eLife

Latest preprint reviews

1. Analysis of long and short enhancers in melanoma cell states

   This article has 9 authors:

   1. David Mauduit
   2. Ibrahim Ihsan Taskiran
   3. Liesbeth Minnoye
   4. Maxime de Waegeneer
   5. Valerie Christiaens
   6. Gert Hulselmans
   7. Jonas Demeulemeester
   8. Jasper Wouters
   9. Stein Aerts

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is a well-executed study describing multiple new findings related to the association between enhancer activity as measured by massively parallel reporter assay (MPRA), chromatin features, and underlying TF binding profiles in the context of different transcriptional states of cutaneous melanoma. There are several technical and conceptual advances including the refinement of MPRA assays and the understanding of regulatory mechanisms controlling cell state-specific enhancer activity that will be valuable for other investigators to adapt the experimental design and data analysis strategies. This work will be of broad interest to those seeking to understand cell type- or cell identify-specific gene regulation at the level of transcription and epigenetic control using these and related approaches.

     (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 agreed to share their name with the authors.)

   Reviewed by eLife

2. NMDA receptors in visual cortex are necessary for normal visuomotor integration and skill learning

   This article has 3 authors:

   1. Felix C Widmer
   2. Sean M O'Toole
   3. Georg B Keller

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study examined the mechanism underlying the development of prediction-error related responses of neurons in the primary visual cortex (V1) evoked by the mismatch between self-generated locomotor movement and visual feedback. The authors show that unilateral gene knockout of NMDA receptors or CaMKII in the primary visual cortex impaired the mismatch-related responses in V1. The experiments are well thought out and the paper is well presented. The results suggesting a role for local plasticity in V1 will be of great interest to those researchers interested in neural circuit development as well as cortical 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. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

3. Reporting and misreporting of sex differences in the biological sciences

   This article has 2 authors:

   1. Yesenia Garcia-Sifuentes
   2. Donna L Maney

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript presents a descriptive audit on statistically treatment, reporting and interpretation of the effects of sex as a biological variable (SABV) on the studied outcomes in articles published across nine scholarly disciplines. The manuscript highlights and provides data on prevalence of several inconsistencies and inaccuracies in the literature regarding treatment of SABV as an important moderator of the effects of an intervention on a considered outcome and how such inconsistencies could lead to biased conclusions regarding the effects of SABV. As such, the manuscript may inform not only funding agencies and grant reviewers, but also researchers in most scientific disciplines regarding the importance of adhering to rigorous methodological standards when examining the effects of SABV.

     (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 names with the authors.)

   Reviewed by eLife

4. Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy

   This article has 10 authors:

   1. Lisa M Strong
   2. Chunmei Chang
   3. Julia F Riley
   4. C Alexander Boecker
   5. Thomas G Flower
   6. Cosmo Z Buffalo
   7. Xuefeng Ren
   8. Andrea KH Stavoe
   9. Erika LF Holzbaur
   10. James H Hurley

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper describes the crystal structure of two key components of the autophagy system, the PI3P-binding protein WIPI2d in complex with its interaction region in the hATG8 E3 ligase scaffold component ATG16L1. The paper provides interesting new data and demonstrates the requirements for association of WIPI2d with membranes. Functional studies in cells provide evidence that mutation of residues at the interface for ATG16L1 binding affects function, although additional studies would support loss of function versus a dominant negative effect.

     (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. Dorsal premammillary projection to periaqueductal gray controls escape vigor from innate and conditioned threats

   This article has 17 authors:

   1. Weisheng Wang
   2. Peter J Schuette
   3. Mimi Q La-Vu
   4. Anita Torossian
   5. Brooke C Tobias
   6. Marta Ceko
   7. Philip A Kragel
   8. Fernando MCV Reis
   9. Shiyu Ji
   10. Megha Sehgal
   11. Sandra Maesta-Pereira
   12. Meghmik Chakerian
   13. Alcino J Silva
   14. Newton S Canteras
   15. Tor Wager
   16. Jonathan C Kao
   17. Avishek Adhikari

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Wang et al. explores the relationship between the vigor of behavioral escape and cholecystokinin-expressing neurons in the premammillary nucleus of the hypothalamus that project to the periaqueductal gray. The experiments presented use a range of complementary approaches and techniques to perform a comprehensive examination of the circuitry underlying a particular aversively motivated behavior. However, a lack of clarity and specificity in how experiments and results are described, as well as a missed opportunity to relate this work to recent publications by many of the same authors, soften the conclusions that can be drawn from the manuscript in its current form.

