Spectral Region Optimization for Raman-Based Optical Biopsy of Inflammatory Lesions

Objective: The biochemical alterations between inflammatory fibrous hyperplasia (IFH) and normal tissues of buccal mucosa were probed by using the FT-Raman spectroscopy technique. The aim was to find the minimal set of Raman bands that would furnish the best discrimination. Background: Raman-based optical biopsy is a widely recognized potential technique for noninvasive real-time diagnosis. However, few studies had been devoted to the discrimination of very common subtle or early pathologic states as inflammatory processes that are always present on, for example, cancer lesion borders. Methods: Seventy spectra of IFH from 14 patients were compared with 30 spectra of normal tissues from six patients. The statistical analysis was performed with principal components analysis and soft independent modeling class analogy cross-validated, leave-one-out methods. Results: Bands close to 574, 1,100, 1,250 to 1,350, and 1,500 cm(-1) (mainly amino acids and collagen bands) showed the main intragroup variations that are due to the acanthosis process in the IFH epithelium. The 1,200 (C-C aromatic/DNA), 1,350 (CH(2) bending/collagen 1), and 1,730 cm(-1) (collagen III) regions presented the main intergroup variations. This finding was interpreted as originating in an extracellular matrix-degeneration process occurring in the inflammatory tissues. The statistical analysis results indicated that the best discrimination capability (sensitivity of 95% and specificity of 100%) was found by using the 530-580 cm(-1) spectral region. Conclusions: The existence of this narrow spectral window enabling normal and inflammatory diagnosis also had useful implications for an in vivo dispersive Raman setup for clinical applications.

The full Bayesian significance test for mixture models: results in gene expression clustering

Gene clustering is a useful exploratory technique to group together genes with similar expression levels under distinct cell cycle phases or distinct conditions. It helps the biologist to identify potentially meaningful relationships between genes. In this study, we propose a clustering method based on multivariate normal mixture models, where the number of clusters is predicted via sequential hypothesis tests: at each step, the method considers a mixture model of m components (m = 2 in the first step) and tests if in fact it should be m - 1. If the hypothesis is rejected, m is increased and a new test is carried out. The method continues (increasing m) until the hypothesis is accepted. The theoretical core of the method is the full Bayesian significance test, an intuitive Bayesian approach, which needs no model complexity penalization nor positive probabilities for sharp hypotheses. Numerical experiments were based on a cDNA microarray dataset consisting of expression levels of 205 genes belonging to four functional categories, for 10 distinct strains of Saccharomyces cerevisiae. To analyze the method's sensitivity to data dimension, we performed principal components analysis on the original dataset and predicted the number of classes using 2 to 10 principal components. Compared to Mclust (model-based clustering), our method shows more consistent results.

Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes

Background: Prostate cancer cells in primary tumors have been typed CD10(-)/CD13(-)/CD24(hi)/CD26(+)/CD38(lo)/CD44(-)/CD104(-). This CD phenotype suggests a lineage relationship between cancer cells and luminal cells. The Gleason grade of tumors is a descriptive of tumor glandular differentiation. Higher Gleason scores are associated with treatment failure. Methods: CD26(+) cancer cells were isolated from Gleason 3+3 (G3) and Gleason 4+4 (G4) tumors by cell sorting, and their gene expression or transcriptome was determined by Affymetrix DNA array analysis. Dataset analysis was used to determine gene expression similarities and differences between G3 and G4 as well as to prostate cancer cell lines and histologically normal prostate luminal cells. Results: The G3 and G4 transcriptomes were compared to those of prostatic cell types of non-cancer, which included luminal, basal, stromal fibromuscular, and endothelial. A principal components analysis of the various transcriptome datasets indicated a closer relationship between luminal and G3 than luminal and G4. Dataset comparison also showed that the cancer transcriptomes differed substantially from those of prostate cancer cell lines. Conclusions: Genes differentially expressed in cancer are potential biomarkers for cancer detection, and those differentially expressed between G3 and G4 are potential biomarkers for disease stratification given that G4 cancer is associated with poor outcomes. Differentially expressed genes likely contribute to the prostate cancer phenotype and constitute the signatures of these particular cancer cell types.

