The Significance Filter, the Winner's Curse and the Need to Shrink

The "significance filter" refers to focusing exclusively on statistically significant results. Since frequentist properties such as unbiasedness and coverage are valid only before the data have been observed, there are no guarantees if we condition on significance. In fact, the significance filter leads to overestimation of the magnitude of the parameter, which has been called the "winner's curse". It can also lead to undercoverage of the confidence interval. Moreover, these problems become more severe if the power is low. While these issues clearly deserve our attention, they have been studied only informally and mathematical results are lacking. Here we study them from the frequentist and the Bayesian perspective. We prove that the relative bias of the magnitude is a decreasing function of the power and that the usual confidence interval undercovers when the power is less than 50%. We conclude that failure to apply the appropriate amount of shrinkage can lead to misleading inferences

First--order continuous models of opinion formation

We study certain nonlinear continuous models of opinion formation derived from a kinetic description involving exchange of opinion between individual agents. These models imply that the only possible final opinions are the extremal ones, and are similar to models of pure drift in magnetization. Both analytical and numerical methods allow to recover the final distribution of opinion between the two extremal ones.Comment: 17 pages, 4 figure

Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project

Providing ostensibly healthy individuals with personal results from whole-genome sequencing could lead to improved health and well-being via enhanced disease risk prediction, prevention, and diagnosis, but also poses practical and ethical challenges. Understanding how individuals react psychologically and behaviourally will be key in assessing the potential utility of personal whole-genome sequencing. We conducted an exploratory longitudinal cohort study in which quantitative surveys and in-depth qualitative interviews were conducted before and after personal results were returned to individuals who underwent whole-genome sequencing. The participants were offered a range of interpreted results, including Alzheimer’s disease, type 2 diabetes, pharmacogenomics, rare disease-associated variants, and ancestry. They were also offered their raw data. Of the 35 participants at baseline, 29 (82.9%) completed the 6-month follow-up. In the quantitative surveys, test-related distress was low, although it was higher at 1-week than 6-month follow-up (Z=2.68, P=0.007). In the 6-month qualitative interviews, most participants felt happy or relieved about their results. A few were concerned, particularly about rare disease-associated variants and Alzheimer’s disease results. Two of the 29 participants had sought clinical follow-up as a direct or indirect consequence of rare disease-associated variants results. Several had mentioned their results to their doctors. Some participants felt having their raw data might be medically useful to them in the future. The majority reported positive reactions to having their genomes sequenced, but there were notable exceptions to this. The impact and value of returning personal results from whole-genome sequencing when implemented on a larger scale remains to be seen

Linear regression for numeric symbolic variables: an ordinary least squares approach based on Wasserstein Distance

In this paper we present a linear regression model for modal symbolic data. The observed variables are histogram variables according to the definition given in the framework of Symbolic Data Analysis and the parameters of the model are estimated using the classic Least Squares method. An appropriate metric is introduced in order to measure the error between the observed and the predicted distributions. In particular, the Wasserstein distance is proposed. Some properties of such metric are exploited to predict the response variable as direct linear combination of other independent histogram variables. Measures of goodness of fit are discussed. An application on real data corroborates the proposed method

On variation and uncertainty

The overall purpose of the 'Statistical Points and Pitfalls' series is to help readers and researchers alike increase awareness of how to use statistics and why/how we fall into inappropriate choices or interpretations. We hope to help readers understand common misconceptions and give clear guidance on how to avoid common pitfalls by offering simple tips to improve your reporting of quantitative research findings. Each entry discusses a commonly encountered inappropriate practice and alternatives from a pragmatic perspective with minimal mathematics involved. We encourage readers to share comments on or suggestions for this section on Twitter, using the hashtag: #mededstats.</p

Clinical relevance of endpoints in clinical trials for acid sphingomyelinase deficiency enzyme replacement therapy

