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.

The Brazilian Seismographic Integrated Systems (BRASIS): Infrastructure and data management

In geophysics and seismology, raw data need to be processed to generate useful information that can be turned into knowledge by researchers. The number of sensors that are acquiring raw data is increasing rapidly. Without good data management systems, more time can be spent in querying and preparing datasets for analyses than in acquiring raw data. Also, a lot of good quality data acquired at great effort can be lost forever if they are not correctly stored. Local and international cooperation will probably be reduced, and a lot of data will never become scientific knowledge. For this reason, the Seismological Laboratory of the Institute of Astronomy, Geophysics and Atmospheric Sciences at the University of São Paulo (IAG-USP) has concentrated fully on its data management system. This report describes the efforts of the IAG-USP to set up a seismology data management system to facilitate local and international cooperation. © 2011 by the Istituto Nazionale di Geofisica e Vulcanologia. All rights reserved.

Mathematical analysis of maximum power generated by photovoltaic systems and fitting curves for standard test conditions

The rural electrification is characterized by geographical dispersion of the population, low consumption, high investment by consumers and high cost. Moreover, solar radiation constitutes an inexhaustible source of energy and in its conversion into electricity photovoltaic panels are used. In this study, equations were adjusted to field conditions presented by the manufacturer for current and power of small photovoltaic systems. The mathematical analysis was performed on the photovoltaic rural system I- 100 from ISOFOTON, with power 300 Wp, located at the Experimental Farm Lageado of FCA/UNESP. For the development of such equations, the circuitry of photovoltaic cells has been studied to apply iterative numerical methods for the determination of electrical parameters and possible errors in the appropriate equations in the literature to reality. Therefore, a simulation of a photovoltaic panel was proposed through mathematical equations that were adjusted according to the data of local radiation. The results have presented equations that provide real answers to the user and may assist in the design of these systems, once calculated that the maximum power limit ensures a supply of energy generated. This real sizing helps establishing the possible applications of solar energy to the rural producer and informing the real possibilities of generating electricity from the sun.

Test systems and mathematical models for transmission network expansion planning

The data of four networks that can be used in carrying out comparative studies with methods for transmission network expansion planning are given. These networks are of various types and different levels of complexity. The main mathematical formulations used in transmission expansion studies-transportation models, hybrid models, DC power flow models, and disjunctive models are also summarised and compared. The main algorithm families are reviewed-both analytical, combinatorial and heuristic approaches. Optimal solutions are not yet known for some of the four networks when more accurate models (e.g. The DC model) are used to represent the power flow equations-the state of the art with regard to this is also summarised. This should serve as a challenge to authors searching for new, more efficient methods.

Corn productivity in function of surface application of lime in differents management systems and cultural preparation

The evaluation of technologies employed at the agricultural production system such as crop rotation and soil preparation, both associated with crop-livestock integration, is crucial. Therefore, the aim of the present study was to evaluate the incorporation of lime for three no-tillage systems and cultural managements in system of crop-livestock integration, with emphasis on corn grain yield. The experiment was conducted from January 2003 to April 2005 at Selvíria city, MS, in Dystroferric Red Latosol, clay texture. The experimental design was randomized blocks with split plots consisted of three main treatments, aimed the soil physics conditioning and the incorporation of lime: PD - No-no-tillage; CM - minimum no-tillage, and PC - conventional no-tillage; and of two secondary treatments related to the management: rotation and crop succession, with four replications. Data on agronomic traits of maize were analyzed: plant height, stem diameter, height of the first spike insertion, 100 grains weight and grain yield. The results showed that the maize produced under the system of crop-livestock integration is quite feasible, showing that grain yields are comparable to averages in the region and the different soil physical conditioning and incorporation of lime did not influence the corn yield as well as the cultural managements, rotation and succession, did not affect the maize crop behavior after two years of cultivation.

Effects of different soil tillage systems and coverages on soybean crop in the Botucatu Region in Brazil

Nowadays, agricultural practices should combine high yields with a sustainable use of resources. Different tillage practices and crop covers, if combined, may help to achieve both objectives. In this work, several traits of a soybean (Glycine max L. Merr) cultivar were studied under different conditions of tillage and previous soil coverages. The experiment was installed at Lageado Research Station, Botucatu county, SP, Brazil, on a Paleudult. It consisted of nine treatments (combining three systems of soil tillage and three cover crops) and 4 replicates, yielding 36 plots of a randomized block experimental design. The soil tillage systems considered were: (i) conventional tillage with two heavy harrowing and a levelling harrowing; (ii) chiseling, and (iii) no-tillage with chemical drying of vegetation. The three cover crops used were: black oat, sorghum and spontaneous vegetation. Analyzed variables were: plant height, initial and final plant densities, height of first pod insertion, weight of a thousand grains, number of pods per plant, number of grains per pod, and crop yield. No significant differences were observed for most of the analyzed variables; however, conventional tillage produced significantly heavier grains and a higher number of pods per plant. The selected covers were considered an excellent coverage prior to planting soybean in a crop rotation. The three tillage systems can be used for deployment of culture without compromising the development of soybean.

