eLife Assessment

This important manuscript presents a thorough analysis of the evolution of Major Histocompatibility Complex gene families across primates. A key strength of this analysis is the use of state-of-the-art phylogenetic methods to estimate rates of gene gain and loss, accounting for the notorious difficulty to properly assemble MHC genomic regions. Overall the evidence for the authors' conclusions – that there is considerable diversity in how MHC diversity is deployed across species – is compelling.

eLife Assessment

This important study demonstrates that some degree of spatial tuning (e.g., place cells) and ability to decode spatial location emerges in sufficiently complex systems trained to process visual information. This intriguing observation challenges existing approaches and findings used in the study of spatial navigation. However, the strength of evidence regarding the nature and quality of spatial tuning, its compatibility with experimental data, and the overall interpretation of the study remains incomplete. This work will be of interest to the research community of spatial navigation.

eLife Assessment

This important study uses an original method to address the longstanding question of why reaching movements are often biased. The combination of a wide range of experimental conditions and computational modeling is a strength. Solid evidence is presented in support of the main claim that most of the biases in 2-D movement planning originate in misalignment between visuo-proprioceptive reference frames.

eLife Assessment

This study provides solid evidence that odor fear conditioning biases olfactory sensory neuron receptor choice in mice and that this bias is detectable in the next generation. The authors use rigorous histological and behavioral analyses, including unsupervised behavioral quantification, to support the conclusion that odor-specific sensory representations can be shaped by experience and partially transmitted across generations. While the behavioral effects in offspring are modest and the mechanistic basis of inheritance remains unresolved, the study offers an important and carefully executed contribution to understanding experience-dependent sensory plasticity and its intergenerational consequences.

eLife Assessment

This useful study characterizes the evolution of medial prefrontal cortex activity during the learning of an odor-based choice task. The evidence provided is solid, providing quantification of functional classes of cells over the course of learning using the longitudinal calcium recordings in prefrontal cortex, and quantification of prefrontal sequences. However, the experimental design appears to provide limited evidence to support strong conclusions regarding pre-existing representations or the functional relevance of neural sequences. The study will be of interest to neuroscientists investigating learning and decision-making processes.

eLife Assessment

This study developed a novel continuous dot-motion decision-making task, in which participants can see another player's responses as well as their own, to measure perceptual performance and confidence judgments in a social context. The study is a valuable contribution to social decision-making primarily by introducing a new task and offering convincing evidence on how participants are impacted by others' decisions during continuous perceptual choices. The manuscript delivers clear evidence that participants judgements are driven by metacognitive confidence over simpler primary uncertainty.

eLife Assessment

This study provides a valuable genome-centric characterization of microbial communities across deep sediment cores from a Spartina patens salt marsh. The study provides claims on the metabolic capabilities of the deep sediment microbiome as well as on a burial microbial assembly process and functional complementarity at depth. However, some of these claims remain incomplete and would benefit from further supporting evidence. Overall, this work will be of interest to microbial ecologists working on wetlands.

eLife Assessment

The authors used a Bayesian modeling framework to fit behavior and serotonin neuron activity to reward history across multiple timescales. A key goal was to distinguish value coding from other influences, particularly thirst, by comparing model fits across neurons. Although the question and approach are valuable, several limitations of the current manuscript mean that support for the conclusions is incomplete.

eLife Assessment

This important study advances our understanding of vertebrate forelimb development, specifically the contribution of Hox genes to zebrafish pectoral fin formation. The authors have employed a robust and extensive genetic approach to tackle a key and unresolved question. The findings are overall convincing and will be of broad interest to developmental and evolutionary biologists.

eLife Assessment

By leveraging optical coherence tomography this study provides important insight into the deformation of human fingertip ridges when contacting raised features such as edges and contours. The study provides compelling evidence that such features tend to cause deformation and relative movement of what the authors term ridge flanks rather than bending of the ridges themselves.

eLife Assessment

The authors have performed a potentially valuable new kind of analysis in connectomics, mapping to an interesting developmental problem of synaptic input to sensory neurons. While the analysis itself is solid, the authors have drawn broader conclusions than are directly supported by the presented data. With more measured claims and greater clarity and explanations for the analysis, the study could potentially become stronger.

eLife Assessment

This study provides a valuable contribution to understanding how negative affect influences food-choice decision making in bulimia nervosa, using a mechanistic approach with a drift diffusion model (DDM) to examine the weighting of tastiness and healthiness attributes. The solid evidence is supported by a robust crossover design and rigorous statistical methods, although concerns about the interpretation of group differences across neutral and negative conditions limit the interpretability of the results.

