Compressive Phase Contrast Tomography

When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. In- terference effects visible with high brightness sources creates higher contrast, edge enhanced images. When the object is piecewise smooth (made of big blocks of a few components), such higher con- trast datasets have a sparse solution. We apply basis pursuit solvers to improve SNR, remove ring artifacts, reduce the number of views and radiation dose from phase contrast datasets collected at the Hard X-Ray Micro Tomography Beamline at the Advanced Light Source. We report a GPU code for the most computationally intensive task, the gridding and inverse gridding algorithm (non uniform sampled Fourier transform).Comment: 5 pages, "Image Reconstruction from Incomplete Data VI" conference 7800, SPIE Optical Engineering + Applications 1-5 August 2010 San Diego, CA United State

Changes in health behaviours in adults at-risk of chronic disease: primary outcomes from the My health for life program.

BACKGROUND: Chronic disease is the leading cause of premature death globally, and many of these deaths are preventable by modifying some key behavioural and metabolic risk factors. This study examines changes in health behaviours among men and women at risk of diabetes or cardiovascular disease (CVD) who participated in a 6-month lifestyle intervention called the My health for life program. METHODS: The My health for life program is a Queensland Government-funded multi-component program designed to reduce chronic disease risk factors amongst at-risk adults in Queensland, Australia. The intervention comprises six sessions over a 6-month period, delivered by a trained facilitator or telephone health coach. The analysis presented in this paper stems from 9,372 participants who participated in the program between July 2017 and December 2019. Primary outcomes included fruit and vegetable intake, consumption of sugar-sweetened drinks and take-away, alcohol consumption, tobacco smoking, and physical activity. Variables were summed to form a single Healthy Lifestyle Index (HLI) ranging from 0 to 13, with higher scores denoting healthier behaviours. Longitudinal associations between lifestyle indices, program characteristics and socio-demographic characteristics were assessed using Gaussian Generalized Estimating Equations (GEE) models with an identity link and robust standard errors. RESULTS: Improvements in HLI scores were noted between baseline (Md = 8.8; IQR = 7.0, 10.0) and 26-weeks (Md = 10.0; IQR = 9.0, 11.0) which corresponded with increases in fruit and vegetable consumption and decreases in takeaway frequency (p < .001 for all) but not risky alcohol intake. Modelling showed higher average HLI among those aged 45 or older (β = 1.00, 95% CI = 0.90, 1.10, p < .001) with vocational educational qualifications (certificate/diploma: β = 0.32, 95% CI = 0.14, 0.50, p < .001; bachelor/post-graduate degree β = 0.79, 95% CI = 0.61, 0.98, p < .001) while being male, Aboriginal or Torres Strait Islander background, or not currently working conferred lower average HLI scores (p < .001 for all). CONCLUSIONS: While participants showed improvements in dietary indicators, changes in alcohol consumption and physical activity were less amenable to the program. Additional research is needed to help understand the multi-level barriers and facilitators of behaviour change in this context to further tailor the intervention for priority groups

Crystal structures of PI3K-C2α PX domain indicate conformational change associated with ligand binding

<p>Abstract</p> <p>Background</p> <p>PX domains have specialized protein structures involved in binding of phosphoinositides (PIs). Through binding to the various PIs PX domains provide site-specific membrane signals to modulate the intracellular localisation and biological activity of effector proteins. Several crystal structures of these domains are now available from a variety of proteins. All PX domains contain a canonical core structure with main differences exhibited within the loop regions forming the phosphoinositide binding pockets. It is within these areas that the molecular basis for ligand specificity originates.</p> <p>Results</p> <p>We now report two new structures of PI3K-C2α PX domain that crystallised in a P3₁21 space group. The two structures, refined to 2.1 Å and 2.5 Å, exhibit significantly different conformations of the phosphoinositide-binding loops. Unexpectedly, in one of the structures, we have detected a putative-ligand trapped in the binding site during the process of protein purification and crystallisation.</p> <p>Conclusion</p> <p>The two structures reported here provide a more complete description of the phosphoinositide binding region compared to the previously reported 2.6 Å crystal structure of human PI3K-C2α PX where this region was highly disordered. The structures enabled us to further analyse PI specificity and to postulate that the observed conformational change could be related to ligand-binding.</p

