eLife

Latest preprint reviews

1. The RNA-binding activity of the TRIM-NHL protein NHL-2 is essential for miRNA-mediated gene regulation

   This article has 10 authors:

   1. Nasim Saadat
   2. Rhys N. Colson
   3. Acadia L. Grimme
   4. Uri Seroussi
   5. Joshua W. Anderson
   6. Julie M. Claycomb
   7. Matthew C. J. Wilce
   8. Katherine McJunkin
   9. Jacqueline A. Wilce
   10. Peter R. Boag

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This useful study identifies amino acid residues in the C. elegans RNA-binding protein NHL-2 that are required for RNA binding in vitro and NHL-2 function in vivo. The evidence in support of the authors' mechanistic model is currently incomplete, as data implicating specific NHL-2 amino acids in RNA binding per se in vivo are not presented. This manuscript will be of interest to scientists working in the area of gene regulation.

   Reviewed by eLife

2. Light-driven synchronization of optogenetic clocks

   This article has 5 authors:

   1. Maria Cristina Cannarsa
   2. Filippo Liguori
   3. Nicola Pellicciotta
   4. Giacomo Frangipane
   5. Roberto Di Leonardo

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a light-entrainable synthetic oscillator in bacteria, the optorepressilator. The authors develop a toolbox using optogenetics that makes the cellular oscillator easily controllable. This toolbox is valuable, contributing both to bioengineering and to the understanding of biological dynamical systems. The comparison with a mathematical model, population, and single-cell measurements demonstrate convincingly that the planned system was achieved and is suitable to control and study biological oscillators.

   Reviewed by eLife

3. PPI-hotspotID for detecting protein–protein interaction hot spots from the free protein structure

   This article has 6 authors:

   1. Yao Chi Chen
   2. Karen Sargsyan
   3. Jon D Wright
   4. Yu-Hsien Chen
   5. Yi-Shuian Huang
   6. Carmay Lim

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The manuscript presents a machine-learning method to predict protein hotspot residues. The validation is incomplete, along with the misinterpretation of the results with other current methods like FTMap.

   Reviewed by eLife

4. Dynamic reinforcement learning reveals time-dependent shifts in strategy during reward learning

   This article has 4 authors:

   1. Sarah Jo C Venditto
   2. Kevin J Miller
   3. Carlos D Brody
   4. Nathaniel D Daw

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important work by Veneditto and colleagues developed a new modeling approach, called a mixture-of-agent hidden Markov model (MoA-HMM), in which choice behaviors are modeled as transitions between discrete states defined by different weighting of several reinforcement learning and decision strategies. The authors apply this approach to their previous data collected from rats performing the two-step task, and show that this method predicts fluctuations in neural and other behavioral data and provides better fits to the data than previous methods. The revision has greatly improved the manuscript, the evidence supporting the conclusions is convincing, and the method is of general interest to the field.

   Reviewed by eLife

5. Blood metabolomic profiling reveals new targets in the management of psychological symptoms associated with severe alcohol use disorder

   This article has 16 authors:

   1. Sophie Leclercq
   2. Hany Ahmed
   3. Camille Amadieu
   4. Géraldine Petit
   5. Ville Koistinen
   6. Quentin Leyrolle
   7. Marie Poncin
   8. Peter Stärkel
   9. Eloise Kok
   10. Pekka J Karhunen
   11. Philippe de Timary
   12. Sophie Laye
   13. Audrey M Neyrinck
   14. Olli K Kärkkäinen
   15. Kati Hanhineva
   16. Nathalie Delzenne

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study provides valuable insights and allows for hypothesis generation around diet-microbe-host interactions in alcohol use disorder. The strength of the evidence is convincing: the work is done in a rigorous manner in a well-described cohort of patients with AUD before and after withdrawal. There are several weaknesses, including validating the metabolites identified by metabolomics, the cross-sectional study design, the lack of a healthy control group, and the descriptive nature of such clinical cohort studies. Nevertheless, the study provides a wealth of new data that may be the basis for future studies that test causality and elucidate the role of single metabolites in the psychiatric sequela of AUD.

