Developmental and structural features of secretory canals in root and shoot wood of Copaifera langsdorffii Desf. (Leguminosae-Caesalpinioideae)

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

In silico network topology-based prediction of gene essentiality

The identification of genes essential for survival is important for the understanding of the minimal requirements for cellular life and for drug design. As experimental studies with the purpose of building a catalog of essential genes for a given organism are time-consuming and laborious, a computational approach which could predict gene essentiality with high accuracy would be of great value. We present here a novel computational approach, called NTPGE (Network Topology-based Prediction of Gene Essentiality), that relies on the network topology features of a gene to estimate its essentiality. The first step of NTPGE is to construct the integrated molecular network for a given organism comprising protein physical, metabolic and transcriptional regulation interactions. The second step consists in training a decision-tree-based machine-learning algorithm on known essential and non-essential genes of the organism of interest, considering as learning attributes the network topology information for each of these genes. Finally, the decision-tree classifier generated is applied to the set of genes of this organism to estimate essentiality for each gene. We applied the NTPGE approach for discovering the essential genes in Escherichia coli and then assessed its performance. (C) 2007 Elsevier B.V. All rights reserved.

A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data

Background: The genome-wide identification of both morbid genes, i.e., those genes whose mutations cause hereditary human diseases, and druggable genes, i.e., genes coding for proteins whose modulation by small molecules elicits phenotypic effects, requires experimental approaches that are time-consuming and laborious. Thus, a computational approach which could accurately predict such genes on a genome-wide scale would be invaluable for accelerating the pace of discovery of causal relationships between genes and diseases as well as the determination of druggability of gene products.Results: In this paper we propose a machine learning-based computational approach to predict morbid and druggable genes on a genome-wide scale. For this purpose, we constructed a decision tree-based meta-classifier and trained it on datasets containing, for each morbid and druggable gene, network topological features, tissue expression profile and subcellular localization data as learning attributes. This meta-classifier correctly recovered 65% of known morbid genes with a precision of 66% and correctly recovered 78% of known druggable genes with a precision of 75%. It was than used to assign morbidity and druggability scores to genes not known to be morbid and druggable and we showed a good match between these scores and literature data. Finally, we generated decision trees by training the J48 algorithm on the morbidity and druggability datasets to discover cellular rules for morbidity and druggability and, among the rules, we found that the number of regulating transcription factors and plasma membrane localization are the most important factors to morbidity and druggability, respectively.Conclusions: We were able to demonstrate that network topological features along with tissue expression profile and subcellular localization can reliably predict human morbid and druggable genes on a genome-wide scale. Moreover, by constructing decision trees based on these data, we could discover cellular rules governing morbidity and druggability.

Strand Analysis, a free online program for the computational identification of the best RNA interference (RNAi) targets based on Gibbs free energy

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

Ultramorphological features of the egg of Telmatoscopus albipunctatus (Williston) (Diptera, Psychodidae)

Aspectos ultramorfológicos do ovo de Telmatoscopus albipunctatus (Williston) (Diptera, Psychodidae). As moscas da família Psychodidae, também conhecidas como moscas de banheiro, são de importância médica e veterinária. Informações gerais sobre ciclo de vida e hábitos do adulto são facilmente encontradas, mas pouco se sabe sobre a morfologia do ovo. Dessa forma, neste estudo, a ultramofologia do ovo de Telmatoscopus albipunctatus (Williston, 1893) foi analisada por microscopia eletrônica de varredura com o objetivo de descrever sua estrutura, provendo importantes dados para futuras comparações entre moscas de diferentes espécies e gêneros. O aspecto geral do ovo de T. albipunctatus é similar a outros Psychodidae, medindo aproximadamente 0.4 mm de comprimento e 0.1 mm de largura. Entretanto, baseado nas esculturas contínuas e descontínuas do exocórion, as quais podem ser espécie-específicas, podemos inferir que os ovos de T. albipunctatus podem sobreviver sob condições de muita umidade ou seca, dificultando o controle da espécie. Nossos resultados ressaltam a importância do uso da microscopia eletrônica como uma ferramenta no estudo dos padrões do exocórion. A morfologia externa do ovo de T. albipunctatus pode ser usada como base para futuros estudos e como ferramenta para comparação de diferentes espécies de moscas do gênero Psychodidae.

