Uniform Local Amenability

The main results of this paper show that various coarse (`large scale') geometric properties are closely related. In particular, we show that property A implies the operator norm localisation property, and thus that norms of operators associated to a very large class of metric spaces can be effectively estimated. The main tool is a new property called uniform local amenability. This property is easy to negate, which we use to study some `bad' spaces. We also generalise and reprove a theorem of Nowak relating amenability and asymptotic dimension in the quantitative setting

Expanders and Property A

We give a cohomological characterisation of expander graphs, and use it to give a direct proof that expander graphs do not have Yu's property A

Reconciling the Classical-Field Method with the Beliaev Broken Symmetry Approach

We present our views on the issues raised in the chapter by Griffin and Zaremba [A. Griffin and E. Zaremba, in Quantum Gases: Finite Temperature and Non-Equilibrium Dynamics, N. P. Proukakis, S. A. Gardiner, M. J. Davis, and M. H. Szymanska, eds., Imperial College Press, London (in press)]. We review some of the strengths and limitations of the Bose symmetry-breaking assumption, and explain how such an approach precludes the description of many important phenomena in degenerate Bose gases. We discuss the theoretical justification for the classical-field (c-field) methods, their relation to other non-perturbative methods for similar systems, and their utility in the description of beyond-mean-field physics. Although it is true that present implementations of c-field methods cannot accurately describe certain collective oscillations of the partially condensed Bose gas, there is no fundamental reason why these methods cannot be extended to treat such scenarios. By contrast, many regimes of non-equilibrium dynamics that can be described with c-field methods are beyond the reach of generalised mean-field kinetic approaches based on symmetry-breaking, such as the ZNG formalism.Comment: 8 pages. Unedited version of chapter to appear in Quantum Gases: Finite Temperature and Non-Equilibrium Dynamics (Vol. 1 Cold Atoms Series). N.P. Proukakis, S.A. Gardiner, M.J. Davis and M.H. Szymanska, eds. Imperial College Press, London (in press). See http://www.icpress.co.uk/physics/p817.html v2: Added arXiv cross-reference

DNA → RNA: What Do Students Think the Arrow Means?

The central dogma of molecular biology, a model that has remained intact for decades, describes the transfer of genetic information from DNA to protein though an RNA intermediate. While recent work has illustrated many exceptions to the central dogma, it is still a common model used to describe and study the relationship between genes and protein products. We investigated understanding of central dogma concepts and found that students are not primed to think about information when presented with the canonical figure of the central dogma. We also uncovered conceptual errors in student interpretation of the meaning of the transcription arrow in the central dogma representation; 36% of students (n = 128; all undergraduate levels) described transcription as a chemical conversion of DNA into RNA or suggested that RNA existed before the process of transcription began. Interviews confirm that students with weak conceptual understanding of information flow find inappropriate meaning in the canonical representation of central dogma. Therefore, we suggest that use of this representation during instruction can be counterproductive unless educators are explicit about the underlying meanin

The stellar activity-rotation relationship

Using a new catalog of 824 solar and late-type stars with measured X-ray luminosities and rotation periods we have studied the relationship between rotation and stellar activity that is believed to be a probe of the underlying stellar dynamo. Using an unbiased subset of the sample we calculate the power law slope of the unsaturated regime of the activity-rotation relationship as LX/Lbol α Roβ, where β = –2.70 ± 0.13. Notably this is inconsistent with the canonical β = –2 slope to a confidence of 5σ are argues for an interface-type dynamo. Super-saturation is observed for the fastest rotators in our sample and its parametric dependencies are explored. Significant correlations are found with both the corotation radius and the excess polar updraft, the latter theory being preferred as it is supported by other observations. We also present a new X-ray population synthesis model of the mature stellar component of our Galaxy and use it to reproduce deep observations of a high Galactic latitude field. The model, XStar, can be used to test models of stellar spin-down and dynamo decay, as well as for estimating stellar X-ray contamination rates for non-stellar studies. (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Development of the Central Dogma Concept Inventory (CDCI) Assessment Tool

