eLife Assessment

This manuscript reports on the application of ribosome profiling (EZRA-seq and eRF1-seq) combined with massively parallel reporter assays to identify and characterize a GA-rich element associated with ribosome pausing during translation termination. While the development of eRF1-seq is useful and the identification of GA-rich elements upstream of stop codons is convincing, the level of support for other claims is inadequate. Specifically, the evidence that GA-rich sequences upstream of stop codons can base-pair with the 3′ end of 18S rRNA to prolong ribosome dwell time, and the evidence that Rps26 interferes with this interaction to regulate translation termination, are not adequate.

eLife Assessment

The authors investigated the epigenetic mechanisms regulating the differentiation of circulating monocytes that infiltrate the CNS and adopt microglia-like characteristics. The work is useful to the field, as the contribution of circulating myeloid cell-derived microglia remains controversial. However, the evidence presented is inadequate as the analyses are based on a very limited set of genes, which does not sufficiently support the authors' central claims.

eLife Assessment

This study presents a role for heparin sulfate in SARS-CoV-2 entry that runs counter to prevailing data in the field. If the conclusions were firmly supported by the data, the work would be a significant contribution to the field. While the use of diverse cellular models, virological tools, and robust microscopy approaches constitutes a useful data set, the proposed model remains incomplete and requires clarification of entry mechanisms, host factors, and viral variant-specific fusion pathways to substantiate it against established entry models.

eLife Assessment

This work details the finding that in at least one of the subunits of the heterohexameric chaperone complex Pfdn5 has additional functions beyond its contribution to cytoskeletal protein folding in Drosophila. The authors provide convincing evidence that it is a hitherto unknown microtubule associated protein in addition to regulating microtubule organization and levels of tubulin monomers. The important findings show that Pfdn5 loss exaggerates pathological manifestations of mutant human Tau bearing FTDP-17 linked mutations in Drosophila, while its overexpression suppresses them, suggesting that the latter may constitute a future therapeutic approach.

eLife Assessment

In this valuable study, the authors used an elegant genetic approach to delete EED at the post-neural crest induction stage. The usage of the single-cell RNA-seq analysis method is extremely suitable to determine changes in the cell type-specific gene expression during development. Results backed by solid evidence demonstrate that Eed is required for craniofacial osteoblast differentiation and mesenchymal proliferation after the induction of the neural crest.

eLife Assessment

This useful study explores the role of RAP2A in asymmetric cell division (ACD) regulation in glioblastoma stem cells (GSCs), drawing parallels to Drosophila ACD mechanisms and proposing that an imbalance toward symmetric divisions drives tumor progression. While findings on RAP2A's role in GSC expansion are promising, and the reviewers found the study innovative and technically solid, the study relies on neurosphere models without in vivo confirmation and will therefore need to be further validated in the future.

eLife Assessment

This important study reveals that connexin43 (Cx43) hemichannels are directly activated by CO₂ through a conserved carbamylation motif, extending a mechanism previously described for β-connexins to α-connexins. The evidence is convincing, supported by complementary biochemical and electrophysiological analyses showing CO₂-induced hemichannel opening and ATP release in cultured cells and hippocampal slices. These findings advance our understanding of connexin regulation by metabolic gases and will be of broad interest to researchers studying cell communication, neural signaling, and gasotransmitter biology.

eLife Assessment

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

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

eLife Assessment

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

eLife Assessment

This study thoroughly assesses tactile acuity on women's breasts, for which no dependable data currently exists. The study provides two important contributions, by convincingly showing that tactile acuity on the breast is poor in comparison to other body parts, and that acuity is worst in larger breasts, indicating that the number of tactile sensors is fixed. However, further arguments concerning the role of the nipple in spatial localisation are not well supported by the current evidence, therefore diluting the overall contribution of the study. This study will be of interest to the broader community of touch, as well as those interested in breast reconstruction and sexual function.

eLife Assessment

This valuable study reports that EEG recordings of the earliest stage of information processing in the human visual cortex can be used to predict subsequent choice responses. The findings provide novel, solid evidence for integrative processing in low-level sensory cortices, though the exact nature of the neural signals measured here requires some clarification. While some conceptual issues need to be addressed, the paper is likely to be of interest to neuroscientists interested in the contribution of early sensory signals to decision-making.

