A series of three cases of severe Clostridium difficile infection in Australia associated with a binary toxin producing clade 2 ribotype 251 strain

Three patients with severe Clostridium difficile infection (CDI) caused by an unusual strain of C. difficile, PCR ribotype (RT) 251, were identified in New South Wales, Australia. All cases presented with severe diarrhoea, two had multiple recurrences and one died following a colectomy. C. difficile RT251 strains were isolated by toxigenic culture. Genetic characterisation was performed using techniques including toxin gene profiling, PCR ribotyping, whole genome sequencing (WGS), in-silico multi-locus-sequence-typing (MLST) and core-genome single nucleotide variant (SNV) analyses. Antimicrobial susceptibility was determined using an agar incorporation method. In vitro toxin production was confirmed by Vero cell cytotoxicity assay and pathogenicity was assessed in a murine model of CDI. All RT251 isolates contained toxin A (tcdA), toxin B (tcdB) and binary toxin (cdtA and cdtB) genes. Core-genome analyses revealed the RT251 strains were clonal, with 0–5 SNVs between isolates. WGS and MLST clustered RT251 in the same evolutionary clade (clade 2) as RT027. Despite comparatively lower levels of in vitro toxin production, in the murine model RT251 infection resembled RT027 infection. Mice showed marked weight loss, severe disease within 48 h post-infection and death. All isolates were susceptible to metronidazole and vancomycin. Our observations suggest C. difficile RT251 causes severe disease and emphasise the importance of ongoing surveillance for new and emerging strains of C. difficile with enhanced virulence

Stationary distributions for diffusions with inert drift

Consider reflecting Brownian motion in a bounded domain in $${\mathbb R^d}$$ that acquires drift in proportion to the amount of local time spent on the boundary of the domain. We show that the stationary distribution for the joint law of the position of the reflecting Brownian motion and the value of the drift vector has a product form. Moreover, the first component is uniformly distributed on the domain, and the second component has a Gaussian distribution. We also consider more general reflecting diffusions with inert drift as well as processes where the drift is given in terms of the gradient of a potential

Stabilization with arbitrary laser polarizations

Published versio

An efficient scheme for the deterministic maximal entanglement of N trapped ions

We propose a method for generating maximally entangled states of N two-level trapped ions. The method is deterministic and independent of the number of ions in the trap. It involves a controlled-NOT acting simultaneously on all the ions through a dispersive interaction. We explore the potential application of our scheme for high precision frequency standards.Comment: 4 pages, no figures, submitted to PRL, under review, Revised Version: Incorporated referee comment

Preparation and control of a cavity-field state through atom-driven field interaction: towards long-lived mesoscopic states

The preparation of mesoscopic states of the radiation and matter fields through atom-field interactions has been achieved in recent years and employed for a range of striking applications in quantum optics. Here we present a technique for the preparation and control of a cavity mode which, besides interacting with a two-level atom, is simultaneously submitted to linear and parametric amplification processes. The role of the amplification-controlling fields in the achievement of real mesoscopic states, is to produce highly-squeezed field states and, consequently, to increase both: i) the distance in phase space between the components of the prepared superpositions and ii) the mean photon number of such superpositions. When submitting the squeezed superposition states to the action of similarly squeezed reservoirs, we demonstrate that under specific conditions the decoherence time of the states becomes independent of both the distance in phase space between their components and their mean photon number. An explanation is presented to support this remarkable result, together with a discussion on the experimental implementation of our proposal. We also show how to produce number states with fidelities higher than those derived as circular states

Anisotropy, Phonon Modes, and Free Charge Carrier Parameters in Monoclinic β-Gallium Oxide Single Crystals

