1. Last 7 days
    1. The diagram compares these two operating modes side-by-side. Batch mode (left) harvests everything at once; perfusion (right) continuously adds fresh media and removes spent media while retaining cells.

      too much white space before and after image

    2. The opportunity: If cultured meat can use simplified food-grade designs (similar to beer brewing at $5-15/L), costs could drop by 10×.

      are they already doing this? If so, maybe adjust the wordking/emphasis here

    3. of cells matters enormously for cost:

      "enormously for cost' Seems potentially too strong here. ... as we have suggested above, the estimated cost share for cell banking is less than 1% of the total cost.

      Am I correct? If so, please moderate this.

    4. Step 1: Cell Banking

      For each step, give a 'tldr' and an estimated cost share, and have the rest be something folded by default, which they can unfold

    5. Today, optimistic projections suggest ~$63/kg (Garrison et al. 2022), with leading companies achieving <$10/kg cell mass.

      Flag a note (more discussion in tooltip) about how this is the cost of pure cell mass, and early/ultimate products might be hybrid CM, plant-based, fungal etc. ... so this overstates the cost, in a sense

      "Achieving $10/kg" is probably too strong. Maybe 'claiming the ability'? And do you have a link to this?

    6. Product

      diagram below a bit small. Last item looks like a drumstick -- maybe make it look like a 'chicken hamburger' instead? (Because early products unlikely to have bones)

    1. teach a lesson” to “inferior” conquered peoples.

      I don't understand why people thought this was ok. Just because you are going to wear with a country doesn't mean you can abuse them because of racism.

    1. State-Controlled Media OrganizationsIran’s state-controlled media has played a key role in the regime’s suppression of protests, including those following the death of Mahsa Amini. Many of these organizations work in tandem with Iranian security and intelligence services, blurring the lines between government and media and extending the regime’s oppressive reach. Press TV is the English language channel for the state broadcaster of the Iranian government, Islamic Republic of Iran Broadcasting (IRIB), which was designated by the United States in 2013 for participating in censorship. Press TV has broadcasted scores of forced confessions and derogatory programs about Iranian activists, in many cases broadcasting forced confessions before detainee trials. Press TV has also been used by Iranian intelligence services to recruit sensitive assets, including U.S. persons. Press TV is being designed pursuant to E.O. 13846 for being owned or controlled by, directly or indirectly, the IRIB. Tasnim News Agency (Tasnim) is a news outlet founded by two IRGC commanders, Majid Gholizadeh and Hamidreza Moghadam Far, who continue to serve as Tasnim executives and exert control over Tasnim on behalf of the IRGC. Tasnim has supported the IRGC and other instruments of the regime in various ways, including suppressing dissent by helping the IRGC, Iran’s Ministry of Intelligence and Security, and LEF to crowdsource the identities of protestors. Majid Gholizadeh, a former IRGC Commander, is Tasnim’s CEO, an important spokesperson for the news agency, and IRGC propagandist. Hamidreza Moghadam Far is the head of the Tasnim board of directors and an IRGC Commander. Hamidreza Moghadam Far has held multiple prominent roles in the IRGC, including as an advisor to IRGC Commander-in-Chief Hossein Salami and the Cultural Deputy of the IRGC.  Tasnim is being designated pursuant to E.O 13553 for being owned or controlled by, or having acted or purported to act for or on behalf of, the IRGC. Hamidreza Moghadam Far is being designated pursuant to E.O. 13553 for acting or purporting to act for or on behalf of, directly or indirectly, the IRGC. Majid Gholizadeh is being designated for having acted or purported to act for or on behalf of, directly or indirectly, Tasnim News Agency.Fars News Agency is closely affiliated with the IRGC and has provided special intelligence reports to Hossein Salami. Fars News Agency closely coordinated with the Basij Resistance Force (Basij) deputy commander on ongoing Iranian domestic concerns. The Basij, a paramilitary force subordinate to the IRGC, was designated pursuant to E.O. 13553 on June 9, 2011 for its involvement in the violent crackdowns and serious human rights abuses occurring in Iran following the disputed June 2009 presidential election. Fars News Agency was also founded by Hamidreza Moghadam Far, and its board of directors is chaired by Mohammad Mehdi Sayyari Zahan, the U.S.-designated deputy head of the IRGC Intelligence Organization. Payam Tirandaz is the CEO of Fars News Agency, a former member of the Basij, and a former employee of IRIB. Payam Tirandaz plays a pivotal role in Fars News Agency’s support to the IRGC’s malign activities. Fars News Agency is being designated pursuant to E.O 13553, for being owned or controlled by, or having acted or purported to act for or on behalf of the IRGC. Payam Tirandaz is being designated for having acted or purported to act for or on behalf of, directly or indirectly, Fars News Agency.
    2. September 15, 2023 WASHINGTON — Today, the U.S. Department of the Treasury’s Office of Foreign Assets Control (OFAC) is designating 29 individuals and entities in connection with the Iranian regime’s violent suppression of nationwide protests following the death of Mahsa “Zhina” Amini in custody of its ‘Morality Police,’ and the regime’s continued efforts to detain dissenting voices and restrict access to a free and open internet. OFAC’s action targets: 18 key members of the regime’s security forces, the Islamic Revolutionary Guard Corps (IRGC) and the Law Enforcement Forces (LEF); the head of Iran’s Prisons Organization; three individuals and one company in connection with the regime’s systematic censorship and blocking of access to the internet; and three IRGC and regime-controlled media outlets––Fars News, Tasnim News and Press TV––and three senior officials. Today’s action is taken in coordination with partners from the United Kingdom, Canada, Australia, and other partners who are also imposing sanctions on those involved in the Iranian regime’s repression.“As we approach one year since Mahsa Amini’s tragic and senseless death in the custody of Iran’s so-called ‘Morality Police,’ we recall that the movement of men and women across Iran, inclusive of different faiths and ethnic groups, was met with horrific violence, mass incarceration, and systemic internet disruption by the Iranian regime,” said Under Secretary of the Treasury for Terrorism and Financial Intelligence, Brian Nelson. “The United States, alongside the United Kingdom, Canada, Australia, and our other international allies and partners, will continue to take collective action against those who suppress Iranians’ exercise of their human rights.”Today’s sanctions are OFAC’s 13th round of designations in connection with the protests that began in September 2022 and are taken pursuant to Executive Order (E.O.) 13553, which imposes sanctions on certain persons with respect to serious human rights abuses by the Government of Iran; E.O. 13846, which authorizes sanctions on persons who engage in censorship or other activities with respect to Iran; and the counterterrorism authority E.O. 13224, as amended.  Concurrently, the Department of State is imposing visa restrictions on 13 Iranian officials and other individuals for their involvement in the detention or killing of peaceful protestors or inhibiting their rights to freedom of expression or assembly, including through censorship via a country-wide internet shutdown in Iran. Since Mahsa Amini’s death and the protests that followed, the Department of State has imposed visa restrictions on 40 Iranian officials and other individuals for their involvement in acts targeting peaceful protestors.
    1. China produced about 33 percent of all the manufactured goods in the world, with India and Europe each contributing about 23 percent

      I find it interesting that china makes up more production than India and Europe together.

    2. Where India and China accounted for a little over half of the wealth in the world in the eighteenth century,

      I find it very interesting that the made up this much of the wealth. That is a lot

    1. For an article with no known author, use the source title in place of the author’s name, formatted as it would be (i.e., italicized or enclosed in quotation marks) in your Works Cited section.You may abbreviate the title, using only the first few words:

      if no author

    2. If you are using a website or other electronic source that does not have page numbers, use only the author’s name or title of the source in the in-text citation.   Here are examples:   If the source has page numbers: (Pauling 113).  If the source does not have page numbers: (Pauling).  If the source has page numbers: (“Bilingual Minds” 113).  If the source does not have page numbers: (“Bilingual Minds”).

      what you need to know when the article does not have page number

    3. Usually, the Works Cited source entry will begin with an author’s last name. If there is no author, then the name of the article is the first information listed.

      some article do not have authors

    4. The purpose of the in-text citation is to show the reader the source of the information the writer is citing. So, the information in the in-text citation needs to lead directly to the source listed in the Works Cited page

      show the reader where you got the information from.

