A heterogeneity-aware approach to load balancing of computational tasks: a theoretical and simulation study

One of the distinct characteristics of computing platforms shared by multiple users such as a cluster and a computational grid is heterogeneity on each computer and/or among computers. Temporal heterogeneity refers to variation, along the time dimension, of computing power available for a task on a computer, and spatial heterogeneity represents the variation among computers. In minimizing the average parallel execution time of a target task on a spatially heterogeneous computing system, it is not optimal to distribute the target task linearly proportional to the average computing powers available on computers. In this paper, effects of the temporal and spatial heterogeneity on performance of a target task have been analyzed in terms of the mean and standard deviation of parallel execution time. Based on the analysis results, an approach to load balancing for minimizing the average parallel execution time of a target task is described. The proposed approach whose validity has been verified through simulation considers temporal and spatial heterogeneities in addition to the average computing power on each computer.

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.

Synchronization properties of networks of electrically coupled neurons in the presence of noise and heterogeneities

We investigate how synchrony can be generated or induced in networks of electrically coupled integrate-and-fire neurons subject to noisy and heterogeneous inputs. Using analytical tools, we find that in a network under constant external inputs, synchrony can appear via a Hopf bifurcation from the asynchronous state to an oscillatory state. In a homogeneous net work, in the oscillatory state all neurons fire in synchrony, while in a heterogeneous network synchrony is looser, many neurons skipping cycles of the oscillation. If the transmission of action potentials via the electrical synapses is effectively excitatory, the Hopf bifurcation is supercritical, while effectively inhibitory transmission due to pronounced hyperpolarization leads to a subcritical bifurcation. In the latter case, the network exhibits bistability between an asynchronous state and an oscillatory state where all the neurons fire in synchrony. Finally we show that for time-varying external inputs, electrical coupling enhances the synchronization in an asynchronous network via a resonance at the firing-rate frequency.

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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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.

Spectral plots and the representation and interpretation of biological data

It is basic question in biology and other fields to identify the characteristic properties that on one hand are shared by structures from a particular realm, like gene regulation, protein–protein interaction or neural networks or foodwebs, and that on the other hand distinguish them from other structures. We introduce and apply a general method, based on the spectrum of the normalized graph Laplacian, that yields representations, the spectral plots, that allow us to find and visualize such properties systematically. We present such visualizations for a wide range of biological networks and compare them with those for networks derived from theoretical schemes. The differences that we find are quite striking and suggest that the search for universal properties of biological networks should be complemented by an understanding of more specific features of biological organization principles at different scales.

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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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.

Spatial variation of airborne pollen over south-east France: characterization and implications for monitoring networks management

The French airborne pollen monitoring network (RNSA) is currently regrouping 70 Hirst-type pollen traps covering the whole French territory. The aim of this paper is to introduce a simple statistical methodology that can be used to characterize pollen spatial variation. This pilot study is restricted to a limited portion of the RNSA network (18 monitoring stations), eight taxa of allergenic relevance, and a 3-year period (2003–2005). The first step of the approach consisted in quantifying the trap-to-trap pollen similarities on the basis of an original index, called mean Pollinic Distance (mPD), that relies on the comparison of pollen concentration time series. Regression analyses were next conducted with different spatial variables. Distance, latitude and altitude differences were identified as significant predictors of pollen variations, as measured by mPD. In order to further characterize pollen spatial properties, cluster analysis was performed with mPD as the distance estimate. Interestingly, the clusters of sites identified on the basis of the similarity of their pollen profiles, correspond to distinct geographic areas that might be interpreted as homogeneous air masses. The results have major implications for monitoring networks management since they provide an objective basis (1) for choosing the relevant scale to elaborate and supply pollen-related information, and (2) for optimizing networks configuration.

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.

Corpus Interruptus: Biotech Drugs, Insurance Providers and the Treatment of Breast Cancer

In researching the biomedically-engineered drug Neulasta (filgrastim), a breast cancer patient becomes aware of the extent to which knowledge about the development and marketing of drugs influences her decisions with regard to treatment. Time spent on understanding the commercial interests of insurers and pharmaceutical companies initially thwarts but ultimately aids the healing process. This first-person narrative calls for physicians to recognize that the alignment of commercial interests transgresses the patient’s humanity.

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.

Basic Semiosis as Code-Based Control

Though the formal coherence and empirical utility of Marcello Barbieri’s concept of organic code have been starting to become established, a general conception of how the semantics of organic codes is related to the pragmatics of their use is still missing. Barbieri took a first step towards such a conception by distinguishing three types of semiosis in living systems: manufacturing, signalling, and interpretive semiosis. This paper integrates Barbieri’s distinction into Roman Jakobson’s systematization of possible functions of messages in order to propose a general conception of possible types of semiosis in living systems. As a result, Barbieri’s thesis that manufacturing and signalling semiosis are basic types of semiosis, can be confirmed and completed communication-theoretically.

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.

Does Investment in the Sexes Differ When Fathers Are Absent?

This study examines child survival and growth in a patrilineal Ethiopian community as a function of father absence and sex. In line with evolutionary predictions for sex-biased parental investment, the absence of a father and associated constraints on household resources is more detrimental for sons’ than daughters’ survival in infancy. Father absence doubles a son’s risk of dying in infancy but has a positive influence on the well-being of female members of the household, improving daughter survival, growth, and maternal nutritional status. Lack of paternal investment may be compensated for by other matrilateral kin through increased reciprocity between mother, daughter, and sister.