Genetic variability and natural selection at the ligand domain of the Duffy binding protein in brazilian Plasmodium vivax populations

Background: Plasmodium vivax malaria is a major public health challenge in Latin America, Asia and Oceania, with 130-435 million clinical cases per year worldwide. Invasion of host blood cells by P. vivax mainly depends on a type I membrane protein called Duffy binding protein (PvDBP). The erythrocyte-binding motif of PvDBP is a 170 amino-acid stretch located in its cysteine-rich region II (PvDBP(II)), which is the most variable segment of the protein. Methods: To test whether diversifying natural selection has shaped the nucleotide diversity of PvDBP(II) in Brazilian populations, this region was sequenced in 122 isolates from six different geographic areas. A Bayesian method was applied to test for the action of natural selection under a population genetic model that incorporates recombination. The analysis was integrated with a structural model of PvDBP(II), and T-and B-cell epitopes were localized on the 3-D structure. Results: The results suggest that: (i) recombination plays an important role in determining the haplotype structure of PvDBP(II), and (ii) PvDBP(II) appears to contain neutrally evolving codons as well as codons evolving under natural selection. Diversifying selection preferentially acts on sites identified as epitopes, particularly on amino acid residues 417, 419, and 424, which show strong linkage disequilibrium. Conclusions: This study shows that some polymorphisms of PvDBP(II) are present near the erythrocyte-binding domain and might serve to elude antibodies that inhibit cell invasion. Therefore, these polymorphisms should be taken into account when designing vaccines aimed at eliciting antibodies to inhibit erythrocyte invasion.

Substrate/semiconductor interface effects on the emission efficiency of luminescent polymers

The importance of interface effects for organic devices has long been recognized, but getting detailed knowledge of the extent of such effects remains a major challenge because of the difficulty in distinguishing from bulk effects. This paper addresses the interface effects on the emission efficiency of poly(p-phenylene vinylene) (PPV), by producing layer-by-layer (LBL) films of PPV alternated with dodecylbenzenesulfonate. Films with thickness varying from similar to 15 to 225 nm had the structural defects controlled empirically by converting the films at two temperatures, 110 and 230 degrees C, while the optical properties were characterized by using optical absorption, photoluminescence (PL), and photoluminescence excitation spectra. Blueshifts in the absorption and PL spectra for LBL films with less than 25 bilayers (<40-50 nm) pointed to a larger number of PPV segments with low conjugation degree, regardless of the conversion temperature. For these thin films, the mean free-path for diffusion of photoexcited carriers decreased, and energy transfer may have been hampered owing to the low mobility of the excited carriers. The emission efficiency was then found to depend on the concentration of structural defects, i.e., on the conversion temperature. For thick films with more than 25 bilayers, on the other hand, the PL signal did not depend on the PPV conversion temperature. We also checked that the interface effects were not caused by waveguiding properties of the excited light. Overall, the electronic states at the interface were more localized, and this applied to film thickness of up to 40-50 nm. Because this is a typical film thickness in devices, the implication from the findings here is that interface phenomena should be a primary concern for the design of any organic device. (C) 2011 American Institute of Physics. [doi:10.1063/1.3622143]

Substrate orientation effect on potential fluctuations in multiquantum wells of GaAs/AlGaAs

The photoluminescence (PL) technique as a function of temperature and excitation intensity was used to study the optical properties of multiquantum wells (MQWs) of GaAs/Al(x)Ga(1-x)As grown by molecular beam epitaxy on GaAs substrates oriented in the [100], [311]A, and [311]B directions. The asymmetry presented by the PL spectra of the MQWs with an apparent exponential tail in the lower-energy side and the unusual behavior of the PL peak energy versus temperature (blueshift) at low temperatures are explained by the exciton localization in the confinement potential fluctuations of the heterostructures. The PL peak energy dependence with temperature was fitted by the expression proposed by Passler [Phys. Status Solidi B 200, 155 (1997)] by subtracting the term sigma(2)(E)/k(B)T, which considers the presence of potential fluctuations. It can be verified from the PL line shape, the full width at half maximum of PL spectra, the sigma(E) values obtained from the adjustment of experimental points, and the blueshift maximum values that the samples grown in the [311]A/B directions have higher potential fluctuation amplitude than the sample grown in the [100] direction. This indicates a higher degree of the superficial corrugations for the MQWs grown in the [311] direction. (C) 2008 American Institute of Physics.

