eLife

Latest preprint reviews

1. Early stage NSCLS patients’ prognostic prediction with multi-information using transformer and graph neural network model

   This article has 7 authors:

   1. Jie Lian
   2. Jiajun Deng
   3. Edward S Hui
   4. Mohamad Koohi-Moghadam
   5. Yunlang She
   6. Chang Chen
   7. Varut Vardhanabhuti

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work presents a new model that leverages imaging and non-imaging data for the prediction of the survival of patients with early-stage NSCLC. The new model sought to demonstrate the roles of imaging and non-imaging features in determining high-risk nodes within the graph neural network, and the results have the potential of broad interest to clinicians within the field of cancer and have a high value towards clinical application.

     (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 reviewer remained anonymous to the authors.)

   Reviewed by eLife

2. Computational model of the full-length TSH receptor

   This article has 3 authors:

   1. Mihaly Mezei
   2. Rauf Latif
   3. Terry F Davies

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript presents the first molecular dynamics (MD) simulations of full-length membrane-bound Thyroid Stimulating Hormone Receptor (TSHR). The authors find that its linker region (LR) is disordered, contrasting previous models. While this is largely a solid study that would interest researchers working in computational modeling, thyroid hormone metabolism, and signaling, the rationale for the arbitrarily chosen starting model and unclear mechanistic relevance need to be clarified further.

     (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. Novel fast pathogen diagnosis method for severe pneumonia patients in the intensive care unit: randomized clinical trial

   This article has 17 authors:

   1. Yan Wang
   2. Xiaohui Liang
   3. Yuqian Jiang
   4. Danjiang Dong
   5. Cong Zhang
   6. Tianqiang Song
   7. Ming Chen
   8. Yong You
   9. Han Liu
   10. Min Ge
   11. Haibin Dai
   12. Fengchan Xi
   13. Wanqing Zhou
   14. Jian-Qun Chen
   15. Qiang Wang
   16. Qihan Chen
   17. Wenkui Yu

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is of broad interest to clinicians focused on improving sepsis outcomes. The method developed by the authors can identify 10 common pathogens with species-specificity in 4 hours, thus significantly reducing the turnaround time compared to conventional diagnostic methods. Using their method to identify sepsis-causing pathogens early to guide antibiotic treatment, the authors demonstrate high clinical sensitivity and specificity, and some clinical benefit in a real-world scenario.

     (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. Kiaa1024L/Minar2 is essential for hearing by regulating cholesterol distribution in hair bundles

   This article has 6 authors:

   1. Ge Gao
   2. Shuyu Guo
   3. Quan Zhang
   4. Hefei Zhang
   5. Cuizhen Zhang
   6. Gang Peng

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Mutations in MINAR2 causes deafness in human and mice. Loss of function of Minar2 in mice causes a reduction of stereocilia and subsequent hair cell degeneration but the underlying mechanism is unclear. This zebrafish study demonstrated that the Minar2 protein interacts with cholesterol and is localized to the stereocilia of hair cells. The loss of Minar2 reduces cholesterol enrichment in the stereocilia with concomitant accumulation in lysosomes. Thus, this study provides the mechanistic insight of Minar2 and the first glimpse at the importance of cholesterol homeostasis in hair cell function.

     (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

5. Hepatic lipid overload triggers biliary epithelial cell activation via E2Fs

   This article has 10 authors:

   1. Ece Yildiz
   2. Gaby El Alam
   3. Alessia Perino
   4. Antoine Jalil
   5. Pierre-Damien Denechaud
   6. Katharina Huber
   7. Lluis Fajas
   8. Johan Auwerx
   9. Giovanni Sorrentino
   10. Kristina Schoonjans

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study reports that a high-fat diet induces biliary epithelial cell proliferation and suggests this may account for the so-called ductular reaction in advanced fatty liver disease. Convincing data support the finding that the transcription factor E2F1 is required for biliary epithelial cell proliferation in mice fed with a high-fat diet, and organoid models indicate that lipid abundance promotes glycolysis in an E2F-dependent manner. These findings are potentially of broad interest to the field of liver biology and disease.

