Moving beyond P values: data analysis with estimation graphics

Ho, Joses; Tumkaya, Tayfun; Aryal, Sameer; Choi, Hyungwon; Claridge‐Chang, Adam

doi:10.1038/s41592-019-0470-3

Cited by 1,234 publications

(995 citation statements)

References 6 publications

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“…Density plots of model risk scores and all other plots were created using the ggplot2 package 32 . Cumming estimation plots and calculations were produced using the dabestr package 33 and 1000 bootstrap resamples were used to visualize robust effect size estimates of model predictions.…”

Section: Methodsmentioning

confidence: 99%

Development of a multivariable risk model integrating urinary cell DNA methylation and cell‐free RNA data for the detection of significant prostate cancer

et al. 2020

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Background Prostate cancer exhibits severe clinical heterogeneity and there is a critical need for clinically implementable tools able to precisely and noninvasively identify patients that can either be safely removed from treatment pathways or those requiring further follow up. Our objectives were to develop a multivariable risk prediction model through the integration of clinical, urine‐derived cell‐free messenger RNA (cf‐RNA) and urine cell DNA methylation data capable of noninvasively detecting significant prostate cancer in biopsy naïve patients. Methods Post‐digital rectal examination urine samples previously analyzed separately for both cellular methylation and cf‐RNA expression within the Movember GAP1 urine biomarker cohort were selected for a fully integrated analysis (n = 207). A robust feature selection framework, based on bootstrap resampling and permutation, was utilized to find the optimal combination of clinical and urinary markers in a random forest model, deemed ExoMeth. Out‐of‐bag predictions from ExoMeth were used for diagnostic evaluation in men with a clinical suspicion of prostate cancer (PSA ≥ 4 ng/mL, adverse digital rectal examination, age, or lower urinary tract symptoms). Results As ExoMeth risk score (range, 0‐1) increased, the likelihood of high‐grade disease being detected on biopsy was significantly greater (odds ratio = 2.04 per 0.1 ExoMeth increase, 95% confidence interval [CI]: 1.78‐2.35). On an initial TRUS biopsy, ExoMeth accurately predicted the presence of Gleason score ≥3 + 4, area under the receiver‐operator characteristic curve (AUC) = 0.89 (95% CI: 0.84‐0.93) and was additionally capable of detecting any cancer on biopsy, AUC = 0.91 (95% CI: 0.87‐0.95). Application of ExoMeth provided a net benefit over current standards of care and has the potential to reduce unnecessary biopsies by 66% when a risk threshold of 0.25 is accepted. Conclusion Integration of urinary biomarkers across multiple assay methods has greater diagnostic ability than either method in isolation, providing superior predictive ability of biopsy outcomes. ExoMeth represents a more holistic view of urinary biomarkers and has the potential to result in substantial changes to how patients suspected of harboring prostate cancer are diagnosed.

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Section: Methodsmentioning

confidence: 99%

Development of a multivariable risk model integrating urinary cell DNA methylation and cell‐free RNA data for the detection of significant prostate cancer

et al. 2020

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“…Peak stress was defined as the 95th percentile of the stress data to avoid extreme outliers that may be sensitive to boundary conditions. Effects sizes (in the mean and peak values) between models were estimated by calculating bootstrapped 95% confidence intervals (25). We also analysed deep tissue stress along a path through the soft tissue directly beneath the ischial tuberosity, and along the surface of the ischial tuberosity.…”

Section: Solution Approach and Outputmentioning

confidence: 99%

Lateral pressure equalisation as a principle for designing support surfaces to prevent deep tissue pressure ulcers

Boyle

Masen

Masouros

2019

Preprint

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When immobile or neuropathic patients are supported by beds or chairs, their soft tissues undergo deformations that can cause pressure ulcers. Current support surfaces that redistribute under-body pressures at vulnerable body sites have not succeeded in reducing pressure ulcer prevalence. Here we show that adding a supporting lateral pressure can counter-act the deformations induced by under-body pressure, and that this 'pressure equalisation' approach is a more effective way to reduce ulcer-inducing deformations than current approaches based on redistributing under-body pressure.A finite element model of the seated pelvis predicts that applying a lateral pressure to the soft tissue reduces peak von Mises stress in the deep tissue by a factor of 2.4 relative to a standard cushion -a greater effect than that achieved by using a more conformable cushion. The ratio of peak lateral pressure to peak underbody pressure was shown to regulate deep tissue stress better than under-body pressure alone. By optimising the magnitude and position of lateral pressure, tissue deformations can be reduced to that induced when suspended in a fluid.Our results explain the lack of efficacy in current support surfaces, and suggest a new approach to designing and evaluating support surfaces: ensuring sufficient lateral pressure is applied to counter-act under-body pressure.

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“…The raw data is plotted on the upper axes (summary measurements are displayed as gapped lines to the right of each plot: means are indicated as a gap in the lines, vertical lines represent standard deviation error bars); each mean difference is plotted on the lower axes as a bootstrap sampling distribution. Mean differences are depicted as dots; 95% confidence intervals are indicated by the ends of the vertical error bars 49 .…”

Section: Figurementioning

confidence: 99%

Mobile Brain/Body Imaging of cognitive-motor impairment in multiple sclerosis: deriving EEG-based neuro-markers during a dual-task walking study

Sanctis

Malcolm

Mabie

et al. 2019

Preprint

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Individuals with a diagnosis of multiple sclerosis (MS) often present with deficits in the cognitive as well as the motor domain. The ability to perform tasks that rely on both domains may therefore be particularly impaired. Yet, behavioral studies designed to measure costs associated with performing two tasks at the same time such as dual-task walking have yielded mixed results. Patients may mobilize additional brain resources to sustain good levels of performance. To test this hypothesis, we acquired event-related potentials (ERP) in thirteen individuals with MS and fifteen healthy control (HC) participants performing a Go/NoGo response inhibition task while sitting (i.e., single task) or walking on a treadmill (i.e., dual-task).In previous work, we showed that the nogo-N2 elicited by the cognitive task was reduced when healthy adults are also asked to walk, and that nogo-N2 reduction was accompanied by sustained dual-task performance. We predicted that some MS patients, similar to their healthy peers, may mobilize N2-indexed brain resources and thereby reduce costs. Somewhat to our surprise, the HC group performed the Go/NoGo task more accurately while walking, thus showing a dual-task benefit, whereas, in line with expectation, the MS group showed a trend towards dual-task costs.The expected nogo-N2 reduction during dual-task walking was found in the HC group, but was not present at the group level in the MS group, suggesting that this group did not modulate the nogo-N2 process in response to higher task load. Regression analysis for the pooled sample revealed a robust link between nogo-N2 reduction and better dual-task performance. We conclude that impaired nogo-N2 adaptation reflects a neurophysiological marker of cognitivemotor dysfunction in MS.

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Moving beyond P values: data analysis with estimation graphics

Cited by 1,234 publications

References 6 publications

Development of a multivariable risk model integrating urinary cell DNA methylation and cell‐free RNA data for the detection of significant prostate cancer

Development of a multivariable risk model integrating urinary cell DNA methylation and cell‐free RNA data for the detection of significant prostate cancer

Lateral pressure equalisation as a principle for designing support surfaces to prevent deep tissue pressure ulcers

Mobile Brain/Body Imaging of cognitive-motor impairment in multiple sclerosis: deriving EEG-based neuro-markers during a dual-task walking study

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