Stromule formation is dependent upon plastid size, plastid differentiation status and the density of plastids within the cell

Stromules are motile extensions of the plastid envelope membrane, whose roles are not fully understood. They are present on all plastid types but are more common and extensive on non-green plastids that are sparsely distributed within the cell. During tomato fruit ripening, chloroplasts in the mesocarp tissue differentiate into chromoplasts and undergo major shifts in morphology. In order to understand what factors regulate stromule formation, we analysed stromule biogenesis in tobacco hypocotyls and in two distinct plastid populations in tomato mesocarp. We show that increases in stromule length and frequency are correlated with chromoplast differentiation, but only in one plastid population where the plastids are larger and less numerous. We used tobacco hypocotyls to confirm that stromule length increases as plastids become further apart, suggesting that stromules optimise the plastid-cytoplasm contact area. Furthermore, we demonstrate that ectopic chloroplast components decrease stromule formation on tomato fruit chromoplasts, whereas preventing chloroplast development leads to increased numbers of stromules. Inhibition of fruit ripening has a dramatic impact on plastid and stromule morphology, underlining that plastid differentiation status, and not cell type, is a significant factor in determining the extent of plastid stromules. By modifying the plastid surface area, we propose that stromules enhance the specific metabolic activities of plastids. This is an electronic version of an Article published in The Plant Journal, August 2004, Volume 39, pp. 655-667. Copyright 2004 Blackwell Publishing Ltd and The Society for Experimental Biology.

Directed percolation in a two dimensional stochastic fire-diffuse-fire model

In this paper we establish, from extensive numerical experiments, that the two dimensional stochastic fire-diffuse-fire model belongs to the directed percolation universality class. This model is an idealized model of intracellular calcium release that retains the both the discrete nature of calcium stores and the stochastic nature of release. It is formed from an array of noisy threshold elements that are coupled only by a diffusing signal. The model supports spontaneous release events that can merge to form spreading circular and spiral waves of activity. The critical level of noise required for the system to exhibit a non-equilibrium phase-transition between propagating and non-propagating waves is obtained by an examination of the \textit{local slope} $\delta(t)$ of the survival probability, $\Pi(t) \propto \exp(- \delta(t))$, for a wave to propagate for a time $t$.

What do universities want from publishing?

At a simple level, universities want publishing to support and further their mission to carry out research and teaching. However at a detailed level there are major differences within and between universities which mean there will be different wants and expectations of publishing. Bearing in mind these complexities, this paper examines universities' various requirements as producers, purchasers and consumers of publications. Some of the key wants of universities include impact, affordability, quality and access. The merits of the established system of subscription-based journal publishing and the emerging system of open-access publishing and dissemination are discussed in relation to universities' wants.

Self-archiving publications

This chapter discusses the historical development, current practice and future prospects of the self-archiving of research papers in open-access repositories (so-called 'e-print archives'). It describes how the development of interoperable e-print repositories in a number of subject communities has shown that self-archiving can benefit academic researchers (and potentially others) by enabling quick and easy access to the research literature and therefore maximising the impact potential of papers. Realising that the possible benefits are high and the technical entry barriers low, many organisations such as universities have recently tried to encourage widespread self-archiving by setting up institutional repositories. However, major barriers to self-archiving remain - most of them cultural and managerial. There are concerns about quality control, intellectual property rights, disturbing the publishing status quo, and workload. Ways in which these issues are currently being addressed are discussed in this chapter. A number of self-archiving initiatives in different countries have been set up to address the concerns and to kick-start e-print repository use. However, issues remain which require further investigation; those discussed in this chapter include discipline differences, definitions of 'publication', versioning problems, digital preservation, costing and funding models, and metadata standards. The ways in which these issues are resolved will be important in determining the future of self-archiving. Possible futures are discussed with particular reference to journal publishing and quality control. If widely adopted, self-archiving might come to assume a central place in the scholarly communication process, but a great deal of restructuring of the process needs to take place before this potential can be realised.

Bumps, breathers, and waves in a neural network with spike frequency adaptation

In this Letter we introduce a continuum model of neural tissue that include the effects of so-called spike frequency adaptation (SFA). The basic model is an integral equation for synaptic activity that depends upon the non-local network connectivity, synaptic response, and firing rate of a single neuron. A phenomenological model of SFA is examined whereby the firing rate is taken to be a simple state-dependent threshold function. As in the case without SFA classical Mexican-Hat connectivity is shown to allow for the existence of spatially localized states (bumps). Importantly an analysis of bump stability using recent Evans function techniques shows that bumps may undergo instabilities leading to the emergence of both breathers and traveling waves. Moreover, a similar analysis for traveling pulses leads to the conditions necessary to observe a stable traveling breather. Direct numerical simulations both confirm our theoretical predictions and illustrate the rich dynamic behavior of this model, including the appearance of self-replicating bumps.

