The carbohydrate-binding specificity and molecular modelling of Canavalia maritima and Dioclea grandiflora lectins

The carbohydrate-binding specificity of lectins from the seeds of Canavalia maritima and Dioclea grandiflora was studied by hapten-inhibition of haemagglutination using various sugars and sugar derivatives as inhibitors, including N-acetylneuraminic acid and N-acetylmuramic acid. Despite some discrepancies, both lectins exhibited a very similar carbohydrate-binding specificity as previously reported for other lectins from Diocleinae (tribe Phaseoleae, sub-tribe Diocleinae). Accordingly, both lectins exhibited almost identical hydropathic profiles and their three-dimensional models built up from the atomic coordinates of ConA looked very similar. However, docking experiments of glucose and mannose in their monosaccharide-binding sites, by comparison with the ConA-mannose complex used as a model, revealed conformational changes in side chains of the amino acid residues involved in the binding of monosaccharides. These results fully agree with crystallographic data showing that binding of specific ligands to ConA requires conformational chances of its monosaccharide-binding site.

Spatial modelling of Lutzomyia (Nyssomyia) whitmani s.l. (Antunes & Coutinho, 1939) (Diptera: Psychodidae: Phlebotominae) habitat suitability in the state of Mato Grosso, Brazil

Lutzomyia (Nyssomyia) whitmani s.l.is the main vector of cutaneous leishmaniasis in state of Mato Grosso, but little is known about environmental determinants of its spatial distribution on a regional scale. Entomologic surveys of this sand fly species, conducted between 1996 and 2001 in 41 state municipalities, were used to investigate the relationships between environmental factors and the presence of the species, and to develop a spatial model of habitat suitability. The relationship between averaged CDC light trap indexes and 15 environmental and socio-economic factors were tested by logistic regression (LR) analysis. Spatial layers of deforestation tax and the Brazilian index of gross net production (IGNP) were identified as significant explanatory variables for vector presence in the LR model, and these were then overlaid with habitat maps. The highest habitat suitability in 2001 was obtained for the heavily deforested areas in the Central-North, South, East, and Southwest of Mato Grosso, particularly in municipalities with lower IGNP values.

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.

Modelling of soil penetration resistance for an oxisol under no-tillage

Soil penetration resistance is an important property that affects root growth and elongation and water movement in the soil. Since no-till systems tend to increase organic matter in the soil, the purpose of this study was to evaluate the efficiency with which soil penetration resistance is estimated using a proposed model based on moisture content, density and organic matter content in an Oxisol containing 665, 221 and 114 g kg-1 of clay, silt and sand respectively under annual no-till cropping, located in Londrina, Paraná State, Brazil. Penetration resistance was evaluated at random locations continually from May 2008 to February 2011, using an impact penetrometer to obtain a total of 960 replications. For the measurements, soil was sampled at depths of 0 to 20 cm to determine gravimetric moisture (G), bulk density (D) and organic matter content (M). The penetration resistance curve (PR) was adjusted using two non-linear models (PR = a Db Gc and PR' = a Db Gc Md), where a, b, c and d are coefficients of the adjusted model. It was found that the model that included M was the most efficient for estimating PR, explaining 91 % of PR variability, compared to 82 % of the other model.

Spatio-temporal modelling of the duration of the cotton cycle in the State Of Goiás, Brazil

The objective of this work was to develop and validate a mathematical model to estimate the duration of cotton (Gossypium hirsutum L. r. latifolium hutch) cycle in the State of Goiás, Brazil, by applying the method of growing degree-days (GD), and considering, simultaneously, its time-space variation. The model was developed as a linear combination of elevation, latitude, longitude, and Fourier series of time variation. The model parameters were adjusted by using multiple-linear regression to the observed GD accumulated with air temperature in the range of 15°C to 40°C. The minimum and maximum temperature records used to calculate the GD were obtained from 21 meteorological stations, considering data varying from 8 to 20 years of observation. The coefficient of determination, resulting from the comparison between the estimated and calculated GD along the year was 0.84. Model validation was done by comparing estimated and measured crop cycle in the period from cotton germination to the stage when 90 percent of bolls were opened in commercial crop fields. Comparative results showed that the model performed very well, as indicated by the Pearson correlation coefficient of 0.90 and Willmott agreement index of 0.94, resulting in a performance index of 0.85.

