eLife

Latest preprint reviews

1. Fluidity and Predictability of Epistasis on an Intragenic Fitness Landscape

   This article has 3 authors:

   1. Sarvesh Baheti
   2. Namratha Raj
   3. Supreet Saini

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This paper addresses the significant question of quantifying epistasis patterns, which affect the predictability of evolution, by reanalyzing a recently published combinatorial deep mutational scan experiment. The findings are useful, showing that epistasis is fluid, i.e. strongly background dependent, but that fitness effects of mutations are statistically predictable based on the background fitness. While the general approach appears solid, some claims remain incompletely supported by the analysis, as arbitrary cutoffs are used and the description of methods lacks specifics. This analysis should be of interest to the community working on fitness landscapes.

   Reviewed by eLife

2. How relevant is the prior? Bayesian causal inference for dynamic perception in volatile environments

   This article has 3 authors:

   1. David Meijer
   2. Roberto Barumerli
   3. Robert Baumgartner

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study makes a valuable contribution to understanding Bayesian inference in dynamic environments by demonstrating how humans integrate prior beliefs with sensory evidence, revealing an overestimation of environmental volatility while accurately tracking noise. The evidence is solid, supported by robust model fitting and principled factorial model set analyses, though limitations in sample size and inconclusive findings on memory capacity tradeoffs reduce the overall impact. Future work should expand validation across datasets, enhance model comparisons, and explore the generalizability of reduced Bayesian frameworks to strengthen the conclusions and broader relevance of the study.

   Reviewed by eLife

3. Mapping the topographic organization of the human zona incerta using diffusion MRI

   This article has 8 authors:

   1. Roy AM Haast
   2. Jason Kai
   3. Alaa Taha
   4. Violet Liu
   5. Greydon Gilmore
   6. Maxime Guye
   7. Ali R Khan
   8. Jonathan C Lau

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study uses diffusion magnetic resonance imaging to non-invasively map the white matter fibres connecting the zona incerta and cortex in humans. The authors present convincing evidence to indicate that these connections are organized along a rostro-caudal axis. The findings will be of interest to researchers interested in neuroanatomy and cortico-subcortical connectivity.

   Reviewed by eLife

4. Biophysically inspired mean-field model of neuronal populations driven by ion exchange mechanisms

   This article has 13 authors:

   1. Giovanni Rabuffo
   2. Abhirup Bandyopadhyay
   3. Carmela Calabrese
   4. Kashyap Gudibanda
   5. Damien Depannemaecker
   6. Lavinia Mitiko Takarabe
   7. Maria Luisa Saggio
   8. Mathieu Desroches
   9. Anton Ivanov
   10. Marja-Leena Linne
   11. Christophe Bernard
   12. Spase Petkoski
   13. Viktor K Jirsa

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript presents a useful mean-field model for a network of Hodgkin-Huxley neurons retaining the equations for ion exchange between the intracellular and extracellular space. The mean-field model derived in this work relies on approximations and heuristic arguments that, on the one hand, allow a closed-form derivation of the mean-field equations, but also raise questions about their justifications and the degree to which the results agree with experiments as well as direct numerical simulations. Therefore, the evidence for the utility of this approach is at present incomplete.

   Reviewed by eLife

5. Reprogramming of GM-CSF-dependent alveolar macrophages through GSK3 activity modulation

   This article has 16 authors:

   1. Israel Ríos
   2. Cristina Herrero
   3. Mónica Torres-Torresano
   4. Baltasar López-Navarro
   5. María Teresa Schiaffino
   6. Francisco Díaz Crespo
   7. Alicia Nieto-Valle
   8. Rafael Samaniego
   9. Yolanda Sierra-Palomares
   10. Eduardo Oliver
   11. Fernando Revuelta-Salgado
   12. Ricardo García-Luján
   13. Paloma Sánchez-Mateos
   14. Rafael Delgado
   15. Amaya Puig-Kröger
   16. Angel L Corbí

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study provides compelling data from in vitro models and patient-derived samples to demonstrate how modulation of GSK3 activity can reprogram macrophages, revealing potential therapeutic applications in inflammatory diseases such as severe COVID-19. The study stands out for its clear and systematic presentation, convincing experimental approach, and the relevance of its findings to the field of immunology.

