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  1. The oneirogen hypothesis: modeling the hallucinatory effects of classical psychedelics in terms of replay-dependent plasticity mechanisms

    This article has 4 authors:
    1. Colin Bredenberg
    2. Fabrice Normandin
    3. Blake Richards
    4. Guillaume Lajoie
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This paper provides a useful new theory of the hallucinatory effects of psychedelics. The authors present convincing evidence that a computational model trained with the Wake-Sleep algorithm can reproduce some features of hallucinations by varying the strength of top-down connections in the model, but discussion of the model's relationships to the psychedelics and sleep literatures is incomplete. The work will be of interest to researchers studying hallucinations or offline activity and learning more broadly.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  2. Trial-level Representational Similarity Analysis

    This article has 7 authors:
    1. Shenyang Huang
    2. Cortney M Howard
    3. Paul C Bogdan
    4. Ricardo Morales-Torres
    5. Matthew Slayton
    6. Roberto Cabeza
    7. Simon W Davis
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study proposes a potentially useful improvement on a popular fMRI method for quantifying representational similarity in brain measurements by focusing on representational strength at the single trial level and adding linear mixed effects modeling for group-level inference. The manuscript demonstrates increased sensitivity with no loss of precision compared to more classic versions of the method. However, the framing of the work with respect to these prior approaches is incomplete, several assumptions are insufficiently motivated, and it is unclear to what extent the approach would generalize to other paradigms.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  3. Neuroanatomical foundations of social tolerance across macaque species

    This article has 6 authors:
    1. S. Silvère
    2. J. Lamy
    3. C. Po
    4. M. Legrand
    5. J. Sallet
    6. S. Ballesta
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    • Curated by eLife

      eLife Assessment

      This important work compares the size of two brain areas, the amygdala and the hippocampus, across 12 species belonging to the Macaca genus. The authors find, using a convincing methodological approach, that amygdala - but not hippocampal - volume varies with social tolerance grade, with high tolerance species showing larger amygdala than low tolerance species of macaques. Interestingly, their findings also suggest an inverted developmental effect, with intolerant species showing an increase in amygdala volume across the lifespan, compared to tolerant species exhibiting the opposite trend. Overall, this paper offers new insights into the neural basis of social and emotional processing.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  4. Coordinated spinal locomotor network dynamics emerge from cell-type-specific connectivity patterns

    This article has 4 authors:
    1. F David Wandler
    2. Benjamin K Lemberger
    3. David L McLean
    4. James M Murray
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    • Curated by eLife

      eLife Assessment

      In this valuable study, Wandler et al. provide convincing theoretical evidence for alternate mechanisms of rhythm generation by CPGs. Their model shows that cell-type-specific connectivity and a dominant inhibitory drive could underlie rhythm generation. Excitatory input could act to enhance the frequency range of these rhythms. This modeling study could motivate further experimental investigation of these mechanisms to understand CPG rhythmogenesis.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  5. A whole-animal phenotypic drug screen identifies suppressors of atherogenic lipoproteins

    This article has 12 authors:
    1. Daniel J Kelpsch
    2. Liyun Zhang
    3. James H Thierer
    4. Kobe Koren
    5. Urmi Kumar
    6. Yuki Lin
    7. Monica R Hensley
    8. Mira Sohn
    9. Jun O Liu
    10. Thomas Lectka
    11. Jeff S Mumm
    12. Steven A Farber
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    • Curated by eLife

      eLife Assessment

      In this important study, the authors have performed a zebrafish drug screen to identify suppressors of atherogenic lipoproteins. They utilize a well-established LipoGlo assay to find molecules that modulate these lipoproteins, identifying 49 potential hits. They perform some validation experiments, including studies linking enoxolone to its likely inhibitory effect on a specific transcription factor, HNF4alpha. Overall, the results are convincing and robust, and will open up new areas of exploration for those investigators interested in in vivo lipid biology.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  6. Distal Gene Expression Governed by Lamins and Nesprins via Chromatin Conformation Change

