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.

Evaluation of the Diramic system for urine cultures

O sistema Diramic foi avaliado para o diagnóstico das infecções do trato urinário (ITU). O sistema Diramic foi desenvolvido em Cuba e possibilita resultados de diagnóstico das infecções do trato urinário (ITU) em quatro horas e baseia-se na variação da turvação do crescimento microbiano no meio de cultura após incubação a 37ºC/4 horas. 396 amostras de urinas provenientes de ambulatórios e enfermarias do HC da FMB-UNESP-Botucatu/SP foram analisadas pelo sistema Diramic. O método da alça calibrada (AC) foi adotado como método de referência. A taxa de coincidência entre os dois métodos foi de 96,46% (382 amostras de urina), não havendo diferença significativa entre os resultados obtidos nos dois métodos. Os resultados para sensibilidade e especificidade foram 84,37 e 98,80% respectivamente e 10 resultados no Diramic foram falsos negativos (2,5%) e 4 falso positivos (1,01%). Os microrganismos identificados nas urinas positivas foram Escherichia coli (68,75%), Klebsiella pneumoniae (10,94%), leveduras (6,25%), Pseudomonas aeruginosa (4,69%), Enterobacter cloacae (3,12%) e Proteus mirabilis, Staphyloccocus coagulase negativo, Morganella morganii e Citrobacter freundii também foram identificadas (1,56% para cada espécie). O método Diramic foi eficiente na triagem das urinoculturas, porém verificou-se algumas restrições quanto ao diagnóstico das infecções do trato urinário quando causadas por leveduras e em pacientes submetidos a antibioticoterapia.

Cytochemical characterization of the endomembranous system during the oocyte primary growth in Serrasalmus spilopleura (Teleostei, Characiformes, Characidae)

The morphophysiological changes that occur during oocyte primary growth in Serrasalmus spilopleura were studied using ultrastructural cytochemical techniques. In the previtellogenic oocytes endoplasmic reticulum components, Golgi complex cisternae and vesicles, lysosomes, multivesicular bodies and some electron-dense vesicles react to acid phosphatase (AcPase) detection. The endoplasmic reticulum components, Golgi complex cisternae and vesicles also react to osmium tetroxide and potassium iodide impregnation (KI). These structures, except for the Golgi complex cisternae, are strongly contrasted by osmium tetroxide and zinc iodide impregnation (ZIO). Some electron-dense vesicles are ZIO-stained, while microvesicles in the multivesicular bodies and other large isolated cytoplasmic vesicles are contrasted by KI. At primary oocyte growth, the activity of the endomembranous system and the proliferation of membranous organelles are intense. The biosynthetic pathway of the lysosomal proteins such as acid phosphatase, involves the endoplasmic reticulum, Golgi complex, vesicles with inactive hydrolytic enzymes and, finally, the lysosomes. The oocyte endomembranous system have reduction capacity and are involved in the metabolism of rich in SH groups. (c) 2005 Published by Elsevier Ltd.

Expression of renin-angiotensin system signalling compounds in maternal protein-restricted rats: effect on renal sodium excretion and blood pressure

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The cross-entropy method and its application to minimize the ripple of magnetic levitation forces of a maglev system

This paper explores firstly the potential of a new evolutionary method - the Cross-Entropy (CE) method in solving continuous inverse electromagnetic problems. For this purpose, an adaptive updating formula for the smoothing parameter, some mutation operation, and a new termination criterion are proposed. The proposed CE based metaheuristics is applied to reduce the ripple of the magnetic levitation forces of a prototype Maglev system. The numerical results have shown that the ripple of the magnetic levitation forces of the prototype system is reduced significantly after the design optimization using the proposed algorithm.

GLOBAL DYNAMICS IN THE POINCARE BALL of THE CHEN SYSTEM HAVING INVARIANT ALGEBRAIC SURFACES

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The effect of porcelain thickness and surface liner application on the fracture behavior of a ceramic system

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

Prediction of R plus R-2 gravity for the deflection of a photon passing close to the Sun

The cross-section for the scattering of a photon by the Sun's gravitational field, treated as an external field, is computed in the framework of R + R-2 gravity. Using this result, we found that for a photon just grazing the Sun's surface the deflection is 1.75 which is exactly the same as that given by Einstein's theory. An explanation for this pseudo-paradox is provided.

