eLife Assessment

This work represents a valuable finding of how single-trial functional connectivity may be used to infer different cognitive states involved in speech perception and production. Although the data and analyses are overall convincing, the theoretical advance and novelty of the finding are less clear. With a clearer idea of the functional significance of the connectivity data, the paper would be of interest to those interested in brain networks and communication.

eLife Assessment

This important study is of relevance for the fields of predictive processing, perception and learning, with a well-designed paradigm allowing the authors to avoid several common confounds in investigating predictions, such as adaptation. Using a state-of-the-art multivariate EEG approach, the authors test the opposing process theory and find evidence in support of it. Overall, the empirical evidence is solid, however, some conclusions rest on limited evidence and need further work to reconcile the present results with previous studies.

eLife Assessment

Muetter et al. provide an important argument that luminescence is a reliable, high-throughput alternative to colony-forming units (CFU) for super-MIC investigations, particularly when the quantity of interest is biomass. By examining 20 antimicrobials spanning 11 classes, the work shows that discrepancies between CFU and luminescence are often biological (filamentation, Viable But Not Culturable). The work provides a compelling view of how these three common measurements (luminescence, optical density, and CFU) relate to one another across a range of drug treatments, although testing on clinical isolates could be of further benefit.

eLife Assessment

This valuable study examined how sensory adaptation supports visual perception in the presence of noise. The authors used a combination of human psychophysics, electroencephalography (EEG), and deep neural networks to show that adaptation to noise can improve perception. The results are solid but are, at present, weakened by a number of concerns, including some related to the experimental design and some regarding the interpretation of the results in terms of particular mechanisms. With these concerns adequately addressed, the study and conclusions would be likely to be of broad interest to the neuroscience community.

eLife Assessment

This study presents a valuable and well-documented computational pipeline for the scalable analysis and spike sorting of large extracellular electrophysiology datasets, with particular relevance for high-density recordings such as Neuropixels. The authors demonstrate the pipeline's utility for benchmarking spike sorter performance and evaluating the effects of data compression, supported by thorough testing, clear figures, and openly available code. The workflow is reproducible, portable, and practical, providing concrete guidance on computational cost and runtime. Overall, the evidence supporting the pipeline's performance and output quality is compelling, and this work will be of broad interest to the systems neuroscience community.

eLife Assessment

This manuscript presents a novel investigation of organizational principles governing brain activity at both global and local scales during naturalistic viewing paradigms, an important advance for theoretical neuroscience, functional neuroimaging, and neurology. The authors demonstrate that brain activity during naturalistic viewing is dominated by two anti-correlated states that toggle between each other with a third transitional state mediating between them. The evidence supporting this finding is compelling, with the successful replication across three independent datasets (StudyForrest, NarrattenTion, and CamCAN) a particular strength.

eLife Assessment

This valuable study uses a computer vision pipeline to infer the motor control of cephalopod skin, revealing that individual chromatophores exhibit anisotropic deformations and can be associated with multiple putative motor units. The evidence supporting these claims is solid, although the study's conclusions are limited to stationary or sedated animals, and the analyses of motor unit characteristics and electrophysiological validation remain incomplete. This work will be of significant interest to biologists studying cephalopod behavior and motor control.

eLife Assessment

This important study addresses the question of how organ-specific blood vessels form during different stages of development, and how specific genes may regulate these processes. New genetic tools were developed to label distinct endothelial cell populations and track them over time in different mutant backgrounds. The results are solid; however, additional data quantification, lineage tracing, and cell autonomy experiments would further strengthen the conclusions.

eLife Assessment

This important work investigates cooperative behaviors in adolescents using a repeated Prisoner's Dilemma game. The approach used in the study is solid. The impact of this work could be further enhanced with more rigorous modelling procedures and more modeling selection/comparison details, as well as by framing the findings in terms of the specific game-theoretic context, rather than general cooperation. Findings from this study will be of interest to developmental psychologists, economists, and social psychologists.

eLife Assessment

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

eLife Assessment

This manuscript describes a series of studies using four different Go/No Go task variants in combination with fast-scan cyclic voltammetry to determine the role of dopamine release in the ventromedial striatum in action selection, controllability of reward pursuit, effort, and reward approach. The authors conclude that dopamine signals in the ventromedial striatum integrate the invigoration of action initiation with continuous estimation of spatial, but not temporal, proximity to rewards. There are, however, a number of concerns regarding methodology that could affect the interpretation of the results. Thus, while the findings are useful, they are considered incomplete, with the primary claims only partially supported.

eLife Assessment

This important study by Zeng et al characterizes a novel Legionella pneumophila effector, Llfat1 (Lpg1387), which binds actin through a newly identified actin-binding domain. Data is convincing; structural analysis of the Llfat1 ABD-F-actin complex enabled the development of this domain as a probe for F-actin. Additionally, the authors show that Llfat1 functions as a lysine fatty acyltransferase targeting small GTPases, highlighting its importance in both bacterial pathogenesis and cytoskeletal biology.

eLife Assessment

This fundamental work by Yamamoto and colleagues advances our understanding of how positional information is coordinated between axes during limb outgrowth and patterning. They provide convincing evidence that the dorsal-ventral axis feeds into anterior-posterior signaling, and identify the responsible molecules by combining transplantations with molecular manipulations. This work will be of broad interest to regeneration, tissue engineering, and evolutionary biologists.

eLife Assessment

This valuable study investigates whether the activity of an ABC transporter, BmrA, can be modulated by mechanical stimuli. The authors develop a single-molecule experimental system to address this question, although aspects of the methodological framework are incomplete. This work also develops a convincing theoretical model to explain the effect of membrane curvature on the conformational transitions observed during the activity cycle of this membrane protein. This study is of interest to the fields of membrane biophysics and membrane transport.

eLife Assessment

This valuable work explores how synaptic activity encodes information during memory tasks. All reviewers agree that the work is of very high quality and that the methodological approach is praiseworthy. The experimental data support the possibility that phospholipase diacylglycerol signaling and synaptotagmin 7 (Syt7) dynamically regulate the vesicle pool required for presynaptic release. Overall, this is a convincing study.

eLife Assessment

This set of experiments provides important knowledge for how the infralimbic cortex is recruited to inhibit behavior after extinction training. The evidence supporting the conclusions is convincing with multiple sophisticated behavioral designs providing converging lines of evidence, though reviewers note possible alternative interpretations and limitations of small group sizes in some cases. This work will be of interest to those interested in cortical function, learning and memory, aversive behavior, and/or related psychiatric factors.

