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.

Bioimpedance spectrometry in the determination of body water compartments: Accuracy and clinical significance

Bioelectrical impedance analysis (BIA) offers the potential for a simple, portable and relatively inexpensive technique for the in vivo measurement of total body water (TBW). The potential of BIA as a technique of body composition analysis is even greater when one considers that body water can be used as a surrogate measure of lean body mass. However, BIA has not found universal acceptance even with the introduction of multi-frequency BIA (MFBIA) which, potentially, may improve the predictive accuracy of the measurement. There are a number of reasons for this lack of acceptance, although perhaps the major reason is that no single algorithm has been developed which can be applied to all subject groups. This may be due, in part, to the commonly used wrist-to-ankle protocol which is not indicated by the basic theory of bioimpedance, where the body is considered as five interconnecting cylinders. Several workers have suggested the use of segmental BIA measurements to provide a protocol more in keeping with basic theory. However, there are other difficulties associated with the application of BIA, such as effects of hydration and ion status, posture and fluid distribution. A further putative advantage of MFBIA is the independent assessment not only of TBW but also of the extracellular fluid volume (ECW), hence heralding the possibility of,being able to assess the fluid distribution between these compartments. Results of studies in this area have been, to date, mixed. Whereas strong relationships of impedance values at low frequencies with ECW, and at high frequencies with TBW, have been reported, changes in impedance are not always well correlated with changes in the size of the fluid compartments (assessed by alternative and more direct means) in pathological conditions. Furthermore, the theoretical advantages of Cole-Cole modelling over selected frequency prediction have not always been apparent. This review will consider the principles, methodology and applications of BIA. The principles and methodology will,be considered in relation to the basic theory of BIA and difficulties experienced in its application. The relative merits of single and multiple frequency BIA will be addressed, with particular attention to the latter's role in the assessment of compartmental fluid volumes. (C) 1998 Elsevier Science Ltd. All rights reserved.

Functional significance of the beta-hairpin in the insecticidal neurotoxin omega-atracotoxin-Hv1a

omega -Atracotoxin-Hv1a is an insect-specific neurotoxin whose phylogenetic specificity derives from its ability to antagonize insect, but not vertebrate, voltage-gated calcium channels. In order to help understand its mechanism of action and to enhance its utility as a lead compound for insecticide development, we used a combination of protein engineering and site-directed mutagenesis to probe the toxin for key functional regions. First, we constructed a Hairpinless mutant in which the C-terminal beta -hairpin, which is highly conserved in this family of neurotoxins, was excised without affecting the fold of the residual disulfide-rich core of the toxin. The Hairpinless mutant was devoid of insecticidal activity, indicating the functional importance of the hairpin. We subsequently developed a highly efficient system for production of recombinant toxin and then probed the hairpin for key functional residues using alanine-scanning mutagenesis followed by a second round of mutagenesis based on initial hits from the alanine scan. This revealed that two spatially proximal residues, Asn(27) and Arg(35), form a contiguous molecular surface that is essential for toxin activity. We propose that this surface of the beta -hairpin is a key site for interaction of the toxin with insect calcium channels.

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.

Transport in bidisperse adsorbents: Significance of the macroscopic adsorbate flux

Transport in bidisperse adsorbents is investigated here, while incorporating a two-dimensional model for adsorbate diffusion in the microparticles. The latter treatment permits consideration of the macropore concentration variation around the microparticle surface, and thereby predicts an adsorbate through-flux on the macroscopic coordinate. Such a through-flux has earlier been postulated in the literature, but with unrealistic mechanistic justification. The new model therefore resolves the existing ambiguity in this regard, and covers the entire spectrum of behaviour between microparticle and macropore diffusion control. Computational results show that if the macroscopic adsorbate flux, ignored in the conventional analysis, has a significant contribution to the total flux under macropore control conditions then it is always important even when the microparticle diffusion resistance is not negligible. The effect of various parameters such as relative microparticle size and isotherm heterogeneity on the uptake is also studied and discussed. (C) 1997 Elsevier Science Ltd.

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.