10,000 Matching Annotations
  1. May 2026
    1. Each of these issues is evident in MULTI-evolve: the engineering success is real, but the source of performance is that mutational effects are sufficiently additive for the proteins and mutations considered, not that the neural network has learned epistatic synergies.

      Thank you for going through the effort of putting together this properly benchmarked analysis, the lack of a purely additive model in the original work is a significant omission. To give credit to the original authors, it seems the biggest success here is their ensemble PLM model, I suppose some claim of 'synergistic epistasis' could be made here, as the mutants the ensemble proposed do seem to be genuinely beneficial. However, it is obvious that this does not extend to the MLP trained by the authors where the claims of epistasis being captured are made.

    2. The FCNN learns additivity but the authors misattribute its performance to epistasis because no linear baseline was tested

      One thing I personally have always wanted to see in these sort of data/experiments is some flavour of variance partitioning as in quantitative genetics. I.e. How much variation does 2nd order epistasis explain in these systems? Consequently what even is the expected improvement we can hope if we train a model that can successfully capture say 2nd order epistasis? It seems from these results it would probably be quite modest (at least in the context of these data). I don't think a proper analysis can be done here due to the experimental design; each mutant combination is measured only once, so epistasis cannot be distinguished from experimental noise. This paper from the Thornton lab has done an analysis along these lines, and the results seem to suggest additivity can get you a lot of the way there...

    1. For example, in the immediate aftermath of the 2013 Boston Marathon bombing, FBI released a security photo of one of the bombers and asked for tips. A group of Reddit users decided to try to identify the bomber(s) themselves. They quickly settled on a missing man (Sunil Tripathi) as the culprit (it turned out had died by suicide and was in no way related to the case), and flooded the Facebook page set up to search for Sunil Tripathi, causing his family unnecessary pain and difficulty. The person who set up the “Find Boston Bomber” Reddit board said “It Was a Disaster” but “Incredible” [p26], and Reddit apologized for online Boston ‘witch hunt’ [p27].

      It is crazy to see how people who probably meant well could mess up so much but it does highlight some of the problems with crowdsourcing information. It is so hard to identify if the crowd sourced info is accurate and if the person providing it knows if its accurate. The example being with this one if they had been trained investigators they would've been able to know the person they had thought it was couldnt have been connected in any way.

    2. Sometimes even well-intentioned efforts can do significant harm. For example, in the immediate aftermath of the 2013 Boston Marathon bombing, FBI released a security photo of one of the bombers and asked for tips. A group of Reddit users decided to try to identify the bomber(s) themselves. They quickly settled on a missing man (Sunil Tripathi) as the culprit (it turned out had died by suicide and was in no way related to the case), and flooded the Facebook page set up to search for Sunil Tripathi, causing his family unnecessary pain and difficulty. The person who set up the “Find Boston Bomber” Reddit board said “It Was a Disaster” but “Incredible” [p26], and Reddit apologized for online Boston ‘witch hunt’ [p27].

      This passage is powerful because it shows how even good intentions on the internet can lead to harmful consequences. The real example of Reddit users wrongly accusing someone makes the issue feel very serious and emotional. I also think the passage does a good job explaining why crowdsourcing and online investigations can become dangerous when people act too quickly without enough evidence.

    3. Disinformation campaigns also make use of crowdsoucing

      This draws a connection between crowdsourcing and organized deception online. I appreciate that it distinguishes between “orchestrated,” “cultivated,” and “emergent and self-sustaining” disinformation, because that shows falsehoods do not always come from a single top‑down source. Platforms can unintentionally provide ideal conditions for users to collaboratively create and amplify misleading narratives. This really complicates the idea of the “wisdom of crowds,” since the same collective processes that can solve problems can also generate and legitimize inaccurate or harmful information.

    4. I think this example shows how dangerous online crowdsourcing can become when people act too quickly. Even though the Reddit users thought they were helping, they ended up hurting an innocent family. This reminds me that information on social media spreads very fast, and people do not always stop to check if it is actually true before sharing it.

    5. I think the section about power users and lurkers is interesting because it shows that “the crowd” is not always equal. A small group often does most of the work, while many people only watch or benefit from it. This makes me wonder whether crowdsourcing really represents everyone’s voice, or mostly the loudest users.

    6. In the case of a missing hiker rescued after Twitter user tracks him down using his last-sent photo [p23], the “problem” was “Where did the hiker disappear?” and the crowd investigated whatever they could to find the solution of the hiker’s location.

      This reminds me of a lot of true crime videos that I have watched where many of the cases were actually cracked by people on the internet. One that I can think of actually has a Netflix documentary called Don't F With Cats, where the internet identified and caught a loser who was killing cats on video and uploading them.

    7. athi, causing his family unnecessary pain and difficulty. The person who set up the “Find Boston Bomber” Reddit board said “It Was a Disaster” but “Incredible” [p26], and Reddit apologized for online Boston ‘witch hunt’ [p27].

      There were some positives in the article of how Reddit helped organize even animal support for victims, but It's insane the personal harassment this innocent person and his family faced. That trauma can't be stopped by a single apology. Just think about how horrible that would be to experience as someone with no idea what's going on.

  2. social-media-ethics-automation.github.io social-media-ethics-automation.github.io
    1. WIRED. How to Not Embarrass Yourself in Front of the Robot at Work. September 2015. URL: https://www.youtube.com/watch?v=ho1RDiZ5Xew (visited on 2023-12-08)

      I found this video to be quite dystopian in my opinion. While I understand it takes the place of remote work with an actual moving thing, it is really weird to me. I would prefer Zoom to have an iPad rolling around an office like that; it seems like it would be more of a distraction rather than a contribution. She can't talk in meetings if she has questions, because the lag so too substantial. I just don't think that the benefits are heavy enough to outweigh the cons.

    2. GoFundMe: #1 Fundraising Platform for Crowdfunding. URL: https://www.gofundme.com/ (visited on 2023-12-08).

      This source is a fundraising website where individuals can post asking for money with photos and a description of why they are asking for money. There are also fundraisers that are run by nonprofit groups that are advertised across the site. Also, from what I have heard, GoFundMe is very on top of their moderation and will strike down any malicious fundraisers.

    3. United States congressional staff edits to Wikipedia. December 2023. Page Version ID: 1188215095. URL: https://en.wikipedia.org/w/index.php?title=United_States_congressional_staff_edits_to_Wikipedia&oldid=1188215095 (visited on 2023-12-08).

      This is a very interesting situation. It seems like wikipedia editing is probably a really important consideration for public relations firms that specialize in limiting public backlash. It's good that there was a public controversy about this, which reflected poorly on the congressmen editing their pages. I'm sure it set a public precedent that edits like this aren't allowed and could backfire on the editor.

    4. GoFundMe: #1 Fundraising Platform for Crowdfunding. URL: https://www.gofundme.com/ (visited on 2023-12-08).

      GoFundMe is one of the largest crowdfunding platforms that helps people raise money for personal needs, emergencies, medical expenses, education, charities, and community causes. They can share their stories and receive support from others online by give them a account to send money through that. GoFundMe help each other during difficult situations like we can see a lot of case like some individuals are able to afford heart transplants or important surgeries through donations because medical treatment can be extremely expensive.

    5. Adriana Diaz. Twitter tracks down mystery couple in viral proposal photos. New York Post, June 2021. URL: https://nypost.com/2021/06/24/twitter-tracks-down-mystery-couple-in-viral-proposal-photos/ (visited on 2023-12-08).

      Adrian Diaz, in this New York Post article, overall mentions a real-life incident where a photographer used Twitter or X now to identify a couple that a photographer had randomly taken a picture of during their surprise proposal, but she did not know who they were. Using the help of random users on Twitter, she was able to find who they were in real life so she could give them the photo she took. One key detail mentioned that really stood out to me was that the post had gone viral with over 691,000 likes and 94k retweets. This virality is what helped the photographer be able to find who the couples were.

    6. Crowdsourcing. December 2023. Page Version ID: 1188348631. URL: https://en.wikipedia.org/w/index.php?title=Crowdsourcing&oldid=1188348631#Historical_examples (visited on 2023-12-08)

      The source itself is Wikipedia, which means the bibliography is citing crowdsourcing as an example of crowdsourcing. That's not just a fun observation: it reveals something real about how crowdsourcing legitimizes itself. Wikipedia's credibility as a reference depends on the same distributed labor model the chapter is analyzing. The citation is doing double duty as both evidence and demonstration.

    7. Jim Hollan and Scott Stornetta. Beyond being there. In Proceedings of the SIGCHI Conference on Human Factors in Computing Systems, CHI '92, 119–125. New York, NY, USA, June 1992. Association for Computing Machinery. URL: https://dl.acm.org/doi/10.1145/142750.142769 (visited on 2023-12-08), doi:10.1145/142750.142769.

      I think "Beyond being there" source is relevent because it shows that online communication is not just a case of copying face-to-face communication. Online tools can also enable people to work together when they are not in the same place. This is similar to crowdsourcing as many people can give an idea or help with a task little by little. I also think this is true today as a lot of online teamwork is done without ever meeting those people in person. It is useful but sometimes at the expense of being personal.

    8. GoFundMe: #1 Fundraising Platform for Crowdfunding. URL: https://www.gofundme.com/ (visited on 2023-12-08).

      I believe that the GoFundMe source is an example of crowdsourcing because it demonstrates how people can use the internet to ask millions of strangers for help at the same time. Previously, all I thought of when it came to crowdfunding was raising money but after reading this chapter now I can refer to it as a form of crowdsourcing as well. It relies on a large group of people to choose to get involved, even if it is a small amount from them. I also think this is kind of neat because it shows the positive and risky side of websites. It can help people in a true emergency but it also involves trust because the donor will not always know the full story behind a fundraiser.

    9. Adriana Diaz. Twitter tracks down mystery couple in viral proposal photos. New York Post, June 2021. URL: https://nypost.com/2021/06/24/twitter-tracks-down-mystery-couple-in-viral-proposal-photos/ (visited on 2023-12-08).

      This article is a good example of ad‑hoc crowdsourcing used in a positive way rather than as harassment or doxxing. A single tweet (“HELP ME FIND THIS COUPLE!”) effectively defines the “problem,” and then thousands of Twitter users collectively solve it by boosting and sharing until the couple surfaces. It shows how social media can turn what would otherwise be a private moment into a kind of public, collaborative project, but in this case the couple consented and appreciated the attention.

    10. Adriana Diaz. Twitter tracks down mystery couple in viral proposal photos. New York Post, June 2021.

      This article is a really cute story about how a photographer accidentally captured a couples proposal but had no way of getting the photos to them except through Twitter, which worked. I think this was such a cute story and an example of how the internet could get people to band together for a good cause.

    11. Amazon Mechanical Turk is a useful example of planned crowdsourcing because it breaks large projects into small “microtasks,” like data validation, surveys, or content moderation. I think it shows both the power and problem of crowdsourcing: companies gain speed and cheap labor, but workers may feel invisible behind the final product.

    12. WIRED. How to Not Embarrass Yourself in Front of the Robot at Work. September 2015. URL: https://www.youtube.com/watch?v=ho1RDiZ5Xew (visited on 2023-12-08).

      The WIRED video was interesting because it showed how people often change their behavior around robots, even when the robot is not very advanced. I thought it was funny but also realistic how people felt awkward or embarrassed interacting with machines in public spaces. I think it connects to topics from this course about how technology shapes human behavior and social interactions. As robots and AI become more common in workplaces and daily life, I think people will slowly start treating them more naturally, similar to how people learn to become comfortable with technological advancements over time.

    13. Mike Gavin. Canucks' staffer uses social media to find fan who saved his life. NBC Sports Philadelphia, January 2022. URL: https://www.nbcsportsphiladelphia.com/nhl/philadelphia-flyers/canucks-staffer-uses-social-media-to-find-fan-who-saved-his-life/196044/ (visited on 2023-12-08).

      This article talks about an incident at a hocky match between the Vancouver Canucks and the Seattle Kraken. In the game, Vancouver's assistant equipment manager got a message from a fan sitting behind the team bench telling him that a mole on the back of his neck was cancer. After the game, he got it checked and found that the fan was correct, it was a malignant melanoma that he had removed days later. After this, the Canucks turned to social media to find the woman who discovered the cancer. The original post was retweeted over 8,000 times, and the woman was found within two hours.

    14. Daniel Oberhaus. Nearly All of Wikipedia Is Written By Just 1 Percent of Its Editors. Vice, November 2017. URL: https://www.vice.com/en/article/7x47bb/wikipedia-editors-elite-diversity-foundation

      First of all, I didn't know that Wikipedia's founder (Jimmy Wales) started his career by linking to internet porn in the 90s. Wikimedia foundation (a non-profit) found that 1 percent of Wikipedia's editors have made 77% of the site's content. Wikipedia is an adhocracy: a stable hierarchy structure which allows for individual mobility The most startlingly thing is that in 2011, 91% of their editors are male and in 2013, 84% were male, a stable decrease, but still overwhelming. This is a struggle for Ai models as AI will use wikipedia for their training data, using date that is geared for western males.

    15. BBC. Reddit apologises for online Boston 'witch hunt'. BBC News, April 2013. URL: https://www.bbc.com/news/technology-22263020 (visited on 2023-12-08).

      This BBC article notes an unfortunate incident where activity on the site of Reddit, which led to effectively a harassment campaign on those Reddit users believed to responsible for the Boston Bombings. The activity began on the subreddit r/FindBostonBombers, with users attempting to find the perpetuators, leading to several false accusations, harassment of those accused, and eventually a formal apology by the Reddit company itself for the incident.

    1. When looking at who contributes in crowdsourcing systems, or with social media in generally, we almost always find that we can split the users into a small group of power users who do the majority of the contributions, and a very large group of lurkers who contribute little to nothing. For example, Nearly All of Wikipedia Is Written By Just 1 Percent of Its Editors [p33], and on StackOverflow “A 2013 study has found that 75% of users only ask one question, 65% only answer one question, and only 8% of users answer more than 5 questions.” [p34]. We see the same phenomenon on Twitter:

      Does this mean that the amount of puts is around 65-75% of users on Twitter? I find that very crazy to believe, because think about the people who think that the country is the most divided right now? probably the people who are more chronically online, witnessing clipped short-form content, where people are constantly fighting and saying outlandish things in comments. They are going to believe the division, but it could all be bots?

    2. This goes back many thousands of years with activities such as collecting obsidian [p36] and making jewelry, to more modern activities like writing books, building cars, reporting on news, and making movies.

      In many terms and other various definitions, this can be looked at simplistically as "teamwork". The idea too of internet lurkers is interesting because it's something every individual has experienced through the use of social media.

    3. This small percentage of people doing most of the work in some areas is not a new phenomenon. In many aspects of our lives, some tasks have been done by a small group of people with specialization or resources. Their work is then shared with others. This goes back many thousands of years with activities such as collecting obsidian [p36] and making jewelry, to more modern activities like writing books, building cars, reporting on news, and making movies.

      I thought the section about power users and lurkers was interesting because it shows how much online spaces are shaped by a very small group of people. Even though social media feels like everyone is contributing equally, most users are actually just watching rather than posting. I also think this helps explain why certain opinions or trends online can feel much bigger than they actually are in real life. Sometimes the loudest voices online are just the most active users, not necessarily the majority.

    1. In what ways do you think you’ve participated in any crowdsourcing online?

      I contribute to crowdsourcing by participating in subreddits that provide expertise, advice, and anecdotal evidence on various topics. Users can ask questions or run ideas by the community, and the community will provide its opinion. I contribute to some of these communities, but I also participate by reading others' contributions. I find looking through Reddit threads extremely useful for making purchasing decisions for tech products, for example.

    2. In what ways do you think you’ve participated in any crowdsourcing online?

      I think an easy answer to this is I have answered quite a few online polls. By doing this, I was part of a group that supplied data voluntarily to both large and small companies. This was an effort that I and many others partook in to improve the quality of websites or make our opinions heard.

    3. In what ways do you think you’ve participated in any crowdsourcing online?

      I think that I have participated in crowdsourcing online when I engage in social media posts intentionally. For instance, I will see lots of posts on TikTok where the poster is asking the viewer to stay for the length of the video, and engage with it by sharing, liking, and commenting. When I do engage with the post in these ways, I believe that I am participating in crowdsourcing.

    4. In what ways do you think you’ve participated in any crowdsourcing online?

      In terms of participating in online crowdsourcing, I have reviewed products I purchased based on my personal experiences. Like if I bought a low-quality/fake product, I would write a review comparing my experience and warning other people to avoid buying that product. When I try a new restaurant, the staff sometimes ask if I would like to write a review in exchange for a 10% discount. I also report posts related to violence to help prevent harmful content from spreading and to improve the quality of online content.

    5. In what ways do you think you’ve participated in any crowdsourcing online?

      I think that one way I have participated in crowdsourcing online is by voting in companies polls via instagram. Sometimes if I see a company that I like or shop from posting ideas of new flavors, products, etc, I will vote in a poll to try and get my input into the production of something new. I feel like this is a prime example of crowdsourcing because they get a ton of responses and use that to source data from their crowd and participants.

    6. What do you think a social media company’s responsibility is for the crowd actions taken by users on its platform?

      I believe that a social media platform shouldn't have different responsibilities for crowd actions than for individual actions. This would mean that the platform should not allow individuals to spread harmful or hateful information, which would prevent groups from doing the same.

    7. In what ways do you think you’ve participated in any crowdsourcing online?

      I use Reddit quite often, essentially a bunch of different forum sites rolled into one website. There, often, people often post questions to the wider community in hopes of getting an answer (I often do this myself), and I have often answered such queries.

    1. research at UVA

      creative projects at UVA?

      1) Your curiosity and research skills help you understand the RMC's systems, allowing you to successfully address patron's questions, as well as property manage digital media equipment 2) Showing up is the only important part. As long as I can check in and out equipment and answer a few basic things, it's okay to rely on my coworkers to figure out the rest

      Your work supports creative media projects at UVA As a Digital Media Consultant, you practice valuable research, problem solving, and communication skills to support the digital media projects being created at UVA and enhance your professional skills.

    1. Caesar’s

      How crazy is it that Jesus and [Augustus] Caesar were roughly contemporaries? According to Claude, not really crazy. First, Julius Caesar was assassinated in 44 BC. Jesus is born ~4 BC and crucified 30-33 AD. The Roman emperors who overlapped with are: Augustus Caesar (27 BC-14 AD) and Tiberius.

      The fall of the Republic is based on Roman sources. Then, the Romans conquered Judaea at around Christ's time, so it is only then that it was possible for someone to be the Messiah (~military leader who would liberate Jews) and later for the religion to spread through Roman roads and trade.

      Also for some reason many figures are documented very well in that 1st century AD era, so it looms very high resolution. It seems Roman literacy peaked in this period (due to prosperity, probably), and also medieval monks selectively preserved this period because it touched the life of Christ.

    2. God’s Kingdom will be taken away from you and will be given to a nation producing its fruit

      Janna explains: because the Jews treated Christ badly, God took away the Kingdom from them and gave it to the gentiles (another nation, which hopefully then produces fruit). Therefore Christianity can hold that Judaism was the true religion up until the arrival of Christ, and thereafter Christianity was the true religion.

    3. They will respect my son.

      The master of the household is the Lord, the servants are prophets, and his Son is Christ. Obviously the Jewish priestly and scholarly class treated them badly, because they didn't believe their slopulism.

    1. You probably already have some ideas of how crowds can work together on things like editing articles on a site like Wikipedia or answer questions on a site like Quora, but let’s look at some other examples of how crowds can work together.

      This sentence is easy to understand and does a good job introducing the topic. I like how it uses familiar examples like Wikipedia and Quora because it helps readers connect the idea of crowdsourcing to real life. The tone also feels conversational and engaging instead of overly academic.

    2. 16.2.1. Crowdsourcing Platforms# Some online platforms are specifically created for crowdsourcing. For example: Wikipedia [p12]: Is an online encyclopedia whose content is crowdsourced. Anyone can contribute, just go to an unlocked Wikipedia page and press the edit button. Institutions don’t get special permissions (e.g., it was a scandal when US congressional staff edited Wikipedia pages [p13]), and the expectation that editors do not have outside institutional support is intended to encourage more people to contribute.

      I think that Wikipedia is one of the biggest platforms for crowd sourcing because of it's versatility, topics can range from history to political. Also since anybody can edit an article on wikipedia.

    1. the strongest causal evidence.

      moderate this. This is vague. and there are a few kinds of field experiments in addition to this, including price shift experiments (esp. Bray et al), although few if any involving PBA

    2. These measurement challenges mean we should interpret existing estimates cautiously, while still extracting what information we can. The workshop will discuss which methods are most trustworthy and what further research could help.

      this is a bit generic, maybe not necessary

    3. One concrete finding worth engaging: The evidence suggests that the vast majority of PBA purchasers are omnivores, not vegetarians or vegans — one study finds that only around 1% of high-spending plant-based meat alternative households are actually vegetarian. This challenges the intuition that "PBA just captures existing vegans" and raises the stakes for substitution estimation: the counterfactual meat consumption displaced may be much larger than assumed.

      This is probly too strong ... needs caveating and referencing and tooltips.

    4. (chicken vs. beef vs. pork),

      make this 'between different animal products' and 'e.g., chicken vs. beef vs. eggs...' -- relevant for AW when considering issues like the AW impact of meat taxes -- which might shift consumption from beef to chicken, with a higher AW burden -- mention this briefly with further details in a tooltip

    1. Both severely limited Populist gains. The alli-ance struggled to balance the pervasive white supremacy of the AmericanSouth with their call for a grand union of the producing class. Americanracial attitudes—and their virulent southern strain—simply proved tooformidable. Democrats race-baited Populists, and Populists capitulated.

      “The alliance struggled to balance the pervasive white supremacy of the American South…”

      The Populists wanted to unite poor people in the “producing class”:

      farmers laborers workers

      including both:

      poor white farmers poor Black farmers

      But in the South, racism and white supremacy were extremely powerful.

      Many white Southerners believed:

      white people should remain socially and politically dominant. “with their call for a grand union of the producing class”

      Populists hoped poor whites and poor Blacks would work together because they shared economic problems:

      debt low crop prices exploitation by banks and railroads

      The idea was:

      economic class unity over racial division.

      “American racial attitudes…proved too formidable”

      This means racism was too strong to overcome.

      White supremacy was deeply rooted, especially after Reconstruction.

      Many white voters refused to cooperate politically with Black Americans even when they shared similar economic struggles.

      “Democrats race-baited Populists”

      Race-baiting means using racist fears or messages to manipulate voters.

      Southern Democrats told white voters that:

      Populists would give Black Americans more political power interracial cooperation threatened white control

      They used racism to divide poor whites and Blacks.

      “Populists capitulated”

      Capitulated means:

      gave in surrendered stopped resisting

      Instead of fully defending interracial cooperation, many Populists eventually:

      accepted racist politics distanced themselves from Black allies

      to try to keep white voters.

    2. Tosave debtors it promoted an inflationary monetary policy by monetiz-ing silver. Direct election of senators and the secret ballot would ensurethat this federal government would serve the interest of the people ratherthan entrenched partisan interests, and a graduated income tax wouldprotect Americans from the establishment of an American aristocracy.Combined, these efforts would, Populists believed, help shift economicand political power back toward the nation’s producing classes.

      “To save debtors it promoted an inflationary monetary policy by monetizing silver”

      This refers to the Populists supporting free silver.

      What does that mean?

      At the time, U.S. money was mainly tied to gold.

      Populists wanted the government to also use large amounts of silver to create money (“monetize silver”).

      Why? Because increasing the money supply would cause:

      inflation = prices rise slightly Why did farmers/debtors want inflation?

      Many farmers were deeply in debt.

      Inflation helped debtors because:

      crops could sell for higher prices debts became easier to repay since money was worth slightly less

      So Populists believed silver money would help struggling farmers and workers.

      “Direct election of senators”

      Originally, U.S. senators were chosen by state legislatures, not directly by voters.

      Populists wanted ordinary citizens to vote for senators themselves because they believed:

      political machines wealthy elites corporations

      had too much control over legislatures.

      (This later became law with the 17th Amendment.)

      “Secret ballot”

      Before secret ballots, voting was often public or controlled by political parties.

      Populists supported private voting because it:

      reduced bribery reduced intimidation protected voters from pressure “Graduated income tax”

      This means:

      richer people pay a higher percentage in taxes than poorer people.

      Populists thought this would:

      reduce inequality prevent wealthy industrialists from becoming a permanent “aristocracy” (a powerful upper class)

      (This later became possible through the 16th Amendment.)

    3. It called forthe establishment of a network of federally managed warehouses—calledsubtreasuries—which would extend government loans to farmers whostored crops in the warehouses as they awaited higher market prices.

      What were “subtreasuries”?

      The proposal was for the federal government to create:

      warehouses owned or managed by the government

      Farmers could:

      store their crops there wait until prices increased later in the year receive government loans in the meantime Why was this important?

      Without this system:

      farmers had to sell crops immediately when the market was flooded prices were lowest at harvest time middlemen and banks benefited more than farmers

      With subtreasuries:

      farmers could avoid desperate low-price sales they could hold onto crops until prices rose government loans would give them temporary money to survive Example

      A farmer harvests corn in October:

      corn prices are very low because everyone is selling at once

      Instead of selling cheaply:

      the farmer stores the corn in a federal warehouse gets a government loan using the crop as collateral waits several months sells later when prices are higher

    4. it advocatedpostal savings banks to protect depositors and extend credit

      People could:

      deposit savings at local post offices safely store money backed by the government

      Postal savings banks were supposed to:

      be safer protect ordinary workers and farmers reduce the risk of losing money if a private bank collapsed

      1. It was widespread

      The United States Postal Service reached:

      small towns rural farming communities remote areas

      People who had no nearby bank still had access to a post office.

      1. It was government-backed

      People trusted the federal government more than unstable private banks.

      If a private bank failed:

      depositors could lose their savings.

      A postal savings system was seen as safer because:

      the government managed it.

    5. pre-emptive injunction

      During the late 1800s and early 1900s, courts often used preemptive injunctions against:

      strikes labor unions protests boycotts

      Judges would order workers:

      not to strike not to gather not to interfere with businesses

      before the workers even acted.

      If workers ignored the injunction, they could:

      be arrested fined jailed for contempt of cour

    6. “producerist” economy

      A “producerist” economy is the idea that the people who actually produce wealth through their labor are the ones who deserve the most economic and political power.

      “Producers” usually meant:

      farmers artisans laborers small business owners skilled workers

    1. The influence ads promote BP’s plan to “transition to net zero” by gradually reducing oil and gas production and investing more in “low carbon” and renewable energy sources.

      Despite sustainability messaging, the company continues major fossil fuel activities that contribute to environmental harm.

    2. “Backing Britain: delivering homegrown energy” read many of the ads in green script across a map of the UK.

      This message may distract consumers from the environmental consequences of fossil fuel production.

    3. company paid about £570,000 to Facebook and Instagram for influence ads that reached tens of millions of viewers in the UK.

      This raises ethical concerns because social media advertising may shape public perception in a misleading way.

    4. champion the company’s investments in green energy

      The company may exaggerate its environmental efforts while still relying heavily on fossil fuel activities.

    5. BP’s ‘greenwashing’ social media ads as anger over fuel costs rose

      This statement directly indicates possible greenwashing because the company promotes a misleading environmentally friendly image.

    1. 16.1. Crowdsourcing Definition# When tasks are done through large groups of people making relatively small contributions, this is called crowdsourcing. The people making the contributions generally come from a crowd of people that aren’t necessarily tied to the task (e.g., all internet users can edit Wikipedia), but then people from the crowd either get chosen to participate, or volunteer themselves. When a crowd is providing financial contributions, that is called crowdfunding (e.g., patreon [p1], kickstarter [p2], gofundme [p3]). Humans have always collaborated on tasks, and crowds have been enlisted in performing tasks long before the internet existed [p4]. What social media (and other internet systems) have done is expand the options for how people can collaborate on tasks.

      Crowdsourcing in its core idea involves the efforts or contributions of a group of people, often random, to achieve a collective goal. The examples are things like Wikipedia for information and GoFundMe for fundraising. I have personally used and participated in crowdsourcing in the past by fundraising for a local non-profit through GoFundMe during high school.

    2. 16.1. Crowdsourcing Definition# When tasks are done through large groups of people making relatively small contributions, this is called crowdsourcing. The people making the contributions generally come from a crowd of people that aren’t necessarily tied to the task (e.g., all internet users can edit Wikipedia), but then people from the crowd either get chosen to participate, or volunteer themselves. When a crowd is providing financial contributions, that is called crowdfunding (e.g., patreon [p1], kickstarter [p2], gofundme [p3]). Humans have always collaborated on tasks, and crowds have been enlisted in performing tasks long before the internet existed [p4]. What social media (and other internet systems) have done is expand the options for how people can collaborate on tasks. 16.1.1. Different Ways of Collaborating and Communicating# There have been many efforts to use computers to replicate the experience of communicating with someone in person, through things like video chats, or even telepresence robots [p5]]. But there are ways that attempts to recreate in-person interactions inevitably fall short and don’t feel the same. Instead though, we can look at different characteristics that computer systems can provide, and find places where computer-based communication works better, and is Beyond Being There [p6] (pdf here [p7]). Some of the different characteristics that means of communication can have include (but are not limited to): Location: Some forms of communication require you to be physically close, some allow you to be located anywhere with an internet signal. Time delay: Some forms of communication are almost instantaneous, some have small delays (you might see this on a video chat system), or have significant delays (like shipping a package). Synchronicity: Some forms of communication require both participants to communicate at the same time (e.g., video chat), while others allow the person to respond when convenient (like a mailed physical letter). Archiving: Some forms of communication automatically produce an archive of the communication (like a chat message history), while others do not (like an in-person conversation) Anonymity: Some forms of communication make anonymity nearly impossible (like an in-person conversation), while others make it easy to remain anonymous. -Audience: Communication could be private or public, and they could be one-way (no ability to reply), or two+-way where others can respond. Because of these (and other) differences, different forms of communication might be preferable for different tasks. For example, you might send an email to the person sitting next at work to you if you want to keep an archive of the communication (which is also conveniently grouped into email threads). Or you might send a text message to the person sitting next to you if you are criticizing the teacher, but want to do so discretely, so the teacher doesn’t notice. These different forms of communication can then support different methods of crowdsourcing.

      The issue with archiving as an element of a communication type for this chapter presents an unexamined conflict in crowdsourcing: while an archive facilitates both searchability and scalability of crowd-sourced input (example: the edit history on Wikipedia) and therefore allows for tracking/monitoring of contributor actions, at the same time it erases anonymity. Therefore, the advantages of computer based communications are not neutral -- they represent design decisions which favor the interests of the platform(s) hosting the crowd, rather than those providing their labor.

    3. Some of the different characteristics that means of communication can have include (but are not limited to):

      I think archiving messages can be both helpful and stressful. Sometimes it is useful because people can go back and check important information in chats or emails. But at the same time, it also makes people more careful about what they say online because messages can stay forever. I noticed that in group chats or social media, people sometimes misunderstand old messages and start arguments again.

    1. eLife Assessment

      The authors make the valuable observation that directional memory during epithelial cell migration is enhanced compared to single-cell migration. They attribute this effect to adherens junctions and vinculin dimerization. In the work, central measures should be defined more precisely, and the support for their claims about the roles of adherens junctions and vinculin dimerization in memory enhancement remains incomplete.

      [Editors' note: this paper was previously reviewed by another journal.]

    2. Reviewer #1 (Public review):

      Summary:

      In this work, the authors study the migration of isolated cells and of cells in ensembles. They quantify several aspects of the corresponding migration patterns and investigate how these quantities depend on molecules that are known to play an important role in migration. Furthermore, they study the effect of external cues on these migration processes.

      Strengths:

      The authors provide a clean and uniform setting for comparing the migration of isolated cells and of cells in an ensemble in control and mutant conditions, and in the presence and absence of external cues. This allows for a meaningful comparison between different conditions. In this way, the authors obtain useful data that link the migration of isolated cells to that of cells in collectives.

      Weaknesses:

      A major weakness of the manuscript is that the authors do not properly introduce the quantities and concepts they are working with. In this way, it is hardly accessible for a reader who does not have a thorough background in cell migration and anomalous transport. In addition, the manuscript uses some notions that are not standard, for example, vinculin or FA stability, which are not properly introduced. Most strikingly, "collective directional memory" is not defined.

      The authors infer relationships between different quantities, but they remain qualitative, even though the authors use a language that suggests otherwise. For example, "The combination of Focal Adhesion stability and force transmission from the cytoskeleton predicts the migration speed of single cells" (p 2). I am not sure what is meant by prediction, but this heading suggests that knowledge of FA stability and force transmission yields the migration speed. Reading this line, I expect that if I give you values for FA stability and force transmission, you would give me a value for the migration speed. Such a quantitative mapping is not provided. In fact, it cannot be provided, because - as mentioned before - these quantities are not properly defined, so I would not know how to measure them. I do not even know their units.

      Furthermore, the authors do interpret some of their results without explaining or justifying the basis for their interpretation. For example, they use the FRET index of vinculin - another notion that is not properly introduced - to make statements about mechanical stress.

      It also seems that the figures could be improved. Some of the sketches are, in my opinion, not helpful. Examples are Figure 3A (how could a cell move while the hexagonal arrangement of the cells is maintained?) or Figures 2F, 4F, and 6F (what do the colored ellipses indicate?). In Figures 1B, 1D, 2A, 2E, 3B, 3D-F, 4A, 4F, 5B-D, it is not clear which lines merely connect data points and which lines are fits to the data.

    3. Reviewer #2 (Public review):

      Summary:

      The manuscript by Canever et al was assessed by three Referees at another journal, who brought up a range of critical points. I will not repeat a summary of the work; this can be found in the first-round reviews.

      Strengths:

      In their revised manuscript, the authors include substantial changes and additional reasoning. Along with their rebuttal letter, I think they make a very convincing case. While the claims are well supported by the analysis, I do not see that the findings need to be universal to be relevant. It might be rather surprising to me if there existed such a universality, in fact. I think that the findings are solid and interesting in their own right and are worthy of publication, especially with the amended discussion in this revision.

      Weaknesses:

      However, while the more bio-oriented parts are not fully accessible to me, I do have a few points from the data analysis point of view that need amendment.

