eLife Assessment

Clonal hematopoiesis of indeterminate potential (CHIP) is a known risk factor for coronary artery disease, though its precise role in disease progression continues to emerge. This study leverages valuable single-cell RNA data from patients with CHIP mutations and controls to predict key interactions between endothelial cells and monocytes. Using an AI prediction model, the authors identify druggable targets that mediate immune cell interactions in CHIP and provide solid evidence to support their findings.

eLife Assessment

This important study presents a thoughtful design and characterization of chimeric influenza hemagglutinin (HA) head domains combining elements of distinct receptor-binding sites. The results provide convincing evidence that polyclonal cross-group responses to influenza A virus can be elicited by a single immunization. While the mechanistic basis of heterotrimer formation and immunodominance differences remains unclear, the authors provide new insights for protein design, vaccinology, and computational vaccine design.

eLife Assessment

This fundamental work reveals that the accessibility of the unstructured C-terminal tails of α- and β-tubulins differs with the state of the microtubule lattice. Their accessibility increases with the expansion of the lattice induced by GTP and certain MAPs, which can then dictate the subsequent interactions between MAPs and microtubules, and post-translational modifications of tubulin tails. The evidence supporting the conclusion is compelling, although the characterisation of the probes does not answer whether they directly affect the lattice or expose the C-terminal tails of tubulin. This work will be of great interest to the cytoskeleton field.

eLife Assessment

This valuable study presents EM structures of new conformational states of the LONP1 AAA+ protease in conjunction with the mitochondrial protein substrates (StAR, TFAM), along with biochemical functional assays. The EM structures revealed new conformational states in a closed configuration. The structures and associated functional results are solid. However, a notable weakness is the absence of substrates found threaded through the ATPase pores.

eLife Assessment

The manuscript concerns a fundamental and controversial question in Trypanosoma brucei biology and the parasite life cycle, providing further evidence that slender bloodstream forms can indeed infect Tsetse flies. The study is solid in design and execution, and addresses several criticisms made of the authors' earlier work. Nevertheless, some of the main conclusions are only partially supported: one issue is how, precisely, a "slender" bloodstream form is defined, and discrepancies with some results from other laboratories remain unexplained.

eLife Assessment

The authors present a set of wrappers around previously developed software and machine-learning toolkits, and demonstrate their use in identifying endogenous sterols binding to a GPCR. The resulting pipeline is potentially useful for molecular pharmacology researchers due to its accessibility and ease of use. However, the evidence supporting the GPCR-related findings remains incomplete, as the machine-learning model shows indications of overfitting, and no direct ligand-binding assays are provided for validation.

eLife Assessment

This study provides valuable insights into the evolutionary conservation of sex determination mechanisms in ants by identifying a candidate sex-determining region in a parthenogenetic species. It uses solid, well-executed genomic analyses based on differences in heterozygosity between females and diploid males. While the candidate locus awaits functional validation in this species, the study provides convincing support for the ancient origin of a non-coding locus implicated in sex determination.

eLife Assessment

The manuscript presents important findings that advance our understanding of how microglia adapt their surveillance strategies during chronic neurodegeneration. The evidence presented is convincing, with appropriate and validated methodology broadly supporting the claims given by the authors.

eLife Assessment

This study introduces a valuable new metric-phenological lag-to help partition the drivers of observed versus expected shifts in spring phenology under climate warming. The conceptual framework is clearly presented and supported by an extensive dataset, and the revisions have improved the manuscript, though some concerns-particularly regarding uncertainty quantification, spatial analysis, and modeling assumptions-remain only partially addressed. The strength of evidence is generally solid, but further analysis would help to validate the study's conclusions.

eLife Assessment

This study provides novel and convincing evidence that both dopamine D1 and D2 expressing neurons in the nucleus accumbens shell are crucial for the expression of cue-guided action selection, a core component of decision-making. The research is systematic and rigorous in using optogenetic inhibition of either D1- or D2-expressing medium spiny neurons in the NAc shell to reveal attenuation of sensory-specific Pavlovian-Instrumental transfer, while largely sparing value-based decision on an instrumental task. The important findings in this report build on prior research and resolve some conflicts in the literature regarding decision-making.

eLife Assessment

This paper addresses the significant question of quantifying epistasis patterns, which affect the predictability of evolution, by reanalyzing a recently published combinatorial deep mutational scan experiment. The findings are useful, showing that epistasis is fluid, i.e. strongly background dependent, but that fitness effects of mutations are statistically predictable based on the background fitness. While the general approach appears solid, some claims remain incompletely supported by the analysis, as arbitrary cutoffs are used and the description of methods lacks specifics. This analysis should be of interest to the community working on fitness landscapes.

eLife Assessment

Computational simulation of neuron function depends on a collection of morphological properties and ion channel biophysics. This manuscript introduces DendroTweaks, a valuable web application and Python library that eases interactive exploration, development, and validation of single-neuron models in an easily installable and well-documented package. The authors provide a convincing demonstration that their software aids with building intuition and rapid prototyping of biophysical models of neurons, which improves the accessibility of dendritic simulation.

eLife Assessment

This is an important study with convincing evidence that multi-voxel fMRI activity patterns for threat-conditioned stimuli are altered by learning CS-US contingencies. The analyses are dense, but rigorous. The protocol is quite nuanced and complex, but the authors have done a fair job of explaining and presenting the results. The work is relevant for our understanding of how effective learning changes neural stimulus representation in the human brain.

eLife Assessment

This important article reports on the role of specific interneurons in the motion processing circuitry of the fruit fly, and marshals convincing evidence from neural recording, genetic manipulation, and behavioral analysis. A significant result ties the activity of C2/C3 neurons to the temporal resolution of the motion vision system. It remains unclear whether disrupting this pathway affects the dynamics of vision more generally.

eLife Assessment

This important and compelling study establishes a robust computational and experimental framework for the large-scale identification of metallophore biosynthetic clusters. The work advances beyond current standards, providing theoretical and practical value across microbiology, bioinformatics, and evolutionary biology.

