Low Dirac Eigenmodes and the Topological and Chiral Structure of the QCD Vacuum

Several lattice calculations which probe the chiral and topological structure of QCD are discussed. The results focus attention on the low-lying eigenmodes of the Dirac operator in typical gauge field configurations.Comment: Talk presented at the DPF2000 Conferenc

Smoothed Particle Hydrodynamics in cosmology: a comparative study of implementations

We analyse the performance of twelve different implementations of Smoothed Particle Hydrodynamics (SPH) using seven tests designed to isolate key hydrodynamic elements of cosmological simulations which are known to cause the SPH algorithm problems. In order, we consider a shock tube, spherical adiabatic collapse, cooling flow model, drag, a cosmological simulation, rotating cloud-collapse and disc stability. In the implementations special attention is given to the way in which force symmetry is enforced in the equations of motion. We study in detail how the hydrodynamics are affected by different implementations of the artificial viscosity including those with a shear-correction modification. We present an improved first-order smoothing-length update algorithm that is designed to remove instabilities that are present in the Hernquist and Katz (1989) algorithm. For all tests we find that the artificial viscosity is the most important factor distinguishing the results from the various implementations. The second most important factor is the way force symmetry is achieved in the equation of motion. Most results favour a kernel symmetrization approach. The exact method by which SPH pressure forces are included has comparatively little effect on the results. Combining the equation of motion presented in Thomas and Couchman (1992) with a modification of the Monaghan and Gingold (1983) artificial viscosity leads to an SPH scheme that is both fast and reliable.Comment: 30 pages, 26 figures and 9 tables included. Submitted to MNRAS. Postscript version available at ftp://phobos.astro.uwo.ca/pub/etittley/papers/sphtest.ps.g

The kunitz domain protein BLI-5 plays a functionally conserved role in cuticle formation in a diverse range of nematodes

The cuticle of parasitic nematodes performs many critical functions and is essential for proper development and for protection from the host immune response. The biosynthesis, assembly, modification and turnover of this exoskeleton have been most extensively studied in the free-living nematode, Caenorhabditis elegans, where it represents a complex multi-step process involving a whole suite of enzymes. The biosynthesis of the cuticle has an additional level of complexity, as many of the enzymes also require additional proteins to aid their activation and selective inhibition. Blister-5 (BLI-5) represents a protein with a kunitz-type serine protease interacting domain and is involved in cuticle collagen biosynthesis in C. elegans, through its interaction with subtilisin-like processing enzymes (such as BLI-4). Mutation of the bli-5 gene causes blistering of the collagenous adult cuticle. Homologues of BLI-5 have been identified in several parasitic species that span different nematode clades. In this study, we molecularly and biochemically characterize BLI-5 homologues from the clade V nematodes C. elegans and Haemonchus contortus and from the clade III filarial nematode Brugia malayi. The nematode BLI-5 orthologues possess a shared domain structure and perform similar in vitro and in vivo functions, performing important proteolytic enzyme functions. The results demonstrate that the bli-5 genes from these diverse parasitic nematodes are able to complement a C. elegansbli-5 mutant and thereby support the use of the C. elegans model system to examine gene function in the experimentally less-amenable parasitic species

Star Formation, Supernovae Feedback and the Angular Momentum Problem in Numerical CDM Cosmogony: Half Way There?

We present a smoothed particle hydrodynamic (SPH) simulation that reproduces a galaxy that is a moderate facsimile of those observed. The primary failing point of previous simulations of disk formation, namely excessive transport of angular momentum from gas to dark matter, is ameliorated by the inclusion of a supernova feedback algorithm that allows energy to persist in the model ISM for a period corresponding to the lifetime of stellar associations. The inclusion of feedback leads to a disk at a redshift $z=0.52$, with a specific angular momentum content within 10% of the value required to fit observations. An exponential fit to the disk baryon surface density gives a scale length within 17% of the theoretical value. Runs without feedback, with or without star formation, exhibit the drastic angular momentum transport observed elsewhere.Comment: 4 pages, 3 figures, accepted for publication in ApJ Letter

A New Method for the High-Precision Assessment of Tumor Changes in Response to Treatment

Imaging demonstrates that preclinical and human tumors are heterogeneous, i.e. a single tumor can exhibit multiple regions that behave differently during both normal development and also in response to treatment. The large variations observed in control group tumors can obscure detection of significant therapeutic effects due to the ambiguity in attributing causes of change. This can hinder development of effective therapies due to limitations in experimental design, rather than due to therapeutic failure. An improved method to model biological variation and heterogeneity in imaging signals is described. Specifically, Linear Poisson modelling (LPM) evaluates changes in apparent diffusion co-efficient (ADC) before and 72 hours after radiotherapy, in two xenograft models of colorectal cancer. The statistical significance of measured changes are compared to those attainable using a conventional t-test analysis on basic ADC distribution parameters. When LPMs were applied to treated tumors, the LPMs detected highly significant changes. The analyses were significant for all tumors, equating to a gain in power of 4 fold (i.e. equivelent to having a sample size 16 times larger), compared with the conventional approach. In contrast, highly significant changes are only detected at a cohort level using t-tests, restricting their potential use within personalised medicine and increasing the number of animals required during testing. Furthermore, LPM enabled the relative volumes of responding and non-responding tissue to be estimated for each xenograft model. Leave-one-out analysis of the treated xenografts provided quality control and identified potential outliers, raising confidence in LPM data at clinically relevant sample sizes