eLife Assessment

This valuable study introduces CAAMO, a computational framework that combines structure prediction, in silico mutagenesis, molecular simulations, and energy calculations to design RNA aptamers with improved binding affinity. The computational methodology is solid, demonstrating strong theoretical foundations and systematic integration of multiple prediction techniques. However, the experimental validation is incomplete, with methodological weaknesses that limit the strength of support for the computational predictions.

eLife Assessment

This fundamental study uses the Drosophila mushroom body as a model to understand the molecular machinery that controls the temporal specification of neuronal cell types. With convincing experimental evidence, the authors make the finding that the Pipsqueak domain-containing transcription factor Eip93F plays a central role in specifying a later-born neuronal subtype while repressing gene expression programs for earlier subtypes.

eLife Assessment

This important study describes a computational model of the rat spinal locomotor circuits and how they could be plastically reconfigured after lateral hemisection or contusion injuries to replicate gaits observed experimentally in vivo. Overall, the simulation results convincingly mirror the gait parameters observed experimentally. The model suggests the emergence of detour circuits after lateral hemisection, whereas after a midline contusion, the model suggests plasticity of left-right and sensory inputs below the injury.

eLife Assessment

This paper provides important findings towards understanding the role of the lncRNA EPB41L4A-AS1 in a human cell line. The data is generally convincing, supported by extensive and clever integrative analysis. The work provides insights into how this lncRNA regulates gene expression via complex mechanisms; however the biological relevance awaits validation in other models.

eLife Assessment

In this important work, it is demonstrated that certain high-resolution cryo-EM structures can be obtained by using concentrated cell extracts without purification. The compelling results with the mammalian ribosomes demonstrate the utility of this approach for this molecule and complexes with elongation factor 2. Moreover, this work also demonstrates the utility of 2D template matching for particle picking for structure determination by single-particle averaging pipelines.

eLife Assessment

This important study provides solid evidence to support the anti-tumor potential of citalopram, originally an anti-depression drug, in hepatocellular carcinoma (HCC). In addition to their previous report on directly targeting tumor cells via glucose transporter 1 (GLUT1), the authors tried to uncover additional working mechanisms of citalopram in HCC treatment in the current study. The data here suggests that citalopram may regulate the phagocytotic function of TAM via C5aR1 or CD8+T cell function to suppress HCC growth in vivo.

eLife Assessment

This fundamental work significantly advances our understanding of gravity sensing and orientation behavior in the ctenophore, an animal of major importance in understanding the evolution of nervous systems. Through comprehensive reconstruction with volumetric electron microscopy, and time-lapse imaging of cilia motion, the authors provide compelling evidence that the aboral nerve net coordinates the activity of balancer cilia. The resemblance to the ciliomotor circuit in marine annelids provides a fascinating example of how neural circuits may convergently evolve to solve common sensorimotor challenges.

eLife Assessment

This study presents an important study into the molecular function of AT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15), a member of the AHL protein family, identifying it as a potential regulator of three-dimensional gene-loop organization within transcribed gene bodies. The authors support this claim with compelling genome-wide evidence, integrating AHL15 binding profiles with transcriptional and chromatin accessibility changes, as well as demonstrating overlap with genes known to form loops across transcribed regions. The evidence supporting the claims of the authors is solid. Collectively, these findings will be of broad interest to biologists seeking to understand the core regulatory mechanisms underlying gene expression.

eLife Assessment

This fundamental study advances our understanding of population-level immune responses to influenza in both children and adults. The strength of the evidence supporting the conclusions is compelling, with high-throughput profiling assays and mathematical modeling. The work will be of interest to immunologists, virologists, vaccine developers, and those working on mathematical modeling of infectious diseases.

eLife Assessment

This important manuscript evaluates how sample size and demographic balance of reference cohorts affect the reliability of normative models. The evidence supporting the conclusions is convincing. This work will be of interest to clinicians and scientists working with normative models.

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, additional experimentation focused on a greater characterization of macrophage phenotypes (e.g., microglia vs circulating monocytes) would enhance this study. 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

This manuscript presents a valuable study of the activity and functional relevance of different circuits in the dentate gyrus of mice performing a pattern separation task. The study is likely to be of interest to those studying the subregional organization and cell type-specific functions of the dentate gyrus. However, the strength of evidence for the study's conclusions is currently incomplete.

eLife Assessment

This useful study by Palo et al proposes that FRG1 functions as a negative regulator of Nonsense-Mediated mRNA decay (NMD) by associating with the exon junction complex (EJC) and destabilizing UPF1 independently of DUX4. The authors present solid evidence to dissect the relationship between FRG1 and DUX4 in NMD. However, the evidence to support the claim that FRG1 is a component of the EJC or the NMD machinery is incomplete.

eLife Assessment

This study presents a valuable finding on maternal SETDB1 as a key chromatin repressor that shuts down the 2C gene program and enables normal mouse embryonic development. The evidence supporting the claims of the authors is solid, although the inclusion of a causality test, a mechanistic understanding of SETDB1 targeting, and phenotypic quantification would have greatly strengthened the study. The work will be of broad interest to biologists working on embryonic development, stem cells and gene regulation.

eLife Assessment

This study presents a method for expressing single-stranded DNA fluorescent aptamers in E. coli using a retron-based strategy. The evidence supporting the successful expression and folding of DNA aptamers is solid, with clear demonstration of fluorescence after extraction, though the aptamers do not function in living cells. The method represents an important technical advance that will likely become standard for DNA aptamer expression in bacterial systems.

eLife Assessment

This study offers important insights into how entorhinal and hippocampal activity support human thinking in feature spaces. It replicates hexagonal symmetry in entorhinal cortex, reports a novel three-fold symmetry in both behavior and hippocampal signals, and links these findings with a computational model. The task and analyses are sophisticated, and the results appear convincing and of broad interest to neuroscientists.

eLife Assessment

This valuable study introduces a model to help researchers understand how multivariate processes affect observed relationships in genetic data. The authors provide a tool to estimate model parameters. Overall, the authors provide solid evidence that their tool can obtain median-unbiased estimates of the true parameters when using simulated data under the model.

eLife Assessment

This manuscript provides valuable insight into how genome organization changes as cells progress through the cell cycle after mitotic exit. The conclusions are supported by solid, rigorous data, and the use of sorted unsynchronized cells rather than cells treated with drugs is a particular strength. Two sharp genome remodeling events are identified at G1-S and to a lesser extent, at S-G2 transitions. A discussion on the limitations of Hi-C and a broader interpretation of results in the context of other mechanistic models would strengthen the overall rigor.

