Hybrid copula mixed models for combining case-control and cohort studies in meta-analysis of diagnostic tests

Copula mixed models for trivariate (or bivariate) meta-analysis of diagnostic test accuracy studies accounting (or not) for disease prevalence have been proposed in the biostatistics literature to synthesize information. However, many systematic reviews often include case-control and cohort studies, so one can either focus on the bivariate meta-analysis of the case-control studies or the trivariate meta-analysis of the cohort studies, as only the latter contains information on disease prevalence. In order to remedy this situation of wasting data we propose a hybrid copula mixed model via a combination of the bivariate and trivariate copula mixed model for the data from the case-control studies and cohort studies, respectively. Hence, this hybrid model can account for study design and also due to its generality can deal with dependence in the joint tails. We apply the proposed hybrid copula mixed model to a review of the performance of contemporary diagnostic imaging modalities for detecting metastases in patients with melanoma

A vine copula mixed effect model for trivariate meta-analysis of diagnostic test accuracy studies accounting for disease prevalence

A bivariate copula mixed model has been recently proposed to synthesize diagnostic test accuracy studies and it has been shown that it is superior to the standard generalized linear mixed model in this context. Here, we call trivariate vine copulas to extend the bivariate meta-analysis of diagnostic test accuracy studies by accounting for disease prevalence. Our vine copula mixed model includes the trivariate generalized linear mixed model as a special case and can also operate on the original scale of sensitivity, specificity, and disease prevalence. Our general methodology is illustrated by re-analyzing the data of two published meta-analyses. Our study suggests that there can be an improvement on trivariate generalized linear mixed model in fit to data and makes the argument for moving to vine copula random effects models especially because of their richness, including reflection asymmetric tail dependence, and computational feasibility despite their three dimensionality

Between tinkering and transformation: A contemporary appraisal of climate change adaptation research on the world's islands

Islands are at the center of discourses on climate change. Yet despite extensive work on diverse island systems in a changing climate, we still lack an understanding of climate change-related responses amongst islands and what shifting from what might be called “tinkering” (perhaps heat warnings) to “transformational” adaptation (perhaps relocation) means for these vastly different landmasses which are often grouped together by default. Through a systematic review of the climate change adaptation scientific literature, this paper critically reflects on how considering islands as a homogenous ensemble and the use of buzzwords such as “transformational adaptation” may be problematic for diverse island realities under climate change. Our findings show that the adaptation evidence base actually provides literature on contrasting island types and cultural and political contexts, including Small Island Developing States as well as other island territories. This study finds research gaps with respect to regions (e.g., South America, Africa, and Mediterranean) and that there is overall both little evidence of and a lack of context-specific definitions of transformational adaptation in island contexts. The adaptation literature does not yet fully reflect the experiences or needs of islands regarding transitions and transformations throughout history

Symplastic scrotal leiomyoma: a case report

<p>Abstract</p> <p>Introduction</p> <p>Scrotal leiomyomas are rare tumours which are essentially benign. Recurrence and malignant transformation to leiomyosarcoma have been reported. However, a specific subgroup with increased bizarre nuclei showing increased mitosis raises the need for a closer follow-up. We report on such a case.</p> <p>Case presentation</p> <p>We report the case of a 65-year-old man who underwent a scrotal lump excision. Histology showed a well defined leiomyoma. The presence of nuclear pleomorphism and mitoses, just falling short of the criteria for malignancy, made prediction of biological behaviour difficult. The patient remains well on 4-year follow-up.</p> <p>Conclusion</p> <p>Histological evidence of increased mitosis raises the need for sustained follow-up in view of the malignant potential from the extent of mitosis. Immunohistochemistry helps in identifying those patients warranting close follow-up.</p

Development of an in vitro periodontal biofilm model for assessing antimicrobial and host modulatory effects of bioactive molecules

