Evaluated articles

eLife Assessment

This study identifies a role for YAP in regulating tumor cell growth and drug response with differential effects noted based upon growth conditions in monolayer vs spheroid culture. This work has the potential to define more biologically relevant cell culture model systems for drug resistance and define targetable pathways to overcome drug resistance. The findings described are important to the cancer biology field and the evidence supporting the key findings is convincing.

eLife Assessment

This fundamental work has the potential to advance our understanding of brain activity using electrophysiological data, by proposing a completely new approach to reconstructing EEG data that challenges the assumptions typically made in the solutions to Maxwell's equations. However, the evidence supporting the approach is incomplete and requires further evaluations, in particular comparisons with existing, standard reconstruction methods. The work may be of broad interest to neuroscientists and neuroimaging.

eLife Assessment

This valuable study introduces a self-supervised machine learning method to classify C. elegans postures and behaviors directly from video data, offering an alternative to the skeleton-based approaches that rely on often error-prone tracking. This novel approach holds promise for advancing ethology research. That said, the strength of evidence is currently incomplete, as key aspects - including measuring head-tail orientation, increased behavioral interpretability, and quantitative comparisons to established methods - are underdeveloped and would benefit from further validation.

eLife Assessment

This paper presents important findings regarding the rhythmicity of overlapping target and distractor processing and how this affects behaviour. The methods are, in general, clearly laid out and defensible; however, the evidence supporting the central claims is incomplete due to potential biases in the analysis methods. Further control analyses would be beneficial and could greatly strengthen the conclusions that can be drawn from these data.

eLife Assessment

This carefully conducted study aims to understand how the early visual experience of premature infants induces lasting deficits, including compromised motion processing. This important question is addressed in a ferret animal model, in which the developing visual system was exposed prematurely to patterned visual input by opening one or both eyes early, at a time when both retinal waves and light traveling through closed lids drive sensory responses. Convincing evidence is presented, suggesting that eye opening at this time impacts temporal frequency tuning and elevates spontaneous firing rates. These findings will have great relevance for neuroscientists studying visual system development, particularly in the context of premature birth.

eLife Assessment

This study proposes an updated analysis technique that allows researchers to identify rhythms in behavior. If the proposed analyses control the rate of false positives, this will be an important contribution for all neuroscientists interested in rhythmic cognition. At present, the strength of evidence is incomplete, as the simulations ignore one crucial aspect of temporal structure in behavior.

eLife Assessment

This important study uses an innovative task design combined with eye tracking and fMRI to distinguish brain regions that encode the value of individual items from those that accumulate those values for value-based choices. It shows that distinct brain regions carry signals for currently evaluated and previously accumulated evidence. The study provides solid evidence in support of most of its claims, albeit with current minor weaknesses concerning the evidence in favour of gaze-modulation of the fMRI signal. The work will be of interest to neuroscientists working on attention and decision-making.

eLife Assessment

This study provides important insights into the CO₂-dependent activation of Cx43 hemichannels through a well-defined carbamylation motif, supported by multiple independent assays and validation in hippocampal tissue. The evidence convincingly demonstrates that increased pCO₂ enhances Cx43 hemichannel activity, which has potential implications for cellular signaling in cardiomyocytes and astrocytes. While further investigation is needed to fully elucidate the structural mechanisms, the findings offer a foundation for future research in gap junction biology and CO₂ regulation of proteins.

eLife Assessment

This important study shows that nutrient stress emanating from the microenvironment induces metabolic vulnerabilities in pancreatic ductal adenocarcinoma (PDAC). Using a combination of cell-based and mouse models, the authors provide compelling evidence showing that arginine restriction in the microenvironment disrupts lipid homeostasis in PDAC, resulting in the induction of ferroptosis upon exposure of tumors to polyunsaturated fatty acids. This report is likely to be of broad interest to researchers interested in studying cancer biology, tumor microenvironment, metabolism, and stress adaptation mechanisms.

eLife Assessment

This study presents a valuable finding that KDM5 inhibition activates the interferon response and antigen presentation genes in breast cancer cells through R-loops. The evidence supporting the claims of the authors is solid, although the inclusion of further in vivo studies displaying the effects of KDM5 inhibitors on the immunotherapy responses of breast tumors would have strengthened the study. The work will be of interest to scientists working in the field of breast cancer immunotherapy.

eLife Assessment

This important study investigates how neural representations in the postrhinal and medial entorhinal cortices evolve with the learning of a visual associative memory task in mice. The findings provide new insights into how non-spatial information is differentially encoded across interconnected brain areas, with strong evidence that stimulus encoding is robust in the postrhinal cortex and emerges more weakly in the medial entorhinal cortex with learning. The evidence is solid overall, particularly in the use of sophisticated population-level analyses and two-photon imaging across learning phases, although the interpretation of regression models and clustering would benefit from additional clarity and control. The work will be of broad interest to systems neuroscientists studying learning, memory, and cortical circuit function.

