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  1. Gene regulatory dynamics during craniofacial development in a carnivorous marsupial

    This article has 6 authors:
    1. Laura E. Cook
    2. Charles Y. Feigin
    3. John Hills
    4. Davide M. Vespasiani
    5. Andrew J. Pask
    6. Irene Gallego Romero
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study of regulatory elements and gene expression in the craniofacial region of the fat-tailed dunnart shows that, compared to placental mammals, marsupial craniofacial tissue develops in a precocious manner, with enhancer regulatory elements as primary driver of this difference. While the results are overall solid, addressing concerns regarding the liftover methods in the context of low conservation of alignable enhancers between dunnart and mouse would benefit the work, enhancing its value for uncovering mechanisms that drive heterochronic processes and as a reference for future mammalian evolution studies.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  2. Barcode activity in a recurrent network model of the hippocampus enables efficient memory binding

    This article has 5 authors:
    1. Ching Fang
    2. Jack Lindsey
    3. L.F. Abbott
    4. Dmitriy Aronov
    5. Selmaan Chettih
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important work substantially advances our understanding of episodic memory by proposing a biologically plausible mechanism through which hippocampal barcode activity enables efficient memory binding and flexible recall. The evidence supporting the conclusions is convincing, with rigorously validated computational models and alignment with experimental findings. The work will be of broad interest to neuroscientists and computational modelers studying memory and hippocampal function.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  3. Control of innate olfactory valence by segregated cortical amygdala circuits

    This article has 12 authors:
    1. James R. Howe
    2. Chung-Lung Chan
    3. Donghyung Lee
    4. Marlon Blanquart
    5. James H. Lee
    6. Haylie K. Romero
    7. Abigail N. Zadina
    8. Mackenzie E. Lemieux
    9. Fergil Mills
    10. Paula A. Desplats
    11. Kay M. Tye
    12. Cory M. Root
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study provides important insights into how a specific brain region controls innate responses to odors, showing that different parts of this region govern behaviors related to attraction and aversion. The findings are convincing and supported by a combination of well-executed experimental approaches, including genetic manipulations and neural activity mapping, though the evidence could be strengthened by addressing certain methodological concerns, such as clarifying the rationale for specific experimental choices and exploring alternative techniques.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  4. Benchmarking and Optimization of Methods for the Detection of Identity-By-Descent in High-Recombining Plasmodium falciparum

    This article has 3 authors:
    1. Bing Guo
    2. Shannon Takala-Harrison
    3. Timothy D. O'Connor
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study presents an evaluation of several tools used for detecting Identity-By-Descent (IBD) segments in highly recombining genomes, using simulated data to replicate the high recombination and low marker density of Plasmodium falciparum, the parasite responsible for malaria. Most of the evidence presented by the authors is solid demonstrating that users should be cautious calling IBD when SNP density is low and recombination rate is high. This study will be of interest to scientists working in the field of genome evolution and infectious diseases.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  5. Human genetic ancestry, Mycobacterium tuberculosis diversity and tuberculosis disease severity in Dar es Salaam, Tanzania

    This article has 15 authors:
    1. Michaela Zwyer
    2. Zhi Ming Xu
    3. Amanda Ross
    4. Jerry Hella
    5. Mohamed Sasamalo
    6. Maxime Rotival
    7. Hellen Hiza
    8. Liliana K. Rutaihwa
    9. Sonia Borrell
    10. Klaus Reither
    11. Jacques Fellay
    12. Damien Portevin
    13. Lluis Quintana-Murci
    14. Sebastien Gagneux
    15. Daniela Brites
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This useful observational study was conducted in Dar es Salaam, Tanzania, to investigate potential associations between genetic variation in Mycobacterium tuberculosis and human host vs. disease severity. The authors conclude that human genetic ancestry did not contribute to tuberculosis severity, but the evidence for this conclusion is currently incomplete, as the analysis did not fully leverage the genome-wide data available in a human-strain association study, and there was no comparison group from the general population (or household controls), to which the ancestry findings could be compared. The findings have significance for the understanding of the influence of host / bacillary genetics on tuberculosis disease.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  6. Multi-dimensional social relationships shape social attention in monkeys

