Embedding Population Dynamics Models in Inference

Increasing pressures on the environment are generating an ever-increasing need to manage animal and plant populations sustainably, and to protect and rebuild endangered populations. Effective management requires reliable mathematical models, so that the effects of management action can be predicted, and the uncertainty in these predictions quantified. These models must be able to predict the response of populations to anthropogenic change, while handling the major sources of uncertainty. We describe a simple ``building block'' approach to formulating discrete-time models. We show how to estimate the parameters of such models from time series of data, and how to quantify uncertainty in those estimates and in numbers of individuals of different types in populations, using computer-intensive Bayesian methods. We also discuss advantages and pitfalls of the approach, and give an example using the British grey seal population.Comment: Published at http://dx.doi.org/10.1214/088342306000000673 in the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

The Clarens web services architecture

Clarens is a uniquely flexible web services infrastructure providing a unified access protocol to a diverse set of functions useful to the HEP community. It uses the standard HTTP protocol combined with application layer, certificate based authentication to provide single sign-on to individuals, organizations and hosts, with fine-grained access control to services, files and virtual organization (VO) management. This contribution describes the server functionality, while client applications are described in a subsequent talk.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 6 pages, LaTeX, 4 figures, PSN MONT00

Clarens Client and Server Applications

Several applications have been implemented with access via the Clarens web service infrastructure, including virtual organization management, JetMET physics data analysis using relational databases, and Storage Resource Broker (SRB) access. This functionality is accessible transparently from Python scripts, the Root analysis framework and from Java applications and browser applets.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 4 pages, LaTeX, no figures, PSN TUCT00

Zeeman Relaxation of Cold Atomic Iron and Nickel in Collisions with 3He

We have measured the ratio of the diffusion cross-section to the angular momentum reorientation cross-section in the colliding Fe-3He and Ni-3He systems. Nickel (Ni) and iron (Fe) atoms are introduced via laser ablation into a cryogenically cooled experimental cell containing cold (< 1 K) 3He buffer gas. Elastic collisions rapidly cool the translational temperature of the ablated atoms to the helium temperature. The cross-section ratio is extracted by measuring the decays of the atomic Zeeman sublevels. For our experimental conditions, thermal energy is comparable to the Zeeman splitting. As a result, thermal excitations between Zeeman sublevels significantly impact the observed decay. To determine the cross-section ratio accurately, we introduce a model of Zeeman state dynamics that includes thermal excitations. We find the cross-section ratio for Ni-3He = 5 x 10^3 and Fe-3He <= 3 x 10^3 at 0.75 K in a 0.8 T magnetic field. These measurements are interpreted in the context of submerged shell suppression of spin relaxation as studied previously in transition metals and rare earth atoms.Comment: 10 pages, 5 figures; submitted to Phys. Rev.

Experienced tutors' deployment of thinking skills and what might be entailed in enhancing such skills

In the context of research that reports weaknesses in adults' critical thinking skills, the primary aim was to examine adults' use of critical thinking skills that are described in taxonomies and to identify areas for development. Position papers written by an opportunity sample of 32 experienced adult educators formed the data for a descriptive sample survey design intended to reveal participants' use of critical thinking skills. Each 6000-word paper was written during a development programme that supported such skills. A content analysis of the papers revealed that when participants drew on personal and published ideas about learning to derive their proposals for change, they accepted the ideas uncritically, thereby implying that they might find it difficult to help learners to examine ideas critically. The evidence supports research that implies that critical thinking skills are unlikely to develop unless overall course design privileges the development of epistemological understanding (King and Kitchener 1994, Kuhn 1999). A fundamental assumption underlying the study is that this understanding influences effective citizenship and personal development, as well as employability. A proposition that merits attention in future research is that the development of epistemological understanding is largely neglected in current curricula in formal post-16 education

Grid enabled data analysis on handheld devices

The requirement for information on portable, handheld devices demands the realization of increasingly complex applications for increasingly small and ubiquitous devices. This trend promotes the migration of technologies that were originally developed for desktop computers to handheld devices. With the onset of grid computing, users of handheld devices should be able to accomplish much more complex tasks, by accessing the processing and storage resources of the grid. This paper describes the development, features, and performance aspects of a grid enabled analysis environment designed for handheld devices. We also describe some differences in the technologies required to run these applications on desktop machines and handheld devices. In addition, we propose a prototype agent-based distributed architecture for carrying out high-speed analysis of physics data on handheld devices

