Evaluation of the carbon content of aerosols from the burning of biomass in the Brazilian Amazon using thermal, optical and thermal-optical analysis methods

Aerosol samples were collected at a pasture site in the Amazon Basin as part of the project LBA-SMOCC-2002 (Large-Scale Biosphere-Atmosphere Experiment in Amazonia - Smoke Aerosols, Clouds, Rainfall and Climate: Aerosols from Biomass Burning Perturb Global and Regional Climate). Sampling was conducted during the late dry season, when the aerosol composition was dominated by biomass burning emissions, especially in the submicron fraction. A 13-stage Dekati low-pressure impactor (DLPI) was used to collect particles with nominal aerodynamic diameters (D(p)) ranging from 0.03 to 0.10 mu m. Gravimetric analyses of the DLPI substrates and filters were performed to obtain aerosol mass concentrations. The concentrations of total, apparent elemental, and organic carbon (TC, EC(a), and OC) were determined using thermal and thermal-optical analysis (TOA) methods. A light transmission method (LTM) was used to determine the concentration of equivalent black carbon (BC(e)) or the absorbing fraction at 880 nm for the size-resolved samples. During the dry period, due to the pervasive presence of fires in the region upwind of the sampling site, concentrations of fine aerosols (D(p) < 2.5 mu m: average 59.8 mu g m(-3)) were higher than coarse aerosols (D(p) > 2.5 mu m: 4.1 mu g m(-3)). Carbonaceous matter, estimated as the sum of the particulate organic matter (i.e., OC x 1.8) plus BC(e), comprised more than 90% to the total aerosol mass. Concentrations of EC(a) (estimated by thermal analysis with a correction for charring) and BC(e) (estimated by LTM) averaged 5.2 +/- 1.3 and 3.1 +/- 0.8 mu g m(-3), respectively. The determination of EC was improved by extracting water-soluble organic material from the samples, which reduced the average light absorption Angstrom exponent of particles in the size range of 0.1 to 1.0 mu m from >2.0 to approximately 1.2. The size-resolved BC(e) measured by the LTM showed a clear maximum between 0.4 and 0.6 mu m in diameter. The concentrations of OC and BC(e) varied diurnally during the dry period, and this variation is related to diurnal changes in boundary layer thickness and in fire frequency.

Runoff sources and land cover change in the Amazon: an end-member mixing analysis from small watersheds

The flowpaths by which water moves from watersheds to streams has important consequences for the runoff dynamics and biogeochemistry of surface waters in the Amazon Basin. The clearing of Amazon forest to cattle pasture has the potential to change runoff sources to streams by shifting runoff to more surficial flow pathways. We applied end-member mixing analysis (EMMA) to 10 small watersheds throughout the Amazon in which solute composition of streamwater and groundwater, overland flow, soil solution, throughfall and rainwater were measured, largely as part of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia. We found a range in the extent to which streamwater samples fell within the mixing space determined by potential flowpath end-members, suggesting that some water sources to streams were not sampled. The contribution of overland flow as a source of stream flow was greater in pasture watersheds than in forest watersheds of comparable size. Increases in overland flow contribution to pasture streams ranged in some cases from 0% in forest to 27-28% in pasture and were broadly consistent with results from hydrometric sampling of Amazon forest and pasture watersheds that indicate 17- to 18-fold increase in the overland flow contribution to stream flow in pastures. In forest, overland flow was an important contribution to stream flow (45-57%) in ephemeral streams where flows were dominated by stormflow. Overland flow contribution to stream flow decreased in importance with increasing watershed area, from 21 to 57% in forest and 60-89% in pasture watersheds of less than 10 ha to 0% in forest and 27-28% in pastures in watersheds greater than 100 ha. Soil solution contributions to stream flow were similar across watershed area and groundwater inputs generally increased in proportion to decreases in overland flow. Application of EMMA across multiple watersheds indicated patterns across gradients of stream size and land cover that were consistent with patterns determined by detailed hydrometric sampling.

