A low cost scheme for high precision dual-wavelength laser metrology

A novel method capable of delivering relative optical path length metrology with nanometer precision is demonstrated. Unlike conventional dual-wavelength metrology which employs heterodyne detection, the method developed in this work utilizes direct detection of interference fringes of two He-Ne lasers as well as a less precise stepper motor open-loop position control system to perform its measurement. Although the method may be applicable to a variety of circumstances, the specific application where this metrology is essential is in an astrometric optical long baseline stellar interferometer dedicated to precise measurement of stellar positions. In our example application of this metrology to a narrow-angle astrometric interferometer, measurement of nanometer precision could be achieved without frequency-stabilized lasers although the use of such lasers would extend the range of optical path length the metrology can accurately measure. Implementation of the method requires very little additional optics or electronics, thus minimizing cost and effort of implementation. Furthermore, the optical path traversed by the metrology lasers is identical with that of the starlight or science beams, even down to using the same photodetectors, thereby minimizing the non-common-path between metrology and science channels.Comment: 17 pages, 4 figures, accepted for publication in Applied Optic

Using the quantum probability ranking principle to rank interdependent documents

A known limitation of the Probability Ranking Principle (PRP) is that it does not cater for dependence between documents. Recently, the Quantum Probability Ranking Principle (QPRP) has been proposed, which implicitly captures dependencies between documents through “quantum interference”. This paper explores whether this new ranking principle leads to improved performance for subtopic retrieval, where novelty and diversity is required. In a thorough empirical investigation, models based on the PRP, as well as other recently proposed ranking strategies for subtopic retrieval (i.e. Maximal Marginal Relevance (MMR) and Portfolio Theory(PT)), are compared against the QPRP. On the given task, it is shown that the QPRP outperforms these other ranking strategies. And unlike MMR and PT, one of the main advantages of the QPRP is that no parameter estimation/tuning is required; making the QPRP both simple and effective. This research demonstrates that the application of quantum theory to problems within information retrieval can lead to significant improvements

Low-cost scheme for high-precision dual-wavelength laser metrology

A method capable of delivering relative optical path length metrology with nanometer precision is demonstrated. Unlike conventional dual-wavelength metrology, which employs heterodyne detection, the method developed in this work utilizes direct detection of interference fringes of two He-Ne lasers as well as a less precise stepper motor open-loop position control system to perform its measurement. Although the method may be applicable to a variety of circumstances, the specific application in which this metrology is essential is in an astrometric optical long baseline stellar interferometer dedicated to precise measurement of stellar positions. In our example application of this metrology to a narrow-angle astrometric interferometer, measurement of nanometer precision could be achieved without frequency-stabilized lasers, although the use of such lasers would extend the range of optical path length the metrology can accurately measure. Implementation of the method requires very little additional optics or electronics, thus minimizing the cost and effort of implementation. Furthermore, the optical path traversed by the metrology lasers is identical to that of the starlight or science beams, even down to using the same photodetectors, thereby minimizing the noncommon path between metrology and science channels.This research was supported under the Australian Research Council’s Discovery Project funding scheme. Y. K. was supported by the University of Sydney International Scholarship (USydIS)

Candida albicans biofilm heterogeneity does not influence denture stomatitis but strongly influences denture cleansing capacity

Approximately 20  % of the UK population wear some form of denture prosthesis, resulting in denture stomatitis in half of these individuals. Candida albicans is primarily attributed as the causative agent, due to its biofilm -forming ability. Recently, there has been increasing evidence of C. albicans biofilm heterogeneity and the negative impact it can have clinically; however, this phenomenon has yet to be studied in relation to denture isolates. The aims of this study were to evaluate C. albicans biofilm formation of clinical denture isolates in a denture environment and to assess antimicrobial activity of common denture cleansers against these tenacious communities. C. albicans isolated from dentures of healthy and diseased individuals was quantified using real-time PCR and biofilm biomass assessed using crystal violet. Biofilm development on the denture substratum poly(methyl methacrylate), Molloplast B and Ufi-gel was determined. Biofilm formation was assessed using metabolic and biomass stains, following treatment with denture hygiene products. Although C. albicans was detected in greater quantities in diseased individuals, it was not associated with increased biofilm biomass. Denture substrata were shown to influence biofilm biomass, with poly(methyl methacrylate) providing the most suitable environment for C. albicans to reside. Of all denture hygiene products tested, Milton had the most effective antimicrobial activity, reducing biofilm biomass and viability the greatest. Overall, our results highlight the complex nature of denture- related disease, and disease development cannot always be attributed to a sole cause. It is the distinct combination of various factors that ultimately determines the pathogenic outcome

