SPH simulations of irradiation-driven warped accretion discs and the long periods in X-ray binaries

We present three dimensional smoothed particle hydrodynamics (SPH) calculations of irradiation-driven warping of accretion discs. Initially unwarped planar discs are unstable to the radiation reaction when the disc is illuminated by a central radiation source. The disc warps and tilts and precesses slowly in a retrograde direction; its shape continuously flexes in response to the changing orientation of the Roche potential. We simulate ten systems: eight X-ray binaries, one cataclysmic variable (CV), and a `generic' low mass X-ray binary (LMXB). We adopt system parameters from observations and tune a single parameter: our model X-ray luminosity ($L_{*}$) to reproduce the observed or inferred super-orbital periods. Without exception, across a wide range of parameter space, we find an astonishingly good match between the observed $L_{X}$ and the model $L_{*}$. We conclude irradiation-driven warping is the mechanism underlying the long periods in X-ray binaries. Our Her X-1 simulation simultaneously reproduces the observed $L_{X}$, the "main-" and "short-high" X-ray states and the orbital inclination. Our simulations of SS 433 give a maximum warp angle of $18.6^{\circ}$, a good match to the cone traced by the jets, but this angle is reached only in the outer disc. In all cases, the overall disc tilt is less than \degrees{13} and the maximum disc warp is less than and or equal to \degrees{21}.Comment: 17 pages, 14 figures, shorter abstract (24 lines limit

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

Three dimensional SPH simulations of radiation-driven warped accretion discs

We present three dimensional smoothed particle hydrodynamics (SPH) calculations of warped accretion discs in X-ray binary systems. Geometrically thin, optically thick accretion discs are illuminated by a central radiation source. This illumination exerts a non-axisymmetric radiation pressure on the surface of the disc resulting in a torque that acts on the disc to induce a twist or warp. Initially planar discs are unstable to warping driven by the radiation torque and in general the warps also precess in a retrograde direction relative to the orbital flow. We simulate a number of X-ray binary systems which have different mass ratios using a number of different luminosities for each. Radiation-driven warping occurs for all systems simulated. For mass ratios q ~ 0.1 a moderate warp occurs in the inner disc while the outer disc remains in the orbital plane (c.f. X 1916-053). For less extreme mass ratios the entire disc tilts out of the orbital plane (c.f. Her X-1). For discs that are tilted out of the orbital plane in which the outer edge material of the disc is precessing in a prograde direction we obtain both positive and negative superhumps simultaneously in the dissipation light curve (c.f. V603 Aql).Comment: 12 pages, 12 figures, paper accepted for publication by MNRA

The Main Injector Beam Position Monitor Front-End Software

The front-end software developed for the Main Injector (MI) BPM upgrade is described. The software is responsible for controlling a VME crate, equipped with a Motorola PowerPC board running the VxWorks operating system, a custom made timing board and up to 10 commercial digitizer boards. The complete MI BPM system is composed of 7 independent units, each collecting data from 19 to 38 BPM pickups. The MI BPM system uses several components already employed on the successful upgrade of another Fermilab machine, the Tevatron. The front-end software framework developed for the Tevatron BPM upgrade is the base for building the MI front-end software. The framework is implemented in C++ as a generic component library (GBPM) that provides an event-driven data acquisition environment. Functionality of GBPM is extended to meet MI BPM requirements, such as the ability to handle and manage data from multiple cycles; perform readout of the digitizer boards without disrupting or missing subsequent cycles; transition between closed orbit and turn-by-turn modes within a cycle, using different filter and timing configurations; and allow the definition of new cycles during normal operation

How old is this mutation? - a study of three Ashkenazi Jewish founder mutations

Abstract Background Several founder mutations leading to increased risk of cancer among Ashkenazi Jewish individuals have been identified, and some estimates of the age of the mutations have been published. A variety of different methods have been used previously to estimate the age of the mutations. Here three datasets containing genotype information near known founder mutations are reanalyzed in order to compare three approaches for estimating the age of a mutation. The methods are: (a) the single marker method used by Risch et al., (1995); (b) the intra-allelic coalescent model known as DMLE, and (c) the Goldgar method proposed in Neuhausen et al. (1996), and modified slightly by our group. The three mutations analyzed were MSH2*1906 G->C, APC*I1307K, and BRCA2*6174delT. Results All methods depend on accurate estimates of inter-marker recombination rates. The modified Goldgar method allows for marker mutation as well as recombination, but requires prior estimates of the possible haplotypes carrying the mutation for each individual. It does not incorporate population growth rates. The DMLE method simultaneously estimates the haplotypes with the mutation age, and builds in the population growth rate. The single marker estimates, however, are more sensitive to the recombination rates and are unstable. Mutation age estimates based on DMLE are 16.8 generations for MSH2 (95% credible interval (13, 23)), 106 generations for I1037K (86-129), and 90 generations for 6174delT (71-114). Conclusions For recent founder mutations where marker mutations are unlikely to have occurred, both DMLE and the Goldgar method can give good results. Caution is necessary for older mutations, especially if the effective population size may have remained small for a long period of time

