eLife Assessment

In this study, the authors investigated how inference about the current task context, by weighting evidence based on surprise and uncertainty in the environment, is encoded in the cortex. Using MEG imaging and an impressive amount of analytic work based on normative decision modeling, they provided solid evidence for the involvement of the visual and parietal cortex. These results are a valuable complement to and extension of a previous study using fMRI measurements, by identifying the candidate regions that are of importance for the inference process, not just for encoding the end product.

eLife Assessment

This important study links blood-derived dietary content to sustained increases in sleep in the mosquito Aedes aegypti. Using multiple independent approaches, the authors provide convincing evidence for blood-induced changes in sleep. These findings have broad implications for understanding how specialized diets regulate sleep across species and for mosquito vector biology.

eLife Assessment

This manuscript reports a potentially valuable modeling study on sequence generation in the hippocampus in a variety of behavioral contexts. While the scope of the model is ambitious, its presentation is incomplete, and there remains some lack of clarity on the methodology and interpretation. The work will interest the broad community of researchers studying cortical-hippocampal interactions and sequences.

eLife Assessment

This is a potentially valuable modeling study on sequence generation in the hippocampus in a variety of behavioral contexts. While the scope of the model is ambitious, its presentation is incomplete and would benefit from substantially more methodological clarity and better biological justification. The work will interest the broad community of researchers studying cortical-hippocampal interactions and sequences.

eLife Assessment

This important paper presents a rigorous and comprehensive deep mutational analysis of the kinase TYK2, revealing how single amino acid substitutions influence protein abundance, signaling activity, and responses to pharmacological inhibitors. By combining high‑quality experimental design with dose‑response signaling assays and multiple inhibitor conditions, the authors generate a robust dataset that identifies variants across all domains of TYK2, including clusters at functionally critical sites and protein-protein interfaces. The study highlights mutations that drive drug resistance or potentiation and shows that reduced TYK2 abundance aligns with protective autoimmune‑associated variants, underscoring the therapeutic relevance of modulating TYK2 stability. Overall, the work provides compelling insights with clear implications for biochemistry, immunology, clinical genetics, and drug discovery.

eLife Assessment

The authors establish solid theoretical principles for designing brain perturbations under the assumption that brain activity evolves under a linear model. By prioritizing low-variance components, resonant frequencies, and hub nodes, this framework provides an important foundation for optimizing information gain, neural state classification, and the control of neural dynamics. However, the lack of investigation of model mismatch makes the study incomplete.

eLife assessment

This important study uses state-of-the-art, multi-region two-photon calcium imaging to characterize the statistics of functional connectivity between visual cortical neurons. Although alternative interpretations may partially account for the data, the study provides solid evidence that functionally distinct classes of neurons convey visual information via parallel channels within and across both primary and higher-order cortical areas.

eLife Assessment

This useful study presents a simple homeostatic-plasticity model in spiking E-I networks to link spontaneous critical dynamics with representational drift and relatively stable stimulus-response geometry in mouse visual cortex. However, the evidence is incomplete because key concepts and analysis details are not well defined, controls are limited, and several results might be the result of specific methodological choices (e.g., dimensionality reduction, aggregation, or tuned parameters) rather than a robust mechanism. As a result, the work currently supports an interesting correlation between these phenomena, but not a clear causal account.

eLife Assessment

Using a combination of innovative and robust techniques, this study outlines cell-type-specific translational landscape changes that occur in the spinal cord neurons in the early and late phases of nerve injury. The authors provided compelling evidence suggesting an essential role of protein synthesis regulation in the chronic phase of neuropathic pain. Although additional mechanisms contributing to late-phase neuropathic pain beyond altered PV+ neuron excitability remain to be elucidated, this is a fundamental and significant study toward a comprehensive understanding of the molecular pathways involved in neuropathic pain.

eLife Assessment

In this manuscript, Wafer and Tandon et al. present a thoughtful and well-designed genetic screen for regulators of adipose remodeling using zebrafish as a model system. This work is valuable because it uncovers several genes associated with adipose tissue hyperplastic hypertrophic morphology and diet-induced remodelingthe hat have considerable potential health impact. The rigorous phenotypic analyses and compelling evidence make this work a key resource for the field.

eLife Assessment

In this important study, the authors provide a simple yet elegant approach to identifying therapeutic targets that synergize to prevent therapeutic resistance in ovarian cancer using cell lines, data-independent acquisition proteomics, and bioinformatic analysis. The authors convincingly identify several combinations of pharmaceuticals that were able to overcome or prevent therapeutic resistance in culture models of ovarian cancer, a disease with an unmet diagnostic and therapeutic need. This work will be of interest to researchers focused on ovarian cancer.

eLife Assessment

This valuable computational study presents a conceptually simple and biologically plausible reinforcement-learning framework for motor learning based on policy-gradient methods. The evidence supporting the conclusions is convincing, including rigorous mathematical derivations of learning rules for the mean and variance of motor commands and simulation results for three sets of experimental data, based on three different motor learning tasks from the literature. However, there is a lack of a clear description of the specific conditions under which this framework yields unique mechanistic insights or predictive values, hence falling short of qualifying as a "general theory of motor learning". The work will be of interest to researchers in computational motor learning and motor neuroscience.

eLife Assessment

This study addresses an important gap in drug discovery by delivering a rigorous, large-scale evaluation of widely used co-folding methods for predicting ligand-bound protein complexes and virtual screening. A key strength is the comprehensive benchmarking framework, which leverages structures and chemical compounds that were absent from the AI models training set, thereby providing particularly compelling and unbiased evidence of co-folding performance. The findings clearly delineate the complementary roles of deep learning-based co-folding and physics-based docking, offering practical guidance for their rational integration into drug discovery workflows. Although the conclusions are convincing, improvements in the test cases, presentation, and usability can further strengthen the overall impact.

eLife Assessment

In this study, the authors describe the degradation of HDACs in late HSV-1 infection and attempt to link this phenomenon to HDAC export to the cytoplasm and to DNA damage response. However, the evidence is incomplete, as many of the experiments are lacking in rigor. As a result, mechanistic links to the proposed model are weak.

eLife Assessment

This useful study examines patterns of clonal reproduction and somatic mutations in 'Pando', a massive, quaking aspen clone consisting of ~47000 stems. Because the study relies on relatively low-coverage, reduced-representation genomic resequencing data for the detection of somatic mutations, the evidence provided for several of the primary conclusions about clone age and the relationship between mutation accumulation and geographic distance is incomplete.

