Nested sampling for Potts models

Nested sampling is a new Monte Carlo method by Skilling [1] intended for general Bayesian computation. Nested sampling provides a robust alternative to annealing-based methods for computing normalizing constants. It can also generate estimates of other quantities such as posterior expectations. The key technical requirement is an ability to draw samples uniformly from the prior subject to a constraint on the likelihood. We provide a demonstration with the Potts model, an undirected graphical model

Kramers-Kronig, Bode, and the meaning of zero

The implications of causality, as captured by the Kramers-Kronig relations between the real and imaginary parts of a linear response function, are familiar parts of the physics curriculum. In 1937, Bode derived a similar relation between the magnitude (response gain) and phase. Although the Kramers-Kronig relations are an equality, Bode's relation is effectively an inequality. This perhaps-surprising difference is explained using elementary examples and ultimately traces back to delays in the flow of information within the system formed by the physical object and measurement apparatus.Comment: 8 pages; American Journal of Physics, to appea

Conformal dimension and random groups

We give a lower and an upper bound for the conformal dimension of the boundaries of certain small cancellation groups. We apply these bounds to the few relator and density models for random groups. This gives generic bounds of the following form, where $l$ is the relator length, going to infinity. (a) 1 + 1/C < \Cdim(\bdry G) < C l / \log(l), for the few relator model, and (b) 1 + l / (C\log(l)) < \Cdim(\bdry G) < C l, for the density model, at densities $d < 1/16$. In particular, for the density model at densities $d < 1/16$, as the relator length $l$ goes to infinity, the random groups will pass through infinitely many different quasi-isometry classes.Comment: 32 pages, 4 figures. v2: Final version. Main result improved to density < 1/16. Many minor improvements. To appear in GAF

The preparation and characterisation of monomeric and linked metal carbonyl clusters containing the closo-Si2Co4 pseudo-octahedral core

PhSiH3 reacts with [Co₄(CO)₁₂] at 50 °C in hydrocarbon solvents to give [(µ₄-SiPh)₂Co₄(CO)₁₁], 2c, shown by an X-ray crystal structure determination to have a pseudo-octahedral Si₂Co₄ core. Substituted aryl-silanes behaved similarly. Mixtures of PhSiH₃, H₃SiC₆H₄SiH₃ and [Co₄(CO)₁₂] in a ca. 2 1 2 ratio gave the dimeric cluster [{Co₄(µ₄-SiPh)(CO)₁₁Si}₂C₆H₄], 3a, which has the two Si₂Co₄ cores linked by a C₆H₄ group to give a rigid molecule which an X-ray structure analysis shows to be over 23 Å long. Related dimers linked by –(CH₂)₈– groups were isolated from mixtures of PhSiH₃, α ,ω-(H₃Si)₂(CH₂)₈ and [Co₄(CO)₁₂]. Electrochemical studies show the two cluster units in 3a do not interact electronically

Estimation of the specificity of an antibody ELISA for paratuberculosis generated from a sector of the UK cattle population using results from a paratuberculosis control programme

In the United Kingdom (UK) a voluntary programme to control paratuberculosis in cattle based on herd management and serological screening has been operating since 1998. The programme assigns a risk level to each participating herd according to the within herd seroprevalence and the confirmation of the presence of infection with Mycobacterium avium subspecies paratuberculosis (MAP) by faecal culture or polymerase chain reaction (PCR). From the outset a general concern over the specificity of the paratuberculosis antibody enzyme-linked immunosorbent assay (ELISA) resulted in the use of a faecal screen for the causal organism to negate or confirm infection in individual seropositive animals. Progress in improving the diagnostic tests has been gradual throughout the life of the programme and the under-pinning approach to using tests to determine the risk of paratuberculosis for a herd required to be re-examined. This study used a large data set of more than 143,000 test results over five years from the lowest paratuberculosis risk level category of herds to estimate the specificity of a commercially available paratuberculosis antibody ELISA for cattle. In each year of the study the estimated specificity reached or exceeded 0.998. We also examined the apparent impact that annual or more frequent application of the single intradermal comparative cervical tuberculin (SICCT) test for tuberculosis (TB), using purified protein derivatives of Mycobacterium bovis and Mycobacterium avium subspecies avium, had on specificity of the antibody ELISA for paratuberculosis. We found a statistically significant difference in three of the five years with herds that were officially tuberculosis free and not subject to frequent SICCT testing. This difference was small and considered to be of little practical importance for the paratuberculosis assurance programme. We concluded that, in the UK the mandatory TB surveillance programme of cattle herds is not a limiting factor in the use of serological testing to support herd-level assurance schemes for paratuberculosis. Furthermore, in paratuberculosis, where shedding of MAP is intermittent and the sensitivity of the commercially available PCR tests for detection MAP is highly variable, faecal screening of seropositive animals is an unreliable method for negating infection in seropositive cattle