eLife Assessment

This study proposes a valuable and interpretable approach for predicting hematoma expansion in patients with spontaneous intracerebral hemorrhage from non-contrast computed tomography. The evidence supporting the proposed method is solid, including predictive performance evaluated through external validation. This quantitative approach has the potential to improve hematoma expansion prediction with better interpretability. The work will be of interest to medical biologists working on stroke and neuroimaging.

eLife Assessment

This important study presents findings on the patterned loss of Purkinje cells in the cerebellum during aging. The compelling data nicely support the conclusions of this study. This work advances understanding of mechanisms underlying neurodegeneration with aging and provides the basis for development of treatments for age-related neurological disorders.

eLife Assessment

The study presents important findings that are highly relevant for research aiming to combine transcriptomics, connectivity studies, and activity profiling in the rodent brain and the revisions improve the study. The evidence overall remains convincing as the authors use appropriate and validated methodology in line with current state-of-the-art.

eLife Assessment

This study provides novel and convincing evidence that both dopamine D1 and D2 expressing neurons in the nucleus accumbens shell are crucial for the expression of cue-guided action selection, a core component of decision-making. The research is systematic and rigorous in using optogenetic inhibition of either D1- or D2-expressing medium spiny neurons in the NAc shell to reveal attenuation of sensory-specific Pavlovian-Instrumental transfer, while largely sparing value-based decision on an instrumental task. The important findings in this report build on prior research and resolve some conflicts in the literature regarding decision-making.

eLife Assessment

This study provides novel and convincing evidence that both dopamine D1 and D2 expressing neurons in the nucleus accumbens shell are crucial for the expression of cue-guided action selection, a core component of decision-making. The research is systematic and rigorous in using optogenetic inhibition of either D1- or D2-expressing medium spiny neurons in the NAc shell to reveal attenuation of sensory-specific Pavlovian-Instrumental transfer, while largely sparing value-based decision on an instrumental task. The important findings in this report build on prior research and resolve some conflicts in the literature regarding decision making.

eLife Assessment

This useful study reports analyses of Neuropixel recordings in the medial prefrontal cortex and hippocampus of rats in a spatial navigation trial, focusing on classifying prefrontal neurons based on SWR modulation and anatomical location. Reviewers were unconvinced by the presented evidence for the claim that distinct populations of mPFC neurons participate in non-local ensemble representations during SWR and non-SWR periods, and were unconvinced by the presented evidence for a previously unrecognized anatomical distinction between these populations. Further analyses might strengthen the incomplete evidence for some conclusions, and some of the strong claims of the paper should likely be moderated.

eLife Assessment

This study provides valuable insights into the mechanisms of remote memory impairment in an Alzheimer's disease mouse model. The evidence is compelling, with careful use of viral-TRAP labeling and patch-clamp electrophysiology to demonstrate altered inhibitory microcircuit function, though the mechanistic link to memory deficits remains correlative. Overall, the work advances understanding of early circuit-level changes in AD, while highlighting open questions regarding causality and broader network contributions.

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 convincing. The authors have addressed most of the reviewers' concerns and help to further clarify the claims. The work will be of interest to neuroscientists working on glia-neuron interaction and synaptic remodeling.

eLife Assessment

This useful study describes a mechanism of microbial modulation of anti-tumor immunity, which is of considerable interest in the field. However, the experimental supports for the key mechanistic claim, the interaction between RadD and NKp46, are not robust. Multiple experimental inconsistencies, especially in vivo, weaken the conclusions, making the strength of evidence incomplete. Additional controls, direct binding assays, and clarification of in vivo mechanistic relevance would strengthen the work.

eLife Assessment

This work is an important contribution to understanding the role of FGF signaling in the induction of primitive-like cells in a 2D system of human gastrulation. The authors provide compelling evidence showing that endogenous FGF ligands, acting through FGF receptors localized basolaterally, are determinant in the acquisition of specific cell fates. These observations will be of broad relevance to the FGF field.

eLife Assessment

This fundamental study substantially advances our current understanding of mechanotransduction within endothelial cells. The evidence provided by the authors in the revised manuscript is compelling, which taken together, provides strong support for the authors' major findings. The work will be of broad interest to cell biologists and vascular biologists.

eLife Assessment

These valuable studies explore the consequences of exposure to the toxin hydrogen sulfide (H2S) on the behavior and physiology of C. elegans. The work finds that behavioral changes evoked by H2S exposure are modulated by several regulatory pathways known to influence chemosensory-evoked locomotor behavior, but there is incomplete data to support the authors' claim of comprehensive mechanistic insight into the consequences of H2S exposure. Nevertheless, the findings may be informative for those studying organismal stress responses and the effects of mitochondrial ROS on behavior and physiology.

eLife Assessment

This valuable study uses EEG and computational modeling to investigate hemispheric oscillatory asymmetries in unilateral spatial neglect. The work benefits from rare patient data and a careful multimethod approach. However, the evidence is incomplete because key assumptions about alpha‑band entrainment and methodological confounds such as lesion variability and eye‑movement artifacts remain insufficiently addressed.

eLife Assessment

This study presents an important toolkit for visualising the endogenous expression of four classes of neurotransmitter vesicular transporters. Using their toolkit, the authors find that there is co-transmission of neurotransmitters in over 10% of neurons tested. Although the evidence presented in the manuscript is solid, one weakness of this study is the failure of the authors to compare and contrast their results with available single-cell sequencing datasets and with well-established synaptic reporter lines (i.e., co-localization experiments). This toolkit will be of great use to multiple labs, and the authors should indicate their plan to disseminate the reagents and the associated information that is part of this kit.

eLife Assessment

This study introduces Megabouts, a transformer-based classifier for larval zebrafish movement bouts. This useful tool is thoughtfully implemented and has clear potential to unify analyses across labs. However, the evidence supporting its robustness is incomplete. How the method generalizes across datasets, how sensitive it is to noise, and the specific sources of misclassification are unclear. The method would also be strengthened by providing options for users to fine-tune the clusters under different experimental conditions, which would further enhance reliability and flexibility.

eLife Assessment

This valuable work potentially advances our understanding of melody extraction in polyphonic music listening by identifying spontaneous attentional focus in uninstructed listening contexts. However, the evidence supporting the main conclusions is incomplete. The work will be of interest to psychologists and neuroscientists working on music listening, attention, and perception in ecological settings.