eLife Assessment

This important study explores whether complex structures that are lost during evolution can re-evolve, which is a long-standing debate in evolutionary and developmental biology. The authors demonstrate that re-evolution can occur if the gene regulatory network that underlies the development of complex traits is maintained. The evidence supporting its conclusions is solid and the work will be of interest to those studying the evolution and development of complex traits.

eLife Assessment

This important study provides new insight into the regulation of cell organization and division in Trypanosoma brucei through the control of a kinesin motor protein by a polo-like kinase. The authors present solid evidence from rigorous biochemical and imaging analyses showing that phosphorylation modulates kinesin function and cellular organization. However, direct in vivo evidence that PLK phosphorylates kinesin-G is lacking.

eLife Assessment

This valuable study uses a large cohort of clinical malaria cases collected over 18 years to address a critical knowledge gap regarding the role of PfEMP1 variants across distinct severe malaria syndromes. The conclusions are potentially of importance and interest to those who study malaria severity, but the evidence is incomplete, largely due to a lack of clarity on data inclusion and the correct use of statistical tests. More up-to-date data analysis methods would further strengthen the conclusions.

eLife Assessment

This important study presents a novel immunotherapy strategy for cancer. The authors develop a whole-tumor cell vaccine comprised of senescent tumor cells and a COX2 inhibitor in a hydrogel matrix. They present convincing evidence of the efficacy of this approach in preclinical models, demonstrating that prostaglandin E2 (PGE2) modulates the senescence-associated secretory phenotype (SASP) toward an immunostimulatory state, although more mechanistic/functional work would strengthen their conclusions. This work is timely and will be of interest to immunologists and others interested in the development of novel cancer therapies.

eLife Assessment

This important work describes systematic computational and experimental approaches to turn a moderately stable α-helical bundle into a very stable fold. The authors advance our understanding of α-helix stabilization providing a convenient framework that has general implications for the protein design field. The main claims have convincing support through a sound methodology, with strong specific conclusions for designing mechanically, thermally, and chemically stable α-helical bundles.

eLife Assessment

This is an important study showing that movement vigor is not solely an individual property but emerges through interaction when two people are physically linked. The evidence is convincing, supported by a well-controlled experimental design and modeling that closely match the observed behavior. While the authors provided a helpful comparison of several candidate models of human-human interaction dynamics, the statistical power remains limited.

eLife Assessment

This valuable work extends a previously published regression framework for trial-aligned photometry data incorporating functional variables. However, the evidence is generally incomplete, due to the way that within-trial changes in variables have been incorporated into an inherently cross-trial analysis framework, which will limit general adoption. The ideas in this work will be of interest to researchers analyzing photometry signals.

eLife Assessment

This manuscript explores the dynamic behaviors of Pol II and Pol III puncta that encompass the SL1 and 5S genes, following up on the authors' prior studies on ATTF-6. The authors show that ATTF-6 is required for RNA Pol II but not RNA Pol III foci, demonstrating that within the gene cluster, the regulation of RNA Pol II and RNA Pol III remain distinct from each other. The study is useful for analyzing understudied gene families, but it is incomplete and needs additional edits and experiments.

eLife Assessment

This fundamental work uncovers an unexpected lysosomal function for NINJ2 and links it to ferroptosis and cancer biology. The evidence supporting the conclusions appears to be convincing. Additional mechanistic clarification, particularly around the NINJ2-LAMP1 interaction and ferroptosis specificity, will further strengthen the manuscript. This work will be of general interest to the community of ferroptosis and cancer biology.

eLife Assessment

This important study addresses the long-debated hypothesis that humans preferentially choose partners with dissimilar immune genes, using data from a small-scale society that allows comparison between arranged and self-chosen partnerships. Across multiple analyses controlling for genome-wide relatedness and examining functional immune diversity, the authors find no evidence of HLA/MHC-based (dis)assortative mating, suggesting that immune gene variation has limited influence on mate choice in this relatively homogeneous population and that the observed patterns instead reflect selection acting directly on immune loci. While the strength of the evidence is compelling for this population, several conclusions rely on indirect reconstruction methods and imputed data for a very complex region of the genome, which may limit how firmly some claims can be supported.

eLife Assessment

This study presents a valuable finding on the condition dependence of autophagy-mediated lifespan regulation in C. elegans. The evidence is solid, as the data broadly support the main claims, although variability between biological replicates and limited mechanistic exploration leave some conclusions less firmly established. The work will be of interest to researchers studying autophagy, ageing, and intracellular trafficking.

eLife Assessment

This study establishes a methodology (machine vision and gaze pose estimation) and behavioral apparatus for examining social interactions between pairs of marmoset monkeys. It has been difficult to study social interactions using artificial stimuli rather than genuine interactions between unrestrained animals. This study makes a fundamental contribution to social neuroscience research in a laboratory setting. Their results are convincing showing that the study of unrestrained social interactions is possible with detailed quantification of position and gaze. The methodology presented here is relevant to research in social neuroscience, neuroethology, and primatology.

eLife Assessment

This important work examines the effects of side-wall confinement on chemotaxis of swimming bacteria in a shallow microfluidic channel. The authors present convincing experimental evidence, combined with geometric analysis and numerical simulations of simplified models, showing that chemotaxis is enhanced when the distance between the side walls is comparable to the intrinsic radius of chiral circular swimming near open surfaces. This study should be of interest to scientists specializing in bacteria-surface interactions.

eLife Assessment

This interesting study presents a multi-OMICs approach to unify different lines of evidence regarding the epigenetic regulation of the key virulence factor causing placental malaria during P. falciparum infection. Most results are confirmatory of previous observations; nonetheless, the claims are supported by convincing evidence. The combinatorial approach chosen here is unprecedented and therefore provides valuable new data. In addition, the comparative investigation of different DNA methylation modifications is novel and disproves a direct role in var gene regulation.

eLife Assessment

This important research investigates the precision of numerosity perception in two types of tasks and concludes that human performance aligns with an efficient coding model optimized for current environmental statistics and task goals. The proposed model receives compelling evidence from two numerosity perception experiments and a reanalysis of an existing dataset of risky decision-making. These findings have theoretical implications for our understanding of numerosity perception and decision-making as well as the ongoing debate on different efficient coding models.

eLife Assessment

This valuable study is an approach to integrating and comparing single-cell genomics data across species. The evidence supporting the conclusions of this work is solid, and ANTIPODE presents an updated methodological approach to determining how gene expression at the cell-type level has evolved. Thus, ANTIPODE should provide broad utility to studies of comparative neurogenomics and be of use to neuroscientists and evolutionary biologists.

eLife Assessment

This manuscript identifies temperature-dependent alternative splicing of PIF4 in Arabidopsis thaliana and shows that heat stress promotes the accumulation of a short exon 5-skipping isoform that is predicted to encode a non-functional protein. This finding is important, and it provides an intriguing new layer of regulation for PIF4; however, the strength of the mechanistic conclusions is limited, and several key conclusions rely on indirect evidence. As a result, while the data robustly demonstrate heat-regulated alternative splicing of PIF4, the causal role of PIF4 isoforms' balance in shaping heat-induced developmental responses remains only partially supported and the strength of the evidence presented is incomplete. This work will be of interest to biologists working on alternative splicing.

eLife Assessment

The revised manuscript by Shukla et al. provides important mechanistic insights into kinesin-1 autoinhibition and cargo-mediated activation. Through a convincing integration of protein engineering, computational modeling, biophysical assays, HDX-MS, and electron microscopy, the study delineates how cargo binding induces an allosteric transition that propagates along the coiled-coil stalk to the motor domains, enhancing MAP7 engagement. The revisions substantially improve clarity, figure annotation, and methodological transparency, leaving the remaining limitations, primarily those inherent to conformational heterogeneity and resolution, appropriately acknowledged. Overall, the updated manuscript presents a coherent mechanism for kinesin-1 activation that will be of broad interest to the motor protein, structural biology, and cell biology communities.

eLife assessment

This manuscript provides an important contribution to the field of platelet biogenesis, and the convincing evidence will advance our understanding of signal transduction driving the development of late megakaryopoiesis and platelet reactivity that results in bleeding diathesis. The paper is noteworthy for analyzing two related, either singly or in combination, tyrosine phosphatases in this conditional, stage development gene knockout. Because SHP1 is a negative regulator and SHP2 is an activator, the synergistic effects found in the double knockout were surprising.

eLife Assessment

This study provides valuable findings in the study of enhancer biology by identifying and dissecting a minimal enhancer regulating dlx2b expression during zebrafish tooth development, supported by promoter dissection, reporter assays, and genome-editing approaches. The work offers a resource and extends previous findings but has limited broader impact, with several conclusions about general cis-regulatory principles and functional consequences remaining only partially supported. Accordingly, the strength of evidence is at present incomplete, as additional functional validation would be needed to fully substantiate some of the claims.

eLife Assessment

This fundamental study presents experimental evidence on how geomagnetic and visual cues are integrated in a nocturnally migrating insect. The evidence supporting the conclusions is compelling. The work will be of broad interest to researchers studying animal migration and navigation.

eLife Assessment

This valuable study advances our understanding of how organisms respond to chronic oxidative stress. Using the nematode C. elegans, the authors identified key neuronal signaling molecules and their receptors that are required for stress signaling and survival. The evidence supporting the conclusions is solid, including rigorous genetics, stress response analysis, and transcriptional profiling. This research will be of broad interest to neuroscientists and researchers working in the field of oxidative stress regulation.

eLife Assessment

This important study shows that orientation tuning of V1 neurons is suppressed during a continuous flash suppression paradigm, especially in neurons with binocular receptive fields. These findings, made using cutting-edge imaging techniques, convincingly implicate early visual processing in continuous flash suppression, in agreement with previous studies suggesting reduced effective contrast of such stimuli in V1.

eLife Assessment

The authors show that innate defensive behavior in mice is shaped by threat intensity, reward value, and social hierarchy, highlighting how value and social context influence instinctive decisions. The authors provide a valuable characterization of escape behavior which approximates naturalistic conditions. The evidence is incomplete due to indirect measures of vigilance and somewhat misleading characterizations of the looming stimulus.

eLife Assessment

This is an important study reporting that activation of the presynaptic GPR55 receptor suppresses synaptic transmission by modulating GABA release through the reduction of the readily releasable pool without affecting the presynaptic AP waveform and calcium influx. The evidence supporting this claim is compelling and based on an impressive array of techniques including patch-clamp recordings from the axon terminals of cerebellar Purkinje cells and fluorescent imaging of vesicular exocytosis. While the authors have strengthened their conclusions on several technical fronts in the revised version, further investigation is needed into the mechanism by which GPR55 activation might make vesicles insensitive to the rise in presynaptic [Ca²⁺] mediated by VGCCs, and the nature of the endogenous process that would activate this pathway in vivo.

eLife Assessment

This important research investigates the precision of numerosity perception in two types of tasks and concludes that human performance aligns with an efficient coding model optimized for current environmental statistics and task goals. The proposed model receives compelling evidence from two numerosity perception experiments and a reanalysis of an existing dataset of risky decision-making. These findings have theoretical implications for our understanding of numerosity perception and decision-making as well as the ongoing debate on different efficient coding models.

eLife Assessment

This study provides important insights into how Trypanosoma cruzi populations diversify surface protein expression, showing through single-cell RNA sequencing that trans-sialidase-like genes are expressed heterogeneously across individual parasites, a pattern with clear implications for immune evasion. The evidence is convincing, supported by robust single-cell transcriptomic analyses, consistent quantitative measures of expression heterogeneity, and integration with genomic organization that together argue against purely stochastic expression.

eLife Assessment

This work of fundamental significance introduces a novel statistical model of spiking activity that incorporates continuous-time gain modulation. The authors provide exceptional evidence that the model outperforms earlier approaches and alternative candidates in capturing spiking responses across multiple visual areas in the macaque. Beyond its methodological contribution, the study offers new insights into how stimulus-driven variability and internally generated gain fluctuations evolve over time and between brain areas. The framework is likely to find broad application beyond the datasets examined here.

eLife Assessment

This valuable study demonstrates how individual taste preferences shift over time, how these changes relate to cortical activity, and how experience reshapes both. The evidence is largely solid, although additional analyses are needed to strengthen some of the conclusions. The results should be of interest to neuroscientists studying sensory physiology.

eLife Assessment

This study presents valuable insights into cellular sites of monoamine production and presence in Pristionchus pacificus, providing a comparative reference for the detailed knowledge of C. elegans, as well as using this information to compare serotonergic anatomy in 22 nematode species. Functional assays support evolved differences in monoaminergic control over certain, but not all, tested behaviors. The evidence is convincing, combining careful genetic experiments and comparative analysis that are well aligned with the conclusions. The results will serve as a basis for (comparative) structural-functional studies of nematode behavior.

eLife Assessment

This study presents valuable findings on how retrieval practice protects memory inferences from stress via covert memory reactivation. Via two EEG experiments manipulating stress and retrieval practice, the authors provide solid evidence supporting the conclusion. This work will be of interest to cognitive and affective neuroscientists working on the intersection between memory and stress.