The Behaviour of Crude Oil Spilled on Snow

Field and laboratory studies of the behavior of isothermal and hot oil spills on snow are described. Alberta crude oil spilled at 0&deg; C is readily absorbed by snow and contaminates an area of about 0.01 square metres per litre. A hot oil spill melts a channel in the snow and flows along the ground under the snow contaminating an area of about 0.024 square metres per litre. There may be considerable spreading of the oil during thaw. The flow regimes by which oil permeates into snow and the clean-up implications are discussed

A detailed binding free energy study of 2 : 1 ligand–DNA complex formation by experiment and simulation

In 2004, we used NMR to solve the structure of the minor groove binder thiazotropsin A bound in a 2 : 1 complex to the DNA duplex, d(CGACTAGTCG)2. In this current work, we have combined theory and experiment to confirm the binding thermodynamics of this system. Molecular dynamics simulations that use polarizable or non-polarizable force fields with single and separate trajectory approaches have been used to explore complexation at the molecular level. We have shown that the binding process invokes large conformational changes in both the receptor and ligand, which is reflected by large adaptation energies. This is compensated for by the net binding free energy, which is enthalpy driven and entropically opposed. Such a conformational change upon binding directly impacts on how the process must be simulated in order to yield accurate results. Our MM-PBSA binding calculations from snapshots obtained from MD simulations of the polarizable force field using separate trajectories yield an absolute binding free energy (-15.4 kcal mol-1) very close to that determined by isothermal titration calorimetry (-10.2 kcal mol-1). Analysis of the major energy components reveals that favorable non-bonded van der Waals and electrostatic interactions contribute predominantly to the enthalpy term, whilst the unfavorable entropy appears to be driven by stabilization of the complex and the associated loss of conformational freedom. Our results have led to a deeper understanding of the nature of side-by-side minor groove ligand binding, which has significant implications for structure-based ligand development

Insect herbivory (Choristoneura fumiferana, Tortricidea) underlies tree population structure (Picea glauca, Pinaceae)

Variation in insect herbivory can lead to population structure in plant hosts as indicated by defence traits. In annual herbaceous, defence traits may vary between geographic areas but evidence of such patterns is lacking for long-lived species. This may result from the variety of selection pressures from herbivores, long distance gene flow, genome properties, and lack of research. We investigated the antagonistic interaction between white spruce (Picea glauca) and spruce budworm (SBW, Choristoneura fumiferana) the most devastating forest insect of eastern North America in common garden experiments. White spruces that are able to resist SBW attack were reported to accumulate the acetophenones piceol and pungenol constitutively in their foliage. We show that levels of these acetophenones and transcripts of the gene responsible for their release is highly heritable and that their accumulation is synchronized with the most devastating stage of SBW. Piceol and pungenol concentrations negatively correlate with rate of development in female SBW and follow a non-random geographic variation pattern that is partially explained by historical damage from SBW and temperature. Our results show that accumulation of acetophenones is an efficient resistance mechanism against SBW in white spruce and that insects can affect population structure of a long-lived plant

ForestTreeDB: a database dedicated to the mining of tree transcriptomes

ForestTreeDB is intended as a resource that centralizes large-scale expressed sequence tag (EST) sequencing results from several tree species (). It currently encompasses 344 878 quality sequences from 68 libraries, from diverse organs of conifer and hybrid poplar trees. It utilizes the Nimbus data model to provide a hosting system for multiple projects, and uses object-relational mapping APIs in Java and Perl for data accesses within an Oracle database designed to be scalable, maintainable and extendable. Transcriptome builds or unigene sets occupy the focal point of the system. Several of the five current species-specific unigenes were used to design microarrays and SNP resources. The ForestTreeDB web application provides the means for multiple combination database queries. It presents the user with a list of discrete queries to retrieve and download large EST datasets or sequences from precompiled unigene assemblies. Functional annotation assignment is not trivial in conifers which are distantly related to angiosperm model plants. Optimal annotations are achieved through database queries that integrate results from several procedures based open-source tools. ForestTreeDB aims to facilitate sequence mining of coherent annotations in multiple species to support comparative genomic approaches. We plan to continuously enrich ForestTreeDB with other resources through collaborations with other genomic projects