Performance of an environmental test to detect Mycobacterium bovis infection in badger social groups

A study by Courtenay and others (2006) demonstrated that the probability of detecting Mycobacterium bovis by PCR in soil samples from the spoil heaps of main badger setts correlated with the prevalence of excretion (infectiousness) of captured badgers belonging to the social group. It has been proposed that such a test could be used to target badger culling to setts containing infectious animals (Anon 2007). This short communication discusses the issues surrounding this concept, with the intention of dispelling any misconceptions among relevant stakeholders (farmers, policy makers and conservationists)

Quantised Vortices in an Exciton-Polariton Fluid

One of the most striking quantum effects in a low temperature interacting Bose gas is superfluidity. First observed in liquid 4He, this phenomenon has been intensively studied in a variety of systems for its amazing features such as the persistence of superflows and the quantization of the angular momentum of vortices. The achievement of Bose-Einstein condensation (BEC) in dilute atomic gases provided an exceptional opportunity to observe and study superfluidity in an extremely clean and controlled environment. In the solid state, Bose-Einstein condensation of exciton polaritons has now been reported several times. Polaritons are strongly interacting light-matter quasi-particles, naturally occurring in semiconductor microcavities in the strong coupling regime and constitute a very interesting example of composite bosons. Even though pioneering experiments have recently addressed the propagation of a fluid of coherent polaritons, still no conclusive evidence is yet available of its superfluid nature. In the present Letter, we report the observation of spontaneous formation of pinned quantised vortices in the Bose-condensed phase of a polariton fluid by means of phase and amplitude imaging. Theoretical insight into the possible origin of such vortices is presented in terms of a generalised Gross-Pitaevskii equation. The implications of our observations concerning the superfluid nature of the non-equilibrium polariton fluid are finally discussed.Comment: 14 pages, 4 figure

Intimate Partner Violence and Abuse Against Men: Voices of Victimization Among Ex-Servicemen of the British Armed Forces

This study presents the personal testimonies of male British ex-Armed Forces personnel who have experienced violence and abuse victimization that was perpetrated by civilian female partners. In this research, we argue that to embark upon any understanding of the domestic lives of military personnel, an appreciation of the linkages to the cultural context of the military institution is necessary. Understanding the influence of the military institution beyond the military domain is crucial. We unveil the nature and character of the violence and abuse and how the servicemen negotiated their relationships. In doing so, we highlight the embodiment of military discipline, skills, and tactics in the home—not ones of violence which may be routinely linked to military masculinities; rather ones of restraint, tolerance, stoicism, and the reduction of a threat to inconsequential individual significance

Josephson dynamics for coupled polariton modes under the atom-field interaction in the cavity

We consider a new approach to the problem of Bose-Einstein condensation (BEC) of polaritons for atom-field interaction under the strong coupling regime in the cavity. We investigate the dynamics of two macroscopically populated polariton modes corresponding to the upper and lower branch energy states coupled via Kerr-like nonlinearity of atomic medium. We found out the dispersion relations for new type of collective excitations in the system under consideration. Various temporal regimes like linear (nonlinear) Josephson transition and/or Rabi oscillations, macroscopic quantum self-trapping (MQST) dynamics for population imbalance of polariton modes are predicted. We also examine the switching properties for time-averaged population imbalance depending on initial conditions, effective nonlinear parameter of atomic medium and kinetic energy of low-branch polaritons.Comment: 10 pages, 6 postscript figures, uses svjour.cl

Stops making sense: translational trade-offs and stop codon reassignment

Background Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature. Results In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences. Conclusions We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants

Disorder Effects on Exciton-Polariton Condensates

The impact of a random disorder potential on the dynamical properties of Bose Einstein condensates is a very wide research field. In microcavities, these studies are even more crucial than in the condensates of cold atoms, since random disorder is naturally present in the semiconductor structures. In this chapter, we consider a stable condensate, defined by a chemical potential, propagating in a random disorder potential, like a liquid flowing through a capillary. We analyze the interplay between the kinetic energy, the localization energy, and the interaction between particles in 1D and 2D polariton condensates. The finite life time of polaritons is taken into account as well. In the first part, we remind the results of [G. Malpuech et al. Phys. Rev. Lett. 98, 206402 (2007).] where we considered the case of a static condensate. In that case, the condensate forms either a glassy insulating phase at low polariton density (strong localization), or a superfluid phase above the percolation threshold. We also show the calculation of the first order spatial coherence of the condensate versus the condensate density. In the second part, we consider the case of a propagating non-interacting condensate which is always localized because of Anderson localization. The localization length is calculated in the Born approximation. The impact of the finite polariton life time is taken into account as well. In the last section we consider the case of a propagating interacting condensate where the three regimes of strong localization, Anderson localization, and superfluid behavior are accessible. The localization length is calculated versus the system parameters. The localization length is strongly modified with respect to the non-interacting case. It is infinite in the superfluid regime whereas it is strongly reduced if the fluid flows with a supersonic velocity.Comment: chapter for a book "Exciton Polaritons in Microcavities: New Frontiers" by Springer (2012), the original publication is available at http://www.springerlink.co

