Modeling of the TCR-MHC-peptide complex.

The methodology for generating a homology model of the T1 TCR-PbCS-K(d) class I major histocompatibility complex (MHC) class I complex is presented. The resulting model provides a qualitative explanation of the effect of over 50 different mutations in the region of the complementarity determining region (CDR) loops of the T cell receptor (TCR), the peptide and the MHC's alpha(1)/alpha(2) helices. The peptide is modified by an azido benzoic acid photoreactive group, which is part of the epitope recognized by the TCR. The construction of the model makes use of closely related homologs (the A6 TCR-Tax-HLA A2 complex, the 2C TCR, the 14.3.d TCR Vbeta chain, the 1934.4 TCR Valpha chain, and the H-2 K(b)-ovalbumine peptide), ab initio sampling of CDR loops conformations and experimental data to select from the set of possibilities. The model shows a complex arrangement of the CDR3alpha, CDR1beta, CDR2beta and CDR3beta loops that leads to the highly specific recognition of the photoreactive group. The protocol can be applied systematically to a series of related sequences, permitting the analysis at the structural level of the large TCR repertoire specific for a given peptide-MHC complex.

Effects of web-based electrocardiography simulation on strategies and learning styles

OBJECTIVETo identify the association between the use of web simulation electrocardiography and the learning approaches, strategies and styles of nursing degree students.METHODA descriptive and correlational design with a one-group pretest-posttest measurement was used. The study sample included 246 students in a Basic and Advanced Cardiac Life Support nursing class of nursing degree.RESULTSNo significant differences between genders were found in any dimension of learning styles and approaches to learning. After the introduction of web simulation electrocardiography, significant differences were found in some item scores of learning styles: theorist (p < 0.040), pragmatic (p < 0.010) and approaches to learning.CONCLUSIONThe use of a web electrocardiogram (ECG) simulation is associated with the development of active and reflexive learning styles, improving motivation and a deep approach in nursing students.

Biana: a software framework for compiling biological interactions and analyzing networks

Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.Results: We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.Conclusions: BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

SIMULIT : un modèle de simulation pour l'analyse et la planification de l'activité hospitalière

Le modèle développé à l'Institut universitaire de médecine sociale et préventive de Lausanne utilise un programme informatique pour simuler les mouvements d'entrées et de sorties des hôpitaux de soins généraux. Cette simulation se fonde sur les données récoltées de routine dans les hôpitaux; elle tient notamment compte de certaines variations journalières et saisonnières, du nombre d'entrées, ainsi que du "Case-Mix" de l'hôpital, c'est-à-dire de la répartition des cas selon les groupes cliniques et l'âge des patients.

Análise de riscos e dificuldades no desenvolvimento de software

O trabalho que ora apresentamos tem como tema “ O Ensino da Expressão e Educação Físico-Motora nas Escolas do Ensino Básico de São Lourenço dos Órgãos – Pós – Reforma.” O mesmo tem como horizonte temporal o ano lectivo 2006/07 e abarca as Escolas Básicas do novel Município de São Lourenço dos Órgãos. O ensino da Expressão e Educação Físico – Motora (E.E.F.M.) reveste-se de enorme importância e, nos últimos anos, tem-se emprestado muita atenção a esta área, quer seja a nível planetário, quer seja a nível nacional. Hoje, muitos estudiosos preocupam-se com o ensino desta área e, em consequência procuram fazer algo que permita a promoção da mesma e seja vista como as outras ditas académicas, isto porque todos estão cientes da sua importância e pertinência dentro do sistema escolar. Diante de tudo o que já foi dito e na possibilidade de poder dar um contributo a bem da educação no nosso pais, em geral, e no Município de São Lourenço dos Órgãos, em particular, pretendemos compreender, entretanto, porque é que muitos professores não leccionam ou raras vezes leccionam a área da Expressão e Educação Físico – Motora.

Intravenous streptomycin dosing regimen in a patient undergoing hemodialysis: Plasma level monitoring and pharmacokinetic simulation

