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  1. Feb 2025
    1. Este punto de vista, a su vez, nos permite colaborar con otros proyectos de humanidades digitales en el mundo pero también cuestionar las presuposiciones con respecto a la interoperabilidad y el ideal de la construcción de un sistema universalizante de comunicación, una intención babélica que se origina en centros de poder que asumen su propia comunicación como línea de base a la que los demás deben adaptarse. Es decir, las humanidades digitales en términos de conservación de la memoria permiten tanto construir lo propio y significativo como dialogar con una tradición más amplia. Lo propio aquí no es una visión nacionalista, por supuesto, sino la visión centrada en los propósitos y usos significativos de las comunidades que contruyen su historia y sus interpretaciones.

      Sin embargo, creo que lo propio y la interoperabilidad no están en riña, sino que tienen que ver con cómo hay acceso diferenciado, pero interoperable a infraestructuras digitales dispuestas por y para las comunidades y alejadas de grandes oligopolios.

      Por ejemplo, nuestro reciente proyecto de Cartofonías para la revitalización lingüística en La Chorrera, Amazonas usa tecnologías interoperables, pero se distancia de tecnologías hegemónicas y sus centros, de este modo no hospedamos el código en el privativo GitHub) ni usamos el motor wiki libre y complicado de la Wikimedia/Wikipedia, ni hospedamos las memorias en Meta/Instagram. Nuestra curaduría e interconexión de alternativas (Fossil, TiddlyWiki, Internet Archive) es interoperable pero alejadas de las hegemonías tecnoeconómicas libres o privativas. Las comunidades además son las que deciden sobre los accesos a los datos y una posible intranet, podría extender el computador en territorio dónde ahora están hospedados localmente, para que evolucione y crezca con condiciones de acceso distintas y más allá de lo que ahora están en línea.

    2. En concreto, Latino/América se ha preguntado innumerables veces por su autenticidad, es decir, acerca de si realmente entra en el grupo de los humanos a los que se refiere el humanismo o si, por el contrario, tiene una forma distinta de humanidad o incluso de no-humanidad. Esta ondulación, que se ha visto como el efecto de un pueblo que no logra construir una identidad propia, puede ser, sin embargo, propiciadora de visiones renovadoras y alternativas de las humanidades tradicionales y puede encontrar en las humanidades digitales una oportunidad para lograr esa renovación. Por lo tanto, unas humanidades digitales desde América Latina no deberían aceptar sin más los principios excluyentes de las humanidades ni actuar sin entender que la crisis no solo es externa sino que es también autoproducida y un efecto de su propia tradición. Por el contrario, las humanidades digitales en nuestro contexto deben asumir la crisis de las humanidades de una forma generativa y productiva, como un espacio para descentrar y repensar el proyecto de lo humano y para promover la interculturalidad dentro de ese proyecto; ese multiculturalismo que justamente se ha visto excluido y que ha dado lugar a la posición ambivalente de lo latinoamericano en el humanismo.

      Tal vez incluso para superar el proyecto de lo humano o enmarcarlo como menos preponderante, en medio de esas otredades de las Humanidades eurocéntricas y con "H" mayúscula han omitido histórcamente.

      En ese sentido valdría la pena explicitar esos vínculos que este y el siguiente párrafo anuncian y cómo las HD, en particular las Latinoamericanas se conectan con esas miradas críticas.

      Al menos pareciera que la mirada lejana de los movivimento hacktivistas y de tecnologías cívicas de las HD ha sido más bien "apolitico" y academicista, aunque quizás, salvo excepciones crítica y políticamente informadas, como las ejemplificadas en este párrafo.

    3. Las grandes instituciones humanísticas como el museo, el archivo, la universidad y la biblioteca son las encargadas de desarrollar este ejercicio de largo aliento, y tienen la misión de velar por los propósitos humanísticos de conservar, interpretar, apreciar tales formas de expresión y propiciar el diálogo público. A su vez, los humanistas trabajan en estas instituciones o en comunidades informales y desde una sensibilidad particular intentan construir y conservar el, una vez más, zigzagueante concepto de lo humano.

      Así como criticar la visibilidad y el papel de las llamadas "grandes instituciones humanistas" en funciones que no sólo las exceden, sino que han estado largamente por fuera a pesar de que esto se reconoce en miradas, precisamente menos institucionalizadas.

    1. he considerado tres formas de sostenimiento comunes en el mundo del software abierto: dar cursos o soporte de usuario personalizado, o recibir donaciones para el mantenimiento de la base de código o la inclusión de nuevas prestaciones y cualidades al sistema. Todas estas opciones tienen como finalidad que el sistema pueda ser gratuito y a la vez reconozca el trabajo —endemoniado, si se quiere— de organizar una infraestructura de las humanidades digitales.

      En el caso de Grafoscopio, que ha sido y sigue sosteniéndose principalmente gracias a las economías de los afectos y cuidados, la sostenibilida económica y de código ha ocurrido en tres frentes:

      • Lo uso para consultorías adaptándolo a necesidades de nuestros clientes. El código resultado queda libre y las narrativas de datos son del cliente.
      • Lo uso para proyectos educativos e investigativos, tanto en la universidad, como en el hackerspace y otras comunidades de base.
      • Aplico a becas que implican la mejora de Grafoscopio, su documentación y adaptación de funcionalidades.

      Las dos primeras han sido fuentes más constantes de mejoras y este año el software cumple su primera década desde el primer commit, transformándose junto con la infraestructura subyacente en la que está basado.

    2. El primer problema implica que el software no es tan accesible ni liviano como se promociona, pues necesita de la instalación de programas que parchen su compatibilidad y que distancian el supuesto uso descomplicado. El segundo problema implica que, con actitud de modulor moral, es necesario entrar en las entrañas del código para reemplazar las palabras en inglés por palabras en español, hacer ajustes a los vacíos de documentación o personalización, y eso requiere conocimientos en programación o recursos para rediseñar interfaces o hacer localización.

      Desde la comunidad de Grafoscopio, hemos encontrado en la metaherramienta TidddlyWiki esta adaptabilidad extrema y facilidad de uso multiplataforma y multilingüe, incluso para procesos de catalogación y memoria viva.

      También hemos acuñado lo que he llamado "programación intersticial" que permite extender las infraestructuras y, en general los sistemas sociotécnicos pequeños, no desde sus entrañas, sino desde los intersticios con otras infraestructuras, comunidades y sistemas. Así, cuando TiddlyWiki no tiene una funcionalidad particular, la conectamos con Grafoscopio/Pharo o con Fossil para tener las ventajas de todas sin las desventajas particulares de sólo una de ellas.

    3. Siendo este el caso, no basta con la actitud de modulor moral, a pesar de su potencial creativo, porque puede llegar a ser una acción sin retroalimentación en la infraestuctura general, sino que se requiere una actitud de demonio moral, por decirlo así, o sea, una actitud de transformación del propio sistema infraestructural.
    4. seguir la lógica definida por Pelacho et al.92Pelacho et al., «Science as Commons». y establecer unas reglas, o tal vez unas heurísticas organizativas, para el funcionamiento de infraestructuras digitales en América Latina con el fin de cerrar tales brechas y, si se quiere, enraizar las infraestructuras enajenadas.

      Precisamente, en aras del establecimiento claro de reglas, es que me parece que el repositorio de esta tesis debería tener una postura explícita frente al licenciamiento que favorezca los comunes.

    5. Podemos llamarla desobediencia, resistencia, insurgencia, hackeo, rebusque, otras computaciones, o de muchas otras formas más; al final, es una forma de relacionamiento tecnológico que surge del intento por desenajenar las infraestructuras, apropiarlas y hacerlas apropiadas.
    6. Por ejemplo, según comentaron, la inversión en desarrollo de interfaces gráficas de usuarios se suele posponer por los altos costos que implica el diseño y la puesta a prueba de ellas. Algo similar sucede con las traducciones y localizaciones, pues requieren de personas con conocimiento situado. Adicionalmente, muchos proyectos paran sus actividades una vez el primer empujón institucional y financiero cesa, y por lo tanto sus características quedan congeladas en el tiempo o caducan por falta de soporte.

      Es interesante como Grafoscopio ha evitado varias de estas fallas al hacer elecciones extrañas como ser desarrollado en Pharo (que de entrada le da interfaz gráfica y modelos de persistencia de datos ad-hoc), organizando talleres informales como las Data Week y las Data Rodas que crean conocimiento localizado y hacen una diglosia puente en lugar de abismo y basarse en las economías del cuidado y los afectos, reconociéndolas para no requerir tanto dinero inicial. Si bien se comparten las fragilidades de los proyectos de pequeña y mediana, por ejemplo respecto a el número pequeño de desarrolladores, vale la pena visibilizar también estas estrategias diferenciadas para lidiar con estos problemas comunes.

    7. "la verdadera esencia del campo son los proyectos únicos [o one-offs, en inglés] y los prototipos"71Alex Gil, «Interview with Ernesto Oroza», Debates in the Digital Humanities 2016, ed. Matthew K. Gold y Lauren F. Klein (University of Minnesota Press, 2016), 184-93, https://doi.org/10.5749/j.ctt1cn6thb..
    8. luego de que el programa de dotación tecnológica en veredas dejara de proveer internet, las tablets perdieron su utilidad y fueron utilizadas por los estudiantes como raquetas de tenis de mesa.

      interesante además que sólo funcionen con conectividad o se vuelvan "tiestos". Soluciones de conectividad nula, baja o intermitente, como las de las infraestructuras de bolsillo, se colocan criticamente en este lugar.

    9. de alguna forma, borrar el relacionamiento con la propia lengua local y su vida cotidiana.

      No sé hasta qué punto se pueda afirmar eso. Depende de lo que si se programa en inglés tiene que ver con la vida cotidiana o no. En el caso de las tecnologías cívicas el código que escribimos en inglés, permanentemente tiene que ver con lo local y el cotidiano. Por eso son los usos significativos, de los que habla este párrafo al final, donde estaría el centro del posible desarraigo (o su ausencia), sin desconocer que hay usos totalmente enagenados de muchos lenguajes de programación.

    10. Tal diglosia produce una separación de la experiencia diaria con respecto a la infraestructura del trabajo técnico y así una forma de desarraigo o alienación en la vida profesional similar a lo ejemplificado con la caña de azúcar.

      No sé si se pueda marcar una relación tan directa entre la diglosia y el desarraigo. Puede ocurrir como diría Freira, que se aprenda el lenguaje colono para decir la voz de colonizando y hablar precisamente de preocupaciones locales. Comentarios de los esfuerzos en ese sentido de reflejar lo local en código, vía narrativas de datos, metaherramientas y alfabetismos críticos, han sido hechos a lo largo del texto.

    11. las infraestructuras deben construirse siguiendo procesos de internacionalización, es decir, procesos a través de los cuales sea posible y se facilite la transformación del estándar para adaptarlo a idiomas concretos y particularidades semánticas locales61Adrian Mackenzie, «Internationalization», Software Studies: A Lexicon, ed. Matthew Fuller, Leonardo Books (Cambridge, Mass: MIT Press, 2008), 153-61.. Así se construye una relación recíproca entre la línea de base de la interfaz que facilita la comunicación entre grupos diversos y la generosidad para retribuir a esos grupos de una forma que se adapte a sus propias visiones de mundo.

      Otra forma es lidiar con la diglosia de maneras similares a como lo hicimos con Grafoscopio, con software, interfaces gráficas y código en inglés, que tiene una amplia documentación y narrativas de datos en español o incluso haciendo puentes con procesos de revitalización lingüística en Lenguas del Amazonas Colombiano.

    12. Es un efecto de fuga —o runaway—59Gregory Bateson, Mind and Nature: A Necessary Unity (New York: Dutton, 1979), https://books.google.com?id=EvXWAAAAMAAJ. como lo describiría el antropólogo y cibernétista Gregory Bateson. Es decir, como un crecimiento que, aparentemente, puede continuar sin destruir al sistema pero que mantiene unas relaciones de poder desiguales. El efecto de fuga es, al final, la coexistencia de escalas diametralmente distintas dentro de un mismo sistema, bajo la apariencia de la competencia equilibrada. Si recordamos lo dicho en el capítulo 7 sobre la formación de comunidades, podemos afirmar que el efecto de fuga existe en los límites de la sostenibilidad del sistema.
    13. En otros términos, la comunidad en general, al seguir las reglas de la lengua franca y la línea de base idiomática, debe adaptarse a usarla como interfaz para la comunicación global, pero no existe la misma generosidad cuando se trata de referenciar o reconocer la producción en otros idiomas. Esto representa un proceso de invisibilización y, en términos infraestructurales, de mayor esfuerzo, en escala exponencial, para quienes no se encuentran ya en el centro.
    14. Por ejemplo, un efecto desencadenado por esta diferencia idiomática es la menor visibilidad de la producción en otros idiomas.

      ¿Podría una métrica de diversidad, como Plurimétrica producir visualizaciones o representaciones bajamente textuales ayudar a visibilizar la producción multilingüe?

    15. Entre ellas, podemos contar brechas idiomáticas, epistemológicas, técnicas, educativas, económicas y organizativas. Podemos además pensar que estas brechas están paradas sobre infraestructuras que facilitan el trabajo a determinados grupos sociales de forma transparente, pero que brillan por su ausencia o por sus fallos para grupos que no las tienen o solo pueden hacer uso de ellas de forma limitada. Las brechas se encadenan unas a otras, pues, como muestra el fenómeno del apego preferencial, unos privilegios pueden llevar consigo otros más. Por ejemplo, las brechas idiomáticas se relacionan también con brechas epistemológicas —el tipo de temas que se estudian en las humanidades digitales— y con brechas técnicas —como el desarrollo y el tipo de tecnologías que se usan en proyectos de humanidades digitales—.
    16. esa ventaja inicial, a su vez, le trae otras ventajas adicionales al hablante nativo, como el tiempo libre que otros deben dedicar a aprender el idioma, o una suposición de validación mayor derivada de una competencia con el lenguaje adquirida más cotidianamente, y así se le aproximan más privilegios que acrecientan las brechas exponencialmente. En otras palabras, continuamente se refuerza su posición central, pues la infraestructura está diseñada para facilitar su trabajo, más no necesariamente el de otros, quienes deben emplear más energía para las mismas acciones y los mismos efectos.
    17. formas de colaboración con las infraestructuras dominantes para, aunque sea mínimamente, intervenir en ellas y retroalimentarlas, si son generosas, o aprender de ellas para crear derivaciones si es suficientemente fuerte el espírtu hacker de deconstruir y reconstruir. Como diría Boaventura de Sousa Santos, "Las personas y los grupos sociales tienen derecho a ser iguales cuando la diferencia los inferioriza, y el derecho a ser diferentes cuando la igualdad los descaracteriza"42Boaventura de Sousa Santos, The End of the Cognitive Empire: The Coming of Age of Epistemologies of the South (Durham: Duke University Press, 2018), 10..
    18. Por supuesto, este demonio es una metáfora de un ejercicio humano que requiere de conocimientos, habilidades, recursos, tiempo y motivación con las que no necesariamente se cuenta en las instituciones y comunidades informales que soportan las humanidades digitales en nuestro contexto. Como afirma Fernández L'Hoeste, "una configuración puede sumar el saber-cómo básico e incluso el nivel de educación necesario para su operación, pero, sin los medios económicos apropiados o la infraestructura, poco parece viable"40Héctor Fernández l'Hoeste y Rodríguez, «Introduction: In and Out of Digital Humanities; Nations, Networks, and Practices in Latinx America», Digital Humanities in Latin America, ed. Héctor D. Fernández l'Hoeste y Juan Carlos Rodríguez (Gainesville: University of Florida Press, 2020), 2.. Una adaptación personalizada de la tecnología, como sucede con el caso de Brasil ejemplificado antes, debe competir con alternativas prehechas, que ya tienen terreno ganado en la oferta gracias al desarrollo de infraestructuras previas

      Colocaría acá las economías de los afectos y cuidados (familia, amigos), que aunque también invisibles, hacen posible el desarollo de infraestructuras propias y apropiadas desde estos contextos y constituyen ese empujón de largo aliento necesario, como evidencié y agradecí en primera persona con el desarrollo de Grafoscopio.

      Otro tanto tiene que ver con encontrar las grietas para ubicarse de manera que no se compita directamente con lo pre-existente, sino que se complemente lo que este no ofrece, como ocurrió con Grafoscopio también, que se ubicó en la intersección de campos como metaherramientas, sistemas malleables investigación/publicación reproducible, tecnologías cívicas, de una forma en que otras herramientas con mayor visibilidad (Jupyter, por ejemplo) no habían hecho y con ventajas y recorridos particulares no suplidos por las alternativas que emergieron luego.

    19. una tensión entre dedicar energía y trabajo en hacer infraestructuras situadas o en dedicarlo a realizar proyectos concretos con infraestructuras existentes. Por supuesto, más que una oposición en blanco y negro, esta tensión establece unos ejes de posibilidad en los cuales distintos agentes practicantes de las humanidades digitales se mueven, como en las nubes metafóricas propuestas y dibujadas en el capítulo 2. Hacer la distinción es útil, de todos modos, para conceptualizar tales posibilidades. Además, se abre espacio para preguntas como ¿cómo intervenir en las infraestructuras ajenas?, ¿cómo apropiarlas adecuadamente?, ¿cómo establecer procesos colaborativos entre distintas escalas infraestructurales y distintos contextos?

      La forma de superar estos binarismos y navegar estas tensiones, al menos desde la comunidad de Grafoscopio es desarrollar tecnologías propias que reorganizan stacks tecnológicos alternos y agregan metaherramientas a la mezcla, de manera que podamos disfrutar las ventajas de la interoperabilidad y la alta localización y recontextualización.

    20. Ocean Arboniés Flores acerca de las industrias de computadores en Puerto Rico o Jorge Rojas Álvarez acerca de las escuelas radiofónicas de Radio Sutatenza en Colombia.

      Agregaría los trabajos de Silvia Buitrago sobre redes inalámbricas de Fusa Libre, los procesos de tecnificación con Arduino del tostado de café y de la comunidad de Grafoscopio; así como el trabajo del profesor Carlos Barreneche sobre la red ciudadana de calidad del aire y sus sensores de hardware abierto, iniciados en HackBo o mi trabajo con Grafoscopio, metaherramientas y las tecnologías cívicas

    21. El enfoque global y de largo plazo de décadas pasadas, adicionalmente, tenía fuera de foco a las formas alternativas de producción tecnológica en los márgenes, que hackean, apropian, transforman o crean infraestructuras propias, no como parte de políticas estatales o de grandes organizaciones sino como formas autónomas de participación ciudadana y resolución de problemas locales. Además, incluso más que proyectos de nación, como sucedía en los sesentas del siglo pasado, hoy hay interés en ver las formas comunitarias de hacer trabajo para facilitar el trabajo y en las formas locales de apropiación y producción infraestructural a pequeña escala36Rosalba Casas y Tania Pérez-Bustos, eds., Ciencia, Tecnología y Sociedad En América Latina: La Mirada de Nuevas Generaciones (Buenos Aires: Clacso, 2019); Óscar Moreno-Martínez y Javier Guerrero-Castro, «The Gray Zones of Innovation: The Illegal and the Informal in Marginal Worlds», Tapuya: Latin American Science, Technology and Society 3, n.º 1 (1 de enero de 2020): 435-40, https://doi.org/10.1080/25729861.2020.1849489..

      De ahí lo importante de señalar críticamente la fascinación de las HD y muchos de sus representantes con el gigantismo de datos en detrimento de estas miradas locales y en pequeño.

    22. Así, en el presente, las discusiones que hubo en esos años han tomado otros rumbos, no porque se hayan resuelto, sino porque se han exacerbado los problemas, han aparecido unos nuevos y se han replanteado los conceptos: el cuestionamiento del desarrollismo, es decir, la creencia de que el desarrollo económico es el propósito primordial de las sociedades; la necesidad de una decolonización del conocimiento; la defensa del pluralismo y la interculturalidad; las intervención en el cierre de las brechas tecnológicas en un mundo globalizado pero muy desigual; la producción de tecnologías marginales y fuera del estado y las instituciones; o el trabajo para frenar grandes procesos de destrucción ecológica como el calentamiento global o los desequilibros sociales y ambientales causados por el extractivismo35Kreimer y Vessuri, «Latin American Science, Technology, and Society»; Eden Medina, Ivan da Costa Marques, y Christina Holmes, eds., Beyond Imported Magic: Essays on Science, Technology, and Society in Latin America, Inside Technology (London, England Cambridge, Massachusetts: The MIT Press, 2014)..
    23. un proceso regional de tecnologización sin industrialización, es decir, una actualización tecnológica a través de la transferencia —sin un fundamento formativo— de los procesos industriales subyacentes para su creación o su desarrollo situado25Sagasti, «Towards Endogenous Science and Technology for Another Development»..
    24. las implementaciones extrañas, exóticas, arcaicas o misteriosas; los archivos, documentos, memorias, colecciones de museos, etc; incluso, propone, hacer historia contrafactual y ciencia ficción19Bruno Latour, Reassembling the Social: An Introduction to Actor-Network-Theory (Oxford ; New York: Oxford University Press, 2005).. Con ese espíritu, este capítulo se centra entonces en las tensiones particulares alrededor de las infraestructuras usadas para las prácticas de las humanidades digitales en América Latina.

      En la comunidad de Grafoscopio hemos curado, usado y desarrollado stacks alternos de infraestructura para recorrer futuros alternos, con inspiraciones frecuentes en cosas como el Solarpunk.

    25. De acuerdo con personas entrevistadas por estos investigadores, los problemas de espalda y las largas horas de trabajo tenían como efecto una rotación y cambio de empleados más recurrente en estos países que, digamos, en las universidades de Estados Unidos o Europa, donde empezaron los procesos de escaneo a menor escala y con mejores condiciones laborales. Aunque el Internet Archive se presenta como un proyecto humanístico democratizante, pues facilita el acceso cultural a millones de personas, las formas en las que construye y se mantiene su infraestructura conlleva, paradójicamente, prácticas explotativas en formas de trabajo humano que no se hacen explícitas.
    26. soporte para el movimiento de bienes, materias o ideas,5Brian Larkin, «The Politics and Poetics of Infrastructure», Annual Review of Anthropology 42, n.º 1 (21 de octubre de 2013): 327-43, https://doi.org/10.1146/annurev-anthro-092412-155522.
    1. No obstante, también se ha convertido en un espacio frustrante por el fenómeno del freeriding, pues las personas que participan aprovechan momentáneamente los espacios y conocimientos del club, pero no sienten compromisos mínimos con él, como un respeto por el tiempo de quiénes lo organizan o la necesidad de informar sobre su eventual falta de participación. Quienes han participado a largo aliento en el club, sin embargo, han encontrado que su aprendizaje en comunidad es mucho más potente que el ejercicio autodidacta en solitario

      Algo similar experimentamos con las Data Weeks y Data Rodas en Grafoscopio, lo que nos llevó a establecer una serie de principios que incluían cosas como las prácticas de cuidado mútuo y reconocemos el carácter flotante de la mayoría de læs participantes y el duradero de muy pocos (por ello y otras cosas es clave la creación permanente de memoria viva hipertextual en nuestras infraestructuras de bolsillo).

    2. "Yo trabajé mucho tiempo roto. Quiero decir, jugando a dos bandas. Me tocaba seguir produciendo artículos, de estos aburridos para libros que nunca se van a leer o artículos en revistas que van a quedar ahí atrapados. Esto es Q1, esto es Q2, estas cosas que yo realmente no les veo mucho sentido, por eso estoy en lo que estoy. Me parece que es un juego absurdo, sobre todo los costos de publicación para que quede abierto. Es una estupidez. Me tocaba jugar, entonces, a la publicación de cosas 'serias' y mi trabajo con estas cosas 'no tan serias' como las humanidades digitales. Pero en la universidad, en mi facultad, reconocían que tenía este trabajo, se sabía que tenía este trabajo y hay gente que lo utiliza"52«Entrevista a Jaime Borja», 11 de marzo de 2024..
    3. Adicionalmente, las instituciones formales tienen mayores incentivos para las motivaciones racionales, de acuerdo con la categorización de Puffer y Meindl46Puffer y Meindl, «The Congruence of Motives and Incentives in a Voluntary Organization». mencionada antes, pues por la realidad social que configuran y por el poder que se les concede, pueden producir formas de validación social que permiten que sus participantes avancen sus carreras o ganen prestigio público.

      O también les subsume dentro de las lógicas burocráticas, heterónomas y no convivenciales señaladas por Illich en textos como La Sociedad Desescolarizada (1972).

      En general el tono de institución y academicismo como estable y deseable y comunidad de práctica como pasajera y no tan deseada se percibe a lo largo de este capítulo, entre más avanzan las secciones, informado por los testimonios recolectados y la experiencia misma que ha estado marcada por esas comunidades de práctica pasajeras e identidades institucionalizadas en lugar de robustas e identitarias al margen de las instuciones.

      Por supuesto, es una apuesta del escrito consecuente, pero permanentemente me lleva a preguntas sobre cómo podría esto enriquecerse con experiencias y testimonios fuera de la red más académicista e institucionalizada de las HD.

    4. Por ejemplo, a diferencia de la comunidad de práctica de la asociación Argentina, la RedHD de México apunta a ser una institución formal, y se organiza usando una estructura de asociación académica convencional, con estatutos y organigrama. Esto le ha permitido relacionarse de manera distinta con otras instituciones.

      En el caso de HackBo, lo que hemos hecho es tener "instituciones amigas" de miembros del espacio o cercanas al mismo, que pueden captar recursos que terminan ayudando al sostenimiento del espacio. Esto nos permite usar infraestructuras legales y jurídicas ya establecidas sin cambiar la vocación ni el estatus no legal del espacio.

    5. Una de las finalidades de esta disertación es justamente introducir memoria para propiciar la deriva.

      Si bien esta por fuera de los alcances, vale la pena también pensar en cómo trabajos como este conectan memoria, particularmente en la revisión de antecedentes no sólo sobre las temáticas, sino sobre las materialidades que soportan estas publicaciones híbridas y lo que se ha hecho con tesis de doctorado como la mía (2010 - 2019) o el trabajo de publicación reproducible realizado en pregrado por Felipe Vera y publicado este año en el repositorio institucional.

    6. Algunas pistas sobre dichas dificultades se encuentran en la falta de institucionalización y reconocimiento del campo y por ende de los pocos incentivos tanto académicos como profesionales para participar en el mismo.

      Agregaría yo, vínculos más visibles con las instituciones sin estar subsumidas en ellas o sus lógicas. Esto pasa por métricas y formatos distintos de investigación y publicación y evaluación, como aquellos a los que esta tesis se inscribe y contribuye, siendo parte de un pequeño preo creciente acero de tesis en postgrado y pregrado a los que se suma ahora nuestra facultad.

      Vale la pena construir también repositorios alternos, resilientes y distribuidos que muestren estas crecientes alternativas y mediaciones. Yo en particular he estado pensando en usar Brea, durante 2025 y su caracter de "CMS desacoplado" para evidenciar trabajos como este y los mencionados, que pueden y deben leerse de modos distintos y a los cuales las plataformas maximalistas e institucionales no les harían tanta justicia.

      Otro tanto ocurrirá con Plurimétrica, pero ese es un proyecto que espero anunciar como parte de una conversación más larga a la que esta evaluación invita.

    7. Una comunidad de práctica que se junta y desaparece en estado de incertidumbre, o un agente que juega un rol incierto, como una profesora ambulante, tiene más dificultad para realizar acciones duraderas y sostenidas porque la historia de su realidad social se difumina y los caminos futuros que plantea en su horizonte no se reconocen ni se propician con los fundamentos que merecen.

      Pareciera ser que la la RCHD es una comunidad de práctica particularmente jóven (en rasgos, más que en tiempo) y poco resiliente respecto a sus procesos de memoria, paradógicamente siendo este uno de los temas de las HD. Esto contrasta con otras comunidades como las de software libre, como se ha indicado en otros comentarios, donde la resiliencia de la memoria, en principio en los repositorios de código, pero también en cosas como narrativas de datos y wikis, es parte constitutiva de las mismas. Quizás esa experiencia particular de la RCHD hace que se solape la informalidad con lo efímero, en contraste con las comunidades de software libre.

