When the path is never shortest: a reality check on shortest path biocomputation

Shortest path problems are a touchstone for evaluating the computing performance and functional range of novel computing substrates. Much has been published in recent years regarding the use of biocomputers to solve minimal path problems such as route optimisation and labyrinth navigation, but their outputs are typically difficult to reproduce and somewhat abstract in nature, suggesting that both experimental design and analysis in the field require standardising. This chapter details laboratory experimental data which probe the path finding process in two single-celled protistic model organisms, Physarum polycephalum and Paramecium caudatum, comprising a shortest path problem and labyrinth navigation, respectively. The results presented illustrate several of the key difficulties that are encountered in categorising biological behaviours in the language of computing, including biological variability, non-halting operations and adverse reactions to experimental stimuli. It is concluded that neither organism examined are able to efficiently or reproducibly solve shortest path problems in the specific experimental conditions that were tested. Data presented are contextualised with biological theory and design principles for maximising the usefulness of experimental biocomputer prototypes.Comment: To appear in: Adamatzky, A (Ed.) Shortest path solvers. From software to wetware. Springer, 201

No evidence for intense, cold accretion onto YSOs from measurements of Li in T-Tauri stars

We have used medium resolution spectra to search for evidence that proto-stellar objects accrete at high rates during their early 'assembly phase'. Models predict that depleted lithium and reduced luminosity in T-Tauri stars are key signatures of 'cold' high-rate accretion occurring early in a star's evolution. We found no evidence in 168 stars in NGC 2264 and the Orion Nebula Cluster for strong lithium depletion through analysis of veiling corrected 6708 angstrom lithium spectral line strengths. This suggests that 'cold' accretion at high rates (M_dot > 5 x 10-4 M_sol yr-1) occurs in the assembly phase of fewer than 0.5 per cent of 0.3 < M < 1.9 M_sol stars. We also find that the dispersion in the strength of the 6708 angstrom lithium line might imply an age spread that is similar in magnitude to the apparent age spread implied by the luminosity dispersion seen in colour magnitude diagrams. Evidence for weak lithium depletion (< 10 per cent in equivalent width) that is correlated with luminosity is also apparent, but we are unable to determine whether age spreads or accretion at rates less than 5 x 10-4 M_sol yr-1 are responsible.Comment: 13 pages, 10 figures; Accepted for publication in Monthly Notices of the Royal Astronomical Society, 2013 June 0

Pre-main-sequence isochrones -- II. Revising star and planet formation timescales

We have derived ages for 13 young (<30 Myr) star-forming regions and find they are up to a factor two older than the ages typically adopted in the literature. This result has wide-ranging implications, including that circumstellar discs survive longer (~10-12 Myr) and that the average Class I lifetime is greater (~1 Myr) than currently believed. For each star-forming region we derived two ages from colour-magnitude diagrams. First we fitted models of the evolution between the zero-age main-sequence and terminal-age main-sequence to derive a homogeneous set of main-sequence ages, distances and reddenings with statistically meaningful uncertainties. Our second age for each star-forming region was derived by fitting pre-main-sequence stars to new semi-empirical model isochrones. For the first time (for a set of clusters younger than 50 Myr) we find broad agreement between these two ages, and since these are derived from two distinct mass regimes that rely on different aspects of stellar physics, it gives us confidence in the new age scale. This agreement is largely due to our adoption of empirical colour-Teff relations and bolometric corrections for pre-main-sequence stars cooler than 4000 K. The revised ages for the star-forming regions in our sample are: ~2 Myr for NGC 6611 (Eagle Nebula; M 16), IC 5146 (Cocoon Nebula), NGC 6530 (Lagoon Nebula; M 8), and NGC 2244 (Rosette Nebula); ~6 Myr for {\sigma} Ori, Cep OB3b, and IC 348; ~10 Myr for {\lambda} Ori (Collinder 69); ~11 Myr for NGC 2169; ~12 Myr for NGC 2362; ~13 Myr for NGC 7160; ~14 Myr for {\chi} Per (NGC 884); and ~20 Myr for NGC 1960 (M 36).Comment: 28 pages, 18 figures, 34 tables, accepted for publication in MNRAS. All photometric catalogues presented in this paper are available online at the Cluster Collaboration homepage http://www.astro.ex.ac.uk/people/timn/Catalogues

A lithium depletion boundary age of 22 Myr for NGC 1960

We present a deep Cousins RI photometric survey of the open cluster NGC 1960, complete to R_C \simeq 22, I_C \simeq 21, that is used to select a sample of very low-mass cluster candidates. Gemini spectroscopy of a subset of these is used to confirm membership and locate the age-dependent "lithium depletion boundary" (LDB) --the luminosity at which lithium remains unburned in its low-mass stars. The LDB implies a cluster age of 22 +/-4 Myr and is quite insensitive to choice of evolutionary model. NGC 1960 is the youngest cluster for which a LDB age has been estimated and possesses a well populated upper main sequence and a rich low-mass pre-main sequence. The LDB age determined here agrees well with precise age estimates made for the same cluster based on isochrone fits to its high- and low-mass populations. The concordance between these three age estimation techniques, that rely on different facets of stellar astrophysics at very different masses, is an important step towards calibrating the absolute ages of young open clusters and lends confidence to ages determined using any one of them.Comment: Accepted for publication in MNRA

