Besnoitia besnoiti protein disulfide isomerase (BbPDI): molecular characterization, expression and in silico modelling

Besnoitia besnoiti is an apicomplexan parasite responsible for bovine besnoitiosis, a disease with a high prevalence in tropical and subtropical regions and re-emerging in Europe. Despite the great economical losses associated with besnoitiosis, this disease has been underestimated and poorly studied, and neither an effective therapy nor an efficacious vaccine is available. Protein disulfide isomerase (PDI) is an essential enzyme for the acquisition of the correct three-dimensional structure of proteins. Current evidence suggests that in Neosporacaninum and Toxoplasmagondii, which are closely related to B. besnoiti, PDI play an important role in host cell invasion, is a relevant target for the host immune response, and represents a promising drug target and/or vaccine candidate. In this work, we present the nucleotide sequence of the B. besnoiti PDI gene. BbPDI belongs to the thioredoxin-like superfamily (cluster 00388) and is included in the PDI_a family (cluster defined cd02961) and the PDI_a_PDI_a'_c subfamily (cd02995). A 3D theoretical model was built by comparative homology using Swiss-Model server, using as a template the crystallographic deduced model of Tapasin-ERp57 (PDB code 3F8U chain C). Analysis of the phylogenetic tree for PDI within the phylum apicomplexa reinforces the close relationship among B. besnoiti, N. caninum and T. gondii. When subjected to a PDI-assay based on the polymerisation of reduced insulin, recombinant BbPDI expressed in E. coli exhibited enzymatic activity, which was inhibited by bacitracin. Antiserum directed against recombinant BbPDI reacted with PDI in Western blots and by immunofluorescence with B. besnoiti tachyzoites and bradyzoites.

Simulation and theory of hybrid aligned liquid crystal films

We present a study of the effects of nanoconfinement on a system of hard Gaussian overlap particles interacting with planar substrates through the hard-needle-wall potential, extending earlier work by two of us [D. J. Cleaver and P. I. C. Teixeira, Chem. Phys. Lett. 338, 1 (2001)]. Here, we consider the case of hybrid films, where one of the substrates induces strongly homeotropic anchoring, while the other favors either weakly homeotropic or planar anchoring. These systems are investigated using both Monte Carlo simulation and density-functional theory, the latter implemented at the level of Onsager's second-virial approximation with Parsons-Lee rescaling. The orientational structure is found to change either continuously or discontinuously depending on substrate separation, in agreement with earlier predictions by others. The theory is seen to perform well in spite of its simplicity, predicting the positional and orientational structure seen in simulations even for small particle elongations.

Estudo comparativo de procedimentos experimentais e computacionais para cálculo da lipofilia molecular

Introdução – A lipofilia é uma das propriedades físico-químicas que mais influencia a capacidade de uma molécula se movimentar através de compartimentos biológicos. O coeficiente de partição octanol/água (log P) permite, assim, obter uma estimativa da absorção dos fármacos no organismo. A existência de métodos indirectos para um cálculo rápido do log P pode revelar-se de grande importância na análise de listas de compostos com potencial acção farmacológica, reduzindo-as àqueles que se prevêem ter um melhor comportamento biológico. Objectivos – O propósito deste estudo é dar a conhecer um método cromatográfico de RP-HPLC desenvolvido para a determinação indirecta da lipofilia molecular e avaliar a performance de vários programas de cálculo computacional desse mesmo parâmetro. Metodologias – Seleccionaram-se 25 compostos químicos, avaliou-se o log P de cada um deles por RP-HPLC e confrontaram-se os resultados obtidos com os de sete programas computacionais. Resultados – O método RP-HPLC testado demonstrou ser vantajoso em comparação com o convencional shake flask. O programa de cálculo indirecto que proporcionou resultados mais próximos dos experimentais foi o ALOGPS© 2.1. Conclusões – A escolha ideal para a determinação da lipofilia de compostos cujo log P estimado esteja entre 0 e 6 é, sobretudo no que diz respeito à rapidez e simplicidade do processo, o método experimental indirecto RP-HPLC. Quanto aos métodos computacionais concluiu-se que nenhum dos programas, incluindo o ALOGPS© 2.1, demonstrou ser eficaz na avaliação de isómeros pelo que, para estes compostos, será sempre necessário recorrer ao método shake flask ou RP-HPLC.