eLife Assessment

This important work demonstrates the role of physically linking the core and CTD kinase modules of TFIIH via separate domains of subunit Tfb3 in confining RNA Polymerase II Serine 5 CTD phosphorylation to promoter regions of transcribed genes in budding yeast. The main findings, resulting from analyses of viable Tfb3 mutants in which the linkage between TFIIH core and kinase modules has been severed, are supported by solid evidence from in vitro and in vivo experiments. There is an intriguing possibility that the Tfb3-mediated connection between core and kinase modules of TFIIH is an evolutionary addition to an ancestral state of physically unconnected enzymes, which could be examined more rigorously with additional evolutionary analyses.

eLife Assessment

This manuscript uses adaptive-bandit simulations to describe the dynamics of the Pseudomonas-derived chephalosporinase PDC-3 β-lactamase and its mutants to better understand antibiotic resistance. The finding, that clinically observed mutations alter the flexibility of the Ω- and R2-loops, reshaping the cavity of the active site, is valuable to the field. The evidence is considered incomplete, however, with the need for analysis to demonstrate equilibrium weighting of adaptive trajectories and related measures of statistical significance.

eLife Assessment

This study presented valuable findings regarding the basic molecular pathways leading to the cystogenesis of Autosomal Dominant Polycystic Kidney Disease, suggesting BICC1 functions as both a minor causative gene for PKD and a modifier of PKD severity. Solid data were supplied to demonstrate the functional and structural interactions between BICC-1, PC1 and PC2, respectively. The characterization of such interactions remains to be developed further, which renders the specific relevance of these findings for the etiology of relevant diseases unclear.

eLife Assessment

This study investigated the dynamics of human cortical network activity with functional magnetic resonance imaging during movie watching and studied the modulation of these dynamics by subcortical areas using an energy landscape mapping method. The authors identified a set of brain states defined at the level of canonical functional networks, quantified how the brain transitions between these states, and related transition probabilities to inter-subject correlations in evoked brain activity. A major emphasis of the work concerns the role of the thalamus, which shows transition-linked activity changes and dynamic connectivity patterns, including differential involvement of parvalbumin- and calbindin-associated thalamic subdivisions. The analytical strategy developed in this study is applicable to other task- and resting-state fMRI data and would be useful for many researchers in the field; however, the evidence supporting the overall conclusions remains incomplete due to limitations associated with fMRI data preprocessing, analysis, and cross-validation.

eLife Assessment

This study investigates whether heavy metal stress can induce maize-like phenotypic and molecular responses in teosinte and whether these responses overlap with genomic regions implicated in domestication. By combining copper and cadmium treatments with quantitative phenotyping, gene-expression analyses, and expanded assessments of nucleotide diversity across a key chromosome 5 interval, the authors provide an integrated view of how abiotic stress responses intersect with domestication-related traits. The significance of the findings is valuable, as the work offers meaningful insights for the subfield of maize evolution and stress biology by extending heavy-metal response analyses to teosinte and linking them to domestication-associated loci, although the evolutionary implications remain indirect. The strength of evidence is solid, with appropriately designed and quantitatively supported experiments that broadly support the claims, but do not yet establish a causal or historical role for heavy metal stress in domestication.

eLife Assessment

This is an important work implementing data mining methods on IMC data to discover spatial protein patterns related to the triple-negative breast cancer patients' chemotherapy response. The evidence supporting the claims of the authors is solid, although more detailed methodology clarification and validation are needed. While the accuracy of the methods is not very high, the work shows potential for translational application.

eLife Assessment

This important study focuses on the molecular mechanisms underlying the generation of neuronal diversity. Taking advantage of a well-defined neuroblast lineage in Drosophila, the authors provide convincing evidence that two transcription factors of the conserved forkhead box (FOX) family offer a mechanistic link between transient spatial cues that specify neuroblast identity and terminal selector genes that define post-mitotic neuron identity. The findings will be of interest to developmental neurobiologists.

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. The authors have also made clear effort to address concerns in revision. However, the strength of evidence remains incomplete. Acquisition of data from additional animals in the primary experiment could bolster these findings.

eLife Assessment

This study provides valuable insight into the role of actin protrusions in mediating early pre-endoyctic steps of human papillomavirus entry at the cell surface. Using state-of-the-art microscopy in an immortalized keratinocyte model, the authors present mostly solid evidence that filopodia actively promote the transfer of heparin sulfate-coated virions from the extracullar matrix to the viral entry factor CD151. Remaining gaps in the mechanistic model could be further supported by including a more expansive analysis of the fixed microscopy samples and live cell imaging to distinguish virion transfer from direct binding.

eLife Assessment

This valuable work advances our understanding of the relationship between multimodal magnetic resonance imaging (MRI) measures, cognition, and mental health. Compelling use of statistical learning techniques in UK Biobank data shows that 48% of the variance between an 11-task derived g-factor and imaging data can be explained. Overall, this paper contributes to the study of brain-behaviour relations and will be of interest for both its methods and its findings on how much variance in g can be explained.

eLife Assessment

This study offers a valuable methodological advance by introducing a gene panel selection approach that captures combinatorial specificity to define cell identity. The findings address key limitations of current single-gene marker methods. The evidence is compelling, but would be strengthened by further validation of rare cell states and unexpected marker categories.

eLife Assessment

This manuscript presents a valuable methodological approach to investigating context-dependent activity of cis-regulatory activity within defined genomic loci. The authors combine a locus-specific massively parallel reporter assay, enabling unbiased and high-coverage profiling of enhancer activity across large genomic regions, with a degenerate reporter assay to identify nucleotides critical for enhancer function. The data supporting the conclusions are solid, highlighted by successful identification and characterization of both previously known and new regulatory elements across multiple developmental stages, cell types, and species. While the approach has inherent limitations in sensitivity, and indirect assignment of regulatory elements to target genes, it provides a flexible platform for nominating candidate cis-regulatory elements across defined loci.

eLife Assessment

This study provides valuable mechanistic insight into the mutually exclusive distributions of the histone variant H2A.Z and DNA methylation by testing two hypotheses: (i) that DNA methylation destabilizes H2A.Z nucleosomes, thereby preventing H2A.Z retention, and (ii) that DNA methylation suppresses H2A.Z deposition by ATP-dependent chromatin remodelling complexes. Through a series of well-designed and carefully executed experiments, findings are presented in support of both hypotheses. However, the evidence in support of either hypothesis is incomplete, so that the proposed mechanisms underlying the enrichment of H2A.Z on unmethylated DNA remain somewhat speculative.

