Reviewer #3 (Public review):

Summary:

The manuscript by Elley and colleagues describes experiments on the effects of synthetic torpor on ex vivo heart ischemia. The key aspect of the study was the use of viral-vector mediated manipulation of the hypothalamic medial preoptic area (MPA) in rats. They used AAV-CaMKIIa-hM3D(Gq). The authors report that chemogenetic activation of the MPA prior to an ex vivo heart ischemia-reperfusion insult induces cardio protection against infarct size that is independent of prior in vivo hypothermia. Phosphoproteomic analysis of cardiac tissue suggested changes in cell survival and death pathways.

Strengths:

This study has important strengths. The idea is novel. The experimental design is appropriately rationalized and fascinating. The manuscript is written and presented concisely.

Weaknesses:

The study has important weaknesses in the experimental design and validation of the model.

(1) The study is based on the use of a DREADD-designed viral vector (AAV-CaMKIIa-hM3D(Gq) -mCherry) that is activated by 2 mg/kg IP injection of CNO. The rationale is to putatively activate the MPA. The authors show no evidence for chemogenetic activation of neurons in the MPA. This could be done using a variety of different approaches, even phosphoproteomics.

(2) The stereotaxic injections are difficult to precisely and locally place, particularly bilaterally. Figure 2F is only a schematic. It would be better to show actual low magnification brain sections (bregma +0.12 to -0.48) from a representative rat to show the placement of the AAV.

(3) The control rats were injected with AAV-CaMKIIa-EGFP. Why was EGFP used instead of mCherry for the control?

(4) Ideally, a mutant non-activatable variant of AAV-CaMKIIa-hM3D(Gq) should have been used for a better control.

(5) The authors should comment on whether there is any neurotoxicity in the MPA associated with the forced AAV expression of hM3D-Gq.

(6) Is there any inflammatory pathology seen in the MPA with AAV transduction?

(7) There are no experiments to show that the systemic torpor is specifically associated with the MPA region. Experiments should be done with injections of AAV-CaMKIIa-hM3D(Gq)-mCherry placed in other brain regions, for example, the nearby nucleus accumbens.

(8) The mapping of the distribution of neurons responsible for synthetic torpor is not mechanistic enough and is not directly to the point. While excitatory and inhibitory markers are examined, a more interesting and deeper approach would have been to use glutamate receptor antagonists to manipulate the torpor response.

(9) The ischemia and reperfusion aspects of the Lagendorff method need to be clarified. The isolated hearts are already ischemic after their removal from the rat. The reperfusion aspect is caused by reflow of blood to generate oxidative stress, but in the ex vivo model, is there really reperfusion injury?

(10) The authors show that whole animal oxygen consumption is reduced in the torpor state. The measurement is crude and most likely reflects the inactivity of the animal's skeletal muscle in the torpor state. A more relevant and direct experiment would be to do oxygen consumption (or Seahorse) assays on extracts of the isolated hearts.

(11) The authors report that the synthetic torpor induces bradycardia. There is no follow-up on this important observation. The MPA-heart connection is not analyzed. (A) Is the link through cardiovascular centers in the brainstem? (B) Is the torpor-induced bradycardia mediated through increased parasympathetic or decreased sympathetic autonomic tone? Pharmacological experiments could also be done.

Reviewer #1 (Public review):

The work corroborates the idea, recently suggested by Rosenthal et al. (2025), that spreading depolarization is involved in the mechanisms of electroconvulsive therapy. Using a mouse model of electroconvulsive therapy and various sophisticated approaches to visualize cortical activity, the authors provide an extensive description of traveling calcium waves induced by electroconvulsive stimulation. The study confirms that the calcium events have properties typical of cortical spreading depolarization and seeks to show that the calcium/SD waves mediate therapeutic and neuroplastic effects of electroconvulsive therapy. The authors find that after electroconvulsive stimulation associated with calcium/SD waves, Fos expression increases widely; in the cortex, this increase is localized to the hemisphere affected by calcium waves. They show that some EEG predictors of the beneficial effects of electroconvulsive therapy correlate with the occurrence of calcium/SD waves. Despite the solid methodology and the study's interesting, its conclusions are not fully supported by the data.

In particular:

(1)The title of the paper claims that "electroconvulsive stimulation drives cortical spreading depolarization dependent immediate early gene expression". However, immunohistochemical staining shows that Fos expression increases not only in the cortex but also in many subcortical regions, including the hippocampus and amygdala (Figure 5A). Really, conventional electroconvulsive therapy stimulates nearly the entire brain volume and induces generalized seizure activity that can trigger SD not only in the cortex but also in other brain sites. Therefore, regions beyond the cortex can also drive the effects of electroconvulsive therapy. Next, the authors use Fos staining as a marker of neuronal plasticity. However, Fos is also a marker of preceding neuronal activation. As electroconvulsive stimulation, seizures, and SD are associated with high neural activity, it is unclear whether the observed Fos upregulation results from the prior activation or heralds the subsequent plastic changes. Other markers of neuroplasticity (e.g., BDNF) should also be examined.

(2) Postictal EEG suppression is one of the most promising correlates of positive clinical outcomes after electroconvulsive therapy. Cortical SD is also tightly coupled with suppression of neuronal activity in affected regions. Although the authors report that postictal suppression is stronger after stimulations with cortical SDs than without SDs, the cortices affected (ipsi) and unaffected (contra) by unilateral cortical calcium/SD events exhibit identical suppression (Figure 6F). The result contradicts established knowledge in the field. If the calcium events are cortical SDs, they should induce EEG suppression only in the affected hemisphere.

(3) The study states a beneficial role of calcium/SD waves in ECS effects. However, SD alters numerous aspects of brain function, leading to a range of effects that can underlie side effects as well. Assessment of the behavioral effects of stimulation with and without calcium/SD waves can help clarify the issue.

The results of the work suggest that cortical SD can contribute to electroconvulsive therapy-related mechanisms and help to optimize the stimulation parameters to achieve maximal therapeutic effect.

Reviewer #2 (Public review):

Summary:

This manuscript addresses the question of mechanisms underlying the therapeutic effects of electroconvulsive therapy (ECT). Clinical efficacy of ECT in major depression (and other disorders) is well established and has often been assumed to be a direct consequence of seizure activity generated by the current application. However, as the authors point out, this explanation is unsatisfactory. A recent study (Rosenthal et al., 2025) provided evidence that ECT generates a wave of cortical spreading depolarization (CSD) in mice, and initial evidence that similar events were generated in patients undergoing ECT. Based on their observations, Rosenthal et al. proposed that CSD, rather than seizure, may engage plasticity mechanisms that contribute to the brain's clinical response to ECT. The current study adds to that prior work by reporting other consequences of CSD, in addition to sustained Ca2+ elevations. The current study also links EEG characteristics immediately following the ECT with the likelihood of generating a CSD, which can help optimize ECT parameters.

Strengths:

An important research topic, linking a large set of rodent studies with a limited clinical EEG data set.

The data acquisition and analyses appear to be of very high quality, and the main results are well illustrated.

Association between EEG characteristics linked to good clinical outcome matched by mouse EEG data linked to CSD.

Characterization of multiple consequences of CSD following ECT in the mouse brain.

Weaknesses:

The main characterization of CSD propagation comes from GCaMP Ca2+ measurements, as previously reported (Rosenthal et al., 2025). That prior study also provided key electrophysiological evidence of CSD with a DC shift after ECT in mice (supplemental data). Given the prior evidence for ECT-CSD, the additional measures shown in the current manuscript are fully expected. Thus, the 2-photon imaging of Ca2+ elevations following CSD (Figure 4) is consistent with prior 2-photon imaging studies of CSD, and the complex hemodynamic and pH changes are expected to contribute to propagation of EGFP fluorescence changes (Supplemental Figure 5). These data are well presented, but, contrary to the results section here, these results appear confirmatory rather than necessary to build a case that the key event generated by ECT is a CSD.

The authors state that "our conclusion that CSD is the primary driver of plasticity is based on its role in driving Fos expression" (line 472). Related to the point above, there is already a very well-established literature showing that CSD leads to rapid and robust Fos expression in rodent cortex, so this is fully consistent with prior work. The prior work, CSD-fos work, should be summarized and/or cited more clearly in the manuscript. Showing that Fos increases only in the hemisphere where there is a large CSD-Ca2+ wave is a clear demonstration of this. While Fos increases can certainly be well linked to plasticity in some experimental paradigms, the implication that Fos increases underlie CSD-induced plasticity and possibly therapeutic effects of ECT is not appropriate. Fos increases after CSD are a reliable marker of the very strong neuronal activation that occurs, but Fos increases are not specific for plasticity and can be activated by challenges that do not generate synaptic plasticity. A range of other gene expression changes have been identified with CSD and may contribute to adaptive plasticity; these could be mentioned alongside speculation about Fos. To support the main conclusions of this paper about CSD driving plasticity via Fos, Fos knockout or knockdown studies are needed, as has been used in prior plasticity studies.

Reviewer #3 (Public review):

Summary:

This manuscript combines widefield calcium imaging, electroencephalography, 2-photon imaging, and immunohistochemistry in mice to re-demonstrate that electroconvulsive stimulation (ECS) induces a seizure followed by cortical spreading depolarization, as previously shown. The putative novel finding - which is not unexpected - is that ECS is also correlated with increased expression of the immediate early gene cFOS, although this has also been shown previously. The authors speculate that CSD drives cFOS expression, which might contribute to the therapeutic effects of ECT; however, experiments performed do not provide causal evidence for this hypothesis. Instead, the authors use expression of cFOS - a nonspecific activity-dependent gene induced in various pathological and non-therapeutic contexts - as a proxy for plasticity and/or therapeutic effect. Hence, overall, the significance of the findings is limited and primarily serves to replicate prior work, with the evidence evaluated as incomplete.

Strengths:

The experiments are generally well executed from a technical perspective.

Main Weaknesses to be addressed in revision:

(1) The main findings of this paper are replication experiments of prior work, and thus, the novelty and significance of this manuscript are relatively limited.

- It is already known that the mean frequency of ECT-induced seizures decays between peak and offset in humans (Stuiver et al. Clin Neurophysiol. 2026 Jan:181:2111439. doi: 10.1016/j.clinph.2025.2111439) and mice (Murakami et al. J Pharmacol Sci 2008 Jan;106(1):78-83. 10.1254/jphs.FP0071453), which the authors re-demonstrate in Figure 1.

- It has already been demonstrated that ECT in mouse models induces lateralized CSD waves in a manner that depends on stimulation parameters and the initial evoked response during stimulation (Rosenthal et al. Nat Comm. 2025 May 18;16(1):4619. doi: 10.1038/s41467-025-59900-1); the authors replicate this in Figures 1, 2, 3, 6.

- It is already widely established that EEG and calcium signals are highly concordant in mouse brain physiology, as shown in Figure 1. It is already known that CSD propagates from supragranular to granular and infragranular layers (Zakharov et al. Epilepsia. 2019 Dec;60(12):2386-2397. doi: 10.1111/epi.16390) as shown in Figure 4.

- It is already known that CSD waves induce cFOS expression (e.g., Dell'Orco et al. Front Cell Neurosci. 2023 Dec 14:17:1292661. doi: 10.3389/fncel.2023.1292661; Hermann and Hossman. Neuroscience. 1999 Jan;88(2):599-608. doi: 10.1016/s0306-4522(98)00249-8) as the authors replicate in Figure 5.

Minimally, the authors should revise claims regarding novelty, as the manuscript, as written, is misleading to a reader not familiar with the field. There is limited innovation in re-demonstrating that these events are seizures and that they involve spreading depolarization.

(2) The authors frame their hypothesis that CSD could be a potential mediator of the therapeutic effects of ECT, but they do not measure therapeutic effects or directly test this hypothesis. The principal advancement of the paper is showing that ECT-induced CSD triggers hemisphere-specific cFOS expression as a proxy of plasticity. However, it is already known that CSD induces cFOS expression (as noted above). The observation that cFOS expression was induced only by CSD, not by the initial seizure, is likely a byproduct of the greater activity induced by CSD than by seizure. cFOS expression is nonspecific to plasticity or therapeutic effects and can be triggered by many non-therapeutic interventions. The cFOS data thus do not meaningfully measure therapeutic plasticity. The authors also selectively cite references suggesting that EEG metrics such as seizure duration predict positive therapeutic outcomes, but this link is controversial and not well established in the clinical literature.

Minor Weaknesses:

(3) For the n=3 mice used for concurrent 2P imaging with microprism implant, these animals also had ChrimsonR co-expression, but there are no optogenetic studies described in this paper, which is confusing. Yet, this co-expression introduces a significant confound, as GCaMP6 emission (525/50nm band in this study) will overlap substantially with the ChrimsonR excitation spectrum. Thus, the fluorescence emission used to image these neurons may be optogenetically activating them at the same time. Please explain.

(4) Incision of the cortex for implantation of a prism is a significant cortical injury that likely induces CSD instantaneously and may change the propensity for CSD in subsequent recordings. Please comment on this limitation and address how much time elapsed after surgery before imaging.

(5) Method details are missing or insufficiently described for location, titer, and injection strategy for 2-photon experiments.

(6) Given the wide range of parameters used for ECS in mice and ECT in humans, the authors should provide tables for what stimulation parameters were used for each recording. These protocols were chosen manually rather than randomly or systematically, which introduces confounding factors into analyses that use parameters as an independent variable.

(7) While much of the cFOS staining after unilateral CSD shows hemisphere-specific asymmetry, several regions (piriform cortex, amygdala, thalamus) do appear to have bilateral cFOS expression. Please comment on this.

(8) The discussion states: "If CSD accounts for plasticity effects, triggering a CSD in a non-seizure context may be sufficient to elicit therapeutic effects. This is supported by the clinical success of ultra-brief stimulation treatments that do not cause seizures, such as rTMS with accelerated protocols, which achieves treatment efficacy on par with ECT for major depressive disorder". Are the authors implying that TMS induces CSD? What evidence supports this idea?

(9) This statement - "Assuming psychosis is the result of thalamocortical coupling that is too weak in frontal areas of the cortex" (lines 583-585) - may be overly speculative.

Reviewer #1 (Public review):

[Editors' note: all three reviewers confirm that all initial concerns have been fully resolved through comprehensive revisions and supplementary analyses.]

Summary:

By imaging the dynamics of synaptic proteins in cultured neurons, this study presents significant findings regarding the dynamics of excitatory and inhibitory synaptic proteins during development. The evidence shows that the ratios of excitatory and inhibitory synaptic proteins are stable during synapse development. This discovery advances our understanding of the complex mechanisms governing synapse formation. The strength of the evidence is robust, as it is supported by a combination of biological assays and endogenous labeling.

Strengths:

This research sheds light on the dynamics of the excitatory and inhibitory synapses during development. It is crucial to understand that while excitatory synapses and inhibitory synapses are developed independently, the ratio of their number is relatively stable during development, maintaining a stable excitatory/inhibitory ratio.

Important findings and implications in the research include:

(1) Persistent Synapse Dynamics: Excitatory and inhibitory synapses remain highly dynamic even in mature neurons (DIV12-14), challenging the dogma that synaptic structures are stable after the synaptogenesis stage.

(2) Maintained E/I Balance: Despite ongoing synapse turnover (formation/elimination) and presynaptic terminal reduction, the overall density and ratio of excitatory-to-inhibitory synapses remain relatively stable during circuit maturation (Figure 7).

(3) Developmental Shifts: While presynaptic compartments decrease over time, postsynaptic sites increase, suggesting independent regulation of pre- and postsynaptic elements within a stable E/I framework.

Weaknesses:

This study focuses on specific synaptic proteins within synapses, which may not fully represent the dynamics of other synaptic machinery; also, whether similar observations exist in vivo is still unknown. Further research is needed to explore the implications of these findings in more complex neuronal environments.

Comments on revised version:

The authors have addressed all my questions/comments. No further questions for this manuscript.

Reviewer #2 (Public review):

Summary:

The Garbett et al. identified a critical need to begin to understand the interplay between the assembly, maturation, and elimination of excitatory and inhibitory synapses. They also detail the lack of reliable tools to address this gap in knowledge. Here, the authors developed synaptic reporters expressed by lentiviruses (mClover3-Homer1c, HaloTag-Syb2, and tdTomato-Gephyrin). They combined these reporters with resonance scanning confocal imaging to measure synapses over a 15-hour period during neuron development and in mature neurons in primary hippocampal cultures. Using these reporters in the same neuron, the authors compared the ratios of postsynaptic excitatory and inhibitory specializations that co-localize with presynaptic terminals during development and in mature neurons and found that they are stable across time points. Finally, the authors developed CRISPR/Cas9 tools (TKIT) to knock-in endogenous fluorescent tags (GFP/tdTomato-Gephyrin) or epitope tags (HA-Bassoon and HA-Homer1) to begin to study synapse dynamics using endogenous proteins. I believe this paper highlights an important gap in knowledge and begins to offer methodologies to determine the dynamic coordination between excitatory and inhibitory synapses.

Strengths:

(1) The experiments are well-designed and carefully controlled.

(2) The authors carefully validated the reporter and TKIT constructs.

(3) The authors provide strong proof-of-principle for the use of the reporter constructs to track synapse formation, maintenance, and elimination over a 15-hour period.

(4) Ingenious use of technologies (reporters, TKIT, and resonance scanning confocal microscopy) to develop a platform for future studies of synapse dynamics.

(5) Strong evidence supporting that the ratio of excitatory and inhibitory synapses (those that oppose syb2) stays constant through development.

Overall, this is a well-executed study that develops tools to simultaneously image excitatory and inhibitory synapse dynamics and represents an important first step to address the fundamental question regarding the coordination between these two types of synapses.

Comments on revised version:

The authors addressed all my questions and comments. Their edits have made this paper significantly stronger. I believe that this is an important paper for the field.

Reviewer #3 (Public review):

In the present study, the authors describe the development of new tools and imaging strategies to assess the concomitant development of excitatory and inhibitory synapses in dissociated neuron cultures. To this end, they generate fluorescently tagged constructs of excitatory and inhibitory synapse marker proteins using either conventional overexpression or CRISPR-based strategies. They then image these marker proteins over a timespan of 15 hours to assess synaptic dynamics at different developmental timepoints. Based on their data, they conclude that excitatory and inhibitory synapse development occur in concert to maintain a functional balance despite individual synapse turnover.

Overall, this study addresses an interesting question, i.e., the interplay between the development of excitatory and inhibitory synapses, which has important implications, particularly for neurodevelopmental disorders in which the balance of excitation and inhibition is disrupted. The experiments are technically solid and well-executed, and the individual images are highly compelling.

Comments on revised version:

The authors have fully addressed my concerns, and this is now a strong manuscript for the synaptic field.

Reviewer #1 (Public review):

Summary:

This study investigates how human temporal voice areas (TVA) respond to vocalizations from nonhuman primates. Using functional MRI during a species-categorization task, the authors compare neural responses to calls from humans, chimpanzees, bonobos, and macaques while modeling both acoustic and phylogenetic factors. They find that bilateral anterior TVA regions respond more strongly to chimpanzee than to other nonhuman primate vocalizations, suggesting that these regions are sensitive not only to human voices but also to acoustically and evolutionarily related sounds.

The work provides important comparative evidence for continuity in primate vocal communication and offers a strong empirical foundation for modeling how specific acoustic features drive TVA activity.

Strengths:

(1) Comparative scope: The inclusion of four primate species, including both great apes and monkeys, provides a rare and valuable cross-species perspective on voice processing.

(2) Methodological rigor: Acoustic and phylogenetic distances are carefully quantified and incorporated into the analyses.

(4) Neuroscientific significance: The finding of TVA sensitivity to chimpanzee calls supports the view that human voice-selective regions are evolutionarily tuned to certain acoustic features shared across primates.

(4) Clear presentation: The study is well organized, the stimuli well controlled, and the imaging analyses transparent and replicable.

(5) Theoretical contribution: The results advance u

Comments on revised version.

I thank the authors for having carefully considered and implemented my remarks on the first version.

Reviewer #2 (Public review):

Summary:

This study investigated how the human brain responds to vocalizations from multiple primate species, including humans, chimpanzees, bonobos, and rhesus macaques. The central finding-that subregions of the temporal voice areas (TVA), particularly in the bilateral anterior superior temporal gyrus, show enhanced responses to chimpanzee vocalizations-suggests a potential neural sensitivity to calls form phylogenetically close nonhuman primates.

Strengths:

The authors employed three analytical models to consistently demonstrate activation in the anterior superior temporal gyrus that is specific to chimpanzee calls. The methodology was logical and robust, and the results supporting these findings appear solid.

Weakness:

The authors only tested vocalizations from three non-human primate species other than humans. In this case, the species specificity of the effect does not fully represent the specificity of evolutionary relatedness.

Comments on revised version.

I have no further comments.

Reviewer #3 (Public review):

Summary:

Using fMRI, the authors demonstrate that human temporal voice areas (TVA) respond not only to human vocalizations but also to those of other primates, particularly chimpanzee calls, which share acoustic features with human voices. These findings provide compelling evidence for cross-species vocal processing in the human auditory system and carry important theoretical implications for understanding the evolutionary underpinnings of speech perception.

Strengths:

The study offers a valuable comparative design, rigorous acoustic and phylogenetic modeling, and consistent evidence that bilateral anterior TVA regions respond more strongly to chimpanzee vocalizations than to other species' calls. The inclusion of both great apes and monkeys provides a rare cross-species perspective.

Weaknesses:

Minor limitations include the acoustic-phylogenetic confound (which the authors partially address with additional analyses), the lack of non-vocal controls to establish true selectivity.

Overall, the methods, data, and analyses broadly support the claims, with only minor weaknesses that do not undermine the main conclusions. The findings are valuable for the subfield of auditory neuroscience and comparative cognition, with solid evidence supporting the primary claims.

Comments on revised version.

After revision, this work has shown great improvement in data analysis, figure organization, and writing. I have no further suggestions.

Reviewer #1 (Public review):

Summary:

Argunşah et al. describe and investigate the mechanisms underlying the differential response dynamics of barrel vs septa domains in the whisker-related primary somatosensory cortex (S1). Upon repeated stimulation, the authors report that the response ratio between multi- and single-whisker stimulation increases in layer (L) 4 neurons of the septal domain, while remaining constant in barrel L4 neurons. The authors attribute this divergence to differences in short-term synaptic plasticity, particularly within somatostatin-expressing (SST⁺) interneurons. This interpretation is supported by 1) the increased density of SST+ neurons in L4 of the septa compared to barrel domain, 2) the stronger response of (L2/3) SST+ neurons to repeated multi- vs single-whisker stimulation and 3) the reduced functional difference in single- versus multi-whisker response ratios across barrel and septal domains in Elfn1 KO mice, which lack a synaptic protein that confers characteristic short-term plasticity, notably in SST+ neurons. Consistently, a decoder trained on WT data fails to generalize to Elfn1 KO responses. Finally, the authors report a relative enrichment of S2- and M1-projecting cell densities in L4 of the septal domain compared to the barrel domain, suggesting that septal and barrel circuits may differentially route information about single vs multi-whisker stimulation downstream of S1.

Strengths:

This paper describes and aims to study a circuit underlying differential response between barrel columns and septal domains of the primary somatosensory cortex. This work supports the view these two domains contribute distinctly to the processing single versus multi-whisker inputs and highlight the role of SST+ neuron and their short-term plasticity. Together, this study suggests that the barrel cortex multiplexes whisker-derived sensory information across its domains, enabling parallel processing within S1.

Weaknesses:

Although the divergence in responses to repeated single- versus multi-whisker stimulation between barrel and septal domains is consistent with a role for SST⁺ neuron short-term plasticity, the evidence presented does not conclusively demonstrate that this mechanism is the critical driver of the difference. The lack of targeted recordings and manipulations limits the strength of this conclusion: SST⁺ neuron activity is not measured in L4, nor is it assessed in a domain-specific manner. The Elfn1 knockout manipulation does not appear to selectively affect either stimulus condition, domain or interneuron subtype. Finally, all experiments were performed under anesthesia, which raises concerns about how well the reported dynamics generalize to awake cortical processing.

Reviewer #3 (Public review):

Summary:

This study investigates the functional differences between barrel and septal columns in the mouse somatosensory cortex, focusing on how local inhibitory dynamics (particularly involving SST⁺ interneurons) may mediate temporal integration of multi-whisker (MW) stimuli in septa. Using a combination of in vivo multi-unit recordings, calcium imaging, and anatomical tracing, the authors propose a model in which Elfn1-dependent synaptic facilitation onto SST⁺ interneurons contribute to the distinct sensory responses to MW input in barrels and septa, enabling functional segregation between these domains.

Strengths:

The study presents a thought-provoking and useful conceptual model for understanding sensory processing in the somatosensory cortex. While barrel columns have been widely studied, septal regions remain relatively understudied in mice. If septa indeed act as selective integrators of distributed sensory input, this would suggest a novel computational role for cortical microcircuits beyond the classical view focused on barrels. Although still hypothetical, the proposed model in which SST⁺ interneurons contribute to domain-specific sensory responses between barrel and septal domains is intriguing and opens new avenues for investigating inhibitory circuit mechanisms.

Weaknesses:

The primary limitation of this study lies in the spatial and cellular specificity of the recording techniques. The physiological data rely predominantly on unsorted multi-unit activity (MUA) recorded with low-channel-count silicon probes. Because MUA aggregates signals from multiple neurons over a radius of approximately 50-100 µm (comparable to or larger than the width of septal domains in mice), it remains difficult to confidently attribute the recorded activity exclusively to septal versus barrel populations. The authors have now addressed this concern more carefully by reframing their interpretation in terms of "septal-enriched" populations and by providing additional threshold-based analyses suggesting that the principal effects are more robust in Layer 4. These additions substantially improve the manuscript and support a more cautious interpretation of the findings. Nevertheless, the proposed Elfn1/SST⁺ mechanism remains supported primarily by indirect evidence. Although the calcium imaging data provide useful support for stimulus-dependent SST⁺ recruitment, these experiments were restricted to L2/3 interneurons and therefore do not directly test the Layer 4 circuit mechanism proposed to underlie the electrophysiological observations. Direct in vivo cell-type-specific recordings and manipulations in Layer 4 would ultimately be required to establish the proposed mechanism more conclusively.

Comments on revised version.

I have read the revised manuscript and overall, I think the authors have addressed my major concerns appropriately. I appreciate the substantially moderated interpretation of the findings and the additional analyses clarifying the limitations of the MUA recordings.

Reviewer #1 (Public review):

The paper uses a passive whisker detection task in mice to identify a behavioral phenomenon that can reasonably be interpreted as spatial attentional capture. The attentional effect occurs transiently after a successful whisker stimulus detection yields reward, and lasts for a few trials before subsiding. The attentional effect is to the right or left whiskers, depending on whether right or left whiskers are rewarded; no finer spatial resolution for attention was tested. By recording whisker-evoked spiking from single units in S1, the authors show that this form of spatial attention increases the gain of whisker-evoked neuronal responses in S1 for a large subset of S1 units. In contrast, neural responses are not modulated by overall task engagement. Together, these findings show a neural signature of spatial attention in S1 cortex. Because whisker or facial movements were not tracked, it is not clear whether this represents covert attention or whisker movement in response to previously rewarded stimuli, which would be a form of overt attention.

Substantial attentional modulation of neural responses was observed for a subset of whisker-responsive S1 units, but the effect size was small on average for the total unit population. The top 25% of units showed a ~12% attentional response modulation (relative to firing rate range for each unit), but the median unit showed only a 1.3% response modulation. It would have been useful to analyze the magnitude or prevalence of attentional modulation across layers or in fast-spiking vs. regular spiking units, but this was not reported.

Major

(1) It is hard to interpret the underlying causes of the attentional modulation of neural activity without having measured whisker and facial movement. This is a particular issue in S1, where whisker movement against the stimulation grid can alter the mechanical efficiency of stimulus delivery. Such movements would represent overt attention, which would engage an entirely different neural mechanism than covert attention.

(2) An interesting debate is whether the behavioral phenomenon is best described as attention or as dynamic learning of the stimulus-response association for that block. In Posner-type cued attention tasks, and also in many block-type attention tasks in rodents, animals receive reward for successfully detecting either cued or uncued stimuli, and thus attention (higher response probability or improved psychometric sensitivity for cued stimuli) is at least partially dissociated from the stimulus-reward contingency. That is not the case here. The fact that mice have difficulty learning the contingency reversal suggests that the phenomenon is better explained by attention than by learning the contingency; however, to prove this clearly, the existence of the attentional effect on neural activity in Block 1 vs. Block 2 would have to be shown.

(3) Some of the graphical representations of the attentional modulation of neural activity are unclear. The single-unit example of attentional modulation is quite strong (Figure 3d). The mean response for the top 25% of units is also visually clear (Figure 3f). But the effect is not apparent at all in Figure 3e, which the figure legend says shows every unit. What is the yellow point and line in this figure? Why isn't the attentional effect visible in this panel? Perhaps I am misunderstanding Figure 3e, but it is not clear to me why it compares Pref>0.5 to Pref<0.5, when the intended analysis suggests it should be Pref>0 to Pref<0? Also in Figure 3, it is critical for the reader to know whether panels 3g-3h represent the top 25% of units or all units. Neither the results text nor the legend is clear on this.

(4) There is a missed opportunity to quantify attentional modulation across cortical layers, since laminar probes and Neuropixels probes were used for the recordings. In addition, there is no separation of fast-spiking from regular-spiking units, and no quantitative metrics are provided to assess the quality of single units. This could reveal key aspects of cortical processing of attentional signals.

Reviewer #2 (Public review):

Summary:

Dyce et al investigate the modulation of sensory responses in the somatosensory 'barrel' cortex during a novel whisker vibration detection task in head-fixed mice, aiming to find correlates of spatial attention in both the animals' behavior and their neuronal activity.

Strengths:

The authors produced an extensive and parameterized dataset of both behavioral responses and neuronal activity, with >3000 single units of which >1400 were responsive.

Weaknesses:

In my view, the main conclusions of the manuscript are not currently well supported by the data.

The authors effectively define "spatial attention" as a state where an animal responds more to a stimulus that gives more rewards (out of two possible stimuli presented on different sides of the snout, i.e., segregated spatially). If one defines spatial attention purely in these terms, then their findings do show neuronal correlates of spatial attention. However, those neuronal correlates can be explained by known aspects of neuronal responses in the barrel cortex.

This plays out in several different ways:

From the behavioral point of view, greater attention may correlate with an increased hit rate to stimuli on the rewarded side, but in the absence of other supporting measurements, the relationship could well be the opposite: an animal could pay more (rather than less) attention to the stimulus delivered on the unrewarded side, to make sure it suppresses the incorrect response. It is impossible to tell, as the data don't provide an independent measurement of whether the animal is paying greater attention to, or is more aware of, one side than the other, nor do they provide an independent measurement of neuronal tuning on either side. There is no separate measurement of arousal either (e.g., via pupillometry or locomotion).

The experimental design involved two blocks on each daily task session, with the second block reversing the side on which rewarded stimuli were delivered. Reinforcing one's doubts about the behavior and its interpretation, mice had much poorer performance on each day's second block, to the extent that perceptual sensitivity (d') was the same for both sides: d' did not increase after reward reversal for stimuli on the initially unrewarded side. This further emphasizes the lack of a separate demonstration of focused "spatial attention".

Much of the data (both behavioral and neuronal) could be accounted for, e.g., by a strategy where the mouse keeps a token in working memory of what side seems to be driving rewards, while maintaining equally strong sensory drive on both sides, but with no attentional shift at all. The policy would be to respond more whenever the stimulated side matches the token in memory (thus also reinforcing the token, thus enhancing performance next time). This would be easily implemented with a disinhibitory reward-modulation signal such as the one multiple researchers have found carried by VIP neurons (e.g., Szadai et al DOI: 10.7554/eLife.78815).

Similarly, the fact that "attended trials" (Pref > 0) produced greater responses than "unattended trials" appears to be explainable as follows. Here, "attended" trials are those where the contralateral stimulus is presented (and, if responded to, is rewarded), "unattended" trials are those where the stimulus is ipsilateral (and not rewarded). The animal responds more (at least in the first block) to stimuli delivered to the contralateral pad - i.e., rewarded as opposed to unrewarded ones. Beyond the knowledge mentioned above that cortex-wide VIP sensitivity to rewards can drive disinhibition in general, activity modulation dependent on rewards and outcomes (and stimulus value) has been established specifically in the barrel cortex (e.g., Lacefield et al DOI: 10.1016/j.celrep.2019.01.093, Bale et al DOI: 10.1016/j.cub.2020.10.059, Banerjee et al DOI: 10.1038/s41586-020-2704-z, Chereau et al 10.1038/s41467-020-17005-x). The reward- and value-evoked activity demonstrated in those papers would suffice to predict more activity at the contralateral electrode on "attended" trials, along the lines of the findings in Ramamurthy et al (DOI: 10.1038/s41467-025-60592-w) and consistent also with the enhanced "attentional modulation" on hit trials.

Other aspects of the analysis and terminology lead to confusing outcomes. For example, in the analysis in Figure 3, Performance averaged in a set of trials around a given trial is defined as the mean rate of responses to stimulation on either side - regardless of whether those responses are correct (since the stimuli can be on either side, but only one side is correct and gets rewarded and putatively reinforced). Thus, this definition of "Performance" can increase with the rate of incorrect licks to the wrong side and is at odds with the normal use of the word. On trials where this Perf = 1 and the stimuli are balanced on either side, this corresponds to a true performance (and reward rate) of only 0.5 - what one would normally consider random discrimination between the sides. Thus, Perf = 1 trials may still give a low reward rate and, if responses scale with reward, a small effect of reward. Hence, based on known properties of reward dependence, greater correlation of neuronal activity with "Preference" than with "Performance" would be expected, rather than reflecting a new aspect of "spatial attention". A definition of performance more in line with established practice and measuring side-to-side discrimination (corresponding more closely to the authors' "Preference" parameter) would have shown this more clearly.

Reviewer #1 (Public review):

Summary:

The authors studied the development of hippocampal connectivity gradients based on open datasets and performed correlation analyses with other MRI features as well as gene expression information from other datasets. Although the main findings are correlational and cross-sectional, the analyses are overall sophisticated and replicated in several datasets.

Strengths:

The hippocampus is a key region in understanding large-scale brain organization and cognition, and the authors applied advanced and suitable analytics to study its development. The paper is overall well-organized and well-written, and the findings are relevant for studying large-scale brain development.

Weaknesses:

While sophisticated, several of the analyses appear mainly correlational, cross-sectional, and rely on cross-dataset contextualization, which should also be stated as a limitation of the current work.

Reviewer #2 (Public review):

Summary:

In this manuscript, the authors aim to assess how the functional organisation of the hippocampus is related to the geometry and neurobiological differences of the hippocampus. In particular, the authors focus on the first three eigenvectors of hippocampal-cortical functional connectivity, based on non-linear dimensionality reduction on resting-state functional MRI data. Furthermore, the work aims to describe changes in these functional axes and their relation to other factors throughout youth and evaluate whether they are predictive of individual variations in cognition.

Strengths:

A major strength of this study is the attempt to replicate key findings across multiple developmental cohorts.

Weaknesses:

The major weaknesses of the manuscript center on gaps in technical transparency and several conceptual inaccuracies. The machine learning methodology used for cognitive prediction is scarce, leaving little means to evaluate whether the behavioral results suffer from data leakage or overfitting. The introduction sets up an oversimplified historical premise regarding the field's understanding and appreciation of hippocampal connectivity, and contains several incorrect references that throw doubt on the argumentation. Additionally, T1w/T2w signal intensity is incorrectly used as synonymous with myelin, despite gold-standard histological validation showing a non-significant correlation between T1w/T2w and myelin staining (Sandrone et al., 2013).

Appraisal of Aims and Conclusions:

The authors partially achieve their aims by illustrating certain age-related changes in hippocampal function; however, the correlative study design is not equipped to examine how these changes are "shaped" by geometry, myelination, or gene expression (especially the latter two). Furthermore, conclusions were often overstated based on small effect sizes.

Context and Field Impact:

This work adds to a growing body of literature focused on gradient-based representations of hippocampal topology. By applying these methods across a wide developmental age bracket, it provides a useful reference point for how the hippocampus and wider cortex interact during maturation. To improve utility to the neuroimaging and cognitive neuroscience communities, the nesting of subfields within the eigenvector topology should be addressed, too.

Reviewer #1 (Public review):

Summary:

Mudunuri et al. investigate the foraging response of Drosophila larvae in response to patchy resources of distinct value (concentration of nutrient or valence). They show that larvae adjust their behavior according to both the quality and valence of available resources. Interestingly, previous exposure to resources of lower value increases the permanence time in resources of greater value. This suggests that larvae can value, remember and adapt their behaviour in response to previous foraging experience.

They perform a simple integration model that recapitulates the larval behaviour.

Strengths:

This paper uses a very well-controlled foraging set-up where larvae are tested individually and for 3 hours, allowing for a good statistical analysis of their behaviour.

They investigate for the first time the ability of Drosophila larvae to perceive, remember and compare the quality and valence of distinct resources. It is very exciting, as it will open up the field of foraging decision studies using the fruitfly larvae.

Weaknesses:

(1) Most of the analysis depends on the thresholding, but it is not clear what increasing the radius of analysis means in terms of foraging. There are two issues here:

a) What is the behaviour of the larvae on the edges of the patch? It is obvious that the fructose or the NaCl will diffuse at the edge, so are they remaining in the proximity because they are actively feeding (exploiting) on this decaying concentration, or are they sensing the lower gradient and they are actually looking (chemosensing) for the higher concentration? The behaviour at the edge is really different (check sucrose in Wosniack et al. 2022), and there might be a way of avoiding the diffusion by actually adding a plastic ring and pouring the agar + resource in there. The effect of the ring, per se, would still have to be tested.

b) How was the threshold selected? It is very likely that the concentration at the patch boundary will be very different for 1M and 0.1 M. Could the authors explain why they chose such a distance? What does majority of larvae mean? Is the "majority" the same for 0.1M and 1M? Is there a relationship between the threshold chosen and the diffusion of fructose and NaCl?

(2) The word exploitation is used in the paper, but there are many instances where it is unclear whether that is the case. This should be clarified since there are no controls for exploitation.

(3) In the experiments analysing the adaptation of foraging behaviour, it is not clear if the first and second patch means that only 2 patches were analysed per larva or the first and second in a sequence of patches visited. I think it is the second option (because of Figure S3D), but the authors should clarify this. Also, we do not know how many animals were tested. The number of data points in 4C (4G) compared to 4D (4H) seems very different.<br /> Regarding the results, which are very interesting, why aren't the larvae spending less time in the 0.1M sucrose patch after having fed on a 1M patch, while they spend more time in a 1M after a 0.1M? Could it be that the difference in residence time is correlated with their hunger rather than the comparison between conditions?

(4) I am not an expert in this type of model, and I would appreciate it if the authors could explain how the values of the drift and leak have been fitted in Figure 5H. If possible, I would recommend adding a graph showing the parameter exploration of distinct possible combinations of values.

Reviewer #2 (Public review):

Summary:

This manuscript investigates how Drosophila larvae make foraging decisions in patchy environments with controlled resource density and valence. Using movement tracking in bounded arenas, the authors show that larvae's patch residence time (PRT) differs depending on resource type, environmental context, and prior experience.

The authors vary whether the environment is homogenous (all patches are equal) or heterogenous (mixed patches) and whether a higher density of the resource is appetitive (food) or aversive (salt). The most salient results are that in heterogeneous environments, larvae remain longer on higher-density patches of fructose, while they stay shorter in higher-density salt patches. The study further demonstrates that prior foraging experience influences subsequent patch residence time (PRT).

A drift-diffusion model is used to describe patch-leaving behavior, suggesting that an integration process may underlie stay-leave decisions during foraging. Overall, the work provides a useful behavioral system for studying foraging behaviour and highlights the role of context and experience in shaping larval foraging strategies.

Strengths:

A major strength of the manuscript is the behavioral system. The assay is simple, well-controlled, and suitable for realistic spatial and temporal scale tracking of individual larvae. The use of non-volatile resources and embedded patches minimizes confounds from olfactory navigation and allows the authors to focus on local patch exploitation, return behavior, and experience-dependent decisions.

The results regarding patch resident time (how long larvae stay in patches of different resource density) are convincing. In homogeneous environments, larvae spend more time on patches with a higher density of food (0.1M > 0.01M) and less time in patches with a lower density of salt (0.01M > 0.1M), indicating that their behaviour is sensitive to the valence of the resource. Further, larvae do not simply respond to current circumstances, since PRT in a given patch is sensitive to the quality of the preceding one encountered, showing some kind of memory.

Weaknesses:

(1) The theoretical background of the experiment, as exposed in the Introduction, is somewhat misleading. The experiment is based on patches of sufficient size for the individual larvae not to deplete them through their activity, so that the intake rate is constant while exploiting a given patch. In those circumstances, the theoretical rate-maximizing strategy would be to either reject a patch on encounter or stay in it indefinitely (until pupation). The threshold for rejection or acceptance will depend on travel time, but patch residence time would be either zero (or minimal identification time) or lifelong. In the introduction, it appears as if the system follows the classical Marginal Value Theorem assumptions as used in classical foraging theory. In that case, patch residence time is fundamentally sensitive to a decline in intake rate while in a patch. This raises questions about what factors drive patch-leaving in the present protocol. A better theoretical framework would focus on behavioural variables that can be expected to depend on the circumstances of the experiment, as discussed below.

(2) Rather than make predictions about time in the patch, which as explained above do not reflect the present system, larval behaviour could be modelled and described as a function of observable properties such as: (a) speed of locomotion; (b) tendency to deviate from straight progress (area restricted searching); (c) probability of return after leaving a patch, possibly controlled through rea restricted searching; (d) a response to concentration gradient, since patch boundaries are probably gradual through diffusion. There is a useful literature in this regard in studies of parasitic wasps such as Venturia canescens (formerly Nemeritis canescens, see Waage 1979). Larva may respond directly to local resource concentration (see van Alphen, J. J., Bernstein, C., & Driessen, G., 2003), where higher concentration leads to increased feeding rate, reduced locomotion, and consequently results in longer time in each patch. This could still be a normative model, but based on realistic driving inputs. The dimensions of the system make it unlikely that larvae have the opportunity to adjust to travel time, or patch composition, on which classical foraging models are based. The original versions of the marginal value theorem were thought for cases where birds exploited pine cones, so that each bird had multiple encounters, and also on dung flies that mated in dung patches, which also dried out. A system with heritable optimised parameters could work for other natural systems where the parameters can be heritable, but not here.

(3) The previous argument indicates that patch time, while it is a real quantitative consequence, is not ideal as the major dependent variable for this system. Given that the authors have the full trajectories, they could treat movement in discrete time bins and ask if the tendency to depart from linear progression (i.e. from moving straight ahead) is a function of the density of the resource. It would appear as if all the results, including return to patches (but not memory), could be explained by area-restricted searching (see Dorfman, A., Hills, T. T., & Scharf, I. (2022). A guide to area‐restricted search: a foundational foraging behaviour. Biological Reviews, 97(6), 2076-2089.). Slower movement (perhaps directly caused by eating) and more twisted progress could generate longer times in higher food densities.

(4) The evidence for an effect of prior experience is interesting but could be strengthened. The authors state that PRT on the second patch depends on the concentration in the first patch. However, statistically significant modulation of prior experience was only found when the second food patch was richer, namely 1M fructose (Figure 4C). If the change in patch time is due to a form of learning and contrast, one might expect significantly shorter times in any second patch if the first one was richer, which is not the case. One difficulty is that the 'patchy' nature of the environment may not be evident to the larvae, because they are much smaller than the patches. From a larva's perspective, a patch is an environment, potentially suitable to remain in until pupation (which is what they ought to do in richer food patches).

(5) The modelling section is promising but currently somewhat underdeveloped relative to the strength of the claims. The authors fit a drift-diffusion model to data and report that a drift-only model captures homogeneous environments, whereas adding a leak term improves the fit in heterogeneous environments. This provides a useful quantitative summary of behavior but the biological interpretation of the leak parameter is not clear. In addition, the valence condition was not modelled.

Reviewer #3 (Public review):

Summary:

The work investigates how the foraging behaviour of Drosophila larvae depends on resource quality, valence, and heterogeneity in the foraging environment. A specific focus of the work was to study how foraging decisions depend on the prior experience of alternative resource patches in the same environment. Moreover, the work presents computational models (drift diffusion models) that recapitulate foraging decisions, and whose parameters appear to depend on resource quality and environment statistics, providing potential insights into the dynamics of the decision-making process.

I am not familiar with previous literature on foraging decisions in Drosophila, but I was specifically consulted to comment on the computational modelling. Therefore, my comments will mostly focus on the modelling aspects.

Strengths:

In my understanding, the two strengths of the current study are that:<br /> (1) it uses non-volatile resources, providing better control of the available cues that could guide foraging decisions, and<br /> (2) it tracks foraging behaviour over an extended period of time (3h), generating a rich dataset of foraging behaviour in the same environment.

Overall, the study appears to have been carefully conducted.

Weaknesses:

The computational modelling currently provides limited additional value beyond the empirical results. There are no prior hypotheses that are addressed by the computational models. Given the flexibility of DDMs, fitting foraging times is expected to be feasible. The question is whether the fits provide mechanistic insight. The main insight appears to be that describing foraging times in a homogeneous environment requires a single free parameter (drift rate), while the heterogenous environment requires a second parameter (leak). However, the effective complexity of the model is higher than the stated parameter count suggests, as each patch quality is fit with a different drift rate, which does not generalise across environments: in the heterogeneous environment, the drift rate differs substantially across fructose concentrations, whereas in the homogeneous environment, the same concentrations yield nearly identical drift rates. Counter their claims, the authors also do not systematically explore the effect of specific prior foraging experience on computational parameters, but only contrast model fits to environments with different statistics, in which prior experiences will be generally different. Overall, at the moment these modelling results have a rather descriptive character, and provide very little insight into the underlying computational principles that drive foraging decisions.

