49,187 research outputs found
On a dynamic reaction-diffusion mechanism: The spatial patterning of teeth primordia in the alligator
It is now well established both theoretically and, more recently, experimentally, that steady-state spatial chemical concentration patterns can be formed by a number of specific reaction–diffusion systems. Reaction–diffusion models have been widely applied to biological pattern formation problems. Here we propose a model mechanism for the initiation and spatial positioning of teeth primordia in the alligator, Alligator mississippiensis, which, from a reaction–diffusion theory, introduces, among other things, a new element, namely the effect of domain growth on dynamic spatial pattern formation. Detailed embryological studies by Westergaard and Ferguson (B. Westergaard and M. W. J. Ferguson, J. Zool. Lond., 1986, 210, 575; 1987, 212, 191; Am. J. Anatomy, 1990, 187, 393) show that jaw growth plays a crucial role in the developmental patterning of the tooth initiation process. Based on biological data we develop a reaction–diffusion mechanism, which crucially includes domain growth. The model can reproduce the spatial pattern development of the first seven teeth primordia in the lower half jaw of A. mississippiensis. The results for the precise spatio temporal sequence compare well with detailed developmental experiments
A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology
Much of the progress in developing our ability to successfully design genetic circuits with predictable dynamics has followed the strategy of molding biological systems to fit into conceptual frameworks used in other disciplines, most notably the engineering sciences. Because biological systems have fundamental differences from systems in these other disciplines, this approach is challenging and the insights obtained from such analyses are often not framed in a biologically-intuitive way. Here, we present a new theoretical framework for analyzing the dynamics of genetic circuits that is tailored towards the unique properties associated with biological systems and experiments. Our framework approximates a complex circuit as a set of simpler circuits, which the system can transition between by saturating its various internal components. These approximations are connected to the intrinsic structure of the system, so this representation allows the analysis of dynamics which emerge solely from the system's structure. Using our framework, we analyze the presence of structural bistability in a leaky autoactivation motif and the presence of structural oscillations in the Repressilator
Dynamic weight parameter for the Random Early Detection (RED) in TCP networks
This paper presents the Weighted Random Early Detection (WTRED) strategy for congestion handling in TCP networks. WTRED provides an adjustable weight parameter to increase the sensitivity of the average queue size in RED gateways to the changes in the actual queue size. This modification, over the original RED proposal, helps gateways minimize the mismatch between average and actual queue sizes in router buffers. WTRED is compared with RED and FRED strategies using the NS-2 simulator. The results suggest that WTRED outperforms RED and FRED. Network performance has been measured using throughput, link utilization, packet loss and delay
Suicide substrate reaction-diffusion equations: varying the source
The suicide substrate reaction is a model for certain enzyme-inhibiting drugs. This reaction system is examined assuming that the substrate diffuses freely while the enzyme remains fixed. Two sets of initial and boundary conditions are examined: one modelling an instantaneous point source, akin to an injection of substrate, the other, a continuous point source, akin to a continuing influx, or intravenous drip, of substrate. The quasi-steady-state assumption is applied to obtain analytical solutions for a limited parameter space. Finally, further applications of numerical and analytical experimentation on pharmaceutical mechanisms are described
Mixtures of Common Skew-t Factor Analyzers
A mixture of common skew-t factor analyzers model is introduced for
model-based clustering of high-dimensional data. By assuming common component
factor loadings, this model allows clustering to be performed in the presence
of a large number of mixture components or when the number of dimensions is too
large to be well-modelled by the mixtures of factor analyzers model or a
variant thereof. Furthermore, assuming that the component densities follow a
skew-t distribution allows robust clustering of skewed data. The alternating
expectation-conditional maximization algorithm is employed for parameter
estimation. We demonstrate excellent clustering performance when our model is
applied to real and simulated data.This paper marks the first time that skewed
common factors have been used
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