eLife

Latest preprint reviews

1. Large scale loss-of-function mutations during chicken evolution and domestication

   This article has 19 authors:

   1. Siwen Wu
   2. Kun Wang
   3. Xuehai Ge
   4. Tengfei Dou
   5. Sisi Yuan
   6. Shixiong Yan
   7. Zhiqiang Xu
   8. Yong Liu
   9. Zonghui Jian
   10. Jingying Zhao
   11. Rouhan Zhao
   12. Xiannian Zi
   13. Dahai Gu
   14. Lixian Liu
   15. Qihua Li
   16. Dong-Dong Wu
   17. Junjing Jia
   18. Changrong Ge
   19. Zhengchang Su

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study reports potential loss-of-function variants, pseudogenes and gene presence-absence variation across multiple chicken genomes, with potential implications for understanding genome evolution and domestication. The evidence for the central claims is unfortunately incomplete, as the inferences of gene loss are not sufficiently robust to account for assembly and annotation artifacts, and, in addition, the analyses can not distinguish between positive selection and relaxed constraint. The overall claim of large-scale gene loss being adaptive and thus being a major driver of chicken evolution and domestication is therefore not sufficiently supported. The area of the study is of interest to colleagues in evolutionary and comparative genomics as well as animal domestication.

   Reviewed by eLife

2. GDNF regenerates the missing enteric nervous system of Hirschsprung mice via non-canonical signaling in diverse subtypes of tissue-resident progenitors

   This article has 7 authors:

   1. Alassane Gary
   2. Rodolphe Soret
   3. Marie A Lefèvre
   4. Nejia Lassoued
   5. Ann Aspirot
   6. Christophe Faure
   7. Nicolas Pilon

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study investigates how GDNF treatment restores nerve cells in the bowel of a mouse model of Hirschsprung disease, and proposes that this regeneration occurs through diverse resident precursor cells and a non-canonical signaling pathway. The evidence is solid for the ability of the treatment to induce new bowel nerve cells and for a contribution from multiple precursor populations, supported by extensive cell tracing and imaging experiments. This work will be of interest to researchers in developmental biology and peripheral neurobiology.

   Reviewed by eLife

3. Hippocampal and prefrontal contributions to memory-guided navigation depend on task epoch

   This article has 4 authors:

   1. Tora Dohi
   2. Lucy Anderson
   3. György Buzsàki
   4. Ipshita Zutshi

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Dohi et al. asked what role the dorsal hippocampus and medial prefrontal cortex play during different temporal epochs of a memory-guided navigation task, a long-standing question for neuroscientists studying hippocampal-prefrontal contributions to working memory. This useful study used a delayed, cue-guided T-maze task in mice and reported impaired choice accuracy when silencing occurred early in the central-arm run but not during the delay. However, the evidence for the study's claim is incomplete in its current form: the silencing windows are not duration-matched across epochs, key negative findings rest on three to four mice without power analysis or reported effect sizes, no non-mnemonic control task distinguishes disrupted memory-guided behavior from a general action-selection deficit, and no neural recordings accompany the causal manipulations to verify the manipulations' assumed mechanistic effects. The reported perseveration also reflects an increased directional bias rather than repetition of the previous choice, and the language should be revised accordingly.

   Reviewed by eLife

4. Uncertainty-aware quantitative analysis of the structure and dynamics of T cell receptor repertoires

   This article has 3 authors:

   1. Simo Kitanovski
   2. Kai Wollek
   3. Daniel Hoffmann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable tool for comparing immune receptor data across multiple samples while properly accounting for statistical uncertainty and receptor similarity. The evidence supporting the tool is solid overall. However, some key concerns regarding potential sequencing artifacts in one of the validation datasets and an unclear strategy for false discovery rate control in the proposed framework remain to be addressed.

   Reviewed by eLife

5. A reinforcement learning framework for goal-directed stimulation of engineered neuronal networks

   This article has 8 authors:

   1. Benedikt Maurer
   2. Vaiva Vasiliauskaitė
   3. Julian Hengsteler
   4. Gino Cathomen
   5. Tobias Ruff
   6. Cedric Schmid
   7. János Vörös
   8. Stephan J Ihle

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents an open-source reinforcement learning framework for the real-time, closed-loop optimization of spatiotemporal electrical stimulation in engineered neuronal networks. Using single-spike-resolution activity as continuous feedback, the authors provide solid evidence that their platform can identify stimulation patterns that drive specific activity motifs within a structurally constrained four-node circuit. While this reproducible system offers a valuable and accessible tool for interacting with biological neural networks in an adaptive manner, further validation is needed to determine how well these stimulation strategies generalize to larger, unstructured, or more conventional network architectures.

