1000 resultados para Ondina Ferreira


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Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun to elucidate the demographic history of the species, as well as patterns of population structure and patterns of linkage disequilibrium within its genome. Such studies will be greatly enhanced by new genomic tools and recent large-scale efforts to map genomic variation. To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum. Results: Using an Affymetrix 3,000 SNP assay array, we found roughly half the assays (1,638) yielded high quality, 100% accurate genotyping calls for both major and minor SNP alleles. Genotype data from 76 global isolates confirm significant genetic differentiation among continental populations and varying levels of SNP diversity and linkage disequilibrium according to geographic location and local epidemiological factors. We further discovered that nonsynonymous and silent (synonymous or noncoding) SNPs differ with respect to within-population diversity, interpopulation differentiation, and the degree to which allele frequencies are correlated between populations. Conclusions: The distinct population profile of nonsynonymous variants indicates that natural selection has a significant influence on genomic diversity in P. falciparum, and that many of these changes may reflect functional variants deserving of follow-up study. Our analysis demonstrates the potential for new high-throughput genotyping technologies to enhance studies of population structure, natural selection, and ultimately enable genome-wide association studies in P. falciparum to find genes underlying key phenotypic traits.

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Background: Plasmodium vivax malaria is a major public health challenge in Latin America, Asia and Oceania, with 130-435 million clinical cases per year worldwide. Invasion of host blood cells by P. vivax mainly depends on a type I membrane protein called Duffy binding protein (PvDBP). The erythrocyte-binding motif of PvDBP is a 170 amino-acid stretch located in its cysteine-rich region II (PvDBP(II)), which is the most variable segment of the protein. Methods: To test whether diversifying natural selection has shaped the nucleotide diversity of PvDBP(II) in Brazilian populations, this region was sequenced in 122 isolates from six different geographic areas. A Bayesian method was applied to test for the action of natural selection under a population genetic model that incorporates recombination. The analysis was integrated with a structural model of PvDBP(II), and T-and B-cell epitopes were localized on the 3-D structure. Results: The results suggest that: (i) recombination plays an important role in determining the haplotype structure of PvDBP(II), and (ii) PvDBP(II) appears to contain neutrally evolving codons as well as codons evolving under natural selection. Diversifying selection preferentially acts on sites identified as epitopes, particularly on amino acid residues 417, 419, and 424, which show strong linkage disequilibrium. Conclusions: This study shows that some polymorphisms of PvDBP(II) are present near the erythrocyte-binding domain and might serve to elude antibodies that inhibit cell invasion. Therefore, these polymorphisms should be taken into account when designing vaccines aimed at eliciting antibodies to inhibit erythrocyte invasion.

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Background: The ideal malaria parasite populations for initial mapping of genomic regions contributing to phenotypes such as drug resistance and virulence, through genome-wide association studies, are those with high genetic diversity, allowing for numerous informative markers, and rare meiotic recombination, allowing for strong linkage disequilibrium (LD) between markers and phenotype-determining loci. However, levels of genetic diversity and LD in field populations of the major human malaria parasite P. vivax remain little characterized. Results: We examined single-nucleotide polymorphisms (SNPs) and LD patterns across a 100-kb chromosome segment of P. vivax in 238 field isolates from areas of low to moderate malaria endemicity in South America and Asia, where LD tends to be more extensive than in holoendemic populations, and in two monkey-adapted strains (Salvador-I, from El Salvador, and Belem, from Brazil). We found varying levels of SNP diversity and LD across populations, with the highest diversity and strongest LD in the area of lowest malaria transmission. We found several clusters of contiguous markers with rare meiotic recombination and characterized a relatively conserved haplotype structure among populations, suggesting the existence of recombination hotspots in the genome region analyzed. Both silent and nonsynonymous SNPs revealed substantial between-population differentiation, which accounted for similar to 40% of the overall genetic diversity observed. Although parasites clustered according to their continental origin, we found evidence for substructure within the Brazilian population of P. vivax. We also explored between-population differentiation patterns revealed by loci putatively affected by natural selection and found marked geographic variation in frequencies of nucleotide substitutions at the pvmdr-1 locus, putatively associated with drug resistance. Conclusion: These findings support the feasibility of genome-wide association studies in carefully selected populations of P. vivax, using relatively low densities of markers, but underscore the risk of false positives caused by population structure at both local and regional levels.

