Generating functions for canonical systems of fermions

The method proposed by Pratt to derive recursion relations for systems of degenerate fermions [Phys. Rev. Lett. 84, 4255 (2000), arXiv:nucl-th/9905055] relies on diagrammatic techniques. This efficient formalism assumes no explicit two-body interactions, makes possible the inclusion of conservation laws and requires low computational time. In this brief report, we show that such recursion relations can be obtained from generating functions, without any restriction as concerns the number of conservation laws (e.g. total energy or angular momentum).Comment: submitted to Physical Review

The performance environment in football

The first phase of this research project focused on developing an understanding of the performance environment in football, that is, the array of factors impacting individual and team performance in competitive situations. Study one was a qualitative investigation of the performance environment of the England youth football teams. National coaches, sport scientists, and players were interviewed regarding the factors that influenced performance at international tournaments. The main positives included: player understanding, strong team cohesion, managed free-time activities, and a detailed knowledge of opposition. The main negatives included: over coaching, player boredom, limited player free-time, player anxiety, and physical fatigue. Overall, results revealed 158 raw data themes, from which eight dimensions were abstracted to describe the performance environment. [Continues.

Improved limits on photon velocity oscillations

The mixing of the photon with a hypothetical sterile paraphotonic state would have consequences on the cosmological propagation of photons. The absence of distortions in the optical spectrum of distant Type Ia supernov\ae allows to extend by two orders of magnitude the previous limit on the Lorentz-violating parameter $\delta$ associated to the photon-paraphoton transition, extracted from the abscence of distortions in the spectrum of the cosmic microwave background. The new limit is consistent with the interpretation of the dimming of distant Type Ia supernov\ae as a consequence of a nonzero cosmological constant. Observations of gamma-rays from active galactic nuclei allow to further extend the limit on $\delta$ by ten orders of magnitude.Comment: 10 pages, 4 Postscript figures, use epsfig, amssym

Higher-order conservative interpolation between control-volume meshes: Application to advection and multiphase flow problems with dynamic mesh adaptivity

© 2016 .A general, higher-order, conservative and bounded interpolation for the dynamic and adaptive meshing of control-volume fields dual to continuous and discontinuous finite element representations is presented. Existing techniques such as node-wise interpolation are not conservative and do not readily generalise to discontinuous fields, whilst conservative methods such as Grandy interpolation are often too diffusive. The new method uses control-volume Galerkin projection to interpolate between control-volume fields. Bounded solutions are ensured by using a post-interpolation diffusive correction. Example applications of the method to interface capturing during advection and also to the modelling of multiphase porous media flow are presented to demonstrate the generality and robustness of the approach

A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data.

BACKGROUND: The advent of next generation sequencing technology has accelerated efforts to map and catalogue copy number variation (CNV) in genomes of important micro-organisms for public health. A typical analysis of the sequence data involves mapping reads onto a reference genome, calculating the respective coverage, and detecting regions with too-low or too-high coverage (deletions and amplifications, respectively). Current CNV detection methods rely on statistical assumptions (e.g., a Poisson model) that may not hold in general, or require fine-tuning the underlying algorithms to detect known hits. We propose a new CNV detection methodology based on two Poisson hierarchical models, the Poisson-Gamma and Poisson-Lognormal, with the advantage of being sufficiently flexible to describe different data patterns, whilst robust against deviations from the often assumed Poisson model. RESULTS: Using sequence coverage data of 7 Plasmodium falciparum malaria genomes (3D7 reference strain, HB3, DD2, 7G8, GB4, OX005, and OX006), we showed that empirical coverage distributions are intrinsically asymmetric and overdispersed in relation to the Poisson model. We also demonstrated a low baseline false positive rate for the proposed methodology using 3D7 resequencing data and simulation. When applied to the non-reference isolate data, our approach detected known CNV hits, including an amplification of the PfMDR1 locus in DD2 and a large deletion in the CLAG3.2 gene in GB4, and putative novel CNV regions. When compared to the recently available FREEC and cn.MOPS approaches, our findings were more concordant with putative hits from the highest quality array data for the 7G8 and GB4 isolates. CONCLUSIONS: In summary, the proposed methodology brings an increase in flexibility, robustness, accuracy and statistical rigour to CNV detection using sequence coverage data

Chicken Embryonic-Stem Cells Are Permissive to Poxvirus Recombinant Vaccine Vectors.