Spatial Distribution of Seropositive Dogs to Leptospira spp. and Evaluation of Leptospirosis Risk Factors Using a Decision Tree

Background: Leptospirosis is an important zoonotic disease associated with poor areas of urban settings of developing countries and early diagnosis and prompt treatment may prevent disease. Although rodents are reportedly considered the main reservoirs of leptospirosis, dogs may develop the disease, may become asymptomatic carriers and may be used as sentinels for disease epidemiology. The use of Geographical Information Systems (GIS) combined with spatial analysis techniques allows the mapping of the disease and the identification and assessment of health risk factors. Besides the use of GIS and spatial analysis, the technique of data mining, decision tree, can provide a great potential to find a pattern in the behavior of the variables that determine the occurrence of leptospirosis. The objective of the present study was to apply Geographical Information Systems and data prospection (decision tree) to evaluate the risk factors for canine leptospirosis in an area of Curitiba, PR.Materials, Methods & Results: The present study was performed on the Vila Pantanal, a urban poor community in the city of Curitiba. A total of 287 dog blood samples were randomly obtained house-by-house in a two-day sampling on January 2010. In addition, a questionnaire was applied to owners at the time of sampling. Geographical coordinates related to each household of tested dog were obtained using a Global Positioning System (GPS) for mapping the spatial distribution of reagent and non-reagent dogs to leptospirosis. For the decision tree, risk factors included results of microagglutination test (MAT) from the serum of dogs, previous disease on the household, contact with rats or other dogs, dog breed, outdoors access, feeding, trash around house or backyard, open sewer proximity and flooding. A total of 189 samples (about 2/3 of overall samples) were randomly selected for the training file and consequent decision rules. The remained 98 samples were used for the testing file. The seroprevalence showed a pattern of spatial distribution that involved all the Pantanal area, without agglomeration of reagent animals. In relation to data mining, from 189 samples used in decision tree, a total of 165 (87.3%) animal samples were correctly classified, generating a Kappa index of 0.413. A total of 154 out of 159 (96.8%) samples were considered non-reagent and were correctly classified and only 5/159 (3.2%) were wrongly identified. on the other hand, only 11 (36.7%) reagent samples were correctly classified, with 19 (63.3%) samples failing diagnosis.Discussion: The spatial distribution that involved all the Pantanal area showed that all the animals in the area are at risk of contamination by Leptospira spp. Although most samples had been classified correctly by the decision tree, a degree of difficulty of separability related to seropositive animals was observed, with only 36.7% of the samples classified correctly. This can occur due to the fact of seronegative animals number is superior to the number of seropositive ones, taking the differences in the pattern of variable behavior. The data mining helped to evaluate the most important risk factors for leptospirosis in an urban poor community of Curitiba. The variables selected by decision tree reflected the important factors about the existence of the disease (default of sewer, presence of rats and rubbish and dogs with free access to street). The analyses showed the multifactorial character of the epidemiology of canine leptospirosis.

Photoelastic Analysis of Implant-Retained and Conventional Obturator Prostheses With Different Attachment Systems and Soft Relining

Complete and partial loss of maxillary bone may jeopardize oral physiology and generate complications as oral-sinus-nasal communication. Palatal obturator prostheses are a treatment alternative for rehabilitation of these patients. The aim of this study was to assess stress distribution, through photoelasticity, on palatal obturator prostheses associated with different attachment systems (o'ring, bar clip, and o'ring/bar clip) of implants and submitted to relining. Two photoelastic models were fabricated according to an experimental maxillary model with oral-sinus-nasal communication. One model did not present implants, whereas the other included 2 implants with 13.0 mm in length in the left ridge. Four colorless maxillary obturator prostheses were fabricated and relined with soft silicone. One of these prostheses presented no attachment system, whereas the remaining prostheses included attachment systems adapted to the implants. The assembly (model/attachment system/prosthesis) was positioned in a circular polariscope during loading with 100 N at 10 mm/s. The results were based on observation during the experiment and photographic records of stress on the photoelastic model. The bar clip system exhibited the highest stress concentration followed by o'ring/bar clip and o'ring systems. The attachment systems presented different stress distribution with greater concentration surrounding the implants and homogenous stress distribution on the photoelastic model without implants. The highest concentration of fringes occurred, in ascending order, with o'ring, o'ring/bar clip, and bar clip systems.