    This article has 5 authors:
    1. Sainan Liu
    2. Jiepin Huang
    3. Suhao Chen
    4. Michael L Platt
    5. Yan Yang
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study examined how multidimensional social relationships influence social attention in rhesus macaques, linking individual and group-level behaviors to attentional processes. The findings that oxytocin altered social attention and its relationship to both social tendencies and dyadic relationships are important, as recent technological advances allow for the exploration of neuronal activities and mechanisms in free-moving macaques. This work is convincing and will be of interest to those studying the interplay between social dynamics and information processing in primates.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  7. Real-Time Closed-Loop Feedback System For Mouse Mesoscale Cortical Signal And Movement Control: CLoPy

    This article has 2 authors:
    1. Pankaj K. Gupta
    2. Timothy H. Murphy
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents a platform to implement closed-loop experiments in mice based on auditory feedback. The authors provide solid evidence that their platform enables a variety of closed-loop experiments using neural or movement signals, indicating that it will be a valuable resource to the neuroscience community. However, the demonstration experiments could be strengthened by increasing the sample size for several groups in the neurofeedback experiments, as well as a more thorough description of the results in the text.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  8. Quantification of the effect of hemodynamic occlusion in two-photon imaging

    This article has 4 authors:
    1. Baba Yogesh
    2. Matthias Heindorf
    3. Rebecca Jordan
    4. Georg B. Keller
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study conducted experiments to quantify how changes in blood flow results in apparent fluorescence changes when imaging neural activity sensors using two-photon microscopy. While the study highlights the prevalence neural-activity independent artifacts in two-photon imaging, the evidence linking the observed signals to hemodynamic occlusion remains incomplete.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  9. Synaptic input architecture of visual cortical neurons revealed by large-scale synapse imaging without backpropagating action potentials

    This article has 3 authors:
    1. Satoru Kondo
    2. Kohei Kikuta
    3. Kenichi Ohki
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study uses a novel method to record spine calcium responses without the confounds of backpropagating action potentials to study how the dendritic integration of large numbers of inputs generates the tuned output of cortical neurons. While the results are generally solid, the study would benefit from more details, characterizations, and quantifications, including better validation of the method to suppress backpropagating action potentials.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  10. CCR5 antagonists as neuroprotective and stroke recovery enhancing agents: a preclinical systematic review and meta-analysis

    This article has 16 authors:
    1. Ayni Sharif
    2. Matthew S. Jeffers
    3. Dean A. Fergusson
    4. Raj Bapuji
    5. Stuart G. Nicholls
    6. John Humphrey
    7. Warren Johnston
    8. Ed Mitchell
    9. Mary-Ann Speirs
    10. Laura Stronghill
    11. Michele Vuckovic
    12. Susan Wulf
    13. Risa Shorr
    14. Dar Dowlatshahi
    15. Dale Corbett
    16. Manoj M. Lalu
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This systematic review presents valuable insights into CCR5 antagonist drugs for neuroprotection and stroke management. The strength of the evidence is convincing, and the review methods and reporting adhere to the expected standards. A sensitivity analysis based on the risk of bias assessment of the included studies would be beneficial, and a more focused/detailed acknowledgment of key limitations of the review would add value to the quality of the reporting and interpretations of the findings.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  11. A differentiable Gillespie algorithm for simulating chemical kinetics, parameter estimation, and designing synthetic biological circuits

