TESTING STATISTICAL HYPOTHESIS ON RANDOM TREES AND APPLICATIONS TO THE PROTEIN CLASSIFICATION PROBLEM

Efficient automatic protein classification is of central importance in genomic annotation. As an independent way to check the reliability of the classification, we propose a statistical approach to test if two sets of protein domain sequences coming from two families of the Pfam database are significantly different. We model protein sequences as realizations of Variable Length Markov Chains (VLMC) and we use the context trees as a signature of each protein family. Our approach is based on a Kolmogorov-Smirnov-type goodness-of-fit test proposed by Balding et at. [Limit theorems for sequences of random trees (2008), DOI: 10.1007/s11749-008-0092-z]. The test statistic is a supremum over the space of trees of a function of the two samples; its computation grows, in principle, exponentially fast with the maximal number of nodes of the potential trees. We show how to transform this problem into a max-flow over a related graph which can be solved using a Ford-Fulkerson algorithm in polynomial time on that number. We apply the test to 10 randomly chosen protein domain families from the seed of Pfam-A database (high quality, manually curated families). The test shows that the distributions of context trees coming from different families are significantly different. We emphasize that this is a novel mathematical approach to validate the automatic clustering of sequences in any context. We also study the performance of the test via simulations on Galton-Watson related processes.

Investigation of the mass transfer processes during the desalination of water containing phenol and sodium chloride by electrodialysis

Oxidation processes are used in wastewater treatment when conventional processes are not effective due to the presence of recalcitrant organic contaminants, like phenol. However, the presence of ionic compounds associated with organic pollutants may retard the oxidation. In this work the transport of species contained in an aqueous solution of phenol containing sodium chloride was evaluated in an electrodialysis (ED) system. An experimental study was carried out in which the influence of the process variables on the phenol loss and sodium chloride removal was investigated. Experiments were also performed without current, in order to determine the phenol transfer due to diffusion. The phenol and salt concentration variations in the ED compartments were measured over time, using dedicated procedures and an experimental design to determine the global characteristic parameters. A phenomenological approach was used to relate the phenol, salt and water fluxes with the driving forces (concentration and electric potential gradients). Under ED conditions, two contributions were pointed out for the phenol transport, i.e. diffusion and convection, this latter coming from the water flux due to electroosmosis related to the migration of salts. The fitting of the parameters of the transport equations resulted in good agreement with the experimental results over the range of conditions investigated. (c) 2008 Elsevier B.V. All rights reserved.

Phylogeography of Chelonus insularis (Hymenoptera: Braconidae) and Campoletis sonorensis (Hymenoptera: Ichneumonidae), Two Primary Neotropical Parasitoids of the Fall Armyworm (Lepidoptera: Noctuidae)

In a previous study, we observed no spatial genetic structure in Mexican populations of the parasitoids Chelonus insularis Cresson (Hymenoptera: Braconidae) and Campoletis sonorensis Cameron (Hymenoptera: Ichneumonidae) by using microsatellite markers In the current study, we Investigated whether for these important parasitoids of the fall armyworm (Lepidoptera: Noctuidae) there is any genetic structure at a larger scale Insects of both species were collected across the American continent and their phylogeography was Investigated using both nuclear and mitochondria] markers Our results suggest an ancient north-south migration of C insularis, whereas no clear pattern] could be determined for C sonorensis. Nonetheless, the resulting topology indicated the existence of a cryptic taxon within this later species. a few Canadian specimens determined as C. sonorensis branch outside a clack composed of the Argentinean Chelonus grioti Blanchard, the Brazilian Chelonus flavicincta Ashmead, and the rest of the C sonorensis individuals The individuals revealing the cryptic taxon were collected from Thichoplusia in (Hubner) (Lepidoptera. Noctuidae) on tomato (Lycopersicon spp) and may represent a biotype that has adapted to the early season phenology of its host. Overall, the loosely defined spatial genetic structure previously shown at a local fine scale also was found at the larger scale, for both species Dispersal of these insects may be partly driven by wind as suggested by genetic similarities between Individuals coming from very distant locations.

