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.

Descriptions and phylogenetic significance of the fronto-lateral gland pores and dorsal lattice organs of cyprid larvae of seven species of barnacles (Cirripedia : Thoracica : Pedunculata)

The paired fronto-lateral gland pores and lattice organs (LO1, 2, 3, 4, and 5) of seven species of pedunculate barnacles belonging to two thoracican suborders, Heteralepadomorpha (family Heteralepadidae: Heteralepas sp. 1 and 2) and Lepadomorpha (families Poecilasmatidae: Poecilasma inaequilaterale and Octolasmis aymonini geryonophila and Lepadidae: Lepas pacifica, Dosima fascicularis, and Conchoderma virgatum), were investigated by scanning electron microscopy (SEM). While the fronto-lateral gland pores exhibit slight variation among species, with only L. pacifica showing a different morphology, the variations in the arrangement of LOs are phylogenetically instructive. The lattice organs in the foregoing species correspond in general to the inferred advanced type (Type C), but the distinct keel in the pore field in P. inaequilaterale and L. pacifica is reminiscent of, but not necessarily identical with the less advanced Type B. The arrangement of the anterior LOs (1-2) is rhomboidal in the two heteralepadomorph species, the two poecilasmatid species, and two of the three lepadid species, as it is in all previously and presently known lepadomorph cyprids except D. fascicularis. In this last species, they are deployed linearly along the hinge line. A linear arrangement of all the lattice organs is presumably the plesiomorphic condition for the Thoracica; an obvious exception being the pattern seen in Ibla cumingi. The arrangement of the first two pairs of posterior LOs (3-4) in O. a. geryonophila and C. virgatum differs from that of all previously described Lepadomorpha in being rhomboidal rather than aligned linearly along the hinge line. This same arrangement of LOs 3 and 4 in the two heteralepadomorph species is notable since it is not known in other thoracicans. Our results concerning variation in lattice organs of the lower Pedunculata are more or less consistent with current phylogenetic speculations and genetic information that ally Heteralepadomorpha with Lepadomorpha. Significance of this variation at lower taxonomic levels is also evident in the two similar forms of Heteralepas.

Enhanced transpiration rate in the high pigment 1 tomato mutant and its physiological significance

Tomato high pigment (hp) mutants represent an interesting horticultural resource due to their enhanced accumulation of carotenoids, flavonoids and vitamin C. Since hp mutants are known for their exaggerated light responses, the molecules accumulated are likely to be antioxidants, recruited to deal with light and others stresses. Further phenotypes displayed by hp mutations are reduced growth and an apparent disturbance in water loss. Here, we examined the impact of the hp1 mutation and its near isogenic line cv Micro-Tom (MT) on stomatal conductance (gs), transpiration (E), CO(2) assimilation (A) and water use efficiency (WUE). Detached hp1 leaves lost water more rapidly than control leaves, but this behaviour was reversed by exogenous abscisic acid (ABA), indicating the ability of hp1 to respond to this hormone. Although attached hp1 leaves had enhanced gs, E and A compared to control leaves, genotypic differences were lost when water was withheld. Both instantaneous leaf-level WUE and long-term whole plant WUE did not differ between hp1 and MT. Our results indicate a link between exaggerated light response and water loss in hp1, which has important implications for the use of this mutant in both basic and horticultural research.

Teacher strikes in Brazil and its representations: ""orderly disciplined class"" and ""education workers"" (Sao Paulo, 1963-1979)

This article analyses the teacher strikes that took place in the state of Sao Paulo ( Brazil). These strikes produced new representations of the profession and gave a particular visibility to its interest aggregation processes. These same strikes appeared as major incentives for the organisation of teachers in Brazil. The October 1963 strike - about six months before the military coup of 1964 - was the first to mobilise the whole of the teaching profession of the Sao Paulo state: primary and secondary education, public and private schools were all involved. The two other strikes, organised by teachers in the public schools in 1978 and 1979, took place under the dictatorship. As such, they had a particular significance in the process of recovering civil liberties in the final stages of the military regime in the 1980s. This article is based on an analysis of the front-page covering of these teacher strikes by the two major journals of the state, O Estado de S. Paulo and Folha de S. Paulo. With Chartier`s concept collective representations in mind, this approach allows us to grasp how large-circulation journals diffuse images of the profession and its organisational configurations. These press pictures are analysed by dint of the analytical frame Roland Barthes advanced in the 1960s, i.e. by reading their denoted, connoted and symbolic messages.

