Modeling AIDS vaccines: the cellular level

This paper discuses current strategies for the development of AIDS vaccines wich allow immunzation to disturb the natural course of HIV at different detailed stages of its life cycle. Mathematical models describing the main biological phenomena (i.e. virus and vaccine induced T4 cell growth; virus and vaccine induced activation latently infected T4 cells; incremental changes immune response as infection progress; antibody dependent enhancement and neutralization of infection) and allowing for different vaccination strategies serve as a backgroud for computer simulations. The mathematical models reproduce updated information on the behavior of immune cells, antibody concentrations and free viruses. The results point to some controversial outcomes of an AIDS vaccine such as an early increase in virus concentration among vaccinated when compared to nonvaccinated individuals.

Balloon-based adjuvant radiotherapy in breast cancer: comparison between 99mTc and HDR 192Ir

Abstract Objective: To perform a comparative dosimetric analysis, based on computer simulations, of temporary balloon implants with 99mTc and balloon brachytherapy with high-dose-rate (HDR) 192Ir, as boosts to radiotherapy. We hypothesized that the two techniques would produce equivalent doses under pre-established conditions of activity and exposure time. Materials and Methods: Simulations of implants with 99mTc-filled and HDR 192Ir-filled balloons were performed with the Siscodes/MCNP5, modeling in voxels a magnetic resonance imaging set related to a young female. Spatial dose rate distributions were determined. In the dosimetric analysis of the protocols, the exposure time and the level of activity required were specified. Results: The 99mTc balloon presented a weighted dose rate in the tumor bed of 0.428 cGy.h-1.mCi-1 and 0.190 cGyh-1.mCi-1 at the balloon surface and at 8-10 mm from the surface, respectively, compared with 0.499 and 0.150 cGyh-1.mCi-1, respectively, for the HDR 192Ir balloon. An exposure time of 24 hours was required for the 99mTc balloon to produce a boost of 10.14 Gy with 1.0 Ci, whereas only 24 minutes with 10.0 Ci segments were required for the HDR 192Ir balloon to produce a boost of 5.14 Gy at the same reference point, or 10.28 Gy in two 24-minutes fractions. Conclusion: Temporary 99mTc balloon implantation is an attractive option for adjuvant radiotherapy in breast cancer, because of its availability, economic viability, and similar dosimetry in comparison with the use of HDR 192Ir balloon implantation, which is the current standard in clinical practice.

Simulações computacionais e ferramentas de modelização em educação química: uma revisão de literatura publicada

This article presents a review of published literature concerning the use of computer simulations and modeling tools in Chemical Education. The findings about the possibilities of their application in the Chemistry curriculum, their effective implementation, the teaching methods involved, the research methodology and also the instruments of evaluation that were used and their results were described and analyzed. The need to develop adequate theory support to educators who want to start using this new technology in their Chemistry classes became evident along the research, as well as the lack of development of model perception among Chemistry educators and learners.

Uma perspectiva computacional sobre catálise enzimática

Enzymes are extremely efficient catalysts. Here, part of the mechanisms proposed to explain this catalytic power will be compared to quantitative experimental results and computer simulations. Influence of the enzymatic environment over species along the reaction coordinate will be analysed. Concepts of transition state stabilisation and reactant destabilisation will be confronted. Divided site model and near-attack conformation hypotheses will also be discussed. Molecular interactions such as covalent catalysis, general acid-base catalysis, electrostatics, entropic effects, steric hindrance, quantum and dynamical effects will also be analysed as sources of catalysis. Reaction mechanisms, in particular that catalysed by protein tyrosine phosphatases, illustrate the concepts.

Do We Understand Hydrodynamic Dispersion in Sedimenting Suspensions?

Microstructural changes, that is an important feature for the understanding of the velocity variance in sedimentation is investigated with numerical simulations. The simulations are used to describe velocity fluctuations and hydrodynamic dispersion in a suspension of interacting point-particles sedimenting in a rectangular box with periodic sides and impenetrable bottom and top. It is observed how the positions of the particles evolve in a finite container. The suspension that was initially random in the gravity direction only, tends to be fully randomized as a result of the relative arrangements of the particles and the hydrodynamic interactions between them. The computer simulations, based on statistics over a significant number of particle configurations, suggest velocity variances and diffusivities dependent on the size of the simulated system but with anisotropy in velocity fluctuations and diffusion coefficients nearly independent of the box size.