Kinematic analysis and modelling of biped locomotion systems

This paper presents the kinematic study of robotic biped locomotion systems. The main purpose is to determine the kinematic characteristics and the system performance during walking. For that objective, the prescribed motion of the biped is completely characterised in terms of five locomotion variables: step length, hip height, maximum hip ripple, maximum foot clearance and link lengths. In this work, we propose four methods to quantitatively measure the performance of the walking robot: energy analysis, perturbation analysis, lowpass frequency response and locomobility measure. These performance measures are discussed and compared in determining the robustness and effectiveness of the resulting locomotion.

Advances in modelling of mechatronic systems: the toolset FASIM_C++ for the simulation of vehicle dynamics

The increasing complexity of controller systems, applied in modern passenger cars, requires adequate simulation tools. The toolset FASIM_C++, described in the following, uses complex vehicle models in three-dimensional vehicle dynamics simulation. The structure of the implemented dynamic models and the generation of the equations of motion applying the method of kinematic differentials is explained briefly. After a short introduction in methods of event handling, several vehicle models and applications like controller development, roll-over simulation and real-time-simulation are explained. Finally some simulation results are presented.

Modelling of mechanical properties of CRFC composites under flexure loading

Carbon Fibre Reinforced Carbon (CFRC) Composites are increasing their applications due to their high strength and Young’s Modulus at high temperatures in inert atmosphere. Although much work has been done on processing and structure and properties relationship, few studies have addressed the modelling of mechanical properties. This work is divided in two parts. In the first part, a modelling of mechanical properties was carried out for two bi-directional composites using a model based on the Bernoulli-Euler theory for symmetric laminated beams. In the second part, acoustic emission (AE) was used as an auxiliary technique for monitoring the failure process of the composites. Differences in fracture behaviour are reflected in patterns of AE.

Seed bank modelling of volunteer oil seed rape: from seeds fate in the soil to seedling emergence

Studies were conducted to estimate parameters and relationships associated with sub-processes in soil seed banks of oilseed rape in Gorgan, Iran. After one month of burial, seed viability decreased to 39%, with a slope of 2.03% per day, and subsequently decreased with a lower slope of 0.01 until 365 days following burial in the soil. Germinability remained at its highest value in autumn and winter and decreased from spring to the last month of summer. Non-dormant seeds of volunteer oilseed rape did not germinate at temperatures lower than 3.8 ºC and a water potential of -1.4 MPa ºd. The hydrothermal values were 36.2 and 42.9 MPa ºd for sub- and supra-optimal temperatures, respectively. Quantification of seed emergence as influenced by burial depth was performed satisfactorily (R² = 0.98 and RMSE = 5.03). The parameters and relationships estimated here can be used for modelling soil seed bank dynamics or establishing a new model for the environment.

Mathematical modelling of the osmotic dehydration of cherry tomato (Lycopersicon esculentum var. cerasiforme)

Osmotic dehydration of cherry tomato as influenced by osmotic agent (sodium chloride and a mixed sodium chloride and sucrose solutions) and solution concentration (10 and 25% w/w) at room temperature (25°C) was studied. Kinetics of water loss and solids uptake were determined by a two parameter model, based on Fick's second law and applied to spherical geometry. The water apparent diffusivity coefficients obtained ranged from 2.17x10-10 to 11.69x10-10 m²/s.

Theoretical modelling of Staphylococcus aureus growth in a cooked meat product kept at ambient temperature using temperature profiles of selected Mexican cities

A theoretical model is used to predict the growth of Staphylococcus aureus in a pasteurized meat product kept at ambient temperatures for several hours. For this purpose, the temperature profiles of some cities of Mexico were combined with literature data on the kinetics of S. aureus growth. As shown by theoretical predictions, if the food is kept at ambient temperature, the average daily temperature may not give accurate predictions.

