Hierarchical analysis of piecewise affine models of gene regulatory networks

A key point in the analysis of dynamical models of biological systems is to handle systems of relatively high dimensions. In the present paper we propose a method to hierarchically organize a certain type of piecewise affine (PWA) differential systems. This specific class of systems has been extensively studied for the past few years, as it provides a good framework to model gene regulatory networks. The method, shown on several examples, allows a qualitative analysis of the asymptotic behavior of a PWA system, decomposing it into several smaller subsystems. This technique, based on the well-known strongly connected components decomposition, is not new. However, its adaptation to the non-smooth PWA differential equations turns out to be quite relevant because of the strong discrete structure underlying these equations. Its biological relevance is shown on a 7-dimensional PWA system modeling the gene network responsible for the carbon starvation response in Escherichia coli.

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Language processing with dynamic fields

We construct a mapping from complex recursive linguistic data structures to spherical wave functions using Smolensky’s filler/role bindings and tensor product representations. Syntactic language processing is then described by the transient evolution of these spherical patterns whose amplitudes are governed by nonlinear order parameter equations. Implications of the model in terms of brain wave dynamics are indicated. Electronic supplementary material  The online version of this article (doi: ) contains supplementary material, which is available to authorized users.

Towards dynamical system models of language-related brain potentials

Event-related brain potentials (ERP) are important neural correlates of cognitive processes. In the domain of language processing, the N400 and P600 reflect lexical-semantic integration and syntactic processing problems, respectively. We suggest an interpretation of these markers in terms of dynamical system theory and present two nonlinear dynamical models for syntactic computations where different processing strategies correspond to functionally different regions in the system’s phase space.

Is it a revolution?

Jablonka and Lamb's claim that evolutionary biology is undergoing a ‘revolution’ is queried. But the very concept of revolutionary change has uncertain application to a field organized in the manner of contemporary biology. The explanatory primacy of sequence properties is also discussed.

Individual variability of behavioural responses by Wandering Albatrosses (Diomedea exulans) to human disturbance

Sub-Antarctic Marion Island has had a permanent research station for 50 years and the islands Wandering Albatrosses have been intensively studied for 20 years. The reactions of breeding birds to approaches by a human on foot were recorded. Three response variables were calculated: intensity of vocal reaction (IVR), intensity of non-vocal reaction (INR) and overall response index (ORI). At 5 m from the nest, twice as many birds stood and/or vocalised as at 15 m. Nearest neighbour distance, age and gender did not explain individual variability of responses. Study colony birds had higher IVR scores than non-study colony birds; birds at colonies closest to the station had the highest ORI scores. A better breeding record was associated with lower IVR and ORI scores, but a causative relationship remains to be demonstrated. A minimum viewing distance of 25 m is recommended for breeding Wandering Albatrosses.

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Realistic threshold policy with hysteresis to control predator–prey continuous dynamics

This paper introduces a threshold policy with hysteresis (TPH) for the control of one-predator one-prey models. The models studied are the Lotka–Volterra and Rosenzweig–MacArthur two species density-dependent predator–prey models and the Arditi–Ginzburg nondimensional ratio-dependent model. The proposed policy (TPH) changes the dynamics of the system in such a way that a bounded oscillation is achieved confined to a region that does not allow extinction of either species. The policy can be designed by a suitable choice of so called virtual equilibrium points in a simple and intuitive manner.

Forty Years of ‘The Strategy’: Levins on Model Building and Idealization

This paper is an interpretation and defense of Richard Levins’ “The Strategy of Model Building in Population Biology,” which has been extremely influential among biologists since its publication 40 years ago. In this article, Levins confronted some of the deepest philosophical issues surrounding modeling and theory construction. By way of interpretation, I discuss each of Levins’ major philosophical themes: the problem of complexity, the brute-force approach, the existence and consequence of tradeoffs, and robustness analysis. I argue that Levins’ article is concerned, at its core, with justifying the use of multiple, idealized models in population biology.

The Cauchy problem for one-dimensional spiking neuron models

I consider spiking neuron models defined by a one-dimensional differential equation and a reset—i.e., neuron models of the integrate-and-fire type. I address the question of the existence and uniqueness of a solution on for a given initial condition. It turns out that the reset introduces a countable and ordered set of backward solutions for a given initial condition. I discuss the implications of these mathematical results in terms of neural coding and spike timing precision.

Adaptationism and the adaptive landscape

Debates over adaptationism can be clarified and partially resolved by careful consideration of the ‘grain’ at which evolutionary processes are described. The framework of ‘adaptive landscapes’ can be used to illustrate and facilitate this investigation. We argue that natural selection may have special status at an intermediate grain of analysis of evolutionary processes. The cases of sickle-cell disease and genomic imprinting are used as case studies.

