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small pieces

some thoughts can only be thought in the dark, but

The LLM leaves a bitter taste but...

I wish people's works were more online—more accessible (preferably, with stable, citable URLs). But to say that the people themselves should be more public in the sense that the author means here is just a continuation and strong endorsement of the modern (Facebook and onwards) social networking era, and it goes against everything we've learned during this time.

It's great if all of a person's interactions across, say, many mailing lists are preserved and available—and aren't just holes, missing from the record.* That's different from whether or not it's great to be able to click on that person's name, find a profile page for them, and then encounter an exhaustive, reverse chronological feed of all of their activity across all mailing lists. Mailing lists rarely enable this, but virtually every modern social network does, and they're actually built around it.

The former is topic-based indexing, and the latter is actor- (person-) based indexing. Actor-based indexing is bad, and we now know that it's bad.

Actor-based indexing is like running into someone you know (or a stranger, even) at the post office and then, through some mechanism where their physical presence is connected to the metaverse, being able to perform some tap/gesture at the virtualized floating bubble over their heads and then get to see all the public places where you would have seen them earlier that day if you had been at any one of those, and then having a log of every interaction for the day prior, and the day before that, and so on, stretching back over their entire life, including the grocery store, the restaurant, the houseparty they were at, their work, etc. This would be bad. That means it's not good. And it's not good "online", either, for the exact same reasons.

* as unfortunately, many Mastodon (and other ActivityPub-powered) interactions turn out; Mastodon happens to achieve the worst of both worlds!

The formal def at the time of a document, every knowledge carrying material, that can be consulted, studied used as proof.

Three essays:

• a technique for knowledge work
• a distinct profession
• a necessity of our times

The first and last sound promising as title.

Qu'est-ce que la documentation? 2024 edition w notes, of the 1951 original 3 essays. In calibre.

Briet published Qu'est-ce que la documentation? at the height of her professional life, working at the national library as head of the reference service, and 3 yrs before her early retirement.

!

!

[[Every Living Thing by Jason Roberts]] Linnaeus as categoriser, applying predefined structure, where the structure is only partly emergent from observation.

Esto tiene que ser centrado en la escuela

The tech is straigthforward: sqlite, node.js and html/css. The value is the combination of different sources into personal tool.

phrased in his 'information capital' terms, he wants the highest possible compounding effect, great service from his tools, high security (locally stored and hosted e.g.), and high speed (reduced friction is higher liquidity)

a life lens magnifies details and shows patterns, by shifting perspective. Finds the constellations in your disparate data sources.

A lens does not create anything new, all the information is already there, but it lives fragmented over a bunch of different apps. Unconnected.

[[Martijn Aslander]] struggled for words to describe what he built for himself, at mix of life tracking, pkm, crm, dashboards and more. What is the amalgam of that?

No shit, Sherlock. Should've researched a bit before jumping into a 6 person project, don't you think?

Molleindustria sorta did this.

Loop games like Rue Valley, 12 minutes, Outer Wilds, Minit, or Oxen Free, hardly portray emancipation pathways. Replayable ones, like I Was a Teenage Exocolonist, or Papers, Please, might, but most roguelikes won't. Hades doesn't.

Yes, but arguably you are talking more about the mind and body, as stated. You are talking about rape, and war, and dick picks, and blackmail, and death threats, doxxing. You are talking about invisible suffering. Depression, anxiety, and problems with addiction are not like a scar or a leg injury. They get often ostracised, and people are not taught how to share them to regulate them with help.

As in mutual respect: I tend for you, and you tend for me. An issue is that people may deny their vulnerability. They may dismiss it as any other attribute or sentiment. They may be infatuated with riches, and think they are immune behind the screen, relying on the trope that only girls cry, and that psych harm is separate from physical one. Further, practicing ethics of care requires a lot of time and continuous effort to minimise oneself, to revise and make one obsolete. To stop creating and start listening, to not pursue firstness, but secondariness, to be invisible, not acknowledged, not praised. It is tough, and can lead to burnout.

If you play defensively, or a support role, or alone; if you have an effeminate name tag, skin, or cosmetics... you may be a target, through chat, for instance (but hackers could also track your IP in other ways).

Two arguments are being made here: First, player events impact non-players. Second: Players, even if thought invisible, leave bodily tracks.

Player events can be festivals, performances, but also cultural shenanigans and terms like inting, or gg ez, which can convey a competitive way of narrating out of the gaming sphere. Players leave tracks the moment they download a game, in the form of cookies, if the game requires Internet connection or has an anti-cheat tool (Riot Vanguard), if it has a log that gets mixed with OS files, or if it has a public profile linkage like a Rocket League ranking tracker, modding store, Mario Maker level, Steam user, or Animal Crossing island. These are our creations, extensions —limbs— of ourselves, of our image, and ideas.

eLife Assessment

This useful study presents Altair-LSFM, a solid and well-documented implementation of a light-sheet fluorescence microscope (LSFM) designed for accessibility and cost reduction. While the approach offers strengths such as the use of custom-machined baseplates and detailed assembly instructions, its overall impact is limited by the lack of live-cell imaging capabilities and the absence of a clear, quantitative comparison to existing LSFM platforms. As such, although technically competent, the broader utility and uptake of this system by the community may be limited.

Reviewer #1 (Public review):

Summary:

The article presents the details of the high-resolution light-sheet microscopy system developed by the group. In addition to presenting the technical details of the system, its resolution has been characterized and its functionality demonstrated by visualizing subcellular structures in a biological sample.

Strengths:

(1) The article includes extensive supplementary material that complements the information in the main article.

(2) However, in some sections, the information provided is somewhat superficial.

Weaknesses:

(1) Although a comparison is made with other light-sheet microscopy systems, the presented system does not represent a significant advance over existing systems. It uses high numerical aperture objectives and Gaussian beams, achieving resolution close to theoretical after deconvolution. The main advantage of the presented system is its ease of construction, thanks to the design of a perforated base plate.

(2) Using similar objectives (Nikon 25x and Thorlabs 20x), the results obtained are similar to those of the LLSM system (using a Gaussian beam without laser modulation). However, the article does not mention the difficulties of mounting the sample in the implemented configuration.

(3) The authors present a low-cost, open-source system. Although they provide open source code for the software (navigate), the use of proprietary electronics (ASI, NI, etc.) makes the system relatively expensive. Its low cost is not justified.

(4) The fibroblast images provided are of exceptional quality. However, these are fixed samples. The system lacks the necessary elements for monitoring cells in vivo, such as temperature or pH control.

Reviewer #2 (Public review):

Summary:

The authors present Altair-LSFM (Light Sheet Fluorescence Microscope), a high-resolution, open-source microscope, that is relatively easy to align and construct and achieves sub-cellular resolution. The authors developed this microscope to fill a perceived need that current open-source systems are primarily designed for large specimens and lack sub-cellular resolution or are difficult to construct and align, and are not stable. While commercial alternatives exist that offer sub-cellular resolution, they are expensive. The authors' manuscript centers around comparisons to the highly successful lattice light-sheet microscope, including the choice of detection and excitation objectives. The authors thus claim that there remains a critical need for high-resolution, economical, and easy-to-implement LSFM systems.

Strengths:

The authors succeed in their goals of implementing a relatively low-cost (~ USD 150K) open-source microscope that is easy to align. The ease of alignment rests on using custom-designed baseplates with dowel pins for precise positioning of optics based on computer analysis of opto-mechanical tolerances, as well as the optical path design. They simplify the excitation optics over Lattice light-sheet microscopes by using a Gaussian beam for illumination while maintaining lateral and axial resolutions of 235 and 350 nm across a 260-um field of view after deconvolution. In doing so they rest on foundational principles of optical microscopy that what matters for lateral resolution is the numerical aperture of the detection objective and proper sampling of the image field on to the detection, and the axial resolution depends on the thickness of the light-sheet when it is thinner than the depth of field of the detection objective. This concept has unfortunately not been completely clear to users of high-resolution light-sheet microscopes and is thus a valuable demonstration. The microscope is controlled by an open-source software, Navigate, developed by the authors, and it is thus foreseeable that different versions of this system could be implemented depending on experimental needs while maintaining easy alignment and low cost. They demonstrate system performance successfully by characterizing their sheet, point-spread function, and visualization of sub-cellular structures in mammalian cells, including microtubules, actin filaments, nuclei, and the Golgi apparatus.

Weaknesses:

There is a fixation on comparison to the first-generation lattice light-sheet microscope, which has evolved significantly since then:

(1) The authors claim that commercial lattice light-sheet microscopes (LLSM) are "complex, expensive, and alignment intensive", I believe this sentence applies to the open-source version of LLSM, which was made available for wide dissemination. Since then, a commercial solution has been provided by 3i, which is now being used in multiple cores and labs but does require routine alignments. However, Zeiss has also released a commercial turn-key system, which, while expensive, is stable, and the complexity does not interfere with the experience of the user. Though in general, statements on ease of use and stability might be considered anecdotal and may not belong in a scientific article, unreferenced or without data.

(2) One of the major limitations of the first generation LLSM was the use of a 5 mm coverslip, which was a hinderance for many users. However, the Zeiss system elegantly solves this problem, and so does Oblique Plane Microscopy (OPM), while the Altair-LSFM retains this feature, which may dissuade widespread adoption. This limitation and how it may be overcome in future iterations is not discussed.

(3) Further, on the point of sample flexibility, all generations of the LLSM, and by the nature of its design, the OPM, can accommodate live-cell imaging with temperature, gas, and humidity control. It is unclear how this would be implemented with the current sample chamber. This limitation would severely limit use cases for cell biologists, for which this microscope is designed. There is no discussion on this limitation or how it may be overcome in future iterations.

(4) The authors' comparison to LLSM is constrained to the "square" lattice, which, as they point out, is the most used optical lattice (though this also might be considered anecdotal). The LLSM original design, however, goes far beyond the square lattice, including hexagonal lattices, the ability to do structured illumination, and greater flexibility in general in terms of light-sheet tuning for different experimental needs, as well as not being limited to just sample scanning. Thus, the Alstair-LSFM cannot compare to the original LLSM in terms of versatility, even if comparisons to the resolution provided by the square lattice are fair.

(5) There is no demonstration of the system's live-imaging capabilities or temporal resolution, which is the main advantage of existing light-sheet systems.

While the microscope is well designed and completely open source, it will require experience with optics, electronics, and microscopy to implement and align properly. Experience with custom machining or soliciting a machine shop is also necessary. Thus, in my opinion, it is unlikely to be implemented by a lab that has zero prior experience with custom optics or can hire someone who does. Altair-LSFM may not be as easily adaptable or implementable as the authors describe or perceive in any lab that is interested, even if they can afford it. The authors indicate they will offer "workshops," but this does not necessarily remove the barrier to entry or lower it, perhaps as significantly as the authors describe.

There is a claim that this design is easily adaptable. However, the requirement of custom-machined baseplates and in silico optimization of the optical path basically means that each new instrument is a new design, even if the Navigate software can be used. It is unclear how Altair-LSFM demonstrates a modular design that reduces times from conception to optimization compared to previous implementations.

Reviewer #3 (Public review):

Summary:

This manuscript introduces a high-resolution, open-source light-sheet fluorescence microscope optimized for sub-cellular imaging.

The system is designed for ease of assembly and use, incorporating a custom-machined baseplate and in silico optimized optical paths to ensure robust alignment and performance. The authors demonstrate lateral and axial resolutions of ~235 nm and ~350 nm after deconvolution, enabling imaging of sub-diffraction structures in mammalian cells.

The important feature of the microscope is the clever and elegant adaptation of simple gaussian beams, smart beam shaping, galvo pivoting and high NA objectives to ensure a uniform thin light-sheet of around 400 nm in thickness, over a 266 micron wide Field of view, pushing the axial resolution of the system beyond the regular diffraction limited-based tradeoffs of light-sheet fluorescence microscopy.

Compelling validation using fluorescent beads and multicolor cellular imaging highlights the system's performance and accessibility. Moreover, a very extensive and comprehensive manual of operation is provided in the form of supplementary materials. This provides a DIY blueprint for researchers who want to implement such a system.

Strengths:

(1) Strong and accessible technical innovation:

With an elegant combination of beam shaping and optical modelling, the authors provide a high-resolution light-sheet system that overcomes the classical light-sheet tradeoff limit of a thin light-sheet and a small field of view. In addition, the integration of in silico modelling with a custom-machined baseplate is very practical and allows for ease of alignment procedures. Combining these features with the solid and super-extensive guide provided in the supplementary information, this provides a protocol for replicating the microscope in any other lab.

(2) Impeccable optical performance and ease of mounting of samples:

The system takes advantage of the same sample-holding method seen already in other implementations, but reduces the optical complexity. At the same time, the authors claim to achieve similar lateral and axial resolution to Lattice-light-sheet microscopy (although without a direct comparison (see below in the "weaknesses" section). The optical characterization of the system is comprehensive and well-detailed. Additionally, the authors validate the system imaging sub-cellular structures in mammalian cells.

(3) Transparency and comprehensiveness of documentation and resources:

A very detailed protocol provides detailed documentation about the setup, the optical modeling, and the total cost.

Weaknesses:

(1) Limited quantitative comparisons:

Although some qualitative comparison with previously published systems (diSPIM, lattice light-sheet) is provided throughout the manuscript, some side-by-side comparison would be of great benefit for the manuscript, even in the form of a theoretical simulation. While having a direct imaging comparison would be ideal, it's understandable that this goes beyond the interest of the paper; however, a table referencing image quality parameters (taken from the literature), such as signal-to-noise ratio, light-sheet thickness, and resolutions, would really enhance the features of the setup presented. Moreover, based also on the necessity for optical simplification, an additional comment on the importance/difference of dual objective/single objective light-sheet systems could really benefit the discussion.

(2) Limitation to a fixed sample:

In the manuscript, there is no mention of incubation temperature, CO₂ regulation, Humidity control, or possible integration of commercial environmental control systems. This is a major limitation for an imaging technique that owes its popularity to fast, volumetric, live-cell imaging of biological samples.

(3) System cost and data storage cost:

While the system presented has the advantage of being open-source, it remains relatively expensive (considering the 150k without laser source and optical table, for example). The manuscript could benefit from a more direct comparison of the performance/cost ratio of existing systems, considering academic settings with budgets that most of the time would not allow for expensive architectures. Moreover, it would also be beneficial to discuss the adaptability of the system, in case a 30k objective could not be feasible. Will this system work with different optics (with the obvious limitations coming with the lower NA objective)? This could be an interesting point of discussion. Adaptability of the system in case of lower budgets or more cost-effective choices, depending on the needs.

Last, not much is said about the need for data storage. Light-sheet microscopy's bottleneck is the creation of increasingly large datasets, and it could be beneficial to discuss more about the storage needs and the quantity of data generated.

Conclusion:

Altair-LSFM represents a well-engineered and accessible light-sheet system that addresses a longstanding need for high-resolution, reproducible, and affordable sub-cellular light-sheet imaging. While some aspects-comparative benchmarking and validation, limitation for fixed samples-would benefit from further development, the manuscript makes a compelling case for Altair-LSFM as a valuable contribution to the open microscopy scientific community.

eLife Assessment

This is an important account of replay as recency-weighted context-guided memory reactivation that explains a number of empirical findings across human and rodent memory literatures. The evidence is compelling and the work is likely to inspire further adaptions to incorporate additional biological and cognitive features.

Reviewer #1 (Public review):

Summary:

Zhou and colleagues developed a computational model of replay that heavily builds on cognitive models of memory in context (e.g., the context-maintenance and retrieval model), which have been successfully used to explain memory phenomena in the past. Their model produces results that mirror previous empirical findings in rodents and offers a new computational framework for thinking about replay.

Strengths:

The model is compelling and seems to explain a number of findings from the rodent literature. It is commendable that the authors implement commonly used algorithms from wakefulness to model sleep/rest, thereby linking wake and sleep phenomena in a parsimonious way. Additionally, the manuscript's comprehensive perspective on replay, bridging humans and non-human animals, enhanced its theoretical contribution.

Weaknesses:

This reviewer is not a computational neuroscientist by training, so some comments may stem from misunderstandings. I hope the authors would see those instances as opportunities to clarify their findings for broader audiences.

(1) The model predicts that temporally close items will be co-reactivated, yet evidence from humans suggests that temporal context doesn't guide sleep benefits (instead, semantic connections seem to be of more importance; Liu and Ranganath 2021, Schechtman et al 2023). Could these findings be reconciled with the model or is this a limitation of the current framework?

(2) During replay, the model is set so that the next reactivated item is sampled without replacement (i.e., the model cannot get "stuck" on a single item). I'm not sure what the biological backing behind this is and why the brain can't reactivate the same item consistently. Furthermore, I'm afraid that such a rule may artificially generate sequential reactivation of items regardless of wake training. Could the authors explain this better or show that this isn't the case?

(3) If I understand correctly, there are two ways in which novelty (i.e., less exposure) is accounted for in the model. The first and more talked about is the suppression mechanism (lines 639-646). The second is a change in learning rates (lines 593-595). It's unclear to me why both procedures are needed, how they differ, and whether these are two different mechanisms that the model implements. Also, since the authors controlled the extent to which each item was experienced during wakefulness, it's not entirely clear to me which of the simulations manipulated novelty on an individual item level, as described in lines 593-595 (if any).

As to the first mechanism - experience-based suppression - I find it challenging to think of a biological mechanism that would achieve this and is selectively activated immediately before sleep (somehow anticipating its onset). In fact, the prominent synaptic homeostasis hypothesis suggests that such suppression, at least on a synaptic level, is exactly what sleep itself does (i.e., prune or weaken synapses that were enhanced due to learning during the day). This begs the question of whether certain sleep stages (or ultradian cycles) may be involved in pruning, whereas others leverage its results for reactivation (e.g., a sequential hypothesis; Rasch & Born, 2013). That could be a compelling synthesis of this literature. Regardless of whether the authors agree, I believe that this point is a major caveat to the current model. It is addressed in the discussion, but perhaps it would be beneficial to explicitly state to what extent the results rely on the assumption of a pre-sleep suppression mechanism.

