H(2) infrared line emission from the ionized region of planetary nebulae

Context. The analysis and interpretation of the H(2) line emission from planetary nebulae have been done in the literature by assuming that the molecule survives only in regions where the hydrogen is neutral, as in photodissociation, neutral clumps, or shocked regions. However, there is strong observational and theoretical evidence that at least part of the H(2) emission is produced inside the ionized region of these objects. Aims. The aim of the present work is to calculate and analyze the infrared line emission of H(2) produced inside the ionized region of planetary nebulae using a one-dimensional photoionization code. Methods. The photoionization code Aangaba was improved in order to calculate the statistical population of the H(2) energy levels, as well as the intensity of the H(2) infrared emission lines in the physical conditions typical of planetary nebulae. A grid of models was obtained and the results then analyzed and compared with the observational data. Results. We show that the contribution of the ionized region to the H(2) line emission can be important, particularly in the case of nebulae with high-temperature central stars. This result explains why H(2) emission is more frequently observed in bipolar planetary nebulae (Gatley's rule), since this kind of object typically has hotter stars. Collisional excitation plays an important role in populating the rovibrational levels of the electronic ground state of H(2) molecules. Radiative mechanisms are also important, particularly for the upper vibrational levels. Formation pumping can have minor effects on the line intensities produced by de-excitation from very high rotational levels, especially in dense and dusty environments. We included the effect of the H(2) molecule on the thermal equilibrium of the gas, concluding that, in the ionized region, H(2) only contributes to the thermal equilibrium in the case of a very high temperature of the central star or a high dust-to-gas ratio, mainly through collisional de-excitation.

Detection of polymorphisms of the mtDNA control region of Caretta caretta (Testudines: Cheloniidae) by PCR-SSCP

Marine turtles are increasingly being threatened worldwide by anthropogenic activities. Better understanding of their life cycle, behavior and population structure is imperative for the design of adequate conservation strategies. The mtDNA control region is a fast-evolving matrilineal marker that has been employed in the study of marine turtle populations. We developed and tested a simple molecular tracing system for Caretta caretta mtDNA haplotypes by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). Using this technique, we were able to distinguish the SSCP patterns of 18 individuals of the haplotypes CC-A4, CC-A24 and CCxLO, which are commonly found in turtles sampled on the Brazilian coast. When we analyzed 15 turtles with previously unknown sequences, we detected two other haplotypes, in addition to the other four. Based on DNA sequencing, they were identified as the CC-A17 and CC-A1 haplotypes. Further analyses were made with the sea turtles, Chelonia mydas (N = 8), Lepidochelys olivacea (N = 3) and Eretmochelys imbricata (N = 1), demonstrating that the PCR-SSCP technique is able to distinguish intra-and interspecific variation in the family Cheloniidae. We found that this technique can be useful for identifying sea turtle mtDNA haplotypes, reducing the need for sequencing.

Bayesian online algorithms for learning in discrete Hidden Markov Models

We propose and analyze two different Bayesian online algorithms for learning in discrete Hidden Markov Models and compare their performance with the already known Baldi-Chauvin Algorithm. Using the Kullback-Leibler divergence as a measure of generalization we draw learning curves in simplified situations for these algorithms and compare their performances.

Analytical results on Muller's ratchet effect in growing populations

Fontanari introduced [Phys. Rev. Lett. 91, 218101 (2003)] a model for studying Muller's ratchet phenomenon in growing asexual populations. They studied two situations, either including a death probability for each newborn or not, but were able to find analytical (recursive) expressions only in the no-decay case. In this Brief Report a branching process formalism is used to find recurrence equations that generalize the analytical results of the original paper besides confirming the interesting effects their simulations revealed.

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.

