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.

Effects of turmeric and its active principle, curcumin, on bleomycin-induced chromosome aberrations in Chinese hamster ovary cells

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

EFFECTS OF INTRAUTERINE AND POSTNATAL PROTEIN-CALORIE MALNUTRITION ON METABOLIC ADAPTATIONS TO EXERCISE IN YOUNG-RATS

The effect of intrauterine and postnatal protein-calorie malnutrition on the biochemical ability to perform exercise was investigated in young male rats. Malnourished rats were obtained by feeding dams a low-protein (6%) casein-based diet prepared in the laboratory during pregnancy and lactation. Control rats received an isocaloric diet containing 25% protein. The low-protein diet contained additional starch and glucose. At 45 days of age, malnourished rats showed lower body weight, serum protein, albumin and glucose levels, hematocrit values and heart glycogen content but higher circulating free fatty acids and gastrocnemius muscle glycogen than control rats. In response to exercise (50 min of swimming), control rats displayed lower heart, gastrocnemius and liver glycogen levels whereas malnourished rats showed low glycogen levels only in the gastrocnemius muscle. Both control and malnourished rats showed high serum glucose and free fatty acid levels after exercise. In conclusion, protein-calorie malnutrition improved muscle glycogen storage but this substrate was broken down to a greater extent in response to exercise. Malnourished rats were able to perform exercise maintaining high blood glucose levels, as observed in control rats, perhaps as a consequence of the elevated availability of circulating free fatty acids.

Influence of TiO2 and AI(2)O(3) on the electrical and microstructural properties of SnO2 ceramics obtained by the Pechini method

Tin oxide has wakened up great scientific and technological interest for its potential use in varistors production and as gas sensor. In order to improve the microstructural and electrical properties in SnO2 varistor ceramics, the influence of differents dopants used, like TiO2 and Al2O3, is under research. The effect of TiO2 and Al2O3 on the properties of Sn-Co-Nb varistor systems obtained by the Pechini method has been investigated in this work. Characterization of synthesized raw material was performed by X-Ray Diffraction (XRD) and Scanning Electronic Microscopy (SEM). The microstructural and electrical characterization of sintered samples show that the TiO2 favors the grain growth and the Al2O3 contributes to the decrease it, effect that is manifested in the Sn-Co-Nb varistor systems. Breakdown field increase up to 6300V/cm with increasing Al2O3 content and non-linear coefficients with alpha=22 were obtained.

Distribution of fluoride and calcium in plaque biofilms after the use of conventional and low-fluoride dentifrices

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

Influence of ideal and non-ideal excitation sources on the dynamics of a nonlinear vibro-impact system

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

Alcohol and Quality of Life Among Social Groups for the Elderly in Sao Jose dos Campos, Brazil

This study aims to investigate alcohol consumption within social groups for the elderly in So Jos, dos Campos-Brazil, and to check for a correlation between alcohol consumption and quality of life. A sample of 500 individuals participating on social groups for the elderly were interviewed by using the Alcohol Use Disorders Identification Test (AUDIT) to verify alcohol consumption; the Medical Outcomes Study 36 Item Short Form (SF-36), for evaluating quality of life; and the Oral Health Impact Profile short form (OHIP-14), for evaluating oral health-related quality of life. The average alcohol consumption was very low (1.48), being higher in men (2.23) than women (1.09). The SF-36 average score for the domain of physical function was 70.5; for role-physical function 64.9; for bodily pain,68.3; for general health 73.8; for vitality,72.4; for social function 82.8; for role-emotional function 72.3 and for mental health 75.0. The OHIP-14 average score was 3.87. AUDIT did not correlate with SF-36 domains, or with OHIP-14. However, there was a negative correlation between OHIP 14 and all SF-36 domains. This elderly sample has a very low consumption of alcohol, and no correlation was found between alcohol consumption and oral and medical quality of life.

Methodological contributions towards the study of health care production: lessons from a research study on barriers and access in mental health

This article presents methodological contributions and a conceptual innovation for thinking about the production of health care, stemming from a study on access and barriers in mental health carried out in the municipality of Campinas (São Paulo, Brazil). The study used a cartographic approach and, after an initial identification of the most complex cases (on the part of the teams of workers), adopted the users as guides to explore the different levels of production of their lives and to evaluate the possibility of forming a network of existential connections that produce life as a fundamental analyzer of access or barriers to care.

Analysis of efficiency and rationality in a sugar-alcohol mill using hyperboloid a-load and potency

Brazil is the world's largest producer of sugar cane and which in the state of São Paulo concentrate the greatest amount of sugar cane field of the country. The sugar-alcohol sector has the capacity to produce sufficient thermal and electrical energy to be used in their process of production and commercialize of surplus in electricity distribution network. Therefore it is necessary to evaluate the energy efficiency and rationality within the mill. Accordingly this research proposed analyze the sugar-alcohol mill's sectors globally and individually, located in the west center of the São Paulo state, using the valuation methodology employed by the Agência Nacional de Energia Elétrica (ANEEL) in the industries that do not have systems of cogeneration. In this analysis, the hyperboloids of load and potency were applied based on the indexes of potency factor and load factor that allow estimate the efficiency and rationality. © 2013 IEEE.