Analyzing the heterogeneity of rule-based EHR phenotyping algorithms in CALIBER and the UK Biobank

Electronic Health Records (EHR) are data generated during routine interactions across healthcare settings and contain rich, longitudinal information on diagnoses, symptoms, medications, investigations and tests. A primary use-case for EHR is the creation of phenotyping algorithms used to identify disease status, onset and progression or extraction of information on risk factors or biomarkers. Phenotyping however is challenging since EHR are collected for different purposes, have variable data quality and often require significant harmonization. While considerable effort goes into the phenotyping process, no consistent methodology for representing algorithms exists in the UK. Creating a national repository of curated algorithms can potentially enable algorithm dissemination and reuse by the wider community. A critical first step is the creation of a robust minimum information standard for phenotyping algorithm components (metadata, implementation logic, validation evidence) which involves identifying and reviewing the complexity and heterogeneity of current UK EHR algorithms. In this study, we analyzed all available EHR phenotyping algorithms (n=70) from two large-scale contemporary EHR resources in the UK (CALIBER and UK Biobank). We documented EHR sources, controlled clinical terminologies, evidence of algorithm validation, representation and implementation logic patterns. Understanding the heterogeneity of UK EHR algorithms and identifying common implementation patterns will facilitate the design of a minimum information standard for representing and curating algorithms nationally and internationally

Study on Doping Prevention: A map of Legal, Regulatory and Prevention Practice Provisions in EU 28

Historically, anti-doping efforts have focused on the detection and deterrence of doping in elite and competitive sport. There is, however, a growing concern that doping is occurring outside the organised sporting system; giving rise to the belief that the misuse of doping agents in recreational sport has become a societal problem and a public health issue that must be addressed. The EU Commission awarded a contract (EAC/2013/0617) to a Consortium to undertake this Study with the aim of developing the evidence-base for policies designed to combat doping in recreational sport. Fourteen internationally recognised experts shaped the Study which comprised (i) the collection of primary data through a structured survey, and (ii) secondary data through literature searches and website analysis. All 28 Member States participated in the information-gathering process. Specifically, this involved a systematic study of the ethical considerations, legal position, prevention research landscape, and current practise in relation to the prevention of doping in recreational sport. The Study provides a comprehensive overview of current practice and legislation as it applies to the prevention of doping and promotes and supports the sharing of best practices in the EU regarding the fight against doping in recreational sport. It concludes with seven recommendations for future action that focus on the need for a coordinated response in relation to the problems arising from doping in recreational sport

Exact solution of A-D Temperley-Lieb Models

We solve for the spectrum of quantum spin chains based on representations of the Temperley-Lieb algebra associated with the quantum groups {\cal U}_q(X_n } for X_n = A_1,B_n,C_n$and$D_n$. We employ a generalization of the coordinate Bethe-Ansatz developed previously for the deformed biquadratic spin one chain. As expected, all these models have equivalent spectra, i.e. they differ only in the degeneracy of their eigenvalues. This is true for finite length and open boundary conditions. For periodic boundary conditions the spectra of the lower dimensional representations are containded entirely in the higher dimensional ones. The Bethe states are highest weight states of the quantum group, except for some states with energy zero

Loop algorithm for Heisenberg models with biquadratic interaction and phase transitions in two dimensions

We present a new algorithm for quantum Monte Carlo simulation based on global updating with loops. While various theoretical predictions are confirmed in one dimension, we find, for S=1 systems on a square lattice with an antiferromagnetic biquadratic interaction, that the intermediate phase between the antiferromagnetic and the ferromagnetic phases is disordered and that the two phase transitions are both of the first order in contrast to the one-dimensional case. It is strongly suggested that the transition points coincide those at which the algorithm changes qualitatively.Comment: 4 pages including 4 figures, to appear in JPS

Understanding implementation success: protocol for an in-depth, mixed-methods process evaluation of a cluster randomised controlled trial testing methods to improve detection of Lynch syndrome in Australian hospitals.

