An automated image analysis framework for segmentation and division plane detection of single live Staphylococcus aureus cells which can operate at millisecond sampling time scales using bespoke Slimfield microscopy

Staphylococcus aureus is an important pathogen, giving rise to antimicrobial resistance in cell strains such as Methicillin Resistant S. aureus (MRSA). Here we report an image analysis framework for automated detection and image segmentation of cells in S. aureus cell clusters, and explicit identification of their cell division planes. We use a new combination of several existing analytical tools of image analysis to detect cellular and subcellular morphological features relevant to cell division from millisecond time scale sampled images of live pathogens at a detection precision of single molecules. We demonstrate this approach using a fluorescent reporter GFP fused to the protein EzrA that localises to a mid-cell plane during division and is involved in regulation of cell size and division. This image analysis framework presents a valuable platform from which to study candidate new antimicrobials which target the cell division machinery, but may also have more general application in detecting morphologically complex structures of fluorescently labelled proteins present in clusters of other types of cells

Symmetric Informationally Complete Measurements of Arbitrary Rank

There has been much interest in so-called SIC-POVMs: rank 1 symmetric informationally complete positive operator valued measures. In this paper we discuss the larger class of POVMs which are symmetric and informationally complete but not necessarily rank 1. This class of POVMs is of some independent interest. In particular it includes a POVM which is closely related to the discrete Wigner function. However, it is interesting mainly because of the light it casts on the problem of constructing rank 1 symmetric informationally complete POVMs. In this connection we derive an extremal condition alternative to the one derived by Renes et al.Comment: Contribution to proceedings of International Conference on Quantum Optics, Minsk, 200

Measuring the Effectiveness of Photoresponsive Nanocomposite Coatings on Aircraft Windshields to Mitigate Laser Intensity

In 2004, pilots reported 46 laser illumination events to the Federal Aviation Administration (FAA), with the number increasing to approximately 3,600 in 2011. Since that time, the number of reported laser incidents has ranged from 3,500 to 4,000. Previous studies indicate the potential for flight crewmember distraction from bright laser light being introduced to the cockpit. Compositional variations of the photoresponsive nanocomposite coatings were applied to an aircraft windscreen using a modified liquid dispersion/heating curing process. The attenuating effects of the deposited films on laser light intensity were evaluated using an optical power meter and the resultant laser intensity data through treated and untreated windscreens was collected. Data revealed a reduction in laser intensity (36–88%) in the presence of the engineered photoresponsive nanocomposite films. Results lend support of the view that the addition of transparent laser attenuating films applied to aircraft windscreens may improve flight safety, and reduce the risk from distraction or disruption of flight crewmembers’ vision

Thermal Density Functional Theory in Context

This chapter introduces thermal density functional theory, starting from the ground-state theory and assuming a background in quantum mechanics and statistical mechanics. We review the foundations of density functional theory (DFT) by illustrating some of its key reformulations. The basics of DFT for thermal ensembles are explained in this context, as are tools useful for analysis and development of approximations. We close by discussing some key ideas relating thermal DFT and the ground state. This review emphasizes thermal DFT's strengths as a consistent and general framework.Comment: Submitted to Spring Verlag as chapter in "Computational Challenges in Warm Dense Matter", F. Graziani et al. ed

Probing the WWγWW\gamma Vertex in e^\pm p\to\nu\gammaX

We study the prospects of testing the $WW\gamma$ vertex in $e^- p\to\nu\gamma X$ and $e^+ p\to\nu\gamma X$ at HERA and LEP/LHC. Destructive interference effects between the Standard Model and the anomalous contributions to the amplitude severely limit the sensitivity of both processes to non-standard $WW\gamma$ couplings. Sensitivity limits for the anomalous $WW\gamma$ couplings $\kappa$ and $\lambda$ at HERA and LEP/LHC are derived, taking into account experimental cuts and uncertainties, and the form factor behaviour of nonstandard couplings. These limits are found to be significantly weaker than those which can be expected from other collider processes within the next few years. At HERA, they are comparable to bounds obtained from $S$-matrix unitarity.Comment: 13 pages, 4 figures (not included

Functional Subsystems and Quantum Redundancy in Photosynthetic Light Harvesting

The Fenna-Matthews-Olson (FMO) antennae complex, responsible for light harvesting in green sulfur bacteria, consists of three monomers, each with seven chromophores. Here we show that multiple subsystems of the seven chromophores can transfer energy from either chromophore 1 or 6 to the reaction center with an efficiency matching or in many cases exceeding that of the full seven chromophore system. In the FMO complex these functional subsystems support multiple quantum pathways for efficient energy transfer that provide a built-in quantum redundancy. There are many instances of redundancy in nature, providing reliability and protection, and in photosynthetic light harvesting this quantum redundancy provides protection against the temporary or permanent loss of one or more chromophores. The complete characterization of functional subsystems within the FMO complex offers a detailed map of the energy flow within the FMO complex, which has potential applications to the design of more efficient photovoltaic devices