A second weakness is that the study does not report the detailed results of the statistical tests, and it seems that the authors interpret several differences that are not marked as statistically significant in the figures. Furthermore, the model comparisons do not account for different degrees of freedom of the models, and the goodness of fit values alone are insufficient to conclude that one model is better than the other (rather than overfitting).

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors address the question of working memory maintenance, starting from the experimental observation that recordings of neural activity during the delay period of working memory tasks are sometimes observed to be dynamic. They introduce a new combination of metrics (noise-robustness and energy efficiency) to quantify the performance of various network mechanisms of memory maintenance, in linear networks. They compared attractor networks, feed-forward networks, and networks trained with a loss that includes a robustness and an energy-efficiency component. They show, by plotting state-space trajectories, that networks optimized with this loss exhibit a form of rotational dynamics. They analyzed the data recorded during the delay of a working memory task in PFC, and observed state-space trajectories similar to those of the trained networks.

The comparison with other network mechanisms is interesting in principle, but limited by the fact that only linear networks are considered. This led to counter-intuitive and misleading statements, like the fact that attractor networks are not robust to noise, or that feed-forward networks have energy consumption that is exponential in the number of neurons.

Strengths:

(1) The idea to use both robustness to noise and energy efficiency to assess the performance of networks on working memory tasks is interesting.

(2) The manuscript is clearly written.

(3) There is an interesting combination of methodologies: theory on simple models, network training, and data analysis.

Weaknesses:

(1) Linear networks only.

The main feature of attractor networks is their robustness to noise, which is typically allowed by the non-linearity of neural responses. To fit their modeling framework, the authors focused only on continuous attractor neural networks (e.g., Seung 1996) and ignored point-attractor models such as the Hopfield model, which are typically used to model WM tasks, and which would presumably lead to very different results, e.g., in Figure 1D.

The linearity assumption is also problematic for the comparison with feed-forward models. It seems that the authors obtained runaway firing rates, explaining Figure 1F middle, which are typically prevented in non-linear networks.

The choice of parameters for the attractor network in Figure 1 is not explained. Why is t_slow = 10^4 chosen, and what does it correspond to? We expect in linear networks that activity goes back to zero or diverges as an exponential, but in principle, the time constant can be chosen to be of the same order as the time delay, with approximately linearly decreasing SNR.

Regarding the comparison of the different mechanisms, it would have been nice to better define the notion of rotational dynamics, beyond only considering state-space analysis, which is limited to providing mechanistic interpretations.

(2) Fixed duration of delay periods.

I have understood that for a given network, the duration of the delay period is fixed, as opposed to a delay duration that would fluctuate from trial to trial. This would be an important assumption to relax as well, to better match common experimental paradigms, as well as to expose a fairer comparison with other network mechanisms. See Orhan and Ma (2023) for such a discussion.

(3) Relationship with previous works

Many other works addressed the question of dynamic firing rates during maintenance periods of WM tasks; they should be discussed and compared to the mechanism proposed here. This includes: Barak et al, Progress in Neurobio. 2013, Pereira-Obilinovic, Aljadeff, Brunel, PRX 2023, Hansel, Mato, 2013, or works pertaining to the activity-silent neural states (allowed by short-term plasticity), the framework in which the data of Panichello et al are interpreted in the original publication.

Reviewer #2 (Public review):

In this manuscript, Ritter et al. propose a model of working memory (WM) that combines feedforward and rotational dynamics. The model is discovered by optimizing a linear RNN using a loss function that encourages maximization of signal-to-noise ratio (SNR) and minimization of activation magnitude. The authors argue that the optimized model outperforms other WM models in terms of SNR and energetic efficiency, while also better replicating key features of neural responses recorded in monkey pre-frontal cortex (PFC) during a WM task. The authors also draw connections to state space models (SSM) used for other machine learning applications.

My main issue with this manuscript is that it does not appear to convincingly demonstrate that rotational dynamics offer any advantage over purely feedforward dynamics. The authors adopt three criteria according to which they compare models:<br /> (1) SNR.<br /> (2) Energy efficiency.<br /> (3) Similarity to neural data.

In terms of SNR, purely feedforward models seem to perform similarly to the optimized models (Figure 1). Figure 1 does seem to show that the optimized network produces responses of smaller magnitude when the number of units is large, but the authors do not explain why adding rotational dynamics would produce such a relationship. In fact, the responses that are plotted for the feedforward network in Figures 1B, 2C, and 5E look similar, if not smaller in magnitude than those of the optimized model. Lastly, while the authors claim in the body of the text that the optimized model replicates key features of monkey PFC responses better than the purely feedforward model, this is not apparent to me from the comparisons plotted in Figure 5E-J. The authors thus do not show strong evidence that the model they propose beats what they claim is an established baseline on any of the three criteria.

Another weakness of the manuscript is that the comparison to attractor and feedforward models seems somewhat unfair. In Figure 1, the rotational model is optimized, while the parameters for the attractor and feedforward models seem to have been at least partially chosen by hand. Figure 5C again shows the three models side by side, but the fact that it compares the same network at different stages during training complicates the comparison. Instead, one should compare the rotational solution to the optimal attractor and feedforward models, respectively (obtained by constrained optimization). From looking at the flow-fields, it seems that a feedforward network with an optimized level of amplification may work just as well. On a mechanistic level, it is unclear what computational advantage rotations offer over feedforward dynamics in the WM context.

The choice of baseline models to compare against might be questionable. The simple line attractor model by Seung et al. (1996) was initially designed to explain oculomotor integration. It is true that a line attractor has been suggested as a mechanism for working memory, e.g., in the seminal work by Machens et al (2005). However, it seems fair to say that most studies employing non-linear networks have focused on point attractors as mechanisms of working memory (e.g., Wong & Wang, 2006; Driscoll, Shenoy, Sussillo, 2024). A point attractor arguably does not suffer the SNR issues of a line attractor, because it does not lead to integration of the noise over time. However, non-trivial point attractors cannot be implemented in linear networks of the kind studied by the authors of the present study.

The authors should expand their discussion to include other, potentially closely related work proposing rotation-like dynamics in artificial neural networks during working memory. In particular, the manuscript does not discuss Sharma, Proca, et al, ICML 2026, which describes a rotational solution to a similar WM task obtained by optimizing linear RNNs (Sharma et al., 2026, Fig. 6). Notably, Sharma et al. arrive at a similar rotational (and likely also non-normal) mechanism without using either noisy inputs or a constraint on energy efficiency. The authors of the present manuscript should discuss to what extent this finding contradicts their claim that "normative pressures on noise-robustness and energetic cost shape the complex dynamics of WM circuits." (present manuscript, Introduction). Given the obvious parallels between the two studies, a comparison between the present work and Sharma et al. (2026) would add necessary context to the Discussion.

The authors should also clarify the significance of the "novel method for optimization of continuous-time RNNs driven by noisy inputs" (see Discussion) that the authors propose. This method is mentioned in the first line of the Discussion section but is barely discussed, let alone sufficiently explained, in the previous Sections. The only time a comparison to BPTT with a simple MSE loss is mentioned, it is stated that the two procedures produce the same results. The novel method appears to consist of a loss with two terms, the second of which is a well-known L2-penalty on unit activations (Sussillo et al., 2015). It is not clear that the method is either novel or necessary to obtain the reported results.

Except for the fact that higher-dimensional networks also converge on rotational solutions, Figure 3 does not add much to the reader's understanding of the optimized model (except for panel F). I find the comparison to SSMs too superficial to provide real insight.

Figure 4 claims to show that the optimized model recapitulates "a range of properties observed in prefrontal cortex and other brain areas during WM tasks" (p. 7) but does not show neural data for comparison.

Reviewer #3 (Public review):

Summary:

The authors optimize continuous-time linear recurrent networks driven by noisy input, computing the gradient of decoding performance numerically and analytically. Optimizing for stimulus discriminability after a delay, with a penalty on firing rate, they find networks that adopt what they call high-dimensional rotational dynamics. They argue that these outperform attractor and feedforward models on noise robustness and energetic cost, and resemble state-of-the-art state-space models. They then fit a targeted dimensionality reduction model to prefrontal recordings from monkeys performing a spatial working memory task and argue that the population structure matches the rotational solution.

Strengths:

The evolution of the dynamics throughout learning is a nice observation, as are the analytical calculations, although I am not sure they are new since there is a fair share of work on the learning dynamics of linear networks.

Weakness:

I see many weaknesses. I will classify them into five groups.

(1) Strawman comparison and no clear definition of what is rotational. The paper is centered on comparing a trained model with two models meant to represent "attractor dynamics" and non-normal dynamics. Both are picked as the weakest member of their class.

I use quotation marks for "attractor dynamics" because I am not sure a linear system with an eigenvalue equal to zero is a representative model for the class. This is a particular linear instantiation of the line attractor from Seung 1996, but most attractor models are nonlinear and far more robust to noise, and they are robust through error correction that this linear model does not have. Even modern continuous attractors (Rivkind and Darshan) are very robust to noise through multiple mechanisms. So what the authors picked as an "attractor model" is a limited zero-eigenvalue case that, of course, will drift. "Attractor networks are highly susceptible to noise" is therefore true only of the toy they built, not of the class.

Second, what they call a non-normal model is in fact a feedforward chain, the extreme of non-normality. There are degrees of non-normality in any matrix, and the homogeneous delay line is the corner that requires the largest firing rates. This is not representative. See Daie et al., which has a skip and recurrent structure, or Stroud, which is not a pure chain. So the feedforward chain was also picked as a strawman, chosen so that the energetic cost they then complain about is guaranteed.

This brings me to the real problem in this section. "Rotational" is never defined. If it means complex eigenvalues, then it is a spectral property of any non-normal matrix, and "rotational versus feedforward" is not a dichotomy; it is two regions of the same continuous space of non-normal connectivity. Their own Figure 2C shows the network passing continuously through an attractor, then feedforward, then rotational during optimization. If these are points on a continuum, then "rotational dynamics is optimal" is just a statement about where the optimizer lands under this particular loss and input normalization, not the discovery of a new dynamical class. They need to define the term operationally and show the solution is qualitatively, not just quantitatively, different from non-normal feedforward. I do not think it survives that test.

This brings me to the references.

(2) The dynamical mechanisms of working memory have been studied for more than two decades, and I am surprised how much directly relevant work is missing. First, Druckmann and Chklovskii 2012, where a linear system produces stable encoding from oscillating modes. This is essentially their result more than a decade earlier, and it is not cited. They also miss Murray et al. on stable encoding and heterogeneous timescales in data. They oversimplify the attractor picture; for example, Pereira-Obilinovic et al. 2023 show you can have genuinely stable attractors. They do cite Daie et al., but they ignore its central claim, that non-normality is the underlying mechanism, which is more troubling than not citing it because it means they read it and did not engage. Overall, the references are idiosyncratic, missing relevant work, and not engaging the results of papers they cite.

This brings me to the third point.

(3) Novelty and the relationship to Stroud and Orhan. Those papers take a similar optimization approach and find that, depending on the task parameters, the optimal solution is non-normal, non-normal plus attractor, or attractor. My impression is that what this work calls rotational is just the dynamics of a strongly non-normal A, selected here by the firing-rate regularizer. They never clarify the connection with Stroud. Is the only difference the energy penalty?

The way to settle this is quantitative, and they have the handle and do not use it: report the Henrici departure-from-normality of their optimized A and place the solution inside Stroud's regime structure.

There is also a tension they leave implicit. In Stroud, the early loading direction is orthogonal to the late persistent readout, and that orthogonality is the source of dynamic coding. This paper's subspace alignment result (Figure 5G, H) shows exactly this early-to-late orthogonalization in both model and data, and then presents it as evidence for the rotational account and against Stroud's hybrid. You cannot reproduce a Strout's stim vs. decoder orthogonality and claim it against Strout's without doing more work.

(4) I did not understand the SSM section, and I think it should be cut. Is this a result? Either "SSM" just means a linear dynamical system, in which case it is trivial since every linear network here, including the LMU is an SSM, or it means the network matches a fixed-connectivity model like the LMU, which it does not seem to either. So in what sense is it a result?

(5) The data analysis is one section, and the analysis could be described as feeling somewhat like an afterthought on a very rich dataset. The coding structure they show for the rotational model also looks like the Stroud non-normal-plus-attractor model to me. They even state that the hybrid reproduces the cross-temporal subspace. What are the quantitative, cross-session metric that discriminates rotational from the non-normal-plus-attractor hybrid? Is it eyeballed trajectories?

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed the comments raised in the previous round of review.]

Summary:

In this manuscript, the authors present comprehensive experimental observations and a theoretical framework to explain the heterogeneous behaviour of sarcomeres in cardiomyocytes. They show that a stochastic component exists in their contractile activity, which may act as a feedback mechanism regulating physiological function.

Strengths:

Experiments and data analysis are robust and valid. The rigorous statistical analysis and unbiased methods enable the authors to draw well-supported conclusions that go beyond the existing literature. Their outcomes inform about cellular activity at the individual level and the authors explain how the transient dynamics of single sarcomeres are governed by a force-velocity relationship and lead to the complex contractile patterns. The similarity of the results to the study cited in [24] demonstrates the validity of the in vitro setup for answering these questions and the feasibility of such in-vitro systems to extend our knowledge of out-of-equilibrium dynamics in cardiac cells.

Very interesting the suggestion that the interplay between intrinsic fluctuations and the dynamic instability are part of a feedback mechanism for maintaining structural and functional homeostasis.

The addition of the theoretical model and the new text of the manuscript improves the clarity of the study.

Reviewer #2 (Public review):

Summary:

Sarcomeres, the contractile units of skeletal and cardiac muscle, contract in a concerted fashion to power myofibril and thus muscle fiber contraction.

Muscle fiber contraction depends on the stiffness of the elastic substrate of the cell, yet it is not known how this dependence emerges from the collective dynamics of sarcomeres. Here, the authors analyze contraction time series of individual sarcomeres using live imaging of fluorescently labeled cardiomyocytes cultured on elastic substrates of different stiffness. They find that a reduced collective contractility of muscle fibers on unphysiologically stiff substrates is partially explained by a lack of synchronization in the contraction of individual sarcomeres.

This lack of synchronization is at least partially stochastic, consistent with the notion of a tug-of-war between sarcomeres on stiff sarcomeres. A particular irregularity of sarcomere contraction cycles is 'popping', the extension of sarcomers beyond their rest length. The statistics of 'popping' suggest that this is a purely random process.

Strengths:

This study thus marks an important shift of perspective from whole-cell analysis towards an understanding the collective dynamics of coupled stochastic sarcomeres.

Reviewer #3 (Public review):

The manuscript of Haertter and coworkers studied the variation of the length of a single sarcomere and the response of microfibrils made by sarcomeres of cardiomyocytes on soft gel substrates of varying stiffness.

The measurements at the level of a single sarcomere are an important new result of this manuscript. They are done by combining the labeling of the sarcomeres z line using genetic manipulation and a sophisticated tracking program using machine learning. This single sarcomere analysis shows strong heterogeneities of the sarcomeres that can show fast oscillations not synchronized with the average behavior of the cell and what the authors call popping events which are large amplitude oscillations. Another important result is the fact that cardiomyocyte contractility decreases with the substrate stiffness, although the properties of single sarcomeres do not seem to depend on substrate stiffness.

The authors suggest that the cardiomyocyte cell behavior is dominated by sarcomere heterogeneity. They show that the heterogeneity between sarcomere is stochastic and that the contribution of static heterogeneity (such as composition differences between sarcomeres) is small.

Strengths:

All the results are, to my knowledge, new and original. The authors also made a theoretical model where each sarcomere is described by a Langevin equation based on a non-linear coupling between force and velocity of the sarcomeres. This model accounts well for the experimental results including the observation of what the authors call popping events.

Reviewer #1 (Public review):

Summary:

Dad et al. explored the roles of cytosolic carboxypeptidase 5（CCP5）in the development of ependymal multicilia in the brain. CCP family are erasers of polyglutamylation of ciliary-axoneme microtubules. The authors generated a new mutant mouse of Agbl5 gene, which encodes CCP5, with deletion of its N-terminus and partial carboxypeptidase (CP) domain (named AGBL5M1/M1).

Strengths:

The mutant mice revealed lethal hydrocephalus due to degeneration of ependymal multicilia. Interestingly, this is in contrast with the phenotype of Agbl5 mutants with disruption solely in the CP domain of CCP5 (named AGBL5M2/M2) that did not develop hydrocephalus despite increased glutamylation levels in ependymal cilia as observed for AGBL5M1/M1 mutants. The study has been well-performed and the findings suggest a unique function of the N-domain of CCP5 in ependymal multicilia stability.

Weaknesses:

The content of this article is relatively descriptive and lacks molecular insights, regarding the function of the CCP5 N-domain.

Comments on revised version.

The authors have appropriately revised the manuscript in response to most of my comments.

Reviewer #2 (Public review):

Summary:

This study analyzed consequences of Agbl5 mutation on ependymal cells development and function. Authors first characterize their mutant mouse line reporting a reduced lifespan and severe hydrocephalus. Next, they report defect in ependymal cell cilia number and motility. They provide evidence for impaired basal bodies organisation, cilia glutamylation.

Strengths:

Description of a mutant mouse which implicate Cytosolic Carboxypeptidase 5 (the product of Agbl5 gene) for proper ependymal cells.

Weaknesses:

Description of phenotype are incomplete:

Previous comment: Microtubules are involved in the local organization of ciliary basal bodies (see Werner et al., Vladar et al.,2011; Boutin et al., 2014). It would be interesting that the author checks whether the subapical network of microtubule is glutamylated or not during ependymal cells differentiation and how this network is affected in their mutants.

Although authors now provide images of glutamylation in figure S8 their conclusion claiming that GT335 signal is increased in cilia of Agbl5M1/M1 mutant is not supported convincingly by those pictures. Quantification would be needed.

Reviewer #3 (Public review):

Summary:

The authors developed a new Agbl5 KO allele by extending the deletion to the N-terminus of CCP5 to investigate its function in mouse ependymal cells and trachea.

Strengths:

They show that the KO mice exhibit severe hydrocephalus due to disorganized and mislocated basal bodies. Additionally, they present evidence of both impaired beating coordination and a reduction in ciliary beating.

The manuscript is well-written, and the experiments are convincing.

Comments on revised version.

The authors have taken all of my comments into account and have revised their manuscript to my satisfaction.

Reviewer #1 (Public review):

Summary:

Gruskin and colleagues use twin data from a movie-watching fMRI paradigm to show how genetic control of cortical function intersects with the processing of naturalistic audiovisual stimuli. They use hyperalignment to dissect heritability into the components that can be explained local differences in cortical-functional topography and those that cannot. They show that heritability is strongest at slower-evolving neural time scales, and more evident in functional connectivity estimates than in response time series.

Strengths:

This is a very thorough paper that tackles this question from several different angles. I very much appreciate the use of hyperalignment to factor our topographic differences and found the relationship between heritability and neural time scales very interesting. The writing is clear and the results are compelling. In general, I don't have many complaints after a couple reads through the manuscript; most of my comments below are relatively minor suggestions and points of clarification.

Weaknesses:

The only "weaknesses" I identified were some points where I think the methods, interpretation, or visualization could be clarified:

On page 16, you compare heritability in functional connectivity (FC) and response time series and find that the heritability effect is larger in FC. In general, I agree with your diagnosis that this is in large part due to the fact that FC captures the covariance structure across parcels, whereas response time series only diverge in terms of univariate time-point-by-time-point differences. Another important factor here is that (within-subject) FC can be driven by intrinsic fluctuations that occur with idiosyncratic timing across subjects and are unrelated to the stimulus (whereas time-locked metrics like ISC and time-series differences cannot, by definition). This makes me wonder how this connectivity result would change if you used intersubject functional connectivity (ISFC) analysis to specifically isolate the stimulus-driven components of functional connectivity (Simony et al., 2016). This, to me, would provide a closer comparison to the ISC and response time series results, and could allow the authors to quantify how much of the heritability in FC is intrinsic versus stimulus-driven. I'm not asking that the authors actually perform this analysis, as I don't think it's critical for the message of the manuscript-but it could be an interesting future direction. As the authors discuss on page 17, I also suspect there's something fundamentally shared between response time series and connectivity as they relate to functional topography (Busch et al., 2021) that drives part of the heritability effect.

The observation that regions with intermediate ISC have the largest differences between MZ, DZ, and UR is very interesting, but it's kind of hard to see in Figure 1B. Is there any other way to plot this that might make the effect more obvious? For example, I could imagine three scatter plots where the x- and y-axes are, e.g., MZ ISC and UR ISC, and each data point is a parcel. In this kind of plot, I would expect to see the middle values lifted visibly off the diagonal/unity line toward MZ. You could even color the data points according to networks like in Figure 3C. (You also might not need to scale the ISC axis all the way to r = 1, which would make the differences more visible.)

On page 9, if I understand correctly, you regress the vector of ISC values across parcels out of the vector of heritability values across parcels and then plot the residual heritability values. Do you center the heritability values (or include some kind of intercept) in the process? I'm trying to understand why the heritability values go from all positive (Figure 2A) to roughly balanced between positive and negative (Figure 2B). Important question for me: How should we interpret negative values in this plot? Can you explain this explicitly in the text? (I also wonder if there's a more intuitive way to control for ISC. For example, instead of regressing out ISC at the parcel/map level, could you go into a single parcel and then regress the subject-level pairwise ISC values out when computing the heritability score?)

On page 4 (line 155), you say "we shuffled dyad labels"-is this equivalent to shuffling rows and columns of the pairwise subject-by-subject matrix combined across groups? I'm trying to make sure your approach here is consistent with recommendations by Chen et al., 2016. Is this the same kind of shuffling used for the kinship matrix mentioned at line 189?

I found panel A in Figure 4 to be a little bit misleading because your parcel-wise approach to hyperalignment won't actually resolve topographic idiosyncrasies across a large cortical distance like what's depicted in the illustration (at the scale of the parcels you're performing hyperalignment within). Maybe just move the green and purple brain areas a bit closer to each other so they could feasibly be "aligned" within a large parcel. Worth keeping in mind when writing that hyperalignment is also not actually going to yield a one-to-one mapping of functionally homologous voxels across individuals: it's effectively going to model any given voxel time series as a linear combination of time series across other voxels in the parcel.

References:

Busch, E. L., Slipski, L., Feilong, M., Guntupalli, J. S., di Oleggio Castello, M. V., Huckins, J. F., Nastase, S. A., Gobbini, M. I., Wager, T. D., & Haxby, J. V. (2021). Hybrid hyperalignment: a single high-dimensional model of shared information embedded in cortical patterns of response and functional connectivity. NeuroImage, 233, 117975. https://doi.org/10.1016/j.neuroimage.2021.117975

Chen, G., Shin, Y. W., Taylor, P. A., Glen, D. R., Reynolds, R. C., Israel, R. B., & Cox, R. W. (2016). Untangling the relatedness among correlations, part I: nonparametric approaches to inter-subject correlation analysis at the group level. NeuroImage, 142, 248-259. https://doi.org/10.1016/j.neuroimage.2016.05.023

Simony, E., Honey, C. J., Chen, J., Lositsky, O., Yeshurun, Y., Wiesel, A., & Hasson, U. (2016). Dynamic reconfiguration of the default mode network during narrative comprehension. Nature Communications, 7, 12141. https://doi.org/10.1038/ncomms12141

Comments on revised version.

The authors have adequately addressed my previous comments. This is a strong contribution: the methods are sophisticated, the statistical treatment is rigorous, and the results are quite interesting/compelling. I'm happy to endorse the revised manuscript as a finalized version.

Just to confirm: The subjects watched all different movies across the two days, right? For a moment I was wondering "are Day 1 and Day 2 repetitions of the same movies?" Given that Day 1 and Day 2 are an organizational feature of several figures, it might be worth making this very explicit in the Methods and reminding the reader in the Results section.

Reviewer #3 (Public review):

Strengths:

It's sort of novel to study the heritability of movie-watching fMRI data. The methodology the authors used in the paper is also supportive of their findings. Figures are nicely organized and plotted. They finally found that sensory processing in the human brain is under genetic control over stable aspects of brain function (here referring to neural timescale and resting state connectivity).

Weaknesses:

What I am worried about most is the sample size and interpretation of heritability.

(1) Figure 1. I assumed that the authors just calculated the ISC within each group (MZ, DZ, and UR). Of course, you can get different variations between each group. Therefore, there is heritability. Why not calculate ISC across the whole sample, then separate MZ, DZ, and UR?

(2) Heritability scores in the paper are sort of small. If the sample size is small, please consider p-values, which will tell more about the trustworthiness of your heritability.

(3) I don't understand the high-frequency signals in fMRI data. It's always regarded as noise, the band 1 here in particular.

(4) The statement "we show that the heritability of brain activity patterns can be partially explained by the heritability of the neural timescale" should come from Figure 5. However, after controlling for NT, the heritability decreased max. 0.025 in temporal areas. I am not sure this change supports the statement. If the visual cortex is outlined, and combining ISC changes in the visual cortex, I think this would somehow be answered. Instead of delta h2, adding a new model h2 would be obvious to the readers.

(5) Figures 7 and 8, when getting the difference of heritability, please also consider the standard errors of the heritability estimates. Then you can compare across networks/regions.

(6) I think movie VS resting state is a really important result in this paper. However, there is almost no discussion. Discussing this part would be more beneficial for understanding the genetic control over the neuron arousal and excitation circuits.

Comments on revised version.

The whole manuscript has been improved a lot, and the concerns have been clarified.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed some of comments raised in the previous round of review and have opted to proceed to a Version of Record without additional review.]

Summary:

This is an excellent and strong paper. The authors not only show the mechanisms of action of destabilizing mutations in VHL, but notably, they also go on to computationally design and experimentally test an inhibitor that restores wild-type pVHL function, offering starting points for a new class of kidney cancer drugs. The approach that the authors take here can be used to target destabilizing mutations in repressor proteins, common in diseases, including cancer.

Strengths:

This paper is the culmination of an extraordinary amount of work, over years, including method development and testing by a broad range of tools and experiments. It is thorough and comprehensive. It is also well-written and easy to follow.

Reviewer #2 (Public review):

Summary:

Inactivating VHL mutations are common in clear cell renal cell carcinoma, and about half of those mutations unfold/destabilize the protein rather than directly interfering with critical protein-protein interactions. The authors identify a compound that can stabilize/refold mutant VHL and seemingly restore its ability to downregulate its major downstream targets.

Strengths:

The authors use a clever combination of virtual and cell-based screens, followed by suitable biophysical and cell-based validation assays, to arrive at a VHL refolder. This compound is suboptimal from an ADME point of view, but could be a starting point for further medicinal chemistry optimization. Success would have implications for other diseases linked to similar loss-of-function mutations.

Weaknesses:

In going from CP4 to CP4.29 the authors screened based on downregulation of HIF. This is logical but also introduces the danger of identifying chemicals that can downregulate HIF in an "off-target" manner i.e. non-specifically. It therefore essential to clearly show that CP4.29 downregulates steady-state levels of HIF and HIF target genes in cells with suitable (hydrophobic core) VHL mutants but not in isogenic cells lacking VHL.

Reviewer #1 (Public review):

Summary:

The authors quantified and compared the 3D kinematics of bill and tongue movements between two seed-eating bird species: one that specializes on soft seeds, and one that is more adapted to feeding on hard seeds. Their goal was to determine specifically what the role of the tongue was for processing (e.g., dehusking) seeds, and to understand how differences in biting strength between species affect other aspects of seed processing. The authors provided intricate (visual) details of seed processing movements, and showed how coordination between the tongue and cranial kinesis (i.e., mobility of the upper bill relative to the cranium) is both critically important for properly positioning seeds to enhance feeding efficiency. Many studies have detailed how seed-eating birds process seeds, but this study has elevated those to a new level of quantification and visualization for readers to fully experience firsthand. Furthermore, the authors established that the force-velocity trade-off that has been observed between bill functions (e.g., feeding and singing) is largely driven by the contractile properties of the muscles. The conclusions are well supported by the results, and the authors placed the results more broadly into the context of manual grasping, making the argument that these birds achieve high levels of dexterity with far fewer degrees of freedom, which could have potential biomimetic applications.

Strengths:

This study builds upon - and advances - our understanding of the feeding mechanics of seed-eating birds using cutting-edge 3-dimensional modeling and kinematics. Their quantitative analyses of upper and lower bill, tongue, and seed displacements are complemented by elegant visualizations of seed processing in each species. Their comprehensive Bayesian modeling statistical framework tackles the issue of small sample sizes (i.e., few subjects) with volumes of data for each (i.e., lots of sequential kinematic variables) that plague comparative biomechanics studies, principally because (a) it is difficult to gather these high resolution XROMM and muscle contractile data on more than just a few subjects, and (b) these data streams are inherently very large, as they are gathered at high frame and sampling rates. Furthermore, I believe their approach to statistically testing for differences between species sets a new standard for our field that could (perhaps should?) be implemented in other similar types of studies. Another strength is in how the results were packaged: each subsection indicated how the objectives were addressed, and there were concluding statements trailing each subsection that helped deliver the key takeaways.

Weaknesses:

A potential weakness is one that the authors themselves mentioned, regarding the body (and skull) size differences between species. Because gape size limits bite force, and given the force-velocity tradeoff in muscle function, there could be limitations on the rapid manipulation of relatively large seeds for similar reasons in the smaller finches. I see that the small finches appear to overcompensate in their beak rotations, but it's not clear how those compensatory movements might affect their seed processing kinematics with their preferred seed sizes. This does not nullify the authors' conclusions, but the results for the smaller finches might not be entirely representative of seed processing mechanics in smaller species.

Reviewer #2 (Public review):

Summary:

This study investigates coordinated beak-tongue movements in seed manipulation, biting, and dehusking in songbirds. A comparative analysis of the seed-eating process in two songbird species with different biting forces, the domestic canary and Java sparrow, was conducted using high-speed XROMM with anatomical marker tracking and quantitative behavioral analysis. The authors have done a great job analyzing upper and lower beak rotation and translation, seed orientation and movement speed, and tongue kinematics.

Strengths:

The methodological approach of using high-speed (500 fps) X-ray reconstruction for 3D kinematic tracking in small animals is novel and powerful. It enables high temporal resolution tracking of orofacial movements and could potentially inspire future orofacial research in mammals, including mice and marmosets. Moreover, this study encompasses a wide range of anatomical components involved in seed manipulation behavior, including the upper and lower beak, the tongue, and jaw muscles. The behavioral quantification of these components is solid. The findings that both the upper and lower beaks contribute to seed processing, that the lower beak exhibits greater up-and-down and left-to-right flexibility than the upper beak during seed processing, and that the tongue plays an important role in transporting seeds into the mouth are all solid conclusions consistent with observations of bird feeding behavior. Nevertheless, it is valuable to confirm and quantitatively characterize these observations experimentally. The videos are excellent and very informative.

Weaknesses:

(1) The paper often resorts to qualitative descriptions (e.g., "a high positive correlation of tongue velocity and seed velocity", "Compared to positioning, the measured velocities of both seed and tongue were much lower") instead of providing exact quantitative measurements or statistical results. The authors stated that temporal autocorrelation biases standard statistical analyses (lines 205-210), but this rationale does not justify the absence of statistical validation. Suggestion: use appropriate methods for time-series data, such as a permutation test, to test the significance of correlations between variables and avoid false positives.

(2) (Minor) The marker-tracking image shown in Figure 1B could benefit from the inclusion of a higher-contrast, zoomed-in frame of the head showing the metal markers without the red tracking points, alongside the same frame with the red tracking points overlaid, to provide readers with a clearer view of the X-ray image and the methodology and its precision.

(3) (Minor: possibly soften the mechanistic claim). The proposed mechanism of lingual papillae on the tongue surface may aid food manipulation and food movement towards the posterior region of the mouth is interesting, yet the evidence describing their morphology is not strong enough to support the claim about their functional roles. Furthermore, the claim that papillae orientation affects food transport in lines 294-296 lacks supporting experimental evidence. In addition, the roles of extrinsic and intrinsic tongue muscles in controlling dexterous tongue shape changes and movements are not discussed.

Reviewer #1 (Public review):

Summary:

The authors seek to understand and identify the neural plasticity that underlies recovery from precise unilateral hemi-pyramidotomy. The corticospinal tract is severed on one side in the pyramids below the exit of corticoreticular projections. Recovery from the injury is achieved with an intensive wheel running rehabilitation regime. The anatomical sites of plasticity, the importance of plasticity in different reticular areas<br /> to recovery, and the impact of the degree of plasticity observed on recovery as correlated predictors, are shown.

Strengths:

Refined anatomical analysis using mouse line and genetic and viral intersectional tracing identifies specific reticular targets of likely enhanced cortical control that correlate with recovery of locomotor skill.

Weaknesses:

(1) The study is correlational at this time. This does not undercut the value of the data and the identification of targets of plasticity achieved in the work.

(2) Generalization of motor gains beyond locomotion was not tested. Reach-to-grasp tasks for feeding were not tested.

(3) Some discussions and use of the terms fine motor and skilled motor are fuzzy, and the limitations of the study are not sufficiently clearly stated.

Reviewer #2 (Public review):

Summary:

Bonanno and colleagues combine unilateral pyramidotomy, continuous voluntary complex-wheel running, whole-brain intersectional CSN tracing, and c-Fos mapping to ask whether rehabilitation reorganizes the supraspinal collaterals of the intact corticospinal tract neurons. The study is technically ambitious and competent, the uPyX + complex-wheel + intersectional-tracing + BrainJ combination is smart and interesting, the behavioral effect is convincing, and the blinding and exclusion criteria are explicit. The central anatomical finding - a CSN-specific, whole-brain projectome comparison with subregional LPGi/GiA/MdV granularity - is a legitimate contribution that builds on Asboth 2018. However, the strength of evidence does not support the strongest causal wording in the current abstract, significance statement, and parts of the discussion: the results remain correlational, the MdV-behavior correlation is modest, and its significance is sensitive to the unit of analysis. A major revision is recommended, primarily of framing and quantitative robustness, rather than because the central dataset is unconvincing.

Strengths:

(1) Technically ambitious and technically competent study addressing a relevant gap: brain-wide mapping of intact-CSN reorganization under continuous voluntary rehabilitation.

(2) The combination of uPyX, complex-wheel running, intersectional tracing, and BrainJ whole-brain projection analysis is novel and well integrated.

(3) Behavioral effect is convincing, blinding, and exclusion criteria are explicit.

(4) The central anatomical finding (CSN-specific whole-brain projectome under rehab, with LPGi/GiA/MdV subregional resolution) is a legitimate contribution that builds on Asboth 2018. The closest recent works (Lemieux et al. 2024, Jeleva et al. 2026) study reticulospinal rather than CSN plasticity and are complementary rather than competing.

Weaknesses:

(1) Causal framing extends beyond what the current evidence supports.

The abstract and significance statement present MdV as a potential mediator, or even a central locus, through which rehabilitation re-establishes descending control of the impaired limb. This is stronger than the evidence. What the paper shows is that CSN collateral projection density in MdV has a mild-to-medium correlation with behavioral recovery, and that this region is already known from prior work (Esposito 2014) to be relevant for skilled forelimb function. That is an interesting anatomical correlation, not a demonstration of mediation. No manipulation of MdV or of MdV-projecting CST terminals is performed; there is no silencing, no pathway-specific perturbation during rehabilitation, and no test showing that the identified sprouting is necessary for recovery. The limitations section acknowledges this, but the prominent claims do not.

(2) The behavioral caveat on what is actually novel.

The cleanest way to state what is genuinely new, clearer than the abstract itself, is this: when a CSN population loses part of its spinal target domain (via contralateral uPyX denervating the opposite cord), some CSNs from the opposite cortex appear to redirect growth into brainstem collaterals (LPGi, GiA, MdV). The compensation is plausibly sufficient to restore gross descending drive to the impaired forelimb, but most probably inadequate for the fractionated, cortico-motoneuronal fine-grain control that the direct CST normally provides. That distinction - recovery of drive and even skilled locomotor control vs. recovery of fine precision - is consistent with the ladder-rung improvements the paper reports (footfall counts are an integrated gross-placement metric) and with the skilled-reaching literature (Esposito 2014 and similar), which suggests precision grip and digit individuation would not be fully recovered by an MdV-centered detour. This note is also translationally important when we ask what humans consider fine motor control, which is mostly object manipulation. Relatedly, the ladder task is "skilled" in the operational sense that it requires cortical control, but the motor output measured (gross paw placement, overreach) is not fine motor function in the sense of digit individuation, grip force modulation, or pellet manipulation. "Skilled" here does not even mean *acquired* skill: classical skilled reaching in rodents involves explicit training to acquire a novel motor program, whereas here mice are only habituated. The brainstem-compensation hypothesis is more comfortable with restoring cortex-dependent gross placement than with restoring acquired fine-motor skills.

(3) The anatomy sample is modest for the precision of the claims.

Projection analysis rests on n = 9 pooled controls, n = 5 uPyX−Rehab, and n = 5 uPyX+Rehab. For a whole-brain subregion analysis, this is not a large dataset, even with the sensible restriction to the Wang et al. spinally-projecting set. The three medullary hits are plausible, but some of the most specific conclusions rely on a relatively small number of animals for its most specific claims. This matters especially for the MdV-behavior correlation.

(4) Normalization enforces a zero-sum structure.

Projection density is normalized to the total CST tract signal. This is a reasonable way to control for tracing variability, but it imposes a relative structure on the data: an apparent increase in one region may partly force an apparent decrease elsewhere. This may matter and has to be looked into by the authors, because the manuscript interprets decreased density in some other targets as meaningful redistribution.

(5) The decision to merge PMn and MdV under a single "MdV" label needs more justification.

Since the discussion relies on prior literature assigning skilled forelimb function to MdV proper, the reader needs to know whether the signal truly localizes there or whether it may partly reflect a neighboring region grouped under the same atlas label. Related to this, laterality would be very informative: since the proposed compensatory route is anatomically directional, showing whether the increased signal is preferentially located on the expected side of the medulla would strengthen the interpretation.

(6) The c-Fos / Fig. 3 section goes beyond what the data directly support.

The section "Complex-wheel running recruits intact corticospinal neurons" and the figure title "Rehabilitation functionally recruits intact CSNs" go beyond the actual observation, which is that a higher fraction of CSNs in M1 and M2 are c-Fos+ in runners than in non-runners. "Functionally" is not supported: c-Fos is a transcriptional marker of recent activity, not a functional readout; it does not show that the CSN's output is used to drive behavior. "Rehabilitation" is not supported either: the contrast is runners vs non-runners, applied uniformly across Sham and uPyX groups - healthy Sham+Rehab animals are on wheels for leisure, and the c-Fos effect is present in them too. The finding is difficult to interpret without thinking of the simpler framing ("moving mice have more motor cortex activity than resting mice"), with no control for generic arousal or ambulation. This section is the softest link in the causal chain running - CSN activity - medullary sprouting - recovery.

(7) MdV-recovery correlation: unstated multiple-comparison correction and possible pseudoreplication.

The correlation (R² ≈ 0.33, p ≈ 0.01) is the backbone of the paper's "causal" claim. Panels L/M/N test three correlations (LPGi, GiA, MdV vs forelimb footfall recovery); only MdV is reported as significant. The Figure 5 legend applies Tukey adjustment to the t-tests in A-C but makes no analogous statement for the correlations in L-N. A 3-test Bonferroni (α = 0.017) would not flip the MdV result, but disclosure is warranted, and the three tested regions were pre-selected from the significant group contrasts in A-C, which, to a statistician, would further shrink effective α. More importantly, the figure legend states that closed and open circles represent CFA- and RFA-traced values, respectively, which suggests the correlation treats the two tracer channels per mouse as independent datapoints - doubling the apparent n (≈ 20 from 10 uPyX mice), with the result of a higher significance than one would have at the mouse level.

(8) Reporting issues.

The reader would benefit from judging statistical choices such as those above directly from a data table rather than interpreting the authors' choices. The SciScore rightfully flags multiple missing components of transparent reporting: missing RRIDs, no code availability, limited data availability, and no power calculation, among others.

Almost all these weaknesses can be addressed with a revision of the manuscript, especially in the framing of results.

Conclusion:

The core message - that rehabilitation is associated with a selective pattern of CSN collateral remodeling in the motor medulla, and that MdV projection density covaries with behavioral recovery - is defensible from the data and already a useful result. The current wording in parts of the abstract, significance statement, and discussion goes beyond this and implies a mechanistic conclusion (mediation, central locus, re-establishment of descending control) that the data do not yet establish. The manuscript would better match its evidence with "associated with", "correlates with", or "candidate locus" framing, unless a causal experiment is added.

Reviewer #3 (Public review):

Summary:

In this study, Bonanno et al. show that after a lesion of the corticospinal tract (CST), rehabilitation running in a complex wheel drives improvement in skilled forelimb performance in mice. Mice with unilateral CST injury can perform gross motor tasks (locomotion) at the same level as the non-injured mice, but injured mice still have deficits in another task involving fine motor control. Thus, it is well-suited to test the efficacy of locomotion-based rehabilitation in fine motor control. Mice that voluntarily engaged in the rehabilitation protocol improved in the fine motor control task more than those mice that did not perform any rehabilitation. Highlighting the role of rehabilitation in the recovery of motor function after the lesion.

The authors aimed to study rehabilitation-driven intact CST sprouting to supraspinal areas. They identified one area in the motor medulla where rehabilitation significantly changes the projection density from the intact cortical spinal neurons. Interestingly, this area has ipsilateral connections and thus could be a pathway to convey motor commands from the intact corticospinal tract to the denervated area. However, as the authors acknowledge in the discussion, they only found a correlation between the change in the synaptic projections from intact CST to the medulla and the recovery. Future work should study if indeed the area of the motor medulla identified here increases its ipsilateral projections to the denervated area, confirming the re-routing of motor commands from the intact cortico spinal tract to the denervated area. The paper is strong and, in general, claims are supported by the data.

Strengths:

In this study, Bonanno et al. show that after a unilateral corticospinal tract lesion (CST), locomotion rehabilitation can improve motor function and improvements generalized to tasks that require fine motor control. Moreover, it identifies a potential pathway that could be used for the intact corticospinal tract to convey motor commands to the denervated area. The pathway identified here could become a target for rehabilitation therapies.

Weaknesses:

As the authors acknowledge in the discussion of the study, the main limitation of this study is that the reorganization observed at the motor medulla is only correlational. Thus, it is possible that the adaptation to running with an injured limb of the intact CST to adapt to an injured limb rather than a re-routing of the intact CST inputs to the denervated area underlies the synaptic changes observed in the motor medulla.

The statistical analysis could be better described.

The generalization of skilled movement is limited to only locomotion tasks.

Reviewer #1 (Public review):

Summary:

Microbialization (bacterial overgrowth) is a recognized component of degraded, eutrophied coral reefs where there is a shift from coral to algal dominance on the benthos. In addition, previous work has demonstrated that virus communities shift from a lytic strategy dominated (kill-the-winner) to a temperate (lysogenic) strategy dominated with reef microbialization. Kelman et al. sought to leverage previously published virus metagenomes produced from the water column of healthy and degraded coral reefs to assess virus community metabolic shifts. The authors also produce a conceptual model to demonstrate the potential impact of the observed metabolism shifts on reef fates.

Strengths:

The main strength of the manuscript is the findings from their metagenomic analyses and results. The virus metagenomes were produced using established approaches in the field and yield sufficient data per sample for their analyses. Interesting results regarding the shift in the types of genes from anaplerotic to cataplerotic provide the foundation for testable hypotheses to determine the magnitude of impact virus strategies have on reef health. The introduction is also well written and sets up the scene very well.

Weaknesses:

(1) The methods text currently omits important information related to the sampling design. It is not clear how many metagenomes are from healthy and degraded communities. This impacts the interpretability and robustness of the statistical results. Furthermore, it is unclear if analyses are based on assembled contigs or read-based alignments. Improving the clarity and organization of the Methods is essential for reproducibility.

(2) Regarding the bioinformatics approach, normalization using the "percent known" approach within samples may not fully account for discovery bias related to sequencing depth. While Supplementary Table 1 shows variability in read counts, the lack of community-level metadata makes it difficult to determine if sequencing depth covaries with community type (healthy vs. degraded). The study would benefit from a rarefaction analysis or subsampling to ensure that gene frequency trends and Spearman correlations are biological signals rather than artifacts of sequencing effort.

(3) The qualitative model in Figure 5 is positioned as evidence for the role of viruses in reef health, but it does not provide independent support for the authors' hypotheses. Since the model is parameterized using "arbitrary units" to reflect the authors' assumptions rather than being derived from the empirical metagenomic data, it serves as a helpful illustration of a hypothesis but not as a validation of the findings.

(4) Results and discussion require revisions to improve readability and connectivity across sections. Ensuring a clear distinction between empirical data and model-based speculation would help the audience better appreciate the science.

