Induction of Heme Oxygenase-1 Can Halt and Even Reverse Renal Tubule-Interstitial Fibrosis

Background: The tubule-interstitial fibrosis is the hallmark of progressive renal disease and is strongly associated with inflammation of this compartment. Heme-oxygenase-1 (HO-1) is a cytoprotective molecule that has been shown to be beneficial in various models of renal injury. However, the role of HO-1 in reversing an established renal scar has not yet been addressed. Aim: We explored the ability of HO-1 to halt and reverse the establishment of fibrosis in an experimental model of chronic renal disease. Methods: Sprague-Dawley male rats were subjected to unilateral ureteral obstruction (UUO) and divided into two groups: non-treated and Hemin-treated. To study the prevention of fibrosis, animals were pre-treated with Hemin at days -2 and -1 prior to UUO. To investigate whether HO-1 could reverse established fibrosis, Hemin therapy was given at days 6 and 7 post-surgery. After 7 and/or 14 days, animals were sacrificed and blood, urine and kidney tissue samples were collected for analyses. Renal function was determined by assessing the serum creatinine, inulin clearance, proteinuria/creatininuria ratio and extent of albuminuria. Arterial blood pressure was measured and fibrosis was quantified by Picrosirius staining. Gene and protein expression of pro-inflammatory and pro-fibrotic molecules, as well as HO-1 were performed. Results: Pre-treatment with Hemin upregulated HO-1 expression and significantly reduced proteinuria, albuminuria, inflammation and pro-fibrotic protein and gene expressions in animals subjected to UUO. Interestingly, the delayed treatment with Hemin was also able to reduce renal dysfunction and to decrease the expression of pro-inflammatory molecules, all in association with significantly reduced levels of fibrosis-related molecules and collagen deposition. Finally, TGF-beta protein production was significantly lower in Hemin-treated animals. Conclusion: Treatment with Hemin was able both to prevent the progression of fibrosis and to reverse an established renal scar. Modulation of inflammation appears to be the major mechanism behind HO-1 cytoprotection.

Spectral dependence of aerosol light absorption over the Amazon Basin

In this study, we examine the spectral dependence of aerosol absorption at different sites and seasons in the Amazon Basin. The analysis is based on measurements performed during three intensive field experiments at a pasture site (Fazenda Nossa Senhora, Rondonia) and at a primary forest site (Cuieiras Reserve, Amazonas), from 1999 to 2004. Aerosol absorption spectra were measured using two Aethalometers: a 7-wavelength Aethalometer (AE30) that covers the visible (VIS) to near-infrared (NIR) spectral range, and a 2-wavelength Aethalometer (AE20) that measures absorption in the UV and in the NIR. As a consequence of biomass burning emissions, about 10 times greater absorption values were observed in the dry season in comparison to the wet season. Power law expressions were fitted to the measurements in order to derive the absorption Angstrom exponent, defined as the negative slope of absorption versus wavelength in a log-log plot. At the pasture site, about 70% of the absorption Angstrom exponents fell between 1.5 and 2.5 during the dry season, indicating that biomass burning aerosols have a stronger spectral dependence than soot carbon particles. Angstrom exponents decreased from the dry to the wet season, in agreement with the shift from biomass burning aerosols, predominant in the fine mode, to biogenic and dust aerosols, predominant in the coarse mode. The lowest absorption Angstrom exponents (90% of data below 1.5) were observed at the forest site during the dry season. Also, results indicate that low absorption coefficients were associated with low Angstrom exponents. This finding suggests that biogenic aerosols from Amazonia have a weaker spectral dependence for absorption than biomass burning aerosols, contradicting our expectations of biogenic particles behaving as brown carbon. In a first order assessment, results indicate a small (<1 %) effect of variations in absorption Angstrom exponents on 24-h aerosol forcings, at least in the spectral range of 450-880 nm. Further studies should be taken to assess the corresponding impact in the UV spectral range. The assumption that soot spectral properties represent all ambient light absorbing particles may cause a misjudgment of absorption towards the UV, especially in remote areas. Therefore, it is recommended to measure aerosol absorption at several wavelengths to accurately assess the impact of non-soot aerosols on climate and on photochemical atmospheric processes.

Combining Monte Carlo simulation and density-functional theory to describe the spectral changes of Na(2) in liquid helium

Spectral changes of Na(2) in liquid helium were studied using the sequential Monte Carlo-quantum mechanics method. Configurations composed by Na(2) surrounded by explicit helium atoms sampled from the Monte Carlo simulation were submitted to time-dependent density-functional theory calculations of the electronic absorption spectrum using different functionals. Attention is given to both line shift and line broadening. The Perdew, Burke, and Ernzerhof (PBE1PBE, also known as PBE0) functional, with the PBE1PBE/6-311++G(2d,2p) basis set, gives the spectral shift, compared to gas phase, of 500 cm(-1) for the allowed X (1)Sigma(+)(g) -> B (1)Pi(u) transition, in very good agreement with the experimental value (700 cm(-1)). For comparison, cluster calculations were also performed and the first X (1)Sigma(+)(g) -> A (1)Sigma(+)(u) transition was also considered.

