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.

Biogeochemical processes and the diversity of Nhecolândia lakes, Brazil

The Pantanal of Nhecolândia, the world's largest and most diversified field of tropical lakes, comprises approximately 10,000 lakes, which cover an area of 24,000 km² and vary greatly in salinity, pH, alkalinity, colour, physiography and biological activity. The hyposaline lakes have variable pHs, low alkalinity, macrophytes and low phytoplankton densities. The saline lakes have pHs above 9 or 10, high alkalinity, a high density of phytoplankton and sand beaches. The cause of the diversity of these lakes has been an open question, which we have addressed in our research. Here we propose a hybrid process, both geochemical and biological, as the main cause, including (1) a climate with an important water deficit and poverty in Ca2+ in both superficial and phreatic waters; and (2) an elevation of pH during cyanobacteria blooms. These two aspects destabilise the general tendency of Earth's surface waters towards a neutral pH. This imbalance results in an increase in the pH and dissolution of previously precipitated amorphous silica and quartzose sand. During extreme droughts, amorphous silica precipitates in the inter-granular spaces of the lake bottom sediment, increasing the isolation of the lake from the phreatic level. This paper discusses this biogeochemical problem in the light of physicochemical, chemical, altimetric and phytoplankton data.

Learning processes and the neural analysis of conditioning

Classical and operant conditioning principles, such as the behavioral discrepancy-derived assumption that reinforcement always selects antecedent stimulus and response relations, have been studied at the neural level, mainly by observing the strengthening of neuronal responses or synaptic connections. A review of the literature on the neural basis of behavior provided extensive scientific data that indicate a synthesis between the two conditioning processes based mainly on stimulus control in learning tasks. The resulting analysis revealed the following aspects. Dopamine acts as a behavioral discrepancy signal in the midbrain pathway of positive reinforcement, leading toward the nucleus accumbens. Dopamine modulates both types of conditioning in the Aplysia mollusk and in mammals. In vivo and in vitro mollusk preparations show convergence of both types of conditioning in the same motor neuron. Frontal cortical neurons are involved in behavioral discrimination in reversal and extinction procedures, and these neurons preferentially deliver glutamate through conditioned stimulus or discriminative stimulus pathways. Discriminative neural responses can reliably precede operant movements and can also be common to stimuli that share complex symbolic relations. The present article discusses convergent and divergent points between conditioning paradigms at the neural level of analysis to advance our knowledge on reinforcement.

Serological Survey for Antibodies to Encephalitozoon cuniculi in Ownerless Dogs From Urban Areas of Brazil and Colombia

There are 3 strains of Encephalitozoon cuniculi that occur in mammals. Strain III is associated with clinical disease in dogs, although some can be asymptomatic carriers and excrete spores in their urine. Several cases of human E. cuniculi infection caused by strain III have been observed in immunocompromised patients, indicating that E. cuniculi should be considered a zoonotic agent. Encephalitozoon cuniculi can cause fatal disease in maternally-infected or young dogs. Clinical signs in these animals included blindness, encephalitis, retarded growth rate, and nephritis. Encephalitozoon cuniculi has also been associated with primary renal failure in adult dogs. The present study used the direct agglutination test (DAT, cut-off 1:50) and the indirect fluorescent antibody test (IFAT, cut-off 1:10) to examine the prevalence of antibodies to E. cuniculi in dogs from Brazil and Colombia. Using the DAG, 31 (27.4%) of 113 dogs from Brazil and 47 (18.5%) of 254 dogs from Colombia were seropositive. Nine (14.3%) of 63 dogs from Brazil and IS (35.3%) of the 51 dogs from Colombia were seropositive by indirect immunofluorescent antibody test. These results indicate that dogs from Brazil and Colombia are exposed to E. cuniculi.

An algorithmic Friedman-Pippenger theorem on tree embeddings and applications

An (n, d)-expander is a graph G = (V, E) such that for every X subset of V with vertical bar X vertical bar <= 2n - 2 we have vertical bar Gamma(G)(X) vertical bar >= (d + 1) vertical bar X vertical bar. A tree T is small if it has at most n vertices and has maximum degree at most d. Friedman and Pippenger (1987) proved that any ( n; d)- expander contains every small tree. However, their elegant proof does not seem to yield an efficient algorithm for obtaining the tree. In this paper, we give an alternative result that does admit a polynomial time algorithm for finding the immersion of any small tree in subgraphs G of (N, D, lambda)-graphs Lambda, as long as G contains a positive fraction of the edges of Lambda and lambda/D is small enough. In several applications of the Friedman-Pippenger theorem, including the ones in the original paper of those authors, the (n, d)-expander G is a subgraph of an (N, D, lambda)-graph as above. Therefore, our result suffices to provide efficient algorithms for such previously non-constructive applications. As an example, we discuss a recent result of Alon, Krivelevich, and Sudakov (2007) concerning embedding nearly spanning bounded degree trees, the proof of which makes use of the Friedman-Pippenger theorem. We shall also show a construction inspired on Wigderson-Zuckerman expander graphs for which any sufficiently dense subgraph contains all trees of sizes and maximum degrees achieving essentially optimal parameters. Our algorithmic approach is based on a reduction of the tree embedding problem to a certain on-line matching problem for bipartite graphs, solved by Aggarwal et al. (1996).