eLife Assessment

This study provides an important contribution by showing that whiteflies and planthoppers use salivary effectors to suppress plant immunity through the receptor-like protein RLP4, suggesting convergent evolution in these insect lineages. The topic is of clear interest for understanding plant-insect interactions and offers ideas that could stimulate further research in the field. However, the strength of evidence is incomplete, as some aspects of the data and experimental design limit the extent to which the main claims are fully supported.

eLife Assessment

This manuscript provides a valuable contribution by identifying stress-responsive neurons in the supramammillary nucleus and their ventral subiculum inputs and assessing the regulation of anxiety-related behaviors. The evidence is convincing that the supramammillary nucleus contains stress-responsive neurons, and activation of these neurons increases anxiety-like behaviors. However, evidence that the ventral subiculum input to the supramammillary nucleus encodes and regulates anxiety and that the supramammillary nucleus generates an anxiety engram is incomplete. This work has the potential to offer new insights into how distinct circuits encode different emotional states and will be of interest to those interested in brain systems of aversive emotional and behavioral states.

eLife Assessment

This valuable study characterises receptors for calcitonin-related peptides from a deuterostomian animal, the echinoderm Apostichopus japonicus, by a combination of heterologous expression, pharmacological experiments, and the quantification of gene-expression levels. The authors provide convincing evidence for a functional calcitonin-related peptide system in the sea cucumber, but further work will be needed to confirm the proposed physiological functions of PDF receptor system in this species. This work should be of interest to scientists studying the signaling pathways, functions, and evolution of neuropeptides, and could be of relevance to improving the culture conditions of this economically key species.

eLife Assessment

This study presents results supporting a model that tumorous germline stem cells (GSCs) in the Drosophila ovary mimic the stem cell niche and inhibit the differentiation of neighboring cells. The valuable findings show that GSC tumors often contain non-mutant cells whose differentiation is suppressed by the GSC tumorous cells. However, the evidence showing that the GSC tumors produce BMP ligands to suppress differentiation of non-mutant cells is incomplete. It could be strengthened by the use of sensitive RNA in situ hybridization approaches.

eLife Assessment

This manuscript presents significant and important work that advances single-molecule imaging technology of transcription with simultaneous analysis of several parameters. However, currently, the evidence is incomplete and requires further quantitation/description of the technologies used, further controls, and additional analysis of the data by other methods.

eLife Assessment

This important study resolves the structure of one missing piece of the eukaryotic DNA replication fork, the leading strand clamp loader. Overall, the data are convincing, with electron microscopy data providing a strong basis for analyzing differences and similarities with other RFC complexes. A minor point is that the evidence supporting the proposed role of the β-hairpin is incomplete.

eLife Assessment

This valuable study uses single-molecule imaging to characterize factors controlling the localization, mobility, and function of RNase E in E. coli, a key bacterial ribonuclease central to mRNA catabolism. The supporting evidence for the differential roles of RNAse E's membrane targeting sequence (MTS) and the C-terminal domain (CTD) to RNAse E's diffusion and membrane association is convincing. It provides insight into how RNAse E shapes the spatiotemporal organization of RNA processing in bacterial cells. This interdisciplinary work will be of interest to cell biologists, microbiologists, biochemists, and biophysicists.

eLife Assessment

In their study, Neiswender et al. provide important insights into how BicD2 variants linked to spinal muscular atrophy alter dynein activity and cargo specificity. The authors present convincing evidence that disease-associated mutations lead to interactome changes, supported by additional validation of the BicD2/HOPS complex and discussion of their functional implications. This well-executed study offers invaluable datasets and a strong foundation for future exploration of disease mechanisms.

eLife Assessment

This study presents a fundamental discovery of how cerebellar climbing fibers modulate plastic changes in the somatosensory cortex by identifying both the responsible cortical circuit and the anatomical pathways. The evidence supporting the conclusions is convincing and well supported by modern neuroscience methodologies. Overall, this work represents a significant contribution that will be of broad interest to neuroscientists, especially those studying the long-distance cerebellar influence on non-motor brain functions.

eLife Assessment

This valuable manuscript presents findings supported by solid data to identify a surprising glia-exclusive function for betapix in vascular integrity and angiogenesis. The manuscript also describes the optimisation of a modified CRISPR-based Zwitch approach to generate conditional knockouts in zebrafish

eLife Assessment

This paper addresses the significant question of quantifying epistasis patterns, which affect the predictability of evolution, by reanalyzing a recently published combinatorial deep mutational scan experiment. The findings are that epistasis is fluid, i.e. strongly background dependent, but that fitness effects of mutations are predictable based on the wild-type phenotype. However, these potentially interesting claims are inadequately supported by the analysis, because measurement noise is not accounted for, arbitrary cutoffs are used, and global nonlinearities are not sufficiently considered. If the results continue to hold after these major improvements in the analysis, they should be of interest to all biologists working in the field of fitness landscapes.

eLife Assessment

This valuable study introduces the peptidisc-TPP approach as a promising solution to challenges in membrane proteomics, enabling thermal proteome profiling in a detergent-free system. The concept is innovative and holds significant potential, and the demonstration of its utility and validation is solid. The method presents a strong foundation for broader applications in identifying physiologically and pharmacologically relevant membrane protein-ligand interactions.

eLife Assessment

This valuable study reports the physiological function of a putative transmembrane UDP-N-acetylglucosamine transporter called SLC35G3 in spermatogenesis. The conclusion that SLC35G3 is a new and essential factor for male fertility in mice and probably in humans is supported by convincing data. This study will be of interest to reproductive biologists and physicians working on male infertility.

eLife Assessment

This study reports important negative results, showing that genetically removing the RNA-binding protein PTBP1 in astrocytes is insufficient to convert them into neurons, thereby challenging previous claims in the field. It also offers a compelling analysis of PTBP1's role in regulating astrocyte-specific splicing. The evidence is strong, as the experiments are technically sound, carefully controlled, and supported by both imaging and transcriptomic analyses.

