Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors

Reverse transcriptase (RT) is a multifunctional enzyme in the human immunodeficiency virus (HIV)-1 life cycle and represents a primary target for drug discovery efforts against HIV-1 infection. Two classes of RT inhibitors, the nucleoside RT inhibitors (NRTIs) and the nonnucleoside transcriptase inhibitors are prominently used in the highly active antiretroviral therapy in combination with other anti-HIV drugs. However, the rapid emergence of drug-resistant viral strains has limited the successful rate of the anti-HIV agents. Computational methods are a significant part of the drug design process and indispensable to study drug resistance. In this review, recent advances in computer-aided drug design for the rational design of new compounds against HIV-1 RT using methods such as molecular docking, molecular dynamics, free energy calculations, quantitative structure-activity relationships, pharmacophore modelling and absorption, distribution, metabolism, excretion and toxicity prediction are discussed. Successful applications of these methodologies are also highlighted.

Loss of ammonia from nitrogen fertilizers applied to maize and soybean straw

In Brazilian agriculture, urea is the most commonly used nitrogen (N) source, in spite of having the disadvantage of losing considerable amounts of N by ammonia-N volatilization. The objectives of this study were to evaluate: N lossby ammonia volatilization from: [urea coated with copper sulfate and boric acid], [urea coated with zeolite], [urea+ammonium sulfate], [urea coated with copper sulfate and boric acid+ammonium sulfate], [common urea] and [ammonium nitrate]; and the effect of these N source son the maize yield in terms of amount and quality. The treatments were applied to the surface of a soil under no-tillage maize, in two growing seasons. The first season (2009/2010) was after a maize crop (maize straw left on the soil surface) and the second cycle (2012/2011) after a soybean crop. Due to the weather conditions during the experiments, the volatilization of ammonia-N was highest in the first four days after application of the N sources. Of all urea sources, under volatilization-favorable conditions, the loss of ammonia from urea coated with copper sulfate and boric acid was lowest, while under high rainfall, the losses from the different urea sources was similar, i.e., an adequate rainfall was favorablet o reduce volatilization. The ammonia volatilization losses were greatest in the first four days after application. Maize grain yield differed due to N application and in the treatments, but this was only observed with cultivation of maize crop residues in 2009/2010. The combination of ammonium+urea coated with copper sulfate and boric acid optimized grain yield compared to the other urea treatments. The crude protein concentration in maize was not influenced by the technologies of urea coating.

Fuzzy logic applied to the modeling of water dynamics in an Oxisol in northeastern Brazil

Modeling of water movement in non-saturated soil usually requires a large number of parameters and variables, such as initial soil water content, saturated water content and saturated hydraulic conductivity, which can be assessed relatively easily. Dimensional flow of water in the soil is usually modeled by a nonlinear partial differential equation, known as the Richards equation. Since this equation cannot be solved analytically in certain cases, one way to approach its solution is by numerical algorithms. The success of numerical models in describing the dynamics of water in the soil is closely related to the accuracy with which the water-physical parameters are determined. That has been a big challenge in the use of numerical models because these parameters are generally difficult to determine since they present great spatial variability in the soil. Therefore, it is necessary to develop and use methods that properly incorporate the uncertainties inherent to water displacement in soils. In this paper, a model based on fuzzy logic is used as an alternative to describe water flow in the vadose zone. This fuzzy model was developed to simulate the displacement of water in a non-vegetated crop soil during the period called the emergency phase. The principle of this model consists of a Mamdani fuzzy rule-based system in which the rules are based on the moisture content of adjacent soil layers. The performances of the results modeled by the fuzzy system were evaluated by the evolution of moisture profiles over time as compared to those obtained in the field. The results obtained through use of the fuzzy model provided satisfactory reproduction of soil moisture profiles.

Método multirresíduo para monitoramento de contaminação ambiental de pesticidas na região de Bauru (SP) usando mel como bio-indicador

The presence of residues of the major groups of pesticides (organohalogen, organophosphorous, pyrethroids and organonitrogen) in representative samples of honey produced in Bauru (state of São Paulo, Brazil) was investigated from 1999 through2004. A multiresidue method was applied to honey samples to determine 48 pesticides with recoveries ranging from 76 to 95%. The limits of detection found were lower than 10 µg/kg for GC-MS-SIM. The results indicated that most pesticides found in the samples belonged to the organohalogen and organonitrogen groups. Residues of malathion were detected in almost all of the samples in high concentration.

