Model selection for prognostic time-to-event gene signature discovery with applications in early breast cancer data

Model selection between competing models is a key consideration in the discovery of prognostic multigene signatures. The use of appropriate statistical performance measures as well as verification of biological significance of the signatures is imperative to maximise the chance of external validation of the generated signatures. Current approaches in time-to-event studies often use only a single measure of performance in model selection, such as logrank test p-values, or dichotomise the follow-up times at some phase of the study to facilitate signature discovery. In this study we improve the prognostic signature discovery process through the application of the multivariate partial Cox model combined with the concordance index, hazard ratio of predictions, independence from available clinical covariates and biological enrichment as measures of signature performance. The proposed framework was applied to discover prognostic multigene signatures from early breast cancer data. The partial Cox model combined with the multiple performance measures were used in both guiding the selection of the optimal panel of prognostic genes and prediction of risk within cross validation without dichotomising the follow-up times at any stage. The signatures were successfully externally cross validated in independent breast cancer datasets, yielding a hazard ratio of 2.55 [1.44, 4.51] for the top ranking signature.

A randomised, phase II trial of the DNA-hypomethylating agent 5-aza-2'-deoxycytidine (decitabine) in combination with carboplatin vs carboplatin alone in patients with recurrent, partially platinum-sensitive ovarian cancer.

Background: Our previous laboratory and clinical data suggested that one mechanism underlying the development of platinum resistance in ovarian cancer is the acquisition of DNA methylation. We therefore tested the hypothesis that the DNA hypomethylating agent 5-aza-2'-deoxycytodine (decitabine) can reverse resistance to carboplatin in women with relapsed ovarian cancer.

Methods: Patients progressing 6-12 months after previous platinum therapy were randomised to decitabine on day 1 and carboplatin (AUC 6) on day 8, every 28 days or carboplatin alone. The primary objective was response rate in patients with methylated hMLH1 tumour DNA in plasma.

Results: After a pre-defined interim analysis, the study closed due to lack of efficacy and poor treatment deliverability in 15 patients treated with the combination. Responses by GCIG criteria were 9 out of 14 vs 3 out of 15 and by RECIST were 6 out of 13 vs 1 out of 12 for carboplatin and carboplatin/decitabine, respectively. Grade 3/4 neutropenia was more common with the combination (60% vs 15.4%) as was G2/3 carboplatin hypersensitivity (47% vs 21%).

Conclusions: With this schedule, the addition of decitabine appears to reduce rather than increase the efficacy of carboplatin in partially platinum-sensitive ovarian cancer and is difficult to deliver. Patient-selection strategies, different schedules and other demethylating agents should be considered in future combination studies.

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture

Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.

Developing a Reporting Guideline for Social and Psychological Intervention Trials

Social and psychological interventions are often complex. Understanding randomized controlled trials (RCTs) of these complex interventions requires a detailed description of the interventions tested and the methods used to evaluate them; however, RCT reports often omit, or inadequately report, this information. Incomplete and inaccurate reporting hinders the optimal use of research, wastes resources, and fails to meet ethical obligations to research participants and consumers. In this article, we explain how reporting guidelines have improved the quality of reports in medicine and describe the ongoing development of a new reporting guideline for RCTs: Consolidated Standards of Reporting Trials-SPI (an extension for social and psychological interventions). We invite readers to participate in the project by visiting our website, in order to help us reach the best-informed consensus on these guidelines (http://tinyurl.com/CONSORT-study).

Trajectories of Learning Dispositions and Attitudes in Upper Primary Schools in Northern Ireland: What exactly is going on?

There is increasing research and policy interest in the importance of attitudes to learning, learning orientations and learning dispositions (however they are labelled), not only because they influence traditional measures of school achievement but also because they facilitate how well children function at school, with implications for their future learning. This paper reports the findings on pupils’ learning dispositions and attitudes from two separate cohorts of pupils as they progress through upper primary school (Key Stage 2) in 50 schools in Northern Ireland. (These data are drawn from two different longitudinal studies and the data collection period predates the introduction of the new Northern Ireland Curriculum.) Approximately 1200 pupils completed seven scales from the Assessment of Learner-Centred Practices, ALCPs (McCombs and Lauer, 1997) at three time points, at the end of P5 (9 year olds), at the end of P6 (10 years olds) and at the end of P7 (11 year olds). ALCPs draws on an extensive research base that has identified cognitive and motivational dispositions and attitudes that are associated with a positive orientation to learning, and ultimately with positive progress in school (Alexander and Murphy, 1998). Although each scale can be considered separately, the seven scales cluster into two groups: self-efficacy, mastery orientation, active learning strategies and curiosity are all predicted to be pro-learning; and challenge avoidance, work avoidance, and – to a lesser extent – performance orientation, are predicted to be negatively associated with learning. The general trajectory in the children’s self-evaluations shows that they are becoming less pro-learning over time, with significant decreases in their self-ratings of active learning, curiosity, mastery orientation and self-efficacy. At the same time, there is some evidence that they work harder and put more effort into their work but this is not accompanied by maintaining their previous pro-learning motivations and strategies. The pattern is consistently more negative for boys than for girls. There are very few differences between the two cohorts indicating that the pattern is not confined to a specific cohort. These findings are challenging and will be interrogated with regard to two questions – are the changes related to the influence of the children’s school experiences per se or are they more related to developmental differences as children adopt more critical appraisals of their personal attributes and efforts as they get older? Whatever the reason, these learning dispositions and attitudes are important as they contribute significantly to school achievement even when the more traditional predictors like gender and ability are taken into account.