Changes in soil organic carbon storage under different agricultural management systems in the Southwest Amazon Region of Brazil

The Cerrado and Amazon regions of Brazil are probably the largest agricultural frontier of the world, and Could be a sink or source for C depending on the net effect of land use change and subsequent management on soil organic C pools. We evaluated the effects of agricultural management systems on soil organic C (SOC) stocks in the Brazilian states of Rondonia and Mato Grosso, and derived regional specific factors for soil C stock change associated with different management systems. We used 50 observations (data points) in this study, including 42 dealing with annual cropping practices and 8 dealing with perennial cropping, and analyzed the data in linear mixed-effect models. No tillage (NT) systems in Cerrado areas increased SOC Storage by 1.08 +/- 0.06 relative to SOC stocks under native conditions, while SOC storage increased by a modest factor of 1.01 +/- 0.17 in Cerradao and Amazon Forest conditions. Full tillage (FT) had negative effect on SOC storage relative to NT, decreasing SOC stocks by a factor of 0.94 +/- 0.04. but did not significantly reduce SOC stocks relative to native levels when adopted in the Cerrado region. Perennial cropping had a minimal impact on SOC stocks, estimated at a factor Value of 0.98 +/- 0.14, suggesting these systems maintain about 98% of the SOC stock found under native vegetation. The results Suggest that NT adoption may be increasing SOC with land use change from native vegetation to cropland management in the Cerrado region of Brazil. (C) 2009 Elsevier B.V. All rights reserved.

Carbon sequestration in agricultural soils in the Cerrado region of the Brazilian Amazon

The introduction of crop management practices after conversion of Amazon Cerrado into cropland influences soil C stocks and has direct and indirect consequences on greenhouse gases (GHG) emissions. The aim of this study was to quantify soil C sequestration, through the evaluation of the changes in C stocks, as well as the GHG fluxes (N(2)O and CH(4)) during the process of conversion of Cerrado into agricultural land in the southwestern Amazon region, comparing no-tillage (NT) and conventional tillage (CT) systems. We collected samples from soils and made gas flux measurements in July 2004 (the dry season) and in January 2005 (the wet season) at six areas: Cerrado, CT cultivated with rice for 1 year (1CT) and 2 years (2CT), and NT cultivated with soybean for 1 year (1NT), 2 years (2NT) and 3 years (3NT), in each case after a 2-year period of rice under CT. Soil samples were analyzed in both seasons for total organic C and bulk density. The soil C stocks, corrected for a mass of soil equivalent to the 0-30-cm layer under Cerrado, indicated that soils under NT had generally higher C storage compared to native Cerrado and CT soils. The annual C accumulation rate in the conversion of rice under CT into soybean under NT was 0.38 Mg ha(-1) year(-1). Although CO(2) emissions were not used in the C sequestration estimates to avoid double counting, we did include the fluxes of this gas in our discussion. In the wet season, CO(2) emissions were twice as high as in the dry season and the highest N(2)O emissions occurred under the NT system. There were no CH(4) emissions to the atmosphere (negative fluxes) and there were no significant seasonal variations. When N(2)O and CH(4) emissions in C-equivalent were subtracted (assuming that the measurements made on 4 days were representative of the whole year), the soil C sequestration rate of the conversion of rice under CT into soybean under NT was 0.23 Mg ha(-1) year(-1). Although there were positive soil C sequestration rates, our results do not present data regarding the full C balance in soil management changes in the Amazon Cerrado. (C) 2008 Elsevier B.V. All rights reserved.

Effects of land cover on chemical characteristics of streams in the Cerrado region of Brazil