Reviewer #2 (Public review):

Summary:

The manuscript by Kelman and coauthors investigates how viral communities differ in the genes they encode in healthy and degraded coral reef ecosystems. Across 19 viral metagenomes from Central Pacific reefs, the authors assess the frequency of integration/excision genes as a proxy for viral community temperateness and ask whether genes associated with central carbon metabolism covary with signatures of temperateness. The main finding is that viral communities with more temperate-related genes encode more genes from the Entner-Doudoroff pathway and other reactions interpreted as anaplerotic, whereas more lytic-associated viral communities show greater representation of some pentose phosphate pathway, TCA, and redox-associated genes interpreted as cataplerotic. The authors propose a model based on these patterns in which lytic viral metabolism helps suppress bacterial overgrowth on healthy reefs, while temperate viral metabolism may promote microbialization on degraded reefs. The study addresses an interesting and potentially important concept - that viral auxiliary metabolic genes are important components of microbial communities and can affect ecosystem functioning. Linking viral metabolism to coral reef microbialization is a creative conceptual advance. The manuscript is clearly written, and the reported enrichment of anaplerotic genes in temperate-associated viromes is an interesting pattern that could motivate future work on how viral metabolic potential varies across reef states.

Strengths:

(1) The study connects viral lifestyle, central carbon metabolism, bacterial overgrowth, and reef degradation in a framework that could be useful for future studies of coral reef ecosystems and viral ecology. This is an interesting synthesis that links viral auxiliary metabolism to broader questions about microbialization and reef state.

(2) The manuscript is generally clearly organized around a testable prediction: viral metabolic gene content should vary along a lytic-to-temperate viral community gradient. The reported enrichment of anaplerotic genes in viromes with a larger fraction of temperate viruses is a compelling result.

(3) The authors highlight several virus-encoded metabolic genes that may not have been previously reported in viral datasets or genomes. If supported by further validation, these observations could expand the known repertoire of viral metabolic potential.

(4) The modeling helps clarify the feedbacks the authors propose may connect viral lifestyle, bacterial metabolism, and coral reef degradation. It provides a foundation for generating hypotheses about how viral metabolic genes could influence reef microbial dynamics.

Weaknesses:

(1) The main limitation is that the evidence for several key claims remains indirect. The core analysis is based on correlations between metabolic gene frequencies and integration/excision-related genes. This does not demonstrate that the metabolic genes occur in temperate viral genomes, are physically linked to lysogeny genes, are expressed during infection, or alter host metabolism. Thus, the data support an association between VLP-associated metabolic annotations and a community-level temperateness proxy, but not a direct link between temperate phages and these metabolic functions.

(2) It is important not to equate community-level gene frequencies with genome-level or infection-level metabolic programs. A virome may contain more anaplerotic genes overall, but that does not demonstrate that individual viruses reprogram their hosts in an anaplerotic manner nor that infection produces a net anaplerotic effect. Individual viruses may encode both anaplerotic and cataplerotic genes, and a smaller number of cataplerotic genes could have stronger metabolic consequences depending on expression, enzyme efficiency, pathway position, and host context. This is an important limitation that should be acknowledged and, if possible, addressed with contig- or genome-level analyses.

(3) The ecological interpretation assumes that viral infection is strong enough to influence reef-scale bacterial population dynamics. However, the study does not directly measure infection frequency, lysis rates, viral production, burst size, lysogeny frequency, prophage induction, gene expression, or bacterial mortality. If viral mortality or lysogenic conversion were rare in these systems, the observed gene-frequency patterns could have limited ecosystem-level consequences. This makes claims about viral metabolism suppressing bacterial overgrowth, accelerating microbialization, or acting as a conservation lever more speculative than suggested.

(4) There are statistical limitations related to the use of relative gene frequencies. Because genes are normalized as percentages of known genes, the data are compositional. Apparent increases in some categories may partly reflect decreases in others. Bootstrapped Spearman correlations are useful for assessing the robustness of these associations, but they do not address compositionality or multiple testing.

(5) The anaplerotic/cataplerotic classification is central to the manuscript's conclusions and would benefit from more support. The framework is useful, but it depends on both annotation confidence and biochemical context. Sequence-similarity annotations alone may be vulnerable to misannotation, especially for central metabolic enzymes that share conserved domains across functionally distinct proteins. Stronger evidence that key genes contain key functional domains and/or are phylogenetically related to characterized enzymes would help support the proposed functions. In addition, many central carbon enzymes are reversible or context-dependent, so a clearer rationale for each classification would strengthen the interpretation.

Overall, the manuscript presents a valuable hypothesis and highlights new ecological patterns in coral reef viral metagenomes, but falls short of the evidence needed for the strongest claims. The work would be strengthened by analyses that directly link metabolic genes to viral genomes or lysogeny markers, address compositional effects, validate key annotations, and more clearly distinguish observed gene-frequency associations from hypothesized effects on infection, host metabolism, and reef state.

The John & Calvin Podcast has just published a pretty critical review of the article.

Reviewer #1 (Public review):

Summary:

The review by Dorrell and Whittington synthesizes the progress made over the past few years with respect to a normative theory of grid cells. The core question addressed by normative frameworks of grid cells is what primary computational function grid cells serve. The review discusses evidence from mechanistic models and experimental data that point to path integration as the computational function of grid cells, consistent with results from normative models. The main goal of the review is to clarify the normative grid cell theory literature. However, the current version of the article reads at times more like a perspective or opinion article in support of the path integration hypothesis rather than a critical review of normative frameworks in the grid cell literature that contrasts the benefits and limitations, as well as pitfalls and caveats, with other modelling approaches.

Some specific comments are as follows:

(1) Abstract: "The first question quickly attracted an answer: grid cells subserve path integration ..." - I am not sure if this statement is correct. The first grid cell paper by Hafting and Fyhn in 2005 suggested that grid cells are part of a path integration-based map, and the paper emphasizes the map part. It remained unclear, and is still debated, whether grid cells are part of a system performing path integration or whether grid maps reflect the output/result of a path integration process. Other theories about the function of grid cells were brought forward as well. Although the main competing theory is discussed in this review, this review article at times appears more as a perspective or opinion article with a clear bias toward the path integration hypothesis rather than objectively discussing the evidence.

(2) Grid cells may serve multiple functions. What would be the implications for our understanding of grid cells and for interpreting the results of normative models? In general, the review could discuss some pitfalls or caveats of normative models in more detail.

(3) A normative framework can be helpful in two ways: (a) Given sufficient details on biological constraints, a normative model can help identify the computational function of grid cells. If a computational function is given and - under the given simulated biological constraints - grid cells were part of the solution, the results of the model would support the hypothesis that grid cells serve the computational function in question. (b) If a computational function were identified beyond any doubt (e.g., assume experimental data demonstrated that grid cells are necessary and sufficient for path integration), a normative model would help identify biological parameters necessary to produce grid cell firing. Unfortunately, the review falls short in making this clear distinction between (a) and (b) and in discussing important caveats regarding mixing up these two ways. E.g., the neural network model approaches by Sorscher et al. and others have been criticized because they try to achieve two things at the same time: find support for the computational function of grid cells and identify optimal parameters that result in grid cells. But doing both at the same time provides a strong bias in tweaking the parameters in exactly the way you need for the model to produce grid cells as a solution (other solutions may be possible given other parameters), preventing strong conclusions regarding the computational function of grid cells and preventing conclusions about what the parameter choices mean for biological connectivity motifs. These caveats in setting up normative models and interpreting them could be discussed in greater detail.

(4) A common assumption underlying most grid cell models is that head direction is viewed as identical to movement direction. However, head direction can differ at times from movement direction, and entorhinal head direction cells code head direction rather than movement direction (Raudies et al., 2015; 10.1016/j.brainres.2014.10.053). This missing link in how movement direction signals reach and inform grid cells could be discussed.

(5) "Knowing that one neuron in a module is active and that you make a movement north uniquely determines which neuron in that module should be active next" - I agree that this rule follows from the fact that grid cells within one module differ in phase but share spacing and orientation. However, I am surprised that the authors do not also make the argument here for the value of a normative model. Rebecca R.G. et al. (10.7554/eLife.96627) use exactly the rule cited above as a normative function. They demonstrate that this rule begets grid cells. Isn't this a prime example of how a normative approach can contribute to scientific inquiry? First, a hypothesis about a computational function is derived from experimental data. And in turn, using a normative framework, the experimental data are derived from the computational function (under appropriate biological results). The paper is discussed later together with Nicolai Waniek's work (10.1162/neco_a_01255). However, in my opinion, their work seems to be somewhat misrepresented in that later paragraph. E.g., velocity is still required as an input to determine which neuron should be active next, neurons do not need to be binary units, and space is not discretized beyond the fact that space is encoded by neurons with spatial firing fields.

Reviewer #2 (Public review):

Summary:

This review by Dorrell and Whittington covers a number of aspects related to normative modeling of grid cells. They begin by discussing key experimental insights on grid cell phenomenology. Then, they discuss how grid cells can be used to perform path integration and how they size up as efficient codes of space. These two sections then lead the authors to discuss how combining path integration and efficient coding objectives leads to models of axis-aligned grid cells in a single module. Discussion on non-linear objectives leading to multi-modules is presented. The review ends with several outstanding questions and an optimistic outlook of how normative models (particularly, task-optimized RNNs) can be used as tools for advancing understanding in neuroscience.

Strengths:

(1) The review is timely and covers an area that has seen a lot of recent activity. This discussion around many of the different results (and kinds of models), I think, will be generally helpful for the field.

(2) Although I think the story could be a little more coherently made (see below), in general I enjoyed the author's flow from efficient coding -> efficient coding + path integration -> efficient coding + path integration + non-linear objective. This framing supports the specific conclusion the authors arrive at.

(3) I also really liked the message that the review made of how normative modeling, despite some of its challenges/limitations, can be used effectively in neuroscience. The discussion of cycling between "experimental" modeling (e.g., vanilla RNNs) and theoretically-grounded models was nice, and I think it helps demonstrate the value of this approach.

(4) Showing how the metric loss could be seen as a bandpass filter (Figure 3C) was nice and a contribution of the review.

(5) While the focus of P4 (conjunctive HD-grid cells) felt initially a little cast aside, the discussion around "brain and task-optimised RNNs with standard architectural choices use fundamentally different path-integration mechanism" was nice and I think helpful for steering the community to an interesting open problem.

(6) Identifying how "non-linear functionality" can lead to multi-modules was nice and not something that I have seen as clearly presented before.

Weaknesses:

(1) The authors view the experimental evidence for grid cells being linked to path integration as "specific and strong" and that the " key computational feature that defines entorhinal cortex [is] path-integration". I think experimentalists (at least the ones I work with) would push back on that. First, it's hard to isolate path integration in rodent experiments. So while Gil et al. (2018) did about as good a job as you could do, there are still other interpretations of the results that are not purely path integration dependent. And second, as the authors point out later in the review, there is experimental work finding that grid cells are disrupted in large environments and 3D. Path integration certainly happens (to some extent) in these spaces, which begs the question of how it is achieved with weakened grid coding. Thus, I think reducing the claims about how strongly grid cells are experimentally linked to path integration is called for.

(2) The authors introduce the idea of efficient coding of space and discuss how grid cells are not optimal. It is later clarified (Sec. 5.3) that multi-module codes can be efficient (even if not the most optimal). I was confused reading Section 3, because in Section 2 the multiple modules are discussed, but then in Section 3, they are dropped, and only a single module is being considered. Equation 2 was also a little confusing to me. Alpha is not defined, and I would have thought that it would be x^Tx' - g(x)^T g(x') and not x^Tx' g(x)^T g(x'). Given that there is no page limit here, I think a little more detail in Section 3 would be helpful.

(3) In Section 3, the authors make use of P2 (translation invariance within a module) to rule out (or, at least, question) certain models/approaches. While this is certainly a standard assumption made in theoretical work, it is not very well supported by experimental findings. In particular, Diehl et al. (2017), Ismakov et al. (2017), and Dunn et al. (2017) all found that individual grid fields systematically vary in their peak firing rate. In addition, Redman et al. (2025) found that, within a given module, there was a small but robust diversity of grid orientations and spacings. These suggest that grid cells within a single module may actually be able to encode properties of local space and give some support to normative models that find efficient space coding with grid cells by finding non-axis-aligned grid fields. I think this is all important to mention because: a) it provides more biological nuance to the question about spatial coding; b) it provides more ways in which to test models. For instance, in Redman et al. (2025), the Sorscher et al. (2022) model was shown to produce variability in grid properties that loosely matched what was found in real data. For tests like this (e.g., how much does a model reproduce variability in grid firing field peak rates), I think it is going to be important for continuing to evaluate models.

(4) The focus of the review, I know, is grid cells, but of course, grid cells are part of the MEC and the larger hippocampal network. I totally understand, at some level, you have to make a decision of what to model, but it seems that there are other functional classes of neurons (border cells, head direction cells) that all play an important role in path integration. And while the models the authors consider at the end of the review capture properties of grid cells really well, they do so at the cost of not modeling anything else. The authors mention this in the context of the models not capturing conjunctive grid-head direction cells, but I think the point is a deeper one, and more discussion of at what level it makes sense to consider grid cells only is important.

(5) As I mentioned in the Strengths section, I did enjoy the flow of the paper on how path integration + efficiency is needed to get grid single modules and path integration + efficiency + non-linearity is needed to get multiple grid modules. This creates the story that adding more of these theory-driven constraints helps lead to more "accurate" models of grid cells. But one alternative view is that, if path integration + efficiency is enough to get a single grid module (but only a single grid module), then maybe the utility (or need) of multiple grid modules comes from something else. That is, instead of saying "we need more constraints to get multiple modules", it could be evidence for "we need to re-think whether multiple modules might need a different theory to explain". While I understand this is a big picture question that maybe isn't entirely fair to ask of the authors, I think: 1) the authors do a nice job of positioning their review as a kind of discussion on what normative modeling can provide to neuroscience, so having this discussion on when the failure of a model to capture ALL aspects of the biological features motivates further constraints as opposed to a new approach, would be useful; 2) this question connects with the title of the paper, i.e. "what is the question?"

Reviewer #3 (Public review):

Summary:

The authors present an extensive review of the literature on normative grid cell theory, asking what kind of cost function might be minimized by the entorhinal grid cell code. The authors show which of the main features of grid cells emerge from combinations of terms in a cost function that optimizes for spatial fidelity, biological plausibility, and path integration. They conclude by outlining potential future directions for the field.

Strengths:

The structure of the review makes it particularly useful for researchers who are familiar with grid cells but not necessarily with normative models. Equations are kept to a minimum and are usually explained conceptually.

Weaknesses:

I identified one main weakness, related to the fact that the introduction to experimental results around grid cells and what they allow us to conclude is less nuanced than the rest of the review. However, since this is not the main focus of the manuscript, I consider this a secondary limitation.

The review organizes the current literature on the subject within a coherent conceptual framework, helping to define possible paths forward for the field.

Reviewer #1 (Public review):

Summary:

Extracellular electrophysiology datasets are growing in both number and size, and recordings with thousands of sites per animal are now commonplace. Analyzing these datasets to extract the activity of single neurons (spike sorting) is challenging: signal to noise is low, the analysis is computationally expensive, and small changes in analysis parameters and code can alter the output. The authors address the problem of volume by packaging the well-characterized SpikeInterface pipeline in a framework that can distribute individual sorting jobs across many workers in a compute cluster or cloud environment. Reproducibility is ensured by running containerized versions of the processing components.

The authors apply the pipeline in two important examples. The first is a thorough study comparing the performance of two widely used spike-sorting algorithms (Kilosort 2.5 and Kilosort 4). They use hybrid datasets created by injecting measured spike waveforms (templates) into existing recordings, adjusting those waveforms according to the measured drift in the recording. These hybrid ground truth datasets preserve the complex noise and background of the original recording. Similar to the original Kilosort 4 paper, which uses a different method for creating ground truth datasets that include drift, the authors find Kilosort 4 significantly outperforms Kilosort 2.5. The second example measures the impact of compression of raw data on spike sorting with Kilosort 4, showing that accuracy, precision, and recall of the ground truth units is not significantly impacted even by lossy compression. As important as the individual results, these studies provide good models for measuring the impact of particular processing steps on the output of spike sorting.

Strengths:

The pipeline uses the Nextflow framework, which makes it adaptable to different job schedulers and environments. The high-level documentation is useful, and the GitHub code is well organized. The two example studies are thorough and well-designed and address important questions in the analysis of extracellular electrophysiology data.

Weaknesses:

There are no major weaknesses in the revised manuscript. While no data analysis pipeline can cover the needs of all experiments, the authors have added and significant flexibility in the pipeline. Even experimenters who might opt for a simpler pipeline will benefit from this work as a model.

Reviewer #2 (Public review):

Summary:

This work presents a reproducible, scalable workflow for spike sorting that leverages parallelization to handle large neural recording datasets. The authors introduce both a processing pipeline and a benchmarking framework that can run across different computing environments (workstations, HPC clusters, cloud). Key findings include demonstrating that Kilosort4 outperforms Kilosort2.5 and that 7× lossy compression has minimal impact on spike sorting performance while substantially reducing storage costs.

Strengths:

(1)Extremely high-quality figures with clear captions that effectively communicate complex workflow information.

(2) Very detailed, well-written methods section providing thorough documentation.

(3) Strong focus on reproducibility, scalability, modularity, and portability using established technologies (Nextflow, SpikeInterface, Code Ocean)

(4) Pipeline publicly available on GitHub with documentation.

(5) Clear cost analysis showing ~$5/hour for AWS processing with transparent breakdown.

(6) Good overview of previous spike sorting benchmarking attempts in the introduction

(7) Practical value for the community by lowering barriers to processing large datasets.

Weaknesses

No significant weaknesses. The authors have responded to all my review critiques and suggestions.

Reviewer #3 (Public review):

Summary:

The authors provide a highly valuable and thoroughly documented pipeline to accelerate the processing and spike sorting of high-density electrophysiology data, particularly from Neuropixels probes. The scale of data collection is increasing across the field, and processing times and data storage are a growing concern. This pipeline provides parallelization and benchmarking of performance after data compression that helps address these concerns. The authors also use their pipeline to benchmark different spike sorting algorithms, providing useful evidence that Kilosort4 performs the best of out the tested options. This work, and the ability to implement this pipeline with minimal effort to standardize and speed up data processing across the field, will be of great interest to many researchers in systems neuroscience.

Strengths:

The paper is very well written and clear. The accompanying GitHub and ReadTheDocs are well organized and thorough. Benchmarks are exceptionally well applied to support the authors' claims, and it is clear that the pipeline has been very thoroughly tested and optimized by users at the Allen Institute for Neural Dynamics. The pipeline incorporates existing software and platforms that have also been thoroughly tested (such as SpikeInterface), so the authors are not reinventing the wheel, but rather putting together the best of many worlds. In the latest revision, the authors add a nice analysis showing that compression mostly affects the lowest SNR units. This is a great contribution to the field and it is clear the authors have put a lot of thought into making the pipeline as accessible as possible.

Weaknesses:

None noted. The authors have addressed all previous questions and requests for clarification.

Reviewer #1 (Public review):

Summary:

This manuscript examines how Streptococcus pyogenes regulates expression of the virulence factor SpeB in response to both bacterial and host-derived cues. The authors propose that Vfr acts as a repressor of speB expression and that degradation of Vfr by SpeB or by neutrophil-derived proteases relieves this repression. This creates a model in which S. pyogenes can sense proteolytic activity during infection and use that information to tune virulence factor expression.

Strengths:

The main strength of the study is the bacterial regulatory mechanism. The dual reporter system provides a useful way to follow speB and hasABC expression, and the genetic analysis of known regulators helps validate the system. The media-swap experiments, recombinant Vfr experiments, and SpeB-mediated degradation of Vfr support the conclusion that Vfr represses speB and that proteolysis can relieve this repression. The finding that SpeB can degrade Vfr is particularly interesting because it suggests an autoregulatory mechanism that could reinforce SpeB expression once it has been initiated.

Weaknesses:

The host side of the model is less completely supported. The authors show that neutrophil lysates and protease-containing fractions can induce the speB reporter and degrade Vfr, which supports the idea that neutrophil-derived proteases can affect this circuit. However, the in vivo interpretation relies heavily on PAD4-deficient mice to implicate neutrophil extracellular traps. PAD4 deficiency is a useful perturbation, but it does not by itself distinguish loss of extracellular trap formation from changes in neutrophil recruitment, survival, degranulation, phagocytosis, oxidative killing, or other neutrophil death pathways. As a result, the current data support a role for neutrophil-associated proteolytic activity more strongly than they support a specific role for extracellular traps. This distinction is important for interpreting the central model. The bacterial circuit is well developed, but the host-derived cue remains somewhat underdefined. If the relevant signal is extracellular protease activity more broadly, then the model is still interesting, but the conclusion should be framed around neutrophil-derived proteolytic stress rather than extracellular traps specifically. If extracellular traps are the key in vivo source of protease exposure, then additional evidence would be needed to separate that mechanism from other neutrophil effector functions that remain intact in PAD4-deficient cells.

Overall:

This is a valuable study with solid evidence for a bacterial protease-sensing regulatory mechanism controlling SpeB expression. The work should be useful to investigators interested in bacterial virulence regulation, host-pathogen interactions, and how pathogens integrate immune-derived cues during infection. The impact of the study would be stronger if the host-derived signal were defined more precisely, but the bacterial Vfr-SpeB circuit provides a compelling framework for thinking about how S. pyogenes links proteolytic activity to virulence gene expression.

Reviewer #2 (Public review):

Summary:

The study examines how Streptococcus pyogenes integrates bacterial and host-derived signals to regulate SpeB, proposing that Vfr acts as a protease-sensitive repressor whose degradation relieves repression of speB. The authors further suggest that neutrophil-derived serine proteases, including those associated with inflammatory conditions, may promote this transition, and thereby counterbalance LL-37/CovRS-associated suppression of speB. The conceptual framework is interesting and potentially important for understanding how host inflammation feeds into bacterial virulence regulation.

Strengths:

The work addresses a biologically significant question and does so using a broad and generally well-integrated experimental approach, including bacterial genetics, reporter assays, recombinant protein analyses, neutrophil-derived material, human blood infection, and mouse infection models. A particular strength is the effort to connect host inflammatory processes to bacterial regulatory behavior, which gives the study conceptual reach beyond a narrow mechanistic observation. The data support the view that Vfr is relevant to speB control and that neutrophil-associated protease activity may influence this pathway.

Weaknesses:

The main limitations are mechanistic. The physiological form, localization, and abundance of Vfr are not sufficiently defined to support the proposed model at full strength, and the evidence that Vfr functions as a SpeB-labile repressor under biologically relevant conditions remains incomplete. The relationship between Vfr and the broader RopB/SIP regulatory framework is also not yet firmly established. In addition, the reporter system is not yet benchmarked closely enough against endogenous SpeB protein output, and its growth-phase dependence is insufficiently resolved, which makes it difficult in some settings to distinguish promoter activity from mature protease production. The neutrophil protease component is likewise not defined beyond a general serine protease signal, and the potentially important LL-37/CovRS/Vfr connection is underdeveloped in the main text. Overall, the conceptual advance is promising, but several of the central mechanistic claims would benefit from more direct experimental support and more cautious framing.

Reviewer #3 (Public review):

Summary:

SpeB is a cysteine protease secreted during infection by Streptococcus pyogenes (Spy). SpeB has been extensively investigated for its role in pathogenesis, which involves proteolytic processing of both Spy virulence factors and host proteins. Regulation of speB expression is complex and includes growth phase regulation, a quorum-sensing system, the transcription factor RopB, and the global regulatory system CovRS (CsrRS). Guerra et al now attempt to refine the current model of regulation of SpeB expression, focusing on the Spy protein Vfr, which has been suggested previously to act as a negative regulator of SpeB expression. In the current study, neutrophil lysates (representing proteases released during NETosis) are shown to degrade Vfr and to relieve repression of SpeB. At high cell density, SpeB itself also degrades Vfr, which may allow autoregulation of SpeB expression. These observations are unsurprising as the broad protease activities of both neutrophil proteases and SpeB are well known. Nonetheless, the data presented fill in additional details in our understanding of the complex regulation of an important Spy virulence factor.

Strengths:

(1) Construction of a GFP reporter strain provided a facile methodology for tracking speB promoter activity in a variety of experimental setups.

(2) A Vfr deletion mutant was a useful tool to investigate the role of Vfr in SpeB regulation, and mutants in speB and ropB were important controls.

(3) Experiments using neutrophil lysates in vitro, as well as in vivo studies of mice depleted of neutrophils with anti-Ly6G or in PAD4-/- mice (that cannot form NETs) support the hypothesis that neutrophil proteases derepress speB expression by degrading Vfr.

Weaknesses:

(1) The introduction and all the experiments in Figure 1 focus on CovRS, which turns out to be largely tangential to the overall story developed by the rest of the study. On the other hand, the complex and well-studied regulation of speB expression by RopB and the SIP quorum-sensing system is only minimally described. A better framing would be a more detailed introduction to the current model of speB/RopB/SIP/quorum sensing/growth phase regulation. CovRS could be introduced later as its relevance is really just to show that neutrophil lysates or NETs do more than simply providing LL-37, which signals through CsrS, as another regulator of speB expression.

(2) Vfr, as the central focus of the paper, also deserves a more thorough introduction to provide context for the study. For example, reference 19 (Shelburne et al, 2011) showed reduced transcription of speB in a vfr mutant, an effect that could be complemented by expressing vfr or a 39-aa N-terminal fragment in trans. That study presented evidence that the N-terminal peptide binds to RopB, which may prevent RopB from upregulating SpeB expression. Do the authors concur with that model? As it stands, the discussion and model in Figure 1A imply a direct regulatory effect of Vfr on speB expression rather than an indirect one through regulation of RopB. If direct regulation of speB by Vfr is a consideration, it should be investigated more thoroughly, e.g., by promoter-binding assays, CHIP-seq, etc.

(3) Use of single-cell flow cytometry generally confirmed results observed in batch culture. The authors also comment repeatedly on the heterogeneity of individual cell fluorescence representing both speB and has operon expression. However, the reason(s) for heterogeneity in gene expression are not explored, e.g., differences in individual cell growth rate in batch culture, variable loss of reporter plasmid during infection experiments, etc).

(4) Lines 116-118 and Figure 3C: Incubation of recombinant Vfr with Spy Dvfr reduced SpeB expression, but the degree of suppression is modest compared to that seen in wild-type Spy. How does the concentration of rVfr added compare to that present in the culture fluid of wild-type Spy? (Also, the concentration of rVfr used is unclear: the figure says 3 µg/ml and the legend says 0.3 mg/ml, i.e., 300 µg/ml).

(5) Lines 125-126: "...the Vfr structure contains several potential protease SpeB cleavage sites..." The role of Vfr in degrading SpeB could be clarified by identifying the predicted cleavage products, e.g., by mass spec, after co-incubation of the two recombinant proteins.

(6) Lines 122-124: "Notably, speB expression in Spy Dvfr is unaffected by LL-37 or MgCl2, further validating its [Vfr's?] dominance over CovRS regulation." This statement is an oversimplification and is potentially misleading: LL-37 is degraded by SpeB (Nyberg et al, JBC 2004), which likely explains why the addition of LL-37 fails to signal through CovRS to repress SpeB in Spy Dvfr since SpeB is produced continuously in that strain. By contrast, SpeB is only produced during the stationary phase in the wild type, so LL-37 remains active throughout the exponential phase and represses SpeB expression. The response to the CovRS ligand MgCl2 is similar (or greater) in Spy Dvfr compared to wild type (Figure S2C).

(7) Lines 153-154 and Figure 6E: Growing wild type Spy in the presence of neutrophil lysates with or without a protease inhibitor stimulated or repressed speB expression in a manner consistent with degradation (or not) of Vfr. It would be confirmatory and informative to do the same experiment with the Spy Dvfr strain.

(8) Clarity of writing could be improved, particularly by eliminating pronouns of indefinite reference (it, its, this) in contexts in which the subject is ambiguous (examples at lines 62, 89, 111, 114, 115, 123, 183, 190, 193, 204, 205, 210, 217, 221, 222, 224).

Reviewer #1 (Public review):

Summary:

The authors presented a simplified E. coli cell-free protein synthesis (eCFPS) system reduces core reaction components from 35 to 7, improving protein expression levels. They also presented a "fast lysate" protocol that simplifies extract preparation, enhancing accessibility and robustness for diverse applications.

Strengths:

The authors present a valuable new protocol for eCFPS, which simplifies its application.

Weaknesses:

The authors provide data for optimization but offer insufficient explanation of the fundamental mechanisms underlying the phenomenon based on data.

Comments on revised version.

The authors have satisfactorily addressed the concerns raised by the reviewers. However, the mechanistic basis of the observed performance gain remains insufficiently substantiated. The attribution of this improvement to enhanced transcription is currently speculative. This point could be directly tested by quantifying mRNA levels, for example, using real-time PCR, in both the initial and optimized systems. Such analysis would significantly strengthen the mechanistic interpretation of the results.

Reviewer #2 (Public review):

Summary:

The authors have made a convincing argument that the current system of in vitro translation using E. coli extracts can be significantly optimized to work with much lesser components, while maintaining activity. They have showcased their improved activity using not only physical but also functional readouts.

Strengths:

The experiments are designed in a very logical and easy to understand manner, which makes it easier not only to follow the paper, but also reproduce the results. Functional assays with the synthesized proteins are a good way to demonstrate functionality and applicability of the system. They also benchmark their system against a commercial kit to show superior performance of their system.

Weaknesses:

The production of the lysate requires special instrumentation, limiting accessibility.

Comments on revised version:

Thank you to the authors for addressing the concerns both textually and experimentally. This work has significant value.

Reviewer #3 (Public review):

Summary:

The authors aimed to overcome the challenges associated with complex, conventional prokaryotic cell-free protein synthesis (CFPS) systems, which require up to thirty-five components, by developing a streamlined and efficient E. coli CFPS platform to encourage broader adoption. The main objective was to reduce the number of reaction components from thirty-five to seven, while also developing an accessible 'fast lysate' preparation protocol that eliminates time-consuming runoff and dialysis steps. The authors also sought to demonstrate the robustness and translational quality of this streamlined system by efficiently synthesising challenging functional proteins, including the cytotoxic restriction endonuclease BsaI and the self-assembling intermediate filament protein vimentin.

Strengths:

This study presents several key strengths of the optimised E. coli cell-free protein synthesis system in terms of its design, performance and accessibility.

- The reaction mixture has been dramatically simplified, with the number of essential core components successfully reduced from up to thirty-five in conventional systems to just seven.

- The "fast lysate" protocol is a significant advance in terms of procedure.

- The system's ability to synthesise challenging, functional proteins is evidence of its robustness.

Weaknesses:

(1) Title: "A simplified and highly efficient cell-free protein synthesis system for prokaryotes".

- This title is misleading since one would expect a simplified and highly efficient cell-free protein synthesis system to yield similar protein levels compared to current cell-free protein synthesis systems. What this study shows is that the composition of cell-free protein synthesis systems can be simplified while maintaining a certain level of protein synthesis. Here, optimisation does not involve maintaining protein synthesis yield while simplifying the cell-free protein synthesis system; rather, it involves developing a simplified cell-free protein synthesis system. As mentioned in my comments below, this study lacks a comparison of protein levels with a typical cell-free protein synthesis system.

- What do the authors mean by "highly efficient"? Highly efficient compared to what experimental conditions? If one is interested by the yield of protein synthesis, is this simplified system highly efficient compared to current systems?

(2) Figure 1, 3-5:

- What do relative luciferase units represent? How are these units calculated?

- In this system, the level of expression depends mainly on the level of NLuc transcripts and the efficiency of NLuc translation. How did the authors ensure that the chemical composition of the different eCFPS buffers only affected protein translation and not transcript levels? In other words, are luciferase units solely an indicator of protein synthesis efficiency, or do they also depend on transcription efficiency, which could vary depending on the experimental conditions?

- How long were the eCFPS reactions allowed to proceed before performing the luciferase activity measurement? Depending on the reaction time, the absence or presence of certain compounds may or may not impact NLuc expression. For example, it can be assumed that tRNA does not significantly affect NLuc levels over a short period of time, and that endogenous tRNA in the lysate is present at sufficient concentrations. However, over a longer period of time, the addition of tRNA could be essential to achieve optimal NLuc levels.

- The authors show that tRNA and amino acids are not strictly essential for the expression of NLuc, likely due to residual amounts within the cell lysate. However, are the protein levels achieved without added amino acids and tRNA sufficient for biochemical assays that require a certain amount of protein? It is important to note that the focus here is on optimising the simplicity of the buffer rather than the level of protein expression. In fact, the simplicity of the buffer is prioritised over the amount of protein produced. This should be made clear.

- How would the NLuc level compare if all the components were optimised individually and present in an optimised buffer, compared to a buffer optimised for simplicity as described by the authors?

(3) Line 71, Streamlining eCFPS: removal of dispensable components. This title is misleading because it creates the false impression that proteins can be produced in vitro without the addition of certain compounds. While this is true, the level of protein produced may not be sufficient for subsequent biochemical analyses. This should be made clear.

(4) Figure 2: In the legend, change "(A) Protein expression levels of the eCFPS system measured at varying concentrations of KGlu and MgGlu2" to "(A) Protein expression levels of the eCFPS system using an Nanoluciferase (NLuc) reporter DNA measured at varying concentrations of KGlu and MgGlu2".

(5) Lanes 302-303: "The thorough optimization of the seven core components was a critical step in achieving high protein expression levels". What are "high expression levels"? Compared to what?

Comments on revised version.

The authors have adequately addressed my previous concerns.

Reviewer #1 (Public review):

Summary:

Pecak et al have deciphered the conformational dynamics of a heterodimeric model ABC transporter, TmrAB, a functional homolog of the human antigen transporter TAP, using single molecule Forster resonance energy and fluorophores attached to residues at either nucleotide binding domains or periplasmic gate. The analysis not only differentiated ATP-free and bound states, but also enabled the real time monitoring of protein conformational changes precisely dissecting transport cycles and resolving transient intermediates. This study is absolutely significant in providing and establishing a general pipeline delineating the conformational dynamics in heterodimeric ABC transporters.

Strengths:

The scientific study is very well documented for experimental design, results and conclusions supported by the experimental data. Authors have determined the conformational dynamics of TmrAB across different ATP concentrations including physiological ones and resolved an outward open state and other conformational states consistent with previous cryoEM and DEER studies. Authors have also mentioned limitations in the study.

Comments on revised version.

Authors have worked on most of the revisions stated in previous feedback and included in the newer version, which has been significantly improved. Other comments have been described to be out of scope from this study.

Reviewer #2 (Public review):

In their manuscript entitled 'ATP-driven conformational dynamics reveal hidden intermediates in a heterodimeric ABC transporter', Pečak et al. use elegant single-molecule FRET experiments in detergent to investigate the heterodimeric ABC transporter TmrAB. By combining simulations of the transporter's accessible volume with elegant trapping strategies, the authors identify an unresolved outward-facing open state and conclude that it is usually obscured by a rapidly interconverting ATP-bound ensemble. Overall, the study demonstrates that smFRET can resolve the short-lived intermediate states of TmrAB and potentially other ABC transporters that are obscured in ensemble measurements.

It is a very interesting study that highlights the power of combining high-resolution structural information with spectroscopic approaches. I had three major concerns with the original version, all of which have been addressed by the authors in this revised version.

Reviewer #1 (Public review):

WIPI1 is a PROPPIN family protein that has been implicated in Retromer-mediated membrane fission events. Although the cargos that it has been tested to be important for are diverse, one of the cargos that is unaffected is Beta1-Integrin. This leads the authors to assess another PROPPIN family protein - WIPI2, which is a homolog of WIPI1. KD using siRNA is effective and had no consequences on LAMP1, EGFR trafficking or GLUT1 trafficking. Integrin-B1, however, had a large and significant defect in its recycling from the endosome, with a clear endosomal colocalisation. Complementation experiments with WT WIPI2 recovered the phenotype, but various mutant WIPI2 complements resulted in elongated tubules, and there was also a dominant negative effect of the mutant. Integrin is a classic retriever cargo, so the authors rationalise that WIPI2 may be playing a role with retriever that WIPI1 plays with retromer. To assess this, they perform a set of immunoprecipitations. SNX17, the retriever-associated sorting nexin, co-IPs with WIPI2 in a VPS26C-dependent manner. VPS26C but not VPS26 co-IPs with WIPI2, and the reciprocal with WIPI1. These interactions were not present for the FSSS mutation of WIPI2. WIPI2 localises to Rab11 endosomes mainly, as does retriever. Mutations of WIPI2 not only affected WIPI2 localisation, but also VPS35L mutations, indicating that there is a functional relationship between the two.

Comments on revised version.

The reviewers have responded appropriately to all the points. I have no remaining concerns.

Reviewer #3 (Public review):

Summary:

The manuscript of Mayer and colleagues analyzes the function of WIPI proteins in mammalian cells. The authors identified previously CROP as a complex consisting of WIPI1 and the retromer complex, primarily in yeast cells. In mammalian cells, both WIPI1 and WIPI2 exist, whereas retromer has a homologous complex termed retriever. The now find that WIPI2 can form a complex with retriever subunits. They name this complex CROP2. Their data further indicate that CROP2 and CROP1 have distinct substrate specificities as knock down of CROP2 subunits affect beta1 integrin sorting, whereas knock down of CROP1 affects EGFR and GLUT1. The further identify a similar sequence (FSSS) in both WIPI1 and WIPI2, which is required for their specific binding to retromer and retriever.

Strengths:

CROP1 and CROP2 seem to use similar features for their formation, and have different substrates, which is convincingly shown.

Weaknesses:

The analysis lacks information that this is a complex as claimed. It can be deduced from the immunoprecipitation analysis.

Comments on revised version.

The authors answered my questions and adjusted the text accordingly. Figure 10 was not part of the submitted version. It should be checked by the editor.

Reviewer #1 (Public review):

Summary:

This paper reports the findings of a neuroimaging experiment that tested the hypothesis that the cortex, specifically early visual areas, reinstates the content from single events during our lives. The researchers tested this hypothesis by presenting to-be-remembered pictures of objects at spatial locations on the computer screen and then testing subjects with both recall and recognition. They show that during memory testing, the spatial location of the object can be decoded from the pattern of cortical BOLD responses measured with fMRI. They go on to show that the spatial tuning is higher during recognition than recall, that the tuning is correlated with memory retrieval accuracy, and that the retrieved precision is predicted by the encoded precision, particularly in the higher-level visual areas. Thus, the paper finds evidence of cortical reinstatement of details from a single event in a human life.

Strengths:

This is a strong manuscript that I have had the luxury of commenting on during a round of review at another prestigious journal. As a result, the authors have already made changes to address previous comments about highlighting the complementary learning systems approach more to motivate the alternative prediction that the cortex should only show evidence of reinstatement after repeated presentations. In addition, the authors have fleshed out the discussion of working memory in this task. They also revised their review of the literature to include citations suggesting spatial locations are normal parts of our episodic representations, likely obligatory in nature, as my group and others have argued in completely unrelated work. I applaud the authors for being responsive to a previous round of review and using the comments to address relatively minor issues with the paper, even though they moved on to a different journal. Thus, I found the paper even stronger than at first approach, and at first blush, the results were intriguing and the paper well written.

Weaknesses:

There is a logical perspective in the narrative that seems to unnecessarily weaken the paper. The paper shows evidence consistent with the conclusion that mnemonic representations are contained in early visual cortex, but then argues that those representations are not actually stored therein. For example, the first half of the last sentence of the conclusions (see page 19 of the manuscript). I understand the perspective that subcortical mechanisms must be involved in the act of retrieval, given the neuropsychology and other evidence. But if storage is elsewhere with the same fidelity so as to code this information, then how would such a memory system work? The MTL neurons would need to have the real, precise representation of all the orientations encoded at all the retinotopic locations, a mirror to V1 in terms of precision, because that's the actual memory representation being retrieved, so its fidelity will be limited by what is stored in the file, so to speak. Then, at retrieval, the paper proposes that the brain just reactivates the encoding context in V1 to help with the response output and ensure the precision of the behavioral responses. This must mean that the hippocampus/MTL has cells and networks with tuning functions that match the precision in all the cortical sensory systems that they are integrating context across, given the episodic memory models like Polyn and colleagues (2009, Psych Rev). So, there are little MTL maps that are completely redundant with V1, M1, A1, S1, etc.? Why such redundancy?

Why not propose that what the subcortical systems do is to encode a unique pattern for that episode, that is separated from others, that just links (or provides pointers to, in computer science jargon) the contextual details stored in the cortical networks themselves? In this way, we can explain why neglected patients also neglect their memories of the town square. This has always been my interpretation of the results of the Polyn et al. (2006, Science) paper and the models tested with those whole-brain results. That is, you see widespread cortical context reinstatement during (one-shot) free recall events that included visual selective cortex for faces when faces were being recalled, but included a broad network, probably V1, and activating sounds in A1, body posture in M1, etc., though the latter three examples did not discriminate between categories of memoranda, in their experiments. Given that you show that activity in V1 during retrieval looks like it is being used, you should propose that the early cortex really participates in memory storage functions. V1 neurons are wired up to neurons of other selectivities in a competitive network with plastic synaptic connections. How would experience be prevented from changing activity in the cortex? Yes, cortical changes slow after the critical periods, as studied in the classic eye suturing experiments to study ocular dominance, but changes in cortical representations do not stop with maturity, with the pinwheel centers looking like they are context sensitive, thus, changing rapidly to events across time (Okamoto, Ikezoe, et al., 2011, Sci Reports). The brain would need a no-plasticity mechanism, and instead, it looks like the cortex can completely rewire even in adulthood (Buonomano & Merzenich, 1998, Annu Rev Neuro).

I believe that the paper needs to describe the strong/radical interpretation of the current findings; that they are consistent with the view that the entire brain may be a memory structure, with encoding linking representations across sensory cortices. But also activating semantic and lexical systems, emotional networks encoding those aspects of context which we know can sometimes strongly drive effects, a nice prediction that could be made in the discussion/conclusions. Here you are looking at how precise the visual reinstatement is in V1 during retrieval following one exposure. One parsimonious mechanism to explain this effect is that the brain stores details of events using the neurons that do the high-fidelity perception of the event. Given that our goal is to stimulate thinking among fellow scientists so that this paper can be a citation classic, I think the paper should be revised so that it paints a complete picture of the theoretical possibilities of its findings.

Reviewer #2 (Public review):

Summary:

The study aims to show that the early visual cortex is not merely a sensory-perceptual region that encodes stimuli while they are physically present, but also supports the formation and retrieval of long-term episodic memories. Instead, the authors demonstrate that spatially tuned reactivation of early visual cortex after a single encoding event supports memory-guided behavior, such as recalling an object's original location.

Strengths:

The study provides solid evidence that location information for single, trial-unique objects is reinstated in early visual cortex during both recognition and recall, even without explicit spatial demands, and the remembered vs. forgotten analyses link spatial tuning to behavior. The one-shot design and absence of explicit spatial instructions are important strengths that bring the paradigm closer to everyday, incidental episodic experiences and go beyond highly trained cue-target associations.

Weaknesses:

(1) Conceptually, the main findings would appear less surprising without a sharper theoretical contrast. Given basic retinotopic coding, it is natural that object identity and location are jointly encoded when an object is presented at a particular position, so spatially tuned reinstatement in V1-V3 can be interpreted as a reconfirmation of known properties unless more clearly contrasted with theories that emphasize more abstract, position-invariant cortical representations following hippocampal-cortical recoding. As currently framed, the introduction does not fully articulate what existing accounts might predict, or what pattern of results would have challenged those accounts, which somewhat weakens the perceived theoretical payoff.

(2) It also remains somewhat unclear why early visual cortex (V1-V3), specifically, is the critical locus for the spatial information of interest, as opposed to higher-level visual or parietal regions that could also provide a spatial scaffold; clearer rationale and, if possible, control analyses in additional regions would help here.

(3) Since gaze behavior is central to any spatial account, it would be helpful to report basic eye-tracking analyses comparing remembered versus forgotten trials, especially at encoding, to rule out systematic differences in fixation patterns that could contribute to the spatial tuning results.

Reviewer #3 (Public review):

Summary and Overall Evaluation:

This is an elegant paper addressing an important question: whether spatial location is automatically activated during the recall of object memories. Building on prior work that relied on trained or repeated stimuli, the present study uses unique objects with one-time encoding across four spatial locations - a meaningful advance in ecological validity. The experimental design is clean, the data analysis is well-executed, and the reported effects, while small, are intriguing and open up interesting questions about the role of spatial structure in visual memory. Overall, this is a solid contribution, and my comments below are intended to help the authors strengthen the paper further.

Major Comments

(1) Incidental encoding.<br /> Was the memory task fully incidental - that is, were participants unaware that a subsequent memory test would follow encoding? This seems important for interpreting the automaticity claim that is central to the paper's contribution, and should be clarified explicitly.

(2) Spatial extent of the analysis - higher visual regions and negative pRFs.<br /> The analysis appears restricted to regions V1-V3. Have the authors examined higher visual areas as well? This seems like an important omission given that object memory likely engages regions well beyond the early visual cortex. Relatedly, recent work by Adam Steel and colleagues suggests that spatially tuned negative pRFs may play an important role in memory. Have the authors considered examining these? Expanding the analysis in these directions could substantially enrich the findings.

(3) Mechanism - retinotopic or spatiotopic?<br /> The paper makes a compelling case that spatial structure supports memory, but the nature of that spatial structure deserves more discussion. Are the effects retinotopic or spatiotopic in nature? The current design may not be able to fully dissociate these possibilities, but this distinction is theoretically important, and the authors should engage with it directly. Even a careful discussion of what the current data can and cannot tell us on this point would be valuable.