Exploring community assembly through an individual-based model for trophic interactions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Quantum spin tunneling in a soluble quasi-spin model: an angle-based potential description

We propose an approach which allows one to construct and use a potential function written in terms of an angle variable to describe interacting spin systems. We show how this can be implemented in the Lipkin-Meshkov-Glick, here considered a paradigmatic spin model. It is shown how some features of the energy gap can be interpreted in terms of a spin tunneling. A discrete Wigner function is constructed for a symmetric combination of two states of the model and its time evolution is obtained. The physical information extracted from that function reinforces our description of phase oscillations in a potential. (c) 2004 Elsevier B.V. All rights reserved.

A note about the appearance of non-hyperbolic solutions in a mechanical pendulum system

The investigation of the behavior of a nonlinear system consists in the analysis of different stages of its motion, where the complexity varies with the proximity of a resonance region. Near this region the stability domain of the system undergoes sudden changes due basically to competition and interaction between periodic and saddle solutions inside the phase portrait, leading to the occurrence of the most different phenomena. Depending of the domain of the chosen control parameter, these events can reveal interesting geometric features of the system so that the phase portrait is not capable to express all them, since the projection of these solutions on the two-dimensional surface can hide some aspects of these events. In this work we will investigate the numerical solutions of a particular pendulum system close to a secondary resonance region, where we vary the control parameter in a restrict domain in order to draw a preliminary identification about what happens with this system. This domain includes the appearance of non-hyperbolic solutions where the basin of attraction in the center of the phase portrait diminishes considerably, almost disappearing, and afterwards its size increases with the direction of motion inverted. This phenomenon delimits a boundary between low and high frequency of the external excitation.

Oil-in-water lecithin-based microemulsions as a potential delivery system for amphotericin B

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

Effect of cerium (IV) ions on the anticorrosion properties of siloxane-poly(methyl methacrylate) based film applied on tin coated steel

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

Grain-boundary segregation and precipitates in La2O3 and Pr2O3 doped SnO2 center dot CoO-based varistors

Structural heterogeneities in SnO2.CoO-based varistors were analyzed by transmission electron microscopy. In SnO2.CoO-based system doped with La2O3 and Pr2O3 two kinds of precipitate phases at grain boundary region were found. Using energy dispersive spectrometry they were found to be Co2SnO4 and Pr2Sn2O7, presenting a defined crystalline structure. It was also identified that such precipitate phases are mainly located in triple-junctions of the microstructure. HRTEM analysis revealed the existence of other two types of junctions, one as being homo-junctions of SnO2 grains and other due to twin grain boundaries inside the SnO2.CoO grain. The role of these types of junction in the overall nonlinear electrical features is also discussed. (C) 2003 Elsevier B.V. Ltd. All rights reserved.

A new approach for determining stability constants of metal ion complexes in aquatic systems based on flow injection-ion exchange-flame atomic absorption spectrometry coupling

A method based an ion exchange(IE)-atomic absorption spectrometry(AAS) coupled by flow techniques, allowing the determination of formation constants of, at least, the first species of complex systems, in aqueous solution, was developed.The IE-AAS coupling reduces significantly the number of experimental steps in comparison with IE batch methods, resulting in an important increase in analytical rate. The method is simple both from experimental and computational points of view, making possible its utilization by workers without special expertise in the field of complex equilibria in solution. on the other hand, taking into account mainly the amount of hollow cathode lamps available to date, the developed procedure may be applied, within certain limitations, to the study of many systems whose features prevent the use of traditional approaches.

The STATFLUX code: a statistical method for calculation of flow and set of parameters, based on the Multiple-Compartment Biokinetical Model