(4) As the manuscript mentions, the only difference between sleep and wake in the model is the initial conditions (a0). This is an obvious simplification, especially given the last author's recent models discussing the very different roles of REM vs NREM. Could the authors suggest how different sleep stages may relate to the model or how it could be developed to interact with other successful models such as the ones the last author has developed (e.g., C-HORSE)? Finally, I wonder how the model would explain findings (including the authors') showing a preference for reactivation of weaker memories. The literature seems to suggest that it isn't just a matter of novelty or exposure, but encoding strength. Can the model explain this? Or would it require additional assumptions or some mechanism for selective endogenous reactivation during sleep and rest?

(5) Lines 186-200 - Perhaps I'm misunderstanding, but wouldn't it be trivial that an external cue at the end-item of Figure 7a would result in backward replay, simply because there is no potential for forward replay for sequences starting at the last item (there simply aren't any subsequent items)? The opposite is true, of course, for the first-item replay, which can't go backward. More generally, my understanding of the literature on forward vs backward replay is that neither is linked to the rodent's location. Both commonly happen at a resting station that is further away from the track. It seems as though the model's result may not hold if replay occurs away from the track (i.e. if a0 would be equal for both pre- and post-run).

(6) The manuscript describes a study by Bendor & Wilson (2012) and tightly mimics their results. However, notably, that study did not find triggered replay immediately following sound presentation, but rather a general bias toward reactivation of the cued sequence over longer stretches of time. In other words, it seems that the model's results don't fully mirror the empirical results. One idea that came to mind is that perhaps it is the R/L context - not the first R/L item - that is cued in this study. This is in line with other TMR studies showing what may be seen as contextual reactivation. If the authors think that such a simulation may better mirror the empirical results, I encourage them to try. If not, however, this limitation should be discussed.

(7) There is some discussion about replay's benefit to memory. One point of interest could be whether this benefit changes between wake and sleep. Relatedly, it would be interesting to see whether the proportion of forward replay, backward replay, or both correlated with memory benefits. I encourage the authors to extend the section on the function of replay and explore these questions.

(8) Replay has been mostly studied in rodents, with few exceptions, whereas CMR and similar models have mostly been used in humans. Although replay is considered a good model of episodic memory, it is still limited due to limited findings of sequential replay in humans and its reliance on very structured and inherently autocorrelated items (i.e., place fields). I'm wondering if the authors could speak to the implications of those limitations on the generalizability of their model. Relatedly, I wonder if the model could or does lead to generalization to some extent in a way that would align with the complementary learning systems framework.

Reviewer #3 (Public review):

In this manuscript, Zhou et al. present a computational model of memory replay. Their model (CMR-replay) draws from temporal context models of human memory (e.g., TCM, CMR) and claims replay may be another instance of a context-guided memory process. During awake learning, CMR-replay (like its predecessors) encodes items alongside a drifting mental context that maintains a recency-weighted history of recently encoded contexts/items. In this way, the presently encoded item becomes associated with other recently learned items via their shared context representation - giving rise to typical effects in recall such as primacy, recency and contiguity. Unlike its predecessors, CMR-replay has built in replay periods. These replay periods are designed to approximate sleep or wakeful quiescence, in which an item is spontaneously reactivated, causing a subsequent cascade of item-context reactivations that further update the model's items-context associations.

Using this model of replay, Zhou et al. were able to reproduce a variety of empirical findings in the replay literature: e.g., greater forward replay at the beginning of a track and more backwards replay at the end; more replay for rewarded events; the occurrence of remote replay; reduced replay for repeated items, etc. Furthermore, the model diverges considerably (in implementation and predictions) from other prominent models of replay that, instead, emphasize replay as a way of predicting value from a reinforcement learning framing (i.e., EVB, expected value backup).

Overall, I found the manuscript clear and easy to follow, despite not being a computational modeller myself. (Which is pretty commendable, I'd say). The model also was effective at capturing several important empirical results from the replay literature while relying on a concise set of mechanisms - which will have implications for subsequent theory building in the field.

The authors addressed my concerns with respect to adding methodological detail. I am satisfied with the changes.

Author response:

The following is the authors’ response to the original reviews.

Public Reviews:

Reviewer #1 (Public Review):

Summary:

Zhou and colleagues developed a computational model of replay that heavily builds on cognitive models of memory in context (e.g., the context-maintenance and retrieval model), which have been successfully used to explain memory phenomena in the past. Their model produces results that mirror previous empirical findings in rodents and offers a new computational framework for thinking about replay.

Strengths:

The model is compelling and seems to explain a number of findings from the rodent literature. It is commendable that the authors implement commonly used algorithms from wakefulness to model sleep/rest, thereby linking wake and sleep phenomena in a parsimonious way. Additionally, the manuscript's comprehensive perspective on replay, bridging humans and non-human animals, enhanced its theoretical contribution.

Weaknesses:

This reviewer is not a computational neuroscientist by training, so some comments may stem from misunderstandings. I hope the authors would see those instances as opportunities to clarify their findings for broader audiences.

(1) The model predicts that temporally close items will be co-reactivated, yet evidence from humans suggests that temporal context doesn't guide sleep benefits (instead, semantic connections seem to be of more importance; Liu and Ranganath 2021, Schechtman et al 2023). Could these findings be reconciled with the model or is this a limitation of the current framework?

We appreciate the encouragement to discuss this connection. Our framework can accommodate semantic associations as determinants of sleep-dependent consolidation, which can in principle outweigh temporal associations. Indeed, prior models in this lineage have extensively simulated how semantic associations support encoding and retrieval alongside temporal associations. It would therefore be straightforward to extend our model to simulate how semantic associations guide sleep benefits, and to compare their contribution against that conferred by temporal associations across different experimental paradigms. In the revised manuscript, we have added a discussion of how our framework may simulate the role of semantic associations in sleep-dependent consolidation.

“Several recent studies have argued for dominance of semantic associations over temporal associations in the process of human sleep-dependent consolidation (Schechtman et al., 2023; Liu and Ranganath 2021; Sherman et al., 2025), with one study observing no role at all for temporal associations (Schechtman et al., 2023). At first glance, these findings appear in tension with our model, where temporal associations drive offline consolidation. Indeed, prior models have accounted for these findings by suppressing temporal context during sleep (Liu and Ranganath 2024; Sherman et al., 2025). However, earlier models in the CMR lineage have successfully captured the joint contributions of semantic and temporal associations to encoding and retrieval (Polyn et al., 2009), and these processes could extend naturally to offline replay. In a paradigm where semantic associations are especially salient during awake learning, the model could weight these associations more and account for greater co-reactivation and sleep-dependent memory benefits for semantically related than temporally related items. Consistent with this idea, Schechtman et al. (2023) speculated that their null temporal effects likely reflected the task’s emphasis on semantic associations. When temporal associations are more salient and task-relevant, sleep-related benefits for temporally contiguous items are more likely to emerge (e.g., Drosopoulos et al., 2007; King et al., 2017).”

The reviewer’s comment points to fruitful directions for future work that could employ our framework to dissect the relative contributions of semantic and temporal associations to memory consolidation.

(2) During replay, the model is set so that the next reactivated item is sampled without replacement (i.e., the model cannot get "stuck" on a single item). I'm not sure what the biological backing behind this is and why the brain can't reactivate the same item consistently.

Furthermore, I'm afraid that such a rule may artificially generate sequential reactivation of items regardless of wake training. Could the authors explain this better or show that this isn't the case?

We appreciate the opportunity to clarify this aspect of the model. We first note that this mechanism has long been a fundamental component of this class of models (Howard & Kahana 2002). Many classic memory models (Brown et al., 2000; Burgess & Hitch, 1991; Lewandowsky & Murdock 1989) incorporate response suppression, in which activated items are temporarily inhibited. The simplest implementation, which we use here, removes activated items from the pool of candidate items. Alternative implementations achieve this through transient inhibition, often conceptualized as neuronal fatigue (Burgess & Hitch, 1991; Grossberg 1978). Our model adopts a similar perspective, interpreting this mechanism as mimicking a brief refractory period that renders reactivated neurons unlikely to fire again within a short physiological event such as a sharp-wave ripple. Importantly, this approach does not generate spurious sequences. Instead, the model’s ability to preserve the structure of wake experience during replay depends entirely on the learned associations between items (without these associations, item order would be random). Similar assumptions are also common in models of replay. For example, reinforcement learning models of replay incorporate mechanisms such as inhibition to prevent repeated reactivations (e.g., Diekmann & Cheng, 2023) or prioritize reactivation based on ranking to limit items to a single replay (e.g., Mattar & Daw, 2018). We now discuss these points in the section titled “A context model of memory replay”

“This mechanism of sampling without replacement, akin to response suppression in established context memory models (Howard & Kahana 2002), could be implemented by neuronal fatigue or refractory dynamics (Burgess & Hitch, 1991; Grossberg 1978). Non-repetition during reactivation is also a common assumption in replay models that regulate reactivation through inhibition or prioritization (Diekmann & Cheng 2023; Mattar & Daw 2018; Singh et al., 2022).”

(3) If I understand correctly, there are two ways in which novelty (i.e., less exposure) is accounted for in the model. The first and more talked about is the suppression mechanism (lines 639-646). The second is a change in learning rates (lines 593-595). It's unclear to me why both procedures are needed, how they differ, and whether these are two different mechanisms that the model implements. Also, since the authors controlled the extent to which each item was experienced during wakefulness, it's not entirely clear to me which of the simulations manipulated novelty on an individual item level, as described in lines 593-595 (if any).

We agree that these mechanisms and their relationships would benefit from clarification. As noted, novelty influences learning through two distinct mechanisms. First, the suppression mechanism is essential for capturing the inverse relationship between the amount of wake experience and the frequency of replay, as observed in several studies. This mechanism ensures that items with high wake activity are less likely to dominate replay. Second, the decrease in learning rates with repetition is crucial for preserving the stochasticity of replay. Without this mechanism, the model would increase weights linearly, leading to an exponential increase in the probability of successive wake items being reactivated back-to-back due to the use of a softmax choice rule. This would result in deterministic replay patterns, which are inconsistent with experimental observations.

We have revised the Methods section to explicitly distinguish these two mechanisms:

“This experience-dependent suppression mechanism is distinct from the reduction of learning rates through repetition; it does not modulate the update of memory associations but exclusively governs which items are most likely to initiate replay.”

We have also clarified our rationale for including a learning rate reduction mechanism:

“The reduction in learning rates with repetition is important for maintaining a degree of stochasticity in the model’s replay during task repetition, since linearly increasing weights would, through the softmax choice rule, exponentially amplify differences in item reactivation probabilities, sharply reducing variability in replay.”

Finally, we now specify exactly where the learning-rate reduction applied, namely in simulations where sequences are repeated across multiple sessions:

“In this simulation, the learning rates progressively decrease across sessions, as described above.“

As to the first mechanism - experience-based suppression - I find it challenging to think of a biological mechanism that would achieve this and is selectively activated immediately before sleep (somehow anticipating its onset). In fact, the prominent synaptic homeostasis hypothesis suggests that such suppression, at least on a synaptic level, is exactly what sleep itself does (i.e., prune or weaken synapses that were enhanced due to learning during the day). This begs the question of whether certain sleep stages (or ultradian cycles) may be involved in pruning, whereas others leverage its results for reactivation (e.g., a sequential hypothesis; Rasch & Born, 2013). That could be a compelling synthesis of this literature. Regardless of whether the authors agree, I believe that this point is a major caveat to the current model. It is addressed in the discussion, but perhaps it would be beneficial to explicitly state to what extent the results rely on the assumption of a pre-sleep suppression mechanism.

We appreciate the reviewer raising this important point. Unlike the mechanism proposed by the synaptic homeostasis hypothesis, the suppression mechanism in our model does not suppress items based on synapse strength, nor does it modify synaptic weights. Instead, it determines the level of suppression for each item based on activity during awake experience. The brain could implement such a mechanism by tagging each item according to its activity level during wakefulness. During subsequent consolidation, the initial reactivation of an item during replay would reflect this tag, influencing how easily it can be reactivated.

A related hypothesis has been proposed in recent work, suggesting that replay avoids recently active trajectories due to spike frequency adaptation in neurons (Mallory et al., 2024). Similarly, the suppression mechanism in our model is critical for explaining the observed negative relationship between the amount of recent wake experience and the degree of replay.

We discuss the biological plausibility of this mechanism and its relationship with existing models in the Introduction. In the section titled “The influence of experience”, we have added the following:

“Our model implements an activity‑dependent suppression mechanism that, at the onset of each offline replay event, assigns each item a selection probability inversely proportional to its activation during preceding wakefulness. The brain could implement this by tagging each memory trace in proportion to its recent activation; during consolidation, that tag would then regulate starting replay probability, making highly active items less likely to be reactivated. A recent paper found that replay avoids recently traversed trajectories through awake spike‑frequency adaptation (Mallory et al., 2025), which could implement this kind of mechanism. In our simulations, this suppression is essential for capturing the inverse relationship between replay frequency and prior experience. Note that, unlike the synaptic homeostasis hypothesis (Tononi & Cirelli 2006), which proposes that the brain globally downscales synaptic weights during sleep, this mechanism leaves synaptic weights unchanged and instead biases the selection process during replay.”

(4) As the manuscript mentions, the only difference between sleep and wake in the model is the initial conditions (a0). This is an obvious simplification, especially given the last author's recent models discussing the very different roles of REM vs NREM. Could the authors suggest how different sleep stages may relate to the model or how it could be developed to interact with other successful models such as the ones the last author has developed (e.g., C-HORSE)? 

We appreciate the encouragement to comment on the roles of different sleep stages in the manuscript, especially since, as noted, the lab is very interested in this and has explored it in other work. We chose to focus on NREM in this work because the vast majority of electrophysiological studies of sleep replay have identified these events during NREM. In addition, our lab’s theory of the role of REM (Singh et al., 2022, PNAS) is that it is a time for the neocortex to replay remote memories, in complement to the more recent memories replayed during NREM. The experiments we simulate all involve recent memories. Indeed, our view is that part of the reason that there is so little data on REM replay may be that experimenters are almost always looking for traces of recent memories (for good practical and technical reasons).

Regarding the simplicity of the distinction between simulated wake and sleep replay, we view it as an asset of the model that it can account for many of the different characteristics of awake and NREM replay with very simple assumptions about differences in the initial conditions. There are of course many other differences between the states that could be relevant to the impact of replay, but the current target empirical data did not necessitate us taking those into account. This allows us to argue that differences in initial conditions should play a substantial role in an account of the differences between wake and sleep replay.

We have added discussion of these ideas and how they might be incorporated into future versions of the model in the Discussion section:

“Our current simulations have focused on NREM, since the vast majority of electrophysiological studies of sleep replay have identified replay events in this stage. We have proposed in other work that replay during REM sleep may provide a complementary role to NREM sleep, allowing neocortical areas to reinstate remote, already-consolidated memories that need to be integrated with the memories that were recently encoded in the hippocampus and replayed during NREM (Singh et al., 2022). An extension of our model could undertake this kind of continual learning setup, where the student but not teacher network retains remote memories, and the driver of replay alternates between hippocampus (NREM) and cortex (REM) over the course of a night of simulated sleep. Other differences between stages of sleep and between sleep and wake states are likely to become important for a full account of how replay impacts memory. Our current model parsimoniously explains a range of differences between awake and sleep replay by assuming simple differences in initial conditions, but we expect many more characteristics of these states (e.g., neural activity levels, oscillatory profiles, neurotransmitter levels, etc.) will be useful to incorporate in the future.”

Finally, I wonder how the model would explain findings (including the authors') showing a preference for reactivation of weaker memories. The literature seems to suggest that it isn't just a matter of novelty or exposure, but encoding strength. Can the model explain this? Or would it require additional assumptions or some mechanism for selective endogenous reactivation during sleep and rest?

We appreciate the encouragement to discuss this, as we do think the model could explain findings showing a preference for reactivation of weaker memories, as in Schapiro et al. (2018). In our framework, memory strength is reflected in the magnitude of each memory’s associated synaptic weights, so that stronger memories yield higher retrieved‑context activity during wake encoding than weaker ones. Because the model’s suppression mechanism reduces an item’s replay probability in proportion to its retrieved‑context activity, items with larger weights (strong memories) are more heavily suppressed at the onset of replay, while those with smaller weights (weaker memories) receive less suppression. When items have matched reward exposure, this dynamic would bias offline replay toward weaker memories, therefore preferentially reactivating weak memories. 

In the section titled “The influence of experience”, we updated a sentence to discuss this idea more explicitly: 

“Such a suppression mechanism may be adaptive, allowing replay to benefit not only the most recently or strongly encoded items but also to provide opportunities for the consolidation of weaker or older memories, consistent with empirical evidence (e.g., Schapiro et al. 2018; Yu et al., 2024).”

(5) Lines 186-200 - Perhaps I'm misunderstanding, but wouldn't it be trivial that an external cue at the end-item of Figure 7a would result in backward replay, simply because there is no potential for forward replay for sequences starting at the last item (there simply aren't any subsequent items)? The opposite is true, of course, for the first-item replay, which can't go backward. More generally, my understanding of the literature on forward vs backward replay is that neither is linked to the rodent's location. Both commonly happen at a resting station that is further away from the track. It seems as though the model's result may not hold if replay occurs away from the track (i.e. if a0 would be equal for both pre- and post-run).