The Cerrado is the second largest Brazilian biome and contains the headwaters of three major hydrological basins in Brazil. In spite of the biological and ecological relevance of this biome, there is little information about how land use changes affect the chemistry of low-order streams in the Cerrado. To evaluate these effects streams that drain areas under natural, rural, and urban land cover were sampled near Brasilia, Brazil. Water samples were collected between September 2004 and December 2006. Chemical concentrations generally followed the pattern of Urban > Rural > Natural. Median conductivity of stream water of 21.6 (interquartile: 22.7) mu S/cm in urban streams was three and five-fold greater relative to rural and natural areas, respectively. In the wet season, despite of increasing discharge, concentration of many solutes were higher, particularly in rural and natural streams. Streams also presented higher total dissolved N (TDN) loads from natural to rural and urban although DIN:DON ratios did not differ significantly. In natural and urban streams TDN was 80 and 77% dissolved organic N, respectively. These results indicate that alterations in land cover from natural to rural and urban are changing stream water chemistry in the Cerrado with increasing solute concentrations, in addition to increased TDN output in areas under urban cover, with potential effects on ecosystem function.

Phosphorus kinetics in growing hair sheep

Kinetics modelling was used to study the effects of different dietary phosphorus (P) levels on P metabolism in young sheep. An experiment was conducted with 12 Santa Ines lambs receiving a basal diet of a hay-concentrate mixture. Different amounts of dicalcium phosphate were added to the basal diet, to give the following treatments levels of 0, 1.5, 3 and 4.5 g/animal/day. The isotopic dilution technique (32 p) was used for analyze four compartments: gastrointestinal tract, plasma, bone and soft tissues (liver, heart, kidney and muscle), as well as nutrient flows between them. All P flows showed a positive linear or exponential relationship with P intake. Both incorporation and reabsorption in bone and soft tissue increased with increasing P levels in the diet, with positive retention above 3 g/day. On the 4.5g P/day treatment, reduced P absorption and increased P in the faeces from dietary origin was noted. Three g/day of P treatment was sufficient to meet soft tissue requirements for young sheep. (C) 2008 Elsevier B.V. All rights reserved.

Frozen Chicken for Wild Fish: Nutritional Transition in the Brazilian Amazon Region Determined by Carbon and Nitrogen Stable Isotope Ratios in Fingernails

Objectives: Amazonian populations are experiencing dietary changes characteristic of the nutrition transition. However, the degree of change appears to vary between urban and rural settings. To investigate this process, we determined carbon and nitrogen stable isotope ratios in fingernails and dietary intake of Amazonian populations living along a rural to urban continuum along the Solimoes River in Brazil. Methods: Carbon and nitrogen stable isotope ratios were analyzed from the fingernails of 431 volunteer subjects living in different settings ranging from rural villages, small towns to urban centers along the Solimoes River. Data from 200 dietary intake surveys were also collected using food frequency questionnaires and 24-h recall interviews in an effort to determine qualitative aspects of diet composition. Results: Fingernail delta(13)C values (mean standard deviation) were -23.2 +/- 1.3, 20.2 +/- 1.5, and 17.4 +/- 1.3 parts per thousand and delta(15)N values were 11.8 +/- 0.6, 10.4 +/- 0.8, and 10.8 +/- 0.7 parts per thousand for those living in rural villages, small towns, and major cities, respectively. We found a gradual increase in the number of food items derived from C(4) plant types (meat and sugar) and the replacement of food items derived from C(3) plant types (fish and manioc flour) with increasing size of urban centers. Conclusion: Increasing urbanization in the Brazilian Amazon is associated with a significant change in food habits with processed and industrialized products playing an increasingly important role in the diet and contributing to the nutrition transition in the region. Am. J. Hum. Biol. 23:642-650, 2011. (C) 2011 Wiley-Liss, Inc.

Analysis of Single-Nucleotide Polymorphisms in the crt-o and mdr1 Genes of Plasmodium vivax among Chloroquine-Resistant Isolates from the Brazilian Amazon Region

Plasmodium vivax parasites with chloroquine resistance (CQR) are already circulating in the Brazilian Amazon. Complete single-nucleotide polymorphism (SNP) analyses of coding and noncoding sequences of the pvmdr1 and pvcrt-o genes revealed no associations with CQR, even if some mutations had not been randomly selected. In addition, striking differences in the topologies and numbers of SNPs in these transporter genes between P. vivax and P. falciparum reinforce the idea that mechanisms other than mutations may explain this virulent phenotype in P. vivax.