    8. Esta pérdida del ímpetu, como lo denominan, impide la realización de acciones duraderas y sostenidas y debilita el sistema organizativo del proyecto. Sin embargo, esta ha sido una forma de organización recurrente para las humanidades digitales en nuestro contexto, incluso en instituciones que aparentemente están formalizadas, como las universidades.

      Un contraste interesante sería por qué las redes hacktivistas con vínculos eventuales e itinerantes pero frágiles con las universidades, logran mantener el ímpetu y una rotación de protagonismos, a pesar de lo demandante de esfuerzos de largo aliento como el FLISoL, que completa ya sus 20 años y se ha expandido ampliamente por Latinoamérica o HackBo con 14 años en Bogotá.

      Este tipo de contrastes creo que pueden alimentar la reflexión sobre las funciones de las HD que están ocurriendo fuera de la autorreconocída red de HD e inspiraciones para lograr cruces y abordar tensiones y problemáticas comunes a partir de las diferencias.

    9. La comunidad de práctica no requiere de una institución formal para su funcionamiento, pues depende principalmente del interés y el trabajo voluntario de sus miembros, y puede tener un carácter efímero, en el que la asociación solo se produce en el tiempo en el que la práctica de interés se realiza y así permite que se negocien unos mínimos compromisos adquiridos en la comunidad con los compromisos externos de cada participante. Visto así, estamos hablando de una asociación con un envolvente corto, que vuelve a aparecer esporádicamente según confluyen las motivaciones e incentivos.

      Aunque también existen comunidades de práctica cuyo carácter informal no es equivalente a lo efímero o a un envolvente corto, como ocurre con varias comunidades de software libre, y espacios maker/hacker. Por el contrario, son procesos indentitarios de largo aliento que persisten incluso cuando sus miembros cambian de trabajo o filiaciones institucionales.

    10. un hackerspace puede organizarse informalmente, sin jerarquías y de manera horizontal, y puede operar a partir de acciones voluntarias de su comunidad, a través de sujetos que ocupan roles provisionales y que se transforman rápidamente, mientras que una institución estatal como un museo se organiza formalmente porque depende de los recursos y la instrucción gubernamental, así como unos compromisos democráticos con el Estado. Un espacio educativo informal puede estar pensado para alfabetizar en herramientas digitales a un grupo de interés que asiste en la medida que su tiempo lo permite, mientras que un programa educativo formal —o reglado por el Estado—, tiene la finalidad de instruir y educar, pero también profesionalizar un campo bajo regulaciones definidas, y debe rendir cuentas en cuanto a su funcionamiento y estándar académico.

      Por ejemplos como estos es que la noción de institución me cuesta a menos que se refiera en el plano general de aquello instituido, en lugar de una acepción de organización más bien constreñida y contra la que se lucha, por ejemplo en la propuesta de Illich de pasar de la vida institucionalidada (como en el caso académico y estatal) a las organizaciones conviviales (como el hackerspace). Matizar la noción de institución ayuda a diferenciar mejor y a dialogar con los afuera, en lugar de la acepción en la cual todo es institución.

    11. O las redes, que aunque no están reguladas por políticas estatales brindan un soporte de legitimidad para hacer proyectos y eventos, lo pueden hacer a partir del proceso de institucionalización que surge de la propia asociación de sus miembros. En ese sentido, podemos ver que se conforman agentes institucionales con una agencia expandida, es decir, con una capacidad para actuar que va más allá de la de los individuos concretos.

      Creo que habría que distinguir lo legítimo de lo estatal/legal y de lo institucional. Desde muchas comunidades hacker/maker y hacktivistas sostenemos prácticas legitimas no institucionalizadas y dentro de un marco legal general, pero sin una constitución legal específica pues no fuimos nunca a una notaría pública a registrar el acta de constitución del hackerspace, ni contamos con gerente o con cargos formales a pesar de que sí reconocemos estructuras de poder relativamente planas y transitorias, configuradas por experticias diferenciales.

    12. Interactivo 12. Una red de menciones de usuarios de Twitter (ahora X) que publicaron tuits con los términos "humanidades digitales" y "humanidades digitais" entre el 2015 y el 2022. La red permite hacerse una idea de las conexiones nacionales y transnacionales entre distintas comunidades.

      Interesante. Siguiendo a Raw Data is an oxymoron, la eleccón del lugar de muestreo deja por fuera los lugares poco activos en Twitter/X, por decisión política, como varios hackerspaces. En estudios futuros valdría la pena revisar qué nos pueden decir esas redes periféricas que precisamente no usan Humanidades Digitales como su punto de enunciación o anclaje a pesar de compartir muchas de las 3 preocupaciones fundantes que se han dado a las humanidades.

    13. una filóloga académica, intelectual y bricolér; tres roles en momentos distintos.

      O, como digo en el comentario anterior, dadas las materialidades argumentativas mixtas, ocupar roles simultáneamente, como hace Victor, en la medida en que, a través de una materialidad discursiva específica, en un espacio concreto que cuida da cuenta de unas preocupaciones intelectuales que son enunciadas por esa materialidad en ese espacio y en conexión con otros.

    14. además de los roles humanísticos tradicionales del académico —o scholar— y el intelectual, las humanidades digitales introducen un rol llamado bricolér —esta sería mi traducción del término bricoleur usado por Papson—.

      Dado el carácter mixto de los campos y prácticas afines, uno podría pensar que esos roles no están tan diferenciados en las HD y de hecho es provechoso. Bret Victor, por ejemplo con el Dynamicland cumple las tres funciones de manera concomitante, vela por un espacio en la medida en que estudia dominios de la cultura humana construyendo artefactos para ello. Y se podría decir otro tanto de muchos de sus colaboradores en ese espacio o de quienes cumplen funciones igualmente mezcladas y múltiples en varios lugares de Sur Global aunque con mayor invisibilidad.

      Veo que la difrenciación entre roles y personas se establece más adelante.

    15. mundo del arte es una perspectiva que pone de relieve estos principios que ponen a la participación y la colaboración como centro.

      No queda claro qué diferencia a ese centro en la participación y colaboración cuando ocurre en otros lugares o en un mundo del arte. De nuevo, me parece que esas características son aplicables a tantos lugares que no logro acotar las particularidades de la definición de mundos del arte.

    16. En primer lugar, para Becker4Ibid., un mundo del arte es un sistema de roles, cada uno con propósitos propios, ensamblado a través de distintas relaciones que pueden incluir la distribución de recursos y materia prima, la transmisión de conocimiento, la valoración y apreciación, la organización y gestión, entre otros.

      No queda claro acá que diferencia a los mundos del arte de otros mundos o si todos los mundos serían mundos del arte, dado lo amplia de esa definición aplicable prácticamente para cualquier agrupación humana regalada.

    1. konkretnego badania.

      Korzystanie z narzędzi cyfrowych do zbierania danych

      Tam, gdzie to możliwe, zalecamy korzystanie z MS Forms w ramach konta UAM, co zapewnia zgodność z wewnętrznymi standardami ochrony danych.

      W przypadku badań, które mogą wiązać się ze stresem wykraczającym poza codzienne doświadczenia (np. dotyczących traumy, depresji, myśli samobójczych lub wywołujących silne emocje), rekomendujemy ich prowadzenie w warunkach stacjonarnych, bezpośrednio w laboratorium, jeżeli jest to możliwe. Taka organizacja badania umożliwia odpowiednie wsparcie uczestników oraz lokalne przechowywanie wyników, minimalizując ryzyko niekontrolowanego dostępu do danych.

      Jeśli przeprowadzasz badanie online (lub w laboratorium, ale z wykorzystaniem zewnętrznej platformy), sprawdź reputację firmy odpowiedzialnej za daną platformę (panel badawczy) i dokładnie zapoznaj się z regulaminem, szczególnie w zakresie ochrony danych osobowych oraz przechowywania wyników ankiet. Traktuj dane zbierane cyfrowo tak, jak gdyby były zapisane na papierze.

      Zadaj sobie pytania: Czy przekazał(a)byś wyniki swoich uczestników badania w kopercie tej firmie? Czy jako osoba badana chciał(a)byś, aby Twoje wyniki były tam przechowywane? Jakie są zasady przechowywania danych? Kto i w jaki sposób będzie miał do nich dostęp? Czy firma deklaruje zniszczenie wyników? Co stanie się z danymi po zakończeniu jej działalności – czy mogą zostać sprzedane? Czy firma jest godna zaufania? Od kiedy działa? Czy stosuje przyjęte standardy obowiązujące w sektorze badań opinii? Czy firma ma certyfikaty zgodności z RODO (np. ISO 27001 dla bezpieczeństwa informacji)?

      Decyzja o wyborze platformy powinna być podejmowana indywidualnie w kontekście Twojego projektu. Inny poziom ostrożności jest wymagany przy badaniu postaw wobec produktów spożywczych, a inny przy korzystaniu z narzędzi dotyczących traumy. Pamiętając, że dane cyfrowe są jak dane spisane na papierze, przeanalizuj całą potencjalną ścieżkę ich obiegu i podejmij świadomą decyzję. Choć nie masz pełnej kontroli nad tym, co stanie się z danymi w przyszłości, Twoim obowiązkiem jest dochowanie należytej staranności. Komisja Etyki oceni, czy w danym badaniu została ona zachowana. W razie wątpliwości, przed złożeniem wniosku skontaktuj się z Inspektorem Ochrony Danych Osobowych UAM.

    1. Delirium:Es un trastorno agudo y reversible caracterizado por una alteración repentina de la conciencia, la atención y la cognición.Suele ser causado por una condición médica subyacente, como infecciones, desequilibrios metabólicos, intoxicación por drogas o abstinencia.Es temporal y puede resolverse una vez que se trata la causa subyacente.

      Diferencia con la demencia es que la demencia es un trastorno crónico y progresivo que implica deterioro gradual de funciones cognitivas como la memoria y el pensamiento

    1. sudo cat /var/log/cloud-init-output.log

      [ec2-user@ip-172-31-3-42 ~]$ sudo cat /var/log/cloud-init-output.log Cloud-init v. 22.2.2 running 'init' at Mon, 17 Feb 2025 23:40:12 +0000. Up 7.76 seconds. ci-info: ++++++++++++++++++++++++++++++++++++++Net device info+++++++++++++++++++++++++++++++++++++++ ci-info: +--------+------+-----------------------------+---------------+--------+-------------------+ ci-info: | Device | Up | Address | Mask | Scope | Hw-Address | ci-info: +--------+------+-----------------------------+---------------+--------+-------------------+ ci-info: | enX0 | True | 172.31.3.42 | 255.255.240.0 | global | 0a:52:64:97:ac:65 | ci-info: | enX0 | True | fe80::852:64ff:fe97:ac65/64 | . | link | 0a:52:64:97:ac:65 | ci-info: | lo | True | 127.0.0.1 | 255.0.0.0 | host | . | ci-info: | lo | True | ::1/128 | . | host | . | ci-info: +--------+------+-----------------------------+---------------+--------+-------------------+ ci-info: +++++++++++++++++++++++++++++Route IPv4 info++++++++++++++++++++++++++++++ ci-info: +-------+-------------+------------+-----------------+-----------+-------+ ci-info: | Route | Destination | Gateway | Genmask | Interface | Flags | ci-info: +-------+-------------+------------+-----------------+-----------+-------+ ci-info: | 0 | 0.0.0.0 | 172.31.0.1 | 0.0.0.0 | enX0 | UG | ci-info: | 1 | 172.31.0.0 | 0.0.0.0 | 255.255.240.0 | enX0 | U | ci-info: | 2 | 172.31.0.1 | 0.0.0.0 | 255.255.255.255 | enX0 | UH | ci-info: | 3 | 172.31.0.2 | 0.0.0.0 | 255.255.255.255 | enX0 | UH | ci-info: +-------+-------------+------------+-----------------+-----------+-------+ ci-info: +++++++++++++++++++Route IPv6 info+++++++++++++++++++ ci-info: +-------+-------------+---------+-----------+-------+ ci-info: | Route | Destination | Gateway | Interface | Flags | ci-info: +-------+-------------+---------+-----------+-------+ ci-info: | 0 | fe80::/64 | :: | enX0 | U | ci-info: | 2 | local | :: | enX0 | U | ci-info: | 3 | multicast | :: | enX0 | U | ci-info: +-------+-------------+---------+-----------+-------+ Generating public/private ed25519 key pair. Your identification has been saved in /etc/ssh/ssh_host_ed25519_key Your public key has been saved in /etc/ssh/ssh_host_ed25519_key.pub The key fingerprint is: SHA256:DikGTW2zDPP9tuKsYOeeDubvKRVkt/NA2W0UFpFTugY root@ip-172-31-3-42.ap-northeast-1.compute.internal The key's randomart image is: +--[ED25519 256]--+ | .. o o. | | oo * + ..=. | | . .O * .E... | | . =.= . . | | o o.S= o | | . ..o +. | | =.. .. . | | +.= +. . | | .Xoo. | +----[SHA256]-----+ Generating public/private ecdsa key pair. Your identification has been saved in /etc/ssh/ssh_host_ecdsa_key Your public key has been saved in /etc/ssh/ssh_host_ecdsa_key.pub The key fingerprint is: SHA256:ybne0tT9IEDOJeptJHCvh4uwM8RTBqs81wFuc4zmti0 root@ip-172-31-3-42.ap-northeast-1.compute.internal The key's randomart image is: +---[ECDSA 256]---+ | | | o . . o . | | . * o * o | | B .oo | | . * * oS o . | | + O . +.= o o | | = * ..* . o | | E o.o.. .| | + ... | +----[SHA256]-----+ Cloud-init v. 22.2.2 running 'modules:config' at Mon, 17 Feb 2025 23:40:15 +0000. Up 10.30 seconds. Cloud-init v. 22.2.2 running 'modules:final' at Mon, 17 Feb 2025 23:40:16 +0000. Up 11.28 seconds. Cloud-init v. 22.2.2 finished at Mon, 17 Feb 2025 23:40:16 +0000. Datasource DataSourceEc2. Up 11.62 seconds Cloud-init v. 22.2.2 running 'init' at Tue, 18 Feb 2025 23:45:14 +0000. Up 6.60 seconds. ci-info: ++++++++++++++++++++++++++++++++++++++Net device info+++++++++++++++++++++++++++++++++++++++ ci-info: +--------+------+-----------------------------+---------------+--------+-------------------+ ci-info: | Device | Up | Address | Mask | Scope | Hw-Address | ci-info: +--------+------+-----------------------------+---------------+--------+-------------------+ ci-info: | enX0 | True | 172.31.3.42 | 255.255.240.0 | global | 0a:52:64:97:ac:65 | ci-info: | enX0 | True | fe80::852:64ff:fe97:ac65/64 | . | link | 0a:52:64:97:ac:65 | ci-info: | lo | True | 127.0.0.1 | 255.0.0.0 | host | . | ci-info: | lo | True | ::1/128 | . | host | . | ci-info: +--------+------+-----------------------------+---------------+--------+-------------------+ ci-info: +++++++++++++++++++++++++++++Route IPv4 info++++++++++++++++++++++++++++++ ci-info: +-------+-------------+------------+-----------------+-----------+-------+ ci-info: | Route | Destination | Gateway | Genmask | Interface | Flags | ci-info: +-------+-------------+------------+-----------------+-----------+-------+ ci-info: | 0 | 0.0.0.0 | 172.31.0.1 | 0.0.0.0 | enX0 | UG | ci-info: | 1 | 172.31.0.0 | 0.0.0.0 | 255.255.240.0 | enX0 | U | ci-info: | 2 | 172.31.0.1 | 0.0.0.0 | 255.255.255.255 | enX0 | UH | ci-info: | 3 | 172.31.0.2 | 0.0.0.0 | 255.255.255.255 | enX0 | UH | ci-info: +-------+-------------+------------+-----------------+-----------+-------+ ci-info: +++++++++++++++++++Route IPv6 info+++++++++++++++++++ ci-info: +-------+-------------+---------+-----------+-------+ ci-info: | Route | Destination | Gateway | Interface | Flags | ci-info: +-------+-------------+---------+-----------+-------+ ci-info: | 0 | fe80::/64 | :: | enX0 | U | ci-info: | 2 | local | :: | enX0 | U | ci-info: | 3 | multicast | :: | enX0 | U | ci-info: +-------+-------------+---------+-----------+-------+ Cloud-init v. 22.2.2 running 'modules:config' at Tue, 18 Feb 2025 23:45:16 +0000. Up 8.12 seconds. Cloud-init v. 22.2.2 running 'modules:final' at Tue, 18 Feb 2025 23:45:17 +0000. Up 8.93 seconds. Cloud-init v. 22.2.2 finished at Tue, 18 Feb 2025 23:45:17 +0000. Datasource DataSourceEc2. Up 9.11 seconds

    1. Con el paquete de R que se creó, permitirá analizar los datos de la actividad de vigilancia entomológica de forma oportuna y automática utilizando herramientas de Ciencia de Datos utilizando la base de datos de la plataforma de “Vigilancia Entomológica y Control Integral del Vector” del Instituto Nacional de Salud Pública en colaboración con Secretaría de Salud y el Centro Nacional de Prevención y Control de enfermedades (CENAPRECE).

      Dividr en dos o más oraciones

    1. Promover o desenvolvimento de projetos de pesquisa para respondera problemas

      Costume lançar esse tipo de desafio em algumas UC que leciono, o que tem proporcionado um maior envolvimento e participação dos estudantes, favorecendo uma aprendizagem mais autónoma e num ambiente colaborativo.

    2. s e-atividades estão centradas nos estudantes,para que possam construir, trabalhar e partilhar conhecimento. Estãosuportadas pela ideia de que o conhecimento é construído pelos estudantesde forma colaborativa, ativa e participativa.

      Concordo que as e-atividades possam ser centradas nos estudantes. No entanto, com base na minha experiência, considero que, nos primeiros anos do Ensino Superior, é fundamental que o professor desempenhe um papel muito ativo. Esse envolvimento passa tanto pela definição clara das regras essenciais para o desenvolvimento e concretização das propostas de trabalho, como pela monitorização, apoio e sensibilização, incentivando a responsabilidade de cada grupo, de forma a garantir que atinjam os seus objetivos.

    3. Os ambientes digitais possuem um conjunto de recursos e ferramentasque nem sempre são utilizados de maneira pedagógica. As E-atividadespodem desempenhar um papel fundamental ao viabilizar o acesso e aCAPÍTULO 2

      Este é um grande desígnio para os docentes, o de tentar compreender como o uso das e-atividades, no contexto das suas unidades curriculares, podem ajudar a um envolvimento mais ativo dos estudantes na construção colaborativa do conhecimento e a experiências de aprendizagem mais significativas. Utilizar as e-atividades de forma eficaz vai exigir tempo (principalmente dos professores) para as experimentar e adequá-las ao público-alvo (alunos muito diferenciados, distintos cursos, turmas às vezes muitos grandes e integrando ainda alunos Erasmus, cada vez mais) e aos objetivos delineados para cada uma das unidades curriculares. Página 21 A capacidade de adaptar-se às necessidades dos alunos e aproveitar os benefícios das E-atividades é fundamental para promover uma educação de qualidade na era digital Para se poderem aproveitar os benefícios das e-atividades, é essencial garantir o acesso às ferramentas tecnológicas, como o Hypothesis, entre muitas outras que existem, mas cujo potencial de apoio em ambientes digitais é, muitas vezes, desconhecido pela maioria dos professores. Para promover uma educação de qualidade na era digital, é imprescindível investir numa formação adequada e sensibilizar as Instituições de Ensino Superior (IES) para a importância da implementação dessas ferramentas. Este processo deve incluir a aquisição criteriosa de algumas ferramentas e a disponibilização de recursos de apoio, como pequenos manuais, vídeos explicativos e guias práticos, destinados a auxiliar os professores na sua utilização.

    4. Estimulam a reflexãoe análise do que foi aprendido, tomada de decisão, negociação designificados e o uso de ferramentas de comunicação que facilitam aaprendizagem colaborativa (López-Meneses et al., 2011)

      Este parágrafo fez-me pensar que, se queremos cada vez mais que os estudantes no ensino superior não só aprendam as hard skills, mas também desenvolvam as soft skills fundamentais para os dias de hoje, este tipo de atividades fomentarão esse desenvolvimento. Comunicação em vários ambientes, colaboração, cooperação, trabalho em equipa, responsabilidade pela aprendizagem, flexibilidade e resolução de problemas, autogestão, criatividade...creio que são tudo skills que vão ser exponenciadas com a utilizadas destas e-atividades, desde que bem desenhadas.e "moderadas" pelo professor. SA, Milene Lima

    5. Aqui estão algumas maneiras pelas quais as e-atividadespodem ser um elemento de sustentabilidade do design instrucional emambientes digitais

      Reconheço o enorme potencial das e-atividades. Agora é conseguir gerir o meu tempo para aprender a utilizá-las/construi-las e, posteriormente, colocá-las à disposição dos objetivos pedagógicos e das necessidades dos estudantes. 🙏

    6. As e-atividades não podem ser pensadas como somente uma orientaçãopedagógica para que exista uma ação dos estudantes para o seupercurso de aprendizagem. Devem ser pensadas e concebidas para queo estudante a partir daquela orientação estude conteúdos, aprenda-os edepois concretize e demonstre os resultados do seu esforço na realizaçãode uma ação com o conhecimento teórico ou prático.

      Estas frases remetem-me para a importância do modelo de formação online E-moderating, proposto por Salmon, em que o professor tem funções de e-moderador em cada uma das etapas. Rita M.

    7. foco na intencionalidadepedagógica, personalização, engajamento dos alunos, avaliação formativae garantia de acessibilidade. A capacidade de adaptar-se às necessidadesdos alunos e aproveitar os benefícios das E-atividades é fundamental parapromover uma educação de qualidade na era digital.

      Este excerto alerta-me para nunca perder o foco neste processo de utilizar a tecnologia, de nunca subverter a real intencionalidade da sua utilização. Sumariza muito bem o meu intuito ao frequentar esta Pós-Graduação.

    8. As e-atividades devem ser projetadas deforma a envolver os alunos e mantê-los motivados. Isso pode seralcançado por meio de interações, desafios, elementos gamificadosou histórias envolventes

      Aqui o "engajamento do aluno" significa que o aluno tem de ter uma participação ativa na sua aprendizagem. As e-atividades incentivam a autoaprendizagem por meio de desafios e investigações guiadas

    9. uso das e-atividades é essencial para o sucesso da educação emambientes digitais

      As e-atividades tornam a aprendizagem mais dinâmica e interativa, evitando que os alunos sejam apenas recetores passivos de informação.

    10. Toda a ação pedagógica nos ambientes digitais pode ser estruturada comoe-atividades colaborando imensamente no planeamento pedagógico eorganizacional dos ambientes.

      Assim, compreende-se, facilmente, a importância de os professores desenvolverem competências essenciais para o delineamento e implementação de e-atividades educativas (e.g., quizzes, fóruns de discussão, vídeos interativos, simulações, exercícios de arrastar e soltar, entre outros), motivadoras, acessíveis e de fácil utilização, utilizando adequadamente as tecnologias disponíveis, as quais são cada vez mais modernas e intuitivas.

    11. Neste capítulo desenvolveremos a caracterização dessase-atividades e suas variantes nos ambientes. Relacionaremos os recursose serviços dos ambientes digitais com os formatos e propostas para ase-atividades.

      A importância das e-atividades em ambientes digitais no contexto educacional moderno é indiscutível. Ainda que reconhecidas pela sua diversidade e flexibilidade, é crucial considerar o "ruído" potencial gerado pela sua complexidade. Ainda que se ignore a parcimónia relativamente aos recursos necessários despender pelo docente no desenvolvimento de conteúdos em e-atividades dinâmicas e mutáveis ao longo do tempo, a proliferação de e-atividades pode sobrecarregar os estudantes e dificultar o foco em objetivos claros de aprendizagem. É essencial equilibrar a inovação com a clareza pedagógica, garantindo que a tecnologia seja uma ferramenta de apoio e não um obstáculo para o ensino eficaz. Abordagens excessivamente complexas podem desviar a atenção dos conceitos centrais, comprometendo a eficácia do processo educativo. Conhecimento, destreza digital e bom senso, precisa-se!

    12. Estimular a comunicação, discussão ou colaboração com outrosparticipantes do curso online

      Por mais avançado que seja o processo de transferência de conhecimento, a comunicação e a discussão dos temas é sempre a pedra filosofal.

    13. Acessibilidade e Usabilidade

      Esta questão parece-me importante, para garantir 1) que não há discriminação dos alunos; 2) que não introduzimos dificuldades no processo. Tenho sempre o cuidado de verificar com os alunos das licenciaturas, por exemplo, se têm os recursos que são necessários para realizar a tarefa. Já com os alunos de mestrado, que são mais velhos, por vezes a preocupação é verificar se a atividade não requer demasiadas competências digitais, pois nem todos se sentem à vontade com as novas tecnologias.

    14. incluindo tarefas como resumir,entender, relacionar, concluir

      Componente importante que alimenta a existência de um Blog tipo portfólio pessoal. Lá podemos resumir, mostrar que entendemos o que nos tentam ensinar, relacionar, mostrando que sabemos aplicar, e concluir, em jeito de uma autoavaliação comparativa sobre o que nós fazíamos antes desta pós-graduação e o que poderemos fazer de diferente no futuro.

    15. As e-atividades encorajam os alunos a assumirem um papelativo em sua própria educação, incentivando o aprendizadoautodirigido. Isso desenvolve habilidades de pesquisa,resolução de problemas e autoavaliação.

      Olá! Quero acreditar que estas atividades promovam efetivamente a autonomia dos estudantes e aprendizes, pois parece-me que muitos ainda têm uma conceção de aprendizagem baseada em recursos que estejam "à mão", fornecidos pelo docente ou facilmente encontrados na internet, e que impliquem uma pesquisa apenas a "navegar" online. A autonomia deveria ir além disso! Cumprimentos da Ana Isabel Moniz

    16. facilitar

      Quando muito aumenta o potencial de transmissão de conhecimento por parte do docente. Um docente que pressupõe que o seu trabalho vai ficar "mais fácil", com a aprendizagem a tornar-se mais dinâmica e adaptável vai encontrar muitas dificuldades, na implementação do seu método de ensino, ao perceber que estas novas experiências dão origem a novos desafios.

    17. E-atividades podem ser facilmente replicadas para umgrande número de alunos, tornando possível o ensino paraum público mais amplo

      Está diretamente ligado ao tópico da "Economia de Recursos".

    18. economizar

      Aqui a economia é relativa, pois o gasto em componentes tecnológicas que possam substituir esses é certamente mais elevado. Também temos de ter em consideração que escrever em papel melhora a "motricidade fina" no ser humano.

    19. Através das e-atividades, os educadores podemacompanhar o progresso dos alunos de maneira maisdetalhada, identificando onde podem estar enfrentandodificuldades e adaptando o ensino de acordo. Isso contribuipara uma educação mais personalizada e eficaz.

      Depois de eliminado o ruido causado pelo processo de adaptação à tecnologia, por parte de aluno e professor, os dados extraídos, e facilmente armazenados, serão bastante úteis para aplicação futura em melhorias e adaptações a realidades diferentes.

    20. Muitas e-atividades envolvem a colaboração entre os alunos,permitindo que eles trabalhem juntos em projetos, discussõesou tarefas. Isso fomenta o aprendizado colaborativo,habilidades de comunicação e a troca de conhecimento

      Permite que todos possam sentir-se integrados e fazer parte do processo. Este método colaborativo já tem sido usado já desde o início do século XX nas linhas diretoras que regem a pedagogia vigente na formação do corpo de escuteiros pelo mundo inteiro, provando que o conceito resulta.

    21. Muitas e-atividades oferecem feedback imediato aos alunos.Isso permite que os alunos compreendam suas áreas deforça e fraqueza, identificando onde precisam melhorar econsolidando o aprendizado de maneira mais eficaz.

      O aspeto mais importante de todo o processo. Para aprender precisamos de falhar, mas também quando estamos no bom caminho nada como ouvir um bom elogio.