Nestmate recognition in the stingless bee Frieseomelitta varia (Hymenoptera, Apidae, Meliponini): sources of chemical signals

Social insects use cuticular lipids for nestmate recognition. These lipids are chiefly hydrocarbons that can be endogenously produced or acquired from the environment. Although these compounds are already described as coming from different sources for different groups of social insects, nothing is known about the source of cuticular hydrocarbons in stingless bees. We used behavioural recognition tests and cuticle chemical investigation to elucidate the role of endogenous and environmentally based cues for nestmate recognition in the stingless bee Frieseomelitta varia. We found that although newly emerged workers present specific cuticle patterns according to their nest origin, these compounds are not used for nestmate recognition, since newly emerged workers are broadly accepted in different colonies. The cerumen used in nest construction played an important role in recognition behaviour. Twenty minutes of contact with foreign cerumen was sufficient to increase the rejection rates of nestmates and separate the groups of workers according to their chemical profile. On the other hand, tests of feeding on a common diet showed no effect on chemical cuticle pattern or recognition behaviour. (C) 2010 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.

Unraveling the Na,K-ATPase alpha(4) Subunit Assembling Induced by Large Amounts of C(12)E(8) by Means of Small-Angle X-ray Scattering

In the current work, we studied the effect of the nonionic detergent dodecyloctaethyleneglycol, C(12)E(8), on the structure and oligomeric form of the Na,K-ATPase membrane enzyme (sodium-potassium pump) in aqueous suspension, by means of small-angle X-ray scattering (SAXS). Samples composed of 2 mg/mL of Na,K-ATPase, extracted from rabbit kidney medulla, in the presence of a small amount of C(12)E(8) (0.005 mg/mL) and in larger concentrations ranging from 2.7 to 27 mg/mL did not present catalytic activity. Under this condition, an oligomerization of the alpha subunits is expected. SAXS data were analyzed by means of a global fitting procedure supposing that the scattering is due to two independent contributions: one coming from the enzyme and the other one from C(12)E(8) micelles. In the small detergent content (0.005 mg/mL), the SAXS results evidenced that Na,K-ATPase is associated into aggregates larger than (alpha beta)(2) form. When 2.7 mg/mL of C(12)E(8) is added, the data analysis revealed the presence of alpha(4) aggregates in the solution and some free micelles. Increasing the detergent amount up to 27 mg/mL does not disturb the alpha(4) aggregate: just more micelles of the same size and shape are proportionally formed in solution. We believe that our results shed light on a better understanding of how nonionic detergents induce subunit dissociation and reassembling to minimize the exposure of hydrophobic residues to the aqueous solvent.

EEG-based Brain-Computer Interfaces: An Overview of Basic Concepts and Clinical Applications in Neurorehabilitation

Some patients are no longer able to communicate effectively or even interact with the outside world in ways that most of us take for granted. In the most severe cases, tetraplegic or post-stroke patients are literally `locked in` their bodies, unable to exert any motor control after, for example, a spinal cord injury or a brainstem stroke, requiring alternative methods of communication and control. But we suggest that, in the near future, their brains may offer them a way out. Non-invasive electroencephalogram (EEG)-based brain-computer interfaces (BCD can be characterized by the technique used to measure brain activity and by the way that different brain signals are translated into commands that control an effector (e.g., controlling a computer cursor for word processing and accessing the internet). This review focuses on the basic concepts of EEG-based BC!, the main advances in communication, motor control restoration and the down-regulation of cortical activity, and the mirror neuron system (MNS) in the context of BCI. The latter appears to be relevant for clinical applications in the coming years, particularly for severely limited patients. Hypothetically, MNS could provide a robust way to map neural activity to behavior, representing the high-level information about goals and intentions of these patients. Non-invasive EEG-based BCIs allow brain-derived communication in patients with amyotrophic lateral sclerosis and motor control restoration in patients after spinal cord injury and stroke. Epilepsy and attention deficit and hyperactive disorder patients were able to down-regulate their cortical activity. Given the rapid progression of EEG-based BCI research over the last few years and the swift ascent of computer processing speeds and signal analysis techniques, we suggest that emerging ideas (e.g., MNS in the context of BC!) related to clinical neuro-rehabilitation of severely limited patients will generate viable clinical applications in the near future.

Development of a digital hearing aid to meet the Brazilian Government`s Ordinance 587 (APAC) - Health Department

The treatment of sensorineural hearing loss is based on hearing aids, also known as individual sound amplification devices. The hearing aids purchased by the Brazilian Government, aiming at fulfilling public policies, are based on dedicated components, which bring about benefits, but also render them expensive and may impair repair services after manufacture`s warranty expires. Aim: to design digital behind-the-ear hearing aids built from standardized components coming from the very supply chain of these manufacturers. Study design: experimental. Materials and Methods: to identify the supply chain of these manufacturers, request samples and set up hearing aids in the laboratory. Results: The developed hearing aids did not show lesser electroacoustic characteristics when compared to those acquired by the Government, also being tested by the same reference international technical standard. Conclusion: It is possible to develop digital behind-the-ear hearing aids based on off-the-shelf components from hearing aid manufacturers` supply chain. Their advantages include low operational costs - for acquisition (with clear advantages for the Government) and service (advantage for the patient).

Involvement of the central nervous system in the chronic form of Chagas` disease

Background and purpose: Apart from the central nervous system parasitic invasion in chagasic immunodeficient patients and strokes due to heart lesions provoked by the disease, the typical neurological syndromes of the chronic phase of Chagas` disease (CD) have not yet been characterized, although involvement of the peripheral nervous system has been well documented. This study aims at investigating whether specific signs of central nervous system impairment might be associated with the disease. Methods: Twenty-seven patients suffering from the chronic form of Chagas` disease (CCD) and an equal number of controls matched for sex, age, educational and socio-cultural background, and coming from the same geographical regions, were studied using neurological examinations, magnetic resonance images, and electroencephalographic frequency analysis. Results: Nineteen patients were at the stage A of the cardiac form of the disease (without documented structural lesions or heart failure). Dizziness, brisk reflexes, and ankle and knee areflexia were significantly more prevalent in the patients than in the controls. The significant findings in quantitative electroencephalogram were an increase in the theta relative power and a decrease in the theta dominant frequency at temporal-occipital derivations. Subcortical, white matter demyelination was associated with diffuse theta bursts and theta-delta slowing in two patients. Conclusions: Our findings suggest a discrete and unspecific functional cortical disorder and possible white matter lesions in CD. The focal nervous system abnormalities in CD documented here did not seem to cause significant functional damage or severely alter the patient`s quality of life. (C) 2008 Elsevier B.V. All rights reserved.

Generation of Polyclonal Antibodies Against Recombinant Human Glucocerebrosidase Produced in Escherichia coli

Deficiency of the lysosomal glucocerebrosidase (GCR) enzyme results in Gaucher`s disease, the most common inherited storage disorder. Treatment consists of enzyme replacement therapy by the administration of recombinant GCR produced in Chinese hamster ovary cells. The production of anti-GCR antibodies has already been described with placenta-derived human GCR that requires successive chromatographic procedures. Here, we report a practical and efficient method to obtain anti-GCR polyclonal antibodies against recombinant GCR produced in Escherichia coli and further purified by a single step through nickel affinity chromatography. The purified GCR was used to immunize BALB/c mice and the induction of anti-GCR antibodies was evaluated by enzyme-linked immunosorbent assay. The specificity of the antiserum was also evaluated by western blot analysis against recombinant GCR produced by COS-7 cells or against endogenous GCR of human cell lines. GCR was strongly recognized by the produced antibodies, either as cell-associated or as secreted forms. The detected molecular masses of 59-66 kDa are in accordance to the expected size for glycosylated GCR. The GCR produced in E. coli would facilitate the production of polyclonal (shown here) and monoclonal antibodies and their use in the characterization of new biosimilar recombinant GCRs coming in the near future.

Histometric Study of Alveolar Bone in Rats Submitted to Ethanol During Lactation

The present work studied the adverse effects of maternal exposure of rats to alcohol during lactation, on the development of their offspring. Histometric evaluation by karyometry and of the alveolar bone at the level of the first upper molar of the sucking was perfomed. Two groups of animals, one coming from mothers exposed to drinking water containing 20% ethanol during the total lactation period and the other of controls coming from mothers receiving only alcohol-free drinking water during this period. On the 21 first day of lactation the young of each group were aleatorily selected and following anesthesia, their heads severed; after histological treatment, serial 6 mu m sections on the frontal plane at the molar level, stained with hematoxilin and eosin, were obtained. The experimental results produced, suggest that sucking from ethanol-treated mothers, show retarded post-natal growth, their alveolar bones presenting scarce, little calcified trabeculae, and a more abundant bone marrow compared to controls.