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  1. Xcr1 + type 1 conventional dendritic cells are essential mediators for atherosclerosis progression

    This article has 17 authors:
    1. Tianhan Li
    2. Liaoxun Lu
    3. Juanjuan Qiu
    4. Xin Dong
    5. Le Yang
    6. Kexin He
    7. Yanrong Gu
    8. Binhui Zhou
    9. Tingting Jia
    10. Toby Lawrence
    11. Marie Malissen
    12. Guixue Wang
    13. Rong Huang
    14. Hui Wang
    15. Bernard Malissen
    16. Yinming Liang
    17. Lichen Zhang
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This manuscript by Li, Lu et al., presents important findings on the role of cDC1 in atherosclerosis and their influence on the adaptive immune system. Using Xcr1Cre-Gfp Rosa26LSL-DTA ApoE-/- mouse models, these data convincingly reveal an unexpected, non-redundant role of the XCL1-XCR1 axis in mediating cDC1 contributions to atherosclerosis.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  2. An abundant merozoite surface protein of Plasmodium falciparum modulates susceptibility to inhibitory antibodies

    This article has 11 authors:
    1. Isabelle G. Henshall
    2. Jill Chmielewski
    3. Dimuthu Angage
    4. Ornella Romeo
    5. Keng Heng Lai
    6. Kaitlin R. Turland
    7. Nicki Badii
    8. Michael Foley
    9. Robin F. Anders
    10. James Beeson
    11. Danny W Wilson
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important work offers a fresh perspective fundamental to merozoite surface biology and potential implications on vaccine design, challenging the dogma that MSPs are indispensable invasion engines. Although the authors only deleted bp 132-819, the data based on Western blot, IFA, and RNA‐seq provide compelling evidence that while MSP2 is dispensable for growth, it serves as an immune modulator for AMA1. This work will be of particular interest to scientists working on different aspects of Plasmodium biology and vaccinology.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  3. REPOP: bacterial population quantification from plate counts

    This article has 6 authors:
    1. Pedro Pessoa
    2. Carol Lu
    3. Stanimir Asenov Tashev
    4. Rory Kruithoff
    5. Douglas P. Shepherd
    6. Steve Pressé
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study introduces a Bayesian method to determine bacterial counts that accounts for the experimental noise inherent to dilution and plating methods, and distinguishes it from biological uncertainty. The evidence supporting the conclusions is convincing, combining simulated data and experimental data. The method will be of interest to microbial ecologists, and potentially to the broader community interested in inference from biological data, even more so if the domain of application and the limitations are further clarified.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  4. Noninvasive ultrasound targeted modulation of calcium influx in splenic immunocytes potentiates antineoplastic immunity attenuating hepatocellular carcinoma proliferation

    This article has 11 authors:
    1. Wei Dong
    2. Guihu Wang
    3. Senyang Li
    4. Yichao Chai
    5. Qian Wang
    6. Yucheng Li
    7. Qiaoman Fei
    8. Yujin Zong
    9. Jing Geng
    10. Pengfei Liu
    11. Zongfang Li
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study presents an innovative noninvasive immunotherapeutic strategy for hepatocellular carcinoma by combining ultrasound stimulation with calcium-loaded nanodroplets to activate splenic immune responses. The authors provide solid preclinical data, including single-cell transcriptomic analyses and evidence of tumor growth suppression, supported by a creative and well-executed methodology. Further validation of the calcium signaling mechanisms and assessment of long-term safety will strengthen the translational potential of this approach. The work will be of broad interest to researchers in oncology, immunotherapy, and biomedical engineering.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  5. The impact of ambient contamination on demultiplexing methods for single-nucleus multiome experiments

    This article has 10 authors:
    1. Terence Li
    2. Marcus Alvarez
    3. Cuining Liu
    4. Kevin Abuhanna
    5. Yu Sun
    6. Jason Ernst
    7. Kathrin Plath
    8. Brunilda Balliu
    9. Chongyuan Luo
    10. Noah Zaitlen
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study introduces ambisim, a rigorously validated and well-documented simulation framework that enables the generation of synthetic, genotype-aware single-cell RNA and ATAC sequencing datasets under realistic conditions. The authors provide solid evidence of its utility by benchmarking multiple demultiplexing methods and proposing a new variant consistency metric. While the tool is valuable for guiding method selection, the interpretation of the new metric requires further clarification.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  6. Neural Representation of Time across Complementary Reference Frames

