The generalized Robinson-Foulds metric

The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to the original one; but the two trees are identical if we remove the single taxon. To this end, we propose a natural extension of the RF metric that does not simply count identical clades but instead, also takes similar clades into consideration. In contrast to previous approaches, our model requires the matching between clades to respect the structure of the two trees, a property that the classical RF metric exhibits, too. We show that computing this generalized RF metric is, unfortunately, NP-hard. We then present a simple Integer Linear Program for its computation, and evaluate it by an all-against-all comparison of 100 trees from a benchmark data set. We find that matchings that respect the tree structure differ significantly from those that do not, underlining the importance of this natural condition.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Corporate financing decisions: UK survey evidence

Despite theoretical developments in recent years, our understanding of corporate capital structure remains incomplete. Prior empirical research has been dominated by archival regression studies which are limited in their ability to fully reflect the diversity found in practice. The present paper reports on a comprehensive survey of corporate financing decision-making in UK listed companies. A key finding is that firms are heterogeneous in their capital structure policies. About half of the firms seek to maintain a target debt level, consistent with trade-off theory, but 60 per cent claim to follow a financing hierarchy, consistent with pecking order theory. These two theories are not viewed by respondents as either mutually exclusive or exhaustive. Many of the theoretical determinants of debt levels are widely accepted by respondents, in particular the importance of interest tax shield, financial distress, agency costs and also, at least implicitly, information asymmetry. Results also indicate that cross-country institutional differences have a significant impact on financial decisions

Phenomenological Tests of Supersymmetric A_4 Family Symmetry Model of Neutrino Mass

Recently Babu, Ma and Valle proposed a model of quark and lepton mixing based on $A_4$ symmetry. Within this model the lepton and slepton mixings are intimately related. We perform a numerical study in order to derive the slepton masses and mixings in agreement with present data from neutrino physics. We show that, starting from three-fold degeneracy of the neutrino masses at a high energy scale, a viable low energy neutrino mass matrix can indeed be obtained in agreement with constraints on lepton flavour violating $\mu$ and $\tau$ decays. The resulting slepton spectrum must necessarily include at least one mass below 200 GeV which can be produced at the LHC. The predictions for the absolute Majorana neutrino mass scale $m_0 \geq 0.3$ eV ensure that the model will be tested by future cosmological tests and $\beta\beta_{0\nu}$ searches. Rates for lepton flavour violating processes $\ell_j \to \ell_i + \gamma$ in the range of sensitivity of current experiments are typical in the model, with BR(\mu \to e \gamma) \gsim 10^{-15} and the lower bound BR$(\tau \to \mu \gamma) > 10^{-9}$. To first approximation, the model leads to maximal leptonic CP violation in neutrino oscillations.Comment: 23 pages, 7 figure

Desempenho da alface em cultivo orgânico com e sem cobertura morta e diferentes lâminas d'água.

O experimento foi conduzido no período de 27/05/2006 a 02/08/2006 no SIPA (Sistema Integrado de Produção Agroecológica), localizado no município de Seropédica-RJ. Nesse trabalho, objetivou-se avaliar o desempenho da cultura da alface (Lactuca sativa L.)cultivada sob diferentes lâminas de irrigação em um solo sem e com cobertura de palhada da leguminosa gliricídia. Foram conduzidos dois experimentos simultâneos, utilizando o delineamento experimental de blocos ao acaso, em ambos os experimentos, nos quais foram aplicadas 5 lâminas de irrigação, correspondendo a 25, 50, 80, 100, 115 % da evapotranspiração da cultura (ETc), sendo a produção final avaliada por meio da determinação da massa fresca, área foliar e número de folhas. Até o nível de 100% ETc, todas as variáveis analisadas tiveram seus valores aumentados, e para o nível de 115%, houve um decrescimento das mesmas. Na produção de massa fresca total, o sistema de cultivo com utilização de cobertura morta foi superior ao sem cobertura não diferenciando estatisticamente ao nível de 5 % probabilidade pelo teste F somente nas lâminas de 25 e 115% ETc

A role for XRCC2 gene polymorphisms in breast cancer risk and survival

Background The XRCC2 gene is a key mediator in the homologous recombination repair of DNA double strand breaks. It is hypothesised that inherited variants in the XRCC2 gene might also affect susceptibility to, and survival from, breast cancer. Methods The study genotyped 12 XRCC2 tagging single nucleotide polymorphisms (SNPs) in 1131 breast cancer cases and 1148 controls from the Sheffield Breast Cancer Study (SBCS), and examined their associations with breast cancer risk and survival by estimating ORs and HRs, and their corresponding 95% CIs. Positive findings were further investigated in 860 cases and 869 controls from the Utah Breast Cancer Study (UBCS) and jointly analysed together with available published data for breast cancer risk. The survival findings were further confirmed in studies (8074 cases) from the Breast Cancer Association Consortium (BCAC). Results The most significant association with breast cancer risk in the SBCS dataset was the XRCC2 rs3218408 SNP (recessive model p=2.3×10−4, minor allele frequency (MAF)=0.23). This SNP yielded an ORrec of 1.64 (95% CI 1.25 to 2.16) in a two-site analysis of SBCS and UBCS, and a meta-ORrec of 1.33 (95% CI 1.12 to 1.57) when all published data were included. This SNP may mark a rare risk haplotype carried by two in 1000 of the control population. Furthermore, the XRCC2 coding R188H SNP (rs3218536, MAF=0.08) was significantly associated with poor survival, with an increased per-allele HR of 1.58 (95% CI 1.01 to 2.49) in a multivariate analysis. This effect was still evident in a pooled meta-analysis of 8781 breast cancer patients from the BCAC (HR 1.19, 95% CI 1.05 to 1.36; p=0.01). Conclusions These findings suggest that XRCC2 SNPs may influence breast cancer risk and survival

Tests of sunspot number sequences: 1. Using ionosonde data

More than 70 years ago it was recognised that ionospheric F2-layer critical frequencies [foF2] had a strong relationship to sunspot number. Using historic datasets from the Slough and Washington ionosondes, we evaluate the best statistical fits of foF2 to sunspot numbers (at each Universal Time [UT] separately) in order to search for drifts and abrupt changes in the fit residuals over Solar Cycles 17-21. This test is carried out for the original composite of the Wolf/Zürich/International sunspot number [R], the new “backbone” group sunspot number [RBB] and the proposed “corrected sunspot number” [RC]. Polynomial fits are made both with and without allowance for the white-light facular area, which has been reported as being associated with cycle-to-cycle changes in the sunspot number - foF2 relationship. Over the interval studied here, R, RBB, and RC largely differ in their allowance for the “Waldmeier discontinuity” around 1945 (the correction factor for which for R, RBB and RC is, respectively, zero, effectively over 20 %, and explicitly 11.6 %). It is shown that for Solar Cycles 18-21, all three sunspot data sequences perform well, but that the fit residuals are lowest and most uniform for RBB. We here use foF2 for those UTs for which R, RBB, and RC all give correlations exceeding 0.99 for intervals both before and after the Waldmeier discontinuity. The error introduced by the Waldmeier discontinuity causes R to underestimate the fitted values based on the foF2 data for 1932-1945 but RBB overestimates them by almost the same factor, implying that the correction for the Waldmeier discontinuity inherent in RBB is too large by a factor of two. Fit residuals are smallest and most uniform for RC and the ionospheric data support the optimum discontinuity multiplicative correction factor derived from the independent Royal Greenwich Observatory (RGO) sunspot group data for the same interval