It Had to Be You Performance at NYCEMF 2014:for Clarinet and Computer

Concert 15: 3:30-5:30 PM: Playhouse

Danny Saul, Glitches/Trajectories
Ethan Greene, Lissajous
Kyong Mee Choi, Ceaseless Cease
Thomas Beverly, Ocotillo

intermission

Paul Wilson, It Had to be You
Kwangrae Kim, Sound Drawing
Steven Kemper, Mythical Spaces
David Durant, FAJI

Improved Thermal Performance of SOI Using Compound Buried Layer

The buried oxide (BOX) layer in silicon on insulator (SOI) was replaced by a compound buried layer (CBL) containing layers of SiO2, polycrystalline silicon (polysilicon), and SiO2. The undoped polysilicon in the CBL acted as a dielectric with a higher thermal conductivity than SiO2. CBL provides a reduced thermal resistance with the same equivalent oxide thickness as a standard SiO2 buried layer. Thermal resistance was further reduced by lateral heat flow through the polysilicon. Reduction in thermal resistance by up to 68% was observed, dependent on polysilicon thickness. CBL SOI substrates were designed and manufactured to achieve a 40% reduction in thermal resistance compared with an 1.0-μm SiO2 BOX. Power bipolar transistors with an active silicon layer thickness of 13.5 μm manufactured on CBL SOI substrates showed a 5%-17% reduction in thermal resistance compared with the standard SOI. This reduction was dependent on transistor layout geometry. Between 65% and 90% of the heat flow from these power transistors is laterally through the thick active silicon layer. Analysis confirmed that CBL SOI provided a 40% reduction in the vertical path thermal resistance. Devices employing thinner active silicon layers will achieve the greater benefit from reduction in vertical path thermal resistance offered by CBL SOI.

Accuracy of LightCycler SeptiFast for the detection and identification of pathogens in the blood of patients with suspected sepsis: a systematic review and meta-analysis

Purpose: There is an urgent need to develop diagnostic tests to improve the detection of pathogens causing life-threatening infection (sepsis). SeptiFast is a CE-marked multi-pathogen real-time PCR system capable of detecting DNA sequences of bacteria and fungi present in blood samples within a few hours. We report here a systematic review and meta-analysis of diagnostic accuracy studies of SeptiFast in the setting of suspected sepsis.

Methods: A comprehensive search strategy was developed to identify studies that compared SeptiFast with blood culture in suspected sepsis. Methodological quality was assessed using QUADAS. Heterogeneity of studies was investigated using a coupled forest plot of sensitivity and specificity and a scatter plot in receiver operator characteristic space. Bivariate model method was used to estimate summary sensitivity and specificity.

Results: From 41 phase III diagnostic accuracy studies, summary sensitivity and specificity for SeptiFast compared with blood culture were 0.68 (95 % CI 0.63–0.73) and 0.86 (95 % CI 0.84–0.89) respectively. Study quality was judged to be variable with important deficiencies overall in design and reporting that could impact on derived diagnostic accuracy metrics.

Conclusions: SeptiFast appears to have higher specificity than sensitivity, but deficiencies in study quality are likely to render this body of work unreliable. Based on the evidence presented here, it remains difficult to make firm recommendations about the likely clinical utility of SeptiFast in the setting of suspected sepsis.

Effects of a demand-led evidence briefing service on the uptake and use of research evidence by commissioners of health services: protocol for a controlled before and after study

Background: Clinical Commissioning Groups (CCGs) are mandated to use research evidence effectively to ensure optimum use of resources by the National Health Service (NHS), both in accelerating innovation and in stopping the use of less effective practices and models of service delivery. We intend to evaluate whether access to a demand-led evidence service improves uptake and use of research evidence by NHS commissioners compared with less intensive and less targeted alternatives. 

Methods/design: This is a controlled before and after study involving CCGs in the North of England. Participating CCGs will receive one of three interventions to support the use of research evidence in their decision-making:1) consulting plus responsive push of tailored evidence; 2) consulting plus an unsolicited push of non-tailored evidence; or 3) standard service unsolicited push of non-tailored evidence. Our primary outcome will be changed at 12 months from baseline of a CCGs ability to acquire, assess, adapt and apply research evidence to support decision-making. Secondary outcomes will measure individual clinical leads and managers’ intentions to use research evidence in decision making. Documentary evidence of the use of the outputs of the service will be sought. A process evaluation will evaluate the nature and success of the interactions both within the sites and between commissioners and researchers delivering the service. 

Discussion: The proposed research will generate new knowledge of direct relevance and value to the NHS. The findings will help to clarify which elements of the service are of value in promoting the use of research evidence.Those involved in NHS commissioning will be able to use the results to inform how best to build the infrastructure they need to acquire, assess, adapt and apply research evidence to support decision-making and to fulfil their statutory duties under the Health and Social Care Act.

Defining the role of common variation in the genomic and biological architecture of adult human height

Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated 1/42,000, 1/43,700 and 1/49,500 SNPs explained 1/421%, 1/424% and 1/429% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/I 2-catenin and chondroitin sulfate-related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.

New genetic loci link adipose and insulin biology to body fat distribution

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms.