eLife

Latest preprint reviews

1. Connectome-Based Attractor Dynamics Underlie Brain Activity in Rest, Task, and Disease

   This article has 11 authors:

   1. Robert Englert
   2. Balint Kincses
   3. Raviteja Kotikalapudi
   4. Giuseppe Gallitto
   5. Jialin Li
   6. Kevin Hoffschlag
   7. Choong-Wan Woo
   8. Tor D Wager
   9. Dagmar Timmann
   10. Ulrike Bingel
   11. Tamas Spisak

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a useful approach for revealing large-scale brain attractor dynamics during resting states, task processing, and disease conditions using insights from Hopfield neural networks. The evidence supporting the findings is solid across the many datasets analysed. The work will be of broad interest to neuroscientists using neuroimaging data with interest in computational modelling of brain activity.

   Reviewed by eLife

2. On the discovered Cancer Driving Nucleotides (CDNs)–Distributions across genes, cancer types and patients

   This article has 16 authors:

   1. Lingjie Zhang
   2. Tong Deng
   3. Zhongqi Liufu
   4. Xiangnyu Chen
   5. Shijie Wu
   6. Xueyu Liu
   7. Changhao Shi
   8. Bingjie Chen
   9. Zheng Hu
   10. Qichun Cai
   11. Chenli Liu
   12. Mengfeng Li
   13. Miles E Tracy
   14. Xuemei Lu
   15. Chung-I Wu
   16. Haijun Wen

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study is a companion to a paper introducing a theoretical framework and methodology for identifying Cancer Driving Nucleotides (CDNs). The evidence that recurrent SNVs or CDNs are common in true cancer driver genes is convincing, with more limited evidence that many more undiscovered cancer driver mutations will have CDNs, and that this approach could identify these undiscovered driver genes with about 100,000 samples.

   Reviewed by eLife

3. Encoding of cerebellar dentate neuron activity during visual attention in rhesus macaques

   This article has 7 authors:

   1. Nico A. Flierman
   2. Sue Ann Koay
   3. Willem S. van Hoogstraten
   4. Tom J.H. Ruigrok
   5. Pieter R. Roelfsema
   6. Aleksandra Badura
   7. Chris I. De Zeeuw

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study examined neuronal activity in the dentate nucleus of the cerebellum when monkeys performed a difficult perceptual decision-making task. The authors provide convincing evidence that the cerebellum represents sensory, motor, and behavioral outcome signals that are sent to the attentional system, but further analysis focusing on the disparity of performance between animals would improve the quality of the paper. This paper is of great general interest in that it shows the involvement of the cerebellum in cognitive processes at the neuronal level.

   Reviewed by eLife

4. A bacterial regulatory uORF senses multiple classes of ribosome-targeting antibiotics

   This article has 2 authors:

   1. Gabriele Baniulyte
   2. Joseph T Wade

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     In this important study, Baniulyte and Wade provide solid evidence that translation of a short ORF denoted toiL positioned upstream of the topAI-yjhQP operon is responsive to different ribosome-targeting antibiotics, consequently controlling translation of the TopAI toxin as well as Rho-dependent transcription termination. Strengths of the study include combining a genetic screen to identify 23S rRNA mutations that affect topA1 expression and a creative approach to map the different locations of ribosome stalling within toiL induced by different antibiotics, with ribosome profiling and RNA structure probing by SHAPE to examine consequences of different antibiotics on toiL-mediated regulation. The work could be improved by examining the physiological consequences of topAI-yjhQP activation on antibiotic exposure and by resolving discrepancies between the SHAPE data and the translation rate of toiL.

   Reviewed by eLife

5. Septins function in exocytosis via physical interactions with the exocyst complex in fission yeast cytokinesis

   This article has 6 authors:

   1. Davinder Singh
   2. Yajun Liu
   3. Yi-Hua Zhu
   4. Sha Zhang
   5. Shelby Naegele
   6. Jian-Qiu Wu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     How secretion is regulated during cell division and how membrane trafficking factors cooperate with the cytoskeleton during cell division remain poorly understood. In this work the authors find potential direct interactions between the polymeric septin cytoskeleton and the exocyst complex, using fission yeast as a model organism. The work provides a valuable body of new information that will be of great interest to the cell biology community. The evidence is strong and rigorous in many places but is incomplete in other respects.

