Feature selection environment for genomic applications

Background: Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction). There are many genomic and proteomic applications that rely on feature selection to answer questions such as selecting signature genes which are informative about some biological state, e. g., normal tissues and several types of cancer; or inferring a prediction network among elements such as genes, proteins and external stimuli. In these applications, a recurrent problem is the lack of samples to perform an adequate estimate of the joint probabilities between element states. A myriad of feature selection algorithms and criterion functions have been proposed, although it is difficult to point the best solution for each application. Results: The intent of this work is to provide an open-source multiplataform graphical environment for bioinformatics problems, which supports many feature selection algorithms, criterion functions and graphic visualization tools such as scatterplots, parallel coordinates and graphs. A feature selection approach for growing genetic networks from seed genes ( targets or predictors) is also implemented in the system. Conclusion: The proposed feature selection environment allows data analysis using several algorithms, criterion functions and graphic visualization tools. Our experiments have shown the software effectiveness in two distinct types of biological problems. Besides, the environment can be used in different pattern recognition applications, although the main concern regards bioinformatics tasks.

Development of Control Systems for Safety Instrumented Systems

Safety Instrumented Systems (SIS) are designed to prevent and / or mitigate accidents, avoiding undesirable high potential risk scenarios, assuring protection of people`s health, protecting the environment and saving costs of industrial equipment. The design of these systems require formal methods for ensuring the safety requirements, but according material published in this area, has not identified a consolidated procedure to match the task. This sense, this article introduces a formal method for diagnosis and treatment of critical faults based on Bayesian network (BN) and Petri net (PN). This approach considers diagnosis and treatment for each safety instrumented function (SIF) including hazard and operability (HAZOP) study in the equipment or system under control. It also uses BN and Behavioral Petri net (BPN) for diagnoses and decision-making and the PN for the synthesis, modeling and control to be implemented by Safety Programmable Logic Controller (PLC). An application example considering the diagnosis and treatment of critical faults is presented and illustrates the methodology proposed.

Effect of the processing conditions and the addition of trans-polyoctenylene rubber on the properties of natural rubber/styrene-butadiene rubber blends

In this study, the influence of the processing conditions and the addition of trans-polyoctenylene rubber (TOR) on Mooney viscosity, tensile properties, hardness, tearing resistance, and resilience of natural rubber/styrene-butadiene rubber blends was investigated. The results obtained are explained in light of dynamic mechanical and morphological analyses. Increasing processing time produced a finer blend morphology, which resulted in an improvement in the mechanical properties. The addition of TOR involved an increase in hardness, a decrease in tear resistance, and no effect on the resilience. It resulted in a large decrease in the Mooney viscosity and a slight decrease in the tensile properties if the components of the compounds were not properly mixed. The results indicate that TOR acted more as a plasticizer than a compatibilizer. (c) 2008 Wiley Periodicals, Inc.

Shedding light on technological development in Brazil

We try to shed some light oil the question of wily technology-intensive businesses often fail in less-developed countries and under what circumstances they are likely to be a Success from the perspective of both domestic and export markets. The answers were drawn from a set of empirical evidences from Brazilian firms applying photonics technologies. Sonic of the issues faced by them are related to the question of state versus private initiative, entering traditional versus niche market, and technology transfer versus product development management. In overall, we concluded that weakness of the institutions and inadequacy of social and organizational demography play a key role in explaining to a large extent wily countries differ in technological development and diffusion. In this context, we point out obstacles, which must be removed in order to make public policies and firm`s achievements more efficient. (C) 2008 Elsevier Ltd. All rights reserved.

Tabasco pepper production with CO(2) application using drip irrigation

Tabasco pepper production with CO(2) application using drip irrigation. Application of CO(2) through water reduces the soil solution pH, causing variations in nutrient mobility and consequent effects on the absorption. The objective of this study was to analyze the effects of carbon dioxide rates supplied by drip irrigation in the production of Capsicum frutescens L. crop. A randomized block design with four treatments and eight replications was used. The treatments were four rates of CO(2): 0 (T1), 451.95 (T2); 677.93 (T3) and 903.92 (T4) kg ha(-1). The fruits were counted and weighed; the length and the diameter were obtained from an average of 20 fruits per plant, randomly taken, from each treatment in the plot. The quadratic effect (p < 0.01) occurred for CO(2) on the yield and there was quadratic effect (p < 0.05) of the rates on the number of fruits. There were no effects of CO(2) rates on the green matter, dry matter and fruit length and diameter. The T2 treatment provided greater yield and higher number of fruits per plant with an increase of 16 and 26%, respectively in relation to T1 (without CO(2)). CO(2) application favored the increase in the yield because of the greater number of fruits per plant in the Tabasco pepper crop.