(4) Relationship between encoding failure and retrieval failure.<br /> For trials where memory performance is worse, and the encoding models fail, is there a systematic relationship between how the pRFs fail at object retrieval versus spatial retrieval? In other words, are the pRFs wrongly tuned in the same way at both stages? This analysis could provide meaningful insight into whether object and location retrieval draw on shared spatial representations.

(5) Object shape and spatial mapping.<br /> Real-world objects vary considerably in surface structure and shape, which may affect how cleanly they map onto a specific spatial location. Was this considered in the analysis? What was taken as the correct or peak location for each object, and how was this defined when objects extended across space? Apologies if this was addressed in the methods and I missed it.

(6) Time course of pRF activation.<br /> Is there a way to examine the time course of pRF activation within a trial? Do the spatially tuned responses arise immediately upon retrieval, or do they build up over time? Even a preliminary analysis of this would be of considerable theoretical interest, as it would speak to whether spatial reinstatement is an early automatic process or a later, more deliberate one.

(7) Effect size and functional significance.<br /> The authors acknowledge that the reported effects are very small, which I appreciate. However, this does raise genuine questions about functional significance that I think deserve a more direct response. One approach that would help contextualize the spatial effects would be to compare their magnitude to that of another feature - object identity, for example - to give readers a sense of the relative importance of spatial versus non-spatial information in memory representations. I recognize this may not be straightforward with the current design, but even a brief discussion of how one might benchmark the spatial effects would be helpful.

(8) The attention account.<br /> I found the discussion of attention less than fully convincing. The authors appear to argue against an attentional interpretation of the spatial effects, but it is not clear why participants wouldn't attend to the encoded location during retrieval - particularly in a design with relatively few retrieval cues, where spatial location may be one of the most useful available. The attention account thus seems difficult to rule out on the basis of the current data, and the discussion should engage more seriously with this alternative rather than setting it aside.

(9) Later-remembered versus later-forgotten objects - BOLD signal.<br /> Were later-remembered objects associated with stronger overall BOLD responses during encoding compared to later-forgotten objects, or was the effect specific to the pRF modelling? Clarifying this would help readers understand whether the spatial effects are part of a broader pattern of stronger encoding or something more specific to the spatial reinstatement mechanism.

Reviewer #1 (Public review):

This study examines the mechanisms underlying retinal toxicity associated with certain AAV gene therapy vectors, particularly in the retinal pigment epithelium (RPE) and photoreceptors following expression of transgenes such as GFP. The findings suggest that AAV-related retinal toxicity is driven less by transgene identity itself and more by distinct pathogenic mechanisms, including stress-induced injury in RPE cells and interferon-mediated damage in photoreceptors. The comments are as follows:

(1) The AAV vectors were manufactured in-house, and the production method is described in sufficient detail. However, were any characterization assays performed beyond qPCR-based titer determination, such as vector genome titer, capsid titer, empty/full capsid ratio, sterility, bioburden, endotoxin, mycoplasma, residual host cell DNA, residual plasmid DNA, or residual host cell protein testing? These analyses, particularly those assessing residual impurities and microbial contamination, are critical, as such contaminants may provoke inflammatory responses following subretinal injection. This, in turn, could confound the interpretation of the results, including the identification of the molecular pathways contributing to toxicity as well as the specific role of GFP-associated toxicity. Please provide any characterization information for the AAV vectors.

(2) The study uses contralateral or uninjected eyes as controls, but this choice may not adequately account for changes induced by the subretinal injection procedure itself. Because the earliest assessment of RPE toxicity was performed at 2 weeks post-injection, any injury, inflammation, retinal detachment-related stress, or wound-healing responses triggered by the surgical procedure could have contributed to the observed phenotype. As a result, comparisons to uninjected eyes alone make it difficult to distinguish vector or transgene-specific toxicity from procedure related effects. Inclusion of a more appropriate procedural control, such as sham-injected eyes or eyes injected with vehicle/buffer alone, would have strengthened the study by enabling clearer discrimination between injection-related retinal responses and toxicity attributable to the AAV construct or transgene expression.

(3) The authors used phalloidin staining on RPE-choroid flatmounts to evaluate RPE toxicity, which provides useful information on RPE morphology and structural disruption. However, it would be highly informative to also assess the presence and distribution of subretinal microglia/macrophages, for example, by Iba1 immunostaining, in the same preparations. Specifically, determining whether Iba1-positive cells accumulate in or around areas of RPE dystrophy would help clarify the contribution of local inflammatory responses to the observed pathology. Such analysis could strengthen the interpretation of the toxicity phenotype by revealing whether RPE degeneration is accompanied by focal immune cell recruitment and whether these cells spatially associate with regions of tissue damage. This would also provide additional insight into whether inflammation is likely to be a downstream consequence of RPE injury or a more direct contributor to disease progression, especially in light of publications by Danial Saban's group regarding the characterization of microglia phenotypes using RNA-seq analysis.

(4) The Discussion should also address the anatomical and procedural differences between neonatal and adult mouse eyes, particularly with respect to retinal thickness and the potential impact of subretinal injection-related injury. Because the RPE toxic effects appeared less severe in adult mice, it would be valuable for the authors to consider whether this difference reflects true age-dependent biological susceptibility or, at least in part, differences in the mechanical consequences of the injection procedure. Neonatal retinas are thinner and structurally less mature than adult retinas, which may render them more vulnerable to injection-associated stress, retinal detachment, or secondary tissue injury following subretinal delivery. In contrast, the greater retinal thickness and maturity of the adult eye may provide some degree of resilience to procedural trauma, thereby reducing the apparent severity of RPE damage. Expanding the Discussion to consider these factors would strengthen the interpretation of the age-related differences observed in toxicity and help distinguish vector- or transgene-driven effects from potential confounding effects introduced by the delivery method itself.

Overall, this manuscript presents a detailed and comprehensive analysis of transgene-induced retinal toxicity and makes effective use of multiple mouse models to dissect the contribution of relevant molecular pathways. The study is particularly strengthened by its systematic approach, combining histologic, transcriptomic, and genetic loss-of-function strategies to distinguish the mechanisms underlying toxicity in the RPE versus photoreceptors. By evaluating several knockout mouse lines, the authors can move beyond descriptive observations and begin to assign causality to specific stress and immune signaling pathways, thereby providing important mechanistic insight into AAV-associated retinal injury. These findings are timely and relevant to the broader field of ocular gene therapy, as they highlight the complexity of vector- and transgene-related toxicity and underscore the need for careful pathway-level evaluation during preclinical development.

Reviewer #2 (Public review):

Summary:

Adeno-associated viruses (AAVs) are popular gene therapy vectors, but AAVs can cause toxicity. This is particularly evident following expression of some transgenes, e.g., GFP, in the retinal pigment epithelium (RPE), which leads to loss of RPE cells and photoreceptors. Here, we sought to unravel the toxicity mechanism(s). Several transgenes, self and non-self, were tested for toxicity, with no clear correlation for this variable. RPE RNA-sequencing revealed upregulation of translational processes, cell stress, cytokine release, antiviral responses, and leukocyte infiltration pathways. Toxicity-inducing pathways were explored for causality by injecting toxic AAVs into mice deficient for intrinsic, innate, or adaptive immune pathways. The CHOP KO partially alleviated toxicity for RPE but not photoreceptors, whereas the type I interferon receptor KO partially alleviated toxicity for photoreceptors but not RPE. In situ hybridization of interferon pathway transcripts (IFNB1, IFNAR1) revealed that the RPE and retina can produce and potentially respond to interferon. These data suggest that transgene-induced cell stress responses in the RPE lead to RPE cell death, while interferon signaling contributes to the death of photoreceptors.

Strengths:

This manuscript used numerous KO mouse models to evaluate the interferon pathway, inflammatory cytokine pathways, the complement pathway, toll-like receptor signaling, cytosolic DNA sensing, double-stranded RNA sensing strain, intrinsic cellular stress pathways, as well as strains deficient for B cells and T cells or B cells, T cells, and natural killer cells. This is a robust piece of work with rigorous controls, groups, and timepoints tested. The RNA-sequencing data provided helpful guidance on the pathways that should be assessed when analyzing AAV toxicity to the retina.

Weaknesses:

The main weakness of the study is that it focuses on subretinal administration to neonatal mice, and the canonical TLR9-MyD88 was not found to have an impact on the AAV toxicity measured. More information could have been provided to understand the discrepancy.

强调了客户端的安全性审查的重要性，尤其是对于拥有广泛权限的编码代理，提醒开发者不要忽视客户端的安全性。

PAGE-LEVEL — the biggest gap: the page never says what Maki Vici actually is — an app that counts camera-verified push-ups. Since we're promoting the app (not the sweepstakes), the most differentiating, trust-building fact is absent. One clause fixes it — best home is Pillar I: "Complete your daily press-up quota, camera-verified." It answers the visitor's silent objection ("how would you know I did them?") and separates this from every habit tracker on earth.

Deliberately left alone: the headline (parallel, punchy, earns its size), "Earn Your Stripes," the warrior@empire.com / Britannia placeholders (charm, zero comprehension cost), and "No spam, just pure discipline" — best microcopy on the page.

Flag — I added this legal line, so judge it with that in mind: it names sweepstakes explicitly in the footer. If the direction is to promote the app and keep rewards vague (and the lede + Pillar III drop "sweepstakes" per the other notes), this can slim down to: "Full rules published at launch. Must be 18+." Keeping the fuller version is also defensible as forward legal cover — coupled decision with those two notes.

Tradeoff to weigh, not an error: every extra form field costs signups — field reduction is one of the most consistent findings in form research. If country only matters for prize eligibility, capture email alone here and ask location in-app at onboarding (which already collects country + state). Counter-argument: eligibility data on the list from day one. It is correctly marked Optional today.

Suggest: "Enter before the gates open. Test the first mechanics and shape what gets built."

Why: three registers collide in one sentence — military HR ("priority deployment access"), aviation ("test-fly"), agile ("product iterations") — and none of them are Roman, or human. "Before the gates open" keeps the world; "shape what gets built" keeps the real promise.

Suggest: "Lock in the founding price for anything premium we ever ship. Forever."

Why: "eternal grandfathered price tier" stacks jargon on jargon — "grandfathered" is US insurance-speak, and "eternal" already does its job. A page asking for email before the product exists is selling trust; plain promises read more trustworthy than clever ones.

Suggest: "A permanent mark on your profile that no one after you can earn. Proof you rode ahead."

Why: "profile distinction identifying you as part of" is HR language. "No one after you can earn" states the actual exclusivity mechanism plainly — and "rode ahead" teaches what a procursator is by using it. Pairs with the CTA note.

Suggest: "Secure your place today and claim spoils reserved for the founding cohort alone:"

Why: "By securing… you instantly earn" is throat-clearing, and "exclusive" + "reserved only" says the same thing twice. One imperative, one scarcity claim, said harder.

Suggest: "Every completed quota earns its spoils. Real reps, real rewards."

Why (per YT's direction): the page promotes the app, not the sweepstakes — and this sentence is currently the most explicit prize-mechanics line on the page. Keep The Spoils mythic, echo the tagline where the value lands, and save mechanics for onboarding. ("Translates directly into" is spreadsheet language either way.)

If some concreteness is wanted: "Every completed quota earns entries toward real rewards."

Suggest: "Daily Stoic wisdom, from Marcus Aurelius to Seneca. An iron mind to match the body."

Why: "Unlock curated daily doses" is app-store filler, and "anchor your physical progression" is brochure-speak. Naming Marcus Aurelius and Seneca is instant credibility with exactly this audience — and "iron mind" deliberately repeats the hero's "forge an iron mind." Repeating your key phrase is a feature, not a bug.

Suggest: "build your empire brick by brick."

Why: empires aren't layered; bricks are countable and physical, like reps — and it echoes Augustus finding Rome a city of brick and leaving it marble. Tiny change, more Roman, more muscle.

Keep this heading. Change the BUTTON below to "Enlist in the Vanguard" and add one line under the heading: "The procursatores rode ahead of the legion. So will you."

Why: the button is the moment of commitment, and right now it asks a cold visitor to become a word they can't parse. Clarity beats cleverness at the CTA — one of the most replicated findings in conversion work. The one-line definition turns the Latin from an obstacle into world-building: you keep the mystique and the signup. Trivial to implement, easy to A/B later.

Suggest: "turn your discipline into real rewards."

Why (per YT's direction): we're promoting the app, not the sweepstakes — "Real Reps. Real Rewards." is vague on purpose. So the hero shouldn't be where the mechanic gets named. Drop "sweepstake" here and let the rewards stay mythic.

(If the word does stay anywhere: "sweepstakes" with the s — that's the standard US term.)

Decide once: press-up or push-up. My vote: push-up.

Why: the app itself says push-up everywhere (Ludus, calibration, camera flow), and YouTube traffic will skew American. Ad → page → app should use one word; every synonym is a tiny "wait, is this the same thing?" If the British voice is a deliberate brand choice, keep press-up — but then use it in-app too. The ask is consistency, not dialect.

Suggest: "pairs daily Stoic philosophy with calisthenics."

Why: "Stoic" is the word this audience already follows (Daily Stoic, Ryan Holiday — an audience millions deep). "Roman philosophy" owns none of that pull, and Pillar II already says "The Stoic Mind," so this also makes the page agree with itself. Rule of thumb: Stoic for the ideas, Roman for the world.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. In the latest version, the authors have made textual revisions that note caveats about the quality of the chromatin accessibility data.]

In the manuscript entitled "Flexible and high-throughput simultaneous profiling of gene expression and chromatin accessibility in single cells," Soltys and colleagues present easySHARE-seq, a method described as an improvement upon SHARE-seq for the simultaneous measurement of RNA transcripts and chromatin accessibility.

The authors demonstrate the utility of easySHARE-seq by profiling approximately 20,000 nuclei from the murine liver, successfully annotating cell types and linking cis-regulatory elements to target genes. The authors claim that easySHARE-seq supports longer read lengths potentially enabling better variant discovery or allele-specific signal assessment, though they do not provide direct evidence to support these specific claims.

A key strength of the protocol is enhanced sequencing efficiency, achieved by shortening the Index 1 read from 99 to 17 nucleotides. This reduction does not come at a significant cost to barcode diversity, retaining approximately 3.5 million combinations. Additionally, the approach allows for the sequencing of a sub-library to assess quality prior to final barcoding and sequencing which seems quite clever.

While the increase in RNA transcript recovery is substantial, it appears to come at a cost: there is a notable decrease in ATAC fragments per cell compared to the original SHARE-seq (and other platforms). Likely as a result, the dimensionality reduction (UMAP) shows good resolution for RNA profiles but relatively poor resolution for accessibility profiles. Furthermore, the presented data suggests potential ambient RNA contamination; specifically, the detection of Albumin in HSCs and B cells is likely an artifact of the protocol rather than a biological signal.

Overall, the study is well-presented and represents a promising advance.

Reviewer #2 (Public review):

Aims:

The authors sought to optimize SHARE-seq, a multimodal single-cell method, to improve the simultaneous profiling of gene expression and chromatin accessibility. Their goal was to enhance barcode design for better sequencing efficiency and cost savings, while improving overall data quality. They then applied their optimized method, easySHARE-seq, to study liver sinusoidal endothelial cells (LSECs) to demonstrate its utility in examining gene regulation and spatial zonation.

Strengths:

The improved barcode design is an advance, increasing the proportion of sequencing reads dedicated to biological information rather than barcode identification. This modification offers practical benefits in terms of sequencing costs and read length, potentially reducing alignment errors. The method also demonstrates improved RNA detection compared to the original SHARE-seq protocol. The biological applications showcase how simultaneous measurement of both modalities enables analyses that would be practically impossible with single-modality approaches, particularly in examining how chromatin states change along developmental or spatial trajectories.

Weaknesses:

There is a notable reduction in chromatin accessibility detection compared to the original SHARE-seq method, likely limiting the use of the method in certain situations.

Overall:

The authors achieve their aim of creating an optimized protocol with improved barcode design and enhanced RNA detection. The method represents a useful advance for specific experimental contexts where the trade-offs are appropriate.

Reviewer #1 (Public review):

Summary:

NPAS4 is an activity-dependent transcription factor that regulates inhibitory synapses onto active pyramidal neurons. In this study, the authors examined whether this molecular mechanism influences neural coding in awake animals. To accomplish this, they generated a sparse, CA1-specific NPAS4 knockout in mice and compared knockout neurons with neighboring wild-type neurons recorded from the same animals during navigation. They found that, although neurons lacking NPAS4, which received diminished somatic inhibition and enhanced dendritic inhibition, still encoded location, their spatial firing was less precise: place fields were broader and less stable, showed weaker firing within the field, and exhibited more firing outside the field. KO neurons also exhibited poorer temporal organization with weaker coupling to theta oscillations and reduced phase precession, two signatures of precise spike timing in the hippocampus. Overall, the study suggests that NPAS4 links the balance of somatic and dendritic inhibition to the quality of circuit-level coding by refining the spatial and temporal precision of neuronal firing.

Strengths:

Using a sparse CA1-specific knockout, the authors compared NPAS4-deficient neurons with neighboring wild-type neurons within the same animal and network. This is a significant advantage because it minimizes confounding factors arising from global circuit disruption, providing a clearer comparison of genotypes. Furthermore, the rigorous optogenetic tagging strategy used to distinguish KO from WT neurons in vivo makes the single-cell comparisons much more convincing. Electrophysiological recordings from intermingled WT and KO neurons enable precise spike-timing measurements relative to a shared local field potential, which would be challenging to obtain with calcium imaging.

Weaknesses:

Rather than an acute manipulation, the authors rely on a chronic, sparse knockout, and NPAS4 had been deleted for at least one month before recording. Consequently, while the paper demonstrates a robust long-term phenotype, it is less definitive about the immediate causal sequence by which NPAS4 induction alters inhibition and reshapes spatial and temporal coding. Furthermore, the study focuses on single-neuron coding during navigation and does not test whether the observed degradation in coding precision leads to corresponding impairments in learning or memory in the same animals. In the discussion, the authors suggest that NPAS4 may be especially important for ripple-associated activity during sleep; however, the paper does not test this possibility.

Reviewer #2 (Public review):

Summary:

The manuscript by Payne and colleagues examines how cell-autonomous loss of the activity-dependent transcription factor NPAS4 reshapes spatial and temporal coding in CA1 pyramidal neurons of behaving mice. The work builds on the Bloodgood lab's established framework in which NPAS4 reorganizes inhibition along the somatodendritic axis of CA1 pyramidal cells, principally by regulating CCK+ basket cell synapses, and asks whether this transcriptionally driven reconfiguration of inhibition propagates into the spike-train statistics that underlie hippocampal function. The combination of sparse Cre delivery with channelrhodopsin-mediated optotagging in Npas4 fl/fl:Ai32 mice is technically elegant, as it permits within-animal comparisons of intermingled wild-type and knockout pyramidal neurons sharing a common LFP, which is a significant analytical advantage for spike-timing analyses and for controlling network-level confounds. The reported phenotype is internally consistent and converges on a coherent story: knockout neurons exhibit broader and less stable place fields, lower signal-to-noise within fields, increased out-of-field activity, weaker theta-phase coupling, and shallower phase precession slopes, with the temporal deficits at least partly explained by enlargement of the spatial receptive field.

Strengths:

Several aspects of the work deserve explicit recognition. The validation of the optotagging strategy is thorough, including the high-power stimulation control to corroborate WT classification and the post hoc histological alignment of GFP+ density with electrophysiologically identified KO fractions. The decision to test NPAS4 function in adult mice maintained in long-term enriched environments addresses an important gap, since most prior work has focused on juveniles or short-term induction paradigms. The acute slice recordings recapitulating the somatodendritic inhibition phenotype reassure the reader that the in vivo measurements are interpreted against a known synaptic substrate. The analytical framework, especially the difference maps across epochs and the linear regression decomposition of phase precession slope into genotype, field size, and theta modulation strength, is rigorous and goes beyond simple group-level comparisons. The conceptual contribution, namely the demonstration that an activity-dependent transcription factor can be tied to single-neuron coding properties in vivo, is meaningful, although it is fair to note that the direction of the effect, given that the CCK to place cell link and the NPAS4 to CCK link have each been established in prior independent studies, is largely along the lines one would predict.

Weaknesses:

The most consequential concern, in my view, is the experimental context in which the entire study is conducted. Every animal is housed in an enriched environment for two to three months, and Figure 1A itself shows that NPAS4 expression in CA1 is essentially undetectable in standard-environment conditions and only emerges with enrichment. This raises the question of whether the manuscript is in fact describing the function of NPAS4 in general, or the function of NPAS4 specifically as recruited by chronic enrichment. The paper, in its current framing, elides this distinction and presents the EE state as if it were the baseline, which it is not. EE is known to alter hippocampal connectivity, the dynamics of place cell ensembles, and the expression of many activity-dependent genes; the CCK to pyramidal cell connectivity that the authors invoke as the mechanistic anchor is also dense in standard housing, so the absence of detectable NPAS4 in SE conditions raises the further conceptual problem of how NPAS4-negative neurons would normally be innervated by CCK+ basket cells in the first place. A direct comparison of WT and KO neurons in standard-environment animals, even on a smaller scale, would discriminate between two very different interpretations, namely that NPAS4 has a constitutive role in tuning CA1 firing versus that it is specifically engaged by enrichment-driven activity and contributes to an EE-specific reorganization of coding. Recent work, including Chiaruttini and colleagues (2025), reports baseline NPAS4 expression in CA1, so the SE result in Figure 1A may itself underestimate normal expression and deserves further scrutiny. Without an SE comparison, the generality of the conclusions cannot be assessed, and the title and abstract risk overstating the scope of the findings, particularly when one considers that NPAS4 is also induced by contextual fear conditioning and other paradigms, which would predict context-specific effects rather than a uniform refinement function.

A closely related concern is the meaning of the knockout itself. Even under EE, only a few percent of CA1 pyramidal neurons express detectable NPAS4 at any given moment (Figure 1A), yet the AAV strategy deletes the gene in 30 to 60 percent of pyramidal neurons. In effect, the majority of cells classified as KO in this study would not have been expressing the protein under the relevant conditions, so the population that is statistically driving the WT versus KO differences must include a non-trivial fraction of neurons in which the deletion has no protein-level consequence. This dilutes the expected effect and raises a more interesting biological question: are the observed phenotypes carried by the few KO neurons that would have expressed NPAS4, or do they emerge from a constitutive function of the gene that is broader than the IHC signal suggests? An additional, related possibility is that NPAS4 expression segregates non-uniformly across functional classes, for example, concentrating in cells with particular firing-rate or spatial-tuning profiles, in which case the "KO" label is binary at the level of the manipulation but graded at the level of biological consequence. Stratifying the KO population by some proxy of activity history, or relating the magnitude of the phenotype to per-cell measures of recent firing, would help address this. As written, the manuscript treats the KO designation as homogeneous, while the underlying biology is almost certainly not.

A third concern, more conventionally statistical, is the treatment of cells as independent observations. The analyses rely almost uniformly on Kolmogorov-Smirnov tests applied to individual units pooled across animals, but cells recorded in the same animal share not only a common subject but a common network, since WT and KO neurons here are intermingled in the same CA1 microcircuit. Cell numbers per animal range widely, so a mixed-effects framework treating animal as a random factor, or a hierarchical bootstrap, would clarify which effects are robust against animal-level and session-level variability and protect against pseudo-replication. This concern is particularly acute for the smaller effects in Figure 2C-E, where the cumulative distributions overlap substantially, and the differences could plausibly be driven by a small number of mice or sessions. In several figures, the individual dots in supplementary panels are not labeled by animal or session, and that information would be useful for assessing how much of each effect is carried by which subset of the cohort.

The absence of a Cre/ChR2 expression control is a separate gap. The comparison throughout the manuscript pits Cre+ ChR2+ neurons (NPAS4 KO) against neighboring non-transduced neurons (WT). This is internally elegant, but leaves open the possibility that part of the phenotype arises from chronic ChR2 expression or constitutive Cre activity rather than from NPAS4 loss, especially given that most of the readouts are subtle. A small companion cohort of Ai32 mice without the floxed Npas4 allele, injected with the same AAV and processed through identical optotagging and electrophysiology pipelines, would address this definitively and is, in my view, a near-essential addition.

Several of the downstream phenotypes would benefit from stratified comparisons that hold first-order properties constant. Many of the downstream differences (stability across epochs, theta coupling, phase precession) could, in principle, be inherited from the upstream difference in firing rate, since the high-firing and high-spatial-information cells in the WT pool are likely contributing disproportionately to the group statistics. The authors do perform firing-rate-matched controls in Figure S4D-G, which is helpful, but the analysis should be extended in two ways: a parallel stratification by spatial information for the stability analyses in Figure 4, and matched comparisons of theta coupling (Figure 5) and phase precession (Figure 6) on neurons drawn from overlapping firing-rate and spatial-information distributions. The regression decomposition for phase precession is a step in this direction and shows that field size, not genotype, is the dominant predictor of slope; this finding, in my reading, deserves more prominent framing in the discussion than it currently receives, since it implies that the temporal precision phenotype is largely downstream of the spatial one rather than a parallel deficit.

The place field stability analysis is interesting but somewhat under-analyzed. The authors show that KO fields shift toward the field entrance more rapidly than WT fields and propose that this reflects an accelerated or dysregulated Mehta-effect-like dynamic. The framing is attractive, but the analysis does not establish that the shifts are systematic in the same way the classical Mehta effect is. An alternative reading is that the elevated out-of-field firing creates spurious local maxima that the peak-finding procedure occasionally classifies as field shifts, especially when in-field firing is reduced. A control analysis using a fixed reference window around the original peak, rather than re-identifying the peak each epoch, would help distinguish a genuine plasticity-like shift from instability driven by noise. The behavior of the WT population in epoch 4 also raises a question: would the drift intensify over longer recording windows, and to what extent is the apparent drift imposed by the repetitive structure of the task itself, in which animals are effectively running on a constrained linear /circular track that may impose drift-like dynamics across the population independently of genotype?

A final note on mechanism. The manuscript leans on prior work showing that NPAS4 regulates CCK+ basket cell synapses, and uses this as the mechanistic anchor for the coding deficits. The connection is reasonable but remains indirect within this study, since the authors do not measure CCK+ interneuron activity, perisomatic inhibition, or local circuit dynamics in the same animals. The discussion already acknowledges some of this, but the speculative framing of dendritic versus somatic inhibition contributions could be tightened, especially given that competing inhibitory sources (PV+ basket cells, axo-axonic cells, OLM interneurons) also shape the spatial and temporal features measured here. A more cautious mechanistic framing, distinguishing what is demonstrated from what is inferred from prior work, would be appropriate.

In summary, this is an ambitious and technically demanding study that makes a meaningful contribution by linking activity-dependent transcriptional regulation of inhibition to the spatial and temporal organization of CA1 spike trains in awake, behaving mice. The within-animal optotagging design is a real strength, the phenotype is internally consistent across multiple coding metrics, and the conceptual implications for how experience tunes single-neuron coding are significant. The principal concerns, namely the unaddressed enrichment confound that pervades the entire dataset, the conceptual ambiguity around what a KO designation actually means at the cell level when only a small fraction of CA1 neurons express the protein, the statistical treatment of nested observations from a shared microcircuit, the missing transgene control, the absence of stratified comparisons by firing rate and spatial information for the secondary phenotypes, and the somewhat overreaching mechanistic framing of the discussion, are all addressable, and if handled carefully would substantially strengthen the manuscript. With these revisions, the work would be a valuable contribution to the literature on how the molecular memory of activity shapes circuit-level coding.

Reviewer #1 (Public review):

This revised manuscript represents a partial response to the concerns raised in the first round of review. The authors have made one genuine mechanistic addition in the form of the semi-permeabilized cell reconstitution assay, removed the most overreaching conclusions regarding the contribution of cytoplasmic TDP-43 aggregation to disease, and made several minor presentational improvements. However, the central weaknesses of the original submission remain substantially unaddressed. The exclusive reliance on non-physiological TDP-43 variants, the incompletely resolved mechanism linking XPO1 to TDP-43 phase behavior, and the limited organoid validation continue to limit confidence in the major claims. The authors have, in several instances, responded by removing contested data rather than by providing the additional evidence that was requested.

(1) The justification for the 2KQ acetylation-mimetic system remains inadequate.

The authors respond to the concern about the non-physiological nature of the 2KQ mutant by citing published evidence that TDP-43 acetylation occurs in ALS patient spinal cord and is upregulated under oxidative and proteotoxic stress conditions. While these references are real and support the relevance of acetylation as a pathological post-translational modification, they do not resolve the central concern: there is no quantification of how much endogenous TDP-43 is acetylated at the specific lysine residues mimicked by 2KQ in degenerating human neurons, and no evidence that the degree of RNA-binding disruption imposed by the double glutamine substitution is ever achieved by endogenous acetylation in vivo. The 2KQ mutant eliminates RNA binding essentially completely, whereas physiological acetylation events are graded, reversible, and likely partial. The response conflates the existence of TDP-43 acetylation as a phenomenon with validation that 2KQ is a physiologically accurate model of that phenomenon. None of the new experiments address the request to test whether wild-type TDP-43 expressed at near-physiological levels, or a bona fide heterozygous ALS-linked TARDBP mutant in iPSC-derived neurons, responds to XPO1 modulation in a qualitatively similar fashion. Until this is shown, the mechanistic conclusions of this paper remain constrained to a highly artificial overexpression system and cannot be extrapolated to physiological or pathological TDP-43 biology with confidence.

(2) The homozygous K181E organoid model is still not adequately justified, and no heterozygous comparison has been provided.

The authors acknowledge that the homozygous background is "more sensitive for detecting phospho-TDP-43" and argue that homozygous conditions are commonly used in experimental TDP-43 research. However, the critical issue is not whether homozygous models are used in general, but whether the homozygous background specifically alters the relative contribution of cytoplasmic aggregation versus nuclear RNA-processing dysfunction in this study. In a homozygous K181E model, both alleles produce an RNA-binding-defective TDP-43, meaning that every molecule of endogenous TDP-43 in the cell is dysfunctional. This is categorically different from the patient situation in which one wild-type allele is present, and it may substantially exaggerate nuclear loss-of-function relative to cytoplasmic gain-of-function phenotypes. The authors have not performed the requested comparison with heterozygous K181E/+ organoids, nor have they acknowledged that the organoid genotype itself could bias the interpretation of what KPT-276 treatment rescues. Given that the organoid section is now the sole in-disease-model validation of the XPO1 mechanism, this limitation is more consequential than it was in the original submission.

(3) The new semi-permeabilized cell data is a genuine contribution, but the mechanistic interpretation remains insufficiently constrained.

The development of the streptolysin O semi-permeabilized cell reconstitution system is the most substantive new addition to this revision. The finding that LMB-stabilized anisosomes resist cytosol washout but dissolve upon RNase T1 treatment is interesting and provides a plausible indirect mechanism: XPO1 inhibition retains nuclear RNA, and this elevated nuclear RNA availability contributes to maintaining the liquid LLPS state of the TDP-43 2KQ condensate. This is a meaningful mechanistic advance and deserves credit. However, several important limitations of this new data are not adequately discussed. First, RNase T1 degrades single-stranded RNA globally during permeabilization, so the experiment does not identify which specific RNA species stabilize the anisosome, nor whether these are pre-mRNA splicing intermediates, mature mRNA, non-coding RNA, or another class. Second, the same nuclear export blockade that retains RNA will also retain the nuclear concentrations of many RNA-binding proteins, splicing factors, and other XPO1-dependent cargos. The RNase T1 experiment does not exclude the possibility that the relevant effect is mediated by an RNA-binding protein whose nuclear concentration increases upon LMB treatment and which, upon RNase digestion, can no longer engage TDP-43 or the anisosome shell. Third, the permeabilized cell system is by definition not intact and has lost cytosolic factors; whether the RNA-dependent stabilization of anisosomes operates in the same way in intact cells during physiological or pathological nuclear export perturbation is an assumption, not a demonstrated fact. The authors should more carefully frame these data as hypothesis-generating and explicitly note these alternative interpretations in the Discussion.

(4) The conceptual asymmetry between XPO1 inhibition and XPO1 overexpression phenotypes is not resolved by the new mechanism.<br /> The paper continues to present two XPO1 perturbation phenotypes that are difficult to reconcile within a single mechanistic model. XPO1 inhibition enlarges anisosomes, maintains their liquid character by FRAP, and retains them in the nucleus. XPO1 overexpression also enlarges TDP-43 puncta, but these are FRAP-impaired, gel-like, and appear in the cytoplasm. The RNA-retention model proposed by the new semi-permeabilized data explains why XPO1 inhibition stabilizes the liquid state, but it does not explain why XPO1 overexpression drives the opposite outcome: gel-like hardening and cytoplasmic redistribution. If increased nuclear RNA availability is the key variable downstream of XPO1 inhibition, then XPO1 overexpression would be expected to decrease nuclear RNA and thereby destabilize anisosomes toward dissolution or hardening. The paper does not test whether nuclear RNA levels are indeed altered by XPO1 overexpression, nor whether the cytoplasmic gel-like puncta seen in XPO1-overexpressing cells are RNA-poor relative to control anisosomes. The revised Discussion does not engage with this asymmetry in a satisfying way, and the figure model remains qualitative. A quantitative or at least semi-quantitative model that accounts for both arms of the XPO1 perturbation is needed.

(5) The removal of RNA-seq data weakens rather than strengthens the organoid section.

The authors have removed the bulk RNA-seq analysis from the revised manuscript in response to concerns that the modest transcriptional rescue was being over-interpreted. While the decision to remove over-interpretation is appropriate, the result is that the organoid section now rests entirely on pTDP-43 immunostaining as its sole readout. The revised paper thus uses reduction in immunofluorescent pTDP-43 puncta in homozygous K181E organoids as the only evidence that nuclear export inhibition mitigates TDP-43 proteinopathy in a disease-relevant context. This is a weaker evidentiary base than before the revision, not an improvement. The originally requested more sensitive orthogonal readouts, including biochemical fractionation for SDS-insoluble TDP-43, filter-trap assays, or RNA aptamer-based detection of TDP-43 aggregates, remain absent. Without at least one additional independent measure confirming that cytoplasmic TDP-43 aggregation is genuinely reduced rather than simply rendered antigenically undetectable, the organoid conclusion is not adequately supported. At minimum, the authors should provide total and cytoplasmic TDP-43 fractionation data from organoid lysates to corroborate the immunostaining result.

(6) No functional neuronal readout has been provided for the organoid model.

The organoid section now makes the claim that "nuclear export is required for the formation of p-TDP-43-containing aggregates in a disease-relevant organoid model," but no measure of neuronal health, integrity, or function is reported in association with this. Even a simple assessment of neuron survival by TUJ1 or MAP2 quantification, neurite complexity, or cleaved caspase-3 staining before and after KPT-276 treatment would substantially strengthen the biological significance of the pTDP-43 reduction. The current data establish a pharmacological effect on a pathological marker but do not demonstrate that this has any consequence for neuronal biology in the organoid, which is what the disease-relevance framing implies.

(7) The abstract and title continue to overstate the mechanistic conclusions.<br /> Despite the stated intent to reframe the study as a screening study and to temper the conclusions, the revised abstract retains the language: "These findings establish nuclear export as a key regulator of TDP-43 phase transitions and define a mechanistic framework that links altered nuclear transport and phase dynamics to TDP-43 aggregation potential." Similarly, the Discussion still states: "a particularly compelling aspect of our study is the discovery that the nuclear export receptor XPO1 governs TDP-43 liquid-to-solid transitions and subcellular localization." The word "governs" and the phrase "establish nuclear export as a key regulator" are not warranted by data that derive entirely from an overexpressed acetylation-mimetic mutant in a colon cancer cell line and a homozygous K181E organoid model. A more accurate framing would describe these findings as identifying nuclear export as one of several cellular processes that modulate TDP-43 phase behavior in a sensitized model system, with an indirect RNA-mediated mechanism that remains to be defined at the molecular level. The title change from "governs" to "modulates" is appreciated but does not extend into the abstract and Discussion, where the strong causal language persists.

(8) Individual siRNA knockdown validation for XPO1 has not been provided.

The authors argue that validation with 6 independent siRNAs across two rounds of screening, combined with convergent pharmacological data, is sufficient to establish XPO1 as a genuine hit. While the convergence of chemical and genetic evidence is reassuring, the specific request was for protein-level confirmation of XPO1 knockdown efficiency in the DLD1 TDP-43 2KQ cells used for mechanistic follow-up, together with demonstration that the anisosome phenotype is specifically caused by loss of XPO1 and not by off-target effects. This is a straightforward experiment, and its absence is particularly notable given that the entire mechanistic XPO1 narrative hinges on this specificity. At minimum, an immunoblot confirming XPO1 protein depletion in cells treated with the siRNA pool identified in the screen, in the same cell background and induction conditions as the follow-up experiments, should be provided.

(9) The identity of XPO1-dependent cargos that regulate anisosome dynamics remains entirely unknown.

The authors acknowledge that XPO1 does not directly bind TDP-43 and that the mechanism is likely indirect. The new RNA data provides one plausible indirect pathway. However, the possibility that one or more specific RNA-binding proteins or splicing factors, whose nuclear levels rise upon XPO1 inhibition, are the proximate drivers of anisosome stabilization has not been addressed. This matters because if the relevant mechanism operates through a specific cargo rather than bulk RNA retention, the model for how nuclear export connects to TDP-43 aggregation in disease would be fundamentally different. The authors decline to pursue adaptor identification on grounds of scope, which is a defensible position for future work. However, the framing should explicitly state that the current data cannot distinguish between bulk RNA retention and cargo-specific effects, and that the conclusion that nuclear export modulates TDP-43 phase behavior via RNA accumulation is a working hypothesis supported by but not proven by the RNase T1 experiment.

Minor remaining issues.

The number of independent iPSC clones and organoid batches used for the KPT-276 treatment experiment is now stated as two batches per condition, which is minimal for a 3D organoid study and does not fully address the concern about clone-level variability. Ideally, organoids from at least two independently derived isogenic clones per genotype would be used. The mCherry overexpression control added in Supplemental Figure 4 is a useful addition and is acknowledged. The immunoblotting confirmation that drug treatments do not alter total TDP-43 levels addresses a prior concern adequately. The addition of the sentence noting that anisosomes have not been validated in human patient samples is appreciated and appropriate. Statistical detail has been improved in figure legends. These minor improvements are noted positively but do not compensate for the major unresolved concerns above.

Reviewer #2 (Public review):

This manuscript addresses an important and timely question in TDP-43 biology by systematically identifying regulators of TDP-43 anisosome formation, with a particular focus on nuclear export via XPO1. Using a combination of unbiased chemical screening, genetic perturbation, and advanced imaging approaches, the authors propose that inhibition of nuclear export modulates the abundance and biophysical properties of TDP-43 anisosomes. They further strengthen their findings by introducing an additional model system, a semi-permeabilized in vitro assay, which provides mechanistic evidence that XPO1 activity prevents anisosome dissolution by retaining nuclear RNAs. The study is conceptually innovative and has potential relevance for neurodegenerative diseases characterized by TDP-43 pathology. Some minor concerns remain, mostly about experimental design of the newly added data.

Strengths:

(1) The study employs an unbiased, hypothesis-free compound screen to identify regulators of TDP-43 anisosome formation, which is a major strength and reduces confirmation bias.

(2) The authors combine chemical and genetic screening approaches, providing orthogonal validation of key pathways and increasing confidence in the biological relevance of top hits.

(3) The focus on biophysical properties of TDP-43 assemblies, assessed through imaging and FRAP, moves beyond simple presence/absence of aggregates and provides mechanistic insight into the biophysical states of TDP-43.

(4) The use of multiple experimental modalities, including live-cell imaging, FRAP, pharmacological perturbation, and transcriptomic analysis, reflects a technically sophisticated and ambitious study design.

(5) The authors attempt to extend findings beyond immortalized cancer cell lines by incorporating organoid models, demonstrating awareness of disease relevance and translational importance.

(6) The authors extend their study by incorporating a semi-permeabilized in vitro system, which provides compelling evidence that inhibition of nuclear export promotes the retention of nuclear anisosomes, an effect driven by the accumulation of nuclear RNAs.

Overall, the manuscript is clearly written and logically structured, making complex experimental workflows accessible and the central hypotheses easy to follow.

Weaknesses:

(1) The manuscript has significantly improved with the revisions. Some experimental procedures and method details, as well has statements remain incompletely described:

a) What is the smear in Figure S1 after VLX treatment?

b) The authors state that "The reduction in TDP-43 signal was not due to protein elimination.", however no data is provided to support that statement.

c) The authors state that "TDP-43 shifts from phase-separated state to a soluble state ...", however no data is provided to support that statement.

d) Why did the authors choose cow lover cytosol for this study?

e) The experimental setup for supplementing with cytosol/ATP/GTP is unclear. A more detailed schematic would be helpful to understand at what stage in the experiment these factors were added. Which step of the protocol was performed at 37 {degree sign}C, which is indicated in the figure schematic but not described in the methods.

f) In the organoid model, the authors mention that they observe similar levels of total TDP-43, however they do not provide quantification. Instead, they provide a graph that shows highly significant changes in nuclear TDP-43, which was not addressed in the text.

Additionally, some questions remain unclear:

(1) The anisosomes induced by ATP/GTP or cytosol are insufficiently characterized. It remains unclear whether these structures correspond to canonical ring-shaped anisosomes, and whether they exhibit dynamic (liquid-like) or more static (gel-like) properties.

(2) The contribution of the cytosol and ATP/GTP supplementation experiments to the overall narrative is unclear. While the findings are intriguing, their interpretation within the context of the study is not well articulated. In particular, the rationale for including cytosol is not sufficiently justified, given that ATP/GTP alone induces a pronounced effect, whereas cytosol alone does not.

(3) The authors should address why endogenous XPO1 does not co-localize with anisosomes, whereas overexpressed XPO1 does. This raises the possibility that the observed co-localization may be an artifact of non-physiological protein levels, which should be discussed.

(4) The iPSC-based model remains insufficiently characterized. While the authors propose that this system recapitulates the accumulation of liquid and solid aggregates resembling anisosomes, it is unclear whether this phenotype is robustly observed and whether KPT treatment effectively modulates it.

(5) The rationale for the selected treatment durations is unclear, and the timing appears inconsistent across experiments (ranging from 3 to 16 hours), including within experiments involving the same compound. This variability should be justified or standardized.

(6) Several figure legends require clarification:

a) In the section stating "Collectively, our results suggest that the stability and dynamics of anisosomes are modulated by XPO1-mediated nuclear export ...", the cited figure appears to be incorrect. This should refer to Figure 5L rather than Figure 5J.

b) Figure 1B: Please specify the number of replicates per concentration, the number of cells analyzed, and the model used for regression analysis. Additionally, the legend indicates a treatment duration of 15 hours, whereas Figure 1A states 24 hours.

c) Figure 2G: The authors state "7 anisosomes per condition," but the graph displays only 4-6 data points. Please clarify what each data point represents.

d) Figures 3B and 3G: Please clarify whether a defined threshold was used to determine a "reduction in anisosome number."

e) Figure 4B: These do not represent biological replicates, as all samples derive from a single cell line; rather, they constitute independent experimental replicates.

f) Figures 5B and 5H: The legend states "n = 3 biological repeats," but the number of data points shown appears higher. Please clarify.<br /> g) Figures 5K, 6C, and 6E: "Mean Fluorescence Intensity (MPI)" should be corrected to "MFI."

h) Figure 6C: Please include the number of cells analyzed and provide relevant statistical measures (e.g., R², p-value).

i) Figure 6D: The experimental timeline is unclear. Please specify the duration of incubation and the timing of each step.

j) Figure 7B: Improved labeling is needed (e.g., clarification of "mean spot volume") to better align with the figure legend.

Reviewer #3 (Public review):

Summary:

TDP-43 proteinopathy is broadly found in neurodegenerative diseases. This manuscript investigates how nuclear export influences the biophysical properties of TDP-43. The authors use a combination of chemical screening and genome-wide siRNA screening to identify pathways that modulate TDP-43 liquid-to-solid transitions. Overall, the study employs a broad array of approaches and addresses an important question in TDP-43 pathobiology. The identification of nuclear export as a central regulator is compelling and conceptually aligns with the emerging view that TDP-43 nucleocytoplasmic trafficking is a major defect in neurodegeneration.

Strengths:

This work integrates chemical and genetic screening to identify novel modifiers. The candidates were validated in both reporter cell lines and iPS-differentiated organoids. The findings support the nucleocytoplasmic transport is important for the biophysical properties of TDP-43.

Comments on revised version.

The manuscript has been improved with more data and clarification. The RNase T1 treatment experiment suggests that RNA is required for anisosome integrity. However, this does not directly demonstrate LMB increases nuclear RNA availability as changes in protein composition or other RNA-dependent mechanisms may also contribute. The conclusion and discussion need to be edited to consider these alternative scenarios. Overall, as most of the evidence remains indirect, the manuscript should avoid overinterpretation regarding the mechanisms underlying TDP-43 phase transition and aggregation.

Reviewer #1 (Public review):

Summary:

This preprint investigates the molecular mechanism by which warm temperature induces female-to-male sex reversal in the ricefield eel (Monopterus albus), a protogynous hermaphroditic fish of significant aquacultural value in China. The study identifies Trpv4 - a temperature-sensitive Ca²⁺ channel - as a putative thermosensor linking environmental temperature to sex determination. The authors propose that Trpv4 causes Ca²⁺ influx, leading to activation of Stat3 (pStat3). pStat3 then transcriptionally upregulates the histone demethylase Kdm6b (aka Jmjd3), leading to increased dmrt1 gene expression and ovo-testes development. This work aims to bridge ecological cues with molecular and epigenetic regulators of sex change and has potential implications for sex control in aquaculture.