eLife Assessment

This study uses a valuable combination of functional magnetic resonance imaging and electroencephalography (EEG) to study brain activity related to prediction errors in relation to both sensorimotor and more complex cognitive functions. It provides incomplete evidence to suggest that prediction error minimisation drives brain activity across both types of processing and that elevated inter-regional functional coupling along a superior-inferior axis is associated with high prediction error, whereas coupling along a posterior-anterior axis is associated with low prediction error. The manuscript will be of interest to neuroscientists working on predictive coding and decision-making, but would benefit from more precise localisation of EEG sources and more rigorous statistical controls.

eLife Assessment

This manuscript provides evidence that mouse germline cysts develop an asymmetric Golgi, ER, and microtubule-associated structure that resembles the fusome in Drosophila germline cysts. This fundamental study provides new evidence that fusome-like structures exist in germ cell cysts across species. Overall, the data are convincing and represent a significant advance in our understanding of germ cell biology.

eLife Assessment

This paper develops a fundamental theory that explains how the brain can hold in working memory not only the identity but also the order of presented stimuli. Previous theories did not explain the ability of people to immediately recall the correct order of the stimulus presentation. The authors present compelling evidence that this can be achieved through synaptic augmentation, an experimentally observed phenomenon with a time scale of tens of seconds.

eLife Assessment

This valuable study a computational language model, i.e., HM-LSTM, to quantify the neural encoding of hierarchical linguistic information in speech, and addresses how hearing impairment affects neural encoding of speech. Overall the evidence for the findings is solid, although the evidence for different speech processing stages could be strengthened by a more rigorous temporal response function (TRF) analysis. The study is of potential interest to audiologists and researchers who are interested in the neural encoding of speech.

eLife Assessment

This study investigates low-affinity Ca2+ binding by WT calreticulin and mutant calreticulin associated with type I myeloproliferative neoplasms, as well as the impact on Ca2+ fluxes in suspension cultures of megakaryocyte-like cells in vitro in response to ER Ca2+ ATPase inhibitors that deplete endoplasmic reticulum (ER) Ca2+ store and open plasma membrane Ca2+ channels through STIM1-Orai interactions. The results are important in that they show that Ca2+ binding by calreticulin and store-operated Ca2+ entry are not fundamentally impacted by the type I deletion mutation in calreticulin, which rules out a direct effect of the calreticulin mutation on its own low-affinity Ca2+ binding and any broad impact on ER Ca2+ regulation. The strength of the data and methods used ranges from solid to convincing, although the use of suspension-based flow cytometric assays to investigate ER Ca2+ levels and Ca2+ entry can be challenged. High-affinity Ca2+ binding sites could be further considered, and possible confounding effects of Abl kinase activity in the megakaryocyte-like cell lines could be offset.

eLife Assessment

This important study combines a two-person joint hand-reaching paradigm with game-theoretical modeling to examine whether, and how, one's reflexive visuomotor responses are modulated by a partner's control policy and cost structure. The study provides a solid and novel set of behavioral findings suggesting that involuntary visuomotor feedback is indeed modulated in the context of interpersonal coordination. The work will be of interest to cognitive scientists studying the motoric and social aspects of action control.

eLife Assessment

This important study addresses a classic debate in visual processing, using a strong method applied to a rare clinical population to evaluate hierarchical models of visual object perception. The paper finds only partial support for the hierarchical model: as expected, neural responses in ventral visual cortex show increased representational selectivity for faces along the posterior-anterior axes, but the onsets of the signals do not show a temporal hierarchy, indicating more parallel processing. The iEEG dataset is impressive, but the evidence for lack of temporal hierarchy is incomplete: essential quality checks need to be performed, and statistical analyses adapted to ensure that the data and analyses would be able to reveal temporal hierarchy if it were present in the data.

eLife Assessment

This valuable study provides a practical computational framework for inferring latent neural states directly from calcium fluorescence recordings, bypassing the traditional need for a separate spike deconvolution step. The evidence supporting the method is solid, featuring rigorous validation across multiple latent variable model families (including HMM, GPFA, and LFADS) using both simulated and experimental data. However, the assessment of the method's generality would be further strengthened by application to a broader range of experimental datasets, such as recordings from different brain regions or using different calcium indicators.

eLife Assessment

Insects can act as vectors of plant diseases, hence the study of insect-pathogen interactions is relevant for agriculture. This important study identifies in Diaphorina citri a dopamine receptor responsive to 'Candidatus Liberibacter asiaticus' infection, demonstrate direct regulation of this receptor by a microRNA, and integrate dopamine signaling into an established insect reproductive hormone framework. Multiple complementary experimental approaches convincingly support the findings, but key conclusions rely on correlative data and the mechanistic evidence for the proposed linear signaling cascade is incomplete. This work will be of interest for insect physiology and vector-pathogen biology, and more broadly for citrus agriculture.

eLife Assessment

The authors address a hard question and propose a pipeline for using Large Language Models to reconstruct signalling networks as well as to benchmark future models. The findings are valuable for a defined subfield, as the proposed framework allows for assessing such approaches systematically. The overall support is solid, although the present evaluation remains limited in scope and would benefit from a wider range of networks and performance metrics.

eLife Assessment

Important findings from this study include clear evidence of the impact of methylphenidate on cognitive control over Pavlovian biasing of actions and decision-making in humans, in a manner dependent on baseline working memory capacity. The design used drug dosing after learning, allowing a compelling test of the influence of catecholamines on decision processes independent of learning. The task is very well designed, using a combination of aversive and appetitive Pavlovian to Instrumental Transfer, and the in-depth behavioural analysis extends the authors' previous work, which will be of interest to those working in cognitive psychopharmacology. The results challenge the view that catecholamines operate by modulating behavioural invigoration alone.

eLife Assessment

This is a valuable polymer model that provides insight into the origin of macromolecular mixed and demixed states within transcription clusters. The simulations are well performed and clearly presented in the context of existing experimental datasets. This compelling study will be of interest to those studying gene expression in the context of chromatin.

eLife Assessment

This important study identifies a metal transporter in the plasma membrane of the obligate intracellular pathogen, Toxoplasma gondii. Using an array of different approaches, the authors convincingly demonstrate that this transporter mediates iron and zinc uptake and regulates diverse cellular processes, including parasite metabolism and differentiation. This work will be of broad interest to cell biologists and biochemists studying metal ion transport mechanisms.

