation channels as in living systems. The main objective is the independent control of constrained trajectories of motion, and control of the corresponding constraint forces. The peripheral controller is a proportional, derivative and integral (PID) controller. A central controller produces, via pattern generators, reference signals that are the desired constrained position and velocity trajectories, and the desired constraint forces. The basic tenet of the this hybrid control strategy is the use of two mechanisms: 1. linear state and force feedback, and 2. non-linear constraint velocity feedback - sliding mode feedback. The first mechanism can be envisioned as a high gain feedback systems. The high gain attribute imitates the agonist-antagonist co-activation in natural systems. The strategy is applied to the control of the force and trajectory of a two-segment thigh-leg planar biped leg with a mass-less foot cranking a pedal that is analogous to a bicycle pedal. Five computational experiments are presented to show the effectiveness of the strategy and the performance of the controller. The findings of this paper are applicable to the design of orthoses and prostheses to supplement functional electrical stimulation for support purposes in the spinally injured cases.     

近40年来辽宁地区气候干湿界线年代际波动及其成因

应用1961～2004年辽宁省内52个气象站的温度、降水、湿度、风和日照等气候资料,采用改进的Penman模型计算了辽宁地区近40年的潜在蒸发量,讨论了其时空代表性及分布特征;以干燥度指数为干湿气候区的划分标准,通过对该地区近40年干湿气候界线波动状况的对比,在10年际尺度上详细分析了其干湿气候界线波动及变化规律.结果表明,20世纪60年代以来,辽宁省干湿气候界线波动显著,呈现出整体移动的特征,但半湿润与湿润、半干旱与半湿润两条界线并未表现出同进、同退的年际变化特征.20世纪90年代辽宁省干湿气候存在一次突变,半湿润与湿润界限明显东移,半干旱与半湿润界线明显西移,半干旱和湿润区面积都显著缩小,半湿润区面积显著扩大.辽宁西部的气候干湿状况主要由西太平洋副热带高压和东南季风控制,辽宁东部的气候干湿状况除受西太平洋副热带高压和东南季风的影响外,还应考虑到地形降水的作用.     

Comparable ecological dynamics underlie early cancer invasion and species dispersal, involving self-organizing processes

Occupancy of new habitats through dispersion is a central process in nature. In particular, long-distance dispersal is involved in the spread of species and epidemics, although it has not been previously related with cancer invasion, a process that involves cell spreading to tissues far away from the primary tumour.Using simulations and real data we show that the early spread of cancer cells is similar to the species individuals spread and we suggest that both processes are represented by a common spatio-temporal signature of long-distance dispersal and subsequent local proliferation. This signature is characterized by a particular fractal geometry of the boundaries of patches generated, and a power-law scaled, disrupted patch size distribution. In contrast, invasions involving only dispersal but not subsequent proliferation (“physiological invasions”) like trophoblast cells invasion during normal human placentation did not show the patch size power-law pattern. Our results are consistent under different temporal and spatial scales, and under different resolution levels of analysis.We conclude that the scaling properties are a hallmark and a direct result of long-distance dispersal and proliferation, and that they could reflect homologous ecological processes of population self-organization during cancer and species spread. Our results are significant for the detection of processes involving long-range dispersal and proliferation like cancer local invasion and metastasis, biological invasions and epidemics, and for the formulation of new cancer therapeutical approaches.     

Oscillations in a Simple Neuromechanical System: Underlying Mechanisms

A half-center neural oscillator was coupled to a simple mechanical system to study the closed-loop interactions between a central pattern generator and its effector muscles. After a review of the open-loop mechanisms that were previously introduced by Skinner et al. (1994), we extend their geometric approach and introduce four additional closed-loop mechanisms by the inclusion of an antagonistic muscle pair acting on a mass and connected to the half-center neural oscillator ipsilaterally. Two of the closed-loop mechanisms, mechanical release mechanisms, have close resemblance to open-loop release mechanisms whereas the latter two, afferent mechanisms, have a strong dependence on the mechanical properties of the system. The results also show that stable oscillations can emerge in the presence of sensory feedback even if the neural system is not oscillatory. Finally, the feasibility of the closed-loop mechanisms was shown by weakening the idealized assumptions of the synaptic and the feedback connections as well as the rapidity of the oscillations.     

