eLife

Latest preprint reviews

1. ZFT is the major iron and zinc transporter in Toxoplasma gondii

   This article has 7 authors:

   1. Dana Aghabi
   2. Cecilia Gallego Rubio
   3. Miguel Cortijo Martinez
   4. Augustin Pouzache
   5. Erin J Gibson
   6. Lucas Pagura
   7. Clare R Harding

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study identifies a putative iron and zinc transporter in the plasma membrane of the obligate intracellular pathogen, Toxoplasma gondii. Using an array of different approaches, the authors convincingly demonstrate that this transporter regulates diverse cellular processes, including parasite metabolism and differentiation. This work will be of broad interest to cell biologists and biochemists studying metal ion transport mechanisms.

   Reviewed by eLife

2. Deep Neural Networks to Register and Annotate Cells in Moving and Deforming Nervous Systems

   This article has 12 authors:

   1. Adam A Atanas
   2. Alicia Kun-Yang Lu
   3. Brian Goodell
   4. Jungsoo Kim
   5. Saba Baskoylu
   6. Di Kang
   7. Talya S Kramer
   8. Eric Bueno
   9. Flossie K Wan
   10. Karen L Cunningham
   11. Brandon Weissbourd
   12. Steven W Flavell

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Whole-brain imaging of neuronal activity in freely behaving animals holds great promise for neuroscience, but numerous technical challenges limit its use. In this important study, the authors describe a new set of deep learning-based tools to track and identify the activity of head neurons in freely moving nematodes (C. elegans) and jellyfish (Clytia hemisphaerica). While the tools convincingly enable high tracking speed and accuracy in the settings in which the authors have evaluated them, the claim that these tools should be easily generalizable to a wide variety of datasets is incompletely supported.

   Reviewed by eLife

3. Punctuated mutagenesis promotes multi-step evolutionary adaptation in human cancers

   This article has 5 authors:

   1. Christopher Graser
   2. Wenbo Wu
   3. Cole Christini
   4. Mia Petljak
   5. Franziska Michor

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study presents a theoretical model of how punctuated mutations influence multistep adaptation, supported by empirical evidence from some TCGA cancer cohorts. This solid model points to the case of possible punctuated evolution rather than gradual genomic change. There was some disagreement amongst the reviewers in terms of how closely the theoretical results apply to the phenomena examined empirically, and alternative explanations should be considered in the future.

   Reviewed by eLife

4. Two classes of amine/glutamate multi-transmitter neurons innervate Drosophila internal male reproductive organs

   This article has 8 authors:

   1. Martha Chaverra
   2. John Paul Toney
   3. Lizetta D Dardenne-Ankringa
   4. Jace Tolleson Knee
   5. Ann R Morris
   6. Joseph B Wadhams
   7. Sarah J Certel
   8. R Steven Stowers

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study characterizes with rigorous methodology anatomical and functional aspects of the peripheral innervation of the Drosophila male reproductive tract. The convincing analysis reveals two distinct types of glutamatergic neurons that co-release either serotonin or octopamine. While serotonergic neurons are required for male fertility, octopaminergic neurons are dispensable. The work is providing invaluable insight into neurochemical control of insemination, peripheral motor control and neuromodulation in the male reproductive tract.

   Reviewed by eLife

5. Adaptive behavior is guided by integrated representations of controlled and non-controlled information

   This article has 3 authors:

   1. Bingfang Huang
   2. Harrison Ritz
   3. Jiefeng Jiang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study uses creative scalp EEG decoding methods to attempt to demonstrate that two forms of learned associations in a Stroop task are dissociable, despite sharing similar temporal dynamics. However, the evidence supporting the conclusions is incomplete due to concerns with the experimental design and methodology. This paper would be of interest to researchers studying cognitive control and adaptive behavior, if the concerns raised in the reviews can be addressed satisfactorily.

