10,000 Matching Annotations
  1. Feb 2026
    1. Begin by reading the assignment instructions. Your instructor will likely have clear goals for the peer review process, and following the instructions will help you provide significant and meaningful revision ideas for your peer. Read your peer’s essay from the beginning to the end without adding any comments. This first read allows you to grasp your peer’s intentions and focus. Complete a second reading of your peer’s draft and start looking for strengths and weaknesses. Make comments on the margins of your peer’s essay. Later, you can further expand on these comments when you complete the peer review form. Stop when you feel stuck and ask yourself, “If this were my paper, how would I revise it?” Set aside time to review the organization of your peer’s essay. Read their thesis statement and make sure their body paragraphs have topic sentences that connect to their thesis statement. If there isn’t a clear connection, consider helping your peer revise their topic sentence so the connection between the thesis and body paragraph is easy to understand. Be honest. Your peers want to earn the best grade they can, and your advice during peer review will help them achieve this goal. Think of every piece of advice as constructive criticism. Your advice will help them to create a stronger, more focused writing sample.

      1.Read the assignment 2.read peer essay begging to end with no comments 3.finish second read to look for strength and weakness 4.stop when stuck 5.set time to review 6.be honest.

    1. merchants are taking every day our natives, sons of the land and the sons of our noblemen and vassals and our relatives, because the thieves and men of bad conscience grab them wishing to have the things and wares of this kingdom which they are ambitious of; they grab them and get them to be sold; and so great, Sir, is the corruption and licentiousness that our country is being completely depopulate

      Afonso helps warn that the slave trade is emptying his kingdom of its people. He does this by showing his people how destructive Portuguese involvement had become.

    2. They even imagine that a priest can never be anything but a priest--that is, he can never become a layman.

      Humans invention think that priest can never become a layman after they have been a priest and Luther doesn't agree with that and agree with what the scripture says.

    3. Therefore the bishop's consecration is just as if in the name of the whole congregation he took one person out of the community, each member of which has equal power, and commanded him to exercise this power for the rest; just as if ten brothers, co-heirs as king's sons, were to choose one from among them to rule over their inheritance, they would all of them still remain kings and have equal power, although one is appointed to govern.

      Luther does not agree with how the bishop's consecration. Luther thinks that everyone had the same amount of power and everything and yet he just picked one person out of those multiple that have all the same abilities.

    4. we are all one body, though each member does its own work so as to serve the others.

      This is a cool line to think about. Through God we are all his followers or one body. And through each member we are doing our own work to help serve the others and spread the work of God.

    5. Now may God help us, and give us one of those trumpets that overthrew the walls of Jericho, so that we may blow down these walls of straw and paper, and that we may have a chance to use Christian rods for the chastisement of sin, and expose the craft and deceit of the devil; thus we may amend ourselves by punishment and again obtain God's favor.

      Luther is asking for God to help them to give them a trumpet to help overthrew the wall of Jericho. He thinks this will help people obtain God's favor.

    6. and others are brought during the night so that they might not be recognized.

      The secrecy indicates awareness that the slave trade was illegal and morally wrong even at the time.

    7. keenly desirous as they are of the wares and things of your kingdoms,

      Alfonso says that dependency on European goods reshaped local desires, making foreign trade central to everyday life and harder to control.

    8. Pray Our Lord in His mercy to have Your Highness under His guard and let you do forever the things of His service. I kiss your hands many times.

      They are praying to ask for the Lord to help watch over the Highness and to help guard him.

    9. the thieves and men of bad conscience grab them wishing to have the things and wares of this kingdom

      This passage acknowledges African participation in kidnapping, but frames it as consequence of foreign economic pressure rather than cultural acceptance of slavery,

    10. And us we have got neither dispensaries nor drugs which might help us in this forlornness, many of those who had been already confirmed and instructed in the holy faith of Our Lord Jesus Christ perish and die; and the rest of the people in their majority cure themselves with herbs and breads and other ancient methods, so that they put all their faith in the mentioned herbs and ceremonies if they live, and believe that they are saved if they die; and this is not much in the service of God

      People who are confirmed in the holy faith will perish and die but those who aren't will just cure themselves with other things. This is another example of how religion was so big during this time. If you were a follower of Christ you would perish and die and if you aren't then you will have to find another way to cure it.

    11. many of our vassals, whom we had in obedience, do not comply because they have the things in greater abundance than we ourselves;

      Alfonso shows that European trade goods undermined traditional systems of loyalty, weakening royal authority and social hierarchy within Kongo.

    12. The ancient Persian city had once been a home for Israelite refugees freed from the Babylonian Captivity by Cyrus the Great in the 6th century BCE. Shah Abbas continued the tradition of settling refugees in Isfahan, welcoming hundreds of thousands of Armenians in the early 1600s from the disputed border region separating the Shiite Safavids from the Sunni Ottoman Empire.

      This policy shows how the Safavid Empire used refugee populations to strengthen their cities and economy.

    13. The arrival of the printing press in Europe in the middle of the fifteenth century began an explosion of literacy.

      The printing press was a major technology invention helped writers publishes books. This could help increase peoples reading abilities and give people better access to written materials since they could be in books now.

    14. Hinduism, which is still the dominant religion of India, is based on ancient traditions and practices originating centuries before the development of Judaism and other religions in the Middle East. It is a polytheistic religion in which stories of the relations and conflicts among the gods and goddesses help explain the human condition.

      Even though Hinduism is still a large and dominant religion of India, you don't really hear about it much. I hear a lot about Christians and Muslims but not a lot about Hinduism. I think this is because of the area I live it. I think if I went somewhere else in the United State I may hear of it a lot more.

    15. For example, young boys were taken as tribute captives from villages in the Balkans. They were converted to Islam, educated, and trained into an elite fighting force called the Janissaries who reported directly to the Emperor.

      People were taken when they couldn't pay in money for certain things so for revenue they took people. When the Ottoman Empire would take people they would have them get trained in to help out their own Empire.

    16. Europe's nations were organized around and identified by factors like ethnicity, language, customs, and religion. Often these nations fought neighbors that were defined by different identities.

      I think that this is strange how each European nation was organized and identified by different factors. They would also fight other nations that were identified differently.

    1. The human cargo taken from Africa by the Portuguese in the 1400s, however, became much more highly favored than slaves from eastern Europe: not only were dark-skinned people considered more exotic for service in royal courts, they also could not easily escape by blending in with the local population.

      With different races, it became a justification for enslavement after the system was established.

    1. "three sisters" of corn, beans, and squash in garden plots they shifted when soil fertility began to wane.

      Why did these become the "Three Sisters"? What is unique about them?

    2. Men hunted big game, defended the band from predatory animals, and fought; women gathered, fished, trapped small animals, and grew the "three sisters" of corn, beans, and squash in garden plots they shifted when soil fertility began to wane. Because they controlled the more dependable food sources, women had social power; they typically were responsible for distributing all the food and often chose the men who led councils and war parties.

      At what point in history did men begin to have more power in leadership roles then, and why?

  2. Jan 2026
    1. ¿Qué cinco acciones

      1 Create a blank Logic app

      2 Add a logic app trigger that fires when one or more messages arrive in the queue

      3 Add an action that reads IoT temperature data from the Service Bus queue

      4 Add a condition that compares the temperature against the upper and lower thresholds

      5 Add an action that sends an email if temperature is outside thresholds

    2. Seleccionar y colocar:

      Orden Acción 1 Create a blank Logic app

      2 Add a logic app trigger that fires when one or more messages arrive in the queue

      3 Add an action that reads IoT temperature data from the Service Bus queue

      4 Add a condition that compares the temperature against the upper and lower thresholds

      5 Add an action that sends an email if temperature is outside thresholds

    1. not only preserved classical Greek philosophy and science that was lost in much of Europe but made important original contributions to knowledge and culture.

      This highlights how, despite Eurocentric thinking, Africa, the Middle East and Asia were responsible for a lot of the world's scientific advancements during the medieval era.

    1. Rapport de Synthèse : Crise et Dérives du Secteur Périscolaire et de l’Enseignement Privé

      Résumé Exécutif

      Une enquête approfondie de l'émission « Cash Investigation » révèle des défaillances systémiques graves au sein du secteur périscolaire et de certains établissements d'enseignement privé sous contrat en France.

      Le constat est alarmant : violences physiques et verbales, suspicions d'agressions sexuelles, et manque de surveillance généralisé.

      Les points clés à retenir :

      Ampleur nationale : À Paris, 128 animateurs ont été suspendus en 10 ans pour suspicion de violences sexuelles.

      Le phénomène touche l'ensemble du territoire, des grandes métropoles aux zones rurales.

      Failles de recrutement : Une infiltration de 27 heures a suffi pour constater des comportements inappropriés (cris, usage de téléphones, gestes déplacés) et un non-respect flagrant des quotas d'encadrement.

      Inertie institutionnelle : Des signalements d'abus restent parfois sans réponse pendant plusieurs années avant qu'une action concrète ne soit entreprise.

      Échec judiciaire : Seules 3 % des plaintes pour violences sexuelles sur mineurs aboutissent à une condamnation, tandis que 73 % sont classées sans suite.

      Manque de contrôle du privé : Les établissements privés sous contrat, financés à 75 % par l'État, échappent à une surveillance rigoureuse malgré des cas de maltraitance institutionnalisée.

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      I. Analyse du Secteur Périscolaire : Un Système en Souffrance

      L'enquête met en lumière une réalité quotidienne brutale dans les accueils périscolaires (cantines, garderies), souvent méconnue des parents qui supposent leurs enfants protégés par l'institution scolaire.

      A. Des conditions d'exercice dégradées

      L'infiltration d'une journaliste, embauchée sans expérience préalable malgré la possession du BAFA, révèle des dérives immédiates après seulement 27 heures d'observation :

      Comportements inappropriés : Animateurs focalisés sur leurs téléphones portables, hurlements constants contre les enfants, et gestes graves comme une animatrice embrassant des enfants de 4 ans sur la bouche.

      Sous-effectif chronique : Dans certains cas, le nombre d'enfants par animateur est plus du double du quota légal (par exemple, une seule personne pour 23 enfants en cour de récréation).

      Manque de considération : Le métier souffre de bas salaires, d'un recrutement précaire et d'une absence de reconnaissance professionnelle, favorisant un climat d'agressivité.

      B. Problématiques de recrutement et de formation

      Les municipalités, responsables du périscolaire, font face à des difficultés majeures pour trouver du personnel qualifié.

      Règles floues : Le recrutement se base parfois uniquement sur la "bienveillance et le bon sens", sans formation approfondie.

      Hétérogénéité de gestion : La qualité de l'encadrement dépend directement des choix budgétaires et politiques de chaque mairie.

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      II. Violences Sexuelles et Impunité

      Le document souligne une défaillance critique dans la protection des mineurs face aux prédateurs potentiels au sein des structures d'accueil.

      A. Données chiffrées et réalité du terrain

      Il n'existe pas de statistiques officielles nationales, forçant les enquêteurs à compiler leurs propres données à partir de la presse quotidienne régionale.

      Suspensions : 128 animateurs suspendus à Paris en une décennie.

      Répartition : Des affaires sont recensées partout en France (Nancy, Marseille, Haute-Savoie, Moselle).

      B. Le traitement des signalements

      Un problème majeur réside dans la lenteur de réaction des autorités face aux alertes :

      Cas du 15e arrondissement : Un animateur a été interpellé en 2023 pour des jeux et danses à caractère sexuel, alors que des signalements le concernant existaient depuis 2019.

      Culture du silence : Trop souvent, les signalements ne sont pas correctement pris en compte, permettant à des individus suspects de rester au contact des enfants pendant des mois, voire des années.

      C. Statistiques Judiciaires (Source : Ciivise)

      | Type de procédure | Pourcentage | | --- | --- | | Plaintes classées sans suite | 73 % | | Plaintes aboutissant à une condamnation | 3 % |

      Cette difficulté de condamnation s'explique souvent par la situation de "parole contre parole", où la parole de l'enfant n'est pas toujours recueillie dans des conditions optimales.

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      III. L'Enseignement Privé sous Contrat : Une Zone d'Ombre

      L'enquête s'étend aux établissements privés catholiques sous contrat, qui scolarisent près de 2 millions d'élèves en France.

      Financement Public : Ces établissements sont financés à environ 75 % par l'argent public.

      Maltraitance Institutionnalisée : Des témoignages font état de violences physiques (ex: "roustes" en public au self) sur des enfants dès l'âge de 12 ans.

      Absence de contrôle : Malgré l'importance des fonds publics engagés, l'État n'exerce pas de contrôle suffisant sur ces établissements.

      Les syndicats dénoncent un silence persistant (omerta) au sein de l'Enseignement catholique.

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      IV. Recommandations et Solutions

      A. Modèles de réussite

      L'enquête cite l'exemple d'un village ayant réussi à transformer son périscolaire en augmentant son budget de seulement 8 %. Cette hausse a permis :

      • La prise en compte du temps de préparation des ateliers.

      • Une formation accrue des animateurs.

      • Un environnement où les enfants se sentent en sécurité et épanouis.

      B. Vigilance des parents

      Face à ces risques, les pédopsychiatres conseillent d'être attentifs aux changements brusques de comportement chez l'enfant :

      • Troubles du sommeil (énurésie nocturne/pipi au lit).

      • Troubles alimentaires (perte d'appétit).

      • Changements d'humeur ou repli sur soi.

      Il est préconisé de favoriser des moments de "parole libre" lors de situations calmes (bain, trajet en voiture, lecture du soir) pour permettre à l'enfant d'exprimer un éventuel malaise.

    1. État des Lieux du Secteur Périscolaire à Paris : Dysfonctionnements et Dérives

      Résumé Exécutif

      Ce document de synthèse expose les défaillances systémiques au sein des structures périscolaires de la Ville de Paris, telles que révélées par une enquête en immersion.

      Le constat met en lumière une gestion de crise permanente caractérisée par un recrutement fondé sur la simple disponibilité plutôt que sur les compétences, une absence de formation réelle et des violations récurrentes des taux d'encadrement légaux.

      L'analyse révèle un environnement où la sécurité affective et physique des enfants est compromise par des violences verbales, un désinvestissement de certains agents et une impunité institutionnalisée pour les titulaires problématiques via un système de "chaises musicales".

      Le manque de contrôle et d'exigence de la hiérarchie favorise l'émergence de dérives graves, allant de la négligence à des signalements d'attouchements sexuels.

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      1. Un Processus de Recrutement Fondé sur l'Urgence

      Le recrutement des animateurs vacataires semble dicté par une nécessité de combler les effectifs plutôt que par une évaluation des aptitudes pédagogiques.

      Critères de sélection minimaux : La mairie exige uniquement d'avoir 18 ans, d'être motivé, d'avoir un casier judiciaire vierge (vérification du FIJAIS) et des vaccins à jour.

      Absence d'évaluation des compétences : Les entretiens ne comportent aucune question sur la gestion des enfants ou l'expérience éducative. L'atout majeur retenu est la disponibilité du candidat.

      Le dogme du "bon sens" : À défaut de directives claires, le recrutement repose sur deux notions vagues : la "bienveillance" et le "bon sens", y compris pour prodiguer des soins en l'absence d'infirmière.

      Profils à risque : Le manque d'exigence conduit au recrutement de profils inadaptés.

      Un témoignage interne (Karim, responsable éducatif ville) rapporte l'envoi de remplaçants arrivant en état d'ébriété ou issus de parcours de réinsertion sans évaluation préalable suffisante, malgré des avis de recrutement signalant une instabilité.

      2. Déficience de la Formation et de l'Intégration

      L'immersion démontre un décalage profond entre les ambitions affichées par la Ville et la réalité du terrain.

      L'inexistence du parcours d'intégration : La formation se résume à un "briefing express" (chronométré à 6 minutes et 42 secondes dans un cas précis) avant une mise en poste immédiate.

      La Charte de l'animateur ignorée : Bien que ce document définisse les missions éducatives et proscrive les comportements ambigus, il n'est souvent ni présenté ni signé par les nouveaux arrivants.

      Improvisation pédagogique : Alors que le temps périscolaire est censé être éducatif, aucune consigne ne soutient les projets pédagogiques.

      Les animateurs sont invités à "faire des dessins" ou à improviser des jeux sur leur temps personnel.

      3. Conditions de Travail et Non-Respect de la Légalité

      La gestion des effectifs se heurte à une pénurie chronique de personnel qualifié, entraînant des entorses régulières à la réglementation.

      Taux d'encadrement

      | Norme Légale (moins de 6 ans) | Réalité constatée sur le terrain | | --- | --- | | 1 animateur pour 14 enfants | Jusqu'à 1 animateur pour 23 enfants | | Surveillance active requise | Sous-effectifs fréquents (ex: 2 animateurs pour 70 enfants) |

      Précarité et rotation : Les postes de vacataires (payés 15 € brut de l'heure) servent à "boucher les trous" sans continuité éducative, les remplaçants changeant de groupe quotidiennement sans présentation préalable.

      Difficulté de recrutement : La mairie peine à trouver des profils compétents en raison des plannings morcelés et des temps partiels, ne parvenant à compléter ses équipes qu'en période de fin d'études universitaires.

      4. Dérives Comportementales et Climat de Violence

      Le manque de cadre et de formation génère des comportements abusifs au sein des écoles.

      Violences verbales systématiques : L'usage des cris, des menaces ("vous allez rien manger") et des humiliations est une pratique quotidienne pour obtenir le silence ou le respect des règles à la cantine.

      Négligence et désinvestissement : De nombreux animateurs privilégient l'usage personnel de leur smartphone au détriment de la surveillance active des enfants, en violation directe de la charte professionnelle.

      Absence de limites physiques : L'immersion a révélé des gestes inappropriés, tels que des baisers forcés sur la bouche imposés aux enfants par certains membres du personnel sous couvert d'affection.

      5. Défaillances de la Hiérarchie et Impunité

      Le système de contrôle interne semble incapable de réguler ou d'écarter les profils dangereux.

      Pilotage à distance : La hiérarchie supérieure se rend rarement sur le terrain (environ trois fois par an), adoptant une posture de "no news good news".

      Le système des "chaises musicales" : Pour les agents titulaires (fonctionnaires) faisant l'objet de signalements pour maltraitance (fessées, secousses par les oreilles), la Ville privilégie le déplacement géographique plutôt que la sanction disciplinaire ou l'exclusion.

      Cela permet à des individus problématiques de poursuivre leur carrière en changeant simplement d'établissement.

      Gravité des faits signalés : L'enquête mentionne une plainte pour attouchements sexuels sur une enfant pendant la sieste, ayant entraîné la suspension d'un agent au nom du principe de précaution.

      Citations Clés

      « Si un enfant se blesse, elle fait comment ? [...] Voilà, c'est votre bon sens. » — Recruteuse de la Ville de Paris.

      « On forme sur le tas. [...] Allez, bienvenue à bord du briefing express. » — Responsable Éducatif Ville (REV).

      « Si ça te fait de la peine [que les enfants pleurent], c'est pas fait pour toi ce travail. Parce que sinon tu vas te faire bouffer. » — Animatrice à une nouvelle recrue.

      « On peut faire une carrière entière en fait en étant déplacé tout le temps, ça il n'y a aucun problème. » — Karim, responsable périscolaire anonyme.

    1. Synthèse Analytique : Les Mécanismes du Contrôle Coercitif et de la Violence Intrafamiliale

      Résumé Exécutif

      Ce document analyse les dynamiques du contrôle coercitif à travers le prisme des audiences judiciaires et des témoignages d'experts présentés dans l'enquête d'ARTE.

      Le contrôle coercitif ne se limite pas à des actes isolés de violence physique, mais constitue un système délibéré de domination visant à aliéner la liberté de la victime. Les points clés identifiés incluent :

      La nature systémique du contrôle : Il s'agit d'une stratégie globale incluant la micro-surveillance, l'isolement social et la dévalorisation psychologique.

      L'arsenal tactique : L'utilisation de technologies (GPS, caméras, accès aux réseaux sociaux) et de pressions économiques pour maintenir une emprise totale.

      La rhétorique de l'agresseur : Une tendance systématique à l'inversion de la culpabilité, à la minimisation des faits et à l'utilisation de prétextes émotionnels pour justifier la violence.

      L'évolution juridique : La nécessité d'intégrer la notion de contrôle coercitif dans le droit pour déconstruire les rapports de domination ancrés historiquement dans le Code civil.

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      1. Définition et Stratégies du Contrôle Coercitif

      Le contrôle coercitif est décrit comme une « arme par excellence » pour soumettre l'autre.

      Contrairement à la violence ponctuelle, il s'inscrit dans la durée et l'omniprésence.

      Mécanismes de surveillance et de micro-contrôle

      L'agresseur cherche à envahir l'espace psychique, intime et professionnel de la victime par divers moyens :

      Surveillance technologique : Installation de traceurs GPS sous les véhicules, utilisation de caméras de surveillance au domicile, et exigence des codes d'accès aux téléphones et réseaux sociaux.

      Intrusion nocturne : Privation de sommeil par la musique forte ou réveils forcés durant la nuit pour obtenir des « aveux » d'infidélité imaginaire.

      Contrôle du corps : Surveillance de la tenue vestimentaire et, dans des cas extrêmes, inspection des sous-vêtements pour déceler des preuves de rapports extra-conjugaux ou de prostitution.

      Isolement et dévalorisation

      Le contrôle passe par la création d'un désert social autour de la victime :

      Rupture des liens : Interdiction ou limitation des visites à la famille (notamment la mère) et aux amis, sauf en présence de l'agresseur.

      Atteinte à la dignité : Utilisation d'un langage dégradant (« pute », « salope », « moins que rien ») et dénigrement constant des capacités professionnelles ou maternelles.

      Pathologisation de la victime : Traiter la victime d'« hystérique » ou de « folle » pour discréditer sa parole et justifier le contrôle.

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      2. Le Cycle de la Domination et de la Contrainte

      Le passage de la violence verbale à la violence physique et à la séquestration suit une progression souvent prévisible.

      La contrainte physique et matérielle

      Séquestration : Fermer la maison à clé pour empêcher la victime de sortir, ou s'enfermer avec elle pour l'empêcher de fuir une dispute.

      Contrôle des besoins vitaux : Interdiction d'accès à la cuisine pour les enfants ou la conjointe, contrôle strict des courses alimentaires (ne rapporter que de l'eau, forcer la victime à consommer des produits périmés).

      Emprise économique : Captation des prestations sociales et reproches systématiques sur la gestion financière, visant à créer une dépendance totale.

      Menaces et terrorisme domestique

      Le climat de peur est maintenu par des menaces de mort explicites et récurrentes :

      Menaces d'homicide : SMS répétés (« je vais te tuer », « je vais te crever »), mise en joue avec une arme à feu chargée, ou menaces de précipiter la victime d'un pont ou contre un mur sur l'autoroute.

      Chantage au suicide : Utilisation de la menace de se donner la mort pour manipuler la victime et l'empêcher de rompre.

      Violence physique directe : Crachats au visage, strangulation jusqu'à la perte de connaissance, coups de tête et pressions physiques pour « faire taire » la victime.

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      3. Analyse de la Défense des Agresseurs

      L'analyse des audiences révèle des schémas de défense récurrents chez les auteurs de violences, visant à éluder leur responsabilité.

      | Tactique de défense | Manifestation constatée dans les sources | | --- | --- | | Inversion de la culpabilité | Affirmer que la victime est « capricieuse », « exigeante » ou qu'elle a « provoqué » l'acte par son comportement ou son infidélité supposée. | | Minimisation | Qualifier un crachat de « simple réaction », ou des menaces de mort de « mots dits sous le coup de la colère ». | | Justification par le trauma personnel | Invoquer le décès d'un proche, une éducation violente ou une surcharge de travail pour excuser le passage à l'acte. | | Déni de la réalité | Contester les faits malgré les preuves matérielles (SMS, rapports de police, expertises médicales). | | Présentation de soi comme victime | Se décrire comme le « véritable lésé » de l'histoire, celui qui a donné tout son amour sans retour. |

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      4. Impact Traumatique et Conséquences Sociales

      La violence ne s'arrête pas à la victime directe ; elle irradie sur l'ensemble du cercle familial.

      Impact sur les enfants : Les enfants sont témoins et parfois cibles des violences.

      Ils vivent dans une atmosphère de terreur (« se cacher dans la chambre », « avoir peur de son père »).

      L'agresseur peut même les rendre responsables de son propre état émotionnel.

      Le cycle intergénérationnel : Les experts et magistrats soulignent le risque que les enfants reproduisent ces schémas de violence une fois adultes s'ils ne sont pas interrompus.

      La période de séparation : Identifiée comme la phase la plus dangereuse.

      C'est souvent au moment où la victime tente de reprendre sa liberté que la violence culmine (harcèlement par SMS, rodéos autour du domicile, usage de traceurs).

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      5. Perspectives Institutionnelles et Juridiques

      Le document souligne le décalage entre la perception de l'agresseur et la norme légale.

      L'héritage historique : Le rappel de l'ancien article 213 du Code civil (1803), qui imposait l'obéissance de la femme à son mari, explique la persistance de structures de domination archaïques dans l'esprit de certains agresseurs.

      Le rôle de la justice : La magistrature, aujourd'hui majoritairement féminine, a pour mission de rappeler la loi et de déconstruire ces rapports de force.

      Le droit doit s'immiscer « au cœur des rapports intimes » pour protéger la liberté individuelle.

      Sanctions et obligations : Les condamnations citées incluent des peines de prison (dont certaines sous surveillance électronique), des amendes pour préjudice moral, des interdictions de paraître au domicile et l'obligation de suivre des stages de responsabilisation contre les violences sexistes.

      --------------------------------------------------------------------------------

      Note finale : Le contrôle coercitif se définit par la volonté de « conserver sous un contrôle permanent, total et absolu » une personne, la réduisant à un objet de propriété plutôt qu'à un sujet de droit.

      Sa reconnaissance judiciaire est l'outil essentiel pour briser ce système d'oppression.

    1. Two pipes of equal and constant diameter leave a water pumping station and dump water out of an open end that is open to the atmosphere (see the following figure). The water enters at a pressure of two atmospheres and a speed of (v1 = 1.0 m/s). One pipe drops a height of 10 m. What is the velocity of the water as the water leaves each pipe?

      Given: Inlet pressure P1​=2 atm=2.026×105 Pa Inlet velocity v1​=1.0 m/s Outlet pressure P2​=P3​=1 atm=1.013×105 Pa Density of water ρ=1000 kg/m3 Acceleration due to gravity g=9.8 m/s2 1. For the horizontal pipe: The problem states the pipes have a constant diameter. According to the equation of continuity: A1​v1​=A2​v2​ Since the diameter is constant, the cross-sectional area A1​=A2​. Therefore: v2​=v1​=1.0 m/s 2. For the pipe with a 10 m drop: Applying Bernoulli's equation between the inlet (point 1) and the outlet (point 3): P1​+21​ρv12​+ρgh1​=P3​+21​ρv32​+ρgh3​ Taking the outlet level as the reference (h3​=0), then h1​=10 m. 2.026×105+21​(1000)(1.0)2+(1000)(9.8)(10)=1.013×105+21​(1000)v32​+0 202600+500+98000=101300+500v32​ 301100=101300+500v32​ 199800=500v32​ v32​=500199800​ v32​=399.6 v3​=399.6​≈19.99 m/s Final velocities: Horizontal pipe: 1.0 m/s Dropping pipe: 20.0 m/s

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

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      Reply to the reviewers

      Reviewer #1 Reviewer 1 Point 1- The authors describe cortical neuronal counts across several mammalian species, which is quite impressive, but the information on the methods of counting is lacking: how representative are the data used / shown; how many individuals / brains / sections were used for each species considered? Much more detailed description of the quantifications should be provided to judge the validity of this first conclusion.

      Response: We sincerely thank the reviewer for this insightful and constructive suggestion. We agree that the methodological description of our comparative histological analysis, which is the fundamental basis of this study, was insufficient in the original manuscript. Following the reviewer’s advice, we have extensively revised the Materials and Methods section entitled “Nissl staining and neuronal cell number count” (Page 32, Line 15).

      Reviewer 1 Point 2- The authors use several markers of cortical neuron identity to confirm their neuron number measurements, but from the data shown in Figure 1D,E it seems that only some markers (Satb2) show species-differences while others do not (CTIP2 / Tbr1). How do the authors explain this discrepancy - does this mean that it is mainly Satb2 neurons that are increased in number? But if so how to explain the relative increase in subcortical projections shown in Figure S7?

      Response: We appreciate the reviewer’s insightful comments regarding the marker expression patterns. Upon re-evaluating our data in light of your feedback, we agree that the species differences in deep-layer (DL) markers such as Ctip2 and Tbr1 in the adult stage appear relatively modest compared to the robust differences observed in Satb2 and the projection data shown in Figure S8.

      To address this point, we have incorporated a comparison between the adult data (Figure 1) and our findings from P7 (Figure S2). As shown in the revised manuscript, the species differences for all markers are significantly more pronounced at P7 than in the adult. Notably, in the lower layers, rats exhibit a significantly higher number of marker-positive cells across all markers, including those newly added in this revision, compared to mice.

      We offer the following interpretation regarding these temporal differences:

      1. Developmental Relevance: The marker molecules analyzed are well-established regulators of neuronal subtype fate and projection identity during development. Their critical fate-determining functions are primarily exercised during the migration and maturation phases of nascent neurons.
      2. Postnatal Expression Shifts: Whether these molecules maintain functional roles in the fully matured adult brain remains less certain. It is plausible that marker expression may diminish in certain neuronal populations during late postnatal development, leading to the attenuated species differences observed in adults. Consequently, we believe the strong correlation between P7 quantitative data and projection fate provides a biologically sound validation of our hypothesis.

      While we have kept the discussion in the main text concise to maintain focus for the general reader, we have provided comprehensive data in Figure 1 and Figure S2. This ensures that the necessary evidence is readily available for specialists interested in these developmental dynamics.

      Reviewer 1 Point 3- The authors focus their study almost exclusively on somatosensory cortex, but can they comment on other areas (motor, visual for instance)? It would be nice to provide additional comparative data on other areas, at least for some of the parameters examined across mouse and rat. Alternatively the authors should be more explicit in the abstract and description of the study that it is limited to a single area.

      Response: We sincerely appreciate the reviewer’s insightful comment. As suggested, we have revised the Abstract to explicitly state that our current analysis is focused on the somatosensory cortex. Furthermore, as demonstrated in Figure 1B, we have added a discussion regarding the possibility that the species differences observed in the primary somatosensory cortex may be a general feature shared across the entire cerebral cortex, as follows: “This DL-biased thickening in rats was evident in the primary somatosensory area, but is consistently observed throughout the rostral-caudal cortical regions. (Page 19, Lines 29-31)“

      Reviewer 1 Point 4- The authors provide convincing evidence of increased Wnt signaling pathway in the rat. They should show more explicitly how other classical pathways of neurogenic balance / temporal patterning are expressed in their mouse and rat transcriptome data sets. These would include Notch, FGF, BMP, for which all the data should be available to provide meaningful species comparison.

      Response: We sincerely thank the reviewer for this insightful suggestion. Following your advice, we have newly included comparative data on key signaling pathways essential for cortical development—namely Wnt, FGF, NOTCH, mTOR, SHH, and BMP—across different species. These results are now presented in Figure S17. Rat progenitors show comparable patterns to other species for FGF, mTOR, and Notch signaling, but elevated Wnt and BMP expression, especially at early stages. A detailed heatmap of raw Wnt pathway gene expression across species is also included in the same supplementary figure. We believe these additions provide a more comprehensive evolutionary perspective and significantly strengthen our findings.

      Reviewer 1 Point 5- The alignment of mouse and rat trajectories is very nicely showing a delay at early-mid-corticogenesis. But there is also heterochronic transcriptome at latest stages (end of 5). How can this be interpreted? Does this mean potentially prolonged astrogliogenesis in the rat cortex?

      Response: We sincerely appreciate the reviewer’s insightful comment and the meticulous attention given to our data. Regarding the heterochronic shift observed at Day 5, we agree that this point was not sufficiently addressed in the original manuscript.

      We would like to clarify the two primary reasons for this omission, which are inherent to the current study’s design:

      1. Resolution of Stage Alignment at Temporal Extremes: In our developmental stage alignment analysis, corresponding stages are defined by pairs showing the highest transcriptomic similarity within the sampled range. By definition, the precision of this alignment tends to decrease at the earliest and latest time points of a dataset. Since the "true" biological equivalent might lie outside our sampling window, we must be cautious in interpreting shifts at these temporal boundaries.
      2. Difference in Validation Rigor: Our study prioritized the early stages of deep-layer (DL) neuron production. Consequently, we rigorously defined the onset of neurogenesis in rats (Day 1) using multiple independent methods, including clonal analysis, immunohistochemistry, and gene expression. In contrast, Day 5 was defined simply as five days post-initiation of neurogenesis, without equivalent multi-modal validation. Given that our primary focus is the early phase of neurogenesis, the precision of the transition from late neurogenesis to gliogenesis is relatively lower. For these reasons, we believe that an in-depth discussion of the heterochronic shift at Day 5 might lead to over-interpretation. To reflect this more accurately and avoid misleading the reader, we have revised Figure 6F to de-emphasize the Day 5 shift. In addition, we revised the manuscript as “Importantly, while this analysis identified stage pairs with the highest similarity, the correspondence at the edges of the temporal sampling window is inherently less certain than at the center. Consequently, we focus on the notable reflection point at the center of our dataset. (Page 13, Lines 37-39)”.

      We believe these changes more faithfully represent the biological scope of our data while maintaining the scientific integrity of our primary conclusions.

      Reviewer 1 Point 6- Figure 7: description implies that module 3 is a subset of module 4, but this is not obvious at all from the panels shown. Please clarify.

      Response: We sincerely appreciate the reviewer’s careful reading of our manuscript. As suggested, we have revised Figure 7 to clarify the hierarchical relationship between Module 3 and Module 4, ensuring that their inclusion is now explicitly presented.


      Reviewer #2 Reviewer 2 Point 1. The introduction lacks sufficient background and fails to convey the significance of the study. Specifically, why the research was undertaken, what knowledge gap it addresses, and how the findings could be applied. Addressing these questions already in the introduction would enhance the impact of the work and broaden its readership.

      Response: We sincerely appreciate the reviewer’s insightful comment on this point. Our study reports evolutionary insights gained through an unconventional approach: a single-cell level comparison between mice and rats. We agree that clarifying the necessity of this specific approach is crucial for the manuscript. Accordingly, we have added the following two points to the Introduction:

      1. At the end of the first paragraph, we emphasized the current lack of research on the evolutionary adaptation of cortical circuits, despite the established functional importance of evolutionarily conserved circuits. (Page 3, Lines 7-10); “Paradoxically, despite the importance of these variations, research has predominantly focused on the conserved aspects of cortical architecture. Consequently, the degree of evolutionary plasticity inherent in these circuits and the cell-intrinsic mechanisms driving their modification remain profoundly enigmatic.”)
      2. At the end of the third paragraph, we revised and added text (Page3, Lines 26-27; “This lack of comparative insight represents a significant gap in our understanding of how conserved developmental programs give rise to species-specific brain architectures.”).

      Reviewer 2 Point 2. In figure 5 the authors conclude that "differences in cell cycle kinetics and indirect neurogenesis are unlikely to be the primary factors driving the species-specific variation in DL neuron production. Instead, the temporal regulation of progenitor neurogenic competence, which determines the duration of the DL production phase, provides a more plausible explanation for the greater number of DL subtypes observed in rats". It is not clear to this reviewer how the authors come to this conclusion. Authors observe a significant proportion of mitotic cells in rat VZ from day 1, and a higher constant proportion of mitotic progenitors in SVZ rats compared to mouse (Figure 5C). This points to an early difference in mitotic progenitors that may also lead to increased IP numbers, and potentially an increased number in DL cells, even before day 1. In addition, the higher abundance of IPs in the G2/S phase (statistically significant in 4 of the 7 time points) (Figure 5F), would suggest that this difference might play a role in the species-specific variation of DL neuron production. The authors should estimate cell cycle length instead of just measuring proportions to conclude something about cell cycle kinetics. They can then model growth curves to predict the effect caused if there were differences in cell cycle length between equivalent cell types across species.

      Response: We sincerely thank the reviewer for their careful reading of our manuscript and for pointing out the overstatements in our original descriptions. We agree that a more nuanced interpretation of the data was necessary. In response to these constructive suggestions, we have made the following revisions:

      1. Refinement of Descriptions: We have revised the text to more accurately reflect our findings, specifically noting that the increase in RG division on Day 1 and IP proliferation throughout the neurogenic period showed a significant trend. These features are now described more fairly and cautiously in the revised manuscript. (Page 11, Lines 42-46; “Remarkably, while the temporal dynamics of mitotic density were strikingly conserved between the two species, subtle yet discernible species-specific signatures emerged. Specifically, rats exhibited a higher ratio of mitotic cells in the VZ at the onset of neurogenesis, the precise period when DL subtypes are generated in both species. Further assessment of G2/S-phase cells via pulse-EdU labeling (Figure 5D, E) “)
      2. Inclusion of Time-lapse Imaging Data: The reviewer is correct that measuring the proportions of M and G2/S phases provides only a limited snapshot of cell cycle dynamics. To gain a more precise insight, we performed primary cultures of neural progenitor cells (NPCs) from Day 1 and conducted live-cell time-lapse imaging. This allowed us to directly quantify the cell cycle duration of mouse and rat NPCs (Figure S9A-C).
      3. Comparative Analysis and Mathematical Modeling: Our new data revealed that the cell cycle lengths of the two species are remarkably similar, with no significant differences observed under these culture conditions. Furthermore, to validate the impact of these findings on overall brain development, we developed a mathematical model based on our experimental data. This model predicts the total number of cells produced over the five-day neurogenic period, providing a more robust theoretical framework for our conclusions (Figure S9D). We believe these additions significantly strengthen the manuscript and address the reviewer's concerns regarding the physiological relevance of our observations.

      Reviewer 2 Point 3. In Figure 6 the authors focus only on the mouse and rat datasets. Given the availability of datasets from primates that the author used already for Figure 7, it would give the reader a broader prospective if also these datasets would be integrated in the analysis done for Figure 6, particularly it would be interesting to integrate them in the pseudotime alignment of cortical progenitor. How do human and/or macaque early and late neurogenic phase would compare to mouse and rat in this model?

      Response: We sincerely appreciate the reviewer’s insightful suggestion. In accordance with this comment, we have now incorporated pseudotime alignments of cortical progenitors between primates (human, macaque) and rodents (mouse, rat), presented as pairwise gene expression distance matrices with dynamic time warping in Figure S13. These heatmaps illustrate temporal compression or stretching in progenitor gene expression progression across species. Notably, macaque progenitors show no definitive deviations from rodents, whereas human progenitors exhibit distinct protraction relative to rats and even more so to mice. These additions provide a more comprehensive cross-species perspective without altering the study's core conclusions.

