Unsupervised Bayesian linear unmixing of gene expression microarrays

Background: This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expression microarrays. The basis for uBLU is a Bayesian model for the data samples which are represented as an additive mixture of random positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a specific sample. The particularity of the proposed method is that uBLU constrains the factor loadings to be non-negative and the factor scores to be probability distributions over the factors. Furthermore, it also provides estimates of the number of factors. A Gibbs sampling strategy is adopted here to generate random samples according to the posterior distribution of the factors, factor scores, and number of factors. These samples are then used to estimate all the unknown parameters. Results: Firstly, the proposed uBLU method is applied to several simulated datasets with known ground truth and compared with previous factor decomposition methods, such as principal component analysis (PCA), non negative matrix factorization (NMF), Bayesian factor regression modeling (BFRM), and the gradient-based algorithm for general matrix factorization (GB-GMF). Secondly, we illustrate the application of uBLU on a real time-evolving gene expression dataset from a recent viral challenge study in which individuals have been inoculated with influenza A/H3N2/Wisconsin. We show that the uBLU method significantly outperforms the other methods on the simulated and real data sets considered here. Conclusions: The results obtained on synthetic and real data illustrate the accuracy of the proposed uBLU method when compared to other factor decomposition methods from the literature (PCA, NMF, BFRM, and GB-GMF). The uBLU method identifies an inflammatory component closely associated with clinical symptom scores collected during the study. Using a constrained model allows recovery of all the inflammatory genes in a single factor

Effect of maternal panic disorder on mother-child interaction and relation to child anxiety and child self-efficacy

To determine whether mothers with panic disorder with or without agoraphobia interacted differently with their children than normal control mothers, 86 mothers and their adolescents (aged between 13 and 23 years) were observed during a structured play situation. Maternal as well as adolescent anxiety status was assessed according to a structured diagnostic interview. Results showed that mothers with panic disorder/agoraphobia showed more verbal control, were more criticizing and less sensitive during mother-child interaction than mothers without current mental disorders. Moreover, more conflicts were observed between mother and child dyadic interactions when the mother suffered from panic disorder. The comparison of parenting behaviors among anxious and non-anxious children did not reveal any significant differences. These findings support an association between parental over-control and rejection and maternal but not child anxiety and suggest that particularly mother anxiety status is an important determinant of parenting behavior. Finally, an association was found between children’s perceived self-efficacy, parental control and child anxiety symptoms

Social and ethical criteria for prioritizing patients: a survey of students and health professionals in Portugal

O estudo quali-quantitativo explora o dilema ético da microalocação dos recursos da saúde. Objetiva identificar e comparar a opinião de dois grupos da sociedade portuguesa - estudantes e profissionais de saúde sobre a importância das características pessoais dos pacientes no momento de os priorizar e se as escolhas se explicam por referenciais bioéticos de caráter utilitaristas ou deontológicos. Os dados foram recolhidos através de um questionário aplicado a uma amostra de 180 estudantes universitários e 60 profissionais de saúde. Os respondentes perante hipotéticos cená- rios de emergência clínica tiveram de escolher de entre dois pacientes (distinguidos por idade, sexo, responsabilidade social, situação económica e laboral, comportamentos lesivos da saúde e registo criminal) quem tratar e justificar a escolha. Foram usados testes estatísticos de associação para comparar as respostas dos dois grupos e análise de conteúdo para categorizar as justificações. Os resultados sugerem a existência de diferenças nas escolhas dos dois grupos, com os profissionais de saúde a revelarem aceitar menos a utilização de critérios sociais em contexto de escassez e coexistência de critérios utilitaristas e deontológicos, com predomínio da eficiência por parte dos profissionais de saúde e da equidade por parte dos estudantesThis qualitative/quantitative study examines the ethical dilemma of microallocation of health resources. It seeks to identify and compare the opinion of two groups in Portuguese society – students and health professionals – on the importance of personal characteristics of patients at the moment of prioritizing them and if the choices can be explained by bioethical references of a utilitarian or deontological nature. Data were collected by means of a questionnaire administered to a sample of 180 students and 60 health professionals. Faced with hypothetical emergency scenarios, the respondents had to choose between two patients (distinguished by: age, gender, social responsibility, economic and employment situation, harmful health behaviors and criminal record), duly selecting who to treat and then justifying their choice. The results suggest the existence of differences in choices between the two groups, with health professionals revealing they are less prepared to accept the use of social criteria in a context of scarce resources and co-existence of utilitarian and deontological criteria, with a predominance of efficiency on the part of health professionals and equity on the part of students.info:eu-repo/semantics/publishedVersio