Accuracy of modelling and identification of malfunctions in rotor systems: experimental results

The accuracy of modelling of rotor systems composed of rotors, oil film bearings and a flexible foundation, is evaluated and discussed in this paper. The model validation of different models has been done by comparing experimental results with numerical results by means. The experimental data have been obtained with a fully instrumented four oil film bearing, two shafts test rig. The fault models are then used in the frame of a model based malfunction identification procedure, based on a least square fitting approach applied in the frequency domain. The capability of distinguishing different malfunctions has been investigated, even if they can create similar effects (such as unbalance, rotor bow, coupling misalignment and others) from shaft vibrations measured in correspondence of the bearings.

Similar understorey structure in spite of edaphic and floristic dissimilarity in Amazonian forests

Forest structure determines light availability for understorey plants. The structure of lowland Amazonian forests is known to vary over long edaphic gradients, but whether more subtle edaphic variation also affects forest structure has not beenresolved. In western Amazonia, the majority of non-flooded forests grow on soils derived either from relatively fertile sediments of the Pebas Formation or from poorer sediments of the Nauta Formation. The objective of this study was to compare structure and light availability in the understorey of forests growing on these two geological formations. We measured canopy openness and tree stem densities in three size classes in northeastern Peru in a total of 275 study points in old-growth terra firme forests representing the two geological formations. We also documented variation in floristic composition (ferns, lycophytes and the palm Iriartea deltoidea) and used Landsat TM satellite image information to model the forest structural and floristic features over a larger area. The floristic compositions of forests on the two formations were clearly different, and this could also be modelled with the satellite imagery. In contrast, the field observations of forest structure gave only a weak indication that forests on the Nauta Formation might be denser than those on the Pebas Formation. The modelling of forest structural features with satellite imagery did not support this result. Our results indicate that the structure of forest understorey varies much less than floristic composition does over the studied edaphic difference.

Intrusive versus domiciliated triatomines and the challenge of adapting vector control practices against Chagas disease

Chagas disease prevention remains mostly based on triatomine vector control to reduce or eliminate house infestation with these bugs. The level of adaptation of triatomines to human housing is a key part of vector competence and needs to be precisely evaluated to allow for the design of effective vector control strategies. In this review, we examine how the domiciliation/intrusion level of different triatomine species/populations has been defined and measured and discuss how these concepts may be improved for a better understanding of their ecology and evolution, as well as for the design of more effective control strategies against a large variety of triatomine species. We suggest that a major limitation of current criteria for classifying triatomines into sylvatic, intrusive, domiciliary and domestic species is that these are essentially qualitative and do not rely on quantitative variables measuring population sustainability and fitness in their different habitats. However, such assessments may be derived from further analysis and modelling of field data. Such approaches can shed new light on the domiciliation process of triatomines and may represent a key tool for decision-making and the design of vector control interventions.

An experimental/numerical study of the turbulent boundary layer development along a surface with a sudden change in roughness

A theory for the description of turbulent boundary layer flows over surfaces with a sudden change in roughness is considered. The theory resorts to the concept of displacement in origin to specify a wall function boundary condition for a kappa-epsilon model. An approximate algebraic expression for the displacement in origin is obtained from the experimental data by using the chart method of Perry and Joubert(J.F.M., vol. 17, pp. 193-122, 1963). This expression is subsequently included in the near wall logarithmic velocity profile, which is then adopted as a boundary condition for a kappa-epsilon modelling of the external flow. The results are compared with the lower atmospheric observations made by Bradley(Q. J. Roy. Meteo. Soc., vol. 94, pp. 361-379, 1968) as well as with velocity profiles extracted from a set of wind tunnel experiments carried out by Avelino et al.( 7th ENCIT, 1998). The measurements are found to be in good agreement with the theoretical computations. The skin-friction coefficient was calculated according to the chart method of Perry and Joubert(J.F.M., vol. 17, pp. 193-122, 1963) and to a balance of the integral momentum equation. In particular, the growth of the internal boundary layer thickness obtained from the numerical simulation is compared with predictions of the experimental data calculated by two methods, the "knee" point method and the "merge" point method.