    5. Place the in-text citation at the end of the sentence containing the information cited. Do not simply put the in-text citation at the end of a paragraph. Show the reader which sentences include source material. If all the sentences in your paragraph comes from one source, that’s your cue to start analyzing and interpreting your sources more. You can learn more about analyzing and interpreting sources in

      where to place your text citation

    6. You must cite your sources as you use them. In the same way that a table or figure should be located right next to the sentence that discusses i

      it important to know where to place your text citation.

    7. In the professional world, plagiarism results in loss of credibility and often compensation, including future opportunities. In a classroom setting, plagiarism results in a range of sanctions, from loss of a grade to expulsion from a school or university. CNM outlines the consequences for academic dishonesty in its Code of Conduct. In both professional and academic settings, the penalties are severe.

      not giving someone credit for their work it is plagiarism and it does not really help us during our future and especially if you goes to collage and university.

    8. If you do not credit the work of other writers –taking credit for their work as if you wrote it—you are committing plagiarism. If you do not enclose direct quotes in quotation marks or cite the source, you are committing plagiarism.

      when using someone's work always cited it

    9. n your paper, when you quote directly from a source in their words, or when you paraphrase someone else’s idea, you need to tell the reader what that source is so the author gets credit for their words and ideas.

      don't use someone's work and get credit for it

    10. In your paper, when you quote directly from a source in their words, or when you paraphrase someone else’s idea, you need to tell the reader what that source is so the author gets credit for their words and ideas.

      tell the reader where the information came from if you were to quote words from sources

    11. This material must always be cited:  A direct quote  A statistic  An idea that is not your own  Someone else’s opinion  Concrete facts, not considered “common knowledge”  Knowledge not considered “common”

      what is need to cited

    12. Your paper should include no more than 25% direct quotes (and many instructors will think this is too high a percentage). If you have too many direct quotes, paraphrase information from your source instead of using direct quotes. Remember: you are writing this paper. Your words should be the most prominent aspect of your paper.

      don't just relay on quotes your words are also important your words are what is need the most

    13. When writing, make sure you inform the reader when you are using information from a source, whether that be direct quotations or paraphrasing information. And, it should be equally clear when you are expressing your own ideas.    If someone else wrote it, said it, drew it, demonstrated it, or otherwise expressed it, you need to cite it.

      let your reader know when you're using information from other source or cited

    14. The ninth edition of the MLA Style Guide states that your in-text, or parenthetical, citations should do the following: Clearly indicate the specific sources also referenced in the works cited Specifically identify the location of the information that you used Carefully create a clear and concise citation, always confirming its accuracy Check out the video below for more discussion of your in-text citations.

      this checklist is need for your MLA

    15. If you follow MLA style and indicate your source both in your essay and in the Works Cited section, you will prevent the possibility of plagiarism. If you follow MLA guidelines, pay attention to detail, and clearly indicate your sources, then this approach to formatting and citation offers a proven way to demonstrate your respect for other authors and artists.

      this will help you to avoid plagiarism.

    16. The in-text citation is offset with parentheses, clearly calling attention to itself for the reader. The reference to the author or title is like a signal to the reader that information was incorporated from a separate source. It also provides the reader with information to then turn to the Works Cited section of the essay (at the end) where they can find the complete reference.

      using the text citation this always help the reader to know where you got your information

    17. In-text citations are used throughout your paper to credit your sources of information. In MLA style, the in-text citation in the body of the essay links to the Works Cited page at the end. This way, the reader will know which item in the Works Cited is the source of the information.

      it is always important to cited your source content

    1. Exploring through colors: Each photo page has a list of the top eight colors in the photo. When you click on a color, you can explore all the other photos in which that color is one of the the main ones. In this way, all my photos are connected aesthetically. The navigation on a photo page is within the event.

      Interesting web design idea for photography websites. Each photo lists with the photo meta data and description the top eight colors in the photo. Visitors can select any one of colors and seen an archive of every photo where that is one of the top eight featured colors.

    1. This model helps evaluators and forecasters:

      But atm we donm't have confidence in this model. I's more about fixing ideas and giving people a sense of what sort of modeling we want (and surfacing doubts and disagreements on this) so that we can productively collaborate.

      Ideally, we'd also have a page/interface where people could 'build their own models' and we compare them.

    1. New to this topic? How Cultured Chicken is Made | 🎧 Audio Review (22 min MP3)

      Skip this last bit. Try to condense the content at the top a bit more for this page

    2. 💬 We Want Your Feedback! Comment directly on this page using Hypothesis — click the < tab on the right edge. Highlight any equation, parameter, or explanation to annotate it. We actively monitor comments and will respond to questions, incorporate suggestions, and improve the documentation based on your feedback.

      Make this list prominent/folded.

    3. 🔬 Workshop: Cultured Meat Cost Trajectories (Late April / Early May 2026) This model feeds into The Unjournal’s upcoming expert workshop on CM production costs. Workshop details & signup →

      Don't need this at the top of the technical reference page.

    1. Cultured Chicken Production Cost Model CodeShow All CodeHide All CodeView Source

      More caveats about this model ... largely AI generated, as of 27 Mar 2026 we can't vouch for the numbers, provided to give a sense of the sort of modeling we're interested in, and present a framework for discussion and comparison

    2. These are like Squiggle/Guesstimate visualizations - they show the full range of possible values, not just a point estimate.

      Based on which parameters? the user-entered ones above?

    3. Basic Parameters Code viewof plant_capacity = Inputs.range([5, 100], { value: 20, step: 5, label: "Plant Capacity (kTA/yr)" })

      Important -- are these means or medians of a distribution used in simulation or are these simple 'degenerate' numbers. Explain and signpost better

      And do they affect the figures and graphs below? #important

    4. Individual distributions for each cost driver: Code function formatCost(val) { if (val >= 30) return Math.round(val).toString(); if (val >= 1) return val.toFixed(1); if (val >= 0.1) return val.toFixed(2); return val.toFixed(3); } { const allComponents = [ {name: "Media", data: results.cost_media, color: "#27ae60"}, {name: "Micronutrients", data: results.cost_comm_micros, color: "#3498db"}, {name: "Growth Factors", data: results.cost_recf, color: "#9b59b6"}, {name: "Other VOC", data: results.cost_other_var, color: "#7f8c8d"}, {name: "CAPEX (annualized)", data: results.cost_capex, color: "#e74c3c"}, {name: "Fixed OPEX", data: results.cost_fixed, color: "#f39c12"}, {name: "Downstream", data: results.cost_downstream, color: "#1abc9c"} ]; // Filter out components with all zeros (e.g., downstream when not included) const components = allComponents.filter(c => mean(c.data) > 0.001); const plotData = components.map(comp => { const p5 = quantile(comp.data, 0.05); const p50 = quantile(comp.data, 0.50); const p95 = quantile(comp.data, 0.95); const clipVal = Math.max(quantile(comp.data, 0.98), 0.1); const clipped = comp.data.filter(x => x <= clipVal && x >= 0); const plot = Plot.plot({ width: 420, height: 180, marginLeft: 45, marginBottom: 35, marginTop: 10, x: { label: "$/kg", domain: [0, clipVal * 1.1] }, y: { label: null, ticks: [] }, marks: [ Plot.rectY(clipped, Plot.binX({y: "count"}, {x: d => d, fill: comp.color, fillOpacity: 0.7})), Plot.ruleX([p5], {stroke: "black", strokeWidth: 1.5, strokeDasharray: "3,3"}), Plot.ruleX([p50], {stroke: "black", strokeWidth: 2}), Plot.ruleX([p95], {stroke: "black", strokeWidth: 1.5, strokeDasharray: "3,3"}) ] }); const label = `${comp.name}: $${formatCost(p50)} (90% CI: ${formatCost(p5)} – ${formatCost(p95)})`; return {plot, label}; }); return html`<div style="display: grid; grid-template-columns: repeat(2, 1fr); gap: 1rem; margin: 1rem 0;"> ${plotData.map(d => html`<div style="font-size: 0.9em;"> <div style="font-weight: normal; margin-bottom: 0.3rem; color: #333;">${d.label}</div> ${d.plot} </div>`)} </div>`; } formatCost = ƒ(val)