eLife Assessment

This important study provides new insights into how Staphylococcus aureus adapts to disulfide stress through the redox-sensitive regulator Spx, which coordinates nutrient uptake, cysteine import, redox homeostasis, and bacterial growth. While the authors present compelling evidence supporting the central role of Spx in managing disulfide stress, several aspects require further clarification. In particular, the precise mechanisms regulating cysteine uptake and the proposed link between disulfide stress responses and iron limitation would benefit from additional explanation and experimental or conceptual justification.

eLife Assessment

Optical tweezers have been instrumental to the determination of mechanical parameters of molecular motors. This study by Takamatsu et al. reports key mechanical parameters of kinesin KIF1A using fluorescence microscopy, wherein the motor is tethered to a DNA nanospring, without the use of an optical trapping apparatus, which represents an exciting development. The approach and the findings reported change current thinking about KIF1A‑mediated transport, with potential implications for understanding human disease. The findings are important and the strength of the evidence is compelling.

eLife Assessment

This study presents a valuable human stem cell-derived organoid model that captures key morphological and cellular features of spinal cord development and provides evidence for a YAP-dependent mechanism of lumen formation relevant to secondary neurulation. Overall, the evidence is convincing, using strong and validated approaches consistent with the current state of the art, including systematic protocol optimisation across multiple cell lines and quantitative analysis of tissue architecture. However, some claims regarding precise anterior-posterior and dorsoventral spinal cord identity, as well as several novelty claims, are at times overstated and would benefit from more direct validation and more careful positioning. The work will be of interest to developmental biologists and researchers studying neural tube defects.

eLife Assessment

In this valuable study, the authors performed cell-specific ribosome pulldown to identify gene expression (translatome) differences in the anterior (NT1) vs middle & posterior (NT2-9) cells of the C. elegans intestine, under fed, starved, or refeeding conditions. The data generated will be very helpful to the C. elegans community, and the evidence supporting the conclusions of the study is assessed to be solid. Some methodological caveats remain and are discussed.

eLife Assessment

In this useful paper, the authors present a comprehensive method for the purification of recombinant Snake Venom Metalloproteinases (SVMPs) using the MultiBac expression system, explain the self-activation of the enzymes by Zn2+ incubation, and establish high-throughput screening (HTS) techniques. The authors addressed a key problem: producing a substantial amount of pure and enzymatically active SVMPs required for structural and functional studies. Altogether, this work builds a solid foundation for the large-scale production of active SVMPs for future biochemical and structural characterization as well as for drug discovery, albeit leaving certain caveats about the universal applicability of the described methodology for the production of any recombinant SVMPs.

eLife Assessment

The authors used genetic mutations in VANGL2 to study cell morphological changes during differentiation of hPSCs and understand the mechanisms underlying neural tube closure defects. The findings are important as they establish a quantitative, reproducible 2D human iPSC-to-neural-progenitor platform for analyzing cell-shape dynamics during differentiation. The convincing evidence provided, combined with the relative simplicity of the model and its tractability as a patient-specific and reverse genetic platform, make it attractive.

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

eLife Assessment

The authors describe an interesting approach to studying the dynamics and function of membrane proteins in different lipid environments. The fundamental findings have theoretical and practical implications beyond the study of EGFR to all membrane signalling proteins. The evidence supporting the conclusions is compelling, based on the use of a nanodisk system to study membrane proteins in vitro, combined with state-of-the-art single-molecule FRET. The work will be of broad interest to cell biologists and biochemists.

eLife Assessment

This valuable paper advances understanding of the role of the HGF receptor, MET, in cancer cell invasion by demonstrating HGF-induced coordinated trafficking of MET and metalloprotease MT1-MMP into invadopodia. The results are generally solid, but there are concerns about the cell biology and whether the trafficking mechanism is clinically relevant. It's also unclear whether this is a general mechanism or specific to triple-negative breast cancer cells. The paper will be of interest to cancer cell biologists.

eLife Assessment

This study presents valuable findings by demonstrating that specific GPCR subtypes induce distinct extracellular vesicle miRNA signatures, highlighting a potential novel mechanism for intercellular communication with implications for receptor pharmacology within the field. The evidence is solid, however, more experiments are needed to determine whether the distinct extracellular vesicle miRNA signatures result from GPCR-dependent miRNA expression or GPCR-dependent incorporation of miRNAs into extracellular vesicles.

eLife Assessment

This valuable study presents a thorough analysis of protein abundance changes caused by amino acid substitutions, using structural context to improve predictive accuracy. By deriving substitution response matrices based on solvent accessibility, the authors demonstrate that simple structural features can predict abundance effects with accuracy comparable to complex methods such as free energy calculations. The strength of the evidence is convincing, supported by robust experimental design and comprehensive analyses.

eLife Assessment

This study reports insights into how the caspase Dcp-1, best known for cell death, can also promote tissue growth in Drosophila, extending the authors' earlier work by identifying regulatory factors that shape this non-lethal activity. The valuable findings identify new Dcp-1-interacting proteins Sirt1, Fkbp59, Debcl, Buffy, Atg2, and Atg8a, and help broaden understanding of how growth and death pathways intersect. The evidence is solid, but some conclusions would be strengthened by additional studies, particularly regarding the nature of the cell death observed and the involvement of autophagy.

eLife Assessment

This study presents a valuable advance by enabling functional mapping of Ca²⁺ responses in live human pancreatic tissue slices, providing new opportunities to study islet heterogeneity and diabetes-related dysfunction in an intact tissue context. The evidence supporting the main conclusions is solid, based on reproducible methodology and functional validation across multiple human donor samples. Key revisions needed include clearer quantification of transduction efficiency and tissue viability, and improved clarification of how CaMPARI2 signals should be interpreted.

eLife Assessment

This paper addresses valuable questions about the evolution of recombination landscape under domestication by examining recombination maps in domesticated chickens and their wild ancestor. However, despite employing a state-of-the-art deep learning method for recombination map inference, the lack of systematic benchmarking and presence of some unexpected patterns raise concerns about the reliability of the inferred maps, thus providing incomplete support for rapid evolution of recombination landscapes. Additionally, due to methodological limitations in testing for intra-genome correlations between evolutionary processes, the current evidence is inadequate to support the associations of recombination with selection and/or introgression in domesticated chickens.

eLife Assessment

Koch et al. describe a valuable novel methodology, SynSAC, to synchronise cells to analyse meiosis I or meiosis II or mitotic metaphase in budding yeast. The authors present convincing data to validate abscisic acid-induced dimerisation to induce a synthetic spindle assembly checkpoint (SAC) arrest that will be of particular importance to analyse meiosis II. The authors use their approach to determine the composition and phosphorylation of kinetochores from meiotic metaphase I and metaphase II that will be of interest to the broader meiosis research community.

