Adaptive, cautious, predictive control with Gaussian process priors

Nonparametric Gaussian Process models, a Bayesian statistics approach, are used to implement a nonlinear adaptive control law. Predictions, including propagation of the state uncertainty are made over a k-step horizon. The expected value of a quadratic cost function is minimised, over this prediction horizon, without ignoring the variance of the model predictions. The general method and its main features are illustrated on a simulation example

Effect of broodstock holding environment on egg quality in farmed brown trout (Salmo trutta)

Brown trout (Salmo trutta) broodstock from a single population were separated prior to spawning and exposed to two different holding environments: a ‘raceway system’ and a ‘tank system’. Eggs were stripped from females and 13 measures of egg quality were collected, analysed individually, combined by principle components analysis into an integrated egg quality score which was validated against egg survival. The multivariate egg quality score (PC1) differed for fish held in the tank and raceway systems. Egg survival, chorion breaking strength and chorion Se concentrations were higher in eggs produced by broodstock held in the tank system compared to those in the raceway system. In contrast, chorion concentrations of P and K were higher in eggs from fish held in the raceway system. The results suggest that brown trout broodstock reared in tank systems produced higher quality eggs compared to trout reared in raceways. Finally, this study also indicates that multivariate statistical analysis can be used to determine egg quality from multiple egg parameters

Metabolically active cytochrome P450 CYP1B1 in solid tumours: a novel target for chemotherapeutic intervention.

Cytochrome P450 CYP1B1 is a member of a superfamily of haemoproteins that are central to the oxidative metabolism of a wide variety of endogenous and exogenous compounds. Several of these enzymes have an established role in the metabolic bio-transformation of a variety of anti-cancer drugs. In this study, we demonstrated both CYP1B1 and CPR activity in the microsomal fraction of ovarian and kidney tumours

Horseshoe-based Bayesian nonparametric estimation of effective population size trajectories

Phylodynamics is an area of population genetics that uses genetic sequence data to estimate past population dynamics. Modern state-of-the-art Bayesian nonparametric methods for recovering population size trajectories of unknown form use either change-point models or Gaussian process priors. Change-point models suffer from computational issues when the number of change-points is unknown and needs to be estimated. Gaussian process-based methods lack local adaptivity and cannot accurately recover trajectories that exhibit features such as abrupt changes in trend or varying levels of smoothness. We propose a novel, locally-adaptive approach to Bayesian nonparametric phylodynamic inference that has the flexibility to accommodate a large class of functional behaviors. Local adaptivity results from modeling the log-transformed effective population size a priori as a horseshoe Markov random field, a recently proposed statistical model that blends together the best properties of the change-point and Gaussian process modeling paradigms. We use simulated data to assess model performance, and find that our proposed method results in reduced bias and increased precision when compared to contemporary methods. We also use our models to reconstruct past changes in genetic diversity of human hepatitis C virus in Egypt and to estimate population size changes of ancient and modern steppe bison. These analyses show that our new method captures features of the population size trajectories that were missed by the state-of-the-art methods.Comment: 36 pages, including supplementary informatio

Grabbing your ear: rapid auditory-somatosensory multisensory interactions in low-level sensory cortices are not constrained by stimulus alignment.

Multisensory interactions are observed in species from single-cell organisms to humans. Important early work was primarily carried out in the cat superior colliculus and a set of critical parameters for their occurrence were defined. Primary among these were temporal synchrony and spatial alignment of bisensory inputs. Here, we assessed whether spatial alignment was also a critical parameter for the temporally earliest multisensory interactions that are observed in lower-level sensory cortices of the human. While multisensory interactions in humans have been shown behaviorally for spatially disparate stimuli (e.g. the ventriloquist effect), it is not clear if such effects are due to early sensory level integration or later perceptual level processing. In the present study, we used psychophysical and electrophysiological indices to show that auditory-somatosensory interactions in humans occur via the same early sensory mechanism both when stimuli are in and out of spatial register. Subjects more rapidly detected multisensory than unisensory events. At just 50 ms post-stimulus, neural responses to the multisensory 'whole' were greater than the summed responses from the constituent unisensory 'parts'. For all spatial configurations, this effect followed from a modulation of the strength of brain responses, rather than the activation of regions specifically responsive to multisensory pairs. Using the local auto-regressive average source estimation, we localized the initial auditory-somatosensory interactions to auditory association areas contralateral to the side of somatosensory stimulation. Thus, multisensory interactions can occur across wide peripersonal spatial separations remarkably early in sensory processing and in cortical regions traditionally considered unisensory