Private valuation of carbon sequestration in forest plantations

Approval of the Clean Development Mechanism, provided for in the Kyoto Protocol, enables countries with afforested land to trade in carbon emissions reduction certificates related to carbon dioxide equivalent quantities (CO(2-e)) stored within a certain forest area. Potential CO(2-e) above base line sequestration was determined for two forest sites on commercial eucalyptus plantations in northern Brazil (Bahia). Compensation values for silvicultural regimes involving rotation lengths greater than economically optimal were computed using the Faustmann formula. Mean values obtained were US$8.16 (MgCO(2-e))(-1) and US $7.19 (MgCO(2-e))(-1) for average and high site indexes, respectively. Results show that carbon supply is more cost-efficient in highly productive sites. Annuities of US$18.8 Mg C(-1) and US$35.1 Mg C(-1) and yearly payments of US$4.4 m(-3) and US$8.2 m(-3) due for each marginal cubic meter produced were computed for high and average sites, respectively. The estimated value of the tonne of carbon defines minimum values to be paid to forest owners, in order to induce a change in silvicultural management regimes. A reduction of carbon supply could be expected as a result of an increase in wood prices, although it would not respond in a regular manner. For both sites, price elasticity of supply was found to be inelastic and increased as rotation length moved further away from economically optimal: 0.24 and 0.27 for age 11 years in average- and high-productivity sites, respectively. This would be due to biomass production potential as a limiting factor; beyond a certain threshold value. an increase in price does not sustain a proportional change in carbon storage supply. The environmental service valuation model proposed might be adequate for assessing potential supply in plantation forestry, from a private landowner perspective, with an economic opportunity cost. The model is not applicable to low commercial value forest plantations. (C) 2009 Elsevier B.V. All rights reserved.

Diversity of endophytic yeasts from sweet orange and their localization by scanning electron microscopy

Endophytes are microorganisms that colonize plant tissues internally without causing harm to the host. Despite the increasing number of studies on sweet orange pathogens and endophytes, yeast has not been described as a sweet orange endophyte. In the present study, endophytic yeasts were isolated from sweet orange plants and identified by sequencing of internal transcribed spacer (ITS) rRNA. Plants sampled from four different sites in the state of Sao Paulo, Brazil exhibited different levels of CVC (citrus variegated chlorosis) development. Three citrus endophytic yeasts (CEYs), chosen as representative examples of the isolates observed, were identified as Rhodotorula mucilaginosa, Pichia guilliermondii and Cryptococcus flavescens. These strains were inoculated into axenic Citrus sinensis seedlings. After 45 days, endophytes were reisolated in populations ranging from 10(6) to 10(9) CFU/g of plant tissue, but, in spite of the high concentrations of yeast cells, no disease symptoms were observed. Colonized plant material was examined by scanning electron microscopy (SEM), and yeast cells were found mainly in the stomata and xylem of plants, reinforcing their endophytic nature. P. guilliermondii was isolated primarily from plants colonized by the causal agent of CVC, Xylella fastidiosa. The supernatant from a culture of P. guilliermondii increased the in vitro growth of X. fastidiosa, suggesting that the yeast could assist in the establishment of this pathogen in its host plant and, therefore, contribute to the development of disease symptoms.

Nickel adsorption in two Oxisols and an Alfisol as affected by pH, nature of the electrolyte, and ionic strength of soil solution