eLife Assessment

This study provides an important advance in credibility-based learning research by demonstrating how feedback reliability can shape reward learning biases within a carefully controlled bandit task. The strength of the main findings, namely greater learning from credible feedback and robust computational modeling supported by strong parameter recovery and cross-fitting analyses, is compelling. The integration of reinforcement learning and Bayesian benchmark models is methodologically rigorous and well-executed, yielding reliable and interpretable results. The revised manuscript shows clear improvements in theoretical framing and transparency regarding limitations. While additional work is warranted to confirm the role of disinformation in amplifying positivity bias and to explore symptom-related variability or richer Bayesian comparators, this paper represents a high-quality and impactful contribution to the study of learning under uncertainty and misinformation.

eLife Assessment

This valuable study provides a large-scale EEG investigation into how visual deep neural networks (DNNs) and large language models (LLMs) differentially explain the temporal dynamics of visuo-semantic processing in the human brain. Although evidence convincingly shows that DNNs account for early perceptual responses, while LLMs capture later, low-frequency activity associated with semantic integration, the theoretical interpretation of LLM contributions and methodological aspects - including task engagement, justification of model choices, and dimensionality reduction - requires further clarification. The work will be of broad interest to fields of psychology, cognitive neuroscience, and artificial intelligence.

eLife Assessment

This valuable work defines a "learning proteome" for a C. elegans gustatory associative learning paradigm. These results provide the field with a new set of genes to further explore their roles in learning and memory, provide new tools for other labs to employ in their investigations of behavior, and molecular pathways revelant for C. elegans learning and memory. The methodological evidence and the quality of the dataset are convincing. The results will be of interest to neuroscientists and developmental biologists seeking to understand the self-assembly and operation of neural circuits for learning and memory.

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

eLife Assessment

This important study identifies a novel CRF-positive projection from the central amygdala and BNST to dorsal striatal cholinergic interneurons, revealing a previously unrecognized pathway by which stress signals modulate striatal function. The authors present strong and convincing evidence for the anatomical and functional connectivity of this circuit and demonstrate that alcohol disrupts CRF-mediated cholinergic activity, supporting its relevance to alcohol use disorder.

eLife Assessment

This study offers a valuable advance for neuroscience by extending a visualization tool that enables intuitive assessment of how dendritic and synaptic currents shape the output of neurons. The evidence supporting the tool's capabilities is convincing and solid, with well-documented code, algorithmic innovation, and application to hippocampal pyramidal neurons - although experimental confirmation of the predictions is not provided. The work will be of interest to computational and systems neuroscientists seeking accessible methods to examine dendritic computations.

eLife Assessment

This study presents valuable findings from a spatiotemporal analysis of arbovirus case notification data from 2013 to 2020 in Brazil, reporting associations between covariates representing potential drivers of arbovirus transmission and recorded incidence. The work is methodologically solid, though it is unclear how much explanatory power inclusion of the covariates adds. The findings will be of interest to researchers working on the epidemiology of arboviruses.

eLife Assessment

This important study investigates how the nervous system adapts to changes in body mechanics using a tendon transfer surgery that imposes a mismatch between muscle contraction and mechanical action. Using electromyography (EMG) to track muscle activity in two macaque monkeys, the authors conclude that there is a two-phase recovery process that reflects different underlying strategies. However, neither monkey's data includes a full set of EMG and kinematic measurements, and the two datasets are not sufficiently aligned with each other from a behavioural point of view; as a result, the evidence supporting the conclusions is solid but could be improved.

eLife Assessment

This paper contains valuable ideas for methodology concerned with the identification of genes associated with disease prognosis in a broad range of cancers. However, there are concerns that the statistical properties of MEMORY are incompletely investigated and described. Further, more precise details about the implementation of the method would increase the replicability of the findings by other researchers.

eLife Assessment

Davies et al. present a valuable study proposing that Shot can act as a molecular linker between microtubules and actin during dendrite pruning, suggesting an intriguing role in non-centrosomal microtubule organization. However, the experimental evidence is incomplete and does not robustly support these claims, and the lack of a cohesive model connecting the findings weakens the overall impact. While the data suggest that Shot, actin, and microtubule nucleation contribute to dendritic pruning, their precise interplay remains unresolved.