      Do these adjust as I change the sliders above? I changed the 'plant capacity' and I did not see any change here. What's going on? #important

    5. Cost Breakdown by Component (Total: $122.51/kg):where(.plot-d6a7b5) { --plot-background: white; display: block; height: auto; height: intrinsic; max-width: 100%; } :where(.plot-d6a7b5 text), :where(.plot-d6a7b5 tspan) { white-space: pre; }

      make the graph below a bit bigger

    6. Price-competitive with conventional chicken

      Wait -- adjust this to consider/note the CM inclusion rate (%) and cost of plant-based or mycoprotein ingredients ($/kg)

    7. edian Cost (p50)

      Have a separate number for each of these boxes (slightly less prominent) for 'hybrid product cost/kg' ...

      User should be able to input a 'CM inclusion rate (%) and cost of plant-based or mycoprotein ingredients ($/kg) as parameters', and this should do a simple auto adjustment.

      First just a simple adjustment, and later we make this part of the simulation model.

      Also allow user to switch this 'hybrid product' on/off (box below 'Include downstream processing'

    8. Why it matters: If production costs reach ~$10/kg (comparable to conventional chicken), cultured meat could compete at scale. If costs remain >$50/kg, the technology may remain niche

      Caveat/note here about cost of producing the pure cultivated chicken cells, vs cost of the product that will have some percentage of these cells mixed with other (plant, fungal, etc.) ingredients.

    9. What these numbers represent: Simulated production cost per kilogram of cultured chicken (wet weight, unprocessed) in 2036, based on 30,000 Monte Carlo simulations. This is the cost to produce meat in a bioreactor — not retail price, which would include processing, distribution, and margins.

      Make it clear that we're giving the cost/kg for pure chicken cells, not the consumer product, which may (likely?) involve a small to moderate fraction of these cells in the output. Thus the 'price parity with conventional meat' might be easier to attain than the raw numbers suggest.

      Make a prominent note (and unfold further discussion) about the production cost of pure cultured chicken cells versus the cost of the products offered, which are likely to include a mix of chicken cells, plant elements, maybe fungal elements, and other things.

      Thus the cost per kg of pure chicken might not be assessed

    10. A key feature is the latent maturity factor that links:

      provide a reference for this approach, and provide and link a more detailed explanation

    11. Lognormal

      Note that we're open to considering other distributional forms, and making the modeling flexible to allow for different (chosen or simulated) distributions

    12. Probabilities, fractions

      Note that for ~switching parameters, the model samples both from the probabilities of a switch to a different regime (a different discrete state of the world, e.g., a new discovery) and then, in each simulation, uses this probability to select a particular state. (word this better, and be sure I'm correct here)

    13. 🔬 Upcoming Workshop: Cultivated Meat Cost Trajectories

      "!" in red seems like a warning. No need for that. Also, Can you make each of these a folding box, initially folded

    1. For Christmas Eve that year, she had chosen all my favorite foods.

      Ending the memoir with this sentence was an excellent choice by the author. As a teenager, Tan hadn't noticed her mother had catered the meal towards her, as she was fully focused on blending in and impressing her white crush. By including this sentence, Tan shows that she has since grown to fully appreciate her culture and family above her desire to assimilate to white American culture.

    1. ⭐ GFI amino acid report (Dec 2025) — GFI. Based on real quotes from amino acid suppliers and CM manufacturers. Found Humbird's amino acid prices overestimated by 2–10x. GFI cell growth modeling (Nov 2025) — GFI. How to model cell growth more realistically than current TEAs. GFI growth factor costs (2023) — PDF. Anticipated growth factor and recombinant protein costs and volumes for cost-competitive CM. GFI medium cost analysis (2020) — GFI. Foundational analysis of media as the dominant variable cost; identifies recombinant proteins and growth factors as key cost drivers. Some companies report 60% media cost reductions using plant-derived protein homologs. GFI scale-up & bioprocessing trends (2024) — GFI. Industry trends in bioreactor scale, continuous perfusion, and food-grade equipment — relevant to CM_16 (cell density) and CM_20

      too many here (and also all from a single source, GFI. Try to diversify sources, but also use folding and tooltips to reduce the clutter

    2. Note: Believer Meats (the authors' company) shut down Dec 2025.

      this feels a bit too ad-hominem an attack. A tooltip can mention the author's relationship to the company but should not imply that it nullifies the arguments made. See if the author themself made any points about this

    3. Lynch & Pierrehumbert (2019) — "Climate impacts of cultured meat and beef cattle." Early TEA with environmental dimension.

      skip this one maybe? I don't want to focus on Climate

    1. The Black Shoals desperately honorsand protects. As a metaphor, the shoal cannot be reduced to the ocean, theshore, or an island. It always has the potential to be something else thatcannot be known in advance.

      I think the author challenges Brathwaite's perception of the older black woman sweeping the sand outside of her home. The author incorporates the black shoal as a representation of the lady performing her morning routine. The sand travelling to her house was also once on shore, now reaching the Land including her house; this completes the black shoal.

    2. I offer thespace of the shoal as simultaneously land and sea to fracture this notionthat Black diaspora studies is overdetermined by rootlessness and onlymetaphorized by water and to disrupt the idea that Indigenous studiesis solely rooted and fixed in imaginaries of land as territory.

      To summarize this introduction, shoals are the outcome of years of friction and contact between Land and Water, often not trackable in certain typography, man-made maps and technologies. Nature forms these shoals at its own time, and not by the expectations of our materialistic times.

    3. When the ocean is at low tide, one might be able to wade from theshore beyond a break in the waves and into deeper water or a trough tothen come upon very shallow water (or a place where the ocean floor sur-faces), where one can finally stand on sand again. Many who fish find theshoal to be an ideal spot. A school, or gathering of fish, also sometimesdescribed as a shoal, often gathers at the sandbar’s edges to feed on vege-tation. Thus, a shoal is a good spot for catching fish. While also used todescribe nongeological matter such as a school of fish, the term is rarelyused in humanistic terms, however. Declining in use after the eighteenth

      The relation of the shoal for other humans and nature. Similar to the Sap Tree story mentioned at the Tipi.

    4. Throughout The Black Shoals, Black thought,movement, aesthetics, resistance, and lived experience will be interpretedas a form of chafing and rubbing up against the normative flows of Westernthought. Specifically, The Black Shoals will interrupt and slow the momen-tum of long-standing and contemporary modes and itineraries for theoriz-ing New World violence, social relations, Indigeneity, and Blackness in theWestern Hemisphere.4

      As Professor Sherwood had mentioned in this week's lecture, a shoal is a natural bank or ridge made up of rocks or gravel in the sea, often hazardous for ships.

    Annotators

    1. ▸ Context & reference points Optimistic TEAs: Pasitka et al. (2024) claims ~$6.2/lb ($13.7/kg) is achievable with continuous production and animal-free medium. Pessimistic TEAs: Humbird (2020) concluded cost parity is "highly unlikely" given biological and engineering constraints. Current conventional chicken: ~$2-4/kg wholesale in the US. Rethink Priorities (2022): Forecasted limited production through 2050 under most scenarios.

