Bayesian generalized linear models for meta-analysis of diagnostic tests

With the recognition of the importance of evidence-based medicine, there is an emerging need for methods to systematically synthesize available data. Specifically, methods to provide accurate estimates of test characteristics for diagnostic tests are needed to help physicians make better clinical decisions. To provide more flexible approaches for meta-analysis of diagnostic tests, we developed three Bayesian generalized linear models. Two of these models, a bivariate normal and a binomial model, analyzed pairs of sensitivity and specificity values while incorporating the correlation between these two outcome variables. Noninformative independent uniform priors were used for the variance of sensitivity, specificity and correlation. We also applied an inverse Wishart prior to check the sensitivity of the results. The third model was a multinomial model where the test results were modeled as multinomial random variables. All three models can include specific imaging techniques as covariates in order to compare performance. Vague normal priors were assigned to the coefficients of the covariates. The computations were carried out using the 'Bayesian inference using Gibbs sampling' implementation of Markov chain Monte Carlo techniques. We investigated the properties of the three proposed models through extensive simulation studies. We also applied these models to a previously published meta-analysis dataset on cervical cancer as well as to an unpublished melanoma dataset. In general, our findings show that the point estimates of sensitivity and specificity were consistent among Bayesian and frequentist bivariate normal and binomial models. However, in the simulation studies, the estimates of the correlation coefficient from Bayesian bivariate models are not as good as those obtained from frequentist estimation regardless of which prior distribution was used for the covariance matrix. The Bayesian multinomial model consistently underestimated the sensitivity and specificity regardless of the sample size and correlation coefficient. In conclusion, the Bayesian bivariate binomial model provides the most flexible framework for future applications because of its following strengths: (1) it facilitates direct comparison between different tests; (2) it captures the variability in both sensitivity and specificity simultaneously as well as the intercorrelation between the two; and (3) it can be directly applied to sparse data without ad hoc correction. ^

A SIMULATION STUDY OF THE SIZE AND POWER OF SOME TWO-SAMPLE TESTS FOR UNEQUALLY CENSORED SURVIVAL DATA (RANK TESTS, LOGRANK, PROPORTIONAL HAZARDS, WILCOXON TESTS, EXPONENTIAL DISTRIBUTION)

Sizes and power of selected two-sample tests of the equality of survival distributions are compared by simulation for small samples from unequally, randomly-censored exponential distributions. The tests investigated include parametric tests (F, Score, Likelihood, Asymptotic), logrank tests (Mantel, Peto-Peto), and Wilcoxon-Type tests (Gehan, Prentice). Equal sized samples, n = 18, 16, 32 with 1000 (size) and 500 (power) simulation trials, are compared for 16 combinations of the censoring proportions 0%, 20%, 40%, and 60%. For n = 8 and 16, the Asymptotic, Peto-Peto, and Wilcoxon tests perform at nominal 5% size expectations, but the F, Score and Mantel tests exceeded 5% size confidence limits for 1/3 of the censoring combinations. For n = 32, all tests showed proper size, with the Peto-Peto test most conservative in the presence of unequal censoring. Powers of all tests are compared for exponential hazard ratios of 1.4 and 2.0. There is little difference in power characteristics of the tests within the classes of tests considered. The Mantel test showed 90% to 95% power efficiency relative to parametric tests. Wilcoxon-type tests have the lowest relative power but are robust to differential censoring patterns. A modified Peto-Peto test shows power comparable to the Mantel test. For n = 32, a specific Weibull-exponential comparison of crossing survival curves suggests that the relative powers of logrank and Wilcoxon-type tests are dependent on the scale parameter of the Weibull distribution. Wilcoxon-type tests appear more powerful than logrank tests in the case of late-crossing and less powerful for early-crossing survival curves. Guidelines for the appropriate selection of two-sample tests are given. ^

False -positives and false-negatives in tests for trend

False-positive and false-negative values were calculated for five different designs of the trend test and it was demonstrated that a design suggested by Portier and Hoel in 1984 for a different problem produced the lowest false-positive and false-negative rates when applied to historical spontaneous tumor rate data for Fischer Rats. ^

Un cambio de paradigma en la evaluación : De los tests tradicionales a la evaluación de desempeño

