eLife

Latest preprint reviews

1. Robotic search for optimal cell culture in regenerative medicine

   This article has 19 authors:

   1. Genki N Kanda
   2. Taku Tsuzuki
   3. Motoki Terada
   4. Noriko Sakai
   5. Naohiro Motozawa
   6. Tomohiro Masuda
   7. Mitsuhiro Nishida
   8. Chihaya T Watanabe
   9. Tatsuki Higashi
   10. Shuhei A Horiguchi
   11. Taku Kudo
   12. Motohisa Kamei
   13. Genshiro A Sunagawa
   14. Kenji Matsukuma
   15. Takeshi Sakurada
   16. Yosuke Ozawa
   17. Masayo Takahashi
   18. Koichi Takahashi
   19. Tohru Natsume

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The manuscript by Kanda GN, Natsume T et al. describes a robotic artificial intelligence system with a batch Bayesian optimization algorithm that allows to optimise and reliably repeat cell culture protocols. The authors utilise induced pluripotent stem cell-derived retinal pigment epithelial cells as a model culture system of broad interest in regenerative medicine. They demonstrate that the robotic system with Bayesian algorithm accelerates the optimisation of cell culture protocols and increases the quality and quantity of cell products, compared with manual operations - these results will likely inform and strongly impact modern cell culture strategies in regenerative medicine.

     (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 name with the authors.)

   Reviewed by eLife

2. Efferocytosis of SARS-CoV-2-infected dying cells impairs macrophage anti-inflammatory functions and clearance of apoptotic cells

   This article has 43 authors:

   1. Ana CG Salina
   2. Douglas dos-Santos
   3. Tamara S Rodrigues
   4. Marlon Fortes-Rocha
   5. Edismauro G Freitas-Filho
   6. Daniel L Alzamora-Terrel
   7. Icaro MS Castro
   8. Thais FC Fraga da Silva
   9. Mikhael HF de Lima
   10. Daniele C Nascimento
   11. Camila M Silva
   12. Juliana E Toller-Kawahisa
   13. Amanda Becerra
   14. Samuel Oliveira
   15. Diego B Caetité
   16. Leticia Almeida
   17. Adriene Y Ishimoto
   18. Thais M Lima
   19. Ronaldo B Martins
   20. Flavio Veras
   21. Natália B do Amaral
   22. Marcela C Giannini
   23. Letícia P Bonjorno
   24. Maria IF Lopes
   25. Maira N Benatti
   26. Sabrina S Batah
   27. Rodrigo C Santana
   28. Fernando C Vilar
   29. Maria A Martins
   30. Rodrigo L Assad
   31. Sergio CL de Almeida
   32. Fabiola R de Oliveira
   33. Eurico Arruda Neto
   34. Thiago M Cunha
   35. José C Alves-Filho
   36. Vania LD Bonato
   37. Fernando Q Cunha
   38. Alexandre T Fabro
   39. Helder I Nakaya
   40. Dario S Zamboni
   41. Paulo Louzada-Junior
   42. Rene DR Oliveira
   43. Larissa D Cunha

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this paper, the authors demonstrate that the macrophage efferocytic response in SARS-CoV-2 infection is compromised for two reasons. Internalization of apoptotic SARS-CoV-2 infected cells leads to: 1) A proinflammatory as opposed to an anti-inflammatory response; and 2) reduction in macrophage capacity to perform further efferocytosis

     (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

3. Flexible utilization of spatial- and motor-based codes for the storage of visuo-spatial information

   This article has 3 authors:

   1. Margaret M Henderson
   2. Rosanne L Rademaker
   3. John T Serences

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This rigorous, carefully designed and executed functional magnetic-resonance imaging study provides compelling evidence against a rigid, fixed model for how working-memory representations are maintained in the human brain. By analyzing patterns and strength of brain activity, the authors show that networks for maintaining contents in mind vary depending on the task demands and foreknowledge of anticipated responses. This manuscript will be of interest to scientists studying working memory, both in humans and in non-human primates.

     (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

4. Decomposing the role of alpha oscillations during brain maturation

   This article has 4 authors:

   1. Marius Tröndle
   2. Tzvetan Popov
   3. Sabine Dziemian
   4. Nicolas Langer

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript will be of interest to cognitive and developmental neuroscientists who are interested in brain oscillations and their changes with development. This study decomposes the EEG alpha power, demonstrating the confound of aperiodic activity in true oscillatory power and elucidating opposing relation of periodic and aperiodic components with age. The main approach of this paper is well motivated, and the main conclusions are supported by the analysis, which is applied to multiple large datasets, though there are some minor issues with some of the follow up analyses. Overall, this manuscript makes a timely and important case for the consideration of aperiodic signals in future research.

     (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

5. A novel lineage-tracing mouse model for studying early MmuPV1 infections

   This article has 5 authors:

   1. Vural Yilmaz
   2. Panayiota Louca
   3. Louiza Potamiti
   4. Mihalis Panayiotidis
   5. Katerina Strati

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is a very significant new model for papillomavirus infection but all the reviewers have major reservations about the data as they stand, and the quality of some of the data. The manuscript is not publishable without better/more data and a re-write. The work has potential but there is quite a bit of essential experimental work required to make this manuscript sound.