Modeling, control and simulation of full-power converter wind turbines equipped with permanent magnet synchronous generator

In this paper, two wind turbines equipped with a permanent magnet synchronous generator (PMSG) and respectively with a two-level or a multilevel converter are simulated in order to access the malfunction transient performance. Three different drive train mass models, respectively, one, two and three mass models, are considered in order to model the bending flexibility of the blades. Moreover, a fractional-order control strategy is studied comparatively to a classical integer-order control strategy. Computer simulations are carried out, and conclusions about the total harmonic distortion (THD) of the electric current injected into the electric grid are in favor of the fractional-order control strategy.

Power converter topologies for wind energy conversion systems: Integrated modeling, control strategy and performance simulation

This paper presents new integrated model for variable-speed wind energy conversion systems, considering a more accurate dynamic of the wind turbine, rotor, generator, power converter and filter. Pulse width modulation by space vector modulation associated with sliding mode is used for controlling the power converters. Also, power factor control is introduced at the output of the power converters. Comprehensive performance simulation studies are carried out with matrix, two-level and multilevel power converter topologies in order to adequately assert the system performance. Conclusions are duly drawn.

Polímeros conjugados baseados em calix[4]arenos: síntese e aplicações em electrónica molecular

Neste trabalho são descritas as sínteses de novos copolímeros do tipo p-fenileno-etinileno (PPE’s) contendo unidades de calix[4]areno com potencial aplicação em electrónica molecular. A preparação destes copolímeros envolveu a síntese e caracterização de duas unidades monoméricas distintas. O 1,4-bis-25-(oximetil) - 26,26,28-tripropoxi-2,5-di-iodo-benzeno-p-terc-butilcalix[4]areno e diferentes 1,4-di-etinil-2,5-bis(alcoxi)benzenos. Os materiais sintesidados foram analisados e caracterizados por espectroscopia de infravermelho por transformada de Fourier (FTIR), ressonância magnética nuclear de protão e de carbono (1H e 13C RMN), análise elementar (AE) e cromatografia de permeação em gel (GPC). Com o objectivo de estudar as suas propriedades espectroscópicas recorreu-se a técnicas de absorção de estado fundamental e luminescência de estado estacionário. O estudo das propriedades quirópticas do CALIX-p-PPE-C5q demonstrou que a homoquiralidade presente nas cadeias laterais de um dos componentes do copolímero é transferida para a cadeia principal do polímero conjugado, originando um polímero quiral. A realização de estudos electroquímicos por voltametria cíclica permitiu identificar nos diferentes polímeros processos oxidativos a potenciais semelhantes; o processo redutivo apenas foi observado no CALIX-p-PPE-C6. Os polímeros sintetizados foram posteriormente testados em duas aplicações de electrónica molecular. Num dos casos, a sua capacidade de funcionar com sensores químicos na detecção de explosivos nitroaromáticos foi avaliada usando técnicas de fotoluminescência enquanto a sua utilização como filmes emissivos em diodos emissores de luz foi avaliada por estudos de electroluminescência.

Fractional-order control and simulation of wind energy systems with PMSG/full-power converter topology

This paper presents a new integrated model for the simulation of wind energy systems. The proposed model is more realistic and accurate, considering a variable-speed wind turbine, two-mass rotor, permanent magnet synchronous generator (PMSG), different power converter topologies, and filters. Additionally, a new control strategy is proposed for the variable-speed operation of wind turbines with PMSG/full-power converter topology, based on fractional-order controllers. Comprehensive simulation studies are carried out with matrix and multilevel power converter topologies, in order to adequately assert the system performance in what regards the quality of the energy injected into the electric grid. Finally, conclusions are duly drawn.

Simulation of defects in bubble clusters

Topological defects in foam, either isolated (disclinations and dislocations) or in pairs, affect the energy and stress, and play an important role in foam deformation. Surface Evolver simulations were performed on large finite clusters of bubbles. These allow us to evaluate the effect of the topology of the defects, and the distance between defects, on the energy and pressure of foam clusters of different sizes. The energy of such defects follows trends similar to known analytical results for a continuous medium.