Development of the rhopalial nervous system in <Emphasis Type="Italic">Aurelia</Emphasis> sp.1 (Cnidaria,Scyphozoa)

We examined the development of the nervous system in the rhopalium, a medusa-specific sensory structure, in Aurelia sp.1 (Cnidaria, Scyphozoa) using confocal microscopy. The rhopalial nervous system appears primarily ectodermal and contains neurons immunoreactive to antibodies against tyrosinated tubulin, taurine, GLWamide, and FMRFamide. The rhopalial nervous system develops in an ordered manner: the presumptive gravity-sensing organ, consisting of the lithocyst and the touch plate, differentiates first; the “marginal center,” which controls swimming activity, second; and finally, the ocelli, the presumptive photoreceptors. At least seven bilaterally arranged neuronal clusters consisting of sensory and ganglion cells and their neuronal processes became evident in the rhopalium during metamorphosis to the medusa stage. Our analysis provides an anatomical framework for future gene expression and experimental studies of development and functions of scyphozoan rhopalia. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

Leitlinien zur molekulargenetischen Diagnostik: Fragiles-X und Fragiles-X assoziiertes Tremor/Ataxie Syndrom

Ohne Zusammenfassung

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Hennigian Phylogenetic Systematics and the ‘Groundplan’ vs. ‘Post-Groundplan’ Approaches: A Reply to Kukalová-Peck

The recent contribution by Jarmila Kukalová-Peck on Hennigian phylogenetics and hexapod limb evolution is critically evaluated.

Organ and tissue safety workshop 2007: advances and challenges

A workshop in June 2005 (“Preventing Organ and Tissue Allograft-Transmitted Infection: Priorities for Public Health Intervention”) identified gaps in organ and tissue safety in the US. Participants developed a series of allograft safety initiatives. “The Organ and Tissue Safety Workshop 2007: Advances and Challenges” assessed progress and identified priorities for future interventions. Awareness of the challenges of allograft-associated disease transmission has increased. The Transplantation Transmission Sentinel Network will enhance communication surrounding allograft-associated disease transmission. Other patient safety initiatives have focused on adverse event reporting and microbiologic screening technologies. Despite progress, improved recognition and prevention of donor-derived transmission events is needed. This requires systems integration across the organ and tissue transplantation communities including organ procurement organizations, eye and tissue banks, and transplant infectious disease experts. Commitment of resources and improved coordination of efforts are required to develop essential tools to enhance safety for allograft recipients.

The Ethics of Birth and Death: Gender Infanticide in India

This paper discusses the persistent devaluation of the girl child in India and the link between the entrenched perception of female valuelessness and the actual practice of infanticide of girl babies or foetuses. It seeks to place female infanticide, or ‘gendercide,’ within the context of Western-derived conceptions of ethics, justice and rights. To date, current ethical theories and internationally purveyed moral frameworks, as well as legal and political declarations, have fallen short of an adequate moral appraisal of infanticide. This paper seeks to rethink the issue.

Voltage-stepping schemes for the simulation of spiking neural networks

The numerical simulation of spiking neural networks requires particular attention. On the one hand, time-stepping methods are generic but they are prone to numerical errors and need specific treatments to deal with the discontinuities of integrate-and-fire models. On the other hand, event-driven methods are more precise but they are restricted to a limited class of neuron models. We present here a voltage-stepping scheme that combines the advantages of these two approaches and consists of a discretization of the voltage state-space. The numerical simulation is reduced to a local event-driven method that induces an implicit activity-dependent time discretization (time-steps automatically increase when the neuron is slowly varying). We show analytically that such a scheme leads to a high-order algorithm so that it accurately approximates the neuronal dynamics. The voltage-stepping method is generic and can be used to simulate any kind of neuron models. We illustrate it on nonlinear integrate-and-fire models and show that it outperforms time-stepping schemes of Runge-Kutta type in terms of simulation time and accuracy.

Causal networks in simulated neural systems

Neurons engage in causal interactions with one another and with the surrounding body and environment. Neural systems can therefore be analyzed in terms of causal networks, without assumptions about information processing, neural coding, and the like. Here, we review a series of studies analyzing causal networks in simulated neural systems using a combination of Granger causality analysis and graph theory. Analysis of a simple target-fixation model shows that causal networks provide intuitive representations of neural dynamics during behavior which can be validated by lesion experiments. Extension of the approach to a neurorobotic model of the hippocampus and surrounding areas identifies shifting causal pathways during learning of a spatial navigation task. Analysis of causal interactions at the population level in the model shows that behavioral learning is accompanied by selection of specific causal pathways—“causal cores”—from among large and variable repertoires of neuronal interactions. Finally, we argue that a causal network perspective may be useful for characterizing the complex neural dynamics underlying consciousness.

Objects limit human comprehension

This paper demonstrates that the human visual system, the primary sensory conduit for primates, processes ambient energy in a way that obligatorily constructs the objects that we ineluctably perceive. And since our perceptual apparatus processes information only in terms of objects (along with the properties and movements of objects), we are limited in our ability to comprehend ‘what is’ when we move beyond our ordinary world of midsize objects—as, for example, when we address the micro microworld of quantum physics.