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  1. The population structure of invasive Lantana camara is shaped by its mating system

    This article has 3 authors:
    1. P. Praveen
    2. Rajesh Gopal
    3. Uma Ramakrishnan
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      The submission by Gopal and colleagues reports important findings describing the structure of genetic and colour variation in its native range for the globally invasive weed Lantana camara. Whilst the importance of the research question and the scale of the sampling is appreciated, the analysis, which is currently incomplete, requires further tests to support the claims made by the authors.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  2. Neocortical Layer-5 tLTD Relies on Non-Ionotropic Presynaptic NMDA Receptor Signaling

    This article has 5 authors:
    1. Aurore Thomazeau
    2. Sabine Rannio
    3. Jennifer A. Brock
    4. Hovy Ho-Wai Wong
    5. P. Jesper Sjöström
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      eLife assessment

      Using an elegant and thorough experimental design, Thomazeau et al show that, in the developing mouse visual cortex, presynaptic NMDA receptors at layer 5 neocortical synapses mediate spike-timing dependent LTD via JNK2, non-ionotropic signaling. These fundamental findings shed light on how NMDA receptors can tune synaptic function without acting as coincidence detectors. The experiments are supported by compelling evidence, gathered through optogenetics and quadruple patch clamp recordings from cortical slices.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  3. Master control genes in the regeneration of rod photoreceptors from endogenous progenitor cells in zebrafish retina

    This article has 9 authors:
    1. Eyad Shihabeddin
    2. Abirami Santhanam
    3. Stephan Tetenborg
    4. Alexandra L. Aronowitz
    5. Haichao Wei
    6. Guoting Qin
    7. Chengzhi Cai
    8. Jiaqian Wu
    9. John O’Brien
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    • Curated by eLife

      eLife Assessment

      Shihabeddin et al utilized single-cell RNA-Seq analysis of adult P23H zebrafish animals to identify transcription factors (e2fs, Prdm1a, Sp1) expressed selectively in neural progenitors and immature rods, and validated their necessity for regeneration using morphant analysis. The finding is useful, and the evidence is convincing. The deeper mechanistic analysis could further strengthen the current work by (1) distinguishing developmental vs regenerative transcriptional factors, (2) the addition of matched scATAC-Seq data, and (3) integration with single-cell multiome data from developing retina.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  4. Gender–specific Single Transcript Level Atlas of Vasopressin and its Receptor (AVPR1a) in the Mouse Brain

    This article has 18 authors:
    1. Anisa Gumerova
    2. Georgii Pevnev
    3. Funda Korkmaz
    4. Uliana Cheliadinova
    5. Guzel Burganova
    6. Darya Vasilyeva
    7. Liam Cullen
    8. Orly Barak
    9. Farhath Sultana
    10. Weibin Zhou
    11. Steven Sims
    12. Victoria Laurencin
    13. Tal Frolinger
    14. Se-Min Kim
    15. Ki A. Goosens
    16. Tony Yuen
    17. Mone Zaidi
    18. Vitaly Ryu
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    • Curated by eLife

      eLife Assessment

      This work presents an atlas of vasopressin (AVP) and its receptor AVPR1a in mouse brains using RNAscope to map single transcript expressions of Avp and Avpr1a across various brain regions in males and females. The findings are valuable in that they identify brain regions expressing Avpr1a mRNA transcript. The impact of findings is decreased by incomplete or inadequate analysis of the data due to limited description of Avpr1a mRNA distribution within brain regions and limited statistical inference.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  5. Separable Dorsal Raphe Dopamine Projections mediate the Facets of Loneliness-like state