   Reviewed by eLife

6. Dissecting infant leukemia developmental origins with a hemogenic gastruloid model

   This article has 19 authors:

   1. Denise Ragusa
   2. Chun Wai Suen
   3. Gabriel Torregrosa Cortes
   4. Fabio Pastorino
   5. Ayona Johns
   6. Ylenia Cicirò
   7. Liza Dijkhuis
   8. Susanne van den Brink
   9. Michele Cilli
   10. Connor Byrne
   11. Giulia-Andreea Ionescu
   12. Joana Cerveira
   13. Kamil R Kranc
   14. Victor Hernandez-Hernandez
   15. Mirco Ponzoni
   16. Anna Bigas
   17. Jordi Garcia-Ojalvo
   18. Alfonso Martínez Arias
   19. Cristina Pina

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study presents a mouse gastruloid system to generate successive waves of hematopoietic progenitors that in vivo would emerge during embryonic development. Although this newly revised manuscript has addressed some of the concerns raised during the first round of review, the study is still considered incomplete, as the claims are only partially supported. In particular, the claim of definitive wave hematopoietic progenitors being produced in the gastruloids, and their engraftment after transplantation, would benefit from further validation.

   Reviewed by eLife

7. Drug combination prediction for cancer treatment using disease-specific drug response profiles and single-cell transcriptional signatures

   This article has 5 authors:

   1. Daniel Osorio
   2. Parastoo Shahrouzi
   3. Xavier Tekpli
   4. Vessela N Kristensen
   5. Marieke L Kuijjer

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The study conducted by Hurtado et al. offers important insights and solid evidence regarding the prediction of drug combinations for cancer treatment. By leveraging disease-specific drug response profiles and single-cell transcriptional signatures, this research not only demonstrates a novel and effective approach to identifying potential drug synergies but it also enhances our understanding of the underlying mechanisms of drug response prediction.

   Reviewed by eLife

8. Human cerebellum and ventral tegmental area interact during extinction of learned fear

   This article has 14 authors:

   1. Enzo Nio
   2. Patrick Pais Pereira
   3. Nicolas Diekmann
   4. Mykola Petrenko
   5. Alice Doubliez
   6. Thomas M Ernst
   7. Giorgi Batsikadze
   8. Stefan Maderwald
   9. Cornelius Deuschl
   10. Metin Üngör
   11. Sen Cheng
   12. Christian J Merz
   13. Harald H Quick
   14. Dagmar Timmann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study provides insights into the role of the cerebellum in fear conditioning, addressing a key gap in the literature. The evidence presented in support of the conclusions is solid. This work will be of interest to both the extinction learning and cerebellar research communities.

   Reviewed by eLife

9. Simulation-based survey of TMEM16 family reveals that robust lipid scrambling requires an open groove

   This article has 4 authors:

   1. Christina Alexandra Stephens
   2. Niek van Hilten
   3. Lisa Zheng
   4. Michael Grabe

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study provides information on the TMEM16 family of membrane proteins, which play roles in lipid scrambling and ion transport. By simulating 27 structures representing five distinct family members, the authors captured hundreds of lipid scrambling events, offering insights into the mechanisms of lipid translocation and the specific protein regions involved in these processes. While the data on comparison of scrambling competence is compelling, the evidence for outside-the-groove scramblase activity without experimental validation is missing and is based on a limited set of observed events.

   Reviewed by eLife

10. Cortical dynamics in hand/forelimb S1 and M1 evoked by brief photostimulation of the mouse’s hand

    This article has 7 authors:

    1. Daniela Piña Novo
    2. Mang Gao
    3. Rita Fischer
    4. Louis Richevaux
    5. Jianing Yu
    6. John M Barrett
    7. Gordon MG Shepherd

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This work defines the response dynamics in forepaw-related cortical circuits of S1 and M1 following stimulation of peripheral mechanoreceptors in the mouse. In this revised version, the authors have addressed the reviewers' prior concerns. The results are convincing and present a valuable comparison to previously published work. This study has implications for understanding the interactions between primary somatosensory and motor cortex, required for active sensing, and will be of interest to scientists seeking to better understand the functions of somatosensory and motor circuits.

    Reviewed by eLife