eLife

Latest preprint reviews

1. A visual sense of number emerges from divisive normalization in a simple center-surround convolutional network

   This article has 2 authors:

   1. Joonkoo Park
   2. David E Huber

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The current manuscript presents a computational model of numerosity estimation. The model relies on center-surround contrast filters at different spatial scales with divisive normalization between their responses. Using dot arrays as visual stimuli, it is shown that the summed normalized responses of the filters are sensitive to numerosity and insensitive to the low-level visual features of dot size and spacing. Importantly, the model provides an explanation of various spatial and temporal illusions in visual numerosity perception.

     (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

2. Activation mechanism of small heat shock protein HSPB5 revealed by disease-associated mutants

   This article has 9 authors:

   1. Christopher N. Woods
   2. Maria K. Janowska
   3. Lindsey D. Ulmer
   4. Jasleen Kaur Sidhu
   5. Natalie L. Stone
   6. Ellie I. James
   7. Miklos Guttman
   8. Matthew F. Bush
   9. Rachel E. Klevit

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The human small heat shock protein (sHSP) HSPB5 is an ATP-independent molecular chaperone involved in maintaining protein homeostasis. This manuscript reports on dynamic interactions between the disordered N-terminal region (NTR) and the structured alpha-crystallin domain (ACD) in HSPB5 oligomers. The authors show that two mutations, associated with early cataract and myopathy development, disrupt the interaction of the ACD core with the unfolded NTRs and generate a much more dynamic and hyperactive version of the chaperone. These findings will be of interest to colleagues studying molecular chaperones and their implications for disease in humans.

     (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. Machine learning-assisted fluoroscopy of bladder function in awake mice

   This article has 5 authors:

   1. Helene De Bruyn
   2. Nikky Corthout
   3. Sebastian Munck
   4. Wouter Everaerts
   5. Thomas Voets

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript is of broad interest to researchers working in the area of lower urinary tract dysfunction. It describes a novel method to reliably study bladder function; the approach allows for monitoring bladder filling and emptying in freely moving, non-anaesthetized animals without the need for catheter implantation. This work has optimized a machine learning algorithm for defining the outline of the urinary bladder border from fluoroscopic images of mice that received subcutaneous injections of iodinated radiocontrast media. The advantage is that with images taken at 30 images/second and with monitoring bladder dynamics requiring hours-long observation periods, this very large number of generated images no longer requires manual analysis.

     (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

4. Multivalency, autoinhibition, and protein disorder in the regulation of interactions of dynein intermediate chain with dynactin and the nuclear distribution protein

   This article has 8 authors:

   1. Kayla A Jara
   2. Nikolaus M Loening
   3. Patrick N Reardon
   4. Zhen Yu
   5. Prajna Woonnimani
   6. Coban Brooks
   7. Cat H Vesely
   8. Elisar J Barbar

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The identification of an autoinhibitory mechanism of the dynein intermediate chain provides an important contribution to our understanding of dynein assembly and illustrates the plethora of regulatory mechanisms attainable by intrinsically disordered proteins. This paper provides insight into the autoinhibited inactive state of dynein as well as the activation mechanism. A wide range of biophysical approaches is used, providing a very nice example of how these diverse technologies can be applied in concert and in a synergistic manner to study an important question in the realm of "unstructured biology".

     (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. Efficient decision-makers evaluate relative reward per effort

   This article has 1 author:

   1. Jan Kubanek

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The paper describes an interesting, but very abstract extension of normative choice theories. By linking economic and foraging theory, the paper would potentially be of interest to a broad audience in behavioral economics and neuroscience. However, the results in their current form have several important limitations: the lack of a significant validation, such as an account for well-known behavioral or neural effects that would not be explained by alternative theories, a quantitative performance comparison between the proposed EDM and other models in realistic behavioral situations, and a specific link between the actual processes and limitations of real brains and the EDM.