Antisymmetric Magnetic Interactions in Oxo-Bridged Copper(II) Bimetallic Systems

The antisymmetric magnetic interaction is studied using correlated wave-function-based calculations in oxo-bridged copper bimetallic complexes. All of the anisotropic multispin Hamiltonian parameters are extracted using spin-orbit state interaction and effective Hamiltonian theory. It is shown that the methodology is accurate enough to calculate the antisymmetric terms, while the small symmetric anisotropic interactions require more sophisticated calculations. The origin of the antisymmetric anisotropy is analyzed, and the effect of geometrical deformations is addressed.

Intermediate mass standard model Higgs boson at the proposed CERN LEP⊗\otimesLHC epep collider

The production of the \sm\ Higgs $\phi$ with intermediate mass at the proposed CERN LEP$\otimes$LHC $ep$ collider in $\gamma q(\bar q)\rightarrow W^\pm\phi q'(\bar q')$, $\gamma q(\bar q)\rightarrow Z^0\phi q(\bar q)$ and $g\gamma\rightarrow q\bar q\phi$ events is studied. This is done for all possible (massive) flavours of the quarks $q(q')$ and using photons generated via Compton back--scattering of laser light. We study signatures in which the Higgs decays to $b\bar b$--pairs and the electroweak vector bosons $W^\pm$ and $Z^0$ decay either hadronically or leptonically. All possible backgrounds to these signals are also computed. Flavour identification on $b$--jets is assumed. Explicit formulae for the helicity amplitudes of the above processes are given.Comment: 31 pages, Latex, 8 figures uuencoded, revised version, significant changes in the discussion of the results, in tables and figure

The Pathway to Detangle a Scrambled Gene

Programmed DNA elimination and reorganization frequently occur during cellular differentiation. Development of the somatic macronucleus in some ciliates presents an extreme case, involving excision of internal eliminated sequences (IESs) that interrupt coding DNA segments (macronuclear destined sequences, MDSs), as well as removal of transposon-like elements and extensive genome fragmentation, leading to 98% genome reduction in Stylonychia lemnae. Approximately 20-30% of the genes are estimated to be scrambled in the germline micronucleus, with coding segment order permuted and present in either orientation on micronuclear chromosomes. Massive genome rearrangements are therefore critical for development.To understand the process of DNA deletion and reorganization during macronuclear development, we examined the population of DNA molecules during assembly of different scrambled genes in two related organisms in a developmental time-course by PCR. The data suggest that removal of conventional IESs usually occurs first, accompanied by a surprising level of error at this step. The complex events of inversion and translocation seem to occur after repair and excision of all conventional IESs and via multiple pathways.This study reveals a temporal order of DNA rearrangements during the processing of a scrambled gene, with simpler events usually preceding more complex ones. The surprising observation of a hidden layer of errors, absent from the mature macronucleus but present during development, also underscores the need for repair or screening of incorrectly-assembled DNA molecules

Single-molecule techniques in biophysics : a review of the progress in methods and applications

Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft matter behaviour, active biological matter lives far from thermal equilibrium, and typically covers multiple length scales from the nanometre level of single molecules up several orders of magnitude to longer length scales in emergent structures of cells, tissues and organisms. Biological molecules are often characterized by an underlying instability, in that multiple metastable free energy states exist which are separated by energy levels of typically just a few multiples of the thermal energy scale of kBT, where kB is the Boltzmann constant and T the absolute temperature, implying complex, dynamic inter-conversion kinetics across this bumpy free energy landscape in the relatively hot, wet environment of real, living biological matter. The key utility of single-molecule biophysics lies in its ability to probe the underlying heterogeneity of free energy states across a population of molecules, which in general is too challenging for conventional ensemble level approaches which measure mean average properties. Parallel developments in both experimental and theoretical techniques have been key to the latest insights and are enabling the development of highly-multiplexed, correlative techniques to tackle previously intractable biological problems. Experimentally, technological developments in the sensitivity and speed of biomolecular detectors, the stability and efficiency of light sources, probes and microfluidics, have enabled and driven the study of heterogeneous behaviours both in vitro and in vivo that were previously undetectable by ensemble methods..