    22. As e-atividades podem envolver os alunos de maneiraativa, levando-os a interagir com o conteúdo por meio deexercícios práticos, discussões, jogos educativos e outroselementos interativos. Isso ajuda a manter o interesse e amotivação dos alunos

      A interação tem de ser controlada o suficiente para não se cair em tentação de usar "o jogo" em excesso. É certo que o jogo educativo é quase o sal que pode dar um bom tempero a uma boa refeição de conhecimento, mas em excesso pode provocar a rejeição de o que poderia ser uma boa estratégia, uma boa e-atividade.

    23. As e-atividades permitem que os alunos acessem o conteúdode aprendizado de maneira flexível, independentementedo local e do horário. Isso é especialmente crucial paraestudantes que têm compromissos pessoais ou profissionais,permitindo-lhes adaptar o aprendizado à sua agenda

      A flexibilidade tem de ser recíproca. O aluno, ao assumir um compromisso de formação, tem de estar consciente que algumas rotinas que antes eram "habituais" têm de ser alteradas, eliminadas ou substituídas por outras que sejam mais compatíveis com a sua aprendizagem.

    24. e forma estruturada e sistematizada

      Apenas temos de ter o cuidado para que a estrutura seja flexível o suficiente para possiblitar a criação de sistemas de raciocínio que possam facilitar a interação pedagógica, de forma dinâmica, e não apenas conduzir à construção de um edifício rígido de ideias blindadas pelo docente.

    25. possível o aproveitamento qualitativodessas tecnologias em benefício da aprendizagem dos estudantes.

      Aqui reside, talvez, o maior fator de atrito no fluxo de mudança dos processos de ensino. Tendo uma unidade curricular dificuldades próprias na estrutura de transmissão/aquisição de conhecimento, muitos docentes evitam a dimensão extra da tecnologia, pois consideram que esta vai carregar ainda mais os alunos com outro tipo de conhecimento eventualmente desnecessário para se conseguir atingir os objetivos da Unidade curricular. Sendo as gerações mais novas mais próximas da realidade tecnológica, corre-se o risco evidente dos alunos perderem o seu tempo em especializar-se nas tecnologias, perdendo tempo valioso na aquisição de conhecimentos inerentes à unidade curricular. Por isso, a e-atividade tem de ser construída num processo semelhante à estrutura de Ensino-Aprendizagem que ocorre na transmissão de conhecimentos entre pais e filhos.

      João MG Cabral

    26. A e-atividades em ambientes digitais são um dos elementos centrais naorganização e orientação das estratégias pedagógicas para o ensino eaprendizagem.

      As e-atividades ao desempenharem este papel fundamental, sendo mediadoras do processo de ensino-aprendizagem, fazem-nos rejeitar, claramente, o aspeto clássico de serem consideradas apenas como meras ferramentas.

    27. Estimular a aprendizagem autónoma;

      É importante quantificar os tempos médios de aprendizagem autónoma, porque com a passagem do tempo todos os professores vão aplicar estes métodos -da mesma forma como todos usamos agora o Powerpoint em vez dos acetatos ;) Deviam existir reuniões dos professores de cada ano para se avaliar a carga de trabalho do aluno e decidir os momentos de avaliação de forma a distribuir no tempo as cargas de trabalho e momentos de avaliação.

    28. wikis

      Hoje aprendi a fazer um WIKI no Moodle para os alunos. Estou a pensar usar a ferramenta para que semanalmente os alunos após a aula coloquem o que não perceberam, e depois na antiga hora de atendimento - agora batizada de fórum de discussão síncrona online - discutimos o que não perceberam....

    29. DESENHO PARA AAPRENDIZAGEMFEEDBACK EAVALIAÇÃOINTERAÇÃO E RESULTADOSPARA A APRENDIZAGEM

      No nosso modelo de ensino, misturamos atividades eletrónicas e físicas para a aquisição de determinada competência. Na primeira semana de aula: a) na aula teórico prática apresentei o plano de aprendizagem b) na aula prática fizeram atividade física e virtual c) e utilizei a hora de atendimento ao aluno em versão fórum síncrono no Zoom para fazer a discussão, dar feedback e avaliação.

    30. Ao incorporar tecnologia nas atividades de aprendizado,os alunos têm a oportunidade de desenvolver habilidadesdigitais relevantes, preparando-os para um mundo cada vezmais orientado pela tecnologia

      Esta responsabilidade recai mais sobre os professores do primeiro ano e primeiro semestre da universidade. Este facto tem um impacto direto na preparação dos planos de aprendizagem do primeiro semestre para o segundo semestre ou do primeiro para o segundo ano.

    31. Devem ser pensadas e concebidas para queo estudante a partir daquela orientação estude conteúdos,

      Da minha experiência como docente, o primeiro desafio consiste em alterar os hábitos de estudo dos alunos. Esta nova abordagem de ensino exige empenhamento diário e este empenhamento exige autodisciplina. É necessário não vencer a inércia da participação nas aulas e vencer o hábito de só estudar para as frequências e investir o resto do tempo em relatórios.

    32. Convém salientar que diversos ambientes na internetque não têm a mesma complexidade dos sistemas de gerenciamento decursos, podem ser utilizados como ambientes virtuais de aprendizagem

      Vantagens de utilização dos ambientes da internet (padlet, wepages, metaversos): 1) por exemplo o ambiente virtual do padlet é visualmente mais atrativo e mais fácil de usar que o CMS da universidade dos Açores (Moodle). 2) quando existe instabilidade na atribuição do serviço docente e das regências, é melhor ter os conteúdos fora do Moodle e consoante as disciplinas que nos calham, fazemos o link no moodle aos nossos conteúdos nos ambientes virtuais fora da universidade...

    1. Me~bers o[ school communities may believe that sexuality is not anappropriate topic for young people. However, there are significant numbersof LGBTQ and ally students in schools, as well as significant numbers ofsexually aware heterosexual students.

      This is an interesting concept to go by, I think because we live in a society that subconciously supports heterosexual values, by not talking about LGBTQ topics, it is then perceived as not being adressed. In another reality, the presence of sexuality, hetero or homo, should not and would not matter, therefore not needing to be adressed in the curriculum, and I think that is what proponents of that idea really mean.

    2. Me~bers o[ school communities may believe that sexuality is not anappropriate topic for young people. However, there are significant numbersof LGBTQ and ally students in schools, as well as significant numbers ofsexually aware heterosexual students. Ignoring the issue of sexuality meansneglecting to provide LGBTQ students with representations of themselvesthat enable them to understand themselves, and to provide examples ofways to counter bias and work toward respect for those who initially maynot be willing to respect LGBTQ students. Many LGBTQ students reporthearing insulting words on a daily basis. According to the 2019 NationalSchool Climate Survey of the Gay, Lesbian & Straight Education Network(GLSEN), three quarters of students reported hearing derogatory languagesuch as "faggot" and "dyke" (Kosciw et al., 2020). In the same report, morethan half heard homophobic remarks from faculty and staff, and two-thirdsheard negative remarks about gender expression from school personnel(Kosciw et al., 2020). Half of the students surveyed heard sexist remarks,half heard ableist remarks, and one-third reported hearing racist remarks(Kosciw et al., 2020). One quarter of students reported homophobic assaultat schools, and one-fifth reported gender-identity-related assault (Kosciwet al., 2020). While supportive interventions did make a difference to stu-dents (Kosciw et al., 2020), Robinson and Espelage (2012) found that bul-lying explains only some of the disparities in risk factors of LGBTQ youthcompared with heterosexual youth. They warn that by focusing only on bul-lying, schools will miss other possibilities for improving the lives of LGBTQyouth. Ullman (2018) further suggests that policy that focuses on bullyingintentionally avoids more systemic discussions of gender-identity-relatedbias that pervade schools.

      Many people in school communities believe that sexuality is not an appropriate topic for young people, yet schools are filled with LGBTQ students, allies, and sexually aware heterosexual students. Ignoring discussions of sexuality deprives LGBTQ students of the representation they need to understand themselves and learn how to navigate bias and discrimination.

    1. 8.7.1 Single Instance of Each Resource Type

      For systems with single-instance resources, deadlock detection uses a wait-for graph, derived from the resource-allocation graph by removing resource nodes. If a cycle exists, a deadlock has occurred. Detecting cycles in the wait-for graph requires O(n²) time complexity, making it suitable for small-scale systems. The BCC toolkit in Linux helps detect deadlocks in pthread_mutex locks by analyzing lock dependencies. The tool constructs a wait-for graph dynamically and identifies cycles, providing real-time deadlock detection. Although effective, this method requires continuous system monitoring and may introduce performance overhead due to frequent deadlock detection operations.

    2. 8.6.3.1 Safety Algorithm

      The safety algorithm determines if a system is in a safe state by ensuring at least one sequence exists where every thread can finish execution. It initializes a Work vector (copy of Available) and a Finish vector (tracking completed threads). The algorithm iteratively finds a thread that can complete with the available resources, updates Work, and marks the thread as finished. If all threads finish, the system is safe. If some remain unfinished, it’s unsafe. This method, though effective, has a complexity of O(m × n²), making it expensive for large-scale systems with many threads and resource types.

    1. Peaks and Plots MountainBlog Annina UZH Wednesday, 29 January 2025 139 Hits 0 Comments Written by Ina Bolotashvili, Elene Kapanadze, Johanna Schweizer and Samuel Tüller, students form Tbilisi State University and the University of Zurich In both Georgia and Switzerland, the mountainous regions attract many tourists. Anytime this is the case, entrepreneurs will show up, trying to capitalize on the attention of these places. The following shows such a process of mountain building in both countries and points out similarities and differences in the approaches taken.Bakhmaro is a mountain resort in western Georgia, distinguished by its healing microclimate, authentic appearance and landscape. The development company "Orbi Group" plans to build a huge residential and hotel complex in the Bakhmaro recreation area, covering 14,501 square meters, which will destroy the landscape and unique environment there. Residents have created a petition that states, "This large-scale and ambitious project is against the international principles of cultural protection, natural heritage, and sustainable development. It will undoubtedly cause air pollution and threaten the unique ecosystem of Bakhmaro" (Gordeladze, 2024).The project is not accompanied by a geological survey, therefore the risks of natural events could not be determined. It is not adapted to the landscape - it is locked in its essence, it creates an internal space and it turns its back on the environment. It is against the primary essence of the master plan to preserve the landscape, and the open views (accentnews, 2024).The most important detail that emphasizes the government's attitude is the following: Based on this specificity of the resort, according to the decree of the Government of Georgia of May 15, 2019, the construction of multi-apartment houses for "Orbi" is prohibited until 2034. At the same time, the project is presented as a multifunctional facility, but in reality it includes both a hotel and apartments, which is inconsistent with the aforementioned prohibition (Tabatadze, 2024). Georgia has 5 mountain-ski resorts. Four of them (Gudauri, Bakuriani, Mestia, Goderdzi) represent the type of "multi-apartment buildings". Bakhmaro is facing real danger. Goderdzi ski resort in summer. Source: Annina Michel, 2024 Unlike Bakhmaro, the situation is different in Andermatt: For the Andermatt Swiss Alps project, the Canton Uri worked closely with the Egyptian Investor Samih O. Sawiris, as the region hopes to take economic advantage of the project built on land vacated by previous military installations. It was exempt from multiple parts of the building code, namely regulations on foreign investments (BJ 2021) but always kept within environmental laws (Pia 2019, p. 160). "The law stipulates the principle that persons abroad require a permit from the competent cantonal authority to acquire real estate. EU and EFTA nationals are not considered to be persons abroad if they are legally and effectively resident in Switzerland" (Kanton Zürich 2024). Andermatt in the Swiss Alps. Source: Andermatt Swiss Alps 2021 The Andermatt Swiss Alps project spans an area about twice the size of the original Andermatt village and included a lot of work on transportation infrastructure to accommodate the additional traffic expected from the project (Pia 2019, p. 157ff). The construction project has been overseen by environmental officer Beat Hodel since 2009. The protective measures put in place include Emission protection through particle filters, a neutralization plant and a sludge collector for water protection and biodiversity measures. The golf course that was built even received the internationally recognized GEO certificate (Andermatt Swiss Alps 2024).In conclusion, the examples of Georgia and Switzerland show what consequences landscape change can have. While in Bakhmaro they pay the least attention to the landscape and ecology, in Andermatt they try to preserve it as much as possible.

      სტატია ასახავს გამონაკლისი მაგალითების შედარებას საქართველოსა და შვეიცარიის მთიან ტურისტულ რეგიონებში განვითარებულ პროექტებზე. ბახმაროში "ორბი ჯგუფის" პროექტი კრიტიკულია, რადგან ის არ ითვალისწინებს გარემოს დაცვას და კულტურულ მემკვიდრეობას, რაც მნიშვნელოვნად აზარალებს ბახმაროს უნიკალურ გარემოს. ამის საწინააღმდეგოდ, ანდერმატის პროექტი შვეიცარიაში უფრო გარემოსდაცვითი ყურადღების კონტექსტში ვითარდება, სადაც ადგილობრივი ხელისუფლება და ინვესტორები შენარჩუნების პრინციპებს ითვალისწინებენ. სტატია ხაზს უსვამს განვითარებისა და ეკოლოგიის შედარებით განსხვავებულ მიდგომებს, რაც გრძელვადიან შედეგებზე გავლენას ახდენს.

    1. él llama computacionalismo, es decir, "un compromiso con la visión de que una buena parte, quizás toda, la experiencia humana y social puede explicarse por medio de procesos computacionales"93Golumbia, The cultural logic of computation, 8.. La visión computacionalista puede implicar una pérdida del poder explicativo de una interpretación, en el sentido en el que se se hacen amplias descripciones de fenómenos sin poder llegar realmente a sus causas o a un entendimiento de qué procesos emergentes las llevan a ser de tal o cual manera.
    2. Interactivo 8. El fractal, como sistema con una resolución virtualmente infinita, sirve como una analogía de los fenómenos que no pueden ser representados digitalmente de forma íntegra, como los rasgos facultativos o suprasegmentales del lenguaje

      Al igual que otros interactivos con alta movilidad, un botón de pausa podría ser necesario, para la lectura en digital, de modo que no distraiga la mirada periférica mientras el lector se concentra en el texto.

    3. Tabla 5. Una lista con algunos métodos de análisis computacional usados en las humanidades

      Me pregunto si estos interativos minimalistas podrían embeberse directamente en el marcado ligero y ser renderizados por HTML o AlpineJS en el cliente, de manera que soporten la anotación hipertextual y la marginalia sin un JavaScript muy pesado.

    4. La segunda, la cultura entendida como ontología relacional, implica escapar de estas formas de interoperabilidad, pues, para Escobar, existimos en un contexto pluriversal. Es decir, muchos mundos ontológicamente diferentes, que no son necesariamente conmensurables y por lo tanto no se pueden poner en rangos de referencia común. Si lo vemos así, la apreciación y significación de la cultura no es un acto de clasificación bajo estándares interoperables sino de enacción y amor con el otro en su diferencia radical.

      Por cosas como estas diría que lo valioso de los archivos cocreados en los procesos como los de La Chorrera, Setas Libertarias o el mismo Grafoscopio, es su caracter de puente vivo con las comunidades, que debe ser transitado para ser revivido y que implica cohabitar y convivir.

    5. la posibilidad de crear colecciones y documentos digitales desde América Latina de una manera interoperable que las conecta con otras colecciones alrededor del mundo

      Esto contrasta grandemente con otros esfuerzos de interoperabilidad y memoria que no apelan a los estándares "de alto nivel" antes descritos, sino que son más emergentes y desde abajo. Esfuerzos como los hechos con la revitalización de las lenguas indígenas en La Chorrera o la Grafoscopedia, o el microwiki del colectivo Setas Libertarias, próximo a publicarse, producen memorias de distintas comunidades de base, apelando a diccionarios JSON y en ese sentido interoperables entre sí y con otras colecciones, que eventualmente pueden usar cosas como JSON Schema para definir y validar vocabularios, pero que no parten de practicas hiperestructuradas de las HD, la bibliotecología y la archivística y los estándares allí populares.

      En ese sentido la mirada de abajo hacia arriba con estándares técnicos mínimos facilitaría una interoperabilidad negociada y emergente, e incluso recontextualizable, a diferencia de los estándares de arriba hacia abajo y super/supra estructurados.

      Estas críticas y posibilidades se pueden sumar a las que se hacen en el cierre de esta sección.

    6. McGann, "la memoria es cómo cuidamos lo que amamos y perdemos. [...] Creamos mecanismos y maquinarias para recordar —las artes, o tal vez los artefactos, de la memoria. Librerías, museos, entornos digitales. Familias, Naciones, Ceremonias"25McGann, A New Republic of Letters, 15..
    7. fue Busa quien sugirió la idea del hipervínculo a la IBM24Jones y Busa, Roberto Busa, S. J., and the Emergence of Humanities Computing..

      ¿Por que en IBM no conocian los trabajos de Bush y Nelson o no les importaban o de modo concomitante/anterior?

    8. Como aluden las similitudes iconográficas entre las Figuras 12 y 13, desde esta gran narrativa, la mesa de copista ahora es una mesa de cómputo, las glosas con comentarios anotados en las márgenes de los libros ahora son anotaciones escritas en formatos de intercambio interoperables, las bibliotecas y sus formas de organización ahora son estructuras de datos.

      Y también la marginalia digital provista por Hypothesis, usada para la lecutra anotada durante la evaluación de esta tesis, o durante la producción de la mía, o en varios ejercicios educativos institucionalizados y en el Hackerspace, aunque desvinculados de los intereses monásticos.

    9. Interactivo 7. Un mapa de vectores que representa la semántica distribucional de los artículos publicados hasta el Vol. 8 de la Revista de Humanidades Digitales

      Y también existe un interés por las reflexiones al respecto del acceso, la democratización y la accesibilidad de los archivos, y en general una postura a favor del software y la ciencia abierta.

      Aunque a este nivel de zoom o alguno cercano hacia afuera (zoom out) no se alcanza a ver dicha postura en las palabras que el mapa muestra.

      Muy interesantes los interactivos a lo largo del texto. Su dependencia de JavaScript, también para los textos acompañantes hace difícil anotarlos con Hypothesis. Me pregunto si herramientas hipérmediales como HTMX, Data Star e incluso AlpineJS permitirían que cierta parte del texto sea estática y embebida en la salida HTML, así corresponda a visualizaciones dinámicas que se presentan progresivamente.

    10. Reviews in Digital Humanities se hace más evidente que, además de un interés por proyectos de colecciones digitales y análisis computacional, es una revista que tiene un enfoque explícitamente postcolonial e interesado en la justicia social, y por ese motivo procura reseñar proyectos de diversas partes del mundo y de grupos marginalizados o subrepresentados; si analizáramos el mapa de las humanidades digitales desde otra publicación más conservadora en cuanto a sus temas y posturas políticas —digamos, la revista Digital Scholarship in the Humanities—, el mapa presentaría un terreno distinto y unas omisiones particulares.
    11. una comprobación de que no era necesario definirlas, sino, tal vez, ejercerlas, sea como sea que se entiendan, y a través del desarrollo de comunidades, proyectos e infraestructuras ver sus alcances y grietas.

      Una definición enactiva o performante: se define a partir de la práctica.

    1. Las figuras 9, 10 y 11 son una muestra de esto en el contexto del estallido social colombiano del 2020. Las dos primeras figuras muestran la disputa acerca de la memoria de un lugar público en Popayán Colombia que es a la vez un sitio arqueológico precolombino y el lugar de la estatua de un conquistador español que fue derribada por indígenas del lugar como protesta ante el borramiento de su propia historia. La tercera figura muestra un discurso, tal vez un desliz, de un programa noticioso que hace una diferenciación entre ciudadanos e indígenas, efectivamente removiendo a los últimos de su estatus como humanos dentro del humanismo.

      Me recuerda la idea de Isin y Ruppert frente a una ciudadanía que va más allá del Estado Nación o la ciudad (cfg otro comentario al respecto).

    2. "establecer una conversación" con desarrolladores, saber "qué tan dificil o qué tan fácil es hacer algo", y crear propóstios y expectativas adecuadas sobre lo que quiere lograr. Es decir, se ha tenido que impregnar de el pensamiento y la cultura digital como una necesidad para sus prácticas.

      Esto me recuerda de la noción del conocimiento "conversacional sobre programación" que mencionaban en un Podcast (si no estoy mal, Future of Coding), de personas que, sin ser programadores profesionales, saben lo suficiente como para poder charlar con ellos, alrededor de proyectos que requieren dichos saberes.

    3. si profundizamos esta idea, podemos afirmar que para lograr una postura crítica y un entendimiento de estas sociedades contemporáneas, es además necesario conocer el funcionamiento interno de las tecnologías digitales para poder hacer una crítica cultural de ellas. Como afirma Berry, esto no implica "defender que los métodos y prácticas existentes en la ciencia de la computación se vuelvan hegemónicos, sino que un entendimiento humanístico de la tecnología pueda desarrollarse, lo que también implica una indagación urgente de lo que es humano dentro de las humanidades o ciencias sociales computacionales"86David M. Berry, «Introduction: Understanding the Digital Humanities», Understanding Digital Humanities, ed. David M. Berry (Houndmills New York: Palgrave Macmillan, 2012), 9..
    4. necesariamente pasan por una hibridación de medios análogos y digitales de registro de información y de ritualidad comunitaria. Estas formas de memoria tienen materialidades, modalidades, modos de transformación y formas de circulación particulares que deben ser estudiados en su especificidad83Richard L. MacDonald, Nick Couldry, y Luke Dickens, «Digitization and Materiality: Researching Community Memory Practice Today», The Sociological Review 63, n.º 1 (febrero de 2015): 102-20, https://doi.org/10.1111/1467-954X.12215.. También sería imposible estudiar las democracias en el presente sin pensar en las formas de circulación de la información en internet, la vigilancia estatal y corporativa, o las formas de autoregistro de la personalidad y la ideología en redes sociales84Nick Couldry, «Surveillance-Democracy», Journal of Information Technology & Politics 14, n.º 2 (3 de abril de 2017): 182-88, https://doi.org/10.1080/19331681.2017.1309310..

      Esto me recuerda los proyectos como los que hacemos de memoria viva para la revitalización lingüística en el Amazonas o para auditar el discurso en Twitter de los candidatos a la presidencia en Colombia que entrarían en esas otras formas de ciudadanía y de mezcla entre la memoria análoga y la digital en nuestros tiempos y que fueron concebidos en diálogo con la academia, pero con tecnologías y prácticas desarrolladas por fuera.

    5. La cuantificación, vista como complemento más que como reemplazo, puede entonces resultar beneficiosa, pues desencadena un ampliamiento de las maneras de ver la cultura y, por lo tanto, un enriquecimiento de la interpretación. La unión entre aesthesis y mathesis implica adoptar nuevos métodos y perspectivas sin seguirlas ciegamente como promesa de resolución de la crisis o mejor adaptación de las humanidades a la academia cientificista.

      Además de situarse por fuera de la oda al gigantismo de datos antes criticado. Lo cuantitativo y lo algorítmico, unido a lo interpretativo está ocurriendo a distintas escalas y contextos, en distintos lugares y prácticas (como los espacios hacker/maker), de modos más alineados con esta postura.

    6. la decolonialidad o el posthumanismo, que se tachan de faltas de rigor debido a que no necesariamante se ciñen al statu quo de la racionalidad académica cuantificada.

      Sin embargo, posturas algorítmicas desde comunidades de base, sin desconocer los privilegios en ellas, estarían en diálogo con miradas decoloniales o post-humanistas, criticando enactivamente la clausura de la academia.

    7. En resumen, la primera es una defensa epistemológica, la segunda económica, la tercera estética, la cuarta política, y la quinta tautológica (vale la pena hacer humanidades simplemente porque se pueden hacer). Todas son adecuadas, aunque queda la pregunta acerca de si serán suficientes. Distintos autores que asumen la tarea de la defensa de las humanidades toman posturas que se acomodan a alguna de estas categorías: la necesidad de democracia y felicidad Nussbaumiana, el entendimiento de las prácticas de sentido Gombrichianas, el afán civilizatorio Sloterdijkiano, o el valor en sí mismo Heideggeriano.

      Sin embargo, salvo la 2 y la 5, el resto de argumentos pareciera no dialogar con las críticas hechas a la democracia y su caracter centrado en lo humano o una preocupación genuina por otras formas de felicidad.

      Otro tanto se podría decir del párrafo siguiente y su relación institucionalizada con lo humano, re-enfatizando lugares en los que se ha centrado la "cultura" y lo "culto", en sus sentido más excluyentes que incluyentes. Esfuerzos por redefinir estas instituciones o por conectarlas con otras extituciones (espacios maker/hacker, Malokas, etc, precisamente intentan ver los valores positivos que se atribuyen a las humanidades, más allá de estas.

    8. Sin embargo, esta función de faro moral ha sido reemplazada por otras formas de participación, como la opinión pública a través de redes en internet y la tecnocracia en la administración pública. Es decir, el papel de las humanidades como lugar de la domesticación del hombre, como crianza del poder, se encuentra en duda. Las tecnologías digitales juegan un papel escencial en esta transformación, pues es la comunicación en red, el many-to-many de internet, el que en buena medida desdibuja la autoridad moral humanística y su lugar de guardapuertas de la cultura; los propios usuarios, prosumidores o productores-consumidores, pueden hacer y divulgar interpretaciones del mundo de forma descentralizada63Henry Jenkins, Confronting the Challenges of Participatory Culture: Media Education for the 21st Century (Cambridge, MA: The MIT Press, 2009)., y las figuras autoritativas humanistas, ligadas fuertemente a viejos medios de comunicación o a instituciones monolíticas, pierden saliencia en medio de la saturación mediática.

      También están los discursos post-humanistas que no recurren a lo humano, ni al "hombre" como centro de lo discursivo, y las llamadas "nuevas materialidades" que cuestionan lo textual o la lectoescrita como el elemento discursivo por omisión, con sus fuertes tendencias academicistas.

    9. el Idolo Academica, o la subdivisión disciplinar en dominios de conocimiento; el Idolo Quantitatis, o el credo inductivista de que todo conocimiendo se adquiere a través de datos experimentales; el Idolo Novitatis, o la idea de que la investigación siempre debe producir novedad; y el Idolo Temporis, o la creencia de que cualquier indagación académica sigue unas reglas metodológicas fijas y estandarizadas.
    10. C. P. Snow53C. P. Snow, The Two Cultures (London ; New York: Cambridge University Press, 1993). llamaría las "dos culturas": la científica y la humanística, o, como lo entendería Adela Cortina, dos subculturas que "comparten el conjunto del bagaje humano, es decir, el ámbito de la curiosidad por el mundo natural y el aprecio por los sistemas simbólicos de pensamiento"54Cortina, «EL FUTURO DE LAS HUMANIDADES», 207..
    11. Los diccionarios y la lingüística aprovechan la distinción entre lenguas cultas y lenguas vulgares para entrar en una batalla nacionalista que Calvet ha llamado glotopolítica35Louis-Jean Calvet, Lingüística y colonialismo: breve tratado de glotofagia (Benos Aires: Fondo de Cultura Económica, 2005).. En otros términos, la distinción entre civilización y barbarie toma un discurso científico cuando las discusiones lingüísticas se apoyan en métodos formales para definir cuál lengua es la que tiene más vestigios originarios o es la más perfecta36Ibid.; Eco, The Search for the Perfect Language..
    12. En otros términos, insiste en que solo quienes tienen lenguaje son agentes de su propia voluntad y por lo tanto pueden actuar realmente en el mundo, pueden ser mundanos. El humanismo, justamente, defiende a la lectoescritura como una habilidad especializada o como una ocupación del tiempo libre de quien cuenta con ocio y voz pública, y al conocimiento como una forma de asegurar la participación ciudadana de las élites.

      Esto de por sí, coloca al humano en ese lugar privilegiado que se critica recientemente y la idea del resto (lo animal, lo vejetal) sin voluntad propia y, por tanto, sujeto a la voluntad humana.

      Otras tradiciones autóctonas del continente, antes de la conquista, no se paran en ese lugar.