Background, aim, and scope The retention of potentially toxic metals in highly weathered soils can follow different pathways that variably affect their mobility and availability in the soil-water-plant system. This study aimed to evaluate the effects of pH, nature of electrolyte, and ionic strength of the solution on nickel (Ni) adsorption by two acric Oxisols and a less weathered Alfisol. Materials and methods The effect of pH on Ni adsorption was evaluated in surface and subsurface samples from a clayey textured Anionic `Rhodic` Acrudox ( RA), a sandy-clayey textured Anionic `Xantic` Acrudox (XA), and a heavy clayey textured Rhodic Kandiudalf (RK). All soil samples were equilibrated with the same concentration of Ni solution (5.0 mg L(-1)) and two electrolyte solutions (CaCl(2) or NaCl) with different ionic strengths (IS) (1.0, 0.1 and 0.01 mol L(-1)). The pH of each sample set varied from 3 to 10 in order to obtain sorption envelopes. Results and discussion Ni adsorption increased as the pH increased, reaching its maximum of nearly pH 6. The adsorption was highest in Alfisol, followed by RA and XA. Competition between Ni(2+) and Ca(2+) was higher than that between Ni(2+) and Na(+) in all soil samples, as shown by the higher percentage of Ni adsorption at pH 5. At pH values below the intersection point of the three ionic strength curves (zero point of salt effect), Ni adsorption was generally higher in the more concentrated solution (highest IS), probably due to the neutralization of positive charges of soil colloids by Cl(-) ions and consequent adsorption of Ni(2+). Above this point, Ni adsorption was higher in the more diluted solution (lowest ionic strength), due to the higher negative potential at the colloid surfaces and the lower ionic competition for exchange sites in soil colloids. Conclusions The effect of ionic strength was lower in the Oxisols than in the Alfisol. The main mechanism that controlled Ni adsorption in the soils was the ionic exchange, since the adsorption of ionic species varied according to the variation of pH values. The ionic competition revealed the importance of electrolyte composition and ionic strength on Ni adsorption in soils from the humid tropics. Recommendations and perspectives The presence of NaCl or CaCl(2) in different ionic strengths affects the availability of heavy metals in contaminated soils. Therefore, the study of heavy metal dynamics in highly weathered soils must consider this behavior, especially in soils with large amounts of acric components.

Trypanosoma cruzi: evaluation of (-)-cubebin derivatives activity in the messenger RNAs processing

No fully effective treatment has been developed since the discovery of Chagas` disease. Since drug-resistant Trypanosoma cruzi strains are occurring and the current therapy is effective in the acute phase but with various adverse side effects, more studies are needed to characterize the susceptibility of T. cruzi to new drugs. Pre-mRNA maturation in trypanosomatids occurs through a process called trans-splicing, which is unusual RNA processing reaction, and it implies the processing of polycistronic transcription units into individual mRNAs; a short transcript spliced leader (SL RNA) is trans-spliced to the acceptor pre-mRNA, giving origin to the mature mRNA. Cubebin derivatives seem to provide treatments with less collateral effects than benznidazole and showed similar or better trypanocidal activities than benznidazole. Therefore, the cubebin derivatives ((-)-6,6`-dinitrohinokinin (DNH) and (-)-hinokinin (HQ)) interference in the mRNA processing was evaluated using T. cruzi permeable cells (Y and BOL (Bolivia) strains) following by RNase protection reaction. These substances seem to intervene in any step of the RNA transcription, promoting alterations in the RNA synthesis, even though the RNA processing mechanism still occurs. Furthermore, HQ presented better activity against the parasites than DNH, meaning that BOL strain seems to be more resistant than Y.

Dendrimer intercalation in layered double hydroxides

New organic/inorganic (O/I) hybrid assemblies based on Layered Double Hydroxide (LDH) with polyamide amine dendrimer (PAMAM, generation -0.5 and generation +0.5) were prepared by two different routes using either the direct coprecipitation at constant pH or the anion exchange procedure in double surfactant S(+)S(-) phases. The obtained materials were characterized by means of powder X-ray diffraction, thermal gravimetric analysis associated with mass spectrometry, and Fourier-transform infrared spectroscopy. X-ray powder diffraction pattern of the O/I LDH assembly exhibit characteristic profiles of LDH-based materials with basal spacing depending on the nature of the dendrimer. Indeed, for both synthetic procedures, interleaved PAMAM -0.5 gives rise to an interlayer space in agreement with a perpendicular molecular arrangement against the layer of the host structure. For PAMAM+0.5, considering its spherical dimension, a much smaller basal spacing was observed. This observation was interpreted as shrinkage of the molecule to accommodate the interlayer LDH gap, which was rendered possible by the bond angle twisting within PAMAM-0.5. FTIR spectra confirm the presence of both moieties inside both Zn(2)Al/PAMAM G-0.5 and Zn(2)Al/PAMAM G+0.5 assemblies. Finally, thermal analysis associated with mass spectrometry confirm this composition, and in situ temperature XRD data reveal that the highly constrained arrangement for the generation +0.5 is not accompanied by a gain in thermal structural stability; in fact, the assembly prepared from PAMAM -0.5 is more stable. Both O/I PAMAM LDH assemblies constitute well-defined materials which are candidate for catalytic applications.