      Reviewer 2 Point 4. In Figures 6C and 6D, the authors distinguish between cycling and non-cycling NECs and RGCs. Could the authors clarify the rationale behind making this distinction? Could the authors comment on how they interpret the impact of cycling versus non-cycling states on species-specific non-uniform scaling? Do they consider the observed non-linear correspondences to be driven by differences in cell cycle activity?

      Response: We are grateful to the reviewer for their insightful observation. We agree that our initial classification of neural progenitor cell (NPC) populations based on proliferation marker expression levels followed a convention used in other studies but was, in the context of this work, unnecessary and potentially misleading. To avoid further confusion and focus on the core biological question, we have re-organized the data by pooling these populations into a single group. Regarding the concern about species differences in cell cycle kinetics, we believe there is no significant divergence between mice and rats that could explain the observed developmental patterns in temporal progression of neurogenesis. This is supported by two lines of evidence:

      1. Quantitative analysis of pH3-positive cells (Figure 5).
      2. New time-lapse imaging data of primary cultured NPCs, which shows no substantial difference in cell cycle length between the two species (Figure S9). These results indicate that the species-specific differences in deep-layer (DL) neuron production are not driven by cell division kinetics. Consequently, we conclude that the non-linear developmental progression of NPCs occurs independently of cell cycle regulation.

      Reviewer 2 Point 5. For the non-uniform scaling in Figure 6F, the authors identify critical inflection points and mention that "the largest delay in rat progenitors occurring where Day 1 and Day 3 progenitors overlapped". It would be good if the authors could discuss what they think all the inflection points represents. How much can it be explained by the heterogeneity within progenitors per time point? There is a clear higher spread of histograms at days 3 and 5, and the histogram at day 5 almost overlaps with day 1. I wonder if the same conclusion about non-uniform scaling would be detected if the distance matrix was built separately for specific cell types, for example only looking at NECs or RGCs.

      Response: We sincerely appreciate the reviewer’s insightful perspective on this point. In alignment with the suggestions from both this reviewer and Reviewer 1 (Point 5), we have updated the manuscript to discuss all identified inflection points. Specifically, we have clarified why our discussion focuses on the correspondence between Mouse D1 and Rat Day 3.

      A recognized limitation of our current analytical approach is that it identifies the closest matching expression profiles within the specific timeframes sampled for each species. For stages at the beginning or end of our sampling window, the "true" corresponding stage in the other species may lie outside our sampled range, which naturally limits the strength of any conclusions regarding those boundary points. Consequently, while we can confidently confirm the correspondence between Mouse Day 1 and Rat Day 3—both of which sit centrally within our sampled window—we have intentionally avoided over-interpreting data near the temporal boundaries.

      Regarding the cell types analyzed, this specific analysis was conducted exclusively on NECs and RGs (now shown in Figure 6F). Extensive prior research (Susan McConnell lab, Sally Temple lab, Fumio Matsuzaki lab, Dennis Jabaudon lab, and more) has established that the time-dependent mechanisms governing the fate determination of cortical excitatory neuron subtypes are encoded within RGs. Therefore, we focused our investigation on these lineages and did not include other cell types in this study. We believe this focused approach maintains the highest degree of biological relevance for our conclusions.

      Reviewer 2 Point 6. The authors conclude that the elevated and prolonged expression of Wnt-ligand genes in rat RGs extend the DL neurogenic window and contribute to rat-specific expansion of deep cortical layer. In order to validate this finding it would be good for the authors to perform a perturbation experiment and reduce Wnt signalling/ Axin 2 levels in rats or depleted the Lmx1a and Lhx2 double-positive population. Response: __We thank the reviewer for this insightful suggestion. We agree that providing direct experimental evidence is crucial to demonstrating that elevated Wnt signaling in RG progenitors drives the production of DL subtype neurons in rats. To address this, we performed a functional intervention on Day 3, a stage when Wnt signaling (indicated by Axin2 expression) is significantly higher in rats than in mice (__Figure 7C, D). By introducing a dominant-negative form of TCF7L2 (dnTCF7L2) to inhibit Wnt signaling specifically in RG progenitors, we tracked the fate of the resulting neurons (Figure 7I, J). Our results showed a clear reduction in the proportion of DL neurons, accompanied by a reciprocal increase in upper-layer (UL) neurons. These findings demonstrate that maintained high levels of Wnt signaling are essential for the prolonged neurogenic capacity for DL neurons in rats. This new data has been incorporated into Figure 7.

      Reviewer 2 Point 7. The authors conclude that Wnt signaling is a rat specific effect since they did not observe any clear temporal change in wnt receptors in gyrencephalic species, and only a subset of RG in rats co-express Lmx1a and Lhx2. However, specific Wntligands and receptors (Wnt5a, Fzd and Lrp6) seem to be upregulated in human as well (Fig 7G), non RG cells could act as wnt ligand inducers in other species, and it has not been demonstrated that Lmx1a and Lhx2 are the source for Wntligand production. I wonder if the authors can completely rule out a role for Wnt in the protracted neurogenesis of other species.

      Response: We sincerely appreciate the reviewer’s insightful and broad perspective regarding Wnt signaling dynamics across diverse species. In this study, our primary focus was to elucidate the specific mechanisms underlying the differences between mice and rats. Consequently, we did not initially explore Wnt dynamics in other species or their roles in developmental timing in great depth in the original manuscript. We fully acknowledge that lineage-specific adaptations occur at the individual gene level; for instance, Silver and colleagues have reported that human-specific upregulation of Wnt receptor gene FZD8 modulates neural progenitor behavior (Boyd et al., Current Biology 2008, Liu et al., Nature 2025). However, our comparative analysis of five mammalian species—carefully aligned by developmental stage—reveals a distinct global trend. While individual gene variations exist like human FZD8, the expression levels of multiple Wnt-related genes, particularly ligands, are markedly higher in rats than in the other four species.

      Following the reviewer’s insightful suggestion, we examined the potential role of Lmx1a in activating Wnt ligand transcription in rat cortical progenitors by analyzing their expression correlation at the single-cell level. Our analysis revealed that several Wnt ligand genes are co-expressed with Lmx1a with a remarkably strong positive correlation. While we have not yet experimentally demonstrated the direct transcriptional activation of Wnt ligands by Lmx1a in these cells, this robust correlation at single-cell resolution strongly suggests that Lmx1a regulates Wnt ligand expression. These new findings are now included in Figure 7 and Figure S16, and the corresponding results section (Page 15, Lines 42-44) has been revised accordingly.

      __Reviewer 2 Point 8 __Minor comments: The RNAscope experiment is currently qualitative. Is it the mRNA copy number per cell equal in both species but more cells are positive in rat, or are there differences in number of mRNA molecules as well? It is not indicated if the RNAscopeprobes are the same for mouse and rat.

      Response: We sincerely thank the reviewer for this insightful suggestion. Following the comment, we performed RNAscope analysis for Axin2 in both mice and rats and quantified the results (now included in Figure 7D). The new data successfully validate the species differences initially observed in our scRNAseq analysis: specifically, the period of high-level Axin2 expression is significantly extended in rats compared to mice. These findings provide histological evidence that reinforces our conclusions regarding the distinct temporal dynamics between the two species.

      Regarding probe design, the Axin2 RNAscope probes target conserved and corresponding sequences between mouse and rat, with species-specific probes optimized for each organism to ensure maximal specificity and sensitivity. We have updated the Methods section ("Fluorescent in situ hybridization with RNAscope") to include these details.

      Reviewer #3

      Reviewer 3 Point 1. Satb2 is also widely recognized as a deep layer marker. The authors need to perform analysis and quantification in Figs 1 and 4 with other II/III and IV markers such as Cux1 and Rorb.

      Response: We thank the reviewer for their insightful comments regarding the marker specificity. We fully agree that while Satb2 is a robust marker for callosal projection identity, its broad distribution across both deep and upper layers limits its utility as a layer-specific marker. As the reviewer suggested, Cux1 (Layers 2/3) and Rorb (Layer 4) are indeed superior markers for defining laminar identity.

      To address this, we have incorporated new immunohistochemical data for these markers in both the quantification of somatosensory cortical neurons (Figure S2) and the birth-dating analysis (Figure 4).

      Our new findings are as follows:

      1. Layer Quantification (Figure S2): By utilizing Cux1 and Rorb as more specific upper-layer (UL) markers, we confirmed that there are no significant differences in the number of these neurons between mice and rats.
      2. Birth-dating Analysis (Figure 4): These markers allowed us to more precisely define the timing of Cux1/Rorb-positive cell generation, revealing subtle but important differences between the two species. While these additions do not alter the fundamental narrative of the original manuscript, they have significantly enhanced the precision and rigor of our analysis. We are grateful to the reviewer for guiding us toward this more robust validation.

      Reviewer 3 Point 2. Rats have larger cortices. Therefore, quantification of neurons should also be normalized to cortical thickness in Fig 1E and also represented with individual data points.

      Response: We sincerely appreciate the reviewer’s constructive suggestion. We agree that normalizing the number of cortical neurons by thickness provides a more rigorous comparison. Accordingly, we have calculated the neuronal density (cell count per unit thickness) for Tbr1- and Ctip2-positive cells and included these data in Figure S2C. Our analysis confirms that these populations are distributed at a significantly higher density in mice compared to rats.

      Furthermore, we have updated the visualization in Figure 1E to display individual data points, ensuring full transparency of the underlying distribution. We believe these revisions, prompted by the reviewer’s insight, have substantially strengthened the clarity and persuasiveness of our manuscript.

      Reviewer 3 Point 3. The clonal analysis in Figs 2 and 3 quantifies GFP and RFP and reports these as neurons. However, without using cell-specific markers, it seems the authors cannot exclude that some progeny are also glia derived from a radial glial progeny. I don't expect all experiments to have this but they must have some measures of both populations to address this possibility. This needs to be addressed to build confidence in the conclusion that there is clonal production of neurons.

      Related to this, the relationship between position and fate is not always 1 to 1. The data summarized in Fig 2G are based on position and not using subtype markers. They should include assessment of markers as they do in Fig 4.

      Response: We sincerely thank the reviewer for this insightful comment. We agree that a clear definition of cell types is essential for the accuracy of clonal analysis.

      In this study, we primarily identified neurons based on their distinct morphological characteristics and performed measurements specifically on these cells. To validate this approach, we confirmed that the vast majority of cells identified as neurons were positive for NeuN and cortical excitatory neuron markers, while remaining negative for glial markers such as Olig2 and SOX9. (Notably, at postnatal day 7, most cells in the glial lineage exist as undifferentiated Olig2-positive progenitors). These observations support our conclusion that the cells analyzed based on morphology are indeed cortical excitatory neurons.

      As the reviewer rightly pointed out, evaluating cell composition using fate-specific marker expression is the ideal approach. However, our current experimental setup required multiple fluorescence channels for DAPI staining (to assess tissue architecture) and immunostaining for GFP and RFP (to identify labeled clones). Due to these technical constraints regarding available detection channels and host species compatibility, we relied on morphological criteria for the primary analysis.

      To address this concern and ensure the reliability of our findings, we performed additional analyses using a subset of samples. By co-staining retrovirally labeled neurons with cell-fate markers, we obtained results consistent with our other data (Figures 1 and 4) regarding laminar position and marker expression. Based on this consistency, we are confident that our classification based on morphology and laminar position does not alter the fundamental conclusions of this study.

      Reviewer 3 Point 4. In Fig 5, the authors use PH3 as well as EdU to measure differences in indirect neurogenesis. Using EdU and Tbr2 they report more dividing IPs. However they need to measure this over the total number of Tbr2 cells as it is not normalized to differences in Tbr2 cells between species. Are there total differences in Tbr2+ cells when normalized to DAPI as well? Moreover, little analyses is performed to measure any impact on radial glia. As no striking differences were observed in IPs this leaves the cellular mechanism a bit unclear and begs the impact on radial glia. Measuring PH3+ cells in VZ and SVZ is not cell specific nor does it yield information to support the prolonged neurogenesis.

      Response: We sincerely thank the reviewer for this insightful suggestion. We agree that quantifying Tbr2+/EdU+ double-positive cells alone was insufficient to fully capture the IP dynamics. Following the reviewer’s advice, we have now quantified the total population of Tbr2+ cells, normalized to the number of DAPI-stained nuclei. This new analysis reveals that mice and rats exhibit nearly indistinguishable temporal dynamics (Figure S10). When integrated with the original Tbr2+/EdU+ data in Figure 5, these findings suggest that rats maintain a slightly higher IP pool throughout the neurogenic period. This implies that the increased neuronal production in rats is not restricted to a specific phase, but rather occurs consistently across all developmental stages. We believe these additional data significantly strengthen our conclusions.


      Reviewer 3 Point 5. The sc-seq is done in rat and compared to published mouse data from corresponding stages. They conclude species specific differences in progenitor gene expression. I am unsure how appropriate this is. Are similar sequencing platforms used? Can they find similar results if using multiple dataset? There are other datasets that may be used to validate these findings beyond DiBella et al.

      Response: We sincerely thank the reviewer for this insightful comment. We agree that establishing the validity of our analytical approach is crucial for the reader’s confidence in our findings. To address this, we have explicitly stated in the revised manuscript that both our rat scRNAseq data and the publicly available datasets were generated using consistent experimental platforms. This ensures that the integration process is technically sound.

      Revised text (Page 13, Lines 16-18): “After quality control, we integrated these profiles with previously published mouse cortical cell data from corresponding neurogenic stages, which is prepared using the consistent platform with ours (35) (Figure S11).”

      Furthermore, to ensure the robustness of our comparative analysis, we have incorporated an additional independent dataset (Ruan et al., PNAS 2021) in addition to the Di Bella et al. Nature 2021 data used in the original manuscript. We confirmed that the results obtained using this second dataset are highly consistent with our initial findings, further validating our conclusions across different studies (Figure S13A).

      Reviewer 3 Point 6. Wnt ligand analysis requires validation in situ across developmental stages, to support their conclusions. Ideally they might consider doing some manipulations to provide context to this observation.

      Response: We sincerely thank the reviewer for these insightful suggestions. We agree that validating the spatial expression patterns of Wnt ligands and confirming their expression in rat-specific RG, as suggested by our scRNAseq data, is crucial for strengthening our conclusions.

      Regarding the expression of Wnt3a, a key ligand in cortical development: although immunohistochemical analysis clearly identified Wnt3a expression in the cortical hem, the expression levels in RG within the cortical area were substantially lower than those in the hem, making definitive visualization challenging. To complement these findings and provide more robust evidence, we performed the following additional experiments:

      1. Validation of Wnt signaling levels: Using RNAscope-based in situ hybridization for Axin2, we successfully confirmed the elevated Wnt signaling levels in rat-specific RG (Figure 7C, D), consistent with our scRNAseq findings.
      2. Elucidating strikingly high correlated expressions of Lmx1a and Wnt ligand genes in the rat cortical progenitors in our scRNAseq dataset (Figure S16B).
      3. Functional analysis: To test the functional significance of this signaling, we inhibited Wnt signaling by electroporating dominant-negative TCF7L2 into rat RG at E15.5. This manipulation resulted in a subtype shift of the generated neurons toward an upper-layer identity (Figure 7I, J). These new results demonstrate that the rat-specific extension of high Wnt signaling levels serves as a fundamental mechanism for the prolonged production of deep-layer (DL) neurons. We are grateful to the reviewer for these suggestions; these additional data have significantly strengthened our core argument that the heterochronic regulation of Wnt signaling states drives the evolution of cortical neuronal composition.

      __Reviewer 3 Point 7 __Minor concerns-1

      Please separate images in Fig 1D it is very strange to have them all on top of each other.

      Response: We sincerely thank the reviewer for this suggestion. As requested, we have provided individual channel images alongside the merged multicolor panels. We agree that this modification significantly enhances the clarity of our data and makes the results much easier to interpret.

      __Reviewer 3 Point 8 __Minor concerns-2

      Are data in Fig 4E Edu+Tbr1+EdU+? This should be clarified and would be most accurate.

      Response: We appreciate the reviewer’s suggestion. We added the label of Y axes of the plots in Figure 4E-K. The procedure of cell count in these analyses are documented in the caption of Figure 4E-K, “Normalized counts of neurons colabeled for EdU and projection-specific markers, relative to the peak of EdU+ and marker+ cells.”.

      __Reviewer 3 Point 9 __Minor concerns-3

      Fig 4 graphs only have titles without Y axis. Please adjust location of title or repeat for clarity.

      Response: We thank the reviewer for this helpful suggestion. To clarify the definition of the Y-axis, we have now added a descriptive label to the axis in the revised figure.

      __Reviewer 3 Point 10 __Minor concerns-4

      Fig 4A implies cumulative incorporation which I don't think is being performed here. They should clarify this in the figure.

      Response: We appreciate the reviewer’s insightful comment. To avoid any potential misunderstanding regarding the additivity of the effect, we have revised the illustration in Figure 4A for greater clarity.

      __Reviewer 3 Point 11 __Minor concerns-5

      Fig 5 needs labels for the actual stages assayed, as illustrated in Fig 4A.

      Response: We thank the reviewer for this helpful suggestion. Following your comment, we have added the developmental stage information (expressed as embryonic days) for both mice and rats in the revised manuscript.

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      Referee #3

      Evidence, reproducibility and clarity

      In this study the authors investigate differences between two closely related species, rats and mice, in terms of cortical development and neuronal composition. They first perform comparative analysis of cortical layers which revealed the density and markers of deep layer neurons of rats is disproportionately larger compared to adult mice. They then use retroviruses for lineage analysis from embryonic stages to P7. They find in general that there are temporal differences in when mice and rats produce upper versus deep layer neurons, with the process being protracted in rats. EdU injections were used to report differences in the timing of cortical neuron generation between species and they note no striking differences in IPs. Sc-sequencing of rat cortices at different stages was then used to measure temporal changes in gene expression and compared to published mouse data. They note that rats have sustained Wnt ligand expression in radial glia highlighting that as a potential mechanism of action.

      Major concerns 1. Satb2 is also widely recognized as a deep layer marker. The authors need to perform analysis and quantification in Figs 1 and 4 with other II/III and IV markers such as Cux1 and Rorb. 2. Rats have larger cortices. Therefore, quantification of neurons should also be normalized to cortical thickness in Fig 1E and also represented with individual data points. 3. The clonal analysis in Figs 2 and 3 quantifies GFP and RFP and reports these as neurons. However, without using cell-specific markers, it seems the authors cannot exclude that some progeny are also glia derived from a radial glial progney. I don't expect all experiments to have this but they must have some measures of both populations to address this possibility. This needs to be addressed to build confidence in the conclusion that there is clonal production of neurons. Related to this, the relationship between position and fate is not always 1 to 1. The data summarized in Fig 2G are based on position and not using subtype markers. They should include assessment of markers as they do in Fig 4. 4. In Fig 5, the authors use PH3 as well as EdU to measure differences in indirect neurogenesis. Using EdU and Tbr2 they report more dividing IPs. However they need to measure this over the total number of Tbr2 cells as it is not normalized to differences in Tbr2 cells between species. Are there total differences in Tbr2+ cells when normalized to DAPI as well? Moreover, little analyses is performed to measure any impact on radial glia. As no striking differences were observed in IPs this leaves the cellular mechanism a bit unclear and begs the impact on radial glia. Measuring PH3+ cells in VZ and SVZ is not cell specific nor does it yield information to support the prolonged neurogenesis. 5. The sc-seq is done in rat and compared to published mouse data from corresponding stages. They conclude species specific differences in progenitor gene expression. I am unsure how appropriate this is. Are similar sequencing platforms used? Can they find similar results if using multiple dataset? There are other datasets that may be used to validate these findings beyond DiBella et al. 6. Wnt ligand analysis requires validation in situ across developmental stages, to support their conclusions. Ideally they might consider doing some manipulations to provide context to this observation.

      Minor concerns 1. Please separate images in Fig 1D it is very strange to have them all on top of each other. 2. Are data in Fig 4E Edu+Tbr1+EdU+? This should be clarified and would be most accurate. 3. Fig 4 graphs only have titles without Y axis. Please adjust location of title or repeat for clarity. 4. Fig 4A implies cumulative incorporation which I don't think is being performed here. They should clarify this in the figure. 5. Fig 5 needs labels for the actual stages assayed, as illustrated in Fig 4A.

      Significance

      Strengths:

      The finding that there are differences in cortical composition between rats and mice and that this is linked to prolonged neurogenesis in rats Use of careful and detailed lineage analysis to define differences in temporal production of neurons Inclusion of single cell sequencing

      Limitations:

      Largely descriptive Requires additional investigation to support some conclusions about neurons Concerns about inferring too much from single cell sequencing done by the authors but compared to publication

      Advance: Finding that there are differences in neurogenesis between closely related species is interesting and provides insight into mechanisms of cortical evolution.

      Audience: Evolution, cortical development

      Expertise: Cortical development, evolution

    3. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons


      Referee #2

      Evidence, reproducibility and clarity

      Summary:

      Yamauchi et al. performed a comparative anatomical analysis of the layer architecture in the primary somatosensory cortex across 8 mammalian species. Unlike primates, which show an expansion of upper layers (UL), rodents, especially rats, display a pronounced thickening of deep layers (DL). In this study they focus on comparing rats and mice, given the higher abundance of DL neuron subtypes in rats. Using histological analysis, they showed that rats possess significantly more DL neurons per cortical column than mice, while UL neuron counts remain similar. Clonal lineage tracing showed that rat radial glial (RG) progenitors generate more DL neurons, indicating species-specific differences in progenitor neurogenic activity. Birth dating assays confirmed an extended DL neurogenesis phase in rats, followed by a conserved UL generation phase. Single-cell RNA sequencing further revealed that rats maintain an early progenitor state longer than mice, marked by sustained expression of DL-associated genes. Specifically, rat RG progenitors exhibit prolonged and elevated expression of Wnt signaling genes, particularly Wnt ligands. Comparative analysis of published single-cell RNA-Seq across species highlighted that this extended Wnt-high period in rats is exceptional, suggesting a species-specific extension of a conserved neurogenic program.

      Major comments:

      This reviewer thinks the topic is exciting, and the experiments elegant, insightful and well described. The paper is well written and follows a very logical flow, the conclusion for each experiment is supported by the data and they are carefully stated. This reviewer really appreciated the summary illustration included as a panel in each figure, they think that this greatly enhanced the clarity and accessibility of the data presented, especially because species comparison can be difficult to follow.

      In this reviewer's opinion, there are some aspects of the findings that the authors would need to clarify/address to explain in clarify the phenotype observed and to enhance the overall significance of this very well-made paper: 1. The introduction lacks sufficient background and fails to convey the significance of the study. Specifically, why the research was undertaken, what knowledge gap it addresses, and how the findings could be applied. Addressing these questions already in the introduction would enhance the impact of the work and broaden its readership. 2. In figure 5 the authors conclude that "differences in cell cycle kinetics and indirect neurogenesis are unlikely to be the primary factors driving the species-specific variation in DL neuron production. Instead, the temporal regulation of progenitor neurogenic competence, which determines the duration of the DL production phase, provides a more plausible explanation for the greater number of DL subtypes observed in rats". It is not clear to this reviewer how the authors come to this conclusion. Authors observe a significant proportion of mitotic cells in rat VZ from day 1, and a higher constant proportion of mitotic progenitors in SVZ rats compared to mouse (Figure 5C). This points to an early difference in mitotic progenitors that may also lead to increased IP numbers, and potentially an increased number in DL cells, even before day 1. In addition, the higher abundance of IPs in the G2/S phase (statistically significant in 4 of the 7 time points) (Figure 5F), would suggest that this difference might play a role in the species-specific variation of DL neuron production. The authors should estimate cell cycle length instead of just measuring proportions to conclude something about cell cycle kinetics. They can then model growth curves to predict the effect caused if there were differences in cell cycle length between equivalent cell types across species. 3. In Figure 6 the authors focus only on the mouse and rat datasets. Given the availability of datasets from primates that the author used already for Figure 7, it would give the reader a broader prospective if also these datasets would be integrated in the analysis done for Figure 6, particularly it would be interesting to integrate them in the pseudotime alignment of cortical progenitor. How do human and/or macaque early and late neurogenic phase would compare to mouse and rat in this model? 4. In Figures 6C and 6D, the authors distinguish between cycling and non-cycling NECs and RGCs. Could the authors clarify the rationale behind making this distinction? Could the authors comment on how they interpret the impact of cycling versus non-cycling states on species-specific non-uniform scaling? Do they consider the observed non-linear correspondences to be driven by differences in cell cycle activity? 5. For the non-uniform scaling in Figure 6F, the authors identify critical inflection points and mention that "the largest delay in rat progenitors occurring where Day 1 and Day 3 progenitors overlapped". It would be good if the authors could discuss what they think all the inflection points represents. How much can it be explained by the heterogeneity within progenitors per time point? There is a clear higher spread of histograms at days 3 and 5, and the histogram at day 5 almost overlaps with day 1. I wonder if the same conclusion about non-uniform scaling would be detected if the distance matrix was built separately for specific cell types, for example only looking at NECs or RGCs. 6. The authors conclude that the elevated and prolonged expression of Wnt-ligand genes in rat RGs extend the DL neurogenic window and contribute to rat-specific expansion of deep cortical layer. In order to validate this finding it would be good for the authors to perform a perturbation experiment and reduce Wnt signalling/ Axin 2 levels in rats or depleted the Lmx1a and Lhx2 double-positive population. 7. The authors conclude that Wnt signaling is a rat specific effect since they did not observe any clear temporal change in wnt receptors in gyrencephalic species, and only a subset of RG in rats co-express Lmx1a and Lhx2. However, specific Wnt ligands and receptors (Wnt5a, Fzd and Lrp6) seem to be upregulated in human as well (Fig 7G), non RG cells could act as wnt ligand inducers in other species, and it has not been demonstrated that Lmx1a and Lhx2 are the source for Wnt ligand production. I wonder if the authors can completely rule out a role for Wnt in the protracted neurogenesis of other species.

      Minor comments:

      The RNAscope experiment is currently qualitative. Is it the mRNA copy number per cell equal in both species but more cells are positive in rat, or are there differences in number of mRNA molecules as well? It is not indicated if the RNAscope probes are the same for mouse and rat.

      Significance

      How different species achieve such remarkable differences in brain shape and size remains poorly understood. A critical aspect of this process is the duration of the neurogenic phase: the period during which neural progenitors generate neurons. This phase tends to be extended in species with larger brains and contains multiple neuronal stem cell types in varying proportions. It is thought that this accounts for their increased neuronal numbers. In their search for mechanisms that prolong neurogenesis across species, the authors propose a rat-specific role for Wnt ligands in expanding the neurogenic period in the rat brain. Importantly, they rule out that this mechanism operates in other species, such as primates or ferrets, to achieve similar extensions.

      The study is of high quality, incorporating rigorous lineage-tracing experiments in two species and single-cell RNA sequencing. Previous work established a role for Wnt signaling in regulating early neurogenesis in mice. Here, the authors characterize a novel population of radial glial cells (Lmx1a and Lhx2 double-positive) that may explain increased Wnt ligand secretion in rats. However, functional validation of this mechanism is still lacking. To strengthen its evolutionary relevance, it would be important to determine whether similar effects occur during earlier neural stages in other species (such as neuroepithelium thickening), or whether other cell types have co-opted the proposed Lmx1a-Lhx2 regulatory module in other species.

      From the perspective of a researcher with a stem cell and developmental background focused on neural evo-devo, this manuscript represents a solid and novel contribution. The proposed model of a rat-specific mechanism for extending the neurogenic phase contrasts with the prevailing concept of convergence in mechanisms underlying species-specific cortical development. This raises intriguing questions about how multiple molecular pathways have been co-opted to achieve similar developmental outcomes. Furthermore, we know very little about what determines the duration of specific developmental processes. This work suggests that extended Wnt signaling may account for prolonged neurogenesis in rats compared to mice. Future studies should aim to validate the proposed rat-specific co-option of an Lmx1a-Wnt ligand cascade in cortical radial glia, potentially through relief of Lhx2-mediated repression of Lmx1a.

    4. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

      Learn more at Review Commons


      Referee #1

      Evidence, reproducibility and clarity

      Yamauchi and colleagues explore how species-specific differences in timing of neurogenesis may contribute to cell composition in the mature brain, using rat and mouse cortex as a main model of study. They first estimate and compare among 8 mammalian species the number of cortical neurons corresponding to deep layer (DL) and upper layer (UL) neurons. They find a species-specific relative increase of DL/UL neurons in rats, compared with all other species tested. They then explore the cellular mechanisms underlying these differences in mouse and rat, using retrovirus-based clonal analyses and EdU nuclear labeling, as well as axonal projection retrograde tracing. They conclude that the increased number of DL neurons in the rat is correlated with an increase in the period of DL neuron generation at early stages of corticogenesis. They also report a lack of obvious difference in cell cycle kinetics and indirect vs direct neurogenesis that could explain the DL/UL differences. Finally, they perform comparative scRNAseq analysis in mouse vs rat embryonic cortical cells. This first confirms at the transcriptomic level an apparent prolonged period of early neurogenesis in the rat cortex. Moreover they find among modules of co-expression detectable at these stages an increase in genes corresponding to Wnt signalling, a pathway previously linked to increased self-renewal and delayed differentiation of radial glial progenitors. They thus conclude that the species-differences in neuronal number in the rat is linked to increased Wnt signaling at a critical time of corticogenesis.

      Overall this is a thorough and elegant study focused on a timely and interesting topic. The data shown are convincing and carefully interpreted. I have however a couple of comments and questions to make the study fully clear and convincing.

      • The authors describe cortical neuronal counts across several mammalian species, which is quite impressive, but the information on the methods of counting is lacking: how representative are the data used / shown; how many individuals / brains / sections were used for each species considered? Much more detailed description of the quantifications should be provicded to judge the validity of this first conclusion.
      • The authors use several markers of cortical neuron identity to confirm their neuron number measurements, but from the data shown in Figure 1D,E it seems that only some markers (Satb2) show species-differences while others do not (CTIP2 / Tbr1). How do the authors explain this discrepancy - does this mean that it is mainly Satb2 neurons that are increased in number? But if so how to explain the relative increase in subcortical projections shown in Figure S7?
      • The authors focus their study almost exclusively on somatosensory cortex, but can they comment on other areas (motor, visual for instance)? It would be nice to provide additional comparative data on other areas, at least for some of the parameters examined acros mouse and rat. Alternatively the authors should be more explicit in the abstract and description of the study that it is limited to a single area.
      • The authors provide convincing evidence of increased Wnt signaling pathway in the rat. They should show more explicitely how other classical pathways of neurogenic balance / temporal patterning are expressed in their mouse and rat transcriptome data sets. These would include Notch, FGF, BMP, for which all the data should be available to provide meaningful species comparison.
      • The alignment of mouse and rat trajectories is very nicely showing a delay at early-mid-corticogenesis. But there is also heterochronic transcriptome at latest stages (end of 5). How can this be interpreted? Does this mean potentially prolonged astrogliogenesis in the rat cortex?
      • Figure 7: description implies that module 3 is a subset of module 4, but this is not obvious at all from the panels shown. Please clarify.

      Significance

      The topic of the study if of general interest and original, and the conclusions original and important. The approaches used are state of the art and applied in an elegant fashion to the topic. This study should be of broad interest to developmental neurobiologists, but also developmental biologists interesting in temporal patterning and developmental timing across species.

    1. 1)How did he learn to read if it was forbidden? So brave! I feel bad for his suffering, it’s so unfair. Wow! His mistress changed because of slavery, that’s sad but interesting. I like how he used kids to learn, so smart. “Columbian Orator”? I need to look this up, sounds important. It’s so intense that learning to read made him suffer more… cruel that freedom was only a dream.

      2) Chattel -someone’s property (like an object) Stratagems -strategies, tricks Emancipation - freedom from slavery Vindication - defense or justification Writhed -twisted, squirmed Unabated - without decreasing

      3) Frederick Douglass was born a slave in Maryland around 1817. - Origin He went to Baltimore and learned to read with his master’s wife’s help. - Learning He escaped in 1838, got married, and changed his name. -Freedom

      Became a speaker, wrote his autobiography, fought for Black rights. - Activism In Master Hugh’s house, he had to use strategies to keep learning, because his mistress stopped teaching him. -Obstacles His mistress was kind at first, but slavery made her harsh and cruel. - Change of people Douglass befriended white kids to teach him how to read more. -Cleverness The book Columbian Orator taught him about freedom and arguing against slavery. - Education Learning to read caused pain because he saw his situation but couldn’t change it. -Pain

      4) “Slavery proved as injurious to her as it did to me.” “Education and slavery were incompatible with each other.” “The more I read, the more I was led to abhor and detest my enslavers.” “The silver trump of freedom had roused my soul to eternal wakefulness.” Freedom was always on his mind, motivating and torturing him at the same time. - Desire for freedom

      5) My thesis: Learning to read was a double-edged sword for Frederick Douglass: it freed him intellectually and gave him power to fight for freedom, but it also caused him pain by revealing the cruelty of slavery and his own oppression.

    1. Database

        1. Relational Database
      • helpful for storing massive amounts of data -able to store diiffernt types of data
      • managed services, provided backup,high availibility, high storage,
      • across muiltiple az
      • able to recover fast --AWS reposibility - making sure its operational, security of storgae, infasturcture mangaement and safaty -Coustomer Resposibil;ity= mangament of data, encryption and access contraol and monitor performance Types" 1) RDS
      • non flexible scheme
      • SQL, POSTGRESS SQL,
      • relational dataset 2) NoSQL
      • flexible scheme
      • 3)Data Warehousing 4)In memory caching Aurora:
      • faster thatn RDS -SQL

      RedShift- Data Warehouse ElasticCache : inmemory cacheing service

    1. and so great, Sir, is the corruption and licentiousness that our country is being completely depopulated, and Your Highness should not agree with this nor accept it as in your service.

      This is a major part of King Afonso I's plea to King João to stop the slave trade in the Kongo, citing its corruption and licentiousness as well as, I believe, trying to appeal to King João's morals.

    2. Because the pope crowns the emperor, it does not follow that the pope is superior to the emperor. Samuel, who crowned Saul and David, was not above these kings, nor Nathan above Solomon, whom he consecrated . . . Let the emperor then be a veritable emperor and no longer allow himself to be stripped of his sword or of his scepter!

      Luther calls on the emperor to defy the pope and says that the Pope is stripping the emperor of his sword or scepter. This is interesting because it doesn't explicitly call for any action, just telling the emperor to stand up for himself.

    3. They even imagine that a priest can never be anything but a priest--that is, he can never become a layman. All this is nothing but mere talk and a figment of human invention.

      The idea in these sentences is that the Catholic Church says that once a man becomes a priest, he cannot revert to a laymen, an idea that Luther points out is a human invention and not supported by Scripture.

    4. There has been a fiction by which the Pope, bishops, priests, and monks are called the 'spiritual estate'; princes, lords, artisans, and peasants are the 'temporal estate.' This is an artful lie and hypocritical invention

      Luther's idea is that the Catholic's distintion between the "spiritual estate" and "temporal estate" is a fundamentally anti-Christian idea because it seperates laymen and priests into different catagories.

    5. Istanbul quickly became the largest Eurasian city outside China. Under Sultans like Suleiman the Magnificent (r. 1520-1566), the Ottomans expanded into Europe and nearly captured Vienna in 1529 and again in 1683.

      The mention of Ottoman battles against the Europeans are very interesting, and I'd like to know exactly why and how these battles happened.

    6. , 'I believe in the holy Christian Church,' the Pope cannot alone be right; else we must say, 'I believe in the Pope of Rome,' and reduce the Christian Church to one man, which is a devilish and damnable heresy.

      That isn't even a matter of conjecture. He's right, that is heresy. I can't imagine how much courage it must have taken for him to do this back when he did. The church was powerful, and he held his ground. It's amazing.

    7. That is why, in cases of necessity, every man can baptize and absolve, which would not be possible if we were not all priests.

      Again, Luther's point is clearly against not the church, but with their dogma. He wants faith to be something for everyone, and that is beautiful.

    8. Christians are truly of the spiritual estate, and there is no difference among them, save of office.

      I like this statement. I don't personally believe in an religions, but this is a truth of them. To claim one part of religion is more holy than the rest only leads to more pain. I think this assertion by Luther is one of his best.

    9. Thirdly, if they are threatened with a council, they invented the notion that no one may call a council but the Pope.

      This makes for a fair complaint. Luther is reasonable in his frustration with this practice. To have authority be the only one to investigate leads to nothing but corruption.

    10. t happens we have continuously many and different diseases

      Although not connected as much to the greater issue, I always want to leave a note mentioning how much of history is just diseases. It's a staggering amount of history. Too much, really.

    11. And to avoid such a great evil we passed a law so that any white man living in our kingdoms and wanting to purchase goods in any way should first inform three of our noblemen and officials of our court whom we rely upon in this matter…who should investigate if the mentioned goods are captives or free men, and if cleared by them there will be no further doubt nor embargo for them to be taken and embarked.

      I understand this action. You don't want war, so you use laws. It's a simple move, but I know it didn't end up working.

    12. immediately ironed and branded with fire, and when they are carried to be embarked, if they are caught by our guards' men the whites allege that they have bought them but they cannot say from whom, so that it is our duty to do justice and to restore to the freemen their freedom, but it cannot be done if your subjects feel offended, as they claim to be.

      This is just disgusting, and more proof of blatant kidnapping. You don't brand people, you don't steal them. Slavery is an evil of history, and even in modern day, but the practice will always leave a bad taste in my mouth.

    13. seize many of our people, freed and exempt men, and very often it happens that they kidnap even noblemen and the sons of noblemen, and our relatives, and take them to be sold to the white men who are in our kingdoms; and for this purpose they have concealed them; and others are brought during the night so that they might not be recognized.

      Again, they just take people. I can't imagine how they got away with it.

    14. since the mentioned merchants are taking every day our natives, sons of the land and the sons of our noblemen and vassals and our relatives,

      This is just baffling to me. Arica wasn't considerably weaker than Europe at this point in history, at least not on the land. I understand the reason you don't retaliate with violence, but I wouldn't be so patient in their shoes.

    15. The Mughal Empire of India was established in 1526 by a Persian-speaking dynasty that traced its authority back to Genghis Khan’s second son, Chagatai.

      I find it hard to believe that Mughal wasn't meant to invoke the same feeling as the Mongols. Brand recognition means a lot, even in terms of empite naming.

    16. After the Armenian genocide in 1915, during World War One, the Armenian quarter of Isfahan became one of the oldest and largest Armenian centers in the world.

      A city with a legacy of protection. I think that's a better legacy than most would end up having, especially i it could help to save a culture like this.

    17. the trade routes and major markets connecting to the Silk Road such as Cairo and Baghdad.