Interaction between alcohol dehydrogenase II gene, alcohol consumption, and risk for breast cancer

MaeIII Restriction Fragment Length Polymorphism in exon 3 of the alcohol dehydrogenase II was assessed in serum from 467 randomly selected German women and 278 women with invasive breast cancer to evaluate the interaction between a polymorphism of the alcohol dehydrogenase II gene, alcohol consumption and risk for breast cancer. In both groups, usual consumption of different alcoholic beverages was asked for using semiquantitative food frequency questionnaires. We used multivariable logistic regression to separately estimate the association between alcohol consumption and alcohol dehydrogenase II polymorphism in the population sample and women with breast cancer. The alcohol dehydrogenase II polymorphism was detected in 14 women from the population sample (3.0%) and in 27 women with invasive breast cancer (9.7%). Frequency of alcohol consumption was independent of the genotype in the population sample. In women with breast cancer, there was a significant inverse association between the alcohol dehydrogenase II polymorphism and frequency of alcohol consumption (adjusted case-only odds ratio over increasing frequency of alcohol consumption=0.5; P for interaction=0.02). We observed a gene-environment interaction between the alcohol dehydrogenase II polymorphism, alcohol consumption, and risk for breast cancer. Breast cancer risk associated with alcohol consumption may vary according to the alcohol dehydrogenase II polymorphism, probably due to differences in alcohol metabolism

Preschoolers' Precision of the Approximate Number System Predicts Later School Mathematics Performance

The Approximate Number System (ANS) is a primitive mental system of nonverbal representations that supports an intuitive sense of number in human adults, children, infants, and other animal species. The numerical approximations produced by the ANS are characteristically imprecise and, in humans, this precision gradually improves from infancy to adulthood. Throughout development, wide ranging individual differences in ANS precision are evident within age groups. These individual differences have been linked to formal mathematics outcomes, based on concurrent, retrospective, or short-term longitudinal correlations observed during the school age years. However, it remains unknown whether this approximate number sense actually serves as a foundation for these school mathematics abilities. Here we show that ANS precision measured at preschool, prior to formal instruction in mathematics, selectively predicts performance on school mathematics at 6 years of age. In contrast, ANS precision does not predict non-numerical cognitive abilities. To our knowledge, these results provide the first evidence for early ANS precision, measured before the onset of formal education, predicting later mathematical abilities

Stand Out in Class: restructuring theclassroom environment to reducesedentary behaviour in 9–10-year-olds—study protocol for a pilot clusterrandomised controlled trial

Background: Sedentary behaviour (sitting) is a highly prevalent negative health behaviour, with individuals of allages exposed to environments that promote prolonged sitting. Excessive sedentary behaviour adversely affects health inchildren and adults. As sedentary behaviour tracks from childhood into adulthood, the reduction of sedentary time inyoung people is key for the prevention of chronic diseases that result from excessive sitting in later life. The sedentaryschool classroom represents an ideal setting for environmentalchange, through the provision of sit-stand desks. Whilstthe use of sit-stand desks in classrooms demonstrates positiveeffects in some key outcomes, evidence is currently limitedby small samples and/or short intervention durations, withfewstudiesadoptingrandomisedcontrolledtrial(RCT)designs. This paper describes the protocol of a pilot cluster RCT of a sit-stand desk interventioninprimaryschoolclassrooms.Methods/Design:A two-arm pilot cluster RCT will be conducted in eight primary schools (four intervention, four control)with at least 120 year 5 children (aged 9–10 years). Sit-stand desks will replace six standard desks in the interventionclassrooms. Teachers will be encouraged to ensure all pupils are exposed to the sit-stand desks for at least 1 h/dayon average using a rotation system. Schools assigned to the control arm will continue with their usual practice, noenvironmental changes will be made to their classrooms. Measurements will be taken at baseline, beforerandomisation, and at the end of the schools’academic year. In this study, the primary outcomes of interest will beschool and participant recruitment and attrition, acceptability of the intervention, and acceptability and complianceto the proposed outcome measures (including activPAL-measured school-time and school-day sitting, accelerometer-measured physical activity, adiposity, blood pressure, cognitive function, academic progress, engagement, andbehaviour) for inclusion in a definitive trial. A full process evaluation and an exploratory economic evaluation willalso be conducted to further inform a definitive tria

Studying the Underlying Event in Drell-Yan and High Transverse Momentum Jet Production at the Tevatron

