The small quinolone derived compound HT61 enhances the effect of tobramycin against Pseudomonas aeruginosa in vitro and in vivo.

HT61 is a small quinolone-derived compound previously demonstrated to exhibit bactericidal activity against gram-positive bacteria including methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA). When combined with the classical antibiotics and antiseptics neomycin, gentamicin, mupirocin and chlorhexidine, HT61 demonstrated synergistic bactericidal activity against both MSSA and MRSA infections in vitro. In this study, we investigated the individual antimicrobial activity of HT61 alongside its capability to increase the efficacy of tobramycin against both a tobramycin sensitive laboratory reference strain (PAO1) and tobramycin resistant clinical isolates (RP73, NN2) of the gram-negative bacteria Pseudomonas aeruginosa (P. aeruginosa). Using broth microdilution methods, the MICs of HT61 against all strains were assessed, as well as the effect of HT61 in combination with tobramycin using both the chequerboard method and bacterial time-kill assays. A murine model of pulmonary infection was also used to evaluate the combination therapy of tobramycin and HT61 in vivo. In these studies, we demonstrated significant synergism between HT61 and Tobramycin against the tobramycin resistant P. aeruginosa strains RP73 and NN2, whilst an additive/intermediate effect was observed for P. aeruginosa strain PA01 which was further confirmed using bacterial time kill analysis. In addition, the enhancement of tobramycin by HT61 was also evident in in vitro assays of biofilm eradication. Finally, in vivo studies revealed analogous effects to those observed in vitro with HT61 when administered in combination with tobramycin against each of the three P. aeruginosa strains at the highest tested dose (10 mg/kg)

How good is damped molecular dynamics as a method to simulate radiation damage in metals?

Published versio

Aiding the design of radiation resistant materials with multiphysics simulations of damage processes

The design of metals and alloys resistant to radiation damage involves the physics of electronic excitations and the creation of defects and microstructure. During irradiation damage of metals by high energy particles, energy is exchanged between ions and electrons. Such non-adiabatic processes violate the Born-Oppenheimer approximation, on which all conservative classical interatomic potentials rest. By treating the electrons of a metal explicitly and quantum mechanically we are able to explore the influence of electronic excitations on the ionic motion during irradiation damage. Simple theories suggest that moving ions should feel a damping force proportional to their velocity and directly opposed to it. In contrast, our simulations of a forced oscillating ion have revealed the full complexity of this force: in reality it is anisotropic and dependent on the ion velocity and local atomic environment. A large set of collision cascade simulations has allowed us to explore the form of the damping force further. We have a means of testing various schemes in the literature for incorporating such a force within molecular dynamics (MD) against our semi-classical evolution with explicitly modelled electrons. We find that a model in which the damping force is dependent upon the local electron density is superior to a simple fixed damping model. We also find that applying a lower kinetic energy cut-off for the damping force results in a worse model. A detailed examination of the nature of the forces reveals that there is much scope for further improving the electronic force models within MD. © 2010 Materials Research Society.Accepted versio

Virtual patients design and its effect on clinical reasoning and student experience : a protocol for a randomised factorial multi-centre study

Background Virtual Patients (VPs) are web-based representations of realistic clinical cases. They are proposed as being an optimal method for teaching clinical reasoning skills. International standards exist which define precisely what constitutes a VP. There are multiple design possibilities for VPs, however there is little formal evidence to support individual design features. The purpose of this trial is to explore the effect of two different potentially important design features on clinical reasoning skills and the student experience. These are the branching case pathways (present or absent) and structured clinical reasoning feedback (present or absent). Methods/Design This is a multi-centre randomised 2x2 factorial design study evaluating two independent variables of VP design, branching (present or absent), and structured clinical reasoning feedback (present or absent).The study will be carried out in medical student volunteers in one year group from three university medical schools in the United Kingdom, Warwick, Keele and Birmingham. There are four core musculoskeletal topics. Each case can be designed in four different ways, equating to 16 VPs required for the research. Students will be randomised to four groups, completing the four VP topics in the same order, but with each group exposed to a different VP design sequentially. All students will be exposed to the four designs. Primary outcomes are performance for each case design in a standardized fifteen item clinical reasoning assessment, integrated into each VP, which is identical for each topic. Additionally a 15-item self-reported evaluation is completed for each VP, based on a widely used EViP tool. Student patterns of use of the VPs will be recorded. In one centre, formative clinical and examination performance will be recorded, along with a self reported pre and post-intervention reasoning score, the DTI. Our power calculations indicate a sample size of 112 is required for both primary outcomes

