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.

Survival time of random walk in random environment among soft obstacles

We consider a Random Walk in Random Environment (RWRE) moving in an i.i.d. random field of obstacles. When the particle hits an obstacle, it disappears with a positive probability. We obtain quenched and annealed bounds on the tails of the survival time in the general d-dimensional case. We then consider a simplified one-dimensional model (where transition probabilities and obstacles are independent and the RWRE only moves to neighbour sites), and obtain finer results for the tail of the survival time. In addition, we study also the ""mixed"" probability measures (quenched with respect to the obstacles and annealed with respect to the transition probabilities and vice-versa) and give results for tails of the survival time with respect to these probability measures. Further, we apply the same methods to obtain bounds for the tails of hitting times of Branching Random Walks in Random Environment (BRWRE).

Random perturbations of stochastic processes with unbounded variable length memory

We consider binary infinite order stochastic chains perturbed by a random noise. This means that at each time step, the value assumed by the chain can be randomly and independently flipped with a small fixed probability. We show that the transition probabilities of the perturbed chain are uniformly close to the corresponding transition probabilities of the original chain. As a consequence, in the case of stochastic chains with unbounded but otherwise finite variable length memory, we show that it is possible to recover the context tree of the original chain, using a suitable version of the algorithm Context, provided that the noise is small enough.

Gibbs random graphs on point processes

Consider a discrete locally finite subset Gamma of R(d) and the cornplete graph (Gamma, E), with vertices Gamma and edges E. We consider Gibbs measures on the set of sub-graphs with vertices Gamma and edges E` subset of E. The Gibbs interaction acts between open edges having a vertex in common. We study percolation properties of the Gibbs distribution of the graph ensemble. The main results concern percolation properties of the open edges in two cases: (a) when Gamma is sampled from a homogeneous Poisson process; and (b) for a fixed Gamma with sufficiently sparse points. (c) 2010 American Institute of Physics. [doi:10.1063/1.3514605]

An oracle approach for interaction neighborhood estimation in random fields

We consider the problem of interaction neighborhood estimation from the partial observation of a finite number of realizations of a random field. We introduce a model selection rule to choose estimators of conditional probabilities among natural candidates. Our main result is an oracle inequality satisfied by the resulting estimator. We use then this selection rule in a two-step procedure to evaluate the interacting neighborhoods. The selection rule selects a small prior set of possible interacting points and a cutting step remove from this prior set the irrelevant points. We also prove that the Ising models satisfy the assumptions of the main theorems, without restrictions on the temperature, on the structure of the interacting graph or on the range of the interactions. It provides therefore a large class of applications for our results. We give a computationally efficient procedure in these models. We finally show the practical efficiency of our approach in a simulation study.

Sensitized formation of oxidatively generated damage to cellular DNA by UVA radiation

The survey is aimed at critically reviewing information on the UVA-mediated oxidative reactions to cellular components with emphasis on DNA as the result of mostly photosensitized pathways. It appears clearly that UVA radiation is relatively much more efficient than UVB photons in inducing oxidative processes. The main UVA-induced oxidative degradation pathways of DNA are reported and discussed mechanistically. They are mostly rationalized in terms of a major contribution of singlet molecular oxygen ((1)O(2)) and to a lesser extent of hydroxyl radical ((center dot)OH), that in the latter case originates from Fenton-type reactions. This leads to the predominant formation of 8-oxo-7,8-dihydroguanine together with smaller amounts of oxidized pyrimidine bases and DNA strand breaks in UVA-irradiated cells.

DNA oxidation, strand-breaks and etheno-adducts formation promoted by Cu, Zn-superoxide dismutase-H(2)O(2) in the presence and absence of bicarbonate

Biomolecule oxidation promoted by Cu, Zn-superoxide dismutase (SOD1) has been studied because of its potential role in neurodegenerative diseases. We studied the mechanism of DNA damage promoted by the SOD1-H(2)O(2) system. The system promoted the formation of strand breaks in plasmid DNA and the formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) in calf thymus DNA. We were also able to detect, for the. first time, 1,N(2)-etheno-2'-deoxyguanosine (1,N(2)-epsilon dGuo) in calf thymus DNA exposed to SOD1-H(2)O(2). The addition of a copper chelator caused a decrease in the frequency of 8-oxodGuo and 1,N(2)-epsilon dGuo, indicating the participation of copper ions lost from SOD1 active sites. The addition of bicarbonate increased the levels of both DNA lesions. We conclude that copper liberated from SOD1 active sites has a central role in the mechanism of DNA damage promoted by SOD1 in the presence of H(2)O(2), and that bicarbonate can modulate the reactivity of released copper.

DNA damage by sulfite autoxidation catalyzed by cobalt complexes

DNA damage was investigated in the presence of sulfite, dissolved oxygen and cobalt(II) complexes with glycylglycylhistidine, glycylhistidyllysine, glycylglycyltyrosylarginine and tetraglycine. These studies indicated that only Co(II) complexed with glycylglycylhistidine (GGH) induced DNA strand breaks at low sulfite concentrations (1-80 mu M) via strong oxidants formed in the reaction. In the presence of the other complexes, some damage occurred only in the presence of high sulfite concentrations (0.1-2.0 mM) after incubation for 4 h. In the presence of GGH, Co(II) and dissolved O(2), DNA damage must involve a reactive high-valent cobalt complex. The damaging effect was increased by adding S(IV), due to the oxysulfur radicals formed as intermediates in S(IV) autoxidation catalyzed by the complex. SO(3)(center dot)-S-, HO(center dot) and H(center dot) radicals were detected by EPR-spin trapping experiments with DMPO (5,5-dimethyl-1-pyrroline N-oxide). The results indicate that Co(II) binds O2 in the presence of GGH, and leads to the formation of a DMPO-HO(center dot) adduct without first forming free superoxide or hydroxyl radical, supporting the participation of a reactive high-valent cobalt complex.

Sequence-specific electrochemical detection of Alicyclobacillus acidoterrestris DNA using electroconductive polymer-modified fluorine tin oxide electrodes

This study outlines the quantification of low levels of Alicyclobacillus acidoterrestris in pure cultures, since this bacterium is not inactivated by pasteurization and may remain in industrialized foods and beverages. Electroconductive polymer-modified fluorine tin oxide (FTO) electrodes and multiple nanoparticle labels were used for biosensing. The detection of A. acidoterrestris in pure cultures was performed by reverse transcription polymerase chain reaction (RT-PCR) and the sensitivity was further increased by asymmetric nested RT-PCR using electrochemical detection for quantification of the amplicon. The quantification of nested RT-PCR products by Ag/Au-based electrochemical detection was able to detect 2 colony forming units per mL (CFU mL(-1)) of spores in pure culture and low detection and quantification limits (7.07 and 23.6 nM, respectively) were obtained for the target A. acidoterrestris on the electrochemical detection bioassay.

A New Generation of X Ray Irradiators for Insect Sterilization

Recent fears of terrorism have provoked an increase in delays and denials of transboundary shipments of radioisotopes. This represents a serious constraint to sterile insect technique (SIT) programs around the world as they rely on the use of ionizing radiation from radioisotopes for insect sterilization. To validate a novel X ray irradiator, a series of studies on Ceratitis capitata (Wiedemann) and Anastrepha fraterculus (Wiedemann) (Diptera: Tephritidae) were carried out, comparing the relative biological effectiveness (RBE) between X rays and traditional gamma radiation from (60)Co. Male C. capitata pupae and pupae of both sexes of A. fraterculus, both 24 - 48 h before adult emergence, were irradiated with doses ranging from 15 to 120 Gy and 10-70 Gy, respectively. Estimated mean doses of 91.2 Gy of X and 124.9 Gy of gamma radiation induced 99% sterility in C. capitata males, Irradiated A. fraterculus were 99% sterile at approximate to 40-60 Gy for both radiation treatments. Standard quality control parameters and mating indices were not significantly affected by the two types of radiation. The RBE did not differ significantly between the tested X and gamma radiation, and X rays are as biologically effective for SIT purposes as gamma rays are. This work confirms the suitability of this new generation of X ray irradiators for pest control programs that integrate the SIT.

A new approach for in vitro bioassay to measure tannin biological effects based on a gas production technique

The aim of this paper was to study a method based on gas production technique to measure the biological effects of tannins on rumen fermentation. Six feeds were used as fermentation substrates in a semi-automated gas method: feed A - aroeira (Astronium urundeuva); feed B - jurema preta (Mimosa hostilis), feed C - sorghum grains (Sorghum bicolor); feed D - Tifton-85 (Cynodon sp.); and two others prepared mixing 450 g sorghum leaves, 450 g concentrate (maize and soybean meal) and 100 g either of acacia (Acacia mearnsii) tannin extract (feed E) or quebracho (Schinopsis lorentzii) tannin extract (feed F) per kg (w:w). Three assays were carried out to standardize the bioassay for tannins. The first assay compared two binding agents (polyethylene glycol - PEG - and polyvinyl polypirrolidone - PVPP) to attenuate the tannin effects. The complex formed by PEG and tannins showed to be more stable than PVPP and tannins. Then, in the second assay, PEG was used as binding agent, and this assay was done to evaluate levels of PEG (0, 500, 750, 1000 and 1250 mg/g DM) to minimize the tannin effect. All the tested levels of PEG produced a response to evaluate tannin effects but the best response was for dose of 1000 mg/g DM. Using this dose of PEG, the final assay was carried out to test three compounds (tannic acid, quebracho extract and acacia extract) to establish a curve of biological equivalent effect of tannins. For this, five levels of each compound were added to I g of a standard feed (Lucerne hay). The equivalent effect showed not to be directly related to the chemical analysis for tannins. It was shown that different sources of tannins had different activities or reactivities. The curves of biological equivalence can provide information about tannin reactivity and its use seems to be important as an additional factor for chemical analysis. (C) 2007 Elsevier B.V. All rights reserved.

Nasopharyngeal Intubation in Robin Sequence: Technique and Management

Objective: To provide a detailed description of the nasopharyngeal intubation (NPI) technique and photographs, which should be helpful for those who may need to perform it for treating the airway obstruction in Robin sequence. Design: To describe and illustrate the NPI technique and the necessary considerations for its application. Setting: Hospital de Reabilitacao de Anomalias Craniofacial of University of Sao Paulo, Brazil. Result: The NPI procedure involves the use of a whitish, Portex, number 3.0 or 3.5, silicone tube, introduced 8 cm deep into the infant`s nostril and fixed with Micropore tape. The tube is to be removed at least twice a day for proper hygiene (with running water, detergent, and swabs) and should be changed every 7 days. This procedure is taught to the children`s parents or caretakers by the nurse during hospitalization. Conclusion: The technique is so simple that it can be performed by the parents themselves, allowing continuation of the treatment at home.

Constant-random practice and the adaptive process in motor learning with varying amounts of constant practice

The adaptive process in motor learning was examined in terms of effects of varying amounts of constant practice performed before random practice. Participants pressed five response keys sequentially, the last one coincident with the lighting of a final visual stimulus provided by a complex coincident timing apparatus. Different visual stimulus speeds were used during the random practice. 33 children (M age=11.6 yr.) were randomly assigned to one of three experimental groups: constant-random, constant-random 33%, and constant-random 66%. The constant-random group practiced constantly until they reached a criterion of performance stabilization three consecutive trials within 50 msec. of error. The other two groups had additional constant practice of 33 and 66%, respectively, of the number of trials needed to achieve the stabilization criterion. All three groups performed 36 trials under random practice; in the adaptation phase, they practiced at a different visual stimulus speed adopted in the stabilization phase. Global performance measures were absolute, constant, and variable errors, and movement pattern was analyzed by relative timing and overall movement time. There was no group difference in relation to global performance measures and overall movement time. However, differences between the groups were observed on movement pattern, since constant-random 66% group changed its relative timing performance in the adaptation phase.

Morphological and mechanical properties of hybrid matrices of polysiloxane-polyvinyl alcohol prepared by sol-gel technique and their potential for immobilizing enzyme

Hybrid matrices of polysiloxane-polyvinyl alcohol (POS-PVA) were prepared by sol-gel technique using different concentrations of the organic component (polyvinyl alcohol, PVA) in the synthesis medium. The goal was to prepare carriers for immobilizing enzyme by taking into consideration properties as hardness, mean pore diameter, specific surface area and pore size distribution. The matrices were activated with sodium metaperiodate to render functional groups for binding the lipase from Candida rugosa, used here as a study model. Results showed that low proportion of PVA gave POS-PVA with low surface area and pore volume, although with higher hardness. The chemical activation decreased the pore volume and increased the pore size with a decrease on the surface area of about 60-75%. The matrices for enzyme immobilization were chosen considering the best combination of high surface area and hardness. Thus, the POS-PVA prepared with 5.56 x 10(-5) M of PVA with a surface area of 123 m(2)/g and hardness of 71 HV (50 gf 30 s) was shown to be suitable to immobilize the lipase, with an immobilization yield of about 40%. (c) 2008 Elsevier B.V. All rights reserved.

Finite element homogenization technique for the characterization of d(15) shear piezoelectric macro-fibre composites

A finite element homogenization method for a shear actuated d(15) macro-fibre composite (MFC) made of seven layers (Kapton, acrylic, electrode, piezoceramic fibre and epoxy composite, electrode, acrylic, Kapton) is proposed and used for the characterization of its effective material properties. The methodology is first validated for the MFC active layer only, made of piezoceramic fibre and epoxy, through comparison with previously published analytical results. Then, the methodology is applied to the seven-layer MFC. It is shown that the packaging reduces significantly the shear stiffness of the piezoceramic material and, thus, leads to significantly smaller effective electromechanical coupling coefficient k(15) and piezoelectric stress constant e(15) when compared to the piezoceramic fibre properties. However, it is found that the piezoelectric charge constant d(15) is less affected by the softer layers required by the MFC packaging.