    This article has 4 authors:
    1. Yangwen Xu
    2. Nicola Sartorato
    3. Léo Dutriaux
    4. Roberto Bottini
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents a valuable finding on the neural representation of time from two distinct egocentric and allocentric reference frames. The presentation of evidence in the version of the original submission is incomplete, as further conceptual clarifications, methodological details, and addressing potential confounds would strengthen the study. The work will be of interest to cognitive neuroscientists working on the perception and memory of time.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  7. Reorganization of spinal neural connectivity following recovery after thoracic spinal cord injury: insights from computational modelling

    This article has 5 authors:
    1. Natalia A. Shevtsova
    2. Andrew B. Lockhart
    3. Ilya A. Rybak
    4. David S. K. Magnuson
    5. Simon M. Danner
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study describes a computational model of the rat spinal locomotor circuits and how they could be plastically reconfigured after lateral hemisection or contusion injuries to replicate gaits observed experimentally in vivo. Overall, the simulation results convincingly mirror the gait parameters observed experimentally. The model suggests the emergence of detour circuits after lateral hemisection, whereas after a midline contusion, the model suggests plasticity of left-right and sensory inputs below the injury.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  8. G protein-coupled receptor diversity and evolution in the closest living relatives of Metazoa

    This article has 2 authors:
    1. Alain Garcia De Las Bayonas
    2. Nicole King
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study fills an gap in our knowledge of the evolution of GPCRs in holozoans, as well as the phylogeny of associated signaling pathway components such as G proteins, GRKs, and RIC8 proteins. The evidence supporting the conclusions is compelling, with the analysis of extensive new genomic data from choanoflagellates and other non-animal holozoans. Overall, the study is thorough and well-executed. It will be a resource for researchers interested in both the comparative genomics of multicellularity and GPCR biology more broadly, especially given the importance of GPCRs as highly druggable targets.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  9. Genetic compensation in podocalyxin-like mutants during zebrafish liver development

    This article has 8 authors:
    1. Alexis N Ross
    2. Natalie M Miscik
    3. Sharanya Maanasi Kalasekar
    4. James D Harris
    5. Mimi Tran
    6. Aavrati Saxena
    7. Steven Andrew Baker
    8. Kimberley Jane Evason
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      The manuscript by Ross, Miscik, and others describes an intriguing series of observations made when investigating the requirement for podxl during hepatic development in zebrafish. Understanding how genetic compensation pathways are involved in gene function is an important question. However, there is incomplete evidence provided in the manuscript at this point to conclude that discrepancies between observed phenotypes are due to genetic compensation.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  10. Insights from aquaporin structures into drug-resistant sleeping sickness

    This article has 23 authors:
    1. Modestas Matusevicius
    2. Robin A Corey
    3. Marcos Gragera
    4. Keitaro Yamashita
    5. Teresa Sprenger
    6. Marzuq A Ungogo
    7. James N Blaza
    8. Pablo Castro-Hartmann
    9. Dimitri Y Chirgadze
    10. Sundeep Chaitanya Vedithi
    11. Pavel Afanasyev
    12. Roberto Melero
    13. Rangana Warshamanage
    14. Anastasiia Gusach
    15. Jose Maria Carazo
    16. Mark Carrington
    17. Tom L Blundell
    18. Garib Murshudov
    19. Phillip Stansfeld
    20. Mark Sansom
    21. Harry P de Koning
    22. Christopher G Tate
    23. Simone N Weyand
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      In this important study, the authors set out to determine the molecular interactions between the AQP2 from Trypanosoma brucei (TbAQP2) and the trypanocidal drugs pentamidine and melarsoprol in order to clarify the origins of clinically observed drug resistance and facilitate future drug design. Using cryo-EM, molecular dynamics simulations, and lysis assays, the authors present a solid theory for how drug resistance mutations in TbAQP2 prevent drug uptake. Overall, even though a few methodological issues still need minor clarification, this study will be of interest to those working on aquaporins and the development of drugs targeting aquaporins.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  11. Glial betaPix is essential for blood vessel integrity in the zebrafish brain