Scientific teaching requires scientifically constructed, field-tested instruments to accurately evaluate student thinking and gauge teacher effectiveness. We have developed a 23-question, multiple select–format assessment of student understanding of the essential concepts of the central dogma of molecular biology that is appropriate for all levels of undergraduate biology. Questions for the Central Dogma Concept Inventory (CDCI) tool were developed and iteratively revised based on student language and review by experts. The ability of the CDCI to discriminate between levels of understanding of the central dogma is supported by field testing (N = 54), and large-scale beta testing (N = 1733). Performance on the assessment increased with experience in biology; scores covered a broad range and showed no ceiling effect, even with senior biology majors, and pre/posttesting of a single class focused on the central dogma showed significant improvement. The multiple-select format reduces the chances of correct answers by random guessing, allows students at different levels to exhibit the extent of their knowledge, and provides deeper insight into the complexity of student thinking on each theme. To date, the CDCI is the first tool dedicated to measuring student thinking about the central dogma of molecular biology, and version 5 is ready to use

Facilitating the operational readiness of the NHS for the in-house manufacture and delivery of autologous cell therapy [210]

Facilitating the operational readiness of the NHS for the in-house manufacture and delivery of autologous cell therapy [210

The statistical mechanics of a polygenic characterunder stabilizing selection, mutation and drift

By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation, and genetic drift. This requires us to track only four macroscopic variables, instead of the distribution of all the allele frequencies that influence the trait. These macroscopic variables are the expectations of: the trait mean and its square, the genetic variance, and of a measure of heterozygosity, and are derived from a generating function that is in turn derived by maximizing an entropy measure. These four macroscopics are enough to accurately describe the dynamics of the trait mean and of its genetic variance (and in principle of any other quantity). Unlike previous approaches that were based on an infinite series of moments or cumulants, which had to be truncated arbitrarily, our calculations provide a well-defined approximation procedure. We apply the framework to abrupt and gradual changes in the optimum, as well as to changes in the strength of stabilizing selection. Our approximations are surprisingly accurate, even for systems with as few as 5 loci. We find that when the effects of drift are included, the expected genetic variance is hardly altered by directional selection, even though it fluctuates in any particular instance. We also find hysteresis, showing that even after averaging over the microscopic variables, the macroscopic trajectories retain a memory of the underlying genetic states.Comment: 35 pages, 8 figure

Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing

The sequence diversity of viral populations within individual hosts is the starting material for selection and subsequent evolution of RNA viruses such as foot-and-mouth disease virus (FMDV). Using next-generation sequencing (NGS) performed on a Genome Analyzer platform (Illumina), this study compared the viral populations within two bovine epithelial samples (foot lesions) from a single animal with the Inoculum used to initiate experimental infection. Genomic sequences were determined in duplicate sequencing runs, and the consensus sequence determined by NGS, for the Inoculum, was identical to that previously determined using the Sanger method. However, NGS reveals the fine polymorphic sub-structure of the viral population, from nucleotide variants present at just below 50% frequency to those present at fractions of 1%. Some of the higher frequency polymorphisms identified encoded changes within codons associated with heparan sulphate binding and were present in both feet lesions revealing intermediate stages in the evolution of a tissue-culture adapted virus replicating within a mammalian host. We identified 2,622, 1,434 and 1,703 polymorphisms in the Inoculum, and in the two foot lesions respectively: most of the substitutions occurred only in a small fraction of the population and represent the progeny from recent cellular replication prior to onset of any selective pressures. We estimated an upper limit for the genome-wide mutation rate of the virus within a cell to be 7.8 x 10-4 per nt. The greater depth of detection, achieved by NGS, demonstrates that this method is a powerful and valuable tool for the dissection of FMDV populations within-hosts