Evidence map›Paper›PMID 39168105›Full record

ArticleBiophysical journal2024

Response to Biophysical Journal comment to the editor by Skóra regarding the article entitled: Vast heterogeneity in cytoplasmic diffusion rates revealed by nanorheology and Doppelgänger simulations.

Rikki M Garner, Arthur T Molines, Julie A Theriot, Fred Chang

Erratum issuedAbstract readEditorial
PubMed Full text at PMC Publisher
In one paragraph

Article in Biophysical journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

4 authors.

Rikki M GarnerBiophysics Program, Stanford University School of Medicine, Stanford, California; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, Washington. Electronic address: rikkimgarner@gmail.com.
Arthur T MolinesDepartment of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California. Electronic address: a.t.molines@gmail.com.
Julie A TheriotBiophysics Program, Stanford University School of Medicine, Stanford, California; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, Washington.
Fred ChangDepartment of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In a Comment to the Editor, Skóra raises a concern that the modeling framework implemented in Garner et al. (Biophysical Journal, 2023) neglects a potentially important term in the Brownian dynamics simulation of diffusion. Omission of this diffusivity gradient term may lead to an underestimation of the mean and overestimation of the variance of the cytoplasmic viscosity. In this response, we directly address this concern by incorporating this term into our model and showing that for this data set, its effect is negligible and does not alter the conclusions of this work.

Indexed as

CytoplasmDiffusionModels, BiologicalNanotechnologyRheologyViscosity

Identifiers

PMID39168105
PMCPMC11365216

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.