eLife Assessment

This computational study examines how neurons in the songbird premotor nucleus HVC might generate the precise, sparse burst sequences that drive adult song. The findings would be useful for understanding how intrinsic conductances and HVC microcircuitry may produce neural sequences, but the work is incomplete because of arbitrary network assumptions, insufficient consideration of biological details such as how silent gaps in song sequences are represented, and failure to incorporate interactions with auditory and brainstem inputs. As a result, the study offers limited advance and only a modest conceptual advance over prior models.

eLife Assessment

This is a valuable analysis of STORM data that characterizes the clustering of active zones in retinogeniculate terminals across ages and in the absence of retinal waves. The design makes it possible to relate fixed time point structural data to a known outcome of activity-dependent remodeling. The latest revision has tempered the causal claims made in previous versions. The result provides solid structural support for the hypotheses regarding how activity influences the clustering of these synapses.

eLife Assessment

This important work advances our understanding of NMDAR diversity in the brain by providing evidence into the subunit arrangement, architecture, and activation mechanism of GluN1-N2-N3A tri-NMDAR. However, the evidence supporting the conclusions provides incomplete proof for the presence and functional properties of this NMDA receptor subtype. The work will be of broad interest to neuroscientists and biophysicists.

eLife Assessment

This important study sought to investigate the role that early childhood malaria exposure plays in the development of antibody responses to unrelated pathogens and vaccine-derived antigens in Kenyan children. In this natural experiment, the authors compare antibody levels among children who have been exposed to different levels of malaria transmission by using protein microarray technology. Although the findings are of importance, the evidence remains incomplete, and the analysis would benefit from a more in-depth evaluation of potential confounders. With the appropriate analysis, the findings will be of great interest for global health, immunology, and vaccine development.

eLife Assessment

This important work combines theoretical analysis with precise experimental perturbation to demonstrate that the Wnt signaling pathway is characterized by anti-resonance, or a suppression of pathway output at intermediate activation frequencies. The authors identify an anti-resonance behavior, with compelling evidence from optogenetic stimulation in multiple cell types, alongside modeling results that corroborate the phenomenon. While the demonstration of this phenomenon has yet to be extended to fully physiological situations, its clear existence within optogenetically stimulated systems shows that it is likely a significant factor that contributes to the behavior of this central signaling pathway.

eLife Assessment

This fundamental study presents a new method for longitudinally tracking cells in two-photon imaging data that addresses the specific challenges of imaging neurons in the developing cortex. It provides compelling evidence demonstrating reliable longitudinal identification of neurons across the second postnatal week in mice. The study should be of interest to development neuroscientists engaged in population-level recordings using two-photon imaging.

eLife Assessment

This is a valuable study that explores the role of the conserved transcription factor POU4-2 in the maintenance, regeneration, and function of planarian mechanosensory neurons. The authors present convincing evidence provided by gene expression and functional studies to demonstrate that POU4-2 is required for the maintenance and regeneration of mechanosensory neurons and mechanosensory function in planarians. Furthermore, the authors identify conserved genes associated with human auditory and rheosensory neurons as potential targets of this transcription factor.

eLife Assessment

This valuable manuscript presents an open-source and low-cost acoustic system for quantifying biting and chewing in mice. The approach is carefully validated against human observers, demonstrating strong methodological reliability and enabling high-resolution analysis of feeding microstructure. The tool has broad relevance for studies of appetite circuits and pharmacological interventions. A significant contribution is the identification of previously unrecognized "meal-related" neurons in the lateral hypothalamus, providing novel biological insight into food consumption. While the support for the methodological advances is compelling and robust, some circuit-level conclusions are preliminary or incomplete, relying on small pilot samples and manual classification, and should be interpreted with caution. This paper will be of interest to those interested in ingestive behavior and/or hypothalamus.

eLife Assessment

This paper is an important overview of the currently published literature on low-intensity focused ultrasound stimulation (TUS) in humans, providing a meta-analysis of this literature that explores which stimulation parameters might predict the directionality of the physiological stimulation effects. The overall synthesis is convincing. The database proposed by the paper has the potential to become a key community resource if carefully curated and developed.

eLife Assessment

This important study addresses a topic that is frequently discussed in the literature but is under-assessed, namely correlations among genome size, repeat content, and pathogenicity in fungi. Contrary to previous assertions, the authors found that repeat content is not associated with pathogenicity. Rather, pathogenic lifestyle was found to be better explained by the number of protein-coding genes, with other genomic features associated with insect association status. The results are considered solid, although there remain concerns about potential biases stemming from the underlying data quality of the analyzed genomes.

eLife Assessment

This valuable study uses a sophisticated array of techniques to investigate the mechanisms through which the chordotonal receptors in the locust ear (Müller's organ) sense auditory signals. Ultrastructural reconstruction of the sensory organ provides convincing evidence of the organization of the scolopidial structure that wraps the sensory neuron cilium. However, the recordings of sound-evoked motion and electrophysiological activity from the chordotonal sensory neurons provide incomplete evidence for the proposed axial stretch model of mechanotransduction.

eLife Assessment

This study provides new and interesting findings that SCoR2 acts as a denitrosylase to control cardioprotective metabolic reprogramming and prevent injury following ischemia/reperfusion. The compelling evidence is supported by a novel multi-omics approach, but questions remain regarding the stability and human relevance of BDH1 as well as the sufficiency of SCoR2. Overall, the work will be of interest to cardiovascular researchers and provides valuable information to the field, though some mechanistic aspects require further clarification.

eLife Assessment

Using high-throughput small-molecule screening, this study discloses novel modulators of the mitochondrial transcription factor A (TFAM), a key regulator of mitochondrial function. Reviewers viewed the targeting of TFAM as innovative and the study's conclusions as potentially important (especially the effects on inflammation). However, the lack of evidence for a direct effect of the compounds on TFAM activity weakens the paper's key conclusion and renders the study incomplete.

eLife Assessment

This study presents a useful inventory of genes that are up- and down-regulated in the mouse small intestine (duodenum and ileum) during the first postnatal month; the data were collected and analyzed using solid and validated methodology and can be used as a starting point for additional validation of specific markers and for follow-up functional studies. Some aspects of the study were incomplete, with claims being only partially supported by the data, and it is suggested that additional validation be performed. The authors attempted to correlate gene expression changes with periods of high and low NEC susceptibility, but these correlations are speculative and not supported by functional follow-up studies. Discussion of gene expression changes with NEC susceptibility would be more appropriate to include in the Discussion section and to be tempered in the results section.