eLife Assessment

This study presents experiments suggesting intriguing mesoscale reorganization of functional connectivity across distributed cortical and subcortical circuits during learning. The approach is technically impressive and the results are potentially of valuable significance. However, in its current form, the strength of evidence is incomplete. More in-depth analyses and the acquisition of data from additional animals in the primary experiment could bolster these findings.

eLife Assessment

This study investigates how sleep loss and circadian disruption affect whole-organ metabolism in flies (Drosophila melanogaster) and reports that wild-type flies align metabolism in anticipation of diurnal rhythm, while mutant flies with impaired sleep or circadian function shift to reactive or misaligned metabolism. The integration of chamber-based flow-through respirometry with LC-MS metabolomics is innovative, and the significance of the findings is valuable. However, the strength of evidence needed to support the conclusions is incomplete based on concerns regarding the inappropriate use of constant darkness to disrupt circadian rhythms and the lack of details justifying the methods used to correlate respirometry data with whole-body metabolomics.

eLife Assessment

This important work presents technical and conceptual advances with the release of MorphoNet 2.0, a versatile and accessible platform for 3D+T segmentation and analysis. The authors provide compelling evidence across diverse datasets, and the clarity of the manuscript together with the software's usability broadens its impact. Although the strength of some improvements is hard to fully gauge given sample complexity, the tool is a significant step forward that will likely impact many biological imaging fields.

eLife Assessment

The study presents important insights into the regulation of muscle hypertrophy, regulated by Muscle Ankyrin Repeat Proteins (MARPs) and mTOR. The methods are overall solid and complementary, with only minor limitations. Overall, the findings will be of interest for both muscle-biology specialists and the broader mechanobiology community.

eLife Assessment

This important study examines the potential role of ARHGAP36 transcriptional regulation by FOXC1 in controlling sonic hedgehog signaling in human neuroblastoma. While there are many solid findings that strongly support this signaling pathway, there are some aspects of the study that are underdeveloped.

eLife Assessment

This study is important as it demonstrates that 4-aminoquinoline antimalarials antagonize artemisinin activity under physiologically relevant conditions. Using isogenic parasite lines and a chemical probe, the authors provide mechanistic insight and compelling evidence implicating PfCRT in this antagonism. However, some weaknesses have been identified that limit full interpretation of the findings, which are based solely on in vitro assays, though the results have implications that will be of importance in optimizing future antimalarial combination strategies.

eLife Assessment

This study presents vassi, a Python package that streamlines the preparation of training data for machine-learning-based classification of social behaviors in animal groups. This package is a valuable resource for researchers with computational expertise, implementing a framework for the detection of directed social interactions within a group and an interactive tool for reviewing and correcting behavior detections. However, the strength of evidence that the method is widely applicable remains incomplete, performance on benchmark dyadic datasets is comparable to existing approaches, and performance scores on collective behavioral datasets are low. While the package can analyze behavior in large groups of animals, it only outputs dyadic interactions within these groups and does not account for behaviors where more than two animals may be interacting.

Summary: The study shows that when students can use their full linguistic repertoires, participation rises and learners demonstrate more creativity and imagination in multilingual classrooms (p. 1). Why it matters: This frames translanguaging as both inclusive and academically productive.

eLife Assessment

This study provides useful insights into the ways in which germinal center B cell metabolism, particularly lipid metabolism, affects cellular responses. The authors use sophisticated mouse models to demonstrate that ether lipids are relevant for B cell homeostasis and efficient humoral responses. Although the data were collected from in vitro and in vivo experiments and analyzed using solid and validated methodology, more careful experiments and extensive revision of the manuscript will be required to strengthen the authors' conclusions.

eLife Assessment

This valuable study proposes a theoretical model of clathrin coat formation based on membrane elasticity that seeks to determine whether this process occurs by increasing the area of a protein-coated patch with constant curvature, or by increasing the curvature of a protein-coated patch that forms in an initially flat conformation (so called constant curvature or constant area models). Identifying energetically favorable pathways and comparing the obtained shapes with experiments provides solid support to the constant-area pathway. This work will be of interest for biologists and biophysicists interested in membrane remodelling and endocytosis. It provides an innovative approach to tackle the question of constant curvature vs. constant area coat protein formation, although some of the model's assumption are only partially supported by experimental evidence.

eLife Assessment

This important manuscript provides compelling evidence that BK and CaV1.3 channels can co-localize as ensembles early in the biosynthetic pathway, including in the ER and Golgi. The findings, supported by a range of imaging and proximity assays, offer insights into channel organization in both heterologous and endogenous systems. While the data broadly support the central claims, mechanistic aspects remain unresolved, particularly regarding the determinants of mRNA co-localization, the temporal dynamics of ensemble trafficking, and the physiological implications of pre-assembly for channel function at the plasma membrane.