      That is some impressive trade routes. So impressive that I want to go around them to find cheaper trade routes.

    18. and the Ottoman Empire in the Middle East.

      This little empire would last all the way into the 20th century, ultimately collapsing after World War I. It's crazy to think about just how long this empire, one that had been an enemy to the late Roman Empire, survived.

    19. Galileo's middle finger, preserved in the science museum of Florence, Italy

      Galileo's middle finger being taken as a relic is akin to the religious relics of saints that would often be preserved as well. This, perhaps not intentionally, relates to the way science was viewed as another religion almost by people at the time.

    20. Ottomans were actually quite tolerant of ethnic, language, and religious diversity, and their empire was multi-ethnic and multicultural.

      If true, this is incredibly ironic considering the Armenian Genocide perpetrated by the Ottoman Empire during WWI. Would be interesting to find out why this shift occured.

    21. The taxes and charges imposed in the Ottoman-controlled Middle East ultimately created an incentive for European merchants to seek other ways of reaching Asia and trading without these high costs

      Because the Ottoman decided to tax high on trade values, it led European merchants to find other ways to trade goods with out having to pay tax or as much tax.

    1. The following table lists kinetics data for this reaction at 25°C. Determine the rate law and calculate the rate constant. kinetics data for this reaction at 25°C. Experiment [S2O82−]0 (M) [I−]0 (M) Initial Rate (M/s) 1 0.27 0.38 2.05 2 0.40 0.38 3.06 3 0.40 0.22 1.76 Answer: rate = k[S2O82−][I−]; k = 20 M−1·s−1

      Maybe I missed it, but I didn't see anywhere in this chapter in an example or in word where it tells you what to do when the math for determining the rate doesn't give you a clean integer.

      Based on the answer it seems like you can round but I don't get how that makes sense . . . ?

    1. Hume left this essay out of the first edition of his book, An Enquiry into Human Understanding, to avoid antagonizing the faithful.

      I wonder if he left out the essay not only because he was not trying to antagonize believers, but also because of he saw how religious authorities persecuted scholars like Galileo.

    1. Feudal lords squeezed their peasants for crops and labor, and states raised taxes. Several million died during the famine, and then about half of Europe’s population disappeared between the plague’s arrival in 1347 and 1353.

      The extra work and taxes required by the Feudal lords was their strategy for making up the revenue they lost because of the massive amount of their peasants dying. It also seems like it could've been an attempt to show the peasant class that the lords were still in control.

    2. For another sixty years there were two competing Papal Courts

      Though it might not seem like it, I know from outside sources just how often they're would be two or even three popes at at time.

    1. Russia became the largest kingdom in the world, stretching from the Black Sea to the Pacific Ocean, but much of it was unoccupied and primitive. Peter I (Peter the Great, r. 1672-1725) visited Europe in disguise for 18 months to study shipbuilding and new administrative techniques that he used to modernize his realm and establish the Russian Empire.

      Peter the Great going to Europe in disguise is a testament to how little his kingdom had developed at that point. The fact that the Tsar had to go undercover just to study modern shipbuilding and learn to be a ruler shows that Russia had very little to work with.

    2. He annexed the khanates of Kazan, Astrakhan, and Siberia and recruited Cossacks from southern Russia and Ukraine to colonize Siberia.

      Interesting how, in addition to the monetary and commercial benefits colonization would bring him, Ivan IV was possibly also inspired to do this in an effort to pay tribute to Rome's colonization efforts.

    1. • Every student will receive 3 late days• A late day is a 1 day extension that can be applied to any programming assignment. They CANNOTbe used for quizzes, exams, in class work, group assignments, or extra credit.• You may use a single extension, or multiple extensions on an assignment• You must indicate on your assignment how many late days you wish to use on the assignmentwhen you turn it in. This can be done in the assignment comment section in Canvas. Do not emailme to state how many late days you want to use.• After all late days have been used up late assignments will not be graded and assigned a score of zero.

      This is a unique late date system. You can submit late work without penalties to the grade but you only have 3 days total for the whole semester. Quite nice as it helps with time management. For example if there is an important exam in another class that coincides with an assignment.

    1. Rick says: I’ve wanted to work in radio since I was in high school and had great opportunities in college to learn at the campus station. I interned for a semester at a local Top 40 station and, after graduation, was offered a position as the producer of the station’s morning show. The only problem: I had to be at the radio station by 4:45 a.m. I couldn’t do it. I tried everything—alarms on my phone, clock radio alarms, friends calling me. This is not a job you can be late for—dead air is a radio DJ’s greatest nightmare. But no matter what I tried, I could not wake up on time. The third time I arrived late, the radio station let me go.

      So sorry for Rick in this situation. situations can make the unexpected things happen.

    1. How to Manage Time The simplest way to manage your time is to accurately plan for how much time it will take to do each task, and then set aside that amount of time. How you divide the time is up to you. If it is going to take you five hours to study for a final exam, you can plan to spread it over five days, with an hour each night, or you can plan on two hours one night and three hours the next. What you would not want to do is plan on studying only a few hours the night before the exam and find that you fell very short on the time you estimated you would need. If that were to happen, you would have run out of time before finishing, with no way to go back and change your decision. In this kind of situation, you might even be tempted to “pull an all-nighter,” which is a phrase that has been used among college students for decades. In essence it means going without sleep for the entire night and using that time to finish an assignment. While this method of trying to make up for poor planning is common enough to have a name, rarely does it produce the best work.

      Time waits for no man, so use it wisely

    1. K–12 College Many class activities are planned. Class time is given to receiving information. Homework is often similar for each student. You may have freedom in homework choices. Time is managed by others more often. Time is managed by the student.

      Now i know better

    2. 3. Find a purpose in what you do. Purpose is truly the driver for anything we pursue. If you have a strong purpose in any activity, you have reason to persist at it. Think in terms of end goals and why doing something is worth it. Purpose answers the question of “Why should I accomplish this?”

      Purpose is driven by Action indeed

    3. Taken as a list or a single sentence, this can be a bit overwhelming to digest. There are many things being said at the same time, and they may not all be immediately clear. To better understand what each of the “areas of concern” are and how they can impact learning, each has been separated and explained in the table below. Area of ConcernWhat it means for youHow it applies to learningReal-world example 1. Social and psychological origins of …Your motivations, not only as a student but as a person, and both the social and psychological factors that influence youThis can be everything from the original motivation behind enrolling in school in the first place, down to more specific goals like why you want to learn to write and communicate well.A drive to be self-supporting and to take on a productive role in society. 2. needs, which generate …Better job, increased income, satisfying career, prestigeThis can include the area of study you select and the school you choose to attend.Pursuing a degree to seek a career in a field you enjoy. 3. expectations of …Expectation and perception (preconceived and continuing) of educational materialWhat you expect to learn to fulfill goals and meet needs.Understanding what you need to accomplish the smaller goals. An example would be “study for an exam.” 4. the mass media or other sources, which lead to…The content and learning activities of the programSelection of content aimed at fulfilling needs. Results are student satisfaction, perceived value, and continued enrollment.Choosing which learning activities to use (e.g., texts, watch videos, research alternative content, etc.). 5. differential patterns of media exposure, resulting in …Frequency and level of participationHow you engage with learning activities and how often. Results are student satisfaction and perceived value, and continued enrollment.When, how often, and how much time you spend in learning activities. 6. needs gratification and …Better job, increased income, satisfying career, prestige, more immediate goals like pass an exam, earn a good grade, etc.Needs fulfillment and completion of goals.Learning activities that meet your learning needs, including fulfillment of your original goals. 7. other unintended consequences.Increased skills and knowledge, entertainment, social involvement and networkingCauses positive loop-back into 4, 5, and 6, reinforcing those positive outcomes.Things you learn beyond your initial goals.

      Helpful.

    4. Common College Terms, What They Mean, and Why You Need to Know TermWhat It MeansWhy You Need to Know Attendance policyA policy that describes the attendance and absence expectations for a classProfessors will have different attendance expectations. Read your syllabus to determine which ones penalize you if you miss too many classes. Final examA comprehensive assessment that is given at the end of a termIf your class has a final exam, you will want to prepare for it well in advance by reading assigned material, taking good notes, reviewing previous tests and assignments, and studying. LearningThe process of acquiring knowledgeIn college, most learning happens outside the classroom. Your professor will only cover the main ideas or the most challenging material in class. The rest of the learning will happen on your own. Office hoursSpecific hours professor is in the office to meet with studentsVisiting your professor during office hours is a good way to get questions answered and to build rapport. PlagiarismUsing someone’s words, images, or ideas as your own, without proper attributionPlagiarism carries much more serious consequences in college, so it is best to speak to your professor about how to avoid it and review your student handbook’s policy. StudyThe process of using learning strategies to understand and recall informationStudying in college may look different than studying in high school in that it may take more effort and more time to learn more complex material. SyllabusThe contract of a course that provides information about course expectations and policiesThe syllabus will provide valuable information that your professor will assume you have read and understood. Refer to it first when you have a question about the course.

      I find this really helpful

    5. Worry about making a mistake. This concern often goes with imposter syndrome. Students who worry about making a mistake don’t like to answer questions in class, volunteer for a challenging assignment, and even ask for help from others. Instead of avoiding situations where you may fail, embrace the process of learning, which includes—is even dependent on—making mistakes. The more you practice courage in these situations and focus on what you are going to learn from failing, the more confident you become about your abilities.

      This is so me, I do not like mistakes at all, but have gotten to know that we learn from our mistakes.

    6. Here is a secret about college success that not many people know: successful students seek help. They use resources. And they do that as often as necessary to get what they need.

      I always think of asking for help as a disturbance to one, if asked severally, but withe the reading of this, i understand it is not rather it is to my own benefit.

    7. Simply put, procrastination is the act of delaying some task that needs to be completed. It is something we all do to greater and lesser degrees. For most people, a little minor procrastination is not a cause for great concern. But there are situations where procrastination can become a serious problem with a lot of risk. These include: when it becomes a chronic habit, when there are a number of tasks to complete and little time, or when the task being avoided is very important. Because we all procrastinate from time to time, we usually do not give it much thought, let alone think about its causes or effects. Ironically, many of the psychological reasons for why we avoid a given task also keep us from using critical thinking to understand why procrastination can be extremely detrimental, and in some cases difficult to overcome. To succeed at time management, you must understand some of the hurdles that may stand in your way. Procrastination is often one of the biggest. What follows is an overview of procrastination with a few suggestions on how to avoid it.

      I think it’s helpful that the reading points out that procrastination isn’t just laziness, it often has psychological causes that make it hard to overcome.

    8. High school homework often consists of worksheets or tasks based on reading or classroom activities. In other words, all the students are doing the same tasks, at relatively the same time, with little autonomy over their own education. Using the earlier example of the presentation assignment, not only will what you do be larger in scale, but the depth of understanding and knowledge you will put into it will be significantly more than you may have encountered in previous assignments. This is because there are greater expectations required of college graduates in the workplace. Nearly any profession that requires a college degree has with it a level of responsibility that demands higher-level thinking and therefore higher learning. An often-cited example of this is the healthcare professional. The learning requirements for that profession are strict because we depend on those graduates for our health and, in some cases, our lives. While not every profession may require the same level of study needed for healthcare, most do require that colleges maintain a certain level of academic rigor to produce graduates who are competent in their fields. Footnotes

      I think this is important because it shows why college prepares students for real-world jobs that require responsibility and problem-solving.

    9. In fact, the estimated time you should spend will be at least two hours of outside learning for every one hour of lecture. Some weeks may be more intense, depending on the time of the semester and the courses you are taking. If those hours are multiplied over several courses in a given session, you can see how there is a significant amount of time to manage. Unfortunately, many students do not always take this into consideration, and they spend far less time than is needed to be successful. The results of poor time management are often a shock to them.

      This explains that students should expect to spend about two hours studying for every one hour of lecture, which adds up quickly across multiple courses.

    10. As an example of how this works, think about a college assignment that involves giving a classroom presentation. To complete the assignment, you are given time to research and reflect on the information found. As a part of the assignment, you must reach your own conclusions and determine which information that you have found is best suited for the presentation. While the date of the actual presentation and how long it will last are usually determined by the instructor, how much time you spend gathering information, the sources you use, and how you use them are left to you.

      This shows that even though the instructor sets the deadline, students are responsible for managing their own research and preparation time.

    11. In the workplace, the situation is not very different, with activities and time on task being monitored by the company and its management. This is so much a part of the working environment that many companies research how much time each task should take, and they hold employees accountable for the time spent on these job functions. In fact, having these skills will help you stand out on the job and in job interviews.

      I like that the reading connects college skills to the workplace, it shows that learning habits are useful beyond school.

    12. Many college students have felt like this before, and they have survived—even thrived—despite them because they were able to identify a strategy or resource that they could use to help themselves. At some point in your academic career, you may do one or more of the following:

      This shows that feeling overwhelmed in college is normal, and that students succeed when they find helpful strategies or resources.

    13. professors and advisors will expect the same from you, and your college will have all kinds of offices, staff, and programs that are designed to help. This bears calling out again: you need to use those resources.

      This is saying that professors and advisors expect students to take responsibility for seeking help, even though many resources are available.

    14. some students struggle at first because they don’t know about these habits, behaviors, and strategies. But once they learn them, they are able to meet them with ease.

      This means students may struggle at first simply because they haven’t learned the expectations yet, not because they aren’t capable

    15. One way to think about the change in how your professors will relate to you is to think about the nature of relationships you have had growing up. In Figure 1.X: You and Your Relationships Before College you will see a representation of what your relationships probably looked like. Your family may have been the greatest influencer on you and your development.

      This makes sense because growing up, most decisions are guided by family, but in college that influence starts to shift.

    16. In the following graphic, based on Dr. Dweck’s research, you can see how many of the components associated with learning are impacted by these two mindsets.

      This graphic makes me think of a Pessimist vs. an Optimist mindset.

    17. Which factors other than intelligence do you think have the greatest influence on learning?

      I agree that learning takes more than just yourself, it takes a village.

    18. If you find that you sometimes lean toward performance-based goals, do not feel discouraged. Many of the best students tend to initially focus on performance until they begin to see the ways it can restrict their learning. The key to switching to learning-based goals is often simply a matter of first recognizing the difference and seeing how making a change can positively impact your own learning.

      I interpret performance based goals as a bad thing, vs learning based goals which is a good thing. We all want to strive for learning-based goals as it seems more beneficial for learning.

    1. About This Chapter In this chapter you will learn about two of the most valuable tools used for academic success: prioritizing and time management. By the time you complete this chapter, you should be able to do the following: Articulate the ways in which time management differs from high school to college. Outline reasons and effects of procrastination, and provide strategies to overcome it. Describe ways to evaluate your own time management skills. Discuss the importance and the process of prioritization. Articulate the importance of goal setting and motivation. Detail strategies and specific tactics for managing your time.

      I feel so.

    2. Chapter Outline 3.1 The Benefits of Time Management 3.2 Time Management in College 3.3 Procrastination: The Enemy Within 3.4 How to Manage Time 3.5 Prioritization: Self-Management of What You Do and When You Do It 3.6 Goal Setting and Motivation 3.7 Enhanced Strategies for Time and Task Management

      Great outline to take something from.

    1. New Netherland

      New Netherland consisted of New Jersey, New York, Delaware, Connecticut, and Pennsylvania on a map. Then, it was broken apart by the English seizing the colony. Once the English seized it, King Charles II gave it to his brother, James. James is also the Duke of York, and after he rose to become king of England. To answer any questions, yes, New York was named after James. I hope this was helpful to some people, because I have a feeling it may be easier to connect to once you know New Netherland's background.

    1. Some of the Spanish explained native success in 1680 as the work of the Devil, who had stirred up the Pueblo to take arms against God’s chosen people.

      I often find Christianity being used to justify all the horrendous deeds of history on a repetitive whim. Instead of taking accountability, people love placing the blame on unproven factors, concepts, and figures. Sometimes it's very hard for me to believe Christianity is a religion full of "love" for one another when people are consistently using it as a weapon. It's also one of many reasons why I left Christianity in the first place... I don't resonate with it as a result. How can someone be actively proud of their religion when it has been used to dehumanize, terrorize, and enact violence on others? It's what I do not understand. I believe it has been stated before in previous annotations I may have placed, but it's truly starting to sink in more whenever I continue to see scenarios like this, and it's disheartening.

    2. Europeans typically built their cities on top of previous native settlements: other examples are Mexico City, Cusco, and Plymouth. The Timucua population had been devastated by diseases introduced by the Spanish, shrinking from around 200,000 before contact to fifty thousand by 1590. By 1700, only one thousand Timucua remained.

      No compensation was provided by the Europeans at all, and after they just acted like they weren't the cause of a mass cultural extinction. It makes me feel sick to my stomach because it's infuriating. Some of these indigenous people truly cared for these European colonizers. But, behind their backs, the Europeans backstabbed them. Didn't matter if it was indirectly/directly, or unintentionally/intentionally. After the course of events, they did nothing to comfort or de-escalate the issue. With this case, they just stole their homes, relabeled and forced cultural assimilation, and erased their history. Rather than making any last efforts to preserve the indigenous tribes' culture.

      Side note or TLDR (too long, didn't read): The Europeans were like, "Free real estate!" after the deaths of the indigenous with a disease the Europeans originally carried. Not once did a majority feel remorse. Which is why I am absolutely upset about this topic every time I am reminded of it.

    3. Only sixty out of 500 settlers survived the winter and some resorted to stealing bodies from graves for food.

      Yes, cannibalism existed during these times. Unfortunately, a lot of middle and high schools do not go over this. I did at Glencoe-Silver Lake Junior High at least and got some reenactments shown to me through the 7th grade Social Studies/History teacher (Ms. Carlson). But, it gets very grim. When some bodies were found, they could even find a few having cracked open skulls, which is assumed to be connected to their brains being eaten. A victim in Jamestown was a 14 year old, and her nickname was Jane. I'm not sure of her nickname either... Because researchers had a hard time of identifying her due to the extreme damages with her bones. It's very scary on what hunger, survival, and greed can do to a human. I'm so glad that many of us now are out of that level of poverty.

    4. many conquistadors took native women as wives and mistresses

      Due to the racism, classism, oppression, and discrimination against indigenous people in the past, I wonder if these women were forced to elope with these conquistadors. By forced, I am meaning through violence, being seen as objects, having economic issues and a poor class status, and/or being sold off to them. I believe this even happened to Pocahontas (held hostage, forced to change her name, and had to marry an English colonizer), so it wouldn't be too far-fetched if that were the case for other women of the similar backgrounds. It's just depressing to learn and hear from others or textbooks about these types of experiences. No one should be dehumanized and treated so wrongly for things they cannot control.

    5. The Spanish imagined themselves to be at the top of a social pyramid, with people of mixed race beneath them and native peoples and Africans at the bottom

      In other words, just like many other Europeans, they are basically white/pale-skinned supremacists. Pale-skinned complexions meant that you never had to go outside and work, unlike the peasants with darker skin (not necessarily with African heritage) working under you. Funny compared to nowadays, where we have teens and young adults going outside, applying tanning lotion, or going under tanning beds to get more tan. Which really tells you that social and beauty standards fluctuate, and often tend to be subjective. Whether they are healthy, or not.

    6. The Spanish word for gentleman, Hidalgo, literally means “son of something” (hijo de algo), suggesting that common men could become noble by acquiring wealth, lands, and status as a conquistador.

      This is interesting because it shows how men would move up by gaining wealth.

    7. The Indians tolerated the newcomers because their numbers were modest and because the French supplied them with firearms for their ongoing wars with the Iroquois, who had received weapons from their Dutch trading partners

      Normally indigenous are quick to defend from any newcomers.

    8. The Spanish image of an ideal colonial society included natives eager to work and embrace Christianity, mountains of gold and silver, and a social order where everyone knew their place. Patriarchy and social hierarchy shaped the Spanish colonial world

      Its so interesting to learn about different cultures.

    1. Component parts refer to the separate elements of a situation or problem. It might include the people involved, the locations of the people, the weather, market fluctuations, or any number of other characteristics of the situation you’re examining. If you don’t identify all parts of a problem, you run the risk of ignoring a critical element when you offer the solution. For example, if you have a scheduling problem at home and seem to never see your loved ones, the first step in thinking through this problem analytically would be to decide what is contributing to this unfavorable result. To begin, you may examine the family members’ individual work, school, and personal schedules, and then create a group calendar to determine if pockets of time exist that are not taken by outside commitments. Perhaps rather than reading your homework assignments at the college library, you could plan to one day a week read with other members of your family who are doing quiet work. You may also need to determine how time is spent to better understand the family’s use of time, perhaps using categories such as work/school, recreation, exercise, sleep, and meals. Once you sort the categories for all the family members, you may see blocks of time spent that would lend themselves to combining with other categories—if you and your significant other both exercise three times a week for an hour each time but at separate locations, one possible solution may be to work out together. You could alternate locations if both people have favorite places to run, or you could compromise and decide on one location for both of you—one week at the park, one week at the campus rec center. This may not ultimately be the solution, but after establishing the component parts and thinking analytically, you have provided at least one viable solution.

      This shows that breaking a problem into component parts helps you understand all the factors before coming up with a solution.

    2. Thinking helps in many situations, as we’ve discussed throughout this chapter. When we work out a problem or situation systematically, breaking the whole into its component parts for separate analysis, to come to a solution or a variety of possible solutions, we call that analytical thinking. Characteristics of analytical thinking include setting up the parts, using information literacy, and verifying the validity of any sources you reference. While the phrase analytical thinking may sound daunting, we actually do this sort of thinking in our everyday lives when we brainstorm, budget, detect patterns, plan, compare, work puzzles, and make decisions based on multiple sources of information. Think of all the thinking that goes into the logistics of a dinner-and-a-movie date—where to eat, what to watch, who to invite, what to wear, popcorn or candy—when choices and decisions are rapid-fire, but we do it relatively successfully all the time.

      I like that the reading shows analytical thinking isn’t just for school or work, it’s something we practice all the time in normal life.

    1. Pocahontas helped end the war in 1614 when she married John Rolfe (not Captain John Smith) and promoters of colonization publicized her story as an example of the good work of converting the uncivilized Powhatan to Christianity.

      Starting a war and ending it with just a marriage is just weird to think about.

    1. When we encounter new ideas, new people, new situations, we try to fit them into that narrative. Chimamanda Adichie, the Nigerian novelist, talks about the power of the single story. It's a natural human tendency to make order out of complexity by simplifying. We feel more comfortable if we can put people and ideas into already established categories.

      My story is based in Macau, China and combines superstition with Christianity, lucky numbers (3, 8, 7 ) and old folk tales. When I am reviewing that part of my life, I view people from different countries as I did when I was a child.

    1. Analyse de la Tendance « Mamans Ghettossori » : Entre Lutte des Classes et Réalités Éducatives

      Résumé Exécutif

      L'émergence de la tendance « mamans ghettossori » sur TikTok à la fin de l'année 2024 marque un tournant dans la représentation de la parentalité sur les réseaux sociaux.

      Née en réaction au modèle « maman Montessori » — perçu comme bourgeois, permissif et déconnecté — cette tendance met en scène une éducation ancrée dans la réalité des milieux populaires.

      Si ce mouvement permet de déculpabiliser de nombreux parents face aux injonctions de la parentalité positive, il soulève également des inquiétudes quant à la validation potentielle des Violences Éducatives Ordinaires (VEO).

      Au-delà du simple contenu viral, ce phénomène cristallise une « lutte des classes 2.0 » et une réponse aux accusations de démission parentale, soulignant la nécessité de retrouver des espaces de dialogue neutres et bienveillants, tels que les associations de parents.

      --------------------------------------------------------------------------------

      1. Genèse et Mécanismes du Phénomène TikTok

      La tendance a été initiée par l'influenceuse niçoise Jessica French Riviera le 13 décembre 2024, avant de se propager massivement sous forme de « reels ».

      Le format « Ghettossori »

      Le modèle type des vidéos repose sur une litanie de phrases commençant par : « Je suis une maman ghettossori, alors bien entendu que... ». Parmi les exemples cités dans les sources :

      Gestion des loisirs : Accepter des soirées pyjamas avec de nombreux copains, pop-corn et chips sans restriction.

      Défense personnelle : Inscrire l'enfant au kickboxing pour qu'il puisse se défendre en cas de conflit (« heja »).

      Rapport à l'autorité : L'enfant craint davantage la réaction de sa mère s'il ne s'est pas défendu que celle de l'école.

      Réalité quotidienne : Commander une pizza par « flemme » de cuisiner tout en le présentant comme un cadeau à l'enfant.

      Compétition : Ne pas laisser gagner l'enfant aux jeux de société (Mario Kart, galette des rois).

      La figure de proue Montessori : Armelle

      En opposition, la maman Montessori type est représentée par Armelle (@moharmelle).

      Ses vidéos, où elle prône une bienveillance absolue (comme attendre des heures dans une voiture qu'un enfant se réveille), cumulent des millions de vues mais suscitent l'incrédulité, voire la moquerie.

      Elle est devenue la cible principale des pastiches et le contre-modèle sur lequel s'est construit l'archétype ghettossori.

      --------------------------------------------------------------------------------

      2. Une Lutte des Classes 2.0 par Réseaux Interposés

      Le conflit entre « Montessori » et « Ghettossori » dépasse le cadre pédagogique pour devenir un enjeu sociologique majeur.

      Une fracture socio-économique : En France, le réseau Montessori est majoritairement privé et coûteux (sur 300 établissements, seuls trois sont sous contrat avec l'État en 2022).

      Cela associe cette pédagogie aux classes supérieures, créant une opposition naturelle avec les milieux populaires.

      Perception culturelle :

      Modèle Montessori : Perçu comme celui des « parents bobos permissifs », prescripteurs d'une morale normative.   

      Modèle Ghettossori : Revendiqué comme celui de la « vraie vie », valorisant l'imperfection et l'authenticité face aux contraintes du quotidien.

      Effet de halo en Belgique : Bien que les vidéos soient principalement d'origine française, le phénomène touche pleinement la Belgique francophone, les archétypes étant facilement identifiables par le public belge.

      --------------------------------------------------------------------------------

      3. Enjeux Éducatifs et Risques de Dérapages

      L'analyse de la FAPEO souligne une tension entre la déculpabilisation nécessaire et le risque de dérive comportementale.

      Le risque de banalisation des VEO

      Certaines affirmations dans les vidéos ghettossori inquiètent les spécialistes. Sous couvert d'humour et de sarcasme, certains propos pourraient valider des Violences Éducatives Ordinaires (VEO).

      Les journaux (Le Figaro, Le Point, RTL) notent que la frontière entre l'éloge de la « parentalité imparfaite » et la promotion d'une éducation « à la dure » est parfois poreuse.

      Une réponse à la « démission parentale »

      La tendance est analysée comme une réponse indirecte aux discours politiques et médiatiques stigmatisants sur la prétendue démission des parents des classes populaires.

      • C'est un refus de la morale normative qui juge les mères.

      • C'est une revendication du droit à l'erreur et une manifestation d'un ras-le-bol face aux injonctions académiques.

      --------------------------------------------------------------------------------

      4. Dynamiques Sociales et Limites de l'Humour

      Un phénomène genré

      Il est frappant de noter l'absence quasi totale de « papas Montessori » ou « papas ghettossori ».

      L'éducation des jeunes enfants reste un domaine fortement imprégné par le genre, où les mères portent l'essentiel de la charge et du jugement social.

      La dérive du « Roasting »

      L'humour utilisé sur TikTok s'inscrit dans la tendance actuelle du roasting (mise en boîte). Cependant, l'analyse rappelle que :

      • Du rire à l'humiliation, il n'y a qu'un pas.

      • La moquerie répétée peut s'apparenter à du harcèlement ou de la maltraitance.

      • L'utilisation de « l'écriture en creux » permet de railler un modèle (et la personne qui l'incarne) sans la nommer explicitement, renforçant l'agressivité du sous-texte.

      --------------------------------------------------------------------------------

      5. Conclusions et Perspectives : Vers un Espace de Dialogue

      Pour sortir de la logique clivante des réseaux sociaux et des algorithmes qui favorisent le « drama », la FAPEO propose plusieurs pistes de réflexion :

      Unir plutôt que diviser : Au-delà des méthodes, toutes ces mères partagent le désir d'épanouissement de leurs enfants.

      Valoriser les associations de parents : Ces structures sont présentées comme des lieux idéaux pour un échange de pair à pair, sans jugement, loin de l'agressivité numérique.

      Promouvoir la « finesse » de l'humour : S'inspirer de figures comme Coluche, qui ridiculisait les faits et les travers collectifs sans jamais s'attaquer à l'individu ou tomber dans la vulgarité.

      Adopter un « regard qui écoute » : Selon Max Dorra, il est crucial de libérer l'autre de toute évaluation permanente pour restaurer un lien social authentique.

      En définitive, l'opposition entre Montessori et Ghettossori ne doit pas masquer l'essentiel : la nécessité de soutenir tous les parents dans leur réalité quotidienne, en favorisant l'entraide plutôt que le clash médiatique.

    1. Author response:

      We thank all reviewers for their comments. We appreciate the acknowledgement that the paper is important and that results support the major conclusions. We are planning to address the specific concerns as noted by the reviewers in the following way:

      Public Reviews:

      Reviewer #2 (Public review):

      (1) The authors generate a new tool, a Gal4 knock-in of the jam2b locus, to track EGFP-expressing cells over time and follow the developmental trajectory of jam2b-expressing cells. Figure 1 characterizes the line. However, it lacks quantification, e.g., how many etv2-expressing cells also show EGFP expression or the contribution of EGFP-expressing cells to different types of blood vessels. This type of quantification would be useful, as it would also allow for comparison of their findings to their previous data examining the contribution of SVF cells to different types of blood vessels. All the authors state that at 30 hpf, EGFP-expressing cells can be seen in the vasculature (apparently the PCV).

      It is not clear why the authors do not use a nuclear marker for both ECs (as they did in their previous publication) and for jam2b-expressing cells. UAS:nEGFP and UAS:NLS-mcherry (e.g. pt424tg) transgenic lines are available. This would circumvent the problem the authors encounter with the strong fluorescence visible in the yolk extension. It would also facilitate quantifying the contribution of jam2b cells to different types of blood vessels.

      We agree with the importance of quantification. We had performed quantification of jam2b<sup>Gt(2A-Gal4)</sup>;UAS:GFP contribution to different vascular beds, which was shown in Suppl. Fig. S3. We will clarify this in the revision. We also agree that nuclear GFP or mCherry would help to visualize and quantify cells. Unfortunately, we do not have nuclear UAS:GFP or UAS:mCherry line in our possession, and it will take too long to import it for the standard revision timeline. We are working on the construct, and will attempt to establish the line; therefore we are hoping to clarify these results with the nuclear line in the revised manuscript.

      (2) The time-lapse movie in Figure 2 is not very informative, as it just provides a single example of a dividing cell contributing to the PCV. Also, quantifications are needed. As SVF cells appear to expand significantly after their initial specification, it would be informative to know how many cell divisions and which types of blood vessels jam2b-expressing cells contribute to. Can the authors observe cells that give rise to different types of blood vessels? Jam2b expression in LPM cells apparently precedes expression of etv2. Is etv2 needed for maintenance, or do Jam2b-expressing cells contribute to different types of tissues in etv2 mutant embryos? Comparing time-lapse analysis in wildtype and etv2 mutant embryos would address this question.

      The time-lapse was meant to serve as an illustration and confirmation of jam2b cell contribution to vasculature. As noted above, Suppl. Fig. S3 provides quantification of jam2b cell contribution to different vascular beds. We had previously performed detailed time-lapse analysis and quantification of SVF cell migration to PCV, SIA and SIV using etv2-2A-Venus line (Metikala et al 2022, Dev Cell), which has some of the same (or similar) information. It is very challenging to obtain this data using jam2b reporter line due to extensive and bright GFP expression in the mesothelial layer over the yolk and yolk extension; for that reason we can only trace some GFP cells but not all of them. Regarding etv2 requirement for jam2b maintenance, we intend to address this question by analyzing jam2b cell contribution in etv2 MO injected embryos, which recapitulates the phenotype in jam2b mutants.

      (3) In Figure 3, the authors generate UAS:Cre and UAS:Cre-ERT2 transgenic lines to lineage trace the jam2b-expressing cells. It is again not clear why the authors do not use a responder line containing nuclear-localized fluorescent proteins to circumvent the strong expression of fluorescent proteins in the yolk extension. It is also unclear why the two transgenic lines give very different results regarding the number of cells being labelled. The ERT2 fusions label around 3 cells in the SIA, while the Cre line labels only about 1.5 cells per embryo, with very little contribution of labelled cells to other blood vessels. One would expect the Cre line requiring tamoxifen induction to label fewer cells when compared to the constitutive Cre line. What is the reason for this discrepancy? Are the lines single integration? Is there silencing? This needs to be better characterized, also regarding the reproducibility of the experiments. If the Cre lines were to be multiple copy integrations, outcrossing the line might lead to lower expression levels in future generations. 

      It is also not clear how the authors conclude from these findings that "SVF cells show major contribution to the SIA and SIV" when only 1.5 or 3 cells of the SIA are labelled, with even fewer cells labelled in other blood vessels. They speculate that this might be due to low recombination efficiency, a question they then set out to answer using photoconversion of etv2:KAEDE expressing cells, an experiment that they also performed in their 2014 and 2022 publications. To check for low recombination efficiency, the authors could examine the expression of Cre mRNA in their transgenic embryos. Do many more jam2b expressing cells express Cre mRNA than they observe in their switch lines? They could also compare their experiments using Cre recombinase with those using EGFP expression in jam2b cells. EGFP is relatively stable, and the time frames the authors analyze are short. As no quantification of EGFP-expressing cells is provided in Figure 1, this comparison is currently not possible. Do these two different approaches answer different questions here? 

      The reviewer brings up important points, we appreciate that. Unfortunately, we do not have a nuclear switch line in our possession, and it is not possible to obtain it in the normal manuscript revision time line. Regarding UAS:Cre and UAS:CreERT2 lines, they both show rather similar labeling, with most labeled cells present in the SIA. The difference in cell number (1.5 versus 3) is likely due to different levels of Cre expression, which may vary dependent on the integration site. The lines most likely are multi-copy integrations, which can be helpful, as this would result in higher Cre expression. We will address the silencing question by performing in situ hybridization or HCR analysis for Cre or CreERT2 and comparing it with endogenous jam2b expression, as the reviewer suggested. We have noticed that the switch line used, actb2:loxP-BFP-loxP-dsRed, exhibits lower recombination frequency compared to other switch lines (we used it because it was compatible with endothelial fli1:GFP line). We will attempt to answer this question by crossing to other switch lines, which may exhibit higher recombination frequency. In principle, UAS:GFP and switch lines should produce a similar result, except that GFP decays over time and therefore our initial expectation was that switch lines may produce a more accurate result. However, this may not be the case due to low recombination efficiency, which we will attempt to address in the revision.

      (4) Concerning the etv2:KAEDE photoconversion experiments: The percentages the authors report for SVF cells' contribution to the SIV and SIA differ from their previous study (Dev Cell, 2022). In that publication, SVF cells contributed 28% to the SIA and 48% to the SIV. In the present study, the numbers are close to 80% for both vessels. The difference is that the previous study analyzed 2dpf old embryos and the new one 4dpf old embryos. Do SVF-derived cells proliferate more than PCV-derived cells, or is there another explanation for this change in percentage contribution? 

      These numbers refer to different experiments; we apologize for the confusion. As reported earlier in Metikala et 2022, 28% of SVF cells contributed to the SIA and 48% to the SIV by 3 dpf (not 2 dpf; only PCV analysis was done at 2 dpf); SIA and SIV analysis was done based on time-lapse image analysis of etv2-2A-Venus line at 3 dpf, shown in Fig. 3C in Metikala et al. However, this only refers to SVF cell contribution. It does not mean that 28% or 48% cells in SIA or SIV are derived from SVF. The total fraction of SIA and SIV cells that are derived from SVF has not been quantified in the previous study, because that would require accurate tracking of all SVF cells, which is experimentally challenging. Etv2:Kaede experiment is slighly different, because it reports newly formed cells after 24 hpf. It cannot tell if new cells are all derived from SVF cells, although we are not aware of any other source of new endothelial cells at these stages. In the previous study by Metikala et al 2022, we reported ~22 newly formed SIA and ~50 newly formed cells in SIV by 3 dpf (Fig. 1 in Metikala et al 2022), although the entire number of cells was not quantified, therefore the percentage was not known. In the current study, we attempted to estimate the entire percentage of green only Kaede cells, which was close to 80% in both SIA or SIV at 4 dpf. Please note that this estimate was performed in the posterior portion of SIA and SIV that overlies the yolk extension and where SVF cells are observed. We did not quantify cells in the anterior SIV portion, which forms the basket over the yolk.

      (5) Single-cell sequencing data: Why do the authors not show jam2b expression in their single-cell sequencing data? They sorted for (presumably) jam2b-expressing cells and hypothesize that jam2b expression in ECs at this time point is important for the generation of intestinal vasculature. Do ECs in cluster 15 express jam2b? Why are no other top marker genes (tal1, etv2, egfl7, npas4l) included in the dot blot in Figure 5b?

      We appreciate the suggestion and will include additional marker genes as well as jam2b in the revised version of the manuscript.

      (6) Concerns about cell autonomy of mutant phenotypes: The authors need to perform in situ hybridization to characterize jam2a expression. Can it be seen in SVF cells? The double mutants show a clear phenotype in intestinal vessel development; however, it is unclear whether this is due to a cell-autonomous function of jam2a/b within SVF cells. The authors need to address this issue, as jam2b and potentially also jam2a are expressed within the tissue surrounding the forming SVF. For instance, do transplanted mutant cells contribute to the intestinal vasculature to the same extent as wild-type cells do?

      jam2a expression has been characterized in the previous studies and it is shown in the Suppl. Fig. S4E. It is primarily enriched in the skeletal muscle. However, our single-cell RNA-seq analysis shows that SVF cells also express jam2a. We will include additional data on jam2a expression in the revised manuscript. We agree that transplation to address cell autonomy is an important experiment, yet there are some practical challenges to it. Jam2a,jam2b mutant phenotype is only partially penetrant, and about 50% reduction in SVF cell number, as well as partial SIA and SIV phenotypes are observed. Only a small number of transplanted cells may contribute to intestinal vasculature, therefore it may be challenging to see the differences, given the partial penetrance. In an attempt to address cell -autonomy question, we will try a different approach. We will overexpress jam2b labeled with 2A-mCherry, and test if it can rescue the mutant phenotype in cell autonomous manner. Overexpression will be done in a mosaic manner, with higher number of cells labeled than in a typical transplantation experiment.