We study the underlying event in proton-antiproton collisions by examining the behavior of charged particles (transverse momentum pT > 0.5 GeV/c, pseudorapidity |\eta| < 1) produced in association with large transverse momentum jets (~2.2 fb-1) or with Drell-Yan lepton-pairs (~2.7 fb-1) in the Z-boson mass region (70 < M(pair) < 110 GeV/c2) as measured by CDF at 1.96 TeV center-of-mass energy. We use the direction of the lepton-pair (in Drell-Yan production) or the leading jet (in high-pT jet production) in each event to define three regions of \eta-\phi space; toward, away, and transverse, where \phi is the azimuthal scattering angle. For Drell-Yan production (excluding the leptons) both the toward and transverse regions are very sensitive to the underlying event. In high-pT jet production the transverse region is very sensitive to the underlying event and is separated into a MAX and MIN transverse region, which helps separate the hard component (initial and final-state radiation) from the beam-beam remnant and multiple parton interaction components of the scattering. The data are corrected to the particle level to remove detector effects and are then compared with several QCD Monte-Carlo models. The goal of this analysis is to provide data that can be used to test and improve the QCD Monte-Carlo models of the underlying event that are used to simulate hadron-hadron collisions.Comment: Submitted to Phys.Rev.

Precision measurement of the top quark mass from dilepton events at CDF II

We report a measurement of the top quark mass, M_t, in the dilepton decay channel of $t\bar{t}\to b\ell'^{+}\nu_{\ell'}\bar{b}\ell^{-}\bar{\nu}_{\ell}$ using an integrated luminosity of 1.0 fb^{-1} of p\bar{p} collisions collected with the CDF II detector. We apply a method that convolutes a leading-order matrix element with detector resolution functions to form event-by-event likelihoods; we have enhanced the leading-order description to describe the effects of initial-state radiation. The joint likelihood is the product of the likelihoods from 78 candidate events in this sample, which yields a measurement of M_{t} = 164.5 \pm 3.9(\textrm{stat.}) \pm 3.9(\textrm{syst.}) \mathrm{GeV}/c^2, the most precise measurement of M_t in the dilepton channel.Comment: 7 pages, 2 figures, version includes changes made prior to publication by journa

Cross Section Measurements of High-pTp_T Dilepton Final-State Processes Using a Global Fitting Method

We present a new method for studying high-$p_T$ dilepton events ($e^{\pm}e^{\mp}$, $\mu^{\pm}\mu^{\mp}$, $e^{\pm}\mu^{\mp}$) and simultaneously extracting the production cross sections of $p\bar{p} \to t\bar{t}$, $p\bar{p} \to W^+W^-$, and p\bar{p} \to \ztt at a center-of-mass energy of $\sqrt{s} = 1.96$ TeV. We perform a likelihood fit to the dilepton data in a parameter space defined by the missing transverse energy and the number of jets in the event. Our results, which use $360 {\rm pb^{-1}}$ of data recorded with the CDF II detector at the Fermilab Tevatron Collider, are $\sigma(t\bar{t}) = 8.5_{-2.2}^{+2.7}$ pb, $\sigma(W^+W^-) = 16.3^{+5.2}_{-4.4}$ pb, and \sigma(\ztt) =291^{+50}_{-46} pb.Comment: 20 pages, 2 figures, to be submitted to PRD-R

Measurement of the Ratios of Branching Fractions B(Bs -> Ds pi pi pi) / B(Bd -> Dd pi pi pi) and B(Bs -> Ds pi) / B(Bd -> Dd pi)

Using 355 pb^-1 of data collected by the CDF II detector in \ppbar collisions at sqrt{s} = 1.96 TeV at the Fermilab Tevatron, we study the fully reconstructed hadronic decays B -> D pi and B -> D pi pi pi. We present the first measurement of the ratio of branching fractions B(Bs -> Ds pi pi pi) / B(Bd -> Dd pi pi pi) = 1.05 pm 0.10 (stat) pm 0.22 (syst). We also update our measurement of B(Bs -> Ds pi) / B(Bd -> Dd pi) to 1.13 pm 0.08 (stat) pm 0.23 (syst) improving the statistical uncertainty by more than a factor of two. We find B(Bs -> Ds pi) = [3.8 pm 0.3 (stat) pm 1.3 (syst)] \times 10^{-3} and B(Bs -> Ds pi pi pi) = [8.4 pm 0.8 (stat) pm 3.2 (syst)] \times 10^{-3}.Comment: 7 pages, 2 figure