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. The data presented are solid, although some concerns persist regarding inconsistencies in molecular weight of the enzyme used. The study will be of interest to those studying protein and metabolic regulation.

eLife Assessment

This paper describes Unbend - a new method for measuring and correcting motions in cryo-EM images, with a particular emphasis on more challenging in situ samples such as lamella and whole cells. The method, which fits a B-spline model using cross-correlation-based local patch alignment of micrograph frames, represents a valuable tool for the cryo-EM community. The authors elegantly use 2D template matching to provide solid evidence that Unbend outperforms the previously reported method of Unblur by the same authors. The paper would benefit from the inclusion of a similar analysis for established alternative methods, such as MotionCor2.

eLife Assessment

This study identifies the Periportal Lamellar Complex (PLC), an important new structure revealed by a novel 3D imaging method. However, the evidence supporting its distinct cellular identity and functional role is currently incomplete, as it relies on transcriptomic re-analysis and correlation without direct experimental validation. Addressing the key issues of methodological rigor and providing functional evidence is essential to fully substantiate these significant claims.

eLife Assessment

This study presents valuable findings on the role of KLF6 in in vitro endothelial cells exposed to altered (high or low) shear stress with a customized microfluidic device to investigate mechanisms of atherosclerosis. The finding that altered shear stress results in endothelial cell ferroptosis through reduced expression of KLF6 is compelling and adds a new layer of complexity to the pathogenesis of atherosclerotic plaques. However, the inclusion of an arterial cell line and re-evaluation of the statistical tests used would strengthen the authors' conclusions.

eLife Assessment

This important study provides new insights into the synchronization of ripple oscillations in the hippocampus, both within and across hemispheres. Using carefully designed statistical methods, it presents compelling evidence that synchrony is significantly higher within a hemisphere than across. This study will be of interest to neuroscientists studying the hippocampus and memory.

eLife Assessment

This important study combines EEG, neural networks and multivariate pattern analysis to show that real-world size, retinal size and real-world depth are represented at different latencies. The evidence presented is convincing and the work will be of broader interest to the experimental and computational vision community.

eLife Assessment

In this important study, the authors set out to determine the molecular interactions between the AQP2 from Trypanosoma brucei (TbAQP2) and the trypanocidal drugs pentamidine and melarsoprol to understand how TbAQP2 mutations lead to drug resistance. Using cryo-EM, molecular dynamics simulations, and lysis assays the authors present convincing evidence that mutations in TbAQP2 make permeation of trypanocidal drugs energetically less favourable, and that this impacts the ability of drugs to achieve a therapeutic dose. Overall, this data will be of interest for those working on aquaporins, and development of trypanosomiasis drugs as well as drugs targeting aquaporins in general.

eLife Assessment

This study by Roseby and colleagues shows that region-specific mechanosensation - especially anterior-dorsal inputs - controls larval self-righting, and links this to Hox gene function in sensory neurons. The work is important for understanding how body plan cues shape sensorimotor behaviour, and the experimental toolkit will be of use to others. The strength of evidence is solid with respect to the assays developed and the involvement of the anterior region; it is incomplete with respect to dorso-ventral involvement in that region and the role of Hox genes in the process. These findings will be of broad interest to researchers studying neural circuits, developmental genetics, and the evolution of behaviour.

eLife Assessment

This important study uses single-neuron Patch-seq RNA sequencing to investigate the process by which RNA editing can produce protein diversity and regulate function in various cellular contexts. The computational analyses of the data collected are convincing, and from an analytical standpoint, this paper is a notable advance in seeking to provide a biological context for massive amounts of data in the field. The study would be of interest to biologists looking at the effects of RNA editing in the diversification of cellular behaviour.

eLife Assessment

This study provides useful insights into the ways in which germinal center B cell metabolism, particularly lipid metabolism, affects cellular responses. The authors use sophisticated mouse models to convincingly demonstrate that ether lipids are relevant for B cell homeostasis and efficient humoral responses. The authors then conducted in vivo as well as in vitro experiments, thereby strengthening their conclusions.