eLife Assessment

In this fundamental work Horne et al present compelling evidence that YbjP is a novel binding partner of the TolC channel protein. The YbjP is characterized using cryo-EM, and its role probed using pull-down experiments, in vivo crosslinking, functional assays along with phylogenetic analysis which are all properly performed and presented and support the main conclusions. While the study does not identify a clear role for this protein, the results contribute to the understanding of this complex system and will be of interest to those working in the fields of membrane transport and antimicrobial resistance.

eLife Assessment

This useful study presents a new method to identify the activity of single motor units from intramuscular EMG recordings. Validation against state-of-the-art techniques is limited to a small sample of simulated motor units; consequently, the evidence supporting the method's accuracy remains incomplete. The manuscript would be significantly strengthened by using more unbiased simulations for validation, validating the method with experimental datasets, comparing it against more recent techniques, and investigating how muscle physiology impacts accuracy.

eLife Assessment

This modeling study proposes important new insights into the circuit mechanisms underlying navigational control in insects. High-speed video recordings of ants are compared to detailed predictions from a new computational model, whose description is incomplete. If the model is sound, the similarities between the model and behavioral data suggest how complex behavioral motifs can emerge from a simple neural circuit. These results will be of interest to scientists studying the neural circuit basis of behavior, particularly in insects.

eLife Assessment

This study provides important insights into the crosstalk between ATG2A with components of the early secretory pathway. While the mechanisms governing autophagic membrane expansion remain yet to be fully understood, in this study the authors employ an elegant proximity labelling approach and identify two ER-Golgi intermediate compartment (ERGIC)-localized proteins. Through a series of complementary experiments combining microscopy and biochemistry, the authors identify ARFGAP1 and Rab1A as components of early autophagic membranes, which accumulate at the periphery of pre-autophagosomal structures induced by loss of ATG2. The overall study is well executed and the evidence supporting the claims is convincing.

eLife Assessment

This study presents valuable findings on the ability of a state-of-the-art method, Temporally Delayed Linear Modelling (TDLM), to detect the replay of sequences in human memory. The investigation provides compelling evidence that TDLM has significant limitations in its sensitivity to detect replay in extended (minutes-long) rest periods. The work will be of strong interest to researchers investigating memory reactivation in humans, especially using iEEG, MEG, and EEG.

eLife Assessment

This study presents an assessment of the effect of lactate dehydrogenase (LDH) inhibition on the activity of glycolysis and tricarboxylic acid cycle. The data were collected and analyzed using solid and validated methodology. This paper makes a useful contribution to the field as it considers a control analysis of LDH flux. The findings differ from other published findings likely due to the time course of the incubations used to assess metabolism. While such comparative studies were not presented in the manuscript, the manuscript should be interpreted in light of this critical distinction.

eLife Assessment

This study presents an important methodological advance-Liver-CUBIC combined with multicolor metallic nanoparticle perfusion-that enables high-resolution 3D visualization of the liver's complex multi-ductal architecture. The identification of the Periportal Lamellar Complex (PLC) as a novel perivascular structure with distinct cellular composition and low-permeability characteristics is convincing, supported by rigorous imaging data. The observed scaffolding role during fibrosis offers intriguing biological insights, though the functional claims would benefit from direct experimental validation.

eLife Assessment

This study now provides solid evidence for a role of EndoA3-mediated trafficking of ICAM-1 to the immune synapse with T cells. The study will be valuable to those studying cell-cell communication in the immune system, and opens additional questions regarding the mechanisms involved and how other adhesion ligands are regulated.

eLife Assessment

This important study investigates how infestation by the small brown planthopper (Laodelphax striatellus) reshapes rice carbohydrate allocation and demonstrates that host-derived glucose enhances insect fecundity and imidacloprid tolerance, through the activation of conserved nutrient-sensing and endocrine pathways. Across extensive and complementary approaches, including plant manipulations, glucose supplementation, RNAi, pharmacological inhibition, rescue experiments, and biochemical assays, the authors provide convincing evidence that glucose activates the TOR-juvenile hormone-vitellogenin axis to promote reproduction and co-regulates GST-mediated detoxification via both TOR-JH signaling and GCL-GSH metabolism. The mechanistic framework is coherent and well supported by hierarchical validation and functional assays. Some limitations remain regarding the generality of the findings across other pest species and insecticides, and aspects of the evolutionary framing would benefit from more cautious interpretation; nonetheless, the work substantially advances our understanding of how plant-derived nutrients interface with conserved insect signaling pathways to shape fitness-related traits, and will be of broad interest to researchers studying plant-insect interactions, insect physiology, and pest management.

eLife Assessment

This manuscript presents a valuable investigation of the peptidoglycan (PG) recycling pathway in Caulobacter crescentus. The authors showed that PG recycling in C. crescentus is essential not only for β-lactam (ampicillin) resistance but also for cell morphology, efficient division, and overall fitness. The study is comprehensive and compelling.

eLife Assessment

This important study introduces an advance in multi-animal tracking by reframing identity assignment as a self-supervised contrastive representation learning problem. It eliminates the need for segments of video where all animals are simultaneously visible and individually identifiable, and significantly improves tracking speed, accuracy, and robustness with respect to occlusion. This innovation, which is supported through compelling evidence, has implications beyond animal tracking, potentially connecting with advances in behavioral analysis and computer vision.

eLife Assessment

Karimian et al. present a valuable new model to explain how gamma-band synchrony (30-80 Hz) can support human visual feature binding by selectively grouping image elements, countering recent criticisms that the stimulus dependence of gamma oscillations limits their functional role. Grounded in the theory of weakly coupled oscillators the model captures behavioural patterns observed in human psychophysics, offering support for the potential role of synchrony-based mechanisms in feature-binding. The development of the model in alignment with primate electrophysiology convincingly supports the paper's claims that gamma synchrony may be the underlying mechanism. While the paper does not present electrophysiological results that directly link gamma oscillations to figure-ground segregation in the presented task, the model makes several predictions that can be tested experimentally.

eLife Assessment

This important study provides a nuanced analysis of the impact of cues on cost/benefit decision-making deficits in male rats that could have translational relevance to many addictive disorders. The main findings are that cues paired with rewarded outcomes increase the proportion of risky outcomes, whereas risky choice is reduced when cues are paired with reward loss. The experimental data are compelling, whereas the computational analysis based on the optimisation of different Q-learning models is solid. The findings will be of interest to behavioural neuroscientists and clinicians with an interest in risk, decision making, and gambling disorders.

eLife Assessment

This study provides a useful analysis of the changes in chromatin organization and gene expression that occur during the differentiation of two cell types (anterior endoderm and prechordal plate) from a common progenitor in zebrafish, together with investigations into the molecular factors involved. Although the findings are consistent with previous work, the evidence presented appears to be incomplete and would benefit from more rigorous quantification of live imaging and Cre-Lox experiments, a stronger rationale and controls for experiments manipulating chromatin remodeling factors, and a strong justification for the explant model especially given differences between explant and whole embryo data. This work may be of interest to zebrafish developmental biologists investigating the mechanisms underlying specification.

eLife Assessment

This important study investigates how the Cdv division proteins of Metallosphaera sedula assemble on and interact with curved membranes in vitro, advancing our understanding of this reduced ESCRT-like machinery. The data provide support for sequential protein recruitment and curvature-dependent enrichment at membrane necks, based on well-controlled reconstitution assays and quantitative analysis. The work establishes a convincing experimental framework for dissecting Cdv-mediated membrane remodeling. The study will be of broad interest to evolutionary and synthetic biologists as well as membrane biophysicists.

eLife Assessment

This study systematically characterizes the activity patterns of a lateral supramammillary nucleus (SuM)-medial septum (MS)-hippocampus circuit across sleep-wake cycles and its role in memory consolidation. This work is fundamental because it identifies a previously unrecognized brain hub that helps coordinate how different types of memory are supported during a specific sleep state, advancing our understanding of how sleep contributes to memory organization. The work is well-designed, and the data are solid, supporting clear and significant conclusions; however, some mechanistic details and causal relationships would benefit from further clarification or additional experiments. The paper provides new insights into how distinct memory modalities could be processed by parallel, sleep-active subcortical-hippocampal circuits, which would be of general interest to a broad neuroscience audience.

eLife Assessment

This paper describes an important advance in a 2D in vitro neural culture system to generate mature, functional, diverse, and geometrically consistent cultures, in a 384-well format with defined dimensions and the absence of the necrotic core, which persists for up to 300 days. The well-based format and conserved geometry make it a promising tool for arrayed screening studies. The evidence is compelling and provides a method for generating consistent 3D cortical layer-like organization.

eLife Assessment

This study presents a valuable finding on the neural representation of time from two distinct egocentric and allocentric reference frames. The evidence is solid and largely supports the hypothesis, with one caveat that the task differences could impact the observed effects. The work will be of interest to cognitive neuroscientists working on the perception and memory of time.

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 important study examines the role of TNF in modulating energy metabolism during parasite infection. The authors perform an elegant set of studies, however the evidence supporting the major claims of the manuscript is incomplete, particularly in highlighting a direct role for GLUT1 in monocytes. This work integrates an interesting set of observations that will be of interest to the Plasmodium and pathogenesis communities with an expanded set of experiments.

eLife Assessment

This study presents a valuable finding on how the GAP DLC1, a deactivator of the small GTPase RhoA, regulates RhoA activity globally as well as at Focal Adhesions. Using a new acute optogenetic system coupled to a RhoA activity biosensor, the authors present convincing evidence that DLC1 amplifies local Rho activity at Focal Adhesions. Thanks to modeling, they show that DLC1 is needed for a negative feedback loop that engage more RhoA deactivators upon RhoA activation, highlighting the complex regulation of RhoGTPases in space and time.

eLife Assessment

This study represents an important advance in our understanding of how certain inhibitors affect the behavior of voltage gated potassium channels. Robust molecular dynamics simulation and analysis methods lead to a new proposed inhibition mechanism with strength of support being mostly convincing, though computational evidence is limited for some conformations discussed. This study has considerable significance for the fields of ion channel physiology and pharmacology and could aid in development of selective inhibitors for protein targets.

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 use of words persistence or tolerance should follow the consensus definition given in the Balaban 2019 Nat Rev Micro paper.

eLife Assessment

This important study analyzed the impact of amino acid homorepeats on protein expression and solubility in yeast and E. coli. The authors provided convincing evidence that hydrophobic and positively charged amino acids are toxic and that counterselection during evolution reduced the occurrence of such proteotoxic protein sequences. This study will be of interest to cell biologists and biochemists, particularly those working on proteostasis.

eLife Assessment

This valuable study identifies a novel neurodevelopmental syndrome caused by variants in ARID5B, supported by solid human genetic evidence from a well-characterized cohort. While the clinical data establish a clear genotype-phenotype correlation, the functional evidence regarding the proposed molecular mechanisms remains incomplete. Addressing the gaps in the functional characterization and refining the clinical assertions would significantly strengthen the conclusions.

eLife Assessment

This study presents important findings by identifying small molecules that can stabilize and refold missense-mutated VHL tumor suppressor protein, offering a potential therapeutic approach for clear cell renal cell carcinoma. The computational design approach is well-executed, but the evidence is incomplete due to insufficient demonstration that HIF2 downregulation occurs through on-target VHL rescue rather than off-target effects. Additional experiments with appropriate controls are needed to establish the specificity of the mechanism.

eLife Assessment

This important study advances our understanding of developmental timing mechanisms by studying the cleavage, nuclear translocation, and oscillation of the transcription factor MYRF-1 (vertebrate MYRF) during C. elegans larval development. The evidence supporting the conclusions is solid, with elegant genome engineering experiments and state-of-the-art microscopy. The work will be of broad interest to cell and developmental biologists.

eLife Assessment

This manuscript by Feng et al. provides valuable evidence regarding the hematopoietic differentiation of bone marrow endothelial cells in the adult mouse. Overall, the authors have addressed our main concerns. Solid data now more strongly support long-term multi-lineage reconstitution of the adult hemogenic endothelial cells. However, critical data, especially regarding the endothelial cells' hematopoietic identity and functional capacity, remain insufficient, which limits the strength of the hemogenic claim, especially the assertion that these adult hemogenic ECs generate bona fide HSCs. Additional experiments would be necessary to fully rule out alternative explanations.

eLife Assessment

This study provides valuable insights into addressing the question of whether the prevalence of autoimmune disease could be driven by sex differences in the T cell receptor (TCR) repertoire, correlating with higher rates of autoimmune disease in females. The authors compared male and female TCR repertoires using bulk RNA sequencing, from sorted thymocyte subpopulations in pediatric and adult human thymuses; however, the analyses provided do not provide sufficient discrimination and incompletely support the central claims regarding sex differences in the TCR repertoire and potential autoimmune bias.

eLife Assessment

This fundamental study investigates whether neural prediction of words can be measured through pre-activation of neural network word representations in the brain; convincing evidence is provided that neural network representations of neighboring words are correlated in natural language. This study urges future studies to carefully differentiate between neural activity that predicts the upcoming word and neural activity that encodes the current words, which contain information that can be used to predict the upcoming word. The study is of potential interest to researchers investigating language encoding in the brain or in large language models.

eLife Assessment

The submission by Praveen et al. reports important findings describing the structure of genetic and colour variation in its native range for the globally invasive weed Lantana camara. Whilst the importance of the research question and the scale of the sampling is appreciated, the analysis, which is currently incomplete, requires further tests to support the claims made by the authors.

eLife Assessment

Winter months with short days are commonly associated with seasonal depression and hypersomnolence; the mechanisms behind this hypersomnolence however, remain unclear. Chen and colleagues identify a genetic basis for this phenomenon in the fly Drosophila - mutations in the circadian photoreceptor cryptochrome resulted in increased sleep under short photoperiods. These findings are valuable insights into the genetic mechanisms regulating sleep under short days. The data supporting the precise neurobiological basis of these effects however, remains incomplete.

eLife Assessment

This important study introduces LUNA, a new autofocusing method that achieves nanoscale precision and robustly corrects focus drift during time-lapse microscopy, improving imaging under temperature shifts. The authors exploit this technical advance to investigate the bacterial cold shock response, providing solid evidence that individual cells continue to grow and divide in a highly coordinated process that cannot be observed in population-level measurements. This work offers a technical and conceptual framework for reconciling discrepancies between bulk and single-cell growth measurements, with broad relevance for cell biology and microbiology.

eLife Assessment

This valuable study introduces MPS, an open-source pipeline that addresses a significant technical bottleneck by making miniscope data analysis more accessible. Characterized by speed and a low barrier to entry, the software's performance is supported by solid evidence. This work will be of interest to miniscope users seeking a streamlined, memory-efficient, end-to-end analysis solution.

eLife Assessment

With the goal of investigating the assembly and fragmentation of cellular aggregates, this manuscript examines cyanobacterial aggregates in a laboratory setting. This quantitative investigation of the conditions and mechanisms behind aggregation is an important contribution as it yields a basic understanding of natural processes and offers potential strategies for control. The combination of computational and experimental investigations in this manuscript provides convincing support for the role of shear on aggregation and fragmentation.

eLife Assessment

There is a growing interest in understanding the individuality of animal behaviours. In this important article, the authors build and use an impressive array of high throughput phenotyping paradigms to examine the 'stability' (consistency) of behavioural characteristics in a range of contexts and over time. The results show that certain behaviours are individualistic and persist robustly across external stimuli while others are less robust to these changing parameters. The data supporting their findings is extensive and convincing. At the same time, the main analyses focus on a selected subset of the many behavioural metrics recorded, so a large fraction of the acquired data remains only lightly explored; by making these additional data available, the authors provide an invaluable resource for future work to apply alternative analytical frameworks and further mine this rich dataset.

eLife Assessment

This valuable study advances our understanding of best practices for analyzing population-level data using advanced functional alignment methods. It provides convincing evidence that demographic-specific functional templates improve functional neuroimaging studies that use hyperalignment. This study will be of interest to cognitive neuroscientists, neuroimaging methodologists, and computational researchers with an interest in the human brain.

eLife Assessment

This important study demonstrates that Mycobacterium tuberculosis suppresses protective Th17/IL-17 responses in C57BL/6 mice via a Tbet-dependent mechanism involving the virulence factors ESX-1 and PDIM, as mutants lacking these factors induce significantly higher IL-17-producing CD4 T cells and IL-17A in the lungs compared to wild-type bacteria. The experiments are rigorous and well-designed, combining host knockouts and bacterial mutants to yield solid evidence pointing to cross-regulation between Th1 and Th17 pathways, including reduced IL-23 in draining lymph node dendritic cells. However, some of the data on IFN-γ effects or lymph node-specific mechanisms are incomplete and require deeper mechanistic insight, such as direct T cell transcription factor analysis in lymph nodes and broader host validation, to strengthen the work. Overall, the findings provide insight into how bacterial virulence factors limit Th17 induction, thereby promoting persistence, and will interest immunologists and TB researchers focused on host-pathogen balance and vaccine strategies.

eLife Assessment

This valuable manuscript demonstrates that embryonic exposure to the pesticide chlorpyrifos (CPF) impairs juvenile zebrafish social behavior and sets out to define the underlying mechanism. The authors provide solid evidence that butyrate and class I histone deacetylases are involved, as their modulation rescues the phenotype. However, claims that CPF acts through the microbiome and nitric oxide signaling remain correlative and incomplete. Additional validation would strengthen the intriguing hypotheses raised by this work.

eLife Assessment

This work provides an important modeling-based framework for understanding the processes of temporal integration in the claustrum. These mechanisms could support a broader range of integrative brain function. However, at present, the evidence remains at least in part incomplete, primarily because of over-interpretation of the results and their connection to neurophysiology.

eLife Assessment

This important study combines electrocardiographic (ECG) and heart/torso anatomy data from subjects included in the UK Biobank to analyze sex-specific differences in relationships between those two characteristics. The study has several compelling strengths, including the development of an open-source pipeline for reconstruction and analysis of heart/torso geometry from a large cohort. Nevertheless, technical analysis of the data as presented is incomplete, specifically as it pertains to assessment of co-linearity between regressed parameters, interpretation of regression coefficients for sex and/or presence of myocardial infarction, and discussion of potential roles played by underlying electrophysiological derangements. With improvements to these aspects of the analysis, the paper would be of interest to the cardiovascular research community, especially those studying highly relevant health and treatment disparities arising from sex differences.

eLife Assessment

This fundamental work shows that a history of cocaine self-administration disrupts the orbitofrontal cortex's ability to encode similarities between distinct sensory stimuli that possess identical task information - hidden states. The evidence supporting these conclusions is compelling, with methods and analyses spanning self-administration, a novel 'figure 8' sequential odor task, recordings from 3,881 single units, and sophisticated firing analyses revealing complex orbitofrontal representations of task structure. These results will be of broad interest to psychologists, neuroscientists, and clinicians.

eLife Assessment

This valuable study provides evidence that locus coeruleus activity is coordinated with heart rate during sleep, confirming previous work in mice and humans, with a possible role for sleep-dependent memory consolidation. The claims are supported by solid evidence, although the underlying mechanisms and the predictive value of the correlative dataset would benefit from additional controls. This work will be of interest to neuroscientists focusing on sleep, memory, and autonomic functions.