INTRODUCTION:In multisite intervention trials, implementation success often varies widely across settings. Process evaluations are crucial to interpreting trial outcomes and understanding contextual factors and causal chains necessary for successful implementation. Lynch syndrome is a hereditary cancer predisposition conferring an increased risk of colorectal, endometrial and other cancer types. Despite systematic screening protocols to identify Lynch syndrome, the condition remains largely underdiagnosed. The Hide and Seek Project ('HaSP') is a cluster randomised controlled trial determining the effectiveness of two approaches to improving Lynch syndrome detection at eight Australian hospital networks. To enhance widespread implementation of optimal Lynch syndrome identification, there is a need to understand not only what works, but also why, in what contexts, and at what costs. Here we describe an in-depth investigation of factors influencing successful implementation of procedures evaluated in the HaSP trial. METHODS AND ANALYSIS:A mixed-methods, theory-driven process evaluation will be undertaken in parallel to the HaSP trial. Data will include: interviews of Implementation Leads and Lynch syndrome stakeholders, pre-post implementation questionnaires, audio analysis of meetings and focus groups, observation of multidisciplinary team meetings, fidelity checklists and project log analysis. Results will be triangulated and coded, drawing on the Theoretical Domains Framework, Consolidated Framework for Implementation Research and Proctor's implementation outcomes. ETHICS AND DISSEMINATION:Use of a theory-based process evaluation will enhance interpretation and generalisability of HaSP trial findings, and contribute to the implementation research field by furthering understanding of the conditions necessary for implementation success. Ethical approval has been granted and results will be disseminated via publications in peer-reviewed journals and conference presentations. At trial completion, key findings will be fed back to sites to enable refinement of intervention strategies, both in the context of Lynch syndrome and for the possible generalisability of intervention components in other genetic and broader clinical specialties. HASP TRIAL REGISTRATION NUMBER:Australian New Zealand Clinical Trials Registry (Identifier: ACTRN12618001072202). Registered 27 June 2018. http://www.ANZCTR.org.au/ACTRN12618001072202.aspx

Accretion disc winds in tidal disruption events: Ultraviolet spectral lines as orientation indicators

ABSTRACT Some tidal disruption events (TDEs) exhibit blueshifted broad absorption lines (BALs) in their rest-frame ultraviolet (UV) spectra, while others display broad emission lines (BELs). Similar phenomenology is observed in quasars and accreting white dwarfs, where it can be interpreted as an orientation effect associated with line formation in an accretion disc wind. We propose and explore a similar unification scheme for TDEs. We present synthetic UV spectra for disc and wind-hosting TDEs, produced by a state-of-the-art Monte Carlo ionization and radiative transfer code. Our models cover a wide range of disc wind geometries and kinematics. Such winds naturally reproduce both BALs and BELs. In general, sightlines looking into the wind cone preferentially produce BALs, while other orientations preferentially produce BELs. We also study the effect of wind clumping and CNO-processed abundances on the observed spectra. Clumpy winds tend to produce stronger UV emission and absorption lines, because clumping increases both the emission measure and the abundances of the relevant ionic species, the latter by reducing the ionization state of the outflow. The main effect of adopting CNO-processed abundances is a weakening of C iv 1550 Å  and an enhancement of N v 1240 Å  in the spectra. We conclude that line formation in an accretion disc wind is a promising mechanism for explaining the diverse UV spectra of TDEs. If this is correct, the relative number of BAL and BEL TDEs can be used to estimate the covering factor of the outflow. The models in this work are publicly available online and upon request.</jats:p