Anthropogenic Renourishment Feedback on Shorebirds: a Multispecies Bayesian Perspective

In this paper the realized niche of the Snowy Plover (Charadrius alexandrinus), a primarily resident Florida shorebird, is described as a function of the scenopoetic and bionomic variables at the nest-, landscape-, and regional-scale. We identified some possible geomorphological controls that influence nest-site selection and survival using data collected along the Florida Gulf coast. In particular we focused on the effects of beach replenishment interventions on the Snowy Plover (SP), and on the migratory Piping Plover	(PP)	(Charadrius	melodus )	and	Red	Knot	(RK)	(Calidris	canutus ).	Additionally, we investigated the potential differences between the SP breeding and wintering distributions using only regional-scale physiognomic variables and the recorded occur- rences. To quantify the relationship between past renourishment projects and shorebird species we used a Monte Carlo procedure to sample from the posterior distribution of the binomial probabilities that a region is not a nesting or a wintering ground conditional on the occurrence of a beach replenishment intervention in the same and the previous year. The results indicate that it was 2.3, 3.1, and 0.8 times more likely that a region was not a wintering ground following a year with a renourishment intervention for the SP, PP and RK respectively. For the SP it was 2.5. times more likely that a region was not a breeding ground after a renourishment event. Through a maximum entropy principle model we observed small differences in the habitat use of the SP during the breeding and the wintering season. However the habitats where RK was observed appeared quite different. While ecological niche models at the macro-scale are useful for determining habitat suitability ranges, the characterization of the species’ local niche is fundamentally important for adopting concrete multi-species management scenarios. Maintaining and creating optimal suitable habitats for SP characterized by sparse low vegetation in the foredunes areas, and uneven/low-slope beach surfaces, is the proposed conservation scenario to convert anthropic beach restorations and SP populations into a positive feedback without impacting other threatened shorebird species

A machine learning based framework to identify and classify long terminal repeat retrotransposons

Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species. Accurate identification and classification of TEs present in a genome is an important step towards understanding their effects on genes and their role in genome evolution. We introduce TE-LEARNER, a framework based on machine learning that automatically identifies TEs in a given genome and assigns a classification to them. We present an implementation of our framework towards LTR retrotransposons, a particular type of TEs characterized by having long terminal repeats (LTRs) at their boundaries. We evaluate the predictive performance of our framework on the well-annotated genomes of Drosophila melanogaster and Arabidopsis thaliana and we compare our results for three LTR retrotransposon superfamilies with the results of three widely used methods for TE identification or classification: REPEATMASKER, CENSOR and LTRDIGEST. In contrast to these methods, TE-LEARNER is the first to incorporate machine learning techniques, outperforming these methods in terms of predictive performance , while able to learn models and make predictions efficiently. Moreover, we show that our method was able to identify TEs that none of the above method could find, and we investigated TE-LEARNER'S predictions which did not correspond to an official annotation. It turns out that many of these predictions are in fact strongly homologous to a known TE

The spherical 2+p spin glass model: an analytically solvable model with a glass-to-glass transition

We present the detailed analysis of the spherical s+p spin glass model with two competing interactions: among p spins and among s spins. The most interesting case is the 2+p model with p > 3 for which a very rich phase diagram occurs, including, next to the paramagnetic and the glassy phase represented by the one step replica symmetry breaking ansatz typical of the spherical p-spin model, other two amorphous phases. Transitions between two contiguous phases can also be of different kind. The model can thus serve as mean-field representation of amorphous-amorphous transitions (or transitions between undercooled liquids of different structure). The model is analytically solvable everywhere in the phase space, even in the limit where the infinite replica symmetry breaking ansatz is required to yield a thermodynamically stable phase.Comment: 21 pages, 18 figure

Faster algorithms for 1-mappability of a sequence

In the k-mappability problem, we are given a string x of length n and integers m and k, and we are asked to count, for each length-m factor y of x, the number of other factors of length m of x that are at Hamming distance at most k from y. We focus here on the version of the problem where k = 1. The fastest known algorithm for k = 1 requires time O(mn log n/ log log n) and space O(n). We present two algorithms that require worst-case time O(mn) and O(n log^2 n), respectively, and space O(n), thus greatly improving the state of the art. Moreover, we present an algorithm that requires average-case time and space O(n) for integer alphabets if m = {\Omega}(log n/ log {\sigma}), where {\sigma} is the alphabet size

Porphyromonas gingivalis lipopolysaccharide alters atherosclerotic-related gene expression in oxidized low-density-lipoprotein-induced macrophages and foam cells

The molecular mechanism between atherosclerosis formation and periodontal pathogens is not clear although positive correlation between periodontal infections and cardiovascular diseases has been reported. Objective: To determine if atherosclerosis related genes were affected in foam cells during and after its formation by P. gingivalis lipopolysaccharide (LPS) stimulation. Methods: Macrophages from human THP-1 monocytes were treated with oxidized low density lipoprotein (oxLDL) to induce the formation of foam cells. P. gingivalis LPS was added to cultures of either oxLDL-induced macrophages or foam cells. The expression of atherosclerosis related genes was assayed by quantitative real time PCR and the protein production of granulocyte-macrophage colony-stimulating factor（GM-CSF）, monocyte chemotactic protein-1 (MCP-1), IL-1β, IL-10 and IL-12 was determined by ELISA. Nuclear translocation of NF-κB P65 was detected by immunocytochemistry and western blot was used to evaluate IKB-α degradation to confirm the NF-κB pathway activation. Results: P. gingivalis LPS stimulated atherosclerosis related gene expression in foam cells and increased oxLDL induced expression of chemokines, adhesion molecules, growth factors, apoptotic genes, and nuclear receptors in macrophages. Transcription of the pro-inflammatory cytokines IL-1β and IL-12 was elevated in response to LPS in both macrophages and foam cells, whereas the anti-inflammatory cytokine IL-10 was not affected. Increased NF-κB pathway activation was also observed in LPS and oxLDL co-stimulated macrophages. Conclusion: P. gingivalis LPS appears to be an important factor in the development of atherosclerosis by stimulation of atherosclerosis related gene expression in both macrophages and foam cells via activation of the NF-κB pathway