In studies where animals run back and forth on a linear track, replay events are decoded separately for left and right runs, identifying both forward and reverse sequences for each direction, for example using direction-specific place cell sequence templates. Accordingly, in our simulation of, e.g., Ambrose et al. (2016), we use two independent sequences, one for left runs and one for right runs (an approach that has been taken in prior replay modeling work). Crucially, our model assumes a context reset between running episodes, preventing the final item of one traversal from acquiring contextual associations with the first item of the next. As a result, learning in the two sequences remains independent, and when an external cue is presented at the track’s end, replay predominantly unfolds in the backward direction, only occasionally producing forward segments when the cue briefly reactivates an earlier sequence item before proceeding forward.

We added a note to the section titled “The context-dependency of memory replay” to clarify this:

“In our model, these patterns are identical to those in our simulation of Ambrose et al. (2016), which uses two independent sequences to mimic the two run directions. This is because the drifting context resets before each run sequence is encoded, with the pause between runs acting as an event boundary that prevents the final item of one traversal from associating with the first item of the next, thereby keeping learning in each direction independent.”

To our knowledge, no study has observed a similar asymmetry when animals are fully removed from the track, although both types of replay can be observed when animals are away from the track. For example, Gupta et al. (2010) demonstrated that when animals replay trajectories far from their current location, the ratio of forward vs. backward replay appears more balanced. We now highlight this result in the manuscript and explain how it aligns with the predictions of our model:

“For example, in tasks where the goal is positioned in the middle of an arm rather than at its end, CMR-replay predicts a more balanced ratio of forward and reverse replay, whereas the EVB model still predicts a dominance of reverse replay due to backward gain propagation from the reward. This contrast aligns with empirical findings showing that when the goal is located in the middle of an arm, replay events are more evenly split between forward and reverse directions (Gupta et al., 2010), whereas placing the goal at the end of a track produces a stronger bias toward reverse replay (Diba & Buzsaki 2007).” 

Although no studies, to our knowledge, have observed a context-dependent asymmetry between forward and backward replay when the animal is away from the track, our model does posit conditions under which it could. Specifically, it predicts that deliberation on a specific memory, such as during planning, could generate an internal context input that biases replay: actively recalling the first item of a sequence may favor forward replay, while thinking about the last item may promote backward replay, even when the individual is physically distant from the track.

We now discuss this prediction in the section titled “The context-dependency of memory replay”:

“Our model also predicts that deliberation on a specific memory, such as during planning, could serve to elicit an internal context cue that biases replay: actively recalling the first item of a sequence may favor forward replay, while thinking about the last item may promote backward replay, even when the individual is physically distant from the track. While not explored here, this mechanism presents a potential avenue for future modeling and empirical work.”

(6) The manuscript describes a study by Bendor & Wilson (2012) and tightly mimics their results. However, notably, that study did not find triggered replay immediately following sound presentation, but rather a general bias toward reactivation of the cued sequence over longer stretches of time. In other words, it seems that the model's results don't fully mirror the empirical results. One idea that came to mind is that perhaps it is the R/L context - not the first R/L item - that is cued in this study. This is in line with other TMR studies showing what may be seen as contextual reactivation. If the authors think that such a simulation may better mirror the empirical results, I encourage them to try. If not, however, this limitation should be discussed.

Although our model predicts that replay is triggered immediately by the sound cue, it also predicts a sustained bias toward the cued sequence. Replay in our model unfolds across the rest phase as multiple successive events, so the bias observed in our sleep simulations indeed reflects a prolonged preference for the cued sequence.

We now discuss this issue, acknowledging the discrepancy:

“Bendor and Wilson (2012) found that sound cues during sleep did not trigger immediate replay, but instead biased reactivation toward the cued sequence over an extended period of time. While the model does exhibit some replay triggered immediately by the cue, it also captures the sustained bias toward the cued sequence over an extended period.”

Second, within this framework, context is modeled as a weighted average of the features associated with items. As a result, cueing the model with the first R/L item produces qualitatively similar outcomes as cueing it with a more extended R/L cue that incorporates features of additional items. This is because both approaches ultimately use context features unique to the two sides.

(7) There is some discussion about replay's benefit to memory. One point of interest could be whether this benefit changes between wake and sleep. Relatedly, it would be interesting to see whether the proportion of forward replay, backward replay, or both correlated with memory benefits. I encourage the authors to extend the section on the function of replay and explore these questions.

We thank the reviewer for this suggestion. Regarding differences in the contribution of wake and sleep to memory, our current simulations predict that compared to rest in the task environment, sleep is less biased toward initiating replay at specific items, leading to a more uniform benefit across all memories. Regarding the contributions of forward and backward replay, our model predicts that both strengthen bidirectional associations between items and contexts, benefiting memory in qualitatively similar ways. Furthermore, we suggest that the offline learning captured  by our teacher-student simulations reflects consolidation processes that are specific to sleep.

We have expanded the section titled “The influence of experience” to discuss these predictions of the model: 

“The results outlined above arise from the model's assumption that replay strengthens bidirectional associations between items and contexts to benefit memory. This assumption leads to several predictions about differences across replay types. First, the model predicts that sleep yields different memory benefits compared to rest in the task environment: Sleep is less biased toward initiating replay at specific items, resulting in a more uniform benefit across all memories. Second, the model predicts that forward and backward replay contribute to memory in qualitatively similar ways but tend to benefit different memories. This divergence arises because forward and backward replay exhibit distinct item preferences, with backward replay being more likely to include rewarded items, thereby preferentially benefiting those memories.”

We also updated the “The function of replay” section to include our teacher-student speculation:

“We speculate that the offline learning observed in these simulations corresponds to consolidation processes that operate specifically during sleep, when hippocampal-neocortical dynamics are especially tightly coupled (Klinzing et al., 2019).”

(8) Replay has been mostly studied in rodents, with few exceptions, whereas CMR and similar models have mostly been used in humans. Although replay is considered a good model of episodic memory, it is still limited due to limited findings of sequential replay in humans and its reliance on very structured and inherently autocorrelated items (i.e., place fields). I'm wondering if the authors could speak to the implications of those limitations on the generalizability of their model. Relatedly, I wonder if the model could or does lead to generalization to some extent in a way that would align with the complementary learning systems framework.

We appreciate these insightful comments. Traditionally, replay studies have focused on spatial tasks with autocorrelated item representations (e.g., place fields). However, an increasing number of human studies have demonstrated sequential replay using stimuli with distinct, unrelated representations. Our model is designed to accommodate both scenarios. In our current simulations, we employ orthogonal item representations while leveraging a shared, temporally autocorrelated context to link successive items. We anticipate that incorporating autocorrelated item representations would further enhance sequence memory by increasing the similarity between successive contexts. Overall, we believe that the model generalizes across a broad range of experimental settings, regardless of the degree of autocorrelation between items. Moreover, the underlying framework has been successfully applied to explain sequential memory in both spatial domains, explaining place cell firing properties (e.g., Howard et al., 2004), and in non-spatial domains, such as free recall experiments where items are arbitrarily related. 

In the section titled “A context model of memory replay”, we added this comment to address this point:

“Its contiguity bias stems from its use of shared, temporally autocorrelated context to link successive items, despite the orthogonal nature of individual item representations. This bias would be even stronger if items had overlapping representations, as observed in place fields.”

Since CMR-replay learns distributed context representations where overlap across context vectors captures associative structure, and replay helps strengthen that overlap, this could indeed be viewed as consonant with complementary learning systems integration processes. 

Reviewer #2 (Public Review):

This manuscript proposes a model of replay that focuses on the relation between an item and its context, without considering the value of the item. The model simulates awake learning, awake replay, and sleep replay, and demonstrates parallels between memory phenomenon driven by encoding strength, replay of sequence learning, and activation of nearest neighbor to infer causality. There is some discussion of the importance of suppression/inhibition to reduce activation of only dominant memories to be replayed, potentially boosting memories that are weakly encoded. Very nice replications of several key replay findings including the effect of reward and remote replay, demonstrating the equally salient cue of context for offline memory consolidation.

I have no suggestions for the main body of the study, including methods and simulations, as the work is comprehensive, transparent, and well-described. However, I would like to understand how the CMRreplay model fits with the current understanding of the importance of excitation vs inhibition, remembering vs forgetting, activation vs deactivation, strengthening vs elimination of synapses, and even NREM vs REM as Schapiro has modeled. There seems to be a strong association with the efforts of the model to instantiate a memory as well as how that reinstantiation changes across time. But that is not all this is to consolidation. The specific roles of different brain states and how they might change replay is also an important consideration.

We are gratified that the reviewer appreciated the work, and we agree that the paper would benefit from comment on the connections to these other features of consolidation.

Excitation vs. inhibition: CMR-replay does not model variations in the excitation-inhibition balance across brain states (as in other models, e.g., Chenkov et al., 2017), since it does not include inhibitory connections. However, we posit that the experience-dependent suppression mechanism in the model might, in the brain, involve inhibitory processes. Supporting this idea, studies have observed increased inhibition with task repetition (Berners-Lee et al., 2022). We hypothesize that such mechanisms may underlie the observed inverse relationship between task experience and replay frequency in many studies. We discuss this in the section titled “A context model of memory replay”:

“The proposal that a suppression mechanism plays a role in replay aligns with models that regulate place cell reactivation via inhibition (Malerba et al., 2016) and with empirical observations of increased hippocampal inhibitory interneuron activity with experience (Berners-Lee et al., 2022). Our model assumes the presence of such inhibitory mechanisms but does not explicitly model them.”

Remembering/forgetting, activation/deactivation, and strengthening/elimination of synapses: The model does not simulate synaptic weight reduction or pruning, so it does not forget memories through the weakening of associated weights. However, forgetting can occur when a memory is replayed less frequently than others, leading to reduced activation of that memory compared to its competitors during context-driven retrieval. In the Discussion section, we acknowledge that a biologically implausible aspect of our model is that it implements only synaptic strengthening: 

“Aspects of the model, such as its lack of regulation of the cumulative positive weight changes that can accrue through repeated replay, are biologically implausible (as biological learning results in both increases and decreases in synaptic weights) and limit the ability to engage with certain forms of low level neural data (e.g., changes in spine density over sleep periods; de Vivo et al., 2017; Maret et al., 2011). It will be useful for future work to explore model variants with more elements of biological plausibility.” Different brain states and NREM vs REM: Reviewer 1 also raised this important issue (see above). We have added the following thoughts on differences between these states and the relationship to our prior work to the Discussion section:

“Our current simulations have focused on NREM, since the vast majority of electrophysiological studies of sleep replay have identified replay events in this stage. We have proposed in other work that replay during REM sleep may provide a complementary role to NREM sleep, allowing neocortical areas to reinstate remote, already-consolidated memories that need to be integrated with the memories that were recently encoded in the hippocampus and replayed during NREM (Singh et al., 2022). An extension of our model could undertake this kind of continual learning setup, where the student but not teacher network retains remote memories, and the driver of replay alternates between hippocampus (NREM) and cortex (REM) over the course of a night of simulated sleep. Other differences between stages of sleep and between sleep and wake states are likely to become important for a full account of how replay impacts memory. Our current model parsimoniously explains a range of differences between awake and sleep replay by assuming simple differences in initial conditions, but we expect many more characteristics of these states (e.g., neural activity levels, oscillatory profiles, neurotransmitter levels, etc.) will be useful to incorporate in the future.”

We hope these points clarify the model’s scope and its potential for future extensions.

Do the authors suggest that these replay systems are more universal to offline processes beyond episodic memory? What about procedural memories and working memory?

We thank the reviewer for raising this important question. We have clarified in the manuscript:

“We focus on the model as a formulation of hippocampal replay, capturing how the hippocampus may replay past experiences through simple and interpretable mechanisms.”

With respect to other forms of memory, we now note that:

“This motor memory simulation using a model of hippocampal replay is consistent with evidence that hippocampal replay can contribute to consolidating memories that are not hippocampally dependent at encoding (Schapiro et al., 2019; Sawangjit et al., 2018). It is possible that replay in other, more domain-specific areas could also contribute (Eichenlaub et al., 2020).”

Though this is not a biophysical model per se, can the authors speak to the neuromodulatory milieus that give rise to the different types of replay?

Our work aligns with the perspective proposed by Hasselmo (1999), which suggests that waking and sleep states differ in the degree to which hippocampal activity is driven by external inputs. Specifically, high acetylcholine levels during waking bias activity to flow into the hippocampus, while low acetylcholine levels during sleep allow hippocampal activity to influence other brain regions. Consistent with this view, our model posits that wake replay is more biased toward items associated with the current resting location due to the presence of external input during waking states. In the Discussion section, we have added a comment on this point:

“Our view aligns with the theory proposed by Hasselmo (1999), which suggests that the degree of hippocampal activity driven by external inputs differs between waking and sleep states: High acetylcholine levels during wakefulness bias activity into the hippocampus, while low acetylcholine levels during slow-wave sleep allow hippocampal activity to influence other brain regions.”

Reviewer #3 (Public Review):

In this manuscript, Zhou et al. present a computational model of memory replay. Their model (CMR-replay) draws from temporal context models of human memory (e.g., TCM, CMR) and claims replay may be another instance of a context-guided memory process. During awake learning, CMR replay (like its predecessors) encodes items alongside a drifting mental context that maintains a recency-weighted history of recently encoded contexts/items. In this way, the presently encoded item becomes associated with other recently learned items via their shared context representation - giving rise to typical effects in recall such as primacy, recency, and contiguity. Unlike its predecessors, CMR-replay has built-in replay periods. These replay periods are designed to approximate sleep or wakeful quiescence, in which an item is spontaneously reactivated, causing a subsequent cascade of item-context reactivations that further update the model's item-context associations.

Using this model of replay, Zhou et al. were able to reproduce a variety of empirical findings in the replay literature: e.g., greater forward replay at the beginning of a track and more backward replay at the end; more replay for rewarded events; the occurrence of remote replay; reduced replay for repeated items, etc. Furthermore, the model diverges considerably (in implementation and predictions) from other prominent models of replay that, instead, emphasize replay as a way of predicting value from a reinforcement learning framing (i.e., EVB, expected value backup).

Overall, I found the manuscript clear and easy to follow, despite not being a computational modeller myself. (Which is pretty commendable, I'd say). The model also was effective at capturing several important empirical results from the replay literature while relying on a concise set of mechanisms - which will have implications for subsequent theory-building in the field.

With respect to weaknesses, additional details for some of the methods and results would help the readers better evaluate the data presented here (e.g., explicitly defining how the various 'proportion of replay' DVs were calculated).

For example, for many of the simulations, the y-axis scale differs from the empirical data despite using comparable units, like the proportion of replay events (e.g., Figures 1B and C). Presumably, this was done to emphasize the similarity between the empirical and model data. But, as a reader, I often found myself doing the mental manipulation myself anyway to better evaluate how the model compared to the empirical data. Please consider using comparable y-axis ranges across empirical and simulated data wherever possible.

We appreciate this point. As in many replay modeling studies, our primary goal is to provide a qualitative fit that demonstrates the general direction of differences between our model and empirical data, without engaging in detailed parameter fitting for a precise quantitative fit. Still, we agree that where possible, it is useful to better match the axes. We have updated figures 2B and 2C so that the y-axis scales are more directly comparable between the empirical and simulated data. 

In a similar vein to the above point, while the DVs in the simulations/empirical data made intuitive sense, I wasn't always sure precisely how they were calculated. Consider the "proportion of replay" in Figure 1A. In the Methods (perhaps under Task Simulations), it should specify exactly how this proportion was calculated (e.g., proportions of all replay events, both forwards and backwards, combining across all simulations from Pre- and Post-run rest periods). In many of the examples, the proportions seem to possibly sum to 1 (e.g., Figure 1A), but in other cases, this doesn't seem to be true (e.g., Figure 3A). More clarity here is critical to help readers evaluate these data. Furthermore, sometimes the labels themselves are not the most informative. For example, in Figure 1A, the y-axis is "Proportion of replay" and in 1C it is the "Proportion of events". I presumed those were the same thing - the proportion of replay events - but it would be best if the axis labels were consistent across figures in this manuscript when they reflect the same DV.

We appreciate these useful suggestions. We have revised the Methods section to explain in detail how DVs are calculated for each simulation. The revisions clarify the differences between related measures, such as those shown in Figures 1A and 1C, so that readers can more easily see how the DVs are defined and interpreted in each case. 

Reviewer #4/Reviewing Editor (Public Review):

Summary:

With their 'CMR-replay' model, Zhou et al. demonstrate that the use of spontaneous neural cascades in a context-maintenance and retrieval (CMR) model significantly expands the range of captured memory phenomena.

Strengths:

The proposed model compellingly outperforms its CMR predecessor and, thus, makes important strides towards understanding the empirical memory literature, as well as highlighting a cognitive function of replay.

Weaknesses:

Competing accounts of replay are acknowledged but there are no formal comparisons and only CMR-replay predictions are visualized. Indeed, other than the CMR model, only one alternative account is given serious consideration: A variant of the 'Dyna-replay' architecture, originally developed in the machine learning literature (Sutton, 1990; Moore & Atkeson, 1993) and modified by Mattar et al (2018) such that previously experienced event-sequences get replayed based on their relevance to future gain. Mattar et al acknowledged that a realistic Dyna-replay mechanism would require a learned representation of transitions between perceptual and motor events, i.e., a 'cognitive map'. While Zhou et al. note that the CMR-replay model might provide such a complementary mechanism, they emphasize that their account captures replay characteristics that Dyna-replay does not (though it is unclear to what extent the reverse is also true).

We thank the reviewer for these thoughtful comments and appreciate the opportunity to clarify our approach. Our goal in this work is to contrast two dominant perspectives in replay research: replay as a mechanism for learning reward predictions and replay as a process for memory consolidation. These models were chosen as representatives of their classes of models because they use simple and interpretable mechanisms that can simulate a wide range of replay phenomena, making them ideal for contrasting these two perspectives.

