MCMC methods for functions modifying old algorithms to make\ud them faster

Many problems arising in applications result in the need\ud to probe a probability distribution for functions. Examples include Bayesian nonparametric statistics and conditioned diffusion processes. Standard MCMC algorithms typically become arbitrarily slow under the mesh refinement dictated by nonparametric description of the unknown function. We describe an approach to modifying a whole range of MCMC methods which ensures that their speed of convergence is robust under mesh refinement. In the applications of interest the data is often sparse and the prior specification is an essential part of the overall modeling strategy. The algorithmic approach that we describe is applicable whenever the desired probability measure has density with respect to a Gaussian process or Gaussian random field prior, and to some useful non-Gaussian priors constructed through random truncation. Applications are shown in density estimation, data assimilation in fluid mechanics, subsurface geophysics and image registration. The key design principle is to formulate the MCMC method for functions. This leads to algorithms which can be implemented via minor modification of existing algorithms, yet which show enormous speed-up on a wide range of applied problems

Continuous and discrete Clebsch variational principles

The Clebsch method provides a unifying approach for deriving variational principles for continuous and discrete dynamical systems where elements of a vector space are used to control dynamics on the cotangent bundle of a Lie group \emph{via} a velocity map. This paper proves a reduction theorem which states that the canonical variables on the Lie group can be eliminated, if and only if the velocity map is a Lie algebra action, thereby producing the Euler-Poincar\'e (EP) equation for the vector space variables. In this case, the map from the canonical variables on the Lie group to the vector space is the standard momentum map defined using the diamond operator. We apply the Clebsch method in examples of the rotating rigid body and the incompressible Euler equations. Along the way, we explain how singular solutions of the EP equation for the diffeomorphism group (EPDiff) arise as momentum maps in the Clebsch approach. In the case of finite dimensional Lie groups, the Clebsch variational principle is discretised to produce a variational integrator for the dynamical system. We obtain a discrete map from which the variables on the cotangent bundle of a Lie group may be eliminated to produce a discrete EP equation for elements of the vector space. We give an integrator for the rotating rigid body as an example. We also briefly discuss how to discretise infinite-dimensional Clebsch systems, so as to produce conservative numerical methods for fluid dynamics

Arthroscopic Anterior Shoulder Stabilization With Incorporation of a Comminuted Bony Bankart Lesion.

Bony Bankart lesions are a common finding in patients with anterior glenohumeral dislocation. Although there are no defined guidelines, small bony Bankart fractures are typically treated arthroscopically with suture anchors. The 2 main techniques used are double- and single-row suture anchor stabilization, with debate over superiority. Biomechanical studies have shown improved reduction and stabilization with the double-row over the single-row suture anchor technique; however, this has not been reported for small or comminuted bony fragments. Both techniques have shown promising preliminary clinical outcomes. In this Technical Note, we describe our preferred technique for arthroscopic instability repair using a single-row all-suture anchor method with the incorporation of a comminuted bony Bankart fragment in the lateral decubitus position

40 Gbit/s asynchronous digital optical regenerator

We present the first experimental demonstration of an asynchronous digital optical regenerator at 42.67 Gbit/s. The system effectively retimes incoming asynchronous data bursts to a local clock without burst mode clock recovery and converts the signal to a desired wavelength and duty cycle

Approaching the non-linear Shannon limit

We review the recent progress of information theory in optical communications, and describe the current experimental results and associated advances in various individual technologies which increase the information capacity. We confirm the widely held belief that the reported capacities are approaching the fundamental limits imposed by signal-to-noise ratio and the distributed non-linearity of conventional optical fibres, resulting in the reduction in the growth rate of communication capacity. We also discuss the techniques which are promising to increase and/or approach the information capacity limit

Bcl-2 resistant mitochondrial toxicity mediated by the isoquinoline carboxamide PK11195 involves de novo generation of reactive oxygen species

Resistance to apoptosis is a major obstacle preventing effective therapy for malignancy. Mitochondria localized anti-death proteins of the Bcl-2 family play a central role in inhibiting apoptosis and therefore present valid targets for novel therapy. The peripheral benzodiazepine receptor (PBR) shares a close physical association with the permeability transition pore complex (PTPC), a pivotal regulator of cell death located at mitochondrial contact sites. In this study we investigated the cytotoxicity of the PBR ligand, PK11195, in the micromolar concentration range. PK11195 induced antioxidant inhibitable collapse of the inner mitochondrial membrane potential (ΔΨm) and mitochondrial swelling in HL60 human leukaemia cells, but not in SUDHL4 lymphoma cells (which exhibited a higher level of reduced glutathione and relative tolerance to chemotherapy or pro-oxidant induced ΔΨm dissipation). PK11195 induced the production of hydrogen peroxide that was not inhibited by Bcl-2 transfection, nor depletion of mitochondrial DNA. ROS production was however blocked by protonophore, implicating a requirement for ΔΨm. Our findings suggest that PK11195-induced cytotoxicity relies upon Bcl-2 resistant generation of oxidative stress; a process only observed at concentrations several orders of magnitude higher that required to saturate its receptor. © 2001 Cancer Research Campaign www.bjcancer.co

Impact of Environmental Factors on Bacteriocin Promoter Activity in Gut-Derived Lactobacillus salivarius

peer-reviewedBacteriocin production is regarded as a desirable probiotic trait that aids in colonization and persistence in the gastrointestinal tract (GIT). Strains of Lactobacillus salivarius, a species associated with the GIT, are regarded as promising probiotic candidates and have a number of associated bacteriocins documented to date. These include multiple class IIb bacteriocins (salivaricin T, salivaricin P, and ABP-118) and the class IId bacteriocin bactofencin A, which show activity against medically important pathogens. However, the production of a bacteriocin in laboratory media does not ensure production under stressful environmental conditions, such as those encountered within the GIT. To allow this issue to be addressed, the promoter regions located upstream of the structural genes encoding the L. salivarius bacteriocins mentioned above were fused to a number of reporter proteins (green fluorescent protein [GFP], red fluorescent protein [RFP], and luciferase [Lux]). Of these, only transcriptional fusions to GFP generated signals of sufficient strength to enable the study of promoter activity in L. salivarius. While analysis of the class IIb bacteriocin promoter regions indicated relatively weak GFP expression, assessment of the promoter of the antistaphylococcal bacteriocin bactofencin A revealed a strong promoter that is most active in the absence of the antimicrobial peptide and is positively induced in the presence of mild environmental stresses, including simulated gastric fluid. Taken together, these data provide information on factors that influence bacteriocin production, which will assist in the development of strategies to optimize in vivo and in vitro production of these antimicrobials.This work was funded by a SFI PI award “Obesibiotics” (11/PI/1137) to PD

A mixed discontinuous/continuous finite element pair for shallow-water ocean modelling

We introduce a mixed discontinuous/continuous finite element pair for ocean modelling, with continuous quadratic pressure/layer depth and discontinuous velocity. We investigate the finite element pair applied to the linear shallow-water equations on an f-plane. The element pair has the property that all geostrophically balanced states which strongly satisfy the boundary conditions have discrete divergence equal to exactly zero and hence are exactly steady states of the discretised equations. This means that the finite element pair has excellent geostrophic balance properties. We illustrate these properties using numerical tests and provide convergence calculations which show that the discretisation has quadratic errors, indicating that the element pair is stable