Spontaneous Symmetry Breaking and the Renormalization of the Chern-Simons Term

We calculate the one-loop perturbative correction to the coefficient of the \cs term in non-abelian gauge theory in the presence of Higgs fields, with a variety of symmetry-breaking structures. In the case of a residual $U(1)$ symmetry, radiative corrections do not change the coefficient of the \cs term. In the case of an unbroken non-abelian subgroup, the coefficient of the relevant \cs term (suitably normalized) attains an integral correction, as required for consistency of the quantum theory. Interestingly, this coefficient arises purely from the unbroken non-abelian sector in question; the orthogonal sector makes no contribution. This implies that the coefficient of the \cs term is a discontinuous function over the phase diagram of the theory.Comment: Version to be published in Phys Lett B., minor additional change

Hierarchical modelling of temperature and habitat size effects on population dynamics of North Atlantic cod

Understanding how temperature affects cod (Gadus morhua) ecology is important for forecasting how populations will develop as climate changes in future. The effects of spawning-season temperature and habitat size on cod recruitment dynamics have been investigated across the North Atlantic. Ricker and Beverton and Holt stock–recruitment (SR) models were extended by applying hierarchical methods, mixed-effects models, and Bayesian inference to incorporate the influence of these ecosystem factors on model parameters representing cod maximum reproductive rate and carrying capacity. We identified the pattern of temperature effects on cod productivity at the species level and estimated SR model parameters with increased precision. Temperature impacts vary geographically, being positive in areas where temperatures are <5°C, and negative for higher temperatures. Using the relationship derived, it is possible to predict expected changes in population-specific reproductive rates and carrying capacities resulting from temperature increases. Further, carrying capacity covaries with available habitat size, explaining at least half its variability across stocks. These patterns improve our understanding of environmental impacts on key population parameters, which is required for an ecosystem approach to cod management, particularly under ocean-warming scenarios. Key words: carrying capacity , cod , hierarchical models , North Atlantic , temperature , uncertaint

Phase transitions in a gas of anyons

We continue our numerical Monte Carlo simulation of a gas of closed loops on a 3 dimensional lattice, however now in the presence of a topological term added to the action corresponding to the total linking number between the loops. We compute the linking number using certain notions from knot theory. Adding the topological term converts the particles into anyons. Using the correspondence that the model is an effective theory that describes the 2+1-dimensional Abelian Higgs model in the asymptotic strong coupling regime, the topological linking number simply corresponds to the addition to the action of the Chern-Simons term. We find the following new results. The system continues to exhibit a phase transition as a function of the anyon mass as it becomes small \cite{mnp}, although the phases do not change the manifestation of the symmetry. The Chern-Simons term has no effect on the Wilson loop, but it does affect the {\rm '}t Hooft loop. For a given configuration it adds the linking number of the 't Hooft loop with all of the dynamical vortex loops to the action. We find that both the Wilson loop and the 't Hooft loop exhibit a perimeter law even though there are no massless particles in the theory, which is unexpected.Comment: 6 pages, 5 figure

Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc

Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves

Maxwell-Chern-Simons Q-balls

We examine the energetics of $Q$-balls in Maxwell-Chern-Simons theory in two space dimensions. Whereas gauged $Q$-balls are unallowed in this dimension in the absence of a Chern-Simons term due to a divergent electromagnetic energy, the addition of a Chern-Simons term introduces a gauge field mass and renders finite the otherwise-divergent electromagnetic energy of the $Q$-ball. Similar to the case of gauged $Q$-balls, Maxwell-Chern-Simons $Q$-balls have a maximal charge. The properties of these solitons are studied as a function of the parameters of the model considered, using a numerical technique known as relaxation. The results are compared to expectations based on qualitative arguments.Comment: 6 pages. Talk given at Theory CANADA 2, Perimeter Institut

Field theoretic description of the abelian and non-abelian Josephson effect

We formulate the Josephson effect in a field theoretic language which affords a straightforward generalization to the non-abelian case. Our formalism interprets Josephson tunneling as the excitation of pseudo-Goldstone bosons. We demonstrate the formalism through the consideration of a single junction separating two regions with a purely non-abelian order parameter and a sandwich of three regions where the central region is in a distinct phase. Applications to various non-abelian symmetry breaking systems in particle and condensed matter physics are given.Comment: 10 pages no figure

DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas)

<p>Abstract</p> <p>Background</p> <p>DNA methylation is an epigenetic mechanism with important regulatory functions in animals. While the mechanism itself is evolutionarily ancient, the distribution and function of DNA methylation is diverse both within and among phylogenetic groups. Although DNA methylation has been well studied in mammals, there are limited data on invertebrates, particularly molluscs. Here we characterize the distribution and investigate potential functions of DNA methylation in the Pacific oyster (<it>Crassostrea gigas</it>).</p> <p>Results</p> <p>Methylation sensitive PCR and bisulfite sequencing PCR approaches were used to identify CpG methylation in <it>C. gigas </it>genes and demonstrated that this species possesses intragenic methylation. <it>In silico </it>analysis of CpGo/e ratios in publicly available sequence data suggests that DNA methylation is a common feature of the <it>C. gigas </it>genome, and that specific functional categories of genes have significantly different levels of methylation.</p> <p>Conclusions</p> <p>The Pacific oyster genome displays intragenic DNA methylation and contains genes necessary for DNA methylation in animals. Results of this investigation suggest that DNA methylation has regulatory functions in <it>Crassostrea gigas</it>, particularly in gene families that have inducible expression, including those involved in stress and environmental responses.</p

Problems With Complex Actions

We consider Euclidean functional integrals involving actions which are not exclusively real. This situation arises, for example, when there are $t$-odd terms in the the Minkowski action. Writing the action in terms of only real fields (which is always possible), such terms appear as explicitly imaginary terms in the Euclidean action. The usual quanization procedure which involves finding the critical points of the action and then quantizing the spectrum of fluctuations about these critical points fails. In the case of complex actions, there do not exist, in general, any critical points of the action on the space of real fields, the critical points are in general complex. The proper definition of the function integral then requires the analytic continuation of the functional integration into the space of complex fields so as to pass through the complex critical points according to the method of steepest descent. We show a simple example where this procedure can be carried out explicitly. The procedure of finding the critical points of the real part of the action and quantizing the corresponding fluctuations, treating the (exponential of the) complex part of the action as a bounded integrable function is shown to fail in our explicit example, at least perturbatively.Comment: 6+epsilon pages, no figures, presented at Theory CANADA

Should tobacco and alcohol companies be allowed to influence Australia's National Drug Strategy?

Formation of Australia's National Drug Strategy (NDS) included an extensive consultation process that was open not only to community and public health stakeholders, but also to representatives of the tobacco and alcohol industries. Australia is bound by the World Health Organization Framework Convention on Tobacco Control, which requires governments to protect tobacco control measures from interference by the tobacco industry. NDS consultation submissions made by these conflicted industries are not publicly available for scrutiny. The NDS goals are at odds with the commercial agenda of industries that support regulatory stagnation, oppose and undermine effective action, ignore and distort evidence, and prioritise profits over health