Better prediction by use of co-data: Adaptive group-regularized ridge regression

For many high-dimensional studies, additional information on the variables, like (genomic) annotation or external p-values, is available. In the context of binary and continuous prediction, we develop a method for adaptive group-regularized (logistic) ridge regression, which makes structural use of such 'co-data'. Here, 'groups' refer to a partition of the variables according to the co-data. We derive empirical Bayes estimates of group-specific penalties, which possess several nice properties: i) they are analytical; ii) they adapt to the informativeness of the co-data for the data at hand; iii) only one global penalty parameter requires tuning by cross-validation. In addition, the method allows use of multiple types of co-data at little extra computational effort. We show that the group-specific penalties may lead to a larger distinction between `near-zero' and relatively large regression parameters, which facilitates post-hoc variable selection. The method, termed GRridge, is implemented in an easy-to-use R-package. It is demonstrated on two cancer genomics studies, which both concern the discrimination of precancerous cervical lesions from normal cervix tissues using methylation microarray data. For both examples, GRridge clearly improves the predictive performances of ordinary logistic ridge regression and the group lasso. In addition, we show that for the second study the relatively good predictive performance is maintained when selecting only 42 variables.Comment: 15 pages, 2 figures. Supplementary Information available on first author's web sit

Penetration of hot electrons through a cold disordered wire

We study a penetration of an electron with high energy E<<T through strongly disordered wire of length L<<a (a being the localization length). Such an electron can loose, but not gain the energy, when hopping from one localized state to another. We have found a distribution function for the transmission coefficient t. The typical t remains exponentially small in L/a, but with the decrement, reduced compared to the case of direct elastic tunnelling. The distribution function has a relatively strong tail in the domain of anomalously high t; the average ~(a/L)^2 is controlled by rare configurations of disorder, corresponding to this tail.Comment: 4 pages, 5 figure

Polymorphisms of SP110 are associated with both pulmonary and extra-pulmonary tuberculosis among the Vietnamese

Background: Tuberculosis (TB) is an infectious disease that remains a major cause of morbidity and mortality worldwide, yet the reasons why only 10% of people infected with Mycobacterium tuberculosis go on to develop clinical disease are poorly understood. Genetically determined variation in the host immune response is one factor influencing the response to M. tuberculosis. SP110 is an interferon-responsive nuclear body protein with critical roles in cell cycling, apoptosis and immunity to infection. However association studies of the gene with clinical TB in different populations have produced conflicting results. Methods: To examine the importance of the SP110 gene in immunity to TB in the Vietnamese we conducted a case-control genetic association study of 24 SP110 variants, in 663 patients with microbiologically proven TB and 566 unaffected control subjects from three tertiary hospitals in northern Vietnam. Results: Five SNPs within SP110 were associated with all forms of TB, including four SNPs at the C terminus (rs10208770, rs10498244, rs16826860, rs11678451) under a dominant model and one SNP under a recessive model, rs7601176. Two of these SNPs were associated with pulmonary TB (rs10208770 and rs16826860) and one with extra-pulmonary TB (rs10498244). Conclusion: SP110 variants were associated with increased susceptibility to both pulmonary and extra-pulmonary TB in the Vietnamese. Genetic variants in SP110 may influence macrophage signaling responses and apoptosis during M. tuberculosis infection, however further research is required to establish the mechanism by which SP110 influences immunity to tuberculosis infection. © 2014 Fox et al

Transport on Directed Percolation Clusters

We study random lattice networks consisting of resistor like and diode like bonds. For investigating the transport properties of these random resistor diode networks we introduce a field theoretic Hamiltonian amenable to renormalization group analysis. We focus on the average two-port resistance at the transition from the nonpercolating to the directed percolating phase and calculate the corresponding resistance exponent $\phi$ to two-loop order. Moreover, we determine the backbone dimension $D_B$ of directed percolation clusters to two-loop order. We obtain a scaling relation for $D_B$ that is in agreement with well known scaling arguments.Comment: 4 page

The epidemiology and aetiology of diarrhoeal disease in infancy in southern Vietnam: a birth cohort study.

OBJECTIVES: Previous studies indicate a high burden of diarrhoeal disease in Vietnamese children, however longitudinal community-based data on burden and aetiology are limited. The findings from a large, prospective cohort study of diarrhoeal disease in infants in southern Vietnam are presented herein. METHODS: Infants were enrolled at birth in urban Ho Chi Minh City and a semi-rural district in southern Vietnam, and followed for 12 months (n=6706). Diarrhoeal illness episodes were identified through clinic-based passive surveillance, hospital admissions, and self-reports. RESULTS: The minimum incidence of diarrhoeal illness in the first year of life was 271/1000 infant-years of observation for the whole cohort. Rotavirus was the most commonly detected pathogen (50% of positive samples), followed by norovirus (24%), Campylobacter (20%), Salmonella (18%), and Shigella (16%). Repeat infections were identified in 9% of infants infected with rotavirus, norovirus, Shigella, or Campylobacter, and 13% of those with Salmonella infections. CONCLUSIONS: The minimum incidence of diarrhoeal disease in infants in both urban and semi-rural settings in southern Vietnam was quantified prospectively. A large proportion of laboratory-diagnosed disease was caused by rotavirus and norovirus. These data highlight the unmet need for a rotavirus vaccine in Vietnam and provide evidence of the previously unrecognized burden of norovirus in infants

Parental influences on adolescent fruit consumption : the role of adolescent self-efficacy

The aims of this study were to examine whether adolescent self-efficacy mediates the associations between parental control, perceptions of the importance of healthy nutrition for child health and barriers to buying fruits and vegetables and adolescent fruit consumption using a theoretically derived explanatory model. Data were drawn from a community-based sample of 1606 adolescents in Years 7 and 9 of secondary school and their parents, from Victoria, Australia. Adolescents completed a web-based survey assessing their fruit consumption and self-efficacy for increasing fruit consumption. Parents completed a survey delivered via mail assessing parental control, perceptions and barriers to buying fruit and vegetables. Adolescent self-efficacy for increasing fruit consumption mediated the positive associations between parental control and perceptions of the importance of healthy nutrition for child health and adolescent fruit consumption. Furthermore, adolescent self-efficacy mediated the negative association between parental barriers to buying fruits and vegetables and adolescent fruit consumption. The importance of explicating the mechanisms through which parental factors influence adolescent fruit consumption not only relates to the advancement of scientific knowledge but also offers potential avenues for intervention. Future research should assess the effectiveness of methods to increase adolescent fruit consumption by focussing on both improving adolescents&rsquo; dietary self-efficacy and on targeting parental control, perceptions and barriers. <br /

Multifractal properties of resistor diode percolation

Focusing on multifractal properties we investigate electric transport on random resistor diode networks at the phase transition between the non-percolating and the directed percolating phase. Building on first principles such as symmetries and relevance we derive a field theoretic Hamiltonian. Based on this Hamiltonian we determine the multifractal moments of the current distribution that are governed by a family of critical exponents $\{\psi_l \}$. We calculate the family $\{\psi_l \}$ to two-loop order in a diagrammatic perturbation calculation augmented by renormalization group methods.Comment: 21 pages, 5 figures, to appear in Phys. Rev.