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

eLife Assessment

This work offers important insights into the protein CHD4's function in chromatin remodeling and gene regulation in embryonic stem cells, supported by extensive biochemical, genomic, and imaging data. The use of an inducible degron system allows precise functional analysis, and the datasets generated represent a key resource for the field. The revised study offers compelling evidence and makes a significant contribution to understanding CHD4's role in epigenetic regulation. This work will be of interest to the epigenetics and stem biology fields.

eLife Assessment

This valuable study presents Altair-LSFM, a well-documented implementation of a light-sheet fluorescence microscope (LSFM) designed for accessibility and reduced cost. The approach provides compelling evidence of its strengths, including the use of custom-machined baseplates, detailed assembly instructions, and demonstrated live-cell imaging capabilities. This manuscript will be of interest to microscopists and potentially biologists seeking accessible LSFM tools.

eLife Assessment

In this study, the authors investigate the role of ZMAT3, a p53 target gene, in tumor suppression and RNA splicing regulation. Using quantitative proteomics, the authors uncover that ZMAT3 knockout leads to upregulation of HKDC1, a gene linked to mitochondrial respiration, and that ZMAT3 suppresses HKDC1 expression by inhibiting c-JUN-mediated transcription. This set of convincing evidence reveals a fundamental mechanism by which ZMAT3 contributes to p53-driven tumor suppression by regulating mitochondrial respiration.

eLife Assessment

This important study provides the first putative evidence that alteration of the Hox code in neck lateral plate mesoderm is sufficient to induce ectopic development of forelimb buds at neck level. The authors use both gain-of-function (GOF) and loss-of-function (LOF) approaches in chick embryos to test the roles of Hox paralogy group (PG) 4-7 genes in limb development. The GOF data provide strong evidence that overexpression of Hox PG6/7 genes are sufficient to induce forelimb buds at neck level. However, the experiments using dominant negative constructs are lacking some key controls that are needed to demonstrate the specificity of the LOF effect rendering the work as a whole incomplete.

eLife Assessment

This study reports useful information on the mechanisms by which a high-fat diet induces arrhythmias in the model organism Drosophila. Specifically, the authors propose that adipokinetic hormone (Akh) secretion is increased with this diet, and through binding of Akh to its receptor on cardiac neurons, arrhythmia is induced. The authors have revised their manuscript, but in some areas the evidence remains incomplete, which the authors say future studies will be directed to closing the present gaps. Nonetheless, the data presented will be helpful to those who wish to extend the research to a more complex model system, such as the mouse.

eLife Assessment

This fundamental study is part of an impressive, large-scale effort to assess the reproducibility of published findings in the field of Drosophila immunity. In a companion article, the authors analyze 400 papers published between 1959 and 2011, and assess how many of the claims in these papers have been tested in subsequent publications. In this article, the authors report the results of validation experiments to assess a subset of the claims that, according to the literature, have not been corroborated. While the evidence reported for some of these validation studies is convincing, it remains incomplete for others.

eLife Assessment

This important study builds on previous work from the same authors to present a conceptually distinct workflow for cryo-EM reconstruction that uses 2D template matching to enable high-resolution structure determination of small (sub-50 kDa) protein targets. The paper describes how density for small-molecule ligands bound to such targets can be reconstructed without these ligands being present in the template. However, the evidence described for the claim that this technique "significantly" improves the alignment of the reconstruction of small complexes is incomplete. The authors could better evaluate the effects of model bias on the reconstructed densities.

eLife Assessment

This work identifies a novel, conserved link between glycolysis and sulfur metabolism that governs fungal morphogenesis and virulence. The compelling evidence, integrating multiple approaches, provides an important conceptual advance. A future mechanistic dissection of how sulfur metabolites interface with known pathways is encouraged.

eLife Assessment

This study presents DeepTX, a valuable methodological tool that integrates mechanistic stochastic models with single-cell RNA sequencing data to infer transcriptional burst kinetics at genome scale. The approach is broadly applicable and of interest to subfields such as systems biology, bioinformatics, and gene regulation. The evidence supporting the findings is solid, with appropriate validation on synthetic data and thoughtful discussion of limitations related to identifiability and model assumptions.

eLife Assessment

This study provides important insights into mural cell dynamics and vascular pathology using a zebrafish model of cerebral small vessel disease. The authors present convincing evidence that partial loss of foxf2 function results in progressive, cell-autonomous defects in pericytes accompanied by endothelial abnormalities across the lifespan. By leveraging advanced in vivo imaging and genetic approaches, the work establishes zebrafish as a powerful and relevant model for dissecting the cellular mechanisms underlying cerebral small vessel disease.

eLife Assessment

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

eLife Assessment

The authors combine a modeling approach, using a digital twin, with electrophysiological evidence in two species to assess the role of inhibition in shaping selectivity in the visual cortex. The results provide an important advance beyond the classic view of sensory coding by proving compelling evidence that many neurons in visual areas exhibit dual-feature selectivity. Overall, the work exceptionally showcases how in silico experiments can generate concrete hypotheses about neuronal coding that are difficult to discover experimentally.

eLife Assessment

This paper represents a valuable contribution to our understanding of how LFP oscillations and beta band coordination between the hippocampus and prefrontal cortex of rats may relate to learning. Enthusiasm for the reported results was moderated by the concern that some key analyses need to be done, and highly relevant details about task, data, and statistics were missing. Consequently, the reviewers considered the evidence to be incomplete in this version of the manuscript.

eLife Assessment

This important study uncovers a previously unrecognized light-responsive pathway in C. elegans that depends on live food bacteria and is mediated by the bZIP factors ZIP-2/CEBP-2 and the cytochrome P450 enzyme, CYP-14A5. The authors show that this bacteria-linked pathway modulates long-term memory and can be harnessed as a low-cost light-inducible expression system, opening new directions for sensory biology and genetic engineering in worms. The exact means by which live bacteria modulate light signal that activates ZIP-2/CEBP-2 in the worm remains to be elucidated. The evidence supporting the pathway's role uses multiple genetic, transcriptional, and behavioural assays, and is convincing.

eLife Assessment

This important study presents a methodologically rigorous framework for stability-guided fine-mapping, extending PICS and generalizing to methods such as SuSiE, supported by comprehensive simulations and functional enrichment analyses. The evidence is now convincing, demonstrating improved causal variant recovery and offering a robust alternative for cross-population fine-mapping. The approach will be of particular interest to statistical geneticists, computational biologists, and biomedical researchers who rely on fine-mapping to interpret genetic association signals.

eLife Assessment

This manuscript presents useful insights into the molecular basis underlying the positive cooperativity between the co-transported substrates (galactoside sugar and sodium ion) in the melibiose transporter MelB. Building on years of previous studies, this convincing study improves on the resolution of previously published structures and reports the presence of a water molecule in the sugar binding site that would appear to be key for its recognition, introduces further structures bound to different substrates, and utilizes binding and transport assays, as well as HDX-MS and molecular dynamics simulations to further understand the positive cooperativity between sugar and the co-transported sodium cation. The work will be of interest to biologists and biochemists working on cation-coupled symporters, which mediate the transport of a wide range of solutes across cell membranes.

eLife Assessment

This important study uses standard single-cell RNA-seq analyses combined with methods from the social sciences to reduce heterogeneity in gene expression in Drosophila imaginal wing disc cells treated with 4000 rads of ionizing radiation. The use of this methodology from social sciences is novel in Drosophila and allows them to identify a subpopulation of cells that is disproportionately responsible for much of the radiation-induced gene expression. Their compelling analyses reveal genes that are expressed regionally after irradiation, including ligands and transcription factors that have been associated with regeneration, as well as others whose roles in response to irradiation are unknown. This paper would be of interest to researchers in the field of DNA damage responses, regeneration, and development.

eLife Assessment

This important study, which tackles the challenge of analyzing genome integrity and instability in unicellular pathogens by introducing a novel single-cell genomics approach, presents compelling evidence that this new tool outperforms standard whole-genome amplification techniques. While thorough and rigorous, the work's impact would increase by providing scripts and data, as well as a description of the biological relevance that would make this method more appealing to the broad community studying genetic heterogeneity in diverse organisms.

eLife Assessment

This work reports the characterization of newly identified genetic variants of SLC4A1 in patients with distal renal tubular acidosis. Cell culture studies supplemented with histological analysis of a previously established disease mouse model provide convincing evidence that some of the variants increase intracellular pH, reduce ATP synthesis, and attenuate autophagic degradative flux. The study is valuable in establishing a mechanistic framework for future exploration of the link between intracellular pH and mutations in SLC4A1 in vivo.

eLife Assessment

This important study reports convincing evidence of associations between 35 polygenic indices (PGIs) for social, behavioural, and psychological traits, as well as other health conditions (e.g., BMI) and all-cause mortality, based on data from Finnish population-based surveys and a twin cohort linked to administrative registers. PGIs for education, depression, alcohol use, smoking, BMI, and self-rated health showed the strongest associations with all-cause mortality, in the order of ~10% increment in risk per PGI standard deviation. Effect sizes from twin-difference analyses tended to be slightly larger than those from population cohorts, a pattern opposite that generally observed when testing PGI associations with their target phenotypes, and supporting the robustness of findings to confounding by population stratification.

eLife Assessment

This work significantly advances our understanding of chromatin organization within regions of repetitive sequences in the parasitic protozoan Trypanosoma brucei. Using cutting edge interdisciplinary tools, the authors provide compelling evidence for two discrete types of repetitive DNA element-associated proteins- one set involved in essential centromere function; and, the other involved in glycoprotein antigenic variation via homologous recombination. Thus, these fundamental findings have implications for this parasite's biology, and for therapeutic targeting in kinetoplastid diseases. This work will be exciting to those in the centromere/mitosis and parasite immunity fields.

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

eLife Assessment

This important study examines the role of map3k1, a MAP3K family member that has both kinase and ubiquitin ligase domains, in the differentiation of progenitors in the flatworm Planaria. The convincing analyses demonstrate that map3k1 acts within progenitors to restrict their premature differentiation and to prevent formation of teratomas. This work would be of interest to researchers in the fields of regeneration, developmental biology, and aging.

eLife Assessment

This important study employs a closed-loop, theta-phase-specific optogenetic manipulation of medial septal parvalbumin-expressing neurons in rats and reports that disrupting theta-timescale coordination impairs performance of challenging aspects of spatial behaviors, while sparing hippocampal replay and spatial coding in hippocampal place cells. The findings are expected to advance theoretical understanding of learning and memory operations and to provide practical implications for the application of similar optogenetic approaches. The experiments were viewed as technically rigorous, but the strength of evidence provided in the current version of the manuscript was viewed as incomplete, mostly due to limited analyses and the descriptions of some of the experimental protocols.

eLife Assessment

This is a useful study that investigates the role of the long non-coding RNA Dreg1 for the development, differentiation, or maintenance of group 2 ILC (ILC2). The authors generate Dreg1-/- mice and show a reduction of group 2 innate lymphoid cells (ILC2). However, the strength of evidence supporting the impact of Dreg1 on Gata3 expression, a transcription factor required for ILC2 cell fate decisions, and the cell-intrinsic requirement of Dreg1 for ILC2 remain incomplete. This study will be of interest to immunologists.

eLife Assessment

This study presents a platform to implement closed-loop experiments in mice based on auditory feedback. The authors provide convincing evidence that their platform enables a variety of closed-loop experiments using neural or movement signals, indicating that it will be a valuable resource to the neuroscience community. The paper could be strengthened by the addition of additional tutorials, such as on how to run an experiment.

eLife Assessment

This is a valuable study that integrates behavioral and molecular approaches to identify neuromodulators influencing blood-feeding behavior in the disease vector Anopheles stephensi. Through gene expression analyses across blood-seeking life stages and RNA interference experiments, the authors present solid evidence that co-knockdown of the neuromodulators short Neuropeptide F and RYamide affects blood-seeking states in A. stephensi. However, evidence demonstrating that these neuropeptides are sufficient to promote host-seeking is lacking.

eLife Assessment

This paper provides a useful new theory of the hallucinatory effects of 5-HT2A psychedelics. The authors present convincing evidence that a computational model trained with the Wake-Sleep algorithm can reproduce some features of hallucinations by varying the strength of top-down connections in the model, though it is not clear that this model applies to 5-HT2A hallucinogens in particular. The work will be of interest to researchers studying hallucinations or offline activity and plasticity more broadly.

eLife Assessment

This valuable study highlights the key role of NK cells and PD-L1+ neutrophils in worsening sepsis responses in the context of MASH (metabolic dysfunction-associated steatohepatitis). It focused on the role of neutrophils in mediating this effect, which is based on a choline-deficient high-fat diet model of various knockouts or selective ablation of immune cell types. While the data presented are of great interest, there are concerns around the reliability of the strength of the evidence provided, which is currently considered incomplete. The study may be of interest to researchers in immunopathological disease mechanisms once confirmatory studies have been completed.

