Merging Resource Availability with Isotope Mixing Models: The Role of Neutral Interaction Assumptions

Background: Bayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predator's diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values. Methodology: We develop a procedure to incorporate prey availability data into Bayesian mixing models conditional on the similarity of isotope values between two prey. If a pair of prey have similar isotope values (resulting in highly uncertain mixing model results), our model increases the weight of availability data in estimating the contribution of prey to a predator's diet. We test the utility of this method in an intertidal community against independently measured feeding rates. Conclusions: Our results indicate that our weighting procedure increases the accuracy by which consumer diets can be inferred in situations where multiple prey have similar isotope values. This suggests that the exchange of formalism for predictive power is merited, particularly when the relationship between prey availability and a predator's diet cannot be assumed for all species in a system.

Preclinical Studies with Umbilical Cord Mesenchymal Stromal Cells in Different Animal Models for Muscular Dystrophy

Umbilical cord mesenchymal stromal cells (MSC) have been widely investigated for cell-based therapy studies as an alternative source to bone marrow transplantation. Umbilical cord tissue is a rich source of MSCs with potential to derivate at least muscle, cartilage, fat, and bone cells in vitro. The possibility to replace the defective muscle cells using cell therapy is a promising approach for the treatment of progressive muscular dystrophies (PMDs), independently of the specific gene mutation. Therefore, preclinical studies in different models of muscular dystrophies are of utmost importance. The main objective of the present study is to evaluate if umbilical cord MSCs have the potential to reach and differentiate into muscle cells in vivo in two animal models of PMDs. In order to address this question we injected (1) human umbilical cord tissue (hUCT) MSCs into the caudal vein of SJL mice; (2) hUCT and canine umbilical cord vein (cUCV) MSCs intra-arterially in GRMD dogs. Our results here reported support the safety of the procedure and indicate that the injected cells could engraft in the host muscle in both animal models but could not differentiate into muscle cells. These observations may provide important information aiming future therapy for muscular dystrophies.

Modeling the skin pattern of fishes

Complicated patterns showing various spatial scales have been obtained in the past by coupling Turing systems in such a way that the scales of the independent systems resonate. This produces superimposed patterns with different length scales. Here we propose a model consisting of two identical reaction-diffusion systems coupled together in such a way that one of them produces a simple Turing pattern of spots or stripes, and the other traveling wave fronts that eventually become stationary. The basic idea is to assume that one of the systems becomes fixed after some time and serves as a source of morphogens for the other system. This mechanism produces patterns very similar to the pigmentation patterns observed in different species of stingrays and other fishes. The biological mechanisms that support the realization of this model are discussed.

Impact of Manaus City on the Amazon Green Ocean atmosphere: ozone production, precursor sensitivity and aerosol load

As a contribution to the Large-Scale Biosphere-Atmosphere Experiment in Amazonia - Cooperative LBA Airborne Regional Experiment (LBA-CLAIRE-2001) field campaign in the heart of the Amazon Basin, we analyzed the temporal and spatial dynamics of the urban plume of Manaus City during the wet-to-dry season transition period in July 2001. During the flights, we performed vertical stacks of crosswind transects in the urban outflow downwind of Manaus City, measuring a comprehensive set of trace constituents including O(3), NO, NO(2), CO, VOC, CO(2), and H(2)O. Aerosol loads were characterized by concentrations of total aerosol number (CN) and cloud condensation nuclei (CCN), and by light scattering properties. Measurements over pristine rainforest areas during the campaign showed low levels of pollution from biomass burning or industrial emissions, representative of wet season background conditions. The urban plume of Manaus City was found to be joined by plumes from power plants south of the city, all showing evidence of very strong photochemical ozone formation. One episode is discussed in detail, where a threefold increase in ozone mixing ratios within the atmospheric boundary layer occurred within a 100 km travel distance downwind of Manaus. Observation-based estimates of the ozone production rates in the plume reached 15 ppb h(-1). Within the plume core, aerosol concentrations were strongly enhanced, with Delta CN/Delta CO ratios about one order of magnitude higher than observed in Amazon biomass burning plumes. Delta CN/Delta CO ratios tended to decrease with increasing transport time, indicative of a significant reduction in particle number by coagulation, and without substantial new particle nucleation occurring within the time/space observed. While in the background atmosphere a large fraction of the total particle number served as CCN (about 60-80% at 0.6% supersaturation), the CCN/CN ratios within the plume indicated that only a small fraction (16 +/- 12 %) of the plume particles were CCN. The fresh plume aerosols showed relatively weak light scattering efficiency. The CO-normalized CCN concentrations and light scattering coefficients increased with plume age in most cases, suggesting particle growth by condensation of soluble organic or inorganic species. We used a Single Column Chemistry and Transport Model (SCM) to infer the urban pollution emission fluxes of Manaus City, implying observed mixing ratios of CO, NO(x) and VOC. The model can reproduce the temporal/spatial distribution of ozone enhancements in the Manaus plume, both with and without accounting for the distinct (high NO(x)) contribution by the power plants; this way examining the sensitivity of ozone production to changes in the emission rates of NO(x). The VOC reactivity in the Manaus region was dominated by a high burden of biogenic isoprene from the background rainforest atmosphere, and therefore NO(x) control is assumed to be the most effective ozone abatement strategy. Both observations and models show that the agglomeration of NO(x) emission sources, like power plants, in a well-arranged area can decrease the ozone production efficiency in the near field of the urban populated cores. But on the other hand remote areas downwind of the city then bear the brunt, being exposed to increased ozone production and N-deposition. The simulated maximum stomatal ozone uptake fluxes were 4 nmol m(-2) s(-1) close to Manaus, and decreased only to about 2 nmol m(-2) s(-1) within a travel distance >1500 km downwind from Manaus, clearly exceeding the critical threshold level for broadleaf trees. Likewise, the simulated N deposition close to Manaus was similar to 70 kg N ha(-1) a(-1) decreasing only to about 30 kg N ha(-1) a(-1) after three days of simulation.