Laüe back-reflection method for crystallographic orientation of a martensitic Cu-Zn-Al single crystal of the monoclinic system

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

Preparation and characterization of new glassy system As2P2S8-Ga2S3

Glasses having the composition (100 - x)As2P2S8-xGa(2)S(3) with x ranging from 0 to 50% were investigated to determine the compositional effect on properties and local structure. The glass transition temperature (T-g) and the stability parameter against crystallization (T-x - T-g) increased with the addition of Ga2S3. The structure of these glasses was probed by Raman scattering, Fourier transform infrared (FT-IR) and P-31 nuclear magnetic resonance. on the basis of the observed vibrations and the strength of the P-31-P-31 homonuclear magnetic dipolar coupling, two scenarios can be proposed for the structural evolution induced by the addition of Ga2S3. For x <= 20% we may have the formation of GaS4E- groups (E = nonbonding electron), and for x >= 30% we have depolymerization of the As2P2S8 units and the formation of a network of GaPS4 units with each PS4/2 unit (Q(4)) species carrying a single positive formal charge.

Carbon Nuclear Magnetic Resonance Spectroscopic Profiles coupled to Partial Least-Squares Multivariate Regression for Prediction of Several Physicochemical Parameters of Brazilian Commercial Gasoline

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Multivariate calibrations on H-1 NMR profiles for prediction of physicochemical parameters of Brazilian commercial gasoline

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Multivariate calibrations in gas chromatographic profiles for prediction of several physicochemical parameters of Brazilian commercial gasoline

Several Brazilian commercial gasoline physicochemical parameters, such as relative density, distillation curve (temperatures related to 10%, 50% and 90% of distilled volume, final boiling point and residue), octane numbers (motor and research octane number and anti-knock index), hydrocarbon compositions (olefins, aromatics and saturates) and anhydrous ethanol and benzene content was predicted from chromatographic profiles obtained by flame ionization detection (GC-FID) and using partial least square regression (PLS). GC-FID is a technique intensively used for fuel quality control due to its convenience, speed, accuracy and simplicity and its profiles are much easier to interpret and understand than results produced by other techniques. Another advantage is that it permits association with multivariate methods of analysis, such as PLS. The chromatogram profiles were recorded and used to deploy PLS models for each property. The standard error of prediction (SEP) has been the main parameter considered to select the "best model". Most of GC-FID-PLS results, when compared to those obtained by the Brazilian Government Petroleum, Natural Gas and Biofuels Agency - ANP Regulation 309 specification methods, were very good. In general, all PLS models developed in these work provide unbiased predictions with lows standard error of prediction and percentage average relative error (below 11.5 and 5.0, respectively). (C) 2007 Elsevier B.V. All rights reserved.

Behavior of cardiac variables in animals exposed to cigarette smoke

OBJECTIVE: To assess the behavior of cardiac variables in animals exposed to cigarette smoke. METHODS: Two groups of Wistar rats were studied as follows: control group (C), comprising 28 animals; and smoking group (S), comprising 23 animals exposed to cigarette smoke for 30 days. Left ventricular cardiac function was assessed in vivo with transthoracic echocardiography, and myocardial performance was analyzed in vitro in preparations of isolated left ventricular papillary muscle. The cardiac muscle was assessed in isometric contractions with an extracellular calcium concentration of 2.5 mmol/L. RESULTS: No statistical difference was observed in the values of the body variables of the rats and in the mechanical data obtained from the papillary muscle between the control and smoking groups. The values of left ventricular systolic diameter were significantly greater in the smoking animals than in the control animals (C= 3.39 ± 0.4 mm and S= 3.71 ± 0.51 mm, P=0.02). A significant reduction was observed in systolic shortening fraction (C= 56.7 ± 4.2% and S= 53.5 ± 5.3%, P=0.02) and in ejection fraction (C= 0.92 ± 0.02 and S= 0.89 ± 0.04, P=0.01). CONCLUSION: The rats exposed to cigarette smoke had a reduction in left ventricular systolic function, although their myocardial function was preserved.