Keck Spectroscopy of 3<z<7 Faint Lyman Break Galaxies: The Importance of Nebular Emission in Understanding the Specific Star Formation Rate and Stellar Mass Density

The physical properties inferred from the SEDs of z>3 galaxies have been influential in shaping our understanding of early galaxy formation and the role galaxies may play in cosmic reionization. Of particular importance is the stellar mass density at early times which represents the integral of earlier star formation. An important puzzle arising from the measurements so far reported is that the specific star formation rates (sSFR) evolve far less rapidly than expected in most theoretical models. Yet the observations underpinning these results remain very uncertain, owing in part to the possible contamination of rest-optical broadband light from strong nebular emission lines. To quantify the contribution of nebular emission to broad-band fluxes, we investigate the SEDs of 92 spectroscopically-confirmed galaxies in the redshift range 3.8<z<5.0 chosen because the H-alpha line lies within the Spitzer/IRAC 3.6 um filter. We demonstrate that the 3.6 um flux is systematically in excess of that expected from stellar continuum, which we derive by fitting the SED with population synthesis models. No such excess is seen in a control sample at 3.1<z<3.6 in which there is no nebular contamination in the IRAC filters. From the distribution of our 3.6 um flux excesses, we derive an H-alpha equivalent width (EW) distribution. The mean rest-frame H-alpha EW we infer at 3.8<z<5.0 (270 A) indicates that nebular emission contributes at least 30% of the 3.6 um flux. Via our empirically-derived EW distribution we correct the available stellar mass densities and show that the sSFR evolves more rapidly at z>4 than previously thought, supporting up to a 5x increase between z~2 and 7. Such a trend is much closer to theoretical expectations. Given our findings, we discuss the prospects for verifying quantitatively the nebular emission line strengths prior to the launch of the James Webb Space Telescope.Comment: 16 pages, 9 figures, submitted to Ap

Designing theoretically-informed implementation interventions

Clinical and health services research is continually producing new findings that may contribute to effective and efficient patient care. However, the transfer of research findings into practice is unpredictable and can be a slow and haphazard process. Ideally, the choice of implementation strategies would be based upon evidence from randomised controlled trials or systematic reviews of a given implementation strategy. Unfortunately, reviews of implementation strategies consistently report effectiveness some, but not all of the time; possible causes of this variation are seldom reported or measured by the investigators in the original studies. Thus, any attempts to extrapolate from study settings to the real world are hampered by a lack of understanding of the effects of key elements of individuals, interventions, and the settings in which they were trialled. The explicit use of theory offers a way of addressing these issues and has a number of advantages, such as providing: a generalisable framework within which to represent the dimensions that implementation studies address, a process by which to inform the development and delivery of interventions, a guide when evaluating, and a way to allow for an exploration of potential causal mechanisms. However, the use of theory in designing implementation interventions is methodologically challenging for a number of reasons, including choosing between theories and faithfully translating theoretical constructs into interventions. The explicit use of theory offers potential advantages in terms of facilitating a better understanding of the generalisability and replicability of implementation interventions. However, this is a relatively unexplored methodological area

Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma

BACKGROUND: Long non-coding RNAs (lncRNAs) are emerging as molecules that significantly impact many cellular processes and have been associated with almost every human cancer. Compared to protein-coding genes, lncRNA genes are often associated with transposable elements, particularly with endogenous retroviral elements (ERVs). ERVs can have potentially deleterious effects on genome structure and function, so these elements are typically silenced in normal somatic tissues, albeit with varying efficiency. The aberrant regulation of ERVs associated with lncRNAs (ERV-lncRNAs), coupled with the diverse range of lncRNA functions, creates significant potential for ERV-lncRNAs to impact cancer biology. METHODS: We used RNA-seq analysis to identify and profile the expression of a novel lncRNA in six large cohorts, including over 7,500 samples from The Cancer Genome Atlas (TCGA). RESULTS: We identified the tumor-specific expression of a novel lncRNA that we have named Endogenous retroViral-associated ADenocarcinoma RNA or ‘EVADR’, by analyzing RNA-seq data derived from colorectal tumors and matched normal control tissues. Subsequent analysis of TCGA RNA-seq data revealed the striking association of EVADR with adenocarcinomas, which are tumors of glandular origin. Moderate to high levels of EVADR were detected in 25 to 53% of colon, rectal, lung, pancreas and stomach adenocarcinomas (mean = 30 to 144 FPKM), and EVADR expression correlated with decreased patient survival (Cox regression; hazard ratio = 1.47, 95% confidence interval = 1.06 to 2.04, P = 0.02). In tumor sites of non-glandular origin, EVADR expression was detectable at only very low levels and in less than 10% of patients. For EVADR, a MER48 ERV element provides an active promoter to drive its transcription. Genome-wide, MER48 insertions are associated with nine lncRNAs, but none of the MER48-associated lncRNAs other than EVADR were consistently expressed in adenocarcinomas, demonstrating the specific activation of EVADR. The sequence and structure of the EVADR locus is highly conserved among Old World monkeys and apes but not New World monkeys or prosimians, where the MER48 insertion is absent. Conservation of the EVADR locus suggests a functional role for this novel lncRNA in humans and our closest primate relatives. CONCLUSIONS: Our results describe the specific activation of a highly conserved ERV-lncRNA in numerous cancers of glandular origin, a finding with diagnostic, prognostic and therapeutic implications. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-015-0142-6) contains supplementary material, which is available to authorized users

Incident venous thromboembolic events in the Prospective Study of Pravastatin in the Elderly at Risk (PROSPER)

&lt;p&gt;Background: Venous thromboembolic events (VTE), including deep venous thrombosis and pulmonary embolism, are common in older age. It has been suggested that statins might reduce the risk of VTE however positive results from studies of middle aged subjects may not be generalisable to elderly people. We aimed to determine the effect of pravastatin on incident VTE in older people; we also studied the impact of clinical and plasma risk variables.&lt;/p&gt; &lt;p&gt;Methods: This study was an analysis of incident VTE using data from the Prospective Study of Pravastatin in the Elderly at Risk (PROSPER), a randomized, double-blind, placebo-controlled trial of pravastatin in men and women aged 70-82. Mean follow-up was 3.2 years. Risk for VTE was examined in non-warfarin treated pravastatin (n = 2834) and placebo (n = 2865) patients using a Cox's proportional hazard model, and the impact of other risk factors assessed in a multivariate forward stepwise regression analysis. Baseline clinical characteristics, blood biochemistry and hematology variables, plasma levels of lipids and lipoproteins, and plasma markers of inflammation and adiposity were compared. Plasma markers of thrombosis and hemostasis were assessed in a nested case (n = 48) control (n = 93) study where the cohort was those participants, not on warfarin, for whom data were available.&lt;/p&gt; &lt;p&gt;Results: There were 28 definite cases (1.0%) of incident VTE in the pravastatin group recipients and 20 cases (0.70%) in placebo recipients. Pravastatin did not reduce VTE in PROSPER compared to placebo [unadjusted hazard ratio (95% confidence interval) 1.42 (0.80, 2.52) p = 0.23]. Higher body mass index (BMI) [1.09 (1.02, 1.15) p = 0.0075], country [Scotland vs Netherlands 4.26 (1.00, 18.21) p = 0.050 and Ireland vs Netherlands 6.16 (1.46, 26.00) p = 0.013], lower systolic blood pressure [1.35 (1.03, 1.75) p = 0.027] and lower baseline Mini Mental State Examination (MMSE) score [1.19 (1.01, 1.41) p = 0.034] were associated with an increased risk of VTE, however only BMI, country and systolic blood pressure remained significant on multivariate analysis. In a nested case control study of definite VTE, plasma Factor VIII levels were associated with VTE [1.52 (1.01, 2.28), p = 0.044]. However no other measure of thrombosis and haemostasis was associated with increased risk of VTE.&lt;/p&gt; &lt;p&gt;Conclusions: Pravastatin does not prevent VTE in elderly people at risk of vascular disease. Blood markers of haemostasis and inflammation are not strongly predictive of VTE in older age however BMI, country and lower systolic blood pressure are independently associated with VTE risk.&lt;/p&gt