Fretting fatigue in overhead conductors: Rig design and failure analysis of a Grosbeak aluminium cable steel reinforced conductor

The performance optimisation of overhead conductors depends on the systematic investigation of the fretting fatigue mechanisms in the conductor/clamping system. As a consequence, a fretting fatigue rig was designed and a limited range of fatigue tests was carried out at the middle high cycle fatigue regime in order to access an exploratory S-N curve for a Grosbeak conductor, which was mounted on a mono-articulated aluminium clamping system. Subsequent to these preliminary fatigue tests, the components of the conductor/clamping system, such as ACSR conductor, upper and lower clamps, bolt and nuts, were subjected to a failure analysis procedure in order to investigate the metallurgical free variables interfering on the fatigue test results, aiming at the optimisation of the testing reproducibility. The results indicated that the rupture of the planar fracture surfaces observed in the external At strands of the conductor tested under lower bending amplitude (0.9 mm) occurred by fatigue cracking (I mm deep), followed by shear overload. The V-type fracture surfaces observed in some At strands of the conductor tested under higher bending amplitude (1.3 mm) were also produced by fatigue cracking (approximately 400 mu m deep), followed by shear overload. Shear overload fracture (45 degrees fracture surface) was also observed on the remaining At wires of the conductor tested under higher bending amplitude (1.3 mm). Additionally, the upper and lower Al-cast clamps presented microstructure-sensitive cracking, which was folowed by particle detachment and formation of abrasive debris on the clamp/conductor tribo-interface, promoting even further the fretting mechanism. The detrimental formation of abrasive debris might be inhibited by the selection of a more suitable class of as-cast At alloy for the production of clamps. Finally, the bolt/nut system showed intense degradation of the carbon steel nut (fabricated in ferritic-pearlitic carbon steel, featuring machined threads with 190 HV), with intense plastic deformation and loss of material. Proper selection of both the bolt and nut materials and the finishing processing might prevent the loss in the clamping pressure during the fretting testing. It is important to control the specification of these components (clamps, bolt and nuts) prior to the start of large scale fretting fatigue testing of the overhead conductors in order to increase the reproducibility of this assessment. (c) 2008 Elsevier Ltd. All rights reserved.

Strategies for genetic model specification in the screening of genome-wide meta-analysis signals for further replication

Background Meta-analysis is increasingly being employed as a screening procedure in large-scale association studies to select promising variants for follow-up studies. However, standard methods for meta-analysis require the assumption of an underlying genetic model, which is typically unknown a priori. This drawback can introduce model misspecifications, causing power to be suboptimal, or the evaluation of multiple genetic models, which augments the number of false-positive associations, ultimately leading to waste of resources with fruitless replication studies. We used simulated meta-analyses of large genetic association studies to investigate naive strategies of genetic model specification to optimize screenings of genome-wide meta-analysis signals for further replication. Methods Different methods, meta-analytical models and strategies were compared in terms of power and type-I error. Simulations were carried out for a binary trait in a wide range of true genetic models, genome-wide thresholds, minor allele frequencies (MAFs), odds ratios and between-study heterogeneity (tau(2)). Results Among the investigated strategies, a simple Bonferroni-corrected approach that fits both multiplicative and recessive models was found to be optimal in most examined scenarios, reducing the likelihood of false discoveries and enhancing power in scenarios with small MAFs either in the presence or in absence of heterogeneity. Nonetheless, this strategy is sensitive to tau(2) whenever the susceptibility allele is common (MAF epsilon 30%), resulting in an increased number of false-positive associations compared with an analysis that considers only the multiplicative model. Conclusion Invoking a simple Bonferroni adjustment and testing for both multiplicative and recessive models is fast and an optimal strategy in large meta-analysis-based screenings. However, care must be taken when examined variants are common, where specification of a multiplicative model alone may be preferable.

XPC polymorphisms play a role in tissue-specific carcinogenesis: a meta-analysis

XPC participates in the initial recognition of DNA damage during the DNA nucleotide excision repair process in global genomic repair. Polymorphisms in XPC gene have been analyzed in case-control studies to assess the cancer risk attributed to these variants, but results are conflicting. To clarify the impact of XPC polymorphisms in cancer risk, we performed a meta-analysis that included 33 published case-control studies. Polymorphisms analyzed were Lys939Gln and Ala499Val. The overall summary odds ratio (OR) for the associations of the 939Gln/Gln genotype with risk of cancer was 1.01 (95% confidence interval (95% CI): 0.94-1.09), but there were statistically significant associations for lung cancer, observed for the recessive genetic model (Lys/Lys + Lys/Gln vs Gln/Gln), (OR 1.30; 95% CI: 1.113-1.53), whereas for breast cancer a reduced but nonsignificant risk was observed for the same model (OR 0.87; 95% CI: 0.74-1.01). The results for Ala499Val showed a significant overall increase in cancer risk (OR 1.15; 95% CI: 1.02-1.31), and for bladder cancer in both the simple genetic model (Ala/Ala vs Val/Val) (OR 1.30; 95% CI: 1.04-1.61) and the recessive genetic model (Ala/Ala + Ala/Val vs Val/Val) (OR 1.32; 95% CI: 1.06-1.63). Our meta-analysis supports that polymorphisms in XPC may represent low-penetrance susceptibility gene variants for breast, bladder, head and neck, and lung cancer. XPC is a good candidate for large-scale epidemiological case-control studies that may lead to improvement in the management of highly prevalent cancers.