Laterally driven interfaces in the three-dimensional Ising lattice gas

We study the steady state of a phase-separated driven Ising lattice gas in three dimensions using computer simulations with Kawasaki dynamics. An external force field F(z) acts in the x direction parallel to the interface, creating a lateral order parameter current j^x(z) which varies with distance z from the interface. Above the roughening temperature, our data for `shear-like' linear variation of F(z) are in agreement with the picture wherein shear acts as effective confinement in this system, thus supressing the interfacial capillary-wave fluctuations. We find sharper magnetisation profiles and reduced interfacial width as compared to equilibrium. Pair correlations are more suppressed in the vorticity direction y than in the driving direction; the opposite holds for the structure factor. Lateral transport of capillary waves occurs for those forms of F(z) for which the current j^x(z) is an odd function of z, for example the shear-like drive, and a `step-like' driving field. For a V-shaped driving force no such motion occurs, but capillary waves are suppressed more strongly than for the shear-like drive. These findings are in agreement with our previous simulation studies in two dimensions. Near and below the (equilibrium) roughening temperature the effective-confinement picture ceases to work, but the lateral motion of the interface persists.Comment: 20 pages, 11 figures, submitted to Phys. Rev.

Diffraction evidence for the structure of cellulose microfibrils in bamboo, a model for grass and cereal celluloses

Background: Cellulose from grasses and cereals makes up much of the potential raw material for biofuel production. It is not clear if cellulose microfibrils from grasses and cereals differ in structure from those of other plants. The structures of the highly oriented cellulose microfibrils in the cell walls of the internodes of the bamboo Pseudosasa amabilis are reported. Strong orientation facilitated the use of a range of scattering techniques. Results: Small-angle neutron scattering provided evidence of extensive aggregation by hydrogen bonding through the hydrophilic edges of the sheets of chains. The microfibrils had a mean centre-to-centre distance of 3.0 nm in the dry state, expanding on hydration. The expansion on hydration suggests that this distance between centres was through the hydrophilic faces of adjacent microfibrils. However in the other direction, perpendicular to the sheets of chains, the mean, disorder-corrected Scherrer dimension from wide-angle X-ray scattering was 3.8 nm. It is possible that this dimension is increased by twinning (crystallographic coalescence) of thinner microfibrils over part of their length, through the hydrophobic faces. The wide-angle scattering data also showed that the microfibrils had a relatively large intersheet d-spacing and small monoclinic angle, features normally considered characteristic of primary-wall cellulose. Conclusions: Bamboo microfibrils have features found in both primary-wall and secondary-wall cellulose, but are crystallographically coalescent to a greater extent than is common in celluloses from other plants. The extensive aggregation and local coalescence of the microfibrils are likely to have parallels in other grass and cereal species and to influence the accessibility of cellulose to degradative enzymes during conversion to liquid biofuel

Universality in phase boundary slopes for spin glasses on self dual lattices

We study the effects of disorder on the slope of the disorder--temperature phase boundary near the Onsager point (Tc = 2.269...) in spin-glass models. So far, studies have focused on marginal or irrelevant cases of disorder. Using duality arguments, as well as exact Pfaffian techniques we reproduce these analytical estimates. In addition, we obtain different estimates for spin-glass models on hierarchical lattices where the effects of disorder are relevant. We show that the phase-boundary slope near the Onsager point can be used to probe for the relevance of disorder effects.Comment: 8 pages, 6 figure

Ontogeny of synaptophysin and synaptoporin in the central nervous system

The expression of the synaptic vesicle antigens synaptophysin (SY) and synaptoporin (SO) was studied in the rat striatum, which contains a nearly homogeneous population of GABAergic neurons. In situ hybridization revealed high levels of SY transcripts in the striatal anlage from embryonic day (E) 14 until birth. In contrast. SO hybridization signals were low, and no immunoreactive cell bodies were detected at these stages of development. At E 14, SY-immunoreactivity was restricted to perikarya. In later prenatal stages of development SY-immunoreactivity appeared in puncta (identified as terminals containing immunostained synaptic vesicles), fibers, thick fiber bundles and ‘patches’. In postnatal and adult animals, perikarya of striatal neurons exhibited immunoreaction for SO; ultrastructurally SO antigen was found in the Golgi apparatus and in multivesicular bodies. SO-positive boutons were rare in the striatum. In the neuropil, numerous presynaptic terminals positive for SY were observed. Our data indicate that the expression of synaptic vesicle proteins in GABAergic neurons of the striatum is developmentally regulated. Whereas SY is prevalent during embryonic development, SO is the major synaptic vesicle antigen expressed postnatally by striatal neurons which project to the globus pallidus and the substantia nigra. In contrast synapses of striatal afferents (predominantly from cortex, thalamus and substantia nigra) contain SY