   Reviewed by eLife

6. Unraveling CRP/cAMP-Mediated Metabolic Regulation In Escherichia coli Persister Cells

   This article has 4 authors:

   1. Han G Ngo
   2. Sayed Golam Mohiuddin
   3. Aina Ananda
   4. Mehmet A Orman

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The study reports an important finding on the role of the global metabolic regulator Crp/cAMP in the formation of antibiotic persister Escherichia coli. The evidence supporting the claims is solid including metabolomic analysis and characterization of many mutant strains. However, batch culture-based methodologies are unreliable for studying the properties of persister cells that comprise only a fraction of the population and therefore leave the work incomplete.

   Reviewed by eLife

7. Lifestyles and their relative contribution to biological aging across multiple organ systems: change analysis from the China Multi-Ethnic Cohort Study

   This article has 12 authors:

   1. Yuan Zhang
   2. Dan Tang
   3. Ning Zhang
   4. Yi Xiang
   5. Yifan Hu
   6. Wen Qian
   7. Yangji Baima
   8. Xianbin Ding
   9. Ziyun Wang
   10. Jianzhong Yin
   11. Xiong Xiao
   12. Xing Zhao

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study examined the associations of a healthy lifestyle with comprehensive and organ-specific biological ages defined using common blood biomarkers and body measures. Its large sample size, longitudinal design, and robust statistical analysis provide solid support for the findings, which will be of interest to epidemiologists and clinicians.

   Reviewed by eLife

8. NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors

   This article has 7 authors:

   1. Connor M Hill
   2. Alexandra Indeglia
   3. Francis Picone
   4. Maureen E Murphy
   5. Cara Cipriano
   6. Robert G Maki
   7. Alessandro Gardini

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study provides compelling data regarding the molecular characterization of a rare tumor type with few treatment options. This fundamental work significantly advances our mechanistic understanding of solitary fibrous tumours, a critical first step towards targeted precision medicine approaches. The results of this study will be of broad interest to cancer biologists and experimental oncologists.

   Reviewed by eLife

9. DeePosit: an AI-based tool for detecting mouse urine and fecal depositions from thermal video clips of behavioral experiments

   This article has 4 authors:

   1. David Peles
   2. Shai Netser
   3. Natalie Ray
   4. Shlomo Wagner

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This manuscript presents a valuable machine-learning-based approach to the automated detection of urine and fecal deposits by rodents, key ethological behaviors that have traditionally been very poorly studied. The strength of evidence for their claim, however, that the method provides "easy, efficient, and unbiased spatiotemporal analysis of scent marking during behavioral experiments" is incomplete. In particular, there were concerns about the generalizability of the approach, the relatively limited detection capabilities of the method, and a lack of rationale for specific design choices. This manuscript could be of interest to researchers in animal behavior, neuroscience, and automated animal tracking.

   Reviewed by eLife

10. The theory of massively repeated evolution and full identifications of Cancer Driving Nucleotides (CDNs)

    This article has 11 authors:

    1. Lingjie Zhang
    2. Tong Deng
    3. Zhongqi Liufu
    4. Xueyu Liu
    5. Bingjie Chen
    6. Zheng Hu
    7. Chenli Liu
    8. Miles E Tracy
    9. Xuemei Lu
    10. Haijun Wen
    11. Chung-I Wu

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This important paper introduces a theoretical framework and methodology for identifying Cancer Driving Nucleotides (CDNs), primarily based on single nucleotide variant (SNV) frequencies. A variety of solid approaches indicate that a mutation recurring three or more times is more likely to reflect selection rather than being the consequence of a mutation hotspot. The method is rigorously quantitative, though the requirement for larger datasets to fully identify all CDNs remains a noted limitation. The work will be of broad interest to cancer geneticists and evolutionary biologists.

    Reviewed by eLife