Analysis of the Nicotiana tabacum Stigma/Style Transcriptome Reveals Gene Expression Differences between Wet and Dry Stigma Species

The success of plant reproduction depends on pollen-pistil interactions occurring at the stigma/style. These interactions vary depending on the stigma type: wet or dry. Tobacco (Nicotiana tabacum) represents a model of wet stigma, and its stigmas/styles express genes to accomplish the appropriate functions. For a large-scale study of gene expression during tobacco pistil development and preparation for pollination, we generated 11,216 high-quality expressed sequence tags (ESTs) from stigmas/styles and created the TOBEST database. These ESTs were assembled in 6,177 clusters, from which 52.1% are pistil transcripts/genes of unknown function. The 21 clusters with the highest number of ESTs (putative higher expression levels) correspond to genes associated with defense mechanisms or pollen-pistil interactions. The database analysis unraveled tobacco sequences homologous to the Arabidopsis (Arabidopsis thaliana) genes involved in specifying pistil identity or determining normal pistil morphology and function. Additionally, 782 independent clusters were examined by macroarray, revealing 46 stigma/style preferentially expressed genes. Real-time reverse transcription-polymerase chain reaction experiments validated the pistil-preferential expression for nine out of 10 genes tested. A search for these 46 genes in the Arabidopsis pistil data sets demonstrated that only 11 sequences, with putative equivalent molecular functions, are expressed in this dry stigma species. The reverse search for the Arabidopsis pistil genes in the TOBEST exposed a partial overlap between these dry and wet stigma transcriptomes. The TOBEST represents the most extensive survey of gene expression in the stigmas/styles of wet stigma plants, and our results indicate that wet and dry stigmas/styles express common as well as distinct genes in preparation for the pollination process.

The Genetics of Alzheimer`s Disease in Brazil: 10 Years of Analysis in a Unique Population

Alzheimer`s Disease (AD) is the most common type of dementia among the elderly, with devastating consequences for the patient, their relatives, and caregivers. More than 300 genetic polymorphisms have been involved with AD, demonstrating that this condition is polygenic and with a complex pattern of inheritance. This paper aims to report and compare the results of AD genetics studies in case-control and familial analysis performed in Brazil since our first publication, 10 years ago. They include the following genes/markers: Apolipoprotein E (APOE), 5-hidroxytryptamine transporter length polymorphic region (5-HTTLPR), brain-derived neurotrophin factor (BDNF), monoamine oxidase A (MAO-A), and two simple-sequence tandem repeat polymorphisms (DXS1047 and D10S1423). Previously unpublished data of the interleukin-1 alpha (IL-1 alpha) and interleukin-1 beta (IL-1 beta) genes are reported here briefly. Results from others Brazilian studies with AD patients are also reported at this short review. Four local families studied with various markers at the chromosome 21, 19, 14, and 1 are briefly reported for the first time. The importance of studying DNA samples from Brazil is highlighted because of the uniqueness of its population, which presents both intense ethnical miscegenation, mainly at the east coast, but also clusters with high inbreeding rates in rural areas at the countryside. We discuss the current stage of extending these studies using high-throughput methods of large-scale genotyping, such as single nucleotide polymorphism microarrays, associated with bioinformatics tools that allow the analysis of such extensive number of genetics variables, with different levels of penetrance. There is still a long way between the huge amount of data gathered so far and the actual application toward the full understanding of AD, but the final goal is to develop precise tools for diagnosis and prognosis, creating new strategies for better treatments based on genetic profile.

