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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Morbid Jealousy and Sex Differences in Partner-Directed Violence

Previous research suggests that individuals diagnosed with morbid jealousy have jealousy mechanisms that are activated at lower thresholds than individuals with normal jealousy, but that these mechanisms produce behavior that is similar to individuals with normal jealousy. We extended previous research documenting these similarities by investigating sex differences in partner-directed violence committed by individuals diagnosed with morbid jealousy. The results support some of our predictions. For example, a greater percentage of men than women diagnosed with morbid jealousy used physical violence, attempted to kill, and actually killed their partners, and used their hands rather than an object to kill their partners. These results replicate results generated for individuals with normal jealousy. Discussion addresses implications of the current research and highlights directions for future research on the psychology of morbid jealousy.

Slow and fast pulses in 1-D cultures of excitatory neurons

We analyze the characteristics of front propagation in activity of 1-D neuronal cultures by numerical simulations, using only excitatory dynamics. Experimental results in 1-D cultures of hippocampal neurons from rats have shown the spontaneous generation of a slow, low amplitude pulse that precedes a high amplitude, fast pulse that propagates through all the system. Notably, this transition appears both with and without the presence of functioning inhibitory synapses. In accordance with previous work, we demonstrate that purely excitatory integrate and fire neurons with depression in the synapses suffice to produce fast and uniform pulses but cannot explain the appearance of slow, weak pulses. We propose to explain the slow pulses by increasing the complexity of the neuron model in a purely excitatory network with connectivity as close to the experiments as possible. This approach allows us to show that spike frequency adaptation is a fundamental ingredient for the initiation process of the pulse. The introduction of a slow variable that mimics the presence of the slow K ⁺ channels in the soma and produces spike frequency adaptation increases strongly the persistence of the transient activity before the emergence of the fast pulse up to temporal and spatial scales comparable with the experiments. Finally, we demonstrate that proper levels of additive white noisy currents generate such pulses spontaneously, fully reproducing the experimental results. 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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How ubiquitous is adaptation? A critique of the epiphenomenist program

It is important to distinguish adaptation per se (adaptedness, or being adapted) from the more specific concept of adaptation for some function. Commonly used criteria for adaptation in either sense have limited applicability. There are, however, a number of widely applicable criteria for adaptation per se, such as several kinds of cost, low variation, the maintenance of integration, and the fitness distribution of mutations. Application of these criteria leads to the conclusion that adaptation is overwhelmingly prevalent for features of organisms. Neither the presence nor the absence of adaptation has a privileged status in inference. Effectively neutral evolution can occur on adaptive buttes while maintaining the same degree of adaptation, but it is likely to be relatively minor.

Global adaptation patterns of Australian and CIMMYT spring bread wheat

The International Adaptation Trial (IAT) is a special purpose nursery designed to investigate the genotype-by-environment interactions and worldwide adaptation for grain yield of Australian and CIMMYT spring bread wheat (Triticum aestivum L.) and durum wheat (T. turgidum L. var. durum). The IAT contains lines representing Australian and CIMMYT wheat breeding programs and was distributed to 91 countries between 2000 and 2004. Yield data of 41 reference lines from 106 trials were analysed. A multiplicative mixed model accounted for trial variance heterogeneity and inter-trial correlations characteristic of multi-environment trials. A factor analytic model explained 48% of the genetic variance for the reference lines. Pedigree information was then incorporated to partition the genetic line effects into additive and non-additive components. This model explained 67 and 56% of the additive by environment and non-additive by environment genetic variances, respectively. Australian and CIMMYT germplasm showed good adaptation to their respective target production environments. In general, Australian lines performed well in south and west Australia, South America, southern Africa, Iran and high latitude European and Canadian locations. CIMMYT lines performed well at CIMMYT’s key yield testing location in Mexico (CIANO), north-eastern Australia, the Indo-Gangetic plains, West Asia North Africa and locations in Europe and Canada. Maturity explained some of the global adaptation patterns. In general, southern Australian germplasm were later maturing than CIMMYT material. While CIANO continues to provide adapted lines to northern Australia, selecting for yield among later maturing CIMMYT material in CIANO may identify lines adapted to southern and western Australian environments. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

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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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Combining data sharing with the master–worker paradigm in the common component architecture

Software component technologies are being accepted as an adequate solution for handling the complexity of applications. However, existing software component models tend to be specialized to some types of resource architectures (e.g. in-process, distributed environments, etc.) and/or do not provide a very high level of abstraction. This paper focuses on handling data sharing on operation invocations between components as a solution allowing applications to be efficiently executed on all kinds of resources. In particular, the data sharing pattern appears in master–worker applications, when workers need to access only a part of a large piece of data, either in read or write mode. This approach is applied to the Common Component Architecture model. Its benefits are discussed using an image rendering application.