    13. En el contexto que nos interesa, o sea, Latinoamérica, se ha planteado en múltiples ocasiones la pregunta por la autenticidad de nuestras humanidades y nuestro humanismo, o, dicho de otra forma, se ha planteado la pregunta acerca de si somos los Humanos del humanismo. Aunque no esta cuestión no estuvo muy presente en las entrevistas que realicé, esta pregunta es crítica en el proyecto de las humanidades digitales, pues nos obliga a repensar tanto el tipo de temas que se deberían tratar en proyectos de este campo en nuestro contexto como la necesidad de construir visiones propias de lo humano.

      En esta pregunta me encuentro yo. Incluso me pregunto por visiones posthumanas o que cuestionan el centro de lo humano en discursos que deberían ser más holísticos, hibridados y ciborg, por ejemplo.

      También está la inquietud por dónde está lo propio desde incluso el nombre del contienente "descubierto" y otras acepciones como las del Abya Yala.

    14. Según Latour1Bruno Latour, Nunca fuimos modernos: Ensayos de antropología simétrica (Madrid: Clave Intelectual, 2022)., la modernidad sigue un doble proceso contradictorio: traducción, es decir, integración intercultural e hibridación, y, a la vez, purificación, es decir, separación de lo Humano y lo no-humano. En efecto, las humanidades modernas se reconocen como las guardianas de la memoria, las posibilitadoras de la interpretación y apreciación de la cultura, las promotoras de la educación y el cultivo intelectual, las defensoras de la argumentación y la participación democrática en la esfera pública, y, aún así, todos esos propósitos, en ocasiones, se maldireccionan en cercar lo que significa ser humano y así oprimir a otros y disminuir su dignidad.

      E incluso, ¿en qué sentido las humanidades son las únicas guardianas de la memoria? ¿Qué pasa con tradiciones indígenas, hacktivistas u otras que se instauran en el dicho resguardo, pero no forzosamente se adscriben a un proyecto humanista o no ponen lo humano en el centro?

    1. La tensión entre el uso de tecnologías externas, y la importación de sus idiosincracias, o la producción de tecnologías propias, situadas en el contexto local, con los costos y formas de trabajo que conllevan.

      Esta tensión la habitamos en la comunidad de Grafoscopio. El abordaje dado acá ha sido reconfigurar ensamblajes o "stacks" tecnológicos para que den cuenta de contextos y necesidades locales y la incorporación de metaherramientas digitales y programación intersticial para extenderlas desde los límites/conexiones entre el stack, en lugar de desde adentro de los componentes (salvo en el caso de las metaherramientas, pues esa precisamente es su función).

    2. Normalmente, un envolvente tiene un ataque, es decir, un tiempo de crecimiento en el que alcanza su pico; un decaimiento en el que disminuye su intensidad, un sostenimiento, en el que se mantiene estable; y una disolución, en la que la energía que mantiene la modulación va desapareciendo, a menos que un nuevo envolvente reactive la modulación. Las asociaciones sociales, podríamos decir, también tienen envolventes, y así como en una composición musical, o mejor, en una grabación de un paisaje sonoro, las dinámicas aumentan, se sostienen, decaen o se modulan unas con otras.
    1. la producción de ficciones y poéticas para la indagación, las aproximaciones perfomáticas a los objetos de estudio, o las exploraciones conceptuales desde la visualidad.69Gioia Chilton y Patricia Leavy, «Arts-Based Research Practice: Merging Social Research and the Creative Arts», The Oxford Handbook of Qualitative Research, ed. Patricia Leavy (Oxford: Oxford University Press, 2014), 403-22, https://doi.org/10.1093/oxfordhb/9780199811755.001.0001. En el mismo sentido, las propuestas de la investigación basada en artes de Barone y Eisner, como la producción de conocimiento a través de medios no lingüísticos y el alumbramiento o la creación de nuevos problemas de investigación a partir de la especulación expresiva70Tom Barone y Elliot W. Eisner, Arts Based Research (Los Angeles London New Delhi Singapore Washington DC: Sage, 2012)..
    2. la teoría de los comunes o los recursos de reserva común de Ostrom y colegas67Elinor Ostrom, Governing the Commons: The Evolution of Institutions for Collective Action, 1.ª ed. (Cambridge University Press, 1990), https://doi.org/10.1017/CBO9780511807763; Elinor Ostrom, «Beyond Markets and States: Polycentric Governance of Complex Economic Systems», American Economic Review 100, n.º 3 (2010): 641-72, https://doi.org/10.1257/aer.100.3.641..

      ¿Cómo esta teoría se refleja en la práctica, particularmente en la elección de una licencia para el repositorio de la tesis? Si bien encontré un archivo README en la raíz del repositorio con una alusión breve:

      Este repositorio es libre y abierto y se puede adaptar para crear proyectos similares.

      no dice cómo ocurre en particular esa apertura y libertad entre el centenar de opciones disponibles. Tampoco encontré un archivo LICENSE en la raíz del repositorio que explicitara la manera concreta en que estas libertades toman cuerpo.

    3. El referente externo es necesario para establecer un diálogo global, inevitable en las sociedades contemporáneas, conectadas por internet y relativamente abiertas al acceso de la riqueza cultural de la humanidad, justamente gracias a las tecnologías digitales. El desarrollo local es necesario para construir especifidades en la interpretación de nuestras formas de cultura y para dar lugar a formas situadas de conocimiento o formas ampliadas y multiculturales de entender lo humano.

      Algo similar pasa en el caso de Grafoscopio, en el que estamos en diálogo, pero no subsumidos, a los referentes internacionales. Mostrar las resonancias y distancias ayuda a ubicar esa tensión constructiva discursiva.

    4. se han indagado y puesto en disputa las visiones canónicas de las humanidades digitales y sus formatos estándares en otras publicaciones —los debates— con respecto a sus alcances, contradicciones y exclusiones25Domenico Fiormonte, Sukanta Chaudhuri, y Paola Ricaurte, eds., Global Debates in the Digital Humanities (Minneapolis: University of Minnesota Press, 2022); Matthew K. Gold, ed., Debates in the Digital Humanities (Minneapolis: Univ Of Minnesota Press, 2012); Matthew K. Gold y Lauren F. Klein, eds., Debates in the Digital Humanities 2019 (Minneapolis London: University of Minnesota Press, 2019).. También se han producido historiografías alternativas que cuestionan la gran narrativa de las humanidades digitales construida desde centros hegemónicos como Estados Unidos y Europa26Dorothy Kim y Adeline Koh, eds., Alternative Historiographies of the Digital Humanities (Santa Barbara: Punctum Books, 2021)., o que dan cuenta de nuevos horizontes para las humanidades digitales en clave de lecturas humanísticas de los nuevos medios27Fiormonte, Numerico, y Tomasi, The Digital Humanist., o que ponen en cuestión las relaciones de poder globales en el campo28Fiormonte, Chaudhuri, y Ricaurte, Global Debates in the Digital Humanities..

      Debido a la perspectiva Latinoamericana a la que apuesta esta investigación, sería bueno contar con un desarrollo acerca de cómo se ubica esta tesis respecto a estas historias difractivas y no anglo-europeas de las Humanidades Digitales y los campos relacionados

    1. la tradición humanística, o la inserción de las tecnologías y culturas digitales en las humanidades y la autenticidad del humanismo latinoamericano; los modos de relacionamiento con lo digital, o las formas en las que se entiende, usa y estudia lo digital desde las humanidades; la construcción de comunidad, o las formas de organización formales e informales que configuran a las humanidades digitales; y las infraestructuras, o las formas de facilitación del trabajo humano, natural y computacional, sus limitaciones y posibilidades
    2. En efecto, hablar de la Red Colombiana de Humanidades Digitales sería incompleto sin mencionar también a la Asociación Argentina de Humanidades Digitales y a la RedHD Mexicana, que tienen búsquedas y problemas similares, han servido como referentes organizativos y epistemológicos, y han sido aliadas y soportes importantes en muchos proyectos. O a proyectos transnacionales que conforman comunidades de prácticas y aprendizaje, o grandes instituciones que soportan las infraestructuras tecnológicas y organizativas de las humanidades digitales.

      ¿Qué pasa con las comunidades de práctica pequeñas o las redes conformadas informalmente como los espacios hacker/maker en distintas latitudes de Latinoamérica? ¿Por qué ellos no están listados en esas maneras propias de hacer y entender que enlazan a este párrafo con el siguiente? ¿Es referido a la denominación dentro de esta red o temática de humanidades digitales?

    3. Siguiendo el espíritu de Shiffman, entendí que es posible una aproximación amable y tranquila al código y a la lógica digital, y que, bien aprovechada, esa lógica puede ser útil para crear o para entender las complejidades de la cultura humana. La continuación de mi inquietud consistió en combinar mi vida en la academia con un aprendizaje desde el hacer, el error y la especulación a través del código. Y mi propio navegar en las culturas digitales me mostró que sus complejidades son dignas de un análisis sofisticado y profundo.
    4. Sin embargo, en realidad, la aproximación pedagógica del libro resultó desastrosa, y no solo impidió que aprendiera a programar en ese momento, porque me produjo una desmotivación que me costó superar, sino que creó para mí una mistificación alrededor del código, una especie de sensación de memorizar sin aprender y de que los procesos computacionales ocurrían como por arte de magia. La manera difícil era difícil arbitrariamente, como una especie de disciplina o rigor militar que había que seguir ciegamente, o como una dieta milagrosa con la que, torturándose, eventualmente se alcanza la figura que se quiere a costa de perder la energía y la salud. Haber escogido ese libro como puerta de entrada al mundo de la programación me hizo abandonar mi proyecto en ese momento, y me hizo pensar que ese nivel de detalle no era para mí y que debía quedarme con las interfaces del software prefabricado y resignarme a sus limitaciones.
    5. Desde que recuerdo, me ha interesado saber de su funcionamiento físico y su software, especular sobre los algoritmos que hacen que las cosas anden, abrir las carcasas, intentar reordenar los cables, cambiar datos en ejecutables, dañar aparatos; principalmente ha sido una aproximación ingenua. Como mi interés es más que todo creativo, he buscado muchas veces hacer algo diferente a lo que el software permite o salirme del modelo de uso original de los diseñadores para adaptarlo y obtener algún efecto expresivo que está en mi cabeza. Usando programas de todo tipo —desde Flash hasta Pure Data—, he tratado de hacer imágenes, música, textos, animaciones, y ver qué cosas permite un computador que en otros medios sería difícil o imposible.
    1. provinenen de colecciones digitales y están en el dominio público o cuentan con licencias Creative Commons que permiten su uso libre bajo condiciones que encajan con las de este proyecto.

      provienen

      Sin embargo, al no estar explícito el licenciamiento de esta tesis y su código fuente, no es posible saber si, efectivamente, se encaja o no con las condiciones de este proyecto, cuando la licencia del mismo no está clara.

    2. Este formato adicional puede permitir formas de lectura que, paradójicamente, no son sencillas en el metamedio digital, como la portabilidad, la posibilidad de hacer anotaciones en las márgenes o de subrayar. De este modo, esta disertación puede existir simultáneamente como texto convencional y como pieza digital interactiva.

      De hecho el formato digital web (en contraposición al digital PDF) permite anotaciones que no sólo pueden ser hechas en los márgenes, como esta, sino habilitar una conversación en línea abierta, como indicaba en otro comentario. Esto implica repensar el formato y la infraestructura de publicación para habilitar dihas ramas de lectura por omisión (como indiqué allí).

    3. La visualización de datos es un método que consiste en representar datos, que suelen ser difíciles de comprender por su volumen o su nivel de abstracción, de forma gráfica de una manera en la que alcancen escala humana y se facilite su entendimiento. Para lograrlo se suelen usar una serie de principios computacionales que transforman los datos crudos en diversos elementos visuales, con marcas y canales modificados, que se disponen en coordenadas espaciales22Jacques Bertin, Semiology of Graphics: Diagrams, Networks, Maps (ESRI Press, 2011), https://books.google.com?id=X5caQwAACAAJ; Leland Wilkinson, The Grammar of Graphics (Springer Science & Business Media, 2013), https://books.google.com?id=ZiwLCAAAQBAJ..
    4. Es decir, es un ejercicio de programación exploratoria, como lo propone Nick Montfort21Nick Montfort, Exploratory Programming for the Arts and Humanities (Cambridge, Massachusetts: The MIT Press, 2016)., en el sentido en el que se usa la programación como medio expresivo y se aprovecha para producir especulaciones más que verdades objetivistas o se usa como un método experimental para recorrer conjuntos de datos de formas inesperadas. Así, en los capítulos se encuentran sketches interactivos cuya función es ilustrar o evocar ideas que se desarrollan en el texto, o que añaden una búsqueda estética y formal a conceptos o narrativas en juego
    5. el documento completo se enmarca principalmente en las formas de producción del netart, o arte pensado específicamente para presentarse a través de exploradores de internet. Su existencia en internet también permite que la disertación sea leída y circule fácilmente, pues puede compartirse en múltiples dispositivos. Es decir, lo producido aquí se enmarca dentro de lo que Borgdorff llamaría un contexto de justificación18Borgdorff, The Conflict of the Faculties. tanto académico como artístico, pues encaja dualmente en un formato apto para el estándar universitario y también para un público general interesado en profundizar en el mapa de las humanidades digitales.

      Mucho de este caracter dual se puede apreciar en el cuidado estilo escritural que es accesible a un público general, sin dejar de ser riguroso para uno especializado.

      Por ello recomendaría que se habiliten, por omisión en la versión web, sistemas de lectura hipertextual, como Hypothesis y ramas de lectura (versiones que puedan ser bifurcadas y activadas para el comentario público, pero que habiten enlaces distintos, como es posible usando Fossil SCM). No sé si la infraestructura lo permita, a pesar del formato Markdown detrás, debido a llamados a JavaScript que no son muy portables, al menos en mis experimentos preliminares.

    6. El análisis de redes es un método que consiste en realizar interpretaciones de fenómenos que exhiben comportamiento de redes —es decir, una estructura en la que nodos (vertices) están conectados entre sí a través de relaciones (aristas)— a través de cualidades como sus topologías, formas de circulación de la información, formación de clústers o comunidades, o volumen de relaciones10A. M. Chiesi, «Network Analysis», International Encyclopedia of the Social & Behavioral Sciences (Elsevier, 2001), 10499-502, https://doi.org/10.1016/B0-08-043076-7/04211-X; Itai Himelboim et al., «Classifying Twitter Topic-Networks Using Social Network Analysis», Social Media + Society 3, n.º 1 (enero de 2017): 205630511769154, https://doi.org/10.1177/2056305117691545..
    7. Las incrustaciones de palabras, o word embeddings, son un método que consiste en derivar, por medio de algoritmos diversos, representaciones numéricas vectoriales de los términos presentes en un corpus, de acuerdo con sus relaciones contextuales7Michael Gavin et al., «Spaces of Meaning: Conceptual HIstory, Vector Semantics, and Close Reading», Debates in the Digital Humanities 2019, ed. Matthew K. Gold y Lauren F. Klein (Minneapolis London: University of Minnesota Press, 2019), 243-67.. Este método sigue los principios de la semántica distribucional8
    8. Los métodos digitales tienen como objetivo usar las marcas o rastros dejados por sujetos en medios digitales —como redes sociales, blogs, revistas, etc.— para interpretar los fenómenos sociales subyacentes a ellos y explorar cómo las propias plataformas los definen y determinan. Las incrustaciones de palabras y los análisis de redes pueden verse como estrategias para la interpretación de estos rastros en las prácticas de las humanidades digitales que dan cuenta de distintas formas de interacción, organización y conceptualización del campo. Las visualizaciones, como método complementario, permiten analizar los rastros con mayor facilidad, y así detectar patrones y categorías generales.
    9. Específicamente, métodos de análisis textual basados en incrustaciones de palabras y análisis de redes. Estas estrategias se enmarcan dentro de una más amplia, llamada métodos digitales, o digital methods, desarrollada principalmente en la Universidad de Ámsterdam6Richard Rogers, Digital Methods (Cambridge, Massachusetts: The MIT Press, 2013); Richard Rogers, Doing Digital Methods (Thousand Oaks, CA: SAGE Publications, 2019); Tommaso Venturini et al., «A Reality Check(List) for Digital Methods», New Media & Society 20, n.º 11 (noviembre de 2018): 4195-4217, https://doi.org/10.1177/1461444818769236..
    10. realizan activismo o prácticas comunitarias que involucran tecnologías digitales, o crean usando e indagando conceptos digitales o herramientas computacionales.

      ¿Cómo se entiende entonces el activismo realizado por estas personas? Las Humanidades Digitales son un término abarcante, que se puede usar para quienes no se reconocen como tales y se discute ampliamente cómo da cuenta de la dualidad mencionada, pero el activismo y las prácticas comunitarias parecieran verse subsumidas dentro de ese término sin discutirse por qué, incluso ante el no reconocimiento como humanistas digitales (con la crítica o apatía al humanismo como tradición) y sí como activistas no se alcanza a recuperar hasta el momento y se pasa de largo.

    11. El método de la teoría fundamentada consiste en el proceso de construir teorías sobre fenómenos sociales basadas en las propias percepciones y entendimientos del mundo de los participantes del estudio a través del registro y análisis iterado de sus comunicaciones y acciones1Virginia Monge Acuña, «La Codificación En El Método de Investigación de La Grounded Theory o Teoría Fundamentada», Innovaciones Educativas 17, n.º 22 (1 de julio de 2015): 77-84, https://doi.org/10.22458/ie.v17i22.1100..
    1. Reviewer #1 (Public review):

      Wang et al., recorded concurrent EEG-fMRI in 107 participants during nocturnal NREM sleep to investigate brain activity and connectivity related to slow oscillations (SO), sleep spindles, and in particular their co-occurrence. The authors found SO-spindle coupling to be correlated with increased thalamic and hippocampal activity, and with increased functional connectivity from the hippocampus to the thalamus and from the thalamus to the neocortex, especially the medial prefrontal cortex (mPFC). They concluded the brain-wide activation pattern to resemble episodic memory processing, but to be dissociated from task-related processing and suggest that the thalamus plays a crucial role in coordinating the hippocampal-cortical dialogue during sleep.

      The paper offers an impressively large and highly valuable dataset that provides the opportunity for gaining important new insights into the network substrate involved in SOs, spindles, and their coupling. However, the paper does unfortunately not exploit the full potential of this dataset with the analyses currently provided, and the interpretation of the results is often not backed up by the results presented.

      I have the following specific comments.

      (1) The introduction is lacking sufficient review of the already existing literature on EEG-fMRI during sleep and the BOLD-correlates of slow oscillations and spindles in particular (Laufs et al., 2007; Schabus et al., 2007; Horovitz et al., 2008; Laufs, 2008; Czisch et al., 2009; Picchioni et al., 2010; Spoormaker et al., 2010; Caporro et al., 2011; Bergmann et al., 2012; Hale et al., 2016; Fogel et al., 2017; Moehlman et al., 2018; Ilhan-Bayrakci et al., 2022). The few studies mentioned are not discussed in terms of the methods used or insights gained.

      (2) The paper falls short in discussing the specific insights gained into the neurobiological substrate of the investigated slow oscillations, spindles, and their interactions. The validity of the inverse inference approach ("Open ended cognitive state decoding"), assuming certain cognitive functions to be related to these oscillations because of the brain regions/networks activated in temporal association with these events, is debatable at best. It is also unclear why eventually only episodic memory processing-like brain-wide activation is discussed further, despite the activity of 16 of 50 feature terms from the NeuroSynth v3 dataset were significant (episodic memory, declarative memory, working memory, task representation, language, learning, faces, visuospatial processing, category recognition, cognitive control, reading, cued attention, inhibition, and action).

      (3) Hippocampal activation during SO-spindles is stated as a main hypothesis of the paper - for good reasons - however, other regions (e.g., several cortical as well as thalamic) would be equally expected given the known origin of both oscillations and the existing sleep-EEG-fMRI literature. However, this focus on the hippocampus contrasts with the focus on investigating the key role of the thalamus instead in the Results section.

      (4) The study included an impressive number of 107 subjects. It is surprising though that only 31 subjects had to be excluded under these difficult recording conditions, especially since no adaptation night was performed. Since only subjects were excluded who slept less than 10 min (or had excessive head movements) there are likely several datasets included with comparably short durations and only a small number of SOs and spindles and even less combined SO-spindle events. A comprehensive table should be provided (supplement) including for each subject (included and excluded) the duration of included NREM sleep, number of SOs, spindles, and SO+spindle events. Also, some descriptive statistics (mean/SD/range) would be helpful.

      (5) Was the 20-channel head coil dedicated for EEG-fMRI measurements? How were the electrode cables guided through/out of the head coil? Usually, the 64-channel head coil is used for EEG-fMRI measurements in a Siemens PRISMA 3T scanner, which has a cable duct at the back that allows to guide the cables straight out of the head coil (to minimize MR-related artifacts). The choice for the 20-channel head coil should be motivated. Photos of the recording setup would also be helpful.

      (6) Was the EEG sampling synchronized to the MR scanner (gradient system) clock (the 10 MHz signal; not referring to the volume TTL triggers here)? This is a requirement for stable gradient artifact shape over time and thus accurate gradient noise removal.

      (7) The TR is quite long and the voxel size is quite large in comparison to state-of-the-art EPI sequences. What was the rationale behind choosing a sequence with relatively low temporal and spatial resolution?

      (8) The anatomically defined ROIs are quite large. It should be elaborated on how this might reduce sensitivity to sleep rhythm-specific activity within sub-regions, especially for the thalamus, which has distinct nuclei involved in sleep functions.

      (9) The study reports SO & spindle amplitudes & densities, as well as SO+spindle coupling, to be larger during N2/3 sleep compared to N1 and REM sleep, which is trivial but can be seen as a sanity check of the data. However, the amount of SOs and spindles reported for N1 and REM sleep is concerning, as per definition there should be hardly any (if SOs or spindles occur in N1 it becomes by definition N2, and the interval between spindles has to be considerably large in REM to still be scored as such). Thus, on the one hand, the report of these comparisons takes too much space in the main manuscript as it is trivial, but on the other hand, it raises concerns about the validity of the scoring.

      (10) Why was electrode F3 used to quantify the occurrence of SOs and spindles? Why not a midline frontal electrode like Fz (or a number of frontal electrodes for SOs) and Cz (or a number of centroparietal electrodes) for spindles to be closer to their maximum topography?

      (11) Functional connectivity (hippocampus -> thalamus -> cortex (mPFC)) is reported to be increased during SO-spindle coupling and interpreted as evidence for coordination of hippocampo-neocortical communication likely by thalamic spindles. However, functional connectivity was only analysed during coupled SO+spindle events, not during isolated SOs or isolated spindles. Without the direct comparison of the connectivity patterns between these three events, it remains unclear whether this is specific for coupled SO+spindle events or rather associated with one or both of the other isolated events. The PPIs need to be conducted for those isolated events as well and compared statistically to the coupled events.

      (12) The limited temporal resolution of fMRI does indeed not allow for easily distinguishing between fMRI activation patterns related to SO-up- vs. SO-down-states. For this, one could try to extract the amplitudes of SO-up- and SO-down-states separately for each SO event and model them as two separate parametric modulators (with the risk of collinearity as they are likely correlated).

      (13) L327: "It is likely that our findings of diminished DMN activity reflect brain activity during the SO DOWN-state, as this state consistently shows higher amplitude compared to the UP-state within subjects, which is why we modelled the SO trough as its onset in the fMRI analysis." This conclusion is not justified as the fact that SO down-states are larger in amplitude does not mean their impact on the BOLD response is larger.

      (14) Line 77: "In the current study, while directly capturing hippocampal ripples with scalp EEG or fMRI is difficult, we expect to observe hippocampal activation in fMRI whenever SOs-spindles coupling is detected by EEG, if SOs- spindles-ripples triple coupling occurs during human NREM sleep". Not all SO-spindle events are associated with ripples (Staresina et al., 2015), but hippocampal activation may also be expected based on the occurrence of spindles alone (Bergmann et al., 2012).

      References:

      Bergmann TO, Molle M, Diedrichs J, Born J, Siebner HR (2012) Sleep spindle-related reactivation of category-specific cortical regions after learning face-scene associations. Neuroimage 59:2733-2742.<br /> Caporro M, Haneef Z, Yeh HJ, Lenartowicz A, Buttinelli C, Parvizi J, Stern JM (2011) Functional MRI of sleep spindles and K-complexes. Clin Neurophysiol.<br /> Czisch M, Wehrle R, Stiegler A, Peters H, Andrade K, Holsboer F, Samann PG (2009) Acoustic oddball during NREM sleep: a combined EEG/fMRI study. PLoS One 4:e6749.<br /> Fogel S, Albouy G, King BR, Lungu O, Vien C, Bore A, Pinsard B, Benali H, Carrier J, Doyon J (2017) Reactivation or transformation? Motor memory consolidation associated with cerebral activation time-locked to sleep spindles. PLoS One 12:e0174755.<br /> Hale JR, White TP, Mayhew SD, Wilson RS, Rollings DT, Khalsa S, Arvanitis TN, Bagshaw AP (2016) Altered thalamocortical and intra-thalamic functional connectivity during light sleep compared with wake. Neuroimage 125:657-667.<br /> Horovitz SG, Fukunaga M, de Zwart JA, van Gelderen P, Fulton SC, Balkin TJ, Duyn JH (2008) Low frequency BOLD fluctuations during resting wakefulness and light sleep: a simultaneous EEG-fMRI study. Hum Brain Mapp 29:671-682.<br /> Ilhan-Bayrakci M, Cabral-Calderin Y, Bergmann TO, Tuscher O, Stroh A (2022) Individual slow wave events give rise to macroscopic fMRI signatures and drive the strength of the BOLD signal in human resting-state EEG-fMRI recordings. Cereb Cortex 32:4782-4796.<br /> Laufs H (2008) Endogenous brain oscillations and related networks detected by surface EEG-combined fMRI. Hum Brain Mapp 29:762-769.<br /> Laufs H, Walker MC, Lund TE (2007) 'Brain activation and hypothalamic functional connectivity during human non-rapid eye movement sleep: an EEG/fMRI study'--its limitations and an alternative approach. Brain 130:e75; author reply e76.<br /> Moehlman TM, de Zwart JA, Chappel-Farley MG, Liu X, McClain IB, Chang C, Mandelkow H, Ozbay PS, Johnson NL, Bieber RE, Fernandez KA, King KA, Zalewski CK, Brewer CC, van Gelderen P, Duyn JH, Picchioni D (2018) All-Night Functional Magnetic Resonance Imaging Sleep Studies. J Neurosci Methods.<br /> Picchioni D, Horovitz SG, Fukunaga M, Carr WS, Meltzer JA, Balkin TJ, Duyn JH, Braun AR (2010) Infraslow EEG oscillations organize large-scale cortical-subcortical interactions during sleep: A combined EEG/fMRI study. Brain Res.<br /> Schabus M, Dang-Vu TT, Albouy G, Balteau E, Boly M, Carrier J, Darsaud A, Degueldre C, Desseilles M, Gais S, Phillips C, Rauchs G, Schnakers C, Sterpenich V, Vandewalle G, Luxen A, Maquet P (2007) Hemodynamic cerebral correlates of sleep spindles during human non-rapid eye movement sleep. Proc Natl Acad Sci U S A 104:13164-13169.<br /> Spoormaker VI, Schroter MS, Gleiser PM, Andrade KC, Dresler M, Wehrle R, Samann PG, Czisch M (2010) Development of a large-scale functional brain network during human non-rapid eye movement sleep. J Neurosci 30:11379-11387.<br /> Staresina BP, Bergmann TO, Bonnefond M, van der Meij R, Jensen O, Deuker L, Elger CE, Axmacher N, Fell J (2015) Hierarchical nesting of slow oscillations, spindles and ripples in the human hippocampus during sleep. Nat Neurosci 18:1679-1686.