eLife Assessment

This valuable study examined the roles of the posterior parietal cortex in rats performing an auditory change-detection decision task. It provided solid evidence for two subpopulations with opposing modulation patterns during decision formation and for a correspondence between neural and behavioral measures of the short timescale used for evidence evaluation.

eLife Assessment

This study presents valuable findings regardingg a rare mode of reproduction called hybridogenesis in a species pair of frogs. While parts of the study provide solid support for the claim of hybridogenesis, other parts are incomplete with certain claims being only partially supported, as alternative modes of reproduction cannot be fully ruled out.

eLife Assessment

This study provides valuable insights into the influence of sex on bile acid metabolism and the risk of hepatocellular carcinoma (HCC). The data to support that there are inter-relationships between sex, bile acids, and HCC in mice are convincing, although this is a largely descriptive study. Future studies are needed to understand the interaction of sex hormones, bile acids, and chronic liver diseases and cancer at a mechanistic level. Also, there is not enough evidence to determine the clinical significance of the findings given the differences in bile acid composition between mice and men.

eLife Assessment

This is an important study of critical period plasticity, focused on temperature manipulations, and how different parts of the Drosophila larval motor circuit adapt or maladapt. The work convincingly demonstrates that components of the motor network respond in distinct ways to the heat shock, and the combination of functional, structural, and electrophysiological approaches makes the study of significant interest. The work points to central interneurons as primary drivers of maladaptive changes, while motoneurons and neuromuscular junctions show compensatory or homeostatic adjustments. The study is methodologically rigorous, contributing significant insights into critical period biology using a tractable invertebrate model.

eLife Assessment

This study provides important evidence that negative affect is associated with slower cognitive processing in daily life, with findings replicated across three independent samples and supported by rigorous statistical analyses. The strength of evidence is convincing, though reliance on a proxy measure of processing speed limits the completeness of the conclusions.

eLife Assessment

This important work develops the C. elegans as a model organism for studying effort-based discounting by asking the worms to choose between patches of easy and hard to digest bacteria. The authors provide convincing evidence that the nematodes are effort discounting. They also provide solid evidence of involvement of dopamine in the food preference and that the finding is not restricted to lab-acclimated strains.

eLife Assessment

This important study combines behavioural psychophysics with image-computable models to contrast a view-selective model of face recognition with a view-tolerant process. Although diagnostic orientations vary with viewpoint (horizontal for frontal, vertical for profile), human recognition remains consistently tuned to horizontal information, aligning with the view-tolerant model's predictions. The evidence for view-invariant recognition is solid, though testing more plausible model variants and considering generalisability to more naturalistic face stimuli would strengthen the conclusions.

eLife Assessment

This important study uses a combination of behavioral and molecular techniques to identify neuromodulators that influence blood-feeding behavior in the disease vector, Anopheles stephensi. Through a combination of gene expression analysis and RNA knockdown, the authors identify neuropeptides RYamide and sNPF as candidate regulators for blood-feeding, demonstrate behavioral changes upon co-knockdown, and anatomically characterize their expression patterns. While the evidence for behavioral characterization and expression mapping is solid, the evidence supporting a direct causal role for these neuropeptides in promoting host-seeking remains unproven.

eLife Assessment

This manuscript investigates inter-hemispheric interactions in the olfactory system of Xenopus tadpoles. Using a combination of electrophysiology, pharmacology, imaging, and uncaging, the transection of the contralateral nerve is shown to lead to larger odor responses in the unmanipulated hemisphere, and implicates dopamine signaling in this process. The study uses a rich and sophisticated array of tools to investigate olfactory coding and uncovers valuable mechanisms of signaling. However, the data is incomplete, with a few of the conclusions not being well-supported by the data; the interpretation should be adjusted with some caveats, or additional experiments should be done to support these conclusions.

eLife Assessment

This valuable developmental study provides intriguing but incomplete evidence suggesting that, relative to adults, the enhancement of instrumental learning by Pavlovian bias is most pronounced in adolescence, while reward-induced memory enhancements are strongest in childhood. Although the authors tackle a key aspect of learning and motivation with rigorous experimental methods and sophisticated modeling techniques, there are substantial concerns about the absence of relevant analyses, the lack of accord between model-based and exploratory analyses, and the lack of an explanation for how the results cohere with inconsistent findings in the literature.

eLife Assessment

This study provides a valuable contribution to understanding the functional and molecular organization of the medial nucleus accumbens shell in feeding. Using in vivo imaging, optogenetics, and genetic engineering, the authors present solid evidence for a rostro-caudal gradient in D1-SPN activity that refines earlier pharmacological models. The identification of Stard5 and Peg10 as molecular markers and the creation of a Stard5-Flp line represent meaningful advances for future circuit-specific studies. While stronger integration of molecular and functional results and additional analyses of other Stard5-expressing cell types (e.g., D2-SPNs, interneurons) would enhance completeness, the overall methodological rigor and convergence of findings make this a well-executed and informative study. This will be of interest to those interested in brain circuits, reward, emotion, and feeding behavior.

eLife Assessment

This study presents a valuable in-depth comparison of statistical methods for the analysis of ecological time series data, and shows that different analyses can generate different conclusions, emphasizing the importance of carefully choosing methods and of reporting methodological details. The evidence supporting the claims, based on simulated data for a two-species ecosystem, is solid, although testing on more complex datasets could be of further benefit. This paper should be of broad interest to researchers in ecology.

eLife Assessment

This important work employed a recent, functional muscle network analysis for evaluating rehabilitation outcomes in post-stroke patients. While the research direction is relevant and suggests the need for further investigation, the strength of evidence supporting the claims is incomplete. Muscle interactions can serve as biomarkers, but improvements in function are not directly demonstrated, and the method's robustness is not benchmarked against existing approaches.

eLife Assessment

The authors collected time-course RNA-seq data from four tree species in natural environments and analyzed seasonal patterns of gene expression. This fundamental study substantially advances our understanding of how seasonal environments shape gene expression. The evolutionary effects of seasonal environments on gene expression are rarely studied at this scale and the dataset is extensive. The evidence supporting the conclusions is compelling, with caveats and limitations clearly described. The work will be of broad interest to colleagues studying evolution and gene expression.

