Lack of alignment across yeast-dependent life-history traits may limit <i>Drosophila melanogaster</i> dietary specialization

Heterogeneity in food resources is a major driver of local adaptation and speciation. Dietary specialization typically involves multiple life-history traits and may thus be limited by the extent to which these traits adapt in concert. Here, we use Drosophila melanogaster, representing an intermediate state in the generalist-specialist continuum, to explore the scope for dietary specialization. D. melanogaster has a close association with yeast, an essential but heterogeneous food resource. We quantify how different D. melanogaster strains from around the globe respond to different yeast species, across multiple yeast-dependent life-history traits including feeding, mating, egg-laying, egg development and survival. We find that D. melanogaster strains respond to different yeast species in different ways, indicating distinct fly strain-yeast interactions. However, we detect no evidence for trade-offs: fly performance tends to be positively rather than negatively correlated across yeast species. We also find that the responses to different yeast species are not aligned across traits: different life-history traits are maximized on different yeast species. Finally, we confirm that D. melanogaster is a resource generalist: it can grow, reproduce and survive on all the yeast species we tested. Together, these findings provide a possible explanation for the limited extent of dietary specialization in D. melanogaster.</p

Seven questions on the chemical ecology and neurogenetics of resource-mediated speciation

Adaptation to different environments can result in reproductive isolation between populations and the formation of new species. Food resources are among the most important environmental factors shaping local adaptation. The chemosensory system, the most ubiquitous sensory channel in the animal kingdom, not only detects food resources and their chemical composition, but also mediates sexual communication and reproductive isolation in many taxa. Chemosensory divergence may thus play a crucial role in resource-mediated adaptation and speciation. Understanding how the chemosensory system can facilitate resource-mediated ecological speciation requires integrating mechanistic studies of the chemosensory system with ecological studies, to link the genetics and physiology of chemosensory properties to divergent adaptation. In this review, we use examples of insect research to present seven key questions that can be used to understand how the chemosensory system can facilitate resource-mediated ecological speciation in consumer populations

The 2+1 flavor topological susceptibility from the asqtad action at 0.06 fm

We report new data for the topological susceptibility computed on 2+1 flavor dynamical configurations with lattice spacing 0.06 fm, generated with the asqtad action. The topological susceptibility is computed by HYP smearing and compared with rooted staggered chiral perturbation theory as the pion mass goes to zero. At 0.06 fm, the raw data is already quite close to the continuum extrapolated values obtained from coarser lattices. These results provide a further test of the asqtad action with rooted staggered flavors.Comment: 7 pages, 5 figures, talk presented at the XXV International Symposium on Lattice Field Theory, July 30 - August 4, 2007, Regensburg, German

Stereo-consistent screen-space ambient occlusion

Screen-space ambient occlusion (SSAO) shows high efficiency and is widely used in real-time 3D applications. However, using SSAO algorithms in stereo rendering can lead to inconsistencies due to the differences in the screen-space information captured by the left and right eye. This will affect the perception of the scene and may be a source of viewer discomfort. In this paper, we show that the raw obscurance estimation part and subsequent filtering are both sources of inconsistencies. We developed a screen-space method involving both views in conjunction, leading to a stereo-aware raw obscurance estimation method and a stereo-aware bilateral filter. The results show that our method reduces stereo inconsistencies to a level comparable to geometry-based AO solutions, while maintaining the performance benefits of a screen-space approach

Topological susceptibility with the asqtad action

Chiral perturbation theory predicts that in quantum chromodynamics (QCD), light dynamical quarks suppress the gauge-field topological susceptibility of the vacuum. The degree of suppression depends on quark multiplicity and masses. It provides a strong consistency test for fermion formulations in lattice QCD. Such tests are especially important for staggered fermion formulations that lack a full chiral symmetry and use the "fourth-root" procedure to achieve the desired number of sea quarks. Over the past few years we have measured the topological susceptibility on a large database of 18 gauge field ensembles, generated in the presence of 2+1 flavors of dynamical asqtad quarks with up and down quark masses ranging from 0.05 to 1 in units of the strange quark mass and lattice spacings ranging from 0.045 fm to 0.12 fm. Our study also includes three quenched ensembles with lattice spacings ranging from 0.06 to 0.12 fm. We construct the topological susceptibility from the integrated point-to-point correlator of the discretized topological charge density F-Fdual. To reduce its variance, we model the asymptotic tail of the correlator. The continuum extrapolation of our results for the topological susceptibility agrees nicely at small quark mass with the predictions of lowest-order SU(3) chiral perturbation theory, thus lending support to the validity of the fourth-root procedure.Comment: 28 pp, 6 figs. Version 2 corrects some discussion, some numbers, and some figures and adds some reference

An Efficient Dual-Hierarchy t-SNE Minimization

t-distributed Stochastic Neighbour Embedding (t-SNE) has become a standard for exploratory data analysis, as it is capable of revealing clusters even in complex data while requiring minimal user input. While its run-time complexity limited it to small datasets in the past, recent efforts improved upon the expensive similarity computations and the previously quadratic minimization. Nevertheless, t-SNE still has high runtime and memory costs when operating on millions of points. We present a novel method for executing the t-SNE minimization. While our method overall retains a linear runtime complexity, we obtain a significant performance increase in the most expensive part of the minimization. We achieve a significant improvement without a noticeable decrease in accuracy even when targeting a 3D embedding. Our method constructs a pair of spatial hierarchies over the embedding, which are simultaneously traversed to approximate many N-body interactions at once. We demonstrate an efficient GPGPU implementation and evaluate its performance against state-of-the-art methods on a variety of datasets

Vaccination of Rhesus Macaques with a Recombinant Measles Virus Expressing Interleukin-12 Alters Humoral and Cellular Immune Responses

Lack of a vaccine for infants and immunosuppression after infection are problems associated with measles virus (MV). Because interleukin (IL)-12 has been used successfully as a vaccine adjuvant and because inhibition of IL-12 expression has been associated with immunosuppression during measles, the addition of IL-12 may enhance the immune response to MV. To determine the effect of IL-12 supplementation, rhesus macaques were vaccinated with a recombinant MV expressing IL-12; these macaques had increased interferon-γ production by CD4+ T cells, decreased production of IL-4, and lower levels of MV-specific immunoglobulin G4 and neutralizing antibody. Lymphoproliferative responses to mitogen were not improved. IL-12 supplementation altered the T helper type 2 bias of the immune response after MV vaccination, had a detrimental effect on the protective neutralizing antibody response, and did not improve other manifestations of immunosuppression. Reduced IL-12 levels are not the sole factor in MV-induced immunosuppressio

Computer simulations of hard pear-shaped particles

We report results obtained from Monte Carlo simulations investi- gating mesophase formation in two model systems of hard pear-shaped particles. The first model considered is a hard variant of the trun- cated Stone-Expansion model previously shown to form nematic and smectic mesophases when embedded within a 12-6 Gay-Berne-like po- tential [1]. When stripped of its attractive interactions, however, this system is found to lose its liquid crystalline phases. For particles of length to breadth ratio k = 3, glassy behaviour is seen at high pressures, whereas for k = 5 several bi-layer-like domains are seen, with high intradomain order but little interdomain orientational correlation. For the second model, which uses a parametric shape parameter based on the generalised Gay-Berne formalism, results are presented for particles with elongation k = 3; 4 and 5. Here, the systems with k = 3 and 4 fail to display orientationally ordered phases, but that with k = 5 shows isotropic, nematic and, unusually for a hard-particle model, interdigitated smectic A2 phases.</p

Constraint methods for determining pathways and free energy of activated processes

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach

Theory of Banana Liquid Crystal Phases and Phase Transitions

We study phases and phase transitions that can take place in the newly discovered banana (bow-shaped or bent-core) liquid crystal molecules. We show that to completely characterize phases exhibited by such bent-core molecules a third-rank tensor $T^{ijk}$ order parameter is necessary in addition to the vector and the nematic (second-rank) tensor order parameters. We present an exhaustive list of possible liquid phases, characterizing them by their space-symmetry group and order parameters, and catalog the universality classes of the corresponding phase transitions that we expect to take place in such bent-core molecular liquid crystals. In addition to the conventional liquid-crystal phases such as the nematic phase, we predict the existence of novel liquid phases, including the spontaneously chiral nematic $(N_T + 2)^*$ and chiral polar $(V_T + 2)^*$ phases, the orientationally-ordered but optically isotropic tetrahedratic $T$ phase, and a novel nematic $N_T$ phase with $D_{2d}$ symmetry that is neither uniaxial nor biaxial. Interestingly, the Isotropic-Tetrahedratic transition is {\em continuous} in mean-field theory, but is likely driven first-order by thermal fluctuations. We conclude with a discussion of smectic analogs of these phases and their experimental signatures.Comment: 28 pgs. RevTex, 32 eps figures, submitted to Phys. Rev.