Determinants of exercise intolerance in breast cancer patients prior to anthracycline chemotherapy

Women with early‐stage breast cancer have reduced peak exercise oxygen uptake (peak V O2). The purpose of this study was to evaluate peak V O2 and right (RV ) and left (LV ) ventricular function prior to adjuvant chemotherapy. Twenty‐nine early‐stage breast cancer patients (mean age: 48 years) and 10 age‐matched healthy women were studied. Participants performed an upright cycle exercise test with expired gas analysis to measure peak V O2. RV and LV volumes and function were measured at rest, submaximal and peak supine cycle exercise using cardiac magnetic resonance imaging. Peak V O2 was significantly lower in breast cancer patients versus controls (1.7 ± 0.4 vs. 2.3 ± 0.5 L/min, P = 0.0013; 25 ± 6 vs. 35 ± 6 mL/kg/min, P = 0.00009). No significant difference was found between groups for peak upright exercise heart rate (174 ± 13 vs. 169 ± 16 bpm, P = 0.39). Rest, submaximal and peak exercise RV and LV end‐diastolic and end‐systolic volume index, stroke index, and cardiac index were significantly lower in breast cancer patients versus controls (P < 0.05 for all). No significant difference was found between groups for rest and exercise RV and LV ejection fraction. Despite preserved RV and LV ejection fraction, the decreased peak V O2 in early‐stage breast cancer patients prior to adjuvant chemotherapy is due in part to decreased peak cardiac index secondary to reductions in RV and LV end‐diastolic volumes

Simulations of spectral lines from an eccentric precessing accretion disc

Two dimensional SPH simulations of a precessing accretion disc in a q=0.1 binary system (such as XTE J1118+480) reveal complex and continuously varying shape, kinematics, and dissipation. The stream-disc impact region and disc spiral density waves are prominent sources of energy dissipation.The dissipated energy is modulated on the period P_{sh} = ({P_{orb}}^{-1}-{P_{prec}}^{-1}^{-1} with which the orientation of the disc relative to the mass donor repeats. This superhump modulation in dissipation energy has a variation in amplitude of ~10% relative to the total dissipation energy and evolves, repeating exactly only after a full disc precession cycle. A sharp component in the light curve is associated with centrifugally expelled material falling back and impacting the disc. Synthetic trailed spectrograms reveal two distinct "S-wave" features, produced respectively by the stream gas and the disc gas at the stream-disc impact shock. These S-waves are non-sinusoidal, and evolve with disc precession phase. We identify the spiral density wave emission in the trailed spectrogram. Instantaneous Doppler maps show how the stream impact moves in velocity space during an orbit. In our maximum entropy Doppler tomogram the stream impact region emission is distorted, and the spiral density wave emission is uppressed. A significant radial velocity modulation of the whole line profile occurs on the disc precession period. We compare our SPH simulation with a simple 3D model: the former is appropriate for comparison with emission lines while the latter is preferable for skewed absorption lines from precessing discs.Comment: See http://physics.open.ac.uk/FHMR/ for associated movie (avi) files. The full paper is in MNRAS press. Limited disk space limit of 650k, hence low resolution figure file

Canopy and Ear Traits Associated With Avoidance of Fusarium Head Blight in Wheat

Doubled haploid and elite wheat genotypes were ground inoculated in three field experiments and head spray inoculated in two glasshouse experiments, using mixed Fusarium and Microdochium species, to identify crop canopy and ear traits associated with Fusarium head blight (FHB) disease. In all experiments, flag leaf length and tiller number were consistently identified as the most significant canopy traits contributing to progression of FHB caused by Fusarium graminearum, F. culmorum, and F. avenaceum. The influence of ear traits was greater for F. poae that may possess more diverse routes for transmission and spread. Consistently, spikelet density was associated with increased disease severity in the field. F. graminearum, F. culmorum, and F. langsethiae were the main mycotoxin producers and their respective toxins were significantly related to fungal biomass and number of spikelets per ear. Genotypes with lower tiller numbers, shorter flag leaves and less dense ears may be able to avoid FHB disease caused by F. graminearum, F. culmorum, F. avenaceum, or Microdochium species however selection for these canopy and ear architectural traits to enable disease avoidance in wheat is likely to result in a potential trade-off with grain yield and therefore only moderately advantageous in susceptible genotypes

Expression and regulation of drug transporters in vertebrate neutrophils.

There remains a need to identify novel pro-resolution drugs for treatment of inflammatory disease. To date, there are no neutrophil-specific anti-inflammatory treatments in clinical use, perhaps due to our lack of understanding of how drugs access this complex cell type. Here we present the first comprehensive description and expression of both major classes of drug transporters, SLC and ABC, in resting human blood neutrophils. Moreover, we have studied the expression of these carriers in the tractable model system, the zebrafish (Danio rerio), additionally examining the evolutionary relationship between drug transporters in zebrafish and humans. We anticipate that this will be a valuable resource to the field of inflammation biology and will be an important asset in future anti-inflammatory drug design