Validation of reference genes for gene expression studies in the honey bee, Apis mellifera, by quantitative real-time RT-PCR

For obtaining accurate and reliable gene expression results it is essential that quantitative real-time RT-PCR (qRT-PCR) data are normalized with appropriate reference genes. The current exponential increase in postgenomic studies on the honey bee, Apis mellifera, makes the standardization of qRT-PCR results an important task for ongoing community efforts. For this aim we selected four candidate reference genes (actin, ribosomal protein 49, elongation factor 1-alpha, tbp-association factor) and used three software-based approaches (geNorm, BestKeeper and NormFinder) to evaluate the suitability of these genes as endogenous controls. Their expression was examined during honey bee development, in different tissues, and after juvenile hormone exposure. Furthermore, the importance of choosing an appropriate reference gene was investigated for two developmentally regulated target genes. The results led us to consider all four candidate genes as suitable genes for normalization in A. mellifera. However, each condition evaluated in this study revealed a specific set of genes as the most appropriated ones.

Data collapse, scaling functions, and analytical solutions of generalized growth models

We consider a nontrivial one-species population dynamics model with finite and infinite carrying capacities. Time-dependent intrinsic and extrinsic growth rates are considered in these models. Through the model per capita growth rate we obtain a heuristic general procedure to generate scaling functions to collapse data into a simple linear behavior even if an extrinsic growth rate is included. With this data collapse, all the models studied become independent from the parameters and initial condition. Analytical solutions are found when time-dependent coefficients are considered. These solutions allow us to perceive nontrivial transitions between species extinction and survival and to calculate the transition's critical exponents. Considering an extrinsic growth rate as a cancer treatment, we show that the relevant quantity depends not only on the intensity of the treatment, but also on when the cancerous cell growth is maximum.

rho(0) photoproduction in ultraperipheral relativistic heavy ion collisions at root s(NN)=200 GeV

Photoproduction reactions occur when the electromagnetic field of a relativistic heavy ion interacts with another heavy ion. The STAR Collaboration presents a measurement of rho(0) and direct pi(+)pi(-) photoproduction in ultraperipheral relativistic heavy ion collisions at root s(NN) = 200 GeV. We observe both exclusive photoproduction and photoproduction accompanied by mutual Coulomb excitation. We find a coherent cross section of sigma(AuAu -> Au*Au*rho(0)) = 530 +/- 19(stat.) +/- 57(syst.) mb, in accord with theoretical calculations based on a Glauber approach, but considerably below the predictions of a color dipole model. The rho 0 transverse momentum spectrum (p(T)(2)) is fit by a double exponential curve including both coherent and incoherent coupling to the target nucleus; we find sigma(inc)/sigma(coh) = 0.29 +/- 0.03 (stat.) +/- 0.08 (syst.). The ratio of direct pi(+)pi(-) to rho(0) production is comparable to that observed in gamma(p) collisions at HERA and appears to be independent of photon energy. Finally, the measured rho(0) spin helicity matrix elements agree within errors with the expected s-channel helicity conservation.

Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in Sao Paulo, Brazil

The dengue virus has a single-stranded positive-sense RNA genome of similar to 10.700 nucleotides with a single open reading frame that encodes three structural (C, prM, and E) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. It possesses four antigenically distinct serotypes (DENV 1-4). Many phylogenetic studies address particularities of the different serotypes using convenience samples that are not conducive to a spatio-temporal analysis in a single urban setting. We describe the pattern of spread of distinct lineages of DENV-3 circulating in Sao Jose do Rio Preto, Brazil, during 2006. Blood samples from patients presenting dengue-like symptoms were collected for DENV testing. We performed M-N-PCR using primers based on NS5 for virus detection and identification. The fragments were purified from PCR mixtures and sequenced. The positive dengue cases were geo-coded. To type the sequenced samples, 52 reference sequences were aligned. The dataset generated was used for iterative phylogenetic reconstruction with the maximum likelihood criterion. The best demographic model, the rate of growth, rate of evolutionary change, and Time to Most Recent Common Ancestor (TMRCA) were estimated. The basic reproductive rate during the epidemics was estimated. We obtained sequences from 82 patients among 174 blood samples. We were able to geo-code 46 sequences. The alignment generated a 399-nucleotide-long dataset with 134 taxa. The phylogenetic analysis indicated that all samples were of DENV-3 and related to strains circulating on the isle of Martinique in 2000-2001. Sixty DENV-3 from Sao Jose do Rio Preto formed a monophyletic group (lineage 1), closely related to the remaining 22 isolates (lineage 2). We assumed that these lineages appeared before 2006 in different occasions. By transforming the inferred exponential growth rates into the basic reproductive rate, we obtained values for lineage 1 of R(0) = 1.53 and values for lineage 2 of R(0) = 1.13. Under the exponential model, TMRCA of lineage 1 dated 1 year and lineage 2 dated 3.4 years before the last sampling. The possibility of inferring the spatio-temporal dynamics from genetic data has been generally little explored, and it may shed light on DENV circulation. The use of both geographic and temporally structured phylogenetic data provided a detailed view on the spread of at least two dengue viral strains in a populated urban area.

Cold Nuclear Matter Effects on J/psi Yields as a Function of Rapidity and Nuclear Geometry in d plus A Collisions at root S(NN)=200 GeV

We present measurements of J/psi yields in d + Au collisions at root S(NN) = 200 GeV recorded by the PHENIX experiment and compare them with yields in p + p collisions at the same energy per nucleon-nucleon collision. The measurements cover a large kinematic range in J/psi rapidity (-2.2 < y < 2.4) with high statistical precision and are compared with two theoretical models: one with nuclear shadowing combined with final state breakup and one with coherent gluon saturation effects. In order to remove model dependent systematic uncertainties we also compare the data to a simple geometric model. The forward rapidity data are inconsistent with nuclear modifications that are linear or exponential in the density weighted longitudinal thickness, such as those from the final state breakup of the bound state.

Enhanced Production of Direct Photons in Au plus Au Collisions at root s(NN)=200 GeV and Implications for the Initial Temperature

The production of e(+)e(-) pairs for m(e+e-) < 0.3 GeV/c(2) and 1< p(T) < 5 GeV/c is measured in p + p and Au + Au collisions at root s(NN) = 200 GeV. An enhanced yield above hadronic sources is observed. Treating the excess as photon internal conversions, the invariant yield of direct photons is deduced. In central Au + Au collisions, the excess of the direct photon yield over p + p is exponential in transverse momentum, with an inverse slope T = 221 +/- 19(stat) +/- 19(syst) MeV. Hydrodynamical models with initial temperatures ranging from T(init) similar to 300-600 MeV at times of similar to 0.6-0.15 fm/c after the collision are in qualitative agreement with the data. Lattice QCD predicts a phase transition to quark gluon plasma at similar to 170 MeV.

Detailed measurement of the e(+)e(-) pair continuum in p plus p and Au plus Au collisions at root s(NN)=200 GeV and implications for direct photon production

PHENIX has measured the e(+)e(-) pair continuum in root s(NN) = 200 GeV Au+Au and p+p collisions over a wide range of mass and transverse momenta. The e(+)e(-) yield is compared to the expectations from hadronic sources, based on PHENIX measurements. In the intermediate-mass region, between the masses of the phi and the J/psi meson, the yield is consistent with expectations from correlated c (c) over bar production, although other mechanisms are not ruled out. In the low-mass region, below the phi, the p+p inclusive mass spectrum is well described by known contributions from light meson decays. In contrast, the Au+Au minimum bias inclusive mass spectrum in this region shows an enhancement by a factor of 4.7 +/- 0.4(stat) +/- 1.5(syst) +/- 0.9(model). At low mass (m(ee) < 0.3 GeV/c(2)) and high p(T) (1 < p(T) < 5 GeV/c) an enhanced e(+)e(-) pair yield is observed that is consistent with production of virtual direct photons. This excess is used to infer the yield of real direct photons. In central Au+Au collisions, the excess of the direct photon yield over the p+p is exponential in p(T), with inverse slope T = 221 +/- 19(stat) +/- 19(syst) MeV. Hydrodynamical models with initial temperatures ranging from T(init) similar or equal to 300-600 MeV at times of 0.6-0.15 fm/c after the collision are in qualitative agreement with the direct photon data in Au+Au. For low p(T) < 1 GeV/c the low-mass region shows a further significant enhancement that increases with centrality and has an inverse slope of T similar or equal to 100 MeV. Theoretical models underpredict the low-mass, low-p(T) enhancement.