Although we implemented CMR-replay as a straightforward example of the memory-focused view, we believe the proposed mechanisms could be extended to other architectures, such as recurrent neural networks, to produce similar results. We now discuss this possibility in the revised manuscript (see below). However, given our primary goal of providing a broad and qualitative contrast of these two broad perspectives, we decided not to undertake simulations with additional individual models for this paper.

Regarding the Mattar & Daw model, it is true that a mechanistic implementation would require a mechanism that avoids precomputing priorities before replay. However, the "need" component of their model already incorporates learned expectations of transitions between actions and events. Thus, the model's limitations are not due to the absence of a cognitive map.

In contrast, while CMR-replay also accumulates memory associations that reflect experienced transitions among events, it generates several qualitatively distinct predictions compared to the Mattar & Daw model. As we note in the manuscript, these distinctions make CMR-replay a contrasting rather than complementary perspective.

Another important consideration, however, is how CMR replay compares to alternative mechanistic accounts of cognitive maps. For example, Recurrent Neural Networks are adept at detecting spatial and temporal dependencies in sequential input; these networks are being increasingly used to capture psychological and neuroscientific data (e.g., Zhang et al, 2020; Spoerer et al, 2020), including hippocampal replay specifically (Haga & Fukai, 2018). Another relevant framework is provided by Associative Learning Theory, in which bidirectional associations between static and transient stimulus elements are commonly used to explain contextual and cue-based phenomena, including associative retrieval of absent events (McLaren et al, 1989; Harris, 2006; Kokkola et al, 2019). Without proper integration with these modeling approaches, it is difficult to gauge the innovation and significance of CMR-replay, particularly since the model is applied post hoc to the relatively narrow domain of rodent maze navigation.

First, we would like to clarify our principal aim in this work is to characterize the nature of replay, rather than to model cognitive maps per se. Accordingly, CMR‑replay is not designed to simulate head‐direction signals, perform path integration, or explain the spatial firing properties of neurons during navigation. Instead, it focuses squarely on sequential replay phenomena, simulating classic rodent maze reactivation studies and human sequence‐learning tasks. These simulations span a broad array of replay experimental paradigms to ensure extensive coverage of the replay findings reported across the literature. As such, the contribution of this work is in explaining the mechanisms and functional roles of replay, and demonstrating that a model that employs simple and interpretable memory mechanisms not only explains replay phenomena traditionally interpreted through a value-based lens but also accounts for findings not addressed by other memory-focused models.

As the reviewer notes, CMR-replay shares features with other memory-focused models. However, to our knowledge, none of these related approaches have yet captured the full suite of empirical replay phenomena, suggesting the combination of mechanisms employed in CMR-replay is essential for explaining these phenomena. In the Discussion section, we now discuss the similarities between CMR-replay and related memory models and the possibility of integrating these approaches:

“Our theory builds on a lineage of memory-focused models, demonstrating the power of this perspective in explaining phenomena that have often been attributed to the optimization of value-based predictions. In this work, we focus on CMR-replay, which exemplifies the memory-centric approach through a set of simple and interpretable mechanisms that we believe are broadly applicable across memory domains. Elements of CMR-replay share similarities with other models that adopt a memory-focused perspective. The model learns distributed context representations whose overlaps encodes associations among items, echoing associative learning theories in which overlapping patterns capture stimulus similarity and learned associations (McLaren & Mackintosh 2002). Context evolves through bidirectional interactions between items and their contextual representations, mirroring the dynamics found in recurrent neural networks (Haga & Futai 2018; Levenstein et al., 2024). However, these related approaches have not been shown to account for the present set of replay findings and lack mechanisms—such as reward-modulated encoding and experience-dependent suppression—that our simulations suggest are essential for capturing these phenomena. While not explored here, we believe these mechanisms could be integrated into architectures like recurrent neural networks (Levenstein et al., 2024) to support a broader range of replay dynamics.”

Recommendations For The Authors

Reviewer #1 (Recommendations For The Authors):

(1) Lines 94-96: These lines may be better positioned earlier in the paragraph.

We now introduce these lines earlier in the paragraph.

(2) Line 103 - It's unclear to me what is meant by the statement that "the current context contains contexts associated with previous items". I understand why a slowly drifting context will coincide and therefore link with multiple items that progress rapidly in time, so multiple items will be linked to the same context and each item will be linked to multiple contexts. Is that the idea conveyed here or am I missing something? I'm similarly confused by line 129, which mentions that a context is updated by incorporating other items' contexts. How could a context contain other contexts?

In the model, each item has an associated context that can be retrieved via Mfc. This is true even before learning, since Mfc is initialized as an identity matrix. During learning and replay, we have a drifting context c that is updated each time an item is presented. At each timestep, the model first retrieves the current item’s associated context cf by Mfc, and incorporates it into c. Equation #2 in the Methods section illustrates this procedure in detail. Because of this procedure, the drifting context c is a weighted sum of past items’ associated contexts. 

We recognize that these descriptions can be confusing. We have updated the Results section to better distinguish the drifting context from items’ associated context. For example, we note that:

“We represent the drifting context during learning and replay with c and an item's associated context with cf.”

We have also updated our description of the context drift procedure to distinguish these two quantities: 

“During awake encoding of a sequence of items, for each item f, the model retrieves its associated context cf via Mfc. The drifting context c incorporates the item's associated context cf and downweights its representation of previous items' associated contexts (Figure 1c). Thus, the context layer maintains a recency weighted sum of past and present items' associated contexts.”

(3) Figure 1b and 1d - please clarify which axis in the association matrices represents the item and the context.

We have added labels to show what the axes represent in Figure 1.

(4) The terms "experience" and "item" are used interchangeably and it may be best to stick to one term.

We now use the term “item” wherever we describe the model results. 

(5) The manuscript describes Figure 6 ahead of earlier figures - the authors may want to reorder their figures to improve readability.

We appreciate this suggestion. We decided to keep the current figure organization since it allows us to group results into different themes and avoid redundancy. 

(6) Lines 662-664 are repeated with a different ending, this is likely an error.

We have fixed this error.

Reviewer #3 (Recommendations For The Authors):

Below, I have outlined some additional points that came to mind in reviewing the manuscript - in no particular order.

(1) Figure 1: I found the ordering of panels a bit confusing in this figure, as the reading direction changes a couple of times in going from A to F. Would perhaps putting panel C in the bottom left corner and then D at the top right, with E and F below (also on the right) work?

We agree that this improves the figure. We have restructured the ordering of panels in this figure. 

(2) Simulation 1: When reading the intro/results for the first simulation (Figure 2a; Diba & Buszaki, 2007; "When animals traverse a linear track...", page 6, line 186). It wasn't clear to me why pre-run rest would have any forward replay, particularly if pre-run implied that the animal had no experience with the track yet. But in the Methods this becomes clearer, as the model encodes the track eight times prior to the rest periods. Making this explicit in the text would make it easier to follow. Also, was there any reason why specifically eight sessions of awake learning, in particular, were used?

We now make more explicit that the animals have experience with the track before pre-run rest recording:

“Animals first acquire experience with a linear track by traversing it to collect a reward. Then, during the pre-run rest recording, forward replay predominates.”

We included eight sessions of awake learning to match with the number of sessions in Shin et al. (2017), since this simulation attempts to explain data from that study. After each repetition, the model engages in rest. We have revised the Methods section to indicate the motivation for this choice: 

“In the simulation that examines context-dependent forward and backward replay through experience (Figs. 2a and 5a), CMR-replay encodes an input sequence shown in Fig. 7a, which simulates a linear track run with no ambiguity in the direction of inputs, over eight awake learning sessions (as in Shin et al. 2019)”

(3) Frequency of remote replay events: In the simulation based on Gupta et al, how frequently overall does remote replay occur? In the main text, the authors mention the mean frequency with which shortcut replay occurs (i.e., the mean proportion of replay events that contain a shortcut sequence = 0.0046), which was helpful. But, it also made me wonder about the likelihood of remote replay events. I would imagine that remote replay events are infrequent as well - given that it is considerably more likely to replay sequences from the local track, given the recency-weighted mental context. Reporting the above mean proportion for remote and local replay events would be helpful context for the reader.

In Figure 4c, we report the proportion of remote replay in the two experimental conditions of Gupta et al. that we simulate. 

(4) Point of clarification re: backwards replay: Is backwards replay less likely to occur than forward replay overall because of the forward asymmetry associated with these models? For example, for a backwards replay event to occur, the context would need to drift backwards at least five times in a row, in spite of a higher probability of moving one step forward at each of those steps. Am I getting that right?

The reviewer’s interpretation is correct: CMR-replay is more likely to produce forward than backward replay in sleep because of its forward asymmetry. We note that this forward asymmetry leads to high likelihood of forward replay in the section titled “The context-dependency of memory replay”: 

“As with prior retrieved context models (Howard & Kahana 2002; Polyn et al., 2009), CMR-replay encodes stronger forward than backward associations. This asymmetry exists because, during the first encoding of a sequence, an item's associated context contributes only to its ensuing items' encoding contexts. Therefore, after encoding, bringing back an item's associated context is more likely to reactivate its ensuing than preceding items, leading to forward asymmetric replay (Fig. 6d left).”

(5) On terminating a replay period: "At any t, the replay period ends with a probability of 0.1 or if a task-irrelevant item is reactivated." (Figure 1 caption; see also pg 18, line 635). How was the 0.1 decided upon? Also, could you please add some detail as to what a 'task-irrelevant item' would be? From what I understood, the model only learns sequences that represent the points in a track - wouldn't all the points in the track be task-relevant?

This value was arbitrarily chosen as a small value that allows probabilistic stopping. It was not motivated by prior modeling or a systematic search. We have added: “At each timestep, the replay period ends either with a stop probability of 0.1 or if a task-irrelevant item becomes reactivated. (The choice of the value 0.1 was arbitrary; future work could explore the implications of varying this parameter).” 

In addition, we now explain in the paper that task irrelevant items “do not appear as inputs during awake encoding, but compete with task-relevant items for reactivation during replay, simulating the idea that other experiences likely compete with current experiences during periods of retrieval and reactivation.”

(6) Minor typos:

Turn all instances of "nonlocal" into "non-local", or vice versa

"For rest at the end of a run, cexternal is the context associated with the final item in the sequence. For rest at the end of a run, cexternal is the context associated with the start item." (pg 20, line 663) - I believe this is a typo and that the second sentence should begin with "For rest at the START of a run".

We have updated the manuscript to correct these typos. 

(7) Code availability: I may have missed it, but it doesn't seem like the code is currently available for these simulations. Including the commented code in a public repository (Github, OSF) would be very useful in this case.

We now include a Github link to our simulation code: https://github.com/schapirolab/CMR-replay.

This is an interesting and likely observation. Although it is disrupting banking increasingly where KYC is causing large groups to become underbanked, out of an excess of caution by the banks.

Not likely. This is an Anglo-saxon perspective, wrt national id's aversion. They've been around digitally for a generation already across the EU, used online and off, and hasn't had that impact (e.g. Denmark, Spain, Estonia, Netherlands)

word. The breakout should be not being reactionary but a forward looking stance.

IndieWeb is a 2011 concept, back when the silos were much less dominant, and a long way from being synonym with the web itself. So slow grow is what it has had for 15 yrs now, making it the most likely path indeed. Not much impact though, the community isn't set up for broader appeal. I moved on too, and I was low hanging fruit for the community to involve. It's not spreading for lack of narrative, appeal and visibility. Spreading is the alternative to silo'd growth, and IndieWeb is not achieving that.

Interop as the longest shot prediction. Vgl the realisation at Semic by the people there that interoperability is actually the single way out of hyperscaler lock-in. Vgl [[Francesca Bria]] So perhaps not that far fetched for the coming 5 years. Def the angle I need to look at more. -[ ] build overview of European interoperability efforts on diff levels / sectors #geonovumtb #120mins

Draws parallel between federation / small multiples, and tech sovereignty from silo'd hyperscalers. Vgl my notes on alternatives to Silicon Valley type scaling as only game in town.

predicts a resurgence in small forums. I see a parallel with small ActivityPub instances. A building block of #netag too, wrt social symmetry

EventPages is a proposed spec for event sharing, by LinkTree and others. #openvraag is it using ActivityPub that has events in its ActivityStreams, that no one ever uses? Vgl https://www.zylstra.org/blog/2023/09/the-search-for-an-os-meet-up-replacement-mobilizon-edition/

Cameron Jones (Austr) 3 views on IndieWeb 1) wish 2) expectation 3) risk

Where do you see the IndieWeb in 2030?

create 已经创建好了

eLife Assessment

This study combines genetic, cell biological, and interaction data to propose a model of meiotic double-strand break regulation in C. elegans. Solid evidence supports the main conclusions, while by nature of a screening-type study, more may be needed to solidify speculations in future studies. Yet, comprehensive cataloging of the physical and genetic interactions of factors required for meiotic double-strand break is useful information for the field.

Joint Public Review:

Meiotic recombination begins with DNA double-strand breaks (DSBs) generated by the conserved enzyme Spo11, which relies on several accessory factors that vary widely across eukaryotes. In C. elegans, multiple proteins have been implicated in promoting DSB formation, but their functional relationships and how they collectively recruit the DSB machinery to chromosome axes have remained unclear.

In this study, Raices et al. investigate the biochemical and genetic interactions among known DSB-promoting factors in C. elegans meiosis. Using yeast two-hybrid assays and co-immunoprecipitation, they map pairwise protein interactions and identify a connection between the chromatin-associated protein HIM-17 and the transcription factor XND-1. They also confirm the established interaction between DSB-1 and SPO-11 and show that DSB-1 associates with the nematode-specific factor HIM-5, which is required for X-chromosome DSB formation.

The authors extend these findings with genetic analyses, placing these factors into four epistasis groups based on single- and double-mutant phenotypes. Together, these biochemical and genetic data support a model describing how these proteins engage chromatin loops and localize to chromosome axes. The work provides a clearer view of how C. elegans assembles its DSB-forming machinery and how this process compares to mechanisms in other organisms.

Comment from the Reviewing Editor on the revised version:

The authors have adequately addressed the prior review comments. At this point, after going through multiple rounds of reviews and revisions, the community will be better served by having this paper out in public. This version was assessed by the editors without further input from the reviewers.

Author response:

The following is the authors’ response to the previous reviews

Public Reviews: 

Reviewer #1 (Public review): 

Summary: 

The manuscript by Raices et al., provides some novel insights into the role and interactions between SPO-11 accessory proteins in C. elegans. The authors propose a model of meiotic DSBs regulation, critical to our understanding of DSB formation and ultimately crossover regulation and accurate chromosome segregation. The work also emphasizes the commonalities and species-specific aspects of DSB regulation. 

Strengths: 

This study capitalizes on the strengths of the C. elegans system to uncover genetic interactions between a lSPO-11 accessory proteins. In combination with physical interactions, the authors synthesize their findings into a model, which will serve as the basis for future work, to determine mechanisms of DSB regulation. 

Weaknesses: 

The methodology, although standard, still lacks some rigor, especially with the IPs. 

Reviewer #2 (Public review): 

Summary: 

Meiotic recombination initiates with the formation of DNA double-strand break (DSB) formation, catalyzed by the conserved topoisomerase-like enzyme Spo11. Spo11 requires accessory factors that are poorly conserved across eukaryotes. Previous genetic studies have identified several proteins required for DSB formation in C. elegans to varying degrees; however, how these proteins interact with each other to recruit the DSB-forming machinery to chromosome axes remains unclear. 

In this study, Raices et al. characterized the biochemical and genetic interactions among proteins that are known to promote DSB formation during C. elegans meiosis. The authors examined pairwise interactions using yeast two-hybrid (Y2H) and co-immunoprecipitation and revealed an interaction between a chromatin-associated protein HIM-17 and a transcription factor XND-1. They further confirmed the previously known interaction between DSB-1 and SPO-11 and showed that DSB-1 also interacts with a nematodespecific HIM-5, which is essential for DSB formation on the X chromosome. They also assessed genetic interactions among these proteins, categorizing them into four epistasis groups by comparing phenotypes in double vs. single mutants. Combining these results, the authors proposed a model of how these proteins interact with chromatin loops and are recruited to chromosome axes, offering insights into the process in C. elegans compared to other organisms. 

Weaknesses: 

This work relies heavily on Y2H, which is notorious for having high rates of false positives and false negatives. Although the interactions between HIM-17 and XND-1 and between DSB-1 and HIM-5 were validated by co-IP, the significance of these interactions was not tested in vivo. Cataloging Y2H and genetic interactions does not yield much more insight. The model proposed in Figure 4 is also highly speculative. 

Reviewer #3 (Public review): 

The goal of this work is to understand the regulation of double-strand break formation during meiosis in C. elegans. The authors have analyzed physical and genetic interactions among a subset of factors that have been previously implicated in DSB formation or the number of timing of DSBs: CEP-1, DSB-1, DSB-2, DSB-3, HIM-5, HIM-17, MRE-11, REC-1, PARG-1, and XND-1. 

The 10 proteins that are analyzed here include a diverse set of factors with different functions, based on prior analyses in many published studies. The term "Spo11 accessory factors" has been used in the meiosis literature to describe proteins that directly promote Spo11 cleavage activity, rather than factors that are important for the expression of meiotic proteins or that influence the genome-wide distribution or timing of DSBs. Based on this definition, the known SPO-11 accessory factors in C. elegans include DSB-1, DSB2, DSB-3, and the MRN complex (at least MRE-11 and RAD-50). These are all homologs of proteins that have been studied biochemically and structurally in other organisms. DSB-1 & DSB-2 are homologs of Rec114, while DSB-3 is a homolog of Mei4. Biochemical and structural studies have shown that Rec114 and Mei4 directly modulate Spo11 activity by recruiting Spo11 to chromatin and promoting its dimerization, which is essential for cleavage. The other factors analyzed in this study affect the timing, distribution, or number of RAD-51 foci, but they likely do so indirectly. As elaborated below, XND-1 and HIM-17 are transcription factors that modulate the expression of other meiotic genes, and their role in DSB formation is parsimoniously explained by this regulatory activity. The roles of HIM-5 and REC-1 remain unclear; the reported localization of HIM-5 to autosomes is consistent with a role in transcription (the autosomes are transcriptionally active in the germline, while the X chromosome is largely silent), but its loss-of-function phenotypes are much more limited than those of HIM-17 and XND-1, so it may play a more direct role in DSB formation. The roles of CEP-1 (a Rad53 homolog) and PARG-1 are also ambiguous, but their homologs in other organisms contribute to DNA repair rather than DSB formation. 