      (7) Finally, the authors analyze the phenotypes of hand2 mutants and their impact on the expression of jam2b and etv2. They observe a reduction in jam2b and etv2 expression in SVF cells. However, they do not show the vascular phenotypes of hand2 mutants. Is the formation of the SIA and SIV disturbed? Is hand2 cell autonomously needed in ECs? The authors suggest that hand2 controls SVF development through the regulation of jam2b. However, they also show that jam2b mutants do not have a phenotype on their own. Clearly, hand2, if it were to be required in ECs, regulates other genes important for SVF development. These might then regulate jam2b expression. The clear linear relationship, as the title suggests, is not convincingly shown by the data.

      As suggested, we will add the analysis of SIA and SIV in hand2 mutants during the revision process. We could not assess that easily because the line was not maintained in vascular fli1:GFP background. We do not know if hand2 is required cell-autonomously. This is an important question, but it may be answered better in a separate study. Regarding hand2-jam2b axis, it is very clear that jam2b expression in the posterior lateral plate mesoderm is completely lost in hand2 mutants, except for its more anterior domain over the yolk. This does support the idea that hand2 functions upstream of jam2b. However, the relationship may not be necessarily direct. We agree that hand2 may regulate additional genes involved in SVF cell development. We will attempt to clarify this relationship and test if jam2b overexpression may rescue hand2 mutant phenotype.

      Reviewer #3 (Public review):

      (1) Overall molecular mechanisms of Jam2 function are not fully uncovered in the study. How do the adhesion molecules Jam2a and Jam2b regulate SVF cell formation? Are they responsible for migration, adhesion or fate determination of these structures? The authors should provide a more in-depth study of the jam2a, jam2b mutations and assess the processes affected in these mutants. Combining these mutants with etv2:Kaede can also provide a stronger causative link between their functions and defects in SVF formation.

      Our data argue that the initial SVF cell specification (based on etv2 expression) is reduced in jam2a;jam2b mutants. We do not know if the migration or fate determination of the remaining SVF cells is also affected, although this may be more challenging to answer, as there are only few SVF cells remaining. We agree that further mechanistic studies of jam2a,jam2b function are needed. However, we think that this would be better addressed in a separate study. We are currently raising mutants crossed into fli1:Kaede line, which should confirm that there are fewer new cells that emerge after Kaede photoconversion in jam2a,jam2b mutants.

      (2) Have the authors tested the specificity of the jam2b knock-in reporter line? This is an important experiment, as many of the conclusions derive from lineage tracing and fluorescence reporting from this knock-in line. One suggestion is to cross the jam2b:GFP or jam2b:Gal4, UAS:GFP line to the generated jam2b mutants, and examine the expression pattern of these lines. Considering that the ISH experiment showed lack of jam2b expression, the reporter line should not be expressed in the jam2b mutants.

      We show in Suppl. Fig. 2 that jam2b<sup>Gt(2A-Gal4)</sup>;UAS:GFP knock-in line has similar expression pattern as jam2b mRNA by in situ hybridization, which argues for its specificity. In the revision, we plan to use HCR analysis to confirm than jam2b mRNA is expressed in the same cells as jam2b<sup>Gt(2A-Gal4)</sup>;UAS:GFP, as an additional evidence for its specificity. Unfortunately, it is not feasible to cross jam2b knock-in line into jam2b mutants, as suggested by the reviewer. Because jam2b knock-in line targets the endogenous jam2b genomic locus, which is very close in the genome to jam2b promoter deletion in jam2b mutants, the recombination frequency would be very low, and we would not get double jam2b knock-in and knock-out events in the same chromosome.

      (3) The rationale behind the regeneration study is not clear, and the mechanisms underlying the phenotype are not well described. How do the authors explain the phenotype with the impaired regeneration, and what is the significance of this finding as it relates to SVF formation and function? 

      We apologize for this omission. This experiment was more thouroughly described in our previous study by Metikala et al 2022. In that study we showed that when endothelial cells are ablated by treating with MTZ from 6 to 45 hpf, this results in ablation of all vascular endothelial cells except for SVF cells, because they originate later than other cells. We subsequently showed that these SVF cells can partially form PCV and intestinal vasculature, helping them regenerate, which was confirmed by time-lapse imaging. In the current study, we tested if jam2a; jam2b double mutants show defects in such vascular regeneration. Indeed, regeneration after cell ablation was reduced, which correlated with reduction in SVF cell number. This argues that jam2a/b function is required for SVF cell emergence and vascular recovery after endothelial cell ablation. We will provide better description of this experiment and discuss interpretations in the revised manuscript.

      (4) The authors need to include representative images of jam2b>CreERT2 with 4-OH activation at different timepoints in Figure 3.

      Yes, thanks for noting this; these images will be included in the revised manuscript.

      (5) The etv2:Kaede photoconversion experiment to show that the majority of intestinal vasculature derives after 24 hours needs to be supplemented with additional data on photoconverted post-24-hour-old endothelial cells, with the expectation that the majority of intestinal endothelial cells at 4 days will then be labeled with red Kaede. In addition, there have been data that show the red Kaede protein is not stable past several days in vivo, and 3 days might be sufficient for the removal or degradation of this photoconverted protein. Thus, the statement that intestinal vasculature forms largely by new vasculogenesis might be too strong based on existing data.

      It is apparent from Fig. 4B that many other vessels, such as the dorsal aorta and many intersegmental vessels show robust red Kaede expression at 4 dpf, arguing that there is sufficient photoconverted Kaede present at this stage, and its degradation is unlikely to be the reason. However, we are planning to include additional control experiments, as suggested by the reviewer, to make this argument stronger.

      (6) To strengthen the claim that hand2 acts upstream of jam2b, the authors can perform combinatorial genetic epistatic analysis and examine whether jam2b mutations worsen hand2 homozygous or heterozygous effects on the SVF. Similarly, overexpressing jam2b might rescue the loss of SVF/etv2 expression in hand2 mutants. 

      We appreciate this suggestion. Double epistatic analysis, while informative, can be tricky. In this case, we are dealing with jam2a; jam2b redundancy and also the maternal effect. It may take a while considerable effort to generate different combinations of tripple mutant lines (jam2a,jam2b,hand2), and it is unclear whether double or tripple heterozygous embryos will show any defects to clarify their epistatic relationship. Instead, as suggested, we are planning to overexpress jam2b in wild-type and hand2 mutants to address this point.

    2. Reviewer #2 (Public review):

      Summary:

      Griciunaite et al. report on the function of jam2b and hand2 in the formation of the intestinal vasculature derived from late-forming endothelial cells (ECs) within the secondary vascular field (SVF). They generate transgenic lines that allow for the tracking of jam2b-expressing cells, both with fluorescent proteins and through Cre-mediated recombination in reporter lines. They also show that double maternal zygotic mutants in jam2a and jam2b, as well as hand2 mutants, display defects in the formation of the intestinal vasculature.

      Strengths:

      The results are interesting, as they address the important question of how blood vessels form during later developmental time points and potentially identify specific genes regulating this process.

      Weaknesses:

      (1) The authors generate a new tool, a Gal4 knock-in of the jam2b locus, to track EGFP-expressing cells over time and follow the developmental trajectory of jam2b-expressing cells. Figure 1 characterizes the line. However, it lacks quantification, e.g., how many etv2-expressing cells also show EGFP expression or the contribution of EGFP-expressing cells to different types of blood vessels. This type of quantification would be useful, as it would also allow for comparison of their findings to their previous data examining the contribution of SVF cells to different types of blood vessels. All the authors state that at 30 hpf, EGFP-expressing cells can be seen in the vasculature (apparently the PCV).

      It is not clear why the authors do not use a nuclear marker for both ECs (as they did in their previous publication) and for jam2b-expressing cells. UAS:nEGFP and UAS:NLS-mcherry (e.g. pt424tg) transgenic lines are available. This would circumvent the problem the authors encounter with the strong fluorescence visible in the yolk extension. It would also facilitate quantifying the contribution of jam2b cells to different types of blood vessels.

      (2) The time-lapse movie in Figure 2 is not very informative, as it just provides a single example of a dividing cell contributing to the PCV. Also, quantifications are needed. As SVF cells appear to expand significantly after their initial specification, it would be informative to know how many cell divisions and which types of blood vessels jam2b-expressing cells contribute to. Can the authors observe cells that give rise to different types of blood vessels? Jam2b expression in LPM cells apparently precedes expression of etv2. Is etv2 needed for maintenance, or do Jam2b-expressing cells contribute to different types of tissues in etv2 mutant embryos? Comparing time-lapse analysis in wildtype and etv2 mutant embryos would address this question.

      (3) In Figure 3, the authors generate UAS:Cre and UAS:Cre-ERT2 transgenic lines to lineage trace the jam2b-expressing cells. It is again not clear why the authors do not use a responder line containing nuclear-localized fluorescent proteins to circumvent the strong expression of fluorescent proteins in the yolk extension. It is also unclear why the two transgenic lines give very different results regarding the number of cells being labelled. The ERT2 fusions label around 3 cells in the SIA, while the Cre line labels only about 1.5 cells per embryo, with very little contribution of labelled cells to other blood vessels. One would expect the Cre line requiring tamoxifen induction to label fewer cells when compared to the constitutive Cre line. What is the reason for this discrepancy? Are the lines single integration? Is there silencing? This needs to be better characterized, also regarding the reproducibility of the experiments. If the Cre lines were to be multiple copy integrations, outcrossing the line might lead to lower expression levels in future generations.

      It is also not clear how the authors conclude from these findings that "SVF cells show major contribution to the SIA and SIV" when only 1.5 or 3 cells of the SIA are labelled, with even fewer cells labelled in other blood vessels. They speculate that this might be due to low recombination efficiency, a question they then set out to answer using photoconversion of etv2:KAEDE expressing cells, an experiment that they also performed in their 2014 and 2022 publications. To check for low recombination efficiency, the authors could examine the expression of Cre mRNA in their transgenic embryos. Do many more jam2b expressing cells express Cre mRNA than they observe in their switch lines? They could also compare their experiments using Cre recombinase with those using EGFP expression in jam2b cells. EGFP is relatively stable, and the time frames the authors analyze are short. As no quantification of EGFP-expressing cells is provided in Figure 1, this comparison is currently not possible. Do these two different approaches answer different questions here?

      (4) Concerning the etv2:KAEDE photoconversion experiments: The percentages the authors report for SVF cells' contribution to the SIV and SIA differ from their previous study (Dev Cell, 2022). In that publication, SVF cells contributed 28% to the SIA and 48% to the SIV. In the present study, the numbers are close to 80% for both vessels. The difference is that the previous study analyzed 2dpf old embryos and the new one 4dpf old embryos. Do SVF-derived cells proliferate more than PCV-derived cells, or is there another explanation for this change in percentage contribution?

      (5) Single-cell sequencing data: Why do the authors not show jam2b expression in their single-cell sequencing data? They sorted for (presumably) jam2b-expressing cells and hypothesize that jam2b expression in ECs at this time point is important for the generation of intestinal vasculature. Do ECs in cluster 15 express jam2b? Why are no other top marker genes (tal1, etv2, egfl7, npas4l) included in the dot blot in Figure 5b?

      (6) Concerns about cell autonomy of mutant phenotypes: The authors need to perform in situ hybridization to characterize jam2a expression. Can it be seen in SVF cells? The double mutants show a clear phenotype in intestinal vessel development; however, it is unclear whether this is due to a cell-autonomous function of jam2a/b within SVF cells. The authors need to address this issue, as jam2b and potentially also jam2a are expressed within the tissue surrounding the forming SVF. For instance, do transplanted mutant cells contribute to the intestinal vasculature to the same extent as wild-type cells do?

      (7) Finally, the authors analyze the phenotypes of hand2 mutants and their impact on the expression of jam2b and etv2. They observe a reduction in jam2b and etv2 expression in SVF cells. However, they do not show the vascular phenotypes of hand2 mutants. Is the formation of the SIA and SIV disturbed? Is hand2 cell autonomously needed in ECs? The authors suggest that hand2 controls SVF development through the regulation of jam2b. However, they also show that jam2b mutants do not have a phenotype on their own. Clearly, hand2, if it were to be required in ECs, regulates other genes important for SVF development. These might then regulate jam2b expression. The clear linear relationship, as the title suggests, is not convincingly shown by the data.

    3. Reviewer #3 (Public review):

      Summary:

      This study by Griciunaite et al. investigates the function of the adhesion molecule Jam2 in initiating the formation of organ (intestinal)-specific vasculature in zebrafish. Their previous studies identified a group of late-forming vascular progenitors from the lateral plate mesoderm along the yolk extension termed the secondary vascular field (SVF), which can contribute to intestinal vasculature. Transcriptomic analysis of the zebrafish trunk region identified SVF-enriched marker genes, which include jam2b. They then performed expression analysis of jam2b using whole-mount in situ hybridization and Gal4 knock-in transgenic line analysis. These analyses show that jam2b is expressed in the SVF cells that correspond to etv2 and kdrl expression past 24 hours. Lineage tracing combining jam2b:Gal4 and UAS:Cre or UAS:CreERT2 show the contribution of jam2b in SVF and intestinal vasculature formation. jam2b mutations did not cause observable defects in the vasculature, but combined jam2a; jam2b mutations led to impaired ISV, PCV, SIA, SIV and thoracic duct lymphatic vasculature formation. Finally, the authors show that mutations in the transcription factor hand2 led to reduced jam2b expression and impaired SVF formation.

      Strengths:

      The authors accomplished many feats in generating new reporter lines and mutations that are valuable to the community. The study provided an interesting perspective on organ-specific vascular development and origin heterogeneity. The genetic aspects of the study are clean, and the mutational phenotypes are convincing.

      Several suggestions and major comments that can improve the manuscript include:

      (1) Overall molecular mechanisms of Jam2 function are not fully uncovered in the study. How do the adhesion molecules Jam2a and Jam2b regulate SVF cell formation? Are they responsible for migration, adhesion or fate determination of these structures? The authors should provide a more in-depth study of the jam2a, jam2b mutations and assess the processes affected in these mutants. Combining these mutants with etv2:Kaede can also provide a stronger causative link between their functions and defects in SVF formation.

      (2) Have the authors tested the specificity of the jam2b knock-in reporter line? This is an important experiment, as many of the conclusions derive from lineage tracing and fluorescence reporting from this knock-in line. One suggestion is to cross the jam2b:GFP or jam2b:Gal4, UAS:GFP line to the generated jam2b mutants, and examine the expression pattern of these lines. Considering that the ISH experiment showed lack of jam2b expression, the reporter line should not be expressed in the jam2b mutants.

      (3) The rationale behind the regeneration study is not clear, and the mechanisms underlying the phenotype are not well described. How do the authors explain the phenotype with the impaired regeneration, and what is the significance of this finding as it relates to SVF formation and function?

      (4) The authors need to include representative images of jam2b>CreERT2 with 4-OH activation at different timepoints in Figure 3.

      (5) The etv2:Kaede photoconversion experiment to show that the majority of intestinal vasculature derives after 24 hours needs to be supplemented with additional data on photoconverted post-24-hour-old endothelial cells, with the expectation that the majority of intestinal endothelial cells at 4 days will then be labeled with red Kaede. In addition, there have been data that show the red Kaede protein is not stable past several days in vivo, and 3 days might be sufficient for the removal or degradation of this photoconverted protein. Thus, the statement that intestinal vasculature forms largely by new vasculogenesis might be too strong based on existing data.

      (6) To strengthen the claim that hand2 acts upstream of jam2b, the authors can perform combinatorial genetic epistatic analysis and examine whether jam2b mutations worsen hand2 homozygous or heterozygous effects on the SVF. Similarly, overexpressing jam2b might rescue the loss of SVF/etv2 expression in hand2 mutants.

    1. Author response:

      The following is the authors’ response to the previous reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Wu and colleagues aimed to explain previous findings that adolescents, compared to adults, show reduced cooperation following cooperative behaviour from a partner in several social scenarios. The authors analysed behavioural data from adolescents and adults performing a zero-sum Prisoner's Dilemma task and compared a range of social and non-social reinforcement learning models to identify potential algorithmic differences. Their findings suggest that adolescents' lower cooperation is best explained by a reduced learning rate for cooperative outcomes, rather than differences in prior expectations about the cooperativeness of a partner. The authors situate their results within the broader literature, proposing that adolescents' behaviour reflects a stronger preference for self-interest rather than a deficit in mentalising.

      Strengths:

      The work as a whole suggests that, in line with past work, adolescents prioritise value accumulation, and this can be, in part, explained by algorithmic differences in weighted value learning. The authors situate their work very clearly in past literature, and make it obvious the gap they are testing and trying to explain. The work also includes social contexts that move the field beyond non-social value accumulation in adolescents. The authors compare a series of formal approaches that might explain the results and establish generative and modelcomparison procedures to demonstrate the validity of their winning model and individual parameters. The writing was clear, and the presentation of the results was logical and wellstructured.

      We thank the reviewer for recognizing the strengths of our work.

      Weaknesses:

      (Q1) I also have some concerns about the methods used to fit and approximate parameters of interest. Namely, the use of maximum likelihood versus hierarchical methods to fit models on an individual level, which may reduce some of the outliers noted in the supplement, and also may improve model identifiability.

      We thank the reviewer for this suggestion. Following the comment, we added a hierarchical Bayesian estimation. We built a hierarchical model with both group-level (adolescent group and adult group) and individual-level structures for the best-fitting model. Four Markov chains with 4,000 samples each were run, and the model converged well (see Figure supplement 7)

      We then analyzed the posterior parameters for adolescents and adults separately. The results were consistent with those from the MLE analysis (see Figure 2—figure supplement 5). These additional results have been included in the Appendix Analysis section (also see Figure supplement 5 and 7). In addition, we have updated the code and provided the link for reference. We appreciate the reviewer’s suggestion, which improved our analysis.

      (Q2) There was also little discussion given the structure of the Prisoner's Dilemma, and the strategy of the game (that defection is always dominant), meaning that the preferences of the adolescents cannot necessarily be distinguished from the incentives of the game, i.e. they may seem less cooperative simply because they want to play the dominant strategy, rather than a lower preferences for cooperation if all else was the same.

      We thank the reviewer for this comment and agree that adolescents’ lower cooperation may partly reflect a rational response to the incentive structure of the Prisoner’s Dilemma.

      However, our computational modeling explicitly addressed this possibility. Model 4 (inequality aversion) captures decisions that are driven purely by self-interest or aversion to unequal outcomes, including a parameter reflecting disutility from advantageous inequality, which represents self-oriented motives. If participants’ behavior were solely guided by the payoff-dominant strategy, this model should have provided the best fit. However, our model comparison showed that Model 5 (social reward) performed better in both adolescents and adults, suggesting that cooperative behavior is better explained by valuing social outcomes beyond payoff structures.

      Besides, if adolescents’ lower cooperation is that they strategically respond to the payoff structure by adopting defection as the more rewarding option. Then, adolescents should show reduced cooperation across all rounds. Instead, adolescents and adults behaved similarly when partners defected, but adolescents cooperated less when partners cooperated and showed little increase in cooperation even after consecutive cooperative responses. This pattern suggests that adolescents’ lower cooperation cannot be explained solely by strategic responses to payoff structures but rather reflects a reduced sensitivity to others’ cooperative behavior or weaker social reciprocity motives. We have expanded our Discussion to acknowledge this important point and to clarify how the behavioral and modeling results address the reviewer’s concern.

      “Overall, these findings indicate that adolescents’ lower cooperation is unlikely to be driven solely by strategic considerations, but may instead reflect differences in the valuation of others’ cooperation or reduced motivation to reciprocate. Although defection is the payoffdominant strategy in the Prisoner’s Dilemma, the selective pattern of adolescents’ cooperation and the model comparison results indicate that their reduced cooperation cannot be fully explained by strategic incentives, but rather reflects weaker valuation of social reciprocity.”

      Appraisal & Discussion:

      (Q3) The authors have partially achieved their aims, but I believe the manuscript would benefit from additional methodological clarification, specifically regarding the use of hierarchical model fitting and the inclusion of Bayes Factors, to more robustly support their conclusions. It would also be important to investigate the source of the model confusion observed in two of their models.

      We thank the reviewer for this comment. In the revised manuscript, we have clarified the hierarchical Bayesian modeling procedure for the best-fitting model, including the group- and individual-level structure and convergence diagnostics. The hierarchical approach produced results that fully replicated those obtained from the original maximumlikelihood estimation, confirming the robustness of our findings. Please also see the response to Q1.

      Regarding the model confusion between the inequality aversion (Model 4) and social reward (Model 5) models in the model recovery analysis, both models’ simulated behaviors were best captured by the baseline model. This pattern arises because neither model includes learning or updating processes. Given that our task involves dynamic, multi-round interactions, models lacking a learning mechanism cannot adequately capture participants’ trial-by-trial adjustments, resulting in similar behavioral patterns that are better explained by the baseline model during model recovery. We have added a clarification of this point to the Results:

      “The overlap between Models 4 and 5 likely arises because neither model incorporates a learning mechanism, making them less able to account for trial-by-trial adjustments in this dynamic task.”

      (Q4) I am unconvinced by the claim that failures in mentalising have been empirically ruled out, even though I am theoretically inclined to believe that adolescents can mentalise using the same procedures as adults. While reinforcement learning models are useful for identifying biases in learning weights, they do not directly capture formal representations of others' mental states. Greater clarity on this point is needed in the discussion, or a toning down of this language.

      We sincerely thank the reviewer for this professional comment. We agree that our prior wording regarding adolescents’ capacity to mentalise was somewhat overgeneralized. Accordingly, we have toned down the language in both the Abstract and the Discussion to better align our statements with what the present study directly tests. Specifically, our revisions focus on adolescents’ and adults’ ability to predict others’ cooperation in social learning. This is consistent with the evidence from our analyses examining adolescents’ and adults’ model-based expectations and self-reported scores on partner cooperativeness (see Figure 4). In the revised Discussion, we state:

      “Our results suggest that the lower levels of cooperation observed in adolescents stem from a stronger motive to prioritize self-interest rather than a deficiency in predicting others’ cooperation in social learning”.

      (Q5) Additionally, a more detailed discussion of the incentives embedded in the Prisoner's Dilemma task would be valuable. In particular, the authors' interpretation of reduced adolescent cooperativeness might be reconsidered in light of the zero-sum nature of the game, which differs from broader conceptualisations of cooperation in contexts where defection is not structurally incentivised.

      We thank the reviewer for this comment and agree that adolescents’ lower cooperation may partly reflect a rational response to the incentive structure of the Prisoner’s Dilemma. However, our behavioral and computational evidence suggests that this pattern cannot be explained solely by strategic responses to payoff structures, but rather reflects a reduced sensitivity to others’ cooperative behavior or weaker social reciprocity motives. We have expanded the Discussion to acknowledge this point and to clarify how both behavioral and modeling results address the reviewer’s concern (see also our response to Q2).

      (Q6) Overall, I believe this work has the potential to make a meaningful contribution to the field. Its impact would be strengthened by more rigorous modelling checks and fitting procedures, as well as by framing the findings in terms of the specific game-theoretic context, rather than general cooperation.

      We thank the reviewer for the professional comments, which have helped us improve our work.

      Reviewer #2 (Public review):

      Summary:

      This manuscript investigates age-related differences in cooperative behavior by comparing adolescents and adults in a repeated Prisoner's Dilemma Game (rPDG). The authors find that adolescents exhibit lower levels of cooperation than adults. Specifically, adolescents reciprocate partners' cooperation to a lesser degree than adults do. Through computational modeling, they show that this relatively low cooperation rate is not due to impaired expectations or mentalizing deficits, but rather a diminished intrinsic reward for reciprocity. A social reinforcement learning model with asymmetric learning rate best captured these dynamics, revealing age-related differences in how positive and negative outcomes drive behavioral updates. These findings contribute to understanding the developmental trajectory of cooperation and highlight adolescence as a period marked by heightened sensitivity to immediate rewards at the expense of long-term prosocial gains.

      Strengths:

      (1) Rigid model comparison and parameter recovery procedure.

      (2) Conceptually comprehensive model space.

      (3) Well-powered samples.

      We thank the reviewer for highlighting the strengths of our work.

      Weaknesses:

      (Q1) A key conceptual distinction between learning from non-human agents (e.g., bandit machines) and human partners is that the latter are typically assumed to possess stable behavioral dispositions or moral traits. When a non-human source abruptly shifts behavior (e.g., from 80% to 20% reward), learners may simply update their expectations. In contrast, a sudden behavioral shift by a previously cooperative human partner can prompt higher-order inferences about the partner's trustworthiness or the integrity of the experimental setup (e.g., whether the partner is truly interactive or human). The authors may consider whether their modeling framework captures such higher-order social inferences. Specifically, trait-based models-such as those explored in Hackel et al. (2015, Nature Neuroscience)-suggest that learners form enduring beliefs about others' moral dispositions, which then modulate trial-bytrial learning. A learner who believes their partner is inherently cooperative may update less in response to a surprising defection, effectively showing a trait-based dampening of learning rate.

      We thank the reviewer for this thoughtful comment. We agree that social learning from human partners may involve higher-order inferences beyond simple reinforcement learning from non-human sources. To address this, we had previously included such mechanisms in our behavioral modeling. In Model 7 (Social Reward Model with Influence), we tested a higher-order belief-updating process in which participants’ expectations about their partner’s cooperation were shaped not only by the partner’s previous choices but also by the inferred influence of their own past actions on the partner’s subsequent behavior. In other words, participants could adjust their belief about the partner’s cooperation by considering how their partner’s belief about them might change. Model comparison showed that Model 7 did not outperform the best-fitting model, suggesting that incorporating higher-order influence updates added limited explanatory value in this context. As suggested by the reviewer, we have further clarified this point in the revised manuscript.

      Regarding trait-based frameworks, we appreciate the reviewer’s reference to Hackel et al. (2015). That study elegantly demonstrated that learners form relatively stable beliefs about others’ social dispositions, such as generosity, especially when the task structure provides explicit cues for trait inference (e.g., resource allocations and giving proportions). By contrast, our study was not designed to isolate trait learning, but rather to capture how participants update their expectations about a partner’s cooperation over repeated interactions. In this sense, cooperativeness in our framework can be viewed as a trait-like latent belief that evolves as evidence accumulates. Thus, while our model does not include a dedicated trait module that directly modulates learning rates, the belief-updating component of our best-fitting model effectively tracks a dynamic, partner-specific cooperativeness, potentially reflecting a prosocial tendency.

      (Q2) This asymmetry in belief updating has been observed in prior work (e.g., Siegel et al., 2018, Nature Human Behaviour) and could be captured using a dynamic or belief-weighted learning rate. Models incorporating such mechanisms (e.g., dynamic learning rate models as in Jian Li et al., 2011, Nature Neuroscience) could better account for flexible adjustments in response to surprising behavior, particularly in the social domain.

      We thank the reviewer for the suggestion. Following the comment, we implemented an additional model incorporating a dynamic learning rate based on the magnitude of prediction errors. Specifically, we developed Model 9:  Social reward model with Pearce–Hall learning algorithm (dynamic learning rate), in which participants’ beliefs about their partner’s cooperation probability are updated using a Rescorla–Wagner rule with a learning rate dynamically modulated by the Pearce–Hall (PH) Error Learning mechanism. In this framework, the learning rate increases following surprising outcomes (larger prediction errors) and decreases as expectations become more stable (see Appendix Analysis section for details).

      The results showed that this dynamic learning rate model did not outperform our bestfitting model in either adolescents or adults (see Figure supplement 6). We greatly appreciate the reviewer’s suggestion, which has strengthened the scope of our analysis. We now have added these analyses to the Appendix Analysis section (also Figure Supplement 6) and expanded the Discussion to acknowledge this modeling extension and further discuss its implications.

      (Q3) Second, the developmental interpretation of the observed effects would be strengthened by considering possible non-linear relationships between age and model parameters. For instance, certain cognitive or affective traits relevant to social learning-such as sensitivity to reciprocity or reward updating-may follow non-monotonic trajectories, peaking in late adolescence or early adulthood. Fitting age as a continuous variable, possibly with quadratic or spline terms, may yield more nuanced developmental insights.

      We thank the reviewer for this professional comment. In addition to the linear analyses, we further conducted exploratory analyses to examine potential non-linear relationships between age and the model parameters. Specifically, we fit LMMs for each of the four parameters as outcomes (α+, α-, β, and ω). The fixed effects included age, a quadratic age term, and gender, and the random effects included subject-specific random intercepts and random slopes for age and gender. Model comparison using BIC did not indicate improvement for the quadratic models over the linear models for α<sup>+</sup> (ΔBIC<sub>quadratic-linear</sub> = 5.09), α<sup>-</sup>(ΔBIC<sub>quadratic-linear</sub> = 3.04), β (ΔBIC<sub>quadratic-linear</sub> = 3.9), or ω (ΔBIC<sub>quadratic-linear</sub>= 0). Moreover, the quadratic age term was not significant for α<sup>+</sup>, α<sup>−</sup>, or β (all ps > 0.10). For ω, we observed a significant linear age effect (b = 1.41, t = 2.65, p = 0.009) and a significant quadratic age effect (b = −0.03, t = −2.39, p = 0.018; see Author response image 1). This pattern is broadly consistent with the group effect reported in the main text. The shaded area in the figure represents the 95% confidence interval. As shown, the interval widens at older ages (≥ 26 years) due to fewer participants in that range, which limits the robustness of the inferred quadratic effect. In consideration of the limited precision at older ages and the lack of BIC improvement, we did not emphasize the quadratic effect in the revised manuscript and present these results here as exploratory.

      Author response image 1.

      Linear and quadratic model fits showing the relationship between age and the ω parameter, with 95% confidence intervals.

      (Q4) Finally, the two age groups compared - adolescents (high school students) and adults (university students) - differ not only in age but also in sociocultural and economic backgrounds. High school students are likely more homogenous in regional background (e.g., Beijing locals), while university students may be drawn from a broader geographic and socioeconomic pool. Additionally, differences in financial independence, family structure (e.g., single-child status), and social network complexity may systematically affect cooperative behavior and valuation of rewards. Although these factors are difficult to control fully, the authors should more explicitly address the extent to which their findings reflect biological development versus social and contextual influences.

      We appreciate this comment. Indeed, adolescents (high school students) and adults (university students) differ not only in age but also in sociocultural and socioeconomic backgrounds. In our study, all participants were recruited from Beijing and surrounding regions, which helps minimize large regional and cultural variability. Moreover, we accounted for individual-level random effects and included participants’ social value orientation (SVO) as an individual difference measure.

      Nonetheless, we acknowledge that other contextual factors, such as differences in financial independence, socioeconomic status, and social experience—may also contribute to group differences in cooperative behavior and reward valuation. Although our results are broadly consistent with developmental theories of reward sensitivity and social decisionmaking, sociocultural influences cannot be entirely ruled out. Future work with more demographically matched samples or with socioeconomic and regional variables explicitly controlled will help clarify the relative contributions of biological and contextual factors. Accordingly, we have revised the Discussion to include the following statement:

      “Third, although both age groups were recruited from Beijing and nearby regions, minimizing major regional and cultural variation, adolescents and adults may still differ in socioeconomic status, financial independence, and social experience. Such contextual differences could interact with developmental processes in shaping cooperative behavior and reward valuation. Future research with demographically matched samples or explicit measures of socioeconomic background will help disentangle biological from sociocultural influences.”

      Reviewer #3 (Public review):

      Summary:

      Wu and colleagues find that in a repeated Prisoner's Dilemma, adolescents, compared to adults, are less likely to increase their cooperation behavior in response to repeated cooperation from a simulated partner. In contrast, after repeated defection by the partner, both age groups show comparable behavior.

      To uncover the mechanisms underlying these patterns, the authors compare eight different models. They report that a social reward learning model, which includes separate learning rates for positive and negative prediction errors, best fits the behavior of both groups. Key parameters in this winning model vary with age: notably, the intrinsic value of cooperating is lower in adolescents. Adults and adolescents also differ in learning rates for positive and negative prediction errors, as well as in the inverse temperature parameter.

      Strengths:

      The modeling results are compelling in their ability to distinguish between learned expectations and the intrinsic value of cooperation. The authors skillfully compare relevant models to demonstrate which mechanisms drive cooperation behavior in the two age groups.

      We thank the reviewer’s recognition of our work’s strengths.

      Weaknesses:

      (Q1) Some of the claims made are not fully supported by the data:

      The central parameter reflecting preference for cooperation is positive in both groups. Thus, framing the results as self-interest versus other-interest may be misleading.

      We thank the reviewer for this insightful comment. In the social reward model, the cooperation preference parameter is positive by definition, as defection in the repeated rPDG always yields a +2 monetary advantage regardless of the partner’s action. This positive value represents the additional subjective reward assigned to mutual cooperation (e.g., reciprocity value) that counterbalances the monetary gain from defection. Although the estimated social reward parameter ω was positive, the effective advantage of cooperation is Δ=p×ω−2. Given participants’ inferred beliefs p, Δ was negative for most trials (p×ω<2), indicating that the social reward was insufficient to offset the +2 advantage of defection. Thus, both adolescents and adults valued cooperation positively, but adolescents’ smaller ω and weaker responsiveness to sustained partner cooperation suggest a stronger weighting on immediate monetary payoffs.

      In this light, our framing of adolescents as more self-interested derives from their behavioral pattern: even when they recognized sustained partner cooperation and held high expectations of partner cooperation, adolescents showed lower cooperative behavior and reciprocity rewards compared with adults. Whereas adults increased cooperation after two or three consecutive partner cooperations, this pattern was absent among adolescents. We therefore interpret their behavior as relatively more self-interested, reflecting reduced sensitivity to the social reward from mutual cooperation rather than a categorical shift from self-interest to other-interest, as elaborated in the Discussion.

      (Q2) It is unclear why the authors assume adolescents and adults have the same expectations about the partner's cooperation, yet simultaneously demonstrate age-related differences in learning about the partner. To support their claim mechanistically, simulations showing that differences in cooperation preference (i.e., the w parameter), rather than differences in learning, drive behavioral differences would be helpful.

      We thank the reviewer for raising this important point. In our model, both adolescents and adults updated their beliefs about partner cooperation using an asymmetric reinforcement learning (RL) rule. Although adolescents exhibited a higher positive and a lower negative learning rate than adults, the two groups did not differ significantly in their overall updating of partner cooperation probability (Fig. 4a-b). We then examined the social reward parameter ω, which was significantly smaller in adolescents and determined the intrinsic value of mutual cooperation (i.e., p×ω). This variable differed significantly between groups and closely matched the behavioral pattern.

      Following the reviewer’s suggestion, we conducted additional simulations varying one model parameter at a time while holding the others constant. The difference in mean cooperation probability between adults and adolescents served as the index (positive = higher cooperation in adults). As shown in the Author response image 2, decreases in ω most effectively reproduced the observed group difference (shaded area), indicating that age-related differences in cooperation are primarily driven by variation in the social reward parameter ω rather than by others.

      Author response image 2.

      Simulation results showing how variations in each model parameter affect the group difference in mean cooperation probability (Adults – Adolescents). Based on the bestfitting Model 8 and parameters estimated from all participants, each line represents one parameter (i.e., α+, α-, ω, β) systematically varied within the tested range (α±:0.1–0.9; ω, β:1–9) while other parameters were held constant. Positive values indicate higher cooperation in adults. Smaller ω values most strongly reproduced the observed group difference, suggesting that reduced social reward weighting primarily drives adolescents’ lower cooperation.

      (Q3) Two different schedules of 120 trials were used: one with stable partner behavior and one with behavior changing after 20 trials. While results for order effects are reported, the results for the stable vs. changing phases within each schedule are not. Since learning is influenced by reward structure, it is important to test whether key findings hold across both phases.

      We thank the reviewer for this thoughtful and professional comment. In our GLMM and LMM analyses, we focused on trial order rather than explicitly including the stable vs. changing phase factor, due to concerns about multicollinearity. In our design, phases occur in specific temporal segments, which introduces strong collinearity with trial order. In multi-round interactions, order effects also capture variance related to phase transitions.

      Nonetheless, to directly address this concern, we conducted additional robustness analyses by adding a phase variable (stable vs. changing) to GLMM1, LMM1, and LMM3 alongside the original covariates. Across these specifications, the key findings were replicated (see GLMM<sub>sup</sub>2 and LMM<sub>sup</sub>4–5; Tables 9-11), and the direction and significance of main effects remained unchanged, indicating that our conclusions are robust to phase differences.

      (Q4) The division of participants at the legal threshold of 18 years should be more explicitly justified. The age distribution appears continuous rather than clearly split. Providing rationale and including continuous analyses would clarify how groupings were determined.

      We thank the reviewer for this thoughtful comment. We divided participants at the legal threshold of 18 years for both conceptual and practical reasons grounded in prior literature and policy. In many countries and regions, 18 marks the age of legal majority and is widely used as the boundary between adolescence and adulthood in behavioral and clinical research. Empirically, prior studies indicate that psychosocial maturity and executive functions approach adult levels around this age, with key cognitive capacities stabilizing in late adolescence (Icenogle et al., 2019; Tervo-Clemmens et al., 2023). We have clarified this rationale in the Introduction section of the revised manuscript.

      “Based on legal criteria for majority and prior empirical work, we adopt 18 years as the boundary between adolescence and adulthood (Icenogle et al., 2019; Tervo-Clemmens et al., 2023).”

      We fully agree that the underlying age distribution is continuous rather than sharply divided. To address this, we conducted additional analyses treating age as a continuous predictor (see GLMM<sub>sup</sub>1 and LMM<sub>sup</sub>1–3; Tables S1-S4), which generally replicated the patterns observed with the categorical grouping. Nevertheless, given the limited age range of our sample, the generalizability of these findings to fine-grained developmental differences remains constrained. Therefore, our primary analyses continue to focus on the contrast between adolescents and adults, rather than attempting to model a full developmental trajectory.

      (Q5) Claims of null effects (e.g., in the abstract: "adults increased their intrinsic reward for reciprocating... a pattern absent in adolescents") should be supported with appropriate statistics, such as Bayesian regression.

      We thank the reviewer for highlighting the importance of rigor when interpreting potential null effects. To address this concern, we conducted Bayes factor analyses of the intrinsic reward for reciprocity and reported the corresponding BF10 for all relevant post hoc comparisons. This approach quantifies the relative evidence for the alternative versus the null hypothesis, thereby providing a more direct assessment of null effects. The analysis procedure is now described in the Methods and Materials section:

      “Post hoc comparisons were conducted using Bayes factor analyses with MATLAB’s bayesFactor Toolbox (version v3.0, Krekelberg, 2024), with a Cauchy prior scale σ = 0.707.”

      (Q6) Once claims are more closely aligned with the data, the study will offer a valuable contribution to the field, given its use of relevant models and a well-established paradigm.

      We are grateful for the reviewer’s generous appraisal and insightful comments.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) I commend the authors on a well-structured, clear, and interesting piece of work. I have several questions and recommendations that, if addressed, I believe will strengthen the manuscript.