eLife Assessment

This study presents a valuable finding on the direct cytotoxic effects of DuoHexaBody-CD37 in diffuse large B-cell lymphoma, mediated via SHP-1 activation and antibody clustering, independent of complement. The evidence supporting this mechanism is incomplete, with additional work needed to clarify SHP-1's role, the contribution of Fc receptor crosslinking, and the biological relevance across normal and malignant B cells. As the findings are based primarily on in vitro models, further validation would be required to support broader translational conclusions.

eLife Assessment

The granularity with which neural activity in the sensorimotor cortex of mice corresponds to voluntary forelimb motion is a key open question. This paper provides convincing evidence for the encoding of low-level features like joint angles and represents an important step forward toward understanding the cortical origins of limb control signals.

eLife Assessment

The article presents important findings describing the role of IL27 in maintaining HSCs at steady state, and in emergency haematopoiesis in response to T. goodii by limiting the inflammatory monocyte outcomes. However, the evidence is still incomplete, as not enough evidence is provided to support that IL27 only acts at the level of HSCs and not downstream. This study will be of interest to immunologists and hematologists, as well as infectious disease researchers.

eLife Assessment

This study addresses the structural basis of voltage-activation of BK channels using atomistic simulations of several microseconds, to assess conformational changes that underlie both voltage-sensing and gating of the pore. Simulated effects of voltage on the movement of charged amino acids appear solid as they are generally consistent qualitatively and quantitatively with previous experimental and structural results, providing a potentially valuable way to calculate the contribution of individual charges to voltage-sensitivity. Simulations of conformational changes and interactions associated with channel opening and K+ conduction are likely incomplete owing to the timescale of the simulation and theoretical limitations in simulating K+ and water movement, but nonetheless provide helpful initial predictions and a framework for future improvement. This paper will likely be of interest to ion channel biologists and biophysicists focused on voltage-dependent channel gating mechanisms.

eLife Assessment

This important study uses standard single-cell RNA-seq analyses combined with methods from the social sciences to assess heterogeneity in gene expression in Drosophila imaginal wing disc cells treated with 4000 rads of ionizing radiation. The use of this methodology from social sciences is novel in Drosophila. A cell cycle based clustering approach allows them to identify a subpopulation of cells that is disproportionately responsible for much of the radiation-induced gene expression. Their convincing analyses reveal genes that are expressed regionally after irradiation, including ligands and transcription factors that have been associated with regeneration, as well as others whose roles in response to irradiation are unknown. This paper would be of interest to researchers in the field of DNA damage responses, regeneration, and development.

eLife Assessment

This useful study reports a method to detect and analyze a novel post-translational modification, lysine acetoacetylation (Kacac), finding it regulates protein metabolism pathways. The study unveils epigenetic modifiers involved in placing this mark, including key histone acetyltransferases such as p300, and concomitant HDACs, which remove the mark. Proteomic and bioinformatics analysis identified many human proteins with Kacac sites, potentially suggesting broad effects on cellular processes and disease mechanisms. While the data presented are solid, the functional validation of the sites would add significantly to the manuscript's description of this modification; the study will be of interest to those studying protein and metabolic regulation.

eLife Assessment

The authors show that an automated approach using artificial neural networks, which focuses on behaviourally relevant dimensions, can predict human similarity data up to a certain level of granularity. This study has the potential to be a valuable contribution to the broader field of cognitive computational neuroscience, as it provides a tool for the automated collection of similarity judgments under certain conditions. However, as of now, the significance of this method is somewhat limited because of its inability to generalise beyond between-category distinctions and the limited model evaluation. In terms of broader implications, the degree to which this work provides insights into DNN-brain alignment and a better understanding of the functional organisation of the visual system is supported by incomplete evidence.

eLife Assessment

This valuable study demonstrates that silencing of inhibitory interneurons in zebra finch HVC, a premotor nucleus critical for song production, disrupts song. However, song naturally recovers in a way that is surprisingly independent of LMAN, a distinct premotor nucleus required for normal song plasticity. The authors provide solid evidence that disruption is associated with microglial activation, activation of MHCI, synaptic changes, and altered neural dynamics in HVC. However, the manuscript would benefit from a clearer narrative structure, contextualization of the microglial results, and quantitative analyses to fully characterize song syntax and recovery after LMAN lesions.

eLife Assessment

This paper describes the study of the evolution of the N-terminal domain of the MSH6 mismatch repair protein in regard to the presence or absence of histone reader domains. While the presence of the histone reader domains was previously known, the phylogenetic analysis of these domains performed here establishing their insertion through convergent evolution is important, definitively done, and establishes an interesting feature of the MSH6 family of proteins. The work is convincing but the presentation of the structural features of MSH6 could be improved.