Purification and characterization of a protein-tyrosine kinase encoded by the Abelson murine leukemia virus

Sequences termed v-abl, which encode the protein-tyrosine kinase activity of Abelson murine leukemia virus, have been expressed in Escherichia coli as a fusion product (ptabl50 kinase). This fusion protein contains 80 amino acids of SV40 small t and the 403 amino acid protein kinase domain of v-abl. We report here the purification and characterization of this kinase. The purified material contains two proteins (Mr = 59,800 and 57,200), both of which possess sequences derived from v-abl. Overall purification was 3,750-fold, with a 31% yield, such that 117 micrograms of kinase could be obtained from 40 g of E. coli within 6-7 days. The specific kinase activity is over 170 mumol of phosphate min-1 mumol-1, comparable to the most active protein- serine kinases. Kinase activity is insensitive to K+, Na+, Ca2+, Ca2+- calmodulin, cAMP, or cAMP-dependent protein kinase inhibitor. The Km for ATP is dependent on the concentration of the second substrate. GTP can also be used as a phosphate donor. The enzyme can phosphorylate peptides consisting of as few as two amino acids and, at a very low rate, free tyrosine. Incubation of the kinase with [gamma-32P]ATP results in incorporation of 1.0 mol of phosphate/mol of protein. This reaction, however, cannot be blocked by prior incubation with unlabeled ATP. Incubation of 32P-labeled kinase with either ADP or ATP results in the synthesis of [32P]ATP. This suggests the phosphotyrosine residue on the Abelson kinase contains a high energy phosphate bond

Discovery of disc precession in the M31 dipping X-ray binary Bo 158

We present results from three XMM-Newton observations of the M31 low mass X-ray binary XMMU J004314.4+410726.3 (Bo 158), spaced over 3 days in 2004, July. Bo 158 was the first dipping LMXB to be discovered in M31. Periodic intensity dips were previously seen to occur on a 2.78-hr period, due to absorption in material that is raised out of the plane of the accretion disc. The report of these observations stated that the dip depth was anti-correlated with source intensity. However, our new observations do not favour a strict intensity dependance, but rather suggest that the dip variation is due to precession of the accretion disc. This is to be expected in LMXBs with a mass ratio <~ 0.3 (period <~ 4 hr), as the disc reaches the 3:1 resonance with the binary companion, causing elongation and precession of the disc. A smoothed particle hydrodynamics simulation of the disc in this system shows retrograde rotation of a disc warp on a period of ~11 P_orb, and prograde disc precession on a period of ~29 P_orb. This is consistent with the observed variation in the depth of the dips. We find that the dipping behaviour is most likely to be modified by the disc precession, hence we predict that the dipping behaviour repeats on a 81+/-3 hr cycle.Comment: 9 pages, 6 figures, accepted for publication by MNRAS, changed conten

Hydrodynamic modelling of accretion flows

In the proceedings of this, and of several recent close binary conferences, there have been several contributions describing smoothed particle hydrodynamics simulations of accretion disks. It is apposite therefore to review the numerical scheme itself with emphasis on its advantages for disk modelling, and the methods used for modelling viscous processes.Comment: 3 pages, to appear in proceedings of IAU Colloquium 194: Compact binaries in the galaxy and beyon

The effect of quantization on the FCIQMC sign problem

The sign problem in Full Configuration Interaction Quantum Monte Carlo (FCIQMC) without annihilation can be understood as an instability of the psi-particle population to the ground state of the matrix obtained by making all off-diagonal elements of the Hamiltonian negative. Such a matrix, and hence the sign problem, is basis dependent. In this paper we discuss the properties of a physically important basis choice: first versus second quantization. For a given choice of single-particle orbitals, we identify the conditions under which the fermion sign problem in the second quantized basis of antisymmetric Slater determinants is identical to the sign problem in the first quantized basis of unsymmetrized Hartree products. We also show that, when the two differ, the fermion sign problem is always less severe in the second quantized basis. This supports the idea that FCIQMC, even in the absence of annihilation, improves the sign problem relative to first quantized methods. Finally, we point out some theoretically interesting classes of Hamiltonians where first and second quantized sign problems differ, and others where they do not.Comment: 4 pages w/ 2 page appendix, 2 figures, 1 tabl