    This article has 20 authors:
    1. Christopher R. Lee
    2. Gillian A. Matthews
    3. Mackenzie E. Lemieux
    4. Elizabeth M. Wasserlein
    5. Matilde Borio
    6. Raymundo L. Miranda
    7. Laurel R. Keyes
    8. Gates P. Schneider
    9. Caroline Jia
    10. Andrea Tran
    11. Faith Aloboudi
    12. May G. Chan
    13. Enzo Peroni
    14. Grace S. Pereira
    15. Alba LĂłpez-Moraga
    16. Anna Pallé
    17. Eyal Y. Kimchi
    18. Nancy Padilla-Coreano
    19. Romy Wichmann
    20. Kay M. Tye
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    • Curated by eLife

      eLife Assessment

      This study dissects the function of 3 outputs of a specific population of modulatory neurons, dorsal raphe dopamine neurons, in social and affective behavior. It provides valuable information that both confirms prior results and provides new insights. The strength of the evidence is convincing, based on cutting-edge approaches and analysis. This study will be of interest to behavioral and systems neuroscientists, especially those interested in social and emotional behavior.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  6. Top-down feedback matters: Functional impact of brainlike connectivity motifs on audiovisual integration

    This article has 4 authors:
    1. Mashbayar Tugsbayar
    2. Mingze Li
    3. Eilif B. Muller
    4. Blake Richards
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    • Curated by eLife

      eLife Assessment

      This valuable study investigates the computational role of top-down feedback -- a property that is found in biological circuits -- in Artificial Neural Network (ANN) models of the neocortex. Using hierarchical recurrent ANNs in an audiovisual integration task, the authors show a visual bias consistent with that observed in human perception, which mildly improves learning speed. While the study offers a tool that is of value for studying top-down feedback in cortical models, with the potential to inspire other fields (e.g. machine learning), the presented evidence for a general framework of deep learning architectures that predict behavior is incomplete, and the methods section lacks sufficient detail in terms of hyperparameter choice and network structures.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  7. Predictive modeling of hematoma expansion from non-contrast computed tomography in spontaneous intracerebral hemorrhage patients

    This article has 14 authors:
    1. Natasha Ironside
    2. Kareem El Naamani
    3. Tanvir Rizvi
    4. Mohammed Shifat E-Rabbi
    5. Shinjini Kundu
    6. Andrea Becceril-Gaitan
    7. Kristofor Pas
    8. Harrison Snyder
    9. Ching-Jen Chen
    10. Carl D. Langefeld
    11. Daniel Woo
    12. Stephan Mayer
    13. E. Sander Connolly
    14. Gustavo Rohde
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study proposes a valuable and interpretable approach for predicting hematoma expansion in patients with spontaneous intracerebral hemorrhage from non-contrast computed tomography. The predictive performance of the proposed method is solid through external validation using two datasets. The work will be of interest to medical biologists working on stroke and neuroimaging.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  8. Audiovisual cues must be predictable and win-paired to drive risky choice

    This article has 9 authors:
    1. Brett A. Hathaway
    2. Dexter R. Kim
    3. Salwa B. A. Malhas
    4. Kelly M. Hrelja
    5. Lauren Kerker
    6. Tristan J. Hynes
    7. Celyn Harris
    8. Angela J. Langdon
    9. Catharine A. Winstanley
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study provides a nuanced analysis of the impact of cues on cost/benefit decision-making deficits in male rats that could have translational relevance to many addictive disorders. The main findings are that cues paired with rewarded outcomes increase the proportion of risky outcomes, whereas risky choice is reduced when cues are paired with reward loss. The experimental data is convincing, but the computational analysis based on the optimisation of different Q-learning models is incomplete. The findings will be of interest to behavioural neuroscientists and clinicians with an interest in risk, decision making, and gambling disorders.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  9. The coarse mental map of the breast is anchored on the nipple

    This article has 7 authors:
    1. Katie H. Long
    2. Emily E. Fitzgerald
    3. Ev I. Berger-Wolf
    4. Amani Fawaz
    5. Stacy Tessler Lindau
    6. Sliman J. Bensmaia
    7. Charles M. Greenspon
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study thoroughly assesses tactile acuity on women's breasts, for which no dependable data currently exists. The study provides two important contributions, by convincingly showing that tactile acuity on the breast is poor in comparison to other body parts, and that acuity is worst in larger breasts, indicating that the number of tactile sensors is fixed. However, further arguments concerning the role of the nipple in spatial localisation are not well supported by the current evidence. This study will be of interest to the broader community of touch, as well as those interested in breast reconstruction and sexual function.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  10. The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells

    This article has 15 authors:
    1. Jun Yang
    2. Jie Fang
    3. Shivendra Singh
    4. Brennan Wells
    5. Qiong Wu
    6. Hongjian Jin
    7. Laura Janke
    8. Shibiao Wan
    9. Jacob Steele
    10. Jon Connelly
    11. Andrew Murphy
    12. Ruoning Wang
    13. Andrew Davidoff
    14. Margaret Ashcroft
    15. Shondra Pruett-Miller
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This manuscript provides potentially important findings examining in 2D and 3D models in MYC liver cancer cells changes in DNA repair genes and programs in response to hypoxia. The authors use convincing methodology in most cases, but there is some concern that the analysis is incomplete.

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    This article has 7 evaluationsAppears in 1 listLatest version Latest activity
  11. Zebrafish Foxl2l suppresses stemness of germline progenitors and directs feminization

    This article has 6 authors:
    1. Chen-wei Hsu
    2. Hao Ho
    3. Ching-Hsin Yang
    4. Yan-wei Wang
    5. Ker-Chau Li
    6. Bon-chu Chung
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This manuscript provides important findings for understanding the mechanisms of a major gene causing the gonad of fish and other vertebrates, including mammals, to become an ovary rather than a testis. Evidence is solid, but alternative explanations for a number of the claims must be considered and discussed. The impact of the work would benefit by placing it in a richer historical context.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  12. Cholesterol taste avoidance in Drosophila melanogaster

    This article has 3 authors:
    1. Roshani Nhuchhen Pradhan
    2. Craig Montell
    3. Youngseok Lee
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    • Curated by eLife

      eLife Assessment

      This useful study provides convincing evidence that Drosophila can taste cholesterol through a subset of bitter-sensing gustatory receptor neurons, and that flies avoid high-cholesterol food. However, the same receptors have been previously found to be involved in the detection of multiple seemingly unrelated chemicals, and the reported expression patterns of these receptors contradict past reports. These caveats are not mentioned in the paper, raising critical concerns about the study's conclusions.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  13. Single-cell RNA-seq reveals trans-sialidase-like superfamily gene expression heterogeneity in Trypanosoma cruzi populations

    This article has 10 authors:
    1. Lucas Inchausti
    2. LucĂ­a Bilbao
    3. Vanina A Campo
    4. JoaquĂ­n Garat
    5. José Sotelo-Silveira
    6. Gabriel Rinaldi
    7. Virginia M Howick
    8. MarĂ­a Ana Duhagon
    9. Javier G De Gaudenzi
    10. Pablo Smircich
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study utilizes single-cell RNA sequencing to reveal the heterogeneity of trans-sialidase-like superfamily gene expression in Trypanosoma cruzi populations. The approach is highly convincing, as it successfully assigns cells to specific developmental forms and highlights the variability in surface protein expression among trypomastigotes. However, while the findings are solid and contribute to the understanding of immune evasion mechanisms, the study would benefit from a more detailed exploration of the regulatory factors governing trans-sialidase expression. Strengthening this aspect would further enhance its impact on researchers studying T. cruzi pathogenesis and host-parasite interactions.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  14. Molecular dynamics of the matrisome across sea anemone life history

    This article has 8 authors:
    1. B Gideon Bergheim
    2. Alison G Cole
    3. Mandy Rettel
    4. Frank Stein
    5. Stefan Redl
    6. Michael W Hess
    7. Aissam Ikmi
    8. Suat Ă–zbek
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study provides a comprehensive description of the Nematostella vectensis matrisome - the genes encoding the proteins of the extracellular matrix. The authors combine new mass spectrometry data with bioinformatic analyses of previously published genomic and single-cell RNAseq data. Although this work will be of interest to biologists working on the evolution of the matrisome, as well as more broadly those working with non-bilaterian animals, in its current state it is incomplete due to the lack of rigorous criteria for manual curation and comprehensive annotation of the predicted matrisome.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  15. A network regularized linear model to infer spatial expression pattern for single cell