      (1) The used mathematical models need to be specified more precisely. First, the authors confuse Levy flights and walks. These are distinct processes in the sense that a Levy flight does not have a finite variance and thus no finite speed. The proper model here would be Levy walks. As in a big body of the literature, both notions are used interchangeably here, while they are distinct processes. Then the authors speak about a "superdiffusive model", for which I do not find a proper definition. There exists an entire range of superdiffusive models, each with a different physical background, so this needs more clarity. The authors may consult one of the standard reviews for more details, e.g., Soft Matter 8, 9043 (2012) or Phys Chem Chem Phys 16, 24128<br /> (2014). Overall, a few equations (maybe in the Supplement) would help to be more specific.

      (2) For fractional Brownian motion, the authors should check the displacement correlation function; it should show slowly decaying, positive correlations. More details on the practical analysis of FBM can be found, e.g., in Phys Chem Chem Phys 27, 14350 (2025). These correlations should decay as a function of the bin time, e.g., as discussed for the opposite case of subdiffusion in Phys Rev E 88, 010101(R) (2013) [cf Fig 3b]. In general, FBM was determined to be a highly relevant process for a number of systems, including amoeba cells at shorter times, see the detailed analysis in Phys Rev Res 4, 033055 (2022). In this paper, there are also different ways to characterise the motion in terms of scaling. Exponents are detailed.

      (3) Some relevant approaches discussed in literature that should be discussed in the context of this work: eLife 9, e52224 (2020); Rep Prog Phys 86, 126601 (2023); Chaos 35, 023145 (2025). In the context of non-Gaussianity for active particles: Phys Rev E 104, 064615 (2021); New J Phys 25, 013010 (2023).

      (4) In the abstract, I am having some issues with the formulation in the sentence: "This directional memory emerges from fractional Brownian motion". It sounds as if FBM were a fully clarified phenomenon. I would prefer some statement along the lines that the data are consistent with such a mathematical modelling approach.

      After fixing these points, I think the manuscript will clearly warrant being shared.

    4. Reviewer #3 (Public review):

      This manuscript focuses on the presence/origin of directional memory during epithelial cell migration. It starts by analyzing single cells and then moves to more complex systems (confluent layers and scratch assays). The paper first demonstrates that the migration in all of these systems is well-described by persistent random walks, which likely emerge from fractional Brownian motion. This is an important demonstration, as it implies orientation memory in the systems. Then the paper proceeds to attempt to discern the origin of this memory and claims to establish key roles for adherens junctions and vinculin dimerization. While for the most part the manuscript is well-written, there are some significant overinterpretations in experimental results. The largest issue is demonstrating the role of vinculin dimerization, which is not a well-studied phenomenon inside living cells, as all data is reliant on a single point mutation (Y1065E). Additionally, the authors seem to be over-interpreting several of the assays; the statistical analysis does not seem to encompass all comparisons made, and the molecular model proposed does not clearly explain the observed results. The discussion could also be strengthened by considering other aspects of vinculin behavior (e.g., vinculin catch bonding) as well as discussing some other recent similar papers.

      (1) Likely the most significant issue with the manuscript is the interpretation of the vinculin Y1065E variant and the assumption that the only defect the mutations cause is a lack of dimerization. Vinculin dimerization is mediated by a conformational change in the vinculin tail domain induced by F-actin binding (Thompson, FEBS Letters, 2013). Dimerization of the vinculin tail domain has been clearly demonstrated in in vitro systems involving purified proteins, as the authors point out in the manuscript. However, the dimerization of full-length vinculin has not been well characterised in living cells. There are several reasons to suspect dimerization is potentially not prevalent in cells. For instance, in the presence of other actin-binding proteins, there may not be sufficient binding sites available on neighboring actin filaments to facilitate dimerization. Additionally, pY1065 vinculin and vinculin Y1065E have been associated with increased vinculin activation (Huang, JBC, 2014), so other effects seem possible. While the Y1065E variant clearly has an effect on the tension sensor readout and vinculin dynamics, further experimental evidence is needed to show that these effects are due to a lack of dimerization in living cells. To justify the definitive claims made in the manuscript, the authors likely need to develop, or employ, an assay for detecting vinculin dimerization in living cells. The authors could choose between intermolecular FRET, proximity labeling assays (i.e., antibodies with DNA for signal amplification), bimolecular fluorescent complementation (i.e., split GFP) based approaches, or some other approach. It should be noted that working with full-length vinculin, not just Vt, and designing an assay that can incorporate vinculin Y1065 variants (Y1065E and potentially Y1065A/F) would strengthen results. Also, the authors should be aware that the observation of strong dimerization may invalidate the use of FRET-based tension sensors in this system or at least necessitate intermolecular FRET control experiments.

      (2) The authors have seemed to assume that FRAP and adhesion stability are interchangeable. To this reviewer's knowledge, this is not the standard in the field. FRAP informs about molecular dynamics. Stability assays, which probe the spatial position of an entire focal adhesion over time (Zaidel-Bar, JCS, 2007, although other approaches are equally suitable), are typically used for assessing adhesion stability. If the authors wish to make strong claims about the stability of the adhesions, non-FRAP-based assays should be employed. Alternatively, the authors could interpret the FRAP data simply in terms of vinculin dynamics.

      (3) A major conclusion in the manuscript is that in response to overexpression of a specific vinculin construct, focal adhesions behave the same in single cells, confluent cells, and collectively migrating cells for all the mutants but Y1065E. However, outside of the FRET measurements, there is not much evidence to support this claim. The authors should perform a greater comparison of the focal adhesions between the systems used in the manuscript (single cell, confluent cells, collectively migrating cells). Key measurements would include focal adhesion number per cell, focal adhesion size, focal adhesion orientation, vinculin dynamics (e.g., FRAP), focal adhesion stability, and some indicators of focal adhesion composition. For the last aspect, focusing on focal adhesion components that also have roles in adherens junctions, such as VASP, seems appropriate. Without such characterization, it is an overinterpretation to assume that focal adhesions are the same in each system and, therefore, effects are due to vinculin behavior in the adherens junctions.

      (4) What is shown in Figure 3G is not clear. How are P/Po and alpha shown on different areas of the same plot?

      (5) It seems that an insufficient statistical test was used in many experiments. There are comparisons being made between systems (cell migration speed, FRET index...) that are not directly compared in a statistical test. Statistical tests are limited to differences from control (over-expression of full-length vinculin), and consistent increases or decreases (not quantitative values) are taken as evidence of similarity across systems. It seems that a more rigorous and standard approach would be to use an ANOVA/MANOVA with a suitable post-hoc test to perform all of these.

      (6) It is unclear how a lack of vinculin dimerization at adherences junctions perturbs epithelial migration, but the complete lack of vinculin tail, which can also not dimerize, does not. In other words, how can TL "have no other role in cell migration at confluence than those at FAs as in single cells." Notably, the authors do not include the tailless variation in the schematic model figures. These results should be included and explained.

    5. Author response:

      [Editors' note: The authors included an author response to reviews from another journal]

      Reviewer #1 (Comments to the Authors):

      In this manuscript the authors describe that cells in collective movements adopt a superdiffusive behavior to out pace individual cells. This behavior is regulated by cell-cell junctional stability and force transmission. The authors state that speed is regulated by vinculin through mechanosensitivity.

      While is makes intuitive sense that cells may move more efficiently collectively as it reduces their exploratory space and therefore increases their efficiency of movement,

      We agree that this is an intuitive explanation. However, previous literature had shown that confluent cells may or may not migrate depending on conditions that do not solely depend on the space available per cell, but also involve the intrinsic activity of the cell, its cortical tension, and its adhesion with its neighbors, with sometimes counterintuitive effects (doi: 10.1016/J.CEB.2021.07.011). This was the reason that motivated us to investigate how these various ingredients affected space exploration efficiency on different time scales.

      Our results indeed refute the intuition that cells move more efficiently when their exploratory space is reduced by showing that the outcome depends on the time scale considered (Fig. S3B). Specifically, on short time scales (less than 3 hours), the area explored by individual MDCK cells is larger than that explored by MDCK cells at confluence. On a longer time scale (greater than 3 hours), however, the area explored by confluent MDCK cells is larger. This switch is a direct consequence of the change in migratory behavior from persistent random walk to superdiffusion, Moreover, its position in time depends on the cell line: extrapolation of our results on RPE-1 cells suggests that it should theoretically occur after approximately 300hrs, if this time scale was experimentally accessible (Fig. S3F).

      …the role of junctions specifically is less clear.

      We are sorry that we were not able to clearly convey the roles of junctions. We have substantially rewritten our text to address this and all the changes are highlighted in orange. As summarized in Fig. 6F, junctions have three roles. The first role is on persistence, through velocity coordination between neighbors, the second is on speed, through the stability of junctions, and the third role is on directionality, through the sensitivity of the monolayer to the wound edge.

      The first role is evidenced thanks to the comparison of the MSD between single cell and confluent migration assays and the use of the alpha-catenin KD cell line. Alpha-catenin depletion is known to be the most potent disruptor of adherens junctions (DOI:10.1091/mbc.e06-05-0471, , DOI:10.1126/science.aaf7119, (DOI:10.1073/pnas.1002662107, DOI:10.1073/pnas.1119313109), and we show that it significantly alters the superdiffusive behavior that emerges in the confluent migration assay (Fig. 3E,F, 5C). Therefore, junction integrity is critical for the control of cell persistence.

      Moreover, alpha-catenin depletion induces a loss of velocity coordination between neighbors (Fig. S3E), which we show through numerical simulations to induce superdiffusion (Fig. 3G). By contrast, E-cadherin KO and vinculin mutants have no effect on the superdiffusion of confluent cells (Fig. 3E, 4A). Therefore, the critical molecular ingredient is the link provided by alpha-catenin to the cytoskeleton that provides junction integrity.

      The second role of junctions is evidenced thanks to the comparison of cell speeds between single and confluent migration assays with the vinculin mutants (Fig. S4A). Results show that cell speed is reduced of about 10µm/h by confluence, regardless of the mutant except for YE, whose only difference with other mutants is its lower stability (Fig. 4F). This supports that junction stability, and not the other effects of mutants, controls cell speed (we provide a detailed demonstration in the response to the following question). As expected, junction integrity is required as well, as seen from the higher cell speed of the alpha-catenin KD cell line compared to WT (first MSD point in Fig. 3B, E).

      The third role of junctions is evidenced thanks to the comparison between confluent and directed migration assays (Fig. 6A). Results show that the wound healing rate is proportional to cell speed at confluence, regardless of the mutant except for YE, which displays no tension gradient in junctions from front to back cells (Fig. 6C). This supports that such gradient is required for cells to identify on which side is the wound edge. As expected, junction integrity is required as well, as seen from the loss of directional bias of the alpha-catenin KD cell line (Fig. 5F).

      The authors chose vinculin as the basis by which to manipulate tensions at cell-cell junctions, but this comes with considerable drawbacks. Namely, since vinculin appears at both cell-cell and cell-matrix junctions, its role and the role of its mutations is not clear here. The authors state that the collective migration speed is related to junctional stability, but because vinculin is also at FA, how can this be concluded?

      We apologize for the lack of clarity. We hope that the highlighted changes in the revised manuscript will improve this point. As exemplified above, comparing cell migration between isolated cells and confluent cells is essential to enable us to distinguish between the contributions of AJs and FAs. Indeed, since isolated cells lack AJs, the impact of vinculin mutants on single cell migration can only be explained by their effects on FAs. This is how we first determine the effects of vinculin mutants on migration that depend on FAs. Because confluent cells also have FAs, we expect that the effects of vinculin mutants on the migration of isolated cells will still be present in confluent cells, to which will be added the effects of these mutants on AJs and their consequences on migration, if any.

      Therefore, when compared to WT cells, if a given mutant decreases or increases migration speed in individual cells, and does so in confluent cells in the same proportion, then its effects at confluence can be entirely explained by its effects in individual cells, and there are no additional effects of that mutant from AJs. This is indeed what we observe for all mutants except the YE mutant (Fig. S4C), leading us to conclude that none of the vinculin mutants, except the YE mutant, have an effect on migration at confluence that results from AJs. In contrast, the YE mutant has effects on migration at confluence that cannot be explained by its effect on individual cell migration. Therefore, the effects of YE at confluence depend on AJs, whether they result from alterations in AJs, FAs, or both. To distinguish between these scenarios, we proceed by elimination, comparing the effects of YE to those of other mutants on force transmission and adhesion stability, and how these two factors associate with migration speed, as explained below. In FAs, YE alters force transmission differently in individual cells and at confluence, but we already know from Fig. 2 that force transmission in FAs cannot alone explain the speed of migration. This result rules out an indirect effect of AJs on cell migration at confluence through FAs. Furthermore, in AJs, YE affects stability and force transmission, but TL has the same effect on force transmission as YE and we already know that none of the effects of TL on migration depend on AJs (Fig. 3, S4C). This result rules out an effect of force transmission in AJs on migration speed at confluence. We conclude that stability at the AJ level, which is the remaining property specifically impaired by YE, is what regulates migration speed at confluence.

      The manuscript's logic and flow are not clear in some places, making the story hard to follow. As one example, the FRAP data, which the authors suggest is used to investigate vinculin's combined role does not help in this capacity as the interpretation and its connection to the bigger story are not clear.

      We are sorry again for the lack of clarity. We used FRAP data to evaluate the effects of vinculin mutants on adhesion stability. Indeed, mutants have different effects on adhesion stability (Fig. 2E, 4F). In addition, they also have different effects on force transmission (Fig. 2D, 4D,E). The partial overlap in functional alterations caused by the mutants allows us to test the involvement of the overlapping function (here stability) in the overall migration outcome. For example, if two mutants have a similar effect on adhesion stability but different effects on migration speed (such as TL and T12), we can then rule out that speed results from adhesion stability. Similarly, if two mutants have different effects on stability but a similar effect on speed (such as TL and YE), we can also rule out that speed results from stability. We applied the same reasoning to force transmission to conclude that neither adhesion stability nor force transmission alone is sufficient for cells to migrate rapidly. However, the combination of the two enables rapid migration.

      As another example, the information derived from the use of the mutants is not clear in the context of the message in the manuscript since they affect cell-cell and cell-matrix junctions and in some places show results that are counter intuitive and not well-explained, to which the authors admit they are surprising but then do not explain their meaning.

      As such, it is very hard to follow the logic with regard to the information resulting from the mutant experiments.

      We provide above a detailed break-down of our strategy to analyze the results. We regret that our manuscript did not adequately convey our conclusions and we hope that the new version of the manuscript improves this point.

      Proliferation has been shown to play a role in wound healing. Does proliferation change in the various conditions?

      This is an important point. The average speed of cells at confluence is approximately 20 µm/h (Fig. 4B), which means that each cell moves approximately its own size in one hour. During this time, assuming a 16-hour cell cycle, 6% of the cells would have divided, each of them likely pushing one of its neighbors a distance equivalent to the size of a cell. Therefore, cell proliferation accounts for at most a few percent of the total cell movement. For this reason, we can assume that growth does not account for a large part of the movement we observe. This is consistent with previous work showing that proliferation does not contribute significantly to wound healing (DOI: 10.1073/pnas.0705062104, DOI: 10.1083/jcb.201207148).

      Minor comments:

      The authors should provide a better description of the mutants: what does a tailless mutant not bind, or bind differently? More context is needed to help interpret the results. While the mutants have all been published on before, it would be helpful to have more information here so that the manuscript is easier to follow.

      We are sorry that the information we provided was insufficient. We have now detailed the mutations to help the reader understand how interactions are altered.

      Figure 1A is not necessary. Figure 1 overall is fairly predictable as there have been many papers using the persistent random walk as the best model to single cell migration (dating back to the early 1990's). The authors define a new term, angular memory, which they show decreases with increasing delta t as one would predict.

      We acknowledge that persistent random walks have already been observed for individual cells, as in references 3-4 cited in the introduction. Nevertheless, we believe that Figure 1 is important because not all cells migrate as persistent random walkers when isolated. Some migrate in a more exotic manner, resulting in superdiffusive behavior, as in references 5-8 cited in the introduction. Since we observe superdiffusive behavior at confluence (Figure 2), it was therefore necessary to show whether or not single cells were superdiffusive too. We also use this figure to introduce angular memory, a measure that, to our knowledge, has never been used before. According to intuition, it decreases to 0 for persistent random walkers, just as another resembling measure, velocity autocorrelation, would do. However, the angular memory of fractional Brownian walkers does not vanish with increasing delta t (Fig. 3D), while velocity correlation would, just as that of persistent random walkers. This difference makes angular memory much more appropriate for distinguishing between the two migration behaviors, and prompted us to introduce it in the first figure as a reference.

      In the wound healing assay, which cells were measured? Leading edge or interior, and does it matter?

      Figure 5A shows that cells behave differently depending on their distance from the wound. This is because the traces shown correspond to the first few hours of the movie, during which the cells at the front begin to move first. Figure S5A shows the speed of the cells over time after the wound and indicates that the cells reach a stable speed after approximately 3 to 4 hours. Figure S5B shows the speed of the cells as a function of distance from the wound at steady state. These results show that the speed of the cells no longer depends on the distance from the wound at this stage. As indicated in the “Materials and Methods” section, we only considered time points beyond this stage for subsequent analyses of population-averaged MSD and velocity presented in Figure 5, so the location of cells at the front or rear was irrelevant.

      Reviewer #2 (Comments to the Authors):

      To migrate cells must spatially explore their environments, a process that is guided by intrinsic signals (adhesive and mechanical properties, etc) and extrinsic (gradient cues) signals. This exploration can occur on the single or multicellular level. In this study, the authors examine the effect of cell-cell interactions, guidance cues, and cell mechanics in the exploratory capacity of MDCK cells. The authors show that cell-cell adhesion provides a "infinite directional memory for migration" and cell speed is dependent upon the focal adhesion stability, cell mechanics, and the mobility of adherens junctions-these processes are modulated by vinculin.

      My three major concerns with the manuscript are as follows:

      (1) While there is potential new information about the role cell-cell junctions and guidance cues play in cell migration, there is not enough NEW insight presented. Rather the role of vinculin in these processes is expected given what is already known about its ability to control focal adhesion stability, mechanics, and adherens junctions.

      We agree that our cell migration results make sense based on the effects of vinculin mutants on the stability and force transmission of adhesions. Nevertheless, we argue that this was not the only possible scenario. Indeed, we find that none of the effects of vinculin mutants on AJs (except YE) have an impact on cell migration (Fig. S4C). One might have expected that the increased stability provided by the TL and T12 mutants would reduce the speed of collective cell migration, just as the YE mutant increased cell speed due to its altered stability. This is not what we found, and this reveals a nonlinear relationship between AJ stability and migration speed that could be investigated more thoroughly in future studies. Another example is that the effects of the mutants on force transmission in AJs do not impact migration speed at confluence but do impact directed collective migration (Fig. 6). One might have expected that vinculin-mediated force transmission in AJs would impact collective migration, whether directed or not.

      More importantly, we show that the role of intercellular adhesion in cell migration is more complex than expected. Indeed, it depends on the timescale considered: intercellular adhesion is detrimental to short-term spatial exploration and beneficial in the long term (Fig. S3B). Such a timescale-dependent behavior is impossible to predict from previously known effects of the mutants or other molecular considerations. Furthermore, we show that this behavior can be fully explained by the coordination of velocities between neighbors, which depends on intact connections between AJs and the cytoskeleton via alpha-catenin, but is independent of vinculin mutants that connect AJs to the cytoskeleton in parallel with alpha-catenin. One might have expected these connections to also have an impact on velocity coordination, and thus on spatial exploration, but we show that this is not the case (Fig. 3). Finally, we show that directed collective migration has a negligible impact on cell exploration at our experimental timescale (Fig. 5), whereas we initially expected the wound to make migration more ballistic. This reveals that such a directional signal affects spatial exploration at much longer timescales than expected.

      Overall, our results quantify the outcome of competing effects and provide timescales at which one effect outweighs the other in influencing cell migration. We believe this is an original approach that provides substantial new insights into collective cell migration.

      (2) The phenotypes of the cells expressing the mutant vinculins varying greatly. These phenotypes are not addressed despite the fact that they could potentially complicate the analyses. For example, there are dramatic differences between focal adhesion numbers and sizes in the cells expressing the different vinculin mutants; cell spreading is also dramatically altered. Likewise, the T12 mutant vinculin has previously been reported to have increased adhesive strength, increased traction forces, and cell spreading. How does this knowledge change the interpretation?

      We agree that vinculin mutants may have effects on the size and number of FAs, cell spreading, and traction forces that we do not examine here. These consequences can be explained by the effects of these mutants on force transmission in FAs and on their stability, which we report in our work. They do not affect our interpretations. Here, we provide a predictive model of migration speed based on the combination of two consequences of vinculin function, namely stability and force transmission. An interesting avenue for future research would be to assess whether these combinations can be reduced to a single higherlevel effect of vinculin on the cellular phenotype that would be sufficient to predict migration speed. This work remains to be done, as neither FA size and number, cell spreading, adhesion force, nor traction forces alone are sufficient to predict migration speed.

      Along the same lines, it has previously been established that tagged version of vinculin do not efficiently integrate into adherens junctions. Published work from the Nelson laboratory suggests that GFP-vinculins do not localize to cell-cell junctions and work from other laboratories suggests localization occurs only when the endogenous vinculin is silenced.

      We are aware that some GFP-vinculin constructs may not localize as well as the endogenous protein at AJs. This is due to the localization of the GFP tag on the head of vinculin and depends on the length of the linker between GFP and the head of vinculin. The longer the linker, the easier the interaction with AJ partners. Unlike these constructs, the vinculinTSMod sensors we use in our work do not carry a GFP on the head and do not suffer from the same limitations.

      Furthermore, vinculin recruitment to AJs depends on force, with little or no recruitment when tension on the AJs is relaxed (DOI: 10.1038/ncb2055). Vinculin recruitment has in fact already been used as an indicator of AJ tension in Drosophila (DOI: 10.1038/s41467-01807448-8). Consequently, the amount of vinculin visible at the AJs varies depending on the tension exerted on the AJs, which our results confirm: vinculin is more difficult to detect at the AJs in cells located at the front of a wound than in those located at the back (Fig. 6B), which is consistent with the difference in vinculin tension between front and back cells (Fig. 6C) and to the E-cadherin tension gradient between front and back cells (DOI: 10.1083/jcb.201706013). Overall, these results show that vinculin is not always easy to detect at AJs, but this is due to the properties of vinculin, which the constructs we use reproduce better than previous constructs (see also below).

      The images in figure S2 and the prebleach images in figure S4 do not show convincing localization of the mutant vinculins to cell-cell adhesions. This is of special concern given that YE mutant protein hardly has any discernable localization to cell-cell junctions; additionally, none of the mutant proteins were tested for their ability to co-localize with adherens junction components. This raises the question if the parameters being examined and the conclusions drawn from them are affected by a difference in localization.

      We agree that the recruitment of vinculin at intercellular contacts may be difficult to see.

      Besides force-dependent effects mentioned above, other factors are involved. The images shown in Figures S2 and S4 are from live cells in which cytoplasmic vinculin is still present, and its level proportional to the mobility of vinculin. Indeed, the TL and T12 mutants show a more marked contrast between intercellular contacts and the cytoplasm, which is consistent with their greater stability at AJs (Fig. 4F). Conversely, YE shows lower contrast, which is consistent with the lower stability of this construct at AJs (Fig. 4F). The FL construct lies between the two. As a result, the cytoplasmic content can variably mask vinculin recruitment at the AJs depending on the mutant.

      We have now performed additional quantifications of mutant recruitment at intercellular contacts as a function of distance from the basal surface of the cells and relative to their recruitment in FAs, in live cells. Results are shown in the new Fig. S4F. We find that all the constructs are recruited to intercellular contacts with a density that is at most half of that in FAs and that varies along the height. FL shows the highest density, localized more apically, consistent with the localization of an AJ-bound actin belt. The mutants appear to be more homogenously distributed along the height of the lateral surface, which may be explained by their impaired autoinhibition (TL, T12), or mechanosensitivity (YE). This variability also contributes to the difficulty in seeing vinculin recruitment in all cells in a single z-slice.

      To confirm the proper recruitment of vinculin constructs to AJs we have performed immunofluorescence against alpha-catenin and phalloidin on each of the stable cell lines. Results are shown in the new Fig. S4D and E. In these experiments, cell permeabilization allows for the release of some of the cytoplasmic pool of vinculin, which highlights the recruitment of all vinculin constructs to intercellular contacts. There, all vinculin constructs colocalize with alpha-catenin and F-actin, as expected. Additionally, images displayed are maximum intensity projections to mitigate recruitment variability along the height.

      Overall, our results clearly support the localization of vinculin at intercellular contacts, and the differences between the constructs are consistent with the effects of their mutations.

      (3) There is a lack of new mechanistic insight. Conclusions are made about a role of vinculin dimerization. This conclusion appears to be based upon the usage of the mutant version of vinculin Y1065. Did the authors directly measure the ability of this mutant protein to dimerize? Is actin binding also affected.

      The binding properties of the Y1065E mutant, including its dimerization and binding to actin, have already been characterized by other researchers (ref. 40 in our manuscript, as well as DOI:10.1111/j.1432-1033. 1997.01136.x or DOI: 10.1016/j.febslet.2013.02.042). We assumed that these properties are now well established and can be used to explain higher-level phenotypes that we show for the first time, to our knowledge.

      Reviewer #3 (Comments to the Authors):

      Canever et al. tracked two epithelial cell lines on collagen coated glass and showed that isolated cells (non confluent) move as persistent random walkers, whereas confluent monolayers migrate super diffusive, with long range directional memory. By systematically perturbing adhesion machinery they found that focal adhesion mutations mainly tune the speed of single cell tracks, but cannot create long range memory, while force bearing adherens junctions are essential for the super diffusive regime-genetically perturbing them collapses collective memory. These interesting results identify junctional tension as important to switch epithelial cells/sheets between individual and collective search modes - an important quantitative insight that is of clear relevance to cell biologists.

      - The presented data is nicely quantitative and convincing, but I have subtle concerns about the generality of the findings. While the authors show that the differential behavior, they describe is not cell-line specific (MDCK, RPE), there are no experiments evaluating the generality of their conclusions across different matrix conditions. How are the measured migration parameters affected by matrix stiffness? Cell migration on collagen coated glass coverslips is a relatively narrow and artificial condition. How is the collective directional memory expected to behave on softer substrates? The generality of the conclusions could be strengthened by repeating measurements using hydrogels of varying stiffness. Further, it should be discussed to which tissues in the body the selected matrix conditions and migration modes plausibly apply.

      We agree that the generality of our results and the relevance of glass-rigid substrates is an important point. In vivo, epithelial cells rest on a basement membrane with a typical stiffness of approximately 10 MPa, as demonstrated by experimental evaluations on various tissue explants, including renal glomeruli and Bruch's membrane, which are relevant to MDCK and RPE-1 cells (DOI: 10.1111/j.1742-4658.2007.05823.x, DOI: 10.1172/JCI106898, DOI:10.1038/eye.1987.35), we have added these references in the manuscript to support our experimental strategy. In vitro, the most significant effects of substrate stiffness on FAs and cell migration generally occur at much lower stiffnesses, between 0.2 and 100 kPa, and cell phenotypes generally plateau at levels comparable to those observed on glass, even below 100 kPa (DOI: 10.1242/jcs.133645, DOI: 10.1038/ncb3268, DOI:10.1039/c5ib00307e, DOI: 10.1039/c9sm01893j). Furthermore, substrate stiffness has much more moderate effects on confluent cells than on isolated cells. For example, it has been previously demonstrated that confluent layers of MCF10A epithelium showed no change in velocity coordination in the range of 3 to 65 kPa (DOI: 10.1083/jcb.201207148). Therefore, collagen-coated glass appears to be a reasonable model for the basement membrane. Overall, we believe that we have conducted our experiments under physiological conditions, and that our results apply to a wide range of substrate stiffnesses.

      - It would be nice to see how long it takes confluent cell layers to close rectangular wounds of defined size when cells migrate as individual (adherens junctions perturbation) versus collective (wt) (on substrates of different stiffness). Presumably, there should be faster wound closure under the collective regime, at least for simple shaped wounds.

      This is an interesting question, which our results indirectly address. In our study, we measured the wound healing speed of the WT MDCK cell line as well as lines expressing mutant vinculin constructs (Fig. 6A). These results show that this speed ranges from 5 to 15 µm/h depending on the construct expressed (and for reasons that we explain in the manuscript). These values make it easy to estimate the time required to close a wound based on its width. For example, it would take 5 hours to close a 100 µm wide wound for the WT cell line, which has a rate of 10 µm/h (on both sides of the wound).

      Wound closure for cells with disrupted adhesive junctions has already been documented (DOI: 10.1083/jcb.200910041). The results show that wound closure is indeed slower than with WT cells. Although this previous study does not reveal the underlying causes, our work now shows that there are two factors: weaker directional memory due to impaired intercellular coordination and, in the longer term, an additional lack of sensitivity to the guidance signal provided by the wound.

      - Akin to substrate stiffness variation, I am missing experiments that test the effect of cytoskeletal tension on these migration modes. Experiments with Rho kinase or myosin inhibitors could meaningfully broaden the scope of this study.

      Rho kinase or myosin inhibitors applied to cells during the time required to assess migration patterns (a movie recorded overnight is necessary to obtain a statistically reliable calculation of MSD over 3 to 4 hours) are likely to affect many other cellular processes in addition to the cytoskeletal tension directly involved in migration. We believe that the accumulation of these effects will make interpretation of the results very difficult. For example, it has been shown that inhibition of ROCK by Y27 promotes healing of corneal endothelial lesions by affecting proliferation through cyclin D and p27 (DOI: 10.1167/iovs.13-12225), or by improving respiration, which would provide the energy necessary for migration (DOI: 10.1096/fj.202101442RR). Consistently, another study on HaCaT epidermal cells confirms that myosin phosphatase accelerates wound healing through proliferation (DOI: 10.1016/j.bbadis.2018.07.013). In contrast, in HUVEC cells, ROCK inhibition significantly impaired the proliferation and migration of vascular endothelial cells in vitro in a dose-dependent manner (DOI: 10.1097/ICO.0000000000000493).

      Furthermore, previous studies have highlighted that differential contractility at the subcellular level is important for collective migration (DOI: 10.1038/ncb2133, DOI: 10.1083/jcb.201706013), which is not possible to examine with global activation or inhibition of contractility. This prompts the development of more refined and specific measurement and disruption strategies to assess the respective impact of cytoskeletal tension on cell-cell and cell-matrix adhesion mechanisms. Our work, which uses biosensors to assess how this tension differentially affects cell-cell and cell-matrix adhesions, is a step in this direction. The localized spatio-temporal activation or inhibition of myosin subtypes or Rho GTPase regulators specific to these adhesion structures will likely answer these questions in the future, but we believe that the development and application of these approaches will require a substantial amount of work that goes beyond the scope of our study.

    1. The German car giant has since admitted cheating emissions tests in the US.

      This creates legal risks because the company intentionally manipulated emissions test results.

    2. up to 40 times above what is allowed in the US.

      This specific data point reveals a massive gap between marketing claims and actual performance. In advertising ethics, this constitutes deceptive communication, leading to severe legal risks and loss of brand integrity.

    3. the Environmental Protection Agency (EPA)

      Detection by a regulatory body like the EPA demonstrates the legal consequences of making unsubstantiated claims. It underscores the importance of third-party verification in ethical environmental marketing.

    4. engines that could detect when they were being tested

      This indicates symbolic communication where the company prioritized "looking green" during inspections over actual environmental accountability, a core issue in modern corporate ethics.

    5. "defeat device"

      The use of a "defeat device" highlights a major ethical failure in communication strategy. It shows that the sustainability messaging was not an operational improvement but a calculated effort to manipulate regulatory data and consumer trust

    1. According to the agreement, what should you do if you are treated disrespectfully by a patron, staff member, or fellow student employee?

      Change to multiple choice / true false question - the answer is too long and open to type in the exact answer they're looking for

    2. supervisors

      "coworkers and supervisors"

      at the RMC, we have a groupme group chat with all of the staff members, where we communicate with each other and help cover shift when anyone needs to step out or miss a shift

    3. Wear a Library Student Worker tag while working.  You'll appear more professional and it will set you apart from student patrons.

      Take this out - we don't have worker tags on the 3rd floor anymore

    4. Assist with Spaces and Equipment Needs

      Assist with Spaces and Equipment Needs

      • You will help visitors use Library equipment and spaces, including the G-Lab and DML computers, VR equipment, and circulating equipment.

      • You may open and close the RMC and the DML, complete opening and closing checklists, and ensure the Vault is secure.

      • You will contact full-time staff when Library infrastructure or equipment is malfunctioning.

      • You will know where to locate the emergency contacts list and who to call for help.

    5. Route Library Materials

      Manage Studio Spaces

      • Using Workflows and LibCAl, you will check out studio binders, 3D Printing passes, and open the studio doors.

      • You will provide assistance and expertise for the patrons working in the studios.

      • You will serve as a steward of library spaces and ensure that they are neat and tidy.

    6. Circulate Library Materials

      Circulate Digital Media Materials

      • Using Workflows and LibCal, you will accurately check in and out equipment including video cameras, audio recorders, and other creative materials.

      • You will accurately assist patrons to check in and out specialized cameras and lights and correctly account for all included accessories.

      • You will accurately scan materials, account for all accessories, and return them to the appropriate place on the shelf.

    7. Answer Questions and Provide Referrals.

      Answer Questions and Provide Referrals

      • As a Consultant, you will answer general questions about Library resources, services, and spaces.

      • You will find accurate answers using reliable sources like full-time library staff, the UVA Library website, and the Library catalog Virgo.

      • Assistants refer complex questions to full-time staff.

    8. Work at the Service and Information Desk

      Work at the RMC and DML Desks

      • As a Consultant, you will welcome, orient, and help patrons access Library resources, services, and studios.
    9. hone your own research skills.