      We thank the reviewer for commending the organization of our paper.

      (2) Introduction: - Why use a zero-sum (Prisoner's Dilemma; PD) versus a mixed-motive game (e.g. Trust Task) to study cooperation? In a finite set of rounds, the dominant strategy can be to defect in a PD.

      We thank the reviewer for this helpful comment. We agree that both the rationale for using the repeated Prisoner’s Dilemma (rPDG) and the limitations of this framework should be clarified. We chose the rPDG to isolate the core motivational conflict between selfinterest and joint welfare, as its symmetric and simultaneous structure avoids the sequential trust and reputation dependencies/accumulation inherent to asymmetric tasks such as the Trust Game (King-Casas et al., 2005; Rilling et al., 2002).

      Although a finitely repeated rPDG theoretically favors defection, extensive prior research shows that cooperation can still emerge in long repeated interactions when players rely on learning and reciprocity rather than backward induction (Rilling et al., 2002; Fareri et al., 2015). Our design employed 120 consecutive rounds, allowing participants to update expectations about partner behavior and to establish stable reciprocity patterns over time. We have added the following clarification to the Introduction:

      “The rPDG provides a symmetric and simultaneous framework that isolates the motivational conflict between self-interest and joint welfare, avoiding the sequential trust and reputation dynamics characteristic of asymmetric tasks such as the Trust Game (Rilling et al., 2002; King-Casas et al., 2005)”

      (3) Methods:

      Did the participants know how long the PD would go on for?

      Were the participants informed that the partner was real/simulated?

      Were the participants informed that the partner was going to be the same for all rounds?

      We thank the reviewer for the meticulous review work, which helped us present the experimental design and reporting details more clearly. the following clarifications: I. Participants were not informed of the total number of rounds in the rPDG. This prevented endgame expectations and avoided distraction from counting rounds, which could introduce additional effects. II. Participants were told that their partner was another human participant in the laboratory. However, the partner’s behavior was predetermined by a computer program. This design enabled tighter experimental control and ensured consistent conditions across age groups, supporting valid comparisons. III. Participants were informed that they would interact with the same partner across all rounds, aligning with the essence of a multiround interaction paradigm and stabilizing partner-related expectations. For transparency, we have clarified these points in the Methods and Materials section:

      “Participants were told that their partner was another human participant in the laboratory and that they would interact with the same partner across all rounds. However, in reality, the actions of the partner were predetermined by a computer program. This setup allowed for a clear comparison of the behavioral responses between adolescents and adults. Participants were not informed of the total number of rounds in the rPDG.”

      (4) The authors mention that an SVO was also recorded to indicate participant prosociality. Where are the results of this? Did this track game play at all? Could cooperativeness be explained broadly as an SVO preference that penetrated into game-play behaviour?

      We thank the reviewer for pointing this out. We agree that individual differences in prosociality may shape cooperative behavior, so we conducted additional analyses incorporating SVO. Specifically, we extended GLMM1 and LMM3 by adding the measured SVO as a fixed effect with random slopes, yielding GLMM<sub>sup</sub>3 and LMM<sub>sup</sub>6 (Tables 12–13). The results showed that higher SVO was associated with greater cooperation, whereas its effect on the reward for reciprocity was not significant. Importantly, the primary findings remained unchanged after controlling for SVO. These results indicate that cooperativeness in our task cannot be explained solely by a broad SVO preference, although a more prosocial orientation was associated with greater cooperation. We have reported these analyses and results in the Appendix Analysis section.

      (5) Why was AIC chosen rather an BIC to compare model dominance?

      Sorry for the lack of clarification. Both the Akaike Information Criterion (AIC, Akaike, 1974) and Bayesian Information Criterion (BIC, Schwarz, 1978) are informationtheoretic criterions for model comparison, neither of which depends on whether the models to be compared are nested to each other or not (Burnham et al., 2002). We have added the following clarification into the Methods.

      “We chose to use the AICc as the metric of goodness-of-fit for model comparison for the following statistical reasons. First, BIC is derived based on the assumption that the “true model” must be one of the models in the limited model set one compares (Burnham et al., 2002; Gelman & Shalizi, 2013), which is unrealistic in our case. In contrast, AIC does not rely on this unrealistic “true model” assumption and instead selects out the model that has the highest predictive power in the model set (Gelman et al., 2014). Second, AIC is also more robust than BIC for finite sample size (Vrieze, 2012).”

      (6) I believe the model fitting procedure might benefit from hierarchical estimation, rather than maximum likelihood methods. Adolescents in particular seem to show multiple outliers in a^+ and w^+ at the lower end of the distributions in Figure S2. There are several packages to allow hierarchical estimation and model comparison in MATLAB (which I believe is the language used for this analysis;

      see https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007043).

      We thank the reviewer for this helpful comment and for referring us to relevant methodological work (Piray et al., 2019). We have addressed this point by incorporating hierarchical Bayesian estimation, which effectively mitigates outlier effects and improves model identifiability. The results replicated those obtained with MLE fitting and further revealed group-level differences in key parameters. Please see our detailed response to Reviewer#1 Q1 for the full description of this analysis and results.

      (7) Results: Model confusion seems to show that the inequality aversion and social reward models were consistently confused with the baseline model. Is this explained or investigated? I could not find an explanation for this.

      The apparent overlap between the inequality aversion (Model 4) and social reward (Model 5) models in the recovery analysis likely arises because neither model includes a learning mechanism, making them unable to capture trial-by-trial adjustments in this dynamic task. Consequently, both were best fit by the baseline model. Please see Response to Reviewer #1 Q3 for related discussion.

      (8) Figures 3e and 3f show the correlation between asymmetric learning rates and age. It seems that both a^+ and a^- are around 0.35-0.40 for young adolescents, and this becomes more polarised with age. Could it be that with age comes an increasing discernment of positive and negative outcomes on beliefs, and younger ages compress both positive and negative values together? Given the higher stochasticity in younger ages (\beta), it may also be that these values simply represent higher uncertainty over how to act in any given situation within a social context (assuming the differences in groups are true).

      We appreciate this insightful interpretation. Indeed, both α+ and α- cluster around 0.35–0.40 in younger adolescents and become increasingly polarized with age, suggesting that sensitivity to positive versus negative feedback is less differentiated early in development and becomes more distinct over time. This interpretation remains tentative and warrants further validation. Based on this comment, we have revised the Discussion to include this developmental interpretation.

      We also clarify that in our model β denotes the inverse temperature parameter; higher β reflects greater choice precision and value sensitivity, not higher stochasticity. Accordingly, adolescents showed higher β values, indicating more value-based and less exploratory choices, whereas adults displayed relatively greater exploratory cooperation. These group differences were also replicated using hierarchical Bayesian estimation (see Response to Reviewer #1 Q1). In response to this comment, we have added a statement in the Discussion highlighting this developmental interpretation.

      “Together, these findings suggest that the differentiation between positive and negative learning rates changes with age, reflecting more selective feedback sensitivity in development, while higher β values in adolescents indicate greater value sensitivity. This interpretation remains tentative and requires further validation in future research.”

      (9) A parameter partial correlation matrix (off-diagonal) would be helpful to understand the relationship between parameters in both adolescents and adults separately. This may provide a good overview of how the model properties may change with age (e.g. a^+'s relation to \beta).

      We thank the reviewer for this helpful comment. We fully agree that a parameter partial correlation matrix can further elucidate the relationships among parameters. Accordingly, we conducted a partial correlation analysis and added the visually presented results to the revised manuscript as Figure 2-figure supplement 4.

      (10) It would be helpful to have Bayes Factors reported with each statistical tests given that several p-values fall within the 0.01 and 0.10.

      We thank the reviewer for this important recommendation. We have conducted Bayes factor analyses and reported BF10 for all relevant post hoc comparisons. We also clarified our analysis in the Methods and Materials section:

      “Post hoc comparisons were conducted using Bayes factor analyses with MATLAB’s bayesFactor Toolbox (version v3.0, Krekelberg, 2024), with a Cauchy prior scale σ = 0.707.”

      (11) Discussion: I believe the language around ruling out failures in mentalising needs to be toned down. RL models do not enable formal representational differences required to assess mentalising, but they can distinguish biases in value learning, which in itself is interesting. If the authors were to show that more complex 'ToM-like' Bayesian models were beaten by RL models across the board, and this did not differ across adults and adolescents, there would be a stronger case to make this claim. I think the authors either need to include Bayesian models in their comparison, or tone down their language on this point, and/or suggest ways in which this point might be more thoroughly investigated (e.g., using structured models on the same task and running comparisons: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087619).

      We thank the reviewer for the comments. Please see our response to Reviewer 1 (Appraisal & Discussion section) for details.

      Reviewer #2 (Recommendations for the authors):

      (1) The authors may want to show the winning model earlier (perhaps near the beginning of the Results section, when model parameters are first mentioned).

      We thank the reviewer for this suggestion. We agree that highlighting the winning model early improves clarity. Currently, we have mentioned the winning model before the beginning of the Results section. Specifically, in the penultimate paragraph of the Introduction we state:

      “We identified the asymmetric RL learning model as the winning model that best explained the cooperative decisions of both adolescents and adults.”

      Reviewer #3 (Recommendations for the authors):

      (1) In addition to the points mentioned above, I suggest the following:

      Clarify plots by clearly explaining each variable. In particular, the indices 1 vs. 1,2 vs 1,2,3 were not immediately understandable.

      We thank the reviewer for this suggestion. We agree that the indices were not immediately clear. We have revised the figure captions (Figure 1 and 4) to explicitly define these terms more clearly:

      “The x-axis represents the consistency of the partner’s actions in previous trials (t<sub>−1</sub>: last trial; t<sub>−1,2</sub>: last two trials;<sub>t−1,2,3</sub>: last three trials).”

      (2) It's unclear why the index stops at 3. If this isn't the maximum possible number of consecutive cooperation trials, please consider including all relevant data, as adolescents might show a trend similar to adults over more trials.

      We thank the reviewer for raising this point. In our exploratory analyses, we also examined longer streaks of consecutive partner cooperation or defection (up to four or five trials). Two empirical considerations led us to set the cutoff at three in the final analyses. First, the influence of partner behavior diminished sharply with temporal distance. In both GLMMs and LMMs, coefficients for earlier partner choices were small and unstable, and their inclusion substantially increased model complexity and multicollinearity. This recency pattern is consistent with learning and decision models emphasizing stronger weighting of recent evidence (Fudenberg & Levine, 2014; Fudenberg & Peysakhovich, 2016). Second, streaks longer than three were rare, especially among some participants, leading to data sparsity and inflated uncertainty. Including these sparse conditions risked biasing group estimates rather than clarifying them. Balancing informativeness and stability, we therefore restricted the index to three consecutive partner choices in the main analyses, which we believe sufficiently capture individuals’ general tendencies in reciprocal cooperation.

      (3) The term "reciprocity" may not be necessary. Since it appears to reflect a general preference for cooperation, it may be clearer to refer to the specific behavior or parameter being measured. This would also avoid confusion, especially since adolescents do show negative reciprocity in response to repeated defection.

      We thank you for this comment. In our work, we compute the intrinsic reward for reciprocity as p × ω, where p is the partner cooperation expectation and ω is the cooperation preference. In the rPDG, this value framework manifests as a reciprocity-derived reward: sustained mutual cooperation maximizes joint benefits, and the resulting choice pattern reflects a value for reciprocity, contingent on the expected cooperation of the partner. This quantity enters the trade-off between U<sub>cooperation</sub> and U<sub>defection</sub> and captures the participant’s intrinsic reward for reciprocity versus the additional monetary reward payoff of defection. Therefore, we consider the term “reciprocity” an acceptable statement for this construct.

      (4) Interpretation of parameters should closely reflect what they specifically measure.

      We thank the reviewer for pointing this out. We have refined the relevant interpretations of parameters in the current Results and Discussion sections.

      (5) Prior research has shown links between Theory of Mind (ToM) and cooperation (e.g., Martínez-Velázquez et al., 2024). It would be valuable to test whether this also holds in your dataset.

      We thank the reviewer for this thoughtful comment. Although we did not directly measure participants’ ToM, our design allowed us to estimate participants’ trial-by-trial inferences (i.e., expectations) about their partner’s cooperation probability. We therefore treat these cooperation expectations as an indirect representation for belief inference, which is related to ToM processes. To test whether this belief-inference component relates to cooperation in our dataset, we further conducted an exploratory analysis (GLMM<sub>sup</sub>4) in which participants’ choices were regressed on their cooperation expectations, group, and the group × cooperation-expectation interaction, controlling for trial number and gender, with random effects. Consistent with the ToM–cooperation link in prior research (MartínezVelázquez et al., 2024), participants’ expectations about their partner’s cooperation significantly predicted their cooperative behavior (Table 14), suggesting that decisions were shaped by social learning about others’ inferred actions. Moreover, the interaction between group and cooperation expectation was not significant, indicating that this inference-driven social learning process likely operates similarly in adolescents and adults. This aligns with our primary modeling results showing that both age groups update beliefs via an asymmetric learning process. We have reported these analyses in the Appendix Analysis section.

      (6) More informative table captions would help the reader. Please clarify how variables are coded (e.g., is female = 0 or 1? Is adolescent = 0 or 1?), to avoid the need to search across the manuscript for this information.

      We thank the reviewer for raising this point. We have added clear and standardized variable coding in the table notes of all tables to make them more informative and avoid the need to search the paper. We have ensured consistent wording and formatting across all tables.

      (7) I hope these comments are helpful and support the authors in further strengthening their manuscript.

      We thank the three reviewers for their comments, which have been helpful in strengthening this work.

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      (7) Tervo-Clemmens, B., Calabro, F. J., Parr, A. C., et al. (2023). A canonical trajectory of executive function maturation from adolescence to adulthood. Nature Communications, 14, 6922. https://doi.org/10.1038/s41467-023-42540-8

      (8) King-Casas, B., Tomlin, D., Anen, C., Camerer, C. F., Quartz, S. R., & Montague, P. R. (2005). Getting to know you: reputation and trust in a two-person economic exchange. Science, 308(5718), 78-83. https://doi.org/10.1126/science.1108062

      (9) Rilling, J. K., Gutman, D. A., Zeh, T. R., Pagnoni, G., Berns, G. S., & Kilts, C. D. (2002).A neural basis for social cooperation. Neuron, 35(2), 395-405. https://doi.org/10.1016/s0896-6273(02)00755-9

      (10) Fareri, D. S., Chang, L. J., & Delgado, M. R. (2015). Computational substrates of social value in interpersonal collaboration. Journal of Neuroscience, 35(21), 8170-8180. https://doi.org/10.1523/JNEUROSCI.4775-14.2015

      (11) Akaike, H. (2003). A new look at the statistical model identification. IEEE transactions on automatic control, 19(6), 716-723. https://doi.org/10.1109/TAC.1974.1100705

      (12) Schwarz, G. (1978). Estimating the dimension of a model. The annals of statistics, 461464. https://doi.org/10.1214/aos/1176344136

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      (16) Vrieze, S. I. (2012). Model selection and psychological theory: A discussion of the differences between the Akaike Information Criterion (AIC) and the Bayesian Information Criterion (BIC). Psychological Methods, 17(2), 228–243. https://doi.org/10.1037/a0027127

    1. Reviewer #2 (Public review):

      Summary:

      This study presents a systematic and well-executed effort to identify and classify bacterial NRP metallophores. The authors curate key chelator biosynthetic genes from previously characterized NRP-metallophore biosynthetic gene clusters (BGCs) and translate these features into an HMM-based detection module integrated within the antiSMASH platform.

      The new algorithm is compared with a transporter-based siderophore prediction approach, demonstrating improved precision and recall. The authors further apply the algorithm to large-scale bacterial genome mining and, through reconciliation of chelator biosynthetic gene trees with the GTDB species tree using eMPRess, infer that several chelating groups may have originated prior to the Great Oxidation Event.<br /> Overall, this work provides a valuable computational framework that will greatly assist future in silico screening and preliminary identification of metallophore-related BGCs across bacterial taxa.

      Strengths:

      (1) The study provides a comprehensive curation of chelator biosynthetic genes involved in NRP-metallophore biosynthesis and translates this knowledge into an HMM-based detection algorithm, which will be highly useful for the initial screening and annotation of metallophore-related BGCs within antiSMASH.

      (2) The genome-wide survey across a large bacterial dataset offers an informative and quantitative overview of the taxonomic distribution of NRP-metallophore biosynthetic chelator groups, thereby expanding our understanding of their phylogenetic prevalence.

      (3) The comparative evolutionary analysis, linking chelator biosynthetic genes to bacterial phylogeny, provides an interesting and valuable perspective on the potential origin and diversification of NRP-metallophore chelating groups.

      Weaknesses:

      (1) Although the rule-based HMM detection performs well in identifying major categories of NRP-metallophore biosynthetic modules, it currently lacks the resolution to discriminate between fine-scale structural or biochemical variations among different metallophore types.

      (2) While the comparison with the transporter-based siderophore prediction approach is convincing overall, more information about the dataset balance and composition would be appreciated. In particular, specifying the BGC identities, source organisms, and Gram-positive versus Gram-negative classification would improve transparency. In the supplementary tables, the "Just TonB" section seems to include only BGCs from Gram-negative bacteria-if so, this should be clearly stated, as Gram type strongly influences siderophore transport systems.

      Comments on revisions:

      The authors have adequately addressed all of my previous comments. I have no further comments on the revised manuscript.

    2. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      This work by Reitz, Z. L. et al. developed an automated tool for high-throughput identification of microbial metallophore biosynthetic gene clusters (BGCs) by integrating knowledge of chelating moiety diversity and transporter gene families. The study aimed to create a comprehensive detection system combining chelator-based and transporter-based identification strategies, validate the tool through large-scale genomic mining, and investigate the evolutionary history of metallophore biosynthesis across bacteria.

      Major strengths include providing the first automated, high-throughput tool for metallophore BGC identification, representing a significant advancement over manual curation approaches. The ensemble strategy effectively combines complementary detection methods, and experimental validation using HPLC-HRMS strengthens confidence in computational predictions. The work pioneers a global analysis of metallophore diversity across the bacterial kingdom and provides a valuable dataset for future computational modeling.

      Some limitations merit consideration. First, ground truth datasets derived from manual curation may introduce selection bias toward well-characterized systems, potentially affecting performance assessment accuracy. Second, the model's dependence on known chelating moieties and transporter families constrains its ability to detect novel metallophore architectures, limiting discovery potential in metagenomic datasets. Third, while the proposed evolutionary hypothesis is internally consistent, it lacks direct validation and remains speculative without additional phylogenetic studies.

      The authors successfully achieved their stated objectives. The tool demonstrates robust performance metrics and practical utility through large-scale application to representative genomes. Results strongly support their conclusions through rigorous validation, including experimental confirmation of predicted metallophores via HPLC-HRMS analysis.

      The work provides a significant and immediate impact by enabling the transition from labor-intensive manual approaches to automated screening. The comprehensive phylogenetic framework advances understanding of bacterial metal acquisition evolution, informing future studies on microbial metal homeostasis. Community utility is substantial, since the tool and accompanying dataset create essential resources for comparative genomics, algorithm development, and targeted experimental validation of novel metallophores.

      We thank the reviewer for their valuable feedback. We appreciate the positive words, and agree with their listed limitations. Regarding the following comment:

      “Third, while the proposed evolutionary hypothesis is internally consistent, it lacks direct validation and remains speculative without additional phylogenetic studies.”

      We agree that additional phylogenetic analyses are needed in future studies. For the revised manuscript, we have validated our evolutionary hypotheses by additionally analyzing two gene families using the likelihood-based tool AleRax, which implements a probabilistic DTL model. The results were consistent with the eMPRess parsimony-based reconstructions, showing comparable patterns of rare duplication, moderate gene loss, and extensive horizontal transfer. Both methods identified similar lineages as the most probable origin and major recipients of transfer events. This agreement between independent reconciliation frameworks supports the reliability of our evolutionary conclusions. We have added a statement referencing this cross-method validation in the revised manuscript.

      Reviewer #2 (Public review):

      Summary:

      This study presents a systematic and well-executed effort to identify and classify bacterial NRP metallophores. The authors curate key chelator biosynthetic genes from previously characterized NRP-metallophore biosynthetic gene clusters (BGCs) and translate these features into an HMM-based detection module integrated within the antiSMASH platform.

      The new algorithm is compared with a transporter-based siderophore prediction approach, demonstrating improved precision and recall. The authors further apply the algorithm to large-scale bacterial genome mining and, through reconciliation of chelator biosynthetic gene trees with the GTDB species tree using eMPRess, infer that several chelating groups may have originated prior to the Great Oxidation Event.

      Overall, this work provides a valuable computational framework that will greatly assist future in silico screening and preliminary identification of metallophore-related BGCs across bacterial taxa.

      Strengths:

      (1) The study provides a comprehensive curation of chelator biosynthetic genes involved in NRP-metallophore biosynthesis and translates this knowledge into an HMM-based detection algorithm, which will be highly useful for the initial screening and annotation of metallophore-related BGCs within antiSMASH.

      (2) The genome-wide survey across a large bacterial dataset offers an informative and quantitative overview of the taxonomic distribution of NRP-metallophore biosynthetic chelator groups, thereby expanding our understanding of their phylogenetic prevalence.

      (3) The comparative evolutionary analysis, linking chelator biosynthetic genes to bacterial phylogeny, provides an interesting and valuable perspective on the potential origin and diversification of NRP-metallophore chelating groups.

      We greatly appreciate these comments.

      Weaknesses:

      (1) Although the rule-based HMM detection performs well in identifying major categories of NRP-metallophore biosynthetic modules, it currently lacks the resolution to discriminate between fine-scale structural or biochemical variations among different metallophore types.

      We agree that this is a current limitation to the methodology. More specific metallophore structural prediction is among our future goals for antiSMASH. We have added a statement to this effect in the conclusion.

      (2) While the comparison with the transporter-based siderophore prediction approach is convincing overall, more information about the dataset balance and composition would be appreciated. In particular, specifying the BGC identities, source organisms, and Gram-positive versus Gram-negative classification would improve transparency. In the supplementary tables, the "Just TonB" section seems to include only BGCs from Gram-negative bacteria - if so, this should be clearly stated, as Gram type strongly influences siderophore transport systems.

      The reviewer raises good points here. An additional ZIP file containing all BGCs used for the manual curation was inadvertently left out of the supplemental dataset for the first version of the manuscript. We have added columns with source organisms and Gram stain (retrieved from Bacdive) to Table S2. F1 scores were similar for Gram positive and negative subsets, as seen in the new Table S2.

      We thank the reviewer for suggesting this additional analysis, and have added a brief statement in the revised manuscript.

      The “Just TonB” section (in which we tested the performance of requiring TonB without another transporter) was not used for the manuscript. We will preserve it in the revised Table S2 for transparency.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In line 43:

      "excreted" should be replace by "secreted".

      Done.

      (2) In lines 158-159:

      "we manually predicted metallophore production among a large set of BGCs."

      If they are first "annotated with default antiSMASH v6.1", then it is not entirely manual, right? I would suggest making this sentence clearer.

      We have revised the language.

      (3) In lines 165-169:

      It would be good to show the confusion matrix of these results.

      The confusion matrices are found in Table S2, columns AL-AR.

      (4) In Table 1:

      Method names (AntiSMASH rules/Transporter genes) could be misleading, since they are all AntiSMASH-based, right?

      We have adjusted the methods to clarify that while the transporter genes were detected using a modified version of antiSMASH, they are not related to our chelator-based detection rule (which is now correctly singular throughout the text).

      (5) Line 198:

      There are accidental spaces and characters inserted here.

      We could not find any accidental spaces and characters here.

      (6) Line 209:

      "In total, 3,264 NRP metallophore BGC regions were detected"

      Is this number correct? I don't see a correspondence in Table 1.

      We have added the following sentence to the Table 1 legend: “An additional 54 BGC regions were detected as NRP metallophores without meeting the requirements for the antiSMASH NRPS rule.”

      (7) Line 294:

      "From B. brennerae, we identified four catecholic compounds"

      From the bacterial cells or the culture supernatant? I think it is important to state this in a more precise way. If it is from the supernatant, it could be from EVs.

      We state in line 292 that “organic compounds were extracted from the culture supernatants”. As our goal was only to confirm the ability of the strains to produce the predicted metallophores, the precise localization (including cell pellet or EVs) was not explored.

      (8) Lines 349-357:

      These results would benefit greatly from a visualization strategy.

      Thank you, we have added a reference to the existing visualization in Fig. 5, Ring C.

      (9) Lines 452-454:

      How could clusters be de-replicated? Is there an identity equivalence scheme or similarity metric?

      The BGC regions were de-replicated with BiG-SCAPE, which uses multiple similarity metrics as described in Navarro-Muñoz et al, 2020. Clusters could be dereplicated further using a more strict cutoff.

      (10) Line 457:

      "relatively low number of published genomes."

      Could metagenome-assembled genomes help in that matter?

      This is a good question, but we find that MAGs are usually too fragmented to yield complete NRPS BGC regions. We’ve added additional sentences earlier in the discussion: “Detection rates were also lower for fragmented genomes; unfortunately, this limitation (inherent to antiSMASH itself) may hinder the identification of metallophore biosynthesis in metagenomes. As long-read sequencing of metagenomes becomes more common, we expect that detection will improve.”

      (11) Lines 514-515:

      "Adequately-performing pHMMs for Asp and His β-hydroxylase subtypes could not be constructed using the above method."

      What is the overall impact of this discrepancy in the methodology for these specific groups?

      The phylogeny-based methodology was used to reduce false positives. We expect this method will have improved precision at the possible expense of recall.

      (12) Lines 543-545:

      "RefSeq representative bacterial genomes were dereplicated at the genus level using R, randomly selecting one genome for each of the 330 genera determined by GTDB"

      Isn't it more of a random sampling than a dereplication? Dereplication would involve methods such as ANI computation.

      You are correct; we have adjusted the language to clarify.

      (13) Lines 559-560: "were filtered to remove clusters on contig edges."

      This sentence is confusing because networks will be mentioned soon, and they also have edges (not the edges mentioned here), and they could also be clustered (not the clusters mentioned here). Is there a way to make the terminology clearer?

      Thank you, we have adjusted the text to read “BGC regions on contig boundaries”

      (14) Line 560:

      "The resulting 2,523 BGC regions, as well as 78 previously reported BGCs "

      How many were there before filtering?

      We have added the number: 3,264

      (15) Lines 579-580:

      Confusing terminology, as mentioned in Lines 559-560.

      Adjusted as above.

      General comments and questions:

      An objective suggestion to enrich the discussion is to address the role of bacterial extracellular vesicles (EVs) as metallophore carriers. Studies show that EVs, such as outer membrane vesicles, can transport siderophores or other metallophores for iron acquisition in various bacteria, functioning as "public goods" for community-wide nutrient sharing. Highlighting this mechanism would add ecological and functional context to the manuscript. In the future, EV-associated metallophore transport could also be considered for integration into computational detection tools.

      We thank the reviewer for the suggestion; however, we do not think that such a discussion is needed. We briefly discuss the ecological function of metallophores as public goods (and public bads) in the first paragraph of the introduction. We did not find any reports that EV-associated genes co-localize with metallophore BGCs, which would be required for their presence to be a useful marker of metallophore production.

      Is there a feasible path to more generalizable detection of chelating motifs using chemistry-aware features? For example, a machine learning classifier trained on submolecular descriptors (e.g., functional groups, coordination motifs, SMARTS patterns, graph fingerprints, metal-binding propensity scores) could complement the current genome-based approach and broaden coverage beyond known metallophore families. While the discussion mentions future extensions centered on genomic features, integrating chemical information from predicted or known products (or biosynthetic logic inferred from BGC composition) could be explored. A hybrid framework-linking BGC-derived features with chemistry-derived features-may improve both recall for novel metallophore classes and precision in distinguishing true chelators from confounders, thereby increasing overall accuracy.

      We can envision a classifier that uses submolecular descriptors to predict the ability of a molecule to bind metal ions. However, starting with a BGC and accurately predicting the structure of a hitherto unknown chelating moiety will likely prove difficult.  We have added a sentence to the discussion stating that a future tool could use accessory genes to more completely predict chemical structure.

      Although the initial analysis was conducted using RefSeq genomes, what are the anticipated challenges and limitations when scaling this method for BGC prospecting in metagenome-assembled genomes (MAGs), particularly considering the inherent quality differences, assembly fragmentation, and taxonomic uncertainties that characterize MAG datasets compared to curated reference genomes?

      Please see our response to comment 10, line 457. Our pHMM-based approach is designed to be robust to organism taxonomy; however, fragmentation is a significant barrier to accurate antiSMASH-based BGC detection (including in contig-level single-isolate genomes, see Table 1).

      Reviewer #2 (Recommendations for the authors):

      (1) In the "Chemical identification of genome-predicted siderophores across taxa" section, it would be helpful to annotate the cross-species similarities between predicted metallophore BGCs and their reference clusters (Ref BGCs). As currently described, the main text seems to highlight the cross-species resolving power of BiG-SCAPE itself rather than demonstrating the taxonomic generalizability of the chelator HMM-based detection module.

      Thank you for this comment. We intended to display that the new rule is useful for detecting BGCs in unexplored taxa, but we acknowledge that there is not a great diversity in the strains we selected. We have removed “across taxa” to avoid misleading the reader and clarify our intent.

      (2) In addition to using eMPRess for gene-species reconciliation, it may be beneficial to explore or at least reference alternative reconciliation tools to validate the inferred duplication, transfer, and loss (DTL) scenarios. Incorporating such cross-method comparisons would enhance the robustness and credibility of the evolutionary conclusions.

      We appreciate this valuable suggestion. To validate the robustness of our reconciliation-based inferences, we additionally analyzed two gene families using the likelihood-based tool AleRax, which implements a probabilistic DTL model. The results were consistent with the eMPRess parsimony-based reconstructions, showing comparable patterns of rare duplication, moderate gene loss, and extensive horizontal transfer. Both methods identified similar lineages as the most probable origin and major recipients of transfer events. This agreement between independent reconciliation frameworks supports the reliability of our evolutionary conclusions. We have added a brief statement referencing this cross-method validation in the revised manuscript.

    1. Éduquons nos fils : Synthèse sur la Déconstruction de la Masculinité et de la Violence

      Résumé Exécutif

      Ce document analyse les mécanismes de construction de la masculinité et leurs conséquences sur la société française, tels qu'exposés dans les témoignages et analyses du projet "Infrarouge - Éduquons nos fils".

      Le constat central est que la violence n'est pas une essence masculine, mais le produit d'un conditionnement éducatif et social profond.

      Les points clés sont les suivants :

      Le poids des stéréotypes : Dès l'enfance, les garçons sont incités à refouler leur vulnérabilité, assimilée à une faiblesse, pour incarner le modèle du "mâle alpha" invulnérable.

      Un coût sociétal colossal : La "virilité" coûte environ 100 milliards d'euros par an à l'État français (justice, santé, insécurité routière).

      La masculinité comme facteur de risque : Les hommes représentent 97 % de la population carcérale et sont responsables de 84 % des accidents de la route mortels. Ils sont également les premières victimes de leur propre conditionnement (morts prématurées, conduites à risques).

      L'urgence éducative : La solution réside dans une réinvention de l'éducation des fils, passant par l'autorisation de l'expression émotionnelle, la déconstruction des modèles de domination et une présence paternelle sécurisante.

      --------------------------------------------------------------------------------

      1. La Construction du "Mâle Alpha" : Un Conditionnement Précoce

      Le document met en lumière un système éducatif et social qui formate les garçons selon des codes de virilité hégémonique.

      L'injonction à l'invulnérabilité

      Refoulement émotionnel : L'éducation traditionnelle enseigne que "pleurer est une affaire de filles".

      Ce blocage des émotions, de l'enfance à l'âge adulte, génère une souffrance psychique et physique (douleurs somatiques, burn-out).

      L'image de la force : Le modèle valorisé est celui de "Superman" : fort, musclé, insensible et protecteur.

      Le culte du corps (musculation à outrance) est souvent utilisé comme une armure pour pallier une insécurité intérieure ou une vulnérabilité passée.

      Modèles culturels : Les figures d'identification des années 80 et 90 (Stallone, Schwarzenegger, James Bond) ont ancré l'image de l'homme "sandwich de l'hypervirilité", où la réussite passe par la puissance physique et la domination.

      L'influence de l'environnement social

      Le groupe de pairs (la "meute") : La bande de copains joue un rôle de renforcement. La peur d'être exclu ou jugé "faible" pousse les jeunes hommes à la surenchère dans la prise de risque ou la violence.

      Le sexisme ordinaire : La publicité et l'espace public ont longtemps objectivé les femmes, renforçant chez les jeunes garçons une vision prédatrice ou supérieure du masculin.

      --------------------------------------------------------------------------------

      2. Les Conséquences de la Virilité : Statistiques et Coûts

      L'adhésion aux stéréotypes masculins n'est pas seulement un enjeu privé ; elle impacte lourdement la structure socio-économique du pays.

      Le coût financier de la virilité (Analyse de Lucile Petavin)

      L'historienne Lucile Petavin estime que les comportements antisociaux et violents des hommes coûtent 100 milliards d'euros par an à la France.

      | Secteur de dépense | Coût estimé (par an) | | --- | --- | | Justice et forces de l'ordre | 7 milliards € (sur 9 au total) | | Coups et violences volontaires | 18 milliards € (sur 26 au total) | | Insécurité routière | 13,3 milliards € | | Total Global estimé | 100 milliards € |

      L'asymétrie de genre dans la criminalité et les risques

      Incarcération : 97 % des personnes détenues sont des hommes.

      Sécurité routière : Les hommes sont responsables de 84 % des accidents mortels.

      Santé : Les hommes ont 2 à 3 fois plus de risques de mourir prématurément (avant 65 ans) à cause de comportements à risques (alcool, tabac, vitesse). À 14 ans, un garçon a déjà 70 % de risques de plus qu'une fille de mourir dans un accident.

      --------------------------------------------------------------------------------

      3. Les Espaces de Reproduction et de Mutation

      La masculinité se joue dans des lieux clés où les stéréotypes sont soit renforcés, soit déconstruits.

      L'école et la cour de récréation

      L'école est décrite comme un concentré de patriarcat où règnent la compétition et la loi du plus fort.

      Violences scolaires : 71 % des élèves de la 6ème à la terminale ont subi des violences.

      Stéréotypes sportifs : Les activités comme la danse classique ou l'équitation restent perçues comme "féminines", tandis que le foot et la boxe sont vus comme le domaine naturel des garçons. Des initiatives pédagogiques tentent de briser ces barrières par la mixité réelle dans l'effort sportif.

      Le danger du numérique et du masculinisme

      Les réseaux sociaux (TikTok, Instagram) servent de vecteurs à des discours de haine misogyne extrêmes.

      Contenus toxiques : Des influenceurs militent pour un retour au patriarcat pur et dur, prônant la soumission des femmes et la violence comme outil de respect.

      Absence de modération : Les plateformes sont critiquées pour leur manque de régulation, privilégiant le profit généré par l'engagement (vues/likes) au détriment de la sécurité des mineurs.

      --------------------------------------------------------------------------------

      n4. Vers une Nouvelle Paternité et Responsabilité

      Le changement passe par une redéfinition du rôle de père et une prise de conscience collective des hommes.

      Le rôle du père "nouveau"

      Expression de l'affection : Dire "je t'aime" et assurer une sécurité émotionnelle sans menace physique est présenté comme le levier principal pour briser le cycle de la violence.

      Implication domestique : Sortir du cliché "l'homme au barbecue, la femme aux légumes" et s'impliquer dans le soin quotidien des enfants (le "care") permet de normaliser une masculinité attentive et non dominante.

      La responsabilité collective (All Men)

      Le champion de MMA Cédric Dumbé souligne que si tous les hommes ne sont pas coupables, ils sont tous responsables du climat social.

      Sortir de l'indifférence : Refuser de rire aux blagues sexistes, ne pas relayer de contenus dégradants et soutenir activement les victimes de violences sont des actes de "vrais hommes".

      Légitimation de la vulnérabilité : Accepter sa propre part de féminité et ses émotions est la clé pour une virilité "réglée" qui ne débouche pas sur l'agression.

      --------------------------------------------------------------------------------

      Conclusion

      Le document conclut sur la nécessité d'une transformation profonde de l'éducation.

      En autorisant les fils à explorer toute la gamme des émotions humaines et en leur offrant des modèles de force qui ne reposent pas sur la domination, la société peut espérer réduire drastiquement la violence masculine et ses coûts humains et financiers.

      Comme l'indique l'un des intervenants : "Tous les hommes ne sont pas violents, mais la violence est masculine. Éduquez vos fils."

    1. Manifeste de l'hostilité misogyne : Analyse de la haine systémique contre les femmes dans l'espace public

      Résumé Exécutif

      Le présent document synthétise les mécanismes, les acteurs et les conséquences de la recrudescence de la violence misogyne, telle qu'analysée dans le contexte européen et international.

      Il apparaît que les femmes occupant des postes à responsabilité ou s'exprimant avec conviction dans la sphère publique — politiciennes, journalistes, activistes — sont les cibles privilégiées d'une haine organisée.

      Cette hostilité se manifeste par un cyber-harcèlement d'une violence extrême, allant de l'insulte sexiste aux menaces de viol et de mort.

      L'analyse révèle que cette haine n'est pas fortuite : elle est instrumentalisée par des mouvements populistes et d'extrême droite, et théorisée par des groupes masculinistes qui perçoivent l'égalité des genres comme une menace identitaire et sociale.

      Le monde numérique, régi par des algorithmes privilégiant l'engagement (souvent généré par la haine) et protégé par un certain vide juridique, sert d'incubateur à une radicalisation pouvant mener au terrorisme (mouvement « Incel »).

      Face à l'insuffisance des réponses institutionnelles, des initiatives de soutien émergent, tandis que des voix s'élèvent pour appeler à une déconstruction systémique des stéréotypes de masculinité.

      --------------------------------------------------------------------------------

      1. Une Violence Ciblée et Systémique

      La haine envers les femmes n'est pas le fait d'individus isolés, mais un phénomène structurel visant à exclure les femmes de la sphère publique.

      Les cibles privilégiées

      Le mépris et l'agressivité visent particulièrement les femmes qui manifestent de l'assurance et occupent des domaines traditionnellement masculins :

      Femmes politiques : En Allemagne (34 % de députées au Bundestag) comme en France (40 % à l'Assemblée nationale), elles subissent des interruptions systématiques et une remise en question de leur légitimité.

      Journalistes sportives : L'exemple de Claudia Neumann illustre l'hostilité rencontrée lorsqu'une femme investit le "pré carré" masculin du football.

      Activistes et Écrivaines : Des figures comme Alice Barbe ou Leila Slimani subissent des campagnes de dénigrement massives en raison de leurs engagements pour les réfugiés ou les droits des femmes.