eLife Assessment

This study shows that excitatory cholecystokinin (CCK)-expressing neurons in hippocampal area CA3 influence hippocampal-dependent memory using multiple methods to manipulate excitatory CCK-expressing CA3 neurons selectively. The work is valuable because most past studies of CCK-expressing neurons have focused on those neurons that co-express CCK and GABA. Currently, the strength of evidence is incomplete; however, if additional evidence were to be presented that the methods were selective, the evaluation would potentially be higher.

eLife Assessment

This study integrates large-scale behavioral, genetic, and molecular analyses in animal models to investigate morphine response. Utilizing high-quality, time-series Quantitative Trait Loci (QTL) mapping, the work provides compelling evidential support for novel, time-dependent genetic interactions (epistasis). A fundamental result of this rigorous analysis is the discovery of a novel Oprm1-Fgf12-MAPK signaling pathway, which offers new insights into the mechanisms of opioid sensitivity.

eLife Assessment

This important study presents JABS, an open-source platform that integrates hardware and user-friendly software for standardized mouse behavioral phenotyping. The work has practical implications for improving reproducibility and accessibility in behavioral neuroscience, especially for linking behavior to genetics across diverse mouse strains. The strength of evidence is convincing, with comprehensive validation of the platform's components and enthusiastic reviewer support.

eLife Assessment

In this important study, the authors conducted extensive atomistic and coarse-grained simulations as well as a lattice Monte Carlo analysis to probe the driving force and functional impact of supercomplex formation in the inner mitochondrial membrane. The study highlighted the major contribution from membrane mechanics to the supercomplex formation and revealed interesting differences in structural and dynamical features of the protein components upon complex formation. Upon revision, the analysis is considered solid, although the magnitude of estimated membrane deformation energies seem somewhat large. Overall, the study is thorough, creative and the impact on the field of bioenergetics is expected to be significant.

eLife Assessment

This study provides important findings on the understanding of circannual timing in mammals, for which iodothyronine deiodinases (DIOs) have been suggested to be of critical importance, yet functional genetic evidence has been missing. The authors convincingly implicate dio3, the major inactivator of the biologically active thyroid hormone T3, in circannual timing in Djungarian hamsters, using a combination of correlative and gene knock-out experiments; thus this provides key insights into the evolution and function of animal annual timing mechanisms.

eLife Assessment

The results in this study are useful because they begin to establish a causal link between physical activity and the cellular mechanisms of regeneration. The evidence presented is largely solid, supporting the conclusion that exercise-induced changes in the extracellular matrix disrupt regeneration; however, some claims are incomplete, requiring additional controls and a clearer distinction between the effects of mechanical loading and mechanical injury to the blastema. The work will be of interest to researchers in regenerative medicine.

eLife Assessment

This important work characterizes layers of neuropeptidergic modulations that collectively regulate the intake of sugar in a hunger state-dependent manner. Combinations of genetic, physiological, and behavioral approaches present convincing evidence that neurons that release Hugin and Allatostatin A are in an active state in sated flies, leading to suppression of sugar feeding behavior by reducing the sensitivity of sugar-sensitive gustatory neurons that express Gr5a. They also demonstrate that neurons that release Neuromedin U, a vertebrate homolog of Hugin, have common physiological properties as the fly Hugin neurons, revealing a similar function of evolutionarily conserved peptides across animal phyla.

eLife Assessment

This important study extends the previous interesting work of this group to address the potentially different control of movement and posture. Through experiments in which stroke participants used a robotic manipulandum, the authors provide solid evidence supporting a lack of a relation between the resting force postural bias they measure (closely related to the flexor synergy in stroke) and kinematic deficits during movement. Based on these results, the authors propose a conceptual framework that differentially weights the two main descending pathways (corticospinal tract and reticulospinal tract) for neurologically intact and stroke patients.

eLife Assessment

This study investigates how people adapt their speech when auditory feedback is altered. The analyses are rigorous and the work makes a valuable contribution by extending methods from limb motor control to speech. However, because the paradigm does not directly measure sensory error, the evidence for the proposed mechanism of sensorimotor learning is incomplete. The findings are best viewed as evidence for how prior motor adjustments influence subsequent behaviour, highlighting the need for future studies to more precisely separate sensory and motor contributions to adaptation.

