Permutation Tests: A Practical Guide to Resampling Methods for Testing Hypotheses.

Modarres, Reza; Good, Phillip I.

doi:10.2307/2291167

Cited by 48 publications

(45 citation statements)

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“…Additionally, canonical variate analyses (CVA) were performed to maximize the differentiation in anchor shape between groups. Procrustes distances between groups were calculated using a permutation test (Good 2001) with 10,000 randomizations ( = 0.05). The main axes of the PCA and CVA were visualized using wireframe diagrams (Klingenberg 2011).…”

Section: Geomorphometric Analyses and Size Of The Anchorsmentioning

confidence: 99%

Morphological and Genetic Divergence in a Gill Monogenean Parasitizing Distant Cichlid Lineages of Lake Tanganyika: Cichlidogyrus nshomboi (Monogenea: Dactylogyridae) from Representatives of Boulengerochromini and Perissodini

et al. 2022

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As hosts constitute the resource for parasites, an adaptive radiation in a host can drive one in a parasite.In Lake Tanganyika, the diversification of cichlids has often led to a diversification of their Cichlidogyrus monogeneans. Hitherto, Cichlidogyrus nshomboi was known only from Boulengerochromis microlepis, the sole member of Boulengerochromini. Surprisingly, we retrieved this monogenean from Perissodus microlepis, P. straeleni and Haplotaxodon microlepis, belonging to Perissodini. We sequenced the nuclear 18S, 28S, ITS1 rDNA, and the mitochondrial COI genes and studied the morphology of the male copulatory organ (MCO) and the anchors of the attachment organ. This confirmed the conspecificity of the specimens. The occurrence of C. nshomboi on unrelated host lineages could be explained by inheritance from a common ancestor, or by host-switching. We further investigated the genetic and morphological variation across taxonomic (host tribes and species) and geographical scales. Results revealed divergence in ITS1 and COI between parasites infecting different tribes, which could indicate incipient speciation. Additionally, morphological differentiation in the shape and size of anchors was found between these groups, which could be attributed to phenotypic plasticity or to adaptation.Monogeneans from large-bodied B. microlepis had significantly larger anchors, whereas only two of the four measurements differed for the MCO. Unexpectedly, no morphological variation was observed between specimens infecting different species of Perissodini from nearby localities. However, differences were found between C. nshomboi infecting P. microlepis from different parts of the lake, which could be linked to the population genetic structure of the host.

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Section: Geomorphometric Analyses and Size Of The Anchorsmentioning

confidence: 99%

Morphological and Genetic Divergence in a Gill Monogenean Parasitizing Distant Cichlid Lineages of Lake Tanganyika: Cichlidogyrus nshomboi (Monogenea: Dactylogyridae) from Representatives of Boulengerochromini and Perissodini

et al. 2022

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“…Although there seems to be a horizontal shift in the estimated x-axis intercepts in different experiments, these intercept values were similar across experiments (2.19 vs. 2.28). We tested whether these mean estimates were statistically different from one another by fitting these iso-effort patterns based on data with shuffled experiment labels, which created an empirical null distribution with minimal statistical assumptions (Good, 2013). Across 10,000 iterations, we found that the observed x-axis intercept difference between experiments was not statistically different from the null values (bootstrapped p = .65).…”

Section: Equating Physical and Cognitive Effortsmentioning

confidence: 97%

Effortfulness of visual working memory: Gauged by physical exertion.

Zhang¹

2023

Journal of Experimental Psychology: General

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Active maintenance of information in working memory (WM) is an essential but effortful cognitive process. Yet, the effortful nature of WM remains poorly understood. Here, we constructed a model to evaluate how perceived effort of WM is directly compared to that of physical exertion. In Experiment 1, participants freely chose to either remember a certain number of colors in a visual WM task or hold a hand dynamometer to a required percentage of maximal voluntary contraction (%MVC) to obtain a fixed task credit upon successful task completion. We found that participants discounted WM-related effort in the same way as they discounted handgrip-related effort based on a computation of expected choice outcomes (hence utility) associated with different task loads. This rationality in an observer's prospective choice in Experiment 1 was generalized to retrospective choice in Experiment 2 where participants reported which task was more effortful immediately after they had performed both tasks in a randomized order without any reward or feedback. Experiment 3 further probed this shared mechanism using a dual-task paradigm. As predicted by our model, we found that physical exertion could disrupt the performance in the concurrent WM task, proportional to the iso-effort relationship between WM and physical exertion when task loads were high for both tasks. Collectively, our findings converge on a shared computational principle connecting task load, perceived effort, and choice utility across physical and cognitive domains.

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“…1. A permutation test (also called randomization test) 45,46 for the co-expression that was used to build the dendrogram. We wanted to determine the statistical significance of the frequencies in the first column of Table 1, which contains the Mus musculus data analyzed with DCS, and we therefore used a control where the ordering of the dendrogram was no longer dependent on the correlation of the receptors' gene expression.…”

Section: Statistical Analysis Of Comberonsmentioning

confidence: 99%

Naturally occurring combinations of receptors from single cell transcriptomics in endothelial cells

Domanskyi

Hakansson

Meng

et al. 2022

Sci Rep

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VEGF inhibitor drugs are part of standard care in oncology and ophthalmology, but not all patients respond to them. Combinations of drugs are likely to be needed for more effective therapies of angiogenesis-related diseases. In this paper we describe naturally occurring combinations of receptors in endothelial cells that might help to understand how cells communicate and to identify targets for drug combinations. We also develop and share a new software tool called DECNEO to identify them. Single-cell gene expression data are used to identify a set of co-expressed endothelial cell receptors, conserved among species (mice and humans) and enriched, within a network, of connections to up-regulated genes. This set includes several receptors previously shown to play a role in angiogenesis. Multiple statistical tests from large datasets, including an independent validation set, support the reproducibility, evolutionary conservation and role in angiogenesis of these naturally occurring combinations of receptors. We also show tissue-specific combinations and, in the case of choroid endothelial cells, consistency with both well-established and recent experimental findings, presented in a separate paper. The results and methods presented here advance the understanding of signaling to endothelial cells. The methods are generally applicable to the decoding of intercellular combinations of signals.

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Permutation Tests: A Practical Guide to Resampling Methods for Testing Hypotheses.

Cited by 48 publications

References 0 publications

Morphological and Genetic Divergence in a Gill Monogenean Parasitizing Distant Cichlid Lineages of Lake Tanganyika: Cichlidogyrus nshomboi (Monogenea: Dactylogyridae) from Representatives of Boulengerochromini and Perissodini

Morphological and Genetic Divergence in a Gill Monogenean Parasitizing Distant Cichlid Lineages of Lake Tanganyika: Cichlidogyrus nshomboi (Monogenea: Dactylogyridae) from Representatives of Boulengerochromini and Perissodini

Effortfulness of visual working memory: Gauged by physical exertion.

Naturally occurring combinations of receptors from single cell transcriptomics in endothelial cells

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