We derive a dielectric function tensor model approach to render the optical response of monoclinic and triclinic symmetry materials with multiple uncoupled infrared and far-infrared active modes. We apply our model approach to monoclinic β-Ga2O3 single-crystal samples. Surfaces cut under different angles from a bulk crystal, (010) and (2̅01), are investigated by generalized spectroscopic ellipsometry within infrared and far-infrared spectral regions. We determine the frequency dependence of 4 independent β-Ga2O3 Cartesian dielectric function tensor elements by matching large sets of experimental data using a point-by-point data inversion approach. From matching our monoclinic model to the obtained 4 dielectric function tensor components, we determine all infrared and far-infrared active transverse optic phonon modes with Au and Bu symmetry, and their eigenvectors within the monoclinic lattice. We find excellent agreement between our model results and results of density functional theory calculations. We derive and discuss the frequencies of longitudinal optical phonons in β-Ga2O3. We derive and report density and anisotropic mobility parameters of the free charge carriers within the tin-doped crystals. We discuss the occurrence of longitudinal phonon plasmon coupled modes in β-Ga2O3 and provide their frequencies and eigenvectors. We also discuss and present monoclinic dielectric constants for static electric fields and frequencies above the reststrahlen range, and we provide a generalization of the Lyddane-Sachs-Teller relation for monoclinic lattices with infrared and far-infrared active modes.We find that the generalized Lyddane-Sachs-Teller relation is fulfilled excellently for β-Ga2O3

Data-driven quality improvement program to prevent hospitalisation and improve care of people living with coronary heart disease: Protocol for a process evaluation

Background: Practice-level quality improvement initiatives using rapidly advancing technology offers a multidimensional approach to reduce cardiovascular disease burden. For the “QUality improvement in primary care to prevent hospitalisations and improve Effectiveness and efficiency of care for people Living with heart disease” (QUEL) cluster randomised controlled trial, a 12-month quality improvement intervention was designed for primary care practices to use data and implement progressive changes using “Plan, Do, Study, Act” cycles within their practices with training in a series of interactive workshops. This protocol aims to describe the systematic methods to conduct a process evaluation of the data-driven intervention within the QUEL study. Methods: A mixed-method approach will be used to conduct the evaluation. Quantitative data collected throughout the intervention period, via surveys and intervention materials, will be used to (1) identify the key elements of the intervention and how, for whom and in what context it was effective; (2) determine if the intervention is delivered as intended; and (3) describe practice engagement, commitment and capacity associated with various intervention components. Qualitative data, collected via semi-structured interviews and open-ended questions, will be used to gather in-depth understanding of the (1) satisfaction, utility, barriers and enablers; (2) acceptability, uptake and feasibility, and (3) effect of the COVID-19 pandemic on the implementation of the intervention. Conclusion: Findings from the evaluation will provide new knowledge on the implementation of a complex, multi-component intervention at practice-level using their own electronic patient data to enhance secondary prevention of cardiovascular disease. Trial registration: Australian New Zealand Clinical Trials Registry (ANZCTR) number ACTRN12619001790134

Stochastic Physics, Complex Systems and Biology

In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated equilibrium, spontaneous random "mutations" and "adaptations". On an evlutionary time scale it produces sustainable diversity among individuals in a homogeneous population rather than convergence as usually predicted by a deterministic dynamics. The emergent discrete states in such a system, i.e., attractors, have natural robustness against both internal and external perturbations. Phenotypic states of a biological cell, a mesoscopic nonlinear stochastic open biochemical system, could be understood through such a perspective.Comment: 10 page

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands of genomes must thus be efficiently scalable and sensitive from closely related strains to divergent phyla. We present PhyloPhlAn 3.0, an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. PhyloPhlAn 3.0 can assign genomes from isolate sequencing or MAGs to species-level genome bins built from >230,000 publically available sequences. For individual clades of interest, it reconstructs strain-level phylogenies from among the closest species using clade-specific maximally informative markers. At the other extreme of resolution, it scales to large phylogenies comprising >17,000 microbial species. Examples including Staphylococcus aureus isolates, gut metagenomes, and meta-analyses demonstrate the ability of PhyloPhlAn 3.0 to support genomic and metagenomic analyses