Dynamical estimates of chaotic systems from Poincare recurrences

We show a function that fits well the probability density of return times between two consecutive visits of a chaotic trajectory to finite size regions in phase space. It deviates from the exponential statistics by a small power-law term, a term that represents the deterministic manifestation of the dynamics. We also show how one can quickly and easily estimate the Kolmogorov-Sinai entropy and the short-term correlation function by realizing observations of high probable returns. Our analyses are performed numerically in the Henon map and experimentally in a Chua's circuit. Finally, we discuss how our approach can be used to treat the data coming from experimental complex systems and for technological applications. (C) 2009 American Institute of Physics. [doi: 10.1063/1.3263943]

Angular-planar CMB power spectrum

Gaussianity and statistical isotropy of the Universe are modern cosmology's minimal set of hypotheses. In this work we introduce a new statistical test to detect observational deviations from this minimal set. By defining the temperature correlation function over the whole celestial sphere, we are able to independently quantify both angular and planar dependence (modulations) of the CMB temperature power spectrum over different slices of this sphere. Given that planar dependence leads to further modulations of the usual angular power spectrum C(l), this test can potentially reveal richer structures in the morphology of the primordial temperature field. We have also constructed an unbiased estimator for this angular-planar power spectrum which naturally generalizes the estimator for the usual C(l)'s. With the help of a chi-square analysis, we have used this estimator to search for observational deviations of statistical isotropy in WMAP's 5 year release data set (ILC5), where we found only slight anomalies on the angular scales l = 7 and l = 8. Since this angular-planar statistic is model-independent, it is ideal to employ in searches of statistical anisotropy (e.g., contaminations from the galactic plane) and to characterize non-Gaussianities.

Long life of Gauss-Bonnet corrected black holes

Dictated by the string theory and various higher dimensional scenarios, black holes in D > 4-dimensional space-times must have higher curvature corrections. The first and dominant term is quadratic in curvature, and called the Gauss-Bonnet (GB) term. We shall show that although the Gauss-Bonnet correction changes black hole's geometry only softly, the emission of gravitons is suppressed by many orders even at quite small values of the GB coupling. The huge suppression of the graviton emission is due to the multiplication of the two effects: the quick cooling of the black hole when one turns on the GB coupling and the exponential decreasing of the gray-body factor of the tensor type of gravitons at small and moderate energies. At higher D the tensor gravitons emission is dominant, so that the overall lifetime of black holes with Gauss-Bonnet corrections is many orders larger than was expected. This effect should be relevant for the future experiments at the Large Hadron Collider (LHC).

Substrate orientation effect on potential fluctuations in multiquantum wells of GaAs/AlGaAs

