The distribution of word matches between Markovian sequences with periodic boundary conditions

Word match counts have traditionally been proposed as an alignment-free measure of similarity for biological sequences. The D2 statistic, which simply counts the number of exact word matches between two sequences, is a useful test bed for developing rigorous mathematical results, which can then be extended to more biologically useful measures. The distributional properties of the D2 statistic under the null hypothesis of identically and independently distributed letters have been studied extensively, but no comprehensive study of the D2 distribution for biologically more realistic higher-order Markovian sequences exists. Here we derive exact formulas for the mean and variance of the D2 statistic for Markovian sequences of any order, and demonstrate through Monte Carlo simulations that the entire distribution is accurately characterized by a Pólya-Aeppli distribution for sequence lengths of biological interest. The approach is novel in that Markovian dependency is defined for sequences with periodic boundary conditions, and this enables exact analytic formulas for the mean and variance to be derived. We also carry out a preliminary comparison between the approximate D2 distribution computed with the theoretical mean and variance under a Markovian hypothesis and an empirical D2 distribution from the human genome

Correction: Ocean acidification at a coastal CO2 vent induces expression of stress-related transcripts and transposable elements in the sea anemone Anemonia viridis.

[This corrects the article DOI: 10.1371/journal.pone.0210358.]

Expression of the neuropeptides RFamide and LWamide during development of the coral Acropora millepora in relation to settlement and metamorphosis

Neuropeptides play critical roles in cnidarian development. However, although they are known to play key roles in settlement and metamorphosis, their temporal and spatial developmental expression has not previously been characterized in any coral. We here describe Acropora millepora LWamide and RFamide and their developmental expression from the time of their first appearance, using in situ hybridization and FMRFamide immunohistochemistry. AmRFamide transcripts first appear in the ectoderm toward the oral end of the planula larva following blastopore closure. This oral bias becomes less apparent as the planula develops. The cell bodies of AmRFamide-expressing cells are centrally located in the ectoderm, with narrow projections to the mesoglea and to the cell surface. As the planula approaches settlement, AmRFamide expression disappears and is undetectable in the newly settled polyp. Expressing cells then gradually reappear as the polyp develops, becoming particularly abundant on the tentacles. AmLWamide transcripts first appear in ectodermal cells of the developing planula, with minimal expression at its two ends. The cell bodies of expressing cells lie just above the mesoglea, in a position distinct from those of AmRFamide-expressing cells, and have a narrow projection extending across the ectoderm to its surface. AmLWamide-expressing cells persist for most of the planula stage, disappearing shortly before settlement, but later than AmRFamide-expressing cells. As is the case with AmRFamide, expressing cells are absent from the polyp immediately after settlement, reappearing later on its oral side. AmLWamide expression lags that of AmRFamide in both its disappearance and reappearance. Antibodies to FMRFamide stain cells in a pattern similar to that of the transcripts, but also cells in areas where there is no expression revealed by in situ hybridization, most notably at the aboral end of the planula and in the adult polyp. Adult polyps have numerous staining cells on the tentacles and oral discs, as well as an immunoreactive nerve ring around the mouth. There are scattered staining cells in the coenosarc between polyps and staining cells are abundant in the mesenterial filaments. The above results are discussed in the context of our knowledge of the behavior of coral planulae at the time of their settlement and metamorphosis. Corals are facing multiple environmental threats, and these results both highlight the need for, and bring us a step closer to, a mechanistic understanding of a process that is critical to their survival.This work was supported by the Australian Research Council through the Centre for Molecular Genetics of Development, the Centre of Excellence for Coral Reef Studies and Discovery Grants DP0209460, DP0344483, and DP1095343