The code STATFLUX, implementing a new and simple statistical procedure for the calculation of transfer coefficients in radionuclide transport to animals and plants, is proposed. The method is based on the general multiple-compartment model, which uses a system of linear equations involving geometrical volume considerations. Flow parameters were estimated by employing two different least-squares procedures: Derivative and Gauss-Marquardt methods, with the available experimental data of radionuclide concentrations as the input functions of time. The solution of the inverse problem, which relates a given set of flow parameter with the time evolution of concentration functions, is achieved via a Monte Carlo Simulation procedure.Program summaryTitle of program: STATFLUXCatalogue identifier: ADYS_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADYS_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions: noneComputer for which the program is designed and others on which it has been tested: Micro-computer with Intel Pentium III, 3.0 GHzInstallation: Laboratory of Linear Accelerator, Department of Experimental Physics, University of São Paulo, BrazilOperating system: Windows 2000 and Windows XPProgramming language used: Fortran-77 as implemented in Microsoft Fortran 4.0. NOTE: Microsoft Fortran includes non-standard features which are used in this program. Standard Fortran compilers such as, g77, f77, ifort and NAG95, are not able to compile the code and therefore it has not been possible for the CPC Program Library to test the program.Memory, required to execute with typical data: 8 Mbytes of RAM memory and 100 MB of Hard disk memoryNo. of bits in a word: 16No. of lines in distributed program, including test data, etc.: 6912No. of bytes in distributed Program, including test data, etc.: 229 541Distribution format: tar.gzNature of the physical problem: the investigation of transport mechanisms for radioactive substances, through environmental pathways, is very important for radiological protection of populations. One such pathway, associated with the food chain, is the grass-animal-man sequence. The distribution of trace elements in humans and laboratory animals has been intensively studied over the past 60 years [R.C. Pendlenton, C.W. Mays, R.D. Lloyd, A.L. Brooks, Differential accumulation of iodine-131 from local fallout in people and milk, Health Phys. 9 (1963) 1253-1262]. In addition, investigations on the incidence of cancer in humans, and a possible causal relationship to radioactive fallout, have been undertaken [E.S. Weiss, M.L. Rallison, W.T. London, W.T. Carlyle Thompson, Thyroid nodularity in southwestern Utah school children exposed to fallout radiation, Amer. J. Public Health 61 (1971) 241-249; M.L. Rallison, B.M. Dobyns, F.R. Keating, J.E. Rall, F.H. Tyler, Thyroid diseases in children, Amer. J. Med. 56 (1974) 457-463; J.L. Lyon, M.R. Klauber, J.W. Gardner, K.S. Udall, Childhood leukemia associated with fallout from nuclear testing, N. Engl. J. Med. 300 (1979) 397-402]. From the pathways of entry of radionuclides in the human (or animal) body, ingestion is the most important because it is closely related to life-long alimentary (or dietary) habits. Those radionuclides which are able to enter the living cells by either metabolic or other processes give rise to localized doses which can be very high. The evaluation of these internally localized doses is of paramount importance for the assessment of radiobiological risks and radiological protection. The time behavior of trace concentration in organs is the principal input for prediction of internal doses after acute or chronic exposure. The General Multiple-Compartment Model (GMCM) is the powerful and more accepted method for biokinetical studies, which allows the calculation of concentration of trace elements in organs as a function of time, when the flow parameters of the model are known. However, few biokinetics data exist in the literature, and the determination of flow and transfer parameters by statistical fitting for each system is an open problem.Restriction on the complexity of the problem: This version of the code works with the constant volume approximation, which is valid for many situations where the biological half-live of a trace is lower than the volume rise time. Another restriction is related to the central flux model. The model considered in the code assumes that exist one central compartment (e.g., blood), that connect the flow with all compartments, and the flow between other compartments is not included.Typical running time: Depends on the choice for calculations. Using the Derivative Method the time is very short (a few minutes) for any number of compartments considered. When the Gauss-Marquardt iterative method is used the calculation time can be approximately 5-6 hours when similar to 15 compartments are considered. (C) 2006 Elsevier B.V. All rights reserved.

The influence of aluminium on the overall properties of SnO2-based varistors

The influence of aluminium on the development of the microstructure and on the electrical behaviour of the SnO2 center dot Co3O4 center dot Nb2O5 typical varistor system was studied. Two sources of Al were used, alumina (Al2O3) and boehmite (AlO(OH)). The microstructural features were characterised with scanning (SEM) and transmission (TEM) electron microscopies. The different phases present in the studied samples were also studied with XRD, EDS and electron diffraction patterns of selected areas (SAED). Particles containing Sri, Co, Al, and O were unveiled with TEM. Impedance spectroscopy measurements and current density versus electric field characteristics revealed superior electrical properties for samples with AlO(OH). The higher non-linearity (alpha = 19) was achieved with the addition of 0.1% mol of boehmite. The influence of the secondary phases on the electrical properties is also addressed in this work.

Analysis of secondary phases segregated and precipitated in SnO2-based varistors

Transmission and scanning electron microscopy techniques were used to study the heterogeneities found in the microstructure of (SnO2Co3O4Nb2O5Fe2O3)-Co-.-Nb-.-Fe-. and (SnO2ZnONb2O5FC2O3)-Zn-.-Nb-.-F-. varistors. Second phases encountered both inside the grains and ingrain boundary regions were identified using energy dispersive spectrometry and electron diffraction patterns. Through the electrical characterisation, the presence of iron oxide among the additives was determined to highlight the non-linear properties of the specimens. A discussion on the influence of second phases on the non-linear features of these systems is also addressed. (C) 2004 Elsevier Ltd. All rights reserved.