      La nature des agressions

      Contrairement aux hommes, les femmes reçoivent des attaques "taillées sur mesure" liées à leur genre :

      Sexualisation et humiliation : Envoi de "dickpics", insultes à caractère sexuel, commentaires sur le physique ou l'âge.

      Menaces extrêmes : Descriptions détaillées de viols, menaces de mutilations génitales ou de mort.

      Invisibilisation : Au sein même des institutions, la parole des femmes est souvent accueillie par un brouhaha ou un désintérêt feint de la part des collègues masculins.

      --------------------------------------------------------------------------------

      2. Les Racines Idéologiques et l'Instrumentalisation Politique

      La misogynie moderne s'appuie sur des discours structurés et une exploitation politique délibérée.

      Le mouvement masculiniste

      Les masculinistes considèrent que les femmes ont pris le dessus et opprimeraient désormais les hommes.

      Rhétorique de la crise : Ils présentent l'égalité comme une "maladie" ou une "injustice" envers les jeunes hommes.

      Défense du patriarcat : Des auteurs comme Julien Rochedy prônent un retour aux codes virils traditionnels, affirmant que le manque de patriarcat est la cause du féminisme actuel.

      L'extrême droite et le populisme

      Des partis comme l'AfD en Allemagne ou des figures comme Éric Zemmour en France utilisent le sexisme comme stratégie électorale :

      Provocation délibérée : Utilisation de termes sexistes pour susciter l'émotion et gagner en visibilité médiatique.

      Lien avec d'autres haines : La misogynie s'accompagne souvent d'idéologies racistes et antisémites. Le féminisme est présenté comme un facteur de "décadence civilisationnelle".

      Déstabilisation : Au Parlement, l'entrée de partis d'extrême droite a entraîné une augmentation nette des exclamations et comportements sexistes.

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      3. L'Espace Numérique : Un "Lieu de Terreur"

      Internet et les réseaux sociaux agissent comme des catalyseurs de haine en raison de leur fonctionnement intrinsèque.

      La mécanique du cyber-harcèlement

      L'anonymat : Il favorise la levée des inhibitions. Les agresseurs peuvent être des "monsieur tout le monde" (professeurs, ingénieurs, avocats).

      Les algorithmes : La haine et l'incitation à la violence génèrent plus de vues et de clics, ce qui est financièrement profitable pour les plateformes.

      La radicalisation en ligne : Des forums privés permettent à des hommes de s'enfermer dans une vision étriquée du monde, se confortant mutuellement dans leur détestation des femmes.

      La menace "Incel" (Célibataires involontaires)

      Cette sous-culture numérique représente un danger sécuritaire réel :

      Idéologie : Conviction que les femmes sont des êtres inférieurs et que l'accès à leur corps est un droit fondamental.

      Apologie de la violence : Célébration de terroristes comme Elliot Rodger ou Alec Minassian.

      Passage à l'acte : Plusieurs attentats (Santa Barbara, Toronto, Halle) ont été motivés, totalement ou partiellement, par cette haine des femmes.

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      4. Conséquences Sociales et Réponses Institutionnelles

      L'impact de cette violence dépasse les victimes individuelles pour menacer la démocratie elle-même.

      L'impact sur les victimes et la démocratie

      Charge mentale et traumatisme : Les victimes doivent mettre en place des protocoles de sécurité lourds et subissent un stress psychologique intense.

      Le recul de la parole : Une femme sur deux craint d'exprimer son opinion en ligne. Ce retrait forcé crée un déséquilibre dans le débat public, laissant le champ libre aux harceleurs.

      Le sentiment d'isolement : Les militantes se sentent souvent seules face à des réseaux d'agresseurs très bien organisés.

      Un cadre juridique et policier défaillant

      Sous-estimation des faits : Les plaintes sont souvent classées sans suite ou banalisées par les forces de l'ordre ("supprimez votre compte").

      Complexité législative : Les plateformes, souvent basées à l'étranger, collaborent peu avec la justice. En France, des tentatives de régulation ont été déclarées inconstitutionnelles au nom de la liberté d'expression.

      Initiatives de soutien : Des structures comme HateAid en Allemagne offrent désormais un accompagnement juridique et psychologique pour pallier les carences de l'État.

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      5. Perspectives de Lutte et Déconstruction

      Pour enrayer ce phénomène, l'analyse suggère des actions à la racine du problème.

      | Axe d'intervention | Actions préconisées | | --- | --- | | Éducation | Déconstruire les stéréotypes de genre dès le plus jeune âge et remettre en question la "masculinité toxique". | | Engagement masculin | Impliquer les hommes dans le discours féministe. Comme le souligne Leila Slimani, les hommes ont tout à gagner à un monde moins violent et moins régi par l'obligation de virilité brute. | | Justice | Former la police et le parquet à reconnaître la misogynie comme un délit grave. Créer une jurisprudence forte, à l'instar du procès remporté par Alice Barbe. | | Régulation | Imposer des règles communes au niveau européen pour contraindre les plateformes à transmettre les données des auteurs de messages haineux. |

      Conclusion : La lutte contre la misogynie organisée est un enjeu de sécurité publique et de survie démocratique.

      Refuser de céder à la peur et briser le silence sont les premiers remparts contre cette tentative de "silencier" les femmes dans l'espace public.

    1. Masculinité en crise : la fin d’Homo Virilus ?

      Ce document de synthèse analyse les fondements, l'évolution historique et la remise en question contemporaine de l'archétype de la virilité, désigné sous le terme d'« Homo Virilus ».

      À travers un prisme historique, sociologique et personnel, il explore comment ce modèle de domination, longtemps hégémonique, fait face à une crise profonde et à une nécessité de redéfinition.

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      Résumé exécutif

      L’idéal de l'« Homo Virilus » repose sur un triptyque de puissance, de courage et de domination.

      Historiquement ancré dans l'héroïsme guerrier, ce modèle a subi des chocs successifs : la déshumanisation par la guerre industrielle en 1914, l'autonomisation des femmes lors des conflits mondiaux, et les révolutions féministes des années 1970.

      Aujourd'hui, la masculinité est à la croisée des chemins. D'un côté, une réaction masculiniste et « viriliste » s'intensifie, portée par la manosphère et des discours réactionnaires.

      De l'autre, des mouvements de déconstruction émergent, portés par de nouvelles formes de paternité et une distinction claire entre masculinité et domination.

      Le coût social de la virilité obligatoire est désormais quantifié (environ 100 milliards d'euros par an en France), soulignant l'urgence d'une transition vers des modèles plus équitables.

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      1. L'Archétype d'Homo Virilus : Un Idéal de Domination

      Le concept d'Homo Virilus n'est pas une donnée biologique, mais une construction culturelle héritée de l'Antiquité gréco-romaine.

      Les piliers de la virilité : Ce modèle exige puissance, courage et domination. Il impose une maîtrise de soi constante, tout en justifiant une violence explosive si nécessaire.

      Une hiérarchie sociale : La vertu virile justifie la domination des femmes et des enfants, mais aussi celle des hommes jugés « non virils ».

      Une fragilité intrinsèque : Contrairement à l'apparence de force, la virilité est décrite comme une « insoutenable fragilité » car elle doit être prouvée et maintenue en permanence. On ne naît pas Homo Virilus, on le devient par des rites de passage, souvent liés au combat.

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      2. Les Ruptures Historiques : De la Tranchée au Foyer

      Le XXe siècle a marqué le début du déclin de l'héroïsme viril traditionnel.

      L'épreuve de la Grande Guerre (1914-1918)

      La fin du romantisme militaire : La guerre industrielle, avec son « orage d'acier », a rendu le courage individuel obsolète face aux obus.

      Le traumatisme et la « dévirilisation » : Les survivants sont revenus démembrés ou atteints de blessures invisibles (« l'obusite » ou syndrome post-traumatique). À l'époque, la psychiatrie associait ces troubles nerveux à une forme de féminisation ou de lâcheté.

      Inversion des rôles : Pendant que les hommes étaient au front, les femmes (« munitionnettes », conductrices, postières) ont prouvé leur capacité à faire fonctionner la société, brisant le mythe de leur infériorité physique et morale.

      La réaction totalitaire des années 1930

      Le fascisme comme rempart : Face à la fluidité de la République de Weimar, les régimes totalitaires (Hitler, Mussolini) ont prôné un retour à une virilité antique et implacable.

      Idéologie et exclusion : La virilité nazie était indissociable de l'antisémitisme et de l'homophobie. Les homosexuels, perçus comme des « hommes-femmes » incapables de combattre, ont été persécutés et envoyés en camps (marqués du triangle rose).

      Relégation des femmes : Le modèle « Kinder, Kuche, Kirche » (Enfant, Cuisine, Église) visait à supprimer les droits politiques des femmes pour les cantonner au rôle d'épouse-mère du guerrier.

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      3. Les Révolutions du Corps et du Pouvoir

      À partir des années 1960, l'hégémonie virile est attaquée de front par les mouvements sociaux.

      L'ère des luttes LGBT et féministes : La dépénalisation de l'homosexualité (1982 en France) et les victoires législatives (contraception, IVG avec la loi Veil) ont dissocié la sexualité de la reproduction.

      La fin du Pater Familias : Le passage de l'autorité paternelle à l'autorité parentale conjointe a mis fin à la domination juridique absolue du père dans le foyer.

      Le sentiment d'humiliation : Pour les nostalgiques de la domination, ces changements sont vécus comme une dépossession de pouvoir et une « féminisation » de la société.

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      4. La Virilité comme Performance Sexuelle et Sociale

      La puissance masculine reste souvent indexée sur des attributs physiques et des performances quantifiables.

      Le Phallus comme sceptre : La puissance virile est fréquemment réduite à la puissance phallique, créant une obsession pour la taille, la durée et le nombre de conquêtes.

      La culture du vestiaire : Dès l'adolescence, la pression des pairs impose un masque de dureté. La sensibilité est assimilée à une défaillance.

      La domination économique : Au travail, Homo Virilus adopte l'uniforme du cadre ou du manager performant. Les « broligarches » (contraction de brothers et oligarques) utilisent des codes de guerre pour écraser la concurrence.

      La détresse silencieuse : L'échec professionnel est vécu comme une perte de valeur sociale totale. Le tabou de la santé mentale masculine mène à une « épidémie silencieuse » de suicides et de consommations excessives de drogues.

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      5. Violences et Consentement : L'impact de MeToo

      La dénonciation des violences sexistes et sexuelles remet en cause le « droit de cuissage » implicite de l'Homo Virilus.

      De la culture du viol au consentement : Des procès historiques (menés par Gisèle Halimi) à l'affaire Mazan, la société prend conscience que le viol n'est pas le fait de marginaux, mais d'hommes « ordinaires » issus de tous les milieux.

      Prise de conscience masculine : Le mouvement MeToo a forcé certains hommes à réévaluer leurs comportements passés, notamment sur la notion de rapport forcé ou de pression exercée sur les femmes.

      Le coût de la virilité : Les statistiques révèlent que les hommes sont responsables de :

      ◦ 91 % des tentatives d'homicides.    ◦ 99 % des incendies volontaires.    ◦ 84 % des accidents de la route mortels.    ◦ Coût total : Près de 100 milliards d'euros par an en France.

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      6. La Montée du Masculinisme et la « Manosphère »

      En réaction à ces évolutions, un courant réactionnaire puissant s'organise, notamment sur les réseaux sociaux.

      Le discours du déclin : Des personnalités politiques et médiatiques prédisent l'effondrement de la civilisation face à la « castration » de l'homme blanc.

      L'influence de TikTok : La « manosphère » attire les jeunes hommes avec des conseils de drague et de fitness qui cachent un agenda antiféministe radical. Les femmes y sont souvent désignées comme des « féminazis ».

      Le mouvement Incel : Les « célibataires involontaires » développent une haine profonde des femmes, allant parfois jusqu'à l'apologie du terrorisme ou au passage à l'acte meurtrier (Montréal, Californie).

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      7. Vers une Déconstruction et de Nouveaux Modèles

      Des alternatives à l'Homo Virilus émergent, cherchant à dissocier la masculinité de la domination.

      La paternité active : Des ateliers de préparation à la paternité aident les hommes à s'approprier les gestes du soin et de l'éducation, sortant du rôle binaire « autorité et finance ».

      La masculinité au pluriel : Les sociologues et les personnes trans (comme Léon) soulignent que la testostérone ne crée pas le comportement dominateur ; c'est l'éducation qui façonne la virilité toxique.

      Distinction clé :

      Les hommes se trouvent aujourd'hui à la croisée des chemins : perpétuer un stéréotype obsolète et coûteux, ou explorer des formes de masculinité fondées sur l'équité, la sensibilité et le partage des responsabilités.

  3. learninglab.gitlabpages.inria.fr learninglab.gitlabpages.inria.fr
    1. Briefing : Sensibilisation au Trouble du Développement Intellectuel (TDI)

      Ce document de synthèse analyse les enjeux, les caractéristiques et les modalités d'accompagnement liés au trouble du développement intellectuel (TDI), sur la base des expertises de Fabienne Rudler et Marie-Thé (Job coaches et spécialistes en neurodéveloppement).

      Résumé Exécutif

      Le trouble du développement intellectuel (TDI), autrefois nommé handicap mental ou déficience intellectuelle, est un trouble neurodéveloppemental (TND) apparaissant durant l'enfance (avant 18 ans).

      Il se définit par l'association de déficits des fonctions intellectuelles et de limitations significatives du comportement adaptatif. Contrairement aux troubles "Dys", le TDI impacte l'intelligence de manière globale, bien que les profils soient hétérogènes.

      La prise en charge efficace repose sur une distinction cruciale entre le langage expressif (ce que la personne dit) et le langage réceptif (ce qu'elle comprend réellement), ainsi que sur une adaptation de l'environnement face aux difficultés d'abstraction, de repérage temporel et de généralisation des apprentissages.

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      I. Cartographie et Typologie du Handicap

      Il est essentiel de situer le TDI parmi les différentes catégories de handicap pour éviter les confusions diagnostiques.

      | Type de Handicap | Caractéristiques Principales | | --- | --- | | Moteur | Limitation de la mobilité (membres) ou troubles d'origine motrice (ex: visuels). | | Sensoriel | Touche la vision et l'auditif (le goût/l'odorat ne sont pas encore reconnus suite au COVID). | | Psychique | Pathologies mentales (psychoses, bipolarité, dépression, TOC). Apparition souvent à l'adolescence ou à l'âge adulte. | | Dégénératif | État qui s'aggrave par paliers (pas de retour en arrière possible). | | Neurodéveloppemental (TND) | Apparaît durant le développement neurologique (0-18 ans). Inclut les troubles "Dys", le TDAH, l'autisme (TSA) et le TDI. |

      Distinction entre "Dys" et TDI

      Troubles Spécifiques des Apprentissages (Dys) : L'intelligence est préservée. Le trouble est spécifique à un domaine (lecture, calcul, geste).

      TDI : Les capacités cognitives globales sont impactées. La pédagogie doit être radicalement différente car elle ne peut pas s'appuyer sur le même bagage cognitif.

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      II. Étiologie et Critères Diagnostiques du TDI

      Le TDI est un trouble dynamique. L'origine du trouble est multiple, bien qu'une part importante reste inexpliquée.

      Les causes (Étiologie)

      80 % d'origine prénatale (anténatale) : Aberrations chromosomiques (Trisomie 21), malformations cérébrales, prématurité, infections (rubéole, toxoplasmose) ou intoxications durant la grossesse.

      10 % d'origine périnatale : Accidents lors de l'accouchement (anoxie cérébrale, hémorragies).

      10 % d'origine postnatale : Séquelles de méningites, traumatismes crâniens (bébé secoué), noyades ou intoxications (plomb).

      Donnée clé : 40 % à 50 % des TDI restent d'origine indéterminée, ce chiffre montant à 80 % pour les déficiences légères.

      Les trois piliers du diagnostic

      1. Déficit des fonctions intellectuelles : Évalué par des tests de QI (inférieur à 70).

      2. Limitation du comportement adaptatif : Difficultés dans la vie quotidienne (autonomie, relations sociales).

      3. Apparition durant la période développementale : Avant l'âge de 18 ans.

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      III. Analyse des Fonctions Cognitives Impactées

      Le TDI se manifeste par des altérations dans plusieurs domaines clés du traitement de l'information.

      1. Le repérage Espace-Temps

      C'est l'un des domaines les plus lourdement impactés.

      Le Temps : Étant abstrait, il est plus difficile à saisir que l'espace.

      Les personnes peuvent savoir lire l'heure (apprentissage mécanique) sans comprendre la notion de durée ou d'anticipation (ex: estimer le temps de trajet ou comprendre qu'un interrupteur s'éteint en secondes et non en minutes).

      L'Espace : Le repérage sur plan est complexe. L'apprentissage est souvent pragmatique (un trajet précis appris par cœur) plutôt que conceptuel (comprendre le réseau de transport).

      2. Les fonctions exécutives

      Inhibition : Difficulté à s'empêcher de dire ou de faire quelque chose (impulsivité sociale).

      Flexibilité : Difficulté à passer d'une tâche à une autre ou à gérer l'imprévu.

      Mémoire de travail : Capacité limitée à maintenir une information à court terme pour réaliser une action immédiate.

      3. La catégorisation

      L'incapacité à regrouper des objets par concepts (ex: fruits et légumes) rend le quotidien coûteux en énergie. Au supermarché, une personne ne sachant pas catégoriser cherchera chaque produit individuellement plutôt que par rayon.

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      IV. Le Comportement Adaptatif

      Aujourd'hui, le degré de sévérité du TDI (léger, moyen, grave, profond) est déterminé par le fonctionnement adaptatif et non plus seulement par le score de QI.

      Les habiletés évaluées (échelle Vineland-II)

      Conceptuelles : Lecture, écriture, calcul, gestion de l'argent.

      Pratiques : Tâches ménagères, déplacements, utilisation d'appareils (automates, machine à laver).

      Sociales : Demander de l'aide, éviter les abus, respecter les distances sociales.

      La généralisation : un défi majeur

      Une personne avec TDI peut apprendre à utiliser une machine à laver spécifique, mais ne saura pas forcément utiliser un autre modèle. Elle ne généralise pas le principe de fonctionnement. L'apprentissage doit être multiplié dans divers contextes.

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      V. Focus sur la Communication et le Langage

      La communication orale est un piège fréquent dans l'accompagnement, car elle repose sur de nombreux codes implicites.

      Le paradoxe "Expressif vs Réceptif"

      Le "beau vernis" : Certaines personnes s'expriment très bien (langage expressif) mais ne comprennent pas les mots qu'elles emploient ou ceux des autres (langage réceptif).

      Vigilance : Il est impératif de vérifier systématiquement la compréhension, même si la personne semble éloquente.

      Les obstacles linguistiques

      L'abstraction : Les mots ne renvoyant pas à un objet physique (ex: "attendre", "organiser", "ailleurs") sont difficiles à saisir.

      Les doubles sens : Mots phonétiquement identiques mais de sens différents (ex: "glace", "moule", "vase").

      Les petits mots "outils" : Les pronoms (je/tu/moi), les articles et les prépositions peuvent brouiller le message.

      La conditionnalité : Les phrases commençant par "Si..." (ex: "Si tu es malade...") sont souvent incomprises car elles demandent de se projeter dans une situation inexistante. La réponse sera souvent : "Mais je ne suis pas malade".

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      VI. Recommandations pour l'Accompagnement

      Pour favoriser l'inclusion et l'apprentissage des personnes avec TDI, plusieurs leviers doivent être activés :

      1. Respecter le temps de latence : Le traitement de l'information est plus lent. Il faut ralentir le débit, poser une seule question à la fois et attendre la réponse sans reformuler trop vite.

      2. Passer par le concret : Utiliser des supports visuels, des objets réels et éviter les métaphores ou le second degré.

      3. Décomposer les tâches : Ce qui semble être une étape pour une personne ordinaire (ex: traverser la rue) est en réalité une succession de traitements cognitifs complexes (vitesse, distance, durée).

      4. Partir de la réponse de la personne : Si une personne répond "à côté", il faut analyser sa logique pour adapter notre message (ex: si elle ne comprend pas "fromage", utiliser le mot "camembert" si c'est sa référence).

      5. Anticiper les ruptures : Les changements de trajets, les grèves ou les pannes d'appareils sont des situations de mise en échec si elles n'ont pas été travaillées de manière pragmatique.

      Conclusion sur l'autonomie

      L'autonomie n'est pas de savoir tout faire seul, mais de savoir quand et comment demander de l'aide.

      C'est sur ce levier social et adaptatif que les éducateurs et employeurs peuvent avoir le plus d'impact, car si le QI est fixe, le comportement adaptatif peut toujours progresser par l'expérience.

    1. Guide de Référence : Le Programme Google Ad Grants pour les Associations

      Résumé Exécutif

      Le programme Google Ad Grants offre aux associations de loi 1901 une enveloppe de publicité gratuite sur le moteur de recherche Google s'élevant à 10 000 dollars par mois.

      Malgré son potentiel massif pour accroître la notoriété, recruter des bénévoles ou collecter des fonds, ce programme reste largement sous-exploité en France, avec seulement 2 000 à 3 000 associations actives sur les millions existantes.

      Ce document détaille les mécanismes du référencement payant, les critères d'éligibilité technique pour les structures, le processus d'activation en quatre étapes, ainsi que les stratégies optimales pour structurer des campagnes performantes.

      Il souligne également les limites du programme, notamment la priorité donnée aux annonceurs payants et la nécessité d'une gestion rigoureuse pour maximiser l'impact du crédit quotidien de 329 dollars.

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      1. Fondamentaux du Référencement Payant (SEA)

      Le programme Google Ad Grants s'inscrit dans le cadre du référencement payant (SEA), qu'il convient de distinguer du référencement naturel (SEO).

      Différences Clés : SEA vs SEO

      | Caractéristique | Référencement Payant (SEA) | Référencement Naturel (SEO) | | --- | --- | --- | | Position | Haut de la page (résultats sponsorisés) | Sous les annonces sponsorisées | | Délai de résultat | Court terme (immédiat après lancement) | Long terme et incertain | | Coût | Paiement au clic (offert par Ad Grants) | "Gratuit" (nécessite du temps/contenu) | | Contrôle | Choix précis des mots-clés et zones | Dépend de l'algorithme de Google |

      Spécificités du Compte Ad Grants

      Contrairement à un compte Google Ads classique, le compte Ad Grants présente des particularités :

      Enveloppe virtuelle : Aucun budget réel n'est déboursé par l'association ; Google déduit les frais de l'enveloppe de 10 000 $.

      Hiérarchie de diffusion : Les annonces Ad Grants apparaissent en dessous des annonces payantes des entreprises privées ou des institutions disposant d'un budget marketing.

      En cas de forte concurrence (ex: "collecte de dons"), il est parfois impossible de diffuser si les espaces publicitaires sont déjà saturés par des annonceurs payants.

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      2. Éligibilité et Critères Techniques

      Pour bénéficier du programme, une organisation doit remplir des critères statutaires et techniques précis.

      Structures Éligibles

      • Associations loi 1901.

      • Fonds de dotation et fondations reconnues d'utilité publique.

      Exclusions : Les entités gouvernementales, les hôpitaux, les centres de soins et les écoles ne sont pas éligibles directement (sauf via une fondation ou une structure associative dédiée).

      Exigences pour le Site Web

      Google effectue une vérification manuelle du site Internet lors de la demande. Celui-ci doit présenter :

      1. Un nom de domaine propre : Les sites hébergés sur des sous-domaines gratuits (ex: .wix.com, .google.site) sont refusés.

      2. Un contenu substantiel : Un minimum de 5 pages est requis.

      3. Une clarté institutionnelle : La mission et le statut associatif doivent être mentionnés en page d'accueil, dans une page "À propos" et dans le pied de page (footer).

      4. Performance technique : Le site doit être "responsive" (adapté aux mobiles) et avoir une vitesse de chargement satisfaisante (idéalement un score > 50/100 sur PageSpeed Insights).

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      3. Processus d'Activation en 4 Étapes

      Le lancement d'un compte Ad Grants suit un parcours structuré :

      1. Création du compte Google pour les associations : Utiliser de préférence une adresse email professionnelle liée au domaine de l'association pour simplifier la validation.

      2. Validation de l'identité : Google vérifie le statut juridique de l'association (via le numéro RNA). Cette étape prend généralement 24 heures.

      3. Activation de Google Ad Grants : Soumission du site web pour examen des critères de contenu et de performance. Le délai varie de 2 à 14 jours.

      4. Configuration finale : Validation du profil de paiement (sans carte bancaire) et accès définitif au compte.

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      4. Stratégie et Structuration des Campagnes

      Une gestion efficace repose sur une structure logique et l'alignement entre l'intention de l'utilisateur et le contenu proposé.

      Les 4 Piliers du Succès

      Le Ciblage : Sélection de mots-clés pertinents (volume de recherche > 50/mois) et spécifiques à la cause, en évitant les termes trop génériques ou ultra-concurrentiels.

      Les Annonces : Rédaction de titres percutants (jusqu'à 15 variantes) qui reprennent les mots-clés tapés par l'utilisateur.

      Les Enchères : Utilisation impérative de la stratégie "Maximiser les conversions" pour permettre à l'algorithme de Google d'optimiser la diffusion.

      Le Tracking : Connexion indispensable avec Google Analytics pour mesurer les actions concrètes (dons, inscriptions bénévoles, téléchargements).

      Exemple de Structure de Compte (Cas d'un refuge animalier)

      Campagne Adoptions : Groupes d'annonces séparés pour "Adopter un chien" et "Adopter un chat" renvoyant vers les pages respectives du site.

      Campagne Bénévolat : Mots-clés sur le don de temps, le soin aux animaux ou le travail associatif.

      Campagne Marque : Protection du nom de l'association pour apparaître systématiquement en haut lors d'une recherche directe.

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      5. Outils et Maintenance

      Le maintien de la performance nécessite l'usage d'outils complémentaires et une surveillance régulière.

      | Outil | Utilité | Niveau de difficulté | | --- | --- | --- | | Google Keyword Planner | Trouver des mots-clés et analyser leur volume/concurrence. | Débutant | | IA (ChatGPT, Gemini) | Aide à la rédaction des titres et descriptions d'annonces. | Débutant | | Google Analytics | Analyser le comportement des visiteurs après le clic. | Intermédiaire | | Google Tag Manager | Installer des marqueurs de conversion précis sans code. | Avancé |

      Conseils de Gestion

      Ne jamais supprimer de campagne : Il est préférable de mettre en pause les campagnes inactives pour conserver l'historique et gagner du temps lors de la réactivation.

      Utilisation du budget : Le plafond de 10 000 $ est réparti à hauteur de 329 $ par jour. Les crédits non utilisés un jour donné sont définitivement perdus et ne sont pas reportables.

      Sécurité des accès : Il est crucial de nommer plusieurs administrateurs pour éviter la perte du compte en cas de départ d'un collaborateur ou d'un bénévole.

      --------------------------------------------------------------------------------

      6. Éthique et Transparence

      Bien que les annonces soient financées par Google, elles portent la mention "Sponsorisé".

      Cette transparence est renforcée par le Google Ads Transparency Center, qui permet au public de consulter les publicités diffusées par n'importe quelle entité.

      Le programme s'inscrit dans la politique de Responsabilité Sociétale des Entreprises (RSE) de Google, agissant comme un don en nature sous forme d'espace publicitaire.

    1. Reviewer #3 (Public review):

      Summary:

      The manuscript by Poh et al. investigated whether dopamine release in the ventral medial striatum integrates information about action selection, controllability of reward pursuit, effort, and reward approach. Rats were implanted with FSCV probes and trained in four Go/No Go task variants:

      (1) trials were self-initiated and had two trial types (Go vs. No Go) that were auditorily cued,

      (2) trials were cue-initiated and had two trial types (Go vs. No Go) that were auditorily cued,

      (3) trials were self-initiated and had three trial types (Go vs. No Go vs. free reward) that were auditorily cued, and effort was increased,

      (4) trials were cue-initiated and had three trial types (Go vs. No Go vs. free reward) that were auditorily cued.

      The authors report that dopamine levels rose during Go trials and slowly rose in No Go trials, but this pattern did not differ across task variants that modified effort and whether trials were cued or initiated. They also report that dopamine levels rose as rats approached the reward location and were greater in rats that bit the noseport while holding during the No Go response.

      Strengths:

      (1) Interesting task and variants within the task paradigm that would allow the authors to isolate specific behavioral metrics.

      (2) The goal of determining precisely what VMS dopamine signals do is highly significant and would be of interest to many researchers.

      Weaknesses:

      (1) This Go/No-Go procedure is different from the traditional tasks, and this leads to several problems with interpreting the results:

      (a) Go/No Go tasks typically require subjects to refrain from doing any action. In this task, a response is still required for the No Go trials (e.g., continue holding the nosepoke). The problem with this modified design is that failure to withhold a response on No Go trials could be because i) rats could not continue holding the response, as holding responses are difficult for rodents, or ii) rats could not suppress the prepotent go response. This makes interpreting the behavior and the dopamine signal in No Go trials very difficult.

      (b) Most Go/No Go tasks bias or overrepresent Go trials so that the Go response is prepotent, and consequently, successful suppression of the Go response is challenging. I didn't see any information in the manuscript about how often each trial type was presented or how the authors ensured that No Go responses (or lack thereof) were reflecting a suppression of the Go response.

      (2) The authors observe relatively consistent differences in the DA signal between Go and No Go trials after the action-cue onset. However, the response type was not randomized between trial type, so there is a confound between trial type (Go/No Go) and response (lever/nosepoke). The difference in DA signal may have nothing to do with the cue type, but reflects differences in DA signal elicited by levers vs. nosepokes.

      (3) Both Go and No Go trials start with the rat having their nose in the noseport. One cue (Go cue) signals the rat to remove their nose from the noseport and make two lever responses in 5 seconds, whereas the other cue (No Go cue) signals the rat to keep their nose in the noseport for an additional 1.7-1.9 s. The authors state that the time between cue onset and reward delivery was kept the same for all trial types, and Figure 1 suggests this is 2 s, so was reward delivered before rats completed the two lever presses? I would imagine reward was only delivered if rats completed the FR requirement, but again, the descriptions in the text and figures are incongruent.

      (4) The manuscript is difficult to understand because key details are not in the main text or are not mentioned at all. I've outlined several points below:

      (a) The author's description in the manuscript makes it appear as a discrimination task versus a Go/No Go task. I suggest including more details in the main text that clarify what is required at each step in the task. Additionally, providing clarity regarding what task events the voltammetry traces are aligned to would be very useful.

      (b) How many subjects were included in each task variant? The text makes it seem like all rats complete each task variant, but the behavioral data suggest otherwise. Moreover, it appears that some rats did more than one version. Was the order counterbalanced? If not, might this influence the DA signal?

      (5) There is a major challenge in their design and interpretation of the dopamine signal. Both trial types (Go and No Go) start with the rat having their nose in the noseport. An auditory cue is presented for 2-3 s signaling to the rat to either leave the noseport and make a lever response (Go trial) or to stay in the noseport (No Go trial). The timing of these actions and/or decisions is entirely independent, so it is not clear to me how the authors would ever align these traces to the exact decision point for each trial type. They attempt to do this with the nose-port exit analysis, but exiting the noseport for a Go trial (a rat needs to make 2 lever presses and then get a reward) versus a No Go trial (a rat needs to go retrieve the reward) is very different and not comparable.

      (6) The voltammetry analysis did not appear to test the hypotheses the authors outlined in the intro. All comparisons were done within task variants (DA dynamics in Go vs. No Go trials, aligned to different task events), but there were no comparisons across task variants to determine if the DA signal differed in cued vs self-initiated trials.

      (7) Classification of No Go behaviors was interesting, but was not well integrated with the rest of the paper and was underdeveloped. It also raised more questions for me than answers. For example:

      (a) Was the behavior classification consistent across rats for all No Go trials? If not, did the DA signal change within subjects between biting vs digging vs calm?

      (b) If "biting rats" were not always biting rats on every No Go trial, then is it fair to collapse animals into a single measure (Figure 3C).

      (c) Some of the classification groups only had 2 or fewer rats in them, making any statistical comparison and inference difficult.

    1. Je retiendrai trois notions principales : l’interdépendance et les interactions, différentes représentations de l’existence fantasmée du groupe, et le groupe en tant qu’espace transitionnel. Ainsi que nous le verrons, celles-ci interrogent une compréhension des processus inconscients : a) centrés principalement sur « le sujet », dont la vie intrapsychique se structure en fonction de la place réelle et imaginaire qu’il occupe dans les différents groupes auxquels il appartient ; b) centrés sur « le groupe », représentation commune à un ensemble d’individus. Ces notions rendent compte de la fluidité des frontières existant entre l’individu et les groupes, et situent l’espace analytique à l’articulation des limites fluctuantes du Je et du Nous, du dedans et du dehors, du morcellement et de l’unité somatique, et de la pluralité psychique des identités singulière et collective.

      L’auteur dit qu’il va s’appuyer sur trois idées clés : 1. l’interdépendance et les interactions → dans un groupe, personne ne fonctionne seul : chacun influence et est influencé. 2. les représentations fantasmées du groupe → le groupe est aussi une construction imaginaire (mère, menace, refuge, etc.), pas seulement un ensemble réel de personnes. 3. le groupe comme espace transitionnel → le groupe est un entre-deux, ni totalement interne ni totalement externe, où peuvent se déposer et se transformer des vécus archaïques.

      À partir de là, il distingue deux façons de penser l’inconscient : • soit centré sur le sujet (comment sa vie psychique dépend de sa place dans les groupes), • soit centré sur le groupe (le groupe comme représentation commune).

      Ces notions montrent que les frontières entre individu et groupe sont mobiles : le travail analytique se situe précisément dans cet espace intermédiaire, entre Je et Nous, dedans et dehors, morcellement et unité, identité individuelle et collective.

      👉 En très court : le groupe est un espace transitionnel où s’entrelacent psychisme individuel et collectif, avec des frontières fluctuantes, permettant l’expression et la transformation de l’archaïque.

    1. AbstractThe growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterised sequences with the few experimentally characterised ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates protein nascent families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage can scale approximately linearly with input size, while the biological benchmarks showed that the generated protein families closely resemble manually curated families found in widely used databases.

      This work has been peer reviewed in GigaScience (see https://doi.org/10.1093/gigascience/giag009), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

      Reviewer 2: Castrense Savojardo

      This manuscript presents a Nextflow pipeline (nf-core/proteinfamilies) for large-scale protein-family generation. Overall, I think the paper is well written and clear. The pipeline appears very useful, and the reported results show good performance in both family reproducibility and computational efficiency.

      I have a few minor comments requesting additional details:

      1) Does the quality-check step only compute statistics, or is it also used to filter/clean the input set? If so, please specify the criteria and whether filtered sequences are excluded downstream.

      2) Which MMseqs2 clustering mode is used (set cover, connected components, or greedy)? Can this be changed within the pipeline? If configurable, please indicate the relevant parameters.

      3) In the reproducibility benchmark, you use DIAMOND BLASTp to assess similarity between the initial sequence set for the selected families and additional Swiss-Prot sequences. Which sequence identity and alignment coverage (if any) thresholds were applied?

      4) Counts and coverage (p. 6): You state that "These 709 families captured 96.66% of the original unique sequence identifiers (103,385 out of 106,959).". However, a few lines above the final input set is reported as 169,605 unique protein sequences. Could you please clarify the initial number of sequences and the actual coverage after family generation and redundancy reduction?

      5) Figures S1 and S2 are difficult to read due to low resolution.

    2. AbstractThe growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterised sequences with the few experimentally characterised ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates protein nascent families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage can scale approximately linearly with input size, while the biological benchmarks showed that the generated protein families closely resemble manually curated families found in widely used databases.

      This work has been peer reviewed in GigaScience (see https://doi.org/10.1093/gigascience/giag009), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

      Reviewer 1: Vikram Alva

      The authors present nf-core/proteinfamilies, a standardized Nextflow workflow that constructs protein families de novo or classifies sequences against existing families. Using a curated 200-family benchmark and a UniRef90-scale run, the authors show that the pipeline attains high recall with efficient runtimes. Given the ever-increasing size of sequence databases, this work is timely and fills a practical gap in reproducible, at-scale family curation; I expect it to be adopted widely by many research groups.

      I have several comments and suggestions below:

      1. In my view, this workflow will, by construction, yield a mixture of families: some anchored on a single conserved domain/segment, others centered on recurrent multi-domain cores, and some that capture the full-length sequence. This differs from widely used family databases: Pfam is largely domain-level, whereas HAMAP and NCBIFAM are mostly full-length/isofunctional (with PANTHER sitting in between). The resulting granularity is largely determined by MMseqs2 settings (sequence identity, query/target coverage, coverage mode) and by any alignment trimming, which biases toward conserved cores. Please add a brief discussion making this explicit, with practical guidance for tuning toward full-length versus domain-centric generation of families.

      I also recommend a parameter-sensitivity analysis on the 200-family set: sequence identity (30-70%), coverage thresholds (50-95%), and coverage mode (query/target/both), with and without trimming. For each setting, report (i) total families and split/merge rates per curated family, and (ii) a simple granularity readout, the proportion classified as domain-anchored, multi-domain, or full-length. This would clarify how parameter choices drive family counts and domain/full-length centricity, and help readers select defaults aligned with their use case.

      1. In the results, the splits/misses are concentrated in Pfam/PANTHER, while HAMAP/NCBIFAM are much closer to one-to-one (HAMAP 50/50). This suggests the inflated family count is driven, in part, by the domain-centric portion of the benchmark rather than the method itself. Please add a brief note in the Discussion to make this explicit.

      2. Since AFDB has models for most UniProt entries, could these models be used as an orthogonal purity check of the generated families; e.g., map members to AFDB and ask whether they cluster to the same fold by TM-score/Foldseek (allowing full-length differences when the family is domain-anchored)?

      3. HHsearch-based merging of divergent splits. In my view, and the authors note this, several curated families split simply because sequences are very divergent. An optional HHsearch (HMM-HMM) pass could merge these back: merge only at high probability (≈≥95%) with reciprocal coverage of the shorter model (≥0.6). It would be useful to include this as an optional stage in the pipeline.

      4. Optional annotation of de novo families. I think it would be useful to add an annotation step that compares each de novo family (family HMM or MSA) against curated resources (Pfam, NCBIFAM, PANTHER/HAMAP).

      5. Could you briefly outline your expectations for how the pipeline handles transmembrane segments, coiled-coils, repeats, and IDRs, classes prone to over-splitting under MMseqs2 seeding and trimming due to short-motif signal, low complexity, and variable lengths?