Mutualism in a community context: the positive feedback between an ant–aphid mutualism and a gall-making midge

Although mutualisms are widespread and often described in natural history accounts, their ecological influences on other community members remain largely unexplored. Many of these influences are likely a result of indirect effects. In this field study, we investigated the indirect effects of an ant–aphid mutualism on the abundance, survival rates and parasitism rates of a co-occurring herbivore. Rabdophaga salicisbrassicoides (Diptera: Cecidomyiidae) induces rosette galls on the developing shoots of Salix exigua trees, and populations can reach outbreak densities (up to 1,000 galls/stem) in central Washington State (USA). Ant-tended aphids feed on these same stems and often feed on gall tissue. In this study we used a combination of manipulative experiments and observational surveys to test the hypothesis that the abundances of aphids, ants, and galls have positive and reciprocal effects on one another, in a manner that would create a positive feedback loop in population growth. In addition, we examined whether the combined presence of ants and aphids reduces parasitism rates for the gallers. In support of the positive feedback loop hypothesis, aphids enjoyed higher population growth rates in the presence of ants and galls, the presence of ants and aphids resulted in increased abundance of galls, and the abundances of ants, aphids and galls were all positively correlated with one another. However, the mechanism underlying the positive effect of ants and aphids on galler density remains unknown, as the mutualism did not affect parasitism rates. More broadly, this study demonstrates that mutualisms can have significant and complex indirect effects on community and population ecology.     

毛乌素沙地农牧生态系统能值分析与耦合关系

针对毛乌素沙地脆弱农业生态系统生产力实际,根据复合生态系统耦合理论,借助能值理论及分析方法,选择毛乌素沙地偏农区的榆阳区和偏牧区的乌审旗为比较研究对象,对两地近27a的农牧耦合系统初级生产力、次级生产力及系统耦合状况进行了对比分析,探讨性提出了区域农牧系统耦合程度的演变规律。结果表明,榆阳区是偏农型的农牧耦合产业发展模式,乌审旗是偏牧型的牧农耦合产业发展模式;榆阳区有以耗粮型生猪、禽类生产为主的势头,乌审旗有以节粮型草食动物生产为主的势头;榆阳区和乌审旗的初级生产力、次级生产力及A(有效能值利用率)、B(单位低质能产品转化成高质能产品率)、SCD(系统耦合度)值均沿时间序列增大,且SCD值有呈三阶段型增长的规律性。依据研究结果,最后提出了毛乌素沙地农牧生态系统耦合发展的途径,以期能为沙地农牧生态系统稳健发展提供可靠的理论支撑与政策导向。     

Pathway-based Analysis Tools for Complex Diseases:A Review

Genetic studies are traditionally based on single-gene analysis. The use of these analyses can pose tremendous challenges for elucidating complicated genetic interplays involved in complex human diseases. Modern pathway-based analysis provides a technique, which allows a comprehen- sive understanding of the molecular mechanisms underlying complex diseases. Extensive studies uti- lizing the methods and applications for pathway-based analysis have significantly advanced our capacity to explore large-scale omics data, which has rapidly accumulated in biomedical fields. This article is a comprehensive review of the pathway-based analysis methods the powerful methods with the potential to uncover the biological depths of the complex diseases. The general concepts and procedures for the pathway-based analysis methods are introduced and then, a comprehensive review of the major approaches for this analysis is presented. In addition, a list of available path- way-based analysis software and databases is provided. Finally, future directions and challenges for the methodological development and applications of pathway-based analysis techniques are dis- cussed. This review will provide a useful guide to dissect complex diseases.     

基于公平与效率视角的中国大陆生态福祉及生态-经济效率评价

基于生态系统服务价值理论,将\"人类从生态系统中直接获取或享有的终端产品和服务\"界定为生态福祉,从公平与效率视角提出相应表征方法。在此基础上,以中国大陆省区为例,对其2001—2013年间的人均生态福祉及生态-经济效率的时空演变格局进行实证分析,结果表明:①整体来看,研究时段内中国大陆省际人均生态福祉的基尼系数介于0.798—0.806之间,处于极不平均状态;省际生态-经济效率的标准差介于2.110—7.716之间,离散程度相对较高;②从时间上看,研究时段内中国大陆省际人均生态福祉及生态-经济效率的收敛趋势(σ-收敛)相对不明显;人均生态福祉具备绝对β-收敛特征但速度较低(0.16%);生态-经济效率在科技进步及科研投入要素的显著驱动作用下,呈现条件β-收敛现象。③从空间上看,研究时段内中国大陆人均生态福祉及生态-经济效率在\"胡焕庸线\"两侧的地域分异现象比较明显,其重心分别位于青海和安徽境内,整体向东北和西北方向移动,移动速度分别为5.76、3.95km/a。在高消耗、高污染产业逐渐向中西部转移的背景下,应当基于公平与效率视角权衡生态保护与经济发展问题,促进西部地区生态-经济效率和东部地区人均生态福祉共同提高。     

Why is it so difficult to identify a single indicator of water stress in plants? A proposal for a multivariate analysis to assess emergent properties

Because of the complexity of plant responses to water deficit, researchers have attempted to identify simplified models to understand critical aspects of the problem by searching for single indicators that would enable evaluations of the effects of environmental changes on the entire plant. However, this reductionist approach, which is often used in plant sciences, makes it difficult to distinguish systemic emergent behaviours. Currently, a new class of models and epistemology have called attention to the fundamental properties of complex systems. These properties, termed ‘emergent’, are observed at a large scale of the system (top hierarchical level) but cannot be observed or inferred from smaller scales of observation in the same system. We propose that multivariate statistical analysis can provide a suitable tool to quantify global responses to water deficit, allowing a specific and partially quantitative assessment of emergent properties. Based on an experimental study, our results showed that the classical approach of the individual analysis of different data sets might provide different interpretations for the observed effects of water deficit. These results support the hypothesis that a cross‐scale multivariate analysis is an appropriate method to establish models for systemic understanding of the interactions between plants and their changing environment.     

Core area analysis at semi-deciduous forest islands in the Comoé National Park,NE Ivory Coast

For the protection of forest-interior species in both natural forest islands and anthropogenic forest fragments knowledge on the size of forest-core areas is a central issue. In an intact mosaic of semi-deciduous forests and savanna in the Comoé National Park 31 forest islands were selected (2.1–146.1 ha). Values for the depth-of-edge influence (DEI) of the study area recently published range from 0 m up to nearly 150 m. Thus, core-area analysis was carried out for this range in 5 m steps. For a DEI of 55 m—e.g. computed for tree-species composition of large trees—half of the total forest area can be considered as core area, but only 9 of the studied forest islands still contained a relative core area (rCA) of more than 50%. From non-linear regression it was estimated that for a DEI of 55 m an rCA of 50% can be expected for forest islands with a size of 36.6 ± 7.6 ha. This value increased exponentially with increasing DEI. The GIS-based core-area analysis presented in this paper proved to be suitable to give a well interpretable overview on rCA with respect to varying DEI, and we recommend to incorporate this type of analysis in existing GIS-tools. As the presented study is the first sound core area analysis at forest islands in West Africa, data contribute to a better understanding of this field of ecology that is of high relevance for planners and decision makers to protect biodiversity.     

Evaluating prognostic accuracy of biomarkers under competing risk

To develop more targeted intervention strategies, an important research goal is to identify markers predictive of clinical events. A crucial step toward this goal is to characterize the clinical performance of a marker for predicting different types of events. In this article, we present statistical methods for evaluating the performance of a prognostic marker in predicting multiple competing events. To capture the potential time-varying predictive performance of the marker and incorporate competing risks, we define time- and cause-specific accuracy summaries by stratifying cases based on causes of failure. Such definition would allow one to evaluate the predictive accuracy of a marker for each type of event and compare its predictiveness across event types. Extending the nonparametric crude cause-specific receiver operating characteristics curve estimators by Saha and Heagerty (2010), we develop inference procedures for a range of cause-specific accuracy summaries. To estimate the accuracy measures and assess how covariates may affect the accuracy of a marker under the competing risk setting, we consider two forms of semiparametric models through the cause-specific hazard framework. These approaches enable a flexible modeling of the relationships between the marker and failure times for each cause, while efficiently accommodating additional covariates. We investigate the asymptotic property of the proposed accuracy estimators and demonstrate the finite sample performance of these estimators through simulation studies. The proposed procedures are illustrated with data from a prostate cancer prognostic study.     

A system for lake ecosystem indices

There is a growing awareness of the need to develop a more rational structure for scientific decision-making in the environmental sphere. The aim of this paper is to present an outline to a system for ecosystem indices (or indicators). This work is based on a holistic ecosystem perspective and the aim is to present an overall concept rather than practical results. One of the purposes of ecosystem indices is to give politicians and the general public a more easily understandable account of the environmental status and how it changes. An ecosystem index should be not only simple and concise, scientifically relevant and practical, but also economically feasible. This approach uses several important concepts, like target organisms, target ecosystems, environmental sensitivity, and environmental cost/benefit analyses related to remedial measures. Some of the ideas brought forward in this work may be unrealistic because of the complexities involved in establishing simple, practical and meaningful ecological indices. Still, the benefits of establishing even crude environmental indicators for certain ecosystems are so great, that this path is well worth pursuing.     

A simple time delay model for eukaryotic cell cycle

We propose a seven variable model with time delay in one of the variables for the cell cycle in higher eukaryotes. The model consists of four important phosphorylation-dephosphorylation (P-D) cycles that govern the cell cycle, namely Pre-MPF-MPF, Cdc25P-Cdc25, Wee1P-Wee1 and APCP-APC. Other variables are cyclin, free cyclin dependent kinase (Cdk) and mass. The mass acts as a G2/M checkpoint and the checkpoint is represented by a saddle node loop bifurcation. The key feature of the model is that a time lag has been introduced in the activation of anaphase promoting complex (APC) by maturation promoting factor (MPF). This is effected by treating MPF as a time-delayed variable in the activation step of APC. The time lag acts as a spindle checkpoint. Absence of time delay induces a bistability in our model. Time delay also brings about variability in G1 phase timings. The model also reproduces the mutant phenotype experiments on wee1 cells. Stochasticity has been introduced in the model to simulate the dependence of the cycle time on cell birth length. Mutant phenotypes in the stochastic model reproduce the experimental observations better than the deterministic model.