eLife Assessment

The authors used comprehensive approaches to identify Gyc76C as an ITPa receptor in Drosophila. They revealed that ITPa acts via Gyc76C in the renal tubules and fat body to modulate osmotic and metabolic homeostasis. The designed experiments, data, and analyses convincingly support the main claims. The findings are important to help us better understand how ITP signals contributes to systemic homeostasis regulation.

eLife Assessment

This study provides convincing evidence that homologous recombination can occur in telophase-arrested cells, independently of cohesin subunits Smc 1-3. These findings are valuable as they point to investigate the role of cohesins re-association with chromatin in the allelic inter-sister repair by homologous recombination.

eLife Assessment

This study provides important insights into bacterial genome evolution by analyzing single-cell genome sequences of cyanobacteria from Yellowstone hot springs. Using compelling evidence, the authors demonstrate that both homologous recombination within species and frequent hybridization across species are major drivers of genome diversification. Despite the challenges that are inherent to sparse and fragmented single-cell data, the analyses are thorough, carefully controlled, and supported by multiple complementary approaches, making the conclusions highly robust. This work represents a significant advance in our understanding of microbial evolution in natural environments.

eLife Assessment

This valuable study uses tools of population and functional genomics to examine long non-coding RNAs (lncRNAs) in the context of human evolution. Analyses of computationally predicted human-specific lncRNAs and their genomic targets lead to the development of hypotheses regarding the potential roles of these genetic elements in human biology. The conclusions regarding evolutionary acceleration and adaptation, however, only incompletely take data and literature on human/chimpanzee genetics and functional genomics into account.

eLife Assessment

This valuable study is a comprehensive investigation into the regulatory mechanisms and regional distribution of enteroendocrine cell subtypes in the Drosophila midgut, significantly advancing the understanding of how WNT and BMP gradients contribute to EE diversity. The methodological foundation and robust genetic evidence are solid in supporting the key roles of compartment boundary signals, particularly WNT and BMP, in specifying EE subtypes and division modes. However, there is a lack of full mechanistic insight regarding Notch pathway involvement, incomplete quantification of phenotype data, and insufficient global pattern analysis, which detracts from fully supporting some proposed models. Overall, the study provides a platform for future work but would benefit from stronger data integration and expanded mechanistic exploration.

eLife Assessment

This valuable study addresses the effects of selection on aggression on fitness and life-history trade-offs in Drosophila melanogaster. However, the evidence presented is incomplete and does not support the claims proposed in the study of increased survival of highly aggressive males at the expense of reproductive success and shorter mating duration. The main limitation of the study is the choice to use males from only one aggressive Drosophila line in combination with CantonS females, that do not allow disambiguation between nonaggression-related factors, such as hybrid vigor and aggression-related factors influencing mating and lifespan.

eLife Assessment

This valuable study examines how mammals descend effectively and securely along vertical substrates. The conclusions from comparative analyses based on behavioral data and morphological measurements collected from 21 species across a wide range of taxa are convincing, making the work of interest to all biologists studying animal locomotion.

eLife Assessment

This important study provides a systematic investigation of parent-of-origin (POE) effects on gene expression using large trio-based data from the Framingham Heart Study, uncovering thousands of potentially novel associations. While the findings are potentially significant, the statistical support for classifying POE eQTLs and some downstream analyses is incomplete, and more stringent re-analysis is needed. With such revisions, the work would serve as a foundation for advancing understanding of POEs and their role in gene regulation.

eLife Assessment

This important study shows that retinal bipolar cell subtype-specific differences in the size of synaptic ribbon-associated vesicle pools contribute to the transient versus sustained kinetics of the responses of retinal ganglion cells. The data are extensive and compelling. This work will be of broad interest to researchers working on synaptic transmission, retinal signal processing, and sensory neurobiology.

eLife Assessment

This important work provides a new method to extract cfDNA from residual plasma from heparin separators for molecular testing. The evidence supporting the authors' claims is convincing, although some further metrics should also be evaluated. This finding will be interesting to people working in epigenomics and infectious disease diagnostics.

eLife Assessment

The characterization of a dissociable Mediator subunit implicated in cellular pathways, particularly lung alveolar function and HIV latency, would be conceptually interesting. The authors have preliminary evidence for a stable Med16 subcomplex that may regulate specific genes. This work is useful in that it points to interactions between Med16 and UBP1, but the evidence is preliminary and incomplete.

eLife Assessment

This important study systematically investigates repeat expansion in the plant Arabidopsis thaliana using a new k-mer-based method, expanding on smaller studies to more comprehensively identify cis- and trans-acting loci associated with repeat dynamics. The approach is methodologically sound and broadly applicable to large-scale short-read datasets for assessing copy number variation and genomic repeat content. While convincing in its scope and novelty, the findings would be further strengthened with exploratory analyses of datasets from other species with more or fewer repeats in their genomes.

eLife Assessment

This work introduces FunC-ESMs, a proteome-scale framework to classify loss-of-function missense variants into distinct mechanistic groups by combining two complementary state-of-the-art machine learning models. The strength of evidence is convincing, supported by solid benchmarking, integration with experimental datasets, and careful methodological design. The significance of the findings is valuable, providing a resource of clear interest to researchers and diagnostic laboratories working on variant interpretation.

eLife Assessment

This work reveals metabolic pathways and molecular events mechanistically linked to B cell activation. Using an unbiased, comprehensive proteome profiling method and various functional validation approaches, this study generated convincing evidence suggesting a role for amino acid uptake, cholesterol accumulation, and protein prenylation in the proliferation, survival, and biogenesis of B cells stimulated with LPS and other activating stimuli. The significance of the findings is considered to be fundamental, in that they will advance our understanding of cell metabolism during B cell activation.