    This article has 7 authors:
    1. ShihChing Chiu
    2. Qinchao Zhou
    3. Chenglu Xiao
    4. Linlu Bai
    5. Xiaojun Zhu
    6. Wanqiu Ding
    7. Jing-Wei Xiong
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable manuscript presents findings supported by solid data to identify a surprising glia-exclusive function for betapix in vascular integrity and angiogenesis. The manuscript also describes the optimisation of a modified CRISPR-based Zwitch approach to generate conditional knockouts in zebrafish.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  12. Molecular Landscape of the Mouse Adrenal Gland and Adjacent Adipose by Spatial Transcriptomics

    This article has 9 authors:
    1. MaƂgorzata Blatkiewicz
    2. Szymon Hryhorowicz
    3. Marta Szyszka
    4. Joanna SuszyƄska-Zajczyk
    5. Andrzej PƂawski
    6. Adam PlewiƄski
    7. Andrea Porzionato
    8. Ludwik K. Malendowicz
    9. Marcin Rucinski
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This useful study provides a spatial transcriptomic analysis of the mouse adrenal gland that could have implications for future research and applications. The authors present solid results that allow the dissection of the cell signalling pathways and cellular composition of different zones of the adrenal glands in the mouse model; they propose new zone-specific gene markers and specific intra- and inter-zonal signaling pathways based on receptor-ligand expression patterns. Their web tool is user-friendly and will be helpful for adrenal scientists; however, the validation of crucial results of the large dataset is necessary. There are also several contradictory results/interpretations, and the opportunity to dissect the sexually dimorphic gene expression pattern and mouse-human interspecies differences is a missed opportunity.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  13. SIRT2 protects against Japanese encephalitis virus infection in mice

    This article has 9 authors:
    1. Perumal Arumugam Desingu
    2. Lavanya Dindi
    3. Krishnega Murugasamy
    4. Ankit Kumar Tamta
    5. Venketsubbu Ramasubbu
    6. Sukanya Raghu
    7. Amarjeet Shrama
    8. Raju S Rajmani
    9. Nagalingam R Sundaresan
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study explores the role of SIRT2 in regulating Japanese encephalitis virus replication and disease progression in rodent models. The findings presented are novel as sirtuins are known for their roles in aging, metabolism, and cell survival, but have not been studied in the context of viral infections until recently. The evidence supporting the claims is solid, although additional experiments to further characterize the clinical outcomes and directly test the link between acetylated NF-kB and SIRT2 expression would have strengthened the study. The work will be of interest to biologists studying viruses, sirtuins, and inflammation.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  14. Doubling dolutegravir dosage reduces the viral reservoir in ART-treated people with HIV

    This article has 16 authors:
    1. Céline Fombellida-Lopez
    2. Aurelija Valaitienė
    3. Lee Winchester
    4. Nathalie Maes
    5. Patricia Dellot
    6. Céline Vanwinge
    7. Aurélie Ladang
    8. Etienne Cavalier
    9. Fabrice Susin
    10. Dolores Vaira
    11. Marie-Pierre Hayette
    12. Catherine Reenaers
    13. Michel Moutschen
    14. Courtney V Fletcher
    15. Alexander O Pasternak
    16. Gilles Darcis
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study tested whether several months of dolutegravir intensification alters the size of the HIV reservoir as well as immune activation in individuals already on suppressive ART. While the general study approach is appropriate and the paper is well written, the evidence supporting the claims of the authors is incomplete. The title of the paper is only partially supported by the data, based on specific issues with the study design and analysis plan highlighted by Reviewer 1. Specifically, the primary study outcomes were not clearly described a priori, the plausibility of a biologic effect is uncertain based on lack of a consistent effect across participants, and sample size is small. Given a possible observed partial effect and relevant hypothesis, this approach warrants study in a larger trial.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  15. Species biology and demographic history determines species vulnerability to climate change in tropical island endemic birds

    This article has 6 authors:
    1. Ratnesh Karjee
    2. Vikram Iyer
    3. Durbadal Chatterjee
    4. Rajasri Ray
    5. Kritika M Garg
    6. Balaji Chattopadhyay
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      Tropical single-island endemic bird populations are particularly vulnerable to climate change. The authors investigate genetic evidence of how such species dealt with climate changes in the past as a possible predictor for how they will respond to change in the future, which could provide an important example for the fields of conservation genetics and island biogeography. The authors' integration of genomics and habitat modeling is commendable, but we find that the support for their conclusions is incomplete: at times, the results presented appear to contradict each other, the authors do not fully account for key variables, and the limited taxonomic scope may cause problematic biases for the conclusions.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  16. Cancer cells differentially modulate mitochondrial respiration to alter redox state and enable biomass synthesis in nutrient-limited environments