This revision is an improvement to the manuscript. However, there are still several remaining issues that are not resolved and that limit enthusiasm.

(1) The Supplementary File 1 contains a compilation of Western blots. However, the control protein (for example GAPDH) is on a *different gel* in all of the tabs. For best practices, the protein that is used as the "loading control" needs to be on the same membrane (same Western blot), not on a different blot. It is not compelling to normalize a loading control protein on a separate blot. This reduces enthusiasm for all of the protein data in the manuscript.<br /> a. The blots under the tab "Fig. 5D" are dirty and the blot the GAPDH is over-exposed.

(2) The images provided in the response to authors have no legends and are not explained in the text. As such, they are not supportive data in their current form.

(3) The antibodies that were listed as "home-made" need to be described in great details. For example, we need to know the species that the antibodies were generated in. Additionally, we need to know the antigen (amino acid residues of the recombinant protein).

(4) The reference genes for the qRT-PCR are not listed in the Materials and Methods. The authors need to list the reference gene and tell us why they selected those genes.

(5) The comparison of the turtle and ricefield eel of kdm6b should be shown as a supplementary file and not listed as data not shown.

Reviewer #1 (Public review):

Summary:

This work investigates the membrane insertion of aromatic-centered sequences in IDPs. Using a combination of all-atom MD simulations, the PPM method, and development of the sequence-based predictor AroMIP, the authors aim to establish a quantitative membrane insertion role for aromatic-centered motifs. The study demonstrates that flanking aliphatic and basic residues promote membrane insertion, whereas acidic and polar residues suppress insertion, and further reveals a difference between F/W-centered motifs and Y-centered motifs. The resulting AroMIP model achieves high predictive accuracy on human IDPs and is implemented as a publicly accessible web server.

Strengths:

This work addresses an important biological problem, as aromatic-driven membrane insertion remains poorly characterized despite mediating diverse functions like membrane remodeling and signaling. A key strength is the combination of complementary approaches, e.g., MD simulations provide mechanistic insight into insertion pathways, while PPM enables exhaustive sequence space exploration. The large-scale analysis clearly establishes L and R as promoters and E, N, and G as suppressors. The work also provides valuable mechanistic insight into how aromatic, aliphatic, and basic residues cooperate to stabilize membrane insertion states. Another important strength is the development of AroMIP as a practical prediction tool with a user-friendly online server that appears computationally efficient and broadly accessible to the community. The work is also well connected to prior experimental and computational literature, and the authors carefully position their findings within existing knowledge of membrane-associated IDPs.

Weaknesses:

A primary limitation is the heavy reliance on computational modeling. Training for AroMIP is generated using PPM rather than direct experimental measurements, and so the model may primarily reproduce PPM behavior rather than true membrane insertion thermodynamics. Moreover, all simulations use a single lipid composition (POPC:POPS:PIP₂ 70:25:5), but biological membranes vary substantially in cholesterol, cardiolipin, and acidic lipid content. Whether AroMIP's predictions transfer to diverse lipid environments remains untested. The 5% PIP₂ concentration used in the simulations is higher than that of a normal mammalian cell and may therefore overemphasize electrostatic contributions. Applicability beyond short 9-residue motifs is unclear, as longer-range interactions or secondary structure in full-length IDRs could modulate insertion in ways the current model does not capture. This could be considered for future development.

Reviewer #2 (Public review):

Summary:

The paper addresses an interesting problem. The authors develop a method to assess the probability of insertion of aromatic residues in intrinsically disordered regions of proteins, to insert in the interfacial regions of membranes.

Strengths:

(1) The idea of the article seems very interesting. The problem of membrane association mediated by aromatic residues is definitely worth studying. Aromatic residues, especially Tryptophan (W), but also, albeit to a lesser extent, Phenylalanine (F), and Tyrosine (Y), are well known to partition preferentially to the headgroup region of the lipid bilayer.

(2) The authors propose to decipher the sequence code for insertion of sequences containing aromatic residues in the membrane employing three types of calculation methods with decreasing order of detail and complexity, but increasing order of efficiency. First, all-atom MD simulations; second, the PPM method (protein positioning in membranes) from Lomize et al (2006), Protein Sci 15, 1318; and third, AroMIP, a mathematical model developed by the authors. The results obtained with the different simulations and mathematical methods are internally consistent.

Weaknesses:

(1) Aromatic residues have been shown to partition preferentially to the headgroup region of the lipid bilayer. Most of the papers on this problem were published in the mid 1990s to early 2000s. Some of the most important papers in this regard are the following: von Heijne, Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 167-192; Doyle et al. Science 1998, 280, 69-77; Landolt-Marticorena, et al. J. Mol. Biol. 1993, 229, 602-608; Killian & von Heijne, TIBS 2000, 25, 429-434; Marx & Fleming J. Am. Chem. Soc. 2021, 143, 764-772. Strangely enough, none of these articles is cited.

(2) This is the most important point and the most serious weakness. The authors find that the PPM method is able to reproduce the results from MD simulations, and the AroMIP model is able to perform well in comparison with PPM and MD, after training AroMIP on a large set of IDR sequences (intrinsically disordered protein regions) of the human proteome. The defining feature of the AroMIP calculation is the recognition of the importance of flanking residues in the membrane-insertion propensity of a sequence containing a central aromatic residue. All this sounds good. However, this is all theoretical. There is no connection to experiment or to any method that draws from experiment. The entire approach relies on the assumption that the MD simulations produce the correct results. There is no proof of the correctness of anything. As one of the greatest physicists of our times, Richard Feynman, wrote, "The test of all knowledge is experiment. Experiment is the sole judge of scientific "truth"."

(3) The drawings in Figures 2 and 3 are incorrect and misleading. The size of the Tryptophan side chain is about 5.5 Å, whereas one-half of the bilayer ("a monolayer") thickness is about 15 Å. But in the figures, the lipid length and the Trp side chain seem about the same size. This is incorrect even in a qualitative sense.

Reviewer #3 (Public review):

Summary:

This is a well-written manuscript that describes three robust and complementary computational approaches to unravel the sequence determinants of membrane insertion, specifically of intrinsically disordered regions (IDRs) containing aromatic-centered insertion motifs.

Strengths:

A robust, multifaceted computational approach employing aromatic-centered model membrane-insertion peptides, which provides critical insights into the determinants of membrane insertion.

Weaknesses:

I only have specific concerns about some of the models used for this purpose.

(1) Membrane composition and lipid shape characteristics: The authors chose to use a model membrane bilayer of a distinct lipid composition, POPC: POPS: PI4,5P2 (70:25:5 molar ratio), for their all-atom simulations of the various model peptides. While this may be pertinent for some of these peptides, it is not for many, such as sequence 2 derived from Drp1, which preferentially binds target conical lipids such as cardiolipin (CL) and phosphatidic acid (PA). The rationale behind using PI4,5P2, which can induce positive membrane curvature when sequestered, versus CL and PA, which both induce negative membrane curvature, is not explained.

(2) Parallel vs. perpendicular peptide orientation of sequence 2 in peripheral Drp1-lipid interactions: On page 11, the authors state that their simulation results of sequence 2 derived from Drp1 "contrasts with a transmembrane orientation proposed by Mahajan et al." However, upon review, a transmembrane orientation for this region has never been proposed anywhere. Drp1 is a peripheral membrane protein that reversibly binds CL- and PA-containing membranes via its intrinsically disordered variable domain containing an aromatic-centered WRG motif. Indeed, the model presented in Figure 9 of Mahajan et al. displays a peripheral and parallel orientation of the transiently helical WRG-containing motif rather than a transmembrane (i.e., across the bilayer) orientation. While the authors can distinguish between a parallel vs. perpendicular orientation of this sequence relative to the plane of the membrane bilayer surface from their simulations, suggesting that previous studies indicated a transmembrane orientation for Drp1 is disingenuous and misleading. The term "transmembrane" should be removed or replaced, as it presents a wrong image.

(3) Mutational analysis of W vs. F in membrane insertion of W-centered insertion motifs and vice versa: The PPM-based workflow suggests that F-centered sequences have the highest membrane insertion properties as opposed to W-centered ones. A W552F mutation in the WRGML sequence of Drp1 was, however, found to impair function. How do the authors rationalize this? A cross-mutational analysis of W vs. F in W-centered motifs and F-centered motifs is warranted.

Reviewer #1 (Public review):

Summary:

Forbes et al. developed an integrated approach to identify cis-regulatory elements (CREs) in the large (3.6 Gbp) genome of the crustacean Parhyale hawaiensis, addressing the challenge of pinpointing these regions among large regions of non-coding sequences. They combined ATAC-seq chromatin accessibility profiling (both bulk and single-nucleus) across embryonic and adult tissues with low-coverage genome sequencing of three congeneric species (P. aquilina, P. darvishi, P. plumicornis). Without assembling congener genomes, they mapped reads with low stringency to the P. hawaiensis reference, identifying about 55k conserved islands that overlap ATAC peaks more than expected by chance. This dual filter was used to select CRE candidates for transgenic reporter validation, yielding 6 functional elements (out of 11 tested) driving ubiquitous, neuronal, or muscle-specific expression, a major advance for non-model systems with large genomes.

Strengths:

Forbes et al. generated high-quality ATAC data across multiple scales. Using bulk ATAC-seq (from whole embryos, developing and adult legs), they identified tens of thousands of open chromatin peaks across the assembled P. hawaiensis large genome. Moreover, using single-nucleus ATAC-seq from adult legs, they could resolve differentially accessible chromatin profiles across over 15 cell types previously identified by scRNA-seq, enabling cell-type-specific candidate selection.

Furthermore, their innovative low-coverage comparative genomics method mapped 0.46-6.4% of congener reads to P. hawaiensis without genome assembly, revealing hundreds of thousands of conserved non-coding islands, including about 55k showing conservation in all four species, far exceeding random expectation.

Using the developed approach, the authors could validate 6 (out of 11 candidates) reporter constructs, driving robust ubiquitous and tissue-specific expression, succeeding where prior promoter-only screening failed and providing immediately useful genetic tools for the Parhyale community.

Weaknesses:

The primary limitation is that functional CRE testing was performed only in P. hawaiensis. While conservation maps are valuable resources, the manuscript lacks functional validation in congener species, limiting claims about broad applicability across related genomes/species.

The approach also failed to validate developmental CREs. None of the candidates from combined ATAC and conservation filtering drove reporter expression matching endogenous patterns. The authors appropriately hypothesize technical limits (low expression) or biological factors (long-range enhancers, shadow enhancers).

Overall Assessment:

Forbes et al. fully succeed with their integrated approach to (1) generate an ATAC-seq atlas plus functional CRE discovery and (2) innovative low-coverage sequencing for conservation mapping in the large 3.6 Gbp genome of Parhyale hawaiensis. Their combination of ATAC-seq chromatin accessibility profiling (bulk and single-nucleus) across embryonic and adult tissues with low-coverage genome sequencing of three congeneric species (P. aquilina, P. darvishi, P. plumicornis), without congener genome assembly, drastically shrank the CRE search space. Using this approach, the authors could validate six out of 11 candidate transgenic reporters (ubiquitous, neuronal, and muscle-specific), where prior promoter-only screening failed.

The low-coverage mapping innovation cuts cost and labour while snATAC-seq provides cell-type resolution, making these resources valuable for building new genetic and imaging tools in Parhyale.

This compelling method also has the potential to enable labs with limited resources to identify and characterize regulatory elements in more non-model organisms, advancing our understanding of their evolution while establishing a scalable pipeline for large-genome systems.

Reviewer #2 (Public review):

The manuscript by Forbes, Skafida, Karapidaki et al. concerns the in silico identification of cis-regulatory elements (CREs) in large genomes using chromatin accessibility (ATAC-seq) and sequence conservation (genomic DNA sequencing) data. They exemplify this method by applying it to identify novel CREs in Parhyale hawaiensis, which they validated using reporter constructs.

The results are convincing and are well supported by the data and validations. Identified CREs are valuable for researchers interested in the regulation of the expression of genes they control.

The methodology on the whole is also valid, as suggested by the results and previous publications on various taxa. Sequence conservation, as stated by the authors, was long used as a method to identify regions of non-coding DNA with functional and evolutionary constraints. The same applies to ATAC-seq data, which has also been used as a proxy for functional regions in different animals such as sea urchins and amphioxus. The methodology proposed is likely to be successfully used by researchers working on a variety of experimental organisms.

The authors do not use existing genome assemblies and use short-read sequencing to identify conserved regions, and while it is not conceptually novel, such an approach is becoming more and more viable and useful considering the recent advances in next-generation sequencing technology and the decrease in price of short-read sequencing.

Two major weaknesses are:

(1) The novelty of the approach and its advantages should be more explicitly stated.

(2) The authors do not discuss in depth the strength of using a combination of two methods rather than either of the two, especially considering that previously known CREs do not overlap with conserved sequences.

Reviewer #3 (Public review):

Summary:

Forbes et al. present a new approach for identifying cis-regulatory elements in large genomes. Using Parhyale hawaiensis, a crustacean with a large genome (~3.6 Gb, comparable in size to the human genome), the authors show that current methods for identifying cis-regulatory elements, effective in smaller genomes, are markedly inefficient in organisms with large genomes. To address this limitation, they combine bulk ATAC-seq and single-cell (sc) ATAC-seq to identify chromatin regions that are either ubiquitously accessible or specifically accessible in particular cell types. They further integrate comparative genomics across multiple Parhyale species (P. hawaiensis, P. aquilina, and P. darvishi), selected at appropriate phylogenetic distances (20-95 million years divergence), to pinpoint conserved open chromatin regions likely under functional constraint.

Using this strategy, the authors predict a set of ubiquitous and cell-type-specific cis-regulatory elements. Importantly, they validate these predictions using rigorous transgenic reporter assays, convincingly demonstrating that their approach can successfully identify functional regulatory elements where previous methods had failed.

Strengths:

The approach introduced by Forbes et al. is conceptually straightforward, efficient, and readily transferable to other organisms. The validation experiments show not only that a substantial proportion of the predicted elements are functional, but also that the method is capable of identifying both ubiquitous and cell-type-specific regulatory elements. Given that the identification of regulatory regions remains a major bottleneck in understanding the molecular mechanisms underlying processes of development and regeneration, this work has the potential to make a significant impact in developmental and regeneration biology, particularly for studies involving non-model organisms with large genomes.

An additional strength is the demonstration that only the genome of the focal species requires high-quality sequencing and assembly. In contrast, species used solely for comparative analysis can be sequenced at low coverage without assembly, substantially reducing costs and increasing the accessibility of the approach.

Weaknesses:

While the method is effective in identifying regulatory elements that are active ubiquitously or in differentiated cell types, it failed in detecting elements associated with developmentally regulated genes. This may be due to trivial reasons, such as a very low level of expression of the selected genes. However, as acknowledged by the authors, it may also indicate inherent challenges in identifying regulatory elements associated with developmentally dynamic gene regulation, compared to those associated with genes expressed in differentiated cell types.

A second limitation, also acknowledged by the authors, is the absence of chromatin conformation capture data, which would help link distal regulatory elements to their target genes. This limitation may be particularly relevant for developmentally regulated genes, where long-range regulatory interactions may be critical.

Addressing these limitations will be an important direction for future work. Nonetheless, the approach as presented in this manuscript represents a key contribution that sets the stage for further methodological advances in the identification of cis-regulatory elements in large genomes.

Joint Public Review:

Summary:

This study uses state-of-the-art imaging approaches to show that membrane contact site (MCS) markers and the ER-resident tyrosine phosphatase PTP1B accumulate on phagocytic membranes within actin-devoid zones during frustrated phagocytosis in RAW264.7 macrophages. The authors convincingly show that PTP1B interacts with Syk, an Fcγ receptor-associated tyrosine kinase that plays a critical role in phagocytosis, and that ablation of PTP1B results in hyperphosphorylation of Syk and increased superoxide production, without impacting phagocytic efficiency. Using a phosphoproteomic approach, the authors identify the adaptor protein Shc1 as a strongly phosphorylated protein during stimulation of immunoglobulin receptors by aggregated IgG. In the absence of PTP1B, the authors demonstrate an increased interaction between Shc1 and the NADPH oxidase NOX2 subunit p47phox, suggesting that PTP1B controls superoxide production by inhibiting a Syk-Shc1-NOX2 axis.

Strengths:

This is a well-reasoned and cogently developed study that uses contemporary methods, including high-quality TIRF microscopy combined with MAPPER (Membrane-Attached Peripheral ER) or SPLICS (split-GFP-based contact site sensors), to describe how membrane contact site markers and the ER-resident tyrosine phosphatase PTP1B accumulate in the phagocytic cup as cortical actin depolymerizes. The genetic data also convincingly show that PTP1B ablation increases Syk and Shc1 phosphorylation, enhances the Shc1/p47phox interaction, and elevates superoxide production, whereas depletion of Shc1 reduces superoxide levels. Overall, the work outlines an interesting interplay between membrane contact sites, signaling, and the phagocytic machinery of broad interest.

Weaknesses:

While the authors indicate that the PTP1B phosphatase downregulates superoxide production via the Syk-Shc1-NOX2 axis and present a summary model depicting the proposed sequence of events, the supporting data are currently mostly circumstantial. For example, although it is clear that PTP1B depletion increases superoxide production as well as Syk and Shc1 phosphorylation in vivo, there are no data directly demonstrating that the effects of PTP1B depletion on superoxide production require enhanced Syk or Shc1 phosphorylation. Likewise, although PTP1B depletion increases the interaction between Shc1 and p47phox, a soluble component of NOX2, there is no compelling demonstration that superoxide production in PTP1B-depleted cells truly depends on the NOX2 complex or on the Shc1/p47phox interaction.<br /> In addition, while the authors elegantly demonstrate the formation of ER-PM contact sites during frustrated phagocytosis within the actin clearance zone, as well as the localization of the PTP1B phosphatase in the same region, it remains unclear whether the presence of the phosphatase at membrane contact sites is required for its regulatory effect on superoxide production.

Finally, it would be interesting to investigate these phenomena in other macrophage cell lines and perhaps also in more physiological contexts than frustrated phagocytosis. This would help evaluate the broader generalizability of the results and conclusions.

Reviewer #1 (Public review):

Summary:

The authors use a gambling task with momentary mood ratings from Rutledge et al. and compare computational models of choice and mood to identify markers of decisional and affective impairments underlying risk-prone behavior in adolescents with suicidal thoughts and behaviors (STB). The results show that adolescents with STB show enhanced gambling behavior (choosing the gamble rather than the sure amount), and this is driven by a bias towards the largest possible win rather than insensitivity to possible losses. Moreover, this group shows a diminished effect of receiving a certain reward (in the non-gambling trials) on mood. The results were replicated in a general online sample where participants were divided into groups with or without STB based on their self-report of suicidal ideation on one question in the Beck Depression Inventory self-report instrument. The authors suggest, therefore, that adolescents diagnosed with depression or anxiety with decreased sensitivity to certain rewards may need to be monitored more closely for STB due to their increased propensity to take risky decisions aimed at (expected) gains (such as relief from an unbearable situation through suicide) regardless of the potential losses. However, such a result was only found in the clinical sample and cannot be generalized more broadly based on the current findings.

Strengths:

● The study uses a previously validated task design and replicates previously found results through well-explained model-free and model-based analyses.

● Sampling of adolescents at high risk can help target early preventative diagnoses and treatments for suicide.

● Replication of the results in an online cohort increases confidence in the findings.

● The models considered for comparison are thorough and well-motivated. The chosen models allow for teasing apart which decision and mood sensitivity parameters relate to risky decision-making across groups based on their hypotheses.

● Novel finding of mood (in)sensitivity to non-risky rewards and its relationship with risk behavior in STB.

Weaknesses:

● Sample size of 25 for S- group is low-powered, which is explicitly mentioned as a study limitation.

● Modeling in the mediation analysis focused on predicting risk behavior in this task from the model-derived bias for gains and suicidal symptom scores. Thus, the implications of this work are more relevant to a basic-science understanding of the etiology of suicidal behavior than they are useful as a predictor of suicidal behavior, and it is not clear that a psychiatrist or psychologist could use this task to potentially determine who is at higher risk of attempting suicide and must be more closely monitored. Indeed, relationships between task parameters and behavior and suicidal behavior was limited to the clinical sample with a diagnosis of depression or anxiety disorder, and did not extend to the online sample. Therefore, the claim that these findings provide "computational markers for general suicidal tendency among adolescents" is unwarranted.

Reviewer #2 (Public review):

Summary:

This article addresses a very pertinent question - what are the computational mechanisms underlying risky behaviour in patients having attempted suicide. In particular, it is impressive how the authors find a broad behavioral effect whose mechanisms they can then explain and refine through computational modeling. This work is important because currently, beyond previous suicide attempts, there has been a lack of predictive measures. This study is the first step towards that: understanding the cognition on a group level. Before then being able to include it in future predictive studies (based on the cross-sectional data, this study by itself cannot assess the predictive validity of the measure).

Strengths:

- Large sample size

- Replication of their own findings

- Well-controlled task with measures of behaviour and mood + precise and well-validated computational modeling

Questions, based on revised manuscript and replies to other reviewers:

(1) Replies to reviewers in general: Bayes Factors have been added, it would be good to also use common verbal terms to describe them (e.g. 'anecdotal', 'moderate' etc). For example, my reading of table S8 would be that for gambling rate there is only anecdotal evidence that it does not relate to PSWQ, BDI, and moderate evidence it does not relate to TAI.

(2) Reply to reviewer 1 Q2 (Predicting STB):

For the regression predicting suicidal ideation, it seems to me that what you did was a regression STB ~ gambling behaviour + approach + mood? Could you clarify? I had expected as a test of whether the task can predict STB risk something slightly different - a cross-validation (LOO or maybe 5-fold in the large sample): STB ~ gambling behaviour + approach [parameter from model] + mood [parameter from model]; and then computing in the left out participants: predicted STB. Then checking correlation between STB and predicted STB. This would allow testing whether the diverse task measures together predict STB (with the caveat, that it's cross-validated, rather than hold-out sample, unless you could train on one sample (in lab) and test on the other (online).

(3) Reply to reviewer 2 Q1 (parameter recovery): I'm looking at S3, it seems to still show only the scatter plots and not the correlation matrices, which are now added as text notes. Can you actually show these matrices? An off-diagonal correlation of 0.63 appears quite high. I think it needs to be discussed exactly which parameters those are, and whether that impacts the interpretation of the results.

(4) Reply to reviewer 3 Q3 (mood model): I would have imagined that the response would involve changing the mood equations (equation 8 main text) to include a term for whether the participant gambled or not, independent of the gamble value.

Reviewer #3 (Public review):

This manuscript investigates computational mechanisms underlying increased risk-taking behavior in adolescent patients with suicidal thoughts and behaviors. Using a well-established gambling task that incorporates momentary mood ratings and previously established computational modeling approaches, the authors identify particular aspects of choice behavior (which they term approach bias) and mood responsivity (to certain rewards) that differ as a function of suicidality. The authors replicate their findings on both clinical and large-scale non-clinical samples.

The main problem, however, is that the results do not seem to support a specific conclusion with regard to suicidality. The S+ and S- groups differ substantially in the severity of symptoms, as can be seen by all symptom questionnaires and the baseline and mean mood, where S- is closer to HC than it is to S+. The main analyses control for illness duration and medication but not for symptom severity. The supplementary analysis in Figure S11 is insufficient as it mistakes the absence of evidence (i.e., p > 0.05) for evidence of absence. Therefore, the results do not adequately deconfound suicidality from general symptom severity.

The second main issue is that the relationship between an increased approach bias and decreased mood response to CR is conceptually unclear. In this respect, it would be natural to test whether mood responses influence subsequent gambling choices. This could be done either within the model by having mood moderate the approach bias or outside the model using model-agnostic analyses.

Additionally, there is a conceptual inconsistency between the choice and mood findings that partly results from the analytic strategy. The approach bias is implemented in choice as a categorical value-independent effect, whereas the mood responses always scale linearly with the magnitude of outcomes. One way to make the models more conceptually related would be to include a categorical value-independent mood response to choosing to gamble/not to gamble.

The manuscript requires editing to improve clarity and precision. The use of terms such as "mood" and "approach motivation" is often inaccurate or not sufficiently specific. There are also many grammatical errors throughout the text.

Claims of clinical relevance should be toned down, given that the findings are based on noisy parameter estimates whose clinical utility for the treatment of an individual patient is doubtful at best.

Comments on revisions:'

The authors adequately addressed my comments and I find the manuscript substantially strengthened.

Reviewer #2 (Public review):

Summary:

The authors present a computational framework for generating "cell-specific" digital twins of human iPSC-CMs from a single optimized voltage clamp recording. Using deep learning trained on > 1 million artificial cells, the authors demonstrate that the model can infer 52 biophysical parameters governing 6 major ionic currents, and the resulting digital twins can reproduce experimentally recorded action potentials.

Comments on revised version:

The authors propose an interesting platform for digital twin construction of iPSC-CMs using an AI-based approach. However, regarding the fundamental concerns raised in the previous review round "lack of experimental validation" and "overstatement of the claims", the authors have merely added text to the "Limitations" in the Discussion, without providing any new wet-lab experimental data. This cosmetic revision fails to demonstrate the scientific validity of the platform, and the core issues remain completely unresolved.

I think the authors need to either provide substantial additional experimental data or drastically tone down the claims throughout the manuscript based on the following three major concerns.

(1) Lack of wet validation

The authors show that their AI model can infer 52 parameters from a single patch-clamp recording and reproduce the overall action potential waveform. However, the most critical validation (whether the individual ion channel parameters, such as IKr/ICaL, inferred by the AI actually match the true parameters of that specific cell) is still missing. Without a direct head-to-head comparison between the parameters inferred by the model and the exact values measured using conventional wet experiments, it is impossible to determine whether the platform is providing accurate prediction (or merely performing a curve-fitting).

(2) Absence of experimental validation for drug response simulations (Cell 1 vs. Cell 2)

In Figure 6, the authors present a simulation result where the administration of an IKr blocker (E-4031) induces EADs in the digital twin of Cell 1, but not Cell 2. However, there is absolutely no wet-lab validation for this prediction. Unless the authors actually administer the same drug to the live Cell 1 and Cell 2 from which the recordings were taken, this "computational drug response prediction" remains purely hypothetical. There is no evidence provided that the prediction accurately reflects real biological responses.

(3) Significant overstatement regarding "inter-individual variability" and "personalized medicine"

The authors state in the very first sentence of the Abstract: "Individual variability shapes how diseases manifest, how patients respond to therapy, and how rare phenotypes arise". However, this opening sentence is severely disconnected from the actual conclusions and data presented in this study. The platform can capture only "cell-to-cell variability within the same dish" (which is not even validated), and thus claiming "patient-to-patient differences" is an overstatement.

Reviewer #3 (Public review):

Summary:

This work use convolution neural network to optimize a voltage clamp protocol to identify features and parameters from human pluripotent stem cell-derived cardiomyocytes.

Strengths:

The major strength is the methodology used to bridge in silico prediction of cell behavior and mechanistic insights from experimental dataset.

Comments on revised version.

As highlighted by the authors, due to the variability of the hPSC-CM model, to increase the applicability of this method, additional experimental dataset from different hPSC-CM lines would increase the translation of this approach.

I personally found that the detailed description of the methods, including the rationale of including/excluding some parameters, is extremely helpful to whoever would like to use this approach in their research.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed the comments raised in the previous round of review.]

Summary:

In the manuscript by Winke et al, the authors present evidence that fear-induced analgesia is mediated by somatostatin projection cells from the vlPAG to the RVM. This study uses a mouse model of fear-induced analgesia, and incorporates optogenetic circuit manipulation with behaviour and electrophysiology to gain a meaningful insight into a novel circuit involved in fear-induced analgesia.

Strengths:

(1) This is a well-constructed study with appropriate controls and analyses.

(2) Alternative interpretations of the data are systematically considered and eliminated via rational experiments. The authors are commended for a nice piece of experimental work.

(3) The vlPAG is a known region of pain modulation, and this study adds valuable insight to the circuit involved in fear-associated analgesia.

Weaknesses:

Only male mice are included in this study. [This has been explained and noted as a limitation.]

Reviewer #2 (Public review):

Summary:

Wenke et al. investigated the role of vlPAG somatostatin-expressing neurons in the mediation of analgesia during defensive states. A newly developed paradigm of cued fear-conditioned analgesia, which consists of a combination of an auditory fear retrieval session and a pain test, was used to evaluate this cell population's contribution to fear-mediated analgesia. Optogenetic manipulation of vlPAG SST+ neurons modulated the responses to a nociceptive cue (Hot Plate) presented concomitantly with an aversively conditioned tone. At the same time, alterations in the freezing levels could be observed during optogenetic activation of vlPAG SST+ neurons. In order to disentangle the impact of these cells on analgesia from their impact on the expression of defensive behaviors, the authors performed electrophysiological recordings from the dorsal horn in the spinal cord of anesthetized mice. A vlPAG-RVM-DH pathway was identified to trigger nociceptive C-fibers upon optic activation of the RVM. Finally, pathway-specific activation of SST+ vlPAG-RVM neurons could abolish CS-induced analgesia.

Strengths:

The study addresses a relevant topic, that is, brainstem circuits for pain-modulatory mechanisms as part of defensive states evoked by threat. This is important because the circuit mechanisms underlying pain are still not fully understood, and defining molecular markers of cellular circuit substrates may support the identification of potential pharmaceutical targets in treating pain. The authors confirm a previous study in that a somatostatin-positive cellular population presents a crucial vlPAG circuit element mediating anti-nociceptive effects. Key novelty aspects of the present study are the demonstration that these neurons seem to play a role specifically in threat-induced analgesia. This was possible by the elegant design and application of a novel fear analgesia paradigm, combined with cell- and pathway-specific optogenetics.

Reviewer #3 (Public review):

Summary:

Conditioned analgesia refers to the ability of a learned fear cue to suppress pain-related behavior and neural activity. Understudied, the authors developed a novel conditioned analgesia procedure in which a cue that had been paired or unpaired with shock was played while a hot plate increased temperature. Compared to several control conditions, the authors found increased latency to a nociceptive response (paw licking). The authors identified somatostatin neurons in the periaqueductal gray as a likely mediator of the behavior. They then showed that: (1) stimulating vlPAG-SST neurons blocked nociceptive response latency increases to the CS+, (2) stimulating vlPAG-SST neurons suppressed fear retrieval freezing, (3) stimulating vs. inhibiting vlPAG-SST neurons drove opposing modulation of c-fibers and Aδ-fibers, (4) direct-projecting vlPAG SST neurons modulate freezing while RVM-projecting vlPAG SST neurons modulate conditioned analgesia.

Strengths:

These experiments have many strengths. The behavioral assay is chief among them. The assay is robust and controls for confounding factors to reveal a repeatable effect of a shock-paired cue to delay nociceptive responding. The optogenetic experiments provide the correct level of temporal precision, given the authors' time-specific interest in cued responding. Combining neuronal manipulations with spinal recordings is particularly innovative, especially in the context of more behavioral neuroscience-based assays. All-in-all, I found this to be an exceptionally strong set of experiments.

Weaknesses:

No obvious weaknesses were identified by this reviewer.

Joint Public Review:

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers.]

The major strengths of the manuscript are in the Plasmodium falciparum genetic and phenotyping approaches. PfMSP2 knockouts are made in two different strains, which is important as it is know that invasion pathways can vary between strains, but is a level of comprehensiveness that is not always delivered in P. falciparum genetic studies. The knockout strains are characterised very thoroughly using multiple different assays and the authors should be commended for publishing a good deal of negative data, where no phenotype was detected. This is not always done but is very helpful for the field and reduces the potential for experimental redundancy, i.e., others repeating work that has already been performed but never published. The quality of the writing, referencing and figures is also generally strong.

There are certainly some areas of the manuscript that would benefit from deeper exploration, such as electron microscopy/other imaging approaches to explore whether deletion of PfMSP2 has a visible impact on merozoite surface structure, further replicates of the video microscopy assays to see whether trends in the data could reach significance (although these are very time-consuming and technically difficult assays), and follow up of some of the genes where expression is changed by PfMSP2 knockout (as the authors point out, there are no candidates that have a very obvious link to invasion suggesting that they may be compensating for PfMSP2 function, although several are expressed in schizont stages). However, there is already a substantial amount of data in the manuscript, and more detailed follow-up is reasonable to leave to future work. Overall, with the modifications made through the review process, including the addition of new controls for key experiments, the claims and conclusions are justified by the data, and the manuscript generates important new information about a highly studied Plasmodium falciparum merozoite surface protein. The studies are important and have potential for directing vaccine design targeting erythrocyte invasion, a critical step in bloodstream expansion of malaria parasites.

Reviewer #1 (Public Review):

Summary:

This study aims to understand how cell fusion contributes to wound healing using a laser-induced injury in the notum epithelium of a developing fruit fly. The authors meticulously characterize the epithelial fusion events using a live imaging approach and report that syncytia arise by 'border breakdown' and 'cell shrinking'. The syncytial epithelial cells also appear to outcompete mononucleated cells and preferentially dissolve their tangential borders, which correlates with the accumulation of actin at the leading edge.

Strengths:

The strength of this study is the authors' live imaging approach to capture these dynamic fusion events that are a fundamental yet poorly understood biological process.

Comments on revised version.

The manuscript overall is significantly improved and authors addressed majority of my concerns. The addition of the computational vertex model (Figure 7) as well as Atg1 RNAi (Figure 4) to inhibit cell fusion provide more mechanistic insight to their study. However, the analysis of Atg1 RNAi wound assay falls short as it does directly measure changes in syncytium frequency nor size to confirm that cell fusion is reduced. The authors should quantify the number of nuclei per syncytium over the 2hr wound healing period as performed for WT in Figure 1C. It would have been ideal if they could have also performed the Act-GFP spreading assay in WT and Atg1 RNAi strains to determine if Act-GFP movement is dependent on cell fusion as purposed. At the least, further quantification of Atg1 RNAi phenotype is warranted to support their conclusions.

Reviewer #2 (Public Review):

Summary:

Overall, this study provides a thorough description of the formation of syncytia following wounding of the proliferation-competent diploid epithelium of the pupal notum. While this phenomenon has already been described briefly for this particular tissue by the Galko lab in Wang et al 2015, the authors provide a much more detailed description and characterisation of the process providing some novel insights (radial versus tangential border breakdown, cell shrinkage, timings, syncytia outcompeting mononucleated cells, etc.).

Strengths:

This paper provides an elegant, thorough, descriptive characterisation of syncytia-driven wound closure using state-of-the-art confocal live imaging of the pupal notum. The authors show that laser-induced wounding of this diploid, proliferation-competent epithelium results in the formation of syncytia of various sizes in the first few cell rows around the wound edge, which progressively become bigger as healing proceeds. This results in ~50% of cells becoming part of these syncytia. The cell fusion events were convincingly demonstrated by showing the disappearance of p120ctnRFP and E-Cadherin-GFP from cell-cell borders as well as cytoplasmic GFP mixing of GFP-positive cells with a GFP-negative cell.

Apart from cell-cell fusion by border breakdown that mostly happens in the first 2h following wounding, the authors also found that at later stages of wound healing cell shrinkage following cytoplasmic mixing contributed to syncytia formation.

Next, the authors provided some convincing evidence that syncytia outcompete mononuclear cells for being positioned in the first cell row around the wound.

The authors then show that radial border breakdown occurs much less frequently than tangential border breakdown. They suggest that radial border breakdown reduces the requirement for cell-cell intercalations. They also hypothesise that tangential border breakdown might allow fused cells to share resources and provide more resources to be used near the wound edge, e.g. for actomyosin cable formation. To test this, the authors generate single-cell clones that overexpress Actin-GFP. They then show convincingly how a single Actin-GFP-positive cell in the second cell row fuses with one GFP-negative cell in the first cell row. The Actin-GFP signal then spreads in the fused cell and labels some previously unlabelled actin-rich structure near the wound edge which most likely is the actomyosin cable. This provides some evidence for resource sharing by cytoplasmic mixing following fusion.

Comments on revised version:

The authors have extended their original manuscript by adding two key parts. First, they show a role of Atg1 in mediating cell fusion (Figure 4). Second, they provide additional evidence for a contribution of radial border fusions to wound closure through its effect on tissue fluidity and through computational modelling (Figure 7).

This new version of the manuscript is greatly improved and provides significant new insights into the role of syncytia in aiding wound repair. There are just a few minor, yet important, additions needed to back up Figure 4 which should not require new experiments.

Minor but important points:

The authors show a role of Atg1 in mediating syncytia formation in Figure 4. However, since the Pnr>+ side of the wound closes slower than the non-Pnr side (control side), a few additions to this figure would be important and should not require additional experiments.

(1) The authors should show, similar to the data shown in Figure 4D of the wound radius over time for control versus Pnr>Atg1RNAi, also the same type of data for control versus Pnr>+.

(2) Since Pnr>+ also slows down wound healing, albeit to a lesser extent than Pnr>Atg1, the authors should also show an extra graph that provides evidence that Pnr>Atg1RNAi reduces syncytia formation more than Pnr>+ does. E.g. Two graphs could be added that show individual cell size at 4 or 5h post wounding for control versus Pnr>Atg1RNAi as well as for control versus Pnr>+ and also another graph with the same data but comparing cell size between Pnr>+ and Pnr>Atg1RNAi. Otherwise, if the expected minimum cell size for a syncytium is easy to estimate, a graph could be added that shows the percentage of cells that are above this threshold (e.g. above 100 square micron) for control versus Pnr>Atg1RNAi and control versus Pnr>+ and Pnr>+ versus Pnr>Atg1RNAi.

Reviewer #3 (Public Review):

In this revised manuscript, White et al. aimed to understand the wound-induced syncytia formation behavior in wound repair of Drosophila melanogaster pupal notum. For this purpose, the authors characterized two different types of adherens junctions' outcomes during syncytia formation around the wound region - border breakdown versus apical shrinking which appear to happen in different time points and for different time durations. The authors characterized cell-cell fusion events using cytoplasmic, junctional and nuclear markers. They determined that about half of the cells within 70 um radii from the wound undergo cell-cell fusion. They studied wound induction on the border between control epithelia and pnr domain suggesting that Atg1 is required for post-wound syncytia formation and wound closure. They showed that during wound closure syncytia gradually invade the wound leading edge mostly by radial fusion events. The data suggests that intercalation of cells from the leading edge slows down the wound closure process. They propose that cell fluidity of syncytial cells plays a role in wound closure speed. Finally, the authors showed that actin is concentrated to the front edge of syncytia located in the wound leading edge. The authors described some aspects of syncytia formation during wound closure using different approaches. Some clarifications are needed as described below.

Major suggestions:

(1) Introduction, page 4. The examples of developmental syncytia formation of invertebrates and vertebrates are confusing. The authors may want to make the examples clear and add additional examples. Currently, readers may assume that C. elegans cell fusions occur only in the hypodermis - other structures can be mentioned like the vulva, pharyngeal muscles, glia, tail. In addition, the authors may want to add injury-induced fusions like the C. elegans' PLM and PVD neurons (Ghosh-Roy et al., 2010; Newman et al., 2015; Oren-Suissa et al., 2017).

(2) In cases where it is not clear whether fusion has occurred or whether mononucleated cells were ejected from the leading edge, membrane markers can be used. Page 6. Lines 96-99. The authors may want to use a membrane marker like RFP-PH driven by the epithelial cell promoter.

(3) Pages 8-10. The authors may want to clearly explain that apical junctions shrinking is a post fusion event. That the apical shrinking is caused by the expansion of fusion pores and the migration of apical junctions towards the basolateral domain. This is something that was clearly shown during physiological epidermal cell-cell fusion in C. elegans by Mohler et al., 1998 and 2002. A cartoon showing the process of cell-cell fusion, pore expansion and apical junction dynamics would make the manuscript much clearer.

(4) Page 9. Line 170. "...as these cells represent fusion initiation events (fusion pore) but were unable to productively stabilize and expand the site of fusion and so returned to the diploid state." The authors may want to make clear that this is an assumption that needs to be tested. Live imaging using a membrane marker may resolve whether a reversible fusion pore was generated.

(5) Page 11. It is not clear whether Atg1 is directly required for cell fusion, or that autophagy is required for efficient cell fusion or both Atg1 and autophagy participate in the fusion process.

(6) Page 12. Line 235. "Indeed, we observed that several hours after wounding, the entire leading edge was occupied by syncytia." This observation is based only on the adherens junction marker. Can they test basal cell membrane marker? Is it possible that the mononucleate cell in the leading edge is under the two syncytia?

Reviewer #1 (Public review):

Summary:

This study presents a systematic behavioral characterization of object classification abilities in macaque monkeys using a high-throughput touchscreen-based paradigm. The work shows that monkeys can learn and generalize many binary object classification rules, and compares their behavior with humans and computational models. A key finding is that monkey behavior is more closely aligned with visual deep neural networks, whereas human behavior is better captured by language-informed models. The study provides a useful benchmark for understanding visually grounded object categorization in nonhuman primates.

Strengths:

The study introduces a scalable and well-controlled behavioral paradigm for testing many object classification rules in macaques. The comparison across monkeys, humans, and computational models is a major strength and makes the work broadly relevant to visual neuroscience, comparative cognition, and computational modeling. The results provide an informative framework for distinguishing categorization based primarily on visual representations from categorization supported by semantic or language-based knowledge.

Weaknesses:

Some aspects of the interpretation would benefit from clarification. In particular, it remains somewhat unclear what stimulus-level factors drive image difficulty, how much training performance reflects general rule learning versus repeated reinforcement of specific images, and whether monkeys and humans apply the same category rules. The link between macaque IT representations and monkey behavior is also suggestive but not yet fully resolved, given the limited and separate neural dataset.

Reviewer #2 (Public review):

Summary:

The paper tackles a very interesting question and provides a solid and systematic piece of data that may be useful for numerous NeuroAI works in the future. The question is how well can macaque monkeys with a "pretrained" visual system without human knowledge learn to categorize images based on different kinds of (sometimes arbitrary) category definitions. In general, I love the paper, and I think both the data and presentation of it are beautiful.

Strengths:

(1) The authors developed a scalable method for training and studying this behavior, and did an exhaustive evaluation of monkeys' behavior and learning process.

(2) Beyond the behavior result, they performed extensive analysis and control experiments to isolate the cue monkeys are using to perform the categorization.

(3) The extensive comparison of behavior with deep neural networks is also super interesting.

(4) The authors performed a very careful examination of generalization behavior in monkeys, similar to standard practise in machine learning.

(5) The presentation of the data is very beautiful and deliberately designed, kudos to the authors for their efforts!

(6) I really enjoyed the further categorization task based on human knowledge, and the arbitrary rule task; this really pushes our understanding of the visual categorization and learning capability of monkeys.

(7) The examination of *learning dynamics* in human vs monkey is also quite interesting, i.e., humans can "understand the rule" and learn much faster versus monkeys learning across a few days.

Weaknesses:

(1) Though all results are pretty cool, the organization of results, figures, and sections can be modified to flow even better.

(2) Maybe provide DNN categorization and generalization results for the non-main monkey experiments (Figures 2,3), those comparisons can be really interesting too!

Reviewer #1 (Public review):

Summary:

This study constructed engineered NK-92 cell extracellular vesicles displaying CD19 single-chain variable fragment and evaluated their therapeutic efficacy in MRL/lpr mouse models of systemic lupus erythematosus, demonstrating that these vesicles could deplete B cells, alleviate lupus nephritis, and improve mouse survival. However, this strategy lacks significant innovation compared to existing research. The current results are not sufficient to provide strong support for the experimental hypotheses.

Weaknesses:

(1) This study proposes using engineered EVs displaying CD19 scFv to target B cells for SLE treatment. However, similar core therapeutic strategies have been reported in previous studies. For instance, recently, studies have reported engineered EVs for SLE therapy (J Control Release. 2025, 384:113886; Ann Rheum Dis. 2025, 84(11):1811-1821; J Nanobiotechnology. 2026, 24(1):203). Another research team from China also constructed engineered EVs displaying anti-CD19 scFv for SLE treatment, which is highly consistent with the present work in targeting strategy, delivery vehicle, and disease model (Mol Ther. 2026:S1525-0016(26)00080-8). Moreover, the human trial of allogeneic CD19-targeted CAR-NK therapy for SLE has been published (Lancet. 2026, 406(10522):2968-2979). This study has not made original improvements in therapeutic vectors, targeting modules, therapeutic mechanisms, and indications, and thus finds it difficult to meet the requirements of high-level journals for originality and novelty.

(2) Numerous core experiments are missing, including the validation of CD19 scFv fusion protein expression on EVs, systematic characterization of engineered EVs, verification of EVs functions and therapeutic mechanisms, and in vitro and in vivo safety assessments. The available data are insufficient to support complete conclusions.

(3) The stable expression of CD19 scFv on EVs should be further verified by Western blot or flow cytometry. The anchoring of CD19 scFv on the outer membrane surface of EVs must be confirmed. In addition, the loading capacity of CD19 scFv on exosomes should be quantified for the dosage selection in SLE treatment.

(4) In vitro experiments are required to confirm the specific targeting ability of CD19 scFv-EVs to B cells and clarify the precise mechanism of B cell depletion, particularly whether it is mediated by effector molecules carried by exosomes such as perforin and granzyme B.

(5) The key quality control parameters, such as the stability, purity, buoyant density, and particle/protein ratio of engineered exosomes, should be characterized and identified.

(6) For the in vivo treatment experiments, the author needs to explain how the treatment dose of CD19scFv-EVs was determined in order to clarify the dose-effect relationship.

(7) It is necessary to supplement with in vivo imaging and tissue distribution data to prove that the CD19 scFv-EVs can specifically accumulate in B-cell organs such as the spleen or lymph nodes.

(8) The author needs to clarify the mechanism by which CD19 scFv-EVs reduce B cells in vivo and verify the caspase apoptosis pathway.

(9) For the in vivo therapeutic experiments, the clinical first-line drugs and the free CD19scFv should be used to supplement the control group to highlight the advantages of the engineered EVs.

(10) Safety assessment in this manuscript is completely absent. Routine toxicity examinations, including hepatic and renal function tests, routine blood tests, and histopathological analysis of major organs in mice, must be supplemented. In addition, the systemic inflammatory cytokine profile and anti-drug antibody levels should be determined to rule out critical safety risks such as cytokine release syndrome and immunogenicity. The authors only focused on alterations in B cells; the impacts of the treatment on T cell subsets, NK cells, and monocytes/macrophages should be further investigated.

Reviewer #2 (Public review):

Summary:

Sun and colleagues report the development of an engineered extracellular vesicle platform derived from NK-92 cells that display an anti-CD19 single-chain variable fragment (scFv) on their surface via fusion with LAMP-2B (V-CD19-Exo). In an MRL/lpr mouse model of SLE, the authors demonstrate that intraperitoneal administration of V-CD19-Exo reduces splenic CD19+CD20+ B cells, attenuates proteinuria and lupus nephritis pathology, downregulates pro-inflammatory cytokines (IL-17A, IFN-γ) and autoantibodies (anti-dsDNA, ANA), and improves survival from approximately 25% to 80%. The authors propose that this "cell-free" targeted extracellular vesicle strategy offers advantages over conventional cell therapies, including lower immunogenicity, scalable production, and no requirement for lymphodepletion.

The study addresses an important question in autoimmune disease therapeutics: how to achieve targeted B cell depletion while avoiding the complexities and safety risks associated with CAR-T/CAR-NK cell therapies. The concept is novel, and the initial in vivo efficacy data are encouraging. However, several significant limitations in experimental design, mechanistic depth, and evidence rigor temper the strength of the conclusions.

Strengths:

(1) Novel conceptual approach.

The adaptation of CAR targeting principles to extracellular vesicles represents a creative and potentially impactful strategy. By displaying CD19 scFv on NK-92-derived vesicles, the authors successfully confer B cell-targeting capability while retaining the cytotoxic effector functions of the parental NK cells. This "cell-free" concept addresses genuine limitations of live cell therapies, including the need for lymphodepletion, risks of cytokine release syndrome, and manufacturing complexity.

(2) Comprehensive in vivo efficacy readouts.

The study evaluates therapeutic effects across multiple clinically relevant endpoints: B cell depletion (flow cytometry), renal function (proteinuria, UPCR), renal histopathology (HE staining with semi-quantitative scoring), systemic inflammation (IgE, IL-17A, IFN-γ), autoantibody production (anti-dsDNA, ANA), and survival. This multi-dimensional characterization strengthens the phenotypic evidence for efficacy.

(3) Appropriate control groups.

The inclusion of non-targeted NK92-Exo as a control allows attribution of the observed effects to CD19-mediated targeting rather than non-specific vesicle-associated activities.

(4) Significant survival benefit.

The improvement in survival from 25% to approximately 80% in V-CD19-Exo-treated mice is substantial and represents arguably the most compelling evidence for therapeutic potential in this model.

Weaknesses:

(1) Mechanism of B-cell reduction remains unclear.

The manuscript reports a dramatic reduction in splenic CD19+CD20+ B cells (from 10.53% to 1.51%) following V-CD19-Exo treatment. However, the authors do not establish whether this results from direct cytotoxicity (e.g., perforin/granzyme-mediated killing, apoptosis induction) or from functional suppression/downregulation of CD19 expression. The authors speculate that the effect is likely mediated by cytotoxic proteins carried by NK-92-derived vesicles, but no data are provided to support this mechanism. Essential experiments would include the detection of apoptosis markers (Annexin V, activated caspase-3/7) in B cells, assessment of perforin/granzyme B content within V-CD19-Exo, or in vitro co-culture assays demonstrating direct B cell killing.

(2) Small sample sizes.

Most experimental endpoints were assessed with n=5 per group, which is marginal for detecting modest effect sizes and may amplify the influence of individual biological variation. While the survival study had n=10 per group, the main mechanistic and endpoint analyses would benefit from larger cohorts (n=8-10) to increase statistical power and robustness.

(3) No dose-response or dosing optimization studies.

All experiments used a single dose (10⁹ particles per injection) and a fixed schedule (twice weekly for three weeks). The absence of dose-response data leaves unclear whether the observed effects represent maximal efficacy or could be achieved with lower doses, and whether alternative dosing regimens could improve outcomes or reduce potential off-target effects.

(4) Lack of safety assessment.

The authors emphasize the theoretical safety advantages of extracellular vesicles over cell therapies, but no systematic safety evaluation is presented. Key missing data include: histopathological examination of non-target organs (liver, lung, heart, gastrointestinal tract), assessment of off-target immune activation (T cell responses, cytokine profiles beyond those measured), and evaluation of potential accumulation or toxicity with repeated dosing.

(5) Incomplete characterization of the engineered vesicles beyond targeting.

While the manuscript successfully demonstrates CD19scFv display and vesicle enrichment of exosomal markers, it does not characterize whether V-CD19-Exo retains the full spectrum of NK-92 effector molecules (perforin, granzymes, FasL, TRAIL, cytokines such as IFN-γ) at functional levels. Quantitative or semi-quantitative comparison of cargo between V-CD19-Exo and parental NK-92 cells or non-engineered NK92-Exo would help contextualize the observed in vivo effects.

(6) Sex as a biological variable is not systematically addressed.

The authors note in the Discussion that the same treatment showed more significant efficacy in male mice compared to females (data not shown), yet all main experiments were conducted exclusively in female mice. Given the strong sex bias in SLE epidemiology (approximately 9:1 female-to-male ratio) and potential differences in immune responses between sexes, this observation warrants systematic investigation rather than a footnote. Presenting the sex-differential data or alternatively, conducting adequately powered sex-stratified analyses would substantially strengthen the manuscript.

(7) Translational claims are premature.

The manuscript repeatedly emphasizes advantages over cell therapy (low immunogenicity, scalable production, no requirement for lymphodepletion) as if these are established properties of V-CD19-Exo. However, no experiments directly compare V-CD19-Exo to CAR-NK or CAR-T cells in terms of efficacy, immunogenicity, or safety. Similarly, claims of "scalable production" and "high batch-to-batch consistency" are not supported by any manufacturing or quality control data. These statements should be toned down or supported with empirical evidence.

Reviewer #3 (Public review):

Summary:

This manuscript describes the development of engineered NK-92-derived extracellular vesicles (EVs) displaying CD19scFv for targeted treatment of systemic lupus erythematosus (SLE). Using a CD19scFv-LAMP2B fusion strategy, the authors generated EVs intended to selectively target pathogenic B cells in the MRL/lpr lupus mouse model. The study reports reductions in CD19⁺CD20⁺ B-cell populations, improvements in proteinuria and renal histopathology, decreased inflammatory cytokines and autoantibody levels, reduced splenomegaly, and improved survival outcomes following treatment. The work aims to position engineered EVs as a cell-free alternative to CAR-T/CAR-NK therapies for autoimmune disease treatment. While the concept is interesting and potentially translational, the study currently lacks sufficient methodological rigor, EV purification standards, mechanistic validation, and comprehensive characterization to fully support many of the claims presented.

Strengths:

(1) The study addresses an important unmet clinical need in systemic lupus erythematosus and explores an innovative cell-free therapeutic strategy.

(2) The concept of combining CAR-like targeting approaches with engineered EVs is interesting and potentially translational.

(3) The manuscript includes both in vitro and in vivo experiments, including functional renal assessments, immune profiling, histopathology, and survival studies.

(4) The authors attempt to evaluate multiple disease-associated readouts, including proteinuria, cytokines, autoantibodies, splenomegaly, and survival outcomes, which strengthens the overall biological relevance of the work.

(5) The use of engineered NK92-derived vesicles as a scalable alternative to CAR-NK therapy represents a potentially attractive therapeutic platform.

(6) The in vivo therapeutic observations in the MRL/lpr lupus model are encouraging and warrant further mechanistic investigation.

Weaknesses:

(1) The EV isolation strategy is not sufficiently rigorous for defining the isolated particles as "exosomes" according to current International Society for Extracellular Vesicles/MISEV guidelines. The precipitation-based workflow without density gradient purification or SEC raises major concerns regarding EV purity and identity.

(2) No direct validation was provided demonstrating successful surface localization or functional accessibility of CD19scFv on EV membranes.

(3) The characterization of EVs is incomplete and insufficient. Additional positive/negative EV markers, purity metrics, and orthogonal characterization methods are required.

(4) The absence of density gradient ultracentrifugation is particularly concerning, given the systemic injection of EV preparations into mice, as contaminating soluble factors and non-vesicular particles may contribute to the observed therapeutic effects.

(5) The manuscript lacks adequate mechanistic studies explaining how engineered EVs mediate B-cell depletion or immune modulation.

(6) The in vitro functional assays are weakly designed, particularly the use of A549 cells for evaluating CD19-targeted vesicle function.

(7) Important methodological details are missing, including EV normalization strategies, flow cytometry gating controls, blinding procedures, and randomization approaches.

(8) Several figures, particularly TEM and western blot images, are of low quality and difficult to interpret.

(9) The study does not sufficiently exclude the possibility that observed therapeutic effects result from contaminating soluble immune mediators rather than EV-specific activity.

(10) Broader immune profiling is lacking despite the systemic immune complexity of SLE.

(11) The statistical analysis section includes tests that are not reflected in the Results section, creating concerns regarding data presentation and consistency.

(12) Overall, while the concept is interesting, the manuscript currently falls short of the experimental rigor expected for high-impact translational EV studies.

Reviewer #1 (Public review):

Summary:

The manuscript from Ali Guler's lab intends to test the impact of an integrated lifestyle around the timing of food, exercise, and light on circadian rhythm, metabolic health, and sleep in wild-type mice. After observing positive outcomes from short-term studies, they applied this integrated chronobiologically anchored lifestyle to mouse models of neurodegenerative diseases. They found some encouraging trends of health improvement that largely did not reach statistical significance.

Strengths:

Good experimental design to systematically test the effects of shorter day, timed voluntary exercise, and time-restricted feeding in rodents. The authors started with an experimental design that incorporated some findings from published papers. They used a shorter photoperiod of 8 h, which was shown to improve SCN synchrony and amplitude of the molecular clock. The use of time-restricted feeding with feeding aligned with the dark phase also has precedence. The late-night access to the running wheel is based on the published data on treadmill exercise in the late active phase, imparting better metabolic benefits. No other study has systematically integrated all three interventions into a single study. This is one of the uniqueness of the study.

Weaknesses:

Since the B6 strain of mice on normal chow does not show many health impairments, the choice of this strain and diet did not enable fine-grained analyses of each intervention on health outcomes. Although the authors used male and female mice, sex differences (if any) should have been explicitly addressed.

Reviewer #2 (Public review):

Summary:

The LiFE protocol provides shortened light exposure, as well as timed food availability and exercise (running wheel) availability. It causes mice to sleep for the first half of the active phase and to be active during the second portion, thus consolidating activity. This has some positive effect on metabolic markers and some (but not other) behavioral markers. In two AD models, there is the suggestion of a protective effect, though most of the data is not significant.

Strengths:

The concept is important and builds on previous studies showing cognitive benefits and decreased brain pathology in mice with time-restricted feeding or shortened light exposure. The comparison to multiple different light, food, and exercise timing regimens in Figure 1 is quite interesting and informative. The use of 2 different mouse models (5xFAD and 5xFAD::PS19) is a strength, as this latter model is rarely used. The pathological endpoints are appropriate.

Weaknesses:

The LiFE protocol is strange in that it induces sleep during the first several hours of the active phase. The mice seem to show food anticipatory activity, then suddenly go to sleep for a few hours during what should be their most active time of day. Is this good? Would we want such a thing in humans? Why does this happen? What is the real-life implication? How do the mice eat if they are sleeping so much during their food period?

While many of the cognition and brain pathology experiments seem to trend in a positive direction, most are not significant, which calls into question the value of the intervention. There are a few that are significant, but the overall effect seems weak. The experiments with AD mouse models are generally underpowered and not controlled for sex, as female mice get pathology much faster in the 5xFAD model, and males have more severe pathology in the PS19 model. Combining them may mask effects.

In all, it is an interesting and thought-provoking study which shows striking effects of the LiFE intervention on activity patterns and sleep, with modest/inconclusive effects on cognition and brain pathology. While it feels very preliminary, the study does provide some valuable information for planning future studies of circadian interventions in neurodegenerative models, even if the protective effects here are not fully solidified.

Reviewer #3 (Public review):

Summary:

This manuscript presents a multimodal circadian intervention ("LiFE") that combines short photoperiod exposure, time-restricted feeding, and scheduled exercise and examines its effects on circadian activity structure, SCN rhythmicity, sleep, glucose regulation, cognition, and Alzheimer's disease-related phenotypes in mice. The study is ambitious in scope and conceptually appealing. In wild-type mice, the authors report that LiFE consolidates activity rhythms, enhances SCN PER2::LUC amplitude, increases sleep, lowers baseline glucose, reduces glycemic variability, and improves novel object recognition. They then extend the paradigm to 5xFAD and 5xFAD/PS19 mice, where the effects are more modest and mostly trend-level, with limited evidence for improved behavior or reduced pathology.

Strengths:

Overall, the work is interesting and potentially important because it moves beyond single-zeitgeber manipulations and tests the idea that combining multiple entrainment cues may produce broader physiological benefits than light, feeding, or exercise alone. The WT dataset is the strongest part of the paper and provides evidence that the combined intervention changes circadian organization and metabolic physiology.

Weaknesses:

Alzheimer's disease claims are considerably less convincing than the title and framing suggest. The manuscript would be stronger if the authors more clearly separated the robust conclusions in WT animals from the preliminary, underpowered, and largely non-significant findings in the disease models. In its current form, the paper contains substantial merit, but several interpretive and methodological issues should be addressed before publication.

Reviewer #2 (Public review):

Summary:

The authors perform confirmation studies of Paul Basch's seminal schistosome work from 1981, demonstrating the development of transformed schistosomules into sexually dimorphic adult parasites, albeit without successful egg production. In addition to the findings from Basch's earlier work, the authors add some new molecular data in the form of analysis of proliferative cells in in-vitro derived animals.

Strengths:

The authors successfully confirm experimental results from earlier schistosome researchers, providing a potential new tool for studying schistosome biology without the need for vertebrate hosts.

Weaknesses:

The display of data from the authors is sometimes difficult to follow/understand where it comes from. For example:

(1) Line 136: the authors claim state that parasites in HS and FBS conditions have substantially different mortality rates (11.3 +/- 2.7 vs 5 +/- 2.3) but a quite high p-value (0.8). Analyzing the raw data myself, this reviewer obtained a mean of 8.2 +/- 1.7% vs 4.8% +/- 4.3% with a p-value 0f 0.15. Either the data are not clearly presented, and this reviewer did not follow them, or the data presented in the text do not match the raw data in the supplemental files.

(2) Line 187/Figure 4: though it is not clearly stated, it appears that the authors treat their EdU counts as an ordinal data set of 61 steps (from 0 to >60) rather than a continuous measure of EdU+ cells per animal. In this author's opinion, the graph strongly suggests a continuous data set, and the fact that this reviewer had to dig through poorly-labeled raw data to discover the nature of the data is problematic. The authors should either switch to a continuous data set or make it explicit that the data shown are ordinal. If counting EdU+ cells is too arduous, the authors could consider comparing the amount of EdU+ area to the amount of DAPI+ area in maximum intensity projections of their confocal images, as this would roughly approximate the amount of proliferative cells in the animals.

There are some minor issues as well:

(1) Line 122: it is perhaps incorrect to refer to humans as "the" definitive host of schistosomes, as S. japonicum is primarily considered a zoonotic infection with water buffalo/cows being the primary definitive host.

(2) Line 185/298 the authors refer to EdU pulse-chase experiments, but the experiments described here are EdU pulse experiments.

Comments on revised version.

Following the initial submission of the manuscript and a round of peer review, the authors updated the manuscript and addressed all of this reviewer's concerns. As such, this reviewer believes that the manuscript is substantially clearer and will serve as useful literature in the field of schistosome research.

Reviewer #3 (Public review):

Summary:

This study is significant as it established a protocol for the long-term culture of Schistosoma mansoni newly transformed cercariae which developed in vitro into sexually dimorphic forms. The impact of two different sera, Fetal Bovine Serum (FBS) and Human Serum (HS), added to the culture medium supplemented with human red blood cells was evaluated. The authors demonstrated that HS-cultured parasites were able to digest red blood cells, a critical step for long term parasite development. Furthermore, while most FBS-cultured parasites did not progress beyond an early liver stage, sexual dimorphism was clearly evident in the HS-cultured worms, albeit delayed compared to in vivo development.

Strengths:

This study could contribute to further in vitro studies for a better understanding of the unique sexual biology of Schistosoma mansoni and for screening novel schistosomicidal compounds. By increasing parasite development in in vitro studies this protocol could have a positive impact on the principles of the 3Rs (Replacement, Reduction and Refinement) for animal research.

Weaknesses:

As the authors mentioned "pairing between male and female parasites was rare. Pairing was rarely observed and only after day ~ 80 in culture. Egg production was also not achieved with this protocol.

Comments on revised version.

Some data presentation has been improved as suggested by other reviewers in the revised manuscript. The authors have also clarified the limitations of their long-term culture protocol for Schistosoma mansoni newly transformed cercariae which develop in vitro into sexually dimorphic forms with regards to male and female pairing. Additionally, they addressed my specific question regarding the culture conditions used for ex vivo/in vitro mating. The experimental conditions tested for in vitro developed parasites were the same as those for the pairing experiments. It remains to be investigated the factors that negatively influence pairing during the long-term in vitro culture of Schistosoma.

Reviewer #1 (Public Review):

Zeng et al.'s work links several key issues in Cryo Electron Tomography in ways that reinforce each other, inspired by the cycleGAN model, leading to very positive results across several benchmark datasets. The related topics include tomogram cleaning and simulations (two crucial areas in the field), with "spin-off" outcomes in automatic annotation and the completion of the missing wedge. The manuscript covers nearly all essential topics in Tomography, making it very comprehensive and potentially critical in the field. The generalization capabilities on the SHREC 2021 data set are very interesting, although difficult to quantify. I appreciate the approach, but I have serious concerns about some of the limitations of the results presented by the authors.

1. Simplified data versus nowadays challenging tomography data. It is acknowledged the difficulty in making general tests. In this work, the method shows excellent results on potentially simple data sets (the SHREC 2021, which was used for a benchmark in ET several years ago, but not much used since then) and, even more, the old Relion data set for picking).

2. Reproducibility by the average user. I have found many cases in which a specific software produces excellent results when run by the authors. Still, the average user is lost with the parameters and cannot reproduce these promising results. I propose that the authors address this issue by involving some experimental colleagues and ask them to repeat the work. This is a general concern that applies not only to this work but to many others. I think this consideration is crucial for a field that is growing very quickly and where method development happens at an extraordinary pace... but are all of them generally useful?

Reviewer #2 (Public Review):

This study introduces DUAL (Deep Unsupervised simultAneous denoising and simuLation), an unsupervised deep learning framework that jointly addresses denoising and realistic data simulation for cryo-electron tomography (cryo-ET). By leveraging a cyclic, unpaired learning strategy, DUAL avoids reliance on paired clean ground-truth tomograms, which represents a practical advantage over many existing supervised approaches.

Through extensive quantitative evaluations on benchmark datasets, together with qualitative and downstream analyses on diverse experimental tomograms, the authors show that DUAL performs robustly across both denoising and simulation tasks. For denoising, DUAL outperforms several widely used methods on the SHREC 2021 benchmark and achieves the highest particle-picking accuracy on the RELION benchmark, indicating strong downstream utility.

For tomogram simulation, the study presents an unsupervised framework that jointly denoises experimental tomograms and generates synthetic volumes that closely resemble experimental data. These simulated tomograms outperform existing approaches in downstream tasks such as particle picking and enable additional applications, including missing-wedge compensation and cross-domain adaptation, without requiring labeled training data.

Overall, this work represents a substantial contribution to the cryo-ET field by providing a versatile unsupervised tool that reduces dependence on labor-intensive manual annotation, enables realistic data augmentation for training downstream models, and facilitates artifact mitigation. As such, DUAL has the potential to accelerate methodological development and progress toward comprehensive in situ structural biology.

Reviewer #3 (Public Review):

The paper is titled "DUAL: Deep Unsupervised Simultaneous Simulation and Denoising for Cryo-Electron Tomography." The authors provided two closely related code branches: one for denoising and one for missing-wedge correction. However, I did not find the simulation component. This is important, as the authors state that "the simulation branch provides learning-based cryo-ET simulation to generate synthetic tomograms indistinguishable from experimental ones."

In addition, no pre-trained models were provided. Given that the authors indicate that all training data are publicly available, sharing trained models together with references to the corresponding datasets would significantly facilitate evaluation of the reported performance.

The provided instructions are quite minimal and do not currently support reproduction of the reported findings. Compared with other cryo-ET software packages, the documentation is insufficient for installation and practical use. The software also does not consistently support standard cryo-ET file formats, particularly during inference for denoising and missing-wedge correction. In particular, volume preparation (in the first notebook of either pipeline) expects MRC input, whereas inference requires NPZ input. This inconsistency makes me believe that the shared code is not tested, and likely is a new wrap up that does not correspond to the version used to generate the results in the paper.

I also found the denoising workflow difficult to interpret. The notebooks require a "clean" target volume as input, but it is not explained how such a volume should be obtained. It is unclear whether any clean volume may be used or whether this should be simulated based on what the user expects to contain in the input. The logic about this introduced prior is not clear. Additionally, it is not clear whether the default configuration parameters provided in the notebooks correspond to those used in the paper or are intended as illustrative examples. I had requested the exact configurations used to produce the reported results to avoid ambiguity.

After many hours of trial, debugging, and experimentation, I was able to train a model for missing-wedge correction using the default parameters, although the process was slow and memory-intensive. However, despite sustained effort over two days, I was not able to perform inference using the trained model. Full-volume inference fails due to shape mismatches, as the network is trained on fixed-size 3D patches but does not support whole-volume inputs. Patch-based inference also fails at the stitching stage due to incompatible output dimensions, even when using standard volume sizes (e.g., 1024 × 1024 × 400 voxels) that work correctly during patch preparation.

While less central, I also found the training time to be close to prohibitive. The notebook sets the number of epochs to two for a toy example and notes that more epochs are required for real experiments. In practice, training for a single tomogram required approximately 16 hours of computation on two high-end GPUs to reach only six epochs, and likely more would be required (100s?). Due to the inference issues described above, I was not able to evaluate the trained model.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed the comments raised in the previous round of review.]

Summary:

The authors provide a resource to the systems neuroscience community by offering their Python-based CLoPy platform for closed-loop feedback training. In addition to using neural feedback, as is common in these experiments, they include a capability to use real-time movement extracted from DeepLabCut as the control signal. The methods and repository are detailed for those who wish to use this resource. Furthermore, they demonstrate the efficacy of their system through a series of mesoscale calcium imaging experiments. These experiments use a large number of cortical regions for the control signal in the neural feedback setup, while the movement feedback experiments are analyzed more extensively. The revised preprint has improved substantially upon the previous submission.

Strengths:

The primary strength of the paper is the availability of their CLoPy platform. Currently, most closed-loop operant conditioning experiments are custom built by each lab, and carry a relatively large startup cost to get running. This platform lowers the barrier to entry for closed-loop operant conditioning experiments, in addition to making the experiments more accessible to those with less technical expertise.

Another strength of the paper is the use of many different cortical regions as control signals for the neurofeedback experiments. Rodent operant conditioning experiments typically record from the motor cortex, and maybe one other region. Here, the authors demonstrate that mice can volitionally control many different cortical regions not limited to those previously studied, recording across many regions in the same experiment. This demonstrates the relative flexibility of modulating neural dynamics, including in non-motor regions.

Finally, adapting the closed-loop platform to use real-time movement as a control signal is a nice addition. Incorporating movement kinematics into operant conditioning experiments has been a challenge due to the increased technical difficulties of extracting real-time kinematic data from video data at a latency where it can be used as a control signal for operant conditioning. In this paper, they demonstrate that the mice can learn the task using their forelimb position, at a rate that is quicker than the neurofeedback experiments.

Reviewer #2 (Public review):

Summary:

In this work, Gupta & Murphy present several parallel efforts. On one side, they present the hardware and software they use to build a head-fixed mouse experimental setup that they use to track in "real-time" the calcium activity in one or two spots at the surface of the cortex. On the other side, they present another setup that they use to take advantage of the "real-time" version of DeepLabCut with their mice. The hardware and software that they used/develop is described at length, both in the article and in a companion GitHub repository. Next, they present experimental work that they have done with these two setups, training mice to max out a virtual cursor to obtain a reward, by taking advantage of auditory tone feedback that is provided to the mice as they modulate either (1) their local cortical calcium activity, or (2) their limb position.

Strengths:

This work illustrates the fact that thanks to readily available experimental building blocks, body movement and calcium imaging can be carried out using readily available components, including imaging the brain using an incredibly cheap consumer electronics RGB camera (RGB Raspberry Pi Camera). It is a useful source of information for researchers that may be interested in building a similar setup, given the highly detailed overview of the system. Finally, it further confirms previous findings regarding the operant conditioning of the calcium dynamics at the surface of the cortex (Clancy et al. 2020) and suggests an alternative based on deeplabcut to the motor tasks that aim to image the brain at the mesoscale during forelimb movements (Quarta et al. 2022).

Reviewer #3 (Public review):

The study demonstrates the effectiveness of a cost-effective closed-loop feedback system for modulating brain activity and behavior in head-fixed mice. Authors have tested real-time closed-loop feedback system in head-fixed mice two types of graded feedback: 1) Closed-loop neurofeedback (CLNF), where feedback is derived from neuronal activity (calcium imaging), and 2) Closed-loop movement feedback (CLMF), where feedback is based on observed body movement. It is a python based opensource system, and the authors call it CLoPy. Authors also claim to provide all software, hardware schematics, and protocols to adapt it to various experimental scenarios. This system is capable and can be adapted for a wide use case scenarios.

Authors have shown that their system can control both positive (water drop) and negative reinforcement (buzzer-vibrator). This study also shows that using the closed-loop system, mice have shown to better performance, learnt arbitrary tasks and can adapt to changes in the rules as well. By integrating real-time feedback based on cortical GCaMP imaging and behavior tracking authors have provided strong evidence that such closed-loop systems can be instrumental in exploring the dynamic interplay between brain activity and behavior.

Reviewer #1 (Public review):

Summary:

This article presents a study consisting of two experiments, which aim to dissociate and quantify the distinct motivational functions of phasic and tonic pain within a naturalistic and immersive VR setting. Specifically, the Authors test two hypotheses: (i) that phasic pain acts as a punishment signal that drives avoidance learning; (ii) that tonic pain reduces motivational vigor, promoting energy conservation and recuperation. In both experiments, participants performed a free-operant foraging task, where they collected virtual pineapples to earn points.

In Experiment 1, phasic pain was delivered as a brief electric shock to the grasping hand when picking up green pineapples. As phasic pain intensity increased, participants were less likely to choose painful fruits. A reinforcement learning model that incorporated reward, pain cost and effort cost was able to successfully capture behavior.

Experiment 2 combined effects of phasic and tonic pain. Tonic pain was induced by a pressure cuff on the non-dominant arm, simulating sustained discomfort. Interestingly, tonic pain did not affect the perceived intensity or avoidance of phasic pain. However, it significantly reduced movement velocity and pineapple collection rate, interpreted as a reduction of motivational vigor. A temporal decision model incorporating vigor cost successfully captured these effects.

Concomitant EEG recordings showed that tonic pain was associated with reduced alpha and beta power in parietal and temporal areas. Phasic pain ratings and decision values distinctively correlated with skin conductance responses.

Overall, these findings indicate that phasic and tonic pain have distinct and dissociable motivational effects.

Strengths:

This is an ambitious study that provides a quantitative dissociation of the roles of phasic and tonic pain in adaptive behavior, by integrating ecological neuroscience, motivational theory, and computational modeling. The use of immersive VR combined with a free-operant foraging task offers a more ecologically valid context to study pain-related behavior compared to traditional paradigms. Furthermore, the study employs a multimodal approach by combining behavioral data, computational frameworks, physiological signals and EEG. In particular, one of the main strengths of the study is the use of sophisticated computational modeling to capture phasic and tonic pain effects. The experiment codes are available on GitHub, increasing reproducibility.

Weaknesses:

As recognized by the Authors, there is no control condition involving an innocuous salient stimulus to rule out non-specific effects of distraction.

Reviewer #2 (Public review):

Summary:

The study investigated the distinct roles of phasic and tonic pain in adaptive behavior. Phasic pain was proposed to function as a teaching signal, promoting avoidance of further injury, while tonic pain was hypothesized to support recuperative behavior by reducing motivational vigor. This hypothesis was tested using an immersive virtual reality (VR) EEG foraging task, in which participants harvested fruit in a forest environment. Some fruits triggered brief phasic pain to the grasping hand, which in turn reduced the likelihood of choosing those fruits. Concurrently, tonic pressure pain applied to the contralateral upper arm was associated with reduced action velocities. The authors employed a free-operant computational framework to quantify how phasic and tonic pain modulate motivational vigor and decision value. Importantly, model parameters were found to correlate with EEG responses, providing neurophysiological support for the hypothesized functional distinctions.

Comments on revised version.

All my comments have been well addressed.

Reviewer #3 (Public review):

Summary:

This study investigates how phasic and tonic pain modulate behaviour in a free-operant foraging paradigm. The authors apply a computational modeling approach to the behavioural data to quantify the decision value of phasic pain, as well as the degree to which tonic pain reduces motivational vigour. EEG assessments showed, e.g., reduced signal power at alpha and beta frequencies in tonic pain conditions compared to no-tonic-pain conditions, but no association between these neural measures and motivational vigour. The authors conclude that tonic and phasic pain serve different motivational functions, with phasic pain acting as a punishment signal promoting avoidance and tonic pain reducing motivational vigour.

Strengths:

The experimental paradigm is highly innovative. Assessing human behaviour in a naturalistic yet highly controlled setting represents a promising approach to pain research. Notably, assessing pain magnitude implicitly, via its motivational value, offers insights about the overall pain experience that are not usually accessible via common pain ratings.

Reviewer #1 (Public review):

Summary:

This manuscript is an excellent follow-up to your 2022 study, in which Sox17 expression was localized to the rete testis and shown to be required for proper formation of the Sertoli cell valve (transition region). By using Nr5a1-Cre to drive conditional deletion of Sox17 specifically in rete testis cells, you demonstrate that testis weights remain normal at 2 weeks of age but become significantly reduced by 8 weeks in Sox17-cKO males. At the later time point, the seminiferous epithelium is severely disrupted, with apparent arrest of spermiogenesis: the epididymal lumen is essentially devoid of sperm, and most tubules lack elongated spermatids.

Strengths:

The study clearly shows the role of Sox17 in Sertoli cells as being important to SV function. The SV (transition region) between the rete testis and seminiferous tubules remains an understudied domain of testicular biology. The present work, together with the authors' prior study, highlights intriguing mechanisms operating in this specialized niche.

Weaknesses:

At the same time, the available data do not yet fully explain either the developmental assembly of the Sertoli valve or the precise consequences of its functional disruption. These studies are nonetheless valuable precisely because they raise more questions than they answer; the conceptual implications are thought-provoking.

Reviewer #2 (Public review):

This manuscript investigates the role of SOX17 in the formation and function of the Sertoli valve (SV) at the interface between seminiferous tubules and the rete testis (RT). Building on previous work showing that rete testis-specific deletion of Sox17 disrupts SV formation, leading to defective spermiogenesis and male infertility, the authors explore how SOX17 overexpression in Sertoli cells regulates the SV of rodent testes.

Using transgenic mouse models with ectopic Sox17 expression in Sertoli cells, the study demonstrates that SOX17 is not only required but can also modulate SV formation. Ectopic expression in Sertoli cells induces expansion of the SV structure and partially rescues SV defects and spermatogenesis in RT-specific Sox17 conditional knockout animals. The data support a model in which SOX17 acts through paracrine signaling to regulate SV formation, although the precise mechanisms remain to be clarified.

Overall, this is a well-executed study with novel and significant findings. The ability to experimentally manipulate SV size is particularly compelling and provides a valuable framework to study fluid dynamics and epithelial interactions in the testis. This work will be of broad interest to the reproductive biology and developmental biology communities.

Reviewer #3 (Public review):

Summary:

These studies are based on previously published work that showed that deletion of expression of the Sox17 gene in the testis essentially deleted the formation of the Sertoli valve in the Rete testis. The authors extended this work by constructing a vector that resulted in increased Sox17 expression by Sertoli cells and enhanced formation of the Sertoli valve in both wild type and Sox17 knockout mice. The work provides strong evidence supporting the requirement for Sox17 expression to allow formation of the Sertoli valve.

Strengths: The general approach was to express Sox17 from a Tg mouse that expressed Sox17 from Sertoli cells. This Tg mouse was bred into both the WT and the Sox17 KO mouse. The Sertoli valve was enhanced in both the WT/Tg mouse and KO/Tg mouse, showing that ectopic Sox17 could compensate in the Sox17 Ko and act in a concentration-dependent manner in the WT mouse. The results are strong and support the conclusions from the authors. The results were as expected from the original paper describing the KO of Sox 17. These results strengthen these conclusions and provide ideas for additional conclusions. These studies were technically challenging, and the authors provided a very solid manuscript.

Weaknesses:

The authors refer several times to high or low expression, but it all appears to be based on immunohistochemistry, and there is no real quantification using PCR, for example. The process used for cell quantification lacks a rationale for why certain numbers were assigned.

Reviewer #1 (Public review):

This study by Li and colleagues examines how defensive responses to visual threats during foraging are modulated by both reward level and social hierarchy. Using a semi-naturalistic paradigm, the authors test how the availability of water or sucrose, with sucrose being more rewarding than water, shapes escape behavior in mice exposed to looming stimuli of different intensities, which are used to probe perceived threat level and defensive responses. In parallel, the study compares dominant and subordinate animals to assess how social rank biases the trade-off between reward seeking and threat avoidance. By combining behavioral analyses with computational modeling, the work addresses how reward level and social context jointly influence escape decisions in an ethological setting.

Across the different experimental conditions, perceived threat level is the main determinant of behavior. The authors show that looming stimuli associated with higher threat (contrast) consistently elicit faster and more robust escape responses than lower threat stimuli. This effect is particularly evident during early exposures, when animals are highly vigilant and have not yet habituated to the looming stimulus (learned that it is not dangerous). Later they described that as animals gain experience and habituate, behavior becomes more flexible, and reward level begins to exert a graded modulation of the escape response. Importantly, the authors show that under high threat conditions increasing reward value leads to more frequent and faster escape rather than greater reward pursuit, specifically in dominant mice. This finding is particularly relevant, as it suggests that highly valued rewards can heighten vigilance and thereby enhance responsiveness to threat, highlighting that reward does not simply compete with defensive behavior but can also reshape it depending on the perceived level of danger, in contrast to low threat conditions, where threat can be more easily outweighed by reward. However, it is worth noting that the authors use an extremely low contrast for the low threat condition (20%), which may to some extent be insufficient to reliably trigger escape responses. Thus, an important conceptual contribution of the study is the introduction of vigilance as a useful framework to interpret these effects. Vigilance is treated as a behavioral state reflecting heightened attention to potential danger. In line with what is known from natural foraging, mice initially maintain high vigilance when confronted with an innate threat. This perspective helps clarify a finding that might otherwise appear counterintuitive. One might expect higher rewards to motivate animals to tolerate risk, explore more, and habituate faster in any scenario. Instead, the data suggest that highly rewarding outcomes can elevate vigilance, making animals more responsive to threat and leading to faster or more frequent escape under high threat conditions. In this sense, reward does not simply compete with threat but can also amplify sensitivity to it, depending on the internal state of the animal.

The social results are particularly interesting in this context as well. Dominant mice consistently prioritize avoidance over reward, showing stronger escape responses and slower habituation than subordinates. This behavior is well captured by the vigilance framework proposed by the authors: dominant animals appear to maintain higher vigilance, which biases decisions toward threat avoidance. The authors further suggest that stable social relationships sustain high vigilance and slow habituation, framing this as an evolutionarily conserved strategy that may enhance survival. This interpretation provides a valuable perspective on how social structure shapes defensive behavior beyond immediate physical interactions. At the same time, there are important limitations to this interpretation. All experiments were conducted in male mice, and it is possible that the relationship between social hierarchy, vigilance, and defensive behavior would differ substantially in females. In addition, the idea that stable social relationships sustain elevated vigilance should be interpreted carefully, as it does not fully align with broader views of social stability as protective against anxiety and stress and generally beneficial for mental health and resilience. These points do not undermine the findings but suggest that the social effects described here should be interpreted with caution and within the specific context of the task and sex studied.

Another important limitation is that the neural mechanisms underlying these effects remain highly speculative. Although the manuscript includes an extensive discussion of candidate circuits, particularly involving the superior colliculus and downstream structures, these interpretations go far beyond the data presented in the study and are not directly supported by experimental evidence within the paper itself. The discussion gives substantial weight to potential circuit mechanisms based primarily on previous literature rather than on findings from the current study. Given the complexity and distributed nature of the circuits likely involved in integrating vigilance, reward, social context, and defensive behavior, the present work is better viewed as providing a strong behavioral framework rather than direct mechanistic insight into the underlying neural substrates. In this context, some references discussing how animals learn to suppress defensive responses to repeated looming threats and the neural mechanisms supporting this process could further strengthen the discussion (Salay et al 2021; Fratzl et al. 2021; Conway et al. 2025; Mederos et al. 2025).

Methodologically, the behavioral paradigm is well suited for studying escape decisions in socially housed animals, and the machine learning based classification of defensive responses is a strength. The computational model provides a useful formalization of how threat level, reward level, and vigilance interact and may be valuable for other laboratories studying escape, approach avoidance, or conflict situations, particularly as a way to classify behavioral outcomes after pose estimation. More generally, the work will be of interest to the neuroethology community for its detailed characterization of escape behavior under naturalistic conditions. At the same time, some statements in the discussion slightly overstate the novelty of the methodological approach. For example, the claim that the study differs from earlier work by using machine learning rather than manual annotation overlooks that several previous studies have already implemented automated or semi-automated strategies to classify looming evoked defensive behaviors beyond manual scoring alone.

Given the ethological nature of the study and the high inter individual variability reported by the authors, clarity and precision in the methods are especially important for reproducibility. While the revised manuscript addresses many earlier concerns, some aspects remain slightly difficult to follow. For example, the main text states that animals were not water deprived to minimize differences in internal state across conditions, whereas parts of the methods describe experiments in which animals were water deprived. This distinction is not always clearly explained across the different experimental sections, despite internal state being central to the interpretation of the behavioral findings. A clearer separation and description of these conditions would further strengthen confidence in the work. In addition, it was somewhat surprising that the low contrast (20%) looming condition was still sufficient to trigger robust escape responses, and additional clarification or discussion regarding stimulus saliency at this contrast level could help readers better contextualize these findings.

Overall, this study provides a rich analysis of how reward level and social hierarchy modulate defensive behavior through changes in vigilance. It offers a useful conceptual advance for thinking about escape behavior in semi-naturalistic settings and lays a solid foundation for future work aimed at linking these behavioral states to underlying neural circuits.

Reviewer #1 (Public review):

Summary:

The manuscript uses large-scale existing datasets that span almost the full range of human life (5-100 years) to identify two distinct architectural cortical gradients within visual cortex. These gradients are distinct in that in one cytoarchitecture and myeloarchitecture converge and in the other they diverge. The authors tested whether these gradients mapped onto known functional properties of visual cortex, as well as accounting for visual behaviours that are impacted throughout the lifespan. The manuscript also reports the identification of a hitherto unknown cluster of visual field maps in the anterior temporal lobe.

Strengths:

A major strength of the current manuscript is the use of large-scale measurements of human brain structure throughout the lifespan, courtesy of the Human Connectome Project Initiative. The scope of this cross-sectional analysis would be rare, if not impossible to achieve through an individual project.

The approach employed holds promise for assessing the link between large-scale anatomical gradients in the brain and functional/behavioural properties. The current manuscript focuses on visual cortex, but the approach could easily be implemented across the brain in general.

Weaknesses:

While the evidence for a new topographic visual field map cluster in the anterior temporal lobe is less convincing than for clusters in posterior cortex, new analyses strengthen the claim for a visuospatially tuned cluster that shared signatures of topographically organised clusters (e.g., contralateral representations) but might lack clear evidence, at present, for such topography. Investigation of how age-related and SNR confounds contribute to gradients and their life-span development could be expanded.

Comments on revised version.

The authors have taken the comments onboard and performed a number of analyses that strengthen the argument for these clusters being visuospatial in nature. I appreciate the additional analyses and effort. It may be helpful to discuss the evidence for contralateral biases in the absence of clear topographic maps in cortex in the context of what others have terms visuospatial coding (Groen et al., 2021, TiCS) where just such a mechanism is described.

Reviewer #1 (Public review):

This manuscript addresses how PGCs migrate towards SGPs in the Drosophila embryo. It's been shown that Hh produced by SGPs acts as an attractive cue, and that Wunnen(s) act as repulsive cues. In this work, the authors propose that Wun and Wun2 refine PGC guidance by attenuating Hedgehog signalling coming from other tissues.

Overall, the study is potentially interesting and could make an important contribution to the field. The data shown support the idea that Wun/Wun2 negatively regulate Hh signalling and produce PGC migration phenotypes associated with Hh. However, in my opinion, there are two major questions that should be addressed.

(1) Which is the mechanism by which Wun/Wun2 attenuates Hh signalling? The authors propose that Wun/Wun2 block Hh ligand transmission, but their data could also be explained by other possibilities, such as altered Hh production, uptake, retention or degradation, among others. The authors should either show the effect of Wun/Wun2 in Hh transmission mechanistically or attenuate their claim.

(2) How do Wun/Wun2 attenuate Hh signalling in PGCs? The authors propose that Wun/Wun2 function both in somatic tissues and in PGCs, but these two sites of action may have very different mechanistic implications. In the soma, Wun/Wun2 could affect Hh transmission, but a PGC-autonomous role cannot be explained simply by reduced Hh ligand transmission from producing cells; it would more likely involve ligand uptake, receptor trafficking, intracellular degradation or altered PGC responsiveness. This distinction should be central to the interpretation of the data.

Reviewer #2 (Public review):

Summary:

In this submission, Roy et al. examine the process of Drosophila PGC migration. Directed cell migration requires the concerted activities of chemoattractants and repellents to guide cells to the correct locale. In their submission, the authors describe a role for regulated Hedgehog (Hh) signaling to inform PGC migration. In prior work, the authors reported that Hmgcr potentiates Hh signaling, providing a permissive axis. A gap in the field, however, was the identification of the repulsive cues that guide PGCs out of the midgut and toward the future gonad. In the current work, the authors report that two wunen genes (wunen and wunen 2) inhibit Hh signaling, thereby repressing Hh activity. The model is that Hmgcr and wunen(s) balance the transmission of Hh signals to enable effective PGC migration.

Strengths:

A strength of this work is the comprehensive genetic analysis performed by the authors. The authors examine zygotic versus maternal contributions, autonomous versus non-autonomous requirements, and use a variety of RNAi and mutant allele combinations to examine genetic requirements and interactions. Another strength is that the data presented are generally clear and well quantified. Insets are provided to enhance visualization, and relevant data are quantified through replicated experiments.

Weaknesses:

Weaknesses of the work include a lack of biochemical data to validate some of the proposed interactions. Although the authors do report lipidomics data, little is done with these findings to validate or place the results in the context of a mechanistic model. Despite these issues, the conclusions stated are generally well supported by the results.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors present a method to detect natural selection on transcription factor binding sites (TFBSs), which is an upgraded version of a previously published method (Liu and Robinson-Rechavi, 2020). This upgraded version of the test implements more explicit models of evolution and is shown to outperform its predecessor in terms of both power and false positive rate. I think this method can be a valuable resource for the community and can be helpful not only to studies of TFBSs but also broader evolutionary questions related to genotype-phenotype maps or fitness landscapes.

Major comments:

(1) Questions related to Figure 1

Figure 1, along with the first section of the Results, shows that the SVM score and its sensitivity to mutations are generally correlated with the strength of ChIP-seq signals. It is not very clear to me, however, what the motivation is behind this part of the paper. It seems that the model used to predict binding strength is a pre-existing one, and it is unclear what is new in this section. Was the prediction model retrained using different data? Was its validity confirmed using new data? I would appreciate some more elaboration on how these results differ from what was presented in the previous study of Liu and Robinson-Rechavi (2020).

The existence of weak or negative correlations between SVM and coverage, which reportedly reflects low-quality peaks, seems applicable not only to this paper, but also to previous ones, so I would like to have it confirmed whether the question and the authors' answers apply to previous studies as well.

