April 2002: Counting the Cost: Human and Financial Resources

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Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies

Paracoccidioides brasiliensis is the etiologic agent of paracoccidioidomycosis, a disease confined to Latin America and of marked importance in the endemic areas due to its frequency and severity. This species is considered to be clonal according to mycological criteria and has been shown to vary in virulence. To characterize natural genetic variation and reproductive mode in this fungus, we analyzed P. brasiliensis phylogenetically in search of cryptic species and possible recombination using concordance and nondiscordance of gene genealogies with respect to phylogenies of eight regions in five nuclear loci. Our data indicate that this fungus consists of at least three distinct, previously unrecognized species: S1 (species 1 with 38 isolates), PS2 (phylogenetic species 2 with six isolates), and PS3 (phylogenetic species 3 with 21 isolates). Genealogies of four of the regions studied strongly supported the PS2 clade, composed of five Brazilian and one Venezuelan isolate. The second clade, PS3, composed solely of 21 Colombian isolates, was strongly supported by the alpha-tubulin genealogy. The remaining 38 individuals formed S1. Two of the three lineages of P. brasiliensis, S1 and PS2, are sympatric across their range, suggesting barriers to gene flow other than geographic isolation. Our study provides the first evidence for possible sexual reproduction in P. brasiliensis S1, but does not rule it out in the other two species.

Renormalization of singular potentials and power counting

We use a toy model to illustrate how to build effective theories for singular potentials. We consider a central attractive 1/r(2) potential perturbed by a 1/r(4) correction. The power-counting rule, an important ingredient of effective theory, is established by seeking the minimum set of short-range counterterms that renormalize the scattering amplitude. We show that leading-order counterterms are needed in all partial waves where the potential overcomes the centrifugal barrier, and that the additional counterterms at next-to-leading order are the ones expected on the basis of dimensional analysis. (C) 2008 Elsevier B.V. All rights reserved.

Reading, equivalence, and recombination of units: A replication with students with different learning histories

First graders, preschoolers, special education students, and adults received a reading program in which they learned to match printed to dictated words and to construct (copy) printed words. The students not only learned to match the training words but also learned to read them. In addition, most of the students learned to read new words that involved recombinations of the syllables of the training words. The results replicate and extend the generality of a prior analysis of a reading program based on stimulus equivalence and recombination of units.

Stress induced ordering due to interstitial elements in Nb and Ta by frequency analysis

It is well known that the interstitial elements present in solid solution in metals interact with the matrix by a relaxation process known as stress induced ordering. Traditionally this relaxation process is observed in the internal friction measurements. It is a common practice that researchers present the results of the frequency together with internal friction without giving any analysis. In this work we apply an expression which relates the variation of frequency with temperature and analyse the experimental results cited in the literature of the relaxation process due to the stress induced ordering of oxygen and nitrogen present in niobium and tantalum.

Recombination nodules in coleopteran species: Palembus dermestoides(Tenebrionidae) and Epicauta atomaria (Meloidae)

This work describes the first report about the occurrence of recombination nodules (RNs) in spread pachytene cells of two species of Coleoptera: Palembus dermestoides (Tenebrionidae) and Epicauta atomaria (Meloidae). The RNs were observed in preparations contrasted with phosphotungstic acid. Considering RN morphology and its occurrence in pachytene bivalents (one per autosome bivalent) these structures were interpreted to be late RNs. P. dermestoides and E. atolraria have 2n = 20 chromosomes including an Xyp sex determination system. In spite of most frequently subtelocentric morphology observed in the autosomes of both species, the occurrence of RNs is limited only to the synaptonemal complex (SC) structure of the long arms. These findings are in agreement with those obtained using light microscopy analysis in which only one chiasma or terminalization event is observed per autosomal bivalent in early or late metaphase I cells. The RNs have the same average width of the SC of each analyzed species, a circular shape, strong electron density, and are observed mainly between the lateral elements of the SC. The RNs of P. dermestoides and E. atomaria have approximately the same average size (width), 180 +/- 20 nm and 160 +/- 80 nm, respectively. The absence of RNs in the short arms and its occurrence in the long arms are discussed considering the short arm pericentromeric and pro-centric heterochromatin. Copyright (C) 2003 S. Karger AG, Basel