Microbial processes and bacterial populations associated to anaerobic treatment of sulfate-rich wastewater

A pilot-scale (1.2 m(3)) anaerobic sequencing batch biofilm reactor (ASBBR) containing mineral coal for biomass attachment was fed with sulfate-rich wastewater at increasing sulfate concentrations. Ethanol was used as the main organic source. Tested COD/sulfate ratios were of 1.8 and 1.5 for sulfate loading rates of 0.65-1.90 kgSO(4)(2-)/cycle (48 h-cycle) or of 1.0 in the trial with 3.0 gSO(4)(2-) l(-1). Sulfate removal efficiencies observed in all trials were as high as 99%. Molecular inventories indicated a shift on the microbial composition and a decrease on species diversity with the increase of sulfate concentration. Beta-proteobacteria species affiliated with Aminomonas spp. and Thermanaerovibrio spp. predominated at 1.0 gSO(4)(2-) l(-1). At higher sulfate concentrations the predominant bacterial group was Delta-proteobacteria mainly Desulfovibrio spp. and Desulfomicrobium spp. at 2.0 gSO(4)(2-) l(-1), whereas Desulfurella spp. and Coprothermobacter spp. predominated at 3.0 gSO(4)(2-) l(-1). These organisms have been commonly associated with sulfate reduction producing acetate, sulfide and sulfur. Methanogenic archaea(Methanosaeta spp.)was found at 1.0 and 2.0 gSO(4)(2-) l(-1). Additionally, a simplified mathematical model was used to infer on metabolic pathways of the biomass involved in sulfate reduction. (C) 2009 Elsevier Ltd. All rights reserved.

Rural and Urban Streams: Anthropogenic Influences and Impacts on Water and Sediment Quality

The Pirapo river watershed (Parana State, Brazil) compounds a relatively industrialized and urbanized region, undergoing great pressure from the discharge of industrial, agricultural and domestic wastes. We evaluated the environmental quality of ten streams belonging to this watershed in April and June 2008 by performing acute and chronic toxicity tests with Daphnia similis and Ceriodaphnia silvestrii from water and sediment samples. We tested the hypothesis that the streams located in urban areas are more exposed to the influence of pollutants, than those outside the city limits. In addition, we obtained the measures of physical and chemical parameters, and identified the main polluted sources. Contrary to what was expected, the rural streams were more toxic than those located in urban area. These results demonstrate that the water bodies located in rural areas are being affected by the pollution of aquatic ecosystems as far as those found in urban areas, requiring the same attention of environmental managers in relation to its monitoring.

On S-asymptotically omega-periodic functions on Banach spaces and applications

This paper is devoted to the study of the class of continuous and bounded functions f : [0, infinity] -> X for which exists omega > 0 such that lim(t ->infinity) (f (t + omega) - f (t)) = 0 (in the sequel called S-asymptotically omega-periodic functions). We discuss qualitative properties and establish some relationships between this type of functions and the class of asymptotically omega-periodic functions. We also study the existence of S-asymptotically omega-periodic mild solutions of the first-order abstract Cauchy problem in Banach spaces. (C) 2008 Elsevier Inc. All rights reserved.

Almost automorphic mild solutions to some partial neutral functional-differential equations and applications

The paper considers the existence and uniqueness of almost automorphic mild solutions to some classes of first-order partial neutral functional-differential equations. Sufficient conditions for the existence and uniqueness of almost automorphic mild solutions to the above-mentioned equations are obtained. As an application, a first-order boundary value problem arising in control systems is considered. (C) 2007 Elsevier Ltd. All fights reserved.

Articular Cartilage in the Knee: Current MR Imaging Techniques and Applications in Clinical Practice and Research

Magnetic resonance (MR) imaging is the most important imaging modality for the evaluation of traumatic or degenerative cartilaginous lesions in the knee. It is a powerful noninvasive tool for detecting such lesions and monitoring the effects of pharmacologic and surgical therapy. The specific MR imaging techniques used for these purposes can be divided into two broad categories according to their usefulness for morphologic or compositional evaluation. To assess the structure of knee cartilage, standard spin-echo (SE) and gradient-recalled echo (GRE) sequences, fast SE sequences, and three-dimensional SE and GRE sequences are available. These techniques allow the detection of morphologic defects in the articular cartilage of the knee and are commonly used in research for semiquantitative and quantitative assessments of cartilage. To evaluate the collagen network and proteoglycan content in the knee cartilage matrix, compositional assessment techniques such as T2 mapping, delayed gadolinium-enhanced MR imaging of cartilage (or dGEMRIC), T1 rho imaging, sodium imaging, and diffusion-weighted imaging are available. These techniques may be used in various combinations and at various magnetic field strengths in clinical and research settings to improve the characterization of changes in cartilage. (C)RSNA, 2011 , radiographics.rsna.org