Background: Acid sphingomyelinase deficiency (ASMD) also known as Niemann-Pick disease, is a rare lysosomal storage disorder with a diverse disease spectrum that includes slowly progressive, chronic visceral (type B) and neurovisceral forms (intermediate type A/B), in addition to infantile, rapidly progressive fatal neurovisceral disease (type A). Purpose and methods: We review the published evidence on the relevance of splenomegaly and reduced lung diffusion capacity to the clinical burden of chronic forms of ASMD. Targeted literature searches were conducted to identify relevant ASMD and non-ASMD studies for associations between diffusing capacity of the lungs for carbon monoxide (DLCO) and splenomegaly, with clinical parameters and outcome measures. Results: Respiratory disease and organomegaly are primary and independent contributors to mortality, disease burden, and morbidity for patients with chronic ASMD. The degree of splenomegaly correlates with short stature, atherogenic lipid profile, and degree of abnormality of hematologic parameters, and thus may be considered a surrogate marker for bleeding risk, abnormal lipid profiles and possibly, liver fibrosis. Progressive lung disease is a prevalent clinical feature of chronic ASMD, contributing to a decreased quality of life (QoL) and an increased disease burden. In addition, respiratory-related complications are a major cause of mortality in ASMD. Conclusions: The reviewed evidence from ASMD natural history and observational studies supports the use of lung function and spleen volume as clinically meaningful endpoints in ASMD trials that translate into important measures of disease burden for patients

Mentoring at the University of Pennsylvania: Results of a Faculty Survey

BACKGROUND: Research suggests mentoring is related to career satisfaction and success. Most studies have focused on junior faculty. OBJECTIVE: To explore multiple aspects of mentoring at an academic medical center in relation to faculty rank, track, and gender. DESIGN: Cross-sectional mail survey in mid-2003. PARTICIPANTS: Faculty members, 1,432, at the University of Pennsylvania School of Medicine MEASUREMENTS: Self-administered survey developed from existing instruments and stakeholders. RESULTS: Response rate was 73% (n = 1,046). Most (92%) assistant and half (48%) of associate professors had a mentor. Assistant professors in the tenure track were most likely to have a mentor (98%). At both ranks, the faculty was given more types of advice than types of opportunities. Satisfaction with mentoring was correlated with the number of types of mentoring received (r = .48 and .53, P < .0001), job satisfaction (r = .44 and .31, P < .0001), meeting frequency (r = .53 and .61, P < .0001), and expectation of leaving the University within 5 years (Spearman r = −.19 and −.18, P < .0001), at the assistant and associate rank, respectively. Significant predictors of higher overall job satisfaction were associate rank [Odds ratio (OR) = 2.04, CI = 1.29–3.21], the 10-point mentoring satisfaction rating (OR = 1.27, CI = 1.17–1.35), and number of mentors (OR = 1.60, CI = 1.20–2.07). CONCLUSIONS: Having a mentor, or preferably, multiple mentors is strongly related to satisfaction with mentoring and overall job satisfaction. Surprisingly, few differences were related to gender. Mentoring of clinician–educators, research track faculty, and senior faculty, and the use of multiple mentors require specific attention of academic leadership and further study

Analytic philosophy for biomedical research: the imperative of applying yesterday's timeless messages to today's impasses

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined

The dose–response relationship between training-load measures and aerobic fitness in elite academy soccer players

The aim of the current study is to examine the dose-response relationships between training load (TL) measures and the consequent changes in aerobic fitness. Data were collected over the 6-week pre-season period in elite youth soccer players. Participants completed a lactate threshold test to identify changes in treadmill speed at 2 mmol · l (S2) and 4 mmol · l (S4). Internal TL was quantified with the following training impulse (TRIMP) methods: Banister TRIMP, Edwards TRIMP, Lucia TRIMP, individual TRIMP (iTRIMP) and rate of perceived exertion was also collected. External TL measures were total distance, PlayerLoad, high speed running (14.4-19.8 km · h ), very high-speed running (19.8-25.2 km · h ) and maximal sprint distance (>25.2 km · h ). Individual high-speed distance was derived from each participants treadmill speed at S4. Different Bayesian regression models were run with different likelihood functions. The best-fitting models with both the lowest out-of-sample prediction error and the highest variance explained ( ) were used. iTRIMP had the strongest relationships with changes in S2 (r = 0.93, = 0.90) and S4 (r = 0.88, = 0.82). Explained variance ranged from 10%-69% and 11%-38% for all other internal TL measures and external measures, respectively. In summary, the iTRIMP method demonstrates a dose-response relationship with changes in aerobic fitness in elite youth soccer players