We appreciate the reviewer’s clarification. However, the definition of Spo11 accessory factors varies across the literature. Only Keeney and colleagues define these as proteins that physically associate with and activate Spo11 to catalyze DSB formation (Keeney, Lange & Mohibullah, 2014; Lam & Keeney, 2015). In contrast, other authors have used the term more broadly to refer to proteins that promote or regulate Spo11-dependent DSB formation, without necessarily implying a direct interaction with Spo11 (e.g., Panizza et al., 2011; Robert et al., 2016; Stanzione et al., 2016; Li et al., 2021; Lange et al., 2016). Thus, our usage of the term follows this broader functional definition.

An additional significant limitation of the study, as stated in my initial review, is that much of the analysis here relies on cytological visualization of RAD-51 foci as a proxy for DSBs. RAD-51 associates transiently with DSB sites as they undergo repair and is thus limited in its ability to reveal details about the timing or abundance of DSBs since its loading and removal involve additional steps that may be influenced by the factors being analyzed. 

We agree with the reviewer that counting RAD-51 foci provides only an indirect measure of SPO-11–dependent DSBs, as RAD-51 marks sites of repair rather than the breaks themselves. However, we would like to clarify that our current study does not rely on RAD51 foci quantification for any of the analyses or conclusions presented. None of the figures or datasets in this manuscript are based on RAD-51 cytology. Instead, our conclusions are drawn from genetic interactions, biochemical assays, and protein–protein interaction analyses.

The paper focuses extensively on HIM-5, which was previously shown through genetic and cytological analysis to be important for breaks on the X chromosome. The revised manuscript still claims that "HIM-5 mediates interactions with the different accessory factors sub-groups, providing insights into how components on the DNA loops may interact with the chromosome axis." The weak interactions between HIM-5 and DSB-1/2 detected in the Y2H assay do not convincingly support such a role. The idea that HIM-5 directly promotes break formation is also inconsistent with genetic data showing that him5 mutants lack breaks on the X chromosomes, while HIM-5 has been shown to be is enriched on autosomes. Additionally, as noted in my comment to the authors, the localization data for HIM-5 shown in this paper are discordant with prior studies; this discrepancy should be addressed experimentally. 

We appreciate the reviewer’s concerns regarding the interpretation of HIM-5 function.  The weak Y2H interactions between HIM-5 and DSB-1 are not interpreted as direct biochemical evidence of a strong physical interaction, but rather as a potential point of regulatory connection between these pathways. Importantly, these Y2H data are further supported by co-immunoprecipitation experiments, genetic interactions, and the observed mislocalization of HIM-5 in the absence of DSB-1. Together, these complementary results strengthen our conclusion that HIM-5 functionally associates with DSB-promoting complexes.

Regarding HIM-5 localization, the pattern we observe using both anti-GFP staining of the eaIs4 transgene (Phim-5::him-5::GFP) and anti-HA staining of the HIM-5::HA strain is consistent with that reported by McClendon et al. (2016), who validated the same eaIs4 transgene. Although the pattern difers slightly from Meneely et al. (2012), that used a HIM5 antibody that is no longer functional and that has been discontinued by the commercial source. In this prior study, a weak signal was detected in the mitotic region and late pachytene, but stronger signal was seen in early to mid-pachytene. Our imaging— optimized for low background and stable signal—similarly shows robust HIM-5 localization in early and mid-pachytene, supporting the reliability of our GFP and HA-tagged analyses.

The recent analysis of DSB formation in C. elegans males (Engebrecht et al; PloS Genetics; PMID: 41124211) shows that in absence of him-5 there is a significant reduction of CO designation (measured as COSA-1 foci) on autosomes. This study strongly supports a direct and general role for HIM-5 in crossover formation— on both autosomes and on the hermaphrodite X.

This paper describes REC-1 and HIM-5 as paralogs, based on prior analysis in a paper that included some of the same authors (Chung et al., 2015; DOI 10.1101/gad.266056.115). In my initial review I mentioned that this earlier conclusion was likely incorrect and should not be propagated uncritically here. Since the authors have rebutted this comment rather than amending it, I feel it is important to explain my concerns about the conclusions of previous study. Chung et al. found a small region of potential homology between the C. elegans rec-1 and him-5 genes and also reported that him-5; rec-1 double mutants have more severe defects than either single mutant, indicative of a stronger reduction in DSBs. Based on these observations and an additional argument based on microsynteny, they concluded that these two genes arose through recent duplication and divergence. However, as they noted, genes resembling rec-1 are absent from all other Caenorhabditis species, even those most closely related to C. elegans. The hypothesis that two genes are paralogs that arose through duplication and divergence is thus based on their presence in a single species, in the absence of extensive homology or evidence for conserved molecular function. Further, the hypothesis that gene duplication and divergence has given rise to two paralogs that share no evident structural similarity or common interaction partners in the few million years since C. elegans diverged from its closest known relatives is implausible. In contrast, DSB-1 and DSB-2 are both homologs of Rec114 that clearly arose through duplication and divergence within the Caenorhabditis lineage, but much earlier than the proposed split between REC-1 and HIM-5. Two genes that can be unambiguously identified as dsb-1 and dsb-2 are present in genomes throughout the Elegans supergroup and absent in the Angaria supergroup, placing the duplication event at around 18-30 MYA, yet DSB-1 and DSB-2 share much greater similarity in their amino acid sequence, predicted structure, and function than HIM-5 and REC-1. Further, Raices place HIM-5 and REC-1 in different functional complexes (Figure 3B). 

We respectfully disagree with the reviewer’s characterization of the relationship between HIM-5 and REC-1. Our use of the term “paralog” follows the conclusions of Chung et al. (2015), a peer-reviewed study that provided both sequence and microsynteny evidence supporting this relationship. While we acknowledge that the degree of sequence conservation is limited, the evolutionary scenario proposed by Chung et al. remains the only published framework addressing this question. Further the degree of homology between either HIM-5 or REC-1 and the ancestral locus are similar to that observed for DSB-1 and DSB-2 with REC-114 (Hinman et al., 2021). We therefore retain the use of the term “paralog” in reference to these genes. Importantly, our conclusions regarding their distinct molecular and functional roles are independent of this classification.

The authors acknowledge that HIM-17 is a transcription factor that regulates many meiotic genes. Like HIM-17, XND-1 is cytologically enriched along the autosomes in germline nuclei, suggestive of a role in transcription. The Reinke lab performed ChIP-seq in a strain expressing an XND-1::GFP fusion protein and showed that it binds to promoter regions, many of which overlap with the HIM-17-regulated promoters characterized by the Ahringer lab (doi: 10.1126/sciadv.abo4082). Work from the Yanowitz lab has shown that XND-1 influences the transcription of many other genes involved in meiosis (doi: 10.1534/g3.116.035725) and work from the Colaiacovo lab has shown that XND-1 regulates the expression of CRA-1 (doi: 10.1371/journal.pgen.1005029). Additionally, loss of HIM-17 or XND-1 causes pleiotropic phenotypes, consistent with a broad role in gene regulation. Collectively, these data indicate that XND-1 and HIM-17 are transcription factors that are important for the proper expression of many germline-expressed genes. Thus, as stated above, the roles of HIM-17 and XND-1 in DSB formation, as well as their effects on histone modification, are parsimoniously explained by their regulation of the expression of factors that contribute more directly to DSB formation and chromatin modification. I feel strongly that transcription factors should not be described as "SPO-11 accessory factors." 

The ChIP analysis of XND-1 binding sites (using the XND-1::GFP transgene we provided to the Reinke lab) was performed, and Table S3 in the Ahringer paper suggests it is found at germline promoters, although the analysis is not actually provided. We completely agree that at least a subset of XND-1 functions is explained by its regulation of transcriptional targets (as we previously showed for HIM-5). However, like the MES proteins, a subset of which are also autosomal and impact X chromosome gene expression, XND-1 could also be directly regulating chromatin architecture which could have profound effects on DSB formation.  As stated in our prior comments, precedent for the involvement of a chromatin factor in DSB formation is provided by yeast Spp1. 

Recommendations for the authors: 

Editor comments: 

As you can see, the reviewers have additional comments, and the authors can include revisions to address those points prior to publicizing 'a version of record' (e.g. hatching rate assay mentioned by reviewer #1). This type of study, trying to catalog interactions of many factors, inevitably has loose ends, but in my opinion, it does not reduce the value of the study, as long as statements are not misleading. I suggest that the authors address issues by making changes to the main text. After the next round of adjustments by authors, I feel that it will be ready for a version of record, based on the spirit of the current eLife publication model. 

Reviewer #1 (Recommendations for the authors): 

I still have concerns about the HIM-17 IP and immunoblot probing with XND-1 antibodies. While the newly provided whole extract immunoblot clearly shows a XND-1 specific band that goes away in the mutant extracts, there is additional bands that are recognized - the pattern looks different than in the input in Figure 1B. Additionally, there is still a band of the corresponding size in the IPs from extracts not containing the tagged allele of HIM-17, calling into question whether XND-1 is specifically pulled down. 

The authors did not include the hatching rate as pointed out in the original reviews. In the rebuttal: 

"Great question. I guess we need to do this while back out for review. If anyone has suggestions of what to say here. Clearly we overlooked this point but do have the strain." 

We thank the reviewer for this suggestion. We had intended to include a hatching analysis; however, during the course of this work we discovered that our him-17 stock had acquired an additional linked mutation(s) that altered its phenotype and led to inconsistent results. This strain was used to rederive the him-17; eaIs4 double mutant after our original did not survive freeze/thaw. Given the abnormal behavior observed in this line, we concluded that proceeding with the hatching assays could yield unreliable data. We are currently reestablishing a verified him-17 strain, but in the interest of accuracy and reproducibility, we have restricted our analysis in this manuscript to validated datasets derived from confirmed strains.

Reviewer #2 (Recommendations for the authors): 

The authors have addressed most of the previous concerns and substantially improved the manuscript. The new data demonstrate that HIM-5 localization depends on DSB-1, and together with the Y2H and Co-PI results, strengthen the link between HIM-5 and the DSBforming machinery in C. elegans. The remaining points are outlined below: 

Specific comments: 

The font size of texts and labels in the Figure is very small and is hardly legible. Please enlarge them and make them clearly visible (Fig 1A, 1B, 2A, 2B, 2C, 2D, 2E, 3A, 3B, 3C, 3D, 3F)

Done

Although the authors have addressed the specificity of the XND-1 antibody, it remains unclear whether the boxed band is specific to the him-17::3xHA IP, since the same band appears in the control IP, albeit with lower intensity (Fig 1B). Is the ~100 kDa band in the him-17::3xHA IP a modified form XND-1? While antibody specificity was previously demonstrated by IF using xnd-1 mutants, it would be ideal to confirm this on a western blot as well. 

A Western Blot performed using whole cell extracts and probed with the anti- XND-1 antibody has been provided in the revised version of the manuscript (Fig. S1A). This confirms that the antibody specifically recognizes XND-1 protein. We believe that the ~100 kDa band mentioned by the reviewer is likely to be a non-specific cross reaction band detected by the antibody, since an identical band of the same mW was also detected in xnd-1 null mutants (Fig. S1A).

Regarding the IP negative controls, we are firmly convinced the boxed band to be specific, and the fact that a (very) low intensity band is also found in the negative control should not infringe the validity of the HIM-17-XND-1 specific interaction. There is a constellation of similar examples present across the literature, as it is widely acknowledged amongst biochemists that some proteins may “stick” to the beads due their intrinsic biochemical properties despite usage of highly stringent IP buffers. However, the high level of enrichment detected in the IP (as also underlined by the reviewer) corroborates that XND-1 specifically immunoprecipitates with HIM-17 despite a low, non-specific binding to the HA beads is present. If interaction between XND-1 and HIM-17 was non-specific, we logically would have found the band in the IP and the band in the negative control to be of very similar intensity, which is clearly not the case. 

Although co-IP assays are generally considered not a strictly quantitative assay, we want to emphasize that a comparable amount of nuclear extract was employed in both samples as also evidenced by the inputs, in which it is also possible to see that if anything, slightly less  nuclear extracts were employed in the him-17::3xHA; him-5::GFP::3xFLAG vs. the him5::GFP::3xFLAG negative control, corroborating the above mentioned points.

Lastly, it is crucial to mention that mass spectrometry analyses performed on HIM17::3xHA pulldowns show XND-1 as a highly enriched interacting protein (Blazickova et al.; 2025 Nature Comms.), which strongly supports our co-IP results.

The subheading "HIM-5 is the essential factor for meiotic breaks in the X chromosome" does not accurately represent the work described in the Results or in Figure 1. I disagree with the authors' response to the earlier criticism. The issue is not merely semantic. The data do not demonstrate that HIM-5 is required for DSB formation on the X chromosome - this conclusion can only be inferred. What Figure 1 shows is that XND-1 and HIM-17 interact, and that pie-1p-driven HIM-5 expression can partially rescue meiotic defects of him-17 mutants. This supports the conclusion that him-5 is a target of HIM-17/XND-1 in promoting CO formation on the X chromosome. However, the data provide no direct evidence for the claim stated in the subheading. I strongly encourage authors to revise the subheading to more accurately represent the findings presented in the paper. 

After considering the reviewer’s comments, we have revised the subheading to more accurately describe our findings.

In Fig1C, please fix the typo in the last row - "pie1p::him5-::GFP" to "pie-1p::him- 5::GFP".

Done

In Fig 2C, "p" is missing from the label on the right for Phim-5::him-5::GFP.

Done

In Fig 3I, bring the labels (DSB-1/2/3) at the lower right to the front.

Done

In Concluding Remarks, please fix the typo "frequently".

Done

Reviewer #3 (Recommendations for the authors): 

The experiments that analyze HIM-5 in dsb-1 mutants should be repeated using antibodies against the endogenous HIM-5 antibody, and localization of the HIM-5::HA and HIM-5::GFP proteins should be compared directly to antibody staining. This work uses an epitopetagged protein and a GFP-tagged protein to analyze the localization of HIM-5, while prior work (Meneely et al., 2012) used an antibody against the endogenous protein. In Figures 2 and S4 of this paper, neither HIM-5::HA nor HIM-5::GFP appears to localize strongly to chromatin, and autosomal enrichment of HIM-5, as previously reported for the endogenous protein based on antibody staining, is not evident. Moreover, HIM-5::GFP and HIM-5::HA look different from each other, and neither resembles the low-resolution images shown in Figure 6 in Meneely et al 2012, which showed nuclear staining throughout the germline, including in the mitotic zone, and also in somatic sheath cells. Given the differences in localization between the tagged transgenes and the endogenous protein, it is important to analyze the behavior of the endogenous, untagged protein. A minor issue: a wild-type control should also be shown for HIM-5::HA in Figure S4. 

Wild type control added to figure S4

Evidence that XND-1 and HIM-17 form a complex is weak; it is supported by the Y2H and co-IP data but opposed by functional analysis or localization. The diversity of proteins found in the Co-IP of HIM-17::GFP (Table S2) indicate that these interactions are unlikely to be specific. The independent localization of these proteins to chromatin is clear evidence that they do not form an obligate complex; additionally, they have been found to regulate distinct (although overlapping) sets of genes. The predicted structure generated by Alphafold3 has very low confidence and should not be taken as evidence for an interaction.The newly added argument about the lack of apparently overlap between HIM-17 and XND1 due to the distance between the HA tag on HIM-17 and XND-1 is flawed and should be removed - the extended C-terminus in the predicted AlphaFold3 C-terminus of HIM-17 has been interpreted as if it were a structured domain. Moreover, the predicted distance of 180 Å (18 nm) is comparable to the distance between a fluorophore on a secondary antibody and the epitope recognized by the primary antibody (~20-25 nm) and is far below than the resolution limit of light microscopy. 

We appreciate the reviewer’s thoughtful comment. The evidence supporting a physical interaction between XND-1 and HIM-17 is not only shown by our co-IP experiments, but it has also been recently shown in an independent study where MS analyses were conducted on HIM-17::3xHA pull downs to identify novel HIM-17 interactors (Blazickova et al.; 2025 Nature Comms). As shown in the data provided in this study, also under these experimental settings XND-1 was identified as a highly enriched putative HIM-17 interactor. We do acknowledge that their chromatin localization patterns are distinct and they regulate overlapping but not identical sets of genes, however, it is worth noting that protein–protein interactions in meiosis are often transient or context-dependent, and may not necessarily result in co-localization detectable by microscopy. In line with this, in the same work cited above, a similar situation for BRA-2 and HIM-17 was reported, as they were shown to interact biochemically despite the absence of overlapping staining patterns. 

Minor issues: 

The images shown in Panel D in Figure 1 seem to have very different resolutions; the HTP3/HIM-17 colocalization image is particularly blurry/low-resolution and should be replaced. The contrast between blue and green cannot be seen clearly; colors with stronger contrast should be used, and grayscale images should also be shown for individual channels. High-resolution images should probably be included for all of the factors analyzed here to facilitate comparisons.

Here is the ending sentence of the song: I could annotate it as I did so far, but by now you are familiar with Eminem's tone and with the themes dealt with in the project... so I would like to hear your interpretations! Try to unpack it on your own.