     (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 name with the authors.)

   Reviewed by eLife

6. Identification of HIV-reservoir cells with reduced susceptibility to antibody-dependent immune response

   This article has 10 authors:

   1. Antonio Astorga-Gamaza
   2. Judith Grau-Expósito
   3. Joaquín Burgos
   4. Jordi Navarro
   5. Adrià Curran
   6. Bibiana Planas
   7. Paula Suanzes
   8. Vicenç Falcó
   9. Meritxell Genescà
   10. Maria J Buzon

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Persistence of the viral reservoir is hampering HIV cure and thus understanding how these cells persist is important. This study describes a possible way that HIV-infected cells in the reservoir may escape antibody killing. The reservoir cells tend to have less availability of a receptor that binds HIV antibodies that would ordinarily help in killing. These cells are not only less susceptible to antibody killing but also seem to be susceptible to proliferation, which helps maintain the reservoir.

     (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

7. Flexible and efficient simulation-based inference for models of decision-making

   This article has 4 authors:

   1. Jan Boelts
   2. Jan-Matthis Lueckmann
   3. Richard Gao
   4. Jakob H Macke

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper provides a new approach, Mixed Neural Likelihood Estimator (MNLE) to build likelihood emulators for simulation-based models where the likelihood is unavailable. The authors show that the MNLE approach is equally accurate but orders of magnitude more efficient than a recent proposal, likelihood approximation networks (LAN), on two variants of the drift-diffusion model (a widely used model in cognitive neuroscience). The comparison between LAN and MNLE approaches could be improved to strengthen the merits of the proposed approach over existing alternatives.

     (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

8. Intestinal GCN2 controls Drosophila systemic growth in response to Lactiplantibacillus plantarum symbiotic cues encoded by r/tRNA operons

   This article has 13 authors:

   1. Théodore Grenier
   2. Jessika Consuegra
   3. Mariana G Ferrarini
   4. Houssam Akherraz
   5. Longwei Bai
   6. Yves Dusabyinema
   7. Isabelle Rahioui
   8. Pedro Da Silva
   9. Benjamin Gillet
   10. Sandrine Hughes
   11. Cathy I Ramos
   12. Renata C Matos
   13. François Leulier

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Previous studies found that a component of the microbiota, Lactobacillus plantarum, can provide support to its host Drosophila melanogaster during development. They further explore this interaction using defined diets where they find that under conditions that have low levels of some essential amino acids, the bacteria can still promote survival even though the bacteria is not synthesizing the amino acid. Through a screen of bacterial transposon insertion mutants, these authors identify bacterial transfer and ribosomal RNAs as necessary for this effect. And studies in the fly demonstrate that the host kinase GCN2, a protein known to associate with host tRNAs, in enterocytes is the mediator of this response. This manuscript links the intestinal microbiota to host protective responses.

     (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. BDNF/TrkB signaling endosomes in axons coordinate CREB/mTOR activation and protein synthesis in the cell body to induce dendritic growth in cortical neurons

   This article has 9 authors:

   1. Guillermo Moya-Alvarado
   2. Reynaldo Tiburcio-Felix
   3. María Raquel Ibáñez
   4. Alejandro A Aguirre-Soto
   5. Miguel V Guerra
   6. Chengbiao Wu
   7. William C Mobley
   8. Eran Perlson
   9. Francisca C Bronfman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Overall, these authors show that BDNF at the axon terminal can be retrogradely transported to promote new protein synthesis in the neuronal cell body and regulate dendritic morphology, which requires activated TrkB, Akt and mTOR in the soma and nuclear phospho-CREB. Although target-derived neurotrophin effects are well-established in the peripheral nervous system, this mechanism of signaling is less well-understood in the CNS. The manuscript presents a comprehensive analysis of the retrograde transport of BDNF/TrkB from the axon terminal to regulate dendritic morphology.

     (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 name with the authors.)

   Reviewed by eLife

10. Closely related type II-C Cas9 orthologs recognize diverse PAMs

    This article has 9 authors:

    1. Jingjing Wei
    2. Linghui Hou
    3. Jingtong Liu
    4. Ziwen Wang
    5. Siqi Gao
    6. Tao Qi
    7. Song Gao
    8. Shuna Sun
    9. Yongming Wang

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This work is relevant to all who are interested in genome editing. The versatile Cas9 nuclease has enabled creative genome editing applications, yet the targetable sequence space is limited by the PAM specificity of the Cas9 RNP. This manuscript expands the Cas9 toolbox by defining the PAM specificity and genome editing activity of a large group of smaller-sized type II-C Cas9s. The results also contribute to our understanding of the diversity of Cas enzymes and show that there is a significant potential in mining for non-trivial genome editing tools amongst highly similar Cas orthologs.

      (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