Using the UM dynamical cores to reproduce idealised 3D flows

We demonstrate that both the current (New Dynamics), and next generation (ENDGame) dynamical cores of the UK Met Office global circulation model, the UM, reproduce consistently, the long-term, large-scale flows found in several published idealised tests. The cases presented are the Held-Suarez test, a simplified model of Earth (including a stratosphere), and a hypothetical tidally locked Earth. Furthermore, we show that using simplifications to the dynamical equations, which are expected to be justified for the physical domains and flow regimes we have studied, and which are supported by the ENDGame dynamical core, also produces matching long-term, large-scale flows. Finally, we present evidence for differences in the detail of the planetary flows and circulations resulting from improvements in the ENDGame formulation over New Dynamics.Comment: 34 Pages, 23 Figures. Accepted for publication in Geoscientific Model Development (pre-proof version

Use of monitoring technology and injury incidence among recreational runners: a cross-sectional study

Abstract Background Monitoring technology is increasingly accessible to recreational runners. Our aim was to examine patterns of technology use in recreational runners, and its potential association with injury. Methods We conducted a cross-sectional questionnaire study in a sample of adult runners. Recruitment took place at three different 5 km parkrun event across Northern Ireland. Demographics, technology use, running behaviour and running-related injury (RRI) history were examined. Regression analyses were performed to determine relationships between variables. Results Responses were obtained from 192 of 483 eligible finishers (39.8% response rate). Average age was 45.9 years (SD 10.3), with males (47.1 years SD 9.7) slightly older than females (44.8 years SD 10.8). On average, participants ran 3.0 days per week (SD 1.3), with an average weekly distance of 22.6 km (SD 19.7). Males typically ran further (MD 6.2 km/week; 95% CI 0.4 to 12.0) than females. Monitoring technology was used by 87.4% (153/175); with GPS watches the most common device (87.6% (134/153)). Runners using monitoring technology ran further (MD 14.4 km/week; 95% CI 10.3 to 18.5) and more frequently (MD 1.3 days/week; 95% CI 0.7 to 1.9) than those who did not use monitoring technology. There was no significant difference in average age between runners who used monitoring technology and those who did not (MD 4.0 years; 95% CI −0.7 to 8.7). RRI was reported by 40.6% (71/175) of participants in the previous 12 months. In a univariate analysis, none of the selected predictors (age, number of days run per week, distance run per week, or usage of technology to modify training pattern) (p > 0.1) were associated with RRI. Conclusions This study found a high prevalence of monitoring technology usage among recreational runners. While the incidence of RRI remains high, it is not associated with the usage of monitoring technology. Further prospective research should examine if monitoring technology can reduce RRI incidence among recreational runners in future

Development and application of the GIM code for the Cyber 203 computer

The GIM computer code for fluid dynamics research was developed. Enhancement of the computer code, implicit algorithm development, turbulence model implementation, chemistry model development, interactive input module coding and wing/body flowfield computation are described. The GIM quasi-parabolic code development was completed, and the code used to compute a number of example cases. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and implicit finite difference scheme were also added. Development was completed on the interactive module for generating the input data for GIM. Solutions for inviscid hypersonic flow over a wing/body configuration are also presented

Luminex-based virtual crossmatching for renal transplantation in South Africa

Background. Current practice in the Johannesburg renal transplantation programme is to perform a transplant when the patient&rsquo;s complement-dependent cytotoxicity and flow cytometric crossmatches are negative. However, even in patients with negative crossmatches early graft rejections have occurred. We retrospectively evaluated the use of Luminex anti-human leukocyte antigen (HLA) antibody detection technology, often termed &lsquo;virtual crossmatching&rsquo;, compared with the flow cytometric crossmatch, for predicting graft outcome in renal transplant patients. Methods. Sixty-four recipients were crossmatched against multiple donors during their routine work-up for transplant (111 crossmatches); 17 of these patients received transplants during the study period. Anti-HLA antibody detection was performed using Luminex technology and the results were compared with the flow cytometric crossmatch results and with short-term graft success. Results. Compared with flow cytometric crossmatch results, the sensitivity and specificity of Luminex virtual crossmatching was 85.7% and 90.7% for the T-cell crossmatch and 100% and 87.2% for the B-cell crossmatch. Both the sensitivity and specificity of Luminex for predicting short-term graft success were 100%. Conclusions. Strong evidence is provided that single-antigen assays provide improved sensitivity to detect clinically relevant anti-HLA antibodies and can reliably be used to predict shortterm graft success. We recommend incorporation of single-antigen Luminex methodology into the routine work-up algorithm of renal transplant recipients in South Africa.S Afr Med J, 2012;102:40-4