6,986 research outputs found
Self-organization of heterogeneous topology and symmetry breaking in networks with adaptive thresholds and rewiring
We study an evolutionary algorithm that locally adapts thresholds and wiring
in Random Threshold Networks, based on measurements of a dynamical order
parameter. A control parameter determines the probability of threshold
adaptations vs. link rewiring. For any , we find spontaneous symmetry
breaking into a new class of self-organized networks, characterized by a much
higher average connectivity than networks without threshold
adaptation (). While and evolved out-degree distributions
are independent from for , in-degree distributions become broader
when , approaching a power-law. In this limit, time scale separation
between threshold adaptions and rewiring also leads to strong correlations
between thresholds and in-degree. Finally, evidence is presented that networks
converge to self-organized criticality for large .Comment: 4 pages revtex, 6 figure
Critical Line in Random Threshold Networks with Inhomogeneous Thresholds
We calculate analytically the critical connectivity of Random Threshold
Networks (RTN) for homogeneous and inhomogeneous thresholds, and confirm the
results by numerical simulations. We find a super-linear increase of with
the (average) absolute threshold , which approaches for large , and show that this asymptotic scaling is
universal for RTN with Poissonian distributed connectivity and threshold
distributions with a variance that grows slower than . Interestingly, we
find that inhomogeneous distribution of thresholds leads to increased
propagation of perturbations for sparsely connected networks, while for densely
connected networks damage is reduced; the cross-over point yields a novel,
characteristic connectivity , that has no counterpart in Boolean networks.
Last, local correlations between node thresholds and in-degree are introduced.
Here, numerical simulations show that even weak (anti-)correlations can lead to
a transition from ordered to chaotic dynamics, and vice versa. It is shown that
the naive mean-field assumption typical for the annealed approximation leads to
false predictions in this case, since correlations between thresholds and
out-degree that emerge as a side-effect strongly modify damage propagation
behavior.Comment: 18 figures, 17 pages revte
The phase diagram of random threshold networks
Threshold networks are used as models for neural or gene regulatory networks.
They show a rich dynamical behaviour with a transition between a frozen and a
chaotic phase. We investigate the phase diagram of randomly connected threshold
networks with real-valued thresholds h and a fixed number of inputs per node.
The nodes are updated according to the same rules as in a model of the
cell-cycle network of Saccharomyces cereviseae [PNAS 101, 4781 (2004)]. Using
the annealed approximation, we derive expressions for the time evolution of the
proportion of nodes in the "on" and "off" state, and for the sensitivity
. The results are compared with simulations of quenched networks. We
find that for integer values of h the simulations show marked deviations from
the annealed approximation even for large networks. This can be attributed to
the particular choice of the updating rule.Comment: 8 pages, 6 figure
Eotvos bounds on couplings of fundamental parameters to gravity
The possible dependence of fundamental couplings and mass ratios on the
gravitational potential has been bounded by comparing atomic clock frequencies
over Earth's elliptical orbit. Here we evaluate bounds on such dependence from
E"otv"os-type experiments that test the Weak Equivalence Principle, including
previously neglected contributions from nuclear binding energy. We find that
variations of fundamental parameters correlated with the gravitational
potential are bounded at 10^-8--10^-9, an improvement of 2--3 orders of
magnitude over atomic clock bounds.Comment: To be published (Phys.Rev.Lett.), minor changes and corrections,
equivalent to journal versio
By hook or by crook? Morphometry, competition and cooperation in rodent sperm
Background
Sperm design varies enormously across species and sperm competition is thought to be a major factor influencing this variation. However, the functional significance of many sperm traits is still poorly understood. The sperm of most murid rodents are characterised by an apical hook of the sperm head that varies markedly in extent across species. In the European woodmouse Apodemus sylvaticus (Muridae), the highly reflected apical hook of sperm is used to form sperm groups, or “trains,” which exhibited increased swimming velocity and thrusting force compared to individual sperm.
Methodology/Principal Findings
Here we use a comparative study of murine rodent sperm and demonstrate that the apical hook and sperm cooperation are likely to be general adaptations to sperm competition in rodents. We found that species with relatively larger testes, and therefore more intense sperm competition, have a longer, more reflected apical sperm hook. In addition, we show that sperm groups also occur in rodents other than the European woodmouse.
Conclusions
Our results suggest that in rodents sperm cooperation is more widespread than assumed so far and highlight the importance of diploid versus haploid selection in the evolution of sperm design and function
Leaf Morphology, Taxonomy and Geometric Morphometrics: A Simplified Protocol for Beginners
Taxonomy relies greatly on morphology to discriminate groups. Computerized geometric morphometric methods for quantitative shape analysis measure, test and visualize differences in form in a highly effective, reproducible, accurate and statistically powerful way. Plant leaves are commonly used in taxonomic analyses and are particularly suitable to landmark based geometric morphometrics. However, botanists do not yet seem to have taken advantage of this set of methods in their studies as much as zoologists have done. Using free software and an example dataset from two geographical populations of sessile oak leaves, we describe in detailed but simple terms how to: a) compute size and shape variables using Procrustes methods; b) test measurement error and the main levels of variation (population and trees) using a hierachical design; c) estimate the accuracy of group discrimination; d) repeat this estimate after controlling for the effect of size differences on shape (i.e., allometry). Measurement error was completely negligible; individual variation in leaf morphology was large and differences between trees were generally bigger than within trees; differences between the two geographic populations were small in both size and shape; despite a weak allometric trend, controlling for the effect of size on shape slighly increased discrimination accuracy. Procrustes based methods for the analysis of landmarks were highly efficient in measuring the hierarchical structure of differences in leaves and in revealing very small-scale variation. In taxonomy and many other fields of botany and biology, the application of geometric morphometrics contributes to increase scientific rigour in the description of important aspects of the phenotypic dimension of biodiversity. Easy to follow but detailed step by step example studies can promote a more extensive use of these numerical methods, as they provide an introduction to the discipline which, for many biologists, is less intimidating than the often inaccessible specialistic literature
Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity
Background: Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective.
Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode
of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric
analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats.
Methodology/Principal Findings: A new phylogenetic analysis supports the monophyly of saber-toothed cats
(Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various sabertoothed
tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear
variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are
consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a
separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae,
we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The
evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the
separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats.
Conclusions/Significance: Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage,
morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions
peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable
morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in
reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional
diversity studies, and may reveal novel patterns of morphospace occupation
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