eLife Assessment

This study extends prior work on head bristle mechanosensation by delivering a synaptic-resolution map of second-order partners that preserves somatotopy and highlights a cholinergic pathway linking sensory input to grooming circuits, providing a valuable resource for the field. The reconstructions and quantitative connectivity analyses provide solid support the main anatomical claims, while causal sufficiency for the behavioral sequence remains inferential and could be strengthened by a simple rank-order test relating wiring to the known grooming hierarchy.

eLife Assessment

This timely and fundamental study introduces a human iPSC-based co-culture system that models Kupffer cell-hepatocyte interactions and aims to recapitulate liver-specific immune-parenchymal dynamics. Direct contact between iMacs and iHeps promotes mutual tissue-specific maturation, with iHeps downregulating fetal genes while iMacs acquire a Kupffer cell-like profile. This convincing in vitro model holds significant promise and is a leap forward; future experimental understanding will enhance its translational impact.

eLife Assessment

This study constitutes a fundamental advance for the uveal melanoma research field that might be exploited to target this deadly cancer and more generally for targeting transcriptional dependency in cancers. This work substantially advances our understanding of pharmacological inhibition of SWI/SNF as a therapeutic approach for cancer. The study is well written and provides compelling evidence, including comprehensive datasets, compound screens, gene expression analysis, epigenetics, as well as animal studies.

eLife Assessment

This manuscript provides a single-cell transcriptomic atlas for AML (222 samples comprising 748,679 cells) integrating data from multiple studies. They use this dataset to investigate t(8;21) AML, and they reconstruct the Gene Regulatory Network and enhancer Gene Regulatory Network, which allowed identification of interesting targets. This aggregation is important and can help infer differences in genetic regulatory modules based on the age of disease onset. Their compelling effort may help explain age-related variations in prognosis and disease development in subtype-specific manner.

eLife Assessment

This study provides a valuable insight into how the medial and lateral entorhinal cortices interact through distinct excitatory and inhibitory pathways. Using anatomical tracing, optogenetics, and electrophysiology, the authors show that glutamatergic medial entorhinal neurons provide broad excitatory input to lateral entorhinal, while long-range SST+ interneurons deliver selective inhibition to layer I. These findings reveal a novel layer- and cell-type-specific organization of medial to lateral entorhinal connectivity with implications for spatial and episodic memory. The work is solid, but validation of injection specificity and viral spread is needed to fully confirm the anatomical interpretations; with these clarifications, this will be a significant contribution to understanding entorhinal-hippocampal circuit organization.

eLife Assessment

This valuable clinical trial compares the impact of dolutegravir intensification on longitudinal measures of total HIV DNA and day 84 measures of intact HIV DNA. The trial was well-designed, and the paper is easy to read and provides hypothesis generation-level evidence that treatment intensification might decrease intact HIV DNA level in some people after 3 months. The findings are solid, with significant limitations being that study endpoints and hypotheses were not precisely defined prior to the trial, and that effect size is limited and inconsistent across trial participants.

eLife Assessment

Using a transposon sequencing (TN-seq) approach, the authors identified key genetic determinants of drug tolerance in Mycobacterium abscessus. Given that M. abscessus is inherently resistant to multiple antibiotics, this valuable study makes a significant contribution by uncovering how antibiotic tolerance is linked to reactive oxygen species (ROS) in this non-tuberculous mycobacterial (NTM) species. The solid findings further strengthen the growing evidence that ROS play a central role in the mechanism of antibiotic action and tolerance in mycobacteria. However, the manuscript would benefit from improved clarity of presentation and corrections in the reference section.

eLife Assessment

The study presents important findings regarding the incidence and clinical impact of a mutation in a cardiac muscle protein and its association with the development of atrial fibrillation. The authors provide convincing evidence of electrophysiological disturbances in cells with this mutation and of its association with atrial fibrillation, which would be of interest to cardiologists. Evidence supporting the conclusion that this mutation causes atrial fibrillation would benefit from more rigorous electrophysiologic approaches.

eLife Assessment

This study provides valuable insights into the role of the NF-kB and IKK signaling pathways in γδ T cell development and survival, using robust genetic mouse models. While the research is methodologically sound, some conclusions require further evidence, with incomplete analyses, particularly regarding cell-intrinsic effects and mechanistic details. Overall, the findings are significant for immunologists interested in innate-like T cell biology and advancing the understanding of γδ T cell differentiation and maintenance.