    This article has 4 authors:
    1. Haihui Zhang
    2. Zhengyang Lei
    3. Fatemeh Momen-Heravi
    4. Peiwu Qin
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    • Curated by eLife

      eLife Assessment

      This study provides useful information on the impact of Lamin A/C knockdown on gene expression using RNA-Seq analysis. In addition, the impact of Lamin A/C knockdown on telomere dynamics is explored using live cell imaging. The conclusions, however, are inadequately supported by the data presented. Weaknesses include excessive reliance on gene ontology analysis without further validation of direct versus indirect effects, use of only one shRNA, which may have off target effects, validation of knockdown only from gene expression rather than protein levels, lack of discussion on previous studies showing the presence of Lamin A/C in the nuclear interior among others.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  7. The Structural Dynamics of IRE1 and its Interaction with Unfolded Peptides

    This article has 3 authors:
    1. Elena Spinetti
    2. G Elif Karagöz
    3. Roberto Covino
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    • Curated by eLife

      eLife Assessment

      In this important study, the authors conducted atomistic molecular dynamics simulations to probe the interactions between IRE and unfolded peptides. The results help reconcile contradicting experimental findings in the literature and offer mechanistic insights into the activation of the unfolded protein response. The level of evidence is considered solid, although the use of enhanced sampling and more quantitative analysis would further strengthen the conclusions.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  8. The influence of heavy metal stress on the evolutionary transition of teosinte to maize

    This article has 3 authors:
    1. Jonathan Acosta-Bayona
    2. Miguel Vallebueno-Estrada
    3. Jean-Philippe Vielle-Calzada
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents a valuable investigation into how heavy metal stress may have influenced the domestication of maize from its wild ancestor, teosinte parviglumis, focusing on specific ATPase genes with proposed roles in heavy metal homeostasis. The evidence supporting the main claims is incomplete, with suggestive but not definitive data linking gene function to domestication traits, and limited environmental context for the hypothesized selection pressures. While the work introduces an interesting model connecting environmental stress responses to evolutionary transitions and highlights underexplored aspects of teosinte plasticity, the conclusions would benefit from more comprehensive analyses such as transcriptomics, a broader survey of loci, and stronger paleoenvironmental validation. The study will be of interest to researchers in plant evolution and domestication, but currently lacks the analytical depth to fully support its central hypothesis.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  9. Assessing plant phenological changes based on drivers of spring phenology

    This article has 7 authors:
    1. Yong Jiang
    2. Stephen J Mayor
    3. Xiuli Chu
    4. Xiaoqi Ye
    5. Rongzhou Man
    6. Jing Tao
    7. Qing-Lai Dang
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study introduces a novel and broadly applicable metric-phenological lag-to partition the effects of spring warming from other abiotic constraints on plant phenology. While the dataset is extensive and the analytical framework is valuable conceptually, the manuscript lacks clarity in its aims and justification for the new metric, and key results are underdeveloped or poorly visualized. The strength of evidence is moderate to solid, but revisions are needed to clarify the study's contribution and improve interpretability.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  10. Calibration and validation strategy for electromechanical cardiac digital twins

    This article has 7 authors:
    1. Zhinuo Jenny Wang
    2. Maxx Holmes
    3. Ruben Doste
    4. Julia Camps
    5. Francesca Margara
    6. Mariano Vazquez
    7. Blanca Rodriguez
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This is a potentially important study that explores the relevant range of parameter values for calibration and validation of cardiac electromechanics in ventricular models. Although much of the work presented is solid, the evidence provided to support the authors' key scientific claims is incomplete, especially as it relates to the emphasis on standardized validation and verification approaches. Notably, the level of model personalization presented in this work falls short of the threshold for what could reasonably be called a "digital twin", even by the relatively relaxed standards that have emerged in computational physiology and related fields in recent years.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  11. A neuromorphic model of active vision shows how spatiotemporal encoding in lobula neurons can aid pattern recognition in bees

