Interactive mathematical models of subjective alertness and cognitive throughput in humans

The authors present here mathematical models in which levels of subjective alertness and cognitive throughput are predicted by three components that interact with one another in a nonlinear manner. These components are (1) a homeostatic component (H) that falls in a sigmoidal manner during wake and rises in a saturating exponential manner at a rate that is determined by circadian phase during sleep; (2) a circadian component (C) that is a function of the output of our mathematical model of the effect of light on the circadian pacemaker, with the amplitude further regulated by the level of H; and (3) a sleep inertia component (W) that rises in a saturating exponential manner after waketime. The authors first construct initial models of subjective alertness and cognitive throughput based on the results of sleep inertia studies, sleep deprivation studies initiated across all circadian phases, 28-h forced desynchrony studies, and alertness and performance dose response curves to sleep. These initial models are then refined using data from nearly one hundred fifty 30- to 50-h sleep deprivation studies in which subjects woke at their habitual times. The interactive three-component models presented here are able to predict even the fine details of neurobehavioral data from sleep deprivation studies and, after further validation, may provide a powerful tool for the design of safe shift work and travel schedules, including those in which people are exposed to unusual patterns of light.     

Neuronal models for cognitive processes: networks for learning, perception and imagination.

Model neuronal mechanisms are described in detail and organized into a functional system which can perform a wide variety of high level visualcognitive tasks. A conservative estimate of the number of nerve cells required to realize the complete system in the human brain indicates that it can be accommodated within the visual areas of a single cortical hemisphere leaving a “surplus” capacity of ～ 6·62 x 10⁸ visual neurons in the occupied hemisphere.     

Stable oscillations in mathematical models of biological control systems

Summary Oscillations in a class of piecewise linear (PL) equations which have been proposed to model biological control systems are considered. The flows in phase space determined by the PL equations can be classified by a directed graph, called a state transition diagram, on anN-cube. Each vertex of theN-cube corresponds to an orthant in phase space and each edge corresponds to an open boundary between neighboring orthants. If the state transition diagram contains a certain configuration called a cyclic attractor, then we prove that for the associated PL equation, all trajectories in the regions of phase space corresponding to the cyclic attractor either (i) approach a unique stable limit cycle attractor, or (ii) approach the origin, in the limitt→∞. An algebraic criterion is given to distinguish the two cases. Equations which can be used to model feedback inhibition are introduced to illustrate the techniques.     

Chebanov law and Vakar formula in mathematical models of complex systems

Ecological models written in a mathematical language L(M) or model language, with a given style or methodology can be considered as a text. It is possible to apply statistical linguistic laws and the experimental results demonstrate that the behaviour of a mathematical model is the same of any literary text of any natural language. A text has the following characteristics: (a) the variables, its transformed functions and parameters are the lexic units or LUN of ecological models; (b) the syllables are constituted by a LUN, or a chain of them, separated by operating or ordering LUNs; (c) the flow equations are words; and (d) the distribution of words (LUM and CLUN) according to their lengths is based on a Poisson distribution, the Chebanov's law. It is founded on Vakar's formula, that is calculated likewise the linguistic entropy for L(M). We will apply these ideas over practical examples using MARIOLA model. In this paper it will be studied the problem of the lengths of the simple lexic units composed lexic units and words of text models, expressing these lengths in number of the primitive symbols, and syllables. The use of these linguistic laws renders it possible to indicate the degree of information given by an ecological model.     

Mutant mice: Experimental organisms as materialised models in biomedicine

Animal models have received particular attention as key examples of material models. In this paper, we argue that the specificities of establishing animal models—acknowledging their status as living beings and as epistemological tools—necessitate a more complex account of animal models as materialised models. This becomes particularly evident in animal-based models of diseases that only occur in humans: in these cases, the representational relation between animal model and human patient needs to be generated and validated. The first part of this paper presents an account of how disease-specific animal models are established by drawing on the example of transgenic mice models for Alzheimer’s disease. We will introduce an account of validation that involves a three-fold process including (1) from human being to experimental organism; (2) from experimental organism to animal model; and (3) from animal model to human patient. This process draws upon clinical relevance as much as scientific practices and results in disease-specific, yet incomplete, animal models. The second part of this paper argues that the incompleteness of models can be described in terms of multi-level abstractions. We qualify this notion by pointing to different experimental techniques and targets of modelling, which give rise to a plurality of models for a specific disease.     

Systems biomedicine: It’s your turn —Recent progress in systems biomedicine

The concept of “systems biology” is raised by Hood in 1999. It means studying all components with a systematic view. Systems biomedicine is the application of systems biology in medicine. It studies all components in a whole system and aims to reveal the patho-physiologic mechanisms of disease. In recent years, with the development of both theory and technology, systems biomedicine has become feasible and popular. In this review, we will talk about applications of some methods of omics in systems biomedicine, including genomics, metabolomics (proteomics, lipidomics, glycomics), and epigenomics. We will particularly talk about microbiomics and omics for common diseases, two fields which are developed rapidly recently. We also give some bioinformatics related methods and databases which are used in the field of systems biomedicine. At last, some examples that illustrate the whole biological system will be given, and development for systems biomedicine in China and the prospect for systems biomedicine will be talked about.“     

Scale-up of microbial processes: impacts, tools and open questions

Industrial biotechnological production is developing rapidly worldwide. Consequently, more and novel bioprocesses need to perform optimally not only in small lab- but also in large production scales. This article shortly reviews typical impacts found when cells are exposed to micro environmental heterogeneities typically occurring in poorly mixed large scale production reactors. The current state-of-the-art of tool development is presented for analyzing these phenomena. Finally, still open questions are formulated and needs for future research are outlined to further support the expansion of biotech industries by successful research results.     

Biological probability: cognitive processes of generating probabilities of events in biological systems.

This paper analyses relationships between probabilities of events happening in biological systems (or probabilistic disposition of systems) and cognitive properties of biological entities comprising such systems. Two kinds of cognitive properties are identified as relevant to the current problem: the ability to respond differently against different configurations of the environment (discriminability of cognition), and the ability to make an appropriate response to maintain a particular relation with the environment (selectivity of cognition). A basic framework bridging the two features of living systems, probabilistic disposition and the cognitive properties, is presented towards a general theory explaining the process generating probabilities of biological events. In this framework, a deterministic model of a system of entities is developed, in which objects are described as subjects that cognize events (i.e. entities as cognizers). Cognition is used in a wider sense, including not only biotic but also abiotic, and cognizers are conceptually distinguished from the meta-observer who describes the system externally. Based on this perspective, this paper seeks to explicate how events can occur in an uncertain, probabilistic manner, if observed from a cognizer viewpoint, even under a deterministic system. Each cognizer is identified with both the set of states that are actually taken, and its motion function which maps its state uniquely to a successor state depending on the current states of itself and of the rest of cognizers constituting the system. The model analysis reveals that the cognitive properties, discriminability and selectivity, of a cognizer can contribute to determining the probability of an event encountered by the cognizer itself-in particular, discrimination reducing the uncertainty in events occurrence for the cognizer. Biological implication of this result is discussed focusing on the concept of the probability of survival and reproduction.     

Quantum processes in evolution of regulation of living systems (mathematical modeling)

We have developed an imitation model of the appearance of regulation of physiological functions of protocell at initial stages of evolution of living system. It is based on suggestion of the appearance of signal function in spontaneously formed products of partial hydrolysis of the protocell polypeptides, based on which there appear the regulatory molecules—quanta of regulation. For construction of the model, the mathematical apparatus of final automats and of genetic algorithm is used. The model has demonstrated the positive role of involvement of regulatory peptides in the system of regulation of protocell functions to provide its viability under the changing envelopment conditions.     

Tav4SB: integrating tools for analysis of kinetic models of biological systems

ABSTRACT: BACKGROUND: Progress in the modeling of biological systems strongly relies on the availability of specialized computer-aided tools. To that end, the Taverna Workbench eases integration of software tools for life science research and provides a common workflow-based framework for computational experiments in Biology. RESULTS: The Taverna services for Systems Biology (Tav4SB) project provides a set of new Web service operations, which extend the functionality of the Taverna Workbench in a domain of systems biology. Tav4SB operations allow you to perform numerical simulations or model checking of, respectively, deterministic or stochastic semantics of biological models. On top of this functionality, Tav4SB enables the construction of high-level experiments. As an illustration of possibilities offered by our project we apply the multi-parameter sensitivity analysis. To visualize the results of model analysis a flexible plotting operation is provided as well. Tav4SB operations are executed in a simple grid environment, integrating heterogeneous software such as Mathematica, PRISM and SBML ODE Solver. The user guide, contact information, full documentation of available Web service operations, workflows and other additional resources can be found at the Tav4SB project's Web page: http://bioputer.mimuw.edu.pl/tav4sb/. CONCLUSIONS: The Tav4SB Web service provides a set of integrated tools in the domain for which Web-based applications are still not as widely available as for other areas of computational biology. Moreover, we extend the dedicated hardware base for computationally expensive task of simulating cellular models. Finally, we promote the standardization of models and experiments as well as accessibility and usability of remote services.     

复杂性-稳定性研究: 数学模型的进展

对自然生态系统的观察给人们以复杂的群落更稳定的直观印象, 但数学模型却得出了截然相反的结论。这一“悖论”使得复杂性-稳定性研究自20世纪70年代以来成为长期的热点。本文对这一领域的数学模型研究进行简要综述。首先对这一论题进行概念剖析, 然后将各类模型分为线性和非线性两大类, 前者即群落矩阵法, 后者包括相互作用矩阵法、复杂网络数值模拟法和食物网构件动力学法。它们分别基于不同的群落构建方法和稳定性判断标准, 探求各物种是如何相互作用并实现共存的。总体而言, 在随机构建的群落模型中, 多样性和连接度的增长不利于系统稳定; 而在更接近真实自然群落的模型中, 相互作用方式、网络拓扑结构、相互作用强度分布等方面的机制提供了稳定效应, 按此组织的生态网络可达到很高的复杂度。然而, 复杂性-稳定性的研究还远未结束, 当前的模型仍不足以反映自然群落中的复杂相互作用, 稳定性的概念也有待拓展。对这一议题的深入研究在生态学理论和生态系统管理实践方面都具有重大价值。     

Theme E: Disabilities: Analysis models and tools

This paper presents the topics and the activity of the theme E “disabilities: analysis models and tools” within the GDR STIC Santé. This group has organized a conference and a workshop during the period 2011–2012. The conference has focused on technologies for cognitive, sensory and motor impairments, assessment and use study of assistive technologies, user centered method design and the place of ethics in these research topics. The objective of “bodily integration of technique” workshop, organized in the framework of Défi Sens (CNRS) was to develop a multidisciplinary approach (physiology, robotics and anthropology) of the relationships between body and technology taking as an example the prostheses for the compensation of sensorimotor disabilities. Efforts will focus on strengthening the development of a multidisciplinary research for the design of assistive technologies for elderly people and people with disabilities. The modelling of the user's abilities and the designing of adaptable AT to the needs of the person will be carried out with other groups of this GDR and also with other GDRs.