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Haest, B.

Publications and source records attributed to Haest, B..

2 recordsLinked to original sources

The unexpected consequences of predictor error in ecological model selection

1O_LIThe ability to select statistical models based on how well they fit an empirical dataset is a central tenet of modern bioscience. How well this works, though, depends on how goodness-of-fit is measured. Likelihood and its derivatives (e.g. AIC) are popular and powerful tools when measuring goodness-of-fit, though inherently make assumptions about the data. One such assumption is absence of error on the x-axis (i.e. no error in the predictor). This, however, is often not correct and deviations from this assumption are often hard (or impossible) to measure. C_LIO_LIHere, we show that, when predictor error is present, goodness-of-fit as perceived using likelihood will increase with decreases in sample size, effect size, predictor error and predictor variance. This results in predictors with increased effect size, predictor variance or predictor error being punished. As a consequence, we suggest that larger effect sizes are biased against in likelihood-based model comparison. Of note: (i) this problem is exacerbated in datasets with larger samples sizes and a broader range of predictor values - typically considered desirable biological data collection; and (ii) the magnitude of this effect is non-trivial given that proxy error (caused by using correlates of a predictor rather than the predictor itself) can lead to unexpectedly high amounts of error. C_LIO_LIWe investigate the effects of our findings in an empirical dataset of wood anemone (Anemone nemorosa) first flowering date regressed against temperature. Our results show that the proxy error caused by using air temperature rather than ground temperature results in a {triangleup}AIC of around 3. We also demonstrate potential consequences for model selection procedures with autocorrelation (e.g. sliding window approaches). Via simulation we show that in the presence of predictor error AIC will favour autocorrelated, lower effect size predictors (such as those found on the edges of predictive windows), rather than the a priori specified true window. C_LIO_LIOur results suggest significant and far-reaching implications for biological inference with model selection for much of todays ecology using observational data under non-experimental conditions. We assert that no obvious, globally-applicable solution to this problem exists; and propose that quantifying predictor error is key in accurate ecological model selection going forward. C_LI

ecology↗

Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches

The liver is the largest solid organ in the body, yet it remains incompletely characterized. Here, we present a spatial proteogenomic atlas of the healthy human and murine liver combining single-cell CITE-seq, single-nuclei sequencing, spatial transcriptomics and spatial proteomics. By integrating these multi-omic datasets, we provide validated strategies to reliably discriminate and localize all hepatic cells. We then align this atlas across seven species, revealing the conserved program of bona fide Kupffer cells and bile-duct macrophages. We also uncover the respective spatially-resolved cellular niches of these macrophages and the microenvironmental circuits driving their unique transcriptomic identities. We demonstrate that bile-duct macrophages are induced by local lipid exposure, while Kupffer cells crucially depend on their crosstalk with hepatic stellate cells via the evolutionarily-conserved ALK1-BMP9/10 axis.

immunology↗