Feature selection environment for genomic applications

Background: Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction). There are many genomic and proteomic applications that rely on feature selection to answer questions such as selecting signature genes which are informative about some biological state, e. g., normal tissues and several types of cancer; or inferring a prediction network among elements such as genes, proteins and external stimuli. In these applications, a recurrent problem is the lack of samples to perform an adequate estimate of the joint probabilities between element states. A myriad of feature selection algorithms and criterion functions have been proposed, although it is difficult to point the best solution for each application. Results: The intent of this work is to provide an open-source multiplataform graphical environment for bioinformatics problems, which supports many feature selection algorithms, criterion functions and graphic visualization tools such as scatterplots, parallel coordinates and graphs. A feature selection approach for growing genetic networks from seed genes ( targets or predictors) is also implemented in the system. Conclusion: The proposed feature selection environment allows data analysis using several algorithms, criterion functions and graphic visualization tools. Our experiments have shown the software effectiveness in two distinct types of biological problems. Besides, the environment can be used in different pattern recognition applications, although the main concern regards bioinformatics tasks.

Context tree selection: A unifying view

Context tree models have been introduced by Rissanen in [25] as a parsimonious generalization of Markov models. Since then, they have been widely used in applied probability and statistics. The present paper investigates non-asymptotic properties of two popular procedures of context tree estimation: Rissanen's algorithm Context and penalized maximum likelihood. First showing how they are related, we prove finite horizon bounds for the probability of over- and under-estimation. Concerning overestimation, no boundedness or loss-of-memory conditions are required: the proof relies on new deviation inequalities for empirical probabilities of independent interest. The under-estimation properties rely on classical hypotheses for processes of infinite memory. These results improve on and generalize the bounds obtained in Duarte et al. (2006) [12], Galves et al. (2008) [18], Galves and Leonardi (2008) [17], Leonardi (2010) [22], refining asymptotic results of Buhlmann and Wyner (1999) [4] and Csiszar and Talata (2006) [9]. (C) 2011 Elsevier B.V. All rights reserved.

Anthropometric characteristics and motor skills in talent selection and development in indoor soccer

Kick performance, anthropometric characteristics, slalom, and linear running were assessed in 49 (24 elite, 25 nonelite) postpubertal indoor soccer players in order to (a) verify whether anthropometric characteristics and physical and technical capacities can distinguish players of different competitive levels, (b) compare the kicking kinematics of these groups, with and without a defined target, and (c) compare results on the assessments and coaches` subjective rankings of the players. Thigh circumference and specific technical capacities differentiated the players by level of play; cluster analysis correctly classified 77.5% of the players. The correlation between players` standardized measures and the coaches` rankings was 0.29. Anthropometric characteristics and physical capacities do not necessarily differentiate players at post-pubertal stages and should not be overvalued during early development. Considering the coaches` rankings, performance measures outside the specific game conditions may not be useful in identification of talented players.

The effect of agitation speed, enzyme loading and substrate concentration on enzymatic hydrolysis of cellulose from brewer`s spent grain

Brewer`s spent grain components (cellulose, hemicellulose and lignin) were fractionated in a two-step chemical pretreatment process using dilute sulfuric acid and sodium hydroxide solutions. The cellulose pulp produced was hydrolyzed with a cellulolytic complex, Celluclast 1.5 L, at 45 degrees C to convert the cellulose into glucose. Several conditions were examined: agitation speed (100, 150 and 200 rpm), enzyme loading (5, 25 and 45 FPU/g substrate), and substrate concentration (2, 5 and 8% w/v), according to a 2(3) full factorial design aiming to maximize the glucose yield. The obtained results were interpreted by analysis of variance and response surface methodology. The optimal conditions for enzymatic hydrolysis of brewer`s spent grain were identified as 100 rpm, 45 FPU/g and 2% w/v substrate. Under these conditions, a glucose yield of 93.1% and a cellulose conversion (into glucose and cellobiose) of 99.4% was achieved. The easiness of glucose release from BSG makes this substrate a raw material with great potential to be used in bioconversion processes.

Raspberry (Rubus idaeus L.) wine: Yeast selection, sensory evaluation and instrumental analysis of volatile and other compounds