      I don't think I want to show these - these will anchor people based on our own previous review in ways that we might not want

    1. To learn more about Quarto books visit https://quarto.org/docs/books. window.document.addEventListener("DOMContentLoaded", function (event) { const icon = ""; const anchorJS = new window.AnchorJS(); anchorJS.options = { placement: 'right', icon: icon }; anchorJS.add('.anchored'); const isCodeAnnotation = (el) => { for (const clz of el.classList) { if (clz.startsWith('code-annotation-')) { return true; } } return false; } const onCopySuccess = function(e) { // button target const button = e.trigger; // don't keep focus button.blur(); // flash "checked" button.classList.add('code-copy-button-checked'); var currentTitle = button.getAttribute("title"); button.setAttribute("title", "Copié"); let tooltip; if (window.bootstrap) { button.setAttribute("data-bs-toggle", "tooltip"); button.setAttribute("data-bs-placement", "left"); button.setAttribute("data-bs-title", "Copié"); tooltip = new bootstrap.Tooltip(button, { trigger: "manual", customClass: "code-copy-button-tooltip", offset: [0, -8]}); tooltip.show(); } setTimeout(function() { if (tooltip) { tooltip.hide(); button.removeAttribute("data-bs-title"); button.removeAttribute("data-bs-toggle"); button.removeAttribute("data-bs-placement"); } button.setAttribute("title", currentTitle); button.classList.remove('code-copy-button-checked'); }, 1000); // clear code selection e.clearSelection(); } const getTextToCopy = function(trigger) { const outerScaffold = trigger.parentElement.cloneNode(true); const codeEl = outerScaffold.querySelector('code'); for (const childEl of codeEl.children) { if (isCodeAnnotation(childEl)) { childEl.remove(); } } return codeEl.innerText; } const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', { text: getTextToCopy }); clipboard.on('success', onCopySuccess); if (window.document.getElementById('quarto-embedded-source-code-modal')) { const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', { text: getTextToCopy, container: window.document.getElementById('quarto-embedded-source-code-modal') }); clipboardModal.on('success', onCopySuccess); } var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//); var mailtoRegex = new RegExp(/^mailto:/); var filterRegex = new RegExp('/' + window.location.host + '/'); var isInternal = (href) => { return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href); } // Inspect non-navigation links and adorn them if external var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)'); for (var i=0; i<links.length; i++) { const link = links[i]; if (!isInternal(link.href)) { // undo the damage that might have been done by quarto-nav.js in the case of // links that we want to consider external if (link.dataset.originalHref !== undefined) { link.href = link.dataset.originalHref; } } } function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) { const config = { allowHTML: true, maxWidth: 500, delay: 100, arrow: false, appendTo: function(el) { return el.parentElement; }, interactive: true, interactiveBorder: 10, theme: 'quarto', placement: 'bottom-start', }; if (contentFn) { config.content = contentFn; } if (onTriggerFn) { config.onTrigger = onTriggerFn; } if (onUntriggerFn) { config.onUntrigger = onUntriggerFn; } window.tippy(el, config); } const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]'); for (var i=0; i<noterefs.length; i++) { const ref = noterefs[i]; tippyHover(ref, function() { // use id or data attribute instead here let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href'); try { href = new URL(href).hash; } catch {} const id = href.replace(/^#\/?/, ""); const note = window.document.getElementById(id); if (note) { return note.innerHTML; } else { return ""; } }); } const xrefs = window.document.querySelectorAll('a.quarto-xref'); const processXRef = (id, note) => { // Strip column container classes const stripColumnClz = (el) => { el.classList.remove("page-full", "page-columns"); if (el.children) { for (const child of el.children) { stripColumnClz(child); } } } stripColumnClz(note) if (id === null || id.startsWith('sec-')) { // Special case sections, only their first couple elements const container = document.createElement("div"); if (note.children && note.children.length > 2) { container.appendChild(note.children[0].cloneNode(true)); for (let i = 1; i < note.children.length; i++) { const child = note.children[i]; if (child.tagName === "P" && child.innerText === "") { continue; } else { container.appendChild(child.cloneNode(true)); break; } } if (window.Quarto?.typesetMath) { window.Quarto.typesetMath(container); } return container.innerHTML } else { if (window.Quarto?.typesetMath) { window.Quarto.typesetMath(note); } return note.innerHTML; } } else { // Remove any anchor links if they are present const anchorLink = note.querySelector('a.anchorjs-link'); if (anchorLink) { anchorLink.remove(); } if (window.Quarto?.typesetMath) { window.Quarto.typesetMath(note); } if (note.classList.contains("callout")) { return note.outerHTML; } else { return note.innerHTML; } } } for (var i=0; i<xrefs.length; i++) { const xref = xrefs[i]; tippyHover(xref, undefined, function(instance) { instance.disable(); let url = xref.getAttribute('href'); let hash = undefined; if (url.startsWith('#')) { hash = url; } else { try { hash = new URL(url).hash; } catch {} } if (hash) { const id = hash.replace(/^#\/?/, ""); const note = window.document.getElementById(id); if (note !== null) { try { const html = processXRef(id, note.cloneNode(true)); instance.setContent(html); } finally { instance.enable(); instance.show(); } } else { // See if we can fetch this fetch(url.split('#')[0]) .then(res => res.text()) .then(html => { const parser = new DOMParser(); const htmlDoc = parser.parseFromString(html, "text/html"); const note = htmlDoc.getElementById(id); if (note !== null) { const html = processXRef(id, note); instance.setContent(html); } }).finally(() => { instance.enable(); instance.show(); }); } } else { // See if we can fetch a full url (with no hash to target) // This is a special case and we should probably do some content thinning / targeting fetch(url) .then(res => res.text()) .then(html => { const parser = new DOMParser(); const htmlDoc = parser.parseFromString(html, "text/html"); const note = htmlDoc.querySelector('main.content'); if (note !== null) { // This should only happen for chapter cross references // (since there is no id in the URL) // remove the first header if (note.children.length > 0 && note.children[0].tagName === "HEADER") { note.children[0].remove(); } const html = processXRef(null, note); instance.setContent(html); } }).finally(() => { instance.enable(); instance.show(); }); } }, function(instance) { }); } let selectedAnnoteEl; const selectorForAnnotation = ( cell, annotation) => { let cellAttr = 'data-code-cell="' + cell + '"'; let lineAttr = 'data-code-annotation="' + annotation + '"'; const selector = 'span[' + cellAttr + '][' + lineAttr + ']'; return selector; } const selectCodeLines = (annoteEl) => { const doc = window.document; const targetCell = annoteEl.getAttribute("data-target-cell"); const targetAnnotation = annoteEl.getAttribute("data-target-annotation"); const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation)); const lines = annoteSpan.getAttribute("data-code-lines").split(","); const lineIds = lines.map((line) => { return targetCell + "-" + line; }) let top = null; let height = null; let parent = null; if (lineIds.length > 0) { //compute the position of the single el (top and bottom and make a div) const el = window.document.getElementById(lineIds[0]); top = el.offsetTop; height = el.offsetHeight; parent = el.parentElement.parentElement; if (lineIds.length > 1) { const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]); const bottom = lastEl.offsetTop + lastEl.offsetHeight; height = bottom - top; } if (top !== null && height !== null && parent !== null) { // cook up a div (if necessary) and position it let div = window.document.getElementById("code-annotation-line-highlight"); if (div === null) { div = window.document.createElement("div"); div.setAttribute("id", "code-annotation-line-highlight"); div.style.position = 'absolute'; parent.appendChild(div); } div.style.top = top - 2 + "px"; div.style.height = height + 4 + "px"; div.style.left = 0; let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter"); if (gutterDiv === null) { gutterDiv = window.document.createElement("div"); gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter"); gutterDiv.style.position = 'absolute'; const codeCell = window.document.getElementById(targetCell); const gutter = codeCell.querySelector('.code-annotation-gutter'); gutter.appendChild(gutterDiv); } gutterDiv.style.top = top - 2 + "px"; gutterDiv.style.height = height + 4 + "px"; } selectedAnnoteEl = annoteEl; } }; const unselectCodeLines = () => { const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"]; elementsIds.forEach((elId) => { const div = window.document.getElementById(elId); if (div) { div.remove(); } }); selectedAnnoteEl = undefined; }; // Handle positioning of the toggle window.addEventListener( "resize", throttle(() => { elRect = undefined; if (selectedAnnoteEl) { selectCodeLines(selectedAnnoteEl); } }, 10) ); function throttle(fn, ms) { let throttle = false; let timer; return (...args) => { if(!throttle) { // first call gets through fn.apply(this, args); throttle = true; } else { // all the others get throttled if(timer) clearTimeout(timer); // cancel #2 timer = setTimeout(() => { fn.apply(this, args); timer = throttle = false; }, ms); } }; } // Attach click handler to the DT const annoteDls = window.document.querySelectorAll('dt[data-target-cell]'); for (const annoteDlNode of annoteDls) { annoteDlNode.addEventListener('click', (event) => { const clickedEl = event.target; if (clickedEl !== selectedAnnoteEl) { unselectCodeLines(); const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active'); if (activeEl) { activeEl.classList.remove('code-annotation-active'); } selectCodeLines(clickedEl); clickedEl.classList.add('code-annotation-active'); } else { // Unselect the line unselectCodeLines(); clickedEl.classList.remove('code-annotation-active'); } }); } const findCites = (el) => { const parentEl = el.parentElement; if (parentEl) { const cites = parentEl.dataset.cites; if (cites) { return { el, cites: cites.split(' ') }; } else { return findCites(el.parentElement) } } else { return undefined; } }; var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]'); for (var i=0; i<bibliorefs.length; i++) { const ref = bibliorefs[i]; const citeInfo = findCites(ref); if (citeInfo) { tippyHover(citeInfo.el, function() { var popup = window.document.createElement('div'); citeInfo.cites.forEach(function(cite) { var citeDiv = window.document.createElement('div'); citeDiv.classList.add('hanging-indent'); citeDiv.classList.add('csl-entry'); var biblioDiv = window.document.getElementById('ref-' + cite); if (biblioDiv) { citeDiv.innerHTML = biblioDiv.innerHTML; } popup.appendChild(citeDiv); }); return popup.innerHTML; }); } } });

