Global QSAR models of skin sensitisers for regulatory purposes

Background

The new European Regulation on chemical safety, REACH, (Registration, Evaluation, Authorisation and Restriction of CHemical substances), is in the process of being implemented. Many chemicals used in industry require additional testing to comply with the REACH regulations. At the same time EU member states are attempting to reduce the number of animals used in experiments under the 3 Rs policy, (refining, reducing, and replacing the use of animals in laboratory procedures). Computational techniques such as QSAR have the potential to offer an alternative for generating REACH data. The FP6 project CAESAR was aimed at developing QSAR models for 5 key toxicological endpoints of which skin sensitisation was one.

Results

This paper reports the development of two global QSAR models using two different computational approaches, which contribute to the hybrid model freely available online.

Conclusions

The QSAR models for assessing skin sensitisation have been developed and tested under stringent quality criteria to fulfil the principles laid down by the OECD. The final models, accessible from CAESAR website, offer a robust and reliable method of assessing skin sensitisation for regulatory use.

     

Paddling mode of forward flight in insects

By analyzing high-speed video of the fruit fly, we discover a swimminglike mode of forward flight characterized by paddling wing motions. We develop a new aerodynamic analysis procedure to show that these insects generate drag-based thrust by slicing their wings forward at low angle of attack and pushing backwards at a higher angle. Reduced-order models and simulations reveal that the law for flight speed is determined by these wing motions but is insensitive to material properties of the fluid. Thus, paddling is as effective in air as in water and represents a common strategy for propulsion through aquatic and aerial environments.     

Intracavity ionization and pulse formation in femtosecond enhancement cavities

We experimentally and numerically investigate the intracavity ionization of a dilute gas target by an ultrashort pulse inside a femtosecond enhancement cavity. Numerical simulations detail how the dynamic ionization of the gas target limits the achievable peak intensity of the evolving intracavity pulse beyond that of linear cavity losses, setting a constraint on the strength of the nonlinear interaction that can be sustained in such optical cavities. Experimental measurements combined with numerical simulations predict ionization levels in a femtosecond enhancement cavity for the first time. We demonstrate how the resonant response of the femtosecond enhancement cavity can itself be used as a sensitive probe of optical nonlinearities at high intensities.     

Precision mass measurements of neutron halo nuclei using the TITAN Penning trap

Precise atomic mass determinations play a key role in various fields of physics, including nuclear physics, testing of fundamental symmetries and constants and atomic physics. Recently, the TITAN Penning trap measured the masses of several neutron halos. These exotic systems have an extended, diluted, matter distribution that can be modelled by considering a nuclear core surrounded by a halo formed by one or more of loosely bound neutrons. Combined with laser spectroscopy measurements of isotopic shifts precise masses can be used to obtain reliable charge radii and two-neutron-seperation energies for these halo nuclei. It is shown that these results can be used as stringent tests of nuclear models and potentials providing an important metric for our understanding of the interactions in all nuclei.     

Collinear laser spectroscopy with reverse-extracted bunched beams at TRIUMF

Collinear laser spectroscopy with reverse-extracted cooled bunched beams was performed at TRIUMF with radioactive ion beams. Surface-ionized ^78,78mRb ions were injected into TITAN??s cooler-buncher, and reverse-extracted to the laser beam line. There they were neutralised and excited with a counter-propagating laser beam. The fluorescence signal from the D ₂ line was recorded with a photomultiplier tube. The cooler provided typically 50 ion bunches per second, with each bunch containing approximately 10⁵ ions, temporally distributed with a 1.6 ??s width. A hardware gate was set on the signal, suppressing the background by four orders of magnitude.     