    This article has 6 authors:
    1. Sarah M Chang
    2. Muhammad Bin Munim
    3. Sonia E Trojan
    4. Anna Shevzov-Zebrun
    5. Keene L Abbott
    6. Matthew G Vander Heiden
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents valuable findings on the relationship between nutrient availability and NAD/NADH levels, which in turn regulate biomass production in cancer cells. The authors provide solid evidence to support their claims, offering insight into why it is difficult to predict which nutrients limit cancer cell growth: both cell type and nutrient availability together determine the oxidative capacity that constrains the synthesis of various metabolic intermediates. The manuscript will be of interest to researchers working in cancer and cell metabolism.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  17. Epidermal Resident Memory T Cell Fitness Requires Antigen Encounter in the Skin

    This article has 17 authors:
    1. Eric S Weiss
    2. Toshiro Hirai
    3. Haiyue Li
    4. Andrew Liu
    5. Shannon Baker
    6. Ian Magill
    7. Jacob Gillis
    8. Youran R Zhang
    9. Torben Ramcke
    10. Kazuo Kurihara
    11. The ImmGen Consortium OpenSource T cell Project
    12. David Masopust
    13. Niroshana Anandasabapathy
    14. Harinder Singh
    15. David Zemmour
    16. Laura K Mackay
    17. Daniel H Kaplan
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      Weiss et al. provide important new insights and convincing evidence to further our mechanistic understanding of how antigen presentation shapes skin persistence of CD8+ TRM. Using a mouse model for inducible genetic ablation of transforming growth factor beta receptor 3 (TGFBR3) in CD8+ T cells, they demonstrate TGFBR3's role in regulating CD8+ TRM persistence in skin. Furthermore, they show that the strength of T cell receptor (TCR) engagement upon initial CD8+ TRM skin seeding has a positive influence on subsequent TRM expansion following a secondary antigen-reencounter. Together, these mechanisms add to our understanding of how the skin CD8+ T cell repertoire is dynamically responsive to topical antigen.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  18. Individuality transfer: Predicting human decision-making across tasks

    This article has 1 author:
    1. Hiroshi Higashi
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents a useful framework to extract the individuality index to predict subjects' behavior in the target tasks. However, the evidence supporting such a framework is somewhat incomplete and would benefit from overall framing and clarity on its approaches. Overall, this study would be of interest to cognitive and AI researchers who work on cognitive models in general.

    Reviewed by eLife

    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  19. When do measured representational distances reflect the neural representational geometry?

    This article has 2 authors:
    1. Veronica Bossio Botero
    2. Nikolaus Kriegeskorte
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This manuscript makes important contributions to the methodology commonly used to assess representational structures in human and animal brain activity recorded using various techniques (especially fMRI). The evidence in the form of mathematical analysis and simulations is solid. The impact of this contribution could be improved by extending the simulations to assess the effects of violations of explicit and implicit assumptions.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  20. Perinatal environmental enrichment affects murine neonates’ brain structure before their active engagement with environment

    This article has 7 authors:
    1. Malte S Kaller
    2. Clémence Ligneul
    3. Rylan Allemang-Grand
    4. Tie Yuan Zhang
    5. Jacob Ellegood
    6. Michael Meaney
    7. Jason P Lerch
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This is an important study that combines replications of findings and novel detailed MRI investigations to assess the impact of environmental enrichment and maternal behavior on mice brain structure at different stages of development. The results and evidence supporting the conclusions are convincing, but in detail, the interpretation is challenging, in particular due to inter-individual and inter-litter variability. The extent to which maternal care mediates the impact of enrichment on brain development during the perinatal period also remains unclear because behavior was observed only during short periods, and the performed analyses are still incomplete. This study will nevertheless be of significant interest to neuroscientists and researchers interested in neurodevelopment in relation to environmental factors because of its in-depth use of MRI to study brain plasticity in mice.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity