Evaluated articles

eLife Assessment

This fundamental work advances our understanding of how SP5 and SP8 promote neuromesodermal competent progenitors in murine embryos. Generally the evidence is compelling, with strong developmental genetics, transcriptomic, and genomic transcription binding surveys contributing to the strength of the data. Some of the language could be softened to avoid overinterpretation of the data, and figures and diagrams could be improved.

eLife Assessment

This study presents a valuable and rigorous molecular resource, offering subtype-specific insight into the composition of ribosome-associated protein complexes in the developing cerebral cortex. The evidence is compelling in terms of data quality and is strongly supported by the results, given the rigorous technical execution. However, the findings remain primarily descriptive, as the study lacks functional validation to support mechanistic conclusions.

eLife Assessment

In this fundamental manuscript, Richter et al. present a thorough anatomical characterization of the Drosophila melanogaster larval pharyngeal sensory system, which is involved in taste-guided behaviors. This study fills a major gap in the larval sensory map, providing a compelling neuroanatomical foundation for future investigations into sensory circuits and behavior. The data presented here are of exceptional quality and will be of interest to the Drosophila neurobiology community.

eLife Assessment

This is an important study on how dissociable emotions of shame and guilt emerge from cognitive processes and guide behavioral responses. The task is well designed and yields compelling behavioral, computational, and neural evidence elucidating the cognitive link between emotions and compensatory decisions. The work has broad theoretical and practical implications across a range of disciplines concerned with human behavior, including psychology, neuroscience, economics, public policy, and psychiatry.

eLife Assessment

This manuscript uses modeling approaches to provide mechanistic insight into the structural and dynamic properties of enhancer-promoter interactions in Drosophila. Given the interest in this field, this is a timely approach, and the results give useful insights by providing predictions about the processivity of cohesin loop extrusion in Drosophila and concluding that the compartmental interaction strength is poised near criticality in the coil-globule phase space. The evidence provided to support some of the conclusions is, however, incomplete and would be strengthened by better considering some of the caveats in the data used to constrain the models, such as the use of "homie" genetic elements in the dynamic data. There is insufficient evidence provided for the dynamics being criticality-driven, and in addition, consideration of alternative models would further strengthen the conclusions of the manuscript.

eLife Assessment

This important work describes the adaptation and evaluation of two red-shifted anion channelrhodopsins (RubyACRs) for optogenetic inhibition in Drosophila. The study provides convincing evidence for the effectiveness of RubyACRs in fly neurons, including electrophysiology, calcium imaging, and behavioral analysis. With minor revisions to address potential toxicity and compatibility with 2-photon imaging, this paper and the publicly available fly lines it describes will be resources that are of value to the neuroscience community.

eLife Assessment

This manuscript is useful as it demonstrates that Rv2577, a Fe³⁺/Zn²⁺-dependent metallophosphatase, is secreted by Mycobacterium bovis BCG and localizes to the nucleus of mammalian cells, altering transcriptional and inflammatory responses. However, the study is incomplete as it lacks activity validation in macrophage cells and with virulent Mycobacterium tuberculosis strains. It is necessary to confirm Rv2577 secretion from a virulent strain and to clarify the direct or indirect role of MmpE in modulating host pathways, together with mechanistic insight into how MmpE influences lysosomal biogenesis and trafficking.

eLife Assessment

Weindel et al examine behavioural and EEG data in an innovative contrast comparison paradigm where they vary mean contrast widely while keeping contrast difference constant. As intended, this allowed an elegant decomposition of processing stages: while sensory encoding shortened with increasing contrast in keeping with Pieron's law, the period of decision formation lengthened, in keeping with Fechner's law, which was applied to drift rates in a diffusion model of that period. This is an important demonstration of how these two laws apply in concert, to two distinct processing levels, and the multivariate topography parsing, mixed effect models and diffusion models are convincing.

eLife Assessment

This manuscript reports the development and characterization of iGABASnFR2, a genetically encoded GABA sensor that demonstrates substantially improved performance compared to its predecessor, iGABASnFR1. The work is comprehensive and methodologically rigorous, combining high-throughput mutagenesis, functional screening, structural analysis, biophysical characterization, and in vivo validation. The significance of the findings is fundamental, and the supporting evidence is compelling. iGABASnFR2 represents a notable advance in GABA sensor engineering, enabling enhanced imaging of GABA transmission both in brain slices and in vivo, and constitutes a timely, technically robust addition to the molecular toolkit for neuroscience research.

eLife Assessment

The study introduces a valuable dataset for investigating the relationship between vision and language in the brain. The authors provide convincing evidence that decoders trained on brain responses to both images and captions outperform those trained on responses to a single modality. The dataset and decoder results will be of interest to communities studying brain and machine decoding.

