Evaluated articles

eLife assessment

The study presents an important ecosystem designed to support literature mining in biomedical research, showcasing a methodological framework that includes tools like Pubget for article collection and labelbuddy for text annotation. The solid evidence presented for these tools suggests they could streamline the analysis and annotation of scientific literature, potentially benefiting research across a range of biomedical disciplines. While the primary focus is on neuroimaging literature, the applicability of these methods and tools might extend further, offering an advance in the practices of meta-research and literature mining.

eLife assessment

This useful manuscript describes a proteomic analysis of plasma from subjects before and after an exercise regime consisting of endurance and resistance exercise. The work identifies a putative new exerkine, CD300LG, and finds associations of this protein with aspects of insulin sensitivity and angiogenesis. The characterization remains incomplete at present. Because CD300LG may have a transmembrane domain, one possibility is that exercise causes the release of extracellular vesicles containing this protein. As this study reports associations, additional studies will be needed to establish causality. The paper will hopefully prompt further studies to more fully elucidate the underlying biology.

eLife assessment

ImmCellTyper presents a useful toolkit for CyTOF data analysis, integrating BinaryClust for semi-supervised clustering and cell type annotation. The evidence supporting the findings is convincing, with appropriate and validated methodology. This tool will be helpful to researchers in immunology and cytometry, offering a robust solution for cell type identification and differential analysis.

eLife Assessment

This work explores the physical principles underlying fluid flow and luminal transport within the endoplasmic reticulum. Its important contribution is to highlight the strong physical constraints imposed by viscous dissipation in nanoscopic tubular networks. In particular, the work presents convincing evidence based on theoretical analysis that commonly discussed mechanisms such as tubular contraction are unlikely to be at the origin of the observed transport velocities. As such, it will be of relevance to cell biologists and physicists interested in organelle dynamics. As this study is solely theoretical and deals with order of magnitude estimates, its main conclusions await experimental validation.

eLife assessment

This study provides important new insight into how non-synaptic interactions affect the activity of adjacent gustatory neurons housed within the same sensillum. The conclusions are supported by convincing electrophysiological, behavioral, and genetic data. This work will be of interest to neuroscientists studying chemosensory processing or regulation of neuronal excitability.

eLife assessment

This important computational study provides new insights into how neural dynamics may lead to time-evolving behavioral errors as observed in certain working-memory tasks. By combining ideas from efficient coding and attractor neural networks, the authors construct a two-module network model to capture the sensory-memory interactions and the distributed nature of working memory representations. They provide convincing evidence supporting that their two-module network, although none of the alternative circuit structures they considered can account for error patterns reported in orientation-estimation tasks with delays.

eLife Assessment

The authors describe a model for tracking time-varying functional connectivity between neurons from multi-electrode spike recordings. This is an interesting and potentially useful approach to an open problem in neural data analysis, and could be an essential tool for investigating the neural code from large-scale in-vivo recordings of spiking activity. However, the evidence is incomplete: systematic comparisons with existing methods and/or demonstration of its utility relative to conventional methods are essential to demonstrate the usefulness of the method.

eLife Assessment

This important study reports human single-neuron recordings in subcortical structures while participants performed a tactile detection task around the perceptual threshold. The study and the analyses are well conducted and provide convincing evidence that the thalamus and the subthalamic nucleus contain neurons whose activity correlates with the task, with stimulus presentation, and even with whether the stimulation is consciously detected or not. The study will be relevant for researchers interested in the role of subcortical structures in tactile perception and the neural correlates of consciousness.

eLife Assessment

This valuable contribution to the field evaluated the function of the cytoskeletal protein ABBA in mediating key aspects of mitosis of neuronal precursor cells. The authors provide compelling evidence that ABBA interactions with its signaling partners is related to the development of at least some cases of microcephaly — a developmental anomaly associated with intellectual disability and other neurological findings.

eLife Assessment

This work describes a circadian regulation in the expression of HERP, a regulator of endoplasmic reticulum calcium, in primary astrocytic cultures. This work is important because it highlights the potential importance of circadian rhythms in astrocytes, even though making a direct comparison between these rhythms in vitro and in vivo remains challenging. The technical approaches used in this work (RNA-seq, siRNA, Ca2+ imaging) are a solid support for data interpretation.

eLife assessment

The authors report that optogenetic inhibition of hippocampal axon terminals in retrosplenial cortex impairs the performance of a delayed non-match to place task. Elucidating the role of hippocampal projections to the retrosplenial cortex in memory and decision-making behaviors is important. However, the strength of evidence for the paper's claims is incomplete.

eLife Assessment

In this useful study, the authors present convincing evidence linking the enzyme D-alanine-D-alanine ligase (Ddl), crucial for cell wall fortification, to organic acid exposure in Staphylococcus aureus. While it's established that organic acids impede bacterial growth, the researchers reveal a novel coping mechanism where S. aureus maintains elevated levels of D-alanine, the substrate for Ddl, to counteract this inhibition. This discovery illuminates a bacterial strategy for organic acid tolerance, offering new insights for microbiologists and potentially informing future antimicrobial approaches.

eLife assessment

This important study reports a novel approach to studying cerebellar function based on the idea of selective recruitment using fMRI. It provides convincing evidence for task-dependent gating of neocortical input to the cerebellum during a motor task and a working memory task. The study will be of interest to a broad cognitive neuroscience audience.

eLife assessment

This elegant study presents important findings into how small molecules that were originally developed to inhibit the oncogenic kinase, BRAF, instead trigger activation of this kinase target. Compelling and comprehensive evidence supports a new allosteric model to explain the paradoxical activation. This rigorous work will be of great interest to biochemists, structural biologists, and those working on strategies to inhibit kinases in the context of human disease.

eLife Assessment

This valuable study provides convincing evidence that white matter diffusion imaging of the right superior longitudinal fasciculus might help to develop a predictive biomarker of chronic back pain chronicity. The results are based on a discovery-replication approach with different cohorts, but the sample size is limited. The findings will interest researchers interested in the brain mechanisms of chronic pain and in developing brain-based biomarkers of chronic pain.

eLife Assessment

In this valuable study the authors use electrophysiology in brain slices and computer modeling and suggest that layer 2/3 pyramidal neurons of the mouse cortex have functional HCN channels on the proximal apical dendrite which allows distinct processing of input at that location from the input to distal apical dendrites. The revisions improved the solid paper but some of the concerns were not addressed sufficiently and many of these concerns could be addressed by further revision.

eLife assessment

In this important study, the authors use a genetically engineered mouse model to reveal a tumor suppressive role for focal adhesion kinase in right-sided colon cancer. The evidence in support of the authors' claims is generally solid, although the data supporting the mechanism through which FAK deletion promotes tumorigenesis are incomplete. This work will be of interest to cancer researchers and others studying the biological consequences of tuning signal transduction pathways.