It is reported that SVM scores capture TF binding signals better than conservation-based statistics do. My intuitive interpretation is that both ChIP-seq peaks and SVM scores are supposed to reflect binding strength, whereas conservation is supposed to reflect selection (i.e., different definitions of "function" as mentioned above). It is not explicitly explained in the Results, however, what the difference indicates, leaving only an impression that the SVM score is "better" than the conservation statistics.

In summary, I think further elaboration on the above problems would make the flow of thought of this paper easier to follow.

(2) Lack of directional selection for low binding affinity

In the analysis of Drosophila melanogaster ChIP-seq peaks, there were more cases of directional selection for higher binding affinity than directional selection for lower binding affinity. The authors suggested that this observation is "likely biological" because the same pattern was not seen in simulations (line 412-413). I wonder if this could have resulted from a difference in the distribution of ancestral binding affinity across TFBSs between real and simulated data. If binding affinity was generally low in the common ancestor of D. melanogaster and D. simulans, selection for low binding affinity would manifest mainly as purifying selection against mutations that increase affinity instead of directional selection. Ancestral sequences for simulations, if I understood correctly, are observed peaks in D. melanogaster (line 715-719), which would include high fraction sequences that could be rarer in the real ancestral sequences.

The description of this particular result does not refer to a figure or table, nor is it revisited in the Discussion. Figure 5 treats peaks under directional selection as a single category. Taken together, it is hard to tell how this observation should be interpreted. If the authors consider this result as biologically meaningful, I would suggest adding more details (e.g., the number of each side).

(3) Selection in non-focal lineages

Regarding the detected signals of directional selection for stronger binding in certain tissues (Figure 6), I wonder if it is the focal species or those very tissues that are "special": did the human lineage undergo more adaptive regulatory evolution than the chimpanzee lineage, or do nervous and male reproductive systems have a high "propensity" for adaptive regulatory evolution? Assuming that the binding preference of the same TF did not undergo a significant change since human-chimpanzee split (which, I believe, is a built-in assumption in both RegEvo and the permutation test), it should be possible to perform the same test using chimpanzee sequences that are homologous to the human ChIP-seq peak regions. In the case of coding sequences, for example, Bakewell et al. (2007) found that it was the chimpanzee that had more genes under positive selection than humans; I wonder if TFBSs show the same or a different pattern.

(4) Comments on terminology

a) Meaning of "function"

The word "function" has had different meanings in the biology literature, with some authors using "functional" to refer to anything with a phenotypic effect and some using it only for targets of selection. A (putative) TFBS would be considered "functional" as long as it has TF binding affinity if we follow the effect-based definition, but only if its binding affinity is under selection if we follow the selection-based definition. In this manuscript, the term "function" appears to have been used to refer to TF binding but not selection, most notably in the first Results section. There are also places where it is less clear what "function" means exactly (e.g., "deeply conserved elements that are likely to be functionally important" of line 61). Since this paper is about evolution, it is likely that many readers prefer the selection-based definition or assume that the selection-based definition would be used. Thus, using "function" to refer to just TF binding could be confusing. To this end, I would suggest that the authors drop the word "function" or give an explicit definition early in this paper.

b) Directional selection in different directions

In this paper, selection for increased TF binding affinity is referred to as "positive directional selection", and selection in the opposite direction is called "negative directional selection" (as exemplified in Figure 2). I understand that using such shorthand names would make the text less clumsy, but these two terms could potentially be confusing, as "positive selection" and "negative (purifying) selection" are also terms referring to specific types of selection and have some connection to directional and stabilizing selection. Therefore, I suggest that the authors use something like "selection for increased/decreased binding affinity" instead, or note explicitly in the text that "positive/negative directional selection" would be used as shorthand.

Reviewer #2 (Public review):

Summary:

The manuscript by Laverre et al. provides an interesting new test of selection on TF binding. Rather than focusing on sequence changes, this test is specifically for changes in predicted TF binding affinity. The authors report directional selection on 5.1% of tested regions in Drosophila, as well as a signal of selection on CTCF binding in the human CNS and male reproductive system.

Strengths:

Overall, I think this represents an important direction for the field of molecular evolution: now that TF binding can be predicted fairly well from sequence, it can be a very useful focus for tests of selection.

Weaknesses:

As mentioned several times in the manuscript, Jiang and Zhang (2024) pointed out some issues with a previous permutation-based version of this test. Foremost among these was the issue of ascertainment bias: when testing only experimentally supported TF binding sites from a focal species, and then asking what type of selection (or lack of selection) led to those sites, one is guaranteed to find more substitutions that increase affinity, simply because the sites were selected in the first place as those with maximum (empirically measured) affinity.

To address this issue, the authors simulated Drosophila CTCF peaks evolving neutrally and then tested different ascertainment cutoffs in Figure 4D. It was not entirely clear to me what is shown in Figure 4D: the text says the bins were stratified by derived delta-SVM, whereas the figure says SVM, and the legend says derived SVM (both without the delta). I was unable to find any clarification of this in the Methods section. In any case, I am not really convinced by this, for two main reasons. First, when analyzing empirical ChIP-seq data, I would guess that only a tiny fraction of the genome is bound (far less than 1%, especially in mammalian genomes). However, the most extreme bin in Figure 4D is taking the top 10% of (delta?) SVM values. What would Figure 4D look like at bins of the highest 0.1%, 0.001%, etc? My guess is there would be a strong uptick in the FPR. The second reason is actually more important and fundamental than the first. As long as this method is working as described, I cannot see any way that it would ‘not’ be impacted by ascertainment bias. As an extreme case, imagine that all TF binding sites tested had the maximum possible SVM scores; then none of them would have any chance of showing directional selection against binding, while even those that evolved neutrally would appear to have directional selection in favor of binding. Of course, real empirical data are not as extreme as this, but the same concept applies in less extreme scenarios.

This bias could explain patterns observed in the real data. For example: "We observe much more positive than negative directional selection, a pattern likely biological rather than methodological, since it is absent from simulations." This is exactly the pattern predicted under ascertainment bias (in the extreme-scenario thought experiment above). I suspect it is absent from simulations simply because the authors did not properly account for this bias in their simulations.

If the main result reported by the authors had been a lack of any directional selection in favor of binding, and instead only neutrality or directional selection against binding, then this ascertainment bias would not be an issue- it would only have made their results conservative. Unfortunately, this is not the case, and the directional selection in favor of binding, which is the main result emphasized from the empirical analysis, could be inflated by this bias.

Minor point:

The following statement: "In contrast, phastCons and phyloP scores lack such enrichment and have a lower dynamic range, suggesting that the conservation scores are less sensitive to fine-scale variation of TF occupancy and thus regulatory region function" is only true if one assumes that TF binding is the only function of this region. One could even turn this around and say the fact that the sites affecting TF binding are not the most conserved is actually evidence that TF binding is not a good indicator of these regions' entire function. I suggest the authors soften this claim that conservation scores are less sensitive to regulatory region function.

Reviewer #1 (Public review):

Summary

The authors aim to understand, in the context of leaf shape, how the constraints imposed by development inform evolution. Leaf shape is a good place to study the influence of development on evolution because it is a trait that exhibits a lot of diversity, and the developmental mechanisms that give rise to leaf shapes are apparently rather conserved across angiosperms.

As part of the motivation for their work, the authors cite a previous study (Geeta et al), which found that in angiosperm phylogenies, transitions from complex to simple leaf shapes occur through evolution more often than transitions in the opposite direction. Is this due to developmental constraints or adaptation?

The authors undertake two parallel lines of work:

(1) Extending the study of Geeta et al with more data, consisting of both phylogenies and a shape classification dataset. The conclusion from this line of inquiry is that transitions from lobed to unlobed leaves are more common than transitions away from unlobed leaves.

(2) The authors conduct evolution simulations in a computational model of leaf development. Here, they look at {\it neutral} mutations and whether simply neutral evolution is sufficient to drive the observed trend.<br /> The conclusion of the second part of the work is that the driver of the evolution toward simple leaf shape is entropy: there are more ways to make unlobed leaves than to make lobed leaves (at least in terms of gene regulation parameters that will produce the two leaf types). The argument is that random gene regulatory networks are more likely to produce unlobed leaves than lobed leaves; therefore, neutral evolution drives this trend.

Data Analysis

Roughly $9000$ images of leaves were classified into 4 categories: unlobed, lobed, dissected, and compound. These labels were applied to the tips of 5 phylogenetic trees of angiosperms (3 resolved at the genus level and 2 at the species level). By fitting a continuous-time Markov chain to the labelled trees, the authors claim that there is a significantly higher rate of transition to the unlobed leaf shape compared to transitions to more complex shapes.

Simulation

First, the authors validate a computational model (Runions et al) for leaf growth on an experimental dataset. By changing parameters in the model, they can recapitulate the morphological changes in the shapes of Arabidopsis leaves engendered by expression of two particular genes.

Then the authors run an evolutionary model (without selection, just random mutations) on top of the computational leaf development model. As the random walk in parameter space reaches a stationary distribution, they look at both the proportions of the leaf categories in the steady state as well as the transition rates between different categories. The result is that transitions to unlobed leaves are more common than from unlobed leaves.

General Comments

The authors use angiosperm phylogenies from other works as the basis for the data analysis part of their work. Given the centrality of these phylogenies for their conclusions, more information is needed about how these phylogenies were constructed and what they mean. What is the timescale that they span? What method is used to infer them? What regions of DNA were sequenced in order to build the phylogenies? Also, maybe some more discussion of angiosperm evolution (e.g., when was the most recent common ancestor of all angiosperms?) would help put the study in context.

We also need a more in-depth discussion of the computational model. What are all the $>100$ parameters doing, and what informs the seemingly strange mutational model that changes parameters by 3 orders of magnitude?

I am confused about how the rates of transitions were inferred from the phylogeny. Here, one has a phylogeny inferred by some method (which needs to be described in more detail), and just the leaves are labelled. It is stated in the methods that BayesTraits was used to infer the transition rates. I realize this method is probably documented elsewhere, but a bit of a summary of how it works and how to interpret its results would (1) make the paper more self-contained and (2) if the algorithm is credible, make the results firmer.

I am a bit skeptical of the authors' interpretation of the biological trend (of complex to simple leaf shapes) as being driven by neutral evolution. Why does one expect that the mutations generated by the random walk models described in the work are in fact neutral mutations?

- If the entropy of simple leaf shapes is higher than that of complex leaf shapes, why did we have complex leaves at all? I suspect the authors might argue that this is due to selection. In that case, what allows these complex shapes to become simpler? Wouldn't they be losing the selective advantage that drove them to be more complex in the first place? Or maybe the idea is that the rates are inferred assuming some steady state that generates the phylogeny? I did not understand this point.

Are the rates of transitions between leaf types inferred for the phylogeny assuming that the phylogeny is generated by the steady state of some Markov process? (I think the answer is no: in that case, how does one explain the initial condition?) If I take the mutation model (random walk) seriously, then shouldn't I expect that this steady state obeys detailed balance? In that case I should have $p_i r_{i\to j} = p_j r_{j\to i}$ for each of the occupancies $\{ p_i\}$ and transition rates $r_{i\to j}$ for the shape categories. How close are the rates inferred from the phylogenies to obeying detailed balance? Presumably, the Markov chain fitted to the simulation data obeys detailed balance because the mutation model itself does?

I find it hard to take the discussion of development seriously without some consideration of mechanics. Presumably, the mechanics are hidden in the computational leaf development model, but this model is not discussed in enough detail for the reader to know. It seems to me that the interesting question is: what are the {\it mechanical} constraints on development that drive the apparent trend in evolution towards simpler leaf shapes? Maybe it is something about the type of differential growth needed to make complex leaf shapes less robust to mutation. But in this case, I would assume that selection plays a role in the complexity of shape. In any case, a better understanding (or explanation) of the computational model is needed to make this interpretation.

Some discussion of timescales is needed, especially when invoking neutral evolutionary arguments. If a neutral mutation occurs, its time to fix in a population of size $N$ is $\sim N$ generations. What are the relevant angiosperm population sizes and the number of mutations that separate branches on the tree? Are timescales remotely consistent with e.g., the age of angiosperms on Earth?

Reviewer #2 (Public review):

Strengths:

The paper's underlying question is interesting, extending the authors' prior work on RNA along similar conceptual lines. The paper combines both image analysis of leaves and a computational analysis of a simple model of leaf development.

Weaknesses:

The entire paper is based on the Runion model. More intuition about the Runion model would be useful for a broader readership that cares about the evolutionary aspect of this, but may not know the developmental model in question. Obviously, this is prior well-established work, but 2 - 3 sentences highlighting the key structural aspects of such a model would be great. Currently, that intuition is found implicitly in a sentence on page 2 ("complex leaf shapes need more specificity in their GRNs than their simpler unlobed leaf shape"), but the reader is left wondering - is the Runion model a detailed mechanistic one with multiple interacting genes/proteins? If so, how many? Or is it just 2 - 3 genes but with complexity entirely in how long they are each expressed/when they are turned off, etc.

The Runions model has nearly 100 free parameters. Random walks in 100-dimensional spaces have generic properties like a tendency to move toward regions of larger volume that have nothing to do with leaf biology. How do you disentangle the geometry of high-dimensional random walks from genuinely biological developmental bias? Would a toy model with 100 parameters and arbitrary phenotype categories also show "bias toward simplicity" if "simple" phenotypes occupy more volume?

The discussion of Figure 4 (PCA of parameter space) uses "area" loosely when what's actually being measured is bin count in a 2D projection of a high-dimensional space. I would think that, in general, PCA projections can be misleading about volume in the full parameter space, but I can't tell if that's an issue in this case. Some comments/thoughts here would be useful.

The classifier validation section is in the Methods section, but it seems critical to the whole story. The < 80% agreement with manual classification could propagate to the rest of the estimates in the paper. Again, some comments/thoughts here would be useful.

The authors should explain Mut2 and Mut5 in the main paper with a sentence or two, at least schematically, because how you mutate is obviously very relevant to interpreting a paper about biases in variation.

The two mutational schemes use additive perturbations to individual parameters. Real mutations presumably affect regulatory networks in more structured ways (e.g., changing binding affinities that affect multiple parameters simultaneously). How sensitive are the results to the assumption of independent single-parameter mutations?

The connectedness argument is made using a 2D PCA projection. Is there a way to check this statement in the full parameter space or perhaps in higher-dimensional projections to test the robustness of this result? Connected components can merge/split under different projections.

Reviewer #1 (Public review):

This study presents a new model of phenotypic variation incorporating direct and indirect genetic effects, as well as a new implementation (RAINBOWR) for quantification, genomic prediction and GWAS. It includes a simulation study to test the model and implementation, and three applications to plant species.

The abstract describes the main novelty and significance of the study as follows: "Recent studies have utilized high-resolution polymorphism data to enable genomic prediction (GP) and genome-wide association study (GWAS) of IGEs, but unified methods remain limited". I disagree with this statement (e.g., using ASREML: https://doi.org/10.1186/s12711-018-0409-7, using LIMIX: https://doi.org/10.1186/s13059-021-02415-x; etc.).

The parameterisation of genetic effects in the model is not standard and complex. Hence, the simulation study is key, and the results need to be presented in a very rigorous manner. I have several points to make on this:

(1) L172 says the estimated parameters are "close to" the real parameters. The results of the simulation study need to be quantitative (see https://www.biorxiv.org/content/10.64898/2026.03.10.710784v1.supplementary-material for example).

(2) Figure 2h: the estimates seem to be biased, no?

(3) Figure 2 in general: why isn't there a difference between cov and noncov? Do we not expect the inclusion or non-inclusion of a covariance term to affect the other genetic parameters and the results presented in Figure 2?

(4) Does "total BLUPs were highly correlated between models with and without 𝜌" really validate the model?

(5) As far as the GWAS is concerned, the results of the simulation study should include a figure showing whether the p-values are inflated (as observed in the grape application), and not just a ROC curve.

The model only includes IID residuals, whereas the importance of including non-genetic social effects (IEE) has been demonstrated in many settings, and other IGE plant studies have used sophisticated spatially structured residuals (e.g. 10.1111/nph.12035). Can the authors justify why they considered only IID residuals? In the three applications presented, wouldn't it be appropriate to include spatially structured residuals and potentially other relevant covariates?

It remains unclear why the authors chose such an unconventional parameterisation of the DGE IGE models for the questions asked in this study. It seemed appropriate to study frequency-dependent selection (previous paper), but for this study, focused on IGE quantification and GWAS, the classical models (e.g. early models by P. Bijma but also more recent models that allow for distance-dependent IGE) seem appropriate, and they are much simpler and easier to interpret, and have been validated in many settings). The Discussion paragraph L274-284 only strengthens my doubts.

Reviewer #2 (Public review):

Summary:

In this study, Sato and Hamazaki have expanded upon previous work, describing quantitative genetic models for direct and indirect genetic effects and applied this to both simulated and real plant datasets of three different tree species. The methods are clearly described and accompanied by a number of R packages freely available to the wider community.

Strengths:

The main strength lies in the joint modelling of DGE, IGE and their covariance while also simultaneously modelling single-SNP fixed effects (including SNP interactions across neighbours) and a polygenic effect that goes beyond a simple kinship correction as found in many traditional GWAS models, to a compound kinship structure that accounts for DGE, IGE and their interaction.

Weaknesses:

There were some aspects that deserved more attention from the authors. For example, the authors found that a very large amount of phenotypic variation in citric acid content in grapes was explained by neighbour identity, along with over 1000 significant SNPs, yet there was little to no discussion of this result and how it could have arisen (apart from some mention of volatiles and ethylene - but without being explicit on the mechanism here). The simulation study also only considered the scenario of equal direct and indirect genetic variances, while previous studies, as well as the 3 real datasets presented in this study, show that DGE variance is almost always larger than IGE variance. A simulation study cannot be exhaustive, of course, but it seems more likely that in reality and for most traits, IGE will be more difficult to detect than DGE.

Reviewer #3 (Public review):

Summary:

The authors aimed at studying the genetics of interactions between individuals, notably the genetic architecture of indirect genetic effects. For that, they mobilized a technique known as "genome-wide association" study. GWASs are typically formalized as linear mixed models (LMMs) with fixed effects to identify the oligogenic component of the genetic architecture (usually SNPs tested one by one, as done here), and with random effects to quantify the overall contribution of the polygenic component of the genetic architecture (using a kinship matrix). They used an LMM with a few corrections and improvements from one of their already-published model, assessed it on data they had already simulated in a previous work, and applied it to three datasets generated and originally analyzed by others, focusing only on direct genetic effects. The results on simulated data confirmed that it was necessary to adapt their previous model. The results on real data confirmed the presence of negative correlation between direct and indirect genetic effects (for two out of three species), as was already known from other studies. They found a few SNPs with significant, indirect effects, which led them to identify candidate genes, but they did not validate them.

Strengths:

The main strength of the manuscript lies in the question tackled by the authors, i.e., related to indirect genetic effects, with the ambition to go beyond the estimation of overall effects towards the distinction between polygenic and oligogenic components of genetic architecture. They also found, in an apple dataset, a significant IGE SNP that also happens to be in a DGE-associated region.

Weaknesses:

(1) Overall, the authors do not engage sufficiently with the existing literature, and do not provide strong evidence that their approach is more powerful or more interpretable than others. Hence, this work seems rather incremental.

(2) The authors used an LMM that corresponds to a previous LMM they already published in 2021, with a few changes that appeared more like corrections than improvements. Their model raised several questions.

(3) First of all, their previous model included the polygenic component of direct genetic effects (modeled as random with a kinship matrix), but not the polygenic component of indirect genetic effects. As a consequence, the initial model did not allow both direct and indirect genetic effects to be correlated, although this correlation is the hallmark of the topic: a negative correlation can lead to selection on direct effects only to deliver a negative genetic gain (Griffing, 1967). This was corrected in their new model here, so that it is similar in this respect to the other models. They highlighted that, on simulated data, their new model could "infer a trade-off between DGEs and IGEs", but that was the very goal of introducing the correlation parameter, so it was reassuring at least to know that they could estimate it on simulated data. On real data, they found evidence for it being negative, which was already the case in Cappa and Cantet (2008) for a tree species, in Haug et al (2023) for annual crops, in Montazeaud et al (2023) for A. thaliana, etc. They tested for significativity but did not provide any confidence interval. They showed the proportion of variance explained by the covariance, but did not discuss the sign or magnitude of this correlation.

(4) Although the authors included a correlation parameter between DGE and IGE in their updated model, they did not specify if the residual errors were correlated, too. In fact, they did not even specify a distribution for them. It is already known that allowing for correlated errors may not change the estimates (Haug et al, 2021), but in some settings it can be important (Bergsma et al, 2008).

(5) In appendix S4, they say that the "ordinal" model (I am not sure of what they meant by this word) "defines polygenic DGE and IGE by random effects without fixed effects for each SNP". However, this is not correct; see Baud et al (2021), for instance. In any LMM, it is straightforward to include a single fixed effect for a given SNP, and to do it one SNP at a time. Moreover, they claimed that "compared to the ordinal model (Equation S4), the proposed model (Equation 1) is more extensible to incorporate SNP-wise fixed effects while distinguishing variance-covariance matrices", without providing more evidence than this statement.

(6) The authors seemed keen to convince us that the fact that their model is analogous to the Ising model of ferromagnetics was an advantage in itself. But why would it be? Beyond the mere analogy, it should be a matter of modelling choice, and thus be clearly motivated. For instance, they chose to assess the strength of the association between the trait in the focal individual (y_{k_i}) and the average (dis)similarity between the focal individual and all its neighbors (in neighborhood k), calling the latter "indirect genetic effect". Moreover, it is not clear if what they called "IGE" is \beta_{q,2}, u_2, both, or also \beta_{q,12}, etc? Furthermore, they should have used another term as this is not the same as the "indirect genetic effects" of the other models. In these models, what is called the indirect genetic effects can be modeled as depending on group size (see Hadfield and Wilson, 2007; Bijma, 2010). In which sense would the approach of the authors be better? How does it relate to the other models? Do they have more power? Is their term more interpretable?

(7) Another way in which the authors' model may be different from the other models is in the way it models interactions between direct genetic effects and aggregate (dis)similarity between focal and neighbors. At the level of the polygenic components, other models simply have a (DGExIGE) term capturing the deviations from the additivity of DGE + IGE (e.g., Wright, 1985, in the multispecific context). Here, the authors indeed mentioned "interactions between polygenic DGEs and IGEs" and introduced the K_12 matrix, but it is not clear how different (or similar) it is from the more classical (DGExIGE) term. At the level of the oligogenic component, the authors introduced \beta_{q,12}, but it is not clear, to me at least, how it relates to K_12 and K_21.

(8) The authors checked their model on simulated data for various levels of correlation between u_1 (GE) and u_2.

(9) It is not clear why they have higher absolute errors with negative covariance than with a positive one.

(10) As a causative IGE SNP, the authors considered one with a beta_{q,2} significantly different from 0. However, they also have two other coefficients, beta{q,_}1 and beta_{q,12}, for each SNP q. How is the FDR in RAINBOW controlled in such a case? This is not detailed.

(11) In their simulations, the causative IGE SNPS were also causative DGE SNPs. However, this may increase power. From the manuscript title, one could assume that the authors' goal was to distinguish between the SNPs that are both DGE and IGE, versus the ones that are IGEs only.

(12) From what I understood, the authors first estimated the (co)variance components once and for all on the model without any SNP, and they then used the values to fit the GWAS model one SNP at a time. This assumes that the inclusion of SNP effects modeled as fixed would not change anything regarding the (co)variance components, but this is not warranted.

(13) The authors applied their model to three datasets of perennial plants.

(14) They only used their model and did not provide evidence that their model gave a significant improvement compared to other models, such as the one of Baud et al (2021).

(15) In Figures 3, 4 and 5, having an indication of which cases have a significant correlation between u1 and u2 would have helped.

(16) Concerning the Aspen dataset, it is not clear why the authors claimed that "the negative effects of neighboring genotypes were amplified as trees matured" as the PVE_cov in Figure 3 in 2015 are not systematically more negative than those of Figure 3 in 2014.

(17) When discussing their results, the authors should engage more with the literature estimating DGE-IGE correlations (see some of the references above).

(18) Concerning the apple dataset, they mentioned that "metabolite accumulation in ripening fruits may be facilitated by volatile chemicals, such as ethylene", but they did not find any evidence for significant IGE SNPs localized close to a gene involved in ethylene production. Claiming that these are testable hypotheses should have been made earlier, in the introduction, than a posteriori in the discussion.

Reviewer #1 (Public review):

Marconcini et al. report results of an ambitious study on the genetic mechanisms that contribute to resistance of Drosophila flies to the toxin octanoic acid (OA). This study was motivated by two observations: first, Drosophila sechellia, a close relative of D. melanogaster, has evolved specialized feeding on fruits of Morinda citrifolia, which contain high concentrations of OA and second, that artificial selection on Drosophila simulans, a sister species of D. melanogaster, can generate higher resistance to OA. Previous studies had performed genetic mapping studies between D. simulans and D. sechellia that implicated certain genomic regions in resistance to OA and, in particular, implicated several Osiris gene paralogs as contributing to resistance, though the molecular mechanisms of resistance remain unclear. In this study, Marconcini et al. performed two major experiments. First, they performed evolution-and-resequence on Drosophila simulans populations exposed to OA for 50 generations and identified candidate regions with excessive shifts in allele frequencies as candidate regions containing OA resistance genes in D. simulans. Second, they performed a CRISPR knock-out screen in a D. melanogaster cell line to identify genes that contribute to OA resistance and susceptibility.

Evolve-and-resequence yielded many candidate genomic regions with extreme allele frequency shifts, which may be regions containing OA resistance genes, or linked genes, or regions that happen to show a strong shift in all replicate populations by chance. As the authors note, detecting significant shifts in allele frequencies is a challenging problem, and the authors use two measures of allele frequency shifts (the Cochran-Mantel-Haenszel method and Bait-ER) and perform simulations under neutrality to estimate a reasonable significance threshold. I am not entirely convinced by this method of estimating significance levels, because the simulations involve assumptions that may not be met by the real populations. I would think that a permutation test would provide an assumption-free method of estimating significance levels. I have tried to think whether there is something about the design of these experiments that would preclude the use of permutation tests (which are used widely for genome-wide studies, such as QTL), but I can't think of one. Perhaps the authors are aware of a reason permutation tests would be invalid here, and if so, they should state this reason.

There is overlap between regions detected by the two methods, but the methods disagree for many regions. The authors state that a "majority of prominent peaks were found by both methods," but I am unclear on what "prominent" means here. It would be more helpful to be more quantitative about the extent of overlap.

The authors hypothesized that the response would be at similar genomic loci in all populations (line 222). It seems at least possible that epistatic interactions would lead to different combinations of alleles evolving in each population. I wonder if it would be possible to test whether there is heterogeneity in the responses across the replicate populations.

The evolve-and-resequence method yielded many possible regions contributing to OA resistance in D. simulans, but perhaps too many regions to test directly or even to build sensible hypotheses about the genes involved. Thus, the authors performed a second experiment to try to narrow down the list of possible candidate genes. They performed a CRISPR knockout screen in a D. melanogaster cell line for genes that contribute to resistance or susceptibility to OA. The authors identify several limitations of this experiment, but they nonetheless identified several genes where knockouts contribute to OA susceptibility or resistance. Intersecting top hits with regions that experienced selection identified two "resistance" genes: kraken and Alkbh7. The selection hit at kraken is quite compelling, whereas the evidence at Alkbh7 is less strong because only two SNPs were marginally significant. Further functional assays, including gene knockouts in D. melanogaster and D. sechellia, provide some support for the claim that both of these genes can contribute to resistance to OA in flies.

Beyond the few issues raised above, I do not have significant questions about methodology or the results. I do think, however, that the authors should be more conservative about the implications and significance of their results. For example, on line 139, the authors claim that this intersection approach provides a "powerful paradigm to investigate ecotoxicology." I am not sure I agree that the identification of two genes that may contribute to OA resistance, after a seemingly heroic selection experiment and CRISPR screen, suggests that this method is all that powerful. It seems that most of the genes that contribute to the selection response remain unidentified.

Finally, given that one motivation of this project was to identify genes that contribute to evolved resistance to OA, I am surprised that the authors did not generate CRISPR alleles of kraken and Alkbh7 in D. simulans and then use these together with the existing alleles in D. sechellia to perform reciprocal hemizygosity tests to determine if these two genes actually contribute to evolved resistance in D. sechellia. This test is simpler to perform and may be more sensitive than the allelic replacement that the authors propose (lines 446-449).

Reviewer #2 (Public review):

Summary:

The authors studied the resistance against octanoic acid, a compound of the noni fruit, in D. simulans, using experimental evolution and resistance/susceptibility in D. melanogaster cells. They identified novel candidate genes and performed functional tests.

Strengths:

The idea of using experimental evolution of a non-resistant species to develop resistance is interesting, and the idea of narrowing down a large list of candidate loci by CRISPR-based gene knockout in cell culture is innovative. The reviewer also liked the (easy) follow-up experiments to validate the results.

Weaknesses:

The reviewer is not convinced of the conceptual idea behind their approach: the intersection of the two approaches implicitly assumes that null alleles (or at least compromised alleles) should be selected during experimental evolution. The reviewer considers this unlikely, and the authors made no attempt to test this implicit hypothesis in their data. Along the same lines, it is not clear how to reconcile an upregulation of candidate genes in resistant flies with the knockout experiments.

The experiments to validate the effect of candidate genes did not match the experimental evolution conditions.

The statistical analysis suffers from some problems and an insufficient description of the analyses performed.

Although D. simulans GWAS data are available, the authors did not make an attempt to estimate the effect of selected variants in the candidate genes in the GWAS data set.

The reviewer would have liked to see more connection between the experimental evolution and the GWAS data. As some D. simulans genotypes have similar resistance to D. sechellia, it would have been interesting to test whether this genotype contributed to the observed resistance.

At several places, the authors discuss the challenge of studying a polygenic trait, but at the same time, they claim to have detected and validated candidate genes. It would be helpful if the authors could discuss why they consider that their assays could really detect the contribution of single loci to the polygenic trait. In particular, when GWAS did not detect their candidate genes.

It is not clear to the reviewer why the authors did not pay more attention to the highly significant peaks emerging from the experimental evolution study. Their functional validation would have been biologically more plausible.

Impact:

Given the obvious challenges of functional testing of polygenic traits and the clear limitations of the interpretation of the results, the study will be helpful for future studies aiming to characterize polygenic traits. Unfortunately, the results are just another piece of controversial results regarding resistance against octanoic acid, a trait that is rather easy to evaluate.

Reviewer #2 (Public review):

Summary:

The authors have used 1477 sequenced trios with available gene expression data in the offsprings to discover eQTLs that act in a parent-of-origin specific manner. The classified their associated SNPs are tested for enrichment for GWAS hits, drug target genes, etc.

Strengths:

The manuscript presents an impressive analysis of a very rich data set of parent-of-origin eQTLs. To my knowledge, it is one of the largest studies of its kind and most analyses are sound and the results are of interest to many in the field and potentially beyond. The different ideas of follow-up analyses are useful and make sense.

Weaknesses:

While in general the analyses are well-conducted, I noticed a major issue with the POE eQTL classification, which puts into question most of the downstream analysis. In the light of this problem, all claims of individual discoveries (apart from those in Table 1) should be removed. The enrichment analyses remain valid and are useful.

Reviewer #1 (Public review):

Summary:

The authors tackle a long-standing question in developmental theory: given a gene-regulatory network that includes extracellular signaling, which topologies are even capable of transforming an initial spatial profile into a genuinely new pattern? Building on the classical reaction-diffusion framework in one dimension, but imposing biologically motivated constraints, they prove that every one-signal sub-network must be either Hierarchical (H), self-activating (L+), or self-inhibiting (L-). They further demonstrate that only three composite classes of full networks - pure H, a coupled L+ L- "Turing" pair, and an L- module fed by an intracellular positive loop ("noise-amplifying")-can create non-trivial spatial transformations. Analytical criteria and illustrative simulations are provided, together providing a closed taxonomy, which is supposed to be relevant for real systems.

Strengths:

(1) Useful classification framework. Reducing a vast number of possible gene circuits to three canonical pattern-forming motifs is a valuable organizing insight for both theorists and experimentalists.

(2) Practical interpretability. Given a reaction network diagram, one can now decide (assuming the model applies to real systems) whether spatial patterning is even possible, saving experimental effort on in silico screens that could never succeed.

Weaknesses:

(1) After the resubmission, I still have concerns regarding the formal definition of "non-trivial transformations" (P1/P2) and its application to noisy or multi-dimensional systems. The criteria rely on counting "new" critical points (maxima/minima). In their response, the authors argue that the diffusion operator instantly smooths discontinuous white noise, allowing critical points to be properly defined. However, this very smoothing process passively generates a landscape of new, smooth local extrema from the initial noise. Consequently, trivial diffusive regularization could inadvertently fulfil the criteria for a "non-trivial" transformation, leaving the definition conceptually problematic. Furthermore, when extending the framework to 2D/3D, the manuscript assumes that starting from a central "spike" will robustly preserve radial symmetry, yielding concentric rings or shells. This overlooks the fundamental nature of macroscopic mean-field models like reaction-diffusion equations. The realization of the final multidimensional pattern depends strictly on the stability of the solution against ubiquitous perturbations (including angular modes) rather than solely on the deterministic symmetry of the initial condition. It remains unclear how the current framework accounts for spontaneous symmetry breaking in cases where these angular modes become unstable, challenging the assumption that radial symmetry will strictly dictate the outcome. We note that the authors' use of noise as an initial condition does not resolve this fundamental issue. Reaction-diffusion equations inherently describe mean-field dynamics, meaning that microscopic fluctuations are continuously present in any real system, regardless of whether explicit stochastic terms are written into the equations. Ultimately, if a symmetric mean-field solution is structurally unstable to these inherent fluctuations, it simply cannot be realized in nature.

(2) Theoretical limitations in the application of Linear Stability Analysis (LSA): I remain uncertain about the framework's reliance on LSA to categorize macroscopic transformations, especially those arising from large initial perturbations (spikes). In their rebuttal letter, the authors justify this by assuming the perturbation remains small over a short time interval. However, because the study aims to describe stationary, asymptotic states, applying a linear approximation that relies on transient t->0 conditions to predict long-term global stability is not fully resolved.

(3) In the previous round of the review, I suggested that a biomolecular sink, such as A+B -> AB reaction, could break the approach. In their response letter, the authors defend their approach by arguing that such reactions can be accommodated by their abstract constraints (R1-R5) as long as the signs of the Jacobian elements remain invariant. However, the problem I see here is not the sign of the interactions, but the severe loss of spatial homogeneity.

When a macroscopic initial perturbation (a "spike" of morphogen) is introduced into a domain with a strong bimolecular sink, it will inevitably cause massive local depletion of the consumed substrate near the source. Consequently, the background state of the system will rapidly evolve into a profile with macroscopic spatial gradients long before any spontaneous pattern-forming instability takes over. Mathematically, this dictates that the system no longer possesses a homogeneous steady state, and the Jacobian matrix becomes explicitly space-dependent, which should break the classical LSA approach.

Discussion:

The study offers a solid conceptual organization of pattern-forming networks. However, the theoretical bridge between infinitesimal linear stability and macroscopic, non-linear pattern emergence still presents some uncertainties. The way the current framework formally treats noise, multi-dimensional symmetry breaking, and large initial perturbations leaves some questions open regarding its broad analytical applicability to real biological tissues.

Reviewer #3 (Public review):

Pattern formation is responsible for generating the spatial organization of cells, tissues, and organs during embryogenesis. It operates within a multifactorial system including initial conditions, gene regulatory networks, extracellular signals, mechanical forces, stochastic noise and environmental inputs, and finally ensures the functional anatomy of an organism.

This study focuses on the one central aspect in pattern formation: how spatial heterogeneity arises from an initial condition and evolves into a more complex or distinct spatial pattern (non-trivial pattern formation as they termed). The authors made efforts to explore and characterize all possible ways to achieve the pattern formation by discussing how extracellular signals spread, how individual cells respond to those signals, and how those responses, in turn, modulate signal propagation.

Finally, their comprehensive analysis summarizes that there are three classes of interactions between extracellular signal and intracellular responses, corresponding to previously known mechanisms that can generate spatial patterns: Difference in morphogen concentrations in space, noise-amplification, and Turing pattern.

Reviewer #1 (Public review):

The manuscript by Lux et al. addresses how T-cell acute lymphoblastic leukemia (T-ALL) cells migrate into the central nervous system (leptomeninges), specifically through VLA-4 and LFA-1 integrins. VLA-4 and LFA-1 are important regulators of normal T-cell migration into the CNS, so the authors tested whether they also mediate T-ALL infiltration. They generated an intracellular NOTCH1 T-ALL mouse model and then used CRISPR/Cas9 gene targeting to delete VLA-4 and LFA-1. They show that integrin-deficient T-ALL cells accumulate in the CNS compared to control T-ALL cells. The authors performed a time course experiment and found that although WT T-ALL cells accumulated in the CNS before DKO T-ALL cells, over time, DKO T-ALL cells outgrew the WT T-ALL cells. Subsequently, they performed bulk RNA-sequencing and revealed that Integrin beta 7 (Itgb7) was upregulated in the DKO T-ALL cells. To test whether Itgb7 was compensating for the loss of VLA-4 and LFA-1, the authors generated a triple KO (TKO). The TKO T-ALL cells migrated to the CNS; however, CNS accumulation between the TKO and the DKO was not significantly different. To evaluate if there is reduced exit of T-ALL DKO cells from the meninges, they inhibited T-ALL exit via the dorsal meningeal lymphatics by generating an AAV VEGF-trap encoding the binding domain of VEGFR3, and then co-injected WT: DKO cells weeks later. There was no effect on the WT:DKO T-ALL ratio or on the overall number of T-ALL cells in the CNS with meningeal lymphatics regression, suggesting that the DKO does not preferentially accumulate in the CNS, or that delayed exit results in DKO T-ALL accumulation in the CNS.

Additionally, the authors tested whether DKO affected immune surveillance by injecting DKO:WT T-ALL cells into NRG mice. DKO T-ALL cells localized in the dura mater and were spread throughout the tissue, whereas WT T-ALL cells clustered near blood vessels. These observations lead the authors to hypothesize that differential access to nutrients or other signals may influence leukemic cell proliferation. However, EdU labeling revealed no differences, leading the authors to hypothesize that the unique stromal cell layer in the meninges supports the DKO proliferative advantage. Finally, the authors tested whether integrin blockade and chemotherapy might chemosensitize T-ALL cells in the CNS. After a single treatment with 5FU, DKO cells were depleted faster than the WT cells; however, a single treatment with integrin blockade was toxic. After combining 5FU with the integrin antibodies, the authors showed that T-ALL cells in the CNS were significantly more depleted than in treatment with either single therapy.

These data highlight how challenging it is to identify regulators of T-ALL migration and adherence. This study highlights the importance of these experiments and the clinical need to identify the molecules that influence leukemic infiltration into the CNS.

Overall, this study was well performed with appropriate statistical power to implicate integrins in T-ALL CNS infiltration and proliferation.

Reviewer #2 (Public review):

Summary:

In this study, the authors set out to understand how T cell leukemia cells enter and persist in the CNS, with a particular focus on the role of adhesion molecules known to regulate normal immune cell trafficking. Contrary to expectations, they find that loss of two key adhesion molecules does not impair CNS entry but instead leads to increased accumulation of leukemia cells, which is associated with enhanced cell proliferation in this environment. These findings challenge prevailing assumptions about how leukemia cells interact with tissue niches and suggest a potential therapeutic strategy combining adhesion blockade with chemotherapy.

Strengths:

The study addresses an important and longstanding question in leukemia biology using well-designed in vivo models and multiple complementary approaches. The key observation is robust and consistently supported across genetic models and experimental systems. The authors systematically test alternative explanations, including altered entry, exit, and immune evasion, which strengthens the interpretation that proliferation differences underlie the phenotype. The work has potential translational relevance, particularly in highlighting a possible strategy to enhance the efficacy of anti-proliferative therapies in the CNS.

Weaknesses:

While the central phenotype is clear, the mechanistic basis remains incompletely defined. Addressing the following points would strengthen the manuscript.

Major critiques:

(1) The central claim that integrin loss enhances CNS accumulation via increased proliferation is not mechanistically resolved; current data are correlative (EdU incorporation, distribution patterns) and do not establish that integrin-mediated signaling directly restrains cell cycle progression in the CNS niche. The authors should perform functional perturbation of candidate pathways identified (e.g., TGF-β) using pharmacologic inhibitors or genetic approaches (dominant-negative receptor or CRISPR knockdown) in vivo or in ex vivo CNS-derived T-ALL co-culture systems to test whether blocking this pathway rescues the WT proliferation phenotype; if not feasible, the mechanistic claims should be toned down and clearly presented as hypotheses.

(2) The relationship between altered spatial distribution and proliferation is suggestive but not directly demonstrated. The imaging data indicate differences in localization, but these observations are not quantitatively linked to cell cycle status. The authors could strengthen this point by incorporating spatially resolved proliferation analyses, such as combining EdU labeling with imaging or quantifying proximity to stromal or vascular niches, or alternatively by providing additional quantitative analysis of the existing imaging data.

(3) The conclusion that CNS accumulation is not due to altered trafficking (entry/exit) is suggestive but not definitive, as early seeding dynamics are not directly assessed. Authors should perform short-term homing or early time-point competitive trafficking assays (e.g., CNS quantification at 6-48h post-transfer) to rigorously exclude differences in entry kinetics; if such experiments are not feasible, this limitation should be explicitly acknowledged in the discussion.

(4) The therapeutic claim that integrin blockade synergizes with chemotherapy is promising but underdeveloped, as it lacks survival outcomes and a broader translational context. The authors should include survival analyses and, if possible, test combination treatment in a more clinically relevant setting (e.g., delayed intervention or alternative standard-of-care agents), or otherwise temper translational conclusions and discuss risks such as inducing proliferation in the absence of chemotherapy.

Reviewer #1 (Public review):

The manuscript by the Deppmann group is an important contribution to understanding how growth factor signaling is controlled at a per-cell basis, in contrast to bulk biochemistry results. Their system uses cell culture and single-cell signalling proteomics methods to measure responses of cells of different developmental stages (from E14 rat) with complex but relatively clear-cut phenotypes, allowing the effects of BDNF to be compared. This work validates the method for the discovery of future insights from less well-studied ligand-receptor investigations.

Strengths include:

(1) The methods are cutting-edge and powerful.

(2) Clearly written. It leads the reader through the rationale of methodological steps.

(3) Step-by-step data interrogation rather than leaping into complex models of analysis.

(4) "sanity check" controls e.g., mimicking bulk culture expected signaling /expression changes.

(5) Testing biologically of certain findings within the presentation of the results ( e.g., progenitors not responding to BDNF also not internalising TrkB).

(6) Effort to make complex figures/data as understandable as possible.

(7) Not overstating conclusions.

(8) Important conclusion of receptor stoichiometry sets the potential for BDNF sensitivity, and that the intrinsic environment allows for a cell to engage that potential, something possibly thought but not demonstrated previously.

Major points:

(1) Apply appropriate statistics: Student's t-tests are used throughout. It would be more appropriate to utilise ANOVA, at least one-way, to compare across timepoints for a given phospho-protein within one treatment condition (e.g., pERK following BDNF stim), or even multiple t-tests. Also, multiple testing adjustments. are likely needed (not my expertise).

(2) Some data points are n=2; for statistical rigour n=>3 would be appropriate.

(3) They measured pTrkB with antibody targeting site Y816, which couples to PLCy/PKC/Ca2+, but not Shc (for PI3K/MEK pathways), why? Did they get any measurements using an antibody targeting the phosphorylation sites in the activation loop of the kinase? Could this explain the relatively low abundance of active TrkB, compared to the measured TrkB-dependent signalling outcomes? Especially considering the "unresponsive" cells. E.g. https://doi.org/10.1016/S0896-6273(00)00035-0.

(4) Was TrkC ( or A) expressed in any TrkB population that could potentially mediate BDNF signaling?

Reviewer #2 (Public review):

In this study, Sewell et al. use a novel approach to understand cell-specific BDNF signaling in the developing spinal cord. Using cultured E14 spinal cord, the authors used a mass cytometry approach to identify the levels of TrkB and p75NTR receptor expression, as well as 19 signaling markers and cell identification markers, to delineate activation of BDNF signaling in different cell types within a complex population. They identified that the level of receptor expression, while necessary, is not sufficient to determine the activation of signaling cascades. It has been known for some time that TrkB, indeed all RTKs, have the capacity to activate certain canonical signaling pathways; however, not all these pathways are always activated upon ligand treatment. This study begins to identify the conditions under which specific signaling pathways are activated by ligand. Specifically, the type of cell and maturation state are critical for determining signaling. The cytometry approach allows the clustering of cell types according to expression of specific markers, and overlaying those clusters onto the expression status of TrkB and p75 receptors, as well as specific activated signaling proteins. This study provides greater insight into when specific signaling events can be activated by BDNF than was previously known.

The comparison of levels of expression of TrkB and p75NTR is interesting to demonstrate which pathways may require one or both receptors for specific signaling responses.

It is very interesting that progenitors do not respond to BDNF despite abundant expression of TrkB, although they responded to the rescue treatment with phosphorylation of Erk and Akt. The development of competence to respond to BDNF is an interesting question for future analysis, and the authors suggest some possibilities in their Discussion.