      You can add annotations like this one to the website by creating an account on the Hypothes.is platform

    1. We need toobserve the intervening political processes—and toaccount for a wide range of alternative mechanisms

      This is where institutions are also probably quite important

    2. nce local demographicsstabilize, and with them residents’ expectations,diverse localities face no special barriers to raisingtaxes.

      Adjustment is one hell of a thing

    3. But the evidence shows the opposite:that increases in diversity shape the holding of votesmore than their eventual success

      So politicians actually have a good finger on the pulse

    4. Preference divergenceis one such mechanism

      This makes intuitive sense to me, for the most part one would think that the public of public goods was generally good fro all

    5. The results are also robust to the inclusion ofseveral economic and fiscal variables (e.g., unemploy-ment rate) and several measures of community stabil-ity (e.g., the percent of people in the same home in1985 and 1990). The results are not driven by housingprices or the change in housing prices, an alternativepathway through which diversity might shape prop-erty tax rates.

      More to be said here but basically the results hold

    6. and included 15indicator variables denoting how long since the lastoccurrence of the dependent variable.15 Year indicatorvariables capture unobserved time effects.

      Like sure, I do not know this stuff yet

    7. it compares towns that pass increases to allothers, limiting the selection bias induced by thetown officials’ decision to hold the vote.

      Also if anything this would lead to an underestimate

    8. leaders in diversecommunities will propose spending initiatives notsupported by their constituents—and so will seethem fail at the ballot box.

      Sort of a subset of different preferences

    9. iverse communities’lower social capital might in turn dampen theircollective willingness to make public investments.

      Might be valid to question whether there is a decrease in social capital

    10. with opportunities toattract new voters, to gain recognition, and to ad-vance their agenda. These divisive questions can alsodivide local leaders and generate lasting cleavages,making it harder to bring together a coalition in sup-port of increased taxes.

      New electoral power among diverse voters

    11. So long as it shapesresidents’ long-term expectations, diversity couldmatter without becoming a visible topic of localpolitics

      Might have to have a history of politicization though

    12. Other work has shown that localdiversity shapes attitudes towards public spendingonly when race and ethnicity are highly politicized

      I mean hypothetically social contact theory could make good relations

    13. When called to the ballot box, local voters are likelyto know when the proposal will come to fruition.While current spending provides tangible benefits inthe near-term, capital investments take years, and sorequire both significant trust in the taxing authorityand a broad construction of one’s self-interest.

      And a more general affect for one's community, but reasonably good proxies

    14. By shaping whether towns ever considernew tax proposals, rising diversity can have a stealthimpact even absent visible and contentious localpolitical battles

      Doesn't even make it to the floor

    15. the effect is strong only on votesabout long-term capital spending, suggesting thatdemographic changes operate in part by narrowingpeople’s time horizons.

      Reminds me of the refugee paper from ethnic conflict

    16. 11 percentage points weighting towns by population.Massachusetts remains more homogeneous than Texas,but the same probability in Texas school districtsdropped by just two percentage points duringthe 1990s.

      The diversity is mass is changing at a greater rate

    Annotators

    1. the most pivotal and tractable question for animal welfare funding decisions.

      That's too strong a claim. Maybe leave that out entirely or change it to something like 'a high-value tractable question'

    1. Risner et al. (2024)"Environmental impacts of cultured meat," ACS Food Science & Technology. Life cycle assessment finding CM's global warming potential could be 4–25x greater than retail beef if pharmaceutical-grade purification is required. GFI published a formal critique. — ACS Food Sci & Tech. LCA raising environmental cost concerns.

      But mention the Swartz rebuttal here too

    2. showing Humbird's AA costs were 2–10x too high.

      Don't say "showing" -- that's too definitive. That's the claim, and perhaps they provide evidence, but we shouldn't agree with them in this doc without further consideration.

    3. The answers also inform animal welfare funding decisions, but the workshop focus is on getting the cost evidence right.

      This last sentence seems out of place.

    4. 4. From TEA to reality: Why did Believer Meats fail?

      I haven't wanted to make this central. It's worth mentioning, but I wouldn't make it the 'headline' of the fourth point

    1. I tell you: suns exist.”

      My favorite line in this poem. “suns” → symbol of light, truth, hope, divine presence plural (“suns”) → abundance of hope, not just one source confident tone → almost like a promise

    2. Do not go in the direction of darkness –

      “darkness” → symbolizes sadness, negativity, loss of faith “direction” → suggests life is a path with choices reinforces idea of agency (you choose where to go)

    3. Do not stray into the neighborhood of despair.

      “neighborhood” is a metaphor → despair is a place you can enter or avoid suggests despair is temporary, not permanent again uses imperative → caution

    4. love of those who are clear joy,

      “clear joy” → pure, authentic happiness (possibly divine love) could refer to people who only uplift you spiritually/emotionally, not pull you down emphasizes choosing positive, meaningful connections

    5. Do not give your heart to anything else

      Our hearts have their own energy, we are not just our minds. warning against distractions (materialism, negativity) imperative tone = guidance/advice

    6. “If you are seeking, seek us with joy

      “seeking” → searching for meaning, truth, love, or God repetition emphasizes importance of how you seek “with joy” → mindset matters, not just the goal

    1. which scheme to use; tokenization is learned from text data based on an algorithm that I will describe later in this post. In OpenAI’s GPT models, most English words are represented using one or a small number of tokens.

