Robust analogs to the coefficient of variation

Arachchige, Chandima N. P. G.; Prendergast, Luke A.; Staudte, Robert G.

doi:10.1080/02664763.2020.1808599

Cited by 87 publications

(53 citation statements)

References 36 publications

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“…Despite data clean-up, single cell data can contain spurious outlier observations, particularly in genetic perturbation experiments. To estimate the population variability, we therefore used a robust analogue of the coefficient of variation given by RCV M = 1.4826 × MAD / median, where MAD is the median absolute deviation, given by MAD ( x ) = median(| x - m |) where m = median ( x ) (Arachchige et al, 2020).…”

Section: Star Methodsmentioning

confidence: 99%

Nuclear RNA concentration coordinates RNA production with cell size in human cells

Berry

Müller

Pelkmans

2021

Preprint

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Unlike its DNA template, RNA abundance and synthesis rates increase with cell size, as part of a mechanism of cellular RNA concentration homeostasis. Here, we study this scaling phenomenon in human cells by combining genome-wide perturbations with quantitative single-cell measurements. Despite relative ease in perturbing RNA synthesis, we find that RNA concentrations remain highly constant. Systems-level analysis indicates that perturbations that would lead to increased nuclear mRNA abundance result in downregulation of mRNA synthesis. This is associated with reduced levels of several transcription-associated proteins and protein states that are normally coordinated with RNA production in single cells, including RNA polymerase II (Pol II) itself. Acute shut-down of nuclear RNA degradation, elevation of nuclear mRNA levels, and mathematical modelling indicate that mammalian cells achieve RNA concentration homeostasis by an mRNA-based negative feedback on transcriptional activity in the nucleus. Ultimately, this acts to robustly scale Pol II abundance with cell volume and coordinate mRNA synthesis and degradation.

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Section: Star Methodsmentioning

confidence: 99%

Nuclear RNA concentration coordinates RNA production with cell size in human cells

Berry

Müller

Pelkmans

2021

Preprint

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“…This simulation is performed for all uncertainty sources, namely: invasion density, curve assignment, age, streamflow reduction curves, additional water availability and precipitation. For each of these scenarios, we summarize the total uncertainty in estimated streamflow reduction at the catchment and pixel level using a robust estimate of dispersion ‐ the median absolute deviation ( MAD ) ‐ and the robust coefficient of variation ( RCV M ) calculated as

{RCV}_{M} = 1.4826 italicMAD / M

where MAD is the median absolute deviation and M median of streamflow reduction estimates across samples (Arachchige et al, 2020).…”

Section: Methodsmentioning

confidence: 99%

“…where MAD is the median absolute deviation and M median of streamflow reduction estimates across samples (Arachchige et al, 2020).…”

Section: Uncertainty Partitioningmentioning

confidence: 99%

Propagating uncertainty from catchment experiments to estimates of streamflow reduction by invasive alien plants in southwestern South Africa

Moncrieff

Slingsby

Maitre

2021

Hydrological Processes

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Long-term catchment experiments from South Africa have demonstrated that afforestation of grasslands and shrublands significantly reduces surface-water runoff.These results have guided the country's forestry policy and the implementation of a national Invasive Alien Plant (IAP) control programme for the past few decades.Unfortunately, woody IAP densities continue to increase, compounding existing threats to water security from population growth and climatic change. Decision makers need defensible estimates of the impacts of afforestation or invasions on runoff to weigh up alternative land use options, or guide investment of limited resources into ecosystem restoration through IAP clearing versus engineering-based wateraugmentation schemes. Existing attempts to extrapolate the impacts observed in catchment afforestation experiments to broad-scale IAP impacts give no indication of uncertainty. Globally, the uncertainty inherent in the results from paired-catchment experiments is seldom propagated into subsequent analyses making use of these data. We present a fully reproducible Bayesian model that propagates uncertainty from input data to final estimates of changes in streamflow when extrapolating from catchment experiments to broader landscapes. We apply our model to South Africa's catchment experiment data, estimating streamflow losses to plantations and analogous plant invasions in the catchments of southwestern South Africa, including uncertainty. We estimate that regional streamflow is reduced by 304 million m 3 or 4.14% annually as a result of IAPs, with an upper estimate of 408 million m 3 (5.54%) and a lower estimate of 267 million m 3 (3.63%). Our model quantifies uncertainty associated with all parameters and their contribution to overall uncertainty, helping guide future research needs. Acknowledging and quantifying inherent uncertainty enables more defensible decisions regarding water resource management.

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“…For example, it is well known that travel times often are susceptible to outliers. There is a rich literature on metrics that are robust to outliers, and these would be natural candidates for new TTR metrics (Arachchige et al 2020;Rousseeuw and Hubert 2011;Spiegelman et al 2011).…”

Section: Proposal For Future Ttr Analysesmentioning

confidence: 99%

Arterial Roadway Travel Time Reliability and the COVID-19 Pandemic

Rilett

Tufuor

Murphy

2021

J. Transp. Eng., Part A: Systems

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This paper evaluated the effect of the COVID-19 preventive orders on arterial roadway travel time reliability (TTR). A comparative analysis was conducted to examine average travel time distributions (TTD), and their associated TTR metrics, before and during the COVID-19 pandemic. Travel time data for four urban arterial corridors in Nebraska, disaggregated by peak period and direction, were analyzed. It was found that in 2020, the average TTD mean and standard deviation values for all 16 scenarios were reduced by an average of 14.0% and 43.4%, respectively. The travel time index, the planning time index, the level of travel time reliability (LOTTR), and the buffer index metrics associated with these TTDs were reduced, on average, by 14.0%, 19.7%, 3.5%, and 35.0%, respectively. In other words, whether the test corridors were more reliable during the pandemic was a function of which TTR metric was used. The paper concludes by arguing for a fundamental change in how arterial TTR is measured and reported to different user groups.

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Robust analogs to the coefficient of variation

Cited by 87 publications

References 36 publications

Nuclear RNA concentration coordinates RNA production with cell size in human cells

Nuclear RNA concentration coordinates RNA production with cell size in human cells

Propagating uncertainty from catchment experiments to estimates of streamflow reduction by invasive alien plants in southwestern South Africa

Arterial Roadway Travel Time Reliability and the COVID-19 Pandemic

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