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

Ohne Zusammenfassung

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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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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.

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.

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.

Strategies of abstraction

Abstraction is seen as an active process which both enlightens and obscures. Abstractions are not true or false but relatively enlightening or obscuring according to the problem under study; different abstractions may grasp different aspects of a problem. Abstractions may be useless if they can answer questions only about themselves. A theoretical enterprise explores reality through acluster of abstractions that use different perspectives, temporal and horizontal scales, and assumes different givens.

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.

Your Liberty or Your Life: Reciprocity in the Use of Restrictive Measures in Contexts of Contagion

In this paper, we explore the role of reciprocity in the employment of restrictive measures in contexts of contagion. Reciprocity should be understood as a substantive value that governs the use, level and extent of restrictive measures. We also argue that independent of the role reciprocity plays in the legitimisation the use of restrictive measures, reciprocity can also motivate support and compliance with legitimate restrictive measures. The importance of reciprocity has implications for how restrictive measures should be undertaken when preparing and evaluating public health responses to contagion.

The connectionist framework for gene regulation

I show that gene regulation networks are qualitatively consistent and therefore sufficiently similar to linearly seperable connectionist networks to warrant that the connectionist framework be applied to gene regulation. On this view, natural selection designs gene regulation networks to overcome the difficulty of development. I offer some general lessons about their evolvability that can be learned by examining the generic features of connectionist networks.

Working memory dynamics and spontaneous activity in a flip-flop oscillations network model with a Milnor attractor

Many cognitive tasks require the ability to maintain and manipulate simultaneously several chunks of information. Numerous neurobiological observations have reported that this ability, known as the working memory, is associated with both a slow oscillation (leading to the up and down states) and the presence of the theta rhythm. Furthermore, during resting state, the spontaneous activity of the cortex exhibits exquisite spatiotemporal patterns sharing similar features with the ones observed during specific memory tasks. Here to enlighten neural implication of working memory under these complicated dynamics, we propose a phenomenological network model with biologically plausible neural dynamics and recurrent connections. Each unit embeds an internal oscillation at the theta rhythm which can be triggered during up-state of the membrane potential. As a result, the resting state of a single unit is no longer a classical fixed point attractor but rather the Milnor attractor, and multiple oscillations appear in the dynamics of a coupled system. In conclusion, the interplay between the up and down states and theta rhythm endows high potential in working memory operation associated with complexity in spontaneous activities.

Formulations for delivery of therapeutic proteins

Advances in biotechnology have now created a capacity to produce therapeutically active proteins on a commercial scale, opening the potential for their application in an array of disease conditions. The process of translation of the variety of different therapeutic proteins into the medicines used in clinics is now occurring. To assist in this translation, new formulations to deliver proteins could play an important role. These new formulations need to more adequately address the pharmacological and therapeutic requirement for each particular protein/peptide and, in that way, either improve present therapies or extend with new entries the current list of protein based medicines used in clinic.

Causal Explanation of Indonesian Forest Fires: Concepts, Applications, and Research Priorities

Problems with studies, claims, and assumptions that have been made about the causes of fires in Indonesia's tropical moist forests are identified, and the kinds of concepts, methods, prioritizing, and data needed to resolve the problems are discussed. Separate sections are devoted to studying ignitions, studying fire susceptibility and fire behavior, and using the goal of causal explanation to guide interdisciplinary research.

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.