Interfacial effects on the polarization of BiFeO3BiFeO_{3} films

By considering an interfacial layer between the electrode and the $BiFeO_{3}$($BFO$) layer, the polarization and the hysteresis behavior of $BFO$ film are simulated. It is found that the non-ferroelectric interface will increase the coercive field, and remarkably suppress the polarization of the ultrathin film under low applied fields. Due to the competition between the interfacial effect and the internal compressive stress, the maximum polarization on the P-E loop of a $BFO$ film can be independent on the film thickness under an adequate applied field.Comment: 3 pages, 2 figure

Time-of-flight imaging of invisibility cloaks

As invisibility cloaking has recently become experimental reality, it is interesting to explore ways to reveal remaining imperfections. In essence, the idea of most invisibility cloaks is to recover the optical path lengths without an object (to be made invisible) by a suitable arrangement around that object. Optical path length is proportional to the time of flight of a light ray or to the optical phase accumulated by a light wave. Thus, time-of-flight images provide a direct and intuitive tool for probing imperfections. Indeed, recent phase-sensitive experiments on the carpet cloak have already made early steps in this direction. In the macroscopic world, time-of-flight images could be measured directly by light detection and ranging (LIDAR). Here, we show calculated time-of-flight images of the conformal Gaussian carpet cloak, the conformal grating cloak, the cylindrical free-space cloak, and of the invisible sphere. All results are obtained by using a ray-velocity equation of motion derived from Fermat's principle.Comment: 11 pages, 6 figures, journal pape

Long-range frustration in T=0 first-step replica-symmetry-broken solutions of finite-connectivity spin glasses

In a finite-connectivity spin-glass at the zero-temperature limit, long-range correlations exist among the unfrozen vertices (whose spin values being non-fixed). Such long-range frustrations are partially removed through the first-step replica-symmetry-broken (1RSB) cavity theory, but residual long-range frustrations may still persist in this mean-field solution. By way of population dynamics, here we perform a perturbation-percolation analysis to calculate the magnitude of long-range frustrations in the 1RSB solution of a given spin-glass system. We study two well-studied model systems, the minimal vertex-cover problem and the maximal 2-satisfiability problem. This work points to a possible way of improving the zero-temperature 1RSB mean-field theory of spin-glasses.Comment: 5 pages, two figures. To be published in JSTA

On the String Consensus Problem and the Manhattan Sequence Consensus Problem

In the Manhattan Sequence Consensus problem (MSC problem) we are given $k$ integer sequences, each of length $l$, and we are to find an integer sequence $x$ of length $l$ (called a consensus sequence), such that the maximum Manhattan distance of $x$ from each of the input sequences is minimized. For binary sequences Manhattan distance coincides with Hamming distance, hence in this case the string consensus problem (also called string center problem or closest string problem) is a special case of MSC. Our main result is a practically efficient $O(l)$-time algorithm solving MSC for $k\le 5$ sequences. Practicality of our algorithms has been verified experimentally. It improves upon the quadratic algorithm by Amir et al.\ (SPIRE 2012) for string consensus problem for $k=5$ binary strings. Similarly as in Amir's algorithm we use a column-based framework. We replace the implied general integer linear programming by its easy special cases, due to combinatorial properties of the MSC for $k\le 5$. We also show that for a general parameter $k$ any instance can be reduced in linear time to a kernel of size $k!$, so the problem is fixed-parameter tractable. Nevertheless, for $k\ge 4$ this is still too large for any naive solution to be feasible in practice.Comment: accepted to SPIRE 201

Manganese mineralogy and diagenesis in the sedimentary rock record

Oxidation of manganese(II) to manganese(III,IV) demands oxidants with very high redox potentials; consequently, manganese oxides are both excellent proxies for molecular oxygen and highly favorable electron acceptors when oxygen is absent. The first of these features results in manganese-enriched sedimentary rocks (manganese deposits, commonly Mn ore deposits), which generally correspond to the availability of molecular oxygen in Earth surface environments. And yet because manganese reduction is promoted by a variety of chemical species, these ancient manganese deposits are often significantly more reduced than modern environmental manganese-rich sediments. We document the impacts of manganese reduction and the mineral phases that form stable manganese deposits from seven sedimentary examples spanning from modern surface environments to rocks over 2 billion years old. Integrating redox and coordination information from synchrotron X-ray absorption spectroscopy and X-ray microprobe imaging with scanning electron microscopy and energy and wavelength-dispersive spectroscopy, we find that unlike the Mn(IV)-dominated modern manganese deposits, three manganese minerals dominate these representative ancient deposits: kutnohorite (CaMn(CO_3)_2), rhodochrosite (MnCO_3), and braunite (Mn(III)_6Mn(II)O_8SiO_4). Pairing these mineral and textural observations with previous studies of manganese geochemistry, we develop a paragenetic model of post-depositional manganese mineralization with kutnohorite and calcian rhodochrosite as the earliest diagenetic mineral phases, rhodochrosite and braunite forming secondarily, and later alteration forming Mn-silicates