Progressive and biased divergent evolution underpins the origin and diversification of peridinin dinoflagellate plastids

Dinoflagellates are algae of tremendous importance to ecosystems and to public health. The cell biology and genome organization of dinoflagellate species is highly unusual. For example, the plastid genomes of peridinin-containing dinoflagellates encode only a minimal number of genes arranged on small elements termed "minicircles". Previous studies of peridinin plastid genes have found evidence for divergent sequence evolution, including extensive substitutions, novel insertions and deletions, and use of alternative translation initiation codons. Understanding the extent of this divergent evolution has been hampered by the lack of characterized peridinin plastid sequences. We have identified over 300 previously unannotated peridinin plastid mRNAs from published transcriptome projects, vastly increasing the number of sequences available. Using these data, we have produced a well-resolved phylogeny of peridinin plastid lineages, which uncovers several novel relationships within the dinoflagellates. This enables us to define changes to plastid sequences that occurred early in dinoflagellate evolution, and that have contributed to the subsequent diversification of individual dinoflagellate clades. We find that the origin of the peridinin dinoflagellates was specifically accompanied by elevations both in the overall number of substitutions that occurred on plastid sequences, and in the Ka/Ks ratio associated with plastid sequences, consistent with changes in selective pressure. These substitutions, alongside other changes, have accumulated progressively in individual peridinin plastid lineages. Throughout our entire dataset, we identify a persistent bias toward non-synonymous substitutions occurring on sequences encoding photosystem I subunits and stromal regions of peridinin plastid proteins, which may have underpinned the evolution of this unusual organelle.Wellcome Trus

Enhanced Identification of Postoperative Infections among Outpatients

Claims data complement other data sources for identification of surgical site infections following breast surgery and cesarean section

Nonaminoglycoside compounds induce readthrough of nonsense mutations

Large numbers of genetic disorders are caused by nonsense mutations for which compound-induced readthrough of premature termination codons (PTCs) might be exploited as a potential treatment strategy. We have successfully developed a sensitive and quantitative high-throughput screening (HTS) assay, protein transcription/translation (PTT)–enzyme-linked immunosorbent assay (ELISA), for identifying novel PTC-readthrough compounds using ataxia-telangiectasia (A-T) as a genetic disease model. This HTS PTT-ELISA assay is based on a coupled PTT that uses plasmid templates containing prototypic A-T mutated (ATM) mutations for HTS. The assay is luciferase independent. We screened ∼34,000 compounds and identified 12 low-molecular-mass nonaminoglycosides with potential PTC-readthrough activity. From these, two leading compounds consistently induced functional ATM protein in ATM-deficient cells containing disease-causing nonsense mutations, as demonstrated by direct measurement of ATM protein, restored ATM kinase activity, and colony survival assays for cellular radiosensitivity. The two compounds also demonstrated readthrough activity in mdx mouse myotube cells carrying a nonsense mutation and induced significant amounts of dystrophin protein

Developing a framework for public involvement in mathematical and economic modelling : bringing new dynamism to vaccination policy recommendations

Objectives The Mathematical and Economic Modelling for Vaccination and Immunisation Evaluation (MEMVIE) programme aimed to explore, capture and support the potential contribution of the public to mathematical and economic modelling, in order to identify the values that underpin public involvement (PI) in modelling and co-produce a framework that identifies the nature and type of PI in modelling and supports its implementation. Methods We established a PI Reference Group, who worked collaboratively with the academic contributors to create a deliberative knowledge space, which valued different forms of knowledge, expertise and evidence. Together, we explored the key steps of mathematical and economic methods in 21 meetings during 2015–2020. These deliberations generated rich discussion, through which we identified potential points of public contribution and the values that underpin PI in modelling. We iteratively developed a framework to guide future practice of PI in modelling. Results We present the MEMVIE Public Involvement Framework in two forms: a short form to summarise key elements, and a long form framework to provide a detailed description of each potential type of public contribution at each stage of the modelling process. At a macro level, the public can contribute to reviewing context, reviewing relevance, assessing data and justifying model choice, troubleshooting, and interpreting and reviewing outcomes and decision making. The underpinning values that drive involvement include the public contributing to the validity of the model, potentially enhancing its relevance, utility and transparency through diverse inputs, and enhancing the credibility, consistency and continuous development through scrutiny, in addition to contextualising the model within a wider societal view. Discussion and Conclusion PI in modelling is in its infancy. The MEMVIE Framework is the first attempt to identify potential points of collaborative public contribution to modelling, but it requires further evaluation and refinement that we are undertaking in a subsequent study