    This article has 2 authors:
    1. Krishna Rijal
    2. Pankaj Mehta
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This important study introduces a fully differentiable variant of the Gillespie algorithm as an approximate stochastic simulation scheme for complex chemical reaction networks, allowing kinetic parameters to be inferred from empirical measurements of network outputs using gradient descent. The concept and algorithm design are convincing and innovative. While the proofs of concept are promising, the determination of the range of applicability and of the errors is incomplete, leaving open some questions about implications for more complex systems that cannot be addressed by existing methods. This work has the potential to be of significant interest to a broad audience of quantitative and synthetic biologists.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  12. Maintenance of neuronal TDP-43 expression requires axonal lysosome transport

    This article has 18 authors:
    1. Veronica H. Ryan
    2. Sydney Lawton
    3. Joel F. Reyes
    4. James Hawrot
    5. Ashley M. Frankenfield
    6. Sahba Seddighi
    7. Daniel M. Ramos
    8. Faraz Faghri
    9. Nicholas L. Johnson
    10. Jizhong Zou
    11. Martin Kampmann
    12. John Replogle
    13. Hebao Yuan
    14. Kory R. Johnson
    15. Dragan Maric
    16. Ling Hao
    17. Mike A. Nalls
    18. Michael E. Ward
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      In this important manuscript, Ryan et al perform a genome-wide CRISPR based screen to identify genes that modulate TDP-43 levels in neurons. They identify a number of genes and pathways and highlight the BORC complex, which is required for anterograde lysosome transport as one such regulator of TDP-43 protein levels. Overall, this is a convincing study, which opens the door for additional future investigations on the regulation of TDP-43.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  13. Peripheral glia and neurons jointly regulate activity-induced synaptic remodeling at the Drosophila neuromuscular junction

    This article has 4 authors:
    1. Yen-Ching Chang
    2. Yi-Jheng Peng
    3. Joo Yeun Lee
    4. Karen T. Chang
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study presents a valuable finding on a new role of glia in activity-dependent synaptic remodeling using the Drosophila NMJ as a model system. The evidence supporting the claims of the authors is solid. However, the unaddressed cell-type specific mechanisms of Shv secretion and regulation on the extracellular glutamate levels and lack of details on the methods for statistical analysis have hindered further evaluation of the claims. The work will be of interest to neuroscientists working on glia-neuron interaction and synaptic remodeling.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  14. Transcriptional antitermination integrates the expression of loci of diverse phage origin in the chimeric Bartonella Gene Transfer Agent BaGTA

    This article has 3 authors:
    1. Aleksandr Korotaev
    2. Quirin Niggli
    3. Christoph Dehio
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This manuscript describes an important finding of the transcriptional control of a chimeric gene transfer agents (GTA) cluster in Bartonella by a processive anti-termination factor (BrrG). The evidence provided is solid. This manuscript will interest researchers working on transcriptional regulation, horizontal gene transfer, and phages.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  15. The eduWOSM: a benchtop advanced microscope for education and research

    This article has 4 authors:
    1. Nicholas J Carter
    2. Douglas S Martin
    3. Justin E Molloy
    4. Robert A Cross
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This is a valuable study and a promising development for the field of open-source microscopy for educational purposes. The strengths include the low cost of constructing the microscope, impressive performance and detailed resources including a dedicated website and YouTube channel. The claims are generally supported by solid evidence, however, the manuscript would be strengthened by inclusion of further details on standard performance metrics (e.g. signal to noise ratio etc.) compared to existing systems and further details and clarification on the microscope, construction and operation.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  16. Function and firing of the Streptomyces coelicolor contractile injection system requires the membrane protein CisA

    This article has 8 authors:
    1. Bastien Casu
    2. Joseph W Sallmen
    3. Peter E Haas
    4. Govind Chandra
    5. Pavel Afanasyev
    6. Jingwei Xu
    7. Susan Schlimpert
    8. Martin Pilhofer
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This valuable study provides insights into the structure and function of bacterial contractile injection systems that are present in the cytoplasm of many Streptomyces strains. A convincing high-resolution model of the structure of extended forms of the cytoplasmic contractile injection system assembly from Streptomyces coelicolor is presented, with some investigation of the membrane protein CisA in attachment of the extended assembly to the inner face of the cytoplasmic membrane and the firing of the system. The work expands the current understanding of these diverse bacterial nanomachines.

