A reiterative method for calculating the early bactericidal activity of antituberculosis drugs.

Studies of early bactericidal activity (EBA) are important in the rapid evaluation of new antituberculosis drugs. Historically, these have concentrated on the log fall in the viable count in sputum during the first 48 hours of therapy. In this paper, we provide a mathematical model that suggests that the viable count in sputum follows an exponential decay curve with the equation V = S + Me(-kt) (where V is the viable count, M the population of bacteria susceptible to the test drug, S the population susceptible only to sterilizing agents, t the day of sputum collection as related to start of therapy, k the rate constant for the bacteria killed each day, and e the Napierian constant). We demonstrate that data from clinical trials fits the exponential decay model. We propose that future EBA studies should be performed by measuring daily quantitative counts for at least 5 days. We also propose that the comparison of the early bactericidal activity of antituberculosis drugs should be evaluated using the time taken to reduce the viable count by 50% (vt(50)). A further reiterative refinement following a rule set based on statistically the best fit to the exponential decay model is described that will allow investigators to identify anomalous results and thus enhance the accuracy in measuring early bactericidal activity

Molecular Clock on a Neutral Network

The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network of high-fitness genotypes, we establish a formalism for computing all cumulants of the full probability distribution of accumulated mutations in terms of graph properties of the neutral network, and use the formalism to prove overdispersion of the molecular clock. We further show that significant overdispersion arises naturally in evolution when the neutral network is highly sparse, exhibits large global fluctuations in neutrality, and small local fluctuations in neutrality. The results are also relevant for elucidating the topological structure of a neutral network from empirical measurements of the substitution process.Comment: 10 page

StochKit-FF: Efficient Systems Biology on Multicore Architectures

The stochastic modelling of biological systems is an informative, and in some cases, very adequate technique, which may however result in being more expensive than other modelling approaches, such as differential equations. We present StochKit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and exploits the novel concept of selective memory. We experiment StochKit-FF on a model of HIV infection dynamics, with the aim of extracting information from efficiently run experiments, here in terms of average and variance and, on a longer term, of more structured data.Comment: 14 pages + cover pag

Analysis of multiple incidence angle SIR-B data for determining forest stand characteristics

For the first time in the U.S. space program, digital synthetic aperture radar (SR) data were obtained from different incidence angles during Space Shuttle Mission 41-G. Shuttle Imaging Radar-B (SIR-B) data were obtained at incidence angles of 58 deg., 45 deg., and 28 deg., on October 9, 10, and 11, 1984, respectively, for a predominantly forested study area in northern Florida. Cloud-free LANDSAT Thematic Mapper (T.M.) data were obtained over the same area on October 12. The SIR-B data were processed and then digitally registered to the LANDSAT T.M. data by scientists at the Jet Propulsion Laboratory. This is the only known digitally registered SIR-B and T.M. data set for which the data were obtained nearly simultaneously. The data analysis of this information is discussed

Stability Properties of Nonhyperbolic Chaotic Attractors under Noise

We study local and global stability of nonhyperbolic chaotic attractors contaminated by noise. The former is given by the maximum distance of a noisy trajectory from the noisefree attractor, while the latter is provided by the minimal escape energy necessary to leave the basin of attraction, calculated with the Hamiltonian theory of large fluctuations. We establish the important and counterintuitive result that both concepts may be opposed to each other. Even when one attractor is globally more stable than another one, it can be locally less stable. Our results are exemplified with the Holmes map, for two different sets of parameter, and with a juxtaposition of the Holmes and the Ikeda maps. Finally, the experimental relevance of these findings is pointed out.Comment: Phys.Rev. Lett., to be publishe

Robust Trapped-Ion Quantum Logic Gates by Continuous Dynamical Decoupling

We introduce a novel scheme that combines phonon-mediated quantum logic gates in trapped ions with the benefits of continuous dynamical decoupling. We demonstrate theoretically that a strong driving of the qubit decouples it from external magnetic-field noise, enhancing the fidelity of two-qubit quantum gates. Moreover, the scheme does not require ground-state cooling, and is inherently robust to undesired ac-Stark shifts. The underlying mechanism can be extended to a variety of other systems where a strong driving protects the quantum coherence of the qubits without compromising the two-qubit couplings.Comment: Slightly longer than the published versio

Inelastic final-state interaction

The final-state interaction in multichannel decay processes is sytematically studied with application to B decay in mind. Since the final-state inteaction is intrinsically interwoven with the decay interaction in this case, no simple phase theorem like "Watson's theorem" holds for experimentally observed final states. We first examine in detail the two-channel problem as a toy-model to clarify the issues and to remedy common mistakes made in earlier literature. Realistic multichannel problems are too challenging for quantitative analysis. To cope with mathematical complexity, we introduce a method of approximation that is applicable to the case where one prominant inelastic channel dominates over all others. We illustrate this approximation method in the amplitude of the decay B to pi K fed by the intermediate states of a charmed meson pair. Even with our approximation we need more accurate information of strong interactions than we have now. Nonethless we are able to obtain some insight in the issue and draw useful conclusions on general fearyres on the strong phases.Comment: The published version. One figure correcte

Stronger computational modelling of signalling pathways using both continuous and discrete-state methods

Starting from a biochemical signalling pathway model expresses in a process algebra enriched with quantitative information, we automatically derive both continuous-space and discrete-space representations suitable for numerical evaluation. We compare results obtained using approximate stochastic simulation thereby exposing a flaw in the use of the differentiation procedure producing misleading results

Disease and insect resistance screening of the national subterranean clover collection

This project commenced in May 1981 primarily to identify sources of resistance to clover scorch (Kabatiella caulivora), root rots (Pythium, Fusarium and Rhizoctonia spp.), and bluegreen aphid (Acyrthospihon kondoi) in the National Subterranean Clover Collection. Screening for resistance to red legged earthmite (Halotydeus destructor) was initiated part way through the project. Since commencement approximately 5,250 introductions and crossbred clover shave been tested for resistance to clover scorch, 420 for resistance to rootrots, 690 for resistance to blue green aphid and 160 for resistance to redlegged earth mite (R.L.E.M.). A large number of clovers possessing resistance to clover scorch have been identified. Approximately 13% of the introductions tested have scored 3.0 or less (0-10 increasing disease scale) indicating good resistance to clover scorch while the proportion of crossbred clovers with resistance has averaged33%. This indicates the considerable success being achieved in breeding for clover scorch resistance using parent lines previously identified in this programme