eLife

Latest preprint reviews

1. Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy

   This article has 8 authors:

   1. Sierra M Barone
   2. Alberta GA Paul
   3. Lyndsey M Muehling
   4. Joanne A Lannigan
   5. William W Kwok
   6. Ronald B Turner
   7. Judith A Woodfolk
   8. Jonathan M Irish

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The three reviewers were overly positive about the stated goal of your T-REX method to characterize rare populations by cytometry. The potential applications in the context of analyzing antigen-specific T cells (as identified as tetramer-positive cells) were not missed on the reviewers and the use of the 2 timepoints-cohort of samples from rhinovirus-infected patients was judged clever. However, all three reviewers requested some edits and additional tests to really distinguish T-REX from other methods in terms of performance, and to better understand its analysis power. Reviewer #1 enjoined you to clarify the improvements of your method compared to previous methods. Reviewer #2 requested more stringent tests of your methods against functional datasets. Reviewer #3 inquired about corrections for batch effects, the result consistency for repeated down-sampling as well as the scalability of the method (especially when UMAP is being used).

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife, ScreenIT

2. A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen

   This article has 11 authors:

   1. Ursula Oggenfuss
   2. Thomas Badet
   3. Thomas Wicker
   4. Fanny E Hartmann
   5. Nikhil Kumar Singh
   6. Leen Abraham
   7. Petteri Karisto
   8. Tiziana Vonlanthen
   9. Christopher Mundt
   10. Bruce A McDonald
   11. Daniel Croll

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study is of potential interest to a broad audience on evolutionary and population genomics, particularly scientists studying genome dynamics, including transposable elements (TE) and their evolution. It takes advantage of genomics datasets from a large population of wheat pathogens collected across the globe at different times (decades) to detect ongoing processes of genome expansion and potential selection mediated by TE insertions. The work provides empirical evidence that drastic demographic processes shape TE dynamics in nature and that these contribute to intraspecific variation in genome sizes, recapitulating the well-stablished association between TE content and genome size observed across the diversity of life forms.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife

3. Identification of neural progenitor cells and their progeny reveals long distance migration in the developing octopus brain

   This article has 5 authors:

   1. Astrid Deryckere
   2. Ruth Styfhals
   3. Ali Murat Elagoz
   4. Gregory E Maes
   5. Eve Seuntjens

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is a well-presented study on the development of the central nervous system in the octopus O. vulgaris which is of broad interest to scientists in the field of evolutionary developmental biology. The authors provide an excellent in situ gene expression study of neural genes whose expression is conserved in the developing CNS across the animal kingdom. To identify the origin of neural progenitors in the early embryo, the study furthermore includes cell lineage tracing and the analysis of mitotic activity.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

   Reviewed by eLife

4. Multiphasic value biases in fast-paced decisions

   This article has 5 authors:

   1. Elaine A Corbett
   2. L Alexandra Martinez-Rodriguez
   3. Cian Judd
   4. Redmond G O'Connell
   5. Simon P Kelly

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Corbett and colleagues developed a novel experimental framework to account for value biases in fast-paced decisions. For this purpose, they developed detailed computational models of how value biases can alter the decision-making process and used EEG data to constrain the estimation of model parameters and their comparison. In contrast to existing accounts which describe value biases using a single bias mechanism, they found that a more complex and dynamic pattern of mechanisms best explains the EEG and behavioral data.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

5. Convalescent plasma use in the USA was inversely correlated with COVID-19 mortality

   This article has 9 authors:

   1. Arturo Casadevall
   2. Quigly Dragotakes
   3. Patrick W Johnson
   4. Jonathon W Senefeld
   5. Stephen A Klassen
   6. R Scott Wright
   7. Michael J Joyner
   8. Nigel Paneth
   9. Rickey E Carter

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work is of interest to clinicians, epidemiologists and policy makers as it raises concerns about under-utilization of convalescent plasma (CCP) therapy during the Covid-19 pandemic, which in turn led to an increased number of preventable patient deaths. The authors demonstrate an inverse correlation between CCP use and mortality per admission in the US. They estimate that reduced use of CCP may have resulted in 29,000 to 36,000 excess deaths over the past year in the US.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife, ScreenIT

