eLife

Latest preprint reviews

1. Separating selection from mutation in antibody language models

   This article has 9 authors:

   1. Frederick A Matsen
   2. Will Dumm
   3. Kevin Sung
   4. Mackenzie M Johnson
   5. David Rich
   6. Tyler Starr
   7. Yun S Song
   8. Julia Fukuyama
   9. Hugh K Haddox

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study introduces a new biology-informed strategy for deep learning models aiming to predict mutational effects in antibody sequences. It provides solid evidence that separating selection from the nucleotide-level mutation process improves performance over the objectives of protein language models inspired by natural language processing. This paper should be of interest to computational immunologists, but also to the broader community interested in deep learning for biological sequence data and evolution.

   Reviewed by eLife

2. Direct MRI of Collagen

   This article has 4 authors:

   1. Jason Daniel van Schoor
   2. Markus Weiger
   3. Emily Louise Baadsvik
   4. Klaas Paul Pruessmann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This fundamental work substantially advances our understanding of a major research question: whether collagen can be directly imaged with MRI. The evidence supporting the conclusion is compelling, with methods, data, and analyses that are more rigorous than those currently considered state-of-the-art. The work will be of high interest to MR physicists and clinicians, as collagen is the most abundant protein in the human body and plays an essential role in health.

   Reviewed by eLife

3. A dual role for PGLYRP1 in host defense and immune regulation during B. pertussis infection

   This article has 6 authors:

   1. David M Rickert
   2. Sasha Cardozo
   3. Nicholas H Carbonetti
   4. William E Goldman
   5. Karen M Scanlon
   6. Ciaran Skerry

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Rickert and colleagues demonstrate that the host peptidoglycan-binding protein PGLYRP1 has both beneficial and detrimental effects on Bordetella pertussis infection in mice. Using a solid array of techniques, the study provides useful insights into how peptidoglycan species may alter host immune responses. The data on the bactericidal effects on B. pertussis are incomplete, and further experiments are needed to draw conclusions on this question.

   Reviewed by eLife

4. Investigating the native functions of [NiFe]-carbon monoxide dehydrogenases through genomic context analysis

   This article has 2 authors:

   1. Maximilian Böhm
   2. Henrik Land

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable analysis of a large dataset of [NiFe]-CODHs, integrating genomic context, operon organization, and clade-specific gene neighborhoods to discern patterns of functional diversification and adaptation. Carefully looking at the CODH genomic context, e.g., CODH-HCP co-occurrence, the authors gain insight into enzymatic activity, biotechnological potential, and differential functional roles. The approach aligns with current standards in genomic enzymology to characterize newly identified enzymes. With solid support, this work provides a broadly informative contribution to the field.

   Reviewed by eLife

5. A conserved Hsp70 phosphorylation regulates cell cycle progression after DNA damage

   This article has 6 authors:

   1. Thomas Moss
   2. Alexandra Wooldredge
   3. Koustav Bhakta
   4. Matthew Cronin
   5. Jason E Gestwicki
   6. Shaeri Mukherjee

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This potentially valuable manuscript focuses on the phosphorylation of residue T495 as a mechanism to inactivate HSP70 and disrupt cell cycle progression in response to DNA damage. The evidence supporting this model is incomplete and would be strengthened by additional studies defining the extent of T495 phosphorylation induced by DNA damage, identifying the kinase responsible for phosphorylating T495 of HSP70, and further elucidation of the functional implications of T495 phosphorylation in human cells. This work will be of interest to scientists focused on topics including chaperone biology, proteostasis, cell cycle progression, and DNA damage.

   Reviewed by eLife, preLights

6. Dynamic updating of spatial working memory across eye movements: a computational investigation of transsaccadic integration

   This article has 9 authors:

   1. Sijia Zhao
   2. Thomas Parr
   3. Rob Udale
   4. Verena Klar
   5. Gabriel David Jones
   6. Anna Scholcz
   7. Sofia Toniolo
   8. Sanjay G Manohar
   9. Masud Husain

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study makes an important contribution by revealing how saccades selectively disrupt spatial working memory while sparing other object features, and by demonstrating how this mechanism is altered in aging and neurodegeneration. The findings are supported by convincing evidence derived from well-controlled eye-tracking experiments and systematic generative model comparisons. Together, the work provides a computationally grounded framework that is of importance for understanding trans-saccadic memory and its clinical relevance.

   Reviewed by eLife

7. From Syllables to Words: EEG Evidence of Different Age Trajectories in Speech Tracking and Statistical Learning in Infants at High and Low Likelihood for Autism

   This article has 5 authors:

   1. Michel Godel
   2. Ana Fló
   3. Lucas Benjamin
   4. Ghislaine Dehaene-Lambertz
   5. Marie Schaer

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study addresses a key question in developmental cognitive neuroscience by identifying early neural correlates of variability in language learning and showing how syllable tracking and word segmentation develop from birth to two years in infants with differing likelihoods of autism. The evidence is generally strong, with rigorous longitudinal EEG acquisition, careful preprocessing, and validated statistical approaches, though several methodological clarifications would further strengthen confidence in the inferences. Overall, the findings offer important insights with clear theoretical implications for understanding early mechanisms of speech perception and statistical learning, supported by convincing evidence.

   Reviewed by eLife

8. Retrosplenial cortex enables context-dependent goal-directed sensorimotor transformation

   This article has 8 authors:

   1. Pol Bech
   2. Robin F Dard
   3. Jules Lebert
   4. Lana Smith
   5. Axel Bisi
   6. Anthony Renard
   7. Sylvain Crochet
   8. Carl CH Petersen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study combines optogenetic manipulations and wide-field imaging to show that the retrosplenial cortex controls behavioral responses to whisker deflection in a context-dependent manner. The evidence is convincing, but the study would benefit from additional analyses to disentangle the contributions of movement initiation to the recorded neural signals. The paper should be of strong interest to neuroscientists studying cortical mechanisms of sensorimotor processing.

   Reviewed by eLife

9. How individual vigor shapes human-human physical interaction

   This article has 3 authors:

   1. Dorian Verdel
   2. Bastien Berret
   3. Etienne Burdet

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important study showing that movement vigor is not solely an individual property but emerges through interaction when two people are physically linked. The evidence is convincing, supported by a well-controlled experimental design and modeling that closely match the observed behavior. While the authors provided a helpful comparison of several candidate models of human-human interaction dynamics, the statistical power and the statistical analyses could be further improved.

   Reviewed by eLife

10. Perceptual predictions track subjective, over objective, statistical structure

    This article has 5 authors:

    1. Jessye Clarke
    2. Kirsten Rittershofer
    3. Emma K Ward
    4. Daniel Yon
    5. Clare Press

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This important study reports three experiments examining how the subjective experience of task regularities influences perceptual decision-making. Although the evidence linking subjective ratings to behavioral measures is solid, the study would be strengthened if potential reverse influences of response times on subjective ratings were ruled out and if more comprehensive model comparisons supporting the main claims were performed. The findings will appeal to a wide range of researchers in decision-making and perception.

    Reviewed by eLife