A simulation study on the abatement of CO2 emissions by de-absorption with monoethanolamine

Because of the adverse effect of CO2 from fossil fuel combustion on the earth's ecosystems, the most cost-effective method for CO2 capture is an important area of research. The predominant process for CO2 capture currently employed by industry is chemical absorption in amine solutions. A dynamic model for the de-absorption process was developed with monoethanolamine (MEA) solution. Henry's law was used for modelling the vapour phase equilibrium of the CO2, and fugacity ratios calculated by the Peng-Robinson equation of state (EOS) were used for H2O, MEA, N-2 and O-2. Chemical reactions between CO2 and MEA were included in the model along with the enhancement factor for chemical absorption. Liquid and vapour energy balances were developed to calculate the liquid and vapour temperature, respectively.

Transport properties in microcrystalline silicon solar cells under AM1.5 illumination analysed by two-dimensional numerical simulation

Microcrystalline silicon is a two-phase material. Its composition can be interpreted as a series of grains of crystalline silicon imbedded in an amorphous silicon tissue, with a high concentration of dangling bonds in the transition regions. In this paper, results for the transport properties of a mu c-Si:H p-i-n junction obtained by means of two-dimensional numerical simulation are reported. The role played by the boundary regions between the crystalline grains and the amorphous matrix is taken into account and these regions are treated similar to a heterojunction interface. The device is analysed under AM1.5 illumination and the paper outlines the influence of the local electric field at the grain boundary transition regions on the internal electric configuration of the device and on the transport mechanism within the mu c-Si:H intrinsic layer.

Simulation of default events in a CDX and estimation of the spread

The portfolio generating the iTraxx EUR index is modeled by coupled Markov chains. Each of the industries of the portfolio evolves according to its own Markov transition matrix. Using a variant of the method of moments, the model parameters are estimated from a data set of Standard and Poor's. Swap spreads are evaluated by Monte-Carlo simulations. Along with an actuarially fair spread, at least squares spread is considered.

Evaluation of the respiratory motion effect in small animal PET images with GATE Monte Carlo simulations

The rapid growth in genetics and molecular biology combined with the development of techniques for genetically engineering small animals has led to increased interest in in vivo small animal imaging. Small animal imaging has been applied frequently to the imaging of small animals (mice and rats), which are ubiquitous in modeling human diseases and testing treatments. The use of PET in small animals allows the use of subjects as their own control, reducing the interanimal variability. This allows performing longitudinal studies on the same animal and improves the accuracy of biological models. However, small animal PET still suffers from several limitations. The amounts of radiotracers needed, limited scanner sensitivity, image resolution and image quantification issues, all could clearly benefit from additional research. Because nuclear medicine imaging deals with radioactive decay, the emission of radiation energy through photons and particles alongside with the detection of these quanta and particles in different materials make Monte Carlo method an important simulation tool in both nuclear medicine research and clinical practice. In order to optimize the quantitative use of PET in clinical practice, data- and image-processing methods are also a field of intense interest and development. The evaluation of such methods often relies on the use of simulated data and images since these offer control of the ground truth. Monte Carlo simulations are widely used for PET simulation since they take into account all the random processes involved in PET imaging, from the emission of the positron to the detection of the photons by the detectors. Simulation techniques have become an importance and indispensable complement to a wide range of problems that could not be addressed by experimental or analytical approaches.