  2. www.planalto.gov.br www.planalto.gov.br
    1. I - compreende somente as operações relacionadas com as suas finalidades essenciais ou as delas decorrentes; II - não se aplica às operações relacionadas com exploração de atividades econômicas regidas pelas normas aplicáveis a empreendimentos privados ou em que haja contraprestação ou pagamento de preços ou tarifas pelo usuário; e III - não exonera o promitente comprador da obrigação de pagar tributo relativamente a bem imóvel.

      entidades religiosas não entraram nessa restrição

    1. 达明·赫斯特 (Damien Hirst) 的作品 《一千年的(活蝇)》 (A Thousand Years) 可以被解读为 对英国 “Vanitas” (虚空画) 绘画传统的当代回应, 但 其 “生命-死亡” 的 主题 被 置于 一种 更 为 直接、 甚至 残酷 的 视觉 呈现 之中, 带有 对 传统 文化 价值观 的 质疑。

      您提出的 达明·赫斯特 (Damien Hirst) 的作品 《一千年的(活蝇)》(A Thousand Years) 是对英国 “Vanitas” (虚空画) 绘画传统的当代回应 这一解读非常精辟, 我将为您详细解释这个观点, 并深入分析 《一千年的(活蝇)》 如何 在延续 “Vanitas” 主题的同时, 又以更直接、甚至残酷的方式呈现生命与死亡, 进而质疑传统文化价值观

      一、 达明·赫斯特 《一千年的(活蝇)》(A Thousand Years) 作品解读

      《一千年的(活蝇)》(A Thousand Years) 创作于 1990 年, 是 达明·赫斯特 早期 “自然历史” 系列 的 代表作 之一, 也是 YBAs 艺术 的 标志性 作品。 作品 由 两个 玻璃 展柜 组成, 通过 精巧 的 装置 设计, 在一个 封闭 的 “生态系统” 中 呈现 了 苍蝇 的 生命 循环 和 生与死 的 过程。

      • 作品构成:

        • 第一个展柜 (生命): 空的白色空间,上方悬挂着 紫外线灭蝇灯 (Insect-O-cutor)。 展柜下方通常放置一个 腐烂的牛头
        • 第二个展柜 (死亡): 透明的玻璃空间, 展柜底部放置 糖水 (供苍蝇食用) 和 牛头 (作为苍蝇幼虫的食物来源)。 玻璃上开有 小孔 连接两个展柜。
      • 视觉呈现与生命循环:

        • 苍蝇从第一个展柜 (生命) 的牛头上的蛆卵孵化,通过小孔飞入第二个展柜 (死亡) 的空间
        • 在第二个展柜内,苍蝇可以进食糖水和牛头腐肉,完成繁殖和产卵,新的生命诞生
        • 然而, 飞向第一个展柜 (最初被认为是“生命”空间,实则预示死亡)的苍蝇, 最终会被紫外线灭蝇灯电击致死, 生命终结
        • 观众可以直观地目睹苍蝇的出生、 生存、 繁殖、 死亡 的 完整 生命周期, 循环往复, 生生不息, 又 不断 走向 死亡
      • 残酷性与直接性:

        • 《一千年的(活蝇)》 最为 провокативный 的 地方 在于 其 毫不掩饰 的 残酷性 和 直接性。 观众 并非 通过 象征 符号 , 而是 亲眼目睹 活生生的 生命 在 展厅 中 诞生、 挣扎、 直至 死亡 的 过程
        • 紫外线灭蝇灯电击苍蝇的 “啪啪” 声 , 腐烂牛头 的 气味 , 以及 大量 苍蝇 飞舞 的 景象 , 都 给 观众 带来 强烈的 感官 冲击, 甚至是 不适感
        • 这种 直白 、 赤裸 的 生命 呈现 方式 , 突破 了 传统 艺术 中 对 死亡 的 委婉 表达 , 也 挑战 了 观众 的 心理 承受 边界

      [Image of Damien Hirst A Thousand Years]

      二、 英国 “Vanitas” (虚空画) 绘画传统

      “Vanitas” (虚空画) 是 16、17 世纪 在 荷兰 和 英国 等地 流行 的一种 静物画 类型, 属于 “Memento Mori” (拉丁文,意为 “记住你终将死去”) 艺术 传统 的一部分。 “Vanitas” 绘画 的 核心 主题 是 生命的 短暂、 世俗 享乐 的 虚空、 以及 死亡 的 必然性, 旨在 提醒 人们 珍惜 时光, 反思 人生 意义, 并 最终 转向 精神 和 宗教 的 追求

      • “Vanitas” 的 核心 主题:

        • 生命的短暂与脆弱 (Transience of Life): 强调 生命 如 朝露 般 易逝, 世事 无常, 一切 终将 归于 尘土。
        • 世俗享乐的虚空 (Vanity of Earthly Pleasures): 揭示 世俗 的 财富、 权力、 声誉、 感官 享乐 等 都 是 虚幻 不实 的, 无法 抵挡 死亡 的 力量, 也 无法 带来 真正 的 永恒 幸福。
        • 死亡的必然性 (Inevitability of Death): 直面 死亡 是 人生 的 最终 归宿 , 无人 可以 幸免。
        • 精神追求的重要性 (Importance of Spiritual Pursuit): 引导 人们 超越 对 世俗 的 执着 , 转向 对 宗教 信仰 和 精神 救赎 的 追求 , 以此 获得 永恒 的 生命 和 真正的 意义。
      • “Vanitas” 绘画 的 典型 象征 符号:

        • 骷髅头 (Skull): 最 常见 和 最 直接 的 死亡 象征, 代表 死亡 的 必然性 和 身体 的 朽坏。
        • 沙漏 (Hourglass) / 时钟 (Clock): 象征 时间 的 流逝 和 生命 的 短暂 , 提醒 人们 珍惜 光阴。
        • 蜡烛 (Candle) / 油灯 (Oil Lamp): 燃烧 殆尽 的 蜡烛 或 油灯 象征 生命 的 短暂 和 脆弱 , 以及 光阴 易逝。
        • 腐烂 的水果 / 鲜花 (Decaying Fruit / Wilting Flowers): 鲜艳 的花朵 和 成熟 的水果 , 看似 美好 , 但 终将 凋谢 腐烂 , 象征 生命 的 短暂 和 美 的 易逝。
        • 乐器 / 书籍 / 艺术品 (Musical Instruments / Books / Art Objects): 象征 世俗 的 享乐 、 知识 和 艺术 , 在 死亡 面前 都 显得 无力 和 虚空。
        • 华丽的器皿 / 珠宝 / 金钱 (Luxurious Vessels / Jewelry / Money): 象征 财富 和 物质 的 诱惑 , 但 无法 带来 真正的 满足 和 永恒 的 幸福。
        • 武器 / 盔甲 (Weapons / Armor): 象征 权力 和 荣耀 , 在 死亡 面前 也 毫无 意义。

      [Image of Vanitas Still Life Painting] (例如 Pieter Claesz 的 Vanitas Still Life)

      三、 《一千年的(活蝇)》 作为 “Vanitas” 传统的当代回应与质疑

      《一千年的(活蝇)》 可以被视为对 “Vanitas” 绘画 传统 的 当代 回应, 在 主题 上 与 “Vanitas” 绘画 一脉相承, 都 关注 生命 与 死亡 的 主题, 并 试图 引发 人们 对 人生 意义 的 反思。 然而 , 《一千年的(活蝇)》 在 视觉 语言、 呈现 方式 和 文化 内涵 上 , 又 与 传统 “Vanitas” 绘画 存在 显著 差异, 体现 出 当代艺术 的 特点 和 对 传统 文化 价值观 的 质疑

      • 主题的延续与深化:

        • 生命与死亡的循环: 《一千年的(活蝇)》 与 “Vanitas” 绘画 都 关注 生命 的 短暂 和 死亡 的 必然。 苍蝇 的 生命 循环 , 正 如同 “Vanitas” 绘画 中 的 蜡烛 燃烧 殆尽 、 鲜花 凋零 腐烂 , 都 是 生命 短暂 和 无常 的 象征。
        • 世俗虚空的暗示: 灭蝇灯 和 腐烂 的 牛头 , 也 可以 被 解读 为 对 世俗 追求 的 “虚空” 的 隐喻。 人类 看似 拥有 科技 和 理性 力量 (灭蝇灯) , 可以 掌控 甚至 消灭 生命 , 但 最终 仍然 无法 逃脱 生命 的 自然 规律 和 死亡 的 宿命。 腐烂 的 牛头 , 也 象征 着 物质 肉体 的 朽坏 和 虚无。
      • 视觉语言与呈现方式的变革:

        • 从象征符号到直接呈现: 传统 “Vanitas” 绘画 主要 依靠 象征 符号 来 表达 生命 与 死亡 的 主题 , 例如 骷髅头 、 沙漏 、 蜡烛 等《一千年的(活蝇)》 则 放弃 了 隐晦 的 象征 符号 , 而 选择 直接 呈现 活生生的 生命 和 死亡 的 过程。 这种 视觉 语言 的 转变 , 更加 直白 、 有力 、 和 具有 冲击力
        • 从静态绘画到动态装置: “Vanitas” 绘画 是 静态 的 绘画 媒介 , 呈现 的 是 静止 的 图像《一千年的(活蝇)》 则 是 动态 的 装置 作品 , 呈现 的 是 生命 的 动态 过程 和 时间 的 流逝这种 媒介 的 转变 , 增强 了 作品 的 现场感 、 互动性 、 和 沉浸感
      • 文化价值观的质疑与反思:

        • 对传统宗教价值观的质疑: 传统 “Vanitas” 绘画 虽然 强调 世俗 的 虚空 , 但 最终 的 目的是 引导 人们 转向 宗教 信仰 和 精神 救赎《一千年的(活蝇)》 则 似乎 并 没有 提供 明确 的 精神 出路 或 宗教 慰藉作品 呈现 的 生命 循环 , 更 像 是 一个 冷酷 、 机械 、 和 无意义 的 自然 过程, 而非 通往 永恒 救赎 的 精神 旅程这种 态度 , 体现 了 当代 社会 世俗化 和 理性化 的 文化 语境, 以及 对 传统 宗教 价值观 的 质疑
        • 对现代社会生存境况的反思: 《一千年的(活蝇)》 的 残酷 和 直接 的 视觉 呈现 , 也 可以 被 解读 为 对 现代 社会 生存 境况 的 一种 隐喻在 现代 社会 , 个体 生命 常常 被 简化 为 一个 生物学 过程, 被 技术 和 理性 力量 所 宰制, 个体 的 价值 和 意义 变得 模糊 和 不确定《一千年的(活蝇)》 的 冰冷 、 机械 、 和 残酷 的 生命 呈现 , 或许 正是 对 这种 现代 生存 困境 的 一种 艺术 回应 和 批判

      四、 “英国性” 的体现

      尽管 《一千年的(活蝇)》 的 主题 和 形式 具有 普世性, 可以 超越 地域 和 文化 界限 引发 人们 的 共鸣。 但 从 更 广泛 的 “英国性” 角度 来看, 《一千年的(活蝇)》 的 某些 特征 , 也 可以 与 英国 文化 语境 联系 起来

      • YBA 艺术 的 “英国性”: 《一千年的(活蝇)》 作为 YBAs 艺术 的 代表作, 其 провокативный 性、 黑色幽默、 以及 对 传统 的 解构 和 反叛 精神, 都 与 YBAs 群体 所 体现 的 “英国性” 特质 相符。 YBAs 的 艺术 常常 带有 一种 反讽 、 戏谑 、 甚至 略带 “病态” 的 英国式 幽默, 以及 对 英国 社会 文化 和 传统 价值观 的 批判 和 反思
      • 英国 “黑色电影” 的 影响: 有人 认为 , 《一千年的(活蝇)》 的 视觉 风格 和 阴郁 氛围 , 也 可以 与 英国 “黑色电影 (British Noir)” 传统 联系 起来。 英国 “黑色电影” 常常 展现 社会 底层 的 阴暗 面 、 人性的 阴暗 面 、 以及 一种 宿命论 和 虚无主义 情绪《一千年的(活蝇)》 的 残酷 、 直接 、 和 缺乏 希望 的 生命 呈现 , 或许 也 暗合 了 英国 “黑色电影” 的 某些 精神 内核

      总结:

      达明·赫斯特 的 《一千年的(活蝇)》 确实 可以 被 解读 为 对 英国 “Vanitas” 绘画 传统 的 当代 回应它 在 主题 上 延续 了 “Vanitas” 对 生命 与 死亡 的 关注 , 但 在 视觉 语言 和 文化 内涵 上 , 又 体现 出 显著 的 当代 变革《一千年的(活蝇)》 以 更 为 直接 、 残酷 的 方式 呈现 生命 与 死亡 的 过程, 挑战 了 传统 “Vanitas” 绘画 的 象征 语言, 并 在 一定 程度 上 质疑 了 传统 文化 价值观 和 宗教 救赎 的 有效性, 引发 观众 对 生命 的 意义 和 现代 生存 境况 的 更 为 深刻 的反思。 其 ** провокативный 性 、 黑色幽默 , 以及 对 传统 的 解构 和 反叛 精神 , 也 体现 了 YBAs 艺术 的 “英国性” 特质**。

      希望以上详细解释能够解答您的疑问, 并帮助您更深入地理解 达明·赫斯特 的 《一千年的(活蝇)》 及其 与 “Vanitas” 绘画 传统 的 关系! 如果您还有其他问题,欢迎随时提出。

    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

      Reply to the Reviewers

      I would like to thank the reviewers for their comments and interest in the manuscript and the study.

      Referee #1

      1. I would assume that there are RNA-seq and/or ChIP-seq data out there produced after knockdown of one or more of these DBPs that show directional positioning.

      Response: The directional positioning of CTCF-binding sites at chromatin interaction sites was analyzed by CRISPR experiment (Guo Y et al. Cell 2015). We found that the machine learning and statistical analysis showed the same directional bias of the CTCF-binding motif sequence at chromatin interaction sites as the experimental analysis of Guo Y et al. (lines 229-245, Figure 3b, c, d and Table 1). Since CTCF is involved in different biological functions (Braccioli L et al. Essays Biochem. 2019 ResearchGate webpage), the directional bias of binding sites may be reduced in all binding sites including those at chromatin interaction sites (lines 68-73). In our study, we investigated the DNA-binding sites of proteins using the ChIP-seq data of DNA-binding proteins and DNase-seq data. We also confirmed that the DNA-binding sites of SMC3 and RAD21, which tend to be found in chromatin loops with CTCF, also showed the same directional bias as CTCF by the computational analysis.

      1. Figure 6 should be expanded to incorporate analysis of DBPs not overlapping CTCF/cohesin in chromatin interaction data that is important and potentially more interesting than the simple DBPs enrichment reported in the present form of the figure.

      Response: Following the reviewer's advice, I performed the same analysis with the DNA-binding sites that do no overlap with the DNA-binding sites of CTCF and cohesin (RAD21 and SMC3) (Fig. 6 and Supplementary Fig. 4). The result showed the same tendency in the distribution of DNA-binding sites. The height of a peak on the graph became lower for some DNA-binding proteins after removing the DNA-binding sites that overlapped with those of CTCF and cohesin. I have added the following sentence on lines 427 and 817: For the insulator-associated DBPs other than CTCF, RAD21, and SMC3, the DNA-binding sites that do not overlap with those of CTCF, RND21, and SMC3 were used to examine their distribution around interaction sites.

      1. Critically, I would like to see use of Micro-C/Hi-C data and ChIP-seq from these factors, where insulation scores around their directionally-bound sites show some sort of an effect like that presumed by the authors - and many such datasets are publicly-available and can be put to good use here.

      Response: As suggested by the reviewer, I have added the insulator scores and boundary sites from the 4D nucleome data portal as tracks in the UCSC genome browser. The insulator scores seem to correspond to some extent to the H3K27me3 histone marks from ChIP-seq (Fig. 4a and Supplementary Fig. 3). The direction of DNA-binding sites on the genome can be shown with different colors (e.g. red and green), but the directionality of insulator-associated DNA-binding sites is their overall tendency, and it may be difficult to notice the directionality from each binding site because the directionality may be weaker than that of CTCF, RAD21, and SMC3 as shown in Table 1 and Supplementary Table 2.

      I found that the CTCF binding sites examined by a wet experiment in the previous study may not always overlap with the boundary sites of chromatin interactions from Micro-C assay (Guo Y et al. Cell 2015). The chromatin interaction data do not include all interactions due to the high sequencing cost of the assay. The number of the boundary sites may be smaller than that of CTCF binding sites acting as insulators and/or some of the CTCF binding sites may not be locate in the boundary sites. It may be difficult for the boundary location algorithm to identify a short boundary location. Due to the limitations of the chromatin interaction data, I planned to search for insulator-associated DNA-binding proteins without using chromatin interaction data in this study. I have added the statistical summary of the analysis in lines 364-387 as follows: Overall, among 20,837 DNA-binding sites of the 97 insulator-associated proteins found at insulator sites identified by H3K27me3 histone modification marks (type 1 insulator sites), 1,315 (6%) overlapped with 264 of 17,126 5kb long boundary sites, and 6,137 (29%) overlapped with 784 of 17,126 25kb long boundary sites in HFF cells. Among 5,205 DNA-binding sites of the 97 insulator-associated DNA-binding proteins found at insulator sites identified by H3K27me3 histone modification marks and transcribed regions (type 2 insulator sites), 383 (7%) overlapped with 74 of 17,126 5-kb long boundary sites, 1,901 (37%) overlapped with 306 of 17,126 25-kb long boundary sites. Although CTCF-binding sites separate active and repressive domains, the limited number of DNA-binding sites of insulator-associated proteins found at type 1 and 2 insulator sites overlapped boundary sites identified by chromatin interaction data. Furthermore, by analyzing the regulatory regions of genes, the DNA-binding sites of the 97 insulator-associated DNA-binding proteins were found (1) at the type 1 insulator sites (based on H3K27me3 marks) in the regulatory regions of 3,170 genes, (2) at the type 2 insulator sites (based on H3K27me3 marks and gene expression levels) in the regulatory regions of 1,044 genes, and (3) at insulator sites as boundary sites identified by chromatin interaction data in the regulatory regions of 6,275 genes. The boundary sites showed the highest number of overlaps with the DNA-binding sites. Comparing the insulator sites identified by (1) and (3), 1,212 (38%) genes have both types of insulator sites. Comparing the insulator sites between (2) and (3), 389 (37%) genes have both types of insulator sites. From the comparison of insulator and boundary sites, we found that (1) or (2) types of insulator sites overlapped or were close to boundary sites identified by chromatin interaction data.

      1. The suggested alternative transcripts function, also highlighted in the manuscripts abstract, is only supported by visual inspection of a few cases for several putative DBPs. I believe this is insufficient to support what looks like one of the major claims of the paper when reading the abstract, and a more quantitative and genome-wide analysis must be adopted, although the authors mention it as just an 'observation'.

      Response: According to the reviewer's comment, I performed the genome-wide analysis of alternative transcripts where the DNA-binding sites of insulator-associated proteins are located near splicing sites. The DNA-binding sites of insulator-associated DNA-binding proteins were found within 200 bp centered on splice sites more significantly than the other DNA-binding proteins (Fig. 4e and Table 2). I have added the following sentences on lines 397 - 404: We performed the statistical test to estimate the enrichment of insulator-associated DNA-binding sites compared to the other DNA-binding proteins, and found that the insulator-associated DNA-binding sites were significantly more abundant at splice sites than the DNA-binding sites of the other proteins (Fig 4e and Table 2; Mann‒Whitney U test, p value 5. Figure 1 serves no purpose in my opinion and can be removed, while figures can generally be improved (e.g., the browser screenshots in Figs 4 and 5) for interpretability from readers outside the immediate research field.

      Response: I believe that the Figure 1 would help researchers in other fields who are not familiar with biological phenomena and functions to understand the study. More explanation has been included in the Figures and legends of Figs. 4 and 5 to help readers outside the immediate research field understand the figures.

      1. Similarly, the text is rather convoluted at places and should be re-approached with more clarity for less specialized readers in mind.

      Response: Reviewer #2's comments would be related to this comment. I have introduced a more detailed explanation of the method in the Results section, as shown in the responses to Reviewer #2's comments.

      Referee #2

      1. Introduction, line 95: CTCF appears two times, it seems redundant.

      Response: On lines 91-93, I deleted the latter CTCF from the sentence "and examined the directional bias of DNA-binding sites of CTCF and insulator-associated DBPs, including those of known DBPs such as RAD21 and SMC3".

      1. Introduction, lines 99-103: Please stress better the novelty of the work. What is the main focus? The new identified DPBs or their binding sites? What are the "novel structural and functional roles of DBPs" mentioned?

      Response: Although CTCF is known to be the main insulator protein in vertebrates, we found that 97 DNA-binding proteins including CTCF and cohesin are associated with insulator sites by modifying and developing a machine learning method to search for insulator-associated DNA-binding proteins. Most of the insulator-associated DNA-binding proteins showed the directional bias of DNA-binding motifs, suggesting that the directional bias is associated with the insulator.

      I have added the sentence in lines 96-99 as follows: Furthermore, statistical testing the contribution scores between the directional and non-directional DNA-binding sites of insulator-associated DBPs revealed that the directional sites contributed more significantly to the prediction of gene expression levels than the non-directional sites. I have revised the statement in lines 101-110 as follows: To validate these findings, we demonstrate that the DNA-binding sites of the identified insulator-associated DBPs are located within potential insulator sites, and some of the DNA-binding sites in the insulator site are found without the nearby DNA-binding sites of CTCF and cohesin. Homologous and heterologous insulator-insulator pairing interactions are orientation-dependent, as suggested by the insulator-pairing model based on experimental analysis in flies. Our method and analyses contribute to the identification of insulator- and chromatin-associated DNA-binding sites that influence EPIs and reveal novel functional roles and molecular mechanisms of DBPs associated with transcriptional condensation, phase separation and transcriptional regulation.

      1. Results, line 111: How do the SNPs come into the procedure? From the figures it seems the input is ChIP-seq peaks of DNBPs around the TSS.

      Response: On lines 121-124, to explain the procedure for the SNP of an eQTL, I have added the sentence in the Methods: "If a DNA-binding site was located within a 100-bp region around a single-nucleotide polymorphism (SNP) of an eQTL, we assumed that the DNA-binding proteins regulated the expression of the transcript corresponding to the eQTL".

      1. Again, are those SNPs coming from the different cell lines? Or are they from individuals w.r.t some reference genome? I suggest a general restructuring of this part to let the reader understand more easily. One option could be simplifying the details here or alternatively including all the necessary details.

      Response: On line 119, I have included the explanation of the eQTL dataset of GTEx v8 as follows: " The eQTL data were derived from the GTEx v8 dataset, after quality control, consisting of 838 donors and 17,382 samples from 52 tissues and two cell lines". On lines 681 and 865, I have added the filename of the eQTL data "(GTEx_Analysis_v8_eQTL.tar)".

      1. Figure 1: panel a and b are misleading. Is the matrix in panel a equivalent to the matrix in panel b? If not please clarify why. Maybe in b it is included the info about the SNPs? And if yes, again, what is then difference with a.

      Response: The reviewer would mention Figure 2, not Figure 1. If so, the matrices in panels a and b in Figure 2 are equivalent. I have shown it in the figure: The same figure in panel a is rotated 90 degrees to the right. The green boxes in the matrix show the regions with the ChIP-seq peak of a DNA-binding protein overlapping with a SNP of an eQTL. I used eQTL data to associate a gene with a ChIP-seq peak that was more than 2 kb upstream and 1 kb downstream of a transcriptional start site of a gene. For each gene, the matrix was produced and the gene expression levels in cells were learned and predicted using the deep learning method. I have added the following sentences to explain the method in lines 133 - 139: Through the training, the tool learned to select the binding sites of DNA-binding proteins from ChIP-seq assays that were suitable for predicting gene expression levels in the cell types. The binding sites of a DNA-binding protein tend to be observed in common across multiple cell and tissue types. Therefore, ChIP-seq data and eQTL data in different cell and tissue types were used as input data for learning, and then the tool selected the data suitable for predicting gene expression levels in the cell types, even if the data were not obtained from the same cell types.

      1. Line 386-388: could the author investigate in more detail this observation? Does it mean that loops driven by other DBPs independent of the known CTCF/Cohesin? Could the author provide examples of chromatin structural data e.g. MicroC?

      Response: As suggested by the reviewer, to help readers understand the observation, I have added Supplementary Fig. S4c to show the distribution of DNA-binding sites of "CTCF, RAD21, and SMC3" and "BACH2, FOS, ATF3, NFE2, and MAFK" around chromatin interaction sites. I have modified the following sentence to indicate the figure on line 493: Although a DNA-binding-site distribution pattern around chromatin interaction sites similar to those of CTCF, RAD21, and SMC3 was observed for DBPs such as BACH2, FOS, ATF3, NFE2, and MAFK, less than 1% of the DNA-binding sites of the latter set of DBPs colocalized with CTCF, RAD21, or SMC3 in a single bin (Fig. S4c).

      In Aljahani A et al. Nature Communications 2022, we find that depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Together, our data show that loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression. Goel VY et al. Nature Genetics 2023 mentioned in the abstract: Microcompartments frequently connect enhancers and promoters and though loss of loop extrusion and inhibition of transcription disrupts some microcompartments, most are largely unaffected. These results suggested that chromatin loops can be driven by other DBPs independent of the known CTCF/Cohesin.

      FOXA1 pioneer factor functions as an initial chromatin-binding and chromatin-remodeling factor and has been reported to form biomolecular condensates (Ji D et al. Molecular Cell 2024). CTCF have also found to form transcriptional condensate and phase separation (Lee R et al. Nucleic acids research 2022). FOS was found to be an insulator-associated DNA-binding protein in this study and is potentially involved in chromatin remodeling, transcription condensation, and phase separation with the other factors such as BACH2, ATF3, NFE2 and MAFK. I have added the following sentence on line 548: FOXA1 pioneer factor functions as an initial chromatin-binding and chromatin-remodeling factor and has been reported to form biomolecular condensates.

      1. In general, how the presented results are related to some models of chromatin architecture, e.g. loop extrusion, in which it is integrated convergent CTCF binding sites?

      Response: Goel VY et al. Nature Genetics 2023 identified highly nested and focal interactions through region capture Micro-C, which resemble fine-scale compartmental interactions and are termed microcompartments. In the section titled "Most microcompartments are robust to loss of loop extrusion," the researchers noted that a small proportion of interactions between CTCF and cohesin-bound sites exhibited significant reductions in strength when cohesin was depleted. In contrast, the majority of microcompartmental interactions remained largely unchanged under cohesin depletion. Our findings indicate that most P-P and E-P interactions, aside from a few CTCF and cohesin-bound enhancers and promoters, are likely facilitated by a compartmentalization mechanism that differs from loop extrusion. We suggest that nested, multiway, and focal microcompartments correspond to small, discrete A-compartments that arise through a compartmentalization process, potentially influenced by factors upstream of RNA Pol II initiation, such as transcription factors, co-factors, or active chromatin states. It follows that if active chromatin regions at microcompartment anchors exhibit selective "stickiness" with one another, they will tend to co-segregate, leading to the development of nested, focal interactions. This microphase separation, driven by preferential interactions among active loci within a block copolymer, may account for the striking interaction patterns we observe.

      The authors of the paper proposed several mechanisms potentially involved in microcompartments. These mechanisms may be involved in looping with insulator function. Another group reported that enhancer-promoter interactions and transcription are largely maintained upon depletion of CTCF, cohesin, WAPL or YY1. Instead, cohesin depletion decreased transcription factor binding to chromatin. Thus, cohesin may allow transcription factors to find and bind their targets more efficiently (Hsieh TS et al. Nature Genetics 2022). Among the identified insulator-associated DNA-binding proteins, Maz and MyoD1 form loops without CTCF (Xiao T et al. Proc Natl Acad Sci USA 2021 ; Ortabozkoyun H et al. Nature genetics 2022 ; Wang R et al. Nature communications 2022). I have added the following sentences on lines 563-567: Another group reported that enhancer-promoter interactions and transcription are largely maintained upon depletion of CTCF, cohesin, WAPL or YY1. Instead, cohesin depletion decreased transcription factor binding to chromatin. Thus, cohesin may allow transcription factors to find and bind their targets more efficiently. I have included the following explanation on lines 574-576: Maz and MyoD1 among the identified insulator-associated DNA-binding proteins form loops without CTCF.

