Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis

Pathogenic bacteria present a large disease burden on human health. Control of these pathogens is hampered by rampant lateral gene transfer, whereby pathogenic strains may acquire genes conferring resistance to common antibiotics. Here we introduce tools from topological data analysis to characterize the frequency and scale of lateral gene transfer in bacteria, focusing on a set of pathogens of significant public health relevance. As a case study, we examine the spread of antibiotic resistance in Staphylococcus aureus. Finally, we consider the possible role of the human microbiome as a reservoir for antibiotic resistance genes.Comment: 12 pages, 6 figures. To appear in AMT 2014 Special Session on Advanced Methods of Interactive Data Mining for Personalized Medicin

Excited nucleon spectrum using a non-perturbatively improved clover fermion action

We discuss the extraction of negative-parity baryon masses from lattice QCD calculations. The mass of the lowest-lying negative-parity $J = 1/2^{-}$ state is computed in quenched lattice QCD using an ${\cal O}(a)$-improved clover fermion action, and a splitting found with the nucleon mass. The calculation is performed on two lattice volumes, and three lattice spacings enabling a study of both finite-volume and finite-lattice-spacing uncertainties. A measurement of the first excited radial excitation of the nucleon finds a mass considerably larger than that of the negative-parity ground state, in accord with other lattice determinations but in disagreement with experiment. Results are also presented for the lightest negative-parity $I=3/2$ state.Comment: 7 pages, 5 figures, uses espcrc2. Talk presented at Workshop on Lattice Hadron Physics, Colonial Club Resort, Cairns, Australia, July 9-18, 2001. Corrected error in determination of mass of excited, positive-parity nucleon resonanc

The spectrum of D_s mesons from lattice QCD

The spectrum of orbitally excited $D_s$ mesons is computed in the continuum limit of quenched lattice QCD. The results are consistent with the interpretation that the narrow resonance in the $D_s \pi^0$ channel discovered by the BABAR Collaboration is a $J^P=0^+$ $c\bar{s}$ meson. Furthermore, within statistical errors, the $1^+-1^-$ and the $0^+-0^-$ mass splittings are equal, in agreement with the chiral multiplet structure predicted by heavy hadron chiral effective theory. On our coarsest lattice we present results from the first study of orbitally excited $D_s$ mesons with two flavors of dynamical quarks, with mass slightly larger than the strange quark mass. These results are consistent with the quenched data.Comment: 8 pages, 2 figure

Negative-parity Baryon Masses using an O(a)-improved Fermion Action

We present a calculation of the mass of the lowest-lying negative-parity J=1/2- state in quenched QCD. Results are obtained using a non-perturbatively O(a)-improved clover fermion action, and a splitting is found between the mass of the nucleon and its parity partner. The calculation is performed on two lattice volumes and at three lattice spacings, enabling a study of both finite-volume and finite lattice-spacing uncertainties. A comparison is made with results obtained using the unimproved Wilson fermion action.Comment: 13 pages, 8 figures, revtex Version accepted for publication in Physics Letters B. Some changes to discussion of chiral extrapolations; primary results unchange

The Initial Mass Function in disc galaxies and in galaxy clusters: the chemo-photometric picture

The observed brightness of the Tully-Fisher relation suggests a low stellar M/L ratio and a "bottom-light" IMF in disc galaxies, but the corresponding efficiency of chemical enrichment tends to exceed the observational estimates. Either suitable tuning of the IMF slope and mass limits or metal outflows from disc galaxies must then be invoked. A standard Solar Neighbourhood IMF cannot explain the high metallicity of the hot intra-cluster medium: a different IMF must be at work in clusters of galaxies. Alternatively, if the IMF is universal and chemical enrichment is everywhere as efficient as observed in clusters, substantial loss of metals must occur from the Solar Neighbourhood and from disc galaxies in general; a "non-standard" scenario challenging our understanding of disc galaxy formation.Comment: 6 pages, 4 figures; in Proceedings of IMF@50: the Initial Mass Function 50 years later; Corbelli, Palla and Zinnecker (eds.

Metabolic phenotyping reveals a potential link between elevated faecal amino acids, diet and symptom severity in individuals with severe mental illness

The brain-gut axis is increasingly recognized as an important contributing factor in the onset and progression of severe mental illnesses such as schizophrenia spectrum disorders and bipolar disorder. This study investigates associations between levels of faecal metabolites identified using 1H-NMR, clinical parameters, and dietary components of forty-two individuals diagnosed in a transdiagnostic approach to have severe mental illness. Faecal levels of the amino acids; alanine, leucine, and valine showed a significant positive correlation with psychiatric symptom severity as well as with dairy intake. Overall, this study proposes a diet-induced link between the brain-gut axis and the severity of psychiatric symptoms, which could be valuable in the design of novel dietary or therapeutic interventions to improve psychiatric symptoms