eLife Assessment

This valuable study uses fiber photometry, implantable lenses, and optogenetics, to show that a subset of subthalamic nucleus neurons are active during movement, and that active but not passive avoidance depends in part on STN projections to substantia nigra. The strength of the evidence for these claims is solid, whereas evidence supporting the claims that STN is involved in cautious responding is unclear as presented. This paper may be of interest to basic and applied behavioural neuroscientists working on movement or avoidance.

eLife Assessment

This is an important study that takes a key step towards understanding developmental disorders linked to mutations in the O-GlcNAc transferase enzyme by generating a mouse model harboring the C921Y mutation. The study thoroughly examines behavioral and anatomical differences in these mice and finds behavioral hyperactivity and learning/memory deficits, as well as phenotypic differences in skull and brain formation. However, the experimental evidence is incomplete owing to discrepancy in OGT protein/RNA levels in the C921Y mutant mice in this paper and the previous paper ("Neurodevelopmental defects in a mouse model of O-GlcNAc transferase intellectual disability "). This line of research will benefit from investigation of the differences in associated glycoproteins and mechanistic insights. This study will be of interest to those studying neurodevelopment, learning and behavior, or associated brain mechanisms.

eLife Assessment

This study provides new important insights concerning pathogen variant-specific reproduction parameters from molecular sequencing and case finding. The methods for inferring which variants will likely emerge in subsequent epidemic cycles are solid. This article is of broad interest to infectious disease epidemiology researchers and mathematical modellers of the COVID-19 pandemic.

eLife Assessment

This valuable study combined careful computational modeling, a large patient sample, and replication in an independent general population sample to provide a computational account of a difference in risk-taking between people who have attempted suicide and those who have not. It is proposed that this difference reflects a general change in the approach to risky (high-reward) options and a lower emotional response to certain rewards. Evidence for the specificity of the effect to suicide, however, is incomplete, which would require additional analyses.

eLife Assessment

This valuable study concerns a highly interesting and biologically relevant topic, the regulation of the PIN auxin transporter, which is of broad interest to the plant biology community. The authors propose NPY1 to act downstream of PID in auxin-mediated development by modulating PIN phosphorylation, which, if experimentally solidified, would expand our understanding of PIN regulation. While the genetic evidence is solid, the mechanistic role of NPY1 and the functional relevance of phosphorylated PIN residues are still uncertain. There are also concerns regarding experimental rigor and methodological transparency.

eLife Assessment:

This study addresses valuable questions about the neural mechanisms underlying statistical learning of room acoustics, combining robust behavioral measures with non-invasive brain stimulation. The behavioral findings are strong and extend previous work in psychoacoustics, but the TMS results are modest, with methodological limitations and over-interpretation that weaken the mechanistic conclusions. The strength of evidence is therefore incomplete, and a more cautious interpretation of the stimulation findings, alongside strengthened analyses, would improve the manuscript.

eLife Assessment

This important study presents a cross-species and cross-disciplinary analysis of cortical folding. The authors use a combination of physical gel models, computational simulations, and morphometric analysis, extending prior work in human brain development to macaques and ferrets. The findings support the hypothesis that mechanical forces driven by differential growth can account for major aspects of gyrification. The evidence presented is overall strong and convincingly supports the central claims; the findings will be of broad interest in developmental neuroscience.

eLife Assessment

This important study characterises the morphogenesis of cortical folding in the ferret and human cerebral cortex using complementary physical and computational modelling. Notably, these approaches are applied to charting, in the ferret model, known abnormalities of cortical folding in humans. The study finds convincing evidence that variation in cortical thickness and expansion account for deviations in morphology, and supports these findings using cutting-edge approaches from both physical gel models and numerical simulations. The study will be of broad interest to the field of developmental neuroscience.

eLife Assessment

This is an important study reporting a new phenotype for a gene cluster that has previously been associated with the responses of the Gram-negative opportunistic pathogen Pseudomonas aeruginosa to flow fluid. Expression of the froABCD gene cluster is induced by HOCl in vitro and by activated immune cells, which produce these types of reactive chlorine species. Overall, the evidence presented by the authors is solid; however, the mechanism of fro-induction by HOCl remains unclear, and the evidence in support of the authors' claims is descriptive, which needs to be improved. This study is of interest to infection biologists interested in mechanisms of bacterial pathogenicity.

eLife Assessment

The authors develop an important microfluidic microvascular model called "Vessel-on-Chip", which they use to study Neisseria meningitidis interactions within this in vitro vascular system. Compelling evidence shows that the fabricated channels are lined by endothelial cells, and these can be colonized by N. meningitidis that in turn triggers neutrophil recruitment. This model has advantages over the human skin xenograft mouse model, which requires complex surgical techniques, however, it also carries limitations in that only endothelial cells and supplied specific immune cells in the microfluidics are present, while true vasculature contains a number of other cell types including smooth muscle cells, pericytes, and components of the immune system.

[Editors' note: this paper was reviewed by Review Commons.]