EEG-based Brain-Computer Interfaces: An Overview of Basic Concepts and Clinical Applications in Neurorehabilitation

Some patients are no longer able to communicate effectively or even interact with the outside world in ways that most of us take for granted. In the most severe cases, tetraplegic or post-stroke patients are literally `locked in` their bodies, unable to exert any motor control after, for example, a spinal cord injury or a brainstem stroke, requiring alternative methods of communication and control. But we suggest that, in the near future, their brains may offer them a way out. Non-invasive electroencephalogram (EEG)-based brain-computer interfaces (BCD can be characterized by the technique used to measure brain activity and by the way that different brain signals are translated into commands that control an effector (e.g., controlling a computer cursor for word processing and accessing the internet). This review focuses on the basic concepts of EEG-based BC!, the main advances in communication, motor control restoration and the down-regulation of cortical activity, and the mirror neuron system (MNS) in the context of BCI. The latter appears to be relevant for clinical applications in the coming years, particularly for severely limited patients. Hypothetically, MNS could provide a robust way to map neural activity to behavior, representing the high-level information about goals and intentions of these patients. Non-invasive EEG-based BCIs allow brain-derived communication in patients with amyotrophic lateral sclerosis and motor control restoration in patients after spinal cord injury and stroke. Epilepsy and attention deficit and hyperactive disorder patients were able to down-regulate their cortical activity. Given the rapid progression of EEG-based BCI research over the last few years and the swift ascent of computer processing speeds and signal analysis techniques, we suggest that emerging ideas (e.g., MNS in the context of BC!) related to clinical neuro-rehabilitation of severely limited patients will generate viable clinical applications in the near future.

Cholinergic Hyperresponsiveness of Peripheral Lung Parenchyma in Chronic Obstructive Pulmonary Disease

Background: Up to 60% of chronic obstructive pulmonary disease ( COPD) patients can present airway hyperresponsiveness. However, it is not known whether the peripheral lung tissue also shows an exaggerated response to agonists in COPD. Objectives: To investigate the in vitro mechanical behavior and the structural and inflammatory changes of peripheral lung tissue in COPD patients and compare to nonsmoking controls. Methods: We measured resistance and elastance at baseline and after acetylcholine (ACh) challenge of lung strips obtained from 10 COPD patients and 10 control subjects. We also assessed the alveolar tissue density of neutrophils, eosinophils, macrophages, mast cells and CD8+ and CD4+ cells, as well as the content of alpha-smooth muscle actin-positive cells and elastic and collagen fibers. We further investigated whether changes in in vitro parenchymal mechanics correlated to structural and inflammatory parameters and to in vivo pulmonary function. Results: Values of resistance after ACh treatment and the percent increase in tissue resistance (%R) were higher in the COPD group (p <= 0.03). There was a higher density of macrophages and CD8+ cells (p < 0.05) and a lower elastic content (p = 0.003) in the COPD group. We observed a positive correlation between %R and eosinophil and CD8+ cell density (r = 0.608, p = 0.002, and r = 0.581, p = 0.001, respectively) and a negative correlation between %R and the ratio of forced expiratory volume in 1 s to forced vital capacity (r = -0.451, p < 0.05). Conclusions: The cholinergic responsiveness of parenchymal lung strips is increased in COPD patients and seems to be related to alveolar tissue eosinophilic and CD8 lymphocytic inflammation and to the degree of airway obstruction on the pulmonary function test. Copyright (C) 2011 S. Karger AG, Basel

Influence of Parasympathetic Modulation in Doppler Mitral Inflow Velocity in Individuals without Heart Disease

