Modeling brain dynamics using computational neurogenetic approach

The paper introduces a novel computational approach to brain dynamics modeling that integrates dynamic gene–protein regulatory networks with a neural network model. Interaction of genes and proteins in neurons affects the dynamics of the whole neural network. Through tuning the gene–protein interaction network and the initial gene/protein expression values, different states of the neural network dynamics can be achieved. A generic computational neurogenetic model is introduced that implements this approach. It is illustrated by means of a simple neurogenetic model of a spiking neural network of the generation of local field potential. Our approach allows for investigation of how deleted or mutated genes can alter the dynamics of a model neural network. We conclude with the proposal how to extend this approach to model cognitive neurodynamics.

A finite volume method for stochastic integrate-and-fire models

The stochastic integrate and fire neuron is one of the most commonly used stochastic models in neuroscience. Although some cases are analytically tractable, a full analysis typically calls for numerical simulations. We present a fast and accurate finite volume method to approximate the solution of the associated Fokker-Planck equation. The discretization of the boundary conditions offers a particular challenge, as standard operator splitting approaches cannot be applied without modification. We demonstrate the method using stationary and time dependent inputs, and compare them with Monte Carlo simulations. Such simulations are relatively easy to implement, but can suffer from convergence difficulties and long run times. In comparison, our method offers improved accuracy, and decreases computation times by several orders of magnitude. The method can easily be extended to two and three dimensional Fokker-Planck equations.

How development changes evolution: conceptual and historical issues in evolutionary developmental biology

Evolutionary developmental biology (Evo-Devo) is a new and rapidly developing field of biology which focuses on questions in the intersection of evolution and development and has been seen by many as a potential synthesis of these two fields. This synthesis is the topic of the books reviewed here. Integrating Evolution and Development (edited by Roger Sansom and Robert Brandon), is a collection of papers on conceptual issues in Evo-Devo, while From Embryology to Evo-Devo (edited by Manfred Laubichler and Jane Maienschein) is a history of the problem of the relations between ontogeny and phylogeny.

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

Ohne Zusammenfassung

---

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.

---

Sexual selection and mate choice in evolutionary psychology

The importance of mate choice and sexual selection has been emphasized by the majority of evolutionary psychologists. This paper assesses three cases of work on mate choice and sexual selection in evolutionary psychology: David Buss on cross-cultural human mate preferences, Randy Thornhill and Steve Gangestad on the link between mate preferences and fluctuating asymmetry, and Geoffrey Miller on the role of Fisher’s runaway process in human evolution. A mixture of conceptual and empirical problems in each case highlights the general weakness of work in evolutionary psychology on these issues.

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.

---

Gridcast—a next generation broadcast infrastructure?

Gridcast is an R&D project investigating grid ideas and technologies in the broadcasting technical infrastructure. In this paper I discuss the business and technical issues in building infrastructures to support broadcasters and outline the structure of the Gridcast grid-based service oriented architecture for broadcasting playout support.

Benchmarking the effects of operating system interference on extreme-scale parallel machines

We investigate operating system noise, which we identify as one of the main reasons for a lack of synchronicity in parallel applications. Using a microbenchmark, we measure the noise on several contemporary platforms and find that, even with a general-purpose operating system, noise can be limited if certain precautions are taken. We then inject artificially generated noise into a massively parallel system and measure its influence on the performance of collective operations. Our experiments indicate that on extreme-scale platforms, the performance is correlated with the largest interruption to the application, even if the probability of such an interruption on a single process is extremely small. We demonstrate that synchronizing the noise can significantly reduce its negative influence.

Individual optimization efforts and population dynamics: a mathematical model for the evolution of resource allocation strategies, with applications to reproductive and mating systems

We develop a formal framework for the optimal allocation of limited resources that includes and clarifies the interplay between individual optimization and the resulting effects at the population level. As an example, in regard to the evolution of sexual recombination, the paradox of the twofold cost of sex is avoided by distinguishing between the evolution of recombination and the subsequent emergence and stability of different mating types as a result of individual optimization within a population that benefits from recombination.

Robust clustering analysis for the management of self-monitoring distributed systems

We present a decentralized algorithm for online clustering analysis used for anomaly detection in self-monitoring distributed systems. In particular, we demonstrate the monitoring of a network of printing devices that can perform the analysis without the use of external computing resources (i.e. in-network analysis). We also show how to ensure the robustness of the algorithm, in terms of anomaly detection accuracy, in the face of failures of the network infrastructure on which the algorithm runs. Further, we evaluate the tradeoff in terms of overhead necessary for ensuring this robustness and present a method to reduce this overhead while maintaining the detection accuracy of the algorithm.

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.

The Evolution of Complex Organs

The origin of complex biological structures has long been a subject of interest and debate. Two centuries ago, natural explanations for their occurrence were considered inconceivable. However, 150 years of scientific investigation have yielded a conceptual framework, abundant data, and a range of analytical tools capable of addressing this question. This article reviews the various direct and indirect evolutionary processes that contribute to the origins of complex organs. The evolution of eyes is used as a case study to illustrate these concepts, and several of the most common misconceptions about complex organ evolution are discussed.

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.

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.