The condensation and ordering of models of empty liquids

We consider a simple model consisting of particles with four bonding sites ("patches"), two of type A and two of type B, on the square lattice, and investigate its global phase behavior by simulations and theory. We set the interaction between B patches to zero and calculate the phase diagram as the ratio between the AB and the AA interactions, epsilon(AB)*, varies. In line with previous work, on three-dimensional off-lattice models, we show that the liquid-vapor phase diagram exhibits a re-entrant or "pinched" shape for the same range of epsilon(AB)*, suggesting that the ratio of the energy scales - and the corresponding empty fluid regime - is independent of the dimensionality of the system and of the lattice structure. In addition, the model exhibits an order-disorder transition that is ferromagnetic in the re-entrant regime. The use of low-dimensional lattice models allows the simulation of sufficiently large systems to establish the nature of the liquid-vapor critical points and to describe the structure of the liquid phase in the empty fluid regime, where the size of the "voids" increases as the temperature decreases. We have found that the liquid-vapor critical point is in the 2D Ising universality class, with a scaling region that decreases rapidly as the temperature decreases. The results of simulations and theoretical analysis suggest that the line of order-disorder transitions intersects the condensation line at a multi-critical point at zero temperature and density, for patchy particle models with a re-entrant, empty fluid, regime. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3657406]

Difusão molecular em ressonância magnética para estudo de lesões mamárias malignas

Objetivos – Com este estudo pretendeu-se i) avaliar o contributo da aplicação da sequência de difusão na caracterização das lesões mamárias malignas; ii) considerar se a sequência de difusão deve incorporar o protocolo standard em RM mamária e iii) correlacionar os resultados dos valores de coeficiente aparente de difusão (ADC) e os resultados histológicos. Metodologia – A amostra incluiu 18 pacientes do sexo feminino, com idades compreendidas entre 38 e 71 anos, que apresentavam lesões mamárias malignas confirmadas histologicamente. Foi adicionado ao protocolo de RM mamária a sequência de difusão, de modo a calcular os valores de ADC das lesões observadas. Resultados – Verificou-se que a range de valores de ADC para lesões malignas em ROI’s calculados no centro da lesão apresentavam uma média e desvio-padrão de (0,89 ± 0,14x10-3mm2/s). O método da utilização dos valores de ADC na caracterização de lesões mamárias malignas demonstrou uma sensibilidade de 100%. Conclusões – Neste estudo, com uma sensibilidade de 100%, a ponderação em difusão demonstrou ser uma técnica vantajosa na caracterização de lesões mamárias malignas pelo que se sugere a sua introdução no protocolo standard da RM mamária. ABSTRACT - Aims – The aim of this study was i) to evaluate the potential of the DWI sequence in the characterization of malignant breast lesions; ii) to verify if this sequence should incorporate the breast MRI protocol and iii) to correlate the apparent diffusion coefficients (ADC) values and histological results. Methodology – The sample includes 18 female patients between the ages of 38 and 71 years, who presented with malignant breast lesion confirmed by histology. The DWI sequence was added to the MRI standard protocol to calculate the ADC values. Results – In the results obtained we observed that the range of the ADC values calculated in the center of the malignant lesions, showed a mean and standard deviation of 0.89 ± 0.14 x10-3 mm2 / s. This method of using the ADC values for the detection of malignant lesions showed a sensitivity of 100%. Conclusion – The DWI technique proved to be a useful method in the characterization of malignant breast lesions, as it showed a sensitivity of 100%, so we suggest its inclusion in the Breast MR standard protocol.

Patching up dipoles: can dipolar particles be viewed as patchy colloids?

We investigate whether the liquid-vapour phase transition of strongly dipolar fluids can be understood using a model of patchy colloids. These consist of hard spherical particles with three short-ranged attractive sites (patches) on their surfaces. Two of the patches are of type A and one is of type B. Patches A on a particle may bond either to a patch A or to a patch B on another particle. Formation of an AA (AB) bond lowers the energy by epsilon AA (epsilon AB). In the limit [image omitted], this patchy model exhibits condensation driven by AB-bonds (Y-junctions). Y-junctions are also present in low-density, strongly dipolar fluids, and have been conjectured to play a key role in determining their critical behaviour. We map the dipolar Yukawa hard-sphere (DYHS) fluid onto this 2A + 1B patchy model by requiring that the latter reproduce the correct DYHS critical point as a function of the isotropic interaction strength epsilon Y. This is achieved for sensible values of epsilon AB and the bond volumes. Results for the internal energy and the particle coordination number are in qualitative agreement with simulations of DYHSs. Finally, by taking the limit [image omitted], we arrive at a new estimate for the critical point of the dipolar hard-sphere fluid, which agrees with extrapolations from simulation.