eLife

Latest preprint reviews

1. The T cell receptor β chain repertoire of tumor infiltrating lymphocytes improves neoantigen prediction and prioritization

   This article has 18 authors:

   1. Thi Mong Quynh Pham
   2. Thanh Nhan Nguyen
   3. Bui Que Tran Nguyen
   4. Thi Phuong Diem Tran
   5. Nguyen My Diem Pham
   6. Hoang Thien Phuc Nguyen
   7. Thi Kim Cuong Ho
   8. Dinh Viet Linh Nguyen
   9. Huu Thinh Nguyen
   10. Duc Huy Tran
   11. Thanh Sang Tran
   12. Truong Vinh Ngoc Pham
   13. Minh Triet Le
   14. Thi Tuong Vy Nguyen
   15. Minh-Duy Phan
   16. Hoa Giang
   17. Hoai-Nghia Nguyen
   18. Le Son Tran

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The study presents a potentially valuable approach by combining two measurements (pHLA binding and pHLA-TCR binding) to improve predictions of which mutations in colorectal cancer are likely to be presented to and recognised by the immune system. While this approach is promising, the evidence supporting the primary claim remains somewhat incomplete. The experimental validation of the computational predictions with actual immune responses is still limited, despite the increase in sample size from 4 to 8 in this revision.

   Reviewed by eLife

2. Embedding stochastic dynamics of the environment in spontaneous activity by prediction-based plasticity

   This article has 2 authors:

   1. Toshitake Asabuki
   2. Claudia Clopath

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is an important study that investigates how neural networks can learn to stochastically replay presented sequences of activity according to learned transition probabilities. The authors use error-based excitatory plasticity to minimize the difference between internally predicted activity and stimulus-driven activity, and inhibitory plasticity to maintain E-I balance. The approach is solid but the choice of learning rules and parameters is not always always justified, with some unclear aspects to the formal derivation.

   Reviewed by eLife

3. GDF2 and BMP10 coordinate liver cellular crosstalk to maintain liver health

   This article has 13 authors:

   1. Dianyuan Zhao
   2. Ziwei Huang
   3. Xiaoyu Li
   4. Huan Wang
   5. Qingwei Hou
   6. Yuyao Wang
   7. Fang Yan
   8. Wenting Yang
   9. Di Liu
   10. Shaoqiong Yi
   11. Chunguang Han
   12. Yanan Hao
   13. Li Tang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study delineates the cellular contributions of BMP signaling in liver development and function. The findings are convincing, and the study employs state-of-the-art molecular, genetic, and cellular approaches to demonstrate that hepatic stellate cells play a central role in liver health by mediating cell-to-cell crosstalk via the production of specific BMP proteins. This study will be of interest to scientists interested in developmental biology and organ physiology.

   Reviewed by eLife

4. Hybrid immunity from severe acute respiratory syndrome coronavirus 2 infection and vaccination in Canadian adults: A cohort study

   This article has 22 authors:

   1. Patrick E Brown
   2. Sze Hang Fu
   3. Leslie Newcombe
   4. Xuyang Tang
   5. Nico Nagelkerke
   6. H Chaim Birnboim
   7. Aiyush Bansal
   8. Karen Colwill
   9. Geneviève Mailhot
   10. Melanie Delgado-Brand
   11. Tulunay Tursun
   12. Freda Qi
   13. Anne-Claude Gingras
   14. Arthur S Slutsky
   15. Maria D Pasic
   16. Jeffrey Companion
   17. Isaac I Bogoch
   18. Ed Morawski
   19. Teresa Lam
   20. Angus Reid
   21. Prabhat Jha
   22. Ab-C Study Collaborators

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study assessed antibody levels, which are indicative of protection, resulting from both COVID-19 vaccination and natural infection in a representative sample of the Canadian population. The work provides solid evidence that Individuals who received a booster vaccination and had a prior infection had the highest antibody levels, particularly when either the vaccination or natural infection had occurred within the past six months. These findings are of fundamental importance in supporting the value of booster vaccination in populations vulnerable to severe COVID-19.