To evaluate the potential for fermentation of raspberry pulp, sixteen yeast strains (S. cerevisiae and S. bayanus) were studied. Volatile compounds were determined by GC-MS, GC-FID, and GC-PFPD. Ethanol. glycerol and organic acids were determined by HPLC. HPLC-DAD was used to analyse phenolic acids. Sensory analysis was performed by trained panellists. After a screening step, CAT-1, UFLA FW 15 and S. bayanus CBS 1505 were previously selected based on their fermentative characteristics and profile of the metabolites identified. The beverage produced with CAT-1 showed the highest volatile fatty acid concentration (1542.6 mu g/L), whereas the beverage produced with UFLA FIN 15 showed the highest concentration of acetates (2211.1 mu g/L) and total volatile compounds (5835 mu g/L). For volatile sulphur compounds. 566.5 mu g/L were found in the beverage produced with S. bayanus CBS 1505. The lowest concentration of volatile sulphur compounds (151.9 mu g/L) was found for the beverage produced with UFLA FW 15. In the sensory analysis, the beverage produced with UFLA FW 15 was characterised by the descriptors raspberry, cherry, sweet, strawberry, floral and violet. In conclusion, strain UFLA FW 15 was the yeast that produced a raspberry wine with a good chemical and sensory quality. (C) 2010 Elsevier Ltd. All rights reserved.

Selection of new glass-forming compositions in Al-La system using a combination of topological instability and thermodynamic criteria

A combination of an extension of the topological instability ""lambda criterion"" and a thermodynamic criterion were applied to the Al-La system, indicating the best range of compositions for glass formation. Alloy compositions in this range were prepared by melt-spinning and casting in an arc-melting furnace with a wedge-section copper mold. The GFA of these samples was evaluated by X-ray diffraction, differential scanning calorimetry and scanning electron microscopy. The results indicated that the gamma* parameter of compositions with high GFA is higher, corresponding to a range in which the lambda parameter is greater than 0.1, which are compositions far from Al solid solution. A new alloy was identified with the best GFA reported so far for this system, showing a maximum thickness of 286 mu m in a wedge-section copper mold. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Performance of a horizontal-flow anaerobic immobilized biomass (HAIB) reactor and dynamics of the microbial community during degradation of pentachlorophenol (PCP)

The anaerobic biological treatment of pentachlorophenol (PCP) and methanol as the main carbon source was investigated in a horizontal-flow anaerobic immobilized biomass (HAIB) reactor at 30 +/- 1 degrees C, during a 220-day trial period. The reactor biomass was developed as an attached biofilm on polyurethane foam particles, with 24 h of hydraulic retention time. The PCP concentrations, which ranged from 2.0 to 13.0 mg/L, were controlled by adding synthetic substrate. The HAIB reactor reduced 97% of COD and removed 99% of PCP. The microbial biofilm communities of the HAIB reactor amended with PCP, without previous acclimatization, were characterized by polymerase chain reaction (PCR) and amplified ribosomal DNA restriction analysis (ARDRA) with specific Archaea oligonucleotide primers. The ARDRA technique provided an adequate analysis of the community, revealing the profile of the selected population along the reactor. The biomass activities in the HAIB reactor at the end of the experiments indicated the development of PCP degraders and the maintenance of the population of methanogenic Archaea, ensuring the high efficiency of the system treating PCP with added methanol as the cosubstrate. The use of the simplified ARDRA method enabled us to monitor the microbial population with the addition of high concentrations of toxic compounds and highlighting a selection of microorganisms in the biofilm. (C) 2008 Published by Elsevier Ltd.

Long-term stability of hydrogen and organic acids production in an anaerobic fluidized-bed reactor using heat treated anaerobic sludge inoculum

This study evaluates the stability of hydrogen and organic acids production in an anaerobic fluidized-bed reactor (AFBR) that contains expanded clay (2.8-3.35 mm in diameter) as a support medium and is operated on a long-term basis. The reactor was inoculated with thermally pre-treated anaerobic sludge and operated with decreasing hydraulic retention time (HRT), from 8 h to 1 h, at a controlled temperature of 30 degrees C and a pH of about 3.8. Glucose (2000 mg L(-1)) was used as the substrate, generating conversion rates of 92-98%. Decreasing the HRT from 8 h to 1 h led to an increase in average hydrogen-production rates, with a maximum value of 1.28 L h(-1) L(-1) for an HRT of 1 h. In general, hydrogen yield production increased as HRT decreased, reaching 2.29 mol of H(2)/mol glucose at an HRT of 2 h and yielding a maximum hydrogen content of 37% in the biogas. No methane was detected in the biogas throughout the period of operation. The main soluble metabolites (SMP) were acetic acid (46.94-53.84% of SMP) and butyric acid (34.51-42.16% of SMP), with less than 15.49% ethanol. The steady performance of the AFBR may be attributed to adequate thermal treatment of the inoculum, the selection of a suitable support medium for microbial adhesion, and the choice of satisfactory environmental conditions imposed on the system. The results show that stable hydrogen production and organic acids production were maintained in the AFBR over a period of 178 days. (C) 2009 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.

Accelerating autonomous learning by using heuristic selection of actions

This paper investigates how to make improved action selection for online policy learning in robotic scenarios using reinforcement learning (RL) algorithms. Since finding control policies using any RL algorithm can be very time consuming, we propose to combine RL algorithms with heuristic functions for selecting promising actions during the learning process. With this aim, we investigate the use of heuristics for increasing the rate of convergence of RL algorithms and contribute with a new learning algorithm, Heuristically Accelerated Q-learning (HAQL), which incorporates heuristics for action selection to the Q-Learning algorithm. Experimental results on robot navigation show that the use of even very simple heuristic functions results in significant performance enhancement of the learning rate.

Residual stresses in titanium nitride thin films obtained with step variation of substrate bias voltage during deposition

In this work, a series of depositions of titanium nitride (TiN) films on M2 and D2 steel substrates were conducted in a Triode Magnetron Sputtering chamber. The temperature; gas flow and pressure were kept constant during each run. The substrate bias was either decreased or increased in a sequence of steps. Residual stress measurements were later conducted through the grazing X-ray diffraction method. Different incident angles were used in order to change the penetration depth and to obtain values of residual stress at different film depths. A model described by Dolle was adapted as an attempt to calculate the values of residual stress at each incident angle as a function of the value from each individual layer. Stress results indicated that the decrease in bias voltage during the deposition has produced compressive residual stress gradients through the film thickness. On the other hand, much less pronounced gradients were found in one of the films deposited with increasing bias voltage. (C) 2010 Elsevier B.V. All rights reserved.

Spontaneous vegetation on overburden piles in the Coal Basin of Santa Catarina, Brazil

The objective of this work was to select indigenous vegetal species for restoration programs aiming at the regeneration of ombrophilous dense forest. Thirty-five spoil piles located in the county of Sideropolis, Santa Catarina, that received overburden disposal for 39 years (1950-1989) were selected for study because they exhibited remarkable spontaneous regrowth of trees compared to surrounding spoil piles. Floristic inventory covered the whole area of the 35 piles, whereas survey on phytosociology and natural regeneration studies were conducted in 70 plots distributed along the 35 piles. Floristic inventory recorded 83 species from 28 botanical families. Herbaceous terricolous plants constituted the predominant species (47.0%), followed by shrubs (26.5%), trees (19.3%), and vines (7.2%). Results from surveys on phytosociology and natural regeneration, focused on shrubs and trees, recorded incipient ecological succession. In addition, the most adapted species recorded on the overburden piles, as ranked by index of natural regeneration (RNT) plus importance value index (IVI), were as follows: Clethra scabra (RNT = 23.93%; IVI = 17.28%), Myrsine coriacea (RNT = 20.93%, IVI = 11.26%), Eupatorium intermedium (RNT 7.56%, IVI 0.40%), Miconia ligustroides (RNT 5.84%, IVI 2.37%), Ossaea amygdaloides (RNT 3.84%, IVI 1.30%), Tibouchina sellowiana (RNT 3.29%, M 1.94%), Eup. inulaefolium (RNT = 2.65%, IVI = 0.80%), and Baccharis dracunculifolia (RNT = 2.28%; IVI = 0.56%). High values of IVI and RNT exhibited by the exotic species Eucalyptus saligna (IVI = 21.73%, RNT = 51.41%) indicated strong competition between exotic and indigenous species. Severe chemical (acidic pH and lack of nutrients) and physical (coarse substrate and slope angle of 40-50 degrees) characteristics displayed by the overburden piles constituted limitations to floristic diversity and size of indigenous trees, indicating the need for substrate reclamation prior to forest restoration.

Risk-based decision making method for maintenance policy selection of thermal power plant equipment

This study presents a decision-making method for maintenance policy selection of power plants equipment. The method is based on risk analysis concepts. The method first step consists in identifying critical equipment both for power plant operational performance and availability based on risk concepts. The second step involves the proposal of a potential maintenance policy that could be applied to critical equipment in order to increase its availability. The costs associated with each potential maintenance policy must be estimated, including the maintenance costs and the cost of failure that measures the critical equipment failure consequences for the power plant operation. Once the failure probabilities and the costs of failures are estimated, a decision-making procedure is applied to select the best maintenance policy. The decision criterion is to minimize the equipment cost of failure, considering the costs and likelihood of occurrence of failure scenarios. The method is applied to the analysis of a lubrication oil system used in gas turbines journal bearings. The turbine has more than 150 MW nominal output, installed in an open cycle thermoelectric power plant. A design modification with the installation of a redundant oil pump is proposed for lubricating oil system availability improvement. (C) 2009 Elsevier Ltd. All rights reserved.