Formal Context Generation using Dirichlet Distributions

We suggest an improved way to randomly generate formal contexts based on Dirichlet distributions. For this purpose we investigate the predominant way to generate formal contexts, a coin-tossing model, recapitulate some of its shortcomings and examine its stochastic model. Building up on this we propose our Dirichlet model and develop an algorithm employing this idea. By comparing our generation model to a coin-tossing model we show that our approach is a significant improvement with respect to the variety of contexts generated. Finally, we outline a possible application in null model generation for formal contexts.Comment: 16 pages, 7 figure

Evolution of virulence: triggering host inflammation allows invading pathogens to exclude competitors.

Virulence is generally considered to benefit parasites by enhancing resource-transfer from host to pathogen. Here, we offer an alternative framework where virulent immune-provoking behaviours and enhanced immune resistance are joint tactics of invading pathogens to eliminate resident competitors (transferring resources from resident to invading pathogen). The pathogen wins by creating a novel immunological challenge to which it is already adapted. We analyse a general ecological model of 'proactive invasion' where invaders not adapted to a local environment can succeed by changing it to one where they are better adapted than residents. However, the two-trait nature of the 'proactive' strategy (provocation of, and adaptation to environmental change) presents an evolutionary conundrum, as neither trait alone is favoured in a homogenous host population. We show that this conundrum can be resolved by allowing for host heterogeneity. We relate our model to emerging empirical findings on immunological mediation of parasite competition

Collaboration between Science and Religious Education teachers in Scottish Secondary schools

The article reports on quantitative research that examines: (1) the current practice in collaboration; and (2) potential for collaboration between Science and Religious Education teachers in a large sample of Scottish secondary schools. The authors adopt and adapt three models (conflict; concordat and consonance) to interrogate the relationship between science and religion (and the perceived relation between these two subjects in schools) (Astley and Francis 2010). The findings indicate that there is evidence of limited collaboration and, in a few cases, a dismissive attitude towards collaboration (conflict and concordat and very weak consonance). There is, however, evidence of a genuine aspiration for greater collaboration among many teachers (moving towards a more robust consonance model). The article concludes by discussing a number of key factors that must be realised for this greater collaboration to be enacted

Dispersive Optical Interface Based on Nanofiber-Trapped Atoms

We dispersively interface an ensemble of one thousand atoms trapped in the evanescent field surrounding a tapered optical nanofiber. This method relies on the azimuthally-asymmetric coupling of the ensemble with the evanescent field of an off-resonant probe beam, transmitted through the nanofiber. The resulting birefringence and dispersion are significant; we observe a phase shift per atom of $\sim$\,1\,mrad at a detuning of six times the natural linewidth, corresponding to an effective resonant optical density per atom of 0.027. Moreover, we utilize this strong dispersion to non-destructively determine the number of atoms.Comment: 4 pages, 4 figure

Photosynthesis, growth, and decay traits in Sphagnum - a multispecies comparison

Peat mosses (Sphagnum) largely govern carbon sequestration in Northern Hemisphere peatlands. We investigated functional traits related to growth and decomposition in Sphagnum species. We tested the importance of environment and phylogeny in driving species traits and investigated trade-offs among them. We selected 15 globally important Sphagnum species, representing four sections (subgenera) and a range of peatland habitats. We measured rates of photosynthesis and decomposition in standard laboratory conditions as measures of innate growth and decay potential, and related this to realized growth, production, and decomposition in their natural habitats. In general, we found support for a trade-off between measures of growth and decomposition. However, the relationships are not strong, with r ranging between 0.24 and 0.45 for different measures of growth versus decomposition. Using photosynthetic rate to predict decomposition in standard conditions yielded R-2 = 0.20. Habitat and section (phylogeny) affected the traits and the trade-offs. In a wet year, species from sections Cuspidata and Sphagnum had the highest production, but in a dry year, differences among species, sections, and habitats evened out. Cuspidata species in general produced easily decomposable litter, but their decay in the field was hampered, probably due to near-surface anoxia in their wet habitats. In a principal components analysis, PCA, photosynthetic capacity, production, and laboratory decomposition acted in the same direction. The species were imperfectly clustered according to vegetation type and phylogeny, so that some species clustered with others in the same section, whereas others clustered more clearly with others from similar vegetation types. Our study includes a wider range of species and habitats than previous trait analyses in Sphagnum and shows that while the previously described growth-decay trade-off exists, it is far from perfect. We therefore suggest that our species-specific trait measures offer opportunities for improvements of peatland ecosystem models. Innate qualities measured in laboratory conditions translate differently to field responses. Most dramatically, fast-growing species could only realize their potential in a wet year. The same species decompose fast in laboratory, but their decomposition was more retarded in the field than that of other species. These relationships are crucial for understanding the long-term dynamics of peatland communities

Extended haplodiploidy hypothesis

Evolution of altruistic behavior was a hurdle for the logic of Darwinian evolution. Soon after Hamilton formalized the concept of inclusive fitness, which explains how altruism can evolve, he suggested that the high sororal relatedness brought by haplodiploidy could be why Hymenopterans have a high prevalence in eusocial species, and why helpers in Hymenoptera are always female. Later it was noted that in order to capitalize on the high sororal relatedness, helpers would need to direct help toward sisters, and this would bias the population sex ratio. Under a 1:3 males:females sex ratio, the inclusive fitness valuation a female places on her sister, brother, and an own offspring are equalapparently removing the benefit of helping over independent reproduction. Based on this argumentation, haplodiploidy hypothesis has been considered a red herring. However, here we show that when population sex ratio, cost of altruism, and population growth rate are considered together, haplodiploidy does promote female helping even with female-biased sex ratio, due the lowered cost of altruism in such populations. Our analysis highlights the need to re-evaluate the role of haplodiploidy in the evolution of helping, and the importance of fully exploring the model assumptions when comparing interactions of population sex ratios and social behaviors.Peer reviewe

Introduction to protein folding for physicists

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day status of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the 'special flavor' of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.Comment: 53 pages, 18 figures, the figures are at a low resolution due to arXiv restrictions, for high-res figures, go to http://www.pabloechenique.co

Uniqueness of quantum states compatible with given measurement results

We discuss the uniqueness of quantum states compatible with given measurement results for a set of observables. For a given pure state, we consider two different types of uniqueness: (1) no other pure state is compatible with the same measurement results and (2) no other state, pure or mixed, is compatible with the same measurement results. For case (1), it was known that for a d-dimensional Hilbert space, there exists a set of 4d-5 observables that uniquely determines any pure state. We show that for case (2), 5d-7 observables suffice to uniquely determine any pure state. Thus, there is a gap between the results for (1) and (2), and we give some examples to illustrate this. Unique determination of a pure state by its reduced density matrices (RDMs), a special case of determination by observables, is also discussed. We improve the best-known bound on local dimensions in which almost all pure states are uniquely determined by their RDMs for case (2). We further discuss circumstances where (1) can imply (2). We use convexity of the numerical range of operators to show that when only two observables are measured, (1) always implies (2). More generally, if there is a compact group of symmetries of the state space which has the span of the observables measured as the set of fixed points, then (1) implies (2). We analyze the possible dimensions for the span of such observables. Our results extend naturally to the case of low-rank quantum states. © 2013 American Physical Society