      As for the directionality of CTCF, if chromatin loop anchors have some structural conformation, as shown in the paper entitled "The structural basis for cohesin-CTCF-anchored loops" (Li Y et al. Nature 2020), directional DNA binding would occur similarly to CTCF binding sites. Moreover, cohesin complexes that interact with convergent CTCF sites, that is, the N-terminus of CTCF, might be protected from WAPL, but those that interact with divergent CTCF sites, that is, the C-terminus of CTCF, might not be protected from WAPL, which could release cohesin from chromatin and thus disrupt cohesin-mediated chromatin loops (Davidson IF et al. Nature Reviews Molecular Cell Biology 2021). Regarding loop extrusion, the 'loop extrusion' hypothesis is motivated by in vitro observations. The experiment in yeast, in which cohesin variants that are unable to extrude DNA loops but retain the ability to topologically entrap DNA, suggested that in vivo chromatin loops are formed independently of loop extrusion. Instead, transcription promotes loop formation and acts as an extrinsic motor that extends these loops and defines their final positions (Guerin TM et al. EMBO Journal 2024). I have added the following sentences on lines 535-539: Cohesin complexes that interact with convergent CTCF sites, that is, the N-terminus of CTCF, might be protected from WAPL, but those that interact with divergent CTCF sites, that is, the C-terminus of CTCF, might not be protected from WAPL, which could release cohesin from chromatin and thus disrupt cohesin-mediated chromatin loops. I have included the following sentences on lines 569-574: The 'loop extrusion' hypothesis is motivated by in vitro observations. The experiment in yeast, in which cohesin variants that are unable to extrude DNA loops but retain the ability to topologically entrap DNA, suggested that in vivo chromatin loops are formed independently of loop extrusion. Instead, transcription promotes loop formation and acts as an extrinsic motor that extends these loops and defines their final positions.

      Another model for the regulation of gene expression by insulators is the boundary-pairing (insulator-pairing) model (Bing X et al. Elife 2024) (Ke W et al. Elife 2024) (Fujioka M et al. PLoS Genetics 2016). Molecules bound to insulators physically pair with their partners, either head-to-head or head-to-tail, with different degrees of specificity at the termini of TADs in flies. Although the experiments do not reveal how partners find each other, the mechanism unlikely requires loop extrusion. Homologous and heterologous insulator-insulator pairing interactions are central to the architectural functions of insulators. The manner of insulator-insulator interactions is orientation-dependent. I have summarized the model on lines 551-559: Other types of chromatin regulation are also expected to be related to the structural interactions of molecules. As the boundary-pairing (insulator-pairing) model, molecules bound to insulators physically pair with their partners, either head-to-head or head-to-tail, with different degrees of specificity at the termini of TADs in flies (Fig. 7). Although the experiments do not reveal how partners find each other, the mechanism unlikely requires loop extrusion. Homologous and heterologous insulator-insulator pairing interactions are central to the architectural functions of insulators. The manner of insulator-insulator interactions is orientation-dependent.

      1. Do the authors think that the identified DBPs could work in that way as well?

      Response: The boundary-pairing (insulator-pairing) model would be applied to the insulator-associated DNA-binding proteins other than CTCF and cohesin that are involved in the loop extrusion mechanism (Bing X et al. Elife 2024) (Ke W et al. Elife 2024) (Fujioka M et al. PLoS Genetics 2016).

      Liquid-liquid phase separation was shown to occur through CTCF-mediated chromatin loops and to act as an insulator (Lee, R et al. Nucleic Acids Research 2022). Among the identified insulator-associated DNA-binding proteins, CEBPA has been found to form hubs that colocalize with transcriptional co-activators in a native cell context, which is associated with transcriptional condensate and phase separation (Christou-Kent M et al. Cell Reports 2023). The proposed microcompartment mechanisms are also associated with phase separation. Thus, the same or similar mechanisms are potentially associated with the insulator function of the identified DNA-binding proteins. I have included the following information on line 546: CEBPA in the identified insulator-associated DNA-binding proteins was also reported to be involved in transcriptional condensates and phase separation.

      1. Also, can the authors comment about the mechanisms those newly identified DBPs mediate contacts by active processes or equilibrium processes?

      Response: Snead WT et al. Molecular Cell 2019 mentioned that protein post-transcriptional modifications (PTMs) facilitate the control of molecular valency and strength of protein-protein interactions. O-GlcNAcylation as a PTM inhibits CTCF binding to chromatin (Tang X et al. Nature Communications 2024). I found that the identified insulator-associated DNA-binding proteins tend to form a cluster at potential insulator sites (Supplementary Fig. 2d). These proteins may interact and actively regulate chromatin interactions, transcriptional condensation, and phase separation by PTMs. I have added the following explanation on lines 576-582: Furthermore, protein post-transcriptional modifications (PTMs) facilitate control over the molecular valency and strength of protein-protein interactions. O-GlcNAcylation as a PTM inhibits CTCF binding to chromatin. We found that the identified insulator-associated DNA-binding proteins tend to form a cluster at potential insulator sites (Fig. 4f and Supplementary Fig. 3c). These proteins may interact and actively regulate chromatin interactions, transcriptional condensation, and phase separation through PTMs.

      1. Can the author provide some real examples along with published structural data (e.g. the mentioned micro-C data) to show the link between protein co-presence, directional bias and contact formation?

      Response: Structural molecular model of cohesin-CTCF-anchored loops has been published by Li Y et al. Nature 2020. The structural conformation of CTCF and cohesin in the loops would be the cause of the directional bias of CTCF binding sites, which I mentioned in lines 531 - 535 as follows: These results suggest that the directional bias of DNA-binding sites of insulator-associated DBPs may be involved in insulator function and chromatin regulation through structural interactions among DBPs, other proteins, DNAs, and RNAs. For example, the N-terminal amino acids of CTCF have been shown to interact with RAD21 in chromatin loops. To investigate the principles underlying the architectural functions of insulator-insulator pairing interactions, two insulators, Homie and Nhomie, flanking the Drosophila even skipped locus were analyzed. Pairing interactions between the transgene Homie and the eve locus are directional. The head-to-head pairing between the transgene and endogenous Homie matches the pattern of activation (Fujioka M et al. PLoS Genetics 2016).

      Referee #3

      1. Some of these TFs do not have specific direct binding to DNA (P300, Cohesin). Since the authors are using binding motifs in their analysis workflow, I would remove those from the analysis.

      Response: When a protein complex binds to DNA, one protein of the complex binds to the DNA directory, and the other proteins may not bind to DNA. However, the DNA motif sequence bound by the protein may be registered as the DNA-binding motif of all the proteins in the complex. The molecular structure of the complex of CTCF and Cohesin showed that both CTCF and Cohesin bind to DNA (Li Y et al. Nature 2020). I think there is a possibility that if the molecular structure of a protein complex becomes available, the previous recognition of the DNA-binding ability of a protein may be changed. Therefore, I searched the Pfam database for 99 insulator-associated DNA-binding proteins identified in this study. I found that 97 are registered as DNA-binding proteins and/or have a known DNA-binding domain, and EP300 and SIN3A do not directory bind to DNA, which was also checked by Google search. I have added the following explanation in line 249 to indicate direct and indirect DNA-binding proteins: Among 99 insulator-associated DBPs, EP300 and SIN3A do not directory interact with DNA, and thus 97 insulator-associated DBPs directory bind to DNA. I have updated the sentence in line 20 of the Abstract as follows: We discovered 97 directional and minor nondirectional motifs in human fibroblast cells that corresponded to 23 DBPs related to insulator function, CTCF, and/or other types of chromosomal transcriptional regulation reported in previous studies.

      1. I am not sure if I understood correctly, by why do the authors consider enhancers spanning 2Mb (200 bins of 10Kb around eSNPs)? This seems wrong. Enhancers are relatively small regions (100bp to 1Kb) and only a very small subset form super enhancers.

      Response: As the reviewer mentioned, I recognize enhancers are relatively small regions. In the paper, I intended to examine further upstream and downstream of promoter regions where enhancers are found. Therefore, I have modified the sentence in lines 917 - 919 of the Fig. 2 legend as follows: Enhancer-gene regulatory interaction regions consist of 200 bins of 10 kbp between -1 Mbp and 1 Mbp region from TSS, not including promoter.

      1. I think the H3K27me3 analysis was very good, but I would have liked to see also constitutive heterochromatin as well, so maybe repeat the analysis for H3K9me3.

      Response: Following the reviewer's advice, I have added the ChIP-seq data of H3K9me3 as a truck of the UCSC Genome Browser. The distribution of H3K9me3 signal was different from that of H3K27me3 in some regions. I also found the insulator-associated DNA-binding sites close to the edges of H3K9me3 regions and took some screenshots of the UCSC Genome Browser of the regions around the sites in Supplementary Fig. 3b. I have modified the following sentence on lines 962 - 964 in the legend of Fig. 4: a Distribution of histone modification marks H3K27me3 (green color) and H3K9me3 (turquoise color) and transcript levels (pink color) in upstream and downstream regions of a potential insulator site (light orange color). I have also added the following result on lines 348 - 352: The same analysis was performed using H3K9me3 marks, instead of H3K27me3 (Fig. S3b). We found that the distribution of H3K9me3 signal was different from that of H3K27me3 in some regions, and discovered the insulator-associated DNA-binding sites close to the edges of H3K9me3 regions (Fig. S3b).

      1. I was not sure I understood the analysis in Figure 6. The binding site is with 500bp of the interaction site, but micro-C interactions are at best at 1Kb resolution. They say they chose the centre of the interaction site, but we don't know exactly where there is the actual interaction. Also, it is not clear what they measure. Is it the number of binding sites of a specific or multiple DBP insulator proteins at a specific distance from this midpoint that they recover in all chromatin loops? Maybe I am missing something. This analysis was not very clear.

      Response: The resolution of the Micro-C assay is considered to be 100 bp and above, as the human nucleome core particle contains 145 bp (and 193 bp with linker) of DNA. However, internucleosomal DNA is cleaved by endonuclease into fragments of multiples of 10 nucleotides (Pospelov VA et al. Nucleic Acids Research 1979). Highly nested focal interactions were observed (Goel VY et al. Nature Genetics 2023). Base pair resolution was reported using Micro Capture-C (Hua P et al. Nature 2021). Sub-kilobase (20 bp resolution) chromatin topology was reported using an MNase-based chromosome conformation capture (3C) approach (Aljahani A et al. Nature Communications 2022). On the other hand, Hi-C data was analyzed at 1 kb resolution. (Gu H et al. bioRxiv 2021). If the resolution of Micro-C interactions is at best at 1 kb, the binding sites of a DNA-binding protein will not show a peak around the center of the genomic locations of interaction edges. Each panel shows the number of binding sites of a specific DNA-binding protein at a specific distance from the midpoint of all chromatin interaction edges. I have modified and added the following sentences in lines 585-589: High-resolution chromatin interaction data from a Micro-C assay indicated that most of the predicted insulator-associated DBPs showed DNA-binding-site distribution peaks around chromatin interaction sites, suggesting that these DBPs are involved in chromatin interactions and that the chromatin interaction data has a high degree of resolution. Base pair resolution was reported using Micro Capture-C.

      Minor comments:

      1. PIQ does not consider TF concentration. Other methods do that and show that TF concentration improves predictions (e.g., https://www.biorxiv.org/content/10.1101/2023.07.15.549134v2 or https://pubmed.ncbi.nlm.nih.gov/37486787/). The authors should discuss how that would impact their results.

      Response: The directional bias of CTCF binding sites was identified by ChIA-pet interactions of CTCF binding sites. The analysis of the contribution scores of DNA-binding sites of proteins considering the binding sites of CTCF as an insulator showed the same tendency of directional bias of CTCF binding sites. In the analysis, to remove the false-positive prediction of DNA-binding sites, I used the binding sites that overlapped with a ChIP-seq peak of the DNA-binding protein. This result suggests that the DNA-binding sites of CTCF obtained by the current analysis have sufficient quality. Therefore, if the accuracy of prediction of DNA-binding sites is improved, althought the number of DNA-binding sites may be different, the overall tendency of the directionality of DNA-binding sites will not change and the results of this study will not change significantly.

      As for the first reference in the reviewer's comment, chromatin interaction data from Micro-C assay does not include all chromatin interactions in a cell or tissue, because it is expensive to cover all interactions. Therefore, it would be difficult to predict all chromatin interactions based on machine learning. As for the second reference in the reviewer's comment, pioneer factors such as FOXA are known to bind to closed chromatin regions, but transcription factors and DNA-binding proteins involved in chromatin interactions and insulators generally bind to open chromatin regions. The search for the DNA-binding motifs is not required in closed chromatin regions.

      1. DeepLIFT is a good approach to interpret complex structures of CNN, but is not truly explainable AI. I think the authors should acknowledge this.

      Response: In the DeepLIFT paper, the authors explain that DeepLIFT is a method for decomposing the output prediction of a neural network on a specific input by backpropagating the contributions of all neurons in the network to every feature of the input (Shrikumar A et al. ICML 2017). DeepLIFT compares the activation of each neuron to its 'reference activation' and assigns contribution scores according to the difference. DeepLIFT calculates a metric to measure the difference between an input and the reference of the input.

      Truly explainable AI would be able to find cause and reason, and to make choices and decisions like humans. DeepLIFT does not perform causal inferences. I did not use the term "Explainable AI" in our manuscript, but I briefly explained it in Discussion. I have added the following explanation in lines 615-620: AI (Artificial Intelligence) is considered as a black box, since the reason and cause of prediction are difficult to know. To solve this issue, tools and methods have been developed to know the reason and cause. These technologies are called Explainable AI. DeepLIFT is considered to be a tool for Explainable AI. However, DeepLIFT does not answer the reason and cause for a prediction. It calculates scores representing the contribution of the input data to the prediction.

      Furthermore, to improve the readability of the manuscript, I have included the following explanation in lines 159-165: we computed DeepLIFT scores of the input data (i.e., each binding site of the ChIP-seq data of DNA-binding proteins) in the deep leaning analysis on gene expression levels. DeepLIFT compares the importance of each input for predicting gene expression levels to its 'reference or background level' and assigns contribution scores according to the difference. DeepLIFT calculates a metric to measure the difference between an input and the reference of the input.

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

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      Reply to the reviewers

      I would like to thank the reviewers for their comments and interest in the manuscript and the study.

      Reviewer #1

      1) I would assume that there are RNA-seq and/or ChIP-seq data out there produced after knockdown of one or more of these DBPs that show directional positioning.

      As the reviewer pointed out, a wet experimental validation of the results of this study would give an opportunity for more biological researchers to have an interest in the study. I plan to promote the wet experimental analysis in collaboration with biological experimental researchers as a next step of this study. The same analysis in this study can be performed in immortalized cells for CRISPR experiment (e.g. Guo Y et al. Cell 2015).

      2) Figure 6 should be expanded to incorporate analysis of DBPs not overlapping CTCF/cohesin in chromatin interaction data that is important and potentially more interesting than the simple DBPs enrichment reported in the present form of the figure.

      Following the reviewer's advice, I performed the same analysis with the DNA-binding sites that do no overlap with the DNA-binding sites of CTCF and cohesin (RAD21 and SMC3) (Fig. 6 and Supplementary Fig. 4). The result showed the same tendency in the distribution of DNA-binding sites. The height of a peak on the graph became lower for some DNA-binding proteins after removing the DNA-binding sites that overlapped with those of CTCF and cohesin. I have added the following sentence on lines 427 and 817: For the insulator-associated DBPs other than CTCF, RAD21, and SMC3, the DNA-binding sites that do not overlap with those of CTCF, RND21, and SMC3 were used to examine their distribution around interaction sites.

      3) Critically, I would like to see use of Micro-C/Hi-C data and ChIP-seq from these factors, where insulation scores around their directionally-bound sites show some sort of an effect like that presumed by the authors - and many such datasets are publicly-available and can be put to good use here.

      As suggested by the reviewer, I have added the insulator scores and boundary sites from the 4D nucleome data portal as tracks in the UCSC genome browser. The insulator scores seem to correspond to some extent to the H3K27me3 histone marks from ChIP-seq (Fig. 4a and Supplementary Fig. 3). The direction of DNA-binding sites on the genome can be shown with different colors (e.g. red and green), but the directionality is their overall tendency, and it may be difficult to notice the directionality from each binding site.

      I found that the CTCF binding sites examined by a wet experiment in the previous study may not always overlap with the boundary sites of chromatin interactions from Micro-C assay (Guo Y et al. Cell 2015). The chromatin interaction data do not include all interactions due to the high sequencing cost of the assay. The number of the boundary sites may be smaller than that of CTCF binding sites acting as insulators and/or some of the CTCF binding sites may not be locate in the boundary sites. It may be difficult for the boundary location algorithm to identify a short boundary location. Due to the limitations of the chromatin interaction data, I planned to search for insulator-associated DNA-binding proteins without using chromatin interaction data in this study. I have added the statistical summary of the analysis in lines 364-387 as follows: Overall, among 20,837 DNA-binding sites of the 97 insulator-associated proteins found at insulator sites identified by H3K27me3 histone modification marks (type 1 insulator sites), 1,315 (6%) overlapped with 264 of 17,126 5kb long boundary sites, and 6,137 (29%) overlapped with 784 of 17,126 25kb long boundary sites in HFF cells. Among 5,205 DNA-binding sites of the 97 insulator-associated DNA-binding proteins found at insulator sites identified by H3K27me3 histone modification marks and transcribed regions (type 2 insulator sites), 383 (7%) overlapped with 74 of 17,126 5-kb long boundary sites, 1,901 (37%) overlapped with 306 of 17,126 25-kb long boundary sites. Although CTCF-binding sites separate active and repressive domains, the limited number of DNA-binding sites of insulator-associated proteins found at type 1 and 2 insulator sites overlapped boundary sites identified by chromatin interaction data. Furthermore, by analyzing the regulatory regions of genes, the DNA-binding sites of the 97 insulator-associated DNA-binding proteins were found (1) at the type 1 insulator sites (based on H3K27me3 marks) in the regulatory regions of 3,170 genes, (2) at the type 2 insulator sites (based on H3K27me3 marks and gene expression levels) in the regulatory regions of 1,044 genes, and (3) at insulator sites as boundary sites identified by chromatin interaction data in the regulatory regions of 6,275 genes. The boundary sites showed the highest number of overlaps with the DNA-binding sites. Comparing the insulator sites identified by (1) and (3), 1,212 (38%) genes have both types of insulator sites. Comparing the insulator sites between (2) and (3), 389 (37%) genes have both types of insulator sites. From the comparison of insulator and boundary sites, we found that (1) or (2) types of insulator sites overlapped or were close to boundary sites identified by chromatin interaction data.

      4) The suggested alternative transcripts function, also highlighted in the manuscripts abstract, is only supported by visual inspection of a few cases for several putative DBPs. I believe this is insufficient to support what looks like one of the major claims of the paper when reading the abstract, and a more quantitative and genome-wide analysis must be adopted, although the authors mention it as just an 'observation'.

      According to the reviewer's comment, I performed the genome-wide analysis of alternative transcripts where the DNA-binding sites of insulator-associated proteins are located near splicing sites. The DNA-binding sites of insulator-associated DNA-binding proteins were found within 200 bp centered on splice sites more significantly than the other DNA-binding proteins (Fig. 4e and Table 2). I have added the following sentences on lines 397 - 404: We performed the statistical test to estimate the enrichment of insulator-associated DNA-binding sites compared to the other DNA-binding proteins, and found that the insulator-associated DNA-binding sites were significantly more abundant at splice sites than the DNA-binding sites of the other proteins (Fig 4e and Table 2; Mann‒Whitney U test, p value < 0.05). The comparison between the splice sites of both ends of first and last introns and those of other introns showed the similar statistical significance of enrichment and number of splice sites with the insulator-associated DNA-binding proteins (Table 2 and Table S9).

      5) Figure 1 serves no purpose in my opinion and can be removed, while figures can generally be improved (e.g., the browser screenshots in Figs 4 and 5) for interpretability from readers outside the immediate research field.

      I believe that the Figure 1 would help researchers in other fields who are not familiar with biological phenomena and functions to understand the study. More explanation has been included in the Figures and legends of Figs. 4 and 5 to help readers outside the immediate research field understand the figures.

      6) Similarly, the text is rather convoluted at places and should be re-approached with more clarity for less specialized readers in mind.

      Reviewer #2's comments would be related to this comment. I have introduced a more detailed explanation of the method in the Results section, as shown in the responses to Reviewer #2’s comments.

      Reviewer #2

      1) Introduction, line 95: CTCF appears two times, it seems redundant.

      On lines 91-93, I deleted the latter CTCF from the sentence "We examine the directional bias of DNA-binding sites of CTCF and insulator-associated DBPs, including those of known DBPs such as RAD21 and SMC3".

      2) Introduction, lines 99-103: Please stress better the novelty of the work. What is the main focus? The new identified DPBs or their binding sites? What are the "novel structural and functional roles of DBPs" mentioned?

      Although CTCF is known to be the main insulator protein in vertebrates, we found that 97 DNA-binding proteins including CTCF and cohesin are associated with insulator sites by modifying and developing a machine learning method to search for insulator-associated DNA-binding proteins. Most of the insulator-associated DNA-binding proteins showed the directional bias of DNA-binding motifs, suggesting that the directional bias is associated with the insulator.

      I have added the sentence in lines 96-99 as follows: Furthermore, statistical testing the contribution scores between the directional and non-directional DNA-binding sites of insulator-associated DBPs revealed that the directional sites contributed more significantly to the prediction of gene expression levels than the non-directional sites. I have revised the statement in lines 101-110 as follows: To validate these findings, we demonstrate that the DNA-binding sites of the identified insulator-associated DBPs are located within potential insulator sites, and some of the DNA-binding sites in the insulator site are found without the nearby DNA-binding sites of CTCF and cohesin. Homologous and heterologous insulator-insulator pairing interactions are orientation-dependent, as suggested by the insulator-pairing model based on experimental analysis in flies. Our method and analyses contribute to the identification of insulator- and chromatin-associated DNA-binding sites that influence EPIs and reveal novel functional roles and molecular mechanisms of DBPs associated with transcriptional condensation, phase separation and transcriptional regulation.

      3) Results, line 111: How do the SNPs come into the procedure? From the figures it seems the input is ChIP-seq peaks of DNBPs around the TSS.

      On lines 121-124, to explain the procedure for the SNP of an eQTL, I have added the sentence in the Methods: "If a DNA-binding site was located within a 100-bp region around a single-nucleotide polymorphism (SNP) of an eQTL, we assumed that the DNA-binding proteins regulated the expression of the transcript corresponding to the eQTL".

      4) Again, are those SNPs coming from the different cell lines? Or are they from individuals w.r.t some reference genome? I suggest a general restructuring of this part to let the reader understand more easily. One option could be simplifying the details here or alternatively including all the necessary details.

      On line 119, I have included the explanation of the eQTL dataset of GTEx v8 as follows: " The eQTL data were derived from the GTEx v8 dataset, after quality control, consisting of 838 donors and 17,382 samples from 52 tissues and two cell lines”. On lines 681 and 865, I have added the filename of the eQTL data "(GTEx_Analysis_v8_eQTL.tar)".

      5) Figure 1: panel a and b are misleading. Is the matrix in panel a equivalent to the matrix in panel b? If not please clarify why. Maybe in b it is included the info about the SNPs? And if yes, again, what is then difference with a.

      The reviewer would mention Figure 2, not Figure 1. If so, the matrices in panels a and b in Figure 2 are equivalent. I have shown it in the figure: The same figure in panel a is rotated 90 degrees to the right. The green boxes in the matrix show the regions with the ChIP-seq peak of a DNA-binding protein overlapping with a SNP of an eQTL. I used eQTL data to associate a gene with a ChIP-seq peak that was more than 2 kb upstream and 1 kb downstream of a transcriptional start site of a gene. For each gene, the matrix was produced and the gene expression levels in cells were learned and predicted using the deep learning method. I have added the following sentences to explain the method in lines 133 - 139: Through the training, the tool learned to select the binding sites of DNA-binding proteins from ChIP-seq assays that were suitable for predicting gene expression levels in the cell types. The binding sites of a DNA-binding protein tend to be observed in common across multiple cell and tissue types. Therefore, ChIP-seq data and eQTL data in different cell and tissue types were used as input data for learning, and then the tool selected the data suitable for predicting gene expression levels in the cell types, even if the data were not obtained from the same cell types.

      6) Line 386-388: could the author investigate in more detail this observation? Does it mean that loops driven by other DBPs independent of the known CTCF/Cohesin? Could the author provide examples of chromatin structural data e.g. MicroC?

      As suggested by the reviewer, to help readers understand the observation, I have added Supplementary Fig. S4c to show the distribution of DNA-binding sites of "CTCF, RAD21, and SMC3" and "BACH2, FOS, ATF3, NFE2, and MAFK" around chromatin interaction sites. I have modified the following sentence to indicate the figure on line 493: Although a DNA-binding-site distribution pattern around chromatin interaction sites similar to those of CTCF, RAD21, and SMC3 was observed for DBPs such as BACH2, FOS, ATF3, NFE2, and MAFK, less than 1% of the DNA-binding sites of the latter set of DBPs colocalized with CTCF, RAD21, or SMC3 in a single bin (Fig. S4c).

      In Aljahani A et al. Nature Communications 2022, we find that depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Together, our data show that loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression. Goel VY et al. Nature Genetics 2023 mentioned in the abstract: Microcompartments frequently connect enhancers and promoters and though loss of loop extrusion and inhibition of transcription disrupts some microcompartments, most are largely unaffected. These results suggested that chromatin loops can be driven by other DBPs independent of the known CTCF/Cohesin.

      I added the following sentence on lines 561-569: The depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Another group reported that enhancer-promoter interactions and transcription are largely maintained upon depletion of CTCF, cohesin, WAPL or YY1. Instead, cohesin depletion decreased transcription factor binding to chromatin. Thus, cohesin may allow transcription factors to find and bind their targets more efficiently. Furthermore, the loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression.

      FOXA1 pioneer factor functions as an initial chromatin-binding and chromatin-remodeling factor and has been reported to form biomolecular condensates (Ji D et al. Molecular Cell 2024). CTCF have also found to form transcriptional condensate and phase separation (Lee R et al. Nucleic acids research 2022). FOS was found to be an insulator-associated DNA-binding protein in this study and is potentially involved in chromatin remodeling, transcription condensation, and phase separation with the other factors such as BACH2, ATF3, NFE2 and MAFK. I have added the following sentence on line 548: FOXA1 pioneer factor functions as an initial chromatin-binding and chromatin-remodeling factor and has been reported to form biomolecular condensates.

      7) In general, how the presented results are related to some models of chromatin architecture, e.g. loop extrusion, in which it is integrated convergent CTCF binding sites?

      Goel VY et al. Nature Genetics 2023 identified highly nested and focal interactions through region capture Micro-C, which resemble fine-scale compartmental interactions and are termed microcompartments. In the section titled "Most microcompartments are robust to loss of loop extrusion," the researchers noted that a small proportion of interactions between CTCF and cohesin-bound sites exhibited significant reductions in strength when cohesin was depleted. In contrast, the majority of microcompartmental interactions remained largely unchanged under cohesin depletion. Our findings indicate that most P-P and E-P interactions, aside from a few CTCF and cohesin-bound enhancers and promoters, are likely facilitated by a compartmentalization mechanism that differs from loop extrusion. We suggest that nested, multiway, and focal microcompartments correspond to small, discrete A-compartments that arise through a compartmentalization process, potentially influenced by factors upstream of RNA Pol II initiation, such as transcription factors, co-factors, or active chromatin states. It follows that if active chromatin regions at microcompartment anchors exhibit selective "stickiness" with one another, they will tend to co-segregate, leading to the development of nested, focal interactions. This microphase separation, driven by preferential interactions among active loci within a block copolymer, may account for the striking interaction patterns we observe.