A self-managing wide-area data streaming service

Efficient and robust data streaming services are a critical requirement of emerging Grid applications, which are based on seamless interactions and coupling between geographically distributed application components. Furthermore the dynamism of Grid environments and applications requires that these services be able to continually manage and optimize their operation based on system state and application requirements. This paper presents a design and implementation of such a self-managing data-streaming service based on online control strategies. A Grid-based fusion workflow scenario is used to evaluate the service and demonstrate its feasibility and performance.

The Behavioral Ecology of Shellfish Gathering in Western Kiribati,Micronesia. 2: Patch Choice,Patch Sampling,and Risk

The prey choice model, previously applied among shellfish gatherers in Kiribati, Micronesia, has shown that they are foraging in a manner that matches the predictions of optimal foraging theory by maximizing their net energy return rates. Similar conclusions can be drawn subsequent to testing the patch choice model, including patch switching; patch sampling; and the analysis of risk. In light of these results, it is argued that natural selection probably never encouraged the persistence of conservation because individuals have nearly always benefited from short-term goals to ensure greater fitness. However, the possibility remains that as a result of changed circumstances brought about by increasing human population, more efficient extractive technologies, and expanding market opportunities, genuine, as opposed to epiphenomenal conservation, may become established in heavily impacted environments.

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.

Genomic Error-Correcting Codes in the Living World

This paper is intended to complement our previous works on the necessary existence of error-correcting codes endowing genomes with the ability of being regenerated, not merely copied. It sketchily recalls some fundamental definitions and results of information theory and error-correcting codes; provides an overview of our research; shows that the disjunction of replication and regeneration enlightens the divide between germinal and somatic cells; suggests that some phenomena referred to as epigenetic may possibly find an explanation within the framework of error-correcting codes; points out some difficulties, especially those related to sexual reproduction; criticizes the template-replication paradigm, and prompts geneticists to become familiar with information theory.

Advertising and the Predation Loop: A Biosemiotic Model

The basic premise of biosemiotics as a discipline is that there are elementary processes linking signifying strategies in all forms of animate life. Correspondingly, the discoveries of biosemiotics should, in principle, be capable of revealing new insights about human signification. In the present article, I show that this is in fact the case by constructing a biosemiotic model that links advertising strategies with corresponding structures in animal predation. The methodological framework for this model is the catastrophe theory of René Thom. The end result is a revised understanding of an ostensibly cultural phenomenon that demonstrates its continuity with signalling processes conventionally associated with the natural world.

At the Sea’s Edge: Elders and Children in the Littorals of Barbados and the Bahamas

Littorals in the in the Exuma Cays, Bahamas and the Bath Plantation, Barbados are comparative in many ways. These edges of the sea have provided critical services to local people during the time of slavery and since. More than food and medicine, the littoral is the nightly sea bath, where children are instructed, and the last ecosystem effectively used by the elderly. Independence and self-respect derive from use and protection of these littoral by individuals and communities. Local patterns of conservation and use are argued to be essential in the ecological structure and functions of the littoral. Development projects and marine protected areas alike are seen as potentially breaking local ties with the littoral causing trophic skew and damaging local society. If development occurs, mitigation solutions potentially derive from legally recognizing local people as partners in the co-management of their traditional littoral.

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.

Are Girls Good and Boys Bad for Parental Longevity?

Using historical data from the Utah Population Database, this analysis finds significant, consistent, but small adverse mortality effects for mothers after age 50 who had mostly sons. Examination of age-dependent effects indicates that this association increases with mother’s age. Additionally, mothers who had mostly daughters faced mortality risks that increased with age. Offspring sex composition did not have a significant effect on paternal mortality. Interaction analyses were conducted to examine the effect of offspring sex composition with regard to historical period, residential location, socioeconomic status, and childhood survival. No other interactions were found to be statistically significant. Having mostly boys remained detrimental to maternal mortality regardless of childhood survival.