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The relativistic heavy ion program developed at RHIC and now at LHC motivated a deeper study of the properties of the quark-gluon plasma (QGP) and, in particular, the study of perturbations in this kind of plasma. We are interested on the time evolution of perturbations in the baryon and energy densities. If a localized pulse in baryon density could propagate throughout the QGP for long distances preserving its shape and without loosing localization, this could have interesting consequences for relativistic heavy ion physics and for astrophysics. A mathematical way to prove that this can happen is to derive (under certain conditions) from the hydrodynamical equations of the QGP a Korteveg-de Vries (KdV) equation. The solution of this equation describes the propagation of a KdV soliton. The derivation of the KdV equation depends crucially on the equation of state (EOS) of the QGP. The use of the simple MIT bag model EOS does not lead to KdV solitons. Recently we have developed an EOS for the QGP which includes both perturbative and nonperturbative corrections to the MIT one and is still simple enough to allow for analytical manipulations. With this EOS we were able to derive a KdV equation for the cold QGP.

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In this paper we study the one-and two-loop contribution to the free energy in QED with Lorentz symmetry breaking introduced via constant CPT-even Lorentz-breaking parameters at the high temperature limit. We find the impact of the Lorentz-violating term for the free energy and carry out a numerical estimation for the Lorentz-breaking parameter.

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The thermodynamic properties of the magnetic semiconductors GaMnAs and GaCrAs are studied under biaxial strain. The calculations are based on the projector augmented wave method combined with the generalized quasichemical approach to treat the disorder and composition effects. Considering the influence of biaxial strain, we find a tendency to the suppression of binodal decomposition mainly for GaMnAs under compressive strain. For a substrate with a lattice constant 5% smaller than the one of GaAs, for GaMnAs, the solubility limit increases up to 40%. Thus, the strain can be a useful tool for tailoring magnetic semiconductors to the formation or not of embedded nanoclusters. (C) 2010 American Institute of Physics. [doi:10.1063/1.3448025]

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The addition of transition metals to III-V semiconductors radically changes their electronic, magnetic, and structural properties. We show by ab initio calculations that in contrast to the conventional semiconductor alloys, the lattice parameter in magnetic semiconductor alloys, including those with diluted concentration, strongly deviates from Vegard's law. We find a direct correlation between the magnetic moment and the anion-transition metal bond lengths and derive a simple and general formula that determines the lattice parameter of a particular magnetic semiconductor by considering both the composition and magnetic moment. This dependence can explain some experimentally observed anomalies and stimulate other kind of investigations.

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We use the density functional theory/local-density approximation (DFT/LDA)-1/2 method [L. G. Ferreira , Phys. Rev. B 78, 125116 (2008)], which attempts to fix the electron self-energy deficiency of DFT/LDA by half-ionizing the whole Bloch band of the crystal, to calculate the band offsets of two Si/SiO(2) interface models. Our results are similar to those obtained with a ""state-of-the-art"" GW approach [R. Shaltaf , Phys. Rev. Lett. 100, 186401 (2008)], with the advantage of being as computationally inexpensive as the usual DFT/LDA. Our band gap and band offset predictions are in excellent agreement with experiments.

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The local-density approximation (LDA) together with the half occupation (transitionstate) is notoriously successful in the calculation of atomic ionization potentials. When it comes to extended systems, such as a semiconductor infinite system, it has been very difficult to find a way to half ionize because the hole tends to be infinitely extended (a Bloch wave). The answer to this problem lies in the LDA formalism itself. One proves that the half occupation is equivalent to introducing the hole self-energy (electrostatic and exchange correlation) into the Schrodinger equation. The argument then becomes simple: The eigenvalue minus the self-energy has to be minimized because the atom has a minimal energy. Then one simply proves that the hole is localized, not infinitely extended, because it must have maximal self-energy. Then one also arrives at an equation similar to the self- interaction correction equation, but corrected for the removal of just 1/2 electron. Applied to the calculation of band gaps and effective masses, we use the self- energy calculated in atoms and attain a precision similar to that of GW, but with the great advantage that it requires no more computational effort than standard LDA.