Las últimas tendencias en la enseñanza de una lengua extranjera muestran una evolución hacia nuevos enfoques. Sin embargo, las estrategias de evaluación no reflejan en forma fehaciente este cambio de paradigma. Mayoritariamente se continúa priorizando la evaluación formal y sumativa y no se le otorga a la evaluación de proceso la importancia que esta conlleva. El presente trabajo intenta demostrar que la evaluación no puede ser solo concebida como instrumento de medición del aprendizaje del alumno sino que también debe constituir un proceso que proporcione información acerca del camino que el alumno transita en la adquisición de conocimiento, habilidades y actitudes. Es por ello que nos centraremos en la evaluación informal y formativa, haciendo especial hincapié en la evaluación de desempeño, lo que no implica dejar de considerar la evaluación sumativa como parte integral del proceso de enseñanza-aprendizaje. Ejemplos de tareas como evaluación de desempeño pensados para la clase de niños formarán parte de esta propuesta

Un cambio de paradigma en la evaluación : De los tests tradicionales a la evaluación de desempeño

Las últimas tendencias en la enseñanza de una lengua extranjera muestran una evolución hacia nuevos enfoques. Sin embargo, las estrategias de evaluación no reflejan en forma fehaciente este cambio de paradigma. Mayoritariamente se continúa priorizando la evaluación formal y sumativa y no se le otorga a la evaluación de proceso la importancia que esta conlleva. El presente trabajo intenta demostrar que la evaluación no puede ser solo concebida como instrumento de medición del aprendizaje del alumno sino que también debe constituir un proceso que proporcione información acerca del camino que el alumno transita en la adquisición de conocimiento, habilidades y actitudes. Es por ello que nos centraremos en la evaluación informal y formativa, haciendo especial hincapié en la evaluación de desempeño, lo que no implica dejar de considerar la evaluación sumativa como parte integral del proceso de enseñanza-aprendizaje. Ejemplos de tareas como evaluación de desempeño pensados para la clase de niños formarán parte de esta propuesta

Un cambio de paradigma en la evaluación : De los tests tradicionales a la evaluación de desempeño

Las últimas tendencias en la enseñanza de una lengua extranjera muestran una evolución hacia nuevos enfoques. Sin embargo, las estrategias de evaluación no reflejan en forma fehaciente este cambio de paradigma. Mayoritariamente se continúa priorizando la evaluación formal y sumativa y no se le otorga a la evaluación de proceso la importancia que esta conlleva. El presente trabajo intenta demostrar que la evaluación no puede ser solo concebida como instrumento de medición del aprendizaje del alumno sino que también debe constituir un proceso que proporcione información acerca del camino que el alumno transita en la adquisición de conocimiento, habilidades y actitudes. Es por ello que nos centraremos en la evaluación informal y formativa, haciendo especial hincapié en la evaluación de desempeño, lo que no implica dejar de considerar la evaluación sumativa como parte integral del proceso de enseñanza-aprendizaje. Ejemplos de tareas como evaluación de desempeño pensados para la clase de niños formarán parte de esta propuesta

Stable isotope ratios measured on carbonate tests from the Kara Sea

River discharge of Ob and Yenisei to the Kara Sea is highly variable on seasonal and interannual time scales. River water dominates the shallow bottom water near the river mouths, making it warmer and less saline but seasonally and interannually more changeable than bottom water on the deeper shelf. This hydrographic pattern shows up in measurements and modelling, and in stable isotope records (delta18O, delta13C) along the growth axis of bivalve shells and in multiple analyses of single benthic foraminiferal shells. Average isotope ratios increase, but sample-internal variability decreases with water depth and distance from river mouths. However, isotope records of bivalves and foraminifera of a sediment core from a former submarine channel of Yenisei River reveal a different pattern. The retreat of the river mouth from this site due to early Holocene sea level rise led to increasing average isotope values up core, but not to the expected decrease of the in-sample isotope variability. Southward advection of cold saline water along the palaeo-river channel probably obscured the hydrographic variability during the early Holocene. Later, when sediment filled the channel, the hydrographic variability at the core location remained low, because the shallowing proceeded synchronously with the retreat of the river mouth.