    1. AbstractCancer cells are heterogeneous, each harboring distinct molecular aberrations and are dependent on different genes for their survival and proliferation. While successful targeted therapies have been developed based on driver DNA mutations, many patient tumors lack druggable mutations and have limited treatment options. Here, we hypothesize that new precision oncology targets may be identified through “expression-driven dependency”, whereby cancer cells with high expression of a targeted gene are more vulnerable to the knockout of that gene. We introduce a Bayesian approach, BEACON, to identify such targets by jointly analyzing global transcriptomic and proteomic profiles with genetic dependency data of cancer cell lines across 17 tissue lineages. BEACON identifies known druggable genes, e.g., BCL2, ERBB2, EGFR, ESR1, MYC, while revealing new targets confirmed by both mRNA- and protein-expression driven dependency. Notably, the identified genes show an overall 3.8-fold enrichment for approved drug targets and enrich for druggable oncology targets by 7 to 10-fold. We experimentally validate that the depletion of GRHL2, TP63, and PAX5 effectively reduce tumor cell growth and survival in their dependent cells. Overall, we present the catalog of express-driven dependency targets as a resource for identifying novel therapeutic targets in precision oncology.

      This work has been peer reviewed in GigaScience (see https://doi.org/10.1093/gigascience/giag011), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

      Reviewer 2

      The authors introduce BEACON, a Bayesian correlation approach designed to identify expression-driven dependency in cancer. Their hypothesis suggests that cancer cells with elevated expression of specific genes demonstrate increased vulnerability to the knockout of those same genes, thereby unveiling a promising new category of targets in precision oncology—particularly valuable for targeting cancer cells lacking druggable mutations. BEACON models expression levels and dependency scores as bivariate Gaussians and employs Markov Chain Monte Carlo (MCMC) sampling to estimate the correlation coefficient between them. They then compute p-values followed by rigorous multiple testing correction (BH based FDR correction). A notable strength of their approach lies in the integration of mass spectrometry proteomics data alongside transcriptomic and perturbation screening data, enhancing the robustness of their findings. Their work highlights some key insights: - Gene expression-driven dependency (GED) candidates identified across lineages demonstrate enrichment for "DNA-binding transcription activator activity" and "DNA-binding transcription activator activity, RNA polymerase II-specific" pathways. - The analysis successfully identifies compelling candidates with robust signals in both GED and PED (FERMT2, GRHL2, KLF5, CDK6, and CCND1), which are well-supported by existing drug evidence or established literature - Clustering analyses reveal that cancer cells from pancreas and biliary tract tissues, as well as kidney and urinary tract tissue lineages, exhibit remarkably similar expression-driven dependency profiles. Additionally, lineage-specific genes such as transcription factors, cluster together in a manner consistent with existing literature - Through Fisher's exact test, the authors demonstrate significant enrichments of druggable gene lists from DrugBank with expression-driven dependency patterns at both proteomic and transcriptomic levels - Experimental validation shows that PAX5 is essential for PAX5-high B cell lymphoma cell growth, while TP63 and GRHL2 are essential for LSCC cell growth.

      However, I have several principal concerns about the study that should be addressed to demonstrate the robust and superior performance of this proposed approach.

      Major Comments:

      1.Quantitative benchmarking: While the authors present a valuable contribution, the concept of correlating gene dependency scores to expression has been explored previously through approaches like Project DRIVE (E. Robert McDonald, III et al.) and APSIC (Montazeri et al.). BEACON demonstrates strong correlations across multiple lineages, representing broader scope compared to existing methods that appear more lineage-restricted. However, establishing BEACON's comparative advantages requires more rigorous evaluation. Notably, Project DRIVE—a foundational paper in this field—already identified several BEACON candidates in their "Expression Correlation Analysis Identifies Oncogenes and Lineage-Specific Transcription Factors" section, while APSIC characterized many lineage-specific discoveries as tumor effector genes. BEACON's strength lies in integrating proteomic data with transcriptomic and perturbation screens, enabling identification of additional candidates like PAX5 for hematopoietic and lymphoid tissue. To demonstrate the method's impact, I recommend systematic quantitative benchmarking against existing approaches.

      Importantly, BEACON utilizes richer/complementary datasets than previous studies. Disentangling contributions of data richness versus methodological innovation would provide valuable insights into whether enhanced performance stems from improved data availability or genuine method improvements.

      Overall for benchmarking, the authors are strongly encouraged to utilize any comprehensive datasets that best demonstrate their method's competitive advantage and are not limited to the specific comparisons recommended above.

      2.Correlation method comparisons: Figure S2 shows that BEACON exhibits higher MSE at extremes, and the claimed advantage over Pearson for small sample sizes is difficult to quantify from the current visualization. While the theoretical expectation that BEACON should outperform Pearson in small samples is reasonable, the practical significance remains unclear from these simulations. I recommend demonstrating BEACON's advantage using real data by creating a curated list of established GEDs/PEDs and comparing performance between the two methods. This is particularly important since several of BEACON's hits were previously reported by Project DRIVE using simple Pearson correlations. Alternatively, if BEACON's advantage is indeed significant, please elaborate on the simulation results to better justify this claim with clearer quantitative metrics.

      3.Validation experiments: I'm seeking clarification on the validation experiments for TP63 and GRHL2. These candidates were not sensitive to predicted dependency and the authors say that "pan-lineage targets may represent universal vulnerability and their inhibition may lead to undesired off-target effects on other cells". Are the authors positioning them as weaker candidates to illustrate the superiority of lineage-specific predictions like PAX5? Additionally, why were different experimental approaches used—CRISPR for PAX5 versus shRNA for TP63 and GRHL2? For a method aimed at identifying druggable targets, would drug based experiments be more relevant than knockdown approaches to better demonstrate clinical applicability?

      Minor comments

      1. In Figure 4A, the caption refers to the plot as a heatmap, but the visualization appears to be a scatterplot. Please clarify whether the heatmap is missing or modify the caption appropriately. Additionally, I recommend using a different shade of green, as the current color choice makes some gene names difficult to read.
      2. In Fig S5A, please add a legend for tumor and normal
      3. For the TP63 and GRHL2 validation experiments, please include results for all four cell lines. The current manuscript is missing HCC15-shTP63, HCC15-shGRHL2, and HARA-shGRHL2 plots.
      4. How many replicates were the experiments performed on? Is it N= 3 for all experiments?
      5. Missing some text here - "BEACON offers the unique advantage of utilizing prior distributions that are less susceptible to outliers, especially in multiple lineages where the number of cell lines."
    2. AbstractCancer cells are heterogeneous, each harboring distinct molecular aberrations and are dependent on different genes for their survival and proliferation. While successful targeted therapies have been developed based on driver DNA mutations, many patient tumors lack druggable mutations and have limited treatment options. Here, we hypothesize that new precision oncology targets may be identified through “expression-driven dependency”, whereby cancer cells with high expression of a targeted gene are more vulnerable to the knockout of that gene. We introduce a Bayesian approach, BEACON, to identify such targets by jointly analyzing global transcriptomic and proteomic profiles with genetic dependency data of cancer cell lines across 17 tissue lineages. BEACON identifies known druggable genes, e.g., BCL2, ERBB2, EGFR, ESR1, MYC, while revealing new targets confirmed by both mRNA- and protein-expression driven dependency. Notably, the identified genes show an overall 3.8-fold enrichment for approved drug targets and enrich for druggable oncology targets by 7 to 10-fold. We experimentally validate that the depletion of GRHL2, TP63, and PAX5 effectively reduce tumor cell growth and survival in their dependent cells. Overall, we present the catalog of express-driven dependency targets as a resource for identifying novel therapeutic targets in precision oncology.

      This work has been peer reviewed in GigaScience (see https://doi.org/10.1093/gigascience/giag011), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

      Reviewer 4

      Reproducibility report for: Expression-Driven Genetic Dependency Reveals Targets for Precision Oncology Journal: Gigascience ID number/DOI: GIGA-D-25-00147 Reviewer(s): Laura Caquelin, Department of Clinical Neuroscience, Karolinska Institutet, Sweden


      1. Summary of the Study The authors developed a Bayesian method called BEACON to integrate multi-omics data. The method was tested on cancer cell lines across 17 tissue types to identify expression- driven dependencies. The method recovered known drug targets and identified novel candidates. The study concludes this method provides a systematic approach to identify precision oncology targets.

      1. Scope of reproducibility According to our assessment the primary objective is: to identify expression-driven dependencies across cancer cell lines from multiple lineages enabling the discovery of genes whose expression levels correlate with cancer cell dependency scores.
      2. Outcome: Identification of genes with significant expression-driven dependencies across pan-lineage cancer cell lines.
      3. Analysis method outcome: "BEACON calculated the Bayesian correlation between the gene's expressions and CERES cancer dependency scores 25 across the pan-lineage cell lines. BEACON modeled expression levels and dependency scores as the bivariate Gaussians and used Markov Chain Monte Carlo (MCMC) sampling to estimate the correlation coefficient rho between them. Given the null hypothesis that the uncorrelated expression and dependency of a gene has the 0 rho coefficient, we statistically tested each gene's rho estimate obtained from the MCMC simulation as follows. Assume that the MCMC sampling is carried out for a null gene's expression and dependency, then we expect that the distribution of the rho estimate accumulated over the MCMC iterations will be centered at zero. Based on this rationale, we computed the z-score of i-th gene as the deviation of the MCMC estimate of rho from the expected (null) value (i.e., zero) in terms of the standard deviation observed in the simulated distribution, i.e., z(i) = rhoMCMC(i) / SDMCMC(i). Since the z-values, by nature, follow a normal distribution with zero-mean and unit-variance, then we computed the p- value for each gene's rho estimate as the probability of observing a value as extreme as the computed z-value for that gene. We multi-testing corrected the resulting p-values using the BH procedure for FDR." (page 19 -Methods section / mRNA expression-driven dependency (GED))
      4. Main result: "We first analyzed the pan-lineage GED by using mRNA levels and the corresponding dependency scores from 854 cell lines with available data across 17 lineages and identified 244 genes showing significant association (correlation coefficient, rho < -0.25, FDR < 0.05)" (page 7 - Results section / Cancer vulnerability targets showing gene expression-driven dependency (GED))

      1. Availability of Materials a. Data
      2. Data availability: Open
      3. Data completeness: Complete, all data necessary to reproduce main results are available.
      4. Access Method: Repository
      5. Repository: https://doi.org/10.6084/m9.figshare.19700056.v2 -Data quality: Structured

      b. Code - Code availability: Open - Programming Language(s): R - Repository link: https://github.com/Huang-lab/BEACON - License: MIT license - Repository status: Public - Documentation: Readme file


      1. Computational environment of reproduction analysis
      2. Operating system for reproduction: MacOS 15.5
      3. Programming Language(s): R
      4. Code implementation approach: Using shared code
      5. Version environment for reproduction: R version 4.5.0/RStudio 2025.05.1

      1. Results 5.1 Original study results
      2. Results 1: Supplementary table S2 5.2 Steps for reproduction -> Run the code PanLineageMCMC.R
      3. Issue 1: File import paths and incorrect file name -- Resolved: In the original code, there were fixed file paths that only worked on one specific computer. This caused problems when running the code on other computers. To fix this, I recommended to use relative paths, which are based on where the script is located. This way, the code can be run on any computer without needing to change the paths each time.

      ------------------ Start of script ------------------ sam.dep = read.csv(file.path(getwd(), "DepMap_data", "sample_info.csv")) ------------------- End of script -------------------

      • Issue 2: Missing function "intsect" at line 162 -- Resolved: The script called a function intsect that was not defined, leading to an error. Upon request, the authors provided the missing function and added it to the main script (PanLineageMCMC.R).

      • Issue 3: Output directory not created. -- Resolved: The script attempted to write output files to a directory that was not created beforehand. This caused errors during the loop execution when trying to save results. A directory check and automatic creation script was added. If the output folder does not exist, it is now created automatically before the loop runs.

      ------------------ Start of script ------------------ dir_path <- paste0('../out/jags.nadapt',n.adapt,'.update',n.update,'.mcmc ',n.iter,'.simulation_SD_22Q2') if (!dir.exists(dir_path)) { dir.create(dir_path, recursive = TRUE) } ------------------- End of script -------------------

      5.3 Statistical comparison Original vs Reproduced results - Results: Table.mRNA.dependency.Bayesian.pancancer file attached - Comments: The Bayesian PanCancer analysis was re-run, but only on the 244 significant genes listed in Supplementary Table S2, not on the full set of 17 285 genes. This choice was made due to limited computational resources, as running the full model would have required an estimated 100 hours. - Errors detected: - - Statistical Consistency: Among the 244 significant genes originally reported, the reproduced analysis confirmed the statistical significance of these same genes. However, the exact numerical values (Mean, standard deviation, Z value, P-value and adjusted P-value) differed slightly. These discrepancies are expected due to the nature of Bayesian inference, the absence of a random seed, and the relatively low number of MCMC iterations used (n.iter = 500). These settings may not be sufficient to ensure full convergence or reproducibility of posterior estimates and should be interpreted with caution. We were unable to compare the rho values because they were not available in the provided Supplementary table S2, nor extracted in the R code to be include in the resulting output files.


      1. Conclusion
      2. Summary of the computational reproducibility review The results of the Supplementary table S2 in the original study was partially reproduced. We were able to confirm the statistical significance of the 244 genes reported in Supplementary Table S2 using the Bayesian PanCancer model in the provided code. However, the numerical results were not always identical. This is expected because Bayesian methods involve random sampling, the original code did not set a fixed random seed, and the number of iterations used was relatively low. Furthermore, the rho values were not available for comparison, limiting a full reproducibility assessment. Several technical issues were also fixed during the reproduction process, such as hardcoded file paths, a missing function, and the absence of output directories, which were resolved to allow the code to run correctly on a different system. Due to computational limitations, running the full model on all 17,285 genes was not performed.

      3. Recommendations for authors While the original analysis code was successfully used to confirm the statistical significance of the 244 genes, we recommend several improvements to enhance reproducibility: -- Code annotation: Adding more detailed comments within the scripts would help users understand the logic behind each step and the purpose of specific commands or operations. -- Set a random seed: Include set.seed() in all scripts to improve reproducibility across different runs. -- Specify R and package versions: Provide the R version and exact package versions needed to run the code, via a requirements file for example. -- Use relative file paths: Ensure that all necessary folders and functions are created or included by default to avoid path issues. -- Increase MCMC robustness: Use a higher number of iterations and appropriate parameter settings to ensure better convergence and stability of posterior estimates. -- Inform users about computation time: Clearly indicate in the README or publication the expected runtime of the code, especially if it requires several hours or days to complete.

    3. AbstractCancer cells are heterogeneous, each harboring distinct molecular aberrations and are dependent on different genes for their survival and proliferation. While successful targeted therapies have been developed based on driver DNA mutations, many patient tumors lack druggable mutations and have limited treatment options. Here, we hypothesize that new precision oncology targets may be identified through “expression-driven dependency”, whereby cancer cells with high expression of a targeted gene are more vulnerable to the knockout of that gene. We introduce a Bayesian approach, BEACON, to identify such targets by jointly analyzing global transcriptomic and proteomic profiles with genetic dependency data of cancer cell lines across 17 tissue lineages. BEACON identifies known druggable genes, e.g., BCL2, ERBB2, EGFR, ESR1, MYC, while revealing new targets confirmed by both mRNA- and protein-expression driven dependency. Notably, the identified genes show an overall 3.8-fold enrichment for approved drug targets and enrich for druggable oncology targets by 7 to 10-fold. We experimentally validate that the depletion of GRHL2, TP63, and PAX5 effectively reduce tumor cell growth and survival in their dependent cells. Overall, we present the catalog of express-driven dependency targets as a resource for identifying novel therapeutic targets in precision oncology.

      This work has been peer reviewed in GigaScience (see https://doi.org/10.1093/gigascience/giag011), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

      Reviewer 3

      The authors develop a method for correlating gene and protein expression with cellular dependencies using the resources of DepMap. The innovation appears to be a Bayesian approach to the correlation analysis. They use this approach to identify potential therapeutic targets and evaluate some top candidates using in vitro experiments. The paper is fairly straightforward to follow.

      Major comments:

      1. Benchmarking - given the non-linear relationships shown in Fig 2, is a comparison with the Pearson method the most appropriate? Would a Spearman's be better?

      2. The analysis identifies dependencies that are proposed as therapeutic targets, however while the proteins can be druggable, what about normal tissue effects? Some of these are likely lineage-defining proteins that could be highly expressed in normal tissues. Is is notable that in Fig 5B, C that the existing drug targets have a lower association strength than other GEDs identified. Does this suggest that the strongest correlations might be lineage-crucial genes that are too important for normal tissue function to make good drug targets? This needs further consideration in the discussion. Are there any pathways differences between these groups (known drug targets vs others)? For example you might expect more tissue lineage Tfs in the "other" category, while the approved drug targets perhaps more cell surface receptors.

      3. The cell assays performed should effectively be replicating the results of the dependencies on which BEACON is based (DepMap), so why do you get different results? Is it because of the different methods used ie shRNA (not seeing the correlation between expression and dependency) vs CRISPR (replicating the correlation)? If you look at older DepMap scores when they used knockdown rather than CRISPR can you replicate your results?

      4. Although mycoplasma testing was done, were the cell lines re-authenticated by STR profiling at any point?

      5. QPCR is mentioned n the methods but not provided in the results that I can find. Did this validate gene knockdown by shRNA? Any correlation between % KD and proliferation/colony forming effect?

      6. In the discussion it should be acknowledged that cancer subtypes exist within lineages that are molecularly and clinically distinct and so the method might be missing targets specific for these eg ER+ and ER- breast cancer.

      Minor comments: 1. Results para 1 "especially in multiple lineages where the number of cell lines." Missing something in this sentence?

      1. Needs some grammar review

      3, Please italicise all gene names (when referring to gene, not protein) eg CCNE1 amplification etc

      1. Fig S5A - legend or axis labels for N and T needed.
      2. Fig S5C, D - these are proliferation not colony forming assays as stated in the text.

      3. Please include number of replicates and type of error bars in figure legends for cell assays

    4. AbstractCancer cells are heterogeneous, each harboring distinct molecular aberrations and are dependent on different genes for their survival and proliferation. While successful targeted therapies have been developed based on driver DNA mutations, many patient tumors lack druggable mutations and have limited treatment options. Here, we hypothesize that new precision oncology targets may be identified through “expression-driven dependency”, whereby cancer cells with high expression of a targeted gene are more vulnerable to the knockout of that gene. We introduce a Bayesian approach, BEACON, to identify such targets by jointly analyzing global transcriptomic and proteomic profiles with genetic dependency data of cancer cell lines across 17 tissue lineages. BEACON identifies known druggable genes, e.g., BCL2, ERBB2, EGFR, ESR1, MYC, while revealing new targets confirmed by both mRNA- and protein-expression driven dependency. Notably, the identified genes show an overall 3.8-fold enrichment for approved drug targets and enrich for druggable oncology targets by 7 to 10-fold. We experimentally validate that the depletion of GRHL2, TP63, and PAX5 effectively reduce tumor cell growth and survival in their dependent cells. Overall, we present the catalog of express-driven dependency targets as a resource for identifying novel therapeutic targets in precision oncology.

      This work has been peer reviewed in GigaScience (see https://doi.org/10.1093/gigascience/giag011), which carries out open, named peer-review. These reviews are published under a CC-BY 4.0 license and were as follows:

      Reviewer 1

      The authors present BEACON, a method for identifying associations between the expression of a gene and sensitivity to the CRISPR knockout of that gene across a panel of cancer cell lines. These 'oncogene like' dependencies represent potential therapeutic targets that might be exploited for the development of new precision medicines in cancer. The issue that BEACON aims to address is the limited sample size (cell line count) in some specific cancer lineages and experimental noise that might result in spurious correlations between expression and CRISPR sensitivity. The authors demonstrate, using a modelling approach, that BEACON is more reliable for estimating correlation than simple Pearson's correlation when there is high-noise in the measurements. The majority of the manuscript focuses on analyses of dependencies systematically identified using the BEACON approach and their enrichment in drug targets and biological pathways. There is some experimental testing of three potential expression driven dependencies presented. The rationale for the overall approach and analyses are clear.

      Major comments

      • Previous efforts have systematically associated gene/protein expression with CRISPR sensitivity across the same or related datasets (e.g. Pacini et al, Cancer Cell 2024 and Rohde et al, Molecular Systems Biology 2025 using CRISPR; McDonald et al, Cell 2017 and Tsherniak et al, Cell 2017 using RNAi) and so the primary contribution of this paper can be considered the development of the BEACON method. It is thus somewhat surprising that there is no real assessment of the improvements offered by BEACON when compared to simpler methods (Pearson correlation, Spearman correlation) or more more complex recent approaches (Rohde et al's BACON approach). The modelling approach suggests some improvements in specific circumstances (especially high noise) but it is not clear that this leads to improved dependency identification in the real data. Does BEACON identify known oncogene addictions better than these methods? Are the associations identified more reproducible (e.g. across alternative CRISPR screens or RNAi screens)?

      • The experimental validation and the conclusions drawn from it are somewhat confusing. The authors assess three potential expression associated dependencies - two pan-cancer dependencies (GRHL2 and TP63) and one lineage specific dependency (PAX5 in myeloid cells). Only the lineage-specific dependency validated in the way that might be expected, with higher expression associated with increased dependency, leading the authors to conclude that lineage-specific dependencies may be more suitable targets than pan-cancer ones. Given the numbers analysed (3 genes) this suggestion is not well supported. Moreover the perturbation was performed using distinct approaches - CRISPR for PAX5 and shRNA for the other two genes - and only the knockdown of PAX5 was validated by Western blot. It is very hard to know what phenotypes might be a false positive from off-target shRNA effects or false-negatives from variable shRNA knockdown of the target. The results in S5C suggest that the two shRNAs for each gene cause somewhat discordant phenotypes, suggesting there may be some issues with knockdown efficiency. This could potentially be addressed by adding additional shRNAs for GRHL2 / TP63 or testing them using CRISPR perturbation as was done for PAX5. Validation of the knockdown of the intended target could also shed some light here. The manuscript also mentions experiments in an additional cell line (HCC15) but I cannot see these results presented in the main figures or supplement. It would be useful if all results for these two genes were presented in a single figure, with high and low expressing cell lines clearly marked,

      Minor:

      • Previous work has established that in some cases lower expression of a gene can make cells more vulnerable to its perturbation (CYCLOPS genes, Nijhawan et al, Cell 2012). While these are not the focus of this manuscript, it would be useful for the authors to comment on the utility of BEACON for their identification.

      • p14 "Moreover, GED/PED targets were depleted of genes that were Essential In Culture" - it's not clear what this means or where the data comes from. By definition the gene set analysed are at least somewhat essential in culture

    1. NOTA: Cada selección correcta vale un punto.

      1.- Devuelva el estado más reciente del paciente.

      2.- Devuelva los datos de supervisión de la salud que no estén retrasados más de una versión.

      3.- Después de que el paciente sea dado de alta y se hayan evaluado todos los cargos, recupere los datos de facturación correctos con los cargos finales.

    2. NOTA: Cada respuesta correcta vale un punto.

      1.- El código registrará la hora en la que el pedido fue procesado desde la cola.

      2.- Cuando la función ProcessOrders falla, la función se reintentará hasta cinco veces para un pedido determinado, incluyendo el primer intento.

      3.- Cuando hay varios pedidos en la cola, se recuperará un lote de pedidos desde la cola y la función ProcessOrders ejecutará múltiples instancias de forma concurrente para procesar los pedidos.

      4.- La función ProcessOrders enviará el pedido como salida a una tabla Orders en Azure Table Storage.

    1. So, at some point between about ten thousand years ago and about seven thousand years ago, there seems to have been a gradual shift in which some people in relatively abundant regions such as river valleys began first cultivating food plants near their camps of villages, and then in several regions began altering the plants to make them more productive.

      before said times what did people do when they needed certain resources and couldn't get them.

    2. The native cultures of the Northeastern woodlands were generally egalitarian. They weren't necessarily peaceful: bands or tribes often fought each other. But they also incorporated captives into their societies, choosing between either killing captives immediately or adopting them as full members of their bands.

      I believe its interesting that if they dint kill the people they adopted them how would them chose which member was viable and which member wasn't

    1. he most important parts of the Constitution that establish the relationship between states and the national government.

      most important parts of constitution dealing with relationship between states and national government

    1. The other widely used citation scheme was more dependent on punched card format. In this scheme, often called "fixed format", every line began with a coded sequence of characters giving citation information. Each unit within the citation was positioned in specific columns across the line, for example the title in columns 1–3, verse number in columns 5–6, and line number in columns 7–9. The entry of this information was speeded up by functions on the punched card machine, but the information also occupied more space within the computer file.

      Like I said before, this feels so cryptic and difficult in comparison to what we have today.

    1. The paper's idea is interesting, but there are some notes that should be handled by the authors: 1- sub-section 1.2 is not required. 2- Figure 2 is not clear at all. 3- Proofreading for the whole article is required.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      We thank the reviewers and editors for their careful evaluation of our manuscript and their positive comments on the importance and rigor of the work. Below you will find our point-by-point response to each reviewer's suggestions. We believe that we have addressed (in the response and the revised manuscript) all of the concerns. Please note that in some cases, we have numbered a reviewer's comments for clarity, however beyond this, we have not altered any of the reviewers' text.

      Reviewer #1 (Evidence, reproducibility and clarity (Required)):

      Lo et al., report a high-throughput functional profiling study on the gene encoding for argininosuccinate synthase (ASS1), done in a yeast experimental system. The study design is robust (see lines 141-143, main text, Methods), whereby "approximately three to four independent transformants of each variant would be isolated and assayed." (lines 140 - 141, main text, Methods). Such a manner of analysis will allow for uncertainty of the functional readout for the tested variants to be accounted for.

      This is an outstanding study providing insights on the functional landscape of ASS1. Functionally impaired ASS1 may cause citrullinemia type I, and disease severity varies according to the degree of enzyme impairment (line 30, main text; Abstract). Data from this study forms a valuable resource in allowing for functional interpretation of protein-altering ASS1 variants that could be newly identified from large-scale whole-genome sequencing efforts done in biobanks or national precision medicine programs. I have some suggestions for the Authors to consider:

      1. The specific function of ASS1 is to condense L-citrulline and L-aspartate to form argininosuccinate. Instead of measuring either depletion of substrate or formation of product, the Authors elected to study 'growth' of the yeast cells. This is a broader phenotype which could be determined by other factors outside of ASS1. Whereas i agree that the experiments were beautifully done, the selection of an indirect phenotype such as ability of the yeast cells to grow could be more vigorously discussed.

      We appreciate the reviewer's point regarding the indirect nature of growth as a functional readout. In our system, yeast growth is tightly and specifically coupled to ASS enzymatic activity. The strains used are isogenic and lack the native yeast argininosuccinate synthetase, such that arginine biosynthesis, and therefore yeast replication on minimal medium lacking arginine, depends exclusively on the activity of human ASS1. Under these defined and limiting conditions, growth provides a quantitative proxy for ASS1 function. However, we acknowledge that this assay does not resolve specific molecular mechanisms underlying reduced function, such as altered catalytic activity versus effects on protein stability. We have updated the text to clarify these points.

      "While growth is an indirect phenotype relative to direct measurement of substrate turnover or product formation, it is tightly coupled to ASS enzymatic activity in this system and is expected to be impaired by amino acid substitutions that reduce catalytic activity or protein stability. Therefore, growth on minimal medium lacking arginine is a quantitative measure of ASS enzyme function, allowing the impact of ASS1 missense variants to be assessed at scale through a high-throughput growth assay, in a single isogenic strain background, under controlled, defined conditions that limit confounding factors unrelated to ASS1 activity. We expect that the assay will detect reductions in both catalytic activity and protein stability but will not distinguish between these mechanisms."

      1. One of the key reasons why studies such as this one are valuable is due to the limitations of current variant classification methods that rely on 'conservation' status of amino acid residues to predict which variants might be 'pathogenic' and which variants might be 'likely benign'. However, there are serious limitations, and Figures 2 and 6 in the main text shows this clearly. Specifically, there is an appreciable number of variants that, despite being classified as "ClinVar Pathogenic", were shown by the assay to unlikely be functionally impaired. This should be discussed vigorously. Could these inconsistencies be potentially due to the read out (growth instead of a more direct evaluation of ASS1 function)?

      We interpret this discrepancy as reflecting a sensitivity limitation of the growth-based readout rather than a fundamental disagreement between functional effect and clinical annotation. Specifically, we believe that our assay is unable to resolve the very mildest hypomorphic variants from true wild type, i.e., the residual activity of these variants is sufficient to fully support yeast growth under the conditions used. On this basis, we have chosen not to treat wild-type-like growth in our assay as informative for benignity; conversely, reduced growth provides evidence supporting pathogenicity (all clinically validated variants examined in this range are pathogenic).

      We have revised the manuscript to clarify this point explicitly and to frame these variants as lying outside the effective resolution limit of the assay rather than representing true false positives. Additional discussion of this limitation and its implications is provided in our responses to Reviewer 2 (points 1 and 4) along with specific changes made to the text.

      1. Figure 3 is very interesting, showing a continuum of functional readout ranging from 'wild-type' to 'null'. It is very interesting that the Authors used a threshold of less than 0.85 as functionally hypomorphic. What does this mean? It would be very nice if they have data from patients carrying two hypomorphic ASS1 alleles, and correlate their functional readout with severity of clinical presentation. The reader might be curious as to the clinical presentation of individuals carrying, for example, two ASS1 alleles with normalized growth of 0.7 to 0.8.

      I hope you will find these suggestions helpful.

      We thank the reviewer for this thoughtful comment. Figure 3 indeed illustrates a continuum of functional effects, and we agree that careful interpretation of the thresholds used is important. To clarify the rationale for the hypomorphic threshold, the interpretation of intermediate growth values, and to emphasize that these labels reflect only behavior in the functional assay, we have rewritten the relevant section of the Results:

      "The normalized growth scores of the 2,193 variants tested in our functional assay form a clear bimodal distribution (Figure 3), with two distinct peaks corresponding to functional extremes, as is commonly reported in large-scale functional assays of protein function [9, 10]. The smaller peak, centered around the null control (normalized growth = 0), represents variants that fail to support growth in the assay (growth 0.85). Variants with growth values falling between these two peak-based thresholds display partial functional impairment and are classified as functionally hypomorphic (n = 323). Crucially, these classifications are entirely derived from the observed peaks in the distribution of growth values and reflect differences in functional activity under the assay conditions. They do not provide direct evidence for clinical pathogenicity or benignity and should not be used for clinical variant interpretation without proper benchmarking against clinical reference datasets, as implemented below within an OddsPath framework."

      We agree with the reviewer that correlating functional measurements with clinical severity in individuals carrying two hypomorphic ASS1 alleles would be highly informative, particularly given that ASS1 deficiency is an autosomal recessive disorder. While mild hypomorphic variants (for example, variants with normalized growth values of 0.7-0.8 in our assay) could plausibly contribute to disease when paired with a complete loss-of-function allele, systematic analysis of combinatorial genotype effects and genotype-phenotype correlations is beyond the scope of the present study, which focuses on the functional effects of individual variants. We view this as an important direction for future work.

      Reviewer #1 (Significance (Required)):

      This is an outstanding study providing insights on the functional landscape of ASS1. Functionally impaired ASS1 may cause citrullinemia type I, and disease severity varies according to the degree of enzyme impairment (line 30, main text; Abstract). Data from this study forms a valuable resource in allowing for functional interpretation of protein-altering ASS1 variants that could be newly identified from large-scale whole-genome sequencing efforts done in biobanks or national precision medicine programs.

      Reviewer #2 (Evidence, reproducibility and clarity (Required)):

      In this manuscript, Lo et al characterize the phenotypic effect of ~90% of all possible ASS1 missense mutations using an elegant yeast-based system, and use this dataset to aid the interpretation of clinical ASS1 variants. Overall, the manuscript is well-written and the experimental data are interpretated rigorously. Of particular interest is the identification of pairs of deleterious alleles that rescue ASS1 activity in trans. My comments mainly pertain to the relevance of using a yeast screening methodology to infer functional effects of human ASS1 mutations.

      1. Since human ASS1 is heterologously expressed in yeast for this mutational screen, direct comparison of native expression levels between human cells and yeast is not possible. Could the expression level of human ASS1 (driven by the pARG1 promoter) in yeast alter the measured fitness defect of each variant? For instance, if ASS1 expression in yeast is sufficiently high to mask modest reductions in catalytic activity, such variants may be misclassified as hypomorphic rather than amorphic. Conversely, if expression is intrinsically low, even mild catalytic impairments could appear deleterious. While it is helpful that the authors used non-human primate SNV data to calibrate their assay, experiments could be performed to directly address this possibility.

      The nature of the relationship between yeast growth and availability of functional ASS1 could also influence the interpretation of results from the yeast-based screen. Does yeast growth scale proportionately with ASS1 enzymatic activity?

      We completely agree that the expression level of human ASS1 in yeast could influence the measured fitness effects of individual variants. We expect the rank ordering of variants in our growth assay to reflect their relative enzymatic activity (i.e. a monotonic relationship) but acknowledge that the precise mapping between activity and growth is unknown and may include ceiling and floor effects that limit the assay's dynamic range. As the reviewer notes, under high expression conditions moderate loss-of-function variants could appear indistinguishable from wild type (ceiling effect), whereas under lower expression the same variants could behave closer to the null control (floor effect).

      In our system, ASS1 is expressed from the pARG1 promoter, chosen under the assumption that the native expression level of ARG1 (the yeast ASS1 ortholog) is appropriately tuned for yeast growth. Crucially, rather than assuming a fixed mapping from assay growth to clinical pathogenicity (given potential nonlinearities in the relationship between ASS function and growth) we benchmark the assay against external data, including known pathogenic and benign variants and non-human primate SNVs, to calibrate thresholds and guide interpretation within an OddsPath framework. This benchmarking indicates that ceiling effects are likely present, with some mild loss-of-function pathogenic variants appearing indistinguishable from wild type in the growth assay. We explicitly account for this by not using high-growth scores as evidence toward benignity. We have made the following changes the manuscript:

      "A subset of clinically pathogenic ASS1 variants exhibit near-wild-type growth in our yeast assay. In general, we expect a monotonic relationship between ASS function and yeast growth, but with the potential for floor and ceiling effects that constrain the assay's dynamic range. In this context, we interpret high-growth pathogenic variants as likely causing mild loss of function that cannot be distinguished from wild type in our assay"

      "Based on these findings and given that 22/56 pathogenic variants show >85% growth, we conclude that growth above this threshold should not be used as evidence toward benignity."

      1. It would be helpful to add an additional diagram to Figure 1A explaining how the screen was performed, in particular: when genotype and phenotype were measured, relative to plating on selective vs non-selective media? This is described in "Variant library sequence confirmation" and "Measuring the growth of individual isolates" of the Methods section but could also be distilled into a diagram.

      We thank the reviewer for this helpful suggestion. We have updated Figure 1 by adding a new schematic panel (Figure 1C) that distills the experimental workflow into a visual overview. This diagram is intended to complement the detailed descriptions in the Methods and improve clarity for the reader.

      1. The authors rationalize the biochemical consequences of ASS1 mutations in the context of ASS1 per se - for example, mutations in the active site pocket impair substrate binding and therefore catalytic activity, which is expected. Does ASS1 physically interact with other proteins in human cells, and could these interactions be altered in the presence of specific ASS1 mutations? Such effects may not be captured by performing mutational scanning in yeast.

      We are not aware of any specific protein-protein interactions involving ASS that are required for its enzymatic function. However, we agree that ASS could engage in non-essential interactions with other human proteins that might be altered by specific missense variants and that such interactions would not necessarily be captured in a yeast-based assay.

      Importantly, our complementation system depends on human ASS providing the essential enzymatic activity required for arginine biosynthesis in yeast. If ASS1 required obligate human-specific protein interactions to function, even the wild-type enzyme would fail to support yeast growth, which is clearly not the case. We therefore conclude that the assay robustly reports on the intrinsic enzymatic activity of ASS, while acknowledging that non-essential human-specific interactions may not be assessed. We have updated the manuscript to reflect this point.

      "Importantly, successful functional complementation indicates that ASS enzymatic activity does not depend on any obligate human-specific protein interactions."

      1. The authors note that only a small number (2/11) of mutations at the ASS1 monomer-monomer interface lead to growth defects in yeast. It would be helpful for the authors to discuss this further.

      As discussed in response to the reviewer's comments on the relationship between ASS activity and yeast growth (point 1 above), we expect growth to be a monotonic but nonlinear function of enzymatic activity, with potential ceiling effects at high activity. Under this model, variants causing weak or moderate loss of function may remain indistinguishable from wild type when residual activity is sufficient to support normal growth. We favor this explanation for the observation that only 2/11 interface variants show reduced growth, as many pathogenic interface substitutions are associated with milder disease presentations, consistent with higher residual enzyme function. Consistent with this interpretation, variants affecting the active site, where substitutions are expected to cause large reductions in catalytic activity, are readily detected by the assay.

      Although we cannot exclude partial buffering of dimerization defects in yeast, we interpret the reduced sensitivity to interface variants primarily as a general limitation of growth-based assays. Accordingly, our decision not to use growth >85% as evidence toward benignity is conservative relative to approaches that would classify high-growth variants as benign except at the monomer-monomer interface, avoiding reliance on structural subclassification and minimizing the risk of false benign interpretation. Reduced growth, by contrast, provides strong evidence of loss of ASS1 function and pathogenicity, validated under the OddsPath framework.

      We have updated the Results and Discussion sections to clarify these points (also see response to the reviewer's point 1).

      "A subset of clinically pathogenic ASS1 variants exhibit near-wild-type growth in our yeast assay. In general, we expect a monotonic relationship between ASS function and yeast growth, but with the potential for floor and ceiling effects that constrain the assay's dynamic range. In this context, we interpret high-growth pathogenic variants as likely causing mild loss of function that cannot be distinguished from wild type in our assay. Consistent with this view, many pathogenic variants with high assay growth are located at the monomer-monomer interface rather than the active site, and are associated with milder or later-onset clinical presentations, suggesting partial enzymatic impairment that is clinically relevant in humans but not resolved by the yeast assay."

      "Based on these findings and given that 22/56 pathogenic variants show >85% growth, we conclude that growth above this threshold should not be used as evidence toward benignity. Notably, this approach is conservative relative to treating high-growth variants as benign except at the monomer-monomer interface, avoiding reliance on structural subclassification and minimizing the risk of false benign interpretation arising from assay ceiling effects. Conversely, the variants with

      Reviewer #2 (Significance (Required)):

      This study presents the first comprehensive mutational profiling of human ASS1 and would be of broad interest to clinical geneticists as well as those seeking biochemical insights into the enzymology of ASS1. The authors' use of a yeast system to profile human mutations would be particularly useful for researchers performing deep mutational scans, given that it provides functional insights in a rapid and inexpensive manner.