Musical genres: beating to the rhythms of different drums

Online music databases have increased significantly as a consequence of the rapid growth of the Internet and digital audio, requiring the development of faster and more efficient tools for music content analysis. Musical genres are widely used to organize music collections. In this paper, the problem of automatic single and multi-label music genre classification is addressed by exploring rhythm-based features obtained from a respective complex network representation. A Markov model is built in order to analyse the temporal sequence of rhythmic notation events. Feature analysis is performed by using two multi-variate statistical approaches: principal components analysis (unsupervised) and linear discriminant analysis (supervised). Similarly, two classifiers are applied in order to identify the category of rhythms: parametric Bayesian classifier under the Gaussian hypothesis (supervised) and agglomerative hierarchical clustering (unsupervised). Qualitative results obtained by using the kappa coefficient and the obtained clusters corroborated the effectiveness of the proposed method.

Bacterial community in the rhizosphere and rhizoplane of wild type and transgenic eucalyptus

The rhizosphere is a niche exploited by a wide variety of bacteria. The expression of heterologous genes by plants might become a factor affecting the structure of bacterial communities in the rhizosphere. In a greenhouse experiment, the bacterial community associated to transgenic eucalyptus, carrying the Lhcb1-2 genes from pea (responsible for a higher photosynthetic capacity), was evaluated. The culturable bacterial community associated to transgenic and wild type plants were not different in density, and the Amplified Ribosomal DNA Restriction Analysis (ARDRA) typing of 124 strains revealed dominant ribotypes representing the bacterial orders Burkholderiales, Rhizobiales, and Actinomycetales, the families Xanthomonadaceae, and Bacillaceae, and the genus Mycobacterium. Principal Component Analysis based on the fingerprints obtained by culture-independent Denaturing Gradient Gel Electrophoresis analysis revealed that Alphaproteobacteria, Betaproteobacteria and Actinobacteria communities responded differently to plant genotypes. Similar effects for the cultivation of transgenic eucalyptus to those observed when two genotype-distinct wild type plants are compared.

Culture-Independent Assessment of Rhizobiales-Related Alphaproteobacteria and the Diversity of Methylobacterium in the Rhizosphere and Rhizoplane of Transgenic Eucalyptus

The rhizosphere is an ecosystem exploited by a variety of organisms involved in plant health and environmental sustainability. Abiotic factors influence microorganism-plant interactions, but the microbial community is also affected by expression of heterologous genes from host plants. In the present work, we assessed the community shifts of Alphaproteobacteria phylogenetically related to the Rhizobiales order (Rhizobiales-like community) in rhizoplane and rhizosphere soils of wild-type and transgenic eucalyptus. A greenhouse experiment was performed and the bacterial communities associated with two wild-type (WT17 and WT18) and four transgenic (TR-9, TR-15, TR-22, and TR-23) eucalyptus plant lines were evaluated. The culture-independent approach consisted of the quantification, by real-time polymerase chain reaction (PCR), of a targeted subset of Alphaproteobacteria and the assessment of its diversity using PCR-denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone libraries. Real-time quantification revealed a lesser density of the targeted community in TR-9 and TR-15 plants and diversity analysis by principal components analysis, based on PCR-DGGE, revealed differences between bacterial communities, not only between transgenic and nontransgenic plants, but also among wild-type plants. The comparison between clone libraries obtained from the transgenic plant TR-15 and wild-type WT17 revealed distinct bacterial communities associated with these plants. In addition, a culturable approach was used to quantify the Methylobacterium spp. in the samples where the identification of isolates, based on 16S rRNA gene sequences, showed similarities to the species Methylobacterium nodulans, Methylobacterium isbiliense, Methylobacterium variable, Methylobacterium fujisawaense, and Methylobacterium radiotolerans. Colonies classified into this genus were not isolated from the rhizosphere but brought in culture from rhizoplane samples, except for one line of the transgenic plants (TR-15). In general, the data suggested that, in most cases, shifts in bacterial communities due to cultivation of transgenic plants are similar to those observed when different wild-type cultivars are compared, although shifts directly correlated to transgenic plant cultivation may be found.

