Implementing vertex dynamics models of cell populations in biology within a consistent computational framework

The dynamic behaviour of epithelial cell sheets plays a central role during development, growth, disease and wound healing. These processes occur as a result of cell adhesion, migration, division, differentiation and death, and involve multiple processes acting at the cellular and molecular level. Computational models offer a useful means by which to investigate and test hypotheses about these processes, and have played a key role in the study of cell–cell interactions. However, the necessarily complex nature of such models means that it is difficult to make accurate comparison between different models, since it is often impossible to distinguish between differences in behaviour that are due to the underlying model assumptions, and those due to differences in the in silico implementation of the model. In this work, an approach is described for the implementation of vertex dynamics models, a discrete approach that represents each cell by a polygon (or polyhedron) whose vertices may move in response to forces. The implementation is undertaken in a consistent manner within a single open source computational framework, Chaste, which comprises fully tested, industrial-grade software that has been developed using an agile approach. This framework allows one to easily change assumptions regarding force generation and cell rearrangement processes within these models. The versatility and generality of this framework is illustrated using a number of biological examples. In each case we provide full details of all technical aspects of our model implementations, and in some cases provide extensions to make the models more generally applicable

NITROGEN MANAGEMENT IN SOUTHEASTERN MINNESOTA

Crop Production/Industries,

A polynomial training algorithm for calculating perceptrons of optimal stability

Recomi (REpeated COrrelation Matrix Inversion) is a polynomially fast algorithm for searching optimally stable solutions of the perceptron learning problem. For random unbiased and biased patterns it is shown that the algorithm is able to find optimal solutions, if any exist, in at worst O(N^4) floating point operations. Even beyond the critical storage capacity alpha_c the algorithm is able to find locally stable solutions (with negative stability) at the same speed. There are no divergent time scales in the learning process. A full proof of convergence cannot yet be given, only major constituents of a proof are shown.Comment: 11 pages, Latex, 4 EPS figure

State of the Fisheries Report 2007/08

The State of the Fisheries Report is published annually to provide a detailed level of reporting on the management of fish stocks and their environment undertaken by the Department of Fisheries. A summary report from this document is included in the Department’s Annual Report to Parliament, which includes the Department’s nonfinancial (fishery) performance indicators. The Annual Report is no longer printed but is available through the Department’s website (www.fish.wa.gov.au).https://researchlibrary.agric.wa.gov.au/an_sofar/1000/thumbnail.jp

Thermo-acoustic wave propagation and reflection near the liquid-gas critical point

We study the thermo-acoustic wave propagation and reflection near the liquid-gas critical point. Specifically, we perform a numerical investigation of the acoustic responses in a near-critical fluid to thermal perturbations based on the same setup of a recent ultrasensitive interferometry measurement in CO2 [Y. Miura et al. Phys. Rev. E 74, 010101(R) (2006)]. The numerical results agree well with the experimental data. New features regarding the reflection pattern of thermo-acoustic waves near the critical point under pulse perturbations are revealed by the proper inclusion of the critically diverging bulk viscosity.Comment: 14 pages, 4 figures, Accepted by PRE (Rapid Communication

Nestling diet, secondary sexual traits and fitness in the zebra finch

We examined the effect of nestling diet quality on a suite of physiological, morphological and life-history traits in adult male zebra finches,Taeniopygia guttata. Compared with birds reared on a supplemented diet, nestlings reared on a seed-only diet showed a reduced rate of growth and reduced cell-mediated immune function as measured by an in vivo response to aT lymphocyte-dependent mitogen. There were no differences between birds reared on the two diets in any of the following adult traits: body size, primary sexual traits (testes mass, numbers of stored sperm, sperm function, velocity and morphology), secondary sexual traits (beak colour and song rate), serological traits or immunological traits. The only differences we detected were a lower body mass and a greater proportion of individuals with plumage abnormalities among those reared on a seed-only diet (this latter effect was transient). The fact that male zebra finches reared on a seed-only diet were, as adults, virtually indistinguishable from those reared on a supple- mented diet, despite having reduced growth and immune function as nestlings, demonstrates that they subsequently compensated through the di¡erential allocation of resources. Our results indicate that differ- ential allocation is costly in terms of fitness since birds reared on a seed-only diet experienced a significantly greater mortality rate than those reared on a supplemented diet. This in turn suggests the existence of a trade-of between the development of traits important for reproduction, such as primary and secondary sexual traits and longevity

Constraining the Atmospheric Composition of the Day-Night Terminators of HD 189733b : Atmospheric Retrieval with Aerosols

A number of observations have shown that Rayleigh scattering by aerosols dominates the transmission spectrum of HD 189733b at wavelengths shortward of 1 $\mu$m. In this study, we retrieve a range of aerosol distributions consistent with transmission spectroscopy between 0.3-24 $\mu$m that were recently re-analyzed by Pont et al. (2013). To constrain the particle size and the optical depth of the aerosol layer, we investigate the degeneracies between aerosol composition, temperature, planetary radius, and molecular abundances that prevent unique solutions for transit spectroscopy. Assuming that the aerosol is composed of MgSiO$_3$, we suggest that a vertically uniform aerosol layer over all pressures with a monodisperse particle size smaller than about 0.1 $\mu$m and an optical depth in the range 0.002-0.02 at 1 $\mu$m provides statistically meaningful solutions for the day/night terminator regions of HD 189733b. Generally, we find that a uniform aerosol layer provide adequate fits to the data if the optical depth is less than 0.1 and the particle size is smaller than 0.1 $\mu$m, irrespective of the atmospheric temperature, planetary radius, aerosol composition, and gaseous molecules. Strong constraints on the aerosol properties are provided by spectra at wavelengths shortward of 1 $\mu$m as well as longward of 8 $\mu$m, if the aerosol material has absorption features in this region. We show that these are the optimal wavelengths for quantifying the effects of aerosols, which may guide the design of future space observations. The present investigation indicates that the current data offer sufficient information to constrain some of the aerosol properties of HD189733b, but the chemistry in the terminator regions remains uncertain.Comment: Transferred to ApJ and accepted. 11 pages, 10 figures, 1 tabl

The optical transmission spectrum of the hot Jupiter HAT-P-32b: clouds explain the absence of broad spectral features?

We report Gemini-North GMOS observations of the inflated hot Jupiter HAT-P-32b during two primary transits. We simultaneously observed two comparison stars and used differential spectro-photometry to produce multi-wavelength light curves. 'White' light curves and 29 'spectral' light curves were extracted for each transit and analysed to refine the system parameters and produce transmission spectra from 520-930nm in ~14nm bins. The light curves contain time-varying white noise as well as time-correlated noise, and we used a Gaussian process model to fit this complex noise model. Common mode corrections derived from the white light curve fits were applied to the spectral light curves which significantly improved our precision, reaching typical uncertainties in the transit depth of ~2x10^-4, corresponding to about half a pressure scale height. The low resolution transmission spectra are consistent with a featureless model, and we can confidently rule out broad features larger than about one scale height. The absence of Na/K wings or prominent TiO/VO features is most easily explained by grey absorption from clouds in the upper atmosphere, masking the spectral features. However, we cannot confidently rule out clear atmosphere models with low abundances (~10^-3 solar) of TiO, VO or even metal hydrides masking the Na and K wings. A smaller scale height or ionisation could also contribute to muted spectral features, but alone are unable to to account for the absence of features reported here.Comment: 17 pages, 11 figures, 2 tables, accepted for publication in MNRA