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

   Reviewed by eLife

6. Modality-specific tracking of attention and sensory statistics in the human electrophysiological spectral exponent

   This article has 7 authors:

   1. Leonhard Waschke
   2. Thomas Donoghue
   3. Lorenz Fiedler
   4. Sydney Smith
   5. Douglas D Garrett
   6. Bradley Voytek
   7. Jonas Obleser

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript reports on two separate investigations. In the first, the authors provide novel evidence from two anaesthesia challenges that the slope of the 1/f structure of the power spectrum of the EEG fluctuates in a manner that tracks the presumed excitation : inhibition (E:I) balance of the tissue generating the EEG signal. Next they show that fluctuations in this slope also covary in systematic and modality- and stimulus-specific ways with behavioural performance on a multimodal attention task. These observations have potential foundational implications for how this previously unappreciated component of the EEG can be interpreted in terms of brain physiology and function. While the methodology employed is novel and interesting, the data as they stand, do not yet support the strong conclusions proposed by the authors.

     (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 names with the authors.)

   Reviewed by eLife

7. Individual history of winning and hierarchy landscape influence stress susceptibility in mice

   This article has 6 authors:

   1. Katherine B LeClair
   2. Kenny L Chan
   3. Manuella P Kaster
   4. Lyonna F Parise
   5. Charles Joseph Burnett
   6. Scott J Russo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This report by LeClair et al. shows the importance of considering social dominance rank and history of winning/losing rank to define susceptibility to stress in mice. It has many strengths, including an elegant experimental design, including experiments in both males and females, and carefully considering two models of social defeat in females, and an excellent writing and representation of the data.

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

   Reviewed by eLife

8. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons

   This article has 9 authors:

   1. Celia Biane
   2. Florian Rückerl
   3. Therese Abrahamsson
   4. Cécile Saint-Cloment
   5. Jean Mariani
   6. Ryuichi Shigemoto
   7. David A DiGregorio
   8. Rachel M Sherrard
   9. Laurence Cathala

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Using a range of cutting-edge techniques, the authors of this manuscript explore the functional consequences of developmental changes in dendritic morphology and synapse distribution in a GABAergic interneuron. The experiments are carefully performed and represent a thorough investigation of the structural and functional changes in synaptic inputs and postsynaptic dendritic branching patterns, an important topic for both developmental neurobiologists and synaptic physiologists. The data support most conclusions, but alternative interpretations remain possible and should be further considered.

     (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

9. End-of-life targeted degradation of DAF-2 insulin/IGF-1 receptor promotes longevity free from growth-related pathologies

   This article has 5 authors:

   1. Richard Venz
   2. Tina Pekec
   3. Iskra Katic
   4. Rafal Ciosk
   5. Collin Yvès Ewald

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper reports careful work using auxin-mediated degradation to manipulate the DAF-2 insulin/IGF-1 receptor in specific tissues and at different ages of the nematode C. elegans. Since its initial discovery as a gene that could dramatically alter lifespan in this organism, daf-2 has been extensively studied. The authors make excellent and thorough use of their novel reagents to successfully add important new findings to our understanding of this broadly conserved aging pathway, including a finer dissection of the spatial and temporal requirements for DAF-2 in multiple processes, such as the decision window for entering dauer arrest and that altering the levels of this protein very late in life can still have dramatic effects on lifespan. Overall the data are convincing, but the presentation and clarity of the text 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. Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

10. Sleep-dependent upscaled excitability, saturated neuroplasticity, and modulated cognition in the human brain

    This article has 6 authors:

    1. Mohammad Ali Salehinejad
    2. Elham Ghanavati
    3. Jörg Reinders
    4. Jan G Hengstler
    5. Min-Fang Kuo
    6. Michael A Nitsche

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      Sleep serves vital functions for the body and particularly the brain, and accordingly these functions are impaired by sleep deprivation, as has been repeatedly shown for different cognitive processes. However, the neural mechanisms of such effects of sleep loss are still poorly understood. This manuscript is of interest to both sleep researchers and cognitive neuroscientists looking for insights into the effects of sleep deprivation across a broad range of methods and measures. The reported studies comprehensively investigate cortical excitability and plasticity with non-invasive brain stimulation, as well as electrophysiological markers and behavior. The studies confirm and extend previous findings, stating that, in general, sleep deprivation results in higher cortical excitability as well as a negative impact on cognitive processes.

      (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