      My MIS class is literally base around AI and creating chats with the AI Bots.

    2. Tokenization is the process of converting written language into integers (an integer is a whole number). You might think that tokenization is as simple as a=1, b=2, c=3, etc. That is one way to tokenize text, but it turns out that it’s not the only way — and certainly not the most optimal way. For example, the figure below shows three ways to represent the word “Hello” using integers.

      This is kind of making me nervous all I see it numbers and numbers equal math INTEGER yikesss!!

    3. Language models like ChatGPT and Claude don’t work with text. That’s because LLMs are based on mathematics, and math works on numbers, not on words. Therefore, LLMs need to work on numbers.

      So, LLMs cannot be text base and can only work with numbers why though ?

    4. Educational material on large language models (LLMs) comes in one of two categories: (1) high-level overviews that avoid details; or (2) highly technical tutorials written for computer scientists.

      Crazy thing is I'm learning about LLMs in my MIS class!!

    1. Although there are many idiosyncrasies in what may trigger a person with misophonia, the most common triggers are created by other humans, such as the sound of someone chewing, clearing their throat, tapping their foot, or typing on a keyboard.

      any sentences referring to misophonia verbatim

    2. an fMRI study found that people with misophonia show increased response in the anterior insular cortex (AIC) in response to misophonic sounds, compared to control participants and other unpleasant or neutral sounds (Kumar et al., 2017).

      any sentences referring to misophonia verbatim

    3. Both the subjective judgment of aversiveness and the physiological measure of skin conductance response (SCR) increase when people with misophonia are presented with triggers (Edelstein et al., 2013).

      any sentences referring to misophonia verbatim

    4. The disorder is not yet recognized by the Diagnostic and Statistical Manual − 5th version (DSM-5; American Psychiatric Association, 2013), but there has been an increasing amount of research on the characterization and treatment of misophonia (Vitoratou et al., 2021; see also Brout et al., 2018, for a review).

      any sentences referring to misophonia verbatim

    1. IRK was supported by funding from the Prins Bernhard Cultuurfonds (The Netherlands). This project was also funded by a Canadian Social Sciences and Humanities Research Council Insight Grant (435-2021-0224), a Social Sciences and Humanities Research Council Partnership Grant (895-2018-1023), and a Canada Research Chair (950-231872) to SMc.

      any sentences alluding to Montreal or something contained in Montreal

    1. Composers and music researchers had previously analyzed and annotated 65 movements from the Classical, Romantic, and early Modern repertoire in terms of the Taxonomy of Orchestral Grouping Effects (McAdams et al., 2022).

      please find any claims that depend on citations referring to works by any of the present authors

    2. These results confirm with orchestral excerpts the findings of studies on isolated tones with dyads or triads of instruments in which the presence of impulsive instruments reduces the perception of blend (Lembke et al., 2019; Reuter, 1996; Tardieu & McAdams, 2012).

      please find any claims that depend on citations referring to works by any of the present authors

    3. structuring by affecting sequential grouping through the segregation of auditory streams played by different instruments and segmental grouping through timbral contrasts (McAdams et al., 2022).

      please find any claims that depend on citations referring to works by any of the present authors

    4. Several other spectral and spectrotemporal descriptors were found to play a role in blend perception in orchestral works by Fischer et al. (2021). These include spectral flatness and spectral crest (different measures of the degree to which the spectrum is denser or has more emergence of spectral components), and spectral variation (the degree of variation of the spectral shape over time).

      please find any claims that depend on citations referring to works by any of the present authors

    5. Fischer et al. (2021) studied the blends of multi-instrument streams in the context of orchestral stream segregation in predominantly Romantic orchestral excerpts. They found that within-family instrument combinations blended better than between-family combinations. They demonstrated the role played by overlap in timbre correlates of spectral flatness (a measure of the tonalness/noisiness or density of the spectrum), spectral skewness (related to the shape of the spectral envelope), and spectral variation (evolution of the spectral envelope over time), as well as cues derived from the scores such as onset synchrony and the consonance of concurrent pitch relations.

      please find any claims that depend on citations referring to works by any of the present authors

    1. When the sudden drop to a pianissimo occurred towards the ending of the piece, the perceived arousal responses of CHM and WM dropped slightly but rose again immediately to end on a high arousal. These two groups of listeners appear to have anticipated a return to a loud and majestic close and therefore kept their arousal responses higher than those of the NM.

      please highlight anything related to music performance practice

    2. CHM, who are more experienced with the instruments and compositional techniques used in Chinese orchestral music, might have had an idea of which features figure more prominently in the communication of particular intentions, and therefore would have more information available for their judgments.

      please highlight anything related to music performance practice

    3. The perception of affective intentions in music is influenced by the degree of familiarity listeners have with a musical tradition, the content implicated in the music, and the complex sonic environment created by the composer's creation and the musicians' interpretation.

      please highlight anything related to music performance practice

    4. Iqa' (plural iqa'at) is used to describe a rhythmic cycle. Iqa'at are made up of two different basic building blocks, the dum and tak, onomatopoeias derived from the sound produced on membranophones such as the darabuka.

      please highlight anything related to music theory

    5. H5. Being more culturally bound, musical cues that are learned, such as modal structures, metrical relations, and so on, will exert a greater influence on listeners' perceived valence ratings than on their arousal ratings.

      please highlight anything related to music theory

    1. eLife Assessment

      This study provides valuable findings regarding potential correlates of protection against the African swine fever virus. The evidence supporting the claims is solid, and the results are highly relevant to the field. Further analysis using larger number of animals and other virus strains will help validate the importance of these findings and assess the relevance of the immune parameters associated with protection. The work will be of broad interest to veterinary immunologists, and particularly those working on African swine fever.

    2. Reviewer #1 (Public review):

      The study by Lotonin et al. investigates correlates of protection against African swine fever virus (ASFV) infection. The study is based on a comprehensive work, including the measurement of immune parameters using complementary methodologies. An important aspect of the work is the temporal analysis of the immune events, allowing to capture the dynamics of the immune responses induced after infection. Also, the work compares responses induced in farm and SPF pigs, showing the later an enhanced capacity to induce a protective immunity. Overall, the results obtained are interesting and relevant for the field. The findings described in the study further validate work form previous studies (critical role of virus-specific T cell responses), and provide new evidence on the importance of a balanced innate immune response during the immunization process. This information increases our knowledge on basic ASF immunology, one of the important gaps in ASF research that needs to be addressed for a more rational design of effective vaccines. As discussed in the manuscript, the results provide targets which can be further validated in other models, such as immunization using live attenuated vaccines.

      Overall the conclusions of the work are well supported by the results, and most of the issues mentioned during the review have been properly addressed during the revision, improving the quality of the final manuscript. While some limitations remain, I consider that they do not invalidate the results obtained and are well discussed by the authors.

      The study is highly relevant for the field, representing a step forward in our understanding of ASF protective immunity, providing immune targets to be further explored in other models and during vaccine development.

    3. Reviewer #2 (Public review):

      Summary:

      In the current study the authors attempt to identify correlates of protection for improved outcomes following re-challenge with ASFV. An advantage is the study design which compares the responses to a vaccine like mild challenge and during a virulent challenge months later. It is a fairly thorough description of the immune status of animals in terms of T cell responses, antibody responses, cytokines and transcriptional responses and the methods appear largely standard. The comparison between SPF and farm animals is interesting and probably useful for the field in that it suggests that SPF conditions might not fully recapitulate immune protection in the real world. I thought some of the conclusions were over-stated and there are several locations where the data could be presented more clearly.

      Strengths:

      The study is fairly comprehensive in the depth of immune read-outs interrogated. The potential pathways are systematically explored. Comparison of farm animals and SPF animals gives insights into how baseline immune function can differ based on hygiene, which would also likely inform interpretation of vaccination studies going forward.

      Weaknesses:

      There are limited numbers of animals assessed.