Determination of Ni(II) in metal alloys by spectrophotometry UV-Vis using dopasemiquinone

A spectrophotometric method was proposed for Ni(II) determination in alloys using a dopa-semiquinone (L-1) to form [Ni(II)(L1-)3]1-, ε = 9.3 x 10³ L mol-1 cm-1. The optimal conditions for the determination were: wavelength 590 nm, temperature 25 °C, reaction time 45 min and pH 7.5. The Beer's law was obeyed for nickel from 3.33 x 10-5 to 1.78 x 10-4 mol L-1. The method was applied to complex samples, such as inox, nickel-titanium and cobalt-chromium alloys. A study of the potential interferents revealed that Mn was the major interferent. The limit of detection and quantification were 2.88 x 10-5 mol L-1 and 3.06 x 10-5 mol L-1, respectively.

A FACTORIAL DESIGN APPLIED TO THE STUDY OF CHROMIUM TOXICITY ON THE GLUTATHIONE LEVELS OF Brachiaria brizantha AND Brachiaria ruziziensis SEEDLINGS

Chromium toxicity affects redox reactions within plant cells, generating detrimental reactive oxygen species. Glutathione is an antioxidant peptide and also a substrate for the production of phytochelatins, which are chelating peptides reported to mitigate Cr3+ toxicity in plants. In this study, Brachiaria brizantha (B. brizantha) and Brachiaria ruziziensis (B. ruziziensis) seedlings were evaluated for physiological responses and glutathione production following the addition of zero or 5 mg L-1 Cr3+ to the nutrient solution. Glutathione levels were determined by colorimetric analysis at 412 nm using 5,5'-dithio-bis(2-nitrobenzoic acid) as a chromophore reagent and recovery with glutathione reductase (with evaluations at days 10 and 20 of continuous growth). The assessments were carried out in a completely randomized design with 2 authentic replications, and arranged in a 23 factorial. Cr3+ caused an average increase of 0.76 mg g-1 in the initial glutathione content. However, by day 20 there was an average reduction of 3.63 mg g-1. Chromium-affected physiological detrimental responses, albeit detected in both species, were less-pronounced in B. ruziziensis, along with a much higher level of glutathione. This study indicates that B. ruziziensis has a greater tolerance for chromium toxicity than B. brizantha, and that glutathione is likely to be involved in the mitigation of chromium stress in B. ruziziensis.

Fast determination of minoxidil by photometric flow titration

A photometric flow titration based on the redox reaction between KMnO4 and minoxidil is described. The best titration results were observed at 3.20 x 10-4 mol L-1 KMnO4 and 1.00 x 10-3 mol L-1 minoxidil, using the minoxidil solutions as titrant. The flow rate was fixed at 17 mL min-1 and the titrant was added to the system in aliquots of 500 µL, the color changes were monitored at 550 nm. The method was applied to commercial samples and compared with the results from a chromatographic procedure. Recoveries from 97.6 to 102.8 % were observed depending on the sample. Comparison with the chromatographic procedure reveled relative errors of 3.5 - 4.0 %.

Determination of copper at wide range concentrations using instrumental features of high-resolution continuum source flame atomic absorption spectrometry

This work describes a method to determine Cu at wide range concentrations in a single run without need of further dilutions employing high-resolution continuum source flame atomic absorption spectrometry. Different atomic lines for Cu at 324.754 nm, 327.396 nm, 222.570 nm, 249.215 nm and 224.426 nm were evaluated and main figures of merit established. Absorbance measurements at 324.754 nm, 249.215 nm and 224.426 nm allows the determination of Cu in the 0.07 - 5.0 mg L-1, 5.0 - 100 mg L-1 and 100 - 800 mg L-1 concentration intervals respectively with linear correlation coefficients better than 0.998. Limits of detection were 21 µg L-1, 310 µg L-1 and 1400 µg L-1 for 324.754 nm, 249.215 nm and 224.426 nm, respectively and relative standard deviations (n = 12) were £ 2.7%. The proposed method was applied to water samples spiked with Cu and the results were in agreement at a 95% of confidence level (paired t-test) with those obtained by line-source flame atomic absorption spectrometry.

Computer tools applied to analysis of solar water heaters

The simulation programs are important tools to analyze the different energetic alternatives, including the use of renewable energy. The objective of this study was to analyze comparatively the different computer tools available for modeling of solar water heaters. Among the main simulation software of solar thermal systems, there are: RETScreen International, EnergyPlus, TRNSYS, SolDesigner, SolarPro, e T*SOL. Among the tools mentioned, only EnergyPlus and RETScreen International are free, but they allow obtaining interesting results when applied together. The first one has a detailed module of energy analysis of solar water heaters, while the second one provides an detailed economic feasibility study and an assessment of emissions of greenhouse gases. RETScreen International and EnergyPlus programs are aimed at a diverse audience, including designers, researchers and energy planners.