Charged inclusion in nematic liquid crystals

We present a general theory of liquid crystals under inhomogeneous electric field in a Ginzburg-Landau scheme. The molecular orientation can be deformed by electric field when the dielectric tensor is orientation-dependent. We then investigate the influence of a charged particle on the orientation order in a nematic state. The director is aligned either along or perpendicular to the local electric field around the charge, depending on the sign of the dielectric anisotropy. The deformation becomes stronger with increasing the ratio $Ze/R$, where $Ze$ is the charge and $R$ is the radius of the particle. Numerical analysis shows the presence of defects around the particle for large $Ze/R$. They are nanometer-scale defects for microscopic ions. If the dielectric anisotropy is positive, a Saturn ring defect appears. If it is negative, a pair of point defects appear apart from the particle surface, each being connected to the surface by a disclination line segment.Comment: 12 figure

Anharmonic vs. relaxational sound damping in glasses: II. Vitreous silica

The temperature dependence of the frequency dispersion in the sound velocity and damping of vitreous silica is reanalyzed. Thermally activated relaxation accounts for the sound attenuation observed above 10 K at sonic and ultrasonic frequencies. Its extrapolation to the hypersonic regime reveals that the anharmonic coupling to the thermal bath becomes important in Brillouin-scattering measurements. At 35 GHz and room temperature, the damping due to this anharmonicity is found to be nearly twice that produced by thermally activated relaxation. The analysis also reveals a sizeable velocity increase with temperature which is not related with sound dispersion. This suggests that silica experiences a gradual structural change that already starts well below room temperature.Comment: 13 pages with 8 figure

Video object tracking by label propagation and backward projection

This paper presents an approach dedicated to the tracking of one or several semantic objects in a video shot. A state of the art on spatio-temporal segmentation techniques allows us to introduce our own approach. It combines three different steps: label prediction based on partition projection, local segmentation associated with a label propagation, and classification by backward projection. Experimental results highlight the visual quality obtained with this method. Different kinds of objects can be accurately tracked in different kinds of video sequences.Cet article présente nos travaux sur le suivi d'objets dans un plan séquence. Un état de l'art sur les techniques de segmentation spatio-temporelle nous permet d'introduire notre propre méthode de suivi temporel d'objets. Elle est constituée de trois phases distinctes : une prédiction d'étiquettes par projection de partition, une segmentation locale associée à une propagation d'étiquettes, et une classification par rétro-projection. L'association de ces trois étapes cumule les avantages de chaque approche pour un suivi rigoureux d'objets et réduit le temps de traitement de chaque image. La qualité visuelle des résultats obtenus par cette méthode est illustrée en fin d'article. Pour cela nous avons considéré le suivi d'objets ayant des caractéristiques différentes au niveau de leur composition et de leur déplacement

Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals

� 2016 Raina et al. Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here, we report the isolation of an antimicrobial compound produced by Pseudovibrio sp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear magnetic resonance (NMR) and mass spectrometry (MS), identified the antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely derived from DMSP catabolism. TDA was produced in large quantities by Pseudovibrio sp., and prevented the growth of two previously identified coral pathogens, Vibrio coralliilyticus and V. owensii, at very low concentrations (0.5 μg/mL) in agar diffusion assays. Genome sequencing of Pseudovibrio sp. P12 identified gene homologs likely involved in the metabolism of DMSP and production of TDA. These results provide additional evidence for the integral role of DMSP in structuring coral-associated bacterial communities and underline the potential of these DMSP-metabolizing microbes to contribute to coral disease prevention

Unconventional ferromagnetic and spin-glass states of the reentrant spin glass Fe0.7Al0.3

Spin excitations of single crystal Fe0.7Al0.3 were investigated over a wide range in energy and reciprocal space with inelastic neutron scattering. In the ferromagnetic phase, propagating spin wave modes become paramagnon-like diffusive modes beyond a critical wave vector q0, indicating substantial disorder in the long-range ordered state. In the spin glass phase, spin dynamics is strongly q-dependent, suggesting remnant short-range spin correlations. Quantitative model for S(energy,q) in the ``ferromagnetic'' phase is determined.Comment: 4 pages, 5 figure