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    This article has 5 evaluationsAppears in 1 listLatest version Latest activity
  17. A pair of congenic mice for imaging of transplants by positron emission tomography using anti-transferrin receptor nanobodies

    This article has 12 authors:
    1. Thomas Balligand
    2. Claire Carpenet
    3. Sergi Olive-Palau
    4. Tom Jaspers
    5. Pavana Suresh
    6. Xin Liu
    7. Himadri Medhi
    8. Yoon Ho Lee
    9. Mohammad Rashidian
    10. Bart De Strooper
    11. Hidde L. Ploegh
    12. Maarten Dewilde
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      In this innovative study, Carpenet C et al explore the use of nanobody-based PET imaging to track proliferative cells after in vivo transplantation in mice, in a fully immunocompetent setting. The development of a unique set of PET tracers and mouse strains to track genetically-unmodified transplanted cells in vivo is an important novel asset that could potentially facilitate cell tracking. The evidence provided is compelling as the new method proposed might facilitate overcoming certain limitations of alternative approaches, such as full sized immunoglobulins and small molecules, while the specific claims would gain further support by additional experimentation and methodological details.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  18. Reactive Oxygen Detoxification Contributes to Mycobacterium abscessus Antibiotic Survival

    This article has 6 authors:
    1. Nicholas A. Bates
    2. Ronald Rodriguez
    3. Rama Drwich
    4. Abigail Ray
    5. Sarah A. Stanley
    6. Bennett H. Penn
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      Using a TN-seq based approach, the authors identified the genetic determinants of drug tolerance in M. abscessus. Since M. abscessus is resistant to multiple antibiotics, the study is valuable in generating new knowledge linking antibiotic tolerance with ROS in this non-tuberculosis mycobacterial (NTM) species. However, the study is incomplete due to a need for more validation of the Tn-seq data, inconsistency with the clinical strains, and insufficient experiments confirming the role of ROS detoxification in drug tolerance.

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    This article has 4 evaluationsAppears in 1 listLatest version Latest activity
  19. Early experience affects foraging behavior of wild fruit-bats more than their original behavioral predispositions

    This article has 7 authors:
    1. Adi Rachum
    2. Lee Harten
    3. Reut Assa
    4. Aya Goldshtein
    5. Xing Chen
    6. Nesim Gonceer
    7. Yossi Yovel
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      The work presented in this paper provides an important insight into how early life experience shapes adult behavior in fruit bats. The authors raised juvenile bats either in an impoverished or enriched environment and studied their foraging behaviors. The evidence is convincing that bats raised in enriched environments are more active, bold, and exploratory, although further exploration of the data and clarification of the analysis would strengthened the evidence. The work will be of interest to ethologists and developmental psychologists.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity
  20. The electrogenicity of the Na + /K + -ATPase poses challenges for computation in highly active spiking cells

    This article has 3 authors:
    1. Liz Weerdmeester
    2. Jan-Hendrik Schleimer
    3. Susanne Schreiber
    This article has been curated by 1 group:
    • Curated by eLife

      eLife Assessment

      This study provides valuable insights into the lesser-known effects of the sodium-potassium pump on how nerve cells process signals, particularly in highly active cells like those of weakly electric fish. The authors use a detailed mathematical model to show how the pump can shift a cell's normal firing patterns and disrupt the coordination of signals when inputs change quickly. The computational methods used to establish the claims in this work are solid and can be used as a starting point for further studies, yet the conclusions would be strengthened with experimental evidence or testable predictions regarding some of the proposed mechanisms across different cell types.

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    This article has 3 evaluationsAppears in 1 listLatest version Latest activity