eLife Assessment

This study is useful because it challenges the widely accepted notion that muscle stem cell numbers decline with aging, providing novel insights into population heterogeneity and the identification of new surface markers for geriatric MuSCs. However, the evidence is considered incomplete due to insufficient quantitative comparisons of absolute cell numbers, limited analysis of age groups (particularly the lack of "aged" mice as opposed to geriatric), and the need for further functional and mechanistic validation of key subpopulations. Additional concerns that require clarification include the lack of statistical rigor in some experiments, the presentation of supporting data not being complete, and the overextension of claims relating to senescence and new marker validation. Overall, while the findings advance understanding of MuSC aging, the conclusions drawn by the authors should be strengthened with expanded experiments and more rigorous data analysis.

eLife Assessment

This useful paper examined the mechanism of planar cell polarity (PCP) using Drosophila pupal wing, investigating how 'cellular level', 'molecular level' and 'tissue level' mechanisms intersect to establish PCP. This represents progress for the field and the conclusions are mostly backed up by solid data. Whereas the manuscript is sound overall, remaining concerns could be addressed by textual clarification of the concepts used in the manuscript.

[Editors' note: this paper was reviewed by Review Commons and revised by the authors.]

eLife assessment

This important study provides novel evidence that navigational experiences can shape perceptual scene representations. The evidence presented is incomplete and would benefit from clearer explanations of the experiment design and careful discussion of alternative interpretations such as contextual associations or familiarity. The work will be of interest to cognitive psychologists and neuroscientists working on perception and navigation.

[Editors’ note: A revised version of this work has been published in the Journal of Cognitive Neuroscience (DOI: https://doi.org/10.1162/JOCN.a.2409).]

eLife Assessment

The reviewers have found that this manuscript is a valuable contribution, and the evidence in support of its conclusions is mostly solid. It provides novel insights and raises interesting possibilities about the functions of an understudied histone modification within the nucleosome core; however, the data are mostly descriptive and correlative, and although this has value, it is not totally persuasive. Short of additional non-genomic experiments, a more detailed analysis of the genomic data and perhaps additional data would strengthen the conclusions. The manuscript crucially needs further antibody validation to raise confidence in the data.

eLife Assessment

This study provides fundamental insights into eukaryotic phosphate homeostasis by demonstrating how yeast vacuoles dynamically regulate cytosolic phosphate levels. The conclusions are convincing, supported by an elegant combination of in vitro assays and in vivo measurements. This study will be of interest to cell biologists, particularly for those who are working in the field of phosphate metabolism.

eLife Assessment

The mechanistic basis for the potential health benefits of NAD⁺ precursors remains incompletely understood. This manuscript provides a useful assessment of the role of SIRT1 in mediating the effects of NMN in mice fed a high-fat diet. The study addresses a key question, though some of the conclusions appear only partially supported by the presented data.

eLife assessment

The authors identify a novel, conserved link between glycolytic flux and sulfur amino acid metabolism that governs fungal morphological differentiation independently of the cAMP-PKA pathway. This represents an important conceptual advance in understanding metabolic control of development and virulence. While the evidence supporting this connection is compelling, the mechanistic basis of how glycolysis regulates the Met30/Met4 axis requires further experimental clarification.

eLife Assessment

This valuable work investigates the role of protein N-glycosylation in regulating T-cell activation and function and suggests that B4GALT1 is a potential target for tumor immunotherapy. The strength of evidence is solid, and further mechanistic validation could be provided.

Baldwin contends that Black English is a legitimate language forged by historical necessity and bound to power and identity, and that contempt for it is contempt for Black experience.

Angle most relevant to my theme: Language as power/identity vs. “neutral standard.”

Alvarez, Wan, and Lee advocate a translingual orientation that treats students as “language architects,” offering concrete strategies to bring full language resources into academic writing.

Angle most relevant to my theme: Pedagogy that legitimizes multilingual voice and challenges monolingual standards.

Young argues that teachers should teach and value code meshing—blending dialects and languages within the same text—and reject a single “standard” as the only acceptable academic or professional English.

Angle most relevant to my theme: Language plurality as both pedagogy and justice.

Heller argues that Bambara’s use of AAVE in “The Lesson” constructs realism, affirms Black identity, and equips the narrator to critique inequality and resist dominant norms.

Angle most relevant to my theme: Vernacular as a tool of critique and agency.

Jenkins argues that mastering Standard American English is essential for professional success and is not inherently discriminatory.