Clues: my personal advice when it comes to understand a text is dividing it into smaller chunks (example: what piece of cloth is Eminem referring to?). If you struggle with understanding what he is trying to say, don't worry: try to read the text again and remember that previous and following sentences can help you out.

The spiel is "a speech, especially one that is long and spoken quickly and is intended to persuade the person listening about something". https://dictionary.cambridge.org/dictionary/english/spiel

In this case, the wordplay is built around the fact that the name of the U.S. national anthem is the "Star-Spangled Banner" (not spiel). Your turn: according to you, what is Eminem insisting upon? Why makes this expression so powerful?

Eminem touches upon another American tragedy: the genocide of Native Americans (which was even celebrated in the movie and comics industry). The present project does not focus on this theme due to limitations in scope; however, here are some resources to explore this topic: https://hmh.org/library/research/genocide-of-indigenous-peoples-guide/, https://study.com/learn/lesson/video/native-american-genocide-history.html, https://sites.uab.edu/humanrights/2017/04/17/indian-removal-act-genocide-native-americans/.

Eminem's wording strikes again: he plays with America's ideals and bitter social reality by pairing the concluding phrase of the U.S. national anthem, the Star-Spangled Banner, ("O'er the land of the free and the home of the brave!") and the expression racist ville (that means the city of racists). https://amhistory.si.edu/starspangledbanner/the-lyrics.aspx

The oxymoronic expression reveals that America's ideals are just aspirations that never became reality.

Dryer lint refers to the buildup that forms in the dryer as a result of hair, textile fibers and other particles clamping together. Normally, it is thrown up after every washing cycle. In Italian, it is translatable as lanugine, but perhaps the following image will clarify any doubt: https://preparedhero.com/it-it/blogs/articles/dryer-lint#:~:text=What%20Is%20Dryer%20Lint?,for%20dryer%20safety%20and%20performance.

This is a reference to a news story which dates back to 2016, when Micah J. Johnson shot five Dallas police officers dead and harmed other eleven people. Since the killer was a Black man and the shooting happened during a peaceful Black Live Matter rally, the assassination was connected to the movement itself. However, "the BLM organization responded to these critiques head-on, calling the attack "the result of the actions of a lone gunman” and calling it “dangerous and irresponsible” to “assign the actions of one person to an entire movement”." https://www.theguardian.com/us-news/2016/jul/09/black-lives-matter-dallas-protest-shooting https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

Your turn: what do you think Eminem is trying to say here? Which other singer (of the ones that are part of the analysis) mentioned the hiring process. Clue: focus on the word hire.

The singer does not pretend to be colorblind and acknowledges the fact that he is white. Nevertheless, his ideals do not coincide with the ones supported by white suprematists; hence, the shame in being white and in having to deal with the white cultural heritage.

This song gives a circular structure to the present analysis: Eminem connects present-day abuse of power, racism and police brutality to 1960s fights for civil rights. The singer underscores how history seems to repeat itself in an endless loop: although more than 50 years have passed, black people still struggle to have their rights recognized and respected. And, if I may add, music keeps being a space in which lack of equality, racism and social injustice are denounced.

Eminem speaks directly at the heart of the white supremacist ideals, which support the idea that whites are considered "untouchable rockstars" just for the color of their skin. Regardless of the crimes they commit (and especially if they are policemen), they won't ever be charged or held accountable for them. As a matter of fact, in most of the cases in which African-Americans were victims of police brutality, white policemen were acquitted (assolti in Italian) of all charges.

It is "a device with meshes or perforations through which finer particles of a mixture (as of ashes, flour, or sand) of various sizes may be passed to separate them from coarser ones, through which the liquid may be drained from liquid-containing material, or through which soft materials may be forced for reduction to fine particles". https://www.merriam-webster.com/dictionary/sieve.

These three lines describe the white policeman's internal monologue and trail of thought. Although he recognizes their negative impact, he keeps justifying his abusive and racist actions in the name of his country, symbolically represented by the colors of the flag.

"Though he’s fully aware that murdering an innocent black man isn’t the right thing to do, he finds peace and comfort deluding himself into thinking that he’s protecting his country, or as he raps, “the red, white and blue.” https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

In this context, it means "to pass unnoticed or unremarked". In Italian, the sentence could be translated into potremmo lasciarti andare. https://www.merriam-webster.com/dictionary/slide

"A house where dope heads (heroin addicts) live" and do drugs. http://dope-house.urbanup.com/7824692

Eminem is criticizing "how African American drivers are often stereotyped as drug dealers with a criminal background". https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/ Indeed, the key word in the sentence is "probably": the policeman does not know who the young man is, where he is going to or where he comes from, so he cannot do anything but hypothesize. The problem is twofold: 1. He mistakes his hypothesis for truth; 2. His hypothesis is biased: there is no logical reason as for why he associates the young black man with the "dope house". However, he does so because he cultivates prejudices against black men.

The scene goes on. Eminem's visual language does not make it hard to picture it: a white cop stopping a black young man who is driving his car. The policeman asks him to pull up (that is, to stop the car at the side of the road), roll his window down and provide a "profile". In this context, "profiling" indicates "the activity of collecting information about someone, especially a criminal, in order to give a description of them". https://dictionary.cambridge.org/dictionary/english/profiling

More specifically, Eminem is directly criticizing the so-called racial profiling, which is an illegal practice relying "on stereotypes of racial or ethnic groups to assist law enforcement in detecting and deterring crime". In other (simpler) words, it means that some people (namely Latinos or Blacks) are stopped and incarcerated only for belonging to a certain ethnicity. Criminal profiling, instead, is a legal practice based on evidence gathered from "previous crimes from witnesses, victims, and the crime scene. The profile includes the potential suspect’s age range, gender, race, possible employment, and other factors to narrow down the group of suspects". https://www.amu.apus.edu/area-of-study/criminal-justice/resources/racial-profiling-vs-criminal-profiling/<br /> https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

In the opening of the song, Eminem's lyrics shape a scene in which a white policeman stops a car driven by a black young man.

February is Black History Month: since being introduced in 1926 by C. G. Woodson (who helped established African American Studies), the birthmonth of former U.S. President Abraham Lincoln and reformer F. Douglass has been dedicated to celebrate African-American history and culture. Every year, the Association for the Study of African American Life and History (ASALH) chooses a theme to focus on; last year, for example, the theme revolved around labour. https://parade.com/living/black-history-month-themes https://www.weforum.org/stories/2024/02/black-history-month-what-is-it-and-why-do-we-need-it/

This expression precedes proof of Kendrick Lamar's effort and interest in promoting African-American culture: * he supports and remembers the Black Panther Party; * he lectures Georgia State college students about pivotal figures in the African-American community, such as Marcus Garvey; * he celebrates Black History month as it were his birthday.

However, the expression "don't matter how much" (just as the haunting repetition of being "the biggest hypocrite of 2015") signals that somehow his committment to the cause is not enough: why? The singer forces the audience to wait until the last lines of the song to clarify the reasons of his internal turmoil.

Lamar compares the civil war between two African ethnic groups (Zulu and Xhosa) to street fights between Crips and Bloods. Indeed, street fighting between local gangs is read by the singer as a form of civil war since it involves people that live in the same area. In both cases, a bitter ending awaits those who kill each other ("only death settle(s) the score").

Southern Black Africans presents four major ethnic divisions; one of them is the Nguni, which, in its turn, can be divided into four groups: Zulu and Xhosa are two of them. https://sahistory.org.za/article/xhosa https://sahistory.org.za/article/zulu

Although they share a common history, Zulu and Xhosa communities were implicated in a civil war from 1990 to 1994. The reason behind this conflict is, actually, linguistic and colonial: the two languages were "created" by colonizers and African interpreters. Before African colonialism, indeed, there weren't any written languages and people did not distinguish themselves on a linguistic basis, but rather on social belonging. This does not mean that "Zulu and Xhosa identities didn’t exist before the languages were well defined, rather that the identities were transformed when these languages came into existence." https://theconversation.com/zulu-vs-xhosa-how-colonialism-used-language-to-divide-south-africas-two-biggest-ethnic-groups-204969

Tyrone is originally an Irish name, but it is increasingly more common in African-American communities. Unfortuntately, for this reason it is also at the center of discrimination: compared to Tyrone, "white" names are twice as likely to receive responses. Also Darius is a typical African-American name. https://www.irishexaminer.com/news/arid-10108995.html https://www.behindthename.com/name/darius

In this scenario dominated by manslaughter and perverse traditions, the pervasive double consciousness that haunts the singer seems to falter: the American heritage, which also entails the bitter history of racism, is too heavy for the singer to carry. Ultimately, he chooses to identify as African.

In this last verse, there is no possible misunderstanding: Lamar directly attacks centuries of racism, whose thousands of deaths he (rightly) labels as genocide. Another striking expression is that of "generational hatred": the singer evokes an atmosphere in which racism is like a twisted tradition which passes down from generation to generation, destroying people in the meantime.

Double consciousness, again, is a key concept to interpret this line: Lamar feels like a prisoner in his own head, enchained by his own thoughts. This occurs because he has internalized a way of perceiving and judging reality which pertains to the oppressor (in this case, whites).

This entire verse is written in Jamaican patois, that is, "an English-lexified creole language spoken by the majority of Jamaicans". https://jamaicanpatwah.com As you will see, some words may be intuitive, but others are definitely not. While I was looking for the lyrics of the song, I found other anglicized versions which were certainly more comprehensible, but, I am afraid, less faithful to the singer's intention. Consequently, I opted for the original, more complex version.

Why has the singer recurred to Jamaican patois? My hypothesis is that he features it as a way to give importance and centrality to a marginal community through its language.

Dem is they. https://jamaicanpatwah.com/term/dem/961

Lamar mangles (storpia, in Italian) the words of the proverb: this modified version seems to represent a counterpart to the original one. If the first one celebrates and honors Black culture, this one seems to connect to the brutality of reality, in which violence dominates and is, apparently, the only possible response.

This word is a highly offensive, derogatory term used to insult Black people by comparing them to animals. The likening of a person to an ape, a monkey or a gorilla is a discriminatory practice that takes the name of simianization. Simianization dates back to the Middle Ages, has progressively taken a racist turn and started only to indicate black-skinned individuals. Reasons for this association may include the prevalence of apes in Africa and the aesthetic difference between whites and blacks. Whatever the reason may be, it is a form of degradation and dehumanization. In this case, it is probable that Lamar is aiming for a reclaiming of the term. In other words, the same reasoning applied for "nigga" in 2Pac's "Changes" is applicable here: the singer uses this term to affirm his identity as an African-American. https://www.dictionary.com/browse/simianization https://theconversation.com/comparing-black-people-to-monkeys-has-a-long-dark-simian-history-55102

Here Lamar denounces a decade-long rage for anti-Black racism and police brutality he himself was a victim of. In a Rolling Stone interview, Lamar declared that as a teenager "the majority of my interactions with the police were not good […] there were a few good ones who were actually protecting the community. But then you have the ones from the Valley. They never met me in my life, but since I'm a kid […] they wanna slam me on the hood of the car. […] Even if he's not a good kid, that don't give you the right to slam a minor on the ground or pull a pistol on him. " […] Indeed, "police pull guns on him on two occasions. The first when he was 17." https://issuu.com/lawrenceambrocio5018/docs/rolling_stone_march_26_2015_usa_1_

Setting the scene: the song was released as a second single from the 2015 album To Pimp A Butterfly. The album (and the song as well) "is firmly in the present. It's [Lamar's] take on what it means to be young and black in America today". https://issuu.com/lawrenceambrocio5018/docs/rolling_stone_march_26_2015_usa_1_ Indeed, the album is deeply connected to contemporary issues in America (police brutality, systemic racism and inequality) and, in particular, to Black Lives Matter. Black Lives Matter is a "Black-centered political-movement-building project" that surged in 2013 as a reaction to the Travyon Martin murder and is still active today. The core beliefs of the movement include: * the affirmation of the importance of Black Lives against police brutality and any other racist manifestation; * transforming the present world in which "Black lives are systemically targeted for deliberate and indirect demise"; * affirmation of Black humanity and contributions; * abolition of mass incarceration to the detriment of Black people; * collective safety.

https://blacklivesmatter.com/our-history/

Here the central critique to the lack of equality and the debunking of the immigration myths appears evident: in particular, Springsteen makes uses of the anaphora "they died" to underscore the timeless sacrifice of immigrants, who are identified with the makers of the United States ("the hands that build the country"). This last part of the song completely overturns what Springsteen has sung so far: there are no streets paved with gold, no diamonds in the sidewalks or "treasure for the taking". What remains is work "to bones and skin". Once again, Springsteen has not departed from the historical truth: despite their hopes, European immigrants who landed in the United States did not improve their status. In other words, if they were poor, they stayed as such; “past European immigrants often struggled when they first arrived, and most of them did not succeed in reaching the American Dream within their lifetimes.” https://ui.charlotte.edu/story/streets-gold-debunking-american-immigration-myths/ Moreover, research shows that from 1880 to 1920 immigrants "were the mainstay of the American industrial workforce". https://pmc.ncbi.nlm.nih.gov/articles/PMC2760060/#abstract1 Making home in the American Land was, therefore, impossible for them because America itself rejected and discriminated immigrants after exploiting them for its own industrial and economic growth. Indeed, "often stereotyped and discriminated against, many immigrants suffered verbal and physical abuse because they were different. […] The newcomers helped transform American society and culture, demonstrating that diversity, as well as unity, is a source of national strength." https://www.loc.gov/classroom-materials/united-states-history-primary-source-timeline/rise-of-industrial-america-1876-1900/immigration-to-united-states-1851-1900/

Springsteen's radical claim is that such discrimination and sacrifice are not limited to a distant past, but have continued up until now ("they're still dyin' now"). When Springsteen released the song, the country was actually undergoing a period of decline in immigration due to measures taken after the terrorist attacks of September 11, 2001 such as the Patriot Act. https://library.law.howard.edu/civilrightshistory/immigration/history. However, it is true that immigration continues to be a divisive topic in the United States, especially in the current presidency: what do you know about Trump's immigration policies?

Again, these sentences make a parallel with "Gold comes rushing out the rivers straight into your hands": they all evoke the illusionary hopes and dreams of immigrants entering a new land and abandoning their own.

"Immigrants entered the United States through several ports. Those from Europe generally came through East Coast facilities, while those from Asia generally entered through West Coast centers. More than 70 percent of all immigrants, however, entered through New York City, which came to be known as the "Golden Door." Throughout the late 1800s, most immigrants arriving in New York entered at the Castle Garden depot near the tip of Manhattan. In 1892, the federal government opened a new immigration processing center on Ellis Island in New York harbor." https://www.loc.gov/classroom-materials/united-states-history-primary-source-timeline/rise-of-industrial-america-1876-1900/immigration-to-united-states-1851-1900/

Ellis Island was chosen as the first federal facility in which immigrants were processed because of its strategic position: it was isolated, far from the mainland and, therefore, considered fitting to carefully inspect immigrants and prevent them from entering the country without being registered. Inspection process was not detached from class distinctions: only indigent, (that is, poor), third-class passengers (also referred to as "steerage") were required to undergo the inspection process as Ellis Island. What was the criterion, then? Those who boarded the ship on first or second class were presumed to be wealthy people, less likely to "become a public charge in America due to medical or legal reasons". After a long trip, which entailed staying for days in unsanitary conditions and overly crowded spaces, poor people were submitted to a minimum of 3\5 hours of inspection in the Great Hall: their health condition was examined and their origins as well as destinations were investigated. https://klagenfurtmigrationstudies.home.blog/understanding-barriers-to-immigration-by-listening-to-ellis-island-oral-histories/ https://www.statueofliberty.org/ellis-island/overview-history/.

Ellis Island is now seat of a National Museum of Immigration which can be visited in person (https://www.statueofliberty.org/visit/); otherwise, the official website offers numerous online resources if you are interested in the topic.

These sentences evoke popular belief among immigrants that in America there were "streets paved with gold" : this rumor (this myth if you want) created anticipation and hope for those who left their homelands in search of better opportunities. The powerful expression gave the name to this interesting exhibit: https://www.nps.gov/elis/learn/education/streets-paved-with-gold.htm.

Setting the scene: the song was first released in 2006 in the We Shall Overcome: the Seeger Sessions album as a bonus live track on a special edition of the album. The recorded version was added in 2012 to the Wrecking Ball album. The song has a long genesis: it is based on Pete Seeger's "He Lies in the American Land" (1956), which, in its turn, was the translation of a text originally written by a Slovak steelworker, Andrew Kovaly, at the beginning of the 20th century. Consequently, Springsteen recovers and adapts a song that deals with a timeless topic, immigration, and ultimately, the lack of equality for those who migrate to the United States. The music itself is a mixture of typical "American" sounds (rock 'n' roll, the electric guitar...) and an Irish-like folk motive.

Since its "discovery", America has been a land of immigration; in particular, the major wave of immigrants landed in America at the end of the 19th century and the beginning of the following one. Indeed, between 1870 and 1900, nearly 12 million people arrived in the United States. Simultaneously, xenophobia and anti-immigration actions gained momentum: differentiations between "desirable" and "undesirable" immigrants based on racist assumptions around ethnicity and religion laid the foundations for the Immigration Act of 1917, which restricted immigration by imposing literacy tests and by preventing immigration from Asia and almost the entire Middle East. Context around this specific period of time is important because it is exactly in those years that Kovaly wrote "He lies in the American Land".