Hidden vorticity in binary Bose-Einstein condensates

We consider a binary Bose-Einstein condensate (BEC) described by a system of two-dimensional (2D) Gross-Pitaevskii equations with the harmonic-oscillator trapping potential. The intraspecies interactions are attractive, while the interaction between the species may have either sign. The same model applies to the copropagation of bimodal beams in photonic-crystal fibers. We consider a family of trapped hidden-vorticity (HV) modes in the form of bound states of two components with opposite vorticities S(1,2) = +/- 1, the total angular momentum being zero. A challenging problem is the stability of the HV modes. By means of a linear-stability analysis and direct simulations, stability domains are identified in a relevant parameter plane. In direct simulations, stable HV modes feature robustness against large perturbations, while unstable ones split into fragments whose number is identical to the azimuthal index of the fastest growing perturbation eigenmode. Conditions allowing for the creation of the HV modes in the experiment are discussed too. For comparison, a similar but simpler problem is studied in an analytical form, viz., the modulational instability of an HV state in a one-dimensional (1D) system with periodic boundary conditions (this system models a counterflow in a binary BEC mixture loaded into a toroidal trap or a bimodal optical beam coupled into a cylindrical shell). We demonstrate that the stabilization of the 1D HV modes is impossible, which stresses the significance of the stabilization of the HV modes in the 2D setting.

Thermodiffusion in a multicomponent lyotropic mixture in the vicinity of the critical micellar concentration by using the Z-scan technique

Thermodiffusion in a lyotropic mixture of water and potassium laurate is investigated by means of an optical technique (Z scan) distinguishing the index variations due to the temperature gradient and the mass gradients. A phenomenological framework allowing for coupled diffusion is developed in order to analyze thermodiffusion in multicomponent systems. An observable parameter relating to the mass gradients is found to exhibit a sharp change around the critical micellar concentration, and thus may be used to detect it. The change in the slope is due to the markedly different values of the Soret coefficients of the surfactant and the micelles. The difference in the Soret coefficients is due to the fact that the micellization process reduces the energy of interaction of the ball of amphiphilic molecules with the solvent.

Phase diagram of a model for a binary mixture of nematic molecules on a Bethe lattice

We investigate the phase diagram of a discrete version of the Maier-Saupe model with the inclusion of additional degrees of freedom to mimic a distribution of rodlike and disklike molecules. Solutions of this problem on a Bethe lattice come from the analysis of the fixed points of a set of nonlinear recursion relations. Besides the fixed points associated with isotropic and uniaxial nematic structures, there is also a fixed point associated with a biaxial nematic structure. Due to the existence of large overlaps of the stability regions, we resorted to a scheme to calculate the free energy of these structures deep in the interior of a large Cayley tree. Both thermodynamic and dynamic-stability analyses rule out the presence of a biaxial phase, in qualitative agreement with previous mean-field results.

Time correlation function in systems with two coexisting biological species

We study a stochastic lattice model describing the dynamics of coexistence of two interacting biological species. The model comprehends the local processes of birth, death, and diffusion of individuals of each species and is grounded on interaction of the predator-prey type. The species coexistence can be of two types: With self-sustained coupled time oscillations of population densities and without oscillations. We perform numerical simulations of the model on a square lattice and analyze the temporal behavior of each species by computing the time correlation functions as well as the spectral densities. This analysis provides an appropriate characterization of the different types of coexistence. It is also used to examine linked population cycles in nature and in experiment.

Bayesian online algorithms for learning in discrete Hidden Markov Models

We propose and analyze two different Bayesian online algorithms for learning in discrete Hidden Markov Models and compare their performance with the already known Baldi-Chauvin Algorithm. Using the Kullback-Leibler divergence as a measure of generalization we draw learning curves in simplified situations for these algorithms and compare their performances.