Transgenic tobacco revealing altered bacterial diversity in the rhizosphere during early plant development

The rhizosphere constitutes a complex niche that may be exploited by a wide variety of bacteria. Bacterium-plant interactions in this niche can be influenced by factors such as the expression of heterologous genes in the plant. The objective of this work was to describe the bacterial communities associated with the rhizosphere and rhizoplane regions of tobacco plants, and to compare communities from transgenic tobacco lines (CAB1, CAB2 and TRP) with those found in wild-type (WT) plants. Samples were collected at two stages of plant development, the vegetative and flowering stages (1 and 3 months after germination). The diversity of the culturable microbial community was assessed by isolation and further characterization of isolates by amplified ribosomal RNA gene restriction analysis (ARDRA) and 16S rRNA sequencing. These analyses revealed the presence of fairly common rhizosphere organisms with the main groups Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacilli. Analysis of the total bacterial communities using PCR-DGGE (denaturing gradient gel electrophoresis) revealed that shifts in bacterial communities occurred during early plant development, but the reestablishment of original community structure was observed over time. The effects were smaller in rhizosphere than in rhizoplane samples, where selection of specific bacterial groups by the different plant lines was demonstrated. Clustering patterns and principal components analysis (PCA) were used to distinguish the plant lines according to the fingerprint of their associated bacterial communities. Bands differentially detected in plant lines were found to be affiliated with the genera Pantoea, Bacillus and Burkholderia in WT, CAB and TRP plants, respectively. The data revealed that, although rhizosphere/rhizoplane microbial communities can be affected by the cultivation of transgenic plants, soil resilience may be able to restore the original bacterial diversity after one cycle of plant cultivation.

Reliability and validity of scores on scales to measure managerial aspirations

The present investigation assessed the reliability and validity of the scores of a subjective measure of desired aspirations and a behavioral measure of enacted aspirations. A sample of 5,655 employees was randomly split into two halves. Principal components analysis on Sample 1, followed by confirmatory factor analysis on Sample 2, confirmed the desired and enacted scales as distinct but related measures of managerial aspirations. The desired and enacted scales had satisfactory levels of internal consistency and temporal stability over a 1-year period. Relationships between the measures of desired and enacted managerial aspirations and both attitudinal and behavioral criteria, measured concurrently and 1 year later, provided preliminary support for convergent and discriminant validity for our sample. Desired aspirations demonstrated stronger validity than enacted aspirations. Although further examination of the psychometric properties of the scales is warranted, the present findings provide promising support for their validity and reliability for our sample.

Limited ecoclinal variation found in Malva parviflora (small-flowered mallow) across the Mediterranean-climatic agricultural region of Western Australia

Malva parviflora L. populations were collected from 24 locations across the Mediterranean-climatic agricultural region of Western Australia and grown in Perth in a common garden experiment. Seventeen morphometric and taxonomic measurements were taken and genetic variation was investigated by performing principal components analysis (PCA). Taxonomic measurements confirmed that all plants used in the study were M. parviflora. Greater variation occurred within populations than between populations. Separation between populations was only evident between northern and southern populations along principal components 2 (PC2), which was due mainly to flowering time. Flowering time and consequently photoperiod were highly correlated with latitude and regression analysis revealed a close relationship (r(2) = 0.6). Additionally, the pollination system of M. parviflora was examined. Plants were able to self-pollinate without the need for external vectors and the pollen ovule ratio (31 +/- 1.3) revealed that M. parviflora is most likely to be an obligate inbreeder with a slight potential for outcrossing. The limited variation of M. parviflora enhances the likelihood of suitable control strategies being effective across a broad area.

The phylogeography of African Brazilians

Background/Aims: Approximately four million Africans were taken as slaves to Brazil, where they interbred extensively with Amerindians and Europeans. We have previously shown that while most White Brazilians carry Y chromosomes of European origin, they display high proportions of African and Amerindian mtDNA lineages, because of sex-biased genetic admixture. Methods: We studied the Y chromosome and mtDNA haplogroup structure of 120 Black males from Sao Paulo, Brazil. Results: Only 48% of the Y chromosomes, but 85% of the mtDNA haplogroups were characteristic of sub-Saharan Africa, confirming our previous observation of sexually biased mating. We mined literature data for mtDNA and Y chromosome haplogroup frequencies for African native populations from regions involved in Atlantic Slave Trade. Principal Components Analysis and Bayesian analysis of population structure revealed no genetic differentiation of Y chromosome marker frequencies between the African regions. However, mtDNA examination unraveled considerable genetic structure, with three clusters at Central-West Africa, West Africa and Southeast Africa. A hypothesis is proposed to explain this structure. Conclusion: Using these mtDNA data we could obtain for the first time an estimate of the relative ancestral contribution of Central-West (0.445), West (0.431) and Southeast Africa (0.123) to African Brazilians from Sao Paulo. These estimates are consistent with historical information. Copyright (c) 2008 S. Karger AG, Basel.

