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.

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.

Prediction of a weakly bound excited state in the He-4(2)-Li-7 molecule

A scale-independent approach, valid for weakly bound three-body systems, is used to analyze the existence of excited Thomas-Efimov states in molecular systems with three atoms: a helium dimer together with isotopes of lithium (Li-6 and Li-7) and sodium (Na-23). With the present study and the available data, we can clearly predict that the He-4(2)-Li-7 system supports an excited state with binding energy close to 2.31 mK. (C) 2000 American Institute of Physics. [S0021-9606(00)30442-1].

Thermal Study in Solid State of Zn(II)-Diclofenac Complex: Behavior Kinetic of the Dehydration, Transition Phase and Thermal Decomposition

The dehydration, thermal decomposition and transition phase stage of Zn(II)-diclofenac compound were studied by simultaneous TG-DTA and DSC techniques. The TG and DSC curves of this compound were obtained with the mass of sample of 2 and 5 mg. Additionally, DSC curves were carried out in opened and closed alpha-alumina pans under static and nitrogen atmosphere. The DTA and DSC curves show that this compound possesses exothermic transition phase between 170-180 degrees C, which it is irreversible (monotropic reaction) The kinetics study of this transition phase stage was evaluated by DSC under non-isothermal conditions. The obtained data were evaluated with the isoconversional method, where the values of activation energy (E(a) / kJ mol(-1)) was plotted in function of the conversion degree (alpha). The results show that due to mass sample, different activation energies were obtained From these curves a tendency can be seen where the plots maintain the same profile for closed lids and almost run parallel to each other.

Thermal behavior studies of solid state compounds of 4-dimethylaminocinnamylidenepyruvate with alkali earth metals, except beryllium and radium

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

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.

Uncertainties in the prediction of spatial variability of soil CO2 emissions and related properties

A emissão de CO2 do solo apresenta alta variabilidade espacial, devido à grande dependência espacial observada nas propriedades do solo que a influenciam. Neste estudo, objetivou-se: caracterizar e relacionar a variabilidade espacial da respiração do solo e propriedades relacionadas; avaliar a acurácia dos resultados fornecidos pelo método da krigagem ordinária e simulação sequencial gaussiana; e avaliar a incerteza na predição da variabilidade espacial da emissão de CO2 do solo e demais propriedades utilizando a simulação sequencial gaussiana. O estudo foi conduzido em uma malha amostral irregular com 141 pontos, instalada sobre a cultura de cana-de-açúcar. Nesses pontos foram avaliados a emissão de CO2 do solo, a temperatura do solo, a porosidade livre de água, o teor de matéria orgânica e a densidade do solo. Todas as variáveis apresentaram estrutura de dependência espacial. A emissão de CO2 do solo mostrou correlações positivas com a matéria orgânica (r = 0,25, p < 0,05) e a porosidade livre de água (r = 0,27, p <0,01) e negativa com a densidade do solo (r = -0,41, p < 0,01). No entanto, quando os valores estimados espacialmente (N=8833) são considerados, a porosidade livre de água passa a ser a principal variável responsável pelas características espaciais da respiração do solo, apresentando correlação de 0,26 (p < 0,01). As simulações individuais propiciaram, para todas as variáveis analisadas, melhor reprodução das funções de distribuição acumuladas e dos variogramas, em comparação à krigagem e estimativa E-type. As maiores incertezas na predição da emissão de CO2 estiveram associadas às regiões da área estudada com maiores valores observados e estimados, produzindo estimativas, ao longo do período estudado, de 0,18 a 1,85 t CO2 ha-1, dependendo dos diferentes cenários simulados. O conhecimento das incertezas gerado por meio dos diferentes cenários de estimativa pode ser incluído em inventários de gases do efeito estufa, resultando em estimativas mais conservadoras do potencial de emissão desses gases.

Prediction of dry matter intake based on ruminal degradation from milking cows grazing coast-cross grass

Dry matter intake (DMI) of coast-cross grazing by crossbred Holstein-Zebu and Zebu lactating cows was calculated using in vitro dry matter digestibility from extrusa (four esophageal fistulated cows) and fecal output estimate with mordent chromium. Pasture was rotationally grazed with three days grazing period and 27 days testing period, adopting a stocking rate of 1.6 and 3.2 cows/ha, during the dry and rainy season respectively. Voluntary DMI was estimated from degradation characteristics using different equations. Predicted coast-cross DMI varied with models. The prediction of tropical forages dry matter intake from equations based in ruminal degradation parameters needs farther investigation before being employed in practice.

