Bayesian Analysis of Inflation II: Model Selection and Constraints on Reheating

We discuss the model selection problem for inflationary cosmology. We couple ModeCode, a publicly-available numerical solver for the primordial perturbation spectra, to the nested sampler MultiNest, in order to efficiently compute Bayesian evidence. Particular attention is paid to the specification of physically realistic priors, including the parametrization of the post-inflationary expansion and associated thermalization scale. It is confirmed that while present-day data tightly constrains the properties of the power spectrum, it cannot usefully distinguish between the members of a large class of simple inflationary models. We also compute evidence using a simulated Planck likelihood, showing that while Planck will have more power than WMAP to discriminate between inflationary models, it will not definitively address the inflationary model selection problem on its own. However, Planck will place very tight constraints on any model with more than one observationally-distinct inflationary regime -- e.g. the large- and small-field limits of the hilltop inflation model -- and put useful limits on different reheating scenarios for a given model.Comment: ModeCode package available from http://zuserver2.star.ucl.ac.uk/~hiranya/ModeCode/ModeCode (requires CosmoMC and MultiNest); to be published in PRD. Typos fixe

Yersinia ruckeri isolates recovered from diseased Atlantic Salmon (Salmo salar) in Scotland are more diverse than those from Rainbow Trout (Oncorhynchus mykiss) and represent distinct subpopulations

Yersinia ruckeri is the etiological agent of enteric redmouth (ERM) disease of farmed salmonids. Enteric redmouth disease is traditionally associated with rainbow trout (Oncorhynchus mykiss, Walbaum), but its incidence in Atlantic salmon (Salmo salar) is increasing. Yersinia ruckeri isolates recovered from diseased Atlantic salmon have been poorly characterized, and very little is known about the relationship of the isolates associated with these two species. Phenotypic approaches were used to characterize 109 Y. ruckeri isolates recovered over a 14-year period from infected Atlantic salmon in Scotland; 26 isolates from infected rainbow trout were also characterized. Biotyping, serotyping, and comparison of outer membrane protein profiles identified 19 Y. ruckeri clones associated with Atlantic salmon but only five associated with rainbow trout; none of the Atlantic salmon clones occurred in rainbow trout and vice versa. These findings suggest that distinct subpopulations of Y. ruckeri are associated with each species. A new O serotype (designated O8) was identified in 56 biotype 1 Atlantic salmon isolates and was the most common serotype identified from 2006 to 2011 and in 2014, suggesting an increased prevalence during the time period sampled. Rainbow trout isolates were represented almost exclusively by the same biotype 2, serotype O1 clone that has been responsible for the majority of ERM outbreaks in this species within the United Kingdom since the 1980s. However, the identification of two biotype 2, serotype O8 isolates in rainbow trout suggests that vaccines containing serotypes O1 and O8 should be evaluated in both rainbow trout and Atlantic salmon for application in Scotland

Tidal Evolution of a Secularly Interacting Planetary System

In a multi-planet system, a gradual change in one planet's semi-major axis will affect the eccentricities of all the planets, as angular momentum is distributed via secular interactions. If tidal dissipation in the planet is the cause of the change in semi-major axis, it also damps that planet's eccentricity, which in turn also contributes to the evolution of all the eccentricities. Formulae quantifying the combined effects on the whole system due to semi-major axis changes, as well as eccentricity damping, are derived here for a two-planet system. The CoRoT 7 system is considered as an example.Comment: Accepted for publication in the Astrophysical Journal, 17 pages, including 1 figur

Bayesian Analysis of Inflation III: Slow Roll Reconstruction Using Model Selection

We implement Slow Roll Reconstruction -- an optimal solution to the inverse problem for inflationary cosmology -- within ModeCode, a publicly available solver for the inflationary dynamics. We obtain up-to-date constraints on the reconstructed inflationary potential, derived from the WMAP 7-year dataset and South Pole Telescope observations, combined with large scale structure data derived from SDSS Data Release 7. Using ModeCode in conjunction with the MultiNest sampler, we compute Bayesian evidence for the reconstructed potential at each order in the truncated slow roll hierarchy. We find that the data are well-described by the first two slow roll parameters, \epsilon and \eta, and that there is no need to include a nontrivial \xi parameter.Comment: 14 pages, 12 figures, minor changes; final version; accepted in PR