Floral developmental morphology of three Indigofera species (Leguminosae) and its systematic significance within Papilionoideae

Inflorescence and floral development of three species of Indigofera (Leguminosae-Papilionoideae), I. lespedezioides, I. spicata, and I. suffruticosa, were investigated and compared with that of other papilionoid groups, especially with members of the recently circumscribed Millettioid clade, which was merged as sister to Indigofereae in a recent cladistic analysis. Although Indigofera is a genus of special interest, because of its great richness in species and its economic importance, few studies have been made of floral development in the genus or in Indigofereae as a whole. Flower buds and inflorescences were analysed at several stages of development in the three species. Our results confirmed that Indigofera species bear a usual inflorescence type among legumes, the raceme, which comprises flowers initiated in acropetal succession, each with a subtending bract and no bracteoles initiated. The inception of the floral organs is as follows: sepals (5), petals (5), carpel (1), outer stamens (5), and, finally, inner stamens (5). Organ initiation in the sepal, petal, and both stamen whorls is unidirectional, from the abaxial side; the carpel cleft is adaxial. The vexillum is larger than other petals at maturity, covering the keels, which are fused edge-to-edge. Nine filaments are fused to form an adaxially open sheath, and the adaxial stamen of the inner whorl remains free (diadelphous androecium) in the mid-stage of development. Most of the infra-generic differences occurred in the later stages of development. Data on floral development in Indigofera obtained here were also compared with those from other members of Papilionoideae. This comparison showed that the early expression of zygomorphy is shared with other members of the Millettioid clade but is rarely found in other papilionoids, corresponding to a hypothetically morphological synapomorphy in the pair Indigoferae plus millettioids.

Prognostic Significance of Myocardial Fibrosis Quantification by Histopathology and Magnetic Resonance Imaging in Patients With Severe Aortic Valve Disease

Objectives We sought to determine whether the quantitative assessment of myocardial fibrosis (MF), either by histopathology or by contrast-enhanced magnetic resonance imaging (ce-MRI), could help predict long-term survival after aortic valve replacement. Background Severe aortic valve disease is characterized by progressive accumulation of interstitial MF. Methods Fifty-four patients scheduled to undergo aortic valve replacement were examined by ce-MRI. Delayed-enhanced images were used for the quantitative assessment of MF. In addition, interstitial MF was quantified by histological analysis of myocardial samples obtained during open-heart surgery and stained with picrosirius red. The ce-MRI study was repeated 27 +/- 22 months after surgery to assess left ventricular functional improvement, and all patients were followed for 52 +/- 17 months to evaluate long-term survival. Results There was a good correlation between the amount of MF measured by histopathology and by ce-MRI (r = 0.69, p < 0.001). In addition, the amount of MF demonstrated a significant inverse correlation with the degree of left ventricular functional improvement after surgery (r = -0.42, p = 0.04 for histopathology; r = -0.47, p = 0.02 for ce-MRI). Kaplan-Meier analyses revealed that higher degrees of MF accumulation were associated with worse long-term survival (chi-square = 6.32, p = 0.01 for histopathology; chi-square = 5.85, p = 0.02 for ce-MRI). On multivariate Cox regression analyses, patient age and the amount of MF were found to be independent predictors of all-cause mortality. Conclusions The amount of MF, either by histopathology or by ce-MRI, is associated with the degree of left ventricular functional improvement and all-cause mortality late after aortic valve replacement in patients with severe aortic valve disease. (J Am Coll Cardiol 2010; 56: 278-87) (c) 2010 by the American College of Cardiology Foundation