Charge-orbital ordering and phase separation in the two-orbital model for manganites: Roles of Jahn-Teller phononic and Coulombic interactions

The main properties of realistic models for manganites are studied using analytic mean-field approximations and computational numerical methods, focusing on the two-orbital model with electrons interacting through Jahn-Teller (JT) phonons and/or Coulombic repulsions. Analyzing the model including both interactions by the combination of the mean-field approximation and the exact diagonalization method, it is argued that the spin-charge-orbital structure in the insulating phase of the purely JT-phononic model with a large Hund couphng J(H) is not qualitatively changed by the inclusion of the Coulomb interactions. As an important application of the present mean-held approximation, the CE-type antiferromagnetic state, the charge-stacked structure along the z axis, and (3x(2) - r(2))/(3y(2) - r(2))-type orbital ordering are successfully reproduced based on the JT-phononic model with large JH for the half-doped manganite, in agreement with recent Monte Carlo simulation results. Topological arguments and the relevance of the Heisenberg exchange among localized t(2g) spins explains why the inclusion of the nearest-neighbor Coulomb interaction does not destroy the charge stacking structure. It is also verified that the phase-separation tendency is observed both in purely JT-phononic (large JH) and purely Coulombic models in the vicinity of the hole undoped region, as long as realistic hopping matrices are used. This highlights the qualitative similarities of both approaches and the relevance of mixed-phase tendencies in the context of manganites. In addition, the rich and complex phase diagram of the two-orbital Coulombic model in one dimension is presented. Our results provide robust evidence that Coulombic and JT-phononic approaches to manganites are not qualitatively different ways to carry out theoretical calculations, but they share a variety of common features.

Photoluminescence activity of Ba1-xCaxTiO3: dependence on particle size and morphology

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Relationship between B-Cell-specific moloney murine leukemia virus integration site 1 (BMI-1) and homologous recombination regulatory genes in invasive ductal breast carcinomas

B-cell-specific Moloney murine leukemia virus integration site 1 (Bmi-1) is a Polycomb group protein that is able to induce telomerase activity, enabling the immortalization of epithelial cells. Immortalized cells are more susceptible to double-strand breaks (DSB), which are subsequently repaired by homologous recombination (HR). BRCA1 is among the HR regulatory genes involved in the response to DNA damage associated with the RAD51 protein, which accumulates in DNA damage foci after signaling H2AX, another important marker of DNA damage. Topoisomerase III beta (topoIII beta) removes HR intermediates before chromosomal segregation, preventing damage to cellular DNA structure. In breast carcinomas positive for BMI-1 the role of proteins involved in HR remains to be investigated. The aim of this study was to evaluate the association between BMI-1 and homologous recombination proteins. Using tissue microarrays containing 239 cases of primary breast tumors, the expression of Bmi-1, BRCA-1, H2AX, Rad51, p53, Ki-67, topoIII beta, estrogen receptors (ER), progesterone receptors (PR), and HER-2 was analyzed by immunohistochemistry. We observed high Bmi-1 expression in 66 cases (27.6%). Immunohistochemical overexpression of BMI-1 was related to ER (p=0.004), PR (p<0.001), Ki-67 (p<0.001), p53 (p=0.003), BRCA1 (p=0.003), H2AX (p=0.024) and topoIII beta (p<0,001). Our results show a relationship between the expression of BMI-1 and HR regulatory genes, suggesting that Bmi-1 overexpression might be an important event in HR regulation. However, further studies are necessary to understand the mechanisms in which Bmi-1 could regulate HR pathways in invasive ductal breast carcinomas.