      Maybe take this one out? Or perhaps just move it further down the list. We do some research, but it wouldn't be one of the top benefits of being an rmc worker

    1. Multidimensional Evaluation of the Quality of Hyperglycemia in Pregnancy Information on WeChat Platform in China: A Cross-Sectional Survey Yihong Zhang;  Yanting Chen;  Linlin Ma;  Bowen Li;  Jing Meng;  Xiaoni Hou;  Ningning Jin ABSTRACT Background: WeChat is a important source of health information for Chinese perinatal women. The quality of its health information and alignment with perinatal women’s needs influence health literacy and self-management in those with hyperglycemia in pregnancy. Objective: This study aimed to multidimensionally evaluate the quality and alignment with perinatal women’s needs of hyperglycemia in pregnancy health information on China’s WeChat platform, and identify its overall multidimensional quality patterns. Methods: The terms “妊娠期” (pregnancy) and “糖尿病” (diabetes), or “妊娠期” (pregnancy) and “高血糖” (hyperglycemia) were used to search in WeChat, the hottest articles on hyperglycemia in pregnancy were selected. DISCERN was used to evaluate the information’s content quality, Patient Education Materials Assessment Tool (PEMAT) was used to evaluate the information’s understandability and actionability. Specific deficiencies identified in low-scoring items are reported herein. Latent profile analysis (LPA) was used to determine the overall performance patterns of multidimensional quality. Frequency statistics and theme extraction from literature were used to determine the alignment with perinatal women’s information needs. ANOVA was used to analyze variations in DISCERN and PEMAT scores across various information sources. Spearman correlation analysis was used to analyze the relationships between DISCERN and PEMAT scores and different traits of information dissemination. Results: A total of 286 hottest articles on the WeChat platform were included, with a DISCERN score of 41.06 (SD 6.46), a PEMAT understandability score of 64.7% (SD 10.3%), an actionability score of 41.6% (SD 20.8%), and a 42.0% (SD 15.7%) alignment between article content and the information needs of perinatal women. The overall performance patterns of information quality falls into three categories: “professional priority-practical lag type” (19%), “usability priority-basic reliability type” (16.5%), and “multidimensional defects-unusable type” (64.5%). The total DISCERN score, scores for the credibility and comprehensiveness dimension scores of DISCERN, and PEMAT actionability scores differed across different sources (p<.05). Weak positive correlations were observed between daily reads counts and likes with comprehensiveness (ρ=0.19, P<.001; ρ=0.15, P=.01), understandability (ρ=0.19, P=.001; ρ=0.171, P=.004), and actionability (ρ=0.21, P<.001; ρ=0.18, P=.002). Additionally, daily retweets counts were weakly positively correlated with actionability (ρ= 0.21 and P<.001). Conclusions: The quality of health information on hyperglycemia in pregnancy on WeChat is generally average, characterized by low actionability, limited understandability, and limited alignment with information needs. Overall, the “multidimensional defects-unusable type” is predominant. It is recommended that authors of health information for users with hyperglycemia in pregnancy respond to the sophisticated information demands of perinatal women and comprehensively improve the multifaceted quality of information, thereby enhancing perinatal women’s health literacy and self-management capabilities.

      This manuscript was previously submitted to JMIR Medical Informatics and declined for publication. This preprint is an initial draft version, substantial revisions have been made in the newly submitted manuscript.

    2. This manuscript was previously submitted to JMIR Medical Informatics and declined for publication. This preprint is an initial draft version, substantial revisions have been made in the newly submitted manuscript.

    1. Trauma-informed approaches can promote the creation of systems that prioritize safety and empowerment to improve patientwell-being. These approaches are especially important in sexual and reproductive health care, where patients are often askedto disclose sensitive and personal information. This disclosure is particularly relevant in the context of endometriosis, acondition that affects 10% of reproductive-aged women and causes debilitating pelvic pain. Our team led a trauma-informedsocial media campaign to raise awareness and improve the understanding of endometriosis by sharing research findings froma photovoice study focusing on Asian women’s experiences of endometriosis during the COVID-19 pandemic in Canada(EndoPhoto Study). In this paper, we describe how we adapted and applied trauma-informed approaches to the developmentand implementation of the social media campaign. To do this, we followed five adapted trauma-informed principles: (1)support and collaboration, (2) trustworthiness and transparency, (3) safety, (4) empowerment and voice, and (5) culturaland gender sensitivity, and four steps: (1) frame the campaign, (2) create content and manage the campaign, (3) measurecampaign impact, and (4) conduct postcampaign reflections. We co-designed this campaign with patient partners having livedexperience of endometriosis to facilitate support and collaboration. Additionally, we shared details about the funders of thisstudy to increase trust and transparency, moderated comments and deidentified images to promote participant safety, chosesafer platforms to enhance empowerment and voice, avoided stereotypes, and shared authentic experiences of Asian womenwith endometriosis to support cultural and gender sensitivity. The campaign launched on Instagram and Pinterest in March2025 to coincide with Endometriosis Awareness Month. The social media campaign received 8,540,528 total impressions overthe course of the month and had engagement rates of 6.23% and 1.4% on Instagram and Pinterest, respectively

      This article outlines a tutorial on designing a trauma-informed social media campaign (on Instagram and Pinterest) to talk about reproductive health findings (specifically endometriosis) among Asian women. It highlights how women's specific health pain is historically minimized or dismissed by public discourses and healthcare systems. To fix this representational gap, the project centered on authentic visual narratives of minority women to ensure digital empowerment and historical sensitivity, while navigating algorithmic biases on Meta platforms that target and suppress women's sexual and reproductive health contents.

    Annotators

    1. Sotorasib

      I like that we show whether a drug is breakthrough therapy designation, orphan or fast track. However this is information is important only if the drug is not approved. If it is approved from fda then there is no need to show them. Thus they should be showed only in the period that the drug is waiting for approval. If the approval fails and the drug is discontinued, it might be better to show this info under a different tab, like 'Regulatory History'.

    2. Indication

      Showing indication for a drug that has been newly approved is possible, but as the label expands it becomes very difficult as there might be more than 10 indications. Thus probably shouldn't be in the main page as an info.

    3. Indications

      What we call now and indication is an overall description of the disease and the population for which the drug can be used. Thus indication as a definition is only valid for approved drugs. Thus in our context there can't be any failed or investigational Indication. We currently show the diseases where the drug is being studied under the Trials tab. And we have a separate tab for indications of approved drugs, please see 'Approvals and Regulatory' tab at https://staging.bioloupe.com/drug/10333

    4. Ownership

      We dont want to show who has owned the drug during the history, just the current organization and also its partners (if there are any). This tab should not exist and also the current organization should show in the main page. It is a very crucial info to be shown under a tab.

    5. Targets

      For we show only the abbreviation of the target and its mode of action thus KRAS G12C | inhibitor in this case. We dont show Organism Evidence or Affinity right now, thus these three fields should be deleted. A drug might have more than 1 target. Also target of the drug and its technology (in this case small molecule) is the first thing the user is interested in a drug, thus it should be shown in the main page and not in a separate tab.

    6. Chemistry

      We do not have the info for most of the fields in Chemistry. We can get them but they are not important. We have atc code and chembl but they are for internal use only and not for display. Especially codes from other databases like drugbank should not be there as we are not allowed to use it for commercial reasons. Thus Chemistry tab should be removed.

  3. pressbooks.library.torontomu.ca pressbooks.library.torontomu.ca
    1. Every morning the world flung itself over and exposed the town to the sun. So Janie had another day. And every day had a store in it, except Sundays. The store itself was a pleasant place if only she didn’t have to sell things. When the people sat around on the porch and passed around the pictures of their thoughts for the others to look at and see, it was nice. The fact that the thought pictures were always crayon enlargements of life made it even nicer to listen to

      It’s talking about how boring Janie’s day was

  4. pressbooks.library.torontomu.ca pressbooks.library.torontomu.ca
    1. On the train the next day, Joe didn’t make many speeches with rhymes to her, but he bought her the best things the butcher had, like apples and a glass lantern full of candies. Mostly he talked about plans for the town when he got there. They were bound to need somebody like him. Janie took a lot of looks at him and she was proud of what she saw. Kind of portly like rich white folks. Strange trains, and people and places didn’t scare him neither. Where they got off the train at Maitland he found a buggy to carry them over to the colored town

      What they saw didn’t exceed their expectations

  5. pressbooks.library.torontomu.ca pressbooks.library.torontomu.ca
  6. pressbooks.library.torontomu.ca pressbooks.library.torontomu.ca
    1. It was like a drug. In a way it was good because it reconciled her to things. She got so she received all things with the stolidness of the earth which soaks up urine and perfume with the same indifference.

      Comparison between drugs and tending the store.

    1. eLife Assessment

      This important study fills a major geographic and temporal gap in understanding Paleocene mammal evolution in Asia and proposes an intriguing "brawn before bite" hypothesis grounded in diverse analytical approaches. The work rests on a solid methodological base. Some limitations remain, including uncertainty introduced by pooling different tooth positions, limited dietary interpretation, and the predominantly herbivorous taxonomic focus, which narrows the ecological scope of the conclusions. However, the manuscript provides a substantially strengthened and well-supported contribution, while appropriately inviting further work to clarify dietary trends, broader ecological context, and links between dental trait evolution and environmental change.

    2. Reviewer #2 (Public review):

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

      Summary:

      This study uses dental traits of a large sample of Chinese mammals to tract evolutionary patterns through the Paleocene. It presents and argues for a 'brawn before bite' hypothesis -- mammals increased in body size disparity before evolving more specialized or adapted dentitions. The study makes use of an impressive array of analyses, including dental topographic, finite element, and integration analyses, which help to provide a unique insight into mammalian evolutionary patterns.

      Strengths:

      This paper helps to fill in a major gap in our knowledge of Paleocene mammal patterns in Asia, which is especially important because of the diversification of placentals at that time. The total sample of teeth is impressive and required considerable effort for scanning and analyzing. And there is a wealth of results for DTA, FEA, and integration analyses. Further, some of the results are especially interesting, such as the novel 'brawn before bite' hypothesis and the possible link between shifts in dental traits and arid environments in the Late Paleocene. Overall, I enjoyed reading the paper and I think the results will be of interest to a broad audience.

      Weaknesses:

      For the original draft of the manuscript, I had four major concerns with the study, especially related to the sampling, diet, and evidence for the 'brawn before bite' hypothesis. I still believe that the original issues that I raised may be weaknesses of the study. For example, there is still limited discussion on diets (even though the dental topographic analyses used in the study are designed for inferring diets). And I find the results a little challenging to interpret because teeth of multiple positions are included in the same samples, which seems problematic. That said, the authors have addressed each of my previous concerns and have made major revisions, including running new analyses, and thus I support the paper.

    3. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #2 (Public review):

      Summary:

      This study uses dental traits of a large sample of Chinese mammals to tract evolutionary patterns through the Paleocene. It presents and argues for a 'brawn before bite' hypothesis -- mammals increased in body size disparity before evolving more specialized or adapted dentitions. The study makes use of an impressive array of analyses, including dental topographic, finite element, and integration analyses, which help to provide a unique insight into mammalian evolutionary patterns.

      Strengths:

      This paper helps to fill in a major gap in our knowledge of Paleocene mammal patterns in Asia, which is especially important because of the diversification of placentals at that time. The total sample of teeth is impressive and required considerable effort for scanning and analyzing. And there is a wealth of results for DTA, FEA, and integration analyses. Further, some of the results are especially interesting, such as the novel 'brawn before bite' hypothesis and the possible link between shifts in dental traits and arid environments in the Late Paleocene. Overall, I enjoyed reading the paper and I think the results will be of interest to a broad audience.

      Weaknesses:

      For the original draft of the manuscript, I had four major concerns with the study, especially related to the sampling, diet, and evidence for the 'brawn before bite' hypothesis. I still believe that the original issues that I raised may be weaknesses of the study. For example, there is still limited discussion on diets (even though the dental topographic analyses used in the study are designed for inferring diets). And I find the results a little challenging to interpret because teeth of multiple positions are included in the same samples, which seems problematic. That said, the authors have addressed each of my previous concerns and have made major revisions, including running new analyses, and thus I support the paper.

      This revised submission includes only minor changes aimed at clarifying the main text.

      Reviewer #2 (Recommendations for the authors):

      I appreciate that the authors made many improvements to their study based on reviewers' comments. I don't have any remaining major issues with the paper, but I do have several minor comments.

      Thank you for taking the time to provide additional helpful feedback on our study. We have made minor revisions to the manuscript based on your suggestions. Please see our point-by-point response below.

      Lines 48-50. I reiterate my suggestion in my previous review to explicitly state which clade is being discussed, which is important because several major mammal groups beyond placentals (metatherians, multituberculates, dryolestoids, gondwanatherians) survived the K-Pg and had very different diversification patterns. You mention "mammal taxonomic diversity" but in the next sentence say "This initial placental mammals diversification ..." and later mention "stem placental/eutherian lineages." To stay consistent, you might replace "mammal" (L48) and "placental mammals" (L50) with "eutherian(s)" (usually defined as stem + crown placentals). If you follow this suggestion, then elsewhere in the paper I recommend replacing "mammals" with "eutherians" for consistency.

      Thank you for this suggestion. We modified the use of “mammals” throughout the text to general reference to the group only; specific mentions of the dataset analyzed are revised to “eutherians.”

      Lines 75-83. I respect the authors' hesitancy to reconstruct specific diets for the fossil taxa (L75-83), especially considering that dental topographic analyses (DTAs) often struggle to differentiate diets in extant taxa (e.g., Pineda-Munoz et al. 2016 Methods Ecol Evol). I still think that the authors might be able to interpret dietary trends from their results (e.g., an increase in average OPCR values indicating a shift toward more herbivorous diets) - I think discussing dietary trends would be an interesting discussion topic later in the paper. That said, I also recognize that different DTA results seem to show conflicting dietary trends (based on my limited knowledge of those metrics) so maybe that complicates things too much.

      We concur with Reviewer 2 that dietary inferences of DTA data are premature, especially given the ongoing controversies of its use in studies of extant mammal teeth. We kept our current scope of discussion unchanged.

      Lines 75-77. "early mammals ... are beyond the reach of conventional phylogenetic bracketing approaches to dietary reconstruction." But your fossils (eutherians) are certainly within 'phylogenetic brackets' of modern clades (therians, i.e. Eutheria + Metatheria). Maybe you're alluding to the fossils being stem lineages of extant subgroups like Ungulata, which means we can't bracket them specifically within those eutherian subgroups? So, I recommend revising or expanding your statement for clarity. Also, the considerable phylogenetic uncertainty for Paleocene groups (e.g., Halliday et al. 2015) complicates this issue, which you could mention.

      We modified the sentence to now say “Additional complications with ecomorphological analysis of these stem eutherians include the uncertainty in their dietary ecology, having diverged prior to the crown radiation, and uncertainty in phylogenetic positions of Paleocene taxa [7]; thus, they are beyond the reach of conventional phylogenetic bracketing approaches to dietary reconstruction.”

      Line 84. "We investigated dental topography-performance shifts ...". You haven't introduced dental topography or even mentioned teeth yet, and "performance shifts" is vague. So, this phrase might confuse readers. Maybe you can just erase it and start the sentence with "We investigated the timing of ecomorphological ..."?

      We made the recommended revision.

      Lines 104-105 (and elsewhere). "Dental traits paralleled Paleocene global and regional environmental conditions" and "We found that dental topographic trait variability in Paleocene mammals in south China tracked global and regional climatic changes". These conclusions seem a little too assertive to me. Your sample is grouped into 3 rough time bins (of somewhat uncertain ages) and is from a relatively small geographic range - that seems like very limited information for inferring links between dental patterns and climatic changes, especially global patterns. I think it's worth HYPOTHESIZING that dental traits are linked to environmental/climatic changes (with results like those in Figure 2A & B as evidence to support that hypothesis), but I wouldn't make that claim with any confidence. So, I recommend that you temper your relevant conclusion statements. For example, for Line 105, you could replace "We found ..." with "We posit ..." (L105). I would make similar changes to similar statements throughout the paper (e.g., L243).

      Thank you for this suggestion to temper our phrasing. We edited throughout the text to make our interpretations less assertive.

      Figure 1 (and your response to reviewers). Why was the timescale changed to 65.5 Ma for the K-Pg boundary? The K-Pg is 66 Ma (not 65.5), which is the age you mention in the text (e.g. Pg 3 L39) and is well established in the literature - see recent papers from the Paul Renne lab for a more exact age.

      We revised the figure to have the K-Pg at 66 Ma.

  7. pressbooks.library.torontomu.ca pressbooks.library.torontomu.ca
    1. Janie and Logan got married in Nanny’s parlor of a Saturday evening with three cakes and big platters of fried rabbit and chicken.

      Signifies the first chapter of Janie’s adult life.

    1. eLife Assessment

      This valuable paper describes the regulation of the association of meiotic chromosome axis proteins on chromosome ends with sub-telomeric elements in budding yeast. The genome-wide analyses of binding of chromosome components as well as chromatin regulators, complemented with the mapping of meiotic DNA double-strand breaks on chromosome ends, provided solid evidence to support the authors' conclusion. The results in the paper are of interest to researchers in meiotic recombination and the structure of genomes and chromosomes.

    2. Reviewer #1 (Public review):

      The revised manuscript includes several useful additions, and I appreciate the efforts to clarify parts of the analysis. The dataset remains valuable. However, several key issues raised previously are not yet fully resolved and continue to limit the clarity of the main conclusions.

      (1) I appreciate that the authors guide the reader to the relevant regions in the analysis of chromosome fusions (Fig. 2b). However, these subtelomeric regions are not clearly visualized, making it difficult to compare fused and unfused profiles, even though the conclusions rely largely on visual inspection of them. A more direct comparison between fused and unfused ends, together with quantitative summaries (e.g., binned Red1 enrichment and comparisons with internal regions), would make this experiment more convincing.

      (2) The SK1/S288c comparison (Fig. 2c) is an excellent approach, but is currently presented just as profiles, which again requires substantial effort from the reader to extract the relevant information. A systematic analysis across all informative chromosome ends-for example, comparing Red1 levels in syntenic regions using binned log2 fold-change-would more directly test the proposed in cis effect (L168) and clarify the contribution and range of Y'-associated effects. Other factors (e.g. distance from chromosome ends) could also be assessed within this framework.

      Related to this, it is unclear if Y' elements themselves exhibit lower Red1 binding than the genome average. Providing the mean Red1 signal per Y' element would clarify this point and may also aid interpretation of the relationship between coding density and Red1 enrichment.

      (3) The Dot1-Sir3 section is now simpler. However, I still find it difficult to follow the underlying rationale. In particular, it is unclear why a Dot1 function dependent on H3K79 methylation is introduced, given that the data in the previous section suggest H3K79 methylation is dispensable for subtelomeric Red1 depletion. A clearer statement of the authors' working model would be helpful.

    3. Reviewer #2 (Public review):

      Summary:

      In this manuscript, Raghavan and his colleagues sought to identify cis-acting elements and/or protein factors that limit meiotic crossover at chromosome ends. This limitation is important for avoiding chromosome rearrangements and preventing chromosome mis-segregation.

      By comparing protein axis recruitment in SK1 and S288C background, which differ in their number and distribution of Y' elements, the authors show that Y' element have a limited impact on axis protein enrichment. Genetic analyses coupled with ChIP experiments revealed that the differential binding of the Red1 protein in subtelomeric regions requires the methyltransferase Dot1. Interestingly, the lack of Red1 depletion in subtelomeric regions in this mutant does not impact DSB formation. Another surprising finding is that deleting DOT1 has no effect on Red1 loading in the absence of the silencing factor Sir3. Unlike Dot1, Sir3 directly impacts DSB formation, probably by limiting promoter access to Spo11. As now clearly stated in the abstract and the discussion, this explains only a small part of the low levels of DSBs forming in subtelomeric regions and the main mechanisms suppressing crossover close to the ends of chromosomes remain to be deciphered.

      Strengths:

      This work provides intriguing observations, such as the impact of Dot1 and Sir3 on Red1 loading and the uncoupling of Red1 loading and DSB induction in subtelomeric regions.

      The separation of axis protein deposition and DSB induction observed in the absence of Dot1 is interesting because it rules out the possibility that the binding pattern of these proteins is sufficient to explain the low level of DSB in subtelomeric regions.

      The demonstration that Sir3 suppresses the induction of DSBs by limiting the openness of promoters in subtelomeric regions is convincing.

      Weaknesses:

      The section examining the impact of Dot1 and Sir3 remains complex, which is partly inherent to the intricate relationship between Dot1 and Sir3. However, the authors conclude that Dot1 acts independently of its catalytic activity based on the phenotype of the H3K79R mutant phenotype. Although this is possible it is not fully demonstrated as the H3K79R mutant may exhibit its own phenotype independently of Dot1. Unless the authors test the impact of the catalytic dead mutant Dot1-G401R on axis protein enrichment at subtelomeres they cannot claim that Dot1 act independently of its catalytic activity.

      Sir3's impact on DSB induction is compelling, yet it only accounts for a small proportion of DSB depletion in subtelomeric regions. Thus, the main mechanisms suppressing crossover close to the ends of chromosomes remain to be deciphered.

    4. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Meiotic recombination at chromosome ends can be deleterious, and its initiation-the programmed formation of DSBs-has long been known to be suppressed. However, the underlying mechanisms of this suppression remained unclear. A bottleneck has been the repetitive sequences embedded within chromosome ends, which make them challenging to analyze using genomic approaches. The authors addressed this issue by developing a new computational pipeline that reliably maps ChIP-seq reads and other genomic data, enabling exploration of previously inaccessible yet biologically important regions of the genome.

      In budding yeast, chromosome ends (~20 kb) show depletion of axis proteins (Red1 and Hop1) important for recruiting DSB-forming proteins. Using their newly developed pipeline, the authors reanalyzed previously published datasets and data generated in this study, revealing heretofore unseen details at chromosome ends. While axis proteins are depleted at chromosome ends, the meiotic cohesin component Rec8 is not. Y' elements play a crucial role in this suppression. The suppression does not depend on the physical chromosome ends but on cis-acting elements. Dot1 suppresses Red1 recruitment at chromosome ends but promotes it in interior regions. Sir complex renders subtelomeric chromatin inaccessible to the DSB-forming machinery.

      The high-quality data and extensive analyses provide important insights into the mechanisms that suppress meiotic DSB formation at chromosome ends. To fully realise this value, several aspects of data presentation and interpretation should be clarified to ensure that the conclusions are stated with appropriate precision and that remaining future issues are clearly articulated.

      (1) To assess the chromosome fusion effects on overall subtelomeric suppression, authors should guide how to look at the data presented in Figure 2b-c. Based on the authors' definition of the terminal 20 kb as the suppressed region, SK1 chrIV-R and S288c chrI-L would be affected by the chromosome fusion, if any. In addition, I find it somewhat challenging to draw clear conclusions from inspecting profiles to compare subtelomeric and internal regions. Perhaps, applying a quantitative approach - such as a bootstrap-based analysis similar to those presented earlier-would be easier to interpret.

      The reviewer is correct that we could not simply fuse two ends but had to create translocations that also removed variable amounts of subtelomeric sequence. Targeted translocations require unique sequences, and thus the extent to which telomeric sequences were deleted varied based on the availability of such sequences. As noted by the reviewer this necessarily limits the conclusions that can be drawn. We have expanded the description of this experiment and also explicitly state the limitations of this assay. To improve clarity, we have also included a schematic to better highlight which chromosomal sequences were removed.

      To further probe our finding that subtelomeric axis protein enrichment may largely be encoded in cis, we now compared axis protein enrichment between S288c and SK1, as suggested by reviewer 2. For this analysis, we took advantage of a dataset we had produced previously that measures Red1 enrichment in SK1/S288c hybrid strains, which provide a powerful internally controlled setup that eliminates effects caused by differential timing and synchrony between samples. As now shown in Supplementary Fig. 5, SK1 and S288c differ substantially in their subtelomeric architecture at many ends, including extensive differences in the number and distribution of Y’ elements. Importantly, axis protein distribution was very consistent between SK1 and S288c when correcting for the differences in length of individual chromosome ends, supporting the conclusion that axis protein enrichment levels are primarily encoded in cis. This analysis is now shown in Fig. 2c. These data also indicate that the presence of a Y’ element does not affect axis protein levels beyond displacing the axis-recruiting sequences further into the chromosome interior.

      (2) The relationship between coding density and Red1 signal needs clarification. An important conclusion from Figure 3 is that the subtelomeric depletion of Red1 primarily reflects suppression of the Rec8-dependent recruitment pathway, whereas Rec8-independent recruitment appears similar between ends and internal regions. Based on the authors' previous papers (referencess 13, 16), I thought coding (or nucleosome) density primarily influences the Rec8-independent pathway. However, the correlations presented in Figure 2d-e (also implied in Figure 3a) appear opposite to my expectation. Specifically, differences in axis protein binding between chromosome ends and internal regions (or within chromosome ends), where the Rec8-dependent pathway dominates, correlate with coding density. In contrast, no such correlation is evident in rec8Δ cells, where only the Rec8-independent pathway is active and end-specific depletion is absent. One possibility is that masking coding regions within Y' elements influences the correlation analysis. Additional analysis and a clearer explanation would be highly appreciated.

      Thank you for pointing this out. We now also included Y’ elements in the analysis in Fig 2d. Including the Y’ elements yielded an increase in average coding density near the very ends of the chromosomes. This increase matches the higher level of axis protein binding seen in rec8 mutants in Fig. 3a and is consistent with the previously noted link between coding density and axis protein deposition. We now provide further description in the text and the figure legends.

      We do not have an explanation for why there is no correlation with coding density in the EARs but assume that this reflects the unique regulation of this region (as also implied by Supplementary Fig. 4d). At present, the signals that establish the EARs remain unknown although our data indicate that the Hop1-CBR as well as Dot1 are important for axis protein enrichment in the EARs.

      (3) The Dot1-Sir3 section staring from L266 should be clarified. I found this section particularly difficult to follow. It begins by stating that dot1∆ leads to Sir complex spreading, but then moves directly to an analysis of Red1 ChIP in sir3∆ without clearly articulating the underlying hypothesis. I wonder if this analysis is intended to explain the differences observed between dot1∆ and H3K79R mutants in the previous section. I also did not get the concluding statement - Dot1 counteracts Sir3 activity. As sir3Δ alone does not affect subtelomeric suppression, it is unclear what Dot1 counteracts. Perhaps, explicitly stating the authors' working model at the outset of this section would greatly clarify the rationale, results, and conclusions.

      Thank you for this comment. We reworked the introduction to this paragraph to be more focused on Sir3 rather than Dot1. We hope that this introduction is less confusing and more in line with the data presented in this paragraph. We also expanded the conclusion to suggest the alternative possibility that the Sir complex only becomes a regulator of axis proteins in the absence of Dot1.

      Reviewer #2 (Public review):

      Summary:

      In this manuscript, Raghavan and his colleagues sought to identify cis-acting elements and/or protein factors that limit meiotic crossover at chromosome ends. This is important for avoiding chromosome rearrangements and preventing chromosome missegregation.

      By reanalyzing published ChIP datasets, the researchers identified a correlation between low levels of protein axis binding - which are known to modulate homologous recombination - and the presence of cis-acting elements such as the subtelomeric element Y' and low gene density. Genetic analyses coupled with ChIP experiments revealed that the differential binding of the Red1 protein in subtelomeric regions requires the methyltransferase Dot1. Interestingly, Red1 depletion in subtelomeric regions does not impact DSB formation. Another surprising finding is that deleting DOT1 has no effect on Red1 loading in the absence of the silencing factor Sir3. Unlike Dot1, Sir3 directly impacts DSB formation, probably by limiting promoter access to Spo11. However, this explains only a small part of the low levels of DSBs forming in subtelomeric regions.

      Strengths:

      (1) This work provides intriguing observations, such as the impact of Dot1 and Sir3 on Red1 loading and the uncoupling of Red1 loading and DSB induction in subtelomeric regions.

      (2) The separation of axis protein deposition and DSB induction observed in the absence of Dot1 is interesting because it rules out the possibility that the binding pattern of these proteins is sufficient to explain the low level of DSB in subtelomeric regions.

      (3) The demonstration that Sir3 suppresses the induction of DSBs by limiting the openness of promoters in subtelomeric regions is convincing.

      Weaknesses:

      (1) The impact of the cis-encoded signal is not demonstrated. Y' containing subtelomeres behave differently from X-only, but this is only correlative. No compelling manipulation has been performed to test the impact of these elements on protein axis recruitment or DSB formation.

      Thank you for this comment. Our data indeed appeared contradictory because XY’ ends showed overall lower axis protein enrichment, yet our analysis of chromosome fusions, which also eliminated Y’ elements at some the fused ends, provided no evidence for an effect of Y’ elements at those ends. As also noted in the response to reviewer 1, we now compared axis protein enrichment between S288c and SK1, which differ substantially in their number and distribution of Y’ elements (Supplementary Fig. 5). We found that axis protein distribution and enrichment was very consistent between SK1 and S288c when correcting for the displacement caused by the presence of Y' elements and other subtelomeric sequences (now shown in Fig. 2d). These data support the conclusion that axis protein enrichment levels are primarily encoded in cis and indicate that the presence of Y’ elements does not affect axis protein levels beyond displacing the axis-recruiting sequences further into the chromosome interior (giving rise to the apparently lower axis protein enrichment on XY’ ends).

      (2) The mechanism by which Dot1 and Sir3 impact Red1 loading is missing.

      Although we do not yet understand the precise molecular details of these effects, we nevertheless believe we have obtained several important insights into this mechanism. First, our data indicate that the suppressive effect of the ends primarily impacts the Rec8-dependent loading of Red1, whereas loading via the Hop1-CBR is largely unaffected. The effect of Dot1 thus likely occurs via the Rec8-Red1 interaction. Second, the increase in Red1 recruitment is fully rescued by deletion of Sir3, suggesting that Sir3 becomes a promoter of axis protein recruitment in the absence of Dot1. These dependencies are now outlined in the model in Fig. 9. We would also like to note that the Sir complex was previously shown to impact cohesin in mitotic cells. Thus, a connection between the Sir complex and cohesin is not without precedent.

      (3) Sir3's impact on DSB induction is compelling, yet it only accounts for a small proportion of DSB depletion in subtelomeric regions. Thus, the main mechanisms suppressing crossover close to the ends of chromosomes remain to be deciphered.

      Thank you, we absolutely agree. We had discussed this point in the discussion but now also explicitly state this point in the abstract and expanded the discussion of these findings in the results and discussion.

      Reviewer #3 (Public review):

      Summary:

      The paper by Raghavan et. al. describes pathways that suppress the formation of meiotic DNA double-strand breaks (DSBs) for interhomolog recombination at the end of chromosomes. Previously, the authors' group showed that meiotic DSB formation is suppressed in a ~20kb region of the telomeres in S. cerevisiae by suppressing the binding of meiosis-specific axis proteins such as Red1 and Hop1. In this study, by precise genome-wide analysis of binding sites of axis proteins, the authors showed that the binding of Red1 and Hop1 to sub-telomeric regions with X and Y' elements is dependent on Rec8 (cohesin) and/or Hop1's chromatin-binding region (CBR). Furthermore, Dot1 functions in a histone H3K79 trimethylation-independent manner, and the silencing proteins Sir2/3 also regulate the binding of Red1 and Hop1 and also the distribution of DSBs in sub-telomeres.

      Strengths:

      The experiments were conducted with high quality and included nice bioinformatic analyses, and the results were mostly convincing. The text is easy to read.

      Weaknesses:

      The paper did not provide any new mechanistic insights into how DSB formation is suppressed at sub-telomeres.

      We respectfully disagree with this assessment. We show that the Sir complex suppresses DSB formation at a number of cryptic hotspots in the X elements and the adjacent subtelomeric sequences by causing chromatin compaction. The role of the Sir complex in transcriptional silencing, chromatin accessibility, and DSB formation had not previously been analyzed in the meiotic subtelomeres. That being said, Sir-dependent suppression is clearly not the only mechanism that suppresses DSBs in the subtelomeres, as we only observed DSB formation at a small number of hotspots. This was in and of itself a surprise, in particular given the large scale effect on chromatin compaction. We made an effort to more strongly emphasize the fact that additional layers of regulation must exist in the abstract and in the discussion.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Evidence for cis-acting suppression by Y' elements requires further support. The authors propose that Y' elements act in cis to suppress axis protein association at chromosome ends. While this is an attractive model, the current analyses do not yet provide sufficient support for it.

      Thank you for this comment. Our data indeed appeared contradictory, because XY’ ends showed overall lower axis protein enrichment, yet our analysis of chromosome fusions, which also eliminated Y’ elements at some the fused ends provided no evidence for an effect of Y’ elements at those ends. As noted above, we now compared axis protein enrichment between S288c and SK1, which differ substantially in their number and distribution of Y’ elements (Supplementary Fig. 5). We found that axis protein distribution and enrichment was very consistent between SK1 and S288c when correcting for the displacement caused by the presence of Y' elements and other subtelomeric sequences. These data support the conclusion that axis protein enrichment levels are primarily encoded in cis and indicate that the presence of Y’ elements does not affect axis protein levels beyond displacing the axis-recruiting sequences further into the chromosome interior (giving rise to the apparently lower axis protein enrichment on XY’ ends).

      (1a) In Figure S4c, the authors masked Y' elements to rule out the possibility that reduced binding within Y' elements themselves accounts for the overall underrepresentation in subtelomeric regions. However, since the authors propose that Y' elements suppress axis protein binding in surrounding regions in cis, it is appropriate to perform this analysis specifically on chromosome ends containing XY'.

      Thank you for this suggestion. We agree that this would specifically affect the XY’ ends. However, given that we did not see a change even with all the ends, we do not expect a change with just the XY’ ends.

      (1b) In Figure 2b-c, the authors conclude that removal of Y' elements by chromosome fusion does not reveal a long-range suppressive effect. However, the spatial extent of Y'-mediated suppression is not defined, making it unclear whether this experiment can test the proposed model. Perhaps plotting the averaged axis protein profile as a function of distance from Y' elements could help define the effective range of suppression and clarify whether the fusion experiment is informative in this context.

      Thank you. As noted above we now compared SK1 and S288c ends, which provided further evidence that Y’ elements do not affect axis protein enrichment beyond displacing binding sites further into the chromosome interior. In addition, we substantially expanded the description of the chromosome fusion experiment to more clearly outline the setup and the limitations of this experiment.

      (2) L402: "one of the first pieces of direct evidence that nucleosomes block meiotic DSB formation in vivo" sounds overstated, considering past publications (e.g., ref 45 and S. pombe ade6-M26 papers).

