Testing significance relative to a fold-change threshold is a TREAT

Motivation: Statistical methods are used to test for the differential expression of genes in microarray experiments. The most widely used methods successfully test whether the true differential expression is different from zero, but give no assurance that the differences found are large enough to be biologically meaningful

Influences on recruitment to randomised controlled trials in mental health settings in England: a national cross-sectional survey of researchers working for the Mental Health Research Network

Background: Recruitment to trials is complex and often protracted; selection bias may compromise generalisability. In the mental health field (as elsewhere), diverse factors have been described as hindering researcher access to potential participants and various strategies have been proposed to overcome barriers. However, the extent to which various influences identified in the literature are operational across mental health settings in England has not been systematically examined. Methods: A cross-sectional, online survey of clinical studies officers employed by the Mental Health Research Network in England to recruit to trials from National Health Service mental health services. The bespoke questionnaire invited participants to report exposure to specified influences on recruitment, the perceived impact of these on access to potential participants, and to describe additional positive or negative influences on recruitment. Analysis employed descriptive statistics, the framework approach and triangulation of data. Results: Questionnaires were returned by 98 (58%) of 170 clinical studies officers who reported diverse experience. Data demonstrated a disjunction between policy and practice. While the particulars of trial design and various marketing and dommunication strategies could influence recruitment, consensus was that the culture of NHS mental health services is not donducive to research. Since financial rewards for recruitment paid to Trusts and feedback about studies seldom reaching frontline services, clinicians were described as distanced from research. Facing continual service change and demanding clinical workloads, clinicians generally did not prioritise recruitment activities. Incentives to trial participants had variable impact on access but recruitment could be enhanced by engagement of senior investigators and integrating referral with routine practice. Comprehensive, robust feasibility studies and reciprocity between researchers and clinicians were considered crucial to successful recruitment. Conclusions: In the mental health context, researcher access to potential trial participants is multiply influenced. Gatekeeping clinicians are faced with competing priorities and resources constrain research activity. It seems that environmental adjustment predicated on equitable resource allocation is needed if clinicians in NHS mental health services are to fully support the conduct of randomised controlled trials. Whilst cultural transformation, requiring changes in assumptions and values, is complex, our findings suggest that attention to practical matters can support this and highlight issues requiring careful consideration

"It's making contacts" : notions of social capital and implications for widening access to medical education

Acknowledgements Our thanks to the Medical Schools Council (MSC) of the UK for funding Study A; REACH Scotland for funding Study B; and Queen Mary University of London, and to the medical school applicants and students who gave their time to be interviewed. Our thanks also to Dr Sean Zhou and Dr Sally Curtis, and Manjul Medhi, for their help with data collection for studies A and B respectively. Our thanks also to Dr Lara Varpio, Uniformed Services University of the USA, for her advice and guidance on collating data sets and her comments on the draft manuscript.Peer reviewedPublisher PD

Bacterial Acquisition in Juveniles of Several Broadcast Spawning Coral Species

Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH) using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals

Weak Decays Beyond Leading Logarithms

We review the present status of QCD corrections to weak decays beyond the leading logarithmic approximation including particle-antiparticle mixing and rare and CP violating decays. After presenting the basic formalism for these calculations we discuss in detail the effective hamiltonians for all decays for which the next-to-leading corrections are known. Subsequently, we present the phenomenological implications of these calculations. In particular we update the values of various parameters and we incorporate new information on m_t in view of the recent top quark discovery. One of the central issues in our review are the theoretical uncertainties related to renormalization scale ambiguities which are substantially reduced by including next-to-leading order corrections. The impact of this theoretical improvement on the determination of the Cabibbo-Kobayashi-Maskawa matrix is then illustrated in various cases.Comment: 229 pages, 32 PostScript figures (included); uses RevTeX, epsf.sty, rotate.sty, rmpbib.sty (included), times.sty (included; requires LaTeX 2e); complete PostScript version available at ftp://feynman.t30.physik.tu-muenchen.de/pub/preprints/tum-100-95.ps.gz or ftp://feynman.t30.physik.tu-muenchen.de/pub/preprints/tum-100-95.ps2.gz (scaled down and rotated version to print two pages on one sheet of paper

MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study

<p>Abstract</p> <p>Background</p> <p>The interactions of multiple single nucleotide polymorphisms (SNPs) are highly hypothesized to affect an individual's susceptibility to complex diseases. Although many works have been done to identify and quantify the importance of multi-SNP interactions, few of them could handle the genome wide data due to the combinatorial explosive search space and the difficulty to statistically evaluate the high-order interactions given limited samples.</p> <p>Results</p> <p>Three comparative experiments are designed to evaluate the performance of MegaSNPHunter. The first experiment uses synthetic data generated on the basis of epistasis models. The second one uses a genome wide study on Parkinson disease (data acquired by using Illumina HumanHap300 SNP chips). The third one chooses the rheumatoid arthritis study from Wellcome Trust Case Control Consortium (WTCCC) using Affymetrix GeneChip 500K Mapping Array Set. MegaSNPHunter outperforms the best solution in this area and reports many potential interactions for the two real studies.</p> <p>Conclusion</p> <p>The experimental results on both synthetic data and two real data sets demonstrate that our proposed approach outperforms the best solution that is currently available in handling large-scale SNP data both in terms of speed and in terms of detection of potential interactions that were not identified before. To our knowledge, MegaSNPHunter is the first approach that is capable of identifying the disease-associated SNP interactions from WTCCC studies and is promising for practical disease prognosis.</p