eLife Assessment

This important study advances our understanding of how cellular quality control machinery influences cystic fibrosis (CF) drug responsiveness by systematically analyzing the effects of the chaperone calnexin on more than two hundreds of CFTR (cystic fibrosis transmembrane regulator) variants. The evidence supporting the conclusions is convincing, with a comprehensive deep mutational scanning methodology and rigorous quantitative analysis. The findings reveal that calnexin is critical for both CFTR protein expression and corrector drug efficacy in a variant-specific manner, providing invaluable insights that could guide the development of personalized CF therapies. This work will be of significant interest to researchers in protein folding, CF drug development, and genetic disease therapeutics.

eLife Assessment

This important study uses data from OpenAlex on more than 50 million journal articles in over 50,000 research journals to examine the dynamics of interdisciplinarity and international collaboration in research journals. The data analytics used to quantify disciplinary and national diversity are convincing, and support the claims that journals have become more diverse in both aspects. The revisions made by the authors have addressed the small number of concerns the reviewers had about the original version.

eLife Assessment

The authors investigated the potential role of IgG N-glycosylation in Haemorrhagic Fever with Renal Syndrome (HFRS), which may offer significant insights for understanding molecular mechanisms and for the development of therapeutic strategies for this infectious disease. The findings are thought to be valuable to the field and the strength of evidence to support the findings is solid.

eLife Assessment

This study addresses an important question in liver biology: how zonal hepatocytes balance survival and proliferation following injury; using spatial transcriptomics, mechanistic perturbations, and functional assays, the authors propose that a mid-zone Atf4-Chop axis to Btg2 program temporarily suppresses proliferation to promote survival during APAP-induced hepatotoxicity. The idea that distinct intrahepatic zones mount tailored stress responses is conceptually significant and has implications for regeneration and toxicology. The dataset is rich and the methodology modern, but several conclusions rely on assumptions about zonation under injury, limited injury models, and incomplete functional validation of the Atf4-Chop-Btg2 axis. With targeted revisions and additional experiments, the work has the potential to provide strong mechanistic insights into liver zonation and injury responses.

eLife Assessment

This study presents an important finding by identifying OPG as a novel stromal checkpoint influencing T-cell anti-tumor responses, thereby shedding new light on the complex interplay between the tumor microenvironment and immune regulation. The data are robust and the experimental approaches are sound, providing solid support for the study's conclusions; however, there are a number of additional questions raised by the data. Of particular note are the questions raised on the mechanistic effects of TRAIL versus RANKL. In addition, it would broaden the interest in this study to include more translational human data to complement the work presented.

eLife Assessment

This useful study attempts to place an ancient maize sample from Bolivia, dated to the end of the Incan empire, in genetic and geographical context. The analyses show that this sample is most closely related to ancient Peruvian maize, but the data remain inadequate to determine the direction of dispersal and the extent of Inca influence over the genetic make up of the analyzed sample. There are additional deficiencies in the statistical analyses and selection inferences. The topic of the study would appeal to researchers studying maize dispersal and adaptation.

eLife Assessment

This study presents a meta-analysis of two independent genome-wide association studies (GWAS) that investigate the role of plasma proteins as potential biomarkers for enhancing the early detection of prostate cancer (PCa). The results provide useful confirmatory data that support existing evidence currently published. The evidence is incomplete: the study does not provide a comprehensive synthesis of all currently published work, does not explore other clinical outcomes related to prostatic disease, and its findings have not been validated through an external cohort study. These shortcomings notwithstanding, the work may be of interest to researchers studying correlates and predictors of prostate cancer risk.

eLife Assessment

This global study compares environmental niche model outputs of avian influenza pathogen niche constructed for two distinct periods, and uses differences between those outputs to suggest that the changed case numbers and distribution relate to intensification of chicken and duck farming, and extensive cultivation. While a useful update to existing niche models of highly pathogenic avian influenza, the justification for the use of environmental niche models to explore correlative relationships between land cover change and changed case epidemiology is incomplete. Key assumptions have not been adequately clarified for the readers benefit, and in consequence the communication of the likely limitations of the work are not sufficiently clear.

eLife Assessment

This study provides new single-cell multi-omics datasets that may be useful in the study of early cardiac lineages. However, the authors' conclusions regarding the mutual regulation of key regulators for cardiac specification and new cardiac lineage trajectories are inadequately supported by persuasive analysis and do not align with prior published studies. If revised to address the serious caveats adequately, the findings may be of interest to researchers in the field of cardiac development and congenital heart disease.

eLife Assessment

This study provides valuable information on the impact of Lamin A/C knockdown on gene expression using RNA-Seq analysis, as well as on telomere dynamics through live cell imaging. However, the conclusions remain inadequately supported by the current data, and several of the major technical concerns raised in the first round have not yet been fully resolved.

eLife Assessment

This important work represents an advance in our understanding of resident myeloid cells in the zebrafish brain, particularly as it provides a molecular definition of dendritic cell subtypes associated with their localization. Combined evidence from single cell transcriptomics and histology is compelling. The associated atlas will be used as a resource by the zebrafish community and beyond.

eLife Assessment

This work provides high-precision single-cell data on the relationship between DnaA activity and cell size, offering important insights for the field of cell cycle control. These findings motivate a novel and intriguing hypothesis for DNA replication initiation -the "extrusion model"- in which DNA-binding proteins modulate free DnaA availability in response to biomass-DNA imbalance. While the current indirect evidence does not fully establish the model, an experimental perturbation involving H-NS offers convincing support for its plausibility, laying the groundwork for future investigation.

eLife Assessment

This manuscript provides an improved version of an important cancer risk estimation tool and refines and expands upon resources that are currently available to the cancer genetics community. The new program is validated in a set of clinical pedigrees demonstrating its practical accuracy and relevance to the field. Collectively, the data are compelling and support the major conclusions of this manuscript.

eLife Assessment

This paper presents a valuable software package, named "Virtual Brain Inference" (VBI), that enables faster and more efficient inference of parameters in dynamical system models of whole-brain activity, grounded in artificial network networks for Bayesian statistical inference. The authors have provided convincing evidence, across several case studies, for the utility and validity of the methods using simulated data from several commonly used models, but more thorough benchmarking could be used to demonstrate the practical utility of the toolkit. This work will be of interest to computational neuroscientists interested in modelling large-scale brain dynamics.