Background: The relation between left ventricular filing velocities determined by Doppler echocardiography and autonomic nervous system function assessed by heart rate variability (HRV) is unclear. The aim of this study was to evaluate the influence of the autonomic nervous system assessed by the time and frequency domain indices of HRV in the Doppler indices of left ventricular diastolic filling velocities in patients without heart disease. Methods: We studied 451 healthy individuals (255 female [56.4%]) with normal blood pressure, electrocardiogram, chest x-ray, and treadmill electrocardiographic exercise stress test results, with a mean age of 43 +/- 12 (range 15-82) years, who underwent transthoracic Doppler echocardiography and 24-hour electrocardiographic ambulatory monitoring. We studied indices of HRV on time (standard deviation [SD] of all normal sinus RR intervals during 24 hours, SD of averaged normal sinus RR intervals for all 5-minute segments, mean of the SD of all normal sinus RR intervals for all 5-minute segments, root-mean-square of the successive normal sinus RR interval difference, and percentage of successive normal sinus RR intervals > 50 ms) and frequency (low frequency, high frequency, very low frequency, low frequency/high frequency ratio) domains relative to peak flow velocity during rapid passive filling phase (E), atrial contraction (A), E/A ratio, E-wave deceleration time, and isovolumic relaxation time. Statistical analysis was performed with Pearson correlation and logistic regression. Results: Peak flow velocity during rapid passive filling phase (E) and atrial contraction (A), E/A ratio, and deceleration time of early mitral inflow did not demonstrate a significant correlation with indices of HRV in time and frequency domain. We found that the E/A ratio was < 1 in 45 individuals (10%). Individuals with an E/A ratio < 1 had lower indices of HRV in frequency domain (except low frequency/high frequency) and lower indices of the mean of the SD of all normal sinus RR intervals for all 5-minute segments, root-mean-square of the successive normal sinus RR interval difference, and percentage of successive normal sinus RR intervals > 50 ms in time domain. Logistic regression demonstrated that an E/A ratio < 1 was associated with lower HF. Conclusion: Individuals with no evidence of heart disease and an E/A ratio < 1 demonstrated a significant decrease in indexes of HRV associated with parasympathetic modulation. (J Am Soc Echocardiogr 2010;23: 762-5.)

Abnormal Amygdala-Prefrontal Effective Connectivity to Happy Faces Differentiates Bipolar from Major Depression

Background: Bipolar disorder is frequently misdiagnosed as major depressive disorder, delaying appropriate treatment and worsening outcome for many bipolar individuals. Emotion dysregulation is a core feature of bipolar disorder. Measures of dysfunction in neural systems supporting emotion regulation might therefore help discriminate bipolar from major depressive disorder. Methods: Thirty-one depressed individuals-15 bipolar depressed (BD) and 16 major depressed (MDD), DSM-IV diagnostic criteria, ages 18-55 years, matched for age, age of illness onset, illness duration, and depression severity-and 16 age- and gender-matched healthy control subjects performed two event-related paradigms: labeling the emotional intensity of happy and sad faces, respectively. We employed dynamic causal modeling to examine significant among-group alterations in effective connectivity (EC) between right- and left-sided neural regions supporting emotion regulation: amygdala and orbitomedial prefrontal cortex (OMPFC). Results: During classification of happy faces, we found profound and asymmetrical differences in EC between the OMPFC and amygdala. Left-sided differences involved top-down connections and discriminated between depressed and control subjects. Furthermore, greater medication load was associated with an amelioration of this abnormal top-down EC. Conversely, on the right side the abnormality was in bottom-up EC that was specific to bipolar disorder. These effects replicated when we considered only female subjects. Conclusions: Abnormal, left-sided, top-down OMPFC-amygdala and right-sided, bottom-up, amygdala-OMPFC EC during happy labeling distinguish BD and MDD, suggesting different pathophysiological mechanisms associated with the two types of depression.

Effects of bromazepam in frontal theta activity on the performance of a sensorimotor integration task: A quantitative electroencephalography study

Our objective is to verify the modulatory effects of bromazepam on EEG theta absolute power when subjects were submitted to a visuomotor task (i.e., car driver task). Sample was composed of 14 students (9 males and 5 females), right handed, with ages varying between 23 and 42 years (mean = 32.5 +/- 9.5), absence of mental or physical impairments, no psychoactive or psychotropic substance use and no neuromuscular disorders (screened by a clinical examination). The results showed an interaction between condition and electrodes (p=0.034) in favor of F8 electrode compared with F7 in both experimental conditions (t-test; p=0.001). Additionally, main effects were observed for condition (p=0.001), period (p=0.001) and electrodes (p=0.031) in favor of F4 electrode compared with F3. In conclusion, Br 6 mg of bromazepam may interfere in sensorimotor processes in the task performance in an unpredictable scenario allowing that certain visuospatial factors were predominant. Therefore, the results may reflect that bromazepam effects influence the performance of the involved areas because of the acquisition and integration of sensory stimuli processes until the development of a motor behavior based on the same stimuli. (C) 2009 Elsevier Ireland Ltd. All rights reserved.