eLife Assessment

This important study investigates the impact of BRCA1/2 mutations on immunotherapy in lung adenocarcinoma using multi-omics approaches. The detailed genetic analysis of two cancer genes (BRCA1 and BRCA2) demonstrated new roles for these genes in causing the tumor microenvironment in lung cancer. Further experimental explorations of the immune-related changes may still be required. The solid findings of this study provide a foundation for further developing drugs targeting BRCA1/2 in lung cancer therapy.

eLife Assessment

The findings of this study are important since they cover the repurposing of small molecules as metalloprotease and phospholipase inhibitors for early intervention in the treatment of bothropic envenoming in the Neotropics, and thus provide a strong rationale for the progression of these inhibitors into future preclinical and clinical evaluation for snakebite indications across various ecological zones. The strength of the evidence is solid; however, there are some weaknesses, such as a lack of translatability of the in vivo model and insufficient venom characterisation. Thus, the strength of the evidence can be enhanced by the use of a mouse model. The paper remains of interest to ophiologists, biochemists and medicinal chemists.

eLife Assessment

This useful study supplements previous publications of willed attention by addressing a frontoparietal network that supports internal goal generation. The evidence is solid in analyzing two datasets collected at different independent sites, using the same willed-attention paradigm and combining fMRI and EEG. This work will interest cognitive psychologists and neuroscience researchers.

eLife Assessment

This study presents a valuable examination of two measurements of physical activity (self-report and objective) in relation to widely studied structural MRI measures of the brain (hippocampal volume and BrainAGE) and cognitive function (Trail Making Test). Cross-sectional and longitudinal data were analyzed using established and validated methodology. The results convincingly suggest that brain health is more likely a cause of physical activity than an outcome of it, although limitations to the data could mask evidence of benefits to brain health. This work will be of interest to neurologists and epidemiologists studying the etiology of cognitive decline, to clinicians interested in advising patients on strategies for preserving brain health in aging, and to members of the lay public.

eLife Assessment

This study provides valuable contributions to establish canonical Dhh signaling as a primary mediator in the differentiation of Leydig cells and their steroidogenic capacity. Together, the experimental design using their established stem Leydig cell line alongside relevant genetically mutated models, both derived using the relevant Nile tilapia animal system, provided largely convincing evidence to support their conclusions. The work could benefit from a more rigorous dissection of current literature on this pathway that might better inform their conclusions. The work will be of broad interest to developmental biologists interested in differentiation of steroidogenic or hormone producing cells.

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

eLife Assessment

This paper presents a computational method to infer from data a key feature of affinity maturation: the relationship between the affinity of B-cell receptors and their fitness. The approach, which is based on a simple population dynamics model but inferred using AI-powered Simulation-Based Inference, is novel and valuable. It exploits recently published data on replay experiments of affinity maturation. While the method is well-argued and the validation solid, the potential impact of the study is hindered by its complex presentation, which makes it hard to assess its claims reliably.

eLife Assessment

This paper presents a computational method to infer from data a key feature of affinity maturation: the relationship between the affinity of B-cell receptors and their fitness. The approach, which is based on a simple population dynamics model but inferred using AI-powered Simulation-Based Inference, is novel and valuable. It exploits recently published data on replay experiments of affinity maturation. The method is well argued and presented, and the validation is compelling.

eLife Assessment

This valuable manuscript provides solid evidence regarding the role of alpha oscillations in sensory gain control. The authors use an attention-cuing task in an initial EEG study followed by a separate MEG replication study to demonstrate that whilst (occipital) alpha oscillations are increased when anticipating an auditory target, so is visual responsiveness as assessed with frequency tagging. The findings offer a re-interpretation of the inhibitory role of the alpha rhythm, supporting that alpha oscillations contribute to interareal communication.

eLife assessment

The ability to estimate the force of infection for Plasmodium falciparum from other more directly measurable epidemiological quantities is a useful contribution to malaria epidemiology. The authors propose a method to accomplish this using genetic data from the var genes of the Pf genome and novel applications of existing methods from queueing theory. While the simulations are sophisticated, the real-world application of the method is incomplete in its analysis and would benefit from clearer articulation of the assumptions being made. Given the lack of clarity in the methods and presentation of results, it is difficult to fully assess the performance of their proposed estimation procedure.

eLife Assessment

The ability to estimate the force of infection for Plasmodium falciparum from other more directly measurable epidemiological quantities would contribute to malaria epidemiology. The authors propose a method to accomplish this using genetic data from the var genes of the Pf genome and novel applications of existing methods from queueing theory. After revising the manuscript, this is a useful contribution to the field and the authors provide solid evidence to support it.

eLife Assessment

This study provides valuable insights through the elucidation of the first full-length structure of the heterohexameric (MmpS4)₃-(MmpL4)₃ transporter complex from Mycobacterium tuberculosis, advancing understanding of its transport mechanism, linked to virulence and drug resistance. The structural analysis is convincing, offering a clear framework for future mechanistic studies. Major strengths include a comprehensive structural characterization of the complex, though some conclusions require further validation.

eLife Assessment

Maloney et al. offer an important contribution to understanding the potential ecological mechanisms behind individual behavioral variation. By providing compelling theoretical and experimental data, the study bridges the gap between individual, apparently stochastic behavior with its evolutionary purpose and consequences. The work further provides a testable and generalizable model framework to explore behavioral drift in other behaviors.

eLife Assessment

This paper describes useful findings on the effects of isoflurane anesthesia on the visual cortical circuitry of the mouse. It provides solid evidence that the visual spatial frequency sensitivity becomes coarser (lower resolution) during anesthesia, with distinct effects described in excitatory neurons, and parvalbumin (PV) and somatostatin (SOM) positive interneurons. This study should be of interest to neuroscientists studying the mouse visual cortex and the effects of anesthesia on cortical circuitry.

eLife Assessment

This important study experimentally probes potential antibiotic activity against hypothetical "mirror bacteria" with reversed chirality, showing that D-enantiomers of several approved antibiotics largely lack activity against natural bacteria (as a proxy for mirror organisms) and that conjugated D-peptides can elicit strong binding antibody responses in mice when adjuvanted. The evidence is solid for these core observations but incomplete on issues of chiral purity, functional antibody assays, replicates, and pharmacodynamic readouts; the work also overreaches in extrapolations without deeper mechanistic integration or native-format validation. Overall, the work offers a cautious, relevant contribution to mirror microbiology discussions and will interest infectious disease researchers.

