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

ANTIMICROBIAL DITERPENOID ALKALOIDS FROM ERYTHROPHLEUM SUAVEOLENS (GUILL. & PERR.) BRENAN

An investigation of the stem bark of Erythrophleum suaveolens (Guill. & Perr.) Brenan yielded the known amide norcassaide (1) and a new diterpenoid alkaloid named norerythrosuaveolide (2) which was characterized as 7β-hydroxy-7-deoxo-6-oxonorcassaide. The structures were established on the basis of one and two-dimensional 1H and 13C NMR spectral data. The compounds showed potent antimicrobial activities against bacteria and yeasts. KEY WORDS: Erythrophleum suaveolens (Guill. & Perr.) Brenan, Norcassaide, Diterpenoid alkaloid, Norerythrosuaveolide, Antimicrobial activities, Bacteria, Yeasts Bull. Chem. Soc. Ethiop. 2005, 19(2), 221-226

Characteristic cohomology of pp-form gauge theories

The characteristic cohomology $H^k_{char}(d)$ for an arbitrary set of free $p$-form gauge fields is explicitly worked out in all form degrees $k<n-1$, where $n$ is the spacetime dimension. It is shown that this cohomology is finite-dimensional and completely generated by the forms dual to the field strengths. The gauge invariant characteristic cohomology is also computed. The results are extended to interacting $p$-form gauge theories with gauge invariant interactions. Implications for the BRST cohomology are mentioned.Comment: Latex file, no figures, 44 page

Constraints on Dark Matter Annihilation in Clusters of Galaxies with the Fermi Large Area Telescope

Nearby clusters and groups of galaxies are potentially bright sources of high-energy gamma-ray emission resulting from the pair-annihilation of dark matter particles. However, no significant gamma-ray emission has been detected so far from clusters in the first 11 months of observations with the Fermi Large Area Telescope. We interpret this non-detection in terms of constraints on dark matter particle properties. In particular for leptonic annihilation final states and particle masses greater than ~200 GeV, gamma-ray emission from inverse Compton scattering of CMB photons is expected to dominate the dark matter annihilation signal from clusters, and our gamma-ray limits exclude large regions of the parameter space that would give a good fit to the recent anomalous Pamela and Fermi-LAT electron-positron measurements. We also present constraints on the annihilation of more standard dark matter candidates, such as the lightest neutralino of supersymmetric models. The constraints are particularly strong when including the fact that clusters are known to contain substructure at least on galaxy scales, increasing the expected gamma-ray flux by a factor of ~5 over a smooth-halo assumption. We also explore the effect of uncertainties in cluster dark matter density profiles, finding a systematic uncertainty in the constraints of roughly a factor of two, but similar overall conclusions. In this work, we focus on deriving limits on dark matter models; a more general consideration of the Fermi-LAT data on clusters and clusters as gamma-ray sources is forthcoming.Comment: accepted to JCAP, Corresponding authors: T.E. Jeltema and S. Profumo, minor revisions to be consistent with accepted versio