      The authors of the paper proposed several mechanisms potentially involved in microcompartments. These mechanisms may be involved in looping with insulator function. Another group reported that enhancer-promoter interactions and transcription are largely maintained upon depletion of CTCF, cohesin, WAPL or YY1. Instead, cohesin depletion decreased transcription factor binding to chromatin. Thus, cohesin may allow transcription factors to find and bind their targets more efficiently (Hsieh TS et al. Nature Genetics 2022). Among the identified insulator-associated DNA-binding proteins, Maz and MyoD1 form loops without CTCF (Xiao T et al. Proc Natl Acad Sci USA 2021 ; Ortabozkoyun H et al. Nature genetics 2022 ; Wang R et al. Nature communications 2022). I have added the following sentences on lines 563-567: Another group reported that enhancer-promoter interactions and transcription are largely maintained upon depletion of CTCF, cohesin, WAPL or YY1. Instead, cohesin depletion decreased transcription factor binding to chromatin. Thus, cohesin may allow transcription factors to find and bind their targets more efficiently. I have included the following explanation on lines 574-576: Maz and MyoD1 among the identified insulator-associated DNA-binding proteins form loops without CTCF.

      As for the directionality of CTCF, if chromatin loop anchors have some structural conformation, as shown in the paper entitled "The structural basis for cohesin-CTCF-anchored loops" (Li Y et al. Nature 2020), directional DNA binding would occur similarly to CTCF binding sites. Moreover, cohesin complexes that interact with convergent CTCF sites, that is, the N-terminus of CTCF, might be protected from WAPL, but those that interact with divergent CTCF sites, that is, the C-terminus of CTCF, might not be protected from WAPL, which could release cohesin from chromatin and thus disrupt cohesin-mediated chromatin loops (Davidson IF et al. Nature Reviews Molecular Cell Biology 2021). Regarding loop extrusion, the ‘loop extrusion’ hypothesis is motivated by in vitro observations. The experiment in yeast, in which cohesin variants that are unable to extrude DNA loops but retain the ability to topologically entrap DNA, suggested that in vivo chromatin loops are formed independently of loop extrusion. Instead, transcription promotes loop formation and acts as an extrinsic motor that extends these loops and defines their final positions (Guerin TM et al. EMBO Journal 2024). I have added the following sentences on lines 535-539: Cohesin complexes that interact with convergent CTCF sites, that is, the N-terminus of CTCF, might be protected from WAPL, but those that interact with divergent CTCF sites, that is, the C-terminus of CTCF, might not be protected from WAPL, which could release cohesin from chromatin and thus disrupt cohesin-mediated chromatin loops. I have included the following sentences on lines 569-574: The ‘loop extrusion’ hypothesis is motivated by in vitro observations. The experiment in yeast, in which cohesin variants that are unable to extrude DNA loops but retain the ability to topologically entrap DNA, suggested that in vivo chromatin loops are formed independently of loop extrusion. Instead, transcription promotes loop formation and acts as an extrinsic motor that extends these loops and defines their final positions.

      Another model for the regulation of gene expression by insulators is the boundary-pairing (insulator-pairing) model (Bing X et al. Elife 2024) (Ke W et al. Elife 2024) (Fujioka M et al. PLoS Genetics 2016). Molecules bound to insulators physically pair with their partners, either head-to-head or head-to-tail, with different degrees of specificity at the termini of TADs in flies. Although the experiments do not reveal how partners find each other, the mechanism unlikely requires loop extrusion. Homologous and heterologous insulator-insulator pairing interactions are central to the architectural functions of insulators. The manner of insulator-insulator interactions is orientation-dependent. I have summarized the model on lines 551-559: Other types of chromatin regulation are also expected to be related to the structural interactions of molecules. As the boundary-pairing (insulator-pairing) model, molecules bound to insulators physically pair with their partners, either head-to-head or head-to-tail, with different degrees of specificity at the termini of TADs in flies (Fig. 7). Although the experiments do not reveal how partners find each other, the mechanism unlikely requires loop extrusion. Homologous and heterologous insulator-insulator pairing interactions are central to the architectural functions of insulators. The manner of insulator-insulator interactions is orientation-dependent.

      8) Do the authors think that the identified DBPs could work in that way as well?

      The boundary-pairing (insulator-pairing) model would be applied to the insulator-associated DNA-binding proteins other than CTCF and cohesin that are involved in the loop extrusion mechanism (Bing X et al. Elife 2024) (Ke W et al. Elife 2024) (Fujioka M et al. PLoS Genetics 2016).

      Liquid-liquid phase separation was shown to occur through CTCF-mediated chromatin loops and to act as an insulator (Lee, R et al. Nucleic Acids Research 2022). Among the identified insulator-associated DNA-binding proteins, CEBPA has been found to form hubs that colocalize with transcriptional co-activators in a native cell context, which is associated with transcriptional condensate and phase separation (Christou-Kent M et al. Cell Reports 2023). The proposed microcompartment mechanisms are also associated with phase separation. Thus, the same or similar mechanisms are potentially associated with the insulator function of the identified DNA-binding proteins. I have included the following information on line 546: CEBPA in the identified insulator-associated DNA-binding proteins was also reported to be involved in transcriptional condensates and phase separation.

      9) Also, can the authors comment about the mechanisms those newly identified DBPs mediate contacts by active processes or equilibrium processes?

      Snead WT et al. Molecular Cell 2019 mentioned that protein post-transcriptional modifications (PTMs) facilitate the control of molecular valency and strength of protein-protein interactions. O-GlcNAcylation as a PTM inhibits CTCF binding to chromatin (Tang X et al. Nature Communications 2024). I found that the identified insulator-associated DNA-binding proteins tend to form a cluster at potential insulator sites (Supplementary Fig. 2d). These proteins may interact and actively regulate chromatin interactions, transcriptional condensation, and phase separation by PTMs. I have added the following explanation on lines 576-582: Furthermore, protein post-transcriptional modifications (PTMs) facilitate control over the molecular valency and strength of protein-protein interactions. O-GlcNAcylation as a PTM inhibits CTCF binding to chromatin. We found that the identified insulator-associated DNA-binding proteins tend to form a cluster at potential insulator sites (Fig. 4f and Supplementary Fig. 3c). These proteins may interact and actively regulate chromatin interactions, transcriptional condensation, and phase separation through PTMs.

      10) Can the author provide some real examples along with published structural data (e.g. the mentioned micro-C data) to show the link between protein co-presence, directional bias and contact formation?

      Structural molecular model of cohesin-CTCF-anchored loops has been published by Li Y et al. Nature 2020. The structural conformation of CTCF and cohesin in the loops would be the cause of the directional bias of CTCF binding sites, which I mentioned in lines 531 – 535 as follows: These results suggest that the directional bias of DNA-binding sites of insulator-associated DBPs may be involved in insulator function and chromatin regulation through structural interactions among DBPs, other proteins, DNAs, and RNAs. For example, the N-terminal amino acids of CTCF have been shown to interact with RAD21 in chromatin loops.

      To investigate the principles underlying the architectural functions of insulator-insulator pairing interactions, two insulators, Homie and Nhomie, flanking the Drosophila even skipped locus were analyzed. Pairing interactions between the transgene Homie and the eve locus are directional. The head-to-head pairing between the transgene and endogenous Homie matches the pattern of activation (Fujioka M et al. PLoS Genetics 2016).

      Reviewer #3

      1. Some of these TFs do not have specific direct binding to DNA (P300, Cohesin). Since the authors are using binding motifs in their analysis workflow, I would remove those from the analysis.

      When a protein complex binds to DNA, one protein of the complex binds to the DNA directory, and the other proteins may not bind to DNA. However, the DNA motif sequence bound by the protein may be registered as the DNA-binding motif of all the proteins in the complex. The molecular structure of the complex of CTCF and Cohesin showed that both CTCF and Cohesin bind to DNA (Li Y et al. Nature 2020). I think there is a possibility that if the molecular structure of a protein complex becomes available, the previous recognition of the DNA-binding ability of a protein may be changed. Therefore, I searched the Pfam database for 99 insulator-associated DNA-binding proteins identified in this study. I found that 97 are registered as DNA-binding proteins and/or have a known DNA-binding domain, and EP300 and SIN3A do not directory bind to DNA, which was also checked by Google search. I have added the following explanation in line 249 to indicate direct and indirect DNA-binding proteins: Among 99 insulator-associated DBPs, EP300 and SIN3A do not directory interact with DNA, and thus 97 insulator-associated DBPs directory bind to DNA. I have updated the sentence in line 22 of the Abstract as follows: We discovered 97 directional and minor nondirectional motifs in human fibroblast cells that corresponded to 23 DBPs related to insulator function, CTCF, and/or other types of chromosomal transcriptional regulation reported in previous studies.

      2. I am not sure if I understood correctly, by why do the authors consider enhancers spanning 2Mb (200 bins of 10Kb around eSNPs)? This seems wrong. Enhancers are relatively small regions (100bp to 1Kb) and only a very small subset form super enhancers.

      As the reviewer mentioned, I recognize enhancers are relatively small regions. In the paper, I intended to examine further upstream and downstream of promoter regions where enhancers are found. Therefore, I have modified the sentence in lines 917 – 919 of the Fig. 2 legend as follows: Enhancer-gene regulatory interaction regions consist of 200 bins of 10 kbp between -1 Mbp and 1 Mbp region from TSS, not including promoter.

      3. I think the H3K27me3 analysis was very good, but I would have liked to see also constitutive heterochromatin as well, so maybe repeat the analysis for H3K9me3.

      Following the reviewer's advice, I have added the ChIP-seq data of H3K9me3 as a truck of the UCSC Genome Browser. The distribution of H3K9me3 signal was different from that of H3K27me3 in some regions. I also found the insulator-associated DNA-binding sites close to the edges of H3K9me3 regions and took some screenshots of the UCSC Genome Browser of the regions around the sites in Supplementary Fig. 3b. I have modified the following sentence on lines 962 – 964 in the legend of Fig. 4: a Distribution of histone modification marks H3K27me3 (green color) and H3K9me3 (turquoise color) and transcript levels (pink color) in upstream and downstream regions of a potential insulator site (light orange color). I have also added the following result on lines 348 – 352: The same analysis was performed using H3K9me3 marks, instead of H3K27me3 (Fig. S3b). We found that the distribution of H3K9me3 signal was different from that of H3K27me3 in some regions, and discovered the insulator-associated DNA-binding sites close to the edges of H3K9me3 regions (Fig. S3b).

      4. I was not sure I understood the analysis in Figure 6. The binding site is with 500bp of the interaction site, but micro-C interactions are at best at 1Kb resolution. They say they chose the centre of the interaction site, but we don't know exactly where there is the actual interaction. Also, it is not clear what they measure. Is it the number of binding sites of a specific or multiple DBP insulator proteins at a specific distance from this midpoint that they recover in all chromatin loops? Maybe I am missing something. This analysis was not very clear.

      The resolution of the Micro-C assay is considered to be 100 bp and above, as the human nucleome core particle contains 145 bp (and 193 bp with linker) of DNA. However, internucleosomal DNA is cleaved by endonuclease into fragments of multiples of 10 nucleotides (Pospelov VA et al. Nucleic Acids Research 1979). Highly nested focal interactions were observed (Goel VY et al. Nature Genetics 2023). Base pair resolution was reported using Micro Capture-C (Hua P et al. Nature 2021). Sub-kilobase (20 bp resolution) chromatin topology was reported using an MNase-based chromosome conformation capture (3C) approach (Aljahani A et al. Nature Communications 2022). On the other hand, Hi-C data was analyzed at 1 kb resolution. (Gu H et al. bioRxiv 2021). If the resolution of Micro-C interactions is at best at 1 kb, the binding sites of a DNA-binding protein will not show a peak around the center of the genomic locations of interaction edges. Each panel shows the number of binding sites of a specific DNA-binding protein at a specific distance from the midpoint of all chromatin interaction edges. I have modified and added the following sentences in lines 585-589: High-resolution chromatin interaction data from a Micro-C assay indicated that most of the predicted insulator-associated DBPs showed DNA-binding-site distribution peaks around chromatin interaction sites, suggesting that these DBPs are involved in chromatin interactions and that the chromatin interaction data has a high degree of resolution. Base pair resolution was reported using Micro Capture-C.

      1.PIQ does not consider TF concentration. Other methods do that and show that TF concentration improves predictions (e.g.,https://www.biorxiv.org/content/10.1101/2023.07.15.549134v2 or https://pubmed.ncbi.nlm.nih.gov/37486787/). The authors should discuss how that would impact their results.

      The directional bias of CTCF binding sites was identified by ChIA-pet interactions of CTCF binding sites. The analysis of the contribution scores of DNA-binding sites of proteins considering the binding sites of CTCF as an insulator showed the same tendency of directional bias of CTCF binding sites. In the analysis, to remove the false-positive prediction of DNA-binding sites, I used the binding sites that overlapped with a ChIP-seq peak of the DNA-binding protein. This result suggests that the DNA-binding sites of CTCF obtained by the current analysis have sufficient quality. Therefore, if the accuracy of prediction of DNA-binding sites is improved, althought the number of DNA-binding sites may be different, the overall tendency of the directionality of DNA-binding sites will not change and the results of this study will not change significantly.

      As for the first reference in the reviewer's comment, chromatin interaction data from Micro-C assay does not include all chromatin interactions in a cell or tissue, because it is expensive to cover all interactions. Therefore, it would be difficult to predict all chromatin interactions based on machine learning. As for the second reference in the reviewer's comment, pioneer factors such as FOXA are known to bind to closed chromatin regions, but transcription factors and DNA-binding proteins involved in chromatin interactions and insulators generally bind to open chromatin regions. The search for the DNA-binding motifs is not required in closed chromatin regions.

      2. DeepLIFT is a good approach to interpret complex structures of CNN, but is not truly explainable AI. I think the authors should acknowledge this.

      In the DeepLIFT paper, the authors explain that DeepLIFT is a method for decomposing the output prediction of a neural network on a specific input by backpropagating the contributions of all neurons in the network to every feature of the input (Shrikumar A et al. ICML 2017). DeepLIFT compares the activation of each neuron to its 'reference activation' and assigns contribution scores according to the difference. DeepLIFT calculates a metric to measure the difference between an input and the reference of the input.

      Truly explainable AI would be able to find cause and reason, and to make choices and decisions like humans. DeepLIFT does not perform causal inferences. I did not use the term "Explainable AI" in our manuscript, but I briefly explained it in Discussion. I have added the following explanation in lines 615-620: AI (Artificial Intelligence) is considered as a black box, since the reason and cause of prediction are difficult to know. To solve this issue, tools and methods have been developed to know the reason and cause. These technologies are called Explainable AI. DeepLIFT is considered to be a tool for Explainable AI. However, DeepLIFT does not answer the reason and cause for a prediction. It calculates scores representing the contribution of the input data to the prediction.

      Furthermore, to improve the readability of the manuscript, I have included the following explanation in lines 159-165: we computed DeepLIFT scores of the input data (i.e., each binding site of the ChIP-seq data of DNA-binding proteins) in the deep leaning analysis on gene expression levels. DeepLIFT compares the importance of each input for predicting gene expression levels to its 'reference or background level' and assigns contribution scores according to the difference. DeepLIFT calculates a metric to measure the difference between an input and the reference of the input.

    1. Os incêndios no Pantanal têm causado prejuízos significativos à fauna e flora locais. O aumento na frequência e na intensidade de incêndios tem sido apontado como causa de declínio de populações de diversos organismos (ver, p. ex., Abreu et al. (2004), Valencia-Zuleta et al. (2024)). A gestão do regime do fogo no Parque Estadual do Pantanal do Rio Negro requer ações integradas e contínuas, combinando ciência, políticas públicas e participação comunitária. A implementação de práticas como o Manejo Integrado do Fogo e a elaboração de planos específicos são essenciais para preservar este ecossistema único e vital, garantindo a sustentabilidade ambiental e a proteção da biodiversidade local. 2 Objetivos

      Créditos de Biodiversidade Padrões de certificação aplicáveis:

      Biodiversity Credit Standard (BCS) Verified Conservation Areas (VCA) Plan Vivo Metodologias aplicáveis:

      Monitoramento de indicadores de biodiversidade. Avaliação da recuperação de habitats e espécies-chave. Estabelecimento de métricas para quantificação da conservação e restauração. Modelagem ecológica para estimativa de impactos positivos na biodiversidade. 2. Créditos Baseados em Manejo Integrado do Fogo Padrões de certificação aplicáveis:

      Australian Savanna Burning Methodology VCS (Verified Carbon Standard – Metodologias para Manejo do Fogo) Metodologias aplicáveis:

      Implementação de queimadas prescritas para mitigação de incêndios descontrolados. Monitoramento de redução de emissões de GEE por manejo do fogo. Uso de técnicas indígenas e conhecimento tradicional na gestão do fogo. 3. Conservação e Restauração de Savanas Naturais Padrões de certificação aplicáveis:

      BioCarbon Registry – Natural Savannas (BCR0005) Metodologias aplicáveis:

      Proteção contra incêndios descontrolados e práticas sustentáveis de manejo. Restauração ecológica e monitoramento da regeneração natural. Estabelecimento de métricas de estoque de carbono e biodiversidade em savanas. 4. Conservação e Restauração de Zonas Úmidas Continentais Padrões de certificação aplicáveis:

      BioCarbon Registry – Conservation and Restoration of Natural Continental Wetlands (BCR0007) Metodologias aplicáveis:

      Avaliação e monitoramento de áreas úmidas degradadas. Implementação de práticas de restauração para aumento da captura de carbono. Estabelecimento de métricas para biodiversidade e qualidade da água. Proteção de serviços ecossistêmicos associados às zonas úmidas.

    2. Análise Queimada

      ESCOPO DO TRABALHO/ATIVIDADES/PRODUTOS

      Padrões de certificação para projetos de Soluções Baseadas em Natureza

      Realizar uma pesquisa aprofundada sobre o potencial de implementação de projetos que utilizam metodologias baseadas em ecossistemas naturais, visando fornecer benefícios diretos à sociedade. Essa pesquisa deve focar nos principais padrões de certificação para projetos de Soluções baseadas na Natureza (SbN), como Créditos de Biodiversidade e Créditos Baseados em Manejo Integrado do Fogo.

      Objetivo: Elaborar uma análise de viabilidade para a metodologia baseada em soluções naturais, como créditos de biodiversidade e crédito de manejo integrado do fogo. Criar um documento diretivo que inclua a determinação do potencial de geração de créditos de carbono, com uma linha de base previamente estabelecida. Definir a metodologia a ser aplicada, demonstrando as premissas legais necessárias para sua aplicação. Apresentar o framework com base na área do Parque Estadual do Pantanal do Rio Negro.

      Produto Esperado: Documento descritivo que detalhe os padrões de certificação para a metodologia escolhida. O documento deve incluir: O potencial de créditos de carbono que podem ser gerados. A definição da área a ser incluída no projeto.

    1. Many rural areas around the world are facing depopulation problems due to factors like migration, declining birth rates, climate change, unemployment and economic circumstances. Resulting is a population that gets older and older while it grows due to births and migration. Europe has been facing this problem since the 19th century (Kohler et al., 2017). These problems can be summarised into demographic change. This post compares the demographic change in mountain villages in the Swiss Alps with the mountain regions in Georgia, which are part of the Caucasus Mountains. The demographic aging of a population is significantly impacted by the migration patterns of specific age groups, particularly the movement of individuals in generative age. In many rural areas of the European Alps, the emigration of young people has historically played an important role with variations in timing and intensity across different regions (Bender & Kanitscheider, 2012)In Switzerland, the last three decades of the 20th century witnessed a trend of depopulation in urbanized regions and a process of counter-urbanization in rural areas, predominantly located in the mountainous zones of Switzerland (Bender & Kanitscheider, 2012). But present, a reversal trend of migration to mountainous regions can be observed. There are people, also younger ones, from the lowland urban areas that are moving to the regions of the Alps to live and work there. Therefore, the population changes back to a more even distribution over the age groups. The migration both ways is mostly due to the idea of better quality of life but as well because of business opportunities (Mayer & Meili, 2016) Figure 1: A mountain village (Corippo) in the canton Tessin in Switzerland. It shows kind of the demographic change where two people seem to move in or move away, therefore it could represent both countries' demographic chance situation in the mountainous villages (20 Minuten, 2019). In Georgia's mountains, the depopulation process started in the 1980s. Georgia was hit hardest between former Soviet republics and Eastern European countries (Salukvadze & Meladze, 2014). The population decreased from 1989 to 2017 by 39.7%. The economic crisis brought on by political and civil unrest is one of the variables contributing to the population shift in Georgia's mountains. In practically every highland region of Georgia, there is a drop in population, nevertheless, Khevi, Racha, Khevsureti, and Tusheti are especially visible. However, despite the similar environment, Khevi has a more favorable demographic situation than the other areas. The reason for this could be that the Georgian military road goes through here. In Oni municipality, there is a dramatic demographic situation because 37.3% of the population is made up of elderly people (Kohler et al., 2017). It can be said that the situation in Georgia still is dominated by a depopulation trend in the mountainous regions because young people are moving away for better perspectives. Switzerland on the other hand has a slight reversal trend, where more and more people are moving back to mountainous regions because of better work-live balance. But Switzerland went through phases of high depopulation rates before. In conclusion, we can say that demographic change is an ongoing process in both countries with similarities but also big differences. Literature:Bender, O., & Kanitscheider, S. (2012). New Immigration Into the European Alps: Emerging Research Issues. Mountain Research and Development, 32(2), 235–241. https://doi.org/10.1659/MRD-JOURNAL-D-12-00030.1Kohler, T., Elizbarashvili, N., Meladze, G., Svanadze, D., & Meessen, H. (2017). The Demogeographic Crisis in Racha, Georgia: Depopulation in the Central Caucasus Mountains. Mountain Research and Development, 37(4), 415–424. https://doi.org/10.1659/MRD-JOURNAL-D-17-00064.1Mayer, H., & Meili, R. (2016). New Highlander Entrepreneurs in the Swiss Alps. Mountain Research and Development, 36(3), 267–275. https://doi.org/10.1659/MRD-JOURNAL-D-16-00040.1Salukvadze, J., & Meladze, G. (2014). Georgia: Migration, a main risk towards demographic future. Discovering migration between visegrad countries and eastern partners, 150–169.20 Minuten (2019). Ohne Touristen verschwinden diese Oasen, URL: <https://www.20min.ch/story/ohne-touristen-verschwinden-diese-oasen-193854970725> (Accessed November 2023).

      აღნიშნული ბლოგი წარმოადგენს ერთგვარ შედარებით ანალიზს შვეიცარიისა და საქართველოს მთიან რეგიონებს შორის დემოგრაფიული ცვლილებების შესახებ. მნიშვნელოვანია, რომ ბლოგის ავტორებს გამოკვეთილი აქვთ რამდენიმე საკითხი, კერძოდ, მოსახლეობის შემცირების პრობლემები, მისი დაბერების პროცესი, დემოგრაფიული კრიზისის დასაწყისი და მისი გამომწვევი ძირითადი მიზეზები. საგულისხმოა, რომ შვეიცარიის მდგომარეობა მკვეთრად განსხვავდება საქართველოსგან. ბლოგში მოხსენიებული პრობლემები (მიგრაცია, შობადობის დაბალი დონე, ეკონომიკური პრობლემები, კლიმატის ცვლილებები და სხვ,) უფრო მკვეთრად გამოხატულია საქართველოში, რამაც, ცხადია, განაპირობა შრომისუნარიანი ახალგაზრდობის ბარში, ქალაქად გადასვლა. მაშინ როცა საქართველოში დღითიდღე უფრო აქტიურია მათი გადინება, შვეიცარიაში ახალგაზრდები ბრუნდებიან მთიან რეგიონებში. რაც შეეხება, დემოგრაფიული ცვლილებების დაწყებასა და განვითარებას, შვეიცარიაში ქალაქიდან სოფლად, მთაში გადასახლების ტენდენცია მე-20 საუკუნის ბოლოს დაიწყო და დღესაც გრძელდება, ცოტა განსხვავებული ფორმით. შედეგად კი ხდება მოსახლეობის ასაკობრივი განაწილების დაბალანსება, ცხოვრების ხარისხის გაუმჯობესება და გარკვეული ტიპის ბიზნესის ხელშეწყობაც. საქართველოსთან მიმართებით კი ბლოგის ავტორს მოხსენიებული აქვს ტერმინი "კრიზისი" და აღნიშნულია, რომ 1980-იანი წლებიდან შეინიშნებოდა მოსახლეობის კლება მთაში სხვადასხვა ეკონომიკური და პოლიტიკური პრობლემების გამო. რომ შევაჯამო, საქართველოშიც და შვეიცარიაშიც მიმდინარეობს დემოგრაფიული ცვლილებების პროცესი, თუმცა საპირისპირო ტენდენციებით.

    1. o at age 5. Interestingly, the most affluent parents have the luxury of doing what Graue and DiPerna (2000) referred to as "academic redshirting." This means they have the resources - both human and fiscal - to hold their children ou

      This is a good point. Working at a high-school level I don't often think about this early education issue. However, the impacts are felt for years.

    1. Overall points: Performed GWAS on VWD factor level variation in Swedish cohort with diagnosed VWD and found no accumulation of rare variants.

      Strongest effect was detected for blood group O coded for by the ABO gene.

      Sequencing identified 146 variants in the following eight genes: VWF, STXBP5, STAB2, SCARA5, STX2, TC2N, CLEC4M

      Excluding variants in the VWF gene, there were 76 variants remaining across the other genes listed above.

      However, caveats/limitations: 1. Study population is rather small, limits absolute number of chromosomes analyzed for rare variants associated with VWF level.

      1. Study population is a mixture of VWD patients who do not always fulfill modern criteria for type 1 VWD.

      2. Absence of detected rare variants in the study could be caused by the inability of the sequencing methodology to detect variants present in the population.

    1. r nee o a venture £ n in Engl cl'' ,, newwork,2the 50 uthe,rn ,~perm Whale Fishe';i ~und~d 9Pon c:~ •. . ,, , ,,,iP person~! exp~rie~c.e, of ~wo years:• and illustratelbn Wild legends~\l'flshould you be ~nc,lme~ to undertak ' rnhore , as a harpo y th~ aut~o,r'sczoo 3 C Id b • , e t e hook I oneer

      It has no romance and the main character has no experience as a harpooneer. The books is not a personal experience either. He is trying to make it sound good that he can get is published.

    2. It is curious, h~w a man may r:cts; b reason of an \n~ , an~ Yet .the grandest or sweetest of prosp h~ t 'f th , 'd I rven,ng h"11ss' , vay to m o e w, e and • edso like all other hedges , as m no v . , scape b &e ,S h 't b 'th me concerning the enchanting landscape in th eyond

      This might showcase how a sailor feels when he goes on a voyage. The person is so focused on the purpose of the voyage they do not try to look at the lesson that they could learn from being exposed to different regions.

    1. Sevdiğin birinin ölümüne tanık olmak o esaretin başlangıcı olabilirdi.

      ölüm; yine ölüm, yine ölüm ve tekrar tekrar eden ölüm... İnsanoğlu olarak alışamayacağımız en büyük kısır döngü fikrimce.

    1. Protein Language Model Fitness Is a Matter of Preference

      I really enjoyed reading your paper and thought it contained many interesting and insightful gems.

      • As someone who has calculated many PLL, which take time and money, I was very interested in your O(1) method for PLL.
      • The predictive power being predicated on wildtype PLL is a very important result.
      • I found Figure 5 to be a beautiful illustration of how homology in training data influences preference
      • In Figure 6, it was incredible to see just how much the Spearman can be increased for the low-likelihood DMS datasets. And surprising to see that low-likelihood DMS datasets do worse. Clearly there is more to learn.

      More broadly, I would be curious to hear your thoughts on alternative PLM training objectives. Specifically, I'm interested in approaches that maintain the BERT-style masked language modeling objective while incorporating additional training signals. One key idea would be to include explicit feedback about sequence fitness ('good' vs 'bad' sequences) alongside the traditional masked prediction task.

      This approach could help move away from preference-oriented behavior. When models are trained solely on naturally occurring proteins, they implicitly learn that all training examples represent 'good' or 'valid' proteins. By incorporating direct fitness measurements as an additional training objective, we could potentially guide the model to learn more nuanced distinctions between functional and non-functional sequences, rather than simply modeling the distribution of extant proteins.

      Thanks again for the insightful paper.