USE OF PROGENY TESTING IN BEEF-CATTLE - PREDICTION OF GENETIC GAIN IN A NELORE CATTLE-BREEDING PROGRAM

Genetic gains predicted for selection, based on both individual performance and progeny testing, were compared to provide information to be used in implementation of progeny testing for a Nelore cattle breeding program. The prediction of genetic gain based on progeny testing was obtained from a formula, derived from methodology of Young and weller (J. Genetics 57: 329-338, 1960) for two-stage selection, which allows prediction of genetic gain per generation when the individuals under test have been pre-selected on the basis of their own performance. The application of this formula also allowed determination of the number of progeny per tested bull needed to maximize genetic gain, when the total number of tested progeny is limited.

Prediction of cassava starch edible film properties by chemometric analysis of infrared spectra

Cassava starch has been shown to make transparent and colorless flexible films without any previous chemical treatment. The functional properties of edible films are influenced by starch properties, including chain conformation, molecular bonding, crystallinity, and water content. Fourier-transform infrared (FTIR) spectroscopy in combination with attenuated total reflectance (ATR) has been applied for the elucidation of the structure and conformation of carbohydrates. This technique associated with chemometric data processing could indicate the relationship between the structural parameters and the functional properties of cassava starch-based edible films. Successful prediction of the functional properties values of the starch-based films was achieved by partial least squares regression data. The results showed that presence of the hydroxyl group on carbon 6 of the cyclic part of glucose is directly correlated with the functional properties of cassava starch films.

Weather-based prediction of anthracnose severity using artificial neural network models

Data were collected and analysed from seven field sites in Australia, Brazil and Colombia on weather conditions and the severity of anthracnose disease of the tropical pasture legume Stylosanthes scabra caused by Colletotrichum gloeosporioides. Disease severity and weather data were analysed using artificial neural network (ANN) models developed using data from some or all field sites in Australia and/or South America to predict severity at other sites. Three series of models were developed using different weather summaries. of these, ANN models with weather for the day of disease assessment and the previous 24 h period had the highest prediction success, and models trained on data from all sites within one continent correctly predicted disease severity in the other continent on more than 75% of days; the overall prediction error was 21.9% for the Australian and 22.1% for the South American model. of the six cross-continent ANN models trained on pooled data for five sites from two continents to predict severity for the remaining sixth site, the model developed without data from Planaltina in Brazil was the most accurate, with >85% prediction success, and the model without Carimagua in Colombia was the least accurate, with only 54% success. In common with multiple regression models, moisture-related variables such as rain, leaf surface wetness and variables that influence moisture availability such as radiation and wind on the day of disease severity assessment or the day before assessment were the most important weather variables in all ANN models. A set of weights from the ANN models was used to calculate the overall risk of anthracnose for the various sites. Sites with high and low anthracnose risk are present in both continents, and weather conditions at centres of diversity in Brazil and Colombia do not appear to be more conducive than conditions in Australia to serious anthracnose development.

Prediction of occurrences of diverse chemical classes in the Asteraceae through artificial neural networks

The training and the application of a neural network system for the prediction of occurrences of secondary metabolites belonging to diverse chemical classes in the Asteraceae is described. From a database containing about 604 genera and 28,000 occurrences of secondary metabolites in the plant family, information was collected encompassing nine chemical classes and their respective occurrences for training of a multi-layer net using the back-propagation algorithm. The net supplied as output the presence or absence of the chemical classes as well as the number of compounds isolated from each taxon. The results provided by the net from the presence or absence of a chemical class showed a 89% hit rate; by excluding triterpenes from the analysis, only 5% of the genera studied exhibited errors greater than 10%. Copyright (C) 2004 John Wiley Sons, Ltd.

Role of early GnRH administration in sexual behavior disorders of rat pups perinatally exposed to lead

The effects of maternal exposure to lead (Pb) during the perinatal ( 1% and 0.1% Pb) periods of sexual brain differentiation were studied in adult male offspring. Maternal Pb levels were measured after treatment. Behavioral (open field and sexual behavior), physical (sexual maturation, body and organ weights), and biochemical (testosterone levels and hypothalamic monoamine and respective metabolite levels) data were assessed in perinatally exposed offspring. The effects of gonadrotopin-releasing hormone (GnRH) administration to pups at birth on puberty and sexual behavior were also investigated in offspring postnatally exposed to the metal. Results showed that perinatal administration of the two Pb concentrations did not modify maternal weight gain; 1% Pb exposure reduced offspring body weight during the 7 days of treatment while no changes were observed after 0.1% Pb exposure; neither ph concentration altered offspring sexual maturation; the higher Pb concentration improved sexual behavior while the 0.1% concentration reduced it; exposure to 0.1% Pb caused decrease in testis weight, an increase in seminal vesicle weight and no changes in plasma testosterone levels; hypothalamic VMA levels were increased compared to the control group; GnRH administration reversed the effects of 0.1% Ph administration on male sexual behavior. These results show that perinatal exposure to ph had a dose-dependent effect on the sexual behavior of rats and that a decrease in GnRH source in the offspring was probably involved in the reduction of their sexual performance. (C) 2001 Elsevier B.V. All rights reserved.