The responses of glial cells in their culture preparation are also interesting. They see signaling responses to BDNF in astrocytes and "laden" microglia (presumably phagocytic). E14 spinal would not be expected to have a large population of glia at this stage of development, although the serum in their plating media would allow for the proliferation of the progenitors. Astrocytes are generally considered to have the truncated TrkB receptor, yet they see P-Erk, P-Akt, etc. in these cells in response to BDNF. This raises the question of which receptors are expressed in the glial populations and whether the responses in these cells are also maturation dependent, since the glia in their culture conditions are also likely to be immature.

Some specific comments:

(1) The authors should specify what is meant by "rescue" in the text. What is rescuing the cells from trophic deprivation when no BDNF is added? Is it the B27 and GlutaMax in the Maintenance media, and does this actually rescue the cells?

(2) Figure 3 - K252a blocked activation in most, but not all, lineages, especially in mature neurons. Is some component of the P-Erk activation in these cells TrkB independent?

(3) Figure 5 E, F - The correlation between receptor surface depletion and signaling is based on "surface-specific staining". Does the staining allow you to see internalized receptors to confirm that the receptors are internalized?

(4) The drawbacks to the study - particularly capturing snapshots in time to represent signaling cascades, are fully acknowledged in the Discussion. The interplay between TrkB-T1, TrkB-FL, and p75NTR cannot be elucidated from this study, but again, that is acknowledged and will require a different approach.

Reviewer #3 (Public review):

This study addresses a fundamental and long-standing question in neurotrophin biology, how cellular context shapes the interpretation of a single trophic message, and tackles it with a technically demanding and well-executed single-cell mass cytometry approach. By simultaneously measuring 19 signaling effectors and 18 identity markers across a developmental gradient of spinal cord cell types, the authors substantially expand our understanding of BDNF signaling and provide a compelling demonstration of the limitations inherent to bulk biochemical readouts, which average across heterogeneous populations and obscure the discrete subpopulation behavior that the present data reveal.

The finding that only 47-75% of cells respond at peak activation, that maturation state dictates both the magnitude and the qualitative "signature" of the response, and that identical receptor stoichiometries can yield divergent outcomes across cell types collectively constitute an important conceptual advance. The proposed framework of "prepared competence" is thought-provoking and likely to stimulate follow-up work.

That said, several aspects of the data interpretation deserve more critical discussion. My specific comments are detailed below.

(1) Interpretation of TrkB-independent ERK activation (lines 194-196).

The authors state that the residual pERK induction observed in TrkB-negative ("None") cells and the incomplete suppression of pERK by K252a support the established notion that BDNF signaling is not mediated solely through TrkB. This interpretation is presented without sufficient mechanistic detail and, in its current form, is difficult to follow. If BDNF-induced ERK activation is not mediated by TrkB, which alternative receptors could account for it? Does this reflect signaling through p75NTR, transactivation of other receptor tyrosine kinases, or another mechanism altogether? Likewise, the partial resistance of pERK to K252a is interpreted as evidence of an additional regulatory layer, but the underlying activity is not specified. Is the authors' hypothesis that a distinct pool of ERK is engaged independently of Trk activity? If so, what kinase activity is proposed to drive it? These results are intriguing yet puzzling and merit a more critical and explicit discussion of the candidate mechanisms.

(2) The "progenitor paradox" in light of prior work on PC12 cells (lines 207-208).

The observation that TrkB-expressing progenitors remain insensitive to BDNF is presented as a paradox and interpreted through the lens of impaired internalization. This interpretation would benefit from explicit discussion in the context of the classical work on PC12 cells (Segal and colleagues, among others), which established that plasma membrane-restricted Trk receptors engage the Ras-MAPK pathway with rapid, short-duration kinetics that drive proliferation rather than differentiation, whereas internalized Trk receptors sustain MAPK signaling and promote differentiation. Under this framework, the apparent signaling silence of progenitors could, in fact, reflect transient plasma membrane signaling that the time points sampled in the present study (5 min onward) may not capture. The single-cell mass cytometry approach used here is, in principle, well-suited to resolving such rapid kinetics, and the authors are encouraged to address this possibility, both as an alternative interpretation of their data and as a potential extension of the study.

(3) Astrocyte responsiveness and the TrkB isoform issue.

The authors report that astrocytes are highly responsive to BDNF and exhibit robust ligand-induced depletion of surface TrkB, which they interpret as evidence of signaling-competent full-length TrkB (TrkB-FL) on these cells. However, it is well established that astrocytes predominantly express the truncated isoform TrkB-T1, which lacks the intracellular kinase domain and is thought to function in BDNF capture, clearance, and recycling at synapses rather than in canonical downstream signaling. The robust phosphorylation events observed in astrocytes are therefore difficult to reconcile with TrkB-T1-mediated signaling alone. Could these responses instead reflect transactivation of other receptors through neuron-astrocyte crosstalk, for instance, via ligands released by neurons in response to BDNF? Because the authors explicitly state that their antibody cannot distinguish TrkB-FL from TrkB-T1, this limitation directly impacts the interpretation of the astrocyte data and of the proposed isoform-switch hypothesis for progenitors. This caveat is briefly acknowledged but deserves more thorough discussion, ideally with explicit consideration of the alternative interpretations outlined above.

(4) Pathways resistant to K252a inhibition.

The authors note that K252a fails to fully abolish pERK induction in several lineages, but the specific pathways, differentiation states, and receptor stoichiometries that remain K252a-resistant are currently insufficiently described. A more systematic description would strengthen this section. In addition, it would be helpful to discuss whether the residual signal could reflect the proximity of the response to the detection threshold rather than a genuinely K252a-insensitive pool of activity. More broadly, K252a is a broad-spectrum tyrosine kinase inhibitor with well-documented off-target effects, and the present study relies on this single pharmacological tool to define Trk-dependence. The limitations of this approach, and the desirability of complementary inhibitors or genetic perturbations in future studies, should be acknowledged in the Discussion.

(5) The 12-hour trophic deprivation paradigm as a potential confounder.

All cells in the present study are trophically deprived for 12 hours prior to stimulation. This is a methodologically convenient choice, but sustained deprivation is not a neutral starting point: it activates stress-responsive pathways (JNK, p38, autophagy), alters receptor surface trafficking, and can sensitize cells to subsequent stimulation. Several of the reported observations - including the apparent synergy of p75NTR with TrkB on stress markers (p-c-Jun, p38) and the strong induction of trophic effectors immediately upon BDNF addition - could be amplified, or qualitatively altered, by the prior deprivation state, which does not reflect baseline in vivo physiology. The Rescue control, with complete medium, partially addresses this concern but is non-specific. The authors should explicitly acknowledge this limitation and, ideally, discuss the extent to which their conclusions about cell-type-specific signaling competence depend on the deprivation paradigm.

(6) Direct comparison of pseudobulk data with conventional bulk biochemistry.

The pseudobulk reconstruction of the single-cell data is presented as recapitulating canonical BDNF responses, but this comparison relies on general agreement with the published literature rather than on a direct, parallel measurement in the same cultures. Given that the central conceptual contribution of the manuscript rests precisely on departures from the bulk biochemical view of BDNF signaling, an explicit side-by-side comparison of the pseudobulk profile against a parallel bulk Western blot from sister cultures - for at least a subset of key markers such as pERK, pAkt, and pCREB - would substantially strengthen the validation of the platform. Such a comparison would reassure the reader that the discrete subpopulation behavior reported here is genuinely biological, and not in part a consequence of methodological differences between mass cytometry and conventional biochemistry (e.g., differences in fixation kinetics, epitope accessibility, or sensitivity to low-abundance phosphoproteins).

(7) Manuscript organization and balance between main and supplementary figures.

The manuscript presents an exceptionally rich dataset, but the current organization - seven main figures supported by thirteen supplementary figures, several of which are explicitly labeled as extensions of main-text figures - makes it difficult to follow the argument without continuous cross-referencing between documents. I would encourage the authors to consider a substantive reorganization with the following suggestions: (i) Figure S2 and Figure S3, which respectively define the threshold-based "responsiveness" criterion and assess its robustness, are foundational to the central 47-75% responsiveness claim and would be better integrated into the main text, for example as additional panels of Figure 2; (ii) the methodological and quality-control components of Figure S1 and Figure S2 would be more naturally placed within the Methods section; and (iii) the four "Extension" figures (S4, S7, S12, S13) contain considerable redundancy with the corresponding main figures and could be consolidated, with only the most diagnostic panels retained. Concurrent trimming of the denser main figures (Fig. 4, 5, and 6 each carry six or seven panels) would further improve readability.

Reviewer #1 (Public review):

[Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed the comments raised in the previous round of review.]

Summary:

In this review paper, the authors describe the concept of neural correlates of consciousness (NCC) and explain how noninvasive neuroimaging methods fall short of being able to properly characterise an unconfounded NCC. They argue that intracranial research is a means to address this gap and provide a review of many intracranial neuroimaging studies that have sought to answer questions regarding the neural basis of perceptual consciousness.

Strengths:

The authors have provided an in-depth, timely, and scholarly contribution to the study of NCCs. First and foremost, the review surveys a vast array of literature. The authors synthesise findings such that a coherent narrative of what invasive electrophysiology studies have revealed about the neural basis of consciousness can be easily grasped by the reader. The authors also succeed in describing how single-cell recordings can interface with task-design to help mitigate the impact of confounded neural activity when searching for NCCs.

The review is also, to the best of my knowledge, the first review to specifically target intracranial approaches to consciousness and to describe their results in a single article. This is a credit to the authors - as it becomes ever harder to apply strict tests to theories of consciousness using methods such as fMRI and M/EEG, it is important to have informative resources describing the results of human intracranial research so that theorists will have to constrain their theories further in accordance with such data. Additionally, the authors provide a compelling case for single-celled research in consciousness science, despite the dominance of theories situated at the system and circuit level of analysis. As far as the authors were aiming to provide a complete and coherent overview of intracranial approaches to the study of NCCs, I believe they have achieved their aim.

Weaknesses:

Overall, I feel positive about this paper. The authors have addressed my comments from my previous review and I see no significant weaknesses in the current version.

Comment on previous version:

No comments - congratulations to the authors!

Reviewer #2 (Public review):

Summary:

In this work, the authors review the study of the neural correlates of consciousness (NCCs). They discuss several of the difficulties that researchers must face when studying NCCs, and argue that several of these difficulties can be alleviated by using intracranial recordings in humans.

They describe what constitutes an NCC, and the difficulties to distinguish between an NCC proper from the prerequisites and consequences of conscious processing.

They also describe the two main types of experimental designs used to study NCCs. These are the contrastive approach (with its report and non-report variants), and the supraliminal approach, each with their own merits and pitfalls.

They discuss the limitations of non-invasive methods, such as fMRI, EEG and MEG, as well as the limitations of the use of invasive recordings in non-human animals.

After setting the stage in this way, the authors provide an extensive review on the knowledge acquired by using invasive recordings in humans. This included population level measurements in vision and in other sensory modalities, as well as single neuron level studies. The authors also discuss studies of subcortical NCCs.

The second half of this work discusses the theoretical insights gained through the use of intracranial recordings, as well as their limitations, and a perspective for future work.

Strengths:

This work offers an impressive review, which will serve as a useful reference document, both for newcomers to the study of NCC as for experienced researchers. The inclusion of non-visual and subcortical NCCs is of particular merit, as these have been understudied.

Besides serving as a review, this work includes a perspective, exploring several directions to pursue for the progress of the field.

Weaknesses:

No major weaknesses.

Appraisal of whether the authors achieved their aims:

In this work, the authors have gathered an impressive review, and have discussed several important problems in the field of study of NCCs, as well as provided a perspective on how the field could move forward.

Discussion of the likely impact of the work on the field:

This work has the potential of becoming a must read for anyone working in the field of consciousness research.

Comment on previous version:

The authors have addressed all my concerns. Once again, my compliments for a nice piece of work.

Reviewer #3 (Public review):

Summary:

This narrative review provides a clear, well-structured, and comprehensive synthesis of intracerebral recording work on the neural correlates of consciousness. It is written in an accessible manner that will be useful to a broad community of researchers, from those new to iEEG to specialists in the field.

Strengths:

The manuscript successfully integrates methodological and theoretical perspectives and offers a balanced overview of current sometimes contradicting evidence. As such, the manuscript is important as call for a concernted better exploration of NCCs using iEEG in the future.

Comments on latest version:

The current version of the manuscript is clear and complete. Kudos to the authors for their thorough revisions.

Reviewer #1 (Public review):

Summary:

This study uses optogenetics to activate CA3 while recordings from CA1 neurons and characterizing the excitation/inhibition (E/I) balance. They observe use-dependent alterations in the E/I balance as a result of STP and they develop a model to describe these observations. This is a very ambitious paper that deals with many issues using both experimental and modeling approaches.

Strengths:

This paper examines important principles regarding the manner in which synaptic circuitry and use-dependent synaptic plasticity can transform inputs and perform computations.

Weaknesses:

There are three issues that cause concern regarding the applicability of their slice recordings to physiological conditions and that make some aspects of their results difficult to interpret. First, they state that 2 mM added external calcium mimics calcium levels in CSF, but this is not the case. This will influence the plasticity they observe. Second, they indicate that there is a 2% decrease in activated fibers per stimulus and attribute this to ChR2 desensitization. Such use-dependent decreases in fiber activation are expected to build during their repetitive activation experiments and artifactually influence their results. Third, they do not know the responses of individual CA3 cells to stimulation. They do not know if each cell fires reliably during repetitive activation and whether each cell only fires once.

Reviewer #3 (Public review):

Summary:

This work shows experimentally and computationally that single CA1 neurons can perform mismatch detection on patterned CA3 inputs and that STP and EI balance underlie this detection.

Strengths:

It has been known that STP can enhance the EPSP when the corresponding presynaptic input exhibits abrupt changes in firing rate. This work provides experimental evidence and further computational support for the hypothesis that the basic computation through STP is useful for detecting abrupt changes in the spatial pattern of synaptic inputs at the Schaffer collaterals. Further, their results indicate the novel view that mismatch detection is most efficient when gamma-frequency bursting inputs exhibit mismatches between theta cycles. The authors included novel results in the revised manuscript to show that the effective frequency range of gamma oscillation is broad, including both slow and fast gamma bands.

In the initial submission, the dependence of mismatch detection performance on model parameters and experimental settings, such as pattern overlaps and other network parameters, was not sufficiently explored. In the revised manuscript, the authors extensively studied these points and summarized the novel results in Fig. 9. Furthermore, the authors clarified that jitters in input spikes can improve detection performance in some cases. These results show the robustness of their results against variations in external and internal conditions.

Weaknesses:

While this study shows an intriguing example of combined experimental and computational studies, some analytic results, for instance, regarding the complex contributions of jitters to detection performance, could have clarified the underlying mechanism deeper and further strengthened the manuscript.

Reviewer #1 (Public review):

Summary:

Using a computational modeling approach based on the Drift and Diffusion Model (DDM) introduced by Ratcliff and McKoon in 2008, the article by Shevlin and colleagues investigates whether there are differences between neutral and negative emotional states in:

(1) The timings of the integration in food choices of the perceived healthiness and tastiness of food options in individuals with bulimia nervosa and healthy participants

(2) The weighting of the perceived healthiness and tastiness of these options.

Strengths:

By looking at the mechanistic part of the decision process, the approach has potential to improve the understanding of pathological food choices.

Comments on revised version:

I went carefully through the answers of the authors to my last concerns - they answered all my points. I am grateful that they obtained consistent results with the different analyses.

Reviewer #1 (Public review):

Summary:

This manuscript examines the frequency-dependent effects of transcutaneous tibial nerve stimulation (TTNS) on bladder function in healthy volunteers, supported by a conductance-based computational model of lower urinary tract (LUT) neural circuitry. The authors show that 1 Hz TTNS modestly hastens the urge to void, while 20 Hz TTNS delays it - a finding with potential therapeutic relevance for underactive bladder (UAB). A computational model incorporating spinal, brainstem, and peripheral circuit elements provides a mechanistic framework suggesting brainstem-mediated pathways underlie these frequency-dependent effects. The revised manuscript addresses the majority of concerns raised in the initial review.

Strengths:

Novelty. Demonstrating a low-frequency excitatory effect of TTNS in humans is genuinely new. The possibility of inverting the therapeutic effect of an established neuromodulation intervention by simply adjusting stimulation frequency is clinically meaningful and opens a plausible treatment avenue for UAB.

Integrated approach. Combining a controlled human pilot study with a systems-level neural model is a notable strength. The model is physiologically grounded and serves well as a proof-of-concept tool for exploring mechanistic hypotheses.<br /> Improved reproducibility. The addition of a public GitHub repository with documented code, supplementary figures detailing electrode placement and stimulation parameters, and removal of the externally derived Figure 3 all meaningfully improve transparency.

Improved statistics. The shift to Bayesian modelling with ROPE analysis is well-justified given the small sample size and more appropriate than frequentist testing in this context.

Improved presentation. Unit standardization, figure label corrections, and replacement of imprecise terminology (e.g., "paradoxical", "analytically") make the revised manuscript considerably clearer.

Remaining Concerns:<br /> Afferent-efferent disconnect. The human study measures urgency (an afferent sensory endpoint), while the model's primary output is contraction duration (an efferent motor endpoint). The authors have added discussion of this mismatch, but should state more explicitly that the two lines of evidence are complementary rather than directly comparable, and that the mechanistic link between them remains a hypothesis.

Clinical contextualization of effect size. The excitatory effect of 1 Hz TTNS is modest. A brief reference to what a minimally clinically important difference might look like in UAB or urodynamics research would help readers gauge the translational significance of the finding.

Overall Appraisal:<br /> The authors have achieved their stated aims: providing proof-of-concept human evidence for frequency-dependent TTNS effects and a plausible neural circuit explanation. The manuscript is now appropriately cautious in its claims. The open-source computational model is a useful community resource. This work is best understood as a well-scoped proof-of-concept study that credibly motivates further investigation.

Reviewer #2 (Public review):

Strengths:

The main strength of the work is to call attention to a new possibility of inverting the effect of TNS in humans by manipulating stimulation frequency, opening new indications for the therapy. This is highly relevant because of the recent popularity of TNS and its non-invasiveness, which lends itself to rapid testing and evaluation for new conditions and high willingness to adopt. The authors convincingly demonstrate a modest excitatory effect on bladder sensation with low-frequency TNS, which clearly warrants further investigation.

The high-level design of the hypotheses, concepts, and experiments are clearly articulated in both the methods and in particularly clear diagrams, letting the reader focus their attention on the most important findings.

It is rare to develop a new computational model of the lower urinary tract at a systems level, and even more so for it to incorporate circuits in the spinal cord and brainstem centers, and this work undoubtedly advances the field's ability to engineer such systems. Further, because the model is comprised of linked conductance-based point-neurons, it is an excellent tool to investigate how an arguably plausible wiring diagram for neural control of the LUT could result in stimulation frequency dependent effects on pelvic efferents. It is a proof of concept demonstrating how their mechanistic hypothesis of TNS could be implemented neurophysiologically by the nervous system. Further, the model is shared openly, which conforms to good modeling practices.

Weaknesses:

The main drawback of the work is the overinterpretation of the results. The human study and computational model are both proof-of-principle. The human study effect size is small and the sample size is modest; the computational model is poorly validated and does not generate physiologically typical urodynamic responses when simulating even healthy nominal LUT conditions. Thus, both the existence of a TNS 1Hz inhibitory effect (human study) and the mechanistic interpretation of its origin (simulations) remain provisional. For example, despite some caveats later in the work, the abstract stating there is a "frequency-dependent effect of TNS via the ability to alter urge perception and down-regulate bladder activity, corroborating model predictions," could easily be misleading, since a) the reduction in time of first urge with 1Hz stimulation was quite small relative to overall void time, b) reported intensity was essentially not impacted, and c) the model does not directly make predictions about these experiment outcome measures. Similar overreaching statements appear in the second to last paragraph of the introduction, the first paragraph of the discussion, and so on throughout the paper. Many of the analyses are bespoke to the idiosyncrasies of the dataset rather than field standards, making spurious results also more likely and the effects provisional. One example is the use of robust linear regression to identify significance in the experiment between the 1Hz and control groups AND removing outliers before the analysis, since the typical approach is to use robust regression when the outliers are left in the data. Taken together, the potential excitatory effect and mechanism are interesting, and perhaps worth further investigation, but are considerably more tentative than stated.

It remains ambiguous whether a TNS excitatory effect size shown (even if it ends up being repeatable) is clinically meaningful. The ROPE analysis is a reasonable start, but no attempt to connect the parameters chosen (e.g. 60s) to clinical outcomes were made. This is especially true given the washout results and lack of effect on perceived urgency.

There remain several reasons to treat the model results questionable. First, as the authors now note, the model under normal conditions does not generate normal function; a voiding efficiency of 15% is severely underactive. Second, the 1 Hz stimulation simulation appears to create normal voiding, suggesting that the implementation of the neural control circuits may not produce results that would generalize to other experiments. Third, analysis focuses on the model outcome of "time to void", but this outcome is not reported for the experiment, so direct comparison is not possible.

Reviewer #1 (Public review):

[Editors' note: Given the minor nature of this revision, the editors have not sent this back to the original reviewers. The original reviews have been included.]

In this study, the authors set out to determine how two classes of kinase inhibitors, which stabilise a disease-relevant enzyme in either an active (Type I) or inactive state (Type II), influence its organisation and interactions with microtubule filaments in cells. Using the state-of-the-art in-cell structural imaging approaches, they examine how these compounds affect the formation of protein filaments and their association with microtubules, and succeed in defining the underlying structural basis for these differences.

A major strength of the work is the application of in-cell cryo-electron tomography combined with correlative imaging, which enables direct visualisation of protein organisation in a near-native cellular context. The data convincingly demonstrate that the Type I inhibitor compound stabilising the active state promotes extensive LRRK2 filament formation and microtubule bundling, whereas compounds stabilising the inactive state markedly reduce these interactions. The structural analysis further provides insight into how conformational states relate to filament organisation, including modelling of previously unresolved regions of the protein.

These findings are internally consistent and align well with prior biochemical and structural studies, many of which were performed by the same team.

There are, however, some limitations that should be noted. The experiments rely on overexpression of the I2020T mutant form of the LRRK2 protein, which is a rare variant, in a single cell type (293T cells), which may not fully reflect endogenous behaviour or wild-type LRRK2 in a physiological context. In addition, while the imaging data are compelling, the functional consequences of the observed filament formation and microtubule association remain unclear.

The study therefore provides strong descriptive and structural insight, but more limited evidence linking these observations to cellular or disease-relevant outcomes.

Overall, the authors largely achieve their aims, and the results support their central conclusion that different classes of kinase inhibitors have distinct effects on protein organisation in cells. The work represents an important advance in understanding how small molecules can reshape protein architecture in a cellular environment, with potential implications for therapeutic strategies. The methodological approach will also be of broad interest to the field, as it highlights the power of in-cell structural biology to study dynamic protein assemblies that are difficult to capture using traditional approaches.

Reviewer #2 (Public review):

Summary:

Mutations in Leucine-Rich Repeat Kinase 2 (LRRK2) are a major cause of Parkinson's disease. LRRK2 PD-related mutations all result in increased kinase activity. Therefore, LRRK2 has been the focus of the development of kinase inhibitors. So far, two classes of kinase inhibitors have been identified: type 1 LRRK2-specific inhibitors that stabilize LRRK2 in a closed active-like conformation and broad-range type 2 inhibitors that stabilize LRRK2 in an open inactive-like conformation. Basiashvili et al. used here in cell structural biology to study the effect of both type 1 and type 2 inhibitors on the localization and structural conformation of LRRK2-I2020T.

Strengths:

They showed that Type 1 and not Type 2 inhibitors induce LRRK2 filament/ on microtubules. Furthermore, they were able to build a structural map of full-length LRRK2 I2020T bound to a Type 1 inhibitor in a closed kinase confirmation. Together, this work thus confirms the data of previous studies that showed that LRRK2 Type 1 and 2 inhibitors differently affect filament formation.

Previous Weaknesses:

All conclusions are fully supported by the provided data. However, as the authors indicated themselves, the physiological relevance of LRRK2 microtubule binding is questionable. Furthermore, although the authors used a full-length LRRK2 protein, like in previously published structures, the resolution of the N-terminal domains is rather poor. Therefore, it also remains unclear what we learn from this structure compared to the previously published structures.

Reviewer #3 (Public review):

Summary:

This paper describes new insights into the effects of type-I and type-II LRRK2 inhibitors on HEK293T cells that over-express GFP-labeled LRRK2-I2020T. Using correlative light microscopy and cryo-electron tomography, a type-I inhibitor leads to the extensive decoration of microtubules with LRRK2, which is not seen for a type-II inhibitor. Subtomogram averaging reveals that LRRK2 binds to the microtubules in a closed-kinase conformation, with density for the N-terminal arms.

Strengths:

The paper is well written; the CLEM and cryo-ET appear to be done to a high standard. Consequently, I have only minor comments.

Weaknesses:

The resolution of the subtomogram averages is somewhat limited, but the authors have adequately limited the number of degrees of freedom in the fitting of their atomic models by only allowing rigid-body transformations of separate parts of LRRK2.

The authors should include FSC curves between the rigid-body fitted atomic models and the various sub-tomogram average maps.

Comment on the current version from the Reviewing Editor:

I do note that Ext Data Fig 8 does not yet contains the requested model-vs-map FSC curves. I guess this is an oversight and trust that the authors will remedy this during the production process. They might also want to explain what the black, red, green and blue FSC curves are in the current figure (or only show the black (solvent-corrected FSC) curve, together with the requested model-vs-map curve.

Reviewer #1 (Public review):

Summary:

In this study, the authors aim to identify the neural circuit mechanisms underlying dystonic crisis, a severe and life-threatening manifestation of dystonia, and to explore potential therapeutic targets. The authors combine retrospective clinical data from pediatric patients with mechanistic experiments in a genetic mouse model of dystonia. They focus on inhibitory cerebellar nuclei neurons (iCNNs), testing whether these neurons can trigger dystonic crisis and whether their modulation can alleviate symptoms. Using optogenetics, anatomical tracing, and deep brain stimulation (DBS), the authors propose that iCNNs drive dystonic crisis via projections to the centrolateral (CL) thalamus and that this pathway can be therapeutically targeted.

Strengths:

A major strength of the study is its integrative approach, bridging human clinical observations and mechanistic animal experiments. The clinical analysis provides suggestive evidence linking cerebellar abnormalities and inhibitory signaling to dystonic crisis, which motivates the subsequent experimental work. In the mouse model, the authors use cell-type-targeted optogenetic manipulation to show that activation of iCNN pathways induces dystonic crisis-like episodes, while inhibition alleviates spontaneous crises. These bidirectional manipulations provide strong support for a causal role of iCNN activity in modulating disease severity. The identification of a monosynaptic projection from iCNNs to the CL thalamus, combined with DBS experiments showing therapeutic effects, further strengthens the proposed circuit mechanism and highlights translational relevance.

The behavioral effects reported are robust and reproducible across animals, and the use of both activation and inhibition paradigms is a notable strength. The DBS experiments are particularly compelling in demonstrating that modulation of a downstream node can mitigate symptoms induced by upstream circuit activation, supporting the functional relevance of the identified pathway.

Weaknesses:

However, several limitations temper the strength of the conclusions.

First, the specificity of the genetic and optogenetic manipulations is not absolute. The Ptf1a-based strategy targets iCNNs but also labels other neuronal populations and projections, raising the possibility that off-target effects contribute to the observed phenotypes. Although the authors argue that light spread and anatomical considerations make this unlikely, more discussion on evidence of circuit specificity would strengthen the claims.

Second, the behavioral definition and quantification of "dystonic crisis" in mice, while carefully described, remain somewhat subjective and may not fully capture the complexity of the human condition. Additional quantitative or automated behavioral analyses could increase confidence in the interpretation of these episodes and facilitate comparison across conditions. If difficult to add, please at least discuss this aspect.

Third, while the anatomical tracing suggests a projection from iCNNs to the CL thalamus, the functional contribution of this specific synaptic connection is inferred rather than directly demonstrated. The DBS experiments support involvement of the CL but do not establish whether the iCNN→CL pathway is necessary or sufficient for the observed effects. More direct circuit-level manipulations would be required to fully validate this mechanism. If difficult to perform these experiments, please at least discuss the importance of such future studies.

Finally, the translational relevance, while promising, remains somewhat speculative. The clinical data are retrospective and correlative, and the therapeutic implications of targeting this pathway in humans will require further validation.

Overall, the authors have achieved their primary aim of identifying a cerebellar inhibitory circuit that can drive and modulate dystonic crisis in a mouse model. The results support their central conclusions, although some mechanistic aspects remain incompletely resolved. The study provides a valuable contribution to the field by highlighting a previously underappreciated role of inhibitory cerebellar output neurons and suggesting a new circuit-based framework for understanding and treating severe dystonia.

Reviewer #2 (Public review):

Summary:

The role of the cerebellum in producing and modifying dystonic motor phenotypes has been of increasing recent interest to understand the pathophysiology of movement disorders, as well as to develop novel pharmacological and surgical interventions to treat these disorders. Previous rodent and human imaging studies have shown that in genetic, drug-induced, and injury-acquired dystonia, cerebellar dysfunction and output from the deep cerebellar nuclei have correlated with the development of dystonia symptoms. In some genetic dystonia patients, the strength of connections between the cerebellum, thalamus, and cortex could explain reduced penetrance or severity of symptoms in these genetically defined dystonia patients. Altogether, these studies have pointed to abnormal output from the cerebellum as a driver of abnormal motor output. Some studies have even gone as far as to suggest that no cerebellum is better than a cerebellum with abnormal output (see PMID 8491286). This indicates a critical need to understand the neural circuits underlying dystonia development, how the cerebellum drives symptom onset or severity, and if the cerebellum could be therapeutically targeted for the benefit of patients with dystonia.

Hipolito et al. use rigorous mouse genetics-based approaches to understand how a specific cell type, inhibitory projection neurons from the cerebellar nuclei, can drive dystonic phenotypes, especially severe dystonic phenotypes. The authors demonstrate a number of novel findings that further support a critical role for disturbed cerebellar output in driving dystonic phenotypes, and that disrupting this disturbed output may provide a novel therapeutic approach for dystonia. Specifically, the authors define a novel role for inhibitory neurons of the cerebellar nuclei in driving disease, and these neurons have not previously been observed to have monosynaptic connections into a specific nucleus of the thalamus. Disruption of these connections via deep-brain stimulation alleviated severe dystonic crisis with quick onset, and repeated stimulation sessions possibly had a long-term disease-modifying effect. Overall, these findings present novel insight into the circuits and mechanisms by which inhibitory neurons of the cerebellar nuclei influence dystonic states, and how these may be a viable therapeutic target for severe dystonia. My specific comments are below:

Strengths:

The manuscript uses rigorous mouse genetics techniques to provide fundamental insight into the role of inhibitory projection neurons of the cerebellar nuclei in influencing dystonic states. Solid experimental evidence is used to step-by-step illustrate circuit-level consequences of inhibitory projections of the cerebellar nuclei, and whether these can be manipulated for therapeutic benefit.

Weaknesses:

There are mild weaknesses in the approach around proving the specificity of the vGlut2 knockout, the long-term effects of silencing inhibitory projections, as well as the degree to which activation specifically drives dystonic crisis. These are addressed in my specific comments below.

Reviewer #1 (Public review):

[Editor's note: This version has been assessed by the Reviewing Editor without further input from the original reviewers. The authors have addressed all concerns raised by the reviewers; no further changes are required at this point.]

Summary:

The manuscript by Yang et al. investigates the relationship between multi-unit activity in the locus coeruleus, putatively noradrenergic locus coeruleus, hippocampus (HP) sharp-wave ripples (SWR) and spindles using multi-site electrophysiology in freely behaving male rats. The study focuses on SWR during quiet wake and non-REM sleep, and their relation to cortical states (identified using EEG recordings in frontal areas) and LC units.

The manuscript highlights differential modulation of LC units as a function of HP-cortical communication during wake and sleep. They establish that ripples and LC units are inversely correlated to levels of arousal: wake, i.e. higher arousal correlates with higher LC unit activity and lower ripple rates. The authors show that LC neuron activity is strongly inhibited just before SWR detected during wake. During non-REM sleep, they distinguish "isolated" ripples from SWR coupled to spindles and show that inhibition of LC neuron activity is absent before spindle-coupled ripples but not before isolated ripples, suggesting a mechanism where noradrenaline (NA) tone is modulated by HP-cortical coupling. This result has interesting implications for the roles of noradrenaline in the modulation of sleep-dependent memory consolidation, as ripple-spindle coupling is a mechanism favoring consolidation. The authors further show that NA neuronal activity is downregulated before spindles.

Strengths:

In continuity with previous work from the laboratory, this work expands our understanding of the activity of neuromodulatory systems in relation to vigilance states and brain oscillations, an area of research that is timely and impactful. The manuscript presents strong results suggesting that NA tone varies differentially depending on coupling of HP SWR with cortical spindles. The authors place their findings back in the context of identified roles of HP ripples and coupling to cortical oscillations for memory formation in a very interesting discussion. The distinction of LC neuron activity between awake, ripple-spindle coupled events and isolated ripples is an exciting result and its relation to arousal and memory opens fascinating lines of research.

Reviewer #2 (Public review):

Summary:

In this study, authors studied the synchrony between ripple events in Hippocampus, cortical spindles and Locus Coeruleus spiking. The results in this study together with the established literature on the relationship of hippocampal ripples with widespread thalamic and cortical waves, guided authors to propose a role for Locus Coeruleus spiking patterns in memory consolidation. The findings provided here, i.e. correlations between LC spiking activity and Hippocampal ripples, could provide basis for future studies probing the directional flow or the necessity of these correlations in the memory consolidation process. Hence, the paper provides enough scientific advance to highlight the elusive yet important role of Norepinephrine circuitry in the memory processes.

Strengths:

Authors were able to demonstrate correlations of Locus Coeruleus spikes with hippocampal ripples as well as with cortical spindles. Specific strength of the paper is in the demonstration that the spindles that activate with the ripples are comparatively different in their correlations with Locus Coeruleus than those which do not.

Reviewer #3 (Public review):

This manuscript examines how locus coeruleus (LC) activity relates to hippocampal ripple events across behavioral states in freely moving rats. Using multi-site electrophysiological recordings, the authors report that LC activity is suppressed prior to ripple events, with the magnitude of suppression depending on ripple subtype. Suppression is stronger during wakefulness than during NREM sleep and least pronounced for ripples coupled to spindles.

The study is technically sound and addresses a timely and important question regarding how LC activity interacts with hippocampal and thalamocortical network events across vigilance states. While the findings are interesting, they remain observational in nature.

Reviewer #1 (Public review):

Summary:

The manuscript examines whether scene meaning guides overt attention in rhesus macaques. Two monkeys freely viewed naturalistic indoor scenes, including laboratory or housing scenes described as familiar and other indoor scenes described as unfamiliar. The authors compare fixation locations with matched non-fixated control locations using predictors derived from center proximity, image salience, and a DeepMeaning model intended to capture the spatial distribution of semantic informativeness. They report that meaning predicts fixation selection beyond salience and center bias, that meaning and salience interact, that familiar scenes produce broader exploration of low-meaning regions, and that the influence of meaning increases with attentional engagement.

Strengths:

A major strength of the study is its use of natural free-viewing behavior in macaques. The experimental approach takes advantage of intrinsic gaze allocation rather than relying on a more artificial task, which makes the work a useful bridge between human scene-viewing studies and future neurophysiological studies in nonhuman primates.

The statistical analyses are extensive. The authors model fixated and matched non-fixated samples with Bayesian generalized linear mixed models, including center proximity and salience as important controls, examined interactions among predictors, and reported diagnostics for multicollinearity and model convergence. These analyses support the basic observation that the human-derived meaning maps are associated with macaque fixation allocation beyond the particular center and salience terms included in the model.

The question is interesting and timely. If meaning-like scene structure can be operationalized for macaque viewing, this would provide a useful behavioral foundation for future work on the neural mechanisms that link scene analysis, gaze allocation, and natural behavior.

Weaknesses:

The main weakness is interpretive. The manuscript often treats the DeepMeaning map as though it measures scene meaning for the monkey, but the map is ultimately human-derived. Some of the examples make this issue especially salient: regions such as clocks, phones, dining tables, or other human artifacts may be meaningful to human observers, but it is not clear that they have semantic meaning for macaques. If meaning-based guidance is argued to emerge through experience, then unfamiliar human indoor scenes that the monkeys have never encountered cannot straightforwardly be meaningful to them in the same sense that they are meaningful to humans. Predictive success for these scenes may therefore indicate sensitivity to visual or object-level structure correlated with human-rated meaning, rather than macaque semantic understanding.

A related concern is that the DeepMeaning predictor may capture forms of visual salience, objectness, or high-level image structure not captured by the particular low-level salience model. For example, a clock or phone may attract gaze because of shape, contrast, face-like configuration, object boundaries, or other mid-level features rather than because it carries semantic meaning for a macaque. The present analyses show that this model is predictive, but they do not by themselves establish that the predictive variable is semantic meaning rather than visual structure beyond Itti-Koch-style salience.

The manuscript relies heavily on fitted model parameters and derived maps, with relatively little return to the raw behavioral data. The main claims would be easier to evaluate if the authors showed more direct fixation-density maps, scene-by-scene examples, and aggregate raw relationships between fixation behavior and map values. At present, much of the argument rests on interpreting fitted coefficients, without enough behavioral visualization to show what the monkeys actually did across the stimulus set.

It is also unclear whether model performance was evaluated on held-out data. The comparison to repeated viewing of the same images is useful as a behavioral benchmark, but a second viewing may itself be affected by familiarity or memory for the image. This makes it a potentially imperfect estimate of a noise ceiling for first-pass fixation predictability. Cross-validation or held-out prediction, ideally across held-out images as well as trials, would make the predictive claims more convincing.

Although the authors describe multicollinearity as negligible, Figure S2B-C appears to show some nontrivial correlations among predictors. These correlations may matter for interpretation even if variance inflation factors fall below conventional thresholds, especially when the signs of fitted effects point in directions that may be expected from the input correlations, such as relationships involving meaning and familiarity. The manuscript would benefit from reporting these correlations quantitatively and relating them to the fitted effects.

The familiarity analysis is interesting but would benefit from further control. Familiar scenes are photographs of the monkeys' housing and laboratory environments, whereas unfamiliar scenes are other indoor environments. These categories may differ not only in familiarity but also in clutter, spatial layout, object density, color distribution, luminance, contrast, edge density, texture statistics, or the distributions of salience and meaning values. Without additional characterization of the image sets, the conclusion that familiarity itself broadens exploration should be treated cautiously.

The engagement effects also appear less consistent across the two monkeys than some of the summary language suggests. The monkey-specific results should be emphasized, and claims about engagement strengthening meaning-based guidance should be stated in proportion to the cross-animal evidence.

Finally, the manuscript sometimes uses language that sounds more mechanistic than the behavioral data can support. The negative interaction between meaning and salience is an interesting result, but terms such as competitive integration in a shared priority map go beyond what can be concluded from overt fixation selection alone. The study lacks a causal or perturbational manipulation, such as image inversion or another transformation that preserves local features while altering semantic organization. The result would be clearer if described first as a model-based association or subadditive interaction in gaze allocation, with the priority-map interpretation presented as a plausible account rather than a direct conclusion.

Reviewer #2 (Public review):

Summary:

In prior work, the authors developed an ML algorithm that computes spatial maps of "meaning": image regions that are likely to be given semantic labels by human observers. They also previously showed that "meaning" predicts fixations in humans and human infants. Here, these observations were extended to macaque monkeys, testing the hypothesis that meaning is a phylogenetically preserved driver of overt attention across primates.

Strengths:

The paper reports that fixated locations had higher values of meaning compared to nearby, non-fixated locations. Specifically, it shows that meaning values - as inferred from a neural network model - are useful in differentiating these two classes of locations, beyond the established effects of image salience and centrality on gaze. The reported results were consistent in both monkeys.

Weaknesses:

It is difficult to understand what, precisely, is meant by meaning from this paper, although the prior work from this group may offer some insight. Given that, it is not clear if "high-meaning" image locations tend to be objects, for example, or faces, or other such behaviorally relevant image features. Indeed, the utility of the meaning maps was not evaluated against other algorithms that consider more complex natural scene information. This is a particular concern as the paper does not demonstrate that meaning predicts where the viewer will look within the image; instead, it shows that meaning is one of the variables that differentiates fixated locations from nearby non-fixated locations. Because this is not a causal study by necessity, caution is also needed in interpreting the results. In our view, the most parsimonious interpretation may not be that meaning guides gaze in monkeys, but instead that people tend to name things that primate brains evolved to fixate on at the expense of neighboring locations.

Reviewer #3 (Public review):

Summary:

This novel study asks whether meaning-based guidance of overt attention, well-established in humans through the "meaning map" framework, extends to non-human primates. The authors recorded eye movements from two rhesus macaques freely viewing naturalistic indoor scenes and modeled fixation selection using DeepMeaning maps, Itti-Koch salience maps, and center proximity. They report that scene meaning robustly predicts fixation selection after controlling for salience and center bias, that meaning and salience interact competitively rather than additively, and that the influence of meaning is modulated by scene familiarity and attentional engagement. The cross-species extension of the meaning map approach is a valuable contribution, and the Bayesian GLMM framework with variance partitioning is well-suited to the question.

Strengths:

(1) The cross-species extension itself is novel and well-motivated. Nobody has applied the meaning map framework to NHP gaze behavior before. Even with the interpretive caveats I raise below, creating this methodological bridge between human scene perception research and NHP circuit neuroscience is a valuable contribution.

(2) The statistical framework is strong. The Bayesian GLMM with posterior distributions, HDIs, and probability of direction is more informative than frequentist alternatives. The variance partitioning with ΔR² is the right approach for disentangling predictor contributions. Random intercepts for scene are appropriate. The convergence diagnostics (R-hat = 1.00, ESS > 8000 across all models) are exemplary.

(3) Transparent individual-subject reporting. With N = 2, reporting each monkey separately rather than pooling or averaging is the correct choice, and the authors do this consistently. The individual differences are visible because the reporting is honest.

(4) The experimental design is excellent. 200 scenes is a substantial stimulus set by NHP standards. The inclusion of both familiar and unfamiliar environments, the repeated-viewing design for reliability estimation, and the 5-second free viewing window that yields ~15 fixations per trial all reflect thoughtful design.

(5) The familiarity and engagement analyses go beyond the basic demonstration. Even with the limitations we identified, asking how behavioral context modulates the meaning-gaze relationship is more ambitious than simply showing that the correlation exists. These analyses generate testable predictions for future work.

(6) Data and code sharing commitment. The authors plan to release raw data, preprocessing, and analysis code on OSF and GitHub.

Weaknesses:

(1) The authors' central claim is that meaning-based attentional guidance is an "evolutionarily conserved component of primate vision." This claim rests on the finding that macaque fixation patterns correlate with DeepMeaning maps. However, DeepMeaning is trained on human ratings of local scene meaning using a vision-language transformer (CoCa) pretrained on billions of human image-text pairs. What the model captures, then, is the spatial distribution of visual structure that humans judge to be semantically informative. The authors acknowledge that DeepMeaning represents "structured visual representations of scene regions containing identifiable objects and informative relationships" (lines 261-262), but this acknowledgment actually highlights the problem: regions containing identifiable objects and informative spatial relationships would plausibly attract fixations in any visual system with object-selective neurons and a bias toward structured content, regardless of whether the observer is processing "meaning" in any semantic sense. That is, the correlation between macaque gaze and DeepMeaning maps is consistent with shared object-level visual processing, but doesn't uniquely implicate shared semantic processing. The critical adversarial test from Hayes & Henderson (2022a)-where meaning maps detected the removal of semantic content via diffeomorphic scrambling while deep saliency models did not-has not been applied to macaque viewing behavior. Importantly, such a test would require new data collection (showing monkeys scrambled scenes), which may not be feasible. A more tractable approach with the existing data would be to compare DeepMeaning against some other model that captures mid-level visual structure without semantic supervision, though this would be a weaker test. Given these constraints, I would ask the authors to (a) acknowledge this limitation explicitly and temper the evolutionary conservation claim accordingly-for example, framing the result as evidence that macaques and humans share attentional biases toward visually structured scene regions, with the semantic interpretation remaining an open question-and (b) note the diffeomorphic scrambling experiment as an important future direction for establishing whether macaque attention is guided by semantic content per se.

(2) The familiar/unfamiliar scene comparison confounds long-term familiarity with systematic differences in scene content. Familiar scenes are photographs of the vivarium and laboratory; unfamiliar scenes are restaurants, bedrooms, kitchens, and offices. These two categories almost certainly differ in visual complexity, object density, spatial layout, clutter, and the types of objects present. The familiar environments (vivarium caging, lab equipment) are likely more spatially repetitive and lower in object diversity than, say, a restaurant or residential kitchen. Any difference attributed to "familiarity" could therefore reflect these systematic content differences. The negative interaction between meaning and familiarity (Monkey V: β = −0.19; Monkey I: β = −0.19), which the authors interpret as familiarity broadening exploration, could instead reflect the fact that vivarium/lab scenes have a different distribution of meaning values or a different relationship between meaning and salience than human domestic environments. The authors should address this confound directly. At minimum, comparing the distributions of meaning and salience values across the two scene categories would help the reader evaluate whether the familiarity effect can be separated from content effects. Ideally, the authors would include a subset analysis using only scenes matched on feature distributions or include scene-level summary statistics of the meaning and salience maps as covariates in the familiarity model.