Comprehensive simulations of superhumps

(Abridged) We use 3D SPH calculations with higher resolution, as well as with more realistic viscosity and sound-speed prescriptions than previous work to examine the eccentric instability which underlies the superhump phenomenon in semi-detached binaries. We illustrate the importance of the two-armed spiral mode in the generation of superhumps. Differential motions in the fluid disc cause converging flows which lead to strong spiral shocks once each superhump cycle. The dissipation associated with these shocks powers the superhump. We compare 2D and 3D results, and conclude that 3D simulations are necessary to faithfully simulate the disc dynamics. We ran our simulations for unprecedented durations, so that an eccentric equilibrium is established except at high mass ratios where the growth rate of the instability is very low. Our improved simulations give a closer match to the observed relationship between superhump period excess and binary mass ratio than previous numerical work. The observed black hole X-ray transient superhumpers appear to have systematically lower disc precession rates than the cataclysmic variables. This could be due to higher disc temperatures and thicknesses. The modulation in total viscous dissipation on the superhump period is overwhelmingly from the region of the disc within the 3:1 resonance radius. As the eccentric instability develops, the viscous torques are enhanced, and the disc consequently adjusts to a new equilibrium state, as suggested in the thermal-tidal instability model. We quantify this enhancement in the viscosity, which is ~10 per cent for q=0.08. We characterise the eccentricity distributions in our accretion discs, and show that the entire body of the disc partakes in the eccentricity.Comment: 18 pages (mn2e LaTeX), 14 figures, 5 tables, Accepted for publication in MNRA

Open-source development experiences in scientific software: the HANDE quantum Monte Carlo project

The HANDE quantum Monte Carlo project offers accessible stochastic algorithms for general use for scientists in the field of quantum chemistry. HANDE is an ambitious and general high-performance code developed by a geographically-dispersed team with a variety of backgrounds in computational science. In the course of preparing a public, open-source release, we have taken this opportunity to step back and look at what we have done and what we hope to do in the future. We pay particular attention to development processes, the approach taken to train students joining the project, and how a flat hierarchical structure aids communicationComment: 6 pages. Submission to WSSSPE

Prediction-based classification for longitudinal biomarkers

Assessment of circulating CD4 count change over time in HIV-infected subjects on antiretroviral therapy (ART) is a central component of disease monitoring. The increasing number of HIV-infected subjects starting therapy and the limited capacity to support CD4 count testing within resource-limited settings have fueled interest in identifying correlates of CD4 count change such as total lymphocyte count, among others. The application of modeling techniques will be essential to this endeavor due to the typically nonlinear CD4 trajectory over time and the multiple input variables necessary for capturing CD4 variability. We propose a prediction-based classification approach that involves first stage modeling and subsequent classification based on clinically meaningful thresholds. This approach draws on existing analytical methods described in the receiver operating characteristic curve literature while presenting an extension for handling a continuous outcome. Application of this method to an independent test sample results in greater than 98% positive predictive value for CD4 count change. The prediction algorithm is derived based on a cohort of $n=270$ HIV-1 infected individuals from the Royal Free Hospital, London who were followed for up to three years from initiation of ART. A test sample comprised of $n=72$ individuals from Philadelphia and followed for a similar length of time is used for validation. Results suggest that this approach may be a useful tool for prioritizing limited laboratory resources for CD4 testing after subjects start antiretroviral therapy.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS326 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Using a model of group psychotherapy to support social research on sensitive topics

This article describes the exploratory use of professional therapeutic support by social researchers working on a sensitive topic. Talking to recently bereaved parents about the financial implications of their child's death was expected to be demanding work, and the research design included access to an independent psychotherapeutic service. Using this kind of professional support is rare within the general social research community, and it is useful to reflect on the process. There are likely to be implications for collection and interpretation of data, research output and the role and experience of the therapist. Here, the primary focus is the potential impact on researcher well-being

Riding a Spiral Wave: Numerical Simulation of Spiral Waves in a Co-Moving Frame of Reference

We describe an approach to numerical simulation of spiral waves dynamics of large spatial extent, using small computational grids.Comment: 15 pages, 14 figures, as accepted by Phys Rev E 2010/03/2