    This article has 6 authors:
    1. HaDi MaBouDi
    2. Mark Roper
    3. Marie-Genevieve Guiraud
    4. Mikko Juusola
    5. Lars Chittka
    6. James A.R. Marshall
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      Inspired by bee's visual behavior, the goal of the manuscript is to develop a model of visual scanning, visual processing and learning to recognize visual patterns. In this model, pre-training with natural images leads to the formation of spatiotemporal receptive fields that can support associative learning. Due to an incomplete test of the necessity and sufficiency of the features included in the model, it cannot be concluded that the model is either the "minimal circuit" or the most biologically plausible circuit of this system. With a more in-depth analysis, the work has the potential of being important and very valuable to both experimental and computational neurobiologists.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  12. The oocyte zinc transporter Slc39a10/Zip10 is a regulator of zinc sparks during fertilization in mice

    This article has 12 authors:
    1. Atsuko Kageyama
    2. Narumi Ogonuki
    3. Takuya Wakai
    4. Takafumi Namiki
    5. Yui Kawata
    6. Manabu Ozawa
    7. Yasuhiro Yamada
    8. Toshiyuki Fukada
    9. Atsuo Ogura
    10. Rafael A Fissore
    11. Naomi Kashiwazaki
    12. Junya Ito
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents significant and novel insights into the roles of zinc in mammalian meiosis/fertilization events. These findings are useful to our understanding of these processes. The evidence presented is solid, with experiments being well-designed, carefully described, and interpreted with appropriate rigor.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  13. Occupancy of the HbYX hydrophobic pocket is sufficient to induce gate opening in the archaeal 20S proteasomes

    This article has 3 authors:
    1. Janelle JY Chuah
    2. Madalena R Daugherty
    3. David M Smith
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This useful manuscript describes cryo-EM structures of archaeal proteasomes that reveal insights into how occupancy of binding pockets on the 20S protease regulates proteasome gating. The evidence supporting these claims is convincing, although inclusion of more quantitative comparisons would help strengthen the conclusions. This work will be of special interest to researchers interested in proteasome structure and regulation.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  14. The integration mechanism of the four positional cues—anterior, posterior, dorsal, and ventral—in axolotl limb regeneration

    This article has 5 authors:
    1. Sakiya Yamamoto
    2. Saya Furukawa
    3. Ayaka Ohashi
    4. Mayuko Hamada
    5. Akira Satoh
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    • Curated by eLife

      eLife Assessment

      This fundamental work by Yamamoto and colleagues advances our understanding of how positional information is coordinated between axes during limb outgrowth and patterning. They provide solid evidence that the dorsal-ventral axis feeds into anterior-posterior signaling, and identify the responsible molecules by combining transplantations with molecular manipulations. This work will be of broad interest to regeneration, tissue engineering, and evolutionary biologists.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  15. Linage priming and cell type proportioning depends on the interplay between stochastic and deterministic factors

    This article has 7 authors:
    1. William M Salvidge
    2. Chris Brimson
    3. Nicole Gruenheit
    4. Li-Yao Huang
    5. Catherine J Pears
    6. Jason B Wolf
    7. Christopher RL Thompson
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study investigates how stochastic and deterministic factors are integrated during cellular decision-making, particularly in situations where cells differentiate into distinct fates despite being exposed to the same environmental conditions. The authors present convincing evidence that gene expression variability contributes to the robustness of cell fate decisions in D. discoideum, which sheds light into the role of stochasticity during cell differentiation.