Study of the optical and magnetic properties of pyrimidine in water combining PCM and QM/MM methodologies

The solvent effects on the low-lying absorption spectrum and on the (15)N chemical shielding of pyrimidine in water are calculated using the combined and sequential Monte Carlo simulation and quantum mechanical calculations. Special attention is devoted to the solute polarization. This is included by an iterative procedure previously developed where the solute is electrostatically equilibrated with the solvent. In addition, we verify the simple yet unexplored alternative of combining the polarizable continuum model (PCM) and the hybrid QM/MM method. We use PCM to obtain the average solute polarization and include this in the MM part of the sequential QM/MM methodology, PCM-MM/QM. These procedures are compared and further used in the discrete and the explicit solvent models. The use of the PCM polarization implemented in the MM part seems to generate a very good description of the average solute polarization leading to very good results for the n-pi* excitation energy and the (15)N nuclear chemical shield of pyrimidine in aqueous environment. The best results obtained here using the solute pyrimidine surrounded by 28 explicit water molecules embedded in the electrostatic field of the remaining 472 molecules give the statistically converged values for the low lying n-pi* absorption transition in water of 36 900 +/- 100 (PCM polarization) and 36 950 +/- 100 cm(-1) (iterative polarization), in excellent agreement among one another and with the experimental value observed with a band maximum at 36 900 cm(-1). For the nuclear shielding (15)N the corresponding gas-water chemical shift obtained using the solute pyrimidine surrounded by 9 explicit water molecules embedded in the electrostatic field of the remaining 491 molecules give the statistically converged values of 24.4 +/- 0.8 and 28.5 +/- 0.8 ppm, compared with the inferred experimental value of 19 +/- 2 ppm. Considering the simplicity of the PCM over the iterative polarization this is an important aspect and the computational savings point to the possibility of dealing with larger solute molecules. This PCM-MM/QM approach reconciles the simplicity of the PCM model with the reliability of the combined QM/MM approaches.

Supergraph techniques for D=3, N=1 broken supersymmetric theories

We enlarge the usual D = 3 N = 1 supergraph techniques to include the case of (explicitly or spontaneously) broken supersymmetric gauge theories. To illustrate the utility of these techniques, we calculate the two-loop effective potential of the SQED(3) by using the tadpole and the vacuum bubble methods. In these methods, to investigate the possibility of supersymmetry breaking, the superfields must be shifted by theta(alpha) dependent classical superfields (vacuum expectation values), what implies in the explicit breakdown of supersymmetry in the intermediate steps of the calculation. Nevertheless, after studying the minimum of the resulting effective potential, we find that supersymmetry is conserved, while gauge symmetry is dynamically broken, with a mass generated for the gauge superfield.

Simple analytic model for astrophysical S factors

We propose a physically transparent analytic model of astrophysical S factors as a function of a center-of-mass energy E of colliding nuclei (below and above the Coulomb barrier) for nonresonant fusion reactions. For any given reaction, the S(E) model contains four parameters [two of which approximate the barrier potential, U(r)]. They are easily interpolated along many reactions involving isotopes of the same elements; they give accurate practical expressions for S(E) with only several input parameters for many reactions. The model reproduces the suppression of S(E) at low energies (of astrophysical importance) due to the shape of the low-r wing of U(r). The model can be used to reconstruct U(r) from computed or measured S(E). For illustration, we parametrize our recent calculations of S(E) (using the Sao Paulo potential and the barrier penetration formalism) for 946 reactions involving stable and unstable isotopes of C, O, Ne, and Mg (with nine parameters for all reactions involving many isotopes of the same elements, e. g., C+O). In addition, we analyze astrophysically important (12)C+(12)C reaction, compare theoretical models with experimental data, and discuss the problem of interpolating reliably known S(E) values to low energies (E less than or similar to 2-3 MeV).

One-loop energy-momentum tensor in QED with electriclike background

We have obtained nonperturbative one-loop expressions for the mean-energy-momentum tensor and current density of Dirac's field on a constant electriclike back-round. One of the goals of this calculation is to give a consistent description of backreaction in such a theory. Two cases of initial states are considered: the vacuum state and the thermal equilibrium state. First, we perform calculations for the vacuum initial state. In the obtained expressions, we separate the contributions due to particle creation and vacuum polarization. The latter contribution,, are related to the Heisenberg-Euler Lagrangian. Then, we Study the case of the thermal initial state. Here, we separate the contributions due to particle creation, vacuum polarization, and the contributions due to the work of the external field on the particles at the initial state. All these contributions are studied in detail, in different regimes of weak and strong fields and low and high temperatures. The obtained results allow us to establish restrictions on the electric field and its duration under which QED with a strong constant electric field is consistent. Under such restrictions, one can neglect the backreaction of particles created by the electric field. Some of the obtained results generalize the calculations of Heisenberg-Euler for energy density to the case of arbitrary strong electric fields.