Autoionizing states and their relevance in electron-ion recombination

Atomic physics plays an important role in determining the evolution stages in a wide range of laboratory and cosmic plasmas. Therefore, the main contribution to our ability to model, infer and control plasma sources is the knowledge of underlying atomic processes. Of particular importance are reliable low temperature dielectronic recombination (DR) rate coefficients. This thesis provides systematically calculated DR rate coefficients of lithium-like beryllium and sodium ions via ∆n = 0 doubly excited resonant states. The calculations are based on complex-scaled relativistic many-body perturbation theory in an all-order formulation within the single- and double-excitation coupled-cluster scheme, including radiative corrections. Comparison of DR resonance parameters (energy levels, autoionization widths, radiative transition probabilities and strengths) between our theoretical predictions and the heavy-ion storage rings experiments (CRYRING-Stockholm and TSRHeidelberg) shows good agreement. The intruder state problem is a principal obstacle for general application of the coupled-cluster formalism on doubly excited states. Thus, we have developed a technique designed to avoid the intruder state problem. It is based on a convenient partitioning of the Hilbert space and reformulation of the conventional set of pairequations. The general aspects of this development are discussed, and the effectiveness of its numerical implementation (within the non-relativistic framework) is selectively illustrated on autoionizing doubly excited states of helium.

Intrinsic ordering, combinatorial numbers and reliability engineering

[EN]A new algorithm for evaluating the top event probability of large fault trees (FTs) is presented. This algorithm does not require any previous qualitative analysis of the FT. Indeed, its efficiency is independent of the FT logic, and it only depends on the number n of basic system components and on their failure probabilities. Our method provides exact lower and upper bounds on the top event probability by using new properties of the intrinsic order relation between binary strings. The intrinsic order enables one to select binary n-tuples with large occurrence probabilities without necessity to evaluate them. This drastically reduces the complexity of the problem from exponential (2n binary n-tuples) to linear (n Boolean variables)...

Computer simulation of ordering and dynamics in liquid crystals in the bulk and close to the surface

The aim of this PhD thesis is to investigate the orientational and dynamical properties of liquid crystalline systems, at molecular level and using atomistic computer simulations, to reach a better understanding of material behavior from a microscopic point view. In perspective this should allow to clarify the relation between the micro and macroscopic properties with the objective of predicting or confirming experimental results on these systems. In this context, we developed four different lines of work in the thesis. The first one concerns the orientational order and alignment mechanism of rigid solutes of small dimensions dissolved in a nematic phase formed by the 4-pentyl,4 cyanobiphenyl (5CB) nematic liquid crystal. The orientational distribution of solutes have been obtained with Molecular Dynamics Simulation (MD) and have been compared with experimental data reported in literature. we have also verified the agreement between order parameters and dipolar coupling values measured in NMR experiments. The MD determined effective orientational potentials have been compared with the predictions of Maier­Saupe and Surface tensor models. The second line concerns the development of a correct parametrization able to reproduce the phase transition properties of a prototype of the oligothiophene semiconductor family: sexithiophene (T6). T6 forms two crystalline polymorphs largely studied, and possesses liquid crystalline phases still not well characterized, From simulations we detected a phase transition from crystal to liquid crystal at about 580 K, in agreement with available experiments, and in particular we found two LC phases, smectic and nematic. The crystal­smectic transition is associated to a relevant density variation and to strong conformational changes of T6, namely the molecules in the liquid crystal phase easily assume a bent shape, deviating from the planar structure typical of the crystal. The third line explores a new approach for calculating the viscosity in a nematic through a virtual exper- iment resembling the classical falling sphere experiment. The falling sphere is replaced by an hydrogenated silicon nanoparticle of spherical shape suspended in 5CB, and gravity effects are replaced by a constant force applied to the nanoparticle in a selected direction. Once the nanoparticle reaches a constant velocity, the viscosity of the medium can be evaluated using Stokes' law. With this method we successfully reproduced experimental viscosities and viscosity anisotropy for the solvent 5CB. The last line deals with the study of order induction on nematic molecules by an hydrogenated silicon surface. Gaining predicting power for the anchoring behavior of liquid crystals at surfaces will be a very desirable capability, as many properties related to devices depend on molecular organization close to surfaces. Here we studied, by means of atomistic MD simulations, the flat interface between an hydrogenated (001) silicon surface in contact with a sample of 5CB molecules. We found a planar anchoring of the first layers of 5CB where surface interactions are dominating with respect to the mesogen intermolecular interactions. We also analyzed the interface 5CB­vacuum, finding a homeotropic orientation of the nematic at this interface.