      We toned this down and added the references.

      (3) Figure 2e and other scatter plots: Correlation coefficients are reported without p-values. If the authors prefer to use confidence intervals from linear regression instead, they should justify this approach.

      We added p-values to all scatter plots.

      (4) Figure 7f. Explain blue dots.

      We apologize for this oversight (also applies to Supplementary Fig. 10). The blue dots are measurements within 5 kb of an X element. The red dots are the rest of the genome. We now included a legend in the panel to clarify this notation.

      (5) Figure 8d. To assess whether the conclusion can be generalized, the authors could plot the MNase and TrAEL-seq signal fold changes (sir3Δ/SIR3) for hotspots within 5 kb of X elements.

      We attempted various analyses in this direction. However, the range of the MNase-seq effect in sir3 mutants is much greater than the effect on DSBs, making it difficult to make any correlative statements. There are clearly additional layers of DSB suppression in the telomeric regions, and loss/gain of nucleosomes is not sufficient to switch hotspots on/off at most hotspots. We now included a statement to this end in the abstract and also further discuss this notion in the discussion.

      (6) Figure S1c. The apparent difference in X-element distribution may be influenced by bin size. This could be tested by repeating the analysis using smaller bins, comparable in size to the X elements, for all regions.

      We thank the reviewer for this thoughtful suggestion. To address this concern, we repeated the analysis using smaller bins comparable in size to X elements (450 bp) across all region types. Specifically, X elements were analyzed per annotated element, while Y′ elements, subtelomeric 20 kb regions, and internal regions were subdivided into fixed 450 bp windows, and mean input coverage was calculated for each window using the same width-weighted approach.

      This reanalysis did not materially alter the overall distribution patterns observed in Figure S1c. We observed only minor shifts in absolute values, which are expected when changing bin granularity.

      Any residual differences likely reflect underlying copy number of X elements at chromosome ends. Importantly, all ChIP signals in the manuscript are normalized to their corresponding input (ChIP/Input), which mitigates potential biases arising from local copy number variation.

      (7) Figure S2. X elements are difficult to find (e.g., chrVII-L).

      We now included arrowheads at locations with full-length X elements. Partial X elements are marked with stars.

      (8) Figure S7. Please indicate the endpoints of spreading.

      As apparent in this figure and also indicated in the quantification in Supplementary Fig. 9a, spreading of the Sir complex is in most cases quite limited. The example in Supplementary Fig. 9b is one of the largest spreads we observed. The scale of the spreading is hard to meaningfully visualize in Supplementary Fig. 8 given the relatively large genomic distances shown in these profiles. We therefore refer the reader to the analyses shown in Supplementary Fig. 9a, which shows chromosome-resolved extent of spreading.

      Reviewer #2 (Recommendations for the authors):

      To go beyond the correlation between the presence of Y' elements and low levels of protein axis binding, subtelomeres could be easily truncated. Analyzing strains with different distributions of Y' elements would also be informative. The correlative analysis could also be expanded to compare how far the influence of Y' elements goes and whether the number of Y' impacts the extent of protein axis depletion.

      We respectfully disagree with the assertion that subtelomeres could easily be truncated. The high repetitiveness of these sequences makes targeted manipulations of the extreme ends where the Y’ elements are located essentially impossible and is the main reasons for the limitations associated with the analysis of the chromosome fusions as outlined in the response to reviewer 1.

      However, we would like to thank the reviewer for their suggestion to analyze different strain backgrounds. We now compared axis protein enrichment between S288c and SK1. For this analysis, we took advantage of a dataset we had produced previously that measures Red1 enrichment in SK1/S288c hybrid strains, which provide a powerful internally controlled setup that eliminates effects caused by differential timing and synchrony between samples. As now shown in Supplementary Fig. 5, SK1 and S288c differ substantially in their subtelomeric architecture at many ends, including extensive differences in the number and distribution of Y’ elements. Importantly, axis protein distribution was very consistent between SK1 and S288c when correcting for the differences in length of individual chromosome ends, supporting the conclusion that axis protein enrichment levels are primarily encoded in cis. This analysis is now shown in Fig. 2c. These data also indicate that the presence of Y’ elements does not affect axis protein levels beyond displacing the axis-recruiting sequences further into the chromosome interior.

      Given the separation between protein axis loading and DSB induction, it would be interesting to test whether the presence of Y' elements influences the frequency and position of DSB induction.

      We agree that this experiment would be very interesting. However, given the experimental challenges associated with targeted manipulation of Y’ elements as outlined above, we believe that this experiment lies outside the scope of this study. Our observations that Y’ elements do not grossly influence axis protein enrichment in their vicinity may also make an effect on DSB formation less likely.

      The effect of Dot1 on Red1 loading is intriguing because it is at least partially independent of its main known target H3K79, yet fully dependent on Sir3. However, this effect extends far beyond Sir3 binding as detected by ChIP. This is surprising because Dot1 has a limited effect on Sir3 binding as detected by ChIP, and SIR3 deletion has no impact on Red1 binding. However, Dot1 was shown to limit Sir3 spreading to 20 kb on average when overexpressed (Katan-Khaykovich and Struhl 2005; Hocher et al, 2018). It would be interesting to test whether the regions affected by DOT1 deletion coincide with the zone covered by Sir3 upon overexpression (Extended Silent Domains: ESDs, Hocher et al., 2018).

      We agree that this would be an interesting analysis. Unfortunately, the available data on the extended silent domains were not obtained in SK1 and, as noted above, the chromosome end structure differs substantially between the strains, preventing direct comparisons without repeating all the relevant analyses in S288c. In addition, the available data was collected in vegetative cells, although this may be less of an issue given that our analyses show similar spreading in vegetative and meiotic cells. However, short of repeating SIR3 overexpression in meiosis (which also would require a different overexpression regimen as galactose interferes with meiosis), we are not in a position to do this analysis.

      As mentioned in the manuscript, the interplay between the Sir complex and Dot1 has been shown to affect checkpoint regulation during meiotic recombination. However, a discussion on how this relates to the observations reported here is missing.

      Thank you. We included a discussion of this role and its relation to our observations.

      Also, it is unclear why the authors did not investigate the impact of Dot1 and Sir3 impact on the binding of Hop1 rather than Red1, given that Hop1 is currently « the most upstream regulator of recombination known to be depleted about 20 kb from chromosome ends. »

      We changed this statement in the introduction to avoid confusion and also included a model figure that specifically highlights the Rec8-dependent recruitment as a regulatory target.

      Our data show that most of the telomere-proximal effects seem to act through the Rec8-dependent recruitment pathway for which Red1 is the most upstream regulator known. So, although the most upstream factor known before this study was Hop1, our data now identify the interaction between Red1 and Rec8 as the most upstream regulatory node.

      Sir3's impact on DSB induction is compelling, yet it only accounts for a small proportion of DSB depletion in subtelomeric regions. Thus, the main mechanisms suppressing crossover close to the ends of chromosomes remain to be deciphered. This should be acknowledged and discussed.

      In addition to the explicit statement of this conclusion in the results, we now added another statement in the abstract and also expanded the discussion of the fact that there are clearly additional levels of regulation that remain to be discovered.

      Reviewer #3 (Recommendations for the authors):

      Major points:

      It would be nice to show a schematic summary of the authors' main conclusion.

      Thank you, we now included a model schematic as Fig. 9.

      Minor points:

      (1) Supplemental Figure 2: A small box for the X element is marked with the same color as the Y' element, and so it is very hard to find the X element. Please use the clearer color, and it would be nice to show the chromosome ends without the X element (lines 129-130).

      We now included arrowheads at locations with full-length X elements. Partial X elements are marked with stars. This notation also makes it obvious which ends lack annotated X elements.

      (2) Line 156-163, Figure 2b: In the main text, "chromosome fusion between chromosome IV right arm and chromosome I left arm" should be mentioned. Moreover, it isn't very clear to have the data in the S288C background. The fusion points are different between S288C and SK1 (the structures of these ends are quite different). Please explain the authors' logic in the text. 

      To improve clarity, we have included a schematic to better highlight which chromosomal sequences were removed. We have also substantially expanded the description of this experiment and explicitly state the limitations of this assay.

      (3) Supplemental Figure 6: Since the sir3 mutation affects the binding of Red1 EARs (and centromeres). It would be nice to show the similar sets for the HML, MAT, and HMR loci (and intergenic regions as a control).

      We are unfortunately statistically underpowered to perform a meta-analysis of just HML, HMR and MAT. However, we now indicated the positions of HML and HMR in Supplementary Fig. 2 and 8, so the binding of the axis proteins and Sir3 can be inspected directly. MAT is not within 50 kb of a chromosome end and thus was not captured in these analyses.

      (4) Line 322-, the section: From here, the authors switched their story from the sir3 to the sir2. It would be nice to provide the logic with a small introduction on the relationship between Sir2 and Sir3.

      We apologize for this confusion. We are not switching our story to Sir2 but rather are taking advantage of an available dataset that analyzed DSBs in sir2 mutants. We then return to Sir3 to also analyze DSBs in the sir3 mutant and analyze its interaction with a dot1 mutation. To better support the logic, we now briefly reiterate that Sir2 and Sir3 are part of the same complex at the beginning of this section.

      (5) Line 330-331, Figure 8a (and also Supplemental Fig. 8c): Would you explain a bit more about matched strain in the text or figure legend? Each dot represents a strain. If so, please show the strains used here.

      Each dot refers to an individual X or Y’ element that is shown matched in WT and mutant to highlight the trends at the level of individual elements. This is noted in the figure legend.

      (6) Supplemental Figure 7 (and 2): It would be nice to show the position of the HML, MAT, and HMR loci as well as the centromeres in the Figure.

      We now indicated the positions of HML and HMR in Supplementary Fig. 2 and 8. MAT and the centromeres are not located within 50 kb from chromosome ends.

    1. eLife Assessment

      This valuable study demonstrates that self-motion strongly affects neural responses to visual stimuli, comparing humans moving through a virtual environment to passive viewing. The evidence for visuomotor mismatch responses is solid, although the interpretation in terms of prediction remains somewhat preliminary. This study bridges human and rodent studies on the role of prediction in sensory processing, and is therefore expected to be of interest to a large community of neuroscientists.

    2. Reviewer #1 (Public review):

      In this paper, Solyga, Zelechowski & Keller study human visuomotor mismatch responses as an alternative instantiation of prediction errors to classic oddball paradigms. Using VR, they created a condition in which participants were moving around thereby creating a visuomotor coupling between physical movement and visual flow. To attempt to isolate the contribution of specifically movement-related predictions in this condition, they contrasted it to a condition in which participants were seated and rewatching their movement trajectory during the 'active' condition. Visuomotor mismatches were created by temporarily decoupling movement and visual experience by halting the VR display as participants continued to move.

      The core finding of the paper is that participants exhibit a positively-valenced response to the visuomotor decoupling in the active but not in the passive condition. Since walking speed only insignificantly slows down following decoupling events in the active conditions, the authors argue that this difference can not be accounted for by "changes in participants' behavior or to simple visual offset responses" with the latter being equal across both conditions. The following reinstatement of the coupling in turn does not differ between the two conditions. The authors additionally show that this mismatch response differs from visual onset responses elicited by checkerboard inversions and that it's "qualitatively" stronger than more commonly studied auditory oddball mismatch responses.

      The design with its focus on ecological validity is impressive, well-rationalized and the results are well illustrated. I additionally appreciate the control analyses with regards to changes in walking speed and playback DOF and, now added, additional participants who experience the passive condition before the active. I have a couple of questions/comments.

      My main question in round 1 regarded the isolation of visuomotor mismatch. Although the comparison with a seated control seems like a very sensible way to control for simple visual responses, there seem to be more differences than just a break in visuomotor coupling between the conditions. I therefore wonder whether the reduced offset response in the seated condition may be, in part, explained differently. For example, given that participants always conduct the active condition before rewatching their movement in the seated condition, it seemed likely that there is a component of learning across the session that flow will sometimes be halted. This is confirmed with the analyses. The explanation that there is a visuomotor component here is given further weight by their conduction of an additional group of participants who perform the conditions in the reverse order, so this has strengthened the manuscript considerably. However, it does of course remain an imperfect control because the visual stimulus is now different between the conditions for these participants. It's the best that can be achieved with this type of paradigm though and of course it yields a great deal of ecological validity.

      I was also wondering whether the authors may consider the findings in frontal electrodes more closely given that the title of the paper focuses on a specifically occipital effect. Their further analyses have confirmed that there are likely interesting frontal effects. From a theoretical point of view, the spatial dissociation in adaptation effects, which were stronger in frontal and weaker in occipital areas, seems interesting and perhaps worth discussing, especially given the interpretation that "mismatch processing may initially arise in sensory visual areas before engaging higher-order frontal regions." How come the frontal decrease in responses is not accompanied by an analogous decrease in its supposed occipital source? Could these two responses reflect different kinds of prediction error signals (i.e. objective vs subjective)?

      I remain concerned that the authors fight too defensively that they have absolutely isolated visuomotor prediction mechanisms with this paradigm. It's a nice, informative study, but it seems odd to argue there are no other possible explanations. One picks a design to optimize some features but they will always come at some cost to others. Prioritising ecological validity, which is a justifiable aim, necessarily usually weakens some control over confounds.

      To outline my reasoning fully: My concerns wrt generic influences of action on perception are reflected in Fig 1. The P1 is smaller when walking than sitting. It seems likely that the mismatch response reflects something about extrapolation or prediction, because it is larger when walking. However, it's not necessarily sensorimotor prediction. Even if you remove action from the equation, the flow can be extrapolated or predicted most of the time in a way it cannot so well when the video is halted. Of course the sitting condition somewhat controls for it, but when it came second the visual flow disruptions were more predictable here. A reduction in effects over time is indeed confirmed with their analyses. They now have conducted a study with the conditions in the reverse order and they find the same thing. But of course this necessitates non-identical visual flow because the sitting condition is playing the previous participant's flow. So it is likely that across all of these comparisons, it is the visuomotor mismatch that is especially salient. It's just that each comparison is a bit messy/confounded. It would strengthen the manuscript if there were some consideration given to the other processes likely at play here.

      As a more minor point in response to our previous review, whether particular accounts represent an 'orthodox' view at present does not determine whether they raise logical issues in need of consideration. The authors may have missed that the papers in question consider mechanisms underlying the attenuation of particular pieces of information *from perception*. Not perceptual processing. We have one percept at any one moment in time and must understand how different population types synergistically generate that percept.

      Similarly a little strange is the way in which the authors aggressively defend the position that self-generated motion is 'the strongest' type of prediction. Sure, we probably experience the effects of our actions more often than ambulances. But what about objects obeying laws of gravity or others' faces being structured and moving in systematic ways? It is hard to quantify, such that presumably many scientists would be skeptical of such a claim, and it is not needed logically to justify the importance of examining mechanisms enabling action to shape perceptual processing. I'd assume it better to fight the battles you need to (and can) fight, such that the robust claims carry more weight.

      Hope these comments are helpful.

    3. Reviewer #2 (Public review):

      Summary:

      This study investigates whether visuomotor mismatch responses can be detected in humans. By adapting paradigms from rodent studies, the authors report EEG evidence of mismatch responses during visuomotor conditions and compare them to visual-only stimulation and mismatch responses in other modalities.

      Strengths:

      - Authors use a creative experimental design to elicit visuomotor mismatch responses in humans.

      - The study provides an initial dataset and analytical framework that could support future research on human visuomotor prediction errors.

      Weaknesses:

      - Methodological issues (e.g., volume conduction) make it difficult to confidently attribute the observed mismatch responses to activity in visual cortical regions. This could be alleviated by increasing the number of channels.

      The authors successfully demonstrate that visuomotor mismatch paradigms can, in principle, be applied in human EEG. This approach provides a translational bridge between rodent and human work on predictive processing.

    4. Reviewer #3 (Public review):

      Solyga, Zelechowski, and Keller present a concise report of an innovative study demonstrating clear visuomotor mismatch responses in ambulating humans, using a mobile EEG setup and virtual reality. Human subjects walked around a virtual corridor while EEGs were recorded. Occasionally, motion and visual flow were uncoupled, and this evoked a mismatch response that was strongest in occipitally placed electrodes and had a considerable signal to noise ratio. It was robust across participants and could not be explained by the visual stimulus alone.

      This is an important extension of their prior work in mice, and represents an elegant translation of those previous findings to humans, where future work can inform theories of e.g. psychiatric diseases that are believed to involve disordered predictive processing. For the most part, the authors are appropriately circumspect in their interpretations and discussions of the implications. The paper in its current form represents an important addition to the literature.

      The authors have included analyses of the auditory mismatch using temporal electrodes, referenced to Cz (and therefore should exhibit a mismatch positivity). This added data clearly and convincingly shows that the sensorimotor mismatch is, indeed, stronger than the passive auditory MMN.

      - The reference electrode placed at Cz makes it is difficult to interpret relative differences between frontal and occipital electrode responses, as the occipital electrodes are placed farther away from the Cz reference than the frontal electrodes. Similarly, signal occuring cortically near the Cz reference might only appear as though it is occipitally distributed in this montage. It is common in EEG research to re-montage the data to an averaged common reference in order to better interpret the scalp distributions. As the electrode coverage was sparse for some subjects, this could be challenging, and this reviewer does not feel that it is necessary to do this analysis step, or even to drastically rewrite the body of the paper. We only request that some discussion, however brief, is included in the discussion section or the methods that recommend more dense electrode coverage in the future to better interpret scalp distributions and potential meso-scale sources.

      - This is just a suggestion. The authors are encouraged to analyse (and report) time-frequency power and phase locking for these mismatch responses, as is common in much of the literature (see Roach et al 2008 Schizophrenia Bulletin). This is not to say that doing so will yield insights into oscillations per se, but converting the data to the time-frequency domain provides another perspective that has some advantages. fosters translations to rodent models, as ERP peaks do not map well between species, but e.g. delta-theta power does (see Lee et al 2018 Neuropsychopharmacology; Javitt et all 2018 Schizophrenia research; Gallimore et al 2023 Cereb Ctx). Further, ERP peaks can be influenced by the actual neuroanatomy of an individual (especially for quantifying V1 responses). Time frequency analyses may aid in interpreting the "early negative deflection with a peak latency of 48 ms " finding as well. As it stands, the report is complete, and it would be acceptable if the authors chose to save this type of analysis for a future publication.

    5. Author response:

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

      We thank you for the time you took to review our work and for your feedback! The main changes to the manuscript are:

      (1) We have performed additional experiments to increase the number of recordings from frontal and occipital electrodes (previously 51 (occipital: O1+O2) and 26 (frontal: Fp1+Fp2), now 133 and 102). The additional data have strengthened many of our results, including for example the trend for a latency difference between occipital and frontal electrodes that was likely underpowered and is now significant (Figure 3E). We have updated all relevant figures to include the additional data (Figures 2–6, Figure S4, Figure S5). None of the main conclusions have changed.

      (2) As suggested by reviewer 1, we have conducted additional experiments to rule out the possibility that the observed effects were driven by the temporal order of open and closed loop sessions (new Figure S6). We also found another 9 participants who were willing to go on the ‘vomit comet’ of six degrees of freedom (6DOF) playback (previously 5, now 14). These data have further strengthened our conclusion that playback halt responses in 4DOF and 6DOF playback are not substantially different (Figure S4).

      (3) To address the point of reviewers 2 and 3, that mismatch negativity (MMN) responses would be larger on temporal electrodes, we conducted additional experiments in which we also recorded from temporal electrodes T3–T6. We have now added a comparison of visuomotor mismatch and MMN responses on T3–T6 electrodes as Figures S8–S9. On all electrodes, visuomotor mismatch responses were larger than MMN responses.

      (4) As suggested by reviewer 1, we have added an analysis of the experience-dependent changes in mismatch responses comparing frontal and occipital responses early and late in the session (new Figure 4).

      (5) As suggested by reviewer 2, we conducted additional experiments in an independent cohort of participants (note, without concurrent EEG) to measure eye movements triggered by visuomotor mismatches. We found eye-movement speed and blink/eye-closure changes, but these had longer latency than visuomotor mismatch responses (Figure S7).

      (6) Finally, as suggested by reviewers 2 and 3, we applied independent component (ICA) and time–frequency analyses to the EEG data. We show these results and explain why they are not applicable or useful in our case in the responses below.

      Please note, during the revision, we found that a part of our analysis used a bandpass of 0.2-100 Hz while a 1-100 Hz bandpass filter was used elsewhere. This has now been standardized to a 1-100 Hz bandpass filter, and the corresponding methods were updated. This resulted in no relevant changes to the figures. Additionally, the 50 Hz band-stop filter was erroneously described in the methods as 49-51 Hz. The filter used was 40-60 Hz, and the methods have been updated to reflect this.

      Reviewer #1 (Public review):

      In this paper, the authors wished to determine human visuomotor mismatch responses in EEG in a VR setting. Participants were required to walk around a virtual corridor, where a mismatch was created by halting the display for 0.5s. This occurred every 10-15 seconds. They observe an occipital mismatch signal at 180 ms. They determine the specificity of this signal to visuomotor mismatch by subsequently playing back the same recording passively. They also show qualitatively that the mismatch response is larger than one generated in a standard auditory oddball paradigm. They conclude that humans therefore exhibit visuomotor mismatch responses like mice, and that this may provide an especially powerful paradigm for studying prediction error more generally.

      Asking about the role of visuomotor prediction in sensory processing is of fundamental importance to understanding perception and action control, but I wasn't entirely sure what to conclude from the present paradigm or findings. Visuomotor prediction did not appear to have been functionally isolated. I hope the comments below are helpful.

      (1) First, isolating visuomotor prediction by contrasting against a condition where the same video stream is played back subsequently does not seem to isolate visuomotor prediction. This condition always comes second, and therefore, predictability (rather than specifically visuomotor predictability) differs. Participants can learn to expect these screen freezes every 10-15 s, even precisely where they are in the session, and this will reduce the prediction error across time. Therefore, the smaller response in the passive condition may be partly explained by such learning. It's impossible to fully remove this confound, because the authors currently play back the visual specifics from the visuomotor condition, but given that the visuomotor correspondences are otherwise pretty stable, they could have an additional control condition where someone else's visual trace is played back instead of their own, and order counterbalanced. Learning that the freezes occur every 10-15 s, or even precisely where they occur, therefore, could not explain condition differences. At a minimum, it would be nice to see the traces for the first and second half of each session to see the extent to which the mismatch response gets smaller. This won't control for learning about the specific separations of the freezes, but it's a step up from the current information.

      In theory, it is correct that the open loop (playback) session is predictable. However, this is relatively unrealistic. The open loop session is a 5-minute sequence that participants have only experienced once before, when they were generating it in the closed loop session a couple of minutes earlier. It is unlikely that participants would remember the entire sequence to a precision of less than a second, which is what they would need to predict the mismatch event. However, the reviewer is correct that it is possible that the mismatch events lose salience with time, for example as a consequence of participants losing interest in the task with time, or by undergoing some form of adaptation. To address this, we repeated the experiments with the sequence of closed and open loop sessions reversed (Figures S6A-S6C), and we analyzed the responses as a function of time within the session (Figures S6D and S6E), as suggested.

      The reversed-order design consisted of (1) open loop session: a playback, in which participants viewed the recorded closed loop session of a previous participant. This was followed by (2) a closed loop session, in which participants actively walked through the tunnel and experienced visuomotor mismatch events. Using this design, we again found that responses in the closed loop session were significantly larger than in the open loop session (Figures S6A-S6C).

      In addition, we analyzed both new and previously collected data as a function of time in the session. We computed moving average responses across 10 mismatch or playback halt trials at different percentages of progress through the paradigm (Figures S6D and S6E). This analysis revealed no consistent experience-dependent changes that could account for the observed differences between closed and open loop session. While there was indeed some form of experience dependent attenuation of visuomotor mismatch responses (see new Figure 4), the difference at the transition from mismatch to playback halt (and vice versa) far exceeded these adaptation effects (Figures S6D and S6E). This analysis was performed only on data from participants for whom we had both closed and open loop sessions and met our inclusion criteria.

      We used a similar analysis to test whether early and late responses within a session systematically differed (new Figure 4). Here, to maximize the chance of finding a difference, we compared early (first five) and late (last five) trials. Behaviorally, participants reduced their walking speed following mismatch events, with a significantly larger reduction during early trials (14.3%) than during late trials (5.7%) (Figure 4A). Neural responses mirrored this pattern primarily on frontal electrodes: frontal activity showed a clear attenuation from early to late trials (Figure 4B), consistent with the reduction in behavioral responses. In contrast, changes on occipital electrodes were much smaller between early and late trials (Figure 4C-4D). Thus, experience-related modulation is substantially stronger in frontal compared to occipital regions.

      In sum, we do not believe that the difference between visuomotor mismatch responses and playback halt responses can be explained by differences in the predictability of mismatch and playback halt events.

      (2) Second, the authors admirably modified their visual-only condition to remove nausea from 6 df of movement (3D position, pitch, yaw, and roll). However, despite the fact it's far from ideal to have nauseous participants, it would appear from the figures that these modifications may have changed the responses (despite some pairwise lack of significance with small N). Specifically, the trace in S3 (6DOF) and 2E look similar - i.e., comparing the visuomotor condition to the visual condition that matches. Mismatch at 4/5 microvolts in both. Do these significantly differ from each other?

      Yes, the 6DOF playback halt response shown in the previous Figure S3 and the mismatch response shown in previous Figure 2E are significantly different (Author response image 1).

      Author response image 1.

      Comparison of visuomotor mismatch response (A) and 6DOF playback halt response (B) from the original submission with statistics of the comparison (C).

      Nevertheless, to strengthen this conclusion, we collected additional data in the 6DOF condition. We show the comparison for participants for whom both closed loop (active) and open loop sessions (6DOF) were recorded within the same recording session (14 participants) in Figure S4. Consistent with our previous findings, visuomotor mismatch responses were significantly larger than 6DOF playback halt responses (Figures S4A-S4C). And we found no evidence of a difference between 6DOF and 4DOF playback halt responses (Figures S4D and S4E).

      (3) It generally seems that if the authors wish to suggest that this paradigm can be used to study prediction error responses, they need to have controlled for the actions performed and the visual events. This logic is outlined in Press, Thomas, and Yon (2023), Neurosci Biobehav Rev, and Press, Kok, and Yon (2020) Trends Cogn Sci ('learning to perceive and perceiving to learn'). For example, always requiring Ps to walk and always concurrently playing similar visual events, but modifying the extent to which the visual events can be anticipated based on action. Otherwise, it seems more accurately described as a paradigm to study the influence of action on perception, which will be generated by a number of intertwined underlying mechanisms.

      We are not entirely sure we understand the point here correctly. If the reviewer is suggesting that visuomotor coupling is not describable by the ideas of predictive processing, we disagree. However, given that the papers the reviewer is pointing to are premised on what seems to be a somewhat unorthodox interpretation of predictive processing when it comes to cortical circuits, we suspect this is contributing to the misunderstanding here. Let us briefly explain. In the two papers, Press and colleagues argue that most experiments cannot distinguish between “predictive cancellation” and “gated suppression”. This is indeed relatively tricky, even when one has single neuron data. The question is, does movement simply suppress sensory feedback (as is likely the case e.g. in the famous example of the cricket), or does movement result in a precise removal of only the self-generated sensory reafference? The first good evidence of the latter happening in any system is quite recent (Keller and Hahnloser, 2009). The premise the authors build their argument on is that the theory posits that “the brain predictively ‘cancels’ expected action outcomes from perception” (from the abstract of one of the papers). This is incomplete. The minimum circuit for predictive processing is composed of 3 neuron types: positive prediction error neurons, negative prediction error neurons, and internal representation neurons. Only the positive prediction error neurons have the predictive cancellation property the authors discuss. This is not the case for either negative prediction error neurons, or for the internal representation neurons. Negative prediction error neurons are excited by predictions and suppressed by sensory input (i.e. if anything, they are “predictively amplified”). This circuit is relatively well characterized in mouse cortex – for a brief summary see (Keller and Mrsic-Flogel, 2018). Note, this is not our idea of course – the original formulation of predictive processing (Rao and Ballard, 1999) was built to explain end-stopping. These are responses to the absence of an expected line that were stronger than would be expected from classical theories (i.e. negative prediction error responses). In mouse visual cortex, we know that a sudden break in the coupling between locomotion and visual flow selectively activates layer 2/3 negative prediction error neurons. Thus, if human cortex also implements a predictive processing like circuit with positive and negative prediction error neurons, we would expect a break in visuomotor coupling to drive a measurable response in visual cortex (by exciting the population of negative prediction error neurons – this is also why we are quite excited by the phase reversal of visual and mismatch responses as this could indicate that mismatch activates negative prediction error neurons first and positive prediction error neurons later, and vice versa for visual stimulation – negative prediction error neurons are more superficial in cortex (O’Toole et al., 2023)). We do indeed find a response over occipital cortex consistent with the negative prediction error response we observe in mouse cortex. The difficulty in distinguishing “predictive cancellation” and “movement driven suppression” comes only when looking at positive prediction error type responses (that are suppressed by predictive inputs) but does not apply to negative prediction error responses. The predictive processing circuit we are testing is the one described by (Keller and Mrsic-Flogel, 2018; Rao and Ballard, 1999), and here the break in visuomotor coupling is a stimulus that drives negative prediction error responses. Note, other authors who have thought about cortical implementations of predictive processing (e.g. (Bastos et al., 2012)) have glossed over the problem that individual neurons cannot trivially encode both positive and negative errors. Prediction errors are a signed quantity. If neurons signal prediction errors in firing rates and are close to zero firing rate at baseline (as is the case in layer 2/3 of cortex), they cannot (short of rather exotic ideas) encode a signed prediction error. Hence such proposals are not very useful for thinking about prediction error responses in cortex. For these reasons, we see no problem with referring to the response as a prediction error response. This is in line with a large body of mouse research (using a nearly identical paradigm) on the topic.

      One could of course argue that gated suppression could also mean that movement relieves suppression. Thus, one could assume that some neurons are suppressed by movement while others are enhanced. If one allows for enough neuron and stimulus specificity in the precision of the movement related suppression and enhancement of responses, the two models (predictive processing and gated suppression) become equivalent, and the discussion becomes semantic. See (Vasilevskaya et al., 2023) for an extended discussion on this point, and the reasons why we think predictive processing is a more useful model than gated suppression (keep in mind, gated suppression only explains the data if we allow for stimulus/neuron specific gain factors of the suppression, in which case the two models are equivalent).

      More minor points:

      (1) I was also wondering whether the authors may consider the findings in frontal electrodes more closely. Within the statistical tests of the frontal electrodes against 0, as displayed in Figure 3c, the insignificance of the effect of Fp2 seems attributable to the small included sample size of just 13 participants for this electrode, as listed in Table S1, in combination with a single outlier skewing the result. The small sample size stands out especially in comparison to the sample size at occipital electrodes, which is double and therefore enjoys far more statistical power. It looks like the selected time window is not perfectly aligned for determining a frontal effect, and also the distribution in 3B looks like responses are absent in more central electrodes but present in occipital and frontal ones. I realise the focus of analysis is on visual processing, but there are likely to be researchers who find the frontal effect just as interesting.

      That is correct; our data in frontal electrodes was likely underpowered. The reason we have fewer data in frontal electrodes is that eye-blink artifacts are particularly strong in frontal channels, resulting in a larger proportion of trials failing to meet our data inclusion criteria. We have now added more data from frontal and occipital electrodes by including additional experimental sessions. In addition, we applied less stringent trial-exclusion criteria, requiring that no artifacts occur within the time window −0.5 to 1 s relative to the event trigger (instead of −0.5 to 2 s). This adjustment allowed us to retain a larger number of trials. As anticipated by the reviewer, this increase in data was sufficient to confirm a significant response to the visuomotor mismatch event at both frontal electrodes (Figure 3C). The expanded dataset also revealed a significant difference in response onset times between occipital and frontal electrodes (Figure 3E), an effect that was not significant previously. In addition, we have included analysis comparing early and late mismatch responses in frontal and occipital electrodes (Figure 4).

      (2) It is claimed throughout the manuscript that the 'strongest predictor (of sensory input) - by consistency of coupling - is self-generated movement'. This claim is going to be hard to validate, and I wonder whether it might be received better by the community to be framed as an especially strong predictor rather than necessarily the strongest. If I hear an ambulance siren, this is an especially strong predictor of subsequent visual events. If I see a traffic light turn red, then yellow, I can be pretty certain what will happen next. Etc.

      This is a statistical argument. Every movement – throughout life – is directly and immediately coupled to sensory feedback and has been throughout evolutionary history. The vast majority of visual input you receive (we estimate, well above 99%) is the consequence of your own movements (e.g. every few 100 ms your eye movements cause a full field change in your visual input). The same is likely true of proprioceptive and somatosensory input – the vast majority is the direct consequence of your own movements (not other people poking you). This is likely different in the auditory system where a much larger fraction of the input is externally driven (depending a bit on how much one likes to talk). But even here the best predictor is self-motion (most non-self-generated sounds one experiences in life are very difficult to predict with millisecond precision). The example the reviewer gives is a good illustration of this. Take the siren that hails the appearance of an ambulance. The siren tells us that an ambulance will appear, but not how it will look, not when exactly it will appear, and with only very low resolution as to where it will appear. Incidentally, if you ask people to draw an ambulance they tend to draw a WWII style white square vehicle with a red cross on the side – a style of ambulance they likely have not ever seen in life. Their visual predictions of what they are about to see are very low resolution. We catastrophically fail at making pixel perfect predictions from learned stimulus associations of this nature. The traffic light example is difficult to compare to visual feedback control of movement as it is a much simpler prediction of a single bit in the form of a change in color of an existing object.

      In addition, consider how often (in life) you have seen an ambulance after hearing it? 100 times maybe? Maybe less. How often have you seen traffic lights change - 10 000 times? 100 000 times? Now consider, how often you have experienced the visual consequences of moving your head or eyes to the left (keep in mind this includes micro saccades) – at a conservative, once per second, that is somewhere on the order of 1 000 000 000. This is not even in the same ballpark. Our brains can certainly learn to make the ambulance and traffic light type predictions - to some extent - but by far the best predictor of sensory feedback (simply by virtue of the physics of how our body interacts with the world) is self-motion.

