eLife

Latest preprint reviews

1. Neural learning rules for generating flexible predictions and computing the successor representation

   This article has 4 authors:

   1. Ching Fang
   2. Dmitriy Aronov
   3. LF Abbott
   4. Emily L Mackevicius

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This important work provides compelling evidence for the biological plausibility of the Successor Representation (SR) algorithm. The SR is a leading computational hypothesis to explore whether neural representations are consistent with the hypothesis that the neural networks in specific brain area perform predictive computations. Establishing a biologically plausible learning rule for SR representations to form is of high importance in the field of neuroscience. This is also important for comparing the predictive ability of neural circuits with other predictive frameworks designed in machine learning.

     (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

2. Individual behavioral trajectories shape whole-brain connectivity in mice

   This article has 10 authors:

   1. Jadna Bogado Lopes
   2. Anna N Senko
   3. Klaas Bahnsen
   4. Daniel Geisler
   5. Eugene Kim
   6. Michel Bernanos
   7. Diana Cash
   8. Stefan Ehrlich
   9. Anthony C Vernon
   10. Gerd Kempermann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This is an important paper that is methodologically solid and highlights structural covariance as the neuroanatomical basis underlying individuality in genetically identical mice. The approach to individuality is very well designed, and the use of brain imaging and anatomical covariance as the underlying mechanism is well thought out. The statistical methods, while overall sound, require further justification and exploration. This paper will be of broad interest to neuroscientists, especially those working in brain plasticity or understanding unique and shared environmental influences on individuality.

   Reviewed by eLife

3. Rapid reconstruction of neural circuits using tissue expansion and light sheet microscopy

   This article has 19 authors:

   1. Joshua L Lillvis
   2. Hideo Otsuna
   3. Xiaoyu Ding
   4. Igor Pisarev
   5. Takashi Kawase
   6. Jennifer Colonell
   7. Konrad Rokicki
   8. Cristian Goina
   9. Ruixuan Gao
   10. Amy Hu
   11. Kaiyu Wang
   12. John Bogovic
   13. Daniel E Milkie
   14. Linus Meienberg
   15. Brett D Mensh
   16. Edward S Boyden
   17. Stephan Saalfeld
   18. Paul W Tillberg
   19. Barry J Dickson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper introduces a light microscopy pipeline for imaging and fast reconstruction of the synaptic connections of individual neuronal types in the fruit fly and for correlated investigation of circuit structure, function and behavior in the same animal. Because of its speed and accessibility, this approach enables mapping of selected neuronal circuits of multiple animals across different conditions and behavioral states, thus filling an important gap in brain 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. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

4. Generative power of a protein language model trained on multiple sequence alignments

   This article has 3 authors:

   1. Damiano Sgarbossa
   2. Umberto Lupo
   3. Anne-Florence Bitbol

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This valuable paper proposes an innovative iterative masking approach that enables models such as the MSA Transformer to generate new protein sequence designs, which are validated using a wide-ranging set of computational experiments. A key strength of the MSA Transformer is the ability to learn and generalize across protein families, enabling impressive performance across a range of downstream tasks. However, to date, these models have not been used to generate new protein sequence designs. The approach proposed in this paper is quite novel, and a number of metrics are used to examine the resulting performance of the MSA Transformer at generating new protein sequences from specific families.

     (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

5. Early myelination involves the dynamic and repetitive ensheathment of axons which resolves through a low and consistent stabilization rate

   This article has 2 authors:

   1. Adam R Almeida
   2. Wendy B Macklin

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Almeida and Macklin provide one of the first studies to closely examine early oligodendrocyte behaviors at high resolution. These studies use live imaging in zebrafish to provide valuable new insights about the earliest onset of myelination in the central nervous system and add to a body of work showing how oligodendrocytes initiate and maintain myelin sheaths.

     (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 #3 agreed to share their name with the authors.)