Compared to the previous songs, which focus mainly on African Americans and racism, this song shifts attention to inequality due to being an immigrant.

https://immigrationhistory.org/lesson-plan/european-migration/ https://voices.pitt.edu/TeachersGuide/Unit10/American%20Land.htm https://alessandroportelli.blogspot.com/2012/03/bruce-springsteen-wrecking-ball.html https://library.law.howard.edu/civilrightshistory/immigration/history

Apart from the reference to crack, this verse has another important element to be noted: 2Pac is trying to debunk the myth that only African-Americans use drugs. In fact, this 1995 report clearly shows racial disparity in connection to arrests for drug sale and possession: https://bjs.ojp.gov/content/pub/pdf/rdusda.pdf. Although it is undeniable that the African-American community was deeply affected by the (ab)use of crack, it is also true that it was widespread among all poors, including whites.

Although in the previous verse Huey Newton seems to be a source of inspiration for the singer, hope seems to be nowhere to be found in this verse. As any African-American, even Huey ends up being another victim of violence. Considering the bigger picture, it can be hypothesized that 2Pac was even questioning the actual impact and ideals that animated the Black Panther Party itself.

The "Huey" mentioned is Huey Newton, the co-founder (with Bobby Seale) of the Black Panther Party in 1966. (https://americansongwriter.com/the-painful-meaning-behind-the-song-changes-by-tupac/) The Black Panther was a 1960s revolutionary party whose original purpose was that of protecting Blacks from the attack of police officers and eventually extended its scope "to a Marxist revolutionary group that called for the arming of all African Americans, the exemption of African Americans from the draft and from all sanctions of so-called white America, the release of all African Americans from jail, and the payment of compensation to African Americans for centuries of exploitation by white Americans". (https://www.britannica.com/topic/Black-Panther-Party)

In this verse and in the previous one, the singer is making explicit reference to white supremacy and police brutality in the U.S.A: excessive use of force (also culminating in murder) by police officers towards specific categories has been documented since the early 19th century. Targets have varied through the centuries, but African-Americans are historically the most targeted group because of racial implications. In this case, the singer emphasizes policemen's impunity before the law; on the contrary, they are acclaimed and welcomed as "heros". https://www.britannica.com/topic/police-brutality-in-the-United-States-2064580/Police-brutality-after-World-War-II

Disclaimer: some of the punctuation marks (commas, mainly) were not present in the original lyrics of the song; I added them later. I found it a useful, non-intrusive alteration of the text which may result in a better understanding of the content. Commas, indeed, help separating sentences and organize the content in a clearer way; in this context, I argue that they are necessary, especially for non-learner students who are approaching a song that employs a variant of English (the African-American Vernacular English) they are probably not familiar with. Apart from punctuation, the lyrics were not altered in any way.

Setting the scene: the song was recorded in 1992 and released six years later in 2Pac's posthumous album Greatest Hits. It features Talent, an R&B trio formed by Ernest “Bishop” Dixon, Marlon “Castor Troy” Hatcher and Keith “Casino” Murrell. As mentioned earlier, the song samples Bruce Hornsby and the Range's The Way It is and addresses the same social themes.

A dive into the historical context: what happened in the 1990s? * A new President, the Democratic Bill Clinton, was elected and stayed in charge from 1993 to 2001. in 1996, he promoted the Personal Responsibility and Work Opportunity Reconciliation Act which restricted governmental assistance to families in distress. * In the early 1990s, the country entered a severe recession, which was apparently overcome by the mid-1990s. * Black businesses bloomed and Black celebrities (such as Micheal Jackson, Michal Jordan and Oprah Winfrey) started to appear and constituted the first "Black bourgeoisie". However, this was not the reality of common, middle or lower-class African-Americans: in some inner cities, between 30% and 43% of the population in poor neighborhoods (such as East New York, the South Bronx, South Central Los Angeles, Chicago's South Side) was jobless. Many of those "who had once held stable blue-color jobs, low-wage service jobs, such as in the fast-food industry" relied on occasional and informal activities (braiding hair, childcare, car repair...). * The abuse of drugs that had exploded the previous decade went on, especially among poors. * Mass incarceration persisted: in 1990, prisoners reached one million. "By 2000, one-third of all black males in their twenties were under the control of the criminal justice system—either in prison or jail, on parole, probation, or awaiting trial. The major reason for this disproportion in incarceration is the stark racism that continues to pervade the criminal justice system. […] The socio-economic and political consequences of mass incarceration for the black community have been profound. Hundreds of thousands of households have been destroyed". (https://www.amistadresource.org/the_future_in_the_present/social_and_economic_issues.html). As a consequence, in many instances, there were one-parent families: mothers were left to raise their children alone. https://www.amistadresource.org/the_future_in_the_present/social_and_economic_issues.html https://www.ncpedia.org/anchor/united-states-1990s#:~:text=Labor%20unions%20believed%20it%20would,countries%20with%20weak%20pollution%20controls

Normally, will is contracted when preceded by there, here and personal pronouns (I, you, she\he\it, we, you, they) only in oral speech or informal writing. https://dictionary.cambridge.org/us/grammar/british-grammar/contractions In everyday casual language, it is quite common to find will contracted even when combined with proper nouns and objects just as in this case. However, it is important to remember that it is not appropriate to use this form in formal writing. In the following video, starting at the minute 4:16, you can see (and hear) other examples similar to things'll: https://youtu.be/tXTu2tpJKaM?si=4e6I2J3wHd7On5i3&t=256

The possibility of changing becomes increasingly more evident in this part of the song, which gives shape to a conversation between a child and an old man. The resignation seems to belong to the viewpoint of the old man, whereas the child questions the very existence of the "rules" who discriminate them for the color of his skin ("you don't look like they do") and the origin of the authority of those who created them. At this point of the song, resignation seems to resemble a compliant attitude, which may be even benefitting from an injust society. Notice that the singer evidently sides with the boy, ultimately converging his point of view with his own.

Here is the chorus of the song: at first, the singer's reaction to the widespread inquality that dominates the society seems to coincide with a resigned acceptation of the status quo. The feeling of quiet resignation amplifies as the song goes on, reaching its climax when the singer makes reference to the Civil Rights Act and, therefore, establishing a parallelism between the present and the past. However, the chorus closes with a glimpse of hope: indeed, the author invites the audience not to believe to inevitability, thus suggesting that things may change if only people started thinking and acting differently. As a matter of fact, the singer himself insists upon this last verse: "Some things will never change is a statement of resignation, but the most important line in that song is the one that comes after that: But don't you believe them. So I've always been about being strong when resignation is a possibility. Trying to pull up from that and have a positive outlook so that things can change" (http://www.musicfordemocracy.org/node/34.html).

Your turn: do you think that injustice and inequality will ever be defeated?

Setting the scene: the song was released in July 1986 as a single from the band's debut album The Way It Is. It was a great success and the band won the 1987 Grammy Awards in the Best New Artist category. The success of the song has had a long-lasting effect in the music industry: it was sampled by other artists and included in songs such as 2Pac's Changes and Polo G's Wishing for a Hero. The singer has "never counted it" but he has read that his song "has now been recorded 17 times by hip-hop artists" (https://www.rollingstone.com/music/music-features/bruce-hornsby-interview-way-it-is-non-secure-connection-1036032/). In order to understand the following lyrics, it is necessary to place the song in its historical context. The 1980s were years in which several issues emerged: * The process of de-industrialization (that is, the process in which American companies moved their seats abroad, outside the country) deeply affected the job market: tens of thousands of workers lost their jobs. In particular, Blacks were the ones who suffered the most since the majority of them were employed in various industrial fields. As a consequence, poverty spread: 30% of black work force was jobless in 1982. * The conservative Reagan presidency (1981-1989) reduced federal (governmental, that is) economic support to people in need by 20%. The cut to financial measures combined with the ongoing industrial crisis was disastrous. * White supremacy movements and groups (such as the Ku Klux Klan) reignited and engaged in violent acts against African Americans, firebombing of churches and campaigns against affirmative actions programs and integration in schools. "Millions of white Americans had become convinced that “too much” had been given to blacks". * Poverty, hunger and hopelessness paved the way to the abuse of drugs; crack was especially consumed by poor Americans as it was inexpensive and easily available. As a consequence of the combination of low employment, educational poverty and drug popularity, drug dealing became the source of income for young people and violence increased significantly in Black neighborhoods.

What was the government's response? Aggravated levels of violence and crime were responded with the "War on Drugs", which entailed: 1. the elimination of parole (that is, the conditional release of a prisoner, often on the basis of good behavior in prison); 2. stricter penalties for drug sale and possession; 3. building a larger network of prisons.

Needless to say, African-Americans were the most targeted ones. Mass incarceration as a system of control (see the "home" of the website for more on the topic) started to bloom.

https://www.amistadresource.org/the_future_in_the_present/social_and_economic_issues.html

Till means until and they are largely interchangeable; however, it is not its abbreviated form because till predates the longer word. https://www.merriam-webster.com/grammar/should-you-use-until-or-till-or-til

Once again, Dylan calls for equality between Black and white people and (ironically) challenges the audience to specify the number of years that takes for someone to be free.

This word presents a common linguistic phenomenon called g-dropping: it consists in the drop of the -g at the end of certain words. In fact, no -g is actually "dropped" because the 'g' is not even pronounced. All English speakers g-drop, but the frequency of this phenomenon is tied to class belonging, race, sex and degree of formality. Generally, it is more common among lower social classes. http://itre.cis.upenn.edu/~myl/languagelog/archives/000878.html

What does this mean in the context of this song? Answer: By adopting g-dropping and thus language-wise, Bob Dylan positions himself in the tradition of folk music and becomes the spokesman of the people.

Eminem refers to the very symbol of slavery, plantation fields.

Eminem mentions "athlete Colin Kaepernick, and shouts him out towards the latter part of his verse. In 2016, Kaepernick drew praise and criticism from differing corners when he stopped standing for the national anthem as a form of protest against police brutality." https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

Another news story: Rodney King was a taxi driver who was stopped for speeding in 1991: after chasing him, police officers beat him to death. His assassination triggered the 1992 Los Angeles Riots. This story shows that race-oriented police brutality has a long story that precedes the rise of the Black Lives Matter Movement and the (sadly) known assassinations of George Floyd and Freddie Gray, among others. https://www.britannica.com/event/Los-Angeles-Riots-of-1992 https://www.britannica.com/biography/Rodney-King If you are interested (or passionate about true crime), here is a clip from the news that digs deeper into Rodney King's beating (Content warning: violence). https://youtu.be/qnCCGIMCoog?si=qtKIXFVvisIx3WGY

The derringer is a type of handgun.

Pull yourself up by the/your (own) bootstraps is an idiomatic expression that means "to improve your situation without any help from other people". https://dictionary.cambridge.org/dictionary/english/pull-haul-up-by-the-your-own-bootstraps With the following question, Eminem flips over the expression and reveals the uselessness of such a mentality: how can someone be independent and self-reliant if they lack the bare minimum to survive?

The reference to President Donald Trump (who is a Republican) could not be more straightforward.

Notice how this part of the song echoes Lamar's lyrics "gang-banging make me kill a nigga blacker than me?": both songs highlight feuds inside the African-American community due to gang divisions. However, Eminem seems to be more reluctant to blame African-Americans: in the following lines, he underscores that said fights are rooted in problems such as single-parenting, drug abuse and struggle with addiction that lead people "with nothin(g) to lose to shoot each other for shoes".

Eminem links high levels of crime to poor neighborhoods and socio-economic status — which singer whose song we analyzed made the same connection? Do you agree with Eminem's viewpoint?

Freddie Gray was a 25-year-old African-American who was arrested in 2015 in Baltimore and then died only a week later due to injuries while in custody of Baltimore policemen. https://www.cbsnews.com/baltimore/news/maryland-freddie-gray-death-unrest-settlement-police-reform/ (see the annotation on "Pull your pants up, we 'bout to roll up and \ Throw your ass in the van").

The Housing Choice Voucher Program (popularly known as Section Eight) is a program aimed to provide financial support to elderly people, low-income families and veterans in the private housing market. https://www.hud.gov/helping-americans/housing-choice-vouchers-tenants#:~:text=Housing%20Choice%20Voucher%20Program,program%20with%20funding%20from%20HUD Eminem "calls out the country for placing African Americans in a system designed to make them lose. With Section 8 housing and a floundering education system in impoverished neighborhoods, there’s no way they can really win when the odds are stacked up against them." https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

In this case, wave acts as a verb, meaning "moving from side to side, or to make something move like this while holding it in the hand". https://dictionary.cambridge.org/dictionary/english/wave

"Once again, he tries to kill stereotypes by denouncing the “crack spot” as a hangout place for blacks. He’s also critical of naive cops who walk into black neighborhoods with no sense of understanding of their behavior or culture. Instead of walking with a fair mind and attitude, their level of fears heighten because of the unknown, and cause them to automatically be racists." https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

Your turn: Do you think hiring more African-American policemen would make a difference?

The expression Black Ops probably refers to the homonymous Call of Duty shooter game. In this context, the game may function as a metaphor to highlight widespread violence.

The repetitive use of the comparative of majority ("madder") highlights the spiral of violence triggered by police officers' increased violence at black people's (legitimate) rage at their racist treatments. This creates a vicious circle that can only result in more violence, as the Black Ops metaphor clearly represents.

The term is used to indicate the act of "speaking or acting playfully or wittily". https://www.merriam-webster.com/dictionary/banter

Die Antwood are "a group that was ostracized for their 2012 video Fatty Boom Boom, which portrayed their female lead singer, Yolandi, protayed in black face." Eminem's message is that "dealing with in-your-face racism is a tough pill to swallow" but "he’d rather endure that than watch white people seemingly destroy the black culture with empty jokes". https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

Eminem abandons the cop's perspective and adopts a black man's viewpoint. The rapper is not far from the truth: life expectancy varies significantly depending on ethnic factors. "Pre-pandemic, the overall life expectancy was 79 years for the white population, compared to 75 years for the Black population, according to the National Institute of Health. […] in 2022, the overall life expectancy was 71 years for the Black population and 77 years for the white population." This is connected to disparity in access to healthcare, stress and living and working condition. https://badgerherald.com/news/science-news/2024/11/07/life-expectancy-gap-between-black-and-white-americans-is-a-systematic-issue-uw-experts-say/

It is the same rationale that we applied to eyesore. In this case, the nouns are back and spinning. If something backspins, it means that...

"The idea of a change in the measurement of time, in which people and events from one part of history are imagined as existing in another part." In Italian, it would be a vortice temporale. https://dictionary.cambridge.org/dictionary/english/time-warp

Swine would be translated as suino. In this case, it is evident that the singer is using it in a metaphorical sens, that is, as "a contemptible person". https://www.merriam-webster.com/dictionary/swine

The rapper uses a metaphor to indicate that, just as cards players, policemen are not willing to show their true intentions and next moves.

"Something (such as a part of a sleeve or glove) encircling the wrist". In Italian, it would be ammanettato. https://www.merriam-webster.com/dictionary/cuffed

This part refers to a news story, specifically the death of 25-year-old Freddie Gray in 2015, "when he was tossed in the back of a police van and sustained serious injuries. Gray died a week later, and many believed his death was a result of police brutality during his ride to the police station." https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/ https://www.cbsnews.com/baltimore/news/maryland-freddie-gray-death-unrest-settlement-police-reform/

"Vexed by the their complaints regarding the government’s wrongdoings, the narrator slanders African Americans." https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

In this second verse, Eminem keeps adopting the white racist viewpoint, which is explored in further detail.

Police brutality and white supremacy combine here: the racist cop's objective is charging the black man with a crime, regardless of the young man's innocence. Another element that I would like to underscore is the word choice: * homie: the policeman uses an informal term to denigrate the young man. In other words, he discursively builds his social superiority. * back inside: the link here is to the prejudice we mentioned before. The policeman ignores whether the young man has been to jail; he simply assumes it.

"The “Heidi Klum” reference plays off the slang term for cocaine". https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

The tail light (or taillight) is "a red light on the back of a road vehicle that makes it possible for the vehicle to be seen in the dark". https://dictionary.cambridge.org/dictionary/english/tail-light

Here Eminem cleverly makes a pun by using the other, more widespread, meaning of the word profile, that is "a side view of a person's face". https://dictionary.cambridge.org/dictionary/english/profile

The entire first verse corresponds to the white policeman's perspective. As you will listen (and read), Eminem's words are explicit in reporting the cop's viewpoint. The truth cannot be sugarcoated: "we (the cops) ain't gonna lie to you" and don't like the sight of you".

eLife Assessment

This study reports important advances in our understanding of how enteropathogenic E. coli (EPEC) interacts at the intestinal interface. Solid data describe a novel model of spatially coordinated calcium signaling to modulate NF-kB activation; additional data and clarification of methods would improve the strength of these conclusions. These findings, which integrate imaging, genetics, and computational modeling, provide a new way to consider host-pathogen interactions in EPEC infections that may lead to improved therapies.

Reviewer #1 (Public review):

Summary:

In their article, Guo and coworkers investigate the Ca²⁺ signaling responses induced by Enteropathogenic Escherichia coli (EPEC) in epithelial cells and how these responses regulate NF-κB activation. The authors show that EPEC induces rapid, spatially coordinated Ca²⁺ transients mediated by extracellular ATP released through the type III secretion system (T3SS). Using high-speed Ca²⁺ imaging and stochastic modeling, they propose that low ATP levels trigger "Coordinated Ca²⁺ Responses from IP₃R Clusters" (CCRICs) via fast Ca²⁺ diffusion and Ca²⁺-induced Ca²⁺ release. These responses may dampen TNF-α-induced NF-κB activation through Ca²⁺-dependent modulation of O-GlcNAcylation of p65. The interdisciplinary work suggests a new perspective on calcium-mediated immune response by combining quantitative imaging, bacterial genetics, and computational modeling.

Strengths:

The study provides a new concept for host responses to bacterial infections and introduces the concept of Coordinated Ca²⁺ Responses from IP₃R Clusters (CCRICs) as synchronized, whole-cell-scale Ca²⁺ transients with the fast kinetics typical of local events. This is elegantly done by an interdisciplinary approach using quantitative measurements and mechanistic modelling.

