Discussion of "Statistical Inference: The Big Picture" by R. E. Kass

Discussion of "Statistical Inference: The Big Picture" by R. E. Kass [arXiv:1106.2895]Comment: Published in at http://dx.doi.org/10.1214/11-STS337A the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

The Proportional Odds Model for Assessing Rater Agreement with Multiple Modalities

In this paper, we develop a model for evaluating an ordinal rating systems where we assume that the true underlying disease state is continuous in nature. Our approach in motivated by a dataset with 35 microscopic slides with 35 representative duct lesions of the pancreas. Each of the slides was evaluated by eight raters using two novel rating systems (PanIN illustrations and PanIN nomenclature),where each rater used each systems to rate the slide with slide identity masked between evaluations. We find that the two methods perform equally well but that differentiation of higher grade lesions is more consistent across raters than differentiation across raters for lower grade lesions. A proportional odds model is assumed, which allows us to estimate rater-specific thresholds for comparing agreement. In this situation where we have two methods of rating, we can determine whether the two methods have the same thresholds and whether or not raters perform equivalently across methods. Unlike some other model-based approaches for measuring agreement, we focus on the interpretation of the model parameters and their scientific relevance. We compare posterior estimates of rater-specific parameters across raters to see if they are implementing the intended rating system in the same manner. Estimated standard deviation distributions are used to make inferences as to whether raters are consistent and whether there are differences in rating behaviors in the two rating systems under comparison

Toward evidence-based medical statistics. 1: The P value fallacy.

An important problem exists in the interpretation of modern medical research data: Biological understanding and previous research play little formal role in the interpretation of quantitative results. This phenomenon is manifest in the discussion sections of research articles and ultimately can affect the reliability of conclusions. The standard statistical approach has created this situation by promoting the illusion that conclusions can be produced with certain "error rates," without consideration of information from outside the experiment. This statistical approach, the key components of which are P values and hypothesis tests, is widely perceived as a mathematically coherent approach to inference. There is little appreciation in the medical community that the methodology is an amalgam of incompatible elements, whose utility for scientific inference has been the subject of intense debate among statisticians for almost 70 years. This article introduces some of the key elements of that debate and traces the appeal and adverse impact of this methodology to the P value fallacy, the mistaken idea that a single number can capture both the long-run outcomes of an experiment and the evidential meaning of a single result. This argument is made as a prelude to the suggestion that another measure of evidence should be used-the Bayes factor, which properly separates issues of long-run behavior from evidential strength and allows the integration of background knowledge with statistical findings

MRI channel flows and their parasites

Local simulations of the magnetorotational instability (MRI) in accretion disks can exhibit recurrent coherent structures called channel flows. The formation and destruction of these structures may play a role in the development and saturation of MRI-induced turbulence, and consequently help us understand the time-dependent accretion behaviour of certain astrophysical objects. Previous investigations have revealed that channel solutions are attacked by various parasitic modes, foremost of which is an analogue of the Kelvin-Helmholtz instability. We revisit these instabilities and show how they relate to the classical instabilities of plasma physics, the kink and pinch modes. However, we argue that in most cases channels emerge from developed turbulence and are eventually destroyed by turbulent mixing, not by the parasites. The exceptions are the clean isolated channels which appear in systems near criticality or which emerge from low amplitude initial conditions. These structures inevitably achieve large amplitudes and are only then destroyed, giving rise to eruptive behaviour.Comment: 17 pages, 17 figures, accepted by MNRA

Association of selenium, tocopherols, carotenoids, retinol, and 15-isoprostane F(2t) in serum or urine with prostate cancer risk: the multiethnic cohort.

We examine the association of antioxidants and 15-isoprostane F(2t) with risk of prostate cancer.We conducted a nested case-control study of serum antioxidant biomarkers (selenium, tocopherols, carotenoids, and retinol) and a urinary oxidation biomarker (15-isoprostane F(2t)) with risk of prostate cancer within the Multiethnic Cohort. Demographic, dietary, and other exposure information was collected by self-administered questionnaire in 1993-1996. We compared prediagnostic biomarker levels from 467 prostate cancer cases and 936 cancer free controls that were matched on several variables. Multivariate conditional logistic regression models were used to compute adjusted odds ratios (ORs) and 95% confidence intervals (CIs).We observed that there was no overall association of serum concentrations of antioxidants and urinary concentrations of 15-isoprostane F(2t) with risk of prostate cancer or risk of advanced prostate cancer. However, we did observe an inverse association for serum selenium only among African-American men (p trend = 0.02); men in the third tertile of selenium concentrations had a 41% lower risk (95% CI: 0.38-0.93) of prostate cancer when compared to men in the first tertile.Overall, our study found no association of serum antioxidants or 15-isoprostane F(2t) with the risk of prostate cancer. The observed inverse association of selenium with prostate cancer in African-Americans needs to be validated in other studies

Six principles for assessing scientists for hiring, promotion, and tenure

The negative consequences of relying too heavily on metrics to assess research quality are well known, potentially fostering practices harmful to scientific research such as p-hacking, salami science, or selective reporting. The "flourish or perish" culture defined by these metrics in turn drives the system of career advancement in academia, a system that empirical evidence has shown to be problematic and which fails to adequately take societal and broader impact into account. To address this systemic problem, Florian Naudet, John P. A. Ioannidis, Frank Miedema, Ioana A. Cristea, Steven N. Goodman and David Moher present six principles for assessing scientists for hiring, promotion, and tenure

Six principles for assessing scientists for hiring, promotion, and tenure

The negative consequences of relying too heavily on metrics to assess research quality are well known, potentially fostering practices harmful to scientific research such as p-hacking, salami science, or selective reporting. The "flourish or perish" culture defined by these metrics in turn drives the system of career advancement in academia, a system that empirical evidence has shown to be problematic and which fails to adequately take societal and broader impact into account. To address this systemic problem, Florian Naudet, John P. A. Ioannidis, Frank Miedema, Ioana A. Cristea, Steven N. Goodman and David Moher present six principles for assessing scientists for hiring, promotion, and tenure

Diversity, host specialization, and geographic structure of filarial nematodes infecting Malagasy bats

We investigated filarial infection in Malagasy bats to gain insights into the diversity of these parasites and explore the factors shaping their distribution. Samples were obtained from 947 individual bats collected from 52 sites on Madagascar and representing 31 of the 44 species currently recognized on the island. Samples were screened for the presence of micro-and macro-parasites through both molecular and morphological approaches. Phylogenetic analyses showed that filarial diversity in Malagasy bats formed three main groups, the most common represented by Litomosa spp. infecting Miniopterus spp. (Miniopteridae); a second group infecting Pipistrellus cf. hesperidus (Vespertilionidae) embedded within the Litomosoides cluster, which is recognized herein for the first time from Madagascar; and a third group composed of lineages with no clear genetic relationship to both previously described filarial nematodes and found in M. griveaudi, Myotis goudoti, Neoromicia matroka (Vespertilionidae), Otomops madagascariensis (Molossidae), and Paratriaenops furculus (Hipposideridae). We further analyzed the infection rates and distribution pattern of Litomosa spp., which was the most diverse and prevalent filarial taxon in our sample. Filarial infection was disproportionally more common in males than females in Miniopterus spp., which might be explained by some aspect of roosting behavior of these cave-dwelling bats. We also found marked geographic structure in the three Litomosa clades, mainly linked to bioclimatic conditions rather than host-parasite associations. While this study demonstrates distinct patterns of filarial nematode infection in Malagasy bats and highlights potential drivers of associated geographic distributions, future work should focus on their alpha taxonomy and characterize arthropod vectors