Sub-tropical urban environment affecting content and composition of non-structural carbohydrates of Lolium multiflorum ssp italicum cv. Lema

This study analyzed the relationship between environmental factors, especially air pollution and climatic conditions, and non-structural carbohydrates (NSC) in plants of Lolium multiflorum exposed during 10 consecutive periods of 28 days at a polluted site (Congonhas) and at a reference site in Sao Paulo city (Brazil). After exposure, NSC composition and leaf concentrations of Al, Fe. Cu, Zn, Pb and Cd were measured. The seasonal pattern of NSC accumulation was quite similar in both sites, but plants at Congonhas showed higher concentrations of these compounds, especially fructans of low and medium degree of polymerization. Regression analysis showed that NSC in plants growing at the polluted site were explained by variations on temperature and leaf concentration of Fe (positive effect), as well as relative humidity and particulate material (negative effect). NSC in the standardized grass culture, in addition to heavy metal accumulation, may indicate stressing conditions in a sub-tropical polluted environment. (C) 2008 Elsevier Ltd. All rights reserved.

Structure and Applications of a Rhamnolipid Surfactant Produced in Soybean Oil Waste

Soybean oil soapstock was utilized as an alternative carbon source for the production of rhamnolipids by Pseudomonas aeruginosa LBI strain. The chemical composition and properties of the rhamnolipid mixture obtained were determined to define its potential applications. The chemical characterization of the rhamnolipid has revealed the presence of ten different homologues. The monorhamnolipid RhaC(10)C(10) and the dirhamnolipid Rha(2)C(10)C(10) were the main components of the mixture that showed predominance of 44% and 29%, respectively, after 144-h of cultivation. The biosurfactant was able to form stable emulsions with several hydrocarbons and showed excellent emulsification for soybean oil and chicken fat (100%). The rhamnolipid removed 67% of crude oil present in sand samples and presented antimicrobial activity against Bacillus cereus and Mucor miehei at 64 mu g/mL and inhibition of Neurospora crassa, Staphylococcus aureus, and Micrococcus luteus at 256 mu g/mL. The results demonstrated that the rhamnolipid produced in soybean oil soapstock can be useful in environmental and food industry applications.

Species richness, abundance, and body size relationships from a neotropical chironomid assemblage: Looking for patterns

We investigated two of the most studied relationships in the macroecological research program (species richness vs. body size and abundance vs. body size) of a local chironomid assemblage from southeastern Brazil. Although numerous Studies have examined these relationships, few have investigated how they vary at different temporal scales. We used data from a forested stream to document and examine these patterns at monthly intervals. Both the species body size distribution and the abundance-body size relationship varied temporally. In some months the body size distribution was skewed to the right. whereas in others it approached normality. We Found both linear relationships (with different values of slopes). and a polygonal pattern in the abundance-body size relationship. This temporal variation was not related to environmental variables. Our results suggest that body size relationships are temporally instable properties of this chironomid assemblage. (C) 2007 Gesellschaft fur Okologie. Published by Elsevier GmbH. All rights reserved.

Hitting and returning to rare events for all alpha-mixing processes

We prove that for any a-mixing stationary process the hitting time of any n-string A(n) converges, when suitably normalized, to an exponential law. We identify the normalization constant lambda(A(n)). A similar statement holds also for the return time. To establish this result we prove two other results of independent interest. First, we show a relation between the rescaled hitting time and the rescaled return time, generalizing a theorem of Haydn, Lacroix and Vaienti. Second, we show that for positive entropy systems, the probability of observing any n-string in n consecutive observations goes to zero as n goes to infinity. (c) 2010 Elsevier B.V. All rights reserved.

Repeated disturbances and canopy disturbance regime in a tropical semi-deciduous forest

The canopy disturbance regime and the influence of gap methods on the interpretation of forest structure and dynamics were evaluated in a tropical semi-deciduous forest in south-eastern Brazil. We encountered a gap density of 11.2 gaps ha(-1) and an average size which varied from 121 to 333 m(2) depending on the gap delimitation method considered (minimum gap size was 10 m(2)). Although average size was slightly higher, the median value obtained (78 m(2)) was comparable to other tropical forest sites and the gap size-class distribution found supported the pattern described for such forest sites. Among 297 gap makers, snapping and uprooting were the most common modes of disturbance. The number and basal area of gap makers were good predictors of gap size. Almost 25% of all gaps suffered from repeated disturbance events that brought about larger gap sizes. Such processes, along with delimitation methods, strongly influenced the estimation of turnover rate and therefore the interpretation of forest dynamics. These results demonstrated the importance of further studies on repeated disturbances, which is often neglected in forest studies.