A virtual species set for robust and reproducible Species Distribution Modelling tests

Predicting species potential and future distribution has become a relevant tool in biodiversity monitoring and conservation. In this data article we present the suitability map of a virtual species generated based on two bioclimatic variables, and a dataset containing more than 700.000 random observations at the extent of Europe. The dataset includes spatial attributes such as, distance to roads, protected areas, country codes, and the habitat suitability of two spatially clustered species (grassland and forest species) and a wide spread species.

(Table 1) Strontium isotope ratios (87Sr/86Sr) of Neogloboquadrina pachyderma (sinistrally coiling) tests from ODP Hole 151-910A

The sediment sequence at Ocean Drilling Program (ODP) Site 910 (556 m water depth) on the Yermak Plateau in the Arctic Ocean features a remarkable "overconsolidated section" from ~19 to 70-95 m below sea floor (m bsf), marked by large increases in bulk density and sediment strength. The ODP Leg 151 Shipboard Scientific Party interpreted the overconsolidated section to be caused by (1) grounding of a marine-based ice sheet, derived from Svalbard and perhaps the Barents Sea ice sheet, and/or (2) coarser-grained glacial sedimentation, which allowed increased compaction. Here I present planktonic foraminiferal d18O data based on Neogloboquadrina pachyderma (sinistrally coiling) that date the termination of overconsolidation near the boundary between isotope stages 16 and 17 (ca. 660 ka). No evidence is found for coarser grained sedimentation, because lithic fragments >150 µm exhibit similar mean concentrations throughout the upper 24.5 m bsf. The overconsolidated section may reflect more extensive ice-sheet grounding prior to ca. 660 ka, suggesting a major change in state of the Svalbard ice sheets during the mid-Quaternary. Furthermore, continuous sedimentation since that time argues against a pervasive Arctic ice shelf impinged on the Yermak Plateau during the past 660 k.y. These findings suggest that Svalbard ice-sheet history was largely independent of circum-Arctic ice-sheet history during the middle to late Quaternary.

Mg/Ca variability in Globigerinoides ruber tests

Laser ablation inductively coupled plasma-mass spectrometry microanalysis of fossil and live Globigerinoides ruber from the eastern Indian Ocean reveals large variations of Mg/Ca composition both within and between individual tests from core top or plankton pump samples. Although the extent of intertest and intratest compositional variability exceeds that attributable to calcification temperature, the pooled mean Mg/Ca molar values obtained for core top samples between the equator and >30°S form a strong exponential correlation with mean annual sea surface temperature (Mg/Ca mmol/mol = 0.52 exp**0.076SST°C, r**2 = 0.99). The intertest Mg/Ca variability within these deep-sea core top samples is a source of significant uncertainty in Mg/Ca seawater temperature estimates and is notable for being site specific. Our results indicate that widely assumed uncertainties in Mg/Ca thermometry may be underestimated. We show that statistical power analysis can be used to evaluate the number of tests needed to achieve a target level of uncertainty on a sample by sample case. A varying bias also arises from the presence and varying mix of two morphotypes (G. ruber ruber and G. ruber pyramidalis), which have different mean Mg/Ca values. Estimated calcification temperature differences between these morphotypes range up to 5°C and are notable for correlating with the seasonal range in seawater temperature at different sites.

Consolidation tests of ODP Leg 113 samples

Examination of the geotechnical characteristics of Weddell Sea, Maud Rise, and South Orkney microcontinental margin sediments recovered during ODP Leg 113 reveals that the reduction in porosity (consolidation) of the siliciclastic, calcareous, and diatomaceous sediments is primarily a process governed by vertical stresses created by overburden. The initial porosity of the sediments in these areas is governed by the amount of diatoms present. The more diatoms, the higher the porosity. Surficial diatom-rich sediments are everywhere overconsolidated. This is attributed to the strong microfabric created by the diatoms, calcareous and clay particles. The deeper diatom-free sediments of Maud Rise range from slightly underconsolidated to normally consolidated. The silty clays and clays of the Weddell Sea and South Orkney margin are underconsolidated. The degree of underconsolidation of these sediments is similar to that determined in a number of different locations throughout the world's oceans. The very low permeability of the Weddell Sea and South Orkney margin sediments appears to account for this underconsolidation.