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We present a class of solutions of the CP(N) model in (3 + 1) dimensions. We suggest that they represent vortexlike configurations. We also discuss some of their properties. We show that some configurations of vortices have a divergent energy per unit length while for the others such an energy has a minimum for a very special orientation of vortices. We also discuss the Noether charge densities of these vortices.

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We study the propagation of perturbations in the quark gluon plasma. This subject has been addressed in other works and in most of the theoretical descriptions of this phenomenon the hydrodynamic equations have been linearized for simplicity. We propose an alternative approach, also based on hydrodynamics but taking into account the nonlinear terms of the equations. We show that these terms may lead to localized waves or even solitons. We use a simple equation of state for the QGP and expand the hydrodynamic equations around equilibrium configurations. The resulting differential equations describe the propagation of perturbations in the energy density. We solve them numerically and find that localized perturbations can propagate for long distances in the plasma. Under certain conditions our solutions mimic the propagation of Korteweg-de Vries solitons.

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The longitudinal resistivity rho(xx) of two-dimensional electron gases formed in wells with two subbands displays ringlike structures when plotted in a density-magnetic-field diagram, due to the crossings of spin-split Landau levels (LLs) from distinct subbands. Using spin density functional theory and linear response, we investigate the shape and spin polarization of these structures as a function of temperature and magnetic-field tilt angle. We find that (i) some of the rings ""break'' at sufficiently low temperatures due to a quantum Hall ferromagnetic phase transition, thus exhibiting a high degree of spin polarization (similar to 50%) within, consistent with the NMR data of Zhang et al. [Phys. Rev. Lett. 98, 246802 (2007)], and (ii) for increasing tilting angles the interplay between the anticrossings due to inter-LL couplings and the exchange-correlation effects leads to a collapse of the rings at some critical angle theta(c), in agreement with the data of Guo et al. [Phys. Rev. B 78, 233305 (2008)].

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We theoretically investigate negative differential resistance (NDR) for ballistic transport in semiconducting armchair graphene nanoribbon (aGNR) superlattices (5 to 20 barriers) at low bias voltages V(SD) < 500 mV. We combine the graphene Dirac Hamiltonian with the Landauer-Buttiker formalism to calculate the current I(SD) through the system. We find three distinct transport regimes in which NDR occurs: (i) a ""classical"" regime for wide layers, through which the transport across band gaps is strongly suppressed, leading to alternating regions of nearly unity and zero transmission probabilities as a function of V(SD) due to crossing of band gaps from different layers; (ii) a quantum regime dominated by superlattice miniband conduction, with current suppression arising from the misalignment of miniband states with increasing V(SD); and (iii) a Wannier-Stark ladder regime with current peaks occurring at the crossings of Wannier-Stark rungs from distinct ladders. We observe NDR at voltage biases as low as 10 mV with a high current density, making the aGNR superlattices attractive for device applications.

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The diluted magnetic semiconductors are promising materials for spintronic applications. Usually one intents to find the ferromagnetic state but recently the antiferromagnetism (AFM) was proposed to have some advantages. In this work, we verify the possibility to obtain spin polarization with an AFM state. In particular, we studied GaN 5% double doped with two different transition metals atoms (Mn and Co or Cr and Ni), forming the Mn(x)Co(0.056-x)Ga(0.944)N and Cr(x)Ni(0.056-x)Ga(0.944)N quaternary alloys. In order to simulate these systems in a more realistic way, and take into account composition fluctuations, we adapted the generalized quasichemical approach to diluted alloys, which is used in combination with spin density-functional theory. We find that is possible to obtain an AFM ground state up to 70% spin polarization.

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We present parameter-free calculations of electronic properties of InGaN, InAlN, and AlGaN alloys. The calculations are based on a generalized quasichemical approach, to account for disorder and composition effects, and first-principles calculations within the density functional theory with the LDA-1/2 approach, to accurately determine the band gaps. We provide precise results for AlGaN, InGaN, and AlInN band gaps for the entire range of compositions, and their respective bowing parameters. (C) 2011 American Institute of Physics. [doi:10.1063/1.3576570]