Developing the digital self-determined learner through heutagogical design

This empirical qualitative study investigates whether the introduction of heutagogy in contemporary nursing education can foster the development of the digital self-determined learner, who is prepared to work and live in the fourth industrial age and beyond. The impact of heutagogical design on learner process and outcomes is explored through qualitative framework analysis of learner data and reflective educator observations. Findings suggest that with careful scaffolding and courage in remaining true to the educational philosophy, this approach has the potential to develop learners who demonstrate key principles of heutagogy including non-linear learning, learner agency, capability, self-reflection and metacognition and double-loop learning. This innovative study provides insight into the process of developing the self-determined learner and encourages further research into flexible and learner-centred approaches across Higher Education

Understanding recovery in the context of lived experience of personality disorders: a collaborative, qualitative research study

Background Concepts of recovery increasingly inform the development and delivery of mental health services internationally. In the UK recent policy advocates the application of recovery concepts to the treatment of personality disorders. However diagnosis and understanding of personality disorders remains contested, challenging any assumption that mainstream recovery thinking can be directly translated into personality disorders services. Methods In a qualitative interview-based study understandings of recovery were explored in extended, in-depth interviews with six people purposively sampled from a specialist personality disorders’ service in the UK. An interpretive, collaborative approach to research was adopted in which university-, clinical- and service user (consumer) researchers were jointly involved in carrying out interviews and analysing interview data. Results Findings suggested that recovery cannot be conceptualised separately from an understanding of the lived experience of personality disorders. This experience was characterised by a complexity of ambiguous, interrelating and conflicting feelings, thoughts and actions as individuals tried to cope with tensions between internally and externally experienced worlds. Our analysis was suggestive of a process of recovering or, for some, discovering a sense of self that can safely coexist in both worlds. Conclusions We conclude that key facilitators of recovery – positive personal relationships and wider social interaction – are also where the core vulnerabilities of individuals with lived experience of personaility disorders can lie. There is a role for personality disorders services in providing a safe space in which to develop positive relationships. Through discursive practice within the research team understandings of recovery were co-produced that responded to the lived experience of personality disorders and were of applied relevance to practitioners

'To take care of the patients': Qualitative analysis of Veterans Health Administration personnel experiences with a clinical informatics system

<p>Abstract</p> <p>Background</p> <p>The Veterans Health Administration (VA) has invested significant resources in designing and implementing a comprehensive electronic health record (EHR) that supports clinical priorities. EHRs in general have been difficult to implement, with unclear cost-effectiveness. We describe VA clinical personnel interactions with and evaluations of the EHR.</p> <p>Methods</p> <p>As part of an evaluation of a quality improvement initiative, we interviewed 72 VA clinicians and managers using a semi-structured interview format. We conducted a qualitative analysis of interview transcripts, examining themes relating to participants' interactions with and evaluations of the VA EHR.</p> <p>Results</p> <p>Participants described their perceptions of the positive and negative effects of the EHR on their clinical workflow. Although they appreciated the speed and ease of documentation that the EHR afforded, they were concerned about the time cost of using the technology and the technology's potential for detracting from interpersonal interactions.</p> <p>Conclusions</p> <p>VA personnel value EHRs' contributions to supporting communication, education, and documentation. However, participants are concerned about EHRs' potential interference with other important aspects of healthcare, such as time for clinical care and interpersonal communication with patients and colleagues. We propose that initial implementation of an EHR is one step in an iterative process of ongoing quality improvement.</p

Impact of the spotted microarray preprocessing method on fold-change compression and variance stability

<p>Abstract</p> <p>Background</p> <p>The standard approach for preprocessing spotted microarray data is to subtract the local background intensity from the spot foreground intensity, to perform a log2 transformation and to normalize the data with a global median or a lowess normalization. Although well motivated, standard approaches for background correction and for transformation have been widely criticized because they produce high variance at low intensities. Whereas various alternatives to the standard background correction methods and to log2 transformation were proposed, impacts of both successive preprocessing steps were not compared in an objective way.</p> <p>Results</p> <p>In this study, we assessed the impact of eight preprocessing methods combining four background correction methods and two transformations (the log2 and the glog), by using data from the MAQC study. The current results indicate that most preprocessing methods produce fold-change compression at low intensities. Fold-change compression was minimized using the Standard and the Edwards background correction methods coupled with a log2 transformation. The drawback of both methods is a high variance at low intensities which consequently produced poor estimations of the p-values. On the other hand, effective stabilization of the variance as well as better estimations of the p-values were observed after the glog transformation.</p> <p>Conclusion</p> <p>As both fold-change magnitudes and p-values are important in the context of microarray class comparison studies, we therefore recommend to combine the Edwards correction with a hybrid transformation method that uses the log2 transformation to estimate fold-change magnitudes and the glog transformation to estimate p-values.</p