eLife

Latest preprint reviews

1. Deciphering early-warning signals of SARS-CoV-2 elimination and resurgence from limited data at multiple scales

   This article has 3 authors:

   1. Kris V. Parag
   2. Benjamin J. Cowling
   3. Christl A. Donnelly

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study is timely and important for all scientists and policymakers with an interest in producing, using or interpreting estimates of the effective reproductive number, R, as an indicator of epidemic growth when case counts are low (e.g. at the very beginning or end of an epidemic). However, the utility and accuracy of these methods is not evaluated in the context of less-than-ideal surveillance, including time-varying case observation and long delays, which is currently the case in most countries and they fail to evaluate the performance of the metrics in real time.

     (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, ScreenIT

2. Reinvestigation of Classic T Cell Subsets and Identification of Novel Cell Subpopulations by Single-Cell RNA Sequencing

   This article has 8 authors:

   1. Xuefei Wang
   2. Xiangru Shen
   3. Shan Chen
   4. Hongyi Liu
   5. Ni Hong
   6. Hanbing Zhong
   7. Xi Chen
   8. Wenfei Jin

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript is of broad interest to readers interested in heterogeneity in immune cell populations with single-cell RNA sequencing, and for students of human T cell biology. It uses and reanalyses published single-cell RNA sequencing data dataset for this purpose. However, it does not adequately address major technical concerns, and therefore the interpretations are not robustly supported.

     (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

3. Immunoelectron Microscopic Characterization of Vasopressin-Producing Neurons in the Hypothalamo-Pituitary Axis of Non-Human Primates by Use of Formaldehyde-Fixed Tissues Stored at −25 °C for Several Years

   This article has 8 authors:

   1. Akito Otubo
   2. Sho Maejima
   3. Takumi Oti
   4. Keita Satoh
   5. Yasumasa Ueda
   6. John F. Morris
   7. Tatsuya Sakamoto
   8. Hirotaka Sakamoto

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript shows that it is possible to detect high-abundance peptide antigens in nerve cells at the electron microscope (EM) level in sections of formaldehyde-fixed monkey brain after the sections have been stored for several years in an antifreeze solution in the freezer. The topic of utilizing formalin fixed tissue for research, especially with the numerous "brain banks" worldwide, is an important topic especially if one wishes to conduct studies in post mortem human tissue. The authors used antibodies to detect the presence of vasopressin gene-related products (i.e., neurophysin II and copeptin) in the hypothalamus and pituitary of the monkey brain. This paper is of interest to anatomists who work on AVP neurons in non-human primate. Due to issues with tissue quality, methodology and interpretation, the experimental approach described in this paper may not be as useful for studying fixed and archived brain sections as the authors conclude.

     (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 #3 agreed to share their name with the authors.)

   Reviewed by eLife

4. Social media study of public opinions on potential COVID-19 vaccines: informing dissent, disparities, and dissemination

   This article has 7 authors:

   1. Hanjia Lyu
   2. Junda Wang
   3. Wei Wu
   4. Viet Duong
   5. Xiyang Zhang
   6. Timothy D. Dye
   7. Jiebo Luo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study uses social media data (namely twitter) to analyse factors of covid-vaccine acceptance. It first trains a classifier to detect whether a tweets pro-vaccine, neutral, or against. Using then a large corpus of accounts, it investigates multiple factors explaining this position in a light counterfactual analysis. The central finding is that the most socioeconomically disadvantaged groups are more likely to hold polarized opinions on COVID-19 vaccines; other findings inclduing that personal pandemic experience has an important impact on acceptance, or that interest in politics modulates acceptance. This study a good example of what machine learning can do with social media data; however it is also a good example of the high data-demands and limitations of a machine learning approach. The correlations found are plausible but the causal implications are not evidenced strongly enough to guide public policy.

     (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, ScreenIT

5. Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness

   This article has 3 authors:

   1. Alexandre Laverré
   2. Eric Tannier
   3. Anamaria Necsulea

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper addresses a subject of potential great interest regarding the evolution of gene regulation and of enhancer landscapes. Available chromatin looping and gene expression data in mouse and human are analyzed to compare diverse properties of genome-wide promoter-centered maps, including associations with gene expression. It is shown that there is conservation of regulatory landscape across the two species, and that the extent of conservation in the TSS-distal landscape is associated with gene expression similarities. These overall results are in agreement with a large body of work in the field.