   Reviewed by eLife

6. Two novel, tightly linked, and rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought

   This article has 11 authors:

   1. Krithika Venkataraman
   2. Nadav Shai
   3. Priyanka Lakhiani
   4. Sarah Zylka
   5. Jieqing Zhao
   6. Margaret Herre
   7. Joshua Zeng
   8. Lauren A Neal
   9. Henrik Molina
   10. Li Zhao
   11. Leslie B Vosshall

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this manuscript, of interest to those studying insect reproductive biology and specifically mosquitoes, the authors show that females of the yellow fever mosquito retain eggs when fresh water is not readily available. The authors then use RNA expression analyses to identify genes potentially involved in the trait. This leads the authors to focus on two genes that seem to be recent duplicates. The authors generate genetic knockouts and use these to show that these two alleles affect the trait in question. The study includes interesting and technically impressive experiments, but the framing in the context of previous work could be improved.

     (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

7. Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor

   This article has 12 authors:

   1. Josephine HR Maidment
   2. Motoki Shimizu
   3. Adam R Bentham
   4. Sham Vera
   5. Marina Franceschetti
   6. Apinya Longya
   7. Clare EM Stevenson
   8. Juan Carlos De la Concepcion
   9. Aleksandra Białas
   10. Sophien Kamoun
   11. Ryohei Terauchi
   12. Mark J Banfield

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Engineering NLR proteins to improve disease resistance in crop plants is a major goal of the field. This study applies knowledge from structural and evolutionary studies of the rice NLR protein Pik-1 and cognate effector protein AVR-Pik to engineering of new disease resistance genes. The authors nicely demonstrate that it is indeed possible to engineer resistance proteins with broad recognition specificity for the rice blast fungus. The work is of interest to colleagues in synthetic biology, protein engineering and plant-pathogen interactions.

     (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. Human thymopoiesis produces polyspecific CD8+ α/β T cells responding to multiple viral antigens

   This article has 18 authors:

   1. Valentin Quiniou
   2. Pierre Barennes
   3. Vanessa Mhanna
   4. Paul Stys
   5. Helene Vantomme
   6. Zhicheng Zhou
   7. Federica Martina
   8. Nicolas Coatnoan
   9. Michele Barbie
   10. Hang-Phuong Pham
   11. Béatrice Clémenceau
   12. Henri Vie
   13. Mikhail Shugay
   14. Adrien Six
   15. Barbara Brandao
   16. Roberto Mallone
   17. Encarnita Mariotti-Ferrandiz
   18. David Klatzmann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This paper reports on important observations regarding human CD8 T cells that express shared T cell receptors amongst individuals and exhibit poly-specificity directed mainly to several unrelated viral antigens. Although the majority of the claims are convincingly supported by results from both in silico and experimental approaches, mechanistic molecular details underlying poly-specificity remain incomplete. The results from these studies will enhance the ongoing debate on T cell specificity and potentially, will impact fields related to immunology, for example, immunoparasitology, cell biology, and vaccine development.

   Reviewed by eLife

9. Identification of phenotypically, functionally, and anatomically distinct stromal niche populations in human bone marrow based on single-cell RNA sequencing

   This article has 6 authors:

   1. Hongzhe Li
   2. Sandro Bräunig
   3. Parashar Dhapolar
   4. Göran Karlsson
   5. Stefan Lang
   6. Stefan Scheding

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The manuscript by Li and coworkers characterizes sorted human non-hematopoietic bone marrow cells by scRNA-seq and predicts their lineage relationships and possible interactions with mature and immature hematopoietic cells. Transcriptionally-different stromal cell subsets are identified, and their lineage relationships, cell-cell interactions and possible specialized functions are inferred or predicted from in-silico studies, paving the way for future functional and validation studies. This resource significantly adds to the current understanding human non-hematopoietic bone marrow stromal cells and their hematopoietic regulatory functions.

     (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

10. Functional gradients in the human lateral prefrontal cortex revealed by a comprehensive coordinate-based meta-analysis

    This article has 4 authors:

    1. Majd Abdallah
    2. Gaston E Zanitti
    3. Valentin Iovene
    4. Demian Wassermann

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      A meta-analysis of over 14,000 fMRI studies revealed a principle rostral-caudal gradient in the lateral prefrontal cortex. This gradient reflected an internal/external axis, which helps to organize the LPFC's involvement in widespread processes from affect, to memory, to control, and action. This is an important contribution to the literature, particularly as a meta-analytic approach has not been applied to this axis of organization and can complement the limitations of single studies. The evidence for the conclusions could be strengthened by ruling out bias in the analysis and drawing a clearer relationship to functional networks.

      (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