When significance becomes insignificant: Effect sizes and their uncertainties in Bayesian and frequentist frameworks as an alternative approach when analyzing ecotoxicological data

Feckler, Alexander; Low, Matthew; Zubrod, Jochen P.; Bundschuh, Mirco

doi:10.1002/etc.4127

Cited by 15 publications

(10 citation statements)

References 34 publications

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“…The magnitude of the relationship (effect size) between magnetic parameters and each bioaccumulated element was evaluated by the coefficient of determination R 2 , which estimates the proportion of variance shared by the two variables, as explained by a linear model. As recommended for environmental data [24], the probability of the effect size was estimated using the highest posterior density intervals following a Bayesian approach [25]. In addition, Cohen's ƒ 2 was also calculated [26] to class the effect size into small, medium and large [27].…”

Section: Discussionmentioning

confidence: 99%

Magnetic Emissions from Brake Wear are the Major Source of Airborne Particulate Matter Bioaccumulated by Lichens Exposed in Milan (Italy)

et al. 2020

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The concentration of selected trace elements and the magnetic properties of samples of the lichen Evernia prunastri exposed for 3 months in Milan (Italy) were investigated to test if magnetic properties can be used as a proxy for the bioaccumulation of chemical elements in airborne particulate matter. Magnetic analysis showed intense properties driven by magnetite-like minerals, leading to significant correlations between magnetic susceptibility and the concentration of Fe, Cr, Cu, and Sb. Selected magnetic particles were characterized by Scanning Electron Microscope and Energy Dispersion System microanalyses, and their composition, morphology and grain size supported their anthropogenic, non-exhaust origin. The overall combination of chemical, morphoscopic and magnetic analyses strongly suggested that brake abrasion from vehicles is the main source of the airborne particles accumulated by lichens. It is concluded that magnetic susceptibility is an excellent parameter for a simple, rapid and cost-effective characterization of atmospheric trace metal pollution using lichens.

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Section: Discussionmentioning

confidence: 99%

Magnetic Emissions from Brake Wear are the Major Source of Airborne Particulate Matter Bioaccumulated by Lichens Exposed in Milan (Italy)

et al. 2020

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“…Bayesian analyses have been repeatedly advocated in ecotoxicology (Billoir et al, 2008; Pollino and Hart, 2005). They are particularly suitable because ecotoxicological assessments are destined to improve decision making, for which quantification of the effect sizes and the uncertainty associated with these predictions are more essential than an arbitrary significance threshold (Feckler et al, 2018). The Bayesian credible intervals of the mutations rate ratios here can be directly interpreted as probabilities of the effect sizes.…”

Section: Discussionmentioning

confidence: 99%

Measuring mutagenicity in ecotoxicology: A case study of Cd exposure inChironomus riparius

Doria

Waldvogel

Pfenninger

2020

Preprint

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Existing mutagenicity tests for metazoans lack the direct observation of enhanced germline mutation rates after exposure to anthropogenic substances, therefore being inefficient. Cadmium (Cd) is a metal described as a mutagen in mammalian cells and listed as a group 1 carcinogenic and mutagenic substance. But Cd mutagenesis mechanism is not yet clear. Therefore, in the present study, we propose a method coupling short-term mutation accumulation (MA) lines with subsequent whole genome sequencing (WGS) and a dedicated data analysis pipeline to investigate if chronic Cd exposure on Chironomus riparius can alter the rate at which de novo point mutations appear. Results show that Cd exposure did not affect the basal germline mutation rate nor the mutational spectrum in C. riparius, thereby arguing that exposed organisms might experience a range of other toxic effects before any mutagenic effect may occur. We show that it is possible to establish a practical and easily implemented pipeline to rapidly detect germ cell mutagens in a metazoan test organism. Furthermore, our data implicate that it is questionable to transfer mutagenicity assessments based on in vitro methods to complex metazoans.

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“…Unlike Bayesian concept to potential markers discovery, under Frequentists approach the effect size is treated as a fixed value addressing the question how much the data differ ‘significantly’ from that expected under the null. The vast majority of research uses the Frequentists concept completely ignoring the probability of raised hypothesis [48] and reporting only those results which are statistically significant. Usually, when replicating the original case-control study under the same conditions or under conditions as much similar to the original study as possible, researchers obtain negative results (zero or small effect).…”

Section: Discussionmentioning

confidence: 99%

Bayesian multilevel model of micro RNA levels in ovarian-cancer and healthy subjects

et al. 2019

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In transcriptomics, micro RNAs (miRNAs) has gained much interest especially as potential disease indicators. However, apart from holding a great promise related to their clinical application, a lot of inconsistent results have been published. Our aim was to compare the miRNA expression levels in ovarian cancer and healthy subjects using the Bayesian multilevel model and to assess their potential usefulness in diagnosis. We have analyzed a case-control observational data on expression profiling of 49 preselected miRNA-based ovarian cancer indicators in 119 controls and 59 patients. A Bayesian multilevel model was used to characterize the effect of disease on miRNA levels controlling for differences in age and body weight. The difference between the miRNA level and health status of the patient on the scale of the data variability were discussed in the context of their potential usefulness in diagnosis. Additionally, the cross-validated area under the ROC curve (AUC) was used to assess the expected out-of-sample discrimination index of a different sets of miRNAs. The proposed model allowed us to describe the set of miRNA levels in patients and controls. Three highly correlated miRNAs: miR-101-3p, miR-142-5p, miR-148a-3p rank the highest with almost identical effect sizes that ranges from 0.45 to 1.0. For those miRNAs the credible interval for AUC ranged from 0.63 to 0.67 indicating their limited discrimination potential. A little benefit in adding information from other miRNAs was observed. There were several miRNAs in the dataset (miR-604, hsa-miR-221-5p) for which inferences were uncertain. For those miRNAs more experimental effort is needed to fully assess their effect in the context of new hits discovery and usefulness as disease indicators. The proposed multilevel Bayesian model can be used to characterize the panel of miRNA profile and to assess the difference in expression levels between healthy and cancer individuals.

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When significance becomes insignificant: Effect sizes and their uncertainties in Bayesian and frequentist frameworks as an alternative approach when analyzing ecotoxicological data

Cited by 15 publications

References 34 publications

Magnetic Emissions from Brake Wear are the Major Source of Airborne Particulate Matter Bioaccumulated by Lichens Exposed in Milan (Italy)

Magnetic Emissions from Brake Wear are the Major Source of Airborne Particulate Matter Bioaccumulated by Lichens Exposed in Milan (Italy)

Measuring mutagenicity in ecotoxicology: A case study of Cd exposure inChironomus riparius

Bayesian multilevel model of micro RNA levels in ovarian-cancer and healthy subjects

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