     (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

6. Predicting mechanisms of action at genetic loci associated with discordant effects on type 2 diabetes and abdominal fat accumulation

   This article has 4 authors:

   1. Yonathan Tamrat Aberra
   2. Lijiang Ma
   3. Johan LM Björkegren
   4. Mete Civelek

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study reports candidate causal genes in genome-wide association studies that exhibit a discordant pattern of association, namely a higher waist-hip ratio simultaneously with a lowered risk of type 2 diabetes. Identification of such genes could provide insights into why some individuals with obesity are not developing type 2 diabetes, knowledge that ultimately could shed light on the complex interplay between fat distribution and type 2 diabetes. The work is of relevance to the fields of genetics of diabetes and obesity.

     (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

7. Notch signaling functions in noncanonical juxtacrine manner in platelets to amplify thrombogenicity

   This article has 6 authors:

   1. Susheel N Chaurasia
   2. Mohammad Ekhlak
   3. Geeta Kushwaha
   4. Vipin Singh
   5. Ram L Mallick
   6. Debabrata Dash

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Advances in the discovery of novel anti-platelet therapeutics remains an unmet need. This manuscript by Chaurasia et al. describes a novel signaling pathway involving Notch1 and its ligand, Delta-like ligand-4 (DLL4) in driving platelet activation and thrombus formation. The authors provide convincing mechanistic studies to show that blockade of this pathway may serve as a new therapeutic approach to prevent/treat thrombosis. The work will be of great interest to individuals in the hematology and thrombosis field.

     (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

8. Recovering mixtures of fast-diffusing states from short single-particle trajectories

   This article has 4 authors:

   1. Alec Heckert
   2. Liza Dahal
   3. Robert Tjian
   4. Xavier Darzacq

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors describe new approaches to improve the analysis of single-molecule tracking data to uncover multiple diffusive states of proteins in living cells. This paper will be of interest to researches from the fields of experimental biology, who are interested in tracking of proteins using microscopy, as well as computational scientists who are interested in devising novel methodologies for analysis of multiple-particle tracking data. The paper presents two advanced techniques for estimation of motion parameters (such as diffusion coefficients) and contains rigorous evaluation using simulated and real biological 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 #3 agreed to share their name with the authors.)

   Reviewed by eLife

9. Single-cell RNA sequencing analysis of shrimp immune cells identifies macrophage-like phagocytes

   This article has 8 authors:

   1. Peng Yang
   2. Yaohui Chen
   3. Zhiqi Huang
   4. Huidan Xia
   5. Ling Cheng
   6. Hao Wu
   7. Yueling Zhang
   8. Fan Wang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The shrimp market is growing globally, with 8.12 tons produced in 2020. The market size is thought to reach $55 billion by 2027. Most of the market comes from farms, the white shrimp, Penaeus vannamei, being one of the most commonly farmed species worldwide. The present study provides a single cell transcriptional atlas of the white shrimp, P. vannamei, immune cells in the hemolymph, known as hemocytes. White shrimp single cell RNA sequencing studies uncovered two macrophage-like populations, one of them with markers similar to mammalian macrophages. These findings redefine the current classification of shrimp immune cells which has been done using morphological approaches and via targeted qPCR studies but never using single cell transcriptomics.

     (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. PLK4 drives centriole amplification and apical surface area expansion in multiciliated cells

    This article has 6 authors:

    1. Gina M LoMastro
    2. Chelsea G Drown
    3. Aubrey L Maryniak
    4. Cayla E Jewett
    5. Margaret A Strong
    6. Andrew Jon Holland

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      PLK4 is the master regulator of centriole biogenesis, but whether it is also key for centriole amplification during differentiation of multiciliated cells (MCCs) has been questioned based on PLK4 chemical inhibition. Here, using mouse models engineered to lack PLK4 or PLK4 activity, LoMastro et al provide very compelling evidence that PLK4 and its activity are essential for centriole amplification in MCCs. Moreover, they show that centriole amplification in MCCs drives expansion of their apical surface. The findings will be of interest to cell biologists and experts interested in multi-ciliogenesis-related pathologies.

      (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