Background: Inflammation within the oral cavity occurs due to dysregulation between microbial biofilms and the host response. Understanding how different oral hygiene products influence inflammatory properties is important for the development of new products. Therefore, creation of a robust host-pathogen biofilm platform capable of evaluating novel oral healthcare compounds is an attractive option. We therefore devised a multi-species biofilm co-culture model to evaluate the naturally derived polyphenol resveratrol (RSV) and gold standard chlorhexidine (CHX) with respect to anti-biofilm and anti-inflammatory properties.&lt;p&gt;&lt;/p&gt; Methods: An in vitro multi-species biofilm containing &lt;i&gt;S. mitis, F. nucleatum, P. Gingivalis&lt;/i&gt; and &lt;i&gt;A. Actinomycetemcomitans&lt;/i&gt; was created to represent a disease-associated biofilm and the oral epithelial cell in OKF6-TERT2. Cytotoxicity studies were performed using RSV and CHX. Multi-species biofilms were either treated with either molecule, or alternatively epithelial cells were treated with these prior to biofilm co-culture. Biofilm composition was evaluated and inflammatory responses quantified at a transcriptional and protein level.&lt;p&gt;&lt;/p&gt; Results: CHX was toxic to epithelial cells and multi-species biofilms at concentrations ranging from 0.01-0.2%. RSV did not effect multi-species biofilm composition, but was toxic to epithelial cells at concentrations greater than 0.01%. In co-culture, CHX-treated biofilms resulted in down regulation of the inflammatory chemokine IL-8 at both mRNA and protein level. RSV-treated epithelial cells in co-culture were down-regulated in the release of IL-8 protein, but not mRNA.&lt;p&gt;&lt;/p&gt; Conclusions: CHX possesses potent bactericidal properties, which may impact downstream inflammatory mediators. RSV does not appear to have bactericidal properties against multi-species biofilms, however it did appear to supress epithelial cells from releasing inflammatory mediators. This study demonstrates the potential to understand the mechanisms by which different oral hygiene products may influence gingival inflammation, thereby validating the use of a biofilm co-culture model.&lt;p&gt;&lt;/p&gt

A new approach to in silico SNP detection and some new SNPs in the Bacillus anthracis genome

<p>Abstract</p> <p>Background</p> <p><it>Bacillus anthracis </it>is one of the most monomorphic pathogens known. Identification of polymorphisms in its genome is essential for taxonomic classification, for determination of recent evolutionary changes, and for evaluation of pathogenic potency.</p> <p>Findings</p> <p>In this work three strains of the <it>Bacillus anthracis </it>genome are compared and previously unpublished single nucleotide polymorphisms (SNPs) are revealed. Moreover, it is shown that, despite the highly monomorphic nature of <it>Bacillus anthracis</it>, the SNPs are (1) abundant in the genome and (2) distributed relatively uniformly across the sequence.</p> <p>Conclusions</p> <p>The findings support the proposition that SNPs, together with indels and variable number tandem repeats (VNTRs), can be used effectively not only for the differentiation of perfect strain data, but also for the comparison of moderately incomplete, noisy and, in some cases, unknown <it>Bacillus anthracis </it>strains. In the case when the data is of still lower quality, a new DNA sequence fingerprinting approach based on recently introduced markers, based on combinatorial-analytic concepts and called cyclic difference sets, can be used.</p

Improving health outcome for young people with long term conditions: The role of digital communication in current and future patient-clinician communication for NHS providers of specialist clinical services for young people receiving specialist clinical services:LYNC study protocol.

Background: Young people living with long term conditions are vulnerable to health service disengagement. This endangers their long term health. Studies report requests for digital forms of communication - email, text, social media - with their health care team. Digital clinical communication is troublesome for the UK NHS. Aim: To present the research protocol for evaluating the impacts and outcomes of digital clinical communications for young people living with long term conditions and provide critical analysis of their use, monitoring and evaluation by NHS providers. Methods: The research involves: 1) Patient and Public Involvement activities with 16-24 year olds with and without long term health conditions; 2) six literature reviews; 3) case studies – the main empirical part of the study – and 4) synthesis and a consensus meeting. Case studies use a mixed methods design. Interviews and non-participant observation of practitioners and patients communicating in up to 20 specialist clinical settings will be combined with data, aggregated at the case level (non-identifiable patient data), on a range of clinical outcomes meaningful within the case and across cases. We will describe the use of digital clinical communication from the perspective of patients, clinical staff, support staff and managers, interviewing up to 15 young people and 15 staff per case study. Outcome data includes emergency admissions, A&E attendance and DNA rates. Case studies will be analysed to understand impacts of digital clinical communication on patient health outcomes, health care costs and consumption, ethics and patient safety

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7. Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000 quasar spectra (g<22) will constrain BAO over the redshift range 2.15<z<3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyman alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance D_A to an accuracy of 1.0% at redshifts z=0.3 and z=0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyman alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D_A(z) and H^{-1}(z) parameters to an accuracy of 1.9% at z~2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.Comment: 49 pages, 16 figures, accepted by A