Diagnostic model based on Raman spectra of normal, hyperplasia and prostate adenocarcinoma tissues in vitro

This study evaluated the use of Raman spectroscopy to identify the spectral differences between normal (N), benign hyperplasia (BPH) and adenocarcinoma (CaP) in fragments of prostate biopsies in vitro with the aim of developing a spectral diagnostic model for tissue classification. A dispersive Raman spectrometer was used with 830 nm wavelength and 80 mW excitation. Following Raman data collection and tissue histopathology (48 fragments diagnosed as N, 43 as BPH and 14 as CaP), two diagnostic models were developed in order to extract diagnostic information: the first using PCA and Mahalanobis analysis techniques and the second one a simplified biochemical model based on spectral features of cholesterol, collagen, smooth muscle cell and adipocyte. Spectral differences between N, BPH and CaP tissues, were observed mainly in the Raman bands associated with proteins, lipids, nucleic and amino acids. The PCA diagnostic model showed a sensitivity and specificity of 100%, which indicates the ability of PCA and Mahalanobis distance techniques to classify tissue changes in vitro. Also, it was found that the relative amount of collagen decreased while the amount of cholesterol and adipocyte increased with severity of the disease. Smooth muscle cell increased in BPH tissue. These characteristics were used for diagnostic purposes.

PM(2.5) and PM(10): The influence of sugarcane burning on potential cancer risk

In Brazil, sugarcane fields are often burned to facilitate manual harvesting, and this burning causes environmental pollution from the large amounts of soot released into the atmosphere. This material contains numerous organic compounds such as PAHs. In this study, the concentrations of PAHs in two particulate-matter fractions (PM(2.5) and PM(10)) in the city of Araraquara (SE Brazil, with around 200,000 inhabitants and surrounded by sugarcane plantations) were determined during the sugarcane harvest (HV) and non-harvest (NHV) seasons in 2008 and 2009. The sampling strategy included four campaigns, with 60 samples in the NHV season and 220 samples in the HV season. The PM(2.5) and PM(10) fractions were collected using a dichotomous sampler (10 L min(-1), 24 h) with Teflon (TM) filters. The filter sets were extracted (ultrasonic bath with hexane/acetone (1:1 v/v)) and analyzed by HPLC/Fluorescence. The median concentration for total PAHs (PM(2.5) in 2009) was 0.99 ng m(-3) (NHV) and 3.3 ng m(-3) (HV). In the HV season, the total concentration of carcinogenic PAHs (benz(a)anthracene, benzo(b)fluoranthene, benzo(k)fluoranthene, and benzo(a)pyrene) was 5 times higher than in the NHV season. B(a)P median concentrations were 0.017 ng m(-3) and 0.12 ng m(-3) for the NHV and HV seasons, respectively. The potential cancer risk associated with exposure through inhalation of these compounds was estimated based on the benzo[a]pyrene toxic equivalence (BaP(eq)), where the overall toxicity of a PAR mixture is defined by the concentration of each compound multiplied by its relative toxic equivalence factor (TEF). BaP(eq) median (2008 and 2009 years) ranged between 0.65 and 1.0 ng m(-3) and 1.2-1.4 ng m(-3) for the NHV and HV seasons, respectively. Considering that the maximum permissible BaPeq in ambient air is 1 ng m(-3), related to the increased carcinogenic risk, our data suggest that the level of human exposure to PAHs in cities surrounded by sugarcane crops where the burning process is used is cause for concern. (C) 2010 Published by Elsevier Ltd.