Gravitational wave recoil in Robinson-Trautman spacetimes

We consider the gravitational recoil due to nonreflection-symmetric gravitational wave emission in the context of axisymmetric Robinson-Trautman spacetimes. We show that regular initial data evolve generically into a final configuration corresponding to a Schwarzschild black hole moving with constant speed. For the case of (reflection-)symmetric initial configurations, the mass of the remnant black hole and the total energy radiated away are completely determined by the initial data, allowing us to obtain analytical expressions for some recent numerical results that have appeared in the literature. Moreover, by using the Galerkin spectral method to analyze the nonlinear regime of the Robinson-Trautman equations, we show that the recoil velocity can be estimated with good accuracy from some asymmetry measures (namely the first odd moments) of the initial data. The extension for the nonaxisymmetric case and the implications of our results for realistic situations involving head-on collision of two black holes are also discussed.

Cooperative scattering and radiation pressure force in dense atomic clouds

Atomic clouds prepared in ""timed Dicke"" states, i.e. states where the phase of the oscillating atomic dipole moments linearly varies along one direction of space, are efficient sources of superradiant light emission [Scully et al., Phys. Rev. Lett. 96, 010501 (2006)]. Here, we show that, in contrast to previous assertions, timed Dicke states are not the states automatically generated by incident laser light. In reality, the atoms act back on the driving field because of the finite refraction of the cloud. This leads to nonuniform phase shifts, which, at higher optical densities, dramatically alter the cooperative scattering properties, as we show by explicit calculation of macroscopic observables, such as the radiation pressure force.

Universal and nonuniversal contributions to block-block entanglement in many-fermion systems

We calculate the entanglement entropy of blocks of size x embedded in a larger system of size L, by means of a combination of analytical and numerical techniques. The complete entanglement entropy in this case is a sum of three terms. One is a universal x- and L-dependent term, first predicted by Calabrese and Cardy, the second is a nonuniversal term arising from the thermodynamic limit, and the third is a finite size correction. We give an explicit expression for the second, nonuniversal, term for the one-dimensional Hubbard model, and numerically assess the importance of all three contributions by comparing to the entropy obtained from fully numerical diagonalization of the many-body Hamiltonian. We find that finite-size corrections are very small. The universal Calabrese-Cardy term is equally small for small blocks, but becomes larger for x > 1. In all investigated situations, however, the by far dominating contribution is the nonuniversal term stemming from the thermodynamic limit.

Energy spectra for quantum wires and two-dimensional electron gases in magnetic fields with Rashba and Dresselhaus spin-orbit interactions

We introduce an analytical approximation scheme to diagonalize parabolically confined two-dimensional (2D) electron systems with both the Rashba and Dresselhaus spin-orbit interactions. The starting point of our perturbative expansion is a zeroth-order Hamiltonian for an electron confined in a quantum wire with an effective spin-orbit induced magnetic field along the wire, obtained by properly rotating the usual spin-orbit Hamiltonian. We find that the spin-orbit-related transverse coupling terms can be recast into two parts W and V, which couple crossing and noncrossing adjacent transverse modes, respectively. Interestingly, the zeroth-order Hamiltonian together with W can be solved exactly, as it maps onto the Jaynes-Cummings model of quantum optics. We treat the V coupling by performing a Schrieffer-Wolff transformation. This allows us to obtain an effective Hamiltonian to third order in the coupling strength k(R)l of V, which can be straightforwardly diagonalized via an additional unitary transformation. We also apply our approach to other types of effective parabolic confinement, e. g., 2D electrons in a perpendicular magnetic field. To demonstrate the usefulness of our approximate eigensolutions, we obtain analytical expressions for the nth Landau-level g(n) factors in the presence of both Rashba and Dresselhaus couplings. For small values of the bulk g factors, we find that spin-orbit effects cancel out entirely for particular values of the spin-orbit couplings. By solving simple transcendental equations we also obtain the band minima of a Rashba-coupled quantum wire as a function of an external magnetic field. These can be used to describe Shubnikov-de Haas oscillations. This procedure makes it easier to extract the strength of the spin-orbit interaction in these systems via proper fitting of the data.

Analytical results on Muller's ratchet effect in growing populations

Fontanari introduced [Phys. Rev. Lett. 91, 218101 (2003)] a model for studying Muller's ratchet phenomenon in growing asexual populations. They studied two situations, either including a death probability for each newborn or not, but were able to find analytical (recursive) expressions only in the no-decay case. In this Brief Report a branching process formalism is used to find recurrence equations that generalize the analytical results of the original paper besides confirming the interesting effects their simulations revealed.

Contribution of the second Landau level to the exchange energy of the three-dimensional electron gas in a high magnetic field

We derive a closed analytical expression for the exchange energy of the three-dimensional interacting electron gas in strong magnetic fields, which goes beyond the quantum limit (L=0) by explicitly including the effect of the second, L=1, Landau level and arbitrary spin polarization. The inclusion of the L=1 level brings the fields to which the formula applies closer to the laboratory range, as compared to previous expressions, valid only for L=0 and complete spin polarization. We identify and explain two distinct regimes separated by a critical density n(c). Below n(c), the per particle exchange energy is lowered by the contribution of L=1, whereas above n(c) it is increased. As special cases of our general equation we recover various known more limited results for higher fields, and we identify and correct a few inconsistencies in some of these earlier expressions.

Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.

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.