   Reviewed by eLife

6. Refining uncertainty about the TAK-003 dengue vaccine with a multi-level model of clinical efficacy trial data

   This article has 3 authors:

   1. Manar Alkuzweny
   2. Guido España
   3. T Alex Perkins

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This paper presents important new findings about the impact of the TAK-003 vaccine against dengue based on a convincing reanalysis of trial data. The results corroborate those of the original trial analyses, but with reduced uncertainty about the estimates of the impact of the vaccine. The findings will be of interest to clinicians, infectious disease epidemiologists, trial statisticians and policymakers seeking to understand the vaccine's efficacy profile and associated uncertainties.

   Reviewed by eLife

7. Two time scales of adaptation in human learning rates

   This article has 8 authors:

   1. Jonas Simoens
   2. Senne Braem
   3. Pieter Verbeke
   4. Haopeng Chen
   5. Stefania Mattioni
   6. Mengqiao Chai
   7. Nicolas W Schuck
   8. Tom Verguts

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study makes a valuable contribution by separating two timescales of adaptation: rapid, within block reductions in learning rate, and slower, location specific, meta-learned adjustments. Behavioural data and computational modeling converge to support both processes. The evidence is solid with neuroimaging results suggesting that meta-learned learning rates are encoded in the orbitofrontal cortex, while prediction errors are represented in a distributed network including the ventral striatum and are modulated by expected error magnitude, though the specificity of these effects requires further contextualization. The manuscript is timely and clearly written; its main limitation is the weak linkage between neural signals and behavior, leaving uncertainty over whether the reported signals play a mechanistic role in learning.

   Reviewed by eLife

8. Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels

   This article has 12 authors:

   1. Kurt Weir
   2. Pin Lyu
   3. Sangeetha Kandoi
   4. Roujin An
   5. Nicole Pannullo
   6. Isabella Palazzo
   7. Jared A Tangeman
   8. Jun Shi
   9. Steven H DeVries
   10. Dana K Merriman
   11. Jiang Qian
   12. Seth Blackshaw

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study investigates why the 13-lined ground squirrel (13LGS) retina is unusually rich in cone photoreceptors, the cells responsible for color and daylight vision. The authors perform deep transcriptomic and epigenetic comparisons between the mouse and the 13-lined ground squirrel (13LGS) to provide convincing evidence that identifies mechanisms that drive rod vs cone-rich retina development. Overall, this key question is investigated using an impressive collection of new data, cross-species analysis, and subsequent in vivo experiments. However, the functional analysis showing the sufficiency and necessity of Zic3 and Mef2C remains incomplete, and further analyses are needed to support the claim that these enhancers are newly evolved in 13LGS.

   Reviewed by eLife

9. Comparing the outputs of intramural and extramural grants funded by National Institutes of Health

   This article has 5 authors:

   1. Xiang Zheng
   2. Qiyao Yang
   3. Jai Potnuri
   4. Chaoqun Ni
   5. B Ian Hutchins

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study used five metrics to compare the cost-effectiveness of intramural and extramural research funded by the National Institutes of Health in the United States between 2009 and 2019. They found that each type of research had its own set of strengths: extramural research was more cost-effective in terms of publications, whereas intramural research was more cost-effective in terms of influencing clinical work. The evidence supporting these findings is mostly solid, but there are a number of questions about the methods and data - notably about indirect cost recovery and other non-NIH sources of funding - that need to be answered.

   Reviewed by PREreview, eLife

10. Squidly: Enzyme Catalytic Residue Prediction Harnessing a Biology-Informed Contrastive Learning Framework

    This article has 4 authors:

    1. William JF Rieger
    2. Mikael Boden
    3. Frances Arnold
    4. Ariane Mora

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      The authors make an important advance in enzyme annotation by fusing biochemical knowledge with language‑model-based learning to predict catalytic residues from sequence alone. Squidly, a new ML method, outperforms existing tools on standard benchmarks and on the CataloDB dataset. The work has solid support, yet clarifications on dataset biases, ablation analyses, and uncertainty filtering would strengthen its efficiency claims.

    Reviewed by eLife