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    This article has 2 evaluationsAppears in 1 listLatest version Latest activity
  16. Uev1A counteracts oncogenic Ras stimuli in both polyploid and diploid cells

    This article has 13 authors:
    1. Qi Zhang
    2. Yunfeng Wang
    3. Xueli Fu
    4. Ziguang Wang
    5. Yang Zhang
    6. Lizhong Yan
    7. Yuejia Wang
    8. Muhan Yang
    9. Dongze Song
    10. Ruixing Zhang
    11. Hongru Zhang
    12. Shian Wu
    13. Shaowei Zhao
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study examines the role of E2 ubiquitin enzyme, Uev1a in tissue resistance to oncogenic RasV12 in Drosophila melanogaster polyploid germline cells and human cancer cell lines. The incomplete evidence suggests that Uev1a works with the E3 ligase APC/C to degrade Cyclin A, and the strength of evidence could be increased by addressing the expression of CycA in the ovaries and the uev1a loss of function in human cancer cells. This work would be of interest to researchers in germline biology and cancer.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  17. Structure of an oxygen-induced tubular nanocompartment in Pyrococcus furiosus

    This article has 11 authors:
    1. Wenfei Song
    2. Jan Fiala
    3. Ioannis Skalidis
    4. Pascal Albanese
    5. Constantinos Patinios
    6. Marten L Chaillet
    7. Servé WM Kengen
    8. Richard A Scheltema
    9. Stuart C Howes
    10. Albert JR Heck
    11. Friedrich Förster
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      Using advanced CryoEM and mass spectrometry, the authors provide compelling evidence of how tubule formation occurs in an oxygen-dependent manner. These fundamental findings offer a novel mechanism by which rubrerythrin tubules encapsulate encapsulin to prevent oxidative stress in Pyrococcus furiosus. However, there are a few reasonable concerns about biochemical validations and the lack of adequate description of results and methodology.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  18. The denitrosylase SCoR2 controls cardioprotective metabolic reprogramming

    This article has 12 authors:
    1. Zachary W Grimmett
    2. Rongli Zhang
    3. Hua-Lin Zhou
    4. Qiuying Chen
    5. Dawson Miller
    6. Zhaoxia Qian
    7. Justin Lin
    8. Riti Kalra
    9. Steven S Gross
    10. Walter J Koch
    11. Richard T Premont
    12. Jonathan S Stamler
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents compelling evidence that the denitrosylase SCoR2 regulates cardioprotective metabolic reprogramming in the heart following ischemia/reperfusion injury. The findings are supported by a novel multi-omics approach and the integration of mouse and human data, which provides valuable insights into S-nitrosylation and cardiac metabolism. However, some conclusions remain limited by unresolved methodological issues that warrant clarification.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  19. SVEP1 enables efficient binding of Angiopoietin-2 to the TIE1 receptor, allowing receptor phosphorylation and downstream signaling

    This article has 9 authors:
    1. Katharina Uphoff
    2. Melina HuĂźmann
    3. Dörte Schulte-Ostermann
    4. Yvonne Huisman
    5. Matthias Mörgelin
    6. Fabian Metzen
    7. J Fernando Bazan
    8. Manuel Koch
    9. Stefan Schulte-Merker
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This manuscript focuses on developing a structural model of how the multidomain ECM protein SVEP1 enables Angiopoietin (ANG) binding to the orphan receptor TIE1, resulting in downstream receptor phosphorylation and signaling. This is a potentially important study, however, it currently lacks key controls and is therefore incomplete. The data will be of interest to scientists working in vascular biology and RTK signaling.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  20. High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains

    This article has 13 authors:
    1. Caroline Kikawa
    2. Andrea N Loes
    3. John Huddleston
    4. Marlin D Figgins
    5. Philippa Steinberg
    6. Tachianna Griffiths
    7. Elizabeth M Drapeau
    8. Heidi Peck
    9. Ian G Barr
    10. Janet A Englund
    11. Scott E Hensley
    12. Trevor Bedford
    13. Jesse D Bloom
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study advances our understanding of population-level immune responses to influenza in both children and adults. The strength of the evidence supporting the conclusions is compelling, with high-throughput profiling assays and mathematical modeling. The work will be of interest to immunologists, virologists, vaccine developers, and those working on mathematical modeling of infectious diseases.

    Reviewed by eLife

    This article has 5 evaluationsAppears in 1 listLatest version Latest activity