      Reviewer #3 (Evidence, reproducibility and clarity (Required)):

      Section 1 - Evidence, reproducibility, and clarity Summary This manuscript presents a comprehensive functional profiling of 2,193 ASS1 missense variants using a yeast complementation assay, providing valuable data for variant interpretation in the rare disease citrullinemia type I. The dataset is extensive, technically sound, and clinically relevant. The demonstration of intragenic complementation in ASS1 is novel and conceptually important. Overall, the study represents a substantial contribution to functional genomics and rare disease variant interpretation.

      Major comments 1. This is an exciting paper as it can provide support to clinicians to make actionable decisions when diagnosing infants. I have a few major comments, but I want to emphasize the label of "functionally unimpaired" variants to be misleading. The authors explain that there are several pathogenic ClinVar variants that fall into this category (above the >.85 growth threshold) but I think this category needs a more specific name and I would ask the authors to reiterate the shortcomings of the assay again in the Discussion section.

      We thank the reviewer for raising this important point. We agree that the label "functionally unimpaired" could be misleading if interpreted as implying clinical benignity rather than assay behavior. We have therefore clarified that this designation refers strictly to variant behavior in the yeast growth assay and does not imply absence of pathogenicity.

      In addition, we have expanded the Discussion to explicitly address the existence of clinically pathogenic variants with high growth scores (>0.85), emphasizing that these likely reflect a ceiling effect of the assay and represent a key limitation for interpretation. This clarification reiterates that high-growth scores should not be used as evidence toward benignity, while reduced growth provides strong functional evidence of pathogenicity. Relevant revisions are described in our responses to Reviewers 1 and 2.

      1. I think there's an important discussion to be had here, is the assay detecting variants that alter the function of ASS or is it detecting a complete ablation of enzymatic activity? The results might be strengthened with a follow-up experiment that identifies stably expressed ASS1 variants.

      We agree with the review that distinguishing between stability and enzyme activity would be valuable information. Unfortunately, we do not currently have the resources to perform this type of large-scale study. We have acknowledged in the text that our assay does not distinguish between enzyme activity and protein stability:

      "We expect that the assay will detect reductions in both catalytic activity and protein stability, but will not distinguish between these mechanisms."

      At the very least, it would be great to see the authors replicate some of their interesting results from the high-throughput screen by down-selecting to ~12 variants of uncertain significance that could be newly considered pathogenic.

      We have included new analysis of all 25 VUS variants falling in the pathogenic range of our assay (Supplemental Table S7). Reclassification under current guidelines (in the absence of our data) shifts six variants to Pathogenic/Likely Pathogenic and 11 more are reclassified to Likely Pathogenic with the application of our functional data as PS3_Supporting. The remaining eight VUS are all reclassified to Likely Pathogenic when inclusion of homozygous PrimateAI-benign variants allows the assay to satisfy full PS3 criteria.

      1. I would ask the authors to provide more citations of the literature in the introduction of the manuscript. I would be especially interested in knowing more about human ASS being identified as a homolog of yeast ARG1, as they share little sequence similarity (27.5%) at the protein level. That said, I find the yeast complementation assay exciting.

      We thank the reviewer for this suggestion. Human ASS and yeast Arg1 catalyze the same biochemical reaction and share approximately 49% amino acid sequence identity. We have revised the Introduction to clarify this relationship and to note explicitly that the Saccharomyces Genome Database (SGD) identifies the human gene encoding argininosuccinate synthase (ASS1) as the ortholog of yeast ARG1. An appropriate citation has been added to support this statement. The protein alignments have been provided as File S2.

      "This assay is based on the ability of human ASS to functionally replace (complement) its yeast ortholog (Arg1) in S. cerevisiae (Saccharomyces Genome Database, 2026). Importantly, successful functional complementation indicates that ASS enzymatic activity does not depend on any obligate human-specific protein interactions. At the protein level, human ASS and yeast Arg1 display 49% sequence identity (File S2) and share identical enzymatic roles in converting citrulline and aspartate into argininisuccinate."

      1. I appreciate the efforts made by the authors to share their work and make this study more reproducible, such as sharing the hASS1 and yASS1 plasmids being shared on NCBI Genbank (Line 121) and publishing the ONT reads on SRA (Line 154). I made a requests for additional data to be shared, such as the custom method/code for codon optimization and a table of Twist variant cassettes that were ordered. I would also love to see these results shared on MaveDB.org.

      We thank the reviewer for these suggestions regarding data sharing and reproducibility. As requested, we have provided the custom codon optimization script as File S1 and the amino acid alignment used to perform codon harmonization as File S2. The sequence of the underlying variant cassette is included in the corresponding GenBank entry, and we have clarified this point in the legend of Figure 1. For each amino acid substitution, Twist Bioscience used a yeast-specific codon scheme with a single consistent codon per amino acid; accordingly, the sequence of each variant cassette can be inferred from the base construct and the specified amino acid change. A complete list of variant amino acid substitutions used in this study is provided in Table S3.

      1. I find this manuscript very exciting as the authors have a compelling assay that identifies pathogenic variants, but I was generally disappointed by the quality and organization of the figures. For example, Figure 4 provides very little insight, but could be dramatically improved with an overlay of the normalized growth score data or highlighting variants surrounding the substrate or ATP interfaces. There are some very interesting aspects of this manuscript that could be shine through with some polished figures.

      We thank the reviewer for this feedback and agree that clear and well-organized figures are essential for conveying the key results of the study. In response, we have substantially revised Figure 4 by adding colored overlays showing residue conservation and median normalized growth scores (new panels Figure 4C and 4D), which more directly link structural context to functional outcomes and highlight patterns surrounding the active site and substrate interfaces.

      I would also encourage the authors to generate a heatmap of the data represented in Figure 2 (see Fowler and Fields 2014 PMID 25075907, Figure 2), this would be more helpful reference to the readers.

      The reviewer also suggested that a heatmap representation, similar to that used in Fowler and Fields (2014), might aid interpretation of the data shown in Figure 2. Because our dataset consists of sparse single-amino acid substitutions rather than a complete mutational scan, such heatmaps are inherently less dense and less effective at conveying patterns than in saturation mutagenesis studies. Nevertheless, to aid readers who may find this visualization useful, we have generated and included a single-nucleotide variant heatmap as Supplemental Figure S1.

      My major comments are as follows: 6. Citations needed - especially in the introduction and for establishing that hASS is a homolog of yARG1

      We have added the requested citations and clarified the ASS1-ARG1 orthology in the Introduction, as described in our response to point 3 above.

      1. Generally, the authors do a nice job distinguishing the ASS1 gene from the ASS enzyme, though I found some ambiguities (Line 685). Please double-check the use of each throughout the manuscript.

      We have edited the manuscript to ensure consistent and unambiguous use of gene and enzyme nomenclature throughout.

      1. Generally, I'm confused about what strain was used for integrating all these variants, was is the arg1 knock-out strain from the yeast knockout collection or was it FY4? I think FY4 was used for the preliminary experiments, then the KO collection strain was used for making the variant library but I think this could be made more clear in the text and figures. Lines 226-229 describes introducing the hASS1 and yASS1 sequences into the native ARG1 locus in strain FY4, but the Fig1A image depicts the ASS1 variants going into arg1 KO locus. Fig1A should be moved to Fig2.

      We agree that the strain construction steps were not described as clearly as they could have been. We have therefore clarified the strain construction workflow in the Materials & Methods and Results sections, as well as in the Figure 1 legend, to explicitly distinguish preliminary experiments performed in strain FY4 from construction of the variant library in the arg1 knockout background.

      As we have also added an additional panel to Figure 1 that schematically explains how the screen was performed (per Reviewer #2's request), we believe that Figure 1A is appropriately placed and should remain in Figure 1.

      1. Line 303 - "We classify these variants as 'functionally unimpaired'", this is not an accurate description of these variants as Figure 2 highlights 24 pathogenic ClinVar variants that would fall into this category of "functionally unimpaired". The yeast growth assay appears to capture pathogenic variants, but there is likely some nuance of human ASS functionality that is not being assessed here. I would make the language more specific, e.g. "complementary to Arg1" or "growth-compatible".

      We agree that the label "functionally unimpaired" could be misinterpreted if read as implying clinical benignity. We have therefore clarified within the manuscript that this designation refers strictly to variant behavior in the yeast growth assay (i.e., wild-type-like growth under assay conditions) and does not imply absence of pathogenicity. We also expanded the Discussion to explicitly address the subset of clinically pathogenic variants with high growth scores (>0.85), consistent with a ceiling effect of the assay and a key limitation for interpretation. See response to reviewer #3 point 1. Relevant revisions are also discussed in our responses to Reviewers #1 and #2.

      1. Lines 345-355 - It is interesting that there are variants that appear functional at the substrate interfacing sites. Is there anything common across these variants? Are they maintaining the polarity or hydrophobicity of the WT residue? Are any of these variants included in ClinVar or gnomAD? Are pathogenic variants found at any of these sites

      Yes. For highly sensitive active-site residues that have few permissible variants, the vast majority of amino acid substitutions that do retain activity preserve key physicochemical properties of the wild-type residue, such as hydrophobicity or charge. We have added this important observation to the manuscript:

      "Any variants at these sensitive residues that are permissive for activity in our assay retain hydrophobicity or charged states relative to the original amino acid side chain (Figure 5A & Table S5)."

      None of these variants are present in ClinVar. Only L15V and E191D are present in gnomAD (Table S4).

      1. Lines 423-430 - The OddsPath calculation would seem to rely heavily on the thresholds of .85 for normalized growth. The OddsPath calculation could be bolstered with some additional analysis that emphasizes the robustness to alternative thresholds.

      We agree that the sensitivity of the OddsPath calculation to the choice of growth thresholds is an important consideration. In our assay, benign ClinVar variants and non-human primate variants are observed exclusively within the peak centered on wild-type growth, whereas clinically annotated variants falling below this peak are exclusively pathogenic. On this basis, we defined the upper boundary of the assay range interpreted as supporting pathogenicity as the lower boundary of the wild-type-centered peak in the growth distribution (as defined in Figure 3), rather than selecting a cutoff by direct optimization of the OddsPath. This choice reflects the observed concordance, in our dataset, between the onset of measurable functional impairment in the assay and clinical pathogenic annotation. Importantly, in practice the OddsPath value is locally robust to the precise placement of this boundary, remaining invariant across the range 0.82-0.88. Supporting our chosen threshold of 0.85, the lowest-growth benign or primate variant observed has a normalized growth value of 0.88, while the lowest growth observed among variants present as homozygotes in gnomAD was 0.86. We have clarified this rationale and analysis in the revised manuscript.

      "Notably, the "Among all nine of the human ASS1 missense variants observed as homozygotes in gnomAD which were tested as amino acid substitutions in our assay, the lowest observed growth value was 0.86 (Ala258Val) consistent with the lower boundary of the PrimateAI variants which was a growth value of 0.87 (Ala81Thr) (Figure 6) and with our use of a 0.85 classification threshold."

      "If we treat PrimateAI variants as benign (solely for OddsPath calculation purposes), the OddsPath for growth

      1. Lines 432-441 - This is an interesting idea to use variants observed in primates, has ACMG weighed in on this? I understand that CTLN1 is an autosomal recessive disorder but I'd still be interested in seeing how the observed ASS1 missense variants in gnomAD perform in your growth assay, possibly a supplemental figure?

      To our knowledge, the ACMG/AMP guidelines do not currently address the use of homozygous missense variants observed in non-human primates. We are currently in discussion with two ClinGen working groups to discuss the possibility of formalizing the use of this data source.

      We agree that comparison with human population data is also important. Accordingly, total gnomAD allele counts and homozygous counts for all applicable ASS1 missense variants are provided in Table S4, and the growth behavior of ASS1 missense variants observed in the homozygous state in gnomAD is shown in Figure 6. These homozygous variants uniformly exhibit high growth in our assay, consistent with the absence of strong loss-of-function effects. We have updated the manuscript text to clarify these points.

      Minor comments 1. Lines 53-59 - This paragraph needs to cite the literature, especially lines 56, 57, and 59 2. Line 61 - no need to repeat "citrullinemia type I", just use the abbreviation as it was introduced in the paragraph above 3. Lines 61-71 - again, this paragraph needs more literature citations 4. Line 62 - change to "results"

      The changes suggested in points 1-4 have all been implemented in the revised manuscript.

      1. Line 74-75 - "RUSP" acronym not needed as it's never used in the manuscript, the same goes for "HHS"

      We agree that the acronyms "RUSP" and "HHS" are not reused elsewhere in the manuscript. We have nevertheless retained them at first mention, alongside the expanded names, because these acronyms are commonly used in newborn screening and public health policy contexts and may be more familiar to some readers than the expanded terms. We would be happy to remove the acronyms if preferred.

      1. Line 86 - "ASS1" I think is referring to the enzyme and should just be "ASS"? If referring to the gene then italicize to "ASS1"
      2. Lines 91-93 - It would be helpful to mention this is a functional screen in yeast
      3. Line 101 - It would be helpful to the readers to define SD before using the acronym, consider changing to "minimal synthetic defined (SD) medium" and afterwards can refer to as "SD medium"
      4. 109-114 - It would be great if you could share your method for designing the codon-harmonized yASS1 gene, consider sharing as a supplemental script or creating a GitHub repository linked to a Zenodo DOI for publication.

      The changes suggested in points 6-9 have all been implemented in the revised manuscript. The codon harmonization script has been provided as File S1.

      1. Lines 135-137 - I think it's helpful to provide a full table of the cassettes ordered from Twist as well as the primers used to amplify them, consider a supplemental table.

      Details of Twist cassette and the primer sequences used for amplification have been added to the Materials & Methods.

      1. Line 138 - "standard methods" is a bit vague, I'm guessing this is a Geitz and Schiestl 2007 LiAc/ssDNA protocol (PMID 17401334)? Also, was ClonNAT used to select for natMX colonies?

      The reviewer is correct about which protocol was used, and we have added the citation. We have also clarified that selection was carried out based on resistance to nourseothricin.

      1. Line 150 - change to "sequence the entire open reading frame, as previously described [4]."
      2. Line 222-223 - remove "replace" and just use "complement" (and remove the parenthesis)
      3. Line 249 - It would be great to see a supplemental alignment of the hASS1 and yASS1 sequences.
      4. Line 261 - spelling "citrullemia" should be corrected to "citrullinemia"
      5. Line 280 - "using Oxford Nanopore sequencing" is a bit vague, I suggest specifying the equipment used (e.g. Oxford Nanopore Technologies MinION platform) or simplify to "via long-read sequencing (see Materials & Methods)"

      The changes suggested in points 12-16 have all been implemented in the revised manuscript. An alignment of the ASS and Arg1 protein sequences has been provided as File S2.

      1. Line 287-289 - It would be great to see the average number of isolates per variant, as well as a plot of the variant growth estimate vs individual isolate growth.

      We agree with the reviewer that conveying measurement precision is important. The number of isolates assayed per variant is provided in Table S4, and we have added explicit mention of this in the text. Because variants were assayed with a mixture of 1, 2, or {greater than or equal to}3 independent isolates, a scatterplot of variant-level growth estimates versus individual isolate measurements would be difficult to interpret and potentially misleading. Instead, we report standard error estimates for each variant in Table S4, derived from the linear model used to estimate growth effects, which more appropriately summarizes measurement uncertainty given the experimental design.

      1. Lines 324-25 - consider removing the last sentence of this paragraph, it is redundant as the following paragraph starts with the same statement.

      We have removed this sentence.

      1. Lines 327-335 - This is interesting and would benefit from its own subpanel or plot in which the normalized growth score is plotted against variants that are at conserved or diverse residues in human ASS, and see if there's a statistical difference in score between the two groupings.

      As suggested by the reviewer, we have added Supplemental Figure 2 (Figure S2) in which the normalized growth score of each variant is plotted against the conservation of the corresponding residue, as measured by ConSurf. The manuscript already includes a statistical analysis of the relationship between residue conservation and functional impact, showing that amorphic variants occur significantly more frequently at highly conserved residues than unimpaired variants do (one-sided Fisher's exact test). We now refer to this new supplemental figure in the relevant Results section.

      1. Lines 339-341 - As written, it is unclear if aspartate interacts with all of the same residues as citrulline or just Asn123 and Thr119.
      2. Lines 345-355 - As with my above comment, I find this interesting and would
      3. Line 353 - add a period to "al" in "Diez-Fernandex et al."

      The issues raised in points 20 and 22 have all addressed. Point 21 appears to be truncated.

      1. Figure 1 a. Remove "Figure" from the subpanels and show just "A" and "B" (as you do for Figure 4) and combine the two images into a single image. Also make this correction to Figure 5 and Figure 8. b. Panel A - I thought the hASS1 and yASS1 were dropped into FY4, not the arg1 KO strain. This needs clarification. c. Panel A - I'm assuming the natMX cassette contains its own promoter, you could use a right-angled arrow to indicate where the promotors are in your construct. d. Panel B - I'm not sure the bar graph is necessary, it would be more helpful to see calculations of the colony size (or growth curves for each strain) and plot the raw values (maybe pixel counts?) for each replicate rather than normalizing to yeast ARG1. I would be great to have a supplemental figure showing all the replicates side-by-side. e. Panel B - Would be helpful to denote the pathogenic and benign ClinVar variants with an icon or colored text.

      f. Figure 1 Caption - make "A)" and "B)" bold.

      We have implemented the requested changes in Figure 1 with the following exceptions. We have retained panels A and B as separate subfigures because they illustrate distinct experimental concepts. In addition, we respectfully disagree with point (d). The bar graph is intended to provide a clear, high-level comparison of functional complementation by hASS1 versus yASS1 and to illustrate the gross differences in growth between benign and pathogenic proof-of-principle variants. As the bar graph includes error bars for standard deviations, presenting raw colony size measurements or growth curves for individual replicates would substantially complicate the figure without materially improving interpretability for this purpose.

      1. Figure 2 a. "Shown in magenta are amino acid substitutions corresponding to ClinVar pathogenic, pathogenic/likely pathogenic, and likely pathogenic variants" is repeated in the figure caption. b. "Shown in green are amino acid substitutions corresponding to ClinVar benign and likely benign variants." I don't see any green points. c. Identify the colors used for ASS1 substrate binding residues. d. This plot would benefit from a depiction of the human ASS secondary structure and any protein domains (nucleotide-binding domain, synthase domain, and C-terminal helix from Fig4B)

      e. Line 685 675 - "ASS1" is being used in reference to the enzyme, is this correct or should it be "ASS"?

      We have made the requested changes to Figure 2. The repeated caption text has been removed, and references to green points have been corrected to orange points to match the figure. The colors used to indicate ASS substrate-binding residues are explicitly described in the figure key. Secondary structure annotations have been added. References to the enzyme have been corrected to "ASS" rather than "ASS1" where appropriate.

      1. Figure 3 a. Rename the "unimpaired" category as there are several pathogenic ClinVar variants that fall into this category.

      To address this point, we have clarified the labeling by adding "in our yeast assay" to the figure legend, making explicit that the "unimpaired" category refers only to wild-type-like behavior under assay conditions and does not imply clinical benignity. See also response to Reviewer #3, Major Comment 1.

      1. Figure 4 a. List the PDB or AlphaFold accession used for this structure b. Panel A - state which colors are used for to depict each monomer. It is confusing to see several shades of pink/purple used to depict a single monomer in Panel A. c. It is very difficult to make out the aspartate and citrulline substrates in the catalytic binding activity, consider making an inset zooming-in on this domain and displaying a ribbon diagram of the structure rather than the surface. d. Generally, it would be more helpful here to label any particular residues that were identified as pathogenic from your screen, or to overlay average grow scores per residue data onto the structure

      We have implemented the requested changes to Figure 4. The relevant PDB/AlphaFold accession is now listed, and the colors used to depict each monomer in Panel A are clarified in the figure legend. An inset focusing on the active site has been added to improve visualization of the citrulline and aspartate substrates. In addition, we have added new panels (Figure 4C and 4D) overlaying pathogenic residues and average growth scores onto the structure to more directly link structural context with functional data.

      1. Figure 5 a. Line 716 - Insert a page break to place Figure 5 on its own page b. I suggest using a heatmap for this type of plot, as it is very difficult to track which color corresponds to which residue.

      c. Fig5A - This plot could be improved by identifying which residue positions interface with which substrate.

      We have placed Figure 5 on its own page and added information to the legend identifying which residue positions interface with each substrate. We have retained the active-site variant strip charts raised in point (b), as we believe they effectively illustrate how the distribution of variant effects differs between residues. In addition, we have provided a supplemental heatmap showing variant growth across the entire protein (Figure S1), and individual variant scores for all residues are provided in Table S4.

      1. Figure 7 a. Line 735 - Insert page break to place figure on a new page

      List the PDB accession used for these images. c. For clarity I would mention "human ASS" in the figure title d. State the colors of the substrates e. Panels A and B could be combined into a single panel, making it easier to distinguish the active site and dimerization variants.

      f. Could be interesting to get SASA scores for the ClinVar structural variants to determine if they are surface-accessible

      We have implemented the requested changes in Figure 7 with the following exceptions. For point (e), there is no single orientation of the structure that allows a clear simultaneous view of both active-site and dimerization variants; accordingly, we have retained panels A and B as separate subfigures to preserve clarity. With respect to point (f), we agree that solvent accessibility analysis could be informative in other contexts. However, such an analysis does not integrate naturally with the functional and assay-based framework of the present study and was therefore not included.

      1. Figure 8 a. Panel B - overlay a square frame in the larger protein structure that depicts where the below inset is focused, and frame inset image as well.

      We have framed the inset image as requested. We did not add a corresponding frame to the full protein structure, as doing so obscured structural details in the region of interest.

      Reviewer #3 (Significance (Required)):

      Section 2 - Significance This study represents a substantial technical, functional, and translational advance in the interpretation of missense variation in ASS1, a gene of high clinical relevance for the rare disease citrullinemia type I. Its principal strength lies in the generation of an experimentally validated functional atlas of ASS1 missense variants that covers ~90% of all SNV-accessible substitutions. The scale, internal reproducibility, and careful benchmarking of the yeast complementation assay against known pathogenic and benign variants provide a robust foundation for identifying pathogenic ASS1 variants. Particularly strong aspects include the rigorous quality control of variant identities, the quantitative nature of the functional readout, and the thoughtful integration of results into the ACMG/AMP OddsPath framework. The discovery of intragenic complementation between variants affecting distinct structural regions of the enzyme is a notable conceptual and mechanistic contribution. Limitations include the assay's reduced sensitivity to variants impacting oligomerization or subtle folding defects, and the use of yeast as a heterologous system, which may mask disease-relevant mechanisms as several pathogenic ClinVar variants were found to be "functionally unimpaired". Future work extending functional testing to additional cellular contexts or expanding genotype-level combinatorial analyses would further enhance clinical applicability. Relative to prior studies, which have relied on small numbers of patient-derived variants or low-throughput biochemical assays, this work extends the field decisively by delivering a comprehensive, variant-resolved functional map for ASS1. To the best of my current knowledge, this is the first systematic functional screen of ASS1 at this scale and the first direct experimental demonstration that ASS active sites span multiple subunits, enabling intragenic complementation consistent with Crick and Orgel's classic variant sequestration model. As such, the advance is simultaneously technical (high-throughput functional genomics), mechanistic (defining structural contributors to catalysis and epistasis), and clinical (enabling evidence-based reclassification of VUS). I find the use of homozygous non-human primate variants as an orthogonal benign calibration set both creative and controversial, my hope would be that this manuscript will prompt a productive discussion.

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      Referee #3

      Evidence, reproducibility and clarity

      Summary

      This manuscript presents a comprehensive functional profiling of 2,193 ASS1 missense variants using a yeast complementation assay, providing valuable data for variant interpretation in the rare disease citrullinemia type I. The dataset is extensive, technically sound, and clinically relevant. The demonstration of intragenic complementation in ASS1 is novel and conceptually important. Overall, the study represents a substantial contribution to functional genomics and rare disease variant interpretation.

      Major comments

      This is an exciting paper as it can provide support to clinicians to make actionable decisions when diagnosing infants. I have a few major comments, but I want to emphasize the label of "functionally unimpaired" variants to be misleading. The authors explain that there are several pathogenic ClinVar variants that fall into this category (above the >.85 growth threshold) but I think this category needs a more specific name and I would ask the authors to reiterate the shortcomings of the assay again in the Discussion section. I think there's an important discussion to be had here, is the assay detecting variants that alter the function of ASS or is it detecting a complete ablation of enzymatic activity? The results might be strengthened with a follow-up experiment that identifies stably expressed ASS1 variants. At the very least, it would be great to see the authors replicate some of their interesting results from the high-throughput screen by down-selecting to ~12 variants of uncertain significance that could be newly considered pathogenic. I would ask the authors to provide more citations of the literature in the introduction of the manuscript. I would be especially interested in knowing more about human ASS being identified as a homolog of yeast ARG1, as they share little sequence similarity (27.5%) at the protein level. That said, I find the yeast complementation assay exciting. I appreciate the efforts made by the authors to share their work and make this study more reproducible, such as sharing the hASS1 and yASS1 plasmids being shared on NCBI Genbank (Line 121) and publishing the ONT reads on SRA (Line 154). I made a requests for additional data to be shared, such as the custom method/code for codon optimization and a table of Twist variant cassettes that were ordered. I would also love to see these results shared on MaveDB.org. I find this manuscript very exciting as the authors have a compelling assay that identifies pathogenic variants, but I was generally disappointed by the quality and organization of the figures. For example, Figure 4 provides very little insight, but could be dramatically improved with an overlay of the normalized growth score data or highlighting variants surrounding the substrate or ATP interfaces. There are some very interesting aspects of this manuscript that could be shine through with some polished figures. I would also encourage the authors to generate a heatmap of the data represented in Figure 2 (see Fowler and Fields 2014 PMID 25075907, Figure 2), this would be more helpful reference to the readers.

      My major comments are as follows:

      1. Citations needed - especially in the introduction and for establishing that hASS is a homolog of yARG1
      2. Generally, the authors do a nice job distinguishing the ASS1 gene from the ASS enzyme, though I found some ambiguities (Line 685). Please double-check the use of each throughout the manuscript
      3. Generally, I'm confused about what strain was used for integrating all these variants, was is the arg1 knock-out strain from the yeast knockout collection or was it FY4? I think FY4 was used for the preliminary experiments, then the KO collection strain was used for making the variant library but I think this could be made more clear in the text and figures. Lines 226-229 describes introducing the hASS1 and yASS1 sequences into the native ARG1 locus in strain FY4, but the Fig1A image depicts the ASS1 variants going into arg1 KO locus. Fig1A should be moved to Fig2.
      4. Line 303 - "We classify these variants as 'functionally unimpaired'", this is not an accurate description of these variants as Figure 2 highlights 24 pathogenic ClinVar variants that would fall into this category of "functionally unimpaired". The yeast growth assay appears to capture pathogenic variants, but there is likely some nuance of human ASS functionality that is not being assessed here. I would make the language more specific, e.g. "complementary to Arg1" or "growth-compatible".
      5. Lines 345-355 - It is interesting that there are variants that appear functional at the substrate interfacing sites. Is there anything common across these variants? Are they maintaining the polarity or hydrophobicity of the WT residue? Are any of these variants included in ClinVar or gnomAD? Are pathogenic variants found at any of these sites
      6. Lines 423-430 - The OddsPath calculation would seem to rely heavily on the thresholds of <.05 and >.85 for normalized growth. The OddsPath calculation could be bolstered with some additional analysis that emphasizes the robustness to alternative thresholds.
      7. Lines 432-441 - This is an interesting idea to use variants observed in primates, has ACMG weighed in on this? I understand that CTLN1 is an autosomal recessive disorder but I'd still be interested in seeing how the observed ASS1 missense variants in gnomAD perform in your growth assay, possibly a supplemental figure?

      Minor comments

      1. Lines 53-59 - This paragraph needs to cite the literature, especially lines 56, 57, and 59
      2. Line 61 - no need to repeat "citrullinemia type I", just use the abbreviation as it was introduced in the paragraph above
      3. Lines 61-71 - again, this paragraph needs more literature citations
      4. Line 62 - change to "results"
      5. Line 74-75 - "RUSP" acronym not needed as it's never used in the manuscript, the same goes for "HHS"
      6. Line 86 - "ASS1" I think is referring to the enzyme and should just be "ASS"? If referring to the gene then italicize to "ASS1"
      7. Lines 91-93 - It would be helpful to mention this is a functional screen in yeast
      8. Line 101 - It would be helpful to the readers to define SD before using the acronym, consider changing to "minimal synthetic defined (SD) medium" and afterwards can refer to as "SD medium"
      9. 109-114 - It would be great if you could share your method for designing the codon-harmonized yASS1 gene, consider sharing as a supplemental script or creating a GitHub repository linked to a Zenodo DOI for publication.
      10. Lines 135-137 - I think it's helpful to provide a full table of the cassettes ordered from Twist as well as the primers used to amplify them, consider a supplemental table
      11. Line 138 - "standard methods" is a bit vague, I'm guessing this is a Geitz and Schiestl 2007 LiAc/ssDNA protocol (PMID 17401334)? Also, was ClonNAT used to select for natMX colonies?
      12. Line 150 - change to "sequence the entire open reading frame, as previously described [4]."
      13. Line 222-223 - remove "replace" and just use "complement" (and remove the parenthesis)
      14. Line 249 - It would be great to see a supplemental alignment of the hASS1 and yASS1 sequences
      15. Line 261 - spelling "citrullemia" should be corrected to "citrullinemia"
      16. Line 280 - "using Oxford Nanopore sequencing" is a bit vague, I suggest specifying the equipment used (e.g. Oxford Nanopore Technologies MinION platform) or simplify to "via long-read sequencing (see Materials & Methods)"
      17. Line 287-289 - It would be great to see the average number of isolates per variant, as well as a plot of the variant growth estimate vs individual isolate growth
      18. Lines 324-25 - consider removing the last sentence of this paragraph, it is redundant as the following paragraph starts with the same statement
      19. Lines 327-335 - This is interesting and would benefit from its own subpanel or plot in which the normalized growth score is plotted against variants that are at conserved or diverse residues in human ASS, and see if there's a statistical difference in score between the two groupings
      20. Lines 339-341 - As written, it is unclear if aspartate interacts with all of the same residues as citrulline or just Asn123 and Thr119.
      21. Lines 345-355 - As with my above comment, I find this interesting and would
      22. Line 353 - add a period to "al" in "Diez-Fernandex et al."
      23. Figure 1

      a. Remove "Figure" from the subpanels and show just "A" and "B" (as you do for Figure 4) and combine the two images into a single image. Also make this correction to Figure 5 and Figure 8

      b. Panel A - I thought the hASS1 and yASS1 were dropped into FY4, not the arg1 KO strain. This needs clarification

      c. Panel A - I'm assuming the natMX cassette contains its own promoter, you could use a right-angled arrow to indicate where the promotors are in your construct

      d. Panel B - I'm not sure the bar graph is necessary, it would be more helpful to see calculations of the colony size (or growth curves for each strain) and plot the raw values (maybe pixel counts?) for each replicate rather than normalizing to yeast ARG1. I would be great to have a supplemental figure showing all the replicates side-by-side

      e. Panel B - Would be helpful to denote the pathogenic and benign ClinVar variants with an icon or colored text

      f. Figure 1 Caption - make "A)" and "B)" bold 24. Figure 2

      a. "Shown in magenta are amino acid substitutions corresponding to ClinVar pathogenic, pathogenic/likely pathogenic, and likely pathogenic variants" is repeated in the figure caption

      b. "Shown in green are amino acid substitutions corresponding to ClinVar benign and likely benign variants." I don't see any green points

      c. Identify the colors used for ASS1 substrate binding residues

      d. This plot would benefit from a depiction of the human ASS secondary structure and any protein domains (nucleotide-binding domain, synthase domain, and C-terminal helix from Fig4B)

      e. Line 685 - "ASS1" is being used in reference to the enzyme, is this correct or should it be "ASS"? 25. Figure 3

      a. Rename the "unimpaired" category as there are several pathogenic ClinVar variants that fall into this category 26. Figure 4

      a. List the PDB or AlphaFold accession used for this structure

      b. Panel A - state which colors are used for to depict each monomer. It is confusing to see several shades of pink/purple used to depict a single monomer in Panel A

      c. It is very difficult to make out the aspartate and citrulline substrates in the catalytic binding activity, consider making an inset zooming-in on this domain and displaying a ribbon diagram of the structure rather than the surface.

      d. Generally, it would be more helpful here to label any particular residues that were identified as pathogenic from your screen, or to overlay average grow scores per residue data onto the structure 27. Figure 5

      a. Line 716 - Insert a page break to place Figure 5 on its own page

      b. I suggest using a heatmap for this type of plot, as it is very difficult to track which color corresponds to which residue

      c. Fig5A - This plot could be improved by identifying which residue positions interface with which substrate 28. Figure 7

      a. Line 735 - Insert page break to place figure on a new page

      b. List the PDB accession used for these images

      c. For clarity I would mention "human ASS" in the figure title

      d. State the colors of the substrates

      e. Panels A and B could be combined into a single panel, making it easier to distinguish the active site and dimerization variants

      f. Could be interesting to get SASA scores for the ClinVar structural variants to determine if they are surface-accessible 29. Figure 8

      a. Panel B - overlay a square frame in the larger protein structure that depicts where the below inset is focused, and frame inset image as well.

      Significance

      This study represents a substantial technical, functional, and translational advance in the interpretation of missense variation in ASS1, a gene of high clinical relevance for the rare disease citrullinemia type I. Its principal strength lies in the generation of an experimentally validated functional atlas of ASS1 missense variants that covers ~90% of all SNV-accessible substitutions. The scale, internal reproducibility, and careful benchmarking of the yeast complementation assay against known pathogenic and benign variants provide a robust foundation for identifying pathogenic ASS1 variants. Particularly strong aspects include the rigorous quality control of variant identities, the quantitative nature of the functional readout, and the thoughtful integration of results into the ACMG/AMP OddsPath framework. The discovery of intragenic complementation between variants affecting distinct structural regions of the enzyme is a notable conceptual and mechanistic contribution. Limitations include the assay's reduced sensitivity to variants impacting oligomerization or subtle folding defects, and the use of yeast as a heterologous system, which may mask disease-relevant mechanisms as several pathogenic ClinVar variants were found to be "functionally unimpaired". Future work extending functional testing to additional cellular contexts or expanding genotype-level combinatorial analyses would further enhance clinical applicability.

      Relative to prior studies, which have relied on small numbers of patient-derived variants or low-throughput biochemical assays, this work extends the field decisively by delivering a comprehensive, variant-resolved functional map for ASS1. To the best of my current knowledge, this is the first systematic functional screen of ASS1 at this scale and the first direct experimental demonstration that ASS active sites span multiple subunits, enabling intragenic complementation consistent with Crick and Orgel's classic variant sequestration model. As such, the advance is simultaneously technical (high-throughput functional genomics), mechanistic (defining structural contributors to catalysis and epistasis), and clinical (enabling evidence-based reclassification of VUS). I find the use of homozygous non-human primate variants as an orthogonal benign calibration set both creative and controversial, my hope would be that this manuscript will prompt a productive discussion.

    3. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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      Referee #1

      Evidence, reproducibility and clarity

      Lo et al., report a high-throughput functional profiling study on the gene encoding for argininosuccinate synthase (ASS1), done in a yeast experimental system. The study design is robust (see lines 141-143, main text, Methods), whereby "approximately three to four independent transformants of each variant would be isolated and assayed." (lines 140 - 141, main text, Methods). Such a manner of analysis will allow for uncertainty of the functional readout for the tested variants to be accounted for.

      This is an outstanding study providing insights on the functional landscape of ASS1. Functionally impaired ASS1 may cause citrullinemia type I, and disease severity varies according to the degree of enzyme impairment (line 30, main text; Abstract). Data from this study forms a valuable resource in allowing for functional interpretation of protein-altering ASS1 variants that could be newly identified from large-scale whole-genome sequencing efforts done in biobanks or national precision medicine programs. I have some suggestions for the Authors to consider:

      1. The specific function of ASS1 is to condense L-citrulline and L-aspartate to form argininosuccinate. Instead of measuring either depletion of substrate or formation of product, the Authors elected to study 'growth' of the yeast cells. This is a broader phenotype which could be determined by other factors outside of ASS1. Whereas i agree that the experiments were beautifully done, the selection of an indirect phenotype such as ability of the yeast cells to grow could be more vigorously discussed.
      2. One of the key reasons why studies such as this one are valuable is due to the limitations of current variant classification methods that rely on 'conservation' status of amino acid residues to predict which variants might be 'pathogenic' and which variants might be 'likely benign'. However, there are serious limitations, and Figures 2 and 6 in the main text shows this clearly. Specifically, there is an appreciable number of variants that, despite being classified as "ClinVar Pathogenic", were shown by the assay to unlikely be functionally impaired. This should be discussed vigorously. Could these inconsistencies be potentially due to the read out (growth instead of a more direct evaluation of ASS1 function)?
      3. Figure 3 is very interesting, showing a continuum of functional readout ranging from 'wild-type' to 'null'. It is very interesting that the Authors used a threshold of less than 0.85 as functionally hypomorphic. What does this mean? It would be very nice if they have data from patients carrying two hypomorphic ASS1 alleles, and correlate their functional readout with severity of clinical presentation. The reader might be curious as to the clinical presentation of individuals carrying, for example, two ASS1 alleles with normalized growth of 0.7 to 0.8.

      I hope you will find these suggestions helpful.

      Significance

      This is an outstanding study providing insights on the functional landscape of ASS1. Functionally impaired ASS1 may cause citrullinemia type I, and disease severity varies according to the degree of enzyme impairment (line 30, main text; Abstract). Data from this study forms a valuable resource in allowing for functional interpretation of protein-altering ASS1 variants that could be newly identified from large-scale whole-genome sequencing efforts done in biobanks or national precision medicine programs.

    1. k entails (1) telling stories in order to texturiexperience of the viewer and to bring substance and greater corporethe area so that viewers can have an enhanced capacity to perceimake sense of perceptions, (2) historicizing (using the combination oftelling and history-telling) based on new perceptions in order to enrground of engagement, and (3) using this re-formed interpretive frawork to re-consider data - that is, to re-envision the landscape, to seeto understand what's visible in more dynamic ways, and to develtheories

      3 things

    1. IAM Guidelines & Best Practices 1) MFA 2) IMA Roles instead of USER 3) Follow the principle of least provilage 4) rotate user credentials 5) use managed policies

      Shared Responsibility | AWS | Security of infastructure , Avalibity of IAM services, Offer Policies for common scenarios.

      | Customer | manage and secure accss keys and user accounts, implement strong passwods, utlized mFA, IAM permision must be implemented correctly and follow the principle of least privilage.