      Comments on revisions:

      The authors mostly addressed my comments to the previous version. However, in the discussion they added comments relating to and an interpretation based on their own unpublished data and I think that those statements should be removed because the data are not included in this publication and cannot be cited.

    4. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      The study by Lotonin et al. investigates correlates of protection against African swine fever virus (ASFV) infection. The study is based on a comprehensive work, including the measurement of immune parameters using complementary methodologies. An important aspect of the work is the temporal analysis of the immune events, allowing for the capture of the dynamics of the immune responses induced after infection. Also, the work compares responses induced in farm and SPF pigs, showing the latter an enhanced capacity to induce a protective immunity. Overall, the results obtained are interesting and relevant for the field. The findings described in the study further validate work from previous studies (critical role of virus-specific T cell responses) and provide new evidence on the importance of a balanced innate immune response during the immunization process. This information increases our knowledge on basic ASF immunology, one of the important gaps in ASF research that needs to be addressed for a more rational design of effective vaccines. Further studies will be required to corroborate that the results obtained based on the immunization of pigs by a not completely attenuated virus strain are also valid in other models, such as immunization using live attenuated vaccines.

      While overall the conclusions of the work are well supported by the results, I consider that the following issues should be addressed to improve the interpretation of the results:

      We thank Reviewer #1 for their thoughtful and constructive feedback, which significantly contributed to improving the clarity and quality of our manuscript. Below, we respond to each of the reviewer’s comments and describe the revisions that were incorporated.

      (1) An important issue in the study is the characterization of the infection outcome observed upon Estonia 2014 inoculation. Infected pigs show a long period of viremia, which is not linked to clinical signs. Indeed, animals are recovered by 20 days post-infection (dpi), but virus levels in blood remain high until 141 dpi. This is uncommon for ASF acute infections and rather indicates a potential induction of a chronic infection. Have the authors analysed this possibility deeply? Are there lesions indicative of chronic ASF in infected pigs at 17 dpi (when they have sacrificed some animals) or, more importantly, at later time points? Does the virus persist in some tissues at late time points, once clinical signs are not observed? Has all this been tested in previous studies?

      Tissue samples were tested for viral loads only at 17 dpi during the immunization phase, and long-term persistence of the virus in tissues has not been assessed in our previous studies. At 17 dpi, lesions were most prominently observed in the lymph nodes of both farm and SPF pigs. In a previous study using the Estonia 2014 strain (doi: 10.1371/journal.ppat.1010522), organs were analyzed at 28 dpi, and no pathological signs were detected. This finding calls into question the likelihood of chronic infection being induced by this strain.

      (2) Virus loads post-Estonia infection significantly differ from whole blood and serum (Figure 1C), while they are very similar in the same samples post-challenge. Have the authors validated these results using methods to quantify infectious particles, such as Hemadsorption or Immunoperoxidase assays? This is important, since it would determine the duration of virus replication post-Estonia inoculation, which is a very relevant parameter of the model.

      We did not perform virus titration but instead used qPCR as a sensitive and standardized method to assess viral genome loads. Although qPCR does not distinguish between infectious and non-infectious virus, it provides a reliable proxy for relative viral replication and clearance dynamics in this model. Unfortunately, no sample material remains from this experiment, but we agree that subsequent studies employing infectious virus quantification would be valuable for further refining our understanding of viral persistence and replication following Estonia 2014 infection.

      (3) Related to the previous points, do the authors consider it expected that the induction of immunosuppressive mechanisms during such a prolonged virus persistence, as described in humans and mouse models? Have the authors analysed the presence of immunosuppressive mechanisms during the virus persistence phase (IL10, myeloid-derived suppressor cells)? Have the authors used T cell exhausting markers to immunophenotype ASFV Estonia-induced T cells?

      We agree with the reviewer that the lack of long-term protection can be linked to immunosuppressive mechanisms, as demonstrated for genotype I strains (doi: 10.1128/JVI.00350-20). The proposed markers were not analyzed in this study but represent important targets for future investigation. We addressed this point in the discussion.

      (4) A broader analysis of inflammatory mediators during the persistence phase would also be very informative. Is the presence of high VLs at late time points linked to a systemic inflammatory response? For instance, levels of IFNa are still higher at 11 dpi than at baseline, but they are not analysed at later time points.

      While IFN-α levels remain elevated at 11 dpi, this response is typically transient in ASFV infection and likely not linked to persistent viremia. We agree that analyzing additional inflammatory markers at later time points would be valuable, and future studies should be designed to further understand viral persistence.

      (5) The authors observed a correlation between IL1b in serum before challenge and protection. The authors also nicely discuss the potential role of this cytokine in promoting memory CD4 T cell functionality, as demonstrated in mice previously. However, the cells producing IL1b before ASFV challenge are not identified. Might it be linked to virus persistence in some organs? This important issue should be discussed in the manuscript.

      We agree that identifying the cellular source of IL-1β prior to challenge is important, and this should be addressed in subsequent studies. We included a discussion on the potential link between elevated IL-1β levels and virus persistence in certain organs.

      (6) The lack of non-immunized controls during the challenge makes the interpretation of the results difficult. Has this challenge dose been previously tested in pigs of the age to demonstrate its 100% lethality? Can the low percentage of protected farm pigs be due to a modulation of memory T and B cell development by the persistence of the virus, or might it be related to the duration of the immunity, which in this model is tested at a very late time point? Related to this, how has the challenge day been selected? Have the authors analysed ASFV Estonia-induced immune responses over time to select it?

      In our previous study, intramuscular infection with ~3–6 × 10<sup>2</sup> TCID<sub>50</sub>/mL led to 100% lethality (doi: 10.1371/journal.ppat.1010522), which is notably lower than the dose used in the present study, although the route here was oronasal. The modulation of memory responses could be more thoroughly assessed in future studies using exhaustion markers. The challenge time point was selected based on the clearance of the virus from blood and serum. We agree that the lack of protection in some animals is puzzling and warrants further investigation, particularly to assess the role of immune duration, potential T cell exhaustion caused by viral persistence, or other immunological factors that may influence protection. Based on our experience, vaccine virus persistence alone does not sufficiently explain the lack-of-protection phenomenon. We incorporated these important aspects into the revised discussion.

      (7) Also, non-immunized controls at 0 dpc would help in the interpretation of the results from Figure 2C. Do the authors consider that the pig's age might influence the immune status (cytokine levels) at the time of challenge and thus the infection outcome?

      We support the view that including non-immunized controls at 0 dpc would strengthen the interpretation of cytokine dynamics and will consider this in future experimental designs. Regarding age, while all animals were within a similar age range at the time of challenge, we acknowledge that age-related differences in immune status could influence baseline cytokine levels and infection outcomes, and this is an important factor to consider.

      (8) Besides anti-CD2v antibodies, anti-C-type lectin antibodies can also inhibit hemadsorption (DOI: 10.1099/jgv.0.000024). Please correct the corresponding text in the results and discussion sections related to humoral responses as correlates of protection. Also, a more extended discussion on the controversial role of neutralizing antibodies (which have not been analysed in this study), or other functional mechanisms such as ADCC against ASFV would improve the discussion.

      The relevant text in the Results and Discussion sections was revised accordingly, and the discussion was extended to more thoroughly address the roles of antibodies.

      Reviewer #2 (Public review):

      Summary:

      In the current study, the authors attempt to identify correlates of protection for improved outcomes following re-challenge with ASFV. An advantage is the study design, which compares the responses to a vaccine-like mild challenge and during a virulent challenge months later. It is a fairly thorough description of the immune status of animals in terms of T cell responses, antibody responses, cytokines, and transcriptional responses, and the methods appear largely standard. The comparison between SPF and farm animals is interesting and probably useful for the field in that it suggests that SPF conditions might not fully recapitulate immune protection in the real world. I thought some of the conclusions were over-stated, and there are several locations where the data could be presented more clearly.