The prevalence and significance of periodic leg movements during sleep in patients with congestive heart failure

The aim of this study was to evaluate (1) the prevalence of periodic leg movements during sleep (PLMs) in a consecutive sample of congestive heart failure (CHF) outpatients; (2) the presence of correlation between PLMs, subjective daytime sleepiness, and sleep architecture; and (3) the heart rate response to PLMs in CHF. Seventy-nine [50 men, age 59 +/- 11 years, body mass index (BMI) 26 +/- 5 kg/m(2)] consecutive adult stable outpatients with CHF [left ventricular ejection fraction (LVEF) 36 +/- 6%] were prospectively evaluated. The patients underwent assessment of echocardiography, sleepiness (Epworth Scale), and overnight in-lab polysomnography. Fifteen patients (19%) had PLM index > 5. These subjects were similar in sex distribution, BMI, subjective somnolence, LVEF, and apnea-hypopnea index (AHI), but were significantly older than subjects without PLMs. Sleep architecture was similar in subjects with and without PLMs. There was a small but significant elevation of heart rate after PLMs (80.1 +/- 9.4 vs. 81.5 +/- 9.2; p < 0.001). The cardiac acceleration was also present in absence of electroencephalogram activation. The prevalence of PLMs in consecutive sample of adult CHF outpatients was 19%. There were no differences in subjective daytime sleepiness, sleep architecture, AHI, and severity of CHF in subjects with and without PLMs. PLMs caused a small but statistically significant cardiac acceleration.

Immunophenotyping and remodeling process in small airways of idiopathic interstitial pneumonias: functional and prognostic significance

Background and Aims: To test whether different degrees of immunologic and fibrotic airway remodeling processes occur in idiopathic interstitial pneumonias (IIPs), with impact on functional tests and survival, we studied the collagen/elastic system and immune cell density in the bronchiolar interstitium of lungs with the major types of IIPs. Materials and Methods: Histochemistry, immunohistochemistry and morphometric analysis were used to evaluate collagen/elastic fibers and immune cells in the bronchiolar interstitium of open lung biopsies of patients with cryptogenic organizing pneumonia [COP/organizing pneumonia (OP) = 10], acute interstitial pneumonia [AIP/diffuse alveolar damage (DAD) = 20], nonspecific interstitial pneumonia (NSIP/NSIP = 20) and idiopathic pulmonary fibrosis/usual interstitial pneumonia (UIP) = 20. Results: OP lungs presented a significant increase in collagenous/elastic fibers and in the total density of immune cells in the bronchiolar interstitium compared to controls, DAD, NSIP and UIP. We observed a significant increase in CD4, CD8 and CD20 lymphocytes, as well as in neutrophils, macrophages and plasma cells in OP. The increased amount of elastic fibers in the bronchiolar interstitium from OP lungs has a direct association with forced vital capacity (FVC) (r(s) = 0.99, P = 0.03). The most important survival predictor was CD20+ lymphocytes in the bronchiolar interstitium. In decreasing order, patients with UIP [Odds Ratio (OR) = 35.01], high forced expiratory volume in 1 s (FEV1)/FVC FVC (OR = 7.01), increased CD20+ lymphocytes (OR = 4.44) and collagenous/elastic fiber densities (OR = 2.03 and OR = 1.49, respectively) in the bronchiolar interstitium were those who had the greatest risk of death, followed by those with AIP, NSIP and COP. Conclusion: Different degrees of immunologic and fibroelastotic airway remodeling processes occur in the major types of IIPs with impact on physiological tests and survival.