eLife Assessment

This is a valuable study that presents convincing evidence on the genesis of the CPSF6 condensates that form upon HIV-1 infection and the specific molecular determinants involved in their formation, as well as their interactions with SRRM. The study could be strengthened by assessing the relevance of their findings to infection, and in particular, with reverse transcription and gene expression

eLife Assessment

The results by Zhu et al provide valuable insights into the representation of border ownership in area V1. They used neuropixel recording to demonstrate the clustering of border ownership, and compared cross-correlation functions between neurons in different layers to demonstrate that they depend on the type of stimulus. The strength of the evidence is solid but can be improved by performing additional analyses and addressing some concerns (as raised in the previous and current review), and accounting for the differences in classical and non-classical receptive field stimulation conditions.

eLife Assessment

This study presents SegPore, a valuable new method for processing direct RNA nanopore sequencing data, which improves the segmentation of raw signals into individual bases and boosts the accuracy of modified base detection. The evidence presented to benchmark SegPore is solid, and the authors provide a fully documented implementation of the method. SegPore will be of particular interest to researchers studying RNA modifications.

eLife assessment

This is a valuable study that combines a wide range of approaches to provide a biophysical and evolutionary mechanism that could explain why some particular mutations in the SARS-CoV-2 protein N arose during the COVID-19 pandemic. The evidence is solid and relies on multiple experimental approaches. However, some of the results were dependent on extremely high protein concentrations, which may affect certain conclusions.

eLife Assessment

The study reports a potential pathway for isoleucine biosynthesis mediated by the underground activity of AHASII, which converts glyoxylate and pyruvate to 2-ketobutyrate. While the findings are valuable in revealing a possible alternative route for isoleucine production, the evidence presented remains incomplete. More comprehensive biochemical experiments are required to substantiate the physiological feasibility of this pathway.

eLife Assessment

This valuable biomechanical analysis of kangaroo kinematics and kinetics across a range of hopping speeds and masses is a step towards understanding a long-standing problem in locomotion biomechanics: the mechanism for how kangaroos, unlike other mammals, can increase hopping speed without a concomitant increase in metabolic cost. The authors convincingly demonstrate that changes in kangaroo posture with speed increase tendon stress/strain and hence elastic energy storage/return. This greater tendon elastic energy storage/return may counteract the increased cost of generating muscular force at faster speeds and thus allows for the invariance in metabolic cost. This methodologically impressive study sets the stage for further work to investigate the relation of hopping speed to metabolic cost more definitively.

eLife Assessment

This important paper employs multiple experimental approaches and presents evidence that changes in membrane voltage directly affect ERK signaling to regulate cell division. This result is relevant because it supports an ion channel-independent pathway by which changes in membrane voltage can affect cell growth. The evidence now presented is solid and the data support the conclusions. This paper should be of interest to a broad readershp in the areas of cell and developemental biology and electrophysiology.

eLife Assessment

This high-N, multi-task study offers a comprehensive examination of rhythmicity in behavioral performance during listening. It presents a valuable set of findings that reveal task- and ear-specific effects, challenging the notion of a universal rhythmicity in auditory perception. The evidence is solid and the work is likely to be of significant interest to behavioral and cognitive scientists focused on perception and neural oscillations.

eLife Assessment

This important study establishes bathy phytochromes, a unique class of bacterial photoreceptors that respond to near-infrared light (NIR), as versatile tools for bacterial optogenetics. NIR light is a key control signal in optogenetics due to its deep tissue penetration and the ability to combine with existing red- and blue-light sensitive systems, but thus far, NIR-activated proteins have been poorly characterized. The strength of evidence is convincing, with comprehensive in vitro characterization, modular design strategies, and validation across different hosts, supporting the versatility and potential for these tools in biotechnological applications. This study should advance the fields of optogenetics and photobiology and inspire future work.

eLife Assessment

This study provides important insights into how researchers can use perceptual metamers to formally explore the limits of visual representations at different processing stages. The framework is compelling and the data largely support the claims, subject to minor caveats.

eLife Assessment

This study presents a valuable finding relating to how the state of arousal is represented within the superior colliculus, a principal visuo-oculomotor structure. The main conclusion that the representation of arousal is segregated, and thus influences visual activity but not motor output, is incompletely supported by the evidence, but could be stronger if a specific concern relating to an alternative explanation for the dichotomy was addressed. The work will be of interest to sensory, motor, and cognitive neuroscientists.

eLife Assessment

This important study presents a novel approach to enhance the therapeutic potential of mesenchymal stromal cells (MSCs) by genetically modifying their glycogen synthesis pathway, resulting in increased glycogen accumulation and improved cell survival under starvation conditions, particularly in the context of experimental pulmonary fibrosis. The methods and findings are generally solid and could be strengthened in the future by investigating the kinetics of persistence, the immunomodulatory effects, and the underlying improved mechanism of action of MSCs in this pulmonary fibrosis model. If confirmed, this approach could suggest potential methods to improve the therapeutic functionality of MSCs in cell therapy strategies.

eLife Assessment

This important manuscript evaluates how sample size and demographic balance of reference cohorts affect the reliability of normative models. The evidence supporting the conclusions is convincing, although some additional analysis and clarifications could improve the generalisability of the conclusions. This work will be of interest to clinicians and scientists working with normative models.

eLife Assessment

This important paper reports the development of proteins and small molecules that induce degradation of a clinically-relevant oncogenic transcription factor, LMO2. The findings provide a proof of concept that PROTAC-type chemicals can be developed against intrinsically disordered proteins. The methods provide a blueprint for rational design of PROTACs starting from intracellular antibody paratopes. Overall, the paper is supported by solid evidence and will be of interest to chemical biologists and cancer pharmacologists.

eLife Assessment

This valuable study concerns a model for transgenerational epigenetic inheritance, the learned avoidance by C. elegans of the PA14 pathogenic strain of Pseudomonas aeruginosa. A recent study questioned whether transgenerational inheritance in this paradigm lacks robustness. The authors of this study have worked independently of the group that reported the original phenomenon and also independently of the group that challenged the original report. With solid data, this study independently validates findings previously reported by the Murphy group, confirming that the paradigm is reproducible elsewhere. The reviewers also appreciated the information on reagent sources used by different groups. The present study is therefore of broad interest to anyone studying genetics, epigenetics, or learned behavior.