      We think this is an argument we can make based on first principles, and one that is frequently overlooked in the field, as experiments often focus on training people or animals to learn novel associations that, especially in the case of mice, we often have no idea whether cortical circuits can even learn. We should focus experiments on the predictive systems our brains have evolved since long before the evolutionary appearance of ambulances and traffic lights. We understand that the reviewer may disagree with this, but unless the reviewer has a concrete example of an even stronger predictor (as measured by frequency of experience, consistency in coupling, and precision in timing – we can’t think of one), it is a point we will make.

      (3) The checkerboard inversion response at 48 ms is incredibly rapid. Can the authors comment more on what may drive this exceptionally fast response? It was my understanding that responses in this time window can only be isolated with human EEG by presenting spatially polarized events (cf. c1, e.g., Alilovic, Timmermans, Reteig, van Gaal, Slagter, 2019, Cerebral Cortex).

      We don’t know, but it is not inconsistent with previous reports. For example, compare the “standing” and “fast walking” target ERP responses in Figure 5 of (Gramann et al., 2010). Both here and in our data, the fast response peak is only really apparent in the direct comparison of visual responses recorded while participants were walking to those when they were stationary.

      While we have taken great care to calibrate the timing of the visual display with the EEG recording, one could be worried that the alignment is off by as much as tens of milliseconds. However, even if this were so, one could use P1 as a reference and determine that the fast peak roughly precedes P1 by about 40 ms. Which again would result in a latency of about 50 ms of the fast walking peak (assuming P1 peaks at about 90 ms). In sum, we have added a reference to the previous work (that we found thanks to the reviewer’s comment) but fear we have nothing intelligent to say beyond that.

      Reviewer #2 (Public review):

      Summary:

      This study investigates whether visuomotor mismatch responses can be detected in humans. By adapting paradigms from rodent studies, the authors report EEG evidence of mismatch responses during visuomotor conditions and compare them to visual-only stimulation and mismatch responses in other modalities.

      Strengths:

      (1) The authors use a creative experimental design to elicit visuomotor mismatch responses in humans.

      (2) The study provides an initial dataset and analytical framework that could support future research on human visuomotor prediction errors.

      Weaknesses:

      (1) Methodological issues (e.g., volume conduction, channel selection, lack of control for eye movements) make it difficult to confidently attribute the observed mismatch responses to activity in visual cortical regions.

      (2) A very large portion of the data was excluded due to motion artefacts, raising concerns about statistical power and representativeness. The criteria for trial inclusion and the number of accepted trials per participant appear arbitrary and not justified with reference to EEG reliability standards.

      (3) The comparison across sensory modalities (e.g., auditory vs. visual mismatch responses) is conceptually interesting, but due to the choice of analyzing auditory mismatch responses over occipital channels, it has limited interpretability.

      We have responded to these points in the more detailed itemization below.

      The authors successfully demonstrate that visuomotor mismatch paradigms can, in principle, be applied in human EEG. However, due to the issues outlined above, the current findings are relatively preliminary. If validated with improved methodology, this approach could significantly advance our understanding of predictive processing in the human visual system and provide a translational bridge between rodent and human work.

      Reviewer #2 (Recommendations for the authors):

      Overall, the study addresses an interesting and underexplored question (translation of the visuomotor mismatch responses observed in rodents to humans). Below, please find a list of specific suggestions for improvement

      Introduction:

      (1) "updating internal representations and internal models" - what is the difference between the two, and why is it relevant to this study?

      In a nutshell, an internal model is the synaptic weight matrix that transforms between coding spaces. An internal representation is the activity pattern coding for the current representation. See (Aizenbud et al., 2025; Keller and Mrsic-Flogel, 2018) for more lengthy elaborations. The fact that the mechanism used for representation update can also be used to update internal models (i.e. solve the credit assignment problem) is likely the prime advantage of predictive processing (see work from the Bogacz lab). The relevance to the current study is justifying why predictive processing is a reasonable hypothesis for the function of cortex.

      (2) "Certain stimuli can be predicted from the preceding sensory input" vs. "Predictions can also be based on memory" - how are these two different? Do you mean specific (e.g., long-term associative or episodic) memory types in the latter?

      Correct, this is an arbitrary distinction that primarily makes sense in the light of experimental approaches. In this particular case, we were talking about spatial memory. We made this explicit to increase clarity.

      (3) "the strongest predictor - by consistency of coupling - is self-generated movement"

      (a) Externally induced movement, while not self-generated and therefore not predicted, will also generate sensory coupling, so is it really only about consistency?

      Externally induced movement (as in somebody else moving one’s arm we are not sure this is what the reviewer means) will induce sensory-sensory coupling but not sensorimotor coupling. We might be misunderstanding the point. In case the reviewer means stimuli that trigger movement as in us asking participants to walk, or a sudden startle stimulus that makes them jump in all such cases there are of course sensorimotor predictions. Sensorimotor predictions are driven by efference copies of the motor command thus all movements whether ‘voluntarily’ executed or triggered by an external stimulus will drive sensorimotor predictions. (All of this of course assumes that the predictive processing theory is correct.)

      (b) Do you mean temporal consistency (minimal lags), statistical contingencies (same movements linked to the same sensory inputs), or both? How does it differentiate sensorimotor/visuomotor mismatch responses from responses to incongruent stimuli in sensory modalities (e.g. audiovisual)?

      Both. We have rephrased the sentence to try to make this clearer. See also response to reviewer 1 minor point 2 above.

      How does it differentiate sensorimotor/visuomotor mismatch responses from responses to incongruent stimuli in sensory modalities (e.g. audiovisual)?

      Most cross-modal associations are much less consistent (the exact sound of a glass shattering is always slightly different and impossible for us to predict), and orders of magnitude less frequently experienced, than sensorimotor associations. Again, see also response to reviewer 1 minor point 2 above.

      (4) "Every movement is directly coupled to sensory feedback throughout life"

      This may be the case for proprioceptive and/or somatosensory feedback, but not necessarily for visual feedback (e.g., a mouse moving its tail), which is the topic of the study.

      Correct, there are movements that can be disconnected from visual feedback. Most of the time, most movements however are not, and we are studying one of the more prominent ones that is clearly not decoupled locomotion. The contrast we aim to highlight here very prominently is that there is still this vague idea in the field that you can take a participant, or a mouse, and expose them/it to a few tens or hundreds of trials of some sensory stimulus contingency and then probe for prediction error responses to a pattern only recently if at all learned. Given the life-long experience of subjects and mice, is it really surprising that oddball responses are less strong than a sensorimotor mismatch?

      (5) "However, the overall level of this motor-related activity is much higher than one would expect simply from predictions of visual feedback that are compared against visual input."

      Could you please clarify what one would expect in this case, and/or back it up with citations?

      This is in reference to the fact that there are very strong movement related signals in the mouse visual cortex that persist even when the mouse is in complete darkness. In darkness, movements should not trigger any visual feedback change hence the activity is difficult to explain as a movement related prediction of visual flow. We have rephrased this section of the introduction to make this clearer.

      (6) "The more precise the prediction and comparison, the less motor-related activity should be detectable in visual cortex."

      I think this conflates two issues. A good match between prediction and input would indeed result in sensory attenuation. However, sensory precision, at least in active inference, can upregulate prediction error responses. Since predictions cannot be assumed to be perfect (due to external or internal noise), increased precision may therefore augment activity. See e.g. https://doi.org/10.1007/s10339-013-0571-3

      We agree with the reviewer – the phrasing here was misleading. We do not mean precision in the predictive processing sense, but the precision of sensorimotor control necessary for the behavior. We have rephrased the corresponding section of the manuscript.

      (7) Neither the introduction nor the discussion refers to previous human EEG studies on sensorimotor mismatch responses, where sensory feedback doesn't match motor actions (e.g. https://doi.org/10.3758/s13423-021-01992-z ; https://www.sciencedirect.com/science/article/pii/S0028393214003777 ; https://www.sciencedirect.com/science/article/pii/S0028393219301265).

      The studies cited by the reviewer primarily test how discrete violations of learned action–outcome associations are represented in the brain, whereas our visuomotor mismatch paradigm probes violations of continuous sensorimotor coupling during ongoing action. The paradigms are conceptually different both in how strong the coupling is (lifelong vs. learned in the experiment), and in how prediction errors are likely used (visuomotor control vs. stimulus detection). We have added a brief part to our introduction discussing this.

      Results:

      (1) A very large proportion of the dataset was excluded due to movement artefacts. This is rather problematic as

      (a) the rationale behind finding mismatch responses is that motion-related (neural) signals should affect visual cortical activity, so it's essential to disentangle these neural signals from artefacts;

      Correct, we excluded 21.7% of the total data for visuomotor mismatch paradigm. Note, this percentage compares to other similar studies of EEG recordings during movement (Oliveira et al., 2016). By “problematic”, we assume the reviewer means the fact that we have artefacts, not that we exclude trials with artefacts. The movement artefacts are typically caused by the acceleration during stepping in participants with a heavy gait. None of these movement artefacts are time locked to any of the responses we investigate. Thus, they should just appear as increased levels of noise if not excluded. We don’t understand why the reviewer thinks this is particularly problematic for our analysis/conclusions (beyond the trivial consequence of increasing noise levels that would only cause us to underestimate the strength of the mismatch signals we report).

      (b) the criterion for the number of trials of 15 triggers (per condition?) is arbitrary and lower than widely used in the literature, so authors should demonstrate that this is a sufficient number to observe a measurable ERP even for those participants with 15 triggers;

      We have between 16 and 25 visuomotor mismatch events per participant. Author response image 2 is a selection of single participant examples with different number of trials. The number of mismatch events is limited by the fact that we introduce them approximately every 10 - 15 s and have a total duration of the closed loop session of 5 minutes. Thus, on average, we expect to have 24 mismatch events. But we are not sure we understand the logic of the comment, if we set exclusion too low, we just risk losing a response in the noise. And we clearly have stronger and higher signal to noise mismatch responses with an average of 20 trials compared to visual responses during movement with an average of 40 trials or MMN responses with an average of 28 trials.

      Author response image 2.

      Reliable ERPs can be observed with as few as 16 trials across EEG channels. (A) Histograms showing the distribution of the number of valid mismatch trials per participant for each electrode pair (Fp1–2, C3–4, P3–4, O1–2). (B) Representative EEG responses to visuomotor mismatch events from a single participant, recorded at electrode pairs Fp1–2, C3–4, P3–4, and O1–2. Waveforms were computed using the indicated number of trials (shown above each trace). Dashed vertical red lines are onset and offset of the visuomotor mismatch.

      (c) it seems that the seemingly static "visual" condition resulted in a larger proportion of data rejected due to movement (or, as later mentioned, nausea) than the "visuomotor" condition, which is counterintuitive and needs further explanation;

      This is a misunderstanding the ‘visual paradigm’ the reviewer is referring to are the experiments shown in Figure 1. Here we record visual responses in both sitting and walking participants. In this experiment, as in others, exclusion was primarily driven by part of the paradigm where the subjects were moving. To make this clearer we have added Table S2 to the manuscript that provides an overview of trials excluded by paradigm and session.

      (d) authors mention eye movements as a potential issue, which should be possible to detect from frontal channels. Additionally, it's not entirely clear how many datasets were discarded (the results section mentions 19/48 in the visual condition, then 4+11 in the playback condition - isn't this the same condition?)

      The visual paradigm corresponds to the data shown in Figure 1, in which participants viewed a flipping checkerboard in both a walking and a stationary session. The open loop session is part of the visuomotor paradigm shown in Figure 2, where participants were exposed to a replay of the visual flow that had been self-generated during the preceding closed loop session, including the visual flow halts that constituted visuomotor mismatches in the closed loop session. Please note, to avoid such confusion, we have attempted to standardize the usage of paradigm (visual vs. visuomotor) and session (sitting vs. walking, and closed loop vs. open loop) throughout. In addition, we have added a table to summarize the number of excluded trials by paradigm and session as Table S2 to the manuscript.

      In comments 1 and 2 of the public review, the reviewer also points out that we did not control for eye movements and we presume relatedly claims that we did not use common EEG reliability standards. Regarding the first point, we performed additional experiments in an independent cohort of participants to test whether eye movements could account for the visuomotor mismatch responses. We recorded eye movements during closed loop sessions and found that changes in eye speed (Figure S7A) or blink rate (Figure S7B) following the mismatch stimulus had a longer latency than visuomotor mismatch responses in EEG. This suggests that the visuomotor mismatch response cannot be explained by eye blinks or changes in eye movement speed. Regarding the second point, we are not sure we understand. Trial exclusion based on a fixed voltage threshold of 100 µV is relatively common, and our rejection rates are on par, and particularly on occipital electrodes even lower, with other work in EEG recordings during locomotion or movement (see e.g. (Oliveira et al., 2016)).

      Nevertheless, we did attempt to apply independent component analysis (ICA) based filtering to the EEG data (Delorme and Makeig, 2004). However, these methods were designed for high channel density recordings. With only 8 channels, ICA is unable to reliably isolate eye movement or motion artefact components of the EEG. To illustrate this, we tested two artifact-rejection strategies. In the first approach, components associated with non-neural artifacts (e.g., muscle activity, line noise, eye movements) were removed only if at least 90% of the component’s variance was assigned to a single artifact class (Author response image 3A). In the second, more permissive approach aimed specifically at reducing eye movement artifacts, components were removed if artifact-related activity exceeded 90% for non-eye artifacts, while the threshold for eye-related components was lowered to 60% (Author response image 3C). We lowered the threshold for excluding eye-related components to ensure that EEG signals influenced by eye movements were effectively removed. In both cases - whether the eye-component threshold was set to 90% or 60% - the averaged responses to visuomotor mismatch trials remained largely similar to the previously reported data, despite higher noise in some traces. Interestingly, when we then followed the ICA filtering by our voltage threshold based exclusion with a threshold of 100 µV, the resulting traces closely resembled the patterns described in the paper (Author response image 3B and 3D). Thus, we conclude the nonICA filtered responses are easier to interpret, free of any potential ICA filtering artifacts, and far less parameter choice (of the ICA filtering) dependent.

      Author response image 3.

      Removal of artifacts identified with ICA does not change the visuomotor mismatch responses. (A) Visuomotor mismatch responses recorded from occipital electrodes after artifact correction. Components associated with non-neural artifacts (e.g., muscle activity, line noise, eye movements) were removed only if ≥90% of the component’s variance was attributed to a single artifact class. Solid black line represents the mean, and shading indicates the SEM across participants. Dashed vertical red lines are onset and offset of the visuomotor mismatch. (B) As in A, but excluding trials with amplitudes exceeding 100 µV. (C) As in A, but components were removed if artifact-related activity exceeded 90% for non-ocular artifacts, while the threshold for eye-related components was lowered to 60%. (D) As in C, but excluding trials with amplitudes exceeding 100 µV.

      (2) The finding that mismatch responses are observed at all channels, with differences in amplitudes but not latencies, indicates that volume conduction may affect the results. I would strongly suggest accounting for this using a method appropriate for the very small number of channels, e.g., phase lag index.

      We are not sure we understand. The phase lag index is a method to estimate functional connectivity in a way that corrects for volume conduction (using phase lag). We make no claims about functional connectivity; thus, we are not sure what the reviewer is suggesting we do. The fact that the visual and visuomotor mismatch responses were measurable on all electrodes could indeed be in part explained by volume conduction, but we see no way to estimate the volume conduction contribution. From mouse calcium imaging data, we know that both visual and visuomotor mismatch responses spread across large parts of dorsal cortex (including frontal regions like the ACC).

      With the addition of new data, the latency difference between occipital and frontal electrodes - previously observed only as a trend - is now statistically significant (Figure 3E). Occipital responses emerge earlier than frontal responses, suggesting that mismatch-related activity likely originates in sensory visual regions and subsequently propagates to more frontal areas, as similar to what had been reported in mouse cortex (Heindorf and Keller, 2024).

      (3) The authors compare different types of mismatch responses (including auditory oddballs) in the same set of (occipital) channels, but doesn't this undermine the spatial specificity of the results? Classical auditory mismatch negativity is typically observed over central channels, so weaker amplitudes of auditory mismatch responses in occipital channels are likely trivially explained by modality differences. As such, I'm not convinced that this comparison is informative even in a qualitative manner.

      To address this point, we conducted additional auditory oddball experiments with recordings over the auditory cortex (channels T3, T4, T5, and T6). Given our central reference, these channels should capture the strongest mismatch negativity. The amplitude of the visuomotor mismatch response exceeded that of mismatch negativity on all tested channels (new Figures S8 and S9).

      (4) On a similar note, is the polarity reversal found for visual vs. mismatch responses specific to occipital channels?

      Thank you for this interesting question. In fact, polarity reversal was consistently observed across all recorded channels; this has now been added as a main figure to the manuscript (Figure 5).

      (5) Figure S4C seems to cut off one outlier, and I don't see this outlier included in the boxplot.

      Correct, that is why we describe the boxplots in the figure legend as: “Boxes mark median, quartiles, and range of data not considered outliers.” The axes were now adjusted to include all data points.

      Discussion:

      "A central tenet of the cortical circuit for predictive processing is the split into separate populations of neurons that compute positive and negative prediction errors (Keller and Mrsic-Flogel, 2018; Rao and Ballard, 1999)" - this may be the case for visuomotor mismatch signals or reward prediction errors, but signed PEs do not play a central role in other proposed microcircuits for predictive processing in the perceptual domain (e.g. Bastos)

      Signed prediction errors do not play a central role in proposed cortical microcircuits for predictive processing that do not burden themselves with making a concrete proposal for the implementation of the prediction error computation. The (Bastos et al., 2012) work is a good example of this. The equation for the error term provided in that paper is clearly signed (nothing stops the error from going negative), but no proposal is made for how layer 2/3 excitatory neurons are supposed to signal this quantity. With baseline activity levels close to zero in layer 2/3, there really is only one way to do this, and that is separate populations of negative and positive prediction error neurons. With non-zero baseline firing rate, one could do this bidirectionally around a mean firing rate (as is typically thought of dopaminergic RPE neurons). There are more abstract Bayesian implementations that assume logarithmic transformations that could also implement a prediction error-like system without negative firing rates. But given the absence of any physiological evidence, we will refrain from discussing these. However, most importantly, there is now considerable evidence for the existence of both negative and positive prediction error neurons in layer 2/3 of mouse visual cortex. Thus, by “cortical circuit for predictive processing” we here mean those that make biologically plausible proposals for prediction error computations. Also note, the (Rao and Ballard, 1999) model is probably the prime example for what the reviewer calls a proposed microcircuit for predictive processing in the “perceptual domain”.

      Reviewer #3 (Public review):

      Summary:

      Solyga, Zelechowski, and Keller present a concise report of an innovative study demonstrating clear visuomotor mismatch responses in ambulating humans, using a mobile EEG setup and virtual reality. Human subjects walked around a virtual corridor while EEGs were recorded. Occasionally, motion and visual flow were uncoupled, and this evoked a mismatch response that was strongest in occipitally placed electrodes and had a considerable signal-to-noise ratio. It was robust across participants and could not be explained by the visual stimulus alone.

      Strengths:

      This is an important extension of their prior work in mice, and represents an elegant translation of those previous findings to humans, where future work can inform theories of e.g., psychiatric diseases that are believed to involve disordered predictive processing. For the most part, the authors are appropriately circumspect in their interpretations and discussions of the implications. I found the discussion of the polarity differences they found in light of separate positive and negative prediction errors, intriguing.

      Weaknesses:

      The primary weaknesses rest in how the results are sold and interpreted.

      Most notably, the interpretation of the results of the comparison of visuomotor mismatches to the passive auditory oddball induced mismatch responses is inappropriate, as suboptimal electrode choices, unclear matching of trial numbers, and other factors. To clarify, regarding the auditory oddball portion in Figure 5, the data quality is a concern for the auditory ERPs, and the choice of Occipital electrodes is a likely culprit. Typically, auditory evoked responses are maximal at Cz or FCz, although these contacts don't seem to be available with this setup. In general, caution is warranted in comparing ERP peaks between two different sensory modalities - especially if attention is directed elsewhere (to a silent movie) during one recording and not during the other. The authors discuss this as a purely "qualitative" comparison in the text, which is appreciated, and do acknowledge the limitations within the results section, but the figure title and, importantly, the abstract set a different tone. At least, for comparisons between auditory mismatch and visuomotor mismatch, trial numbers need to be equated, as ERP magnitude can be augmented by noise (which reduces with increased numbers of trials in the average).

      To address this point, we conducted additional auditory oddball experiments with recordings over the auditory cortex (channels T3, T4, T5, and T6). Given our central reference, these channels should capture the strongest mismatch negativity. Nevertheless, the amplitude of the visuomotor mismatch response exceeded that of mismatch negativity on all tested channels (these results are now shown in the new Figures S8 and S9), and the response power was significantly greater for the visuomotor mismatch than for mismatch negativity. Independent of electrode we test, the visuomotor mismatch response has a power 5 to 10 times higher than that of the MMN response. And the number of trials per participant that met quality criteria was comparable between the visuomotor mismatch paradigm (mean = 23 trials) and the auditory mismatch paradigm (mean = 28 trials) (Author response image 4).

      Author response image 4.

      Number of trials included for analysis is comparable between visuomotor and oddball paradigm. (A) Histogram showing the distribution of the number of valid trials per participant for O1-2 electrode pair in visuomotor mismatch paradigm. (B) Same as in A but for deviant stimulus presentations in the oddball paradigm.

      And more generally, the size of the mismatch event at the scalp does not scale one-to-one with the size at the level of the neural tissue. One can imagine a number of variables that impact scalp level magnitudes, which are orthogonal to actual cortex-level activation - the size, spread, and polarity variance of the activated source (which all would diminish amplitude at the scalp due to polyphasic summation/cancelation). The variance of phase to a stimulus across trials (cross trial phase locking) vs magnitude of underlying power - the former, in theory, relates to bottom-up activity and the latter can reflect feedback (which has more variability in time across trials; the distance of the scalp electrode from the activated tissue (which, for the auditory system, would be larger (FCz to superior temporal gyrus) than for the visual system (O1 to V1/2)). None of this precludes the inclusion of the auditory mismatch, which is a strength of the study, but interpretations about this supporting a supremacy of sensory-motor mismatch - regardless of validity - are not warranted. I would recommend changing the way this is presented in the abstract.

      We agree with the point that the EEG response does not need to reflect the total cortical activation. However, the discussion in the abstract (and elsewhere) is in the context of clinical experiments where the underlying cortical activity pattern is irrelevant if it does not trigger a clinically measurable (by EEG in this case) response. The abstract only makes a comparison to MMN implicitly in this sentence “Second, a paradigm that can trigger strong prediction error responses and consequently requires shorter recording times could simplify experiments in a clinical setting.” We are not sure how to phrase this even more carefully – the statement at face value is a truism. The reviewer, we assume, takes exception to the unstated implication that visuomotor prediction errors trigger stronger responses than MMN. Given the data we have, we assume most authors would not consider it an overstatement to make that claim outright.

      Otherwise, the data are of adequate quality to derive most of their conclusions.

      The authors claim that the mismatch responses emanate from within the occipital cortex, but I would require denser scalp coverage or a demonstration of consistent impedances across electrodes and across subjects to make conclusions about the underlying cortical sources (especially given the latencies of their peaks). In EEG, the distribution of voltage on the scalp is, of course, related to but not directly reflective of the distribution of the underlying sources. The authors are mostly careful in their discussion of this, but I would strongly recommend changing the work choice of "in occipital cortex" to "over occipital cortex" or even "posteriorly distributed". Even with very dense electrode coverage and co-registration to MRIs for the generation of forward models that constrain solutions, source localization of EEG signals is very challenging and not a simple problem. Given the convoluted and interior nature of human V1, the ability to reliably detect early evoked responses (which show the mismatch in mouse models) at the scalp in ERP peaks is challenging - especially if one is collapsing ERPs across subjects. And - given the latency of the mismatch responses, I'd imagine that many distributed cortical regions contribute to the responses seen at the scalp.

      This is an excellent point we have rephrased throughout to “over occipital cortex” instead of “in occipital cortex”.

      I think that Figure 3C, but as a difference of visual mismatch vs halting flow alone (in the open loop) might be additionally informative, as it clarifies exactly where the pure "mismatch" or prediction error is represented.

      We performed the analysis as suggested (Author response image 5). Visuomotor mismatch responses are stronger on all electrodes compared to playback halt responses. This difference is also larger in data recorded on occipital electrodes.

      Author response image 5.

      Comparison of the difference between visuomotor mismatch and playback halt on all electrodes. Average response strength was calculated within a 100 ms window centered on the peak of the average visuomotor mismatch response across all electrodes. Boxes mark median, quartiles, and range of data not considered outliers. Each circle represents data from one participant. **: p<0.01, *: p<0.05, Fp1-2: 20 participants, C3-4: 31 participants, P3-4: 35 participants, O1-2: 32 participants.

      As a suggestion, the authors are encouraged to analyse time-frequency power and phase locking for these mismatch responses, as is common in much of the literature (see Roach et al 2008, Schizophrenia Bulletin). This is not to say that doing so will yield insights into oscillations per se, but converting the data to the time-frequency domain provides another perspective that has some advantages. It fosters translations to rodent models, as ERP peaks do not map well between species, but e.g., delta-theta power does (see Lee et al 2018, Neuropsychopharmacology; Javitt et al 2018, Schizophrenia research; Gallimore et al 2023, Cereb Ctx). Further, ERP peaks can be influenced by the actual neuroanatomy of an individual (especially for quantifying V1 responses). Time frequency analyses may aid in interpreting the "early negative deflection with a peak latency of 48 ms " finding as well.

      We have performed time–frequency power and phase-locking analyses for both visual responses (Author response image 6 and Author response image 7) and visuomotor mismatch and playback halt responses (Author response image 8 and Author response image 9), as suggested. We have added the results of these analyses here, as these are not fully developed yet. We may add these to a future publication, for which we would properly want to quantify stability of these effects.

      In brief, time–frequency representations of power did identify potentially interesting differences between walking and sitting sessions in the visual paradigm. Inter-trial phase coherence (ITPC) revealed an early increase in alpha-band synchronization suggesting that phase alignment of alpha oscillations may contribute to the early differences in visual responses between walking and sitting. The same analyses were applied to visuomotor mismatch and playback halt responses. Time–frequency power analysis revealed an increase in delta-band power during visuomotor mismatch, consistent with previous reports linking delta activity to prediction error processing, including reward prediction errors (Cavanagh, 2015), unexpected final words (Webb and Sohoglu, 2025), and visual deviance detection (West et al., 2024). Notably, it appears as if the increase in delta power emerged first over occipital electrodes and appeared later over more frontal electrodes, forming a spatiotemporal gradient of onset across the scalp.

      Delta power changes were markedly reduced in the playback halt responses at the time of visual flow cessation. While some power changes were observed, they occurred primarily at visual flow onset rather than at flow offset. Inter-trial phase coherence analysis further revealed delta-band synchronization over occipital electrodes following visuomotor mismatch, whereas the playback halt response showed strong phase synchronization in both delta and theta bands following visual flow onset.

      Author response image 6.

      Time–frequency representations of EEG power changes during the visual paradigm. (A) Time–frequency maps showing changes in spectral power relative to baseline for electrodes Fp1–2, C3–4, P3–4, and O1–2 following checkerboard reversal in the sitting session. The dashed red vertical line indicates the time of the checkerboard reversal (0 s). (B) As in A, but recorded while participants were walking.

      Author response image 7.

      Inter-trial phase coherence (ITPC) for visual trials during sitting and walking. (A) ITPC across trials for electrode pairs Fp1–2, C3–4, P3–4, and O1–2 following checkerboard reversal in the sitting session. The dashed red vertical line marks the time of the checkerboard reversal (0 s). (B) As in A, but recorded during walking.

      Author response image 8.

      Time–frequency representations of EEG power changes during visuomotor mismatch and playback halt responses. (A) Time–frequency maps showing changes in spectral power relative to baseline for electrodes Fp1–2, C3–4, P3–4, and O1–2 following visuomotor mismatch presentation. Dashed vertical red lines are onset and offset of the visuomotor mismatch. (B) As in A, but for playback halts.

      Author response image 9.

      Inter-trial phase coherence (ITPC) for the visuomotor mismatch and playback halt responses. (A) ITPC across trials for electrode pairs Fp1–2, C3–4, P3–4, and O1–2 following visuomotor mismatch presentation. Dashed vertical red lines are onset and offset of the visuomotor mismatch. (B) As in A, but for playback halts.

      Finally, the sentence in the abstract that this paradigm " can trigger strong prediction error responses and consequently requires shorter recording times would simplify experiments in a clinical setting" is a nice setup to the paper, but the very fact that one third of recordings had to be removed due to movement artifact, and that hairstyle modulates the recording SnR, is reason that this paradigm, using the reported equipment, may have limited clinical utility in its current form. Further, auditory oddball paradigms are of great clinical utility because they do not require explicit attention and can be recorded very quickly with no behavioral involvement of a hospitalized patient. This should be discussed, although it does not detract from the overall scientific importance of the study. The authors should reconsider putting this statement in the abstract.

      We have added a paragraph to the discussion to address these points. Note, we get robust and strong responses with very few trials (Author response image 2). The fact that we need to discard up to 21.7 % of trials due to movement/eye blink artefacts, does little to change the fact that we need much fewer trials and have larger and more robust responses compared to other EEG paradigms. Finally, we understand that sometimes not needing participants to pay attention to the task is useful. However, having a paradigm that is engaging and fun for participants and takes 5 minutes of recording time is probably equally often of advantage.

      Reviewer #3 (Recommendations for the authors):

      Minor points:

      (1) In the Introduction, I'm not sure that the logic comes through as to what the authors aim to illustrate by comparing mice to humans, in terms of precision and "movement modulation". In some cases, the precision of the comparison is referred to, and in others, the precision of the prediction (I think?). I'm not sure if they mean for this to be different or not. Simlarly, on line 81, "If indeed the precision of visuomotor coupling determines the amount of motor modulation of visual responses" - here I'm a little confused, as "amount of motor modulation" to me, the term "modulation" refers to a conditional modifier (if moving, than suppress visual movement resposnes. if not moving, then amplify visual movement repssones) rather than movement driven activity. The way I'm reading it, the authors mean the latter, but I could be misunderstanding.

      We have rephrased this section of the introduction.

      (2) I think it could be helpful, in the sentence starting on line 65, to reiterate that this observation of higher-than-expected motor activity in V1 is in mice (if I'm understanding it correctly). I also found myself tangled up in the difference between motor-related activity in V1 and motor-modulation in V1 in this paragraph.

      We have rephrased this section of the introduction.

      (3) For signal power, was the amplitude squared on individual trials prior to averaging, or after averaging? If prior, it would help with separating amplitude modulations from phase variance.

      In our previous analysis, power was computed by squaring the amplitude after trial averaging (Author response image 10A). We repeated the analysis using the alternative approach in which power was calculated for individual trials and then averaged (Author response image 10B). Although this method yields substantially higher absolute power values, the overall pattern of results remains unchanged: visuomotor mismatch responses continue to show significantly higher power than visual responses. To look at the phase variance we additionally analyze inter-trial phase coherence (Author response image 7 and Author response image 9).

      Author response image 10.

      Visuomotor mismatch responses have more power compared to visual responses. (A) Comparison of power between visuomotor mismatch and visual responses, calculated within a 0 - 0.5 s time window following stimulus onset. Power was computed by squaring the amplitude after trial averaging. Boxes indicate the median and interquartile range, with whiskers showing the range excluding outliers; circles represent data from individual participants. ***p < 0.001. (B) Same comparison as in (A), but with power calculated by squaring the amplitude of individual trials prior to averaging.

      (4) The "the world suddenly flew forward!" response from the participant, I understand, and I believe that it is useful to illustrate a point. I do not understand the "Are you printing this? - Hi Mom! " part of the participant response, and I'm not sure it adds to the paper, beyond amusement, which seems inappropriate.

      One of the authors (the one who did none of the experiments) finds this endlessly hilarious and as the reviewer notes, it might add amusement more generally. “Inappropriate” might be a bit harsh – according to our favorite AI chatbot: “Amusement provides significant mental, physical, and social value by offering a necessary escape from routine, reducing stress, and fostering a connection. It enhances well-being through endorphin-releasing experiences and encourages social bonding, learning, and joy.” Nevertheless, we have censored the offending passage.

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    1. eLife Assessment

      This important study convincingly shows that Vibrio bacteria act as predators of ecologically significant algae that contribute to harmful blooms in the lab and in their natural habitat, and that predation is induced by starvation. The authors suggest a working model that can be the basis for future work on this system. The study will be very impactful to those interested in the diversity of microbial predator-prey interactions and controlling toxic algal bloom.

    2. Reviewer #1 (Public review):

      [Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. We appreciate the revisions and the authors addressed all of the remaining minor concerns listed by the reviewers. We have no further suggestions for revision.]

      Summary:

      Rolland and colleagues investigated the interaction between Vibrio bacteria and Alexandrium algae. The authors found a correlation between the abundance of the two in the Thau Lagoon and observed in the laboratory that Vibrio grows to higher numbers in the presence of the algae than in monoculture. Timelapse imaging of Alexandrium in coculture with Vibrio enabled the authors to observe Vibrio bacteria in proximity to the algae and subsequent algae death. The authors further determine the mechanism of the interaction between the two and point out similarities between the observed phenotypes and predator prey behaviours across organisms.

      Strengths:

      The study combines field work with mechanistic studies in the laboratory and uses a wide array of techniques ranging from co-cultivation experiments to genetic engineering, microscopy and proteomics. Further, the authors test multiple Vibrio and Alexandria species and claim a wide spread of the observed phenotypes.

      Comments on revisions:

      I thank the authors for their additional work on the manuscript. My comments were addressed to my satisfaction.

    3. Reviewer #2 (Public review):

      Goal summary:

      The authors sought to (i) demonstrate correlations between the dynamics of the dinoflagellate Alexandrium pacificum and the bacterim Vibrio atlanticus in natural populations, ii) demonstrate the occurrence of predation in laboratory experiments, iii) demonstrate that predation is induced by predator starvation, and iv) test for effects of quorum sensing and iron-uptake genes on the predation process.