Monodisperse lignin fractions as standards in size-exclusion analysis Comparison with polystyrene standards

The difficulty of preparing monodisperse lignin fractions on a large scale is a limiting factor in many applications. The present paper addresses this problem by examining the properties and size-exclusion behavior of lignin isolated by the acetosolv pulping process from post-extraction crushed sugarcane bagasse. The isolated lignin was subjected to a solvent pretreatment, followed by preparative gel permeation chromatography fractionation. The fractions were analyzed by high-performance size-exclusion chromatography (HPSEC) and these samples showed a great decrease in polydispersity, compared to the original acetosolv lignin. Several fractions of very low polydispersity, close to unity, were employed as calibration curve standards in HPSEC analysis. This original analytical approach allowed calibration with these lignin fractions to be compared with the polystyrene standards that are universally employed for lignin molecular mass determination. This led to a noteworthy result, namely that the lignin fractions and polystyrene standards showed very similar behavior over a large range of molecular masses in a typical HPSEC analysis of acetosolv lignin. (C) 2009 Elsevier B.V. All rights reserved.

Características sociodemográficas da mortalidade por câncer de boca em Bauru, SP, no período de 1991 a 2001: uso de geoprocessamento

O objetivo deste estudo foi avaliar as taxas de mortalidade por câncer de boca no período de 1991-2001, no município de Bauru-SP. A fonte de informação utilizada para o reconhecimento e seleção da população-alvo foram Certidões de Óbito dos Cartórios do município de Bauru com dados relativos ao período 1991-2001. Foram coletadas informações referentes a sexo, idade, localização da lesão e endereço. A coleta dos endereços visou à identificação no mapa do município de Bauru da localização geográfica do domicílio. Utilizando ferramentas do geoprocessamento, foi feita a inserção no mapa dos casos identificados. Foram registrados 67 casos de morte por câncer de boca na cidade de Bauru entre 1991 e 2001, com maiores taxas no sexo masculino e sexta década de vida. A análise da distribuição espacial mostra que a maioria dos casos encontra-se próxima à linha férrea que corta o município e foi responsável, em grande parte, pela ocupação territorial pela população, sendo esta também uma área que abrange os bairros mais antigos do município. O câncer de boca constitui importante causa de óbito no município, requerendo um planejamento de ações georreferenciadas pelo sistema local de saúde.

Time evolution of the South Atlantic Magnetic Anomaly

The South Atlantic Magnetic Anomaly (SAMA) is one of the most outstanding anomalies of the geomagnetic field. The SAMA secular variation was obtained and compared to the evolution of other anomalies using spherical harmonic field models for the 1590-2005 period. An analysis of data from four South American observatories shows how this large scale anomaly affected their measurements. Since SAMA is a low total field anomaly, the field was separated into its nondipolar, quadrupolar and octupolar parts. The time evolution of the non-dipole/total, quadrupolar/total and octupolar/total field ratios yielded increasingly high values for the South Atlantic since 1750. The SAMA evolution is compared to the evolution of other large scale surface geomagnetic features like the North and the South Pole and the Siberia High, and this comparison shows the intensity equilibrium between these anomalies in both hemispheres. The analysis of non-dipole fields in historical period suggests that SAMA is governed by (i) quadrupolar field for drift, and (ii) quadrupolar and octupolar fields for intensity and area of influence. Furthermore, our study reinforces the possibility that SAMA may be related to reverse fluxes in the outer core under the South Atlantic region.

Anomalous somatic embryos in Acca sellowiana (O. Berg) Burret (Myrtaceae)

Somatic embryogenesis represents a valuable tool for the studies on the basic aspects of plant embryo development. Today this process is used as a potencial technique for large-scale plant micropropagation although, so far, it has been applied to only a small number of species. However, when somatic embryos are malformed they are considered economically useless. In Acca sellowiana (O. Berg) Burret, an important fruit-producing crop, large amounts of anomalous somatic embryos (76.3%) were found just after 40 days of culture of explants in a 2,4-D containing medium. Among the anomalous forms found in the cotiledonary stage, 12.2% consisted of fused embryos, 40.4% displayed fused cotyledons, 13.0% presented supernumerary cotyledons, and 10.7% showed absence or poorly developed cotyledons, including those without the shoot apical meristem. Histological analyses indicated that the altered embryos were formed either directly from cotyledons, hypocotyl and radicle of the zygotic embryos used as explants, or indirectly from calli formed from these tissue parts. It is suggested that the formation of anomalous somatic embryos, as well as a low frequency of conversion into emblings reflect physiological and/or genetic disturbances triggered by the presence of 2,4-D in the medium. In vitro experimental alternative approaches are discussed in order to lessen the occurrence of malformed somatic embryos.