Evaluation of the prognostic significance of serum galectin-3 in American Joint Committee on Cancer stage III and stage IV melanoma patients

Galectin-3 (Gal-3) is a member of the P-galactoside-binding lectins family and has been implicated in angiogenesis, tumor invasion, and metastatic process in vitro and in vivo. As we showed recently that advanced melanoma patients presented high serum level of Gal-3, we investigated the association of this protein with the outcome of melanoma patients. Whether this protein could be a biomarker has riot been assessed, and we compared the prognostic value of serum Gal-3 in multivariate analysis with lactate dehydrogenase, C-reactive protein and S100B. We conclude that Gal-3 could be of prognostic value in melanoma patients; more precisely, this protein has a strong independent prognostic signification with a cut-off value of 10 ng/ml. After these data, we believe that serum Gal-3 measurement can have an important role in the follow-up and management of advanced American Joint Commission on Cancer stage III and stage IV melanoma patients. Further studies will uncover whether Gal-3 will be able to open new therapeutic perspectives. Melanoma Res 19:316-320 (C) 2009 Wolters Kluwer Health | Lippincott Williams & Wilkins.

Influence of third-generation oral contraceptives on the complexity analysis and symbolic dynamics of heart rate variability

Objective To evaluate the influence of oral contraceptives (OCs) containing 20 mu mu g ethinylestradiol (EE) and 150 mu mu g gestodene (GEST) on the autonomic modulation of heart rate (HR) in women. Methods One-hundred and fifty-five women aged 24 +/-+/- 2 years were divided into four groups according to their physical activity and the use or not of an OC: active-OC, active-non-OC (NOC), sedentary-OC, and sedentary-NOC. The heart rate was registered in real time based on the electrocardiogram signal for 15 minutes, in the supine-position. The heart rate variability (HRV) was analysed using Shannon`s entropy (SE), conditional entropy (complexity index [CInd] and normalised CInd [NCI]), and symbolic analysis (0V%, 1V%, 2LV%, and 2ULV%). For statistical analysis the Kruskal-Wallis test with Dunn post hoc and the Wilcoxon test (p < 0.05 was considered significant) were applied. Results Treatment with this COC caused no significant changes in SE, CInd, NCI, or symbolic analysis in either active or sedentary groups. Active groups presented higher values for SE and 2ULV%, and lower values for 0V% when compared to sedentary groups (p < 0.05). Conclusion HRV patterns differed depending on life style; the non-linear method applied was highly reliable for identifying these changes. The use of OCs containing 20 mu mu g EE and 150 mu mu g GEST does not influence HR autonomic modulation.

Significance of topoisomerase III beta expression in breast ductal carcinomas: strong associations with disease-specific survival and metastasis

Topoisomerases are ubiquitous nuclear enzymes that regulate DNA structure in eukaryotic cells. The role of topoisomerase III beta, the newest member of the topoisomerase family, in the clinical outcome of breast cancer is still poorly understood. This study aims to investigate the immunoexpression of topoisomerase III beta in breast cancer and its relationships with clinicopathologic features and immunohistochemical markers of prognostic significance in breast pathology. Using tissue microarrays containing 171 cases of primary invasive breast cancer, we analyzed the immunoexpression of topoisomerase III beta, estrogen receptor, progesterone receptor, HER-2, BRCA-1, p53, and Ki67. Immunostaining for topoisomerase III beta was found in 33.9% of breast carcinomas, and immunopositivity was correlated with distant metastasis (P = .036) and death (P = .006). Decreased expression of topoisomerase III beta correlated with low expression of Ki67 (P < .001) and negativity for HER-2 (P < .001), BRCA-1 (P = .001), and p53 (P < .001). In the multivariate analysis, topoisomerase Hip expression was a significant predictor of survival (hazard ratio, 3.006 [95% confidence interval, 1.582-5.715]; P = .001). In conclusion, topoisomerase III beta expression can be a useful marker in assessing the prognosis of patients with breast cancer and is an independent predictor of survival. (C) 2010 Elsevier Inc. All rights reserved.