Reliability and validity of the Brazilian-Portuguese version of the Burns Specific Pain Anxiety Scale (BSPAS)

Background: Pain and anxiety are a common problem in all recovery phases after a burn. The Burns Specific Pain Anxiety Scale (BSPAS) was proposed to assess anxiety in burn patients related to painful procedures. Objectives: To assess internal consistency, discriminative construct validity, dimensionality and convergent construct validity of the Brazilian-Portuguese version of the Burns Specific Pain Anxiety Scale. Design: In this cross-sectional study, the original version of the BSPAS, adapted into Brazilian Portuguese, was tested for internal consistency (Cronbach`s Alpha), discriminative validity (related to total body surface area burned and sex), dimensionality (through factor analysis), and convergent construct validity (applying the Visual Analogue Scale for pain and State-Anxiety-STAI) in a group of 91 adult burn patients. Results: The adapted version of the BSPAS displayed a moderate and positive correlation with pain assessments: immediately before baths and dressings (r = 0.32; p < 0.001), immediately after baths and dressings (r = 0.31; p < 0.001) and during the relaxation period (r= 0.31; p < 0.001) and with anxiety assessments (r = 0.34; p < 0.001). No statistically significant differences were observed when comparing the mean of the adapted version of the BSPAS scores with sex (p = 0.194) and total body surface area burned (p = 0.162) (discriminative validity). The principal components analysis applied to our sample seems to confirm anxiety as one single domain of the Brazilian-Portuguese version of the BSPAS. Cronbach`s Alpha showed high internal consistency of the adapted version of the scale (0.90). Conclusion: The Brazilian-Portuguese version of the BSPAS 9-items has shown statically acceptable levels of reliability and validity for pain-related anxiety evaluation in burn patients. This scale can be used to assess nursing interventions aimed at decreasing pain and anxiety related to the performance of painful procedures. (c) 2010 Elsevier Ltd. All rights reserved.

Spatial and temporal patterns in Australian wheat yield and their relationship with ENSO

Spatial and temporal variability in wheat production in Australia is dominated by rainfall occurrence. The length of historical production records is inadequate, however, to analyse spatial and temporal patterns conclusively. In this study we used modelling and simulation to identify key spatial patterns in Australian wheat yield, identify groups of years in the historical record in which spatial patterns were similar, and examine association of those wheat yield year groups with indicators of the El Nino Southern Oscillation (ENSO). A simple stress index model was trained on 19 years of Australian Bureau of Statistics shire yield data (1975-93). The model was then used to simulate shire yield from 1901 to 1999 for all wheat-producing shires. Principal components analysis was used to determine the dominating spatial relationships in wheat yield among shires. Six major components of spatial variability were found. Five of these represented near spatially independent zones across the Australian wheatbelt that demonstrated coherent temporal (annual) variability in wheat yield. A second orthogonal component was required to explain the temporal variation in New South Wales. The principal component scores were used to identify high- and low-yielding years in each zone. Year type groupings identified in this way were tested for association with indicators of ENSO. Significant associations were found for all zones in the Australian wheatbelt. Associations were as strong or stronger when ENSO indicators preceding the wheat season (April-May phases of the Southern Oscillation Index) were used rather than indicators based on classification during the wheat season. Although this association suggests an obvious role for seasonal climate forecasting in national wheat crop forecasting, the discriminatory power of the ENSO indicators, although significant, was not strong. By examining the historical years forming the wheat yield analog sets within each zone, it may be possible to identify novel climate system or ocean-atmosphere features that may be causal and, hence, most useful in improving seasonal forecasting schemes.

??ndice de gest??o municipal em cultura

O objetivo deste trabalho ?? o de construir um ??ndice de gest??o municipal em cultura, com o potencial de servir de balizador para as a????es nesta ??rea tanto no ??mbito municipal quanto no das esferas estaduais e federal. Para tanto s??o utilizados dados do ???Perfil dos Munic??pios Brasileiros ??? Cultura 2006???, publicado pelo IBGE, o qual disp??e das respostas de 5.562 munic??pios sobre cultura e gest??o cultural. As respostas foram tabuladas e combinadas de forma a produzir vari??veis espec??ficas para a constru????o do ??ndice. O m??todo utilizado para a constru????o do ??ndice de Gest??o Municipal em Cultura (IGMC) foi o de an??lise de componentes principais, que permite ?? pr??pria amostra definir os pesos que cada vari??vel exercer?? na computa????o do ??ndice final. Al??m do IGMC geral, foram computados no processo tr??s sub??ndices, cada um deles procurando refletir um aspecto espec??fico da gest??o municipal em cultura, a saber: fortalecimento institucional e gest??o democr??tica, infraestrutura e recursos humanos, e a????o cultural. Os resultados obtidos permitem diversos tipos de compara????es intermunicipais e regionais, bem como a prescri????o de a????es locais na ??rea de gest??o que visem ?? melhoria da administra????o cultural dos munic??pios.