Probing neutrino oscillations in supersymmetric models at the Large Hadron Collider

The lightest supersymmetric particle may decay with branching ratios that correlate with neutrino oscillation parameters. In this case the CERN Large Hadron Collider (LHC) has the potential to probe the atmospheric neutrino mixing angle with sensitivity competitive to its low-energy determination by underground experiments. Under realistic detection assumptions, we identify the necessary conditions for the experiments at CERN's LHC to probe the simplest scenario for neutrino masses induced by minimal supergravity with bilinear R parity violation.

Nonsingular bounce in modified gravity

We investigate bouncing solutions in the framework of the nonsingular gravity model of Brandenberger, Mukhanov and Sornborger. We show that a spatially flat universe filled with ordinary matter undergoing a phase of contraction reaches a stage of minimal expansion factor before bouncing in a regular way to reach the expanding phase. The expansion can be connected to the usual radiation-and matter-dominated epochs before reaching a final expanding de Sitter phase. In general relativity (GR), a bounce can only take place provided that the spatial sections are positively curved, a fact that has been shown to translate into a constraint on the characteristic duration of the bounce. In our model, on the other hand, a bounce can occur also in the absence of spatial curvature, which means that the time scale for the bounce can be made arbitrarily short or long. The implication is that constraints on the bounce characteristic time obtained in GR rely heavily on the assumed theory of gravity. Although the model we investigate is fourth order in the derivatives of the metric (and therefore unstable vis-a-vis the perturbations), this generic bounce dynamics should extend to string-motivated nonsingular models which can accommodate a spatially flat bounce.

Deciphering the spin of new resonances in Higgsless models

We study the potential of the CERN large hadron collider to probe the spin of new massive vector boson resonances predicted by Higgsless models. We consider its production via weak boson fusion which relies only on the coupling between the new resonances and the weak gauge bosons. We show that the large hadron collider will be able to unravel the spin of the particles associated with the partial restoration of unitarity in vector boson scattering for integrated luminosities of 150-560 fb(-1), depending on the new state mass and on the method used in the analyses.

Temperature-driven collapse of a coherent binary mixture of condensates

We present a temperature- dependent Hartree- Fock- Bogoliubov- Popov theory to analyze the properties of the equilibrium states of an homogeneous mixture of bosonic atoms in two different hyperfine states and in the presence of an internal Josephson coupling. In our calculation we show that the bistable structure of the equilibrium states at zero temperature changes when we increase the temperature of the system. We investigate two mechanisms of the disappearance of bistability. In one, near the collapse of one of the equilibrium states, the acoustical branch becomes unstable and the gap of the optical branch goes to zero. In the other, there is no divergent behavior of the system and bistability disappears at a temperature in which the two equilibrium states merge at a zero- population fraction imbalance. When we further increase the temperature, this state remains as a unique equilibrium configuration.

Anisotropic singularities in modified gravity models

We show that the common singularities present in generic modified gravity models governed by actions of the type S = integral d(4)x root-gf(R, phi, X). with X = -1/2 g(ab)partial derivative(a)phi partial derivative(b)phi, are essentially the same anisotropic instabilities associated to the hypersurface F(phi) = 0 in the case of a nonminimal coupling of the type F(phi)R, enlightening the physical origin of such singularities that typically arise in rather complex and cumbersome inhomogeneous perturbation analyses. We show, moreover, that such anisotropic instabilities typically give rise to dynamically unavoidable singularities, precluding completely the possibility of having physically viable models for which the hypersurface partial derivative f/partial derivative R = 0 is attained. Some examples are explicitly discussed.

Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation

Positional information in developing embryos is specified by spatial gradients of transcriptional regulators. One of the classic systems for studying this is the activation of the hunchback (hb) gene in early fruit fly (Drosophila) segmentation by the maternally-derived gradient of the Bicoid (Bcd) protein. Gene regulation is subject to intrinsic noise which can produce variable expression. This variability must be constrained in the highly reproducible and coordinated events of development. We identify means by which noise is controlled during gene expression by characterizing the dependence of hb mRNA and protein output noise on hb promoter structure and transcriptional dynamics. We use a stochastic model of the hb promoter in which the number and strength of Bcd and Hb (self-regulatory) binding sites can be varied. Model parameters are fit to data from WT embryos, the self-regulation mutant hb(14F), and lacZ reporter constructs using different portions of the hb promoter. We have corroborated model noise predictions experimentally. The results indicate that WT (self-regulatory) Hb output noise is predominantly dependent on the transcription and translation dynamics of its own expression, rather than on Bcd fluctuations. The constructs and mutant, which lack self-regulation, indicate that the multiple Bcd binding sites in the hb promoter (and their strengths) also play a role in buffering noise. The model is robust to the variation in Bcd binding site number across a number of fly species. This study identifies particular ways in which promoter structure and regulatory dynamics reduce hb output noise. Insofar as many of these are common features of genes (e. g. multiple regulatory sites, cooperativity, self-feedback), the current results contribute to the general understanding of the reproducibility and determinacy of spatial patterning in early development.