Angle most relevant to my theme: SAE as pragmatic, workplace-driven convention for cross-audience communication.

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 valuable study provides insights into the role of Pten mutations in SHH-medulloblastoma, by using mouse models to resolve the effects of heterozygous vs homozygous mutations on proliferation and cell death throughout tumorigenesis. The experiments presented are convincing, with rigorous quantifications and orthogonal experimentation provided throughout, and the models employing sporadic oncogene induction, rather than EGL-wide genetic modifications, represent an advancement in experimental design. However, the study remains limited, such that the biological conclusions do not extend greatly from those in the extant literature. This could be addressed with additional experimentation focused on cell cycle kinetic changes at early stages, as well as greater characterization of macrophage phenotypes (e.g., microglia vs circulating monocytes). The work will be of interest to medical biologists studying general cancer mechanisms, as the function of Pten may be similar across tumor types.

eLife Assessment

Pinho et al use in vivo calcium imaging and chemogenetic approaches to examine the involvement of hippocampal sub-regions across the different stages of a sensory preconditioning task in mice. They find evidence for sensory preconditioning in male mice. They also find that, in these mice, CaMKII-positive neurons in the dorsal hippocampus encode the audio-visual association that forms in stage 1 of the task. The evidence in support of these findings is convincing. The important study will be of interest to researchers in the fields of learning and memory and/or hippocampus function.

eLife Assessment

This Research Advance manuscript further elucidates the roles of SMC5/6 loader proteins and associated factors in the silencing of extrachromosomal circular DNA by the SMC5/6 complex. While the findings are largely in line with expectations, they are valuable, representing a meaningful advance beyond the recent study from the same laboratories (PMC9708086), validating the previous model that distinct SMC5/6 subcomplexes, SIMC1-SLF2 and SLF1/2, separately control its transcriptional repression and DNA repair activities on extrachromosomal DNA. Solid evidence is presented for a role for SIMC1/SLF2 in localization of the SMC5/6 complex to plasmid DNA, and the distinct requirements as compared to recruitment of SMC5/6 to chromosomal DNA lesions.

eLife Assessment

This paper provides potentially valuable insight into why memory consolidation may differ between children (5-7 years of age) and adults. The work hints at developmental differences in neural engagement during the retrieval of recent and remote memories. However, there are several major concerns with the analyses not alleviated by included controls, and as such the evidence supporting the authors' main claims remains incomplete.

eLife Assessment

This study presents fundamental insights into overcoming resistance in hormone receptor-positive breast cancer by demonstrating that sustained CDK4/6 inhibitor treatment, either alone or in combination with CDK2 inhibitors, significantly suppresses the growth of drug-resistant cancer cells. The findings are supported by compelling evidence from both in vitro cell line experiments and in vivo mouse models, highlighting the therapeutic potential of maintaining CDK4/6 inhibitors beyond disease progression. Additionally, the identification of cyclin E overexpression as a key driver of resistance offers a target that will be of value for future therapeutic strategies, potentially improving outcomes for patients with advanced breast cancer.

eLife Assessment

The study provides important mechanistic insight into the transcriptional control of γδT17 development, elegantly demonstrating how HEB and Id3 act sequentially and cooperatively to regulate γδT17 cell specification and maturation. The study provides compelling evidence that advances the understanding of E-Id protein dynamics in thymic T cell specification. The work is comprehensive, technically rigorous, and conceptually clear, and will be of interest to immunologists, developmental biologists, and those studying the molecular underpinnings of physiological outcomes.

eLife Assessment

This useful manuscript reports findings indicating that cell cycle progression and cytokinesis both play a role in the transition of early to late neural stem cell fates. The imaging data are solid and mostly support the conclusions. However, experimental details are missing, the method of quantitation could be improved, and orthogonal approaches are needed to confirm the findings, which are based on loss-of-function approaches and are not sufficient to support some of the authors' conclusions. Lastly, there is no investigation of the underlying mechanism linking the cell cycle or cytokinesis to the changes (or lack thereof) of early and late NSC fates.

eLife Assessment

The manuscript by Hensley and Yildez studies the mechanical behavior of kinesin under conditions where the z-component of the applied force is minimized. The important study shows that much of the mechanical information gleaned from the traditional "one bead" with attached kinesin approach was probably profoundly influenced by the direction of the applied force. The data are convincing, but in some cases the amount of data collected appears to be smaller than optimal.

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.