eLife Assessment

AIRE has been well known to contribute to immune self-tolerance in the thymus by expressing auto-antigens; in this manuscript, the authors describe unexpected findings about the interaction of AIRE with AID in B cells, and its function in the immune system, thereby contributing to a fundamental understanding of the broader functions of AIRE. The strength of this manuscript is that, by employing biochemical and genetic experiments, the authors convincingly show interaction between AIRE and AID and subsequent AIRE's function in the GC responses. However, two weak points exist: first, the connection between AIRE, auto-anti IL17 Abs, and IL17-positive effector T cells, and second, like the thymus, expression of auto-antigens by AIRE in the GC B cells has not been tested.

eLife Assessment

This study used pupillometry to provide an objective assessment of a form of synesthesia in which people see additional color when reading numbers. It provides convincing evidence that subjective color ratings are matched by changes in pupil size that recapitulate brightness-mediated changes when exposed to the real color. The work provides a valuable contribution to the literature on both synesthetic perception and the use of pupillometry to probe perception and related psychological processes.

eLife Assessment

This study provides an important, comprehensive, large-scale dataset on transcription factor binding in Pseudomonas aeruginosa, along with analyses of its regulatory network, key virulence and metabolic regulators, and a pangenomic examination of transcription factors. Utilizing large-scale ChIP-seq and multi-omics integration, the research convincingly supports the hierarchical regulatory structures and offers insights into virulence mechanisms. This dataset, made available through an online database, should be an invaluable resource to the research community studying P. aeruginosa, a key pathogen at risk for hospital infections and development of antibiotic resistance.

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 the functional relevance of neural sequences. The study will be of interest to neuroscientists investigating learning and decision-making processes.

eLife Assessment

The authors make an important contribution to comparative functional genomics by developing a semi-automated computational pipeline that integrates classification and marker-based cluster annotation to identify orthologous cell types. Using a single-cell RNA-seq dataset of induced pluripotent stem cells and derived embryonic bodies from four primate species: humans, orangutans, cynomolgus macaques, and rhesus macaques, the authors provide convincing evidence that cell type-specific marker genes are substantially less transferable across species than broadly expressed genes, with transferability declining as phylogenetic distance increases. This study establishes a key framework and reference dataset for comparative single-cell analyses and encourages more rigorous evaluation of marker gene transferability across species.

eLife Assessment

Varani et al present important findings regarding the role of distinct cerebellothalamic connections in motor learning and performance. The evidence supporting the main claims is convincing, with multiple replications, validation of their techniques, and appropriate controls. The work will be of broad interest to neuroscientists interested in central mechanisms of motor learning and control, as well as thalamic physiology.

eLife Assessment

In this valuable study, the authors report on an innovative chemostat propagation system to reduce eukaryotic viruses while retaining phages in mixtures used for FVTs (fecal virome transplant). The authors hypothesized that chemostat-propagated viromes could modulate the gut microbiota and reduce necrotizing enterocolitis (NEC) lesions while avoiding potential side effects, such as earlier onset of diarrhea. Although no effect on NEC could be demonstrated, the revised document addressed the other concerns and is much improved from its original version. The study is convincing in that it integrates in vitro fermentation, high-resolution metagenomics, immunogenicity assays, and in vivo validation, demonstrating the potential of FVT using eukaryotic-free virome-based therapeutics.

eLife Assessment

This important study combines microfluidic experiments with mathematical modeling to elucidate the reciprocal interplay between flow dynamics and biofilm growth and detachment. Using Pseudomonas aeruginosa as a model organism, the authors identify several key regimes and stages of biofilm development. Overall, the comparison between experimental observations of biofilm behavior under varying flow conditions and corresponding theoretical predictions forms a compelling understanding of the processes involved in biofilm dynamics. The results will be of interest to researchers studying biofilms and their technological and biological applications.

eLife Assessment

This fundamental study introduces a new biology-informed strategy for deep learning models aiming to predict mutational effects in antibody sequences. It provides convincing evidence that separating selection from the nucleotide-level mutation process improves performance over the objectives of protein language models inspired by natural language processing. This paper should be of interest to computational immunologists, but also to the broader community interested in deep learning for biological sequence data and evolution.

eLife Assessment

This valuable study identifies a novel regulator of stress-induced gene quiescence in C. elegans: the multi-Zinc-finger protein ZNF-236. The work provides evidence for an active mechanism that maintains the repressed state of inducible genes under basal conditions in the absence of stress. The claims for discovery made in the title and abstract are supported by solid experimental data. However, a deeper investigation into the mechanisms of ZNF-236 action could substantially enhance the manuscript's impact and value.

eLife Assessment

This important work by Qin et al. delineates layered neuropeptidergic mechanisms that regulate sugar intake in a hunger state-dependent manner. Using a combination of genetic, physiological, and behavioral experiments, the authors convincingly show that Hugin- and Allatostatin A-releasing neurons are selectively active in sated flies and suppress sugar feeding by reducing the sensitivity of Gr5a-expressing gustatory neurons. They further demonstrate that Neuromedin U neurons share key physiological properties with fly Hugin neurons, highlighting conserved peptide functions across animal phyla.

eLife Assessment

This study introduces a novel method for estimating spatial spectra from irregularly sampled intracranial EEG data, revealing cortical activity across all spatial frequencies, which supports the global and integrated nature of cortical dynamics. It showcases important technical innovations and rigorous analyses, including tests to rule out potential confounds. However, further direct evaluation of the model, for example by using simulated cortical activity with a known spatial spectrum (e.g., an iEEG volume-conductor model that describes the mapping from cortical current source density to iEEG signals, and that incorporates the reference electrodes and the particular montage used), would even further strengthen the solid evidence.

eLife Assessment

In this important work, the authors present a new transformer-based neural network designed to isolate and quantify higher-order epistasis in protein sequences. They provide solid evidence that higher-order epistasis can play key roles in protein function. This work will be of interest to the communities interested in modeling biological sequence data and understanding mutational effects.

eLife Assessment

This study uses the yeast two-hybrid assay to identify proteins that may interact with yeast Set1 and other subunits of COMPASS/Set1C, the histone H3K4 methyltransferase, providing also some evidence for Set1 sumoylation and a role of SET1C methylating other factors in vitro. The results are valuable, and they should contribute to understanding the functions of the conserved SET1C complex, as they suggest potential functional connections with RNA biogenesis, chromatin remodeling, and non-histone methylation, whose implications would yet need to be explored. Nevertheless, apart from the fact that only a small subset of the Y2H interactions is further examined, the validating experiments are only partial or inconclusive, the strength of evidence being at this point incomplete.