6. Motor planning under uncertainty

   This article has 2 authors:

   1. Laith Alhussein
   2. Maurice A Smith

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study addresses an important debate in the field of motor control: Can motor commands generated under uncertain conditions be better explained as an average of different candidate motor programs, or by a single motor plan that minimizes the expected costs? The paper provides evidence for the latter hypothesis. Previous studies have provided clear evidence against the motor averaging hypothesis, however the present study provides the most elegant and conclusive examination of these two ideas to date. While some of the interpretation, especially of Experiment 2, requires more nuanced consideration, overall we thought the evidence presented supported the key conclusion.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

7. Assembly of higher-order SMN oligomers is essential for metazoan viability and requires an exposed structural motif present in the YG zipper dimer

   This article has 10 authors:

   1. Kushol Gupta
   2. Ying Wen
   3. Nisha S Ninan
   4. Amanda C Raimer
   5. Robert Sharp
   6. Ashlyn M Spring
   7. Kathryn L Sarachan
   8. Meghan C Johnson
   9. Gregory D Van Duyne
   10. A Gregory Matera

   This article has been curated by 1 group:

   • Curated by eLife

     Summary:

     The manuscript describes a very detailed mutagenesis analysis of the dimerization / oligomerization behavior of the protein Survival Motor Neuron. Mutations in this protein cause Spinal Muscular Atrophy. Analysis of disease causing mutations show a correlation with their impact on oligomerization. A structural model that includes different domains of the protein involved in oligomerization is built from these analyses.

     This analysis is an excellent source for researchers working in the field of SMN proteins. A mechanistic interpretation of how changes in the oligomerization lead to the disease or impact the formation of membraneless organelles, is however missing. Thus, the manuscript provides an enormous amount of important mutational analysis data but does not lead to a significant advancement in our understanding of the disease mechanism.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

8. Organelle calcium-derived voltage oscillations in pacemaker neurons drive the motor program for food-seeking behavior in Aplysia

   This article has 6 authors:

   1. Alexis Bédécarrats
   2. Laura Puygrenier
   3. John Castro O'Byrne
   4. Quentin Lade
   5. John Simmers
   6. Romuald Nargeot

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this report the authors demonstrate convincingly that rhythmic activity in neurons that are part of the feeding CPG in Aplysia is generated via an unusual mechanism, organelle-derived intracellular calcium fluxes. The neurons that are studied (B63 neurons) play an important role in triggering cycles of motor activity and previous work from this group has demonstrated that activity in these neurons can be modified by operant conditioning. The paper was very well received by the reviewers who were impressed by the novelty of the mechanism uncovered as a driver of a fictive motor program and thus likely behavior.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

   Reviewed by eLife

9. Quantitative control of noise in mammalian gene expression by dynamic histone regulation

   This article has 13 authors:

   1. Deng Tan
   2. Rui Chen
   3. Yuejian Mo
   4. Shu Gu
   5. Jiao Ma
   6. Wei Xu
   7. Xibin Lu
   8. Huiyu He
   9. Fan Jiang
   10. Weimin Fan
   11. Yili Wang
   12. Xi Chen
   13. Wei Huang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to biologists who study mechanisms of cell-to-cell variability in gene expression and those who wish to have a tool to alter variability in mammalian cells. Key regulators of gene expression variability in mammalian cells are identified and noise modulation in a synthetic system is shown. The data quality is high. A model for the origin of the observed noise is proposed, but will require some additional experimental evidence.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

10. The human cerebellum is essential for modulating perceptual sensitivity based on temporal expectations

    This article has 2 authors:

    1. Assaf Breska
    2. Richard B Ivry

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This study provides evidence that individuals with cerebellar degeneration show reduced effects of temporal expectation on perceptual discriminability with interval timing cues, but intact effects with rhythmic cues. The authors compare individuals with cerebellar degeneration to controls, and find a selective impairment of the individuals with cerebellar degeneration to use interval-based temporal predictions to facilitate visual discrimination, whereas rhythm-based performance benefits are spared. This study is of interest to psychologists and neuroscientists investigating prediction, perception, attention, and motor control, as it demonstrates a key role for the cerebellum in mediating the effects of interval-based temporal expectation on perception.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

    Reviewed by eLife