      Strengths:

      The study is fairly comprehensive in the depth of immune read-outs interrogated. The potential pathways are systematically explored. Comparison of farm animals and SPF animals gives insights into how baseline immune function can differ based on hygiene, which would also likely inform interpretation of vaccination studies going forward.

      Weaknesses:

      Some of the conclusions are over-interpreted and should be more robustly shown or toned down. There are also some issues with data presentation that need to be resolved and data that aren't provided that should be, like flow cytometry plots.

      We appreciate the feedback from the Reviewer #2 and acknowledge the concerns raised regarding data presentation. In the revised manuscript, we clarified our conclusions where needed and ensured that interpretations were better aligned with the data shown.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In the Introduction, more details on the experimental model would be appreciated. A short summary of findings obtained with this model in previous works from the authors would help to better understand the context of the study.

      Basic information on the model was added in the Introduction section of the revised manuscript.

      (2) In Figure 1, the addition of more time points on the x-axes would help the interpretation of the figures.

      We agree and have added extra time points to the x-axes.

      (3) To better understand the results in Figure 2A, a figure showing cytokine levels post-Estonia infection of only challenged pigs would help, indicating protected and non-protected animals as in Figure 2C. This figure would be better linked to the corresponding dot plot (Figure 2B).

      Our statistical analyses in Figure 2A are based on using both challenged and non-challenged pigs to assess differences between SPF and farm pigs. We prefer not to remove the non-challenged pigs in order to avoid losing statistical power. Moreover, even when non-challenged and challenged pigs are displayed in the plots, upregulation of IFN-α and IL-8 can be visualized and remains consistent with the positive and negative correlates of protection shown in Figure 2C.

      (4) Dark red colour associated with SPF non-protected is difficult to differentiate from light red in some figures.

      We thank the reviewer for this remark. To preserve the color scheme across the paper, we changed the circle data points to squares for the non-protected SPF pig in the most crowded figures: Figures 1–3 and Supplementary Figures 2 and 8.

      (5) In Supplementary figures 12-16, grouping of the animal numbers (SPF vs farm) would facilitate the interpretation of the results.

      Information on the animal numbers for each group (SPF vs. farm) has been added to the figure captions.

      (6) Are the results shown in Figure 8 based on absolute scores as mentioned? Results from 0 dpc are not shown. Is that correct?

      That is correct. BTM expression values are absolute and could not be normalized, as RNA was not isolated either immediately before the challenge or on day 0 post-challenge. This information is now clarified in the figure captions.

      Reviewer #2 (Recommendations for the authors):

      (1) The authors use the words "predicted" and "predicts" although they haven't used any methods to show that this is true, such as a multivariate analysis. I don't think correlation coefficients are sufficient to indicate prediction. This needs to be fixed.

      We agree with this and have made changes in the text to avoid this impression.

      (2) "Lower baseline immune activation was linked to increased protective immunity." Presumably, the authors mean prior to challenge, not prior to "vaccination"?

      In this sentence written in the Abstract, we refer to baseline immune activation in the steady state, i.e., prior to any infection, as demonstrated in a previous study by Radulovic et al. (2022). The sentence was adapted accordingly. This concept is further explored in the Discussion section.

      (3) The abstract mentioned the comparison between farm and SPF pigs, but didn't provide any context for those findings. It could be added here.

      In the new version, we have added information on this model in the Introduction section.

      (4) Figure legends need N to be indicated. For example, the viral load figures don't appear to be representative of all 9 or 5 animals. Is there a reason why not all were challenged, and how were those 5 challenged selected?

      Numbers of animals in each group were added to the figure captions. We have also provided details regarding the animals sacrificed at different time points of the experiment in the ‘Animal experiment’ section of the Methods.

      (5) 1A doesn't have a legend to indicate whether dark or light color indicates sampling.

      Fair point. We have added the information to the figure.

      (6) For Figure 3C, it's not clear how the correlation is presented. The legend indicates in writing that the color indicates the outcome it correlates with, but the legend suggests that it is r.

      The method of presenting correlation data is consistent across all figures, including Figure 3C. The color reflects the direction and strength of the correlation, corresponding to the r coefficient obtained from correlating immunological parameters with clinical scores. We have clarified this description in the figure caption to improve readability.

      (7) For some of the correlation data in 2D and 3C, it would be nice to provide the plots in the supplemental. Also, are there enough data points for a robust interpretation of correlation curves?

      We agree that providing the plots will improve clarity and have included them in the supplementary material. While we acknowledge that the number of data points is modest, we believe it is sufficient to support a robust interpretation of the correlation curves. Corresponding p-value cutoffs are noted in the figure captions.

      (8) The figure 2C method of indicating significance is confusing. There must be a clearer way to present this figure.

      Analyzing statistical significance for the dataset shown in Figure 2C is challenging due to the small number of animals. We carefully considered alternative ways of presenting statistical significance, however, given the limited group sizes, we believe that the current approach provides the most transparent and informative representation of the data.

      For clarity, we divided the animals into SPF and farm groups, as well as into protected (4 SPF, 2 farm pigs) and non-protected (1 SPF, 3 farm pigs) categories, and performed both group-based (unpaired t-test) and time-based (mixed-effects analysis) comparisons. All significant differences were added to the plots so that readers could directly visualize the observed trends and compare them with the correlation analysis presented in Figure 2D.

      (9) Please note that "viremia" means the presence of a virus specifically in the blood. Other descriptions of viral load should be used if this was not measured.

      We have clarified this in the text. When referring to organs, we use the term “viral loads.”

      (10) The way of putting a square around boxes that are significant can be misleading when a box is surrounded by other significant comparisons. Like for Figure 6B - probably all of these are really significant, but I can't tell for sure.

      Good point. We changed rectangles to circles for better readability of the figures.

      (11) There is a potential argument that these correlates of protection might only be valid for this specific vaccine. It should be noted that comparisons of multiple vaccines would be needed before assuming the correlates are broadly relevant.

      We agree with this statement and address it in the Discussion section.

      (12) For the circled pathways in Figure 9, it is not clear from the diagram if there is a directionality to the involvement of those pathways. Modulated or induced?

      When discussing pathways identified by transcriptome analysis, we are always referring to their induction, as this is based on the normalized enrichment score (NES). We have now specified this in the figure caption.

      (13) The authors speculate about NK cells, but this is based on transcriptional pathways identified and the literature. Is there any indication from the flow cytometry data whether activated NK cells versus NKT cells are associated with protection? Also, the memory phenotype of those cells?

      Regarding NK cells, the BTM analysis was corroborated by the flow cytometry data shown in Supplementary Figure 8. NK cells were defined as CD3<sup>-</sup>CD8α<sup>+</sup>. Specific markers to distinguish NKT cells or to assess memory phenotypes were not included in our panel.

      (14) In the discussion, "Our study demonstrates that T cell activation represents a robust correlate of protection against ASFV" doesn't indicate whether they mean after vaccination or after challenge. Re-using the same time points throughout the manuscript compounds this confusion.

      In this case, we mean that T cell activation upon immunization/vaccination and challenge correlates with protection. This information has been added to the sentence. Although some time points overlap between the immunization and challenge phases, we consistently use “dpi” and “dpc” to clearly distinguish them.

      (15) Flow cytometry gating strategies should be provided in the supplemental, particularly since this species is less frequently studied using flow cytometry; it would be helpful to understand gating and expression levels of key markers.

      We have provided the gating strategy in Supplementary Figure 7, which is also referenced in the “Flow cytometry and hematology analysis” section of the Methods.

      (16) Some of the discussion is a bit long and repetitive - e.g. the parts on antibodies and the last paragraph with multiple other parts of the discussion and manuscript.

      While we agree that some sections are extensive, we think that this level of detail is necessary to integrate the different datasets and to place our findings in the context of previous literature.