The effect of sodium chloride on the formation of W/O microemulsions in soy bean oil/surfactant/water systems and the solubilization of small hydrophilic molecules

Partial pseudoternary phase diagrams were constructed for soy bean oil (SBO)/surfactant/NaCl aqueous solution systems, at 25 degrees C, using the anionic sodium bis(2-ethylhexyl) sulfosuccinate (ACT) and zwiterionic phosphatidylcholine (PC) or mixtures of these surfactants. The isotropic single phase of water-in-oil (W/O) microemulsions (MEs) is shown in the phase diagram and their viscosity reported. ME samples containing small amount of surfactant exhibit slightly higher viscosity than pure SBO, and were used in the solubilization of small water soluble molecules. NaCl enhances the area of the ME phase and MEs with different surfactant composition exhibit different induction time as obtained from tests of oxidative stability, and so are the MEs enriched with ascorbic acid, folic acid and FeSO4, with the latter exhibiting lower stability. The so prepared enriched soy bean oil has potential application in food industry since the surfactants are food grade. (C) 2007 Elsevier B.V. All rights reserved.

Non-involutive constrained systems and Hamilton-Jacobi formalism

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Cold-atom systems and the scaling limit

With perspective to applications of cold-atom systems, some aspects of few-body physics at very low energies will be reviewed. By exploring the possibilities of varying the two-body interaction via the Feshbach resonance mechanism, some recent results are reported for condensed systems in optical lattices.

EthoSeq: A tool for phylogenetic analysis and data mining in behavioral sequences

This article introduces the software program called EthoSeq, which is designed to extract probabilistic behavioral sequences (tree-generated sequences, or TGSs) from observational data and to prepare a TGS-species matrix for phylogenetic analysis. The program uses Graph Theory algorithms to automatically detect behavioral patterns within the observational sessions. It includes filtering tools to adjust the search procedure to user-specified statistical needs. Preliminary analyses of data sets, such as grooming sequences in birds and foraging tactics in spiders, uncover a large number of TGSs which together yield single phylogenetic trees. An example of the use of the program is our analysis of felid grooming sequences, in which we have obtained 1,386 felid grooming TGSs for seven species, resulting in a single phylogeny. These results show that behavior is definitely useful in phylogenetic analysis. EthoSeq simplifies and automates such analyses, uncovers much of the hidden patterns of long behavioral sequences, and prepares this data for further analysis with standard phylogenetic programs. We hope it will encourage many empirical studies on the evolution of behavior.

On the existence of infinite heteroclinic cycles in polynomial systems and its dynamic consequences

In this work we consider the dynamic consequences of the existence of infinite heteroclinic cycle in planar polynomial vector fields, which is a trajectory connecting two saddle points at infinity. It is stated that, although the saddles which form the cycle belong to infinity, for certain types of nonautonomous perturbations the perturbed system may present a complex dynamic behavior of the solutions in a finite part of the phase plane, due to the existence of tangencies and transversal intersections of their stable and unstable manifolds. This phenomenon might be called the chaos arising from infinity. The global study at infinity is made via the Poincare Compactification and the argument used to prove the statement is the Birkhoff-Smale Theorem. (c) 2004 WILEY-NCH Verlag GmbH & Co. KGaA, Weinheim.

RESTRUCTURING of SYSTEMS and LOGISTICS of MOVEMENT and ITS IMPACT on URBAN and REGIONAL PLANNING PAULISTA

Report some of the changes in production and consumption occurring in the state of São Paulo. through the restructuring in motion systems, logistics and standards and taxation, as well as the impacts on urban spaces through new economic dynamics, imposed by the demands of corporate, is the purpose of this article. The decentralization of production and consumption towards the interior was made possible by the combination of hierarchical and ordered some basic elements such as technological innovations (ways and means of transport) and organizational (logistics, standards and taxation) which optimized the flow territorial state São Paulo. It is noteworthy, therefore: 1) the improvement of logistics as a strategy, planning and management of transport, storage and communications (including the granting of public services to private), 2) the technological improvement and expansion of motion systems (infrastructure, means of transport) and 3) the systems of rules and regulations through taxation and deregulation affect the circulatory system of a given space. Thus, both systems aims to disentangle the economic flows (goods, services, information, capital and people) and provide a more fluid territorial. The impacts on the State of São Paulo, mainly through its economic dynamics, revert positively and negatively, by changing the way one thinks and performs planning.

Cultivation systems and planting seasons effects on the vegetative growing of net melon cultivars

Growth effects of cultivation on soil, sand and commercial substrate, on summer and winter time, of 'Bonus #2', 'Don Carlo's and 'Hy Mark' were assessed. The experiments were conducted in a greenhouse of FCAV-UNESP, in Jaboticabal- SP, Brazil, 21° 15' 22 S, 48° 18'58 W, and an altitude of 595 m, comprising the period from November '99 to April 2000 (Summer), and from July to November 2000 (Winter). On soil cultivation, chemical nutrients were used, and the plants received drip irrigation. On sand, fertigation with recirculation of the nutrient solution were used, and slabs and fertigation with non circulating nutrient solution was used with commercial substrate. 'Bonus #2', grown on sand and in the summer season had improved plant height, internodes length, stem diameter, leaf area and dry matter of shoots and roots. 'Hy Mark', when cultivated on commercial substrate had lower growth. During winter season, the growth was slower.