Tidal Evolution of Close-in Extra-Solar Planets

The distribution of eccentricities e of extra-solar planets with semi-major axes a > 0.2 AU is very uniform, and values for e are relatively large, averaging 0.3 and broadly distributed up to near 1. For a < 0.2 AU, eccentricities are much smaller (most e < 0.2), a characteristic widely attributed to damping by tides after the planets formed and the protoplanetary gas disk dissipated. Most previous estimates of the tidal damping considered the tides raised on the planets, but ignored the tides raised on the stars. Most also assumed specific values for the planets' poorly constrained tidal dissipation parameter Qp. Perhaps most important, in many studies, the strongly coupled evolution between e and a was ignored. We have now integrated the coupled tidal evolution equations for e and a over the estimated age of each planet, and confirmed that the distribution of initial e values of close-in planets matches that of the general population for reasonable Q values, with the best fits for stellar and planetary Q being ~10^5.5 and ~10^6.5, respectively. The accompanying evolution of a values shows most close-in planets had significantly larger a at the start of tidal migration. The earlier gas disk migration did not bring all planets to their current orbits. The current small values of a were only reached gradually due to tides over the lifetimes of the planets. These results may have important implications for planet formation models, atmospheric models of "hot Jupiters", and the success of transit surveys.Comment: accepted to Ap

Time from diagnosis to surgery and prostate cancer survival: a retrospective cohort study

Background: A diagnosis of prostate cancer leads to emotional distress and anxiety, prompting calls for rapid diagnostic pathways. Nevertheless, it remains unclear what impact time between diagnosis and surgery has upon prostate cancer survival. Methods: Using national databases for England (cancer registries, Hospital Episode Statistics and Office of National Statistics), we identified 17,043 men with prostate cancer, aged 15 years and older, diagnosed in 1996–2009, and who had surgical resection with curative intent within 6 months of diagnosis. We used relative survival to investigate associations between waiting times and five- and ten-year survival. Results: Five- and ten-year relative survival estimates for the total study sample were 1.04 (95% CI: 1.04 to 1.05) and 1.08 (95% CI: 1.06-1.09), respectively. There were no notable differences in survival between patients who had surgery at 0–3 and 4–6 months after diagnosis. Relative survival was higher among the elderly (>65) and those with well and moderately differentiated tumours. Conclusion: The high relative survival in our cohort probably reflects adherence to selection criteria for surgery among men with localised prostate cancer. Among men treated with surgery within 6 months of diagnosis, we found little evidence of an association between time from diagnosis to surgery and survival.6 page(s

Megasatellites: a peculiar class of giant minisatellites in genes involved in cell adhesion and pathogenicity in Candida glabrata

Minisatellites are DNA tandem repeats that are found in all sequenced genomes. In the yeast Saccharomyces cerevisiae, they are frequently encountered in genes encoding cell wall proteins. Minisatellites present in the completely sequenced genome of the pathogenic yeast Candida glabrata were similarly analyzed, and two new types of minisatellites were discovered: minisatellites that are composed of two different intermingled repeats (called compound minisatellites), and minisatellites containing unusually long repeated motifs (126–429 bp). These long repeat minisatellites may reach unusual length for such elements (up to 10 kb). Due to these peculiar properties, they have been named ‘megasatellites’. They are found essentially in genes involved in cell–cell adhesion, and could therefore be involved in the ability of this opportunistic pathogen to colonize the human host. In addition to megasatellites, found in large paralogous gene families, there are 93 minisatellites with simple shorter motifs, comparable to those found in S. cerevisiae. Most of the time, these minisatellites are not conserved between C. glabrata and S. cerevisiae, although their host genes are well conserved, raising the question of an active mechanism creating minisatellites de novo in hemiascomycetes

Through a Glass, Darkly:The CIA and Oral History

This article broaches the thorny issue of how we may study the history of the CIA by utilizing oral history interviews. This article argues that while oral history interviews impose particular demands upon the researcher, they are particularly pronounced in relation to studying the history of intelligence services. This article, nevertheless, also argues that while intelligence history and oral history each harbour their own epistemological perils and biases, pitfalls which may in fact be pronounced when they are conjoined, the relationship between them may nevertheless be a productive one. Indeed, each field may enrich the other provided we have thought carefully about the linkages between them: this article's point of departure. The first part of this article outlines some of the problems encountered in studying the CIA by relating them to the author's own work. This involved researching the CIA's role in US foreign policy towards Afghanistan since a landmark year in the history of the late Cold War, 1979 (i.e. the year the Soviet Union invaded that country). The second part of this article then considers some of the issues historians must confront when applying oral history to the study of the CIA. To bring this within the sphere of cognition of the reader the author recounts some of his own experiences interviewing CIA officers in and around Washington DC. The third part then looks at some of the contributions oral history in particular can make towards a better understanding of the history of intelligence services and the CIA