High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

Background: High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. Results: We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species. SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. Conclusions: This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity >= 2%. The development of a much larger array of informative SNPs across multiple Eucalyptus species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in Eucalyptus.

Poly (A)(+) Transcriptome Assessment of ERBB2-Induced Alterations in Breast Cell Lines

We report the first quantitative and qualitative analysis of the poly (A)(+) transcriptome of two human mammary cell lines, differentially expressing (human epidermal growth factor receptor) an oncogene over-expressed in approximately 25% of human breast tumors. Full-length cDNA populations from the two cell lines were digested enzymatically, individually tagged according to a customized method for library construction, and simultaneously sequenced by the use of the Titanium 454-Roche-platform. Comprehensive bioinformatics analysis followed by experimental validation confirmed novel genes, splicing variants, single nucleotide polymorphisms, and gene fusions indicated by RNA-seq data from both samples. Moreover, comparative analysis showed enrichment in alternative events, especially in the exon usage category, in ERBB2 over-expressing cells, data indicating regulation of alternative splicing mediated by the oncogene. Alterations in expression levels of genes, such as LOX, ATP5L, GALNT3, and MME revealed by large-scale sequencing were confirmed between cell lines as well as in tumor specimens with different ERBB2 backgrounds. This approach was shown to be suitable for structural, quantitative, and qualitative assessment of complex transcriptomes and revealed new events mediated by ERBB2 overexpression, in addition to potential molecular targets for breast cancer that are driven by this oncogene.

The role of the observed tropical convection in the generation of frost events in the southern cone of South America

Based on previous results obtained from observations and linear wave theory analysis, the hypothesis that large-scale patterns can generate extreme cold events in southeast South America through the propagation of remotely excited Rossby waves was already suggested. This work will confirm these findings and extend their analysis through a series of numerical experiments using a primitive equation model where waves are excited by a thermal forcing situated in positions chosen according to observed convection anomalies over the equatorial region. The basic state used for these experiments is a composite of austral winters with maximum and minimum frequency of occurrence of generalized frosts that can affect a large area known as the Wet Pampas located in the central and eastern part of Argentina. The results suggest that stationary Rossby waves may be one important mechanism linking anomalous tropical convection with the extreme cold events in the Wet Pampas. The combination of tropical convection and a specific basic state can generate the right environment to guide the Rossby waves trigged by the tropical forcing towards South America. Depending on the phase of the waves entering the South American continent, they can favour the advection of anomalous wind at low levels from the south carrying cold and dry air over the whole southern extreme of the continent, producing a generalized frost in the Wet Pampa region. On the other hand, when a basic state based on the composites of minimum frosts is used, an anomalous anticyclone over the southern part of the continent generates a circulation with a south-southeast wind which brings maritime air and therefore humidity over the Wet Pampas region, creating negative temperature anomalies only over the northeastern part of the region. Under these conditions even if frosts occur they would not be generalized, as observed for the other basic state with maximum frequency of occurrence of generalized frosts.

Constraints on cold dark matter accelerating cosmologies and cluster formation

We discuss the properties of homogeneous and isotropic flat cosmologies in which the present accelerating stage is powered only by the gravitationally induced creation of cold dark matter (CCDM) particles (Omega(m) = 1). For some matter creation rates proposed in the literature, we show that the main cosmological functions such as the scale factor of the universe, the Hubble expansion rate, the growth factor, and the cluster formation rate are analytically defined. The best CCDM scenario has only one free parameter and our joint analysis involving baryonic acoustic oscillations + cosmic microwave background (CMB) + SNe Ia data yields (Omega) over tilde = 0.28 +/- 0.01 (1 sigma), where (Omega) over tilde (m) is the observed matter density parameter. In particular, this implies that the model has no dark energy but the part of the matter that is effectively clustering is in good agreement with the latest determinations from the large- scale structure. The growth of perturbation and the formation of galaxy clusters in such scenarios are also investigated. Despite the fact that both scenarios may share the same Hubble expansion, we find that matter creation cosmologies predict stronger small scale dynamics which implies a faster growth rate of perturbations with respect to the usual Lambda CDM cosmology. Such results point to the possibility of a crucial observational test confronting CCDM with Lambda CDM scenarios through a more detailed analysis involving CMB, weak lensing, as well as the large-scale structure.