    This article has 3 authors:
    1. Chaohao Gu
    2. Hu Chen
    3. Zhandong Liu
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      The study is useful for advancing spatial transcriptomics through its novel regression-based linear model (glmSMA) that integrates single-cell RNA-seq with spatial reference atlases, though its methodological framework remains incomplete regarding spatial communication applications and feature dependence. The approach demonstrates notable utility by enabling higher-resolution cell mapping across multiple biological systems and spatial platforms compared to existing tools.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  16. scRNA+TCR-seq Reveals the Proportion and Characteristics of Dual TCR Treg Cells in Mouse Lymphoid and Non-lymphoid Tissues

    This article has 6 authors:
    1. Yuanyuan Xu
    2. Qipeng
    3. Xiaoping Lu
    4. Long Ma
    5. Jun Li
    6. Xinsheng Yao
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study reanalyzed previously published scRNA-seq and TCR-seq data to examine the proportion and characteristics of dual-TCR-expressing Treg cells in mice, presenting some useful insights into TCR diversity and immune regulation. However, the evidence is incomplete, particularly with respect to data interpretation, statistical rigor, and the functionality of dual -TCR Treg cells. The study is potentially of interest to immunologists studying T-cell biology.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  17. Estimation of Rotavirus Vaccine Effectiveness Based on Whole Genome Sequences

    This article has 15 authors:
    1. Jiye Kwon
    2. Jose Jaimes
    3. Mary E Wikswo
    4. Eileen J Klein
    5. Mary Allen Staat
    6. James D Chappell
    7. Geoffrey A Weinberg
    8. Christopher J Harrison
    9. Rangaraj Selvarangan
    10. Coreen Johnson
    11. Daniel M Weinberger
    12. Joshua L Warren
    13. Mathew D Esona
    14. Michael D Bowen
    15. Virginia E Pitzer
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    • Curated by eLife

      eLife Assessment

      Kwon et al. present an important paper using a novel approach to estimating rotavirus vaccine efficacy using data from a passive surveillance network in the US. They provide convincing evidence to support their conclusion that using the whole genome, rather than previous use of two surface proteins, enhances our understanding of strain-specific vaccine efficacy. These findings have implications for this vaccine specifically as well as type-specific vaccine evaluation more generally.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  18. Broad-spectrum immune suppression encoded in self-amplifying RNA enables non-cytotoxic, non-immunostimulatory, externally controllable transgene expression

    This article has 6 authors:
    1. Tony KY Lim
    2. Anne Ritoux
    3. Luke W Paine
    4. Larissa Ferguson
    5. Tawab Abdul
    6. Ewan St John Smith
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    • Curated by eLife

      eLife Assessment

      In this manuscript, Lim and collaborators present a useful system for developing self-amplifying RNA that should not provoke a strong host inflammatory response. However, some of the claims are incomplete; additional experiments to investigate the effects on translation of the gene of interest and replication efficiency of the self-amplifying RNA could strengthen the manuscript.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  19. Dimerization and dynamics of angiotensin-I converting enzyme revealed by cryoEM and MD simulations

    This article has 4 authors:
    1. Jordan M Mancl
    2. Xiaoyang Wu
    3. Minglei Zhao
    4. Wei-Jen Tang
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study shows, for the first time, the structure and snapshots of the dynamics of the full-length soluble Angiotensin-I converting enzyme dimer. The combination of structural and computational approaches elucidates with convincing evidence the conformational dynamics of the complex and key regions mediating the conformational change. This work provides an example of how conformational heterogeneity can be used to gain insights into protein function.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity