Extending Seqenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences

Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients

Diquark effects in light baryon correlators from lattice QCD

We study the role of diquarks in light baryons through point to point baryon correlators. We contrast results from quenched simulations with ones with two flavors of dynamical overlap fermions. The scalar, pseudoscalar and axial vector diquarks are combined with light quarks to form color singlets. The quenched simulation shows large zero mode effects in correlators containing the scalar and pseudoscalar diquark. The two scalar diquarks created by gamma_5 and gamma_0gamma_5 lead to different behavior in baryon correlators, showing that the interaction of diquarks with the third light quark matters: we do not see an isolated diquark. In our quark mass range, the scalar diquark created by gamma_5 seems to play a greater role than the others.Comment: 12 pages, 11 figure

Asymptotic analysis of a size-structured cannibalism model with infinite dimensional environmental feedback

In this work we consider a size-structured cannibalism model with the model ingredients (fertility, growth, and mortality rate) depending on size (ranging over an infinite domain) and on a general function of the standing population (environmental feedback). Our focus is on the asymptotic behavior of the system, in particular on the effect of cannibalism on the long-term dynamics. To this end, we formally linearize the system about steady state and establish conditions in terms of the model ingredients which yield uniform exponential stability of the governing linear semigroup. We also show how the point spectrum of the linearized semigroup generator can be characterized in the special case of a separable attack rate and establish a general instability result. Further spectral analysis allows us to give conditions for asynchronous exponential growth of the linear semigroup

Electron transport through antidot superlattices in Si/SiGeSi/SiGe heterostructures: new magnetoresistance resonances in lattices with large diameter antidots

In the present work we have investigated the transport properties in a number of Si/SiGe samples with square antidot lattices of different periods. In samples with lattice periods equal to 700 nm and 850 nm we have observed the conventional low-field commensurability magnetoresistance peaks consistent with the previous observations in GaAs/AlGaAs and Si/SiGe samples with antidot lattices. In samples with a 600 nm lattice period a new series of well-developed magnetoresistance oscillations has been found beyond the last commensurability peak which are supposed to originate from periodic skipping orbits encircling an antidot with a particular number of bounds.Comment: To appear in EuroPhys. Let

Drosophila olfactory receptors as classifiers for volatiles from disparate real world applications

Olfactory receptors evolved to provide animals with ecologically and behaviourally relevant information. The resulting extreme sensitivity and discrimination has proven useful to humans, who have therefore co-opted some animals' sense of smell. One aim of machine olfaction research is to replace the use of animal noses and one avenue of such research aims to incorporate olfactory receptors into artificial noses. Here, we investigate how well the olfactory receptors of the fruit fly, Drosophila melanogaster, perform in classifying volatile odourants that they would not normally encounter. We collected a large number of in vivo recordings from individual Drosophila olfactory receptor neurons in response to an ecologically relevant set of 36 chemicals related to wine ('wine set') and an ecologically irrelevant set of 35 chemicals related to chemical hazards ('industrial set'), each chemical at a single concentration. Resampled response sets were used to classify the chemicals against all others within each set, using a standard linear support vector machine classifier and a wrapper approach. Drosophila receptors appear highly capable of distinguishing chemicals that they have not evolved to process. In contrast to previous work with metal oxide sensors, Drosophila receptors achieved the best recognition accuracy if the outputs of all 20 receptor types were used

Multiple-crystal X-ray topographic characterization of periodically domain-inverted KTiOPO4 crystal

A periodically domain-inverted KTiOPO4 crystal has been characterized for the first time by multiple-crystal multiple-reflection x-ray topography. The striation contrast within the domain- inverted regions has been revealed in high strain-sensitivity reflection topographs. The origin of formation of the striation contrast and the mechanism of domain inversion in KTiOPO4 are discussed in terms of the structural characteristics of KTiOPO4

Supernova explosions and the birth of neutron stars

We report here on recent progress in understanding the birth conditions of neutron stars and the way how supernovae explode. More sophisticated numerical models have led to the discovery of new phenomena in the supernova core, for example a generic hydrodynamic instability of the stagnant supernova shock against low-mode nonradial deformation and the excitation of gravity-wave activity in the surface and core of the nascent neutron star. Both can have supportive or decisive influence on the inauguration of the explosion, the former by improving the conditions for energy deposition by neutrino heating in the postshock gas, the latter by supplying the developing blast with a flux of acoustic power that adds to the energy transfer by neutrinos. While recent two-dimensional models suggest that the neutrino-driven mechanism may be viable for stars from about 8 solar masses to at least 15 solar masses, acoustic energy input has been advocated as an alternative if neutrino heating fails. Magnetohydrodynamic effects constitute another way to trigger explosions in connection with the collapse of sufficiently rapidly rotating stellar cores, perhaps linked to the birth of magnetars. The global explosion asymmetries seen in the recent simulations offer an explanation of even the highest measured kick velocities of young neutron stars.Comment: 10 pages, 8 figures, 19 ps files; to be published in Proc. of Conf. "40 Years of Pulsars: Millisecond Pulsars, Magnetars, and More", August 12-17, 2007, McGill Univ., Montreal, Canada; high-resolution images can be obtained upon request; incorrect panel in fig.8 replace