Biology subjects

Tumkaya, T.

Publications and source records attributed to Tumkaya, T..

3 recordsLinked to original sources

bioRxiv2018

Moving beyond P values: Everyday data analysis with estimation plots

Introduction Introduction The two-groups design is... Significance testing obscures... Even when fully visualized,... Five key advantages of... Estimation graphics are... Conclusion Author Contributions Funding sources Code Availability Guide to using DABEST Web application Google Colaboratory Python Matlab DABEST-Python in R References Over the past 75 years, a number of statisticians have advised that the data-analysis method known as null- hypothesis significance testing (NHST) should be deprecated (Berkson, 1942; Halsey et al., 2015). The l ...

bioinformatics↗

bioRxiv2018

The Drosophila microbiome has a limited influence on sleep, activity, and courtship behaviors

In animals, commensal microbes modulate various physiological functions, including behavior. While microbiota exposure is required for normal behavior in mammals, it is not known how widely this dependency is present in other animal species. We proposed the hypothesis that the microbiome has a major influence on the behavior of the vinegar fly (Drosophila melanogaster), a major invertebrate model organism. Several assays were used to test the contribution of the microbiome on some well-characterized behaviors: defensive behavior, sleep, locomotion, and courtship in microbe-bearing, control flies and two generations of germ-free animals. None of the behaviors were largely influenced by the absence of a microbiome, and the small or moderate effects were not generalizable between replicates and/or generations. These results refute the hypothesis, indicating that the Drosophila microbiome does not have a major influence over several behaviors fundamental to the animals survival and reproduction. The impact of commensal microbes on animal behaviour may not be broadly conserved.

neuroscience↗

bioRxiv2018

A systematic review and meta-analysis of Drosophila short-term-memory genetics: robust reproducibility, but little independent replication

Geneticists use olfactory conditioning in Drosophila to identify learning genes; however, little is known about how these genes are integrated into short-term memory (STM) pathways. Here, we investigated the hypothesis that the STM evidence base is weak. We performed systematic review and meta-analysis of the field. Using metrics to quantify variation between discovery articles and follow-up studies, we found that seven genes were both highly replicated, and highly reproducible. However, ~80% of STM genes have never been replicated. While only a few studies investigated interactions, the reviewed genes could account for >1000% memory. This large summed effect size could indicate irreproducibility, many shared pathways, or that current assay protocols lack the specificity needed to identify core plasticity genes. Mechanistic theories of memory will require the convergence of evidence from system, circuit, cellular, molecular, and genetic experiments; systematic data synthesis is an essential tool for integrated neuroscience.

animal behavior and cognition↗