Biomedical subjects

Wiebe R Pestman

Publications and source records attributed to Wiebe R Pestman.

3 recordsLinked to original sources

PubMed2006

Instrumental variables: application and limitations.

To correct for confounding, the method of instrumental variables (IV) has been proposed. Its use in medical literature is still rather limited because of unfamiliarity or inapplicability. By introducing the method in a nontechnical way, we show that IV in a linear model is quite easy to understand and easy to apply once an appropriate instrumental variable has been identified. We also point out some limitations of the IV estimator when the instrumental variable is only weakly correlated with the exposure. The IV estimator will be imprecise (large standard error), biased when sample size is small, and biased in large samples when one of the assumptions is only slightly violated. For these reasons, it is advised to use an IV that is strongly correlated with exposure. However, we further show that under the assumptions required for the validity of the method, this correlation between IV and exposure is limited. Its maximum is low when confounding is strong, such as in case of confounding by indication. Finally, we show that in a study in which strong confounding is to be expected and an IV has been used that is moderately or strongly related to exposure, it is likely that the assumptions of IV are violated, resulting in a biased effect estimate. We conclude that instrumental variables can be useful in case of moderate confounding but are less useful when strong confounding exists, because strong instruments cannot be found and assumptions will be easily violated.

Bias↗

PubMed2005

Distributions of alternation rates in various forms of bistable perception.

Studying the temporal dynamics of bistable perception can be useful for understanding neural mechanisms underlying the phenomenon. We take a closer look at those temporal dynamics, using data from four different ambiguous stimuli. We focus our analyses on two recurrent themes in bistable perception literature. First, we address the question whether percept durations follow a gamma distribution, as is commonly assumed. We conclude that this assumption is not justified by the gamma distribution's approximate resemblance to distributions of percept durations. We instead present two straightforward distributions of reciprocal percept durations (i.e., rates) that both easily surpass the classic gamma distribution in terms of resemblance to empirical data. Second, we compare the distributions arising from binocular rivalry with those from other forms of bistable perception. Parallels in temporal dynamics between those classes of stimuli are often mentioned as an indication of a similar neural basis, but have never been studied in detail. Our results demonstrate that the distributions arising from binocular rivalry and other forms of bistable perception are indeed similar up to a high level of detail.

Attention↗

PubMed2005

Hyphal differentiation in the exploring mycelium of Aspergillus niger.

Mycelial fungi play a central role in element cycling in nature by degrading dead organic material such as wood. Fungal colonization of a substrate starts with the invasion of exploring hyphae. These hyphae secrete enzymes that convert the organic material into small molecules that can be taken up by the fungus to serve as nutrients. Using green fluorescent protein (GFP) as a reporter, we show for the first time that exploring hyphae of Aspergillus niger differentiate with respect to enzyme secretion; some strongly express the glucoamylase gene glaA, while others hardly express it at all. When a cytoplasmic GFP was used, 27% of the exploring hyphae of a 5-day-old colony belonged to the low expressing hyphae. By fusing GFP to glucoamylase and by introducing an ER retention signal, this number increased to 50%. This difference is due to cytoplasmic streaming of the reporter in the former case, as was shown by using a photo-activatable GFP. Our findings indicate that a fungal mycelium is highly differentiated, especially when taking into account that hyphae in the exploration zone were exposed to the same nutritional conditions.

Aspergillus niger↗