      Strengths include:

      - Data indicating correlated dynamics in a natural environment that increase the motivation for study of in vitro interactions<br /> - Experimental design allowing clear inference of predation based on population counts of both prey and predators in addition to microscopy-based evidence<br /> - Supplementation of population-level data with molecular approaches to test hypotheses regarding possible involvement of quorum sensing and iron update in predation

      Weaknesses include:

      - A quantitative analysis of effects of manipulating V. atlanticus density on rates of predation would have been valuable

      Appraisal:

      The authors convincingly demonstrate that V. atlanticus can prey on A. pacificum, provide strongly suggestive evidence that such predation is induced by starvation and clearly demonstrate that both iron availability and correspondingly the presence of genes involved in iron uptake strongly influence the efficacy of predation.

      Discussion of impact:

      This paper will interest those interested in the diversity of forms of microbial predation and how microbial predatory behavior responds to environmental fluctuations. It will also interest those investigating bacteria-algae interactions and potential ecological controls of algal blooms. It may also interest researchers of microbial cooperation in light of the suggestion of communication between predator cells.

    4. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Rolland and colleagues investigated the interaction between Vibrio bacteria and Alexandrium algae. The authors found a correlation between the abundance of the two in the Thau Lagoon and observed in the laboratory that Vibrio grows to higher numbers in the presence of the algae than in monoculture. Timelapse imaging of Alexandrium in coculture with Vibrio enabled the authors to observe Vibrio bacteria in proximity to the algae and subsequent algae death. The authors further determine the mechanism of the interaction between the two and point out similarities between the observed phenotypes and predator prey behaviours across organisms.

      Strengths:

      The study combines field work with mechanistic studies in the laboratory and uses a wide array of techniques ranging from co-cultivation experiments to genetic engineering, microscopy and proteomics. Further, the authors test multiple Vibrio and Alexandria species and claim a wide spread of the observed phenotypes.

      Comments on revisions:

      I thank the authors for their additional work on the manuscript. My comments were addressed to my satisfaction.

      Dear Reviewer #1, we thank you for your careful evaluation of our manuscript and for the time and effort you dedicated to this review. We are pleased that the revised version has addressed your concerns to your satisfaction.

      Reviewer #2 (Public review):

      Goal summary

      The authors sought to (i) demonstrate correlations between the dynamics of the dinoflagellate Alexandrium pacificum and the bacterim Vibrio atlanticus in natural populations, ii) demonstrate the occurrence of predation in laboratory experiments, iii) demonstrate that predation is induced by predator starvation, and iv) test for effects of quorum sensing and iron-uptake genes on the predation process.

      Strengths include

      - Data indicating correlated dynamics in a natural environment that increase the motivation for study of in vitro interactions

      - Experimental design allowing clear inference of predation based on population counts of both prey and predators in addition to microscopy-based evidence

      - Supplementation of population-level data with molecular approaches to test hypotheses regarding possible involvement of quorum sensing and iron update in predation

      Weaknesses include

      - A quantitative analysis of effects of manipulating V. atlanticus density on rates of predation would have been valuable

      - Lack of clarity in some of the methodological descriptions

      Appraisal

      The authors convincingly demonstrate that V. atlanticus can prey on A. pacificum, provide strongly suggestive evidence that such predation is induced by starvation and clearly demonstrate that both iron availability and correspondingly the presence of genes involved in iron uptake strongly influence the efficacy of predation.

      Discussion of impact

      This paper will interest those interested in the diversity of forms of microbial predation and how microbial predatory behavior responds to environmental fluctuations. It will also interest those investigating bacteria-algae interactions and potential ecological controls of algal blooms. It may also interest researchers of microbial cooperation in light of the suggestion of communication between predator cells.

      Dear Reviewer #2, we sincerely thank you for the time you devoted to this second review of our manuscript. We greatly appreciate your thoughtful comments, which helped us further improve the clarity and precision of the manuscript. All your additional recommendations have been carefully considered and addressed in the revised version and in our responses below.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (2) The authors' reference to Fig. 4a did not address our concern about density potentially affecting the outcomes shown in Fig. 3. Fig. 4a does not provide any quantitative effects of manipulating Vibrio density. But the new density numbers the authors added in response to point (33) do seem to address our concern, because Vibrio densities become lower in the older cultures, excluding the possibility that the increased predation in older cultures might have been due higher Vibrio densities. We think this should be stated explicitly.

      (33) See point (2) above. We think the authors should explicitly state in the text that the increased predation in older cultures was not due higher Vibrio densities in those older cultures, referring to their data.

      As recommended by Reviewer#2, we added the sentence “Importantly, Vibrio densities decreased with culture age, ruling out the possibility that the stronger predation observed in older cultures was driven by higher bacterial densities” in the results section “Attack of A. pacificum ACT03 is activated by V. atlanticus LGP32 starvation.”

      (45) Is it known that bacterial predators collectively feed more on other bacteria than on microbial eukaryotes in natural habitats? While this certainly seems most likely, it's stated as fact and so should either the statement should be supported with relevant citations or phrased as a likely hypothesis.

      As suggested, we rephrased this sentence “Predatory bacteria are found in a wide variety of environments and are commonly described as feeding on other bacteria, although some cases of predation on microbial eukaryotes have also been hypothesized” in the discussion section.

      (46) Perhaps "Conceiving predators as free-living organisms that kill other organisms and feed on them, this study suggest that Vibrios engage in a novel form of predation in which they kill and feed on algae."

      The reference to 'developing' a predator behavior is not clear. What is meant by 'develop'? It seems unnecessary.

      The use of italics when writing Vibrio is inconsistent.

      We agree that the reference to “developing” a predatory behavior was unclear and unnecessary. We therefore revised the sentence as follows: “Conceiving predators as free-living organisms that kill other organisms and feed on them, this study suggests that Vibrio engages in a novel form of predation in which it kills and feeds on algae.” We also corrected the inconsistent use of italics for Vibrio throughout the manuscript.

      (48) The authors might wish to revise this sentence, as although M. xanxthus does have contact-dependent killing mechanism, it is our understanding that both Lysobacter and myxobacteria can kill some prey at a distance with diffusible secretions.

      The sentence “These bacteria must be in close proximity to their prey in order to cause lysis and utilize their biomass, regardless of the prey's species” was replaced by “These bacteria may require close proximity to their prey to cause lysis and utilize their biomass, although some can also kill prey at a distance through diffusible secretions”.

      (50) Why not directly say 'predatory behavior?

      We totally agree and have reworded the sentence.

      Line by line feedback:

      28 '...the phycosphere, an interface ...'

      We agree and have revised the wording.

      24 'In the attack stage, Vibrios...'

      This sentence has been rephrased as recommended.

      35 surrounds -> surround

      The correction has been done.

      36 The lysis is induced by the cells not by the 'stage'. We would rephrase to 'in which the lysis and consumption of the dinoflagellates occurs'

      This sentence has been rephrased as recommended.

      41 'a new mechanism that could to be involved' -> 'a new mechanism that could be involved ...'

      The correction has been done.

      61 forms

      The correction has been done.

      98 'the role...in'

      The suggested correction has been performed.

      103 'Qpcr' -> 'qPCR'

      Thank you for spotting this typo. “Qpcr” was corrected to “qPCR” in the manuscript.

      125 Misplaced punctuation

      The punctuation was corrected.

      152 The use of '.' vs 'x' to indicate multiplication when writing numbers is inconsistent. In some cases both are missing.

      Numbers have been corrected throughout the manuscript.

      231 I would rephrase 'poor nutrient stress' to 'little nutrient stress' or 'no nutrient stress'

      The rephrasing was carried out as suggested.

      310 R and used packages are not cited

      We added the citation (R Core Team, 2024). Linear models, QQ plots (which are part of linear models), tests, and AICs are included in R by default and are credited to the R Core Team.

      The sentence “Statistical analyses were performed using R 3.6.3 software” was replaced by “Statistical analyses were performed using R 3.6.3 software (R Core Team, 2024) using Rstudio”.

      358 'are capable of simultaneously attacking'

      The expression “are capable of simultaneously attacking” was revised in the manuscript to improve clarity and readability.

      366 'exponential growth phase'

      We have corrected the wording to “exponential growth phase” in the revised manuscript.

      430 The large difference in incubation time between the sea-water vs nutrient-rich treatments and use of different media are unfortunate. These additional variables compromise the ability to directly ascribe observed differences to starvation.

      We agree, the sentence “The comparative analysis of the proteome of V. atlanticus LGP32 incubated 60 h in artificial seawater (ENSW) versus V. atlanticus LGP32 grown 12 h in Zobell nutrient-rich medium revealed 10 proteins modulated by nutrient stress (Fig. S2)” was replaced by “The comparative analysis of the proteome of V. atlanticus LGP32 incubated 60 h in artificial seawater (ENSW) versus V. atlanticus LGP32 grown 12 h in Zobell nutrient-rich medium revealed 10 proteins that were differentially abundant under these two contrasting conditions (Fig. S2)”

      443 Somewhat unclear sentence. I would rephrase this to "Remarkably, of the 10 proteins identified by proteomic analysis and eliminated by mutation, only elimination of PvuB prevented V. atlanticus from attacking A. pacificum ACT03."

      To clarify this point, the sentence “Remarkably, among the 10 proteins identified by proteomic analysis only V. atlanticus LGP32 mutant lacking pvuB failed to attack A. pacificum ACT03 (Fig. 4C; ANOVA p <0.001)” was replaced by “Remarkably, of the 10 proteins identified by proteomic analysis and eliminated by mutation, only elimination of PvuB prevented V. atlanticus from attacking A. pacificum ACT03 (Fig. 4C; ANOVA p <0.001).”

      445 'attack simultaneously' -> 'simultaneously attack'

      The suggested modification has been done.

      450 H3BO4 is written as Boron later, it would be good to call it boron here as well so that it is easier to make the connection for the reader.

      We agree, we modified the manuscript and called it boron.

      459 'no linked' -> 'no link'

      The text was modified accordingly.

      483 'which induces' -> 'which induce'

      The correction has been made.

      519 The use of Vibrio atlanticus and V. atlanticus is inconsistent within the text.

      We have checked and modified the manuscript in accordance with the recommendations.

      807-808 The use of the phrase 'Akaike information criterion (AICc) models' is confusing. Aren't these models just generalized linear models? It should be rephrased to make clear that the AICc is just a test that is used to select which model to use.

      We clarified this point by revising Figure 1 legend. The sentences “(C) Result of Akaike information criterion (AICc) models tested to explain the mean value of degraded Alexandrium cells (dead cells) in spring. (D) Wald test of the AICc model attributing the mean value of degraded cells of Alexandrium in spring to free Vibrio “were replaced by “(C) Results of the Akaike Information Criterion (AICc) test conducted to select a model for explaining the mean value of dead Alexandrium (degraded cells) in spring. (D) Wald test of the AICc model explaining the mean value of dead Alexandrium in spring by free Vibrio”

      827 The chronological sequence of snapshots is not very clear. Perhaps it would be clearer if pictures over a shorter timeframe were used to clearly show the gathering of the V. atlanticus cells near the algal cells.

      To address this point, we removed the first and the last 14 seconds of the snapshots to clearly show the gathering of the V. atlanticus cells near the algal cells, and we added an arrow on Fig. 2D to indicate the chronological order.

    1. eLife Assessment

      This important study describes a novel Bayesian psychophysical approach that efficiently measures how well humans can discriminate between colors across the entire isoluminant plane. The evidence was considered compelling, as it included successful model validation against hold-out data and published datasets. This approach could prove to be of use to color vision scientists, as well as to those who employ computational psychophysics and attempt to model perceptual stimulus fields with smooth variations over coordinate spaces.

    2. Reviewer #1 (Public review):

      Summary:

      This paper presents an ambitious and technically impressive attempt to map how well humans can discriminate between colours across the entire isoluminant plane. The authors introduce a novel Wishart Process Psychophysical Model (WPPM) - a Bayesian method that estimates how visual noise varies across colour space. Using an adaptive sampling procedure, they then obtain a dense set of discrimination thresholds from relatively few trials, producing a smooth, continuous map of perceptual sensitivity. They validate their procedure by comparing actual and predicted thresholds at an independent set of sample points. The work is a valuable contribution to computational psychophysics and offers a promising framework for modelling other perceptual stimulus fields more generally.

      Strengths:

      The approach is elegant and well-described, and the data are of high quality. The writing throughout is clear and the figures are clean (elegant in fact) and do a good job of explaining how the analysis was performed. The whole paper is tremendously thorough and the technical appendices and attention to detail are impressive (for example, a huge amount of data about calibration, variability of the stim system over time etc). This should be a touchstone for other papers that use calibrated colour stimuli.

      Comments on revised version:

      The authors have addressed all the issues I raised to my satisfaction.

    3. Reviewer #3 (Public review):

      Summary:

      This study presents a powerful and rigorous approach for characterizing stimulus discriminability throughout a sensory manifold, and is applied to the specific context of predicting color discrimination thresholds across the chromatic plane.

      Strengths:

      Color discrimination has played a fundamental role in studies of human color vision and for color applications, but as the authors note, remains poorly characterized. The study leverages the assumption that thresholds should vary smoothly and systematically within the space, and validates this with their own tests and comparisons with previous studies.

      Comments on revised version:

      My comments have been addressed.

    4. Author response:

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

      We would like to thank the editors and the reviewers for the thorough and insightful comments and suggestions. Addressing them has strengthened our manuscript. We have carefully addressed all reviewer comments, as described in detail below, as well as additional comments we received from others. In addition, we made two substantive updates to the manuscript:

      (1) We improved the estimation of uncertainty in the model predictions by computing 95% confidence intervals using 120 bootstrapped datasets (instead of the 100% of 10 bootstrapped datasets in the original submission) to match the number of bootstrap for the validation dataset.

      (2) We selected a slightly different hyperparameter value based on follow-up analyses suggested by Reviewer 1, which provided very useful information.

      Importantly, none of these changes alter the main results or conclusions of the paper.

      Beyond these changes and those outlined below, we also worked to improve the clarity of the prose throughout as well as added various additional citations to the literature.

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This paper presents an ambitious and technically impressive attempt to map how well humans can discriminate between colours across the entire isoluminant plane. The authors introduce a novel Wishart Process Psychophysical Model (WPPM) - a Bayesian method that estimates how visual noise varies across colour space. Using an adaptive sampling procedure, they then obtain a dense set of discrimination thresholds from relatively few trials, producing a smooth, continuous map of perceptual sensitivity. They validate their procedure by comparing actual and predicted thresholds at an independent set of sample points. The work is a valuable contribution to computational psychophysics and offers a promising framework for modelling other perceptual stimulus fields more generally.

      Strengths:

      The approach is elegant and well-described (I learned a lot!), and the data are of high quality. The writing throughout is clear, and the figures are clean (elegant in fact) and do a good job of explaining how the analysis was performed. The whole paper is tremendously thorough, and the technical appendices and attention to detail are impressive (for example, a huge amount of data about calibration, variability of the stim system over time, etc). This should be a touchstone for other papers that use calibrated colour stimuli.

      Weaknesses:

      Overall, the paper works as a general validation of the WPPM approach. Importantly, the authors validate the model for the particular stimuli that they use by testing model predictions against novel sample locations that were not part of the fitting procedure (Figure 2). The agreement is pretty good, and there is no overall bias (perhaps local bias?), but they do note a statistically-significant deviation in the shape of the threshold ellipses. The data also deviate significantly from historical measurements, and I think the paper would be considerably stronger with additional analyses to test the generality of its conclusions and to make clearer how they connect with classical colour vision research. In particular, three points could use some extra work:

      (1) Smoothness prior.

      The WPPM assumes that perceptual noise changes smoothly across colour space, but the degree of smoothness (the eta parameter) must affect the results. I did not see an analysis of its effects - it seems to be fixed at 0.5 (line 650). The authors claim that because the confidence intervals of the MOCS and the model thresholds overlap (line 223), the smoothing is not a problem, but this might just be because the thresholds are noisy. A systematic analysis varying this parameter (or at least testing a few other values), and reporting both predictive accuracy and anisotropy magnitude, would clarify whether the model's smoothness assumption is permitting or suppressing genuine structure in the data. Is the gamma parameter also similarly important? In particular, does changing the underlying smoothness constraint alter the systematic deviation between the model and the MOCS thresholds? The authors have thought about this (of course! - line 224), but also note a discrepancy (line 238). I also wonder if it would be possible to do some analysis on the posterior, which might also show if there are some regions of color space where this matters more than others? The reason for doing this is, in part, motivated by the third point below - it's not clear how well the fits here agree with historical data.

      Thank you for raising this important point. We have now added analyses of the effects of the two smoothness-related hyperparameters, ε and γ (see Appendix 10).

      First, we swept a range of values for each hyperparameter (ε: 0.1 – 1; γ: 0.000001 – 0.003) and evaluated model performance using 5-fold cross-validation of the dataset used to fit the WPPM, quantifying predictive accuracy on held-out test data. We used the mean negative log likelihood averaged across the held-out data in the cross validation as our measure of predictive accuracy (Figs. S27-31).

      The two hyperparameters affect cross-validation accuracy in a similar manner. With γ fixed at 0.0003, predictive accuracy is highest for ε in the range of approximately 0.3–0.5 and drops quite rapidly for ε < 0.3. We attribute this drop to oversmoothing. Cross-validation accuracy also decreases, albeit more gradually, for ε > 0.5. We attribute this to increased variance due to undersmoothing relative to the power of our datasets. Similarly, with ε fixed at 0.4, predictive accuracy is highest for γ values between approximately 0.0001 and 0.001, declines rapidly for smaller γ (oversmoothing), and more slowly for larger γ (undersmoothing).

      Second, we examined how the hyperparameter ε affected the agreement between the WPPM fit and the MOCS validation data. Specifically, at each ε, for each participant, we computed the linear regression between WPPM thresholds and validation thresholds at 25 reference locations. Then, we examined the slope and correlation coefficient of all participants as a function of ε. We found a classic bias–variance tradeoff. Excessive smoothness introduces bias by failing to capture structure in the data, whereas insufficient smoothness increases variance in model predictions. These results further support a choice of ε = 0.4 as lying near the optimal balance between bias and variance (Fig. S32).

      Based on these analyses, we selected for the final analysis ε = 0.4, slightly smaller than the preregistered value used in the original submission (0.5), while retaining the original value of γ (0.0003).

      We now discuss these reasons for changing this value in the revision, as well as provide a more general discussion of the importance and practicalities of hyperparameter choice in Bayesian approaches to analyzing data (Discussion / Prior specification).

      (2) Comparison with simpler models. It would help to see whether the full WPPM is genuinely required. Clearly, the data (both here and from historical papers) require some sort of anisotropy in the fitting - the sensitivities decrease as the stimuli move away from the adaptation point. But it's >not< clear how much the fits benefit from the full parameterisation used here. Perhaps fits for a small hierarchy of simpler models - starting with isotropic Gaussian noise (as a sort of 'null baseline') and progressing to a few low-dimensional variants - would reveal how much predictive power is gained by adding spatially varying anisotropy. This would demonstrate that the model's complexity is justified by the data.

      In the 5-fold cross-validation analysis described above (and now presented in Appendix 10), we found that when ε or γ is small, the stronger smoothness constraint leads to threshold ellipses that are nearly identical to each other across color space. Under these conditions, model predictions show poor accuracy on held-out test data and lead to poor predictions of the validation data. This observation addresses the underlying point raised by the reviewer, albeit in a different way than suggested: it shows that a degree of spatially varying anisotropy is necessary to capture the structure of the data. We now make this point in the paper (Discussion / Prior specification).

      More broadly, we employed the WPPM as a prior that imposed smoothness but not much other obvious structure, and used this to learn about the psychometric field. We are currently working to understand how we can best use our current data to improve the prior we would apply to future measurements. There are a number of approaches to this. One would be to seek a parametric mechanistic model that can describe the current data, and to the extent this is possible formulate prior distributions over the parameters of the model. The results reported here thus provide a foundation for deriving and evaluating more structured priors that would even more efficiently leverage future datasets, but with the feature that they impose more structure. We have added this perspective to the Discussion / Extensions of the WPPM framework.

      (3) Quantitative comparison to historical data. The paper currently compares its results to MacAdam, Krauskopf & Karl, and Danilova & Mollon only by visual inspection. It is hard to extract and scale actual data from historical papers, but from the quality of the plotting here, it looks like the authors have achieved this, and so quantitative comparisons are possible. The MacAdam data comparisons are pretty interesting - in particular, the orientations of the long axes of the threshold ellipses do not really seem to line up between the two datasets - and I thought that the orientation of those ellipses was a critical feature of the MacAdam data. Quantitative comparisons (perhaps overall correlations, which should be immune to scaling issues, axis-ratio, orientation, or RMS differences) would give concrete measures of the quality of the model. I know the authors spend a lot of time comparing to the CIE data, and this is great.... But re-expressing the fitted thresholds in CIE or DKL coordinates, and comparing them directly with classical datasets, would make the paper's claims of "agreement" much more convincing.

      Although we are sympathetic to this request, we have chosen not to implement the sort of quantitative comparison requested by the reviewer. The reason is that an important feature of color thresholds is that they depend on the spatial (e.g. Kelly, 1974; Poirson & Wandell, 1996; Danilova & Mollon, 2025) and temporal (e.g. Kelly, 1974) properties of the stimuli, and on the observer’s state of adaptation (e.g. Loomis & Berger, 1979; Krauskopf & Gegenfurtner, 1992). Because (as the reviewer notes below) the spatial and temporal properties of our stimuli were not matched to those of the comparison datasets, our purpose in making these comparisons was to examine qualitative agreement, as well as to situate our results in the literature and to demonstrate that our approach allows us to read out thresholds around the references and in the color spaces used in other studies. We would not expect detailed quantitative agreement with the current dataset because of differences in stimuli.

      As a consequence of this, we think we would be overreaching to quantify the differences between our data and classic datasets. This consideration is particularly important for the MacAdam measurements, where because of the matching adjustment procedure used, the observer’s state of adaptation is likely to have varied (by amounts that are difficult to estimate) from one reference to the next (e.g. Danilova & Mollon, 2025). We have clarified the manuscript with respect to these points (Results / Comparison with previous measurements).

      A point to make on this topic is that an important and interesting future direction that emerges from our work is to develop efficient methods to characterize the dependence of the full discrimination field on ancillary variables, such as those that describe spatial and temporal properties and/or the state of adaptation, which we now also mention in the paper (Discussion / Implications for the mechanisms of color perception). Although not the primary motivation, doing so would enable comparison of data with a wider range of studies.

      We do agree that the comparisons to CIELAB predictions work better when we express them in CIELAB, and have now done so (Fig. 3D; Fig. S24-S26).

      Kelly, D. H. (1974). "Spatio-temporal frequency characteristics of color-vision mechanisms." Journal of the Optical Society of America 64(7): 983–990.

      Poirson, A. B. and B. A. Wandell (1996). "Pattern-color separable pathways predict sensitivity to simple colored patterns " Vision Research 36(4): 515–526.

      Danilova, M. V. and J. D. Mollon (2025). "Effect of stimulus size on chromatic discrimination." Journal of the Optical Society of America A 42(5).

      Loomis, J. M. and T. Berger (1979). "Effects of chromatic adaptation on color discrimination and color appearance." Vision Research 19(8): 891–901.

      Krauskopf, J., Gegenfurtner, K. (1992). "Color discrimination and adaptation." Vision Research 32(11): 2165–2175.

      Overall, this is a creative and technically sophisticated paper that will be of broad interest to vision scientists. It is probably already a definitive method paper showing how we can sample sensitivity accurately across colour space (and other visual stimulus spaces). But I think that until the comparison with historical datasets is made clear (and, for example, how the optimal smoothness parameters are estimated), it has slightly less to tell us about human colour vision. This might actually be fine - perhaps we just need the methods?

      Related to this, I'd also note that the authors chose a very non-standard stimulus to perform these measurements with (a rendered 3D 'Greebley' blob). This does have the advantage of some sort of ecological validity. But it has the significant disadvantage that it is unlike all the other (much simpler) stimuli that have been used in the past - and this is likely to be one of the reasons why the current (fitted) data do not seem to sit in very good agreement with historical measurements.

      As the reviewer notes, our stimuli head in the direction of ecological validity (see also Hedjar et al., 2025) and indeed this was a consideration when we chose them, at the cost of limiting the degree of comparison we can make with prior studies (as discussed above). Another reason we chose our stimuli is that they enable the current data to be used as a basis of comparison with stimuli where we add specularity, change object shape, and vary object pose in the future. These manipulations are not possible with flat matte patches. Such experiments are of interest to us, as they will tell us about how effectively color may be used to differentiate stimuli in cases where other ecologically important variables co-vary. We now mention this motivation in the paper (Results / Task and Stimuli).

      Hedjar, L., M. Toscani and K. R. Gegenfurtner (2025). "Importance of hue: color discrimination of three-dimensional objects and two-dimensional discs." Journal of the Optical Society of America A 42(5).

      Reviewer #2 (Public review):

      Summary:

      Hong et al. present a new method that uses a Wishart process to dramatically increase the efficiency of measuring visual sensitivity as a function of stimulus parameters for stimuli that vary in a multidimensional space. Importantly, they have validated their model against their own hold-out data and against 3 published datasets, as well as against colour spaces aimed at 'perceptual uniformity' by equating JNDs. Their model achieves high predictive success and could be usefully applied in colour vision science and psychophysics more generally, and to tackle analogous problems in neuroscience featuring smooth variation over coordinate spaces.

      Strengths:

      (1) This research makes a substantial contribution by providing a new method to very significantly increase the efficiency with which inferences about visual sensitivity can be drawn, so much so that it will open up new research avenues that were previously not feasible. Secondly, the methods are well thought out and unusually robust. The authors made a lot of effort to validate their model, but also to put their results in the context of existing results on colour discrimination, transforming their results to present them in the same colour spaces as used by previous authors to allow direct comparisons. Hold-out validation is a great way to test the model, and this has been done for an unusually large number of observers (by the standards of colour discrimination research). Thirdly, they make their code and materials freely available with the intention of supporting progress and innovation. These tools are likely to be widely used in vision science, and could of course be used to address analogous problems for other sensory modalities and beyond.

      Weaknesses:

      It would be nice to better understand what constraints the choice of basis functions puts on the space of possible solutions. More generally, could there be particular features of colour discrimination (e.g., rapid changes near the white point) that the model captures less well.

      This comment bears conceptual similarity to Reviewer 1’s question about the hyperparameters of our prior, as it is basically asking whether we might be oversmoothing through the choice of form and number of basis functions. The hyperparameter sweeps we now present suggest that within the choice of basis functions we used, we are operating at a reasonable point on the bias-variance tradeoff curve - we can see bias emerging with a smoother prior, and variance increasing with a less smooth prior. Our expectation is that varying the smoothness of the prior in other ways, such as by varying the form and number of the basis functions, would lead to similar tradeoffs.

      We did perform one additional check that shows, within our current framework, that adding more basis functions is unlikely to change things much. This was to plot the fit weights as a function of Chebyshev basis order (Figure S4 in Appendix 2). These decline to near zero at the highest order we used, suggesting that adding more would not alter the inferred psychometric field, given our hyperparameter choices. Although we could explore this question further by explicitly fitting the data using more basis functions along with different hyperparameter choices, or different functional forms for the basis functions, we decided not to pursue this in favor of performing the other additional analyses we now present.

      We resonate with the reviewer’s concern that assuming smoothness, both by assuming that isoperformance contours are elliptical and by assuming that these vary smoothly with reference, might cause us to miss features of the true underlying field in cases where that field varies rapidly or the isoperformance contours are asymmetric or non-elliptical. Our approach to this was to measure the validation thresholds and demonstrate that any bias in our WPPM-inferred field is small for these measurements. Because we shared the reviewer’s intuition that the adapting point is a candidate location where there might be less smooth variation, we measured a validation threshold at this reference for every subject. Nonetheless, we only measured in one direction around the adapting reference for each subject. We considered validation approaches where we measured full ellipses at a set of validation references, but we were worried about effects of uncertainty reduction and perceptual learning which might distort thresholds at highly sampled locations.

      It is the case that if one wanted to study the discrimination field in more detail around a particular reference, one could concentrate trials in a smaller model space around that reference, and for the same number of trials use a prior with less smoothness relative to the underlying stimulus space. Indeed, simply halving the size of the stimulus space that maps onto the [-1,1] model space and keeping the same prior over the model space effectively halves the degree of smoothness expressed with respect to the stimulus space. Thus our methods could prove useful in studying more rapid variations in the discrimination field if one hypothesized that they might occur around particular reference choices, but this would still rest upon the elliptical assumption. To relax that assumption, one could use the threshold field estimation methods implemented in AEPsych, which incorporate a smoothness assumption but do not assume elliptical isoperformance contours. Weakening the prior in this way would, however, increase trial demand to obtain similar measurement precision.

      As a general matter, we don’t think it is possible to leverage smoothness for trial efficiency on the one hand and at the same time be completely sure that there isn’t some aspect to the underlying ground truth that has been smoothed over. Carefully choosing the degree of prior smoothness together with the number of experimental trials in the context of a particular content problem is an important part of bringing the WPPM and related methods to bear, and one where simulation and held-out data both play an important role.

      We now bring these points out more fully in the paper (Discussion / Extensions of the WPPM framework; Discussion / Prior specification).

      Chen, C.-C., J. M. Foley and D. H. Brainard (2000). "Detection of chromoluminance patterns on chromoluminance pedestals I: threshold measurements." Vision Research 40(7): 773–788.

      The substantial individual differences evident in Figure S20 (comparison with Krauskopf and Gegenfurtner, 1992) are interesting in this context. Some observers show radial biases for the discrimination ellipses away from the white point, some show biases along the negative diagonal (with major axes oriented parallel to the blue-yellow axis), and others show a mixture of the two biases. Are these genuine individual differences, or could the model be performing less accurately in this desaturated region of colour space?

      We agree that these differences are interesting. We have now added more complete bootstrapped confidence regions in these (Appendix 8) and the other comparison figures (Appendix 6, 7, 9), so that an estimate of measurement precision is directly available in these figures. These confidence regions suggest that the individual differences in this region of color space are real. A longer-term goal is to develop more mechanistic models that can account for individual subject data through parameter choice. This might lead to insight into what differs in the visual system across individuals.

      Reviewer #3 (Public review):

      Summary:

      This study presents a powerful and rigorous approach for characterizing stimulus discriminability throughout a sensory manifold, and is applied to the specific context of predicting color discrimination thresholds across the chromatic plane.

      Strengths:

      Color discrimination has played a fundamental role in studies of human color vision and for color applications, but as the authors note, it remains poorly characterized. The study leverages the assumption that thresholds should vary smoothly and systematically within the space, and validates this with their own tests and comparisons with previous studies.

      Weaknesses:

      The paper assumes that threshold variations are due to changes in the level of intrinsic noise at different stimulus levels. However, it's not clear to me why they could not also be explained by nonlinearities in the responses, with fixed noise. Indeed, most accounts of contrast coding (which the study is at least in part measuring because the presentation kept the adapt point close to the gray background chromaticity, and thus measured increment thresholds), assume a nonlinear contrast response function, which can at least as easily explain why the thresholds were higher for colors farther from the gray point. It would be very helpful if a section could be added that explains why noise differences rather than signal differences are assumed and how these could be distinguished. If they cannot, then it would be better to allow for both and refer to the variation in terms of S/N rather than N alone.

      We agree with the reviewer. We are measuring SNR and attributing it to noise, but cannot identify from the data whether changes in SNR across color spaces are due to changes in noise, to a nonlinear relationship between stimulus space and the observer’s response space with noise in the response space held fixed, or both. We now make this point where we introduce the Results / Wishart Process Psychophysical Model and reiterate it in the Discussion / Extensions of the

      WPPM framework.

      Related to this point, the authors note that the thresholds should depend on a number of additional factors, including the spatial and temporal properties and the state of adaptation. However, many of these again seem to be more likely to affect the signal than the noise.

      We don’t disagree. Indeed, as we noted in our response to a comment by Reviewer 1 and above in the context of individual differences, we are very interested in developing a mechanistically plausible model that accounts for the data. If we or others are able to do so, that would provide a basis for parsing performance into separate signal and noise effects. And if such a model has natural ways in which additional variables affect its predictions, measuring the effects of these variables would be a way to provide evidence in favor of the model (Discussion / Implication for the mechanisms of color perception - Extensions of the WPPM framework).

      An advantage of the approach is that it makes no assumptions about the underlying mechanisms. However, the choice to sample only within the equiluminant plane is itself a mechanistic assumption, and these could potentially be leveraged for deciding how to sample to improve the characterization and efficiency. For example, given what we know about early color coding, would it be more (or less) efficient to select samples based on a DKL space, etc?

      The more we are willing to assume about the structure of the psychometric field, the more efficiently we can measure it. As the reviewer correctly notes, this principle applies to trial placement as well. We are currently using an adaptive method (AEPsych) that starts with a fairly weak smoothness prior and attempts to place trials using heuristics that aim to minimize the expected uncertainty in the posterior. As we learn more about the discrimination field, we should be able to leverage stronger priors to increase trial efficiency. This point is closely related to one we made above about developing stronger priors that capture what we have learned in this study. Such priors could also help improve trial placement. For a prior that has a relatively small number of parameters, for example, perhaps a mechanistic prior, methods such as Quest+ (Watson, 2017) may be used for trial placement.

      Watson, A. B. (2017). "QUEST+: A general multidimensional Bayesian adaptive psychometric method." J Vis 17(3): 10.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      I do not think that the authors need to perform additional experiments. However, I would like to see some additional analyses regarding the assumptions made in the fitting procedure and how they affect the final maps.

      I also think some more quantitative comparisons with historical data would be valuable - at the moment, a lot of the comparisons are simply 'by eye'.

      It would have been nice to have the code and data available during the review procedure - I'm sure these will be released with excellent documentation?

      We addressed the first two points in the public review section. The code is now available online as is the data. These links are now provided in the paper (Methods and Materials / Data and code availability).

      Reviewer #2 (Recommendations for the authors):

      Minor points

      I have a few suggestions for additions and small changes.

      (1) Several examples of covariance matrix fields are shown in Figure 1, 4, but these are for simulated examples. It would be nice to see the fields actually fit the data! I would be interested in seeing this for all participants in an Appendix, and maybe for participant CH in the main paper?

      We have made the changes (see Figure 4 and Figure S3).

      (2) I have not worked through all the math in the appendices line by line, but it seems to be complete, and the model validation results speak for themselves. I think the authors have done a pretty good job of explaining the model conceptually (not easy), but I struggled with the 'weighted sum' step in Figure 4 and the main text. I would appreciate a bit more hand-holding here, e.g, why is an 'overcomplete' representation needed as an intermediate, and providing an intuition of why there are 12 matrices in the overcomplete representation and what each matrix in this representation represents.

      We have now added more explanations in the figure legend and text (Fig. 4 and Methods and Materials / The Wishart Process Psychometric Model).

      (3) Individual differences: There is a section on this in the manuscript, and it's concluded that there are only "modest" individual differences. However, in Figure S20, the individual differences, I think, are huge and place observers almost in qualitatively different categories! Some observers show a radial bias in discrimination ellipses, others seem to show basically a bias along the negative diagonal, and others a mixture of both biases. These ellipses are at a desaturated part of colour space - is it possible that there are some rapid changes in the underlying noise in this region that the Wishart fit has not captured due to relatively sparse sampling or the fact that the basis functions are all fairly low spatial frequency? I wondered whether the results are constrained by the choice of Cartesian rather than polar basis functions, e.g, polar basis functions may have better allowed fine-grained changes near the white point but slower changes at higher saturations away from the white point.

      We agree that the individual differences are meaningful and, in some cases, quite pronounced. Our intent in describing the differences as “modest” was to emphasize that the overall structure of the psychometric fields remains broadly consistent across observers. We have revised the Results to note and more fully describe these differences.

      Regarding the possibility that sharp changes in the underlying noise near the achromatic point might not be fully captured by the current model, we agree that this is an important consideration. The current implementation uses relatively low-order Chebyshev basis functions that primarily capture smooth global variations in the psychometric field. While validation analyses indicate that these basis functions capture the dominant structure in the data, they may be less sensitive to sharp local variations such as those that could occur near the white point. Future work could address this by mapping the model space to a smaller region around the achromatic reference or by exploring alternative basis sets (e.g., polar or Zernike functions) that may better capture such localized structure. This is discussed above in this response and now addressed in Discussion / Extensions of the WPPM framework.

      On sampling, I wondered if the results might have been biased by the strongly biased ellipse that occurs at the grey point. If not, and the model is accurate in this region of colour space, I think this figure does show some large individual differences, and it would be good to comment on these in the individual differences section of the manuscript.

      Based on our analysis of trial placement (Fig. S1), the adaptive algorithm does not appear to have disproportionately concentrated trials near the gray point. In fact, more trials were allocated to the edges of the stimulus space than to the center. This suggests that the WPPM estimates are unlikely to be driven primarily by performance in the gray region. In addition, we examined the threshold ellipses around the gray reference in DKL space and found that they are broadly consistent across participants (Figs. S22–S23). Together, these analyses suggest that the anisotropy observed near the gray point reflects a genuine property of the psychometric field rather than an artifact of the sampling procedure.

      As noted just above, we have added additional text about individual differences in the Results and referenced it in the Discussion.

      (4) The manuscript seems unusually free of typographical errors, but I noticed that in many places "Krauskopf and Karl 1992" is cited! Also, I think something has gone wrong with the legend to Figure 2 - perhaps the order of panels was swapped around, but the legend was not fully updated. There is a repeated reference to the "summary of regression slopes" which seems to be in 2 positions, after C and G. It would make more sense to label panel G as D and progress from there, or switch the order of the panels so that G is on the bottom row.

      Thank you for catching those errors. They are now fixed.

      Reviewer #3 (Recommendations for the authors):

      A minor point (or perhaps major if your last name is Gegenfurtner) is that the reference to Krauskopf and Karl is incorrect.

      They are now fixed.

    1. Thank you very much for publishing this manuscript on bioRxiv. I consider it regrettable to continue promoting the existence of the type III effector XopAZ, as the only evidence reported to date comes from a poster abstract at the 2017 APS Annual Meeting. This protein, which is thought to be an FKBP-like peptidyl-prolyl cis-trans isomerase, is even conserved in Escherichia coli K-12, a bacterium lacking a type III secretion system. I doubt that this is a type III effector.

    1. eLife Assessment

      This study addresses the mechanism of action of benzoylurea insecticides and explores the metabolic consequences of inhibiting glycogen breakdown in insects. Both reviewers identify major flaws with the premise of the work. The strength of the provided evidence is inadequate as the data do not, or poorly, support several central claims. The significance of the findings is considered marginal.

    2. Reviewer #1 (Public review):

      Summary:

      In this study, the authors investigate whether glycogen phosphorylase is a potential molecular target of benzoylphenylurea insecticides and examine the physiological consequences of inhibiting glycogen breakdown in the diamondback moth Plutella xylostella. The authors express and characterize recombinant glycogen phosphorylase, test its inhibition by a mammalian glycogen phosphorylase inhibitor and by the insecticide diflubenzuron, and assess the physiological effects of glycogen phosphorylase inhibition through chemical exposure and RNA interference. Based on these experiments, the authors conclude that benzoylphenylurea insecticides do not target glycogen phosphorylase and propose that insects compensate for glycogen phosphorylase inhibition through activation of gluconeogenesis, allowing them to maintain glucose homeostasis and complete development despite strong suppression of the enzyme.

      Strengths:

      The study addresses an interesting and long-standing question in insect toxicology regarding the mechanism of action of benzoylphenylurea insecticides. The authors combine several complementary approaches, including recombinant enzyme characterization, inhibitor assays, RNA interference, gene expression analyses, and metabolite measurements. The biochemical characterization of the recombinant glycogen phosphorylase and the demonstration that the tested glycogen phosphorylase inhibitor can strongly inhibit enzyme activity represent important technical strengths. In addition, the study integrates biochemical and physiological observations to explore how insects might compensate for disruptions in central carbohydrate metabolism.

      Weaknesses:

      Several aspects of the central conclusions rely on indirect evidence and would benefit from additional validation. The proposed compensatory mechanism (gluconeogenesis supported by amino acid mobilization) is inferred primarily from transcriptional changes in gluconeogenic genes, reduced protein levels, and changes in metabolite concentrations. While these observations are consistent with increased gluconeogenic activity, they do not directly demonstrate metabolic flux through this pathway. Direct measurements of gluconeogenic flux would be required to confirm that carbon derived from non-carbohydrate substrates contributes to glucose production.

      Some interpretations are also speculative. For example, the lack of glycogen accumulation following glycogen phosphorylase knockdown is attributed to alternative glycogen degradation pathways, such as α-amylase or glycogen debranching enzymes, but these possibilities are not experimentally examined. Measuring the expression or activity of these enzymes would help evaluate whether such pathways contribute to the observed metabolic response.

      The physiological consequences of the proposed metabolic compensation are also not fully explored. If proteins are mobilized to support gluconeogenesis, this shift might be expected to affect organismal traits such as adult body size, flight capacity, or reproductive performance. Assessing these traits could provide valuable insight into whether the proposed compensatory metabolism carries fitness costs.

      Finally, some conclusions extend beyond the direct evidence presented. The study shows that diflubenzuron does not inhibit glycogen phosphorylase in vitro, but broader conclusions regarding the mechanism of action of benzoylphenylurea insecticides as a class may require additional evidence. In addition, some biochemical and cell-based observations would benefit from confirmation in whole insects, given that metabolic regulation can differ substantially between isolated enzyme or cell-based systems and intact larvae, where hormonal signaling, tissue interactions, and nutrient availability influence metabolic responses.

    3. Reviewer #2 (Public review):

      (1) Significance of the findings and strength of the evidence

      This manuscript evaluates the hypothesis that benzoylurea (BPU) insecticides exert their effects through inhibition of glycogen phosphorylase rather than chitin synthase (CHS). The central premise-that structural similarity among acylurea compounds implies shared molecular targets-is not supported by existing evidence.

      Extensive genetic and biochemical studies, including Reference 5, demonstrate that chitin synthase is the primary insecticidal target of BPUs. In particular, amino acid substitutions at a single site in CHS confer high levels of resistance to diflubenzuron and related compounds, with causality established through CRISPR/Cas9 editing in Drosophila melanogaster. This body of evidence substantially weakens the rationale for proposing glycogen phosphorylase as an alternative primary target.

      The manuscript reports that an acylurea compound previously identified as an inhibitor of mammalian glycogen phosphorylase also inhibits glycogen phosphorylase from Plutella xylostella, while diflubenzuron does not. This observation is consistent with prior work showing that glycogen phosphorylase inhibition among acylureas depends on specific side chain substitutions rather than the shared acylurea core. Consequently, the finding does not support the broader inference that acylurea structure predicts common biological function.

      The manuscript further argues that inhibition of glycogen phosphorylase is not insecticidal and attributes this to metabolic compensation through alternative glucose producing pathways. While it is well established that eukaryotic cells possess multiple mechanisms for maintaining glucose availability, the evidence provided here does not fully support the broader claim that this mechanism explains the lack of insecticidal activity. In particular, the conclusion that the study "resolves" the primary hypothesis is not justified by the data presented.

      Overall, while some experimental observations are sound in isolation, the overarching conclusions are not supported by the strength of the evidence. The significance of the findings is therefore limited.

      (2) Interpretation in the context of existing literature

      The introduction states that the molecular target of BPU insecticides remains a major unresolved controversy. However, multiple prior studies, including References 1, 4, and 5, provide strong genetic evidence that CHS is the primary and essential target of BPUs. These results demonstrate causality rather than simple correlation, particularly through targeted gene editing approaches.

      The manuscript further claims that biochemical studies have failed to demonstrate CHS inhibition by BPUs in cell free assays. However, the cited references (6-9) did not express CHS in such assays and therefore do not directly address this question. As a result, the suggested discrepancy between genetic and enzymatic evidence is not well founded.<br /> Structural analysis of acylurea compounds indicates that biological activity depends on side chain composition rather than the conserved acylurea core. Prior screening studies (Reference 11) show substantial variability in glycogen phosphorylase inhibition among acylureas despite a shared core structure. This undermines the proposal that the acylurea moiety itself constitutes a meaningful clue to a shared molecular mechanism.

      Regarding implications for pesticide design, targeting chitin synthesis remains an attractive strategy because chitin is essential for arthropods and absent in mammals, providing both efficacy and specificity. By contrast, metabolic enzymes such as glycogen phosphorylase are widely conserved, making them less suitable targets from a toxicological and safety perspective.

      (3) Specific technical comments

      The manuscript uses the term "dataology," which is neither defined nor contextualized within the text. As currently used, the term appears unrelated to the subject matter and may be confusing to readers. Clarification or removal would improve clarity.

    4. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      (1) The proposed compensatory mechanism is inferred primarily from transcriptional changes and metabolite levels; direct measurements of gluconeogenic flux are lacking.

      We agree that isotopic tracer experiments would provide the most direct evidence for gluconeogenic flux. While such experiments are beyond the scope of the current revision, we will explicitly acknowledge this as a key limitation and clearly state it as an important direction for future research. We note, however, that the convergent evidence from multiple independent lines, transcriptional upregulation of PEPCK and G-6-Pase, declining protein levels, altered amino acid profiles, and maintained trehalose levels, collectively supports gluconeogenic activation, even though each individual line is indirect. In the revised manuscript, we will present this evidence more cautiously, framing it as “consistent with gluconeogenic compensation” rather than definitively establishing metabolic flux.

      (2) Alternative glycogen degradation pathways (α-amylase, glycogen debranching enzymes) are proposed but not experimentally examined.

      We have now directly addressed this by measuring, via RT-qPCR, the expression of glycogen branching enzyme (GBE) and α-amylase following PxGP knockdown. Our preliminary results reveal a striking and informative pattern:

      GBE was significantly upregulated at 24 h (+29.24%), 48 h (+16.78%), and 96 h (+44.46%) post-injection, indicating transcriptional activation of an alternative glycogen-metabolizing enzyme in response to GP suppression.

      α-Amylase showed no significant change at any time point, suggesting that the compensatory response is pathway-specific rather than a generalized upregulation of all starch/glycogen-degrading enzymes.

      This differential response, GBE up while α-amylase unchanged, provides the first direct evidence that P. xylostella selectively activates specific alternative glycogen catabolic pathways when GP function is compromised. These data will be incorporated into the revised manuscript as a new figure panel.

      (3) Physiological consequences of the proposed metabolic compensation (fitness costs) are not explored.

      We have now assessed fitness consequences of PxGP knockdown by measuring feeding rate, larval body weight, and pupal weight. The results reveal a transient but significant fitness cost:

      Feeding rate: no significant difference between dsGP and dsGFP groups across all time points (24–120 h), indicating that the observed metabolic changes are not attributable to reduced food intake.

      Larval weight: significantly reduced at 24 h (−29.10%) and 48 h (−25.38%) in the dsGP group, demonstrating that metabolic compensation carries a measurable short-term cost.

      Pupal weight: no significant difference, indicating that larvae recover from the transient weight deficit before pupation.

      This pattern, transient larval weight loss with full pupal recovery, is consistent with our proposed model: GP suppression triggers protein catabolism to fuel gluconeogenesis (explaining the weight loss), but the compensatory mechanism is sufficiently effective to restore metabolic homeostasis before the pupal transition. Adult wing area and female fecundity measurements are currently in progress and will be included in the revised manuscript.

      (4) Enzyme activity is not measured in RNAi-treated insects; only transcript-level knockdown is reported.

      We have now measured GP enzyme activity (GPa) in crude extracts from RNAi-treated larvae using the coupled-enzyme spectrophotometric assay. The results provide important new insights:

      Per-larva GP activity was significantly reduced at 24 h (−27.57%) and 48 h (−29.28%), confirming that RNAi-mediated transcript suppression translates to reduced enzyme function in vivo.

      Per-protein GP activity showed a significant reduction only at 48 h (−10.35%). This apparent discrepancy is explained by a substantial decrease in total protein concentration at 24 h (−44.48%), which then gradually recovered. When enzyme activity is normalized to a declining protein pool, the per-protein reduction appears smaller.

      Importantly, the 44.48% decline in total protein at 24 h provides independent biochemical confirmation of our proposed protein catabolism: it is consistent with the mobilization of protein stores to supply amino acids for gluconeogenesis, directly supporting the compensatory mechanism described in our manuscript.

      These enzyme activity data will be presented alongside the existing transcript-level data in the revised manuscript, providing a complete picture from gene expression through enzyme function.

      (5) Conclusions regarding BPU class may require testing additional compounds beyond diflubenzuron.

      We agree and will explicitly limit our conclusion to diflubenzuron in the revised manuscript. The relevant text will be revised to state that “DFB does not inhibit PxGP” rather than making broader claims about the BPU class as a whole.

      (6) Structural evidence that GPI can bind PxGP in a comparable manner to its mammalian target is lacking.

      We have performed molecular docking and binding free energy analysis to address this concern directly. The PxGP homodimer structure was modeled using SWISS-MODEL with the rabbit muscle GP–acyl urea co-crystal structure (PDB: 2ATI; Klabunde et al., 2005) as the template. Molecular docking and MM/GBSA calculations were performed using Cresset Flare V11.

      Key findings:

      GPI exhibited substantially stronger binding to PxGP (ΔG = −34.63 kcal/mol) compared to DFB (ΔG = −29.29 kcal/mol), with a ΔΔG of −5.34 kcal/mol.

      Energy decomposition revealed that van der Waals interactions are the primary driver of selectivity (ΔG<sub>VDW</sub> = −11.49 kcal/mol), reflecting superior shape complementarity of GPI within the binding pocket.

      GPI was predicted to bind at the allosteric site at the dimer interface, engaging seven residues across both subunits (Asn44 and Val45 from chain A; Trp67, Gln71, Tyr75, Arg193, and Asp227 from chain B), a binding mode consistent with the experimentally determined site of acyl urea inhibitors in mammalian GP.

      DFB contacted only six residues, primarily from a single subunit, and its difluorobenzoyl moiety remained entirely solvent-exposed without productive protein contacts, explaining its inability to achieve effective target engagement.

      These structural data, together with the biochemical inhibition data (IC<sub>50</sub> = 2.96 nM for GPI; no inhibition by DFB), provide a comprehensive molecular explanation for the observed selectivity. The results will be presented as a new figure and table in the revised manuscript.

      (7) Dietary carbohydrates could mask the metabolic effects of GP inhibition.

      Our new data showing no difference in feeding rate between dsGP and dsGFP groups addresses this concern from one angle: the metabolic changes we observe are not attributable to altered food intake. We will also add a discussion of the potential contribution of dietary carbohydrates to glucose homeostasis and acknowledge this as a caveat in interpreting the metabolite data.

      Minor points: All terminology errors (“gluconeogenolysis” → “gluconeogenesis”), typographical errors (“over over four decades”), and formatting inconsistencies will be corrected. We will clarify the metabolite normalization approach and improve figure labeling and pathway schematics.

      Reviewer #2 (Public review):

      (1) The central premise — that structural similarity among acylurea compounds implies shared molecular targets — is not supported by existing evidence.

      We agree that the original manuscript overstated the significance of the shared acylurea core as a predictor of common biological activity. In the revised manuscript, we will substantially restructure the Introduction to:

      (1) Explicitly acknowledge the compelling genetic evidence from CRISPR/Cas9 experiments (Reference 5) establishing CHS as the primary site conferring BPU resistance.

      (2) Reframe the study’s objective: rather than proposing to “resolve” the BPU target controversy, the revised manuscript will focus on the systematic evaluation of GP as an independent insecticidal target and the discovery of a gluconeogenic compensation mechanism, questions that have scientific value independent of the BPU mechanism debate.

      (3) Remove the claim that the study “resolves the primary hypothesis.” The conclusion will instead state that our biochemical data demonstrate DFB does not inhibit PxGP, adding enzyme-level evidence to the existing genetic framework.

      (2) Target selectivity among acylurea compounds is determined by side-chain composition, not the shared core.

      We fully agree, and our new structural data now provide a molecular explanation for this principle at the atomic level. Molecular docking reveals that both GPI and DFB anchor to PxGP through their common acylurea carbonyl groups (forming hydrogen bonds with Arg193), but diverge dramatically in their side-chain engagement: GPI’s methoxyphenyl-methylurea moiety engages five additional residues across the dimer interface, while DFB’s difluorobenzoyl group remains entirely solvent-exposed. The van der Waals energy difference (ΔΔG<sub>VDW</sub> = −11.49 kcal/mol) quantitatively reflects this differential shape complementarity. These data directly support Reviewer 2’s point and will be presented as new evidence in the revised manuscript.

      (3) References 6–9 did not express CHS in cell-free assays.

      We will revise the relevant passage for greater precision. Our revised text will distinguish between (a) the absence of direct biochemical evidence for BPU-mediated CHS inhibition in cell-free systems and (b) the technical challenge of expressing and purifying functional CHS for such assays. This distinction will be stated more carefully to avoid any mischaracterization of the cited literature.

      (4) The term “dataology” is non-standard.

      This term has been removed and replaced with “data.” In accordance with eLife’s policy on the use of AI tools and technology, we will include a statement in the Materials and Methods section declaring that AI-based language editing tools were used for English grammar and style refinement. All scientific content was generated entirely by the authors.

      Author response table 1.

      We are confident that the substantial new experimental data and restructured narrative will meaningfully strengthen the manuscript.

    1. eLife Assessment

      The study provides valuable findings suggesting that modifying the donor's diet improves the effectiveness of fecal transplant therapies for liver disease. Although the reported results are of value, the evidence supporting the overall conclusions is incomplete. In particular, causal inferences regarding the effects of microbiota composition, as well as caproic acid signaling on the phenotypes studied, need further confirmation.

    2. Reviewer #1 (Public review):

      Summary:

      The authors aimed to determine whether dietary conditioning of fecal microbiota donors can influence the therapeutic efficacy of fecal microbiota transplantation (FMT) in alcohol-associated liver disease (ALD). Specifically, they tested whether donor diets enriched in vegetable or egg-derived proteins alter microbiota composition and function in ways that enhance recovery from alcohol-induced liver injury. Using a murine ALD model, the study integrates microbiome profiling, metabolomics, proteomics, and functional assays to identify mechanisms underlying improved outcomes. The authors propose that vegetable protein-conditioned microbiota promote beneficial microbial remodeling and increased production of caproic acid, which in turn activates hepatic PPARα signaling and enhances fatty acid β-oxidation, thereby reducing steatosis and inflammation.

      Strengths:

      The study is ambitious and methodologically comprehensive. The central idea, that donor diet can modulate FMT efficacy in ALD, is compelling and potentially impactful. It combines in vivo disease models, microbiome analysis (16S rRNA sequencing), metabolomics and proteomics, pharmacological inhibition experiments, and in vitro validation in hepatocytes. This multi-layered approach is a clear strength and allows the authors to explore the gut-liver axis. The comparison between different protein sources (vegetable vs egg) is very interesting, and the PPARα inhibition experiments provide relatively strong functional support for the involvement of host metabolic signaling pathways in mediating the observed effects.

      Weaknesses:

      Despite the comprehensive scope of the manuscript, several aspects of the study limit the strength of its mechanistic conclusions. The causal attribution to caproic acid remains incomplete. While caproic acid is identified and functionally tested, there is no direct demonstration that it is necessary for the Veg-FMT phenotype in vivo. The metabolomics data suggest multiple candidate metabolites, but these are not systematically explored. The study identifies specific bacterial taxa and, separately, key metabolites, but does not establish a direct connection between microbial composition and metabolite production. The use of GW6471 supports involvement of PPARα but does not fully establish specificity, as off-target effects cannot be excluded. Finally, it is not fully clear whether effects are exclusively microbiota-driven or could partially reflect the transfer of diet-derived metabolites.

      The authors successfully demonstrate that donor dietary conditioning influences the therapeutic efficacy of FMT in a murine model of ALD. The data convincingly show that vegetable protein-conditioned microbiota is associated with improved liver injury, reduced inflammation, and enhanced intestinal barrier integrity compared with controls or an egg protein-enriched diet. While the proteomic and gene expression data suggest activation of pathways related to fatty acid β-oxidation, these measurements do not directly demonstrate increased metabolic flux. The use of the PPARα antagonist GW6471 provides important functional support for the involvement of this pathway, as inhibition attenuates the protective effects of Veg-FMT. However, this approach primarily establishes pathway dependency rather than directly confirming enhanced β-oxidation activity. The authors may therefore wish to moderate their interpretation or clarify this distinction, particularly given the relatively modest fold changes observed in several targets. The role of caproic acid as a central mediator is plausible but not definitively established. Finally, the link between microbiota composition, metabolic function, and host signaling remains partly correlative. Overall, the study achieves its primary aim at a phenotypic level, but some of the mechanistic claims would benefit from more cautious interpretation or additional validation.

      Likely impact of the work on the field, and the utility of the methods and data to the community:

      The work addresses an important and underexplored question: how donor characteristics influence FMT efficacy. By introducing donor diet as a modifiable variable, the study has potential implications for optimizing microbiota-based therapies. The datasets (microbiome, metabolomics, and proteomics) may also be valuable to the community, as they provide a resource for exploring gut-liver metabolic interactions. The translational impact will, however, depend on validation in human systems and a clearer identification of causal mechanisms.

    3. Reviewer #2 (Public review):

      The manuscript explores a valuable strategy for optimizing Fecal Microbiota Transplantation (FMT) efficacy in alcoholic liver disease through donor dietary intervention. I have identified several critical logical gaps, missing links in the evidence chain, and methodological ambiguities that require detailed explanation and supplementation.

      (1) While the Methods section states that each recipient mouse group consisted of 16 animals, microbiome sequencing was performed on only 4 samples per group. This sample size is insufficient, and the high inter-individual variability observed reduces the statistical power and representativeness of the data. I recommend increasing the sequencing sample size or, at a minimum, explicitly acknowledging the risk of false positives due to the small sample size in the Discussion.

      (2) The layout of Figure 4 should be adjusted. Panel A should be enlarged for better visibility, while Panel B should be reduced in size to balance the figure composition.

      (3) A rationale should be provided for the selection of egg white protein as the animal protein control. Does this adequately represent animal proteins in general? Could the results differ if casein or whey protein were used? The current choice limits the generalizability of the conclusions, and this limitation should be addressed.

      (4) The ALD model was established over 12 weeks, yet the FMT intervention consisted of only 3 administrations with a 1-week observation period. In the context of such a severe liver injury model, a 1-week recovery period appears insufficient to observe genuine fibrosis reversal, which typically requires a longer timeframe. The authors should discuss whether short-term FMT can truly induce structural remodeling or if the observed effects are transient.

      (5) The results rely heavily on PICRUSt2 for functional prediction. As prediction does not equate to factual validation, the authors should exercise caution in their wording within the Discussion. Alternatively, I recommend supplementing the study with shotgun metagenomic sequencing to verify the existence of these pathways rather than relying solely on predictive algorithms.

      (6) Although Egg-FMT was less effective than Veg-FMT, it performed better than the standard FMT or abstinence groups. Why is the effect of egg white protein intermediate? Is this due to rapid digestion resulting in insufficient substrate, or differences in metabolite production? A deeper comparative analysis of the Egg-FMT group is required, rather than treating it merely as a negative control.

      (7) Relying solely on the "inhibitor blocking effect" proves only that Caproic acid's function is dependent on the PPARα pathway, not that it directly acts on PPARα. To claim direct activation, the authors must demonstrate direct binding between Caproic acid and the PPARα protein (e.g., via SPR or MST assays). Alternatively, a luciferase reporter assay driven specifically by PPARα response elements (PPRE) should be conducted. If Caproic acid induces luminescence, it would confirm transcriptional activation of PPARα rather than mere downstream activation.

    4. Author response:

      We thank the Reviewing Editor, Senior Editor, and both reviewers for their constructive evaluation of our manuscript. We are encouraged that the reviewers found the central question, whether donor dietary conditioning modulates FMT efficacy in ALD, compelling and the multi-omics framework a strength. Their critiques converge on a shared theme: the manuscript's mechanistic claims around caproic acid and PPARα signaling currently rest on associative and pathway-level evidence, and would benefit from more direct causal testing and more guarded language. We agree, and we outline below the revisions we plan to undertake.

      Public Reviews:

      Reviewer #1 (Public review):

      While the proteomic and gene expression data suggest activation of pathways related to fatty acid β-oxidation, these measurements do not directly demonstrate increased metabolic flux. The use of the PPARα antagonist GW6471 provides important functional support for the involvement of this pathway; however, this approach primarily establishes pathway dependency rather than directly confirming enhanced β-oxidation activity. The role of caproic acid as a central mediator is plausible but not definitively established. Finally, the link between microbiota composition, metabolic function, and host signaling remains partly correlative.

      We thank the reviewer for this thoughtful assessment. We agree that the GW6471 inhibition experiments primarily support pathway dependency rather than direct activation of PPARα by caproic acid, and we will revise the manuscript accordingly to avoid overstating mechanistic conclusions. However, we would like to clarify that the objective of the current study was not to directly quantify metabolic flux. We agree that metabolic flux should not be used here. We will be modifying this in the text to make it clear that we measured mitochondrial beta oxidation as a response to caproic acid.

      To functionally assess alterations in fatty acid β-oxidation capacity, we performed Seahorse Mito Fuel Flex assays, which demonstrated altered dependency and utilization of fatty acid oxidation pathways in response to caproic acid treatment. We will further clarify this distinction in the revised.

      In addition, we agree that the role of caproic acid as a central mediator and the relationship between microbiota composition, metabolite production, and host signaling remain partly correlative. Therefore, we will moderate the interpretation throughout the manuscript and incorporate additional correlation analyses between microbial taxa, caproic acid levels, and disease-associated metabolic parameters to strengthen the microbiota-metabolite-host association while acknowledging the associative nature of these findings.

      Reviewer #2 (Public review):

      (1) While the Methods section states that each recipient mouse group consisted of 16 animals, microbiome sequencing was performed on only 4 samples per group. This sample size is insufficient, and the high inter-individual variability observed reduces the statistical power and representativeness of the data. I recommend increasing the sequencing sample size or, at a minimum, explicitly acknowledging the risk of false positives due to the small sample size in the Discussion.

      We thank the reviewer for this important comment. We would like to clarify that microbiome sequencing was performed on 6 samples per group and not on 4 samples per group, and we will revise the Methods section to improve clarity regarding the number of biological replicates analyzed. The 4 samples were used only for whole proteome analysis.

      In addition, several previously published murine microbiome studies investigating gut microbial alterations in liver disease and FMT interventions have used comparable sample sizes (typically 5-8 animals per group) for 16S rRNA sequencing analyses [1–3]. Nevertheless, we agree that inter individual variability may influence microbiome analyses, and therefore we will explicitly acknowledge this limitation and the possibility of reduced statistical power in the revised Discussion section. We will also ensure that interpretations derived from microbiome compositional analyses are presented more cautiously.

      (2) The layout of Figure 4 should be adjusted. Panel A should be enlarged for better visibility, while Panel B should be reduced in size to balance the figure composition.

      We thank the reviewer for this suggestion. We will revise the layout of Figure 4 accordingly by enlarging Panel A for improved visibility and reducing the size of Panel B to achieve a more balanced figure composition.

      (3) A rationale should be provided for the selection of egg white protein as the animal protein control. Does this adequately represent animal proteins in general? Could the results differ if casein or whey protein were used? The current choice limits the generalizability of the conclusions, and this limitation should be addressed.

      We thank the reviewer for this important suggestion. In the revised manuscript, we will provide additional rationale for selecting egg albumin as the animal-derived protein source. Egg albumin was chosen because it is a well-characterized protein with high biological value, rapid digestibility, standardized composition, and has also been used in our previous ALD-related dietary intervention studies for experimental consistency [4].

      We agree that egg albumin does not represent all animal protein sources. Due to its rapid digestion and absorption, relatively less substrate may reach the distal gut for microbial fermentation compared with more complex proteins. In contrast, proteins such as casein or whey may generate distinct microbial and metabolite profiles and potentially different host responses.

      Accordingly, we will explicitly acknowledge this limitation in the revised manuscript and clarify that our findings should not be generalized to all animal-derived proteins.

      (4) The ALD model was established over 12 weeks, yet the FMT intervention consisted of only 3 administrations with a 1-week observation period. In the context of such a severe liver injury model, a 1-week recovery period appears insufficient to observe genuine fibrosis reversal, which typically requires a longer timeframe. The authors should discuss whether short-term FMT can truly induce structural remodeling or if the observed effects are transient.

      We thank the reviewer for this important and thoughtful observation. We agree that a one-week post-FMT observation period appears insufficient to conclude complete structural remodeling or durable fibrosis reversal in a chronic 12-week ALD model. Though it should be noted that the results achieved with the one week intervention suggest otherwise in this animal model of ALD. As can be observed from the immunohistochemistry of abstinence and treatment groups, which was further quantified for steatosis and fibrosis, there is a __% and __% reduction respectively in the treatment group. Thus we can safely conclude that in the given animal model, an alternate day FMT for 3 doses can reverse steatosis and fibrosis.

      In the revised manuscript, we will explicitly clarify this distinction.

      (5) The results rely heavily on PICRUSt2 for functional prediction. As prediction does not equate to factual validation, the authors should exercise caution in their wording within the Discussion. Alternatively, I recommend supplementing the study with shotgun metagenomic sequencing to verify the existence of these pathways rather than relying solely on predictive algorithms.

      We thank the reviewer for this important suggestion and agree that PICRUSt2-based analyses represent predictive functional inference rather than direct validation of microbial metabolic activity. We will explicitly acknowledge in the Results and Discussion that PICRUSt2 outputs are inferences rather than measurements, and we will integrate our metabolomics data to show where predicted microbial pathways (fatty acid salvage, β-oxidation related pathways) coincide with measurable metabolite shifts, providing observational support for the predictions.

      We would like to avoid doing metagenomic analysis to substantiate PICRUST2 findings primarily because metagenomic analysis would provide information on the set of genes each species carries, and not the functional state of the resulting pathways. To read out the pathways we would be left with the same two options of PICRUS2 or metabolome analysis. Yes, if we perform transcriptome analysis we can reach to a conclusion on which pathways are active. Which is likely to be similar to the readout we get from the end result of these pathways – the metabolome.

      (6) Although Egg-FMT was less effective than Veg-FMT, it performed better than the standard FMT or abstinence groups. Why is the effect of egg white protein intermediate? Is this due to rapid digestion resulting in insufficient substrate, or differences in metabolite production? A deeper comparative analysis of the Egg-FMT group is required, rather than treating it merely as a negative control.

      We thank the reviewer for this insightful observation. We agree that the Egg-FMT group demonstrated an intermediate phenotype and should not be interpreted merely as a negative control. We will modify the text in the manuscript to mention the outcomes with egg protein, wherever it missing. In the revised manuscript, we will modify the language accordingly and expand the Discussion.

      (7) “Relying solely on the ‘inhibitor blocking effect’ proves only that Caproic acid's function is dependent on the PPARα pathway, not that it directly acts on PPARα. To claim direct activation, the authors must demonstrate direct binding between Caproic acid and the PPARα protein (e.g., via SPR or MST assays). Alternatively, a luciferase reporter assay driven specifically by PPARα response elements (PPRE) should be conducted. If Caproic acid induces luminescence, it would confirm transcriptional activation of PPARα rather than mere downstream activation.”

      We thank the reviewer for this important and insightful suggestion. We agree that the current inhibitor-based experiments primarily support the involvement of the PPARα pathway and do not definitively establish direct interaction or transcriptional activation of PPARα by caproic acid. Accordingly, in the revised manuscript, we will moderate our interpretation and avoid statements implying direct activation based solely on the current data.

      We also agree that direct validation experiments such as SPR/MST-based binding assays or PPREdriven luciferase reporter assays would substantially strengthen the mechanistic conclusions. We are currently planning additional experiments to further evaluate the direct action of caproic acid on PPARα and will incorporate these analyses in future revisions and follow-up studies.

      With the pending experiments we request the Editors to kindly provide us a time of about 2 months to send back the revised manuscript.

      References:

      (1) Mitsinikos, F. T., Chac, D., Schillingford, N. & DePaolo, R. W. Modifying macronutrients is superior to microbiome transplantation in treating nonalcoholic fatty liver disease. Gut Microbes 12, 1792256.

      (2) Ferrere, G. et al. Fecal microbiota manipulation prevents dysbiosis and alcohol-induced liver injury in mice. J. Hepatol. 66, 806–815 (2017).