[Editors' note: the authors no longer have access to the original flow cytometry data and plan to compile new datasets for further consideration.]

eLife Assessment

This work describes the establishment of an image analysis pipeline for signal correction, segmentation and quantitative data analysis of multilayered organoid and tumoroid systems. The revised study is important for the field to address many practical challenges in deep-tissue visualization. The image analysis pipeline is well-designed and compelling.

eLife Assessment

This important work compares the size of two brain areas, the amygdala and the hippocampus, across 12 species belonging to the Macaca genus. The authors find, using a convincing methodological approach, that amygdala - but not hippocampal - volume varies with social tolerance grade, with high tolerance species showing larger amygdala than low tolerance species of macaques. Interestingly, their findings also suggest an inverted developmental effect, with intolerant species showing an increase in amygdala volume across the lifespan, compared to tolerant species exhibiting the opposite trend. Overall, this paper offers new insights into the neural basis of social and emotional processing.

eLife Assessment

The current work uses DNA-tethered motor trapping to reduce vertical forces and improve datasets for kinesin-1 motility under load. The evidence is compelling and the significance is important to the kinesin field. Kinesin-1 is more robust and less prone to premature detachment than previously indicated. This represents a significant advancement in the field and is generally applicable to work with optical tweezers.

eLife Assessment

This paper undertakes an important investigation to determine whether movement slowing in microgravity is due to a strategic conservative approach or rather due to an underestimation of the mass of the arm. The experimental dataset is unique, the coupled experimental and computational analyses comprehensive, and the effect is strong. However, the authors present incomplete results to support the claim that movement slowing is due to mass underestimation. Further analysis is needed to rule out alternative explanations.

eLife Assessment

In this useful study, the authors conducted an impressive amount of atomistic simulations with a realistic asymmetric lipid bilayer to probe how the HIV-1 envelope glycoprotein (Env) transmembrane domain, cytoplasmic tail, and membrane environment influence ectodomain orientation and antibody epitope exposure. The simulations convincingly show that ectodomain motion is dominated by tilting relative to the membrane and explicitly demonstrate the role of membrane asymmetry in modulating the protein conformation and orientation. However, due to the qualitative nature of the conducted analyses, the evidence for the coupling between membrane-proximal regions and the antigenic surface is considered incomplete. With stronger integration of prior experimental and computational literature, this work has the potential to serve as a reference for how Env behaves in a realistic, glycosylated, membrane-embedded context.

eLife Assessment

This valuable study uses NAD(P)H fluorescence lifetime imaging (FLIM) to map metabolic states in the Drosophila brain. The authors reveal subtype-specific metabolic profiles in Kenyon cells and report learning-related changes, supported by solid evidence and careful methodology. However, the FLIM shifts observed after memory formation in α/β neurons are small and only weakly significant, so the ability of FLIM to detect subtle physiological changes still requires further validation. Nevertheless, this work provides a strong starting point and demonstrates the promising potential of FLIM for probing neural metabolism in vivo.

eLife Assessment

This study provides a useful application of computational modelling to examine how people with chronic pain learn under uncertainty, contributing to efforts to link pain with motivational processes. However, the evidence supporting the main claims is incomplete, as the modelling differences are not reflected in observable behaviour or pain measures, and the interpretation extends beyond what the data can substantiate. The conclusions would benefit from a clearer explanation of the behavioural differences that underlie the computational findings.

eLife Assessment

This manuscript proposes a lateralized, lobe-specific brain-liver sympathetic neurocircuit regulating hepatic glucose metabolism and presents anatomical evidence for sympathetic crossover at the porta hepatis using viral tracing and neuromodulation approaches. While the topic is of important significance and the methodologies are, in principle, state-of-the-art, significant concerns regarding experimental design, incomplete methodological reporting, sparse and ambiguous labeling, and overi-nterpretation of the data substantially weaken support for the study's central conclusions, thereby limiting the study's completeness. The work will be of interest to biologists, clinicians, and physiologists.

eLife Assessment

The findings are important, as they identify MIRO1 as a central regulator linking mitochondrial positioning and respiratory chain function to VSMC proliferation, neointima formation, and human vasoproliferative disease. Overall, the strength of evidence is convincing, with comprehensive in vivo and in vitro data, including human cells and added bioenergetic analyses, that broadly support the main claims despite some remaining limitations in mechanistic and mitochondrial assays.

eLife Assessment

This manuscript provides useful insights into how the brain can simultaneously represent events and the times when they occurred. The results include a comparison between two different basis functions for temporal selectivity and how these generate different predictions for the dynamics of neural populations. The conclusions are partly incomplete because of questions such as the impact of the linear separability assumption and whether joint encodings of event type and time can be made without it.

eLife Assessment

The authors provide a scholarly review of intracranial research into the neural correlates of consciousness (NCCs). To our knowledge, this is the first such review, and it therefore may become a must-read for anyone working in the field of consciousness research. It is not so persuasive that intracranial recordings are better suited to identifying pure NCCs than other methods, which appears a problem instead solved through novel paradigms and better-developed theories - but this no doubt reflects an in-depth, timely, and insightful contribution to the literature.

eLife Assessment

This important study establishes a workflow based on environmental sampling for the discovery of bacteriophages capable of infecting antibiotic-resistant pathogens. The experimental design, analysis, and results demonstrating the effectiveness of the workflow are convincing, although a broader sampling scheme and more careful framing of the data within the current limitations of viral taxonomy could strengthen the work. This study will interest researchers working on bacterial infections, environmental microbiology, and phage-based alternatives for addressing antimicrobial resistance.

eLife Assessment

This important 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 important study provides the first direct neuroimaging evidence for the integration-segregation theory of exogenous attention underlying inhibition of return, using an optimized IOR-Stroop fMRI paradigm to dissociate integration and segregation processes and to demonstrate that attentional orienting modulates semantic- and response-level conflict processing. Although the empirical evidence is compelling, clearer justification of the experimental logic, more cautious framing of behavioral and regional interpretations, and greater transparency in reporting and presentation are needed to strengthen the conclusions. The work will be of broad interest to researchers investigating visual attention, perception, cognitive control, and conflict processing.