Noninvasive observation of cervical spinal cord activity in children by functional MRI during cold thermal stimulation

Functional magnetic resonance imaging (fMRI) is a non-invasive neuroimaging tool that indirectly identifies areas of neural activity in the brain and more recently has been applied to the adult spinal cord (spinal fMRI). Spinal fMRI could clearly benefit pediatric populations as well. The purpose of this work was to characterize the response observed with spinal fMRI in the brainstem and cervical (C) spinal cord of awake, healthy children during thermal stimulation (17°C and 27°C) applied to the right hand. Functional MRI detected neuronal activity in the expected region of the spinal cord (C6 and C7) as well as in the brainstem and thalamus. The observed magnitudes of signal change of the responses to 17°C and 27°C were similar; however, the spatial distribution of active pixels was greater during 17°C stimulation. The results of this study indicate that fMRI can be used to assess activity in the spinal cords of children, with good sensitivity and reliability.     

A general dual-bolus approach for quantitative DCE-MRI

Purpose

To present a dual-bolus technique for quantitative dynamic contrast-enhanced MRI (DCE-MRI) and show that it can give an arterial input function (AIF) measurement equivalent to that from a single-bolus protocol.

Methods

Five rabbits were imaged using a dual-bolus technique applicable for high-resolution DCE-MRI, incorporating a time resolved imaging of contrast kinetics (TRICKS) sequence for rapid temporal sampling. AIFs were measured from both the low-dose prebolus and the high-dose main bolus in the abdominal aorta. In one animal, TRICKS and fast spoiled gradient echo (FSPGR) acquisitions were compared.

Results

The scaled prebolus AIF was shown to match the main bolus AIF, with 95% confidence intervals overlapping for fits of gamma-variate functions to the first pass and linear fits to the washout phase, with the exception of one case. The AIFs measured using TRICKS and FSPGR were shown to be equivalent in one animal.

Conclusion

The proposed technique can capture even the rapid circulation kinetics in the rabbit aorta, and the scaled prebolus AIF is equivalent to the AIF from a high-dose injection. This allows separate measurements of the AIF and tissue uptake curves, meaning that each curve can then be acquired using a protocol tailored to its specific requirements.     

A delay-dependent model with HIV drug resistance during therapy

The use of combination antiretroviral therapy has proven remarkably effective in controlling HIV disease progression and prolonging survival. However, the emergence of drug resistance can occur. It is necessary that we gain a greater understanding of the evolution of drug resistance. Here, we consider an HIV viral dynamical model with general form of target cell density, drug resistance and intracellular delay incorporating antiretroviral therapy. The model includes two strains: wild-type and drug-resistant. The basic reproductive ratio for each strain is obtained for the existence of steady states. Qualitative analysis of the model such as the well-posedness of the solutions and the equilibrium stability is provided. Global asymptotic stability of the disease-free and drug-resistant steady states is shown by constructing Lyapunov functions. Furthermore, sufficient conditions related to the properties of the target cell density are obtained for the local asymptotic stability of the positive steady state. Numerical simulations are conducted to study the impact of target cell density and intracellular delay focusing on the stability of the positive steady state. The occurrence of Hopf bifurcation of periodic solutions is shown to depend on the target cell density.     

Enhanced Karush–Kuhn–Tucker Conditions for Mathematical Programs with Equilibrium Constraints

In this paper, we study necessary optimality conditions for nonsmooth mathematical programs with equilibrium constraints. We first show that, unlike the smooth case, the mathematical program with equilibrium constraints linear independent constraint qualification is not a constraint qualification for the strong stationary condition when the objective function is nonsmooth. We then focus on the study of the enhanced version of the Mordukhovich stationary condition, which is a weaker optimality condition than the strong stationary condition. We introduce the quasi-normality and several other new constraint qualifications and show that the enhanced Mordukhovich stationary condition holds under them. Finally, we prove that quasi-normality with regularity implies the existence of a local error bound.     

Boundary of Anosov dynamics and evolution equations for surfaces

We show that a compact surface of genus greater than one, without focal points and a finite number of bubbles (“good” shaped regions of positive curvature) is in the closure of Anosov metrics. Compact surfaces of nonpositive curvature and genus greater than one are in the closure of Anosov metrics, by Hamilton's work about the Ricci flow. We generalize this fact to the above surfaces without focal points admitting regions of positive curvature using a “magnetic” version of the Ricci flow, the so‐called Ricci Yang‐Mills flow.