   Reviewed by eLife

5. Obox4 promotes zygotic genome activation upon loss of Dux

   This article has 13 authors:

   1. Youjia Guo
   2. Tomohiro Kitano
   3. Kimiko Inoue
   4. Kensaku Murano
   5. Michiko Hirose
   6. Ten D Li
   7. Akihiko Sakashita
   8. Hirotsugu Ishizu
   9. Narumi Ogonuki
   10. Shogo Matoba
   11. Masayuki Sato
   12. Atsuo Ogura
   13. Haruhiko Siomi

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents an important finding that Obox4 and Dux act redundantly in regulating zygotic genome activation in mice. The evidence supporting the claims of the authors is solid. The work will be of interest to researchers interested in early embryo development and epigenetic reprogramming.

   Reviewed by eLife

6. Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank

   This article has 3 authors:

   1. Ardalan Naseri
   2. Degui Zhi
   3. Shaojie Zhang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study is of potential interest to readers in human genetics and quantitative genetics, as it presents a new method for homozygosity mapping in population-scale datasets, based on an innovative computational algorithm that efficiently identifies runs-of-homozygosity (ROH) segments shared by many individuals. Although the method is innovative and has the potential to be broadly useful, its power and limitations have not yet been adequately evaluated. The application of this new method to the UK Biobank dataset identifies several interesting associations, but it remains currently unclear under what conditions the new approach can provide additional power over existing genome-wide association study methods.

   Reviewed by eLife

7. Neuropilin-1 controls vascular permeability through juxtacrine regulation of endothelial adherens junctions

   This article has 5 authors:

   1. Sagnik Pal
   2. Yangyang Su
   3. Emmanuel Nwadozi
   4. Lena Claesson-Welsh
   5. Mark Richards

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study is focused on the question of how Nrp1 contributes to the regulation of vascular permeability and whether or why there are differences between different vascular beds. The scientific concept of this paper suggests a possible role of Nrp1 on perivascular cells as a participant in the regulation of vascular permeability. This concept is interesting and potentially useful. However, the methodology and quantitative analysis are currently inadequate to fully support the claims.

   Reviewed by eLife

8. The French flag problem revisited: Creating robust and tunable axial patterns without global signaling

   This article has 3 authors:

   1. Stephan Kremser
   2. Gabriel Vercelli
   3. Ulrich Gerland

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study uses cellular automata and evolution algorithms to offer an alternative to long-range signalling models of developmental patterning. The computational evidence that local rules suffice to produce a robust and global pattern is convincing. With some additional insights that connect the theoretical findings back to real biological examples, this work could be of interest to the broad community of developmental and systems biologists.

   Reviewed by eLife

9. In mice, discrete odors can selectively promote the neurogenesis of sensory neuron subtypes that they stimulate

   This article has 5 authors:

   1. Kawsar Hossain
   2. Madeline Smith
   3. Karlin E Rufenacht
   4. Rebecca O'Rourke
   5. Stephen W Santoro

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides valuable insights into the role of sensory stimulation in neurogenesis in the mammalian olfactory epithelium, where new olfactory sensory neurons are continually born throughout an animal's lifespan. The authors show that exposure to two different musk-related odors specifically increases the birth rates of those neurons that respond to these odors. This potentially results in adaptive changes in the subtype composition of the olfactory sensory neuron population. Solid evidence, well supported by control experiments, is presented to support these findings, though further work is needed to confirm that this phenomenon generalizes to olfactory sensory neurons expressing other types of odorant receptor and to explore the mechanisms underlying the stimulus specificity of neurogenesis.

   Reviewed by eLife

10. Cardiac afferent signals can facilitate visual dominance in binocular rivalry

    This article has 3 authors:

    1. John P Veillette
    2. Fan Gao
    3. Howard C Nusbaum

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This is a binocular rivalry study that uses ECG to present visual stimuli pulsing in line with cardiac events, to examine whether systole-entrained stimuli (i.e. presented during the period where the heart has contracted) are suppressed within visual awareness. Arguably out of line with this idea, the dominance durations were increased for systole-entrained stimuli. The manuscript addresses an important, precisely defined, and theoretically well-motivated question using sophisticated experimental and statistical methods. The interpretation of these results is not straightforward, however, such that they currently only provide incomplete support for the claims.

    Reviewed by eLife