   Reviewed by eLife

6. Limitations of pupil diameter as a proxy for modes of locus coeruleus activity

   This article has 3 authors:

   1. Lowell W. Thompson
   2. Siddhartha Joshi
   3. Joshua I. Gold

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study examines the relationship between simultaneous LC single-unit recordings and pupillometry, both within and across baseline and evoked epochs, finding that cross-epoch relationships are unreliable. The evidence is solid and suggests that care should be taken when interpreting pupil responses as reflecting LC activity. This manuscript will be interesting to basic and clinical researchers working in cognitive and decision neuroscience as well as computational psychiatry.

   Reviewed by eLife

7. Neurofeedback enhances a neural signature of selective attention to speech in cocktail-party settings

   This article has 10 authors:

   1. Ram K Pari
   2. Marina Inyutina
   3. Hoang Lam Thanh Hoang
   4. Camille Dedies
   5. Manuela Jaeger
   6. Stefanie Enriquez-Geppert
   7. Mathieu Marx
   8. Stefan Debener
   9. Christoph S Herrmann
   10. Benedikt Zoefel

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study addresses a key question concerning whether neurofeedback can enhance the neural representation of a selected speaker during competing continuous speech and whether such enhancement translates into behavioral benefits. The solid findings provide important insights into the online modulation of auditory attention and the extent to which selective listening can be voluntarily controlled. Although the observed effects were relatively small and did not consistently persist beyond the feedback period, the study advances understanding in an under-explored area and provides a helpful foundation for future research on sustained learning and behavioral transfer.

   Reviewed by eLife

8. Top-down processing alone activates the early somatosensory nuclei

   This article has 8 authors:

   1. Paige Howell
   2. Lynn Farner
   3. Finn Rabe
   4. Tim Emmenegger
   5. Maryam Seif
   6. Patrick Freund
   7. Nicole Wenderoth
   8. Sanne Kikkert

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study provides convincing evidence that somatosensory relay nuclei remain engaged during attempted hand movements following chronic cervical spinal cord injury, including in individuals with severe motor impairment. The combination of functional and quantitative MRI with physiological controls supports the main findings and may have implications that are of importance in understanding sensorimotor processing after spinal cord injury. However, the interpretation of this activity as specifically reflecting top-down, and particularly corticocuneate, signaling may be overstated. The origin and anatomical route of the observed activity appears to remain less firmly established.

   Reviewed by eLife

9. Thermodynamic principles of enzymatic regulation in biomolecular condensates from reaction-coupled molecular modeling

   This article has 6 authors:

   1. Enrico Lavagna
   2. Francesco Delfino
   3. Georgii Koniukov
   4. Matteo Paloni
   5. Luca Ciandrini
   6. Alessandro Barducci

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a reaction-coupled molecular simulation framework to investigate how enzymatic post-translational modifications regulate biomolecular condensates and where reactions preferentially occur within them. These findings are important, in particular, to the emergence of spatially heterogeneous reaction fluxes and enhanced activity at condensate interfaces. The work is timely and has implications beyond the immediate subfield, especially for understanding condensates as biochemical reaction centers. The strength of evidence is solid overall: the computational framework is well motivated and broadly supports the main conclusions, although some aspects of the model implementation, parameter choices, and controls would benefit from further clarification and validation.

   Reviewed by eLife

10. Reassessing Choice Probability: What 59 Macaque Studies Tell Us About Decision-Related Activity in Visual Cortex

    This article has 22 authors:

    1. Anton Pletenev
    2. Richard T Born
    3. Gregory C DeAngelis
    4. Raymond Doudlah
    5. Ichiro Fujita
    6. Joshua I Gold
    7. Robbe LT Goris
    8. Alexander C Huk
    9. Kristine Krug
    10. Pooya Laamerad
    11. Richard D Lange
    12. Aaron J Levi
    13. Hendrikje Nienborg
    14. Christopher C Pack
    15. Andrew J Parker
    16. Ari Rosenberg
    17. Mehdi Sanayei
    18. Takanori Uka
    19. Xuefei Yu
    20. Adam Zaidel
    21. Corey M Ziemba
    22. Ralf M Haefner

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This meta-analysis provides a valuable contribution by integrating findings from dozens of macaque electrophysiology studies to reconcile discrepancies in choice probability and identify factors that robustly influence choice signals in the visual cortex. Such systematic synthesis across studies is rare in this field, and the analysis provides solid evidence for several conclusions, including the cross-study consistency of the relationship between choice probability and sensitivity and the distinctiveness of V1.

    Reviewed by eLife