Mechanics and dynamics of X-chromosome pairing at X inactivation

At the onset of X-chromosome inactivation, the vital process whereby female mammalian cells equalize X products with respect to males, the X chromosomes are colocalized along their Xic (X-inactivation center) regions. The mechanism inducing recognition and pairing of the X’s remains, though, elusive. Starting from recent discoveries on the molecular factors and on the DNA sequences (the so-called "pairing sites") involved, we dissect the mechanical basis of Xic colocalization by using a statistical physics model. We show that soluble DNA-specific binding molecules, such as those experimentally identified, can be indeed sufficient to induce the spontaneous colocalization of the homologous chromosomes but only when their concentration, or chemical affinity, rises above a threshold value as a consequence of a thermodynamic phase transition. We derive the likelihood of pairing and its probability distribution. Chromosome dynamics has two stages: an initial independent Brownian diffusion followed, after a characteristic time scale, by recognition and pairing. Finally, we investigate the effects of DNA deletion/insertions in the region of pairing sites and compare model predictions to available experimental data

A soliton menagerie in AdS

We explore the behaviour of charged scalar solitons in asymptotically global AdS4 spacetimes. This is motivated in part by attempting to identify under what circumstances such objects can become large relative to the AdS length scale. We demonstrate that such solitons generically do get large and in fact in the planar limit smoothly connect up with the zero temperature limit of planar scalar hair black holes. In particular, for given Lagrangian parameters we encounter multiple branches of solitons: some which are perturbatively connected to the AdS vacuum and surprisingly, some which are not. We explore the phase space of solutions by tuning the charge of the scalar field and changing scalar boundary conditions at AdS asymptopia, finding intriguing critical behaviour as a function of these parameters. We demonstrate these features not only for phenomenologically motivated gravitational Abelian-Higgs models, but also for models that can be consistently embedded into eleven dimensional supergravity.Comment: 62 pages, 21 figures. v2: added refs and comments and updated appendice

Quantum Criticality and Holographic Superconductors in M-theory

We present a consistent Kaluza-Klein truncation of D=11 supergravity on an arbitrary seven-dimensional Sasaki-Einstein space (SE_7) to a D=4 theory containing a metric, a gauge-field, a complex scalar field and a real scalar field. We use this D=4 theory to construct various black hole solutions that describe the thermodynamics of the d=3 CFTs dual to skew-whiffed AdS_4 X SE_7 solutions. We show that these CFTs have a rich phase diagram, including holographic superconductivity with, generically, broken parity and time reversal invariance. At zero temperature the superconducting solutions are charged domain walls with a universal emergent conformal symmetry in the far infrared.Comment: 52 pages, 16 figures, 3 appendices; minor changes, version to be published in JHE

Emergent Quantum Near-Criticality from Baryonic Black Branes

We find new black 3-brane solutions describing the "conifold gauge theory" at nonzero temperature and baryonic chemical potential. Of particular interest is the low-temperature limit where we find a new kind of weakly curved near-horizon geometry; it is a warped product AdS_2 x R^3 x T^{1,1} with warp factors that are powers of the logarithm of the AdS radius. Thus, our solution encodes a new type of emergent quantum near-criticality. We carry out some stability checks for our solutions. We also set up a consistent ansatz for baryonic black 2-branes of M-theory that are asymptotic to AdS_4 x Q^{1,1,1}.Comment: 29 pages, 4 figures; v2 discussion of entropy revised, minor changes; v3 note added, minor improvements, version published in JHE

COGA phenotypes and linkages on chromosome 2

An initial linkage analysis of the alcoholism phenotype as defined by DSM-III-R criteria and alcoholism defined by DSM-IV criteria showed many, sometimes striking, inconsistencies. These inconsistencies are greatly reduced by making the definition of alcoholism more specific. We defined new phenotypes combining the alcoholism definitions and the latent variables, defining an individual as affected if that individual is alcoholic under one of the definitions (either DSM-III-R or DSM-IV), and indicated having a symptom defined by one of the latent variables. This was done for each of the two alcoholism definitions and five latent variables, selected from a canonical discriminant analyses indicating they formed significant groupings using the electrophysiological variables. We found that linkage analyses utilizing these latent variables were much more robust and consistent than the linkage results based on DSM-III-R or DSM-IV criteria for definition of alcoholism. We also performed linkage analyses on two first prinicipal components derived phenotypes, one derived from the electrophysiolocical variables, and the other derived from the latent variables. A region on chromosome 2 at 250 cM was found to be linked to both of these derived phenotypes. Further examination of the SNPs in this region identified several haplotypes strongly associated with these derived phenotypes