   Reviewed by eLife

6. Maternal obesity blunts antimicrobial responses in fetal monocytes

   This article has 7 authors:

   1. Suhas Sureshchandra
   2. Brianna M Doratt
   3. Norma Mendza
   4. Oleg Varlamov
   5. Monica Rincon
   6. Nicole E Marshall
   7. Ilhem Messaoudi

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This is an important manuscript that will be of interest to a broad range of researchers studying immunology, obesity and metabolism, as well as the links between maternal health and pathophysiological responses in the offspring. The comprehensive studies using RNA-seq, scRNA-seq, ATAC-seq and scATAC-seq in human umbilical cord monocytes represent an important resource for understanding the transcriptomic and epigenetic shifts in the monocytes of newborns. The experiments involving stimulation of monocytes with pathogens offer convincing evidence for the dysfunction of monocytes in the newborn.

   Reviewed by eLife

7. Invigorating human MSCs for transplantation therapy via Nrf2/DKK1 co-stimulation in a mice acute-on-chronic liver failure model

   This article has 16 authors:

   1. Feng Chen
   2. Zhaodi Che
   3. Yingxia Liu
   4. Pingping Luo
   5. Lu Xiao
   6. Yali Song
   7. Cunchuan Wang
   8. Zhiyong Dong
   9. Mianhuan Li
   10. George L. Tipoe
   11. Dongqing Wu
   12. Min Yang
   13. Yi Lv
   14. Fei Wang
   15. Hua Wang
   16. Jia Xiao

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Chen et al. demonstrate a pro-survival role of the NRF2/DKK1 axis in mesenchymal stem cells. Furthermore, the authors provide evidence that targeting this pathway can enhance survival in response to liver failure in vivo. These data highlight a novel signaling pathway to enhance efficacy of MSCs in promoting regeneration.

     (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. Dissecting the phase separation and oligomerization activities of the carboxysome positioning protein McdB

   This article has 6 authors:

   1. Joseph L Basalla
   2. Claudia A Mak
   3. Jordan A Byrne
   4. Maria Ghalmi
   5. Y Hoang
   6. Anthony G Vecchiarelli

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Carboxysomes enable the efficient fixation of carbon dioxide in specific bacteria. Phase separation has been invoked as a mechanism that drives the formation of carboxysomes. The current work focuses on the biophysical principles of how one of two essential specific protein components enable spatial regulation over carboxysomes. This important work highlights the connection between oligomerization via specific molecular interactions and phase separation. The work is of interest to the areas of biochemistry and carbon dioxide fixation as well as phase separation.

     (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 Arcadia Science, eLife

9. Single-cell transcriptomics identifies Keap1-Nrf2 regulated collective invasion in a Drosophila tumor model

   This article has 6 authors:

   1. Deeptiman Chatterjee
   2. Caique Almeida Machado Costa
   3. Xian-Feng Wang
   4. Allison Jevitt
   5. Yi-Chun Huang
   6. Wu-Min Deng

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Drosophila ovarian follicle cells have been utilized as a model system to study organogenesis and epithelial tumorigenesis. The analysis of single-cell transcriptomes of follicle cells now shows that transcriptionally distinct cell populations emerge shortly after induction of loss of polarity. Strengths of the work include the use of advanced single cell omics and imaging analyses to identify cell types and factors playing a role the disruption of polarity and the implications of this work for epithelial cancers. The authors' claims are generally well supported by the data and analyses. Weaknesses include the lack of high magnification images and need to clarify motivation for the study and highlight the biology rather than technical advances in the results section. Overall, this work is viewed as an important contribution to cell biologists who work on the epithelial morphogenesis or tumorigenesis.

     (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, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

10. Discrete GPCR-triggered endocytic modes enable β-arrestins to flexibly regulate cell signaling

    This article has 3 authors:

    1. Benjamin Barsi-Rhyne
    2. Aashish Manglik
    3. Mark von Zastrow

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This manuscript addresses G protein-coupled receptor signaling and proposes an additional site on Beta-arrestin2 (arrestin 3) as being responsible, in significant part, for the downregulation and likely onward signalling from endosomes of a range of GPCRs. The cell biology appears to be thoroughly carried out and data presented in a statistically appropriate manner. With some textual changes and minor experimental clarification of the route taken and molecules involved, this work will be of broad interest.

      (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