The discovery of mammalian pluripotent embryonic stem cells (ESC) has revolutionised cell research and regenerative medicine. More recently discovered chicken ESC (cESC), though less intensively studied, are increasingly popular as vaccine substrates due to a dearth of avian cell lines. Information on the comparative performance of cESC with common vaccine viruses is limited. Using RNA-sequencing, we compared cESC transcriptional programmes elicited by stimulation with chicken type I interferon or infection with vaccine viruses routinely propagated in primary chicken embryo fibroblasts (CEF). We used poxviruses (fowlpox virus (FWPV) FP9, canarypox virus (CNPV), and modified vaccinia virus Ankara (MVA)) and a birnavirus (infectious bursal disease virus (IBDV) PBG98). Interferon-stimulated genes (ISGs) were induced in cESC to levels comparable to those in CEF and immortalised chicken fibroblast DF-1 cells. cESC are permissive (with distinct host transcriptional responses) to MVA, FP9, and CNPV but, surprisingly, not to PBG98. MVA, CNPV, and FP9 suppressed innate immune responses, while PBG98 induced a subset of ISGs. Dysregulation of signalling pathways (i.e., NFκB, TRAF) was observed, which might affect immune responses and viral replication. In conclusion, we show that cESC are an attractive alternative substrate to study and propagate poxvirus recombinant vaccine vectors

Effect of heat treatment and aging on the mechanical loss and strength of hydroxide catalysis bonds between fused silica samples

Hydroxide catalysis bonds are used in the aLIGO gravitational wave detectors and are an essential technology within the mirror suspensions which allowed for detector sensitivities to be reached that enabled the first direct detections of gravitational waves. Methods aimed at further improving hydroxide catalysis bonds for future upgrades to these detectors, in order to increase detection rates and the number of detectable sources, are explored. Also, the effect on the bonds of an aLIGO suspension construction procedure involving heat, the fibre welding process, is investigated. Here we show that thermal treatments can be beneficial to improving some of the bond properties important to the mirror suspensions in interferometric gravitational wave detectors. It was found that heat treating bonds at 150\,^\circC increases bond strength by a factor of approximately 1.5 and a combination of bond ageing and heat treatment of the optics at 150\,\circC reduces the mechanical loss of a bond from 0.10 to 0.05. It is also shown that current construction procedures do not reduce bond strength

Targeted disruption of py235ebp-1: Invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein

Plasmodium yoelii YM asexual blood stage parasites express multiple members of the py235 gene family, part of the super-family of genes including those coding for Plasmodium vivax reticulocyte binding proteins and Plasmodium falciparum RH proteins. We previously identified a Py235 erythrocyte binding protein (Py235EBP-1, encoded by the PY01365 gene) that is recognized by protective mAb 25.77. Proteins recognized by a second protective mAb 25.37 have been identified by mass spectrometry and are encoded by two genes, PY01185 and PY05995/PY03534. We deleted the PY01365 gene and examined the phenotype. The expression of the members of the py235 family in both the WT and gene deletion parasites was measured by quantitative RT-PCR and RNA-Seq. py235ebp-1 expression was undetectable in the knockout parasite, but transcription of other members of the family was essentially unaffected. The knockout parasites continued to react with mAb 25.77; and the 25.77-binding proteins in these parasites were the PY01185 and PY05995/PY03534 products. The PY01185 product was also identified as erythrocyte binding. There was no clear change in erythrocyte invasion profile suggesting that the PY01185 gene product (designated PY235EBP-2) is able to fulfill the role of EBP-1 by serving as an invasion ligand although the molecular details of its interaction with erythrocytes have not been examined. The PY01365, PY01185, and PY05995/PY03534 genes are part of a distinct subset of the py235 family. In P. falciparum, the RH protein genes are under epigenetic control and expression correlates with binding to distinct erythrocyte receptors and specific invasion pathways, whereas in P. yoelii YM all the genes are expressed and deletion of one does not result in upregulation of another. We propose that simultaneous expression of multiple Py235 ligands enables invasion of a wide range of host erythrocytes even in the presence of antibodies to one or more of the proteins and that this functional redundancy at the protein level gives the parasite phenotypic plasticity in the absence of differences in gene expression

Lagrangian Framework for Systems Composed of High-Loss and Lossless Components

Using a Lagrangian mechanics approach, we construct a framework to study the dissipative properties of systems composed of two components one of which is highly lossy and the other is lossless. We have shown in our previous work that for such a composite system the modes split into two distinct classes, high-loss and low-loss, according to their dissipative behavior. A principal result of this paper is that for any such dissipative Lagrangian system, with losses accounted by a Rayleigh dissipative function, a rather universal phenomenon occurs, namely, selective overdamping: The high-loss modes are all overdamped, i.e., non-oscillatory, as are an equal number of low-loss modes, but the rest of the low-loss modes remain oscillatory each with an extremely high quality factor that actually increases as the loss of the lossy component increases. We prove this result using a new time dynamical characterization of overdamping in terms of a virial theorem for dissipative systems and the breaking of an equipartition of energy.Comment: 53 pages, 1 figure; Revision of our original manuscript to incorporate suggestions from refere