      (3) Zhang, Y., Li, P., Chen, B. & Zheng, R. Therapeutic effects of fecal microbial transplantation on alcoholic liver injury in rat models. Clin. Res. Hepatol. Gastroenterol. 48, 102478 (2024).

      (4) Mittal, A. et al. Protein supplementation differentially alters gut microbiota and associated liver injury recovery in mouse model of alcohol-related liver disease. Clin. Nutr. 46, 96–106 (2025).

    1. eLife Assessment

      This Review Article provides a compendium of advice for MD-PhD students to consider when deciding which, if any, clinical field they will select for residency training. It is grounded in published data and effectively considers factors including the potential for clinical disciplines to sustain research integration, provide mentorship, meet lifestyle expectations, and foster a long-term career as a research-focused physician-scientist.

    2. Reviewer #1 (Public review):

      [Editors' note: this version has been assessed by the Reviewing Editor without further input from the original reviewers. The review comments were minor and constructive, and the authors have been very responsive.]

      Summary:

      This brief piece by Swartz and colleagues outlines the complexities surrounding the choice of clinical specialty for physician-scientists. It is, in general, clear and well-written, and it will be useful to research-oriented medical students choosing a path and to the mentors who are guiding them.

      Strengths:

      The writing is clear. The points made are not profound, but they are important and will be of use to the intended audience.

    3. Reviewer #2 (Public review):

      Summary:

      This article is a useful compendium of advice for MD/PhD students (and research-focused MD students) to consider when it is time to decide on a clinical field for residency training. The authors are a distinguished group of physician-scientists and program directors who are drawing on published data and their own experience as mentors to provide advice and resources to students about to make what can be a career-defining choice. It makes an effective argument for considering important differences between clinical fields in their ability to sustain research integration, provide mentorship, meet lifestyle expectations, and foster a long-term career as a research-focused physician-scientist.

      Strengths:

      (1) A lot has been written about physician-scientists as an endangered species. Given the important role that physician-scientists can play if they engage in research that is informed by experience in patient care, not nearly enough has been written about the choices that students make during training that can keep them on track or throw them off.

      (2) The article provides not only general advice, but specific information in the 2 tables that can help trainees to weigh their priorities and consider their options.

      (3) Among the best advice is to weigh clinical demands, maintenance of procedural skills, recognition of the impact of research time on salary, and the impact of high salaries on the tension between research effort and clinical effort in clinical departments, which is where most physician-scientists in academia are employed.

    4. Author response:

      The following is the authors’ response to the original reviews

      eLife Assessment

      This Review Article provides a compendium of advice for MD-PhD students to consider when deciding which, if any, clinical field they will select for residency training. It is grounded in published data and effectively considers factors including the potential for clinical disciplines to sustain research integration, provide mentorship, meet lifestyle expectations, and foster a long-term career as a research-focused physician-scientist.

      We thank the editors for this positive assessment. We have revised the manuscript to sharpen the decision-making framework and make the advice more actionable, as detailed below.

      Public reviews:

      Reviewer #1 (Public review):

      This brief piece by Swartz and colleagues outlines the complexities surrounding the choice of clinical specialty for physician-scientists. It is, in general, clear and well-written, and it will be useful to research-oriented medical students choosing a path and to the mentors who are guiding them.

      We thank Reviewer #1 for these supportive comments.

      Strengths:

      The writing is clear. The points made are not profound, but they are important and will be of use to the intended audience.

      We appreciate this assessment and agree that the value of this piece lies in consolidating practical, experience-based guidance in one resource for trainees and mentors.

      Weaknesses:

      I have only minor suggestions for improvement. There are some areas of redundancy where the article could be tightened up by consolidating.

      We agree and have made substantial revisions to reduce redundancy throughout the manuscript. Specifically, we have streamlined the Introduction by removing a lengthy paragraph that previewed the article’s contents in a way that overlapped with later sections. The revised Introduction now concisely introduces five core decision-making factors (alignment between clinical and research interests, the structure of clinical work, availability of mentorship and research pathways, institutional culture, and financial sustainability) and directs readers to the new Table 1 and Figure 1 as organizing frameworks.

      We have also consolidated overlapping discussions of research alignment, protected time, and clinical demands. The sections on clinical workload and protected research time have been tightened to minimize repeated points about specialty-specific demands, and we now cross-reference Table 1 rather than re-stating the same considerations in multiple places. Prose has been revised throughout for concision and clarity.

      Reviewer #2 (Public review):

      This article is a useful compendium of advice for MD/PhD students (and research-focused MD students) to consider when it is time to decide on a clinical field for residency training. The authors are a distinguished group of physician-scientists and program directors who are drawing on published data and their own experience as mentors to provide advice and resources to students about to make what can be a career-defining choice.

      We thank Reviewer #2 for this generous and thoughtful evaluation.

      Strengths:

      (1) A lot has been written about physician-scientists as an endangered species. Given the important role that physician-scientists can play if they engage in research that is informed by experience in patient care, not nearly enough has been written about the choices that students make during training that can keep them on track or throw them off.

      We share this perspective and appreciate the reviewer’s recognition of this gap in the literature. Our goal was precisely to address the decision-making process itself, which is often under-discussed in formal publications despite being a frequent topic in mentoring conversations.

      (2) The article provides not only general advice, but specific information in the 2 tables that can help trainees to weigh their priorities and consider their options.

      Thank you. We have further strengthened the tabular content in this revision by adding a new Table 1 (described below) and renumbering the original tables accordingly.

      (3) Among the best advice is to weigh clinical demands, maintenance of procedural skills, recognition of the impact of research time on salary, and the impact of high salaries on the tension between research effort and clinical effort in clinical departments, which is where most physician-scientists in academia are employed.

      We appreciate this feedback and have made this advice more prominent by incorporating these factors explicitly into the new Table 1 framework and by adding a more direct statement in the text about how specialty-specific structural differences affect the ease of sustaining a research career.

      Area for Improvement

      (1) Some of the most useful pieces of advice are scattered through the text when they might be more impactful if focused. For example, what are the 4 or 5 most essential factors that someone in an MD/PhD or an MD program should weigh when they are deciding between clinical disciplines? There are also published data on the experience of past graduates in achieving a research-focused career in each clinical discipline. How should that data be applied by trainees? What are the factors that should be weighed in deciding where to work as a research-focused physician once training has been completed?

      We agree that the most critical decision-making factors were insufficiently distilled. To address this, we have made two major changes.

      First, we have added a new Table 1: “Key Decision Factors for Physician-Scientists Choosing a Clinical Specialty.” This table identifies five essential factors—(i) Alignment of Clinical Specialty with Research Focus, (ii) Structure of Clinical Work and Its Impact on Research Time, (iii) Availability of Structured Research Pathways and Mentorship, (iv) Institutional Environment and Culture, and (v) Financial Model and Long-Term Sustainability—and for each provides columns describing Why It Matters, What to Look For, and Potential Red Flags. This table is designed to be directly actionable for trainees comparing specialties and programs.

      Second, the Introduction now explicitly names these five factors as the organizing framework for the article and directs readers to Table 1 as a synthesis tool. The prior introductory paragraph, which previewed the article’s structure in a general way, has been replaced with a more focused synthesis.

      Regarding the published outcomes data: we have retained the specialty-specific outcomes data in what is now Table 2 (previously Table 1) and have added context in the text about how trainees should interpret these data—specifically, that published graduation and career outcome data provide a useful baseline but should be weighed alongside institutional context, since the same specialty can look very different at different institutions.

      Regarding factors for evaluating post-training positions: we have added a new paragraph in the section on Protected Research Time that addresses how trainees can evaluate the institutional environment at the faculty level, including specific metrics trainees can examine (see response to Points #4 and #5 below).

      (2) Some clinical fields at academic institutions have proved to be much more hospitable to careers as research-focused physicians than others. Published data highlight the challenges. I believe the authors have tried very hard to present a balanced perspective, but in the process, they have, I believe, missed an opportunity to guide trainees and make them aware of what they should look for to avoid making a decision that may prove incompatible with their long-term goals.

      We appreciate this candid observation and agree that our prior draft was overly cautious in this regard. In the revision, we have added a more explicit statement acknowledging that while successful physician-scientists exist across all specialties, the structural ease of sustaining a research-intensive career varies substantially by field. Specifically, we have added the following language to the section on Balancing Clinical and Research Responsibilities:

      “In practice, specialties with high procedural demands and unpredictable clinical schedules are often more challenging environments for sustaining research-intensive careers unless strong institutional protections are in place. While successful physician-scientists exist across all specialties, the structural ease of sustaining a research-intensive career varies substantially by field, and trainees should approach certain specialties with a clear understanding of the additional negotiation and institutional support required.”

      Additionally, the new Table 1 includes a “Potential Red Flags” column that gives trainees concrete warning signs to watch for when evaluating specialties and programs (e.g., departments primarily driven by clinical revenue with limited research infrastructure; absence of physician-scientists in leadership roles; inability to reduce clinical effort).

      (3) Where will be the jobs for physician-scientists who have an MD ± PhD and want to do research and discovery? How many openings will there be for physician-scientists in academia 5–10 years from now? In industry? How are recent events in Washington affecting the continuation of those jobs?

      after careful consideration, we believe that a detailed treatment of labor market projections, industry trends, and the effects of federal funding policy on the physician-scientist workforce falls outside the scope of this article, which is focused on the decision-making process for specialty selection. We note that the workforce question has been the subject of several recent analyses and commentaries (e.g., Milewicz et al., ASCI/AAP/APSA workforce reports) and feel that a thorough treatment would warrant a dedicated manuscript. We have not added this content but acknowledge the reviewer’s point in our thinking about future work.

      (4) Should one of the “smart choices” in the article’s title be where you do the residency, and not just which residency you do? How important is it to be at a successful, research-intensive medical center/university, both during and after residency and fellowship training? If being in an institution where there are numerous very successful physician-scientists and scientists improves the likelihood of being able to sustain a physician-scientist career, how should graduating students improve their chances of being at one of those institutions?

      This is an excellent point, and we agree that institutional environment is at least as important as specialty choice itself. We have made several changes to address this.

      In the Introduction, we have added the statement: “Importantly, the ability to sustain a physician-scientist career is often determined as much by the institutional environment and training program as by the specialty itself.” This signals early in the manuscript that “where” is as critical as “which.”

      In the new Table 1, we have included a row on “Institutional Environment and Culture” as one of the five key decision factors, with the explicit note that institutional commitment is often more determinative than specialty alone in enabling long-term success as a physician-scientist.

      We have also added a dedicated paragraph advising trainees to assess the broader institutional environment by examining: (i) the number of R01-funded investigators within the department, (ii) the presence of institutional training grants (e.g., T32 programs), and (iii) the track record of trainees transitioning from mentored (K) awards to independent (R) funding. We direct trainees to publicly available resources such as NIH RePORTER and the Blue Ridge Institute for Medical Research rankings.

      Finally, we have added a concluding sentence to the protected time section: “Taken together, these factors reinforce that institutional environment and departmental culture are often as determinative as specialty choice itself in shaping a sustainable physician-scientist career.”

      (5) In every clinical discipline, there are departments that value physician-scientists more than other departments and invest accordingly. What advice would the authors give to help graduating students identify those departments?

      This point is closely related to Point #4, and we have addressed it through the same set of revisions. The new paragraph on evaluating institutional environments provides concrete, actionable guidance for trainees on how to assess departmental commitment to physician-scientists, including specific metrics (R01 density, T32 presence, K-to-R transition rates) and publicly accessible tools (NIH RePORTER, Blue Ridge Institute rankings).

      The new Table 1 “Potential Red Flags” column highlights warning signs that a department may not be supportive of physician-scientist careers, including: departments primarily driven by clinical revenue (RVUs) with limited research infrastructure; lack of protected time enforcement; minimal NIH funding; and absence of physician-scientists in leadership roles.

      We have also expanded the existing discussion in the section on mentorship and residency selection, where we already noted the value of identifying departments with T32 grants and active physician-scientist mentors. The revised text now more explicitly connects these markers to the departmental evaluation process.

      We believe these revisions substantially strengthen the manuscript and are grateful for the reviewers’ constructive feedback.

    1. According to the abstract, “For the classification of deficiency, the ROC-AUC, sensitivity, and specificity for spectrophotometry vs. biomarker-based diagnosis were for iron deficiency 0.62, 68% and 55%, respectively, and for zinc deficiency 0.55, 33% and 91%, respectively.” I do not see how for zinc, a sensitivity of 33% and at the same time a specificity of 91% would be possible given the data in Fig. 2a. According to Tab. 2, of the 72 participants, 6 individuals were classified as zinc-deficient by the reference method (serum zinc) and 17 by spectrophotometry. These individuals should be the six individuals with the lowest serum zinc and the 17 individuals with the lowest spectrophotometer zinc in Fig. 2a, respectively. It can be seen from Fig. 2a that in order to find at least one of the six individuals classified as zinc deficient by the reference method, at least 11 or 12 individuals that are not zinc-deficient according to the reference method would need to be classified as zinc deficient by spectrophotometry. Thus, when incrementally increasing the cutoff value from the minimum to the maximum observed spectrophotometer value, specificity would have already dropped to about 82% by the time the first true positive is found. For the same reason, the ROC-plot (Fig. 4a) seems to contradict the data shown in Fig. 2a. I suspect that when creating the plot, the “direction” might have been set incorrectly, so that spectrophotometer readings higher than the cutoff value were interpreted as zinc-deficient, instead of spectrophotometer readings lower than the cutoff value. With the “direction” set correctly, I’m getting an AUC of about 0.38 and the maximum specificity that would be possible at a sensitivity of 33% would be about 47%. However, since these values of sensitivity and specificity are just the result of an arbitrarily picked cutoff value and it has already been shown that the method does not perform better than chance at identifying zinc-deficiency, these values should not be used for characterizing the performance of the spectrophotometer method.

    1. flourish

      I think this is true in education - you have to go into any class with the belief that you have something to learn or you won't. If you walk into a class feeling that you already know it or that the teacher has nothing to offer you, you won't learn. A humble student knows they have much to learn. But the same is also true of the teacher - they need to make sure they realize they have things to learn as well as that symbiotic relationship can be magic.

    2. others

      I think this also is crucial for students with bad experiences in education - they need to forgive the educator that they feel wronged them or they can't often move on and focus on learning new material as they continually just feel bad about it.

    1. human strengths.

      This can be very helpful to students - not what they are bad at, but what they are good at. The difference between you got 2 wrong rather than 18 right.

    2. I think this can be very helpful with students - seeing their strengths. The focus not on what they are bad at, but what they are good at and how to enhance that.

    1. Thirty needle blights (in six groups of five)

      DM INFO: Modify as 2024 rules give them more HP than 5. does so send out four groups of 5

    2. Unless they have been drawn outside, five needle blights and one druid (NE male human) lurk in the eastern portion of the cellar. If they are here when the characters enter that part of the cellar, read:

      the druid and three needle blights were drawn outside. two remain be hind the wine racks

      PC INFO: Something moves behind the eastern wine rack. Through the holes, you glimpse two humanoid figures.

    1. Ancestor worshipis rooted in the belief that happiness of the deceased in the afterlife depends on thesacrifices of the living

      I believe the Chinese (or more cultures, I'm unsure) leave things made out of paper for the deceased. Such as paper iphones, paper cars, paper stacks of money. I knew it was because they were "providing" for the deceased but didn't know that the deceased depended on them. Also, contrasts other religions in which in death we leave all material posessions as we don't need them anymore.

    2. The debate over whether kinship is a process of ‘doing’ through love and care, orwhether it is essentialized through blood and marital ties (‘kinship as being’), runs therisk of overlooking its more fluid dimensions.

      The concept of filial piety being complex and nuanced gets watered down by these assumptions.

    3. Curiously, when caregiving is unpaid, ‘filial heart’ can erode over time.This occurs because society tends to expect filial heart from kin, without recognizingor appreciating it fully. In contrast, paid care means there is no moral debt betweencaregivers and recipients, leading to a different power dynamic in the care practices.

      Reenforces that obligate filial piety can be emotionally, and physically, draining.

    4. However, as the old saying suggests, a lengthy and taxing commitment would eventuallydeplete both affection and patience, leading to a loss of ‘filial heart’.

      The correlation between this belief and the feeling of filial piety carried by caretakers might be correlated.

    5. They also appreciate the social and emotionalvalue added to this service, which grows into a family-like bond of trust over time. Haialso sees his role as fostering this kind of fictive kinship, making caregiving feel muchlike visiting his own family

      I wonder if outside of family filial piety cultivates a reciprocal feeling of familial bonds because of the value of filial piety or is it just a human nature thing to become close to those we spend a lot of time with. Family in a social context seems to be ever-growing as well.

    1. Gripp is the operating system for farms, manufacturers, and dealers. Built for the field.

      We're not going to be able to blanket 1 phrase to cover both Pulse and Rendezvoo, we'll need to split these out. We are definitely not the operating system for OEMs and Dealers, and I'm not sure it's clear enough to say it for farms, no body is looking for an operating system, and I'd like to use something that is easily applied outside of Ag.

    1. What share of cultured meat companies (those with capex over $10 million) will design and build their own bioreactors by 2036?

      Consider: is this more about fit-for-purpose equipment vs. pharma-grade-- the former could also include CM-specific B2B offerings.

    1. has existed in aparallel universe to social and personality psycholog

      because it is not scientifically backed up by social psychology, social psychology actually tends to disagree with the mbti theory

      his ideas were based on argumentation and anecdotal observation rather than empirical evidence, Sperber (2010) suggested that there is the existence of a "guru effect" where people assume statements from authority figures have truth

    Annotators

    1. Regulatorydata: confirmed

      Maybe this could be removed. It doesn't fit under epidemiology.

      We could include more data under epidemiology: 1. Rate of New Cases and Deaths per 100,000 - this is line graph 2. Percent of Cases by Stage 3. Year Relative Survival by Stage at Diagnosis - two graphs here 4. Percent of New Cases by Age Group

      You can find the above data at https://seer.cancer.gov/statfacts/

      1. Regional differences - some cancer types have regional differences (e.g. Esophageal Squamous Cell Carcinoma is mostly commin in East Asia)
    1. For related information

      Looks like the de Mul citation is not linked, just the doi:

      De Mul N, de Jong V, Cremer O ... Practical guidance for validating the predictive performance in the presence of missing data: a guide for the clinical researcher Journal of Clinical Epidemiology, 2026; 192

    1. . It is also linked to higher levels ofsatisfaction with the international student experience (Rohrlichand Martin, 1991) as well as lower levels of homesickness andsocial isolation

      this insinuates that international students may feel better when they feel more integrated with the home culture they are in

    Annotators

    1. Ethnic Studies is the critical and interdisciplinary study of race, ethnicity, and Indigeneity, focusing on the experiences and perspectives of diverse Black, Indigenous, and People of Color (BIPOC) communities.

      feels great to be a indigenous person of earth ( ethnic studies the critical study of indigenous black people . )

    1. In the over fifty years since the founding of Ethnic Studies as an academic field, it has grown substantially to include a range of scholarly associations, degree-granting programs at all levels of higher education, growth in the K-12 education system, inclusion within general education curricula, and as a site of struggle and solidarity for racial justice, decolonization, and intersectionality. S

      12 education system , has grown substatially in 2026

    1. Ethnic Studies is literally my life. It’s helped me understand my life. Seeing that my challenges and my mother’s challenges were mirrored in the classroom, I began to understand that the hardships I’ve endured as a woman of color is not mythical (it can feel that way when it’s not legitimized, because our society acts like we’re past issues of racism, sexism, and so forth). In navigating my own life, Ethnic Studies taught me how to decide for myself.

      while navigating challenges were mirrored in the classroom

    1. Our work in the classroom inspired my peers and myself to advocate for justice and equity for our communities, including creating the group SLO Solidarity to demand recognition of the racism on campus and that administrators develop policies, resources, and services to address the needs of historically underrepresented groups. This led to the creation of new initiatives for transfer students, undocumented students, students of color, and first-generation college students, which continue to this day.

      classrooms inspired my peers and myself to advocate for justice

    2. Oregon State University (OSU) didn’t have an ‘official’ Ethnic Studies department when I arrived, but they had one when I left. We also had a Native American Longhouse/cultural center which was why I went to OSU in the first place. You could major in American Studies with an Ethnic Studies emphasis in a specific core discipline area.

      wow that's great to add ethnic studies . What would you have added ? A great introduction to students .

    3. Just as some students express being saved by Ethnic Studies,

      wow ethnic studies acts as a superhero, cant wait till the update to the alphabet. Knowing that blacks created the alphabet .

    1. As Ethnic Studies has recently become a requirement for the California State University (CSU) system,

      Ethnic studies is a requirement for California state university's

  8. markusstrasser.org markusstrasser.org
    1. Malcolm pretends to be worse

      according to Bishal it's not a pretense, it's rather that the circumstances that came up for Macbeth won't come up

      Or rather, it's making the point that virtue only comes up from circumstance.

    2. How tender ’tis to love the babe that milks me: 61 I would, while it was smiling in my face, 62 Have pluck’d my nipple from his boneless gums

      Judy Dench delivers this line in a sad way. She's saying that the ambition of Macbeth becoming king is so strong, that if she had it she would be forced by it to murder her babe.

    1. My AI Workflow (Without Losing My Skills)
      • The Risk of Skill Erosion: The author highlights the danger of automation leading to an engineering skill deficit. Similar to how ORMs or Garbage Collection can distance developers from underlying SQL or memory management, over-relying on AI agents risks creating developers who cannot debug or evaluate AI-generated production code.
      • The "Remote Work" Parallel: Drawing an analogy to post-COVID remote work, senior engineers can currently leverage AI effectively because they already possess pre-existing, co-located-style foundational engineering skills. The true challenge lies in how newcomers will develop these baseline skills in an AI-first environment.
      • Dual-Track Approach to Coding:
        • Vibe Coding (Internal/Prototypes): For internal productivity tools, quick local prototypes, and automation scripting (e.g., audio manipulation with ffmpeg), the author embraces complete AI delegation, ignoring code quality entirely.
        • Production Engineering: Every single line of AI code shipped to production is reviewed 100%. The author actively aims to write code manually roughly 50% of the time using traditional text editors to maintain sharp, fundamental skills.
      • Strategic Leverage of Claude Code:
        • Planning: The author drafts structural plans independently first, then compares them against Claude's suggestions to ensure critical thinking isn't outsourced.
        • Omega Messes: Claude Code is intentionally deployed to write highly isolated, heavily tested components (referred to as Sandi Metz's "Omega Messes") to maximize speed without polluting core architectural layers.
      • Reallocating Saved Time: Instead of using a 5x velocity boost to hyper-focus on building a frenzy of unneeded features (which ultimately increases stress and decreases user value), the saved time is strategically spent on deliberate breaks, deep architectural thinking, and vetting the actual product utility.
      • Real-World Case Study (Shadow Boxing App): The author details migrating a 5-year-old app from Apple's legacy Speech Synthesis framework to an MP3-based ElevenLabs API approach:
        • Vibe Coded the batch audio processors, silence-removers, and config verification tools.
        • Manually Coded the initial core legacy API refactoring and the user interface layout.
        • Delegated to Claude the tedious edge-case handling for the stateful AudioManager (managing Bluetooth latencies, AirPlay interruptions, Siri, and incoming phone calls).
    1. See biostat.app.vumc.org/DynamitePlots for a list of the many problems caused by dynamite plots, plus some solutions.

      Link is dead, but the original is available here as "24-dynamite.pdf"

    1. Three AI principles every exec leader needs to understand
      • AI operates on statistical patterns, not semantic understanding: Modern AI systems function as pattern-matching engines trained on historical data. They don't understand context or meaning the way humans do, meaning they cannot organically distinguish fact from fiction.
      • AI is inherently non-deterministic and probabilistic: Unlike traditional software which is deterministic (Input X always equals Output Y), AI is probabilistic (Input X yields Output Y with a confidence level of Z). The same input can produce different outputs every time.
      • Errors, bias, and hallucinations cannot be entirely eliminated: Because AI reproduces historical data patterns and hallucinates plausible-sounding fabrications, errors are a native feature rather than a fixable bug. Improving accuracy comes with exponential costs in data, fine-tuning, and human review.
      • Risk tolerance and governance are strategic decisions: Because AI errors are inevitable, executives must determine what error rate their specific business use case can tolerate. Compliance and governance are becoming mandatory as frameworks like Article 4 of the EU AI Act demand demonstrable oversight and sufficient AI literacy among personnel.
      • Data integration is essential but insufficient on its own: Clean, structured, and accessible data is required for AI to work at all. However, long-term competitive advantage relies on intentional design and proprietary data layers (such as semantic layers) rather than just connecting to third-party models.
      • True business advantage lies in the application and organizational layer: Redesigning operational workflows, changing the business operating model, and integrating AI into daily operations dictate where the real value and step-change productivity gains are realized.
      • Human-in-the-loop collaboration outperforms full automation: While AI can boost individual productivity on specific tasks by 30–50%, the most robust results come from human-AI partnerships (diagnostic complementarity) where humans catch errors and AI scales expertise.
    1. 15 principles for managing up
      1. Treat managing up as a true partnership: Proactively adapt to and embrace collaboration with your manager rather than remaining passive or treating the relationship as a purely top-down power dynamic.
      2. Lead with the punchline: Reverse traditional storytelling by stating your conclusion, headline, or recommendation first, ensuring busy executives know exactly why they should care right away.
      3. Show your thinking process: Map out the logical steps and considerations behind your conclusions so your manager can easily follow and trust your rationale.
      4. Flag potential risks early: Surface issues or roadblocks before they escalate into an immediate crisis, giving your manager time to help course-correct.
      5. Bring solutions, not complaints: When presenting a problem, always pair it with actionable solutions or structured options rather than simply unloading the issue onto your manager.
      6. Prioritize the information you share: Filter out noise and organize updates by importance to significantly reduce the cognitive load on your manager.
      7. Keep your manager loop-aware: Provide consistent, predictable updates so your manager is never left in the dark or caught off-guard by external inquiries.
      8. Differentiate micromanagement from under-communication: Evaluate whether a manager's constant hovering is actually due to your own lack of proactive communication and visibility.
      9. Over-communication is often the baseline: What feels like "too much" communication to you is frequently just the right amount of context and security required by a busy leader.
      10. Proactively suggest next steps: Take immediate ownership of your workflow by mapping out and presenting the logical follow-up actions yourself.
      11. State assertions and opinions, don’t just ask questions: Move away from open-ended questions and instead state clear recommendations, backing them up with data or reasoned perspectives.
      12. Anticipate your manager’s questions: Pre-emptively think through the pushback, blind spots, or clarifying details your manager will likely ask about, and address them upfront.
      13. Adapt strictly to their preferred communication channels: Match your manager’s style—whether they prefer quick Slack updates, structured formal documents, or async deep dives.
      14. Build trust before you actually need it: Consistently deliver on small commitments over time to establish a reliable track record, securing autonomy and leeway for future high-stakes initiatives.
      15. Be direct and honest with feedback: When explicitly asked for your opinion or critique, respect the trust given to you by offering specific, actionable, and psychologically safe feedback.
    1. The ZOE Daily30+ trial is interesting, but its claims should be interpreted narrowly.

      The study shows that a fixed high-fibre, plant-based prebiotic blend can shift gut microbiome composition over six weeks in healthy adults. It also reports improvements in some subjective outcomes, including gut symptoms, hunger, satiety, energy and anxiousness. However, the trial does not establish that the supplement produces meaningful clinical benefit, nor that it is superior to a well-designed dietary intervention.

      The main limitation is the comparator. Daily30+ was compared with bread croutons and a single-strain probiotic, Lacticaseibacillus rhamnosus GG. That is not a strong ecological comparison. A 30-plant fibre/polyphenol blend is metabolically and ecologically much broader than one probiotic strain. It is therefore unsurprising that it produced broader microbiome shifts.

      A more meaningful trial would compare Daily30+ against Mediterranean-diet advice, a diverse whole-food high-fibre intervention, or a broad-spectrum probiotic combined with the same dietary guidance. Without that, the trial cannot answer the practical question: does this supplement add anything important beyond eating a diverse Mediterranean-style diet?

      The diversity findings also need careful interpretation. The intervention appears to shift the microbiome toward species ZOE classifies as favourable and away from species it classifies as unfavourable. But that is not the same as showing improved alpha diversity. In fact, the paper reports only limited alpha-diversity improvement, and observed richness decreased in the prebiotic arm. This suggests ecological steering, not simple enrichment.

      There is also a broader immunological concern. Daily30+ is an invariant ecological input applied across diverse hosts. A Mediterranean dietary pattern preserves variability: different plants, fibres, polyphenols, fermented foods, oils, fish, regional traditions and individual choices. A fixed supplement applies the same selective pressure across people with different HLA backgrounds, immune histories, inflammatory states and microbiome equilibria.

      That matters because host–microbiome interactions are not purely metabolic. They are immunological. The same microbial or metabolite shift may be beneficial in one host but provocative in another, especially where HLA-associated antigen presentation or autoimmune susceptibility is relevant.

      The trial does not resolve this. It was short, conducted in healthy adults, and not designed to test autoimmune safety, inflammatory subgroups, HLA-defined risk, or long-term ecological consequences.

      So the strongest interpretation is modest: Daily30+ can alter the microbiome and may improve some self-reported gut and satiety-related symptoms over six weeks. But the trial does not show superiority over Mediterranean-style eating, does not prove broad clinical benefit, and does not address whether imposing a fixed ecological pressure is appropriate across immunogenetically diverse populations.

      From a pragmatic public-health perspective, the cheaper and better-supported advice remains: eat a diverse Mediterranean-style diet rich in whole plants, fibre, legumes, nuts, olive oil, fish and minimally processed foods.

    1. Dirichlet Priors With Concentration Parameter 0.148 for Intercepts

      Prior on the Intercepts: depend on number of levels; automatically estimated by the function.

    1. We've made the world too complicated
      • Overwhelming Systemic Complexity: The author feels crushed by a hyper-complex world characterized by incomprehensible technology, rigid urban zoning, and top-down laws beyond ordinary citizen control.
      • The Cost of Abstraction: Modern life is lived in an abstract, compressed environment that inflicts continuous, unconscious physical and mental stress (e.g., clenched jaws, shallow breathing, persistent confusion).
      • The AGI Illusion: While the tech industry presents Advanced General Intelligence (AGI) as a ultimate savior for human issues, the author notes that society often convinces itself of noble intentions while actually engineering deeper cycles of manipulation and destruction.
      • The Desire to Disconnect: There is a raw, instinctual urge to destroy devices and completely abandon modern societal obligations, even though acting on these impulses risks being labeled an isolated lunatic.
      • Radical Simplification: The initial essay suggests that humanity's greatest gift to itself and the planet might be "to do as little as possible"—relying on primitive intuition and simply appreciating nature (birds, wind, water) and core human emotions.
      • Re-evaluation and Engagement: In a post-script written after watching Adam Curtis' Hypernormalisation, the author acknowledges their original thoughts as somewhat naive. They conclude that simply retreating into an imagined simple past is dangerous and renders an individual powerless; instead, one must strive to critically understand the world's complexities to gain the knowledge and leverage necessary to effect real change and alleviate human suffering.

      Hacker News Discussion

      • The Reality of Engineering: Some commenters suggest the essay reads like an engineer or software professional waking up to the reality that the world possesses far more multi-faceted complexity than any one person can ever master in a lifetime.
      • Alienation and Abstract Labor: Many users attribute this feeling of overwhelm to white-collar remote work. Unlike immediate, local trades (e.g., cooking, baking, bike repair) where tasks start and finish quickly for real people, modern abstract corporate loops remain open for months or years, fostering a deep sense of Marxian "alienation" and lack of control.
      • Shrinking the Circle of Concern: It is argued that technological societies are inherently engineered to perpetually increase in complexity. The only way to make life manageable is to artificially minimize one's own "world" by prioritizing local communities and immediate surroundings rather than trying to fix or process the whole globe.
      • Systemic Traps and "Moloch": Commenters note that the "we" who built this complexity is a vast, hyper-connected collective stretching across generations. This web is so intricate that even good intentions backfire, with some comparing the unstoppable march of systemic complexity to "entropy" or the coordination failure concept of Moloch.
      • The Morality of Doing Nothing: The author's idea of "doing as little as possible" sparked a debate on systemic impact. Commenters point out that for employees at toxic corporations (e.g., Meta or Philip Morris), staying home and doing nothing is indeed a net moral good; however, for essential roles like teachers and nurses, passive withdrawal harms society.
    1. being able to access resources to afford the necessities of life — like affordable housing, healthy foods, and adequate health care. But in the United States, nearly 1 in 10 older adults lives6 in poverty

      This is such an unfortunate statistic. We are noticing nowadays the severity in inflation that has made the prices of housing, groceries, gas, etc. all excessively expensive. People are having hard times affording basic life needs which is not okay. There is ongoing increase in the amount of individuals living in poverty which has yet to be addressed efficiently. As the prices of things go up, we notice that pay and assistance from the states are not meeting people at a common ground. When a person is making less than it cost to live, there is a problem. These issues only promote further health challenges like being able to afford medications, appointments/check ups, etc. People are unable to take care of themselves sufficiently which is a huge issue.

    2. accessible homes and reliable public transit can allow older adults to live independently. And safe, wheelchair-accessible sidewalks, trails, and green spaces make it easier for everyone, including older adults, to get regular physical activity.

      Access to safe transportation is huge in implementing healthier behaviors for aging individuals. For hose who require advanced modes of transportation or help from another individual to get them to their appointments, public transit is essential. Some states even organize transportation groups that are designed to help older individuals who may be disabled or need the assistance. Access to such transportation allows people to stay on top of their own health and be able to make their appointments adn continue care with providers. For those who aim to maintain their independence as long as they can, public transportation is a great way to do so. Even if they cannot drive themselves they still have options to keep mobility.

    3. And transitioning from employer-sponsored health insurance plans to Medicare can complicate coverage and require people to switch providers

      There are so many limiting factors to healthcare that we are noticing in todays society. Medicare is a widely used form of insurance provided through the government for lower income individuals, yet it does not provide access to all possible needs. Many are limited to the type of care they receive solely based on what organizations accept Medicare. Many offices choose to not work with this program so that they can make more profit. It is a sad reality that even aging individuals who need the extra help for possible health conditions are limited to what they can recieve and afford.