A mandate to self archive? The role of open access institutional repositories

This paper argues that the best way to achieve major improvements in scholarly communication in the short and medium term is to make it mandatory to deposit research papers in open access institutional repositories. This is what the House of Commons Science and Technology Committee report of 2004 on scientific publishing recommended. The paper defines what open access repositories are and explains why they should be institutional. It also deals with question of what should be deposited in institutional repositories and why these improve scholarly communication. It then deals with the issue of mandating deposition: why deposition should be mandatory, who should mandate deposition and who should carry out deposition. The paper concludes with an analysis of the wider implications of mandating deposition in institutional repositories and a summary of the existing situation in the UK and elsewhere. The paper discusses the Select Committee report and the UK Government response in relation to institutional repositories.

Waves, bumps, and patterns in neural field theories

Neural field models of firing rate activity have had a major impact in helping to develop an understanding of the dynamics seen in brain slice preparations. These models typically take the form of integro-differential equations. Their non-local nature has led to the development of a set of analytical and numerical tools for the study of waves, bumps and patterns, based around natural extensions of those used for local differential equation models. In this paper we present a review of such techniques and show how recent advances have opened the way for future studies of neural fields in both one and two dimensions that can incorporate realistic forms of axo-dendritic interactions and the slow intrinsic currents that underlie bursting behaviour in single neurons.

A posteriori error estimation for discontinuous Galerkin discretizations of H(curl)-elliptic partial differential equations

We develop the a posteriori error estimation of interior penalty discontinuous Galerkin discretizations for H(curl)-elliptic problems that arise in eddy current models. Computable upper and lower bounds on the error measured in terms of a natural (mesh-dependent) energy norm are derived. The proposed a posteriori error estimator is validated by numerical experiments, illustrating its reliability and efficiency for a range of test problems.

Calculation of electric field strengths at a sharp edge

Sharp edges were first used for field ionisation mass spectrometry by Beckey. Although Cross and Robertson found that etched metal foils were more effective than razor blades for field ionisation, blades are very convenient for determination of field ionisation mass spectra, as reported by Robertson and Viney. The electric field at the vertex of a sharp edge can be calculated by the method of the conformal transformation. Here we give some equations for the field deduced with the assumption that the edge surface can be approximated by a hyperbola. We also compare two hyperbolae with radii of curvature at the vertex of 500 Angstrom and 1000 Angstrom with the profile of a commercial carbon-steel razor blade.

Electric field strengths and ion trajectories in sharp-edge field ionization sources

On the presumption that a sharp edge may be represented by a hyperbola, a conformal transformation method is used to derive electric field equations for a sharp edge suspended above a flat plate. A further transformation is then introduced to give electric field components for a sharp edge suspended above a thin slit. Expressions are deduced for the field strength at the vertex of the edge in both arrangements. The calculated electric field components are used to compute ion trajectories in the simple edge/flat-plate case. The results are considered in relation to future study of ion focusing and unimolecular decomposition of ions in field ionization mass spectrometers.

Symmetry properties of one- and two- electron molecular integrals

The maximum numbers of distinct one- and two-electron integrals that arise in calculating the electronic energy of a molecule are discussed. It is shown that these may be calculated easily using the character table of the symmetry group of the set of basis functions used to express the wave function. Complications arising from complex group representations and from a conflict of symmetry between the basis set and the nuclear configuration are considered and illustrated by examples.

Approximate ab initio calculations and the method of molecular fragments

A two stage approach to performing ab initio calculations on medium and large sized molecules is described. The first step is to perform SCF calculations on small molecules or molecular fragments using the OPIT Program. This employs a small basis set of spherical and p-type Gaussian functions. The Gaussian functions can be identified very closely with atomic cores, bond pairs, lone pairs, etc. The position and exponent of any of the Gaussian functions can be varied by OPIT to produce a small but fully optimised basis set. The second stage is the molecular fragments method. As an example of this, Gaussian exponents and distances are taken from an OPIT calculation on ethylene and used unchanged in a single SCF calculation on benzene. Approximate ab initio calculations of this type give much useful information and are often preferable to semi-empirical approaches, since the nature of the approximations involved is much better defined.

Symmetric Interior Penalty DG Methods for the Compressible Navier-Stokes Equations I: Method Formulation

In this article we consider the development of discontinuous Galerkin finite element methods for the numerical approximation of the compressible Navier-Stokes equations. For the discretization of the leading order terms, we propose employing the generalization of the symmetric version of the interior penalty method, originally developed for the numerical approximation of linear self-adjoint second-order elliptic partial differential equations. In order to solve the resulting system of nonlinear equations, we exploit a (damped) Newton-GMRES algorithm. Numerical experiments demonstrating the practical performance of the proposed discontinuous Galerkin method with higher-order polynomials are presented.