Spatial statistics applied to soybean production data from Paraná State for 2003-04 to 2009-10 crop-years

In the current study, we performed a soybean production spatial distribution analysis in Paraná State. Seven crop-year data, from 2003-04 to 2009-10, obtained from the Paraná Department of Agriculture and Supply (SEAB) were used to develop a Boxmap for each crop-year, show soybean production throughout this time interval. Moran's index was used to measure spatial autocorrelation among municipalities at an aggregate level, while LISA index local correlation. For each index, different contiguity matrix and order were used and there was a significance level study. As a result, we have showed spatial relationship among cities regarding the production, which allowed the indication of high and low production clusters. Finally, identifying main soybean-producing cities, what may provide supply chain members with information to strengthen the crop production in Paraná.

Shewhart's control charts and process capability ratio applied to a sewage treatment station

The current study used statistical methods of quality control to evaluate the performance of a sewage treatment station. The concerned station is located in Cascavel city, Paraná State. The evaluated parameters were hydrogenionic potential, settleable solids, total suspended solids, chemical oxygen demand and biochemical oxygen demand in five days. Statistical analysis was performed through Shewhart control charts and process capability ratio. According to Shewhart charts, only the BOD(5.20) variable was under statistical control. Through capability ratios, we observed that except for pH the sewage treatment station is not capable to produce effluents under characteristics that fulfill specifications or standard launching required by environmental legislation.

Mathematical modeling applied to the growth of tilapia in net cages in the sub middle of the São Francisco river

This study aimed to apply mathematical models to the growth of Nile tilapia (Oreochromis niloticus) reared in net cages in the lower São Francisco basin and choose the model(s) that best represents the conditions of rearing for the region. Nonlinear models of Brody, Bertalanffy, Logistic, Gompertz, and Richards were tested. The models were adjusted to the series of weight for age according to the methods of Gauss, Newton, Gradiente and Marquardt. It was used the procedure "NLIN" of the System SAS® (2003) to obtain estimates of the parameters from the available data. The best adjustment of the data were performed by the Bertalanffy, Gompertz and Logistic models which are equivalent to explain the growth of the animals up to 270 days of rearing. From the commercial point of view, it is recommended that commercialization of tilapia from at least 600 g, which is estimated in the Bertalanffy, Gompertz and Logistic models for creating over 183, 181 and 184 days, and up to 1 Kg of mass , it is suggested the suspension of the rearing up to 244, 244 and 243 days, respectively.

Simulation of Active Control Using Fuzzy Logic Applied to a Pulse Combustor

This work analyzes an active fuzzy logic control system in a Rijke type pulse combustor. During the system development, a study of the existing types of control for pulse combustion was carried out and a simulation model was implemented to be used with the package Matlab and Simulink. Blocks which were not available in the simulator library were developed. A fuzzy controller was developed and its membership functions and inference rules were established. The obtained simulation showed that fuzzy logic is viable in the control of combustion instabilities. The obtained results indicated that the control system responded to pulses in an efficient and desirable way. It was verified that the system needed approximately 0.2 s to increase the tube internal pressure from 30 to 90 mbar, with an assumed total delay of 2 ms. The effects of delay variation were studied. Convergence was always obtained and general performance was not affected by the delay. The controller sends a pressure signal in phase with the Rijke tube internal pressure signal, through the speakers, when an increase the oscillations pressure amplitude is desired. On the other hand, when a decrease of the tube internal pressure amplitude is desired, the controller sends a signal 180º out of phase.

Experimental validation of a 3-D vision-based measurement system applied to robot calibration

One of the problems that slows the development of off-line programming is the low static and dynamic positioning accuracy of robots. Robot calibration improves the positioning accuracy and can also be used as a diagnostic tool in robot production and maintenance. A large number of robot measurement systems are now available commercially. Yet, there is a dearth of systems that are portable, accurate and low cost. In this work a measurement system that can fill this gap in local calibration is presented. The measurement system consists of a single CCD camera mounted on the robot tool flange with a wide angle lens, and uses space resection models to measure the end-effector pose relative to a world coordinate system, considering radial distortions. Scale factors and image center are obtained with innovative techniques, making use of a multiview approach. The target plate consists of a grid of white dots impressed on a black photographic paper, and mounted on the sides of a 90-degree angle plate. Results show that the achieved average accuracy varies from 0.2mm to 0.4mm, at distances from the target from 600mm to 1000mm respectively, with different camera orientations.

Experimental study applied to an industrial robot by using variable structure controllers and friction compensation

Control of an industrial robot is mainly a problem of dynamics. It includes non-linearities, uncertainties and external perturbations that should be considered in the design of control laws. In this work, two control strategies based on variable structure controllers (VSC) and a PD control algorithm are compared in relation to the tracking errors considering friction. The controller's performances are evaluated by adding an static friction model. Simulations and experimental results show it is possible to diminish tracking errors by using a model based friction compensation scheme. A SCARA robot is used to illustrate the conclusions of this paper.