A programme for computer aided identification of Phlebotomine sandflies of the Americas (CIPA): presentation and check-list of American species

The CIPA programme is a collaborative project including two entomologists from France and seven South and Central America countries. Its objective is the development of an expert system for computer aided identification of phlebotomine sandflies from the Americas. It also includes the formation of data bases for bibliographic, taxonomic and biogeographic data. Participant consensus on taxonomic prerequisites, standardization in bibliographic data collections and selection of descriptive variables for the final programme has been established through continous communication among participants and annual meetings. The adopted check-list of American sandflies presented here includes 386 specific taxa, ordered into genera and 28 sub-genera or species groups.

Computer-assisted cartography using topographic properties: precision and accuracy of local soil maps in central Mexico

Map units directly related to properties of soil-landscape are generated by local soil classes. Therefore to take into consideration the knowledge of farmers is essential to automate the procedure. The aim of this study was to map local soil classes by computer-assisted cartography (CAC), using several combinations of topographic properties produced by GIS (digital elevation model, aspect, slope, and profile curvature). A decision tree was used to find the number of topographic properties required for digital cartography of the local soil classes. The maps produced were evaluated based on the attributes of map quality defined as precision and accuracy of the CAC-based maps. The evaluation was carried out in Central Mexico using three maps of local soil classes with contrasting landscape and climatic conditions (desert, temperate, and tropical). In the three areas the precision (56 %) of the CAC maps based on elevation as topographical feature was higher than when based on slope, aspect and profile curvature. The accuracy of the maps (boundary locations) was however low (33 %), in other words, further research is required to improve this indicator.

Evaluation of a computer model to simulate water table response to subirrigation

The objective of this work was to evaluate the water flow computer model, WATABLE, using experimental field observations on water table management plots from a site located near Hastings, FL, USA. The experimental field had scale drainage systems with provisions for subirrigation with buried microirrigation and conventional seepage irrigation systems. Potato (Solanum tuberosum L.) growing seasons from years 1996 and 1997 were used to simulate the hydrology of the area. Water table levels, precipitation, irrigation and runoff volumes were continuously monitored. The model simulated the water movement from a buried microirrigation line source and the response of the water table to irrigation, precipitation, evapotranspiration, and deep percolation. The model was calibrated and verified by comparing simulated results with experimental field observations. The model performed very well in simulating seasonal runoff, irrigation volumes, and water table levels during crop growth. The two-dimensional model can be used to investigate different irrigation strategies involving water table management control. Applications of the model include optimization of the water table depth for each growth stage, and duration, frequency, and rate of irrigation.

Accuracy of computer-aided ultrasound as compared with magnetic resonance imaging in the evaluation of nonalcoholic fatty liver disease in obese and eutrophic adolescents

AbstractObjective:To compare the accuracy of computer-aided ultrasound (US) and magnetic resonance imaging (MRI) by means of hepatorenal gradient analysis in the evaluation of nonalcoholic fatty liver disease (NAFLD) in adolescents.Materials and Methods:This prospective, cross-sectional study evaluated 50 adolescents (aged 11–17 years), including 24 obese and 26 eutrophic individuals. All adolescents underwent computer-aided US, MRI, laboratory tests, and anthropometric evaluation. Sensitivity, specificity, positive and negative predictive values and accuracy were evaluated for both imaging methods, with subsequent generation of the receiver operating characteristic (ROC) curve and calculation of the area under the ROC curve to determine the most appropriate cutoff point for the hepatorenal gradient in order to predict the degree of steatosis, utilizing MRI results as the gold-standard.Results:The obese group included 29.2% girls and 70.8% boys, and the eutrophic group, 69.2% girls and 30.8% boys. The prevalence of NAFLD corresponded to 19.2% for the eutrophic group and 83% for the obese group. The ROC curve generated for the hepatorenal gradient with a cutoff point of 13 presented 100% sensitivity and 100% specificity. As the same cutoff point was considered for the eutrophic group, false-positive results were observed in 9.5% of cases (90.5% specificity) and false-negative results in 0% (100% sensitivity).Conclusion:Computer-aided US with hepatorenal gradient calculation is a simple and noninvasive technique for semiquantitative evaluation of hepatic echogenicity and could be useful in the follow-up of adolescents with NAFLD, population screening for this disease as well as for clinical studies.