The PAX 2 picture processing system

PAX 2 digital picture processing program written in FORTRAN - subroutine annotation

Jet-Induced Nucleosynthesis in Misaligned Microquasars

The jet axes and the orbital planes of microquasar systems are usually assumed to be approximately perpendicular, eventhough this is not currently an observational requirement. On the contrary, in one of the few systems where the relative orientations are well-constrained, V4641Sgr, the jet axis is known to lie not more than ~36 degrees from the binary plane. Such a jet, lying close to the binary plane, and traveling at a significant fraction of the speed of light may periodically impact the secondary star initiating nuclear reactions on its surface. The integrated yield of such nuclear reactions over the age of the binary system (less the radiative mass loss) will detectably alter the elemental abundances of the companion star. This scenario may explain the anomalously high Li enhancements (roughly ~20-200 times the sun's photospheric value; or, equivalently, 0.1-1 times the average solar system value) seen in the companions of some black-hole X-ray binary systems. (Such enhancements are puzzling since Li nuclei are exceedingly fragile - being easily destroyed in the interiors of stars - and Li would be expected to be depleted rather than enhanced there.) Gamma-ray line signatures of the proposed process could include the 2.22 MeV neutron capture line as well as the 0.478 MeV 7Li* de-excitation line, both of which may be discernable with the INTEGRAL satellite if produced in an optically thin region during a large outburst. For very energetic jets, a relatively narrow neutral pion gamma-decay signature at 67.5 MeV could also be measurable with the GLAST satellite. We argue that about 10-20% of all microquasar systems ought to be sufficiently misaligned as to be undergoing the proposed jet-secondary impacts.Comment: ApJ, accepted. Includes referee's suggestions and some minor clarifications over previous versio

Functional Analysis of the Role of Toxin-Antitoxin (TA) Loci in Bacterial Persistence.

Bacterial Persistence: Methods and ProtocolsThe final publication is available at Springer via http://dx.doi.org/10.1007/978-1-4939-2854-5_11We have developed a method to analyze the functionality of putative TA loci by expressing them in Escherichia coli. Here, we describe the procedure for cloning recombinant TA genes into inducible plasmids and expressing these in E. coli. Following expression, toxicity, resuscitation of growth, and changes in persister cell formation are assayed. This can confirm whether predicted TA loci are active in E. coli and whether expression can affect persister cell formation

Identification of type II toxin-antitoxin modules in Burkholderia pseudomallei

© 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reservedThis is an open access article that is freely available in ORE or from the publisher's web site. Please cite the published version.Type II toxin-antitoxin (TA) systems are believed to be widely distributed amongst bacteria although their biological functions are not clear. We have identified eight candidate TA systems in the genome of the human pathogen Burkholderia pseudomallei. Five of these were located in genome islands. Of the candidate toxins, BPSL0175 (RelE1) or BPSS1060 (RelE2) caused growth to cease when expressed in Escherichia coli, whereas expression of BPSS0390 (HicA) or BPSS1584 (HipA) (in an E. coli ΔhipBA background) caused a reduction in the number of culturable bacteria. The cognate antitoxins could restore growth and culturability of cells.Wellcome Trus

Subclinical myocardial disease by cardiac magnetic resonance imaging and spectroscopy in healthy HIV/Hepatitis C virus-coinfected persons.

Objective The contribution of hepatitis C virus (HCV) infection to the risk of heart failure in human immunodeficiency virus (HIV)-coinfected persons is unknown. The objective was to characterize cardiac function and morphology in HIV-treated coinfected persons. Methods In a cross-sectional study, HIV-infected patients virologically suppressed on antiretroviral therapy without known cardiovascular disease or diabetes mellitus underwent cardiac magnetic resonance imaging and spectroscopy for measures of cardiac function, myocardial fibrosis, and steatosis. Results The study included 18 male patients with a median age of 44 years. Of these, 10 had untreated HCV coinfection and eight had HIV monoinfection. Global systolic and diastolic function in the cohort were normal, and median myocardial fat content was 0.48% (interquartile range 0.35-1.54). Left ventricular (LV) mass index and LV mass/volume ratio were significantly greater in the HIV/HCV-coinfected group compared with the HIV-monoinfected group. In the HIV-monoinfected group, there was more myocardial fibrosis as measured by extracellular volume fraction. Conclusions There were differences between HIV/HCV-coinfected and HIV-monoinfected patients in cardiac structure and morphology. Larger studies are needed to examine whether HIV and HCV independently contribute to mechanisms of heart failure

Discrete breathers in a two-dimensional hexagonal Fermi-Pasta-Ulam lattice

We consider a two-dimensional Fermi-Pasta-Ulam (FPU) lattice with hexagonal symmetry. Using asymptotic methods based on small amplitude ansatz, at third order we obtain a reduction to a cubic nonlinear Schrodinger equation (NLS) for the breather envelope. However, this does not support stable soliton solutions, so we pursue a higher-order analysis yielding a generalised NLS, which includes known stabilising terms. We present numerical results which suggest that long-lived stationary and moving breathers are supported by the lattice. We find breather solutions which move in an arbitrary direction, an ellipticity criterion for the wavenumbers of the carrier wave, asymptotic estimates for the breather energy, and a minimum threshold energy below which breathers cannot be found. This energy threshold is maximised for stationary breathers, and becomes vanishingly small near the boundary of the elliptic domain where breathers attain a maximum speed. Several of the results obtained are similar to those obtained for the square FPU lattice (Butt & Wattis, J Phys A, 39, 4955, (2006)), though we find that the square and hexagonal lattices exhibit different properties in regard to the generation of harmonics, and the isotropy of the generalised NLS equation.Comment: 29 pages, 14 Figure