Weaknesses:

(1) The effect of coordination by fast diffusion for small eATP concentrations is explained by the resulting low Ca2+ concentration that is not as strongly affected by calcium buffers compared to higher concentrations. While I agree with this statement on the relative level, CICR is based on the resulting absolute concentration at neighboring IP3Rs (to activate them). Thus, I do not fully agree with the explanation, or at least would expect to use the modelling approach to demonstrate this effect. Simulations for different activation and buffer concentrations could strengthen this point and exclude potential inhibition of channels at higher stimulation levels.

In this respect, I would also include the details of the modelling, such as implementation environment, parameters, and benchmarking. The description in the Supplementary Methods is very similar to the description in the main text. In terms of reproducibility, it would be important to at least provide simulation parameters, and providing the code would align with the emerging standards for reproducible science.

(2) Quantitative characterization of CCRICs:

The paper would benefit from a clearer definition of the term CCRICs and quantitative descriptors like duration, amplitude distribution, frequency, and spatial extent (also in relation to the comment on the EGTA measurements below). Furthermore, it remains unclear to me whether CCRICs represent a population of rapidly propagating micro-waves or truly simultaneous events. Maybe kymographs or wave-front propagation analyses (at least from simulations if experimental resolution is too bad) would strengthen this point.

(3) Specificity of pharmacological tools:

Suramin and U73122 are known to have off-target effects. Control experiments using alternative P2 receptor antagonists like PPADS or inactive U73343 analogs would strengthen the causal link.

Reviewer #2 (Public review):

Summary:

The authors of this study are trying to resolve how cellular infection by enteropathogenic E. coli (EPEC) subverts cellular signaling pathways to promote infection and dampen immune responses. Specifically, alteration in calcium dynamics has been evidenced in the prior literature as a potential initiator of these adaptations, and this study provides ideas and mechanistic detail as to how cellular calcium dynamics may be subverted by pathogens.

Strengths:

The clear strengths of this paper relate to the new ideas inherent in the proposed hypothesis and their support from the experimental approaches used. Overall, the proposed work provides new ideas in this area, which will benefit from further investigation. Certainly, this is an interesting and challenging paradigm to pick apart mechanistically, and is important for improving treatments from intestinal infections.

Weaknesses:

Additional insight is needed in three specific areas to convincingly support the conclusions drawn by the authors. These three areas are: first, a better description of the infection-associated calcium signals. Second, a mechanistic definition of the relevant purinoceptors versus other pathways to increase cellular calcium. Third, an effort to show that the proposed pathways have relevance in a polarized epithelial cell.

DOI: 10.1016/j.isci.2025.114498

Resource: (IMSR Cat# JAX_013786,RRID:IMSR_JAX:013786)

Curator: @areedewitt04

SciCrunch record: RRID:IMSR_JAX:013786

What is this?

DOI: 10.1136/jitc-2025-013577

Resource: The Cancer Genome Atlas (RRID:SCR_003193)

Curator: @scibot

SciCrunch record: RRID:SCR_003193

What is this?

Any relationship of Wren Day to Ma

Juxtaposition of men and women. Men have dreams; women don't have that opportunity (early 1900s). The truth is their only dream implies that they are often deceived or tricked. The statement "They act accordingly" illustrates their determination and matter-of-fact pragmatism.

The boats that carry men's dreams seem rudderless (maybe they anchor - be actualized - maybe they won't. They're distant, meaning unattainable, inaccessible for most who lack choice due to lack of opportunities and inequality for all.

What Is the Spoon Theory Metaphor for Chronic Illness? 2021-11-16<br /> accessed on 2025-12-22T20:30:22

https://udel.edu/~mcdonald/mythptc.html

Was this the white substance mentioned in Erwin Schrodinger's Mind and Matter (Schrodinger1992b) chapter 6?

https://en.wikipedia.org/wiki/Democritus

Was the epithet "laughing philosopher" used as a mnemonic device for Democritus?

This is really interesting, what do you think?

Doesn't the GAE(Great American Empire) have a history of injecting democracy where it is needed most?

Thinking of Intellectual Discourse and meme distribution pre internet, the context of which this book was written is something I am having a hard time understanding.

I bet Civil Liberties as a concept is not in the average liberal's lexicon these days. The state must force WOC's and gays into everything.

I believe that the Gay stuff is all about population control, it's much more moral than the Nazi's so I am not complaining.

Like Historically it does seem to just popped up and taken over institutions.

The "Empire of Love" as Moldbug calls it.

Those that want to win will always beat those that want to be left alone.

bad action space

expecting to represent a high-complexity complete Turing machine as the vision space seems weak (s_i -> 1024x768x3). exaggerated info loss. images cound only retain the relevant tile for vision encoder

string only makes sense in OOP, the OS deals with stdio

This is the best to thing to start with

That's "garbage-collected language implementations" (or, in this context, just "garbage collection").

Programming languages are languages. They're notation. They're inert. They can't have garbage collectors.

The presence of GC is a memory management implementation strategy—a choice—of a given programming language implementation. C, for example, is neither a "garbage-collected language" nor a "non-garbage-collected language".

GCC doesn't have a garbage collector for C programs, and neither does Clang, but GCC and Clang are not "C"; C is a programming language, and GCC and Clang are programming language implementations. You could write a C implementation in the vein of SpiderMonkey or the compiler/runtime from the golang.org toolchain (one designed to parse and run programs written C instead of JS or Go) if you wanted to.

It seems totally reasonable to use convolution across spectral space because any one place in the spectrum should contain information about proximal spaces. Similarly though, it seems reasonable to expect that there should be shared information across proximal pixels across the imaging space. Likely, pixels that are on the boundary between the nucleus and outside of the nucleus seem likely to have different spectra than those within the nucleus. As a result, combining convolutions across both physical and spectral space (a truly hyper-spectral convolutional autoencoder) seems both reasonable and like it would leverage the spatial information to further refine the endmember definitions. Did you try something like this?

Report on adapting the 2023-2027 Open government action plan. [[Paul Suijkerbuijk]] had a role in this report, MCOIG.

Advies Herijking Actieplan Open Overheid 2025 in Zotero

Ah, it uses the CBS protected data working environment (also for the DGA). This means the debiasing is not done without personal data but without the organisation concerned seeing that data. Third party testing basically, with CBS being that party.

Here is the ending sentence of the song: I could annotate it as I did so far, but by now you are familiar with Eminem's tone and with the themes dealt with in the project... so I would like to hear your interpretations! Try to unpack it on your own. Clues: my personal advice when it comes to understand a text is dividing it into smaller chunks (example: what piece of cloth is Eminem referring to?). If you struggle with understanding what he is trying to say, don't worry: try to read the text again and remember that previous and following sentences can help you out.

The spiel is "a speech, especially one that is long and spoken quickly and is intended to persuade the person listening about something". https://dictionary.cambridge.org/dictionary/english/spiel In this case, the wordplay is built around the fact that the name of the U.S. national anthem is the "Star-Spangled Banner" (not spiel).

Your turn: according to you, what is Eminem insisting upon? Why makes this expression so powerful?

Eminem touches upon another American tragedy: the genocide of Native Americans (which was even celebrated in the movie and comic industry). The present project does not focus on this theme; however, here are some resources to explore this topic: https://hmh.org/library/research/genocide-of-indigenous-peoples-guide/, https://study.com/learn/lesson/video/native-american-genocide-history.html, https://sites.uab.edu/humanrights/2017/04/17/indian-removal-act-genocide-native-americans/.

Eminem mentions "athlete Colin Kaepernick, and shouts him out towards the latter part of his verse. In 2016, Kaepernick drew praise and criticism from differing corners when he stopped standing for the national anthem as a form of protest against police brutality." https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

Another news story: Rodney King was a taxi driver who was stopped for speeding in 1991: after chasing him, police officers beat him to death. His assassination triggered the 1992 Los Angeles Riots. This story shows that race-oriented police brutality has a long story that precedes the rise of the Black Lives Matter Movement and the (sadly) known assassinations of George Floyd and Freddie Gray, among others. https://www.britannica.com/event/Los-Angeles-Riots-of-1992 https://www.britannica.com/biography/Rodney-King If you are interested (or passionate about true crime), here is a clip from the news that digs deeper into Rodney King's beating (Content warning: violence). https://youtu.be/qnCCGIMCoog?si=qtKIXFVvisIx3WGY

Pull yourself up by the/your (own) bootstraps is an idiomatic expression that means "to improve your situation without any help from other people". https://dictionary.cambridge.org/dictionary/english/pull-haul-up-by-the-your-own-bootstraps With the following question, Eminem flips over the expression and reveals the uselessness of such a mentality: how can someone be independent and self-reliant if they lack the bare minimum to survive?

Dryer lint refers to the buildup that forms in the dryer after doing laundry as a result of hair, textile fibers and other particles clamping together. Normally, it is thrown up after every washing cycle. In Italian, it is translatable as lanugine, but perhaps the following image will clarify any doubt: https://preparedhero.com/it-it/blogs/articles/dryer-lint#:~:text=What%20Is%20Dryer%20Lint?,for%20dryer%20safety%20and%20performance.

Freddie Gray was a 25-year-old African-American who was arrested in 2015 in Baltimore and then died only a week later due to injuries while in custody of Baltimore policemen. https://www.cbsnews.com/baltimore/news/maryland-freddie-gray-death-unrest-settlement-police-reform/ (see the annotation on "Pull your pants up, we 'bout to roll up and \ Throw your ass in the van").

The Housing Choice Voucher Program (popularly known as Section Eight) is a program aimed to provide financial support to elderly people, low-income families and veterans in the private housing market. https://www.hud.gov/helping-americans/housing-choice-vouchers-tenants#:~:text=Housing%20Choice%20Voucher%20Program,program%20with%20funding%20from%20HUD Eminem "calls out the country for placing African Americans in a system designed to make them lose. With Section 8 housing and a floundering education system in impoverished neighborhoods, there’s no way they can really win when the odds are stacked up against them." https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

In this case, wave acts as a verb, meaning "moving from side to side, or to make something move like this while holding it in the hand". https://dictionary.cambridge.org/dictionary/english/wave

The expression Black Ops probably refers to the homonymous Call of Duty shooter game. In this context, the game may function as a metaphor to highlight widespread violence.

The repetitive use of the comparative of majority ("madder") highlights the spiral of violence triggered by police officers' increased violence at black people's (legitimate) rage at their racist treatments. This creates a vicious circle that can only result in more violence, as the Black Ops metaphor clearly represents.

This is a reference to a news story which dates back to 2016: Micah J. Johnson, shot five Dallas police officers dead and harmed other eleven people. Since the killer was a Black man and the shooting happened during a peaceful Black Live Matter rally, the assassination was connected to the movement itself. However, "the BLM organization responded to these critiques head-on, calling the attack "the result of the actions of a lone gunman” and calling it “dangerous and irresponsible” to “assign the actions of one person to an entire movement”." https://www.theguardian.com/us-news/2016/jul/09/black-lives-matter-dallas-protest-shooting https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

Your turn: what do you think Eminem is trying to say here? Clue: focus on the word hire.

The term is used to indicate the act of "speaking or acting playfully or wittily". https://www.merriam-webster.com/dictionary/banter

Die Antwood are "a group that was ostracized for their 2012 video Fatty Boom Boom, which portrayed their female lead singer, Yolandi, protayed in black face." Eminem's message is that "dealing with in-your-face racism is a tough pill to swallow" but "he’d rather endure that than watch white people seemingly destroy the black culture with empty jokes". https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

Eminem abandons the cop's perspective and adopts a black man's viewpoint. The rapper is accurate: life expectancy varies significantly depending on ethnic factors. "Pre-pandemic, the overall life expectancy was 79 years for the white population, compared to 75 years for the Black population, according to the National Institute of Health. […] in 2022, the overall life expectancy was 71 years for the Black population and 77 years for the white population." This is connected to disparity in access to healthcare, stress and living and working condition. https://badgerherald.com/news/science-news/2024/11/07/life-expectancy-gap-between-black-and-white-americans-is-a-systematic-issue-uw-experts-say/

This song gives a circular structure to the present analysis: Eminem connects present-day abuse of power, racism and police brutality to 1960s fights for civil rights. The singer underscores how history seems to repeat itself in an endless loop: although more than 50 years have passed, black people still struggle to have their rights recognized and respected. And, I add, music keeps being a space in which lack of equality, racism and social injustice are denounced.

It is the same rationale that we applied to eyesore. In this case, the nouns are back and spinning. If something backspins, it means that...

"The idea of a change in the measurement of time, in which people and events from one part of history are imagined as existing in another part." In Italian, it would be a vortice temporale. https://dictionary.cambridge.org/dictionary/english/time-warp

Swine would be translated as suino. In this case, it is evident that the singer is using it in a metaphorical sens, that is, as "a contemptible person". https://www.merriam-webster.com/dictionary/swine

The rapper uses a metaphor to indicate that, just as cards players, policemen are not willing to show their true intentions and next moves.

"Something (such as a part of a sleeve or glove) encircling the wrist". In Italian, it would be ammanettato. https://www.merriam-webster.com/dictionary/cuffed

This part refers to a news story, specifically the death of 25-year-old Freddie Gray in 2015, "when he was tossed in the back of a police van and sustained serious injuries. Gray died a week later, and many believed his death was a result of police brutality during his ride to the police station." https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/ https://www.cbsnews.com/baltimore/news/maryland-freddie-gray-death-unrest-settlement-police-reform/

"Vexed by the their complaints regarding the government’s wrongdoings, the narrator slanders African Americans." https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

In this second verse, the white racist viewpoint is explored further.

It is "a device with meshes or perforations through which finer particles of a mixture (as of ashes, flour, or sand) of various sizes may be passed to separate them from coarser ones, through which the liquid may be drained from liquid-containing material, or through which soft materials may be forced for reduction to fine particles". https://www.merriam-webster.com/dictionary/sieve In Italian, setaccio, colabrodo.

These three lines channel the white policeman's internal monologue and trail of thought. Although he recognizes their negative impact, he keeps justifying his abusive and racist actions in the name of his country, symbolically represented by the colors of the flag.

"Though he’s fully aware that murdering an innocent black man isn’t the right thing to do, he finds peace and comfort deluding himself into thinking that he’s protecting his country, or as he raps, “the red, white and blue.” https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

Police brutality and white supremacy combine here: the racist cop's objective is charging the black man with a crime, regardless of the young man's innocence. Another element that I would like to underscore is the word choice: * homie: the policeman uses an informal term to denigrate the young man. In other words, he discursively builds his social superiority. * back inside: the link here is to the prejudice we mentioned before. The policeman ignores whether the young man has been to jail; he simply assumes it.

"The “Heidi Klum” reference plays off the slang term for cocaine". https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

The tail light (or taillight) is "a red light on the back of a road vehicle that makes it possible for the vehicle to be seen in the dark". https://dictionary.cambridge.org/dictionary/english/tail-light

In this context, it means "to pass unnoticed or unremarked". In Italian, the sentence could be translated into "potremmo lasciarti andare". https://www.merriam-webster.com/dictionary/slide

"A house where dope heads (heroin addicts) live" and do drugs. http://dope-house.urbanup.com/7824692 Eminem is criticizing "how African American drivers are often stereotyped as drug dealers with a criminal background". https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/ Indeed, the key word in the sentence is "probably": the policeman does not know who the young man is, where he is going to or where he comes from, so he cannot do anything but hypothesize. The problem is twofold: 1. He mistakes his hypothesis for truth; 2. His hypothesis is biased: there is no logical reason as for why he associates the young black man with the "dope house". However, he does so because he cultivates prejudices against black men.

Here Eminem cleverly makes a pun by using the other, more widespread, meaning of the word profile, that is "a side view of a person's face". https://dictionary.cambridge.org/dictionary/english/profile

The scene goes on. Eminem's visual language does not make it hard to picture it: a white cop stopping a black young man who is driving his car. The policeman asks him to pull up (that is, to stop the car at the side of the road), roll his window down and provide a "profile". In this context, "profiling" indicates "the activity of collecting information about someone, especially a criminal, in order to give a description of them". https://dictionary.cambridge.org/dictionary/english/profiling More specifically, Eminem is directly criticizing the so-called racial profiling, which is an illegal practice relying "on stereotypes of racial or ethnic groups to assist law enforcement in detecting and deterring crime". In other (simpler) words, it means that some people (namely Latinos or Blacks) are stopped and incarcerated only for belonging to a certain ethnicity. Criminal profiling, instead, is a legal practice based on evidence gathered from "previous crimes from witnesses, victims, and the crime scene. The profile includes the potential suspect’s age range, gender, race, possible employment, and other factors to narrow down the group of suspects". https://www.amu.apus.edu/area-of-study/criminal-justice/resources/racial-profiling-vs-criminal-profiling/<br /> https://www.billboard.com/music/rb-hip-hop/eminem-untouchable-lyrics-decoded-8062711/

The entire first verse corresponds to the white policeman's perspective. As you will listen (and read), Eminem's words are explicit in reporting the cop's viewpoint. The truth cannot be sugarcoated: "we (the cops) ain't gonna lie to you" and don't like the sight of you".

They just completed a stricter regime by the DPA, and then immediately this comes up afterwards. Ouch. It surfaced bc they were monitoring network traffic volumes. That says to me they also know who did the uploading

Eindhoven monitors their network for the type of outgoing connections. Apparently that until now dit not include publicly available algogens

As result of the data breach, all OpenAI products have been banned internally. Only MS Copilot, embedded in their MS office suite is available.

Do you have resolution specifications for a higher NA objective? For folks who might want higher spatial resolution than 2.5um it would be great to know how far the system could be pushed. Related, have you tried a 'true' confocal light path with focusing optics and a pinhole? Again, it would be great to know how far the system could be pushed.