Introduction: Streptomycin, as other aminoglycosides, exhibits concentration-dependent bacterial killing but has a narrow therapeutic window. It is primarily eliminated unchanged by the kidneys. Data and dosing information to achieve a safe regimen in patients with chronic renal failure undergoing hemodialysis (HD) are scarce. Although main adverse reactions are related to prolonged, elevated serum concentrations, literature recommendation is to administer streptomycin after each HD. Patients (or Materials) and Methods: We report the case of a patient with end-stage renal failure, undergoing HD, who was successfully treated with streptomycin for gentamicin-resistant Enterococcus faecalis bacteremia with prosthetic arteriovenous fistula infection. Streptomycin was administered intravenously 7.5 mg/kg, 3 hours before each dialysis (3 times a week) during 6 weeks in combination with amoxicillin. Streptomycin plasma levels were monitored with repeated blood sampling before, after, and between HD sessions. A 2-compartment model was used to reconstruct the concentration time profile over days on and off HD. Results: Streptomycin trough plasma-concentration was 2.8 mg/L. It peaked to 21.4 mg/L 30 minutes after intravenous administration, decreased to 18.2 mg/L immediately before HD, and dropped to 4.5 mg/L at the end of a 4-hour HD session. Plasma level increased again to 5.7 mg/L 2 hours after the end of HD and was 2.8 mg/L 48 hours later, before the next administration and HD. The pharmacokinetics of streptomycin was best described with a 2-compartment model. The computer simulation fitted fairly well to the observed concentrations during or between HD sessions. Redistribution between the 2 compartments after the end of HD reproduced the rebound of plasma concentrations after HD. No significant toxicity was observed during treatment. The outcome of the infection was favorable, and no sign of relapse was observed after a follow-up of 3 months. Conclusion: Streptomycin administration of 7.5 mg/kg 3 hours before HD sessions in a patient with end-stage renal failure resulted in an effective and safe dosing regimen. Monitoring plasma levels along with pharmacokinetic simulation document the suitability of this dosing scheme, which should replace current dosage recommendations for streptomycin in HD.

Simulation in Third Cycle English Language Teaching

Many researchers have suggested simulation as a powerful tool to transpose the normal classroom into an authentic setting where language skills can be performed under more realistic conditions. This paper will outline the benefits of simulation in the classroom, provide additional topics to Third Cycle English Language National Syllabus to be discussed / simulated in the classroom and also provide two simulation lesson plans with samples for Capeverdean Third Cycle English Language Students.

Integração de Sistemas de Bombas de Calor Geotérmicas em Edifícios

A simulação de edifícios e sistemas de aquecimento está na base deste trabalho. O edifício em estudo é a Residência Universitária Polo-II-1, com o objectivo de adaptar utilização de “Ground Source Heat Pumps” (GSHP) para satisfazer a necessidade de aquecimento do edifício. Para determinar a carga térmica, o edifício terá que ser modelado no software de simulação dinâmica multizona TRNSYS (TRaNsient SYstems Simulation). Da mesma forma que o edifício, o sistema também é modelado no TRNSYS a fim de obter o desempenho da GSHP a ser utilizado no edifício. Para melhor avaliar os benefícios do sistema, vai ser preciso uma análise comparativa da GSHP com outros sistemas normalmente utilizados para o aquecimento doméstico.

A pseudo-spectral method for the simulation of poro-elastic seismic wave propagation in 2D polar coordinates using domain decomposition

We present a novel numerical approach for the comprehensive, flexible, and accurate simulation of poro-elastic wave propagation in 2D polar coordinates. An important application of this method and its extensions will be the modeling of complex seismic wave phenomena in fluid-filled boreholes, which represents a major, and as of yet largely unresolved, computational problem in exploration geophysics. In view of this, we consider a numerical mesh, which can be arbitrarily heterogeneous, consisting of two or more concentric rings representing the fluid in the center and the surrounding porous medium. The spatial discretization is based on a Chebyshev expansion in the radial direction and a Fourier expansion in the azimuthal direction and a Runge-Kutta integration scheme for the time evolution. A domain decomposition method is used to match the fluid-solid boundary conditions based on the method of characteristics. This multi-domain approach allows for significant reductions of the number of grid points in the azimuthal direction for the inner grid domain and thus for corresponding increases of the time step and enhancements of computational efficiency. The viability and accuracy of the proposed method has been rigorously tested and verified through comparisons with analytical solutions as well as with the results obtained with a corresponding, previously published, and independently bench-marked solution for 2D Cartesian coordinates. Finally, the proposed numerical solution also satisfies the reciprocity theorem, which indicates that the inherent singularity associated with the origin of the polar coordinate system is adequately handled.

Viability and Management of an Endangered Capercaillie (Tetrao urogallus) Metapopulation in the Jura Mountains, Western Switzerland

The populations of Capercaillie (Tetrao urogallus), the largest European grouse, have seriously declined during the last century over most of their distribution in western and central Europe. In the Jura mountains, the relict population is now isolated and critically endangered (about 500 breeding adults). We developed a simulation software (TetrasPool) that accounts for age and spatial structure as well as stochastic processes, to perform a viability analysis and explore management scenarios for this population, capitalizing on a 24 years-long series of field data. Simulations predict a marked decline and a significant extinction risk over the next century, largely due to environmental and demographic stochasticity (average values of life-history parameters would otherwise allow stability). Variances among scenarios mainly stem from uncertainties about the shape and intensity of density dependence. Uncertainty analyses suggest to focus conservation efforts on enhancing, not only adult survival (as often advocated for long-lived species), but also recruitment. The juvenile stage matters when local populations undergo extinctions, because it ensures connectivity and recolonization. Besides limiting human perturbations, a silvicultural strategy aimed at opening forest structure should improve the quality and surface of available patches, independent of their size and localization. Such measures are to be taken urgently, if the population is to be saved.