Statistics of extinction and survival in Lotka-Volterra systems

We analyze purely competitive many-species Lotka-Volterra systems with random interaction matrices, focusing the attention on statistical properties of their asymptotic states. Generic features of the evolution are outlined from a semiquantitative analysis of the phase-space structure, and extensive numerical simulations are performed to study the statistics of the extinctions. We find that the number of surviving species depends strongly on the statistical properties of the interaction matrix, and that the probability of survival is weakly correlated to specific initial conditions.Comment: Previous version had error in authors. 11 pages, including 5 figure

REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform

Motivation: Proteins with solenoid repeats evolve more quickly than non-repetitive ones and their periodicity may be rapidly hidden at sequence level, while still evident in structure. In order to identify these repeats, we propose here a novel method based on a metric characterizing amino-acid properties (polarity, secondary structure, molecular volume, codon diversity, electric charge) using five previously derived numerical functions

T-cell number and subtype influence the disease course of primary chronic lymphocytic leukaemia xenografts in alymphoid mice.

Chronic lymphocytic leukaemia (CLL) cells require microenvironmental support for their proliferation. This can be recapitulated in highly immunocompromised hosts in the presence of T cells and other supporting cells. Current primary CLL xenograft models suffer from limited duration of tumour cell engraftment coupled with gradual T-cell outgrowth. Thus, a greater understanding of the interaction between CLL and T cells could improve their utility. In this study, using two distinct mouse xenograft models, we investigated whether xenografts recapitulate CLL biology, including natural environmental interactions with B-cell receptors and T cells, and whether manipulation of autologous T cells can expand the duration of CLL engraftment. We observed that primary CLL xenografts recapitulated both the tumour phenotype and T-cell repertoire observed in patients and that engraftment was significantly shorter for progressive tumours. A reduction in the number of patient T cells that were injected into the mice to 2-5% of the initial number or specific depletion of CD8+ cells extended the limited xenograft duration of progressive cases to that characteristic of indolent disease. We conclude that manipulation of T cells can enhance current CLL xenograft models and thus expand their utility for investigation of tumour biology and pre-clinical drug assessment

Is null-point reconnection important for solar flux emergence?

The role of null-point reconnection in a 3D numerical MHD model of solar emerging flux is investigated. The model consists of a twisted magnetic flux tube rising through a stratified convection zone and atmosphere to interact and reconnect with a horizontal overlying magnetic field in the atmosphere. Null points appear as the reconnection begins and persist throughout the rest of the emergence, where they can be found mostly in the model photosphere and transition region, forming two loose clusters on either side of the emerging flux tube. Up to 26 nulls are present at any one time, and tracking in time shows that there is a total of 305 overall, despite the initial simplicity of the magnetic field configuration. We find evidence for the reality of the nulls in terms of their methods of creation and destruction, their balance of signs, their long lifetimes, and their geometrical stability. We then show that due to the low parallel electric fields associated with the nulls, null-point reconnection is not the main type of magnetic reconnection involved in the interaction of the newly emerged flux with the overlying field. However, the large number of nulls implies that the topological structure of the magnetic field must be very complex and the importance of reconnection along separators or separatrix surfaces for flux emergence cannot be ruled out.Comment: 26 pages, 12 figures. Added one referenc

Review article: MHD wave propagation near coronal null points of magnetic fields

We present a comprehensive review of MHD wave behaviour in the neighbourhood of coronal null points: locations where the magnetic field, and hence the local Alfven speed, is zero. The behaviour of all three MHD wave modes, i.e. the Alfven wave and the fast and slow magnetoacoustic waves, has been investigated in the neighbourhood of 2D, 2.5D and (to a certain extent) 3D magnetic null points, for a variety of assumptions, configurations and geometries. In general, it is found that the fast magnetoacoustic wave behaviour is dictated by the Alfven-speed profile. In a $\beta=0$ plasma, the fast wave is focused towards the null point by a refraction effect and all the wave energy, and thus current density, accumulates close to the null point. Thus, null points will be locations for preferential heating by fast waves. Independently, the Alfven wave is found to propagate along magnetic fieldlines and is confined to the fieldlines it is generated on. As the wave approaches the null point, it spreads out due to the diverging fieldlines. Eventually, the Alfven wave accumulates along the separatrices (in 2D) or along the spine or fan-plane (in 3D). Hence, Alfven wave energy will be preferentially dissipated at these locations. It is clear that the magnetic field plays a fundamental role in the propagation and properties of MHD waves in the neighbourhood of coronal null points. This topic is a fundamental plasma process and results so far have also lead to critical insights into reconnection, mode-coupling, quasi-periodic pulsations and phase-mixing.Comment: 34 pages, 5 figures, invited review in Space Science Reviews => Note this is a 2011 paper, not a 2010 pape