The photoluminescence (PL) technique as a function of temperature and excitation intensity was used to study the optical properties of multiquantum wells (MQWs) of GaAs/Al(x)Ga(1-x)As grown by molecular beam epitaxy on GaAs substrates oriented in the [100], [311]A, and [311]B directions. The asymmetry presented by the PL spectra of the MQWs with an apparent exponential tail in the lower-energy side and the unusual behavior of the PL peak energy versus temperature (blueshift) at low temperatures are explained by the exciton localization in the confinement potential fluctuations of the heterostructures. The PL peak energy dependence with temperature was fitted by the expression proposed by Passler [Phys. Status Solidi B 200, 155 (1997)] by subtracting the term sigma(2)(E)/k(B)T, which considers the presence of potential fluctuations. It can be verified from the PL line shape, the full width at half maximum of PL spectra, the sigma(E) values obtained from the adjustment of experimental points, and the blueshift maximum values that the samples grown in the [311]A/B directions have higher potential fluctuation amplitude than the sample grown in the [100] direction. This indicates a higher degree of the superficial corrugations for the MQWs grown in the [311] direction. (C) 2008 American Institute of Physics.

Awaking the Vacuum in Relativistic Stars

Void of any inherent structure in classical physics, the vacuum has revealed to be incredibly crowded with all sorts of processes in relativistic quantum physics. Yet, its direct effects are usually so subtle that its structure remains almost as evasive as in classical physics. Here, in contrast, we report on the discovery of a novel effect according to which the vacuum is compelled to play an unexpected central role in an astrophysical context. We show that the formation of relativistic stars may lead the vacuum energy density of a quantum field to an exponential growth. The vacuum-driven evolution which would then follow may lead to unexpected implications for astrophysics, while the observation of stable neutron-star configurations may teach us much on the field content of our Universe.

INFERENCE FOR EIGENVALUES AND EIGENVECTORS OF GAUSSIAN SYMMETRIC MATRICES

This article presents maximum likelihood estimators (MLEs) and log-likelihood ratio (LLR) tests for the eigenvalues and eigenvectors of Gaussian random symmetric matrices of arbitrary dimension, where the observations are independent repeated samples from one or two populations. These inference problems are relevant in the analysis of diffusion tensor imaging data and polarized cosmic background radiation data, where the observations are, respectively, 3 x 3 and 2 x 2 symmetric positive definite matrices. The parameter sets involved in the inference problems for eigenvalues and eigenvectors are subsets of Euclidean space that are either affine subspaces, embedded submanifolds that are invariant under orthogonal transformations or polyhedral convex cones. We show that for a class of sets that includes the ones considered in this paper, the MLEs of the mean parameter do not depend on the covariance parameters if and only if the covariance structure is orthogonally invariant. Closed-form expressions for the MLEs and the associated LLRs are derived for this covariance structure.

Hitting and returning to rare events for all alpha-mixing processes

We prove that for any a-mixing stationary process the hitting time of any n-string A(n) converges, when suitably normalized, to an exponential law. We identify the normalization constant lambda(A(n)). A similar statement holds also for the return time. To establish this result we prove two other results of independent interest. First, we show a relation between the rescaled hitting time and the rescaled return time, generalizing a theorem of Haydn, Lacroix and Vaienti. Second, we show that for positive entropy systems, the probability of observing any n-string in n consecutive observations goes to zero as n goes to infinity. (c) 2010 Elsevier B.V. All rights reserved.

Phosphorus kinetics in growing hair sheep

Kinetics modelling was used to study the effects of different dietary phosphorus (P) levels on P metabolism in young sheep. An experiment was conducted with 12 Santa Ines lambs receiving a basal diet of a hay-concentrate mixture. Different amounts of dicalcium phosphate were added to the basal diet, to give the following treatments levels of 0, 1.5, 3 and 4.5 g/animal/day. The isotopic dilution technique (32 p) was used for analyze four compartments: gastrointestinal tract, plasma, bone and soft tissues (liver, heart, kidney and muscle), as well as nutrient flows between them. All P flows showed a positive linear or exponential relationship with P intake. Both incorporation and reabsorption in bone and soft tissue increased with increasing P levels in the diet, with positive retention above 3 g/day. On the 4.5g P/day treatment, reduced P absorption and increased P in the faeces from dietary origin was noted. Three g/day of P treatment was sufficient to meet soft tissue requirements for young sheep. (C) 2008 Elsevier B.V. All rights reserved.