DFT Study on Ce-Doped Anatase TiO2: Nature of Ce3+ and Ti3+ Centers Triggered by Oxygen Vacancy Formation

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

Environmental Fate of Neonicotinoids and Classification of Their Potential Risks to Hypogean, Epygean, and Surface Water Ecosystems in Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Theoretical study on the molecular mechanism for the reaction of VO2+ with C2H4

The complex reaction between VO2+ ((1)A(1)/(3)A) and C2H4 (Ag-1(g)/(3)A(1)) to yield VO+ ((1)Delta/(3)Sigma) and CH3CHO ('A'/(3)A) has been studied by means of B3LYP/6-31G* and B3LYP/6-311G(2d,p) calculations. The structures of all reactants, products, intermediates, and transition structures of this reaction have been optimized and characterized at the fundamental singlet and first excited triplet electronic states. Crossing points are localized, and possible spin inversion processes are discussed by means of the intrinsic reaction coordinate approach. Relevant stationary points along the most favorable reaction pathways have been studied at the CCSD/6-311G(2d,p)//B3LYP/6-311G(2d,p) calculation level. The theoretical results allow the development of thermodynamic and kinetic arguments about the reaction pathways of the title process. In the singlet state, the first step is the barrierless obtention of a reactant complex associated with the formation of a V-C bond, while in the triplet state a three-membered ring addition complex with the V bonded to the two C atoms is obtained. Similar behavior is found in the exit channels: the product complexes can be formed from isolated products without barriers. The reactant and product complexes are the most stable stationary points in the singlet and triplet electronic states. From the singlet state reactant complex, two reaction pathways are posssible to reach the triplet state product complex. (i) A mechanism in which a hydrogen transfer process is the first and rate limiting step and the second step is an oxygen transfer between vanadium and carbon atoms with a concomitant change in the spin state. The crossing point between singlet and triplet spin states is not kinetically relevant because it takes place at a later stage occurring in the exit channel. (ii) A mechanism in which the first stage renders a four-membered ring between vanadyl cation and the ethylene fragment and an oxygencarbon bond is formed; on going from this minimum to the second transition structure, associated with a carbon-vanadium bond breaking process, the crossing point between singlet and triplet spin states is reached. The final step is the hydrogen transfer between both carbon atoms to yield the product complex. In this case the spin change opens a lower barrier pathway. The transition structures with larger values of relative energies for both reactive channels of VO2+ ((1)A(1)) + C2H4 (Ag-1) --> VO+ ((3)Sigma) + CH3CHO ((1)A') present similar energies, and the two reaction pathways can be considered as competitive.

Theoretical study on the reaction mechanism of VO2+ with propyne in gas phase

Possible molecular mechanisms of the gas-phase ion/molecule reaction of VO2+ in its lowest singlet and triplet states ((1)A(1)/(3)A '') with propyne have been investigated theoretically by density functional theory (DFT) methods. The geometries, energetic values, and bonding features of all stationary and intersystem crossing points involved in the five different reaction pathways (paths 1-5), in both high-spin (triplet) and low-spin (singlet) surfaces, are reported and analyzed. The oxidation reaction starts by a hydrogen transfer from propyne molecule to the vanadyl complex, followed by oxygen migration to the hydrocarbon moiety. A hydride transfer process to the vanadium atom opens four different reaction courses, paths 1-4, while path 5 arises from a hydrogen transfer process to the hydroxyl group. Five crossing points between high- and low-spin states are found: one of them takes place before the first branching point, while the others occur along path 1. Four different exit channels are found: elimination of hydrogen molecule to yield propynaldehyde and VO+ ((1)Sigma/(3)Sigma); formation of propynaldehyde and the moiety V-(OH2)(+); and two elimination processes of water molecule to yield cationic products, Prod-fc(+) and Prod-dc(+) where the vanadium atom adopts a four- and di-coordinate structure, respectively.

The use of landforms to predict the variability of soil and orange attributes

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

Productivity of beet and roquette cultivation as a function of time of establishing intercropping

With the aim of evaluating the effect of intercropping on the productivity of beet and roquette crops, a study was conducted in the Section of Vegetable and Aromatic-Medicinal Plants, FCAV-UNESP, Jaboticabal/SP. The treatments consisted of co-cultivations of roquette (Cultivada) and beets (Early Wonder) established at 0, 7, 14 and 21 days after the transplanting of beets, and as monocultures of beets and roquette. The experiments were delineated in a randomized block design. The productivity of beets in monoculture was not superior to that obtained with intercropping with roquette. The production of dry mass of roquette with intercropping was less than that with monoculture and the reduction was more marked with more delayed establishment of co-cultivation. Intercropping established at 0 and 7 days after the transplanting of beets was the most efficient, with indices of efficient use of land of 1.26 and 1.27, respectively.