eLife Assessment

The authors quantified intentions and knowledge gaps in scientists' use of sex as a biological variable in their work, and used a workshop intervention to show that while willingness was high, pressure points centered on statistical knowledge and perceived additional monetary costs to research. These important findings demonstrate the difficulty in changing understanding: while interventions can improve knowledge and decrease perceived barriers, the impact was small. The evidence for the findings is solid.

eLife Assessment

This valuable study reports a critical role of the axonemal protein ANKRD5 in sperm motility and male fertility. Convincing data were presented to support the main conclusion. This work will be of interest to biomedical researchers who study ciliogenesis, sperm biology, and male fertility.

eLife Assessment

This manuscript revisits the well-studied KdpFABC potassium transport system from bacteria with a convincing set of new higher resolution structures, a protein expression strategy that permits purification of the active wildtype protein, and insight obtained from mutagenesis and activity assays. The thorough and thoughtful mechanistic analyses make this a valuable contribution to the membrane transport field.

eLife Assessment

In flies defective for axonal transport of mitochondria, the authors report the upregulation of one subunit, the beta subunit, of the heterotrimeric eIF2 complex via mass spectroscopy proteomics. Neuronal overexpression of eIF2β phenocopied aspects of neuronal dysfunction observed when axonal transport of mitochondria was compromised. Conversely, lowering eIF2β expression suppressed aspects of neuronal dysfunction. While these are intriguing and useful observations, technical weaknesses limit the interpretation. On balance, the evidence supporting the current claims is suggestive but incomplete, especially concerning the characterization of the eIF2 heterotrimer and the data regarding translational regulation.

eLife Assessment

Xenacoelomorpha is an enigmatic phylum, displaying various presumably simple or ancestral bilaterian features. This valuable study characterises the reproductive life history of Hofstenia miamia, a member of class Acoela in this phylum. The authors describe the morphology and development of the reproductive system, its changes upon degrowth and regeneration, and the animals' egg-laying behaviour. The evidence is convincing, with fluorescent microscopy and quantitative measurements as a considerable improvement to historical reports based mostly on histology and qualitative observations.

eLife Assessment

This is a valuable manuscript that reframes Gaucher's disease pathology through the analysis of renal health, using a Drosophila model mutant for glucocerebrosidase (GBA1). The authors provide physiological and cellular data showing that renal dysfunction may be a critical disease-modifying feature. This work broadens the field's focus beyond the nervous system to include systemic ionic regulation as a potential contributor to disease initiation and progression. The genetic and experimental approaches are solid and offer a rationale for investigating analogous dysfunction in human tissues; however, several claims extend beyond the presented evidence and would benefit from additional experimental support to fully support the conclusions.

eLife Assessment

This work uses enhanced sampling molecular dynamics methods to generate potentially useful information about a conformational change (the DFG flip) that plays a key role in regulating kinase function and inhibitor binding. The focus of the work is on the mechanism of conformational change and how mutations affect the transition. The evidence supporting the conclusions is incomplete.

eLife Assessment

This work uses enhanced sampling molecular dynamics methods to generate potentially useful information about a conformational change (the DFG flip) that plays a key role in regulating kinase function and inhibitor binding. The focus of the work is on the mechanism of conformational change and how mutations affect the transition. The evidence supporting the conclusions is incomplete.

eLife Assessment

In this valuable study, the authors present traces of bone modification on ~1.8 million-year-old proboscidean remains from Tanzania, which they infer to be the earliest evidence for stone-tool-assisted megafaunal consumption by hominins. Challenging published claims, the authors argue that persistent megafaunal exploitation roughly coincided with the earliest Achulean tools. Notwithstanding the rich descriptive and spatial data, the behavioral inferences about hominin agency rely on traces (such as bone fracture patterns and spatial overlap) that are not unequivocal; the evidence presented to support the inferences thus remains incomplete. Given the implications of the timing and extent of hominin consumption of nutritious and energy-dense food resources, as well as of bone toolmaking, the findings of this study will be of interest to paleoanthropologists and other evolutionary biologists.

eLife Assessment

This study presents a valuable finding on mutations in ZNF217, ZNF703, and ZNF750 through 23 breast cancer samples alongside matched normal tissues in Kenyan breast cancer patients. The evidence supporting the claims of the authors is solid, yet the analysis of the manuscript lacks methodological transparency, statistical detail, and sufficient comparison with existing large-scale datasets. The work will be of interest to medical biologists and scientists working in the field of breast cancer.

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.