Determination of nutritional and toxic elements in pasteurized bovine milk from Vale do Paraiba region (Brazil)

Throughout the year of 2004, 54 samples (I L each) were collected from commercial sources in the Vale do Paraiba region (eastern portion of Sao Paulo State, Brazil). The concentrations of (Ca, Cr, Cu, Fe, Mg, Mn, Ni, Se, Zn, Cd and Pb) in these samples were analyzed by two atomic-absorption spectroscopy (AAS) methods. Ca, Cu, Fe, Mg and Zn were determined by flame atomic-absorption spectroscopy (FAAS) and (Cd, Cr, Mn, Ni, Pb and Se) were determined by electrothermal atomic-absorption spectroscopy (ETAAS). Tests to determine and quantify essential, nonessential and toxic elements present in bovine milk are rare in Brazil, especially so for Vale do Paraiba region. Tests were performed on standard NIST-certified milk-powder to validate the reliability of subsequently collected analytical data. Ca presented a lower recovery value (85.3%). The finding for Ca macro-nutrient was found to be below recommended international standards (1300 mg/L) for all samples possibly due to milk heterogeneity and losses in the pasteurization process. Significant results for Pb were found in all milk samples with average values at 0.230 mg/L from a minimum of 0.062 mg/L and maximum of 0.476 mg/L (C) 2009 Elsevier Ltd. All rights reserved.

Stability region bifurcations of nonlinear autonomous dynamical systems: Type-zero saddle-node bifurcations

The behavior of stability regions of nonlinear autonomous dynamical systems subjected to parameter variation is studied in this paper. In particular, the behavior of stability regions and stability boundaries when the system undergoes a type-zero sadle-node bifurcation on the stability boundary is investigated in this paper. It is shown that the stability regions suffer drastic changes with parameter variation if type-zero saddle-node bifurcations occur on the stability boundary. A complete characterization of these changes in the neighborhood of a type-zero saddle-node bifurcation value is presented in this paper. Copyright (C) 2010 John Wiley & Sons, Ltd.

Power imbalance application region method for distributed synchronous generator anti-islanding protection design and evaluation

This paper presents a novel graphical approach to adjust and evaluate frequency-based relays employed in anti-islanding protection schemes of distributed synchronous generators, in order to meet the anti-islanding and abnormal frequency variation requirements, simultaneously. The proposed method defines a region in the power mismatch space, inside which the relay non-detection zone should be located, if the above-mentioned requirements must be met. Such region is called power imbalance application region. Results show that this method can help protection engineers to adjust frequency-based relays to improve the anti-islanding capability and to minimize false operation occurrences, keeping the abnormal frequency variation utility requirements satisfied. Moreover, the proposed method can be employed to coordinate different types of frequency-based relays, aiming at improving overall performance of the distributed generator frequency protection scheme. (C) 2011 Elsevier B.V. All rights reserved.

Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp RFLP/PCR data set

The taxonomy of the N(2)-fixing bacteria belonging to the genus Bradyrhizobium is still poorly refined, mainly due to conflicting results obtained by the analysis of the phenotypic and genotypic properties. This paper presents an application of a method aiming at the identification of possible new clusters within a Brazilian collection of 119 Bradryrhizobium strains showing phenotypic characteristics of B. japonicum and B. elkanii. The stability was studied as a function of the number of restriction enzymes used in the RFLP-PCR analysis of three ribosomal regions with three restriction enzymes per region. The method proposed here uses Clustering algorithms with distances calculated by average-linkage clustering. Introducing perturbations using sub-sampling techniques makes the stability analysis. The method showed efficacy in the grouping of the species B. japonicum and B. elkanii. Furthermore, two new clusters were clearly defined, indicating possible new species, and sub-clusters within each detected cluster. (C) 2008 Elsevier B.V. All rights reserved.