     (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

6. Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states

   This article has 17 authors:

   1. Francisco Rodriguez-Algarra
   2. Robert A. E. Seaborne
   3. Amy F. Danson
   4. Selin Yildizoglu
   5. Harunori Yoshikawa
   6. Pui Pik Law
   7. Zakaryya Ahmad
   8. Victoria A. Maudsley
   9. Ama Brew
   10. Nadine Holmes
   11. Mateus Ochôa
   12. Alan Hodgkinson
   13. Sarah J. Marzi
   14. Madapura M. Pradeepa
   15. Matthew Loose
   16. Michelle L. Holland
   17. Vardhman K. Rakyan

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript extends the evidence that ribosomal DNA has substantial interindividual variation, and presents evidence that variants are associated with differences in DNA methylation. The authors show that some rDNA types respond to environmental signals during in utero development, whereas others are changed during the aging process - thus broadening the known communication between development/nutrition/aging and the cellular protein synthesis machinery. These findings have relevance for the influence of such epialleles on gene expression and disease risk.

     (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

7. Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes

   This article has 3 authors:

   1. Martina Milighetti
   2. John Shawe-Taylor
   3. Benny Chain

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript reports a new approach to the important and challenging problem of predicting T cell receptor:peptide-MHC interactions, one that relies on molecular model building (with previously published tools) followed by feature extraction and machine learning. The strengths of the study are more conceptual than practical: the overall framework and analytical approach; a balanced, critical assessment of the method's performance (which does not shy away from negative results); some observations on TCR:pMHC docking geometry. On the practical side, the classifier does not appear to generalize well to unseen epitopes (neither do the published tools it's compared to), so at the end of the day it's not clear that it will be preferable to simpler sequence-based approaches.

     (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

8. TALPID3/KIAA0586 Regulates Multiple Aspects of Neuromuscular Patterning During Gastrointestinal Development in Animal Models and Human

   This article has 20 authors:

   1. Jean Marie Delalande
   2. Nandor Nagy
   3. Conor J. McCann
   4. Dipa Natarajan
   5. Julie E. Cooper
   6. Gabriela Carreno
   7. David Dora
   8. Alison Campbell
   9. Nicole Laurent
   10. Polychronis Kemos
   11. Sophie Thomas
   12. Caroline Alby
   13. Tania Attié-Bitach
   14. Stanislas Lyonnet
   15. Malcolm P. Logan
   16. Allan M. Goldstein
   17. Megan G. Davey
   18. Robert M. W. Hofstra
   19. Nikhil Thapar
   20. Alan J. Burns

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this study, the authors used a chick and a mouse model and human tissues to analyze the role of the conserved protein TALPID3/KIAA0586, previously linked to ciliogenesis, in gut development. Using a multi-species approach, the authors conclude that TALPID3 has an evolutionary conserved role in regulating gut patterning along the radial axis, apparently orchestrated by neural crest cells in a non-cell-autonomous manner and mediated by perturbation of Sonic Hedgehog signaling and the composition of extracellular matrix.

     (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

9. All-Optical Electrophysiology in hiPSC-Derived Neurons With Synthetic Voltage Sensors

   This article has 17 authors:

   1. Francesca Puppo
   2. Sanaz Sadegh
   3. Cleber A. Trujillo
   4. Martin Thunemann
   5. Evan P. Campbell
   6. Matthieu Vandenberghe
   7. Xiwei Shan
   8. Ibrahim A. Akkouh
   9. Evan W. Miller
   10. Brenda L. Bloodgood
   11. Gabriel A. Silva
   12. Anders M. Dale
   13. Gaute T. Einevoll
   14. Srdjan Djurovic
   15. Ole A. Andreassen
   16. Alysson R. Muotri
   17. Anna Devor

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be interesting for people performing all optical electrophysiology. It describes a new combination of previously available genetic tools to allow simultaneous optogenetic manipulation and optical electrophysiology. The manuscript does not provide a major conceptual advance but provides good evidence that this assay can be employed for large-scale screening in hIPSC-derived neurons.

     (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. Transthyretin Promotes Axon Growth via Regulation of Microtubule Dynamics and Tubulin Acetylation

    This article has 8 authors:

    1. Jessica Eira
    2. Joana Magalhães
    3. Nídia Macedo
    4. Maria Elena Pero
    5. Thomas Misgeld
    6. Mónica M. Sousa
    7. Francesca Bartolini
    8. Márcia A. Liz

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      In their manuscript, Eira et al. investigate the role of transthyretin in promoting axon elongation by modulating microtubule dynamics. The data point to a possible role of transthyretin in regulating microtubule dynamics by modulating tubulin acetylation levels during axon outgrowth. With additional support to strengthen this conclusion, the paper will be of interest to those in the neurodevelopment, neurodegeneration, and microtubule cytoskeleton fields.

      (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