Foliar cuticular alkanes of Camarea (Malpighiaceae) and their taxonomic significance

Camarea is a South-American endemic genus comprising eight species. In the present work n-alkanes from foliar cuticular waxes of 23 specimens, representing seven species of Camarea were analyzed, aiming at establishing interspecific affinities and evaluating the usefulness of n-alkane distribution as species characteristic. The sampling included also specimens of Peixotoa rericulata and Janusia guaronitica (both Malpighiaceae). The results were used to obtain a phenogram indicating chemical affinities between species. The results are in agreement with morphological similarities among some Camarea species. Intraspecific variability was small, suggesting that n-alkane distribution may be useful for species characterization and establishment of links among Camarea species. The results support the recognition of Camarea triphylla as a synonym of Camarea axillaris and are not coherent with a hybrid condition of a population exhibiting morphological characteristics combining Camarea affinis and Camarea hirsuta, suggesting instead that the individuals analyzed belong either to Camarea hirsuta or a close species. Distribution of n-alkanes is inadequate to distinguish among Malpighiaceae genera: P reticulata has n-alkane distribution similar to several Cumarea species. (C) 2008 Elsevier Ltd. All rights reserved.

Clinical significance of lifetime panic disorder in the course of bipolar disorder type I

Objectives: The aim of the study was to analyze the impact of lifetime panic disorder (PD) diagnosis in a sample of patients with bipolar disorder type I (BPI), evaluating clinical and demographic variables. Methods: Ninety-five outpatients from the Bipolar Disorder Research Program at the Institute of Psychiatry of the University of Sao Paulo Medical School were enrolled. Twenty-seven BPI patients with PD were compared to 68 BPI patients without any anxiety disorders regarding clinical and demographic variables. Results: Compared to BPI patients without any anxiety disorders, patients with BPI + PD presented significantly higher number of mood episodes (18.9 +/- 13.8 vs 8.5 +/- 7.8; P < .001), depressive episodes (10.8 +/- 8.2 vs 4.6 +/- 4,8; P = .001), and manic episodes (7.4 +/- 7.3 vs 3.6 +/- 3.6; P = .008). Patients with BPI + PD had more frequently a depressive episode as their first one compared to BPI patients without anxiety disorders (94.1% vs 57.5%; P = .011). Patients with BPI + PD had more comorbidity with lifetime diagnosis of drug abuse or dependence (33.3% vs 8.8%; P = .010) and eating disorders (29.6% vs 6.0%; P = .004). Conclusions: The higher number of mood episodes in general presented by patients with BPI + PD when compared with BPI patients without any anxiety disorders, along with the higher frequencies of drug misuse and eating disorders, indicates that PD comorbidity is associated with a poorer Course and outcome of BPI. The higher frequency of depression as the onset mood episode and the higher number of manic episodes in the group with PD may have important treatment implications and should be further investigated. (C) 2009 Elsevier Inc. All rights reserved.

ASSOCIATED A-TYPE SUBALKALINE AND HIGH-K CALC-ALKALINE GRANITES IN THE ITU GRANITE PROVINCE, SOUTHEASTERN BRAZIL: PETROLOGICAL AND TECTONIC SIGNIFICANCE

The 590-580 Ma Itu Granite Province (IGP) is a roughly linear belt of post-orogenic granite plutons similar to 60 km wide extending for some 350 km along the southern edge of the Apia-Guaxupe Terrane in southeastern Brazil. Typical components are subalkaline A-type granites (some with rapakivi texture) that crystallized at varied, but mostly strongly oxidizing conditions, and contrast with a coeval association of also oxidized high-K calc-alkaline granites in terms of major (e. g., lower Ca/Fe) and trace elements (higher Nb, Y, Zr). Mantle-derived magmas (such as those forming the LILE-rich Piracaia Monzodiorite, with epsilon(Nd(t)) = -7 to -10, (87)Sr/(86)Sr((t)) = 0.7045-0.7055) are inferred to derive from enriched subcontinental lithosphere modified during previous subduction, and may have played a role in the generation of the A-type granites, adding melts or fluids or both to the lower crust from which the latter were generated. The IGP is interpreted as a reflection of crust uplift and increased heat flux during ascent of hot, less dense asthenosphere after continental collision, probably reflecting breakoff of an oceanic slab coeval to the right-lateral accretion of a terrane related to the Mantiqueira Orogenic System.