   Reviewed by eLife

6. Geometry and dynamics of representations in a precisely balanced memory network related to olfactory cortex

   This article has 3 authors:

   1. Claire Meissner-Bernard
   2. Friedemann Zenke
   3. Rainer W Friedrich

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study introduces a biologically constrained model of telencephalic area of adult zebrafish to highlight the significance of precisely balanced memory networks in olfactory processing. The authors provide compelling evidence that their model performs better in multiple situations (for e.g. in terms of network stability and shaping the geometry of representations), compared to traditional attractor networks and persistent activity. The work supports recent studies reporting functional E/I subnetworks in several sensory cortexes, and will be of interest to both theoretical and experimental neuroscientists studying network dynamics based on structured excitatory and inhibitory interactions.

   Reviewed by eLife

7. Deconstructing Complexity: A Computational Topology Approach to Trajectory Inference in the Human Thymus with tviblindi

   This article has 14 authors:

   1. Jan Stuchly
   2. David Novak
   3. Nadezda Brdickova
   4. Petra Hadlova
   5. Vojen Sadilek
   6. Ahmad Iksi
   7. Daniela Kuzilkova
   8. Michael Svaton
   9. George Alehandro Saad
   10. Pablo Engel
   11. Herve Luche
   12. Ana E Sousa
   13. Afonso RM Almeida
   14. Tomas Kalina

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors present an algorithm and workflow for the inference of developmental trajectories from single-cell data, including a mathematical approach to increase computational efficiency. In this latest version, the authors addressed the benchmarking of the novel method, but the absence of quantitative comparisons to state-of-the-art methods still make this study incomplete. Based on the shown validation approaches, one can neither ultimately judge if the shown method will be an advance over previous work nor whether the approach will be of general useful applicability.

   Reviewed by eLife

8. Shortcutting from self-motion signals reveals a cognitive map in mice

   This article has 5 authors:

   1. Jiayun Xu
   2. Mauricio Girardi-Schappo
   3. Jean-Claude Beique
   4. André Longtin
   5. Leonard Maler

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This fundamental work provides creative and thoughtful analysis of rodent foraging behavior and its dependence on body reference frame-based vs world reference frame-based cues. Compelling evidence demonstrates that a robust map, capable of supporting taking novel shortcuts, can be learned primarily if not exclusively based on self-motion cues, which has rarely if ever been reported outside of the human literature. The work, which will be of interest to a broad audience of neuroscientists, provides a rich discussion about the role of the hippocampus in supporting the behavior that should guide future neurophysiological investigations.

   Reviewed by eLife

9. Purging viral latency by a bifunctional HSV-vectored therapeutic vaccine in chronically SIV-infected macaques

   This article has 11 authors:

   1. Ziyu Wen
   2. Pingchao Li
   3. Yue Yuan
   4. Congcong Wang
   5. Minchao Li
   6. Haohang Wang
   7. Minjuan Shi
   8. Yizi He
   9. Mingting Cui
   10. Ling Chen
   11. Caijun Sun

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this useful study, the authors tested a novel approach to eradicate the HIV reservoir by constructing a herpes simplex virus (HSV)-based therapeutic vaccine designed to reactivate HIV from latently infected cells and induce an immune response to kill such infected cells. Testing this approach with SIV in a primate model, the authors report that the SIV reservoir was reduced. However, the evidence presented appears to be incomplete because the animal group size was small and the SIV reservoir size highly variable.

   Reviewed by eLife

10. Unveiling chemotherapy-induced immune landscape remodeling and metabolic reprogramming in lung adenocarcinoma by scRNA-sequencing

    This article has 16 authors:

    1. Yiwei Huang
    2. Gujie Wu
    3. Guoshu Bi
    4. Lin Cheng
    5. Jiaqi Liang
    6. Ming Li
    7. Huan Zhang
    8. Guangyao Shan
    9. Zhengyang Hu
    10. Zhencong Chen
    11. Zongwu Lin
    12. Wei Jiang
    13. Qun Wang
    14. Junjie Xi
    15. Shanye Yin
    16. Cheng Zhan

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This study reports single-cell RNA sequencing results of lung adenocarcinoma, comparing 4 treatment-naive and 5 post-neoadjuvant chemotherapy tumor samples. Of interest is the delineation of two macrophage subtypes: Anti-mac cells (CD45+CD11b+CD86+) and Pro-mac cells (CD45+CD11b+ARG+), with the proportion of Pro-mac/pro-tumorigenic cells significantly increasing in LUAD tissues after neoadjuvant chemotherapy. In terms of significance, the findings might be useful. However issues remain after the revision with lengthy descriptive clustering type analysis, insufficient statistical support, and inefficient figure presentation. As it stands, the level of supportive evidence is inadequate.

    Reviewed by eLife