    2. Unlike autoregressive language models, masked language models don’t have a natural way to immediately compute the joint likelihood of a sequence. As a result, Wang and Cho (2019) proposed to mask every index of a sequence one-at-a-time then average to derive a PLL (Wang and Cho, 2019): <img class="highwire-embed" alt="Embedded Image" src="https://www.biorxiv.org/sites/default/files/highwire/biorxiv/early/2024/10/03/2024.10.03.616542/embed/inline-graphic-2.gif"/>.This formulation suffers from the need to run 𝒪 (L) forward passes to compute a perplexity or log likelihood. In response to this, the community only considers autoregressive pLMs when computing fitness values for proteins containing insertions or deletions.

      There is a lot of overlap between this paragraph and the next.

    1. o use an ArrayList instead

      )%3B%0A%0A++++++++//+remove+item+0+and+move+everything+down%0A++++++++//++(this+can+be+done+in+one+method+call+with+ArrayList)%0A++++++++/toDoList%5B0%5D+%3D+toDoList%5B1%5D%3B%0A++++++++toDoList%5B1%5D+%3D+toDoList%5B2%5D%3B%0A++++++++toDoList%5B2%5D+%3D+%22%22%3B%0A/%0A+++++++toDoList.remove(0)%3B%0A%0A++++++++System.out.println(%22Here's+the+next+thing+to+do%3A+%22+%2B+toDoList.get(0))%3B%0A%0A++++++++//+Why+is+an+ArrayList+better+than+an+array+for+a+toDoList%3F%0A++++++++//+Answer%3A%0A++++%7D%0A%7D%0A%0A&mode=edit)

    1. No más conjeturas sobre la capacidad que necesita: si opta por poca capacidad al implementar una carga de trabajo, puede terminar con recursos inactivos caros o lidiando con las implicaciones de rendimiento de una capacidad limitada. Con los servicios de computación en la nube, estos problemas pueden desaparecer. Puede usar tanta capacidad como necesite y escalar a

      hola

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public Review):

      The authors studied how hippocampal connectivity gradients across the lifespan, and how these relate to memory function and neurotransmitter distributions. They observed older age with less distinct transitions and observed an association between gradient de-differentiation and cognitive decline.

      This is overall an innovative and interesting study to assess gradient alterations across the lifespan and its associations to cognition.

      The paper is well-written, and the methods appear sound and thoughtful. There are several strengths, including the inclusion of two independent cohorts, the use of gradient mapping and alignment techniques, and an overall sound statistical and analysis framework. There are several areas for potential improvements in the paper, and these are listed below:

      We thank the Reviewer for their positive assessment and summary of our work. We address each of the Reviewer’s comments below, and outline the revisions we have made to the manuscript based on the Reviewer’s suggestions.

      (1) The reported D1 associations appear a bit post-hoc in the current work and I was unclear why the authors specifically focussed on dopamine here, as other transmitter systems are similar present at the level of the hippocampus and implicated in aging.

      Other neurotransmitter systems may indeed be relevant in the context of hippocampal function in aging. In this study, however, we included a specific research question about the DA D1 receptor (D1DR) based on previous research 1) emphasizing the role of DA neuromodulation in maintaining functional network segregation in aging to support cognition (Pedersen et al., 2023), 2) reporting heterogeneous distribution of DA markers across the hippocampus, supporting efficient modulation of distinct behaviors (Dubovyk & ManahanVaughan, 2019; Edelmann & Lessmann, 2018; Gasbarri et al., 1994; Kempadoo et al., 2016), and 3) demonstrating the spatial distribution of D1DRs as varying across neocortex along a unimodal-transmodal gradient (Pedersen et al., 2024). To which degree this variation might be reflected in cortico-hippocampal connectivity, however, remained to be investigated. As such, one of the study’s specific aims was to evaluate the spatial distribution of D1DRs as a molecular correlate of the hippocampus’ functional organization. Importantly, we were interested in mapping associations between individual differences in the organization of connectivity and D1DRs. This was uniquely enabled by utilizing the DyNAMiC sample, as it includes structural and functional MRI data in combination with D1DR PET in the same individuals across the adult lifespan (n=180). However, after observing significant spatial correspondence between functional organization and D1DR expressed by the second hippocampal gradient (G2), we did indeed perform complimentary analyses with group-averaged data of additional dopamine markers (D2DR from a subsample of our participants, as well as DAT and FDOPA from open sources) to test the generalizability of the original finding. Taken together, the original analyses based on subject-level data and complimentary group-level analyses provided support for the interpretation of G2 as a dopaminergic mode.

      We have updated the manuscript to clarify the focus on the D1 receptor and the contribution of including additional DA markers.

      Updated paragraph in the Introduction, pages 5-6:

      “Dopamine (DA) is one of the most important modulators of hippocampus-dependent function(47,48), and influences the brain’s functional architecture through enhancing specificity of neuronal signaling(49). Consistently, there is a DA-dependent aspect of maintained functional network segregation in aging which supports cognition(50). Animal models suggest heterogeneous patterns of DA innervation(51,52) and postsynaptic DA receptors(53), across both transverse and longitudinal hippocampal axes, likely allowing for separation between DA modulation of distinct hippocampus-dependent behaviors(47). Moreover, the human hippocampus has been linked to distinct DA circuits on the basis of long-axis variation in functional connectivity with midbrain and striatal regions(54,55). Taken together with recent findings revealing a unimodal-transmodal organization of the most abundantly expressed DA receptor subtype, D1 (D1DR), across cortex(56), we tested the hypothesis that the organization of hippocampal-neocortical connectivity partly reflects the underlying distribution of hippocampal DA receptors, predicting predominant spatial correspondence for any hippocampal gradient conveying a unimodal-transmodal pattern across cortex.”

      Updated sections in the Results, page 13-14:

      “Our next aim was to investigate to which extent the distribution of hippocampal DA D1 receptors (D1DRs), measured by [<sup>11</sup>C]SCH23390 PET in the DyNAMiC(58) sample, may serve as a molecular correlate of the hippocampus’ functional organization.”

      “Complimentary analyses were then conducted to further evaluate G2 as a dopaminergic hippocampal mode by utilizing additional DA markers at group-level.”

      Moreover, the authors may be aware that multiple PET tracers are somewhat challenged in the mesiotemporal region. Is this the case for the D1 receptor as well? The hippocampus is a small and complex structure, and PET more of a low res technique so one would want to highlight and discuss the limitations of the correlations with PET maps here and/or evaluate whether the analysis adds necessary findings to the study.

      We thank the Reviewer for raising this point. The lower resolution of PET is indeed a relevant aspect to consider when quantifying D1DR availability in the hippocampus, even though previous research indicate high test-retest reliability of [<sup>11</sup>C]SCH23390 PET measurement in this region (Kaller et al., 2017). We have now elaborated on PET limitations in the Discussion of the revised manuscript.

      In our study, we made efforts to reduce potential partial volume effects (PVE) by correcting our PET data, and tested spatial associations between our functional gradients and D1DR maps using trend-surface modelling (TSM), rather than through voxel-wise comparisons. This allowed us to evaluate the spatial correspondence between functional connectivity and D1DRs at a level of spatial trends, estimated using TSM models computed at increasing levels of complexity. The results showed consistent spatial overlap between G2 and D1DRs across these models, that is, across spatial trends described at coarser-to-finer scales. Furthermore, this was replicated across several DA markers with PET and SPECT data from independent samples.

      Taken together, we agree with the Reviewer that the spatial correspondence observed between G2 and hippocampal D1DRs should be interpreted in the context of resolution-related limitations inherent to PET imaging. However, we strongly believe that our DA analyses offer valuable insight to the molecular underpinnings of hippocampal functional organization.

      Updated paragraph in the Discussion, pages 25-26:

      “We discovered that G2, specifically, manifested organizational principles shared among function, behavior, and neuromodulation. Meta-analytical decoding reproduced a unimodalassociative axis across G2 (Figure 3B), and analyses in relation to the distribution of D1DRs – which vary across cortex along a unimodal-transmodal axis(76,77) – demonstrated topographic correspondence both at the level of individual differences and across the group. It should, however, be acknowledged that PET imaging in the hippocampus is associated with resolutionrelated limitations, although previous research indicate high test-retest reliability of [<sup>11</sup>C]SCH23390 PET to quantify D1DR availability in this region(78). As such, mapping the distribution of hippocampal D1DRs at a fine spatial scale remains challenging, and replication of our results in terms of overlap with G2 is needed in independent samples. Here, we evaluated the observed spatial overlap between G2 topography and D1DRs across multiple TSM model orders, showing correspondence between modalities from simple to more complex parameterizations of their spatial properties. Topographic correspondence was additionally observed between G2 and other DA markers from independent datasets (Figure 3B), suggesting that G2 may constitute a mode reflecting a dopaminergic phenotype, which contributes to the currently limited understanding of its biological underpinnings.”

      From my (perhaps somewhat biased) perspective, it might be valuable to instead or in addition look at measures of hippocampal microstructure and how these relate to the functional aging effects. This could be done, if available, using data from the same subjects (eg based on quantitative MRI contrasts and/or structural MRI) and/or using contextualization findings as implemented in eg hippomaps.readthedocs.io

      We thank the Reviewer for this suggestion. We performed additional analyses investigating the spatial overlap between our connectivity gradients and estimates of hippocampal microstructure, computed as the ratio of T1- over T2-weighted (T1w/T2w) images (Glasser & Von Essen, 2011; vos de Wael et al., 2018). Analyses of spatial correspondence then followed the TSM-based method used to test the spatial overlap between functional connectivity gradients and D1DR distribution. Applying TSM to the T1w/T2w image computed for each participant yielded subject-level model parameters describing microstructure topography, which were then entered as predictors of connectivity topography in multivariate GLMs (separate models for each gradient and hemisphere, 6 models in total).

      Analyses revealed that microstructure of the right hippocampus significantly predicted gradient topography of right-hemisphere G1 (F = 1.325, p \= 0.034), while no other links between connectivity gradients and microstructure emerged as significant (F 0.930-1.184, ps 0.7060.079).

      These results, suggesting an association along the anteroposterior axis, deviate from previous findings linking hippocampal microstructure to G3-like, medial-lateral, connectivity organization (vos de Wael et al., 2018). As we believe that comprehensive analyses of our gradients in relation to microstructure across the lifespan would be best addressed in future work, we have not included these analyses of microstructure in the revised manuscript.

      (2) Can the authors clarify why they did not replicate based on cohorts that are more widely used in the community and open access, such as CamCAN and/or HCP-Aging? It might connect their results with other studies if an attempt was made to also show that findings persist in either of these repositories.

      We agree with the Reviewer that replication in samples such as CamCAN and/or HCP-Aging would provide valuable opportunities to connect our findings with those of other studies using those datasets. Here, we included the Betula dataset (Nilsson et al., 2004) as our replication sample, as it was immediately available to us, included a large sample of adults in a comparable age, and a word recall episodic memory task closely aligned with the one included in DyNAMiC. Importantly, leveraging the Betula dataset as our replication sample allows us to link our findings to a wide range of previous studies central to the understanding of neurocognitive aging in general, and hippocampal aging in particular (Nyberg, 2017; Nyberg et al., 2020). Betula is a large longitudinal project that has been tracking individuals since 1988, and is part of the National E-infrastructure for Aging Research (NEAR: www.near-aging.se), through which data from several Swedish studies are made available to both national and international researchers. While we acknowledge the value of extending replication efforts to datasets like CamCAN and HCP-Aging, we emphasize the significant contribution of having replicated our connectivity gradients in the Betula dataset.

      (3) The authors applied TSM and related these parameters to topographic changes in the gradients. I was wondering whether and how such an approach controls for autocorrelation present in both the PET map and gradients. Could the authors clarify?

      The Reviewer raises an important topic in spatial autocorrelation. The TSM approach used to parameterize the topography of the functional gradients and D1DR distribution, and to test the spatial correspondence between modalities, did not include any specific method to control for autocorrelation. Here, we highlight two aspects of our study in relation to this point. First, we demonstrated in the Supplementary information (S. Figure 4) that autocorrelation induced by spatial smoothing likely has limited effects on overall gradient topography and the ability of TSM parameters to capture meaningful inter-individual differences in terms of age. Second, in the case of spatial overlap effects being significantly impacted by autocorrelation, we would expect the association between right-hemisphere G2 and D1DR topography to similarly emerge for G2 in the left hemisphere. The absence of such an association may speak to a limited effect of spatial autocorrelation.

      (4) The TSM approach quantifies the gradients in terms of x/y/z direction in a cartesian coordinate system. Wouldn't a shape intrinsic coordinate system in the hippocampus also be interesting, and perhaps even be more efficient to look at here (see eg DeKraker 2022 eLife or Paquola et al 2020 eLife)?

      This is a very relevant question and we appreciate the Reviewer’s suggestion. We recognize that there may be several benefits associated with adopting a shape-intrinsic coordinate system when characterizing effects in the hippocampus, given its curved/folded anatomy. Approaches like the ones adopted in DeKraker et al., 2022 and Paquola et al., 2020, utilizes geodesic coordinate frameworks to represent the hippocampus in surface space, enabling mapping of connectivity onto the hippocampal surface while respecting its inherent curvature and topology. We anticipate that quantifying gradients within such a framework would especially benefit identification of connectivity change across the hippocampal surface relative to reference points such as subfield boundaries, while minimizing effects of interindividual differences in hippocampal shape and folding. In our study, hippocampal gradients and their associated cortical patterns were computed in volumetric space, with TSM subsequently used to parameterize the change in connectivity along these gradients. This indeed yields a description of connectivity change within a coordinate system less specific to hippocampal anatomy, but may favor generalizability and integration with previous gradient findings within and beyond the hippocampus (e.g., Przeździk et al., 2019; Tian et al., 2020; Katsumi et al., 2023; Navarro-Schröder et al., 2015), as well as connections with broader neuroimaging frameworks through techniques such as meta-analytical decoding. In our view, the different coordinate frameworks offer complimentary insight to hippocampal organization, and while we have opted to not undertake novel analyses to explore our gradients within a geodesic coordinate system for the purposes of this paper, we recognize the importance of such evaluation of our gradients in future analyses. We have made updates to the Discussion in the revised manuscript on this topic (pages 23-24):

      “Greater anatomical specificity, with more precise characterization of connectivity in relation to subfield boundaries while minimizing effects of inter-individual differences in hippocampal shape and folding, might be achieved by adopting techniques implementing a geodesic coordinate system to represent effects within the hippocampus(68,69).”

      Reviewer #2 (Public Review):

      Summary:

      This paper derives the first three functional gradients in the left and right hippocampus across two datasets. These gradient maps are then compared to dopamine receptor maps obtained with PET, associated with age, and linked to memory. Results reveal links between dopamine maps and gradient 2, age with gradients 1 and 2, and memory performance.

      Strengths:

      This paper investigates how hippocampal gradients relate to aging, memory, and dopamine receptors, which are interesting and important questions. A strength of the paper is that some of the findings were replicated in a separate sample.

      Weaknesses:

      The paper would benefit from added clarification on the number of models/comparisons for each test. Furthermore, it would be helpful to clarify whether or not multiple comparison correction was performed and - if so - what type or - if not - to provide a justification. The manuscript would furthermore benefit from code sharing and clarifying which results did/did not replicate.

      We thank the Reviewer for their positive assessment and suggestions regarding further clarifications. We have addressed the Reviewer’s comments in a point-by-point manner under the “Recommendations for the authors” section.

      Reviewer #3 (Public Review):

      Summary:

      In this study, the authors analyzed the complex functional organization of the hippocampus using two separate adult lifespan datasets. They investigated how individual variations in the detailed connectivity patterns within the hippocampus relate to behavioral and molecular traits. The findings confirm three overlapping hippocampal gradients and reveal that each is linked to established functional patterns in the cortex, the arrangement of dopamine receptors within the hippocampus, and differences in memory abilities among individuals. By employing multivariate data analysis techniques, they identified older adults who display a hippocampal gradient pattern resembling that of younger individuals and exhibit better memory performance compared to their age-matched peers. This underscores the behavioral importance of maintaining a specific functional organization within the hippocampus as people age.

      Strengths:

      The evidence supporting the conclusions is overall compelling, based on a unique dataset, rich set of carefully unpacked results, and an in-depth data analysis. Possible confounds are carefully considered and ruled out.

      Weaknesses:

      No major weaknesses. The transparency of the statistical analyses could be improved by explicitly (1) stating what tests and corrections (if any) were performed, and (2) justifying the elected statistical approaches. Further, some of the findings related to the DA markers are borderline statistically significant and therefore perhaps less compelling but they line up nicely with results obtained using experimental animals and I expect the small effect sizes to be largely related to the quality and specificity of the PET data rather than the derived functional connectivity gradients.

      We thank the Reviewer for the thoughtful summary and positive assessment of our work. To increase transparency of the statistical analyses, we have in the revised manuscript added information regarding statistical tests and corrections for multiple comparisons. In the Results, p-values were reported at an uncorrected statistical threshold, and we have in the revised manuscript included the corresponding p-values adjusted for multiple comparisons using the Benjamini-Hochberg method to control the false discovery rate (FDR). Finally, in the revised manuscript, we have now elaborated on the potential limitations of our PET analyses and we include the updated paragraph below.

      Addition made to the Results section, page 13:

      “Individual maps of D1DR binding potential (BP) were also submitted to TSM, yielding a set of spatial model parameters describing the topographic characteristics of hippocampal D1DR distribution for each participant. D1DR parameters were subsequently used as predictors of gradient parameters in one multivariate GLM per gradient (in total 6 GLMs, controlled for age, sex, and mean FD). Results are reported with p-values at an uncorrected statistical threshold and p-values after adjustment for multiple comparisons using the Benjamini-Hochberg method to control the false discovery rate (FDR).”

      Addition made to the Results section, page 15:

      “Effects of age on gradient topography were assessed using multivariate GLMs including age as the predictor and gradient TSM parameters as dependent variables (controlling for sex and mean frame-wise displacement; FD). One model was fitted per gradient and hemisphere, each model including all TSM parameters belonging to a gradient (in total, 6 GLMs).”

      Addition made to the Results section, page 17:

      “Models were assessed separately for left and right hemispheres, across the full sample and within age groups, yielding eight hierarchical models in total. Results are reported with p-values at an uncorrected statistical threshold and p-values after FDR adjustment.”

      Updated paragraph in the Discussion, pages 25-26:

      “We discovered that G2, specifically, manifested organizational principles shared among function, behavior, and neuromodulation. Meta-analytical decoding reproduced a unimodalassociative axis across G2 (Figure 3B), and analyses in relation to the distribution of D1DRs – which vary across cortex along a unimodal-transmodal axis(76,77) – demonstrated topographic correspondence both at the level of individual differences and across the group. It should, however, be acknowledged that PET imaging in the hippocampus is associated with resolutionrelated limitations, although previous research indicate high test-retest reliability of [<sup>11</sup>C]SCH23390 PET to quantify D1DR availability in this region(78). As such, mapping the distribution of hippocampal D1DRs at a fine spatial scale remains challenging, and replication of our results in terms of overlap with G2 is needed in independent samples. Here, we evaluated the observed spatial overlap between G2 topography and D1DRs across multiple TSM model orders, showing correspondence between modalities from simple to more complex parameterizations of their spatial properties. Topographic correspondence was additionally observed between G2 and other DA markers from independent datasets (Figure 3B), suggesting that G2 may constitute a mode reflecting a dopaminergic phenotype, which contributes to the currently limited understanding of its biological underpinnings.”

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      Please see the comments in the public review.

      We thank the Reviewer for their comments and recommendations, and have addressed them in the “Public review” section.

      Reviewer #2 (Recommendations For The Authors):

      (1) All statistical analyses are based on linear regressions using trend surface modeling (TSM) parameters that parameterize gradients at the subject level. These models resulted in 9 parameters for gradient 1 and 12 parameters each for gradients 2 and 3. The text states that 'Effects of age on gradient topography was assessed using multivariate GLMs including age as the predictor and gradient TSM parameters as dependent variables (controlling for sex and mean frame-wise displacement; FD)'. Please clarify whether these GLMs were fitted separately for each TSM parameter (i.e., 9+12+12=33 models for both left and right = 66 total models) or on the overall model?

      We appreciate the Reviewer’s request for clarification on this matter. These GLMs were fitted on the overall TSM model, that is, through one GLM per gradient (3) and hemisphere (2), each one including all TSM parameters belonging to a gradient (in total, 6 GLMs).

      In the revised manuscript, we have added more details to the Results section, page 15: “Effects of age on gradient topography were assessed using multivariate GLMs including age as the predictor and gradient TSM parameters as dependent variables (controlling for sex and mean frame-wise displacement; FD). One model was fitted per gradient and hemisphere, each model including all TSM parameters belonging to a gradient (in total, 6 GLMs).”

      (2) Similarly, for memory it appears that multiple models were performed (left and right, young, middle-aged, old, whole groups). Please clarify whether and how multiple comparison correction was performed in this case.

      In the revised manuscript, we have now specified the number of analyses conducted in relation to memory performance. We have also clarified that p-values were reported at an uncorrected statistical threshold, and we have in the revised manuscript included the corresponding p-values adjusted for multiple comparisons using the Benjamini-Hochberg method to control the FDR.

      Updated section in the Results, page 17:

      “Models were assessed separately for left and right hemispheres, across the full sample and within age groups, yielding eight hierarchical models in total. Results are reported with p-values at an uncorrected statistical threshold and p-values after FDR adjustment.”

      (3) Although I applaud the authors for their replication efforts, the results do not appear to replicate well. For example, memory was linked to gradient 2 in the whole group but to gradient 1 in the young group. Furthermore, dopamine was linked to gradient 2 in the right but not the left hemisphere. Although the overall group-level gradients were very stable between the two datasets, it is not clear whether the age findings replicated and the memory subgroup findings only replicated at trend level for memory and only partially replicated at the TSM parameter level.

      We thank the Reviewer for highlighting the inclusion of a replication dataset as a strength of our study, and we appreciate the recommendation to clarify to which extent results replicated. We provide a response to the Reviewer’s points below, and specify the revisions made to the manuscript in relation to this topic.

      The main aim of our study was to characterize the topographic organization of functional hippocampal-neocortical connectivity within the hippocampus across the adult lifespan, as previous studies have limited their focus to younger adults. Given the lack of previous studies for comparison, together with our identification of a novel secondary long-axis connectivity gradient (G2) taking precedence over the previously established medial-lateral G3, we included the Betula sample (Nilsson et al., 2004) for the purpose of replication. There was a high level of consistency between our main dataset and our replication dataset, with gradients 1-3 in left and right hemispheres identified in both samples.

      Further use of the replication dataset, beyond the identification of the connectivity gradients, was originally not planned. As such, not all subsequent analyses in the main dataset were conducted in the replication dataset. However, we found it critical to evaluate the observation that older individuals who maintained a youth-like gradient topography also exhibited higher levels of memory performance in an independent sample. This was possible given that the replication dataset included a comparable number of participants in similar ages and a word recall episodic memory task corresponding well to the one used in DyNAMiC. Overall, we conclude that these analyses replicated well across samples. Firstly, topography of lefthemisphere G1 informed the classification of older adults into youth-like and aged subgroups in both samples. Furthermore, in both samples, we observed that the older subgroups identified based on G1 topography also exhibited the youth-like vs. aged pattern in G2 topography. This pattern was, however, evident also in G3 only in the main sample, possibly suggesting a limited contribution of G3 topography in determining overall functional profiles in older age. In terms of the behavioral relevance of maintaining youth-like gradient topography in older age, we observed effects on word recall performance in both samples; although the Reviewer correctly points out that, the difference between subgroups was significant at trend-level (p = 0.058) in the replication dataset. While this indeed underscores the importance of replication efforts in additional samples, we argue that the pattern observed in our replication dataset is overall consistent with, and conveys effects in the expected direction based on, the original observations in our main dataset.

      In revising the manuscript, we have performed additional analyses for replication purposes in terms of memory. Originally, we observed a significant association between G2 topography and episodic memory across the main sample. However, this effect did not remain significant after FDR adjustment for multiple comparisons. To evaluate this association further, we conducted a corresponding hierarchical multiple regression analysis in the replication dataset, which supported a role of G2 in memory (Adj. R<sup>2</sup> = 0.368, ΔR<sup>2</sup> = 0.081, F= 1.992, p = 0.028). Together, these analyses suggest that inter-individual differences in episodic memory performance may in part be explained by the spatial characteristics of G2 across the adult lifespan, although increased statistical power in relation to the large number of TSM parameters included in the hierarchical regression models may be needed to explore this association in smaller, age-stratified, groups. Relatedly, it is worth mentioning that higher levels of memory performance in older age were linked to the maintenance of youth-like G2 topography in both our main and replication datasets.

      In parallel, topographic parameters of G1 predicted memory performance in the younger adults, which successfully replicates TSM-based results previously reported in Przeździk et al., 2019. Although similar associations were not evident within the other age groups, a link between G1 topography and memory was demonstrated in older age based on a) the identification of individuals maintaining a youth-like G1 profile and higher levels of memory, within which b) memory performance was, as in young adults, significantly predicted by G1 topography.

      The spatial correspondence between G2 topography and distribution of hippocampal D1DRs was lateralized to the right, and as the Reviewer points out, as such did not replicate across hemispheres. To which extent replication across hemispheres should be expected in this case is, however, difficult to determine. Lateralization and/or hemispheric asymmetry is commonly observed in numerous hippocampal features, from the molecular level to its functional involvement in behavior (Nematis et al., 2023; Persson & Söderlund, 2015), including various dopaminergic markers tested in the animal literature (Afonso et al., 1993; Sadeghi et al., 2017). Yet, potential differences between hemispheres in D1DR availability and the spatial distribution of receptors along hippocampal axes remain less studied in humans. More data is therefore needed to determine the nature of this right-hemisphere lateralization.

      In sum, we argue that our results show a good level of replication across independent datasets and across analyses in our main dataset. Whereas this study did not attempt replication of all analyses conducted in the main dataset, it has through replication across independent samples provided support for its main findings – the organization of hippocampal-neocortical connectivity along three main hippocampal gradients across the adult lifespan, and the gradient topography-based identification of older individuals maintaining a youth-like hippocampal organization in older age.

      The revised manuscript includes edits made to incorporate the new analyses and clarifications of observations in relation to memory.

      In the Results, page 17:

      “Observing that the association between G2 and memory did not remain significant after FDR adjustment, we performed the same analysis in our replication dataset, which also included episodic memory testing. Consistent with the observation in our main dataset, G2 significantly predicted memory performance (Adj. R<sup>2</sup> = 0.368, ΔR<sup>2</sup> = 0.081, F= 1.992, p = 0.028) over and above covariates and topography of G1. Here, the analysis also showed that G1 topography predicted performance across the sample (Adj. R<sup>2</sup> = 0.325, ΔR<sup>2</sup> = 0.112, F= 3.431, p < 0.001).”

      In the Discussion, page 26:

      “Results linked both G1 and G2 to episodic memory, suggesting complimentary contributions of these two overlapping long-axis modes. Considered together, analyses in the main and replication datasets indicated a role of G2 topography in memory across the adult lifespan, independent of age. A similar association with G1 was only evident across the entire sample in the replication dataset, whereas results in the main sample seemed to emphasize a role of youthlike G1 topography in memory performance. In line with previous research, memory was successfully predicted by G1 topography in young adults(30), and similarly predicted by G1 in older adults exhibiting a youth-like functional profile.”

      (4) Please share the data and code and add a description of data and code availability in the manuscript.

      We have now made our code available, and added a statement on data and code availability in the revised manuscript.

      On page 37: “Data from the DyNAMiC study are not publicly available. Access to the original data may be shared upon request from the Principal investigator, Dr. Alireza Salami. The Matlab, R, and FSL codes used for analyses included in this study are openly available at https://github.com/kristinnordin/hcgradients. Computation of gradients was done using the freely available toolbox ConGrads: https://github.com/koenhaak/congrads.”

      Reviewer #3 (Recommendations For The Authors):

      Please see the comments in the public review.

      We thank the Reviewer for their comments and recommendations, and have addressed them in the “Public review” section.

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    1. Author response:

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

      Reviewer #1:

      Regarding the manuscript's clarity, the sentence on page 5, "We also stained VTA sections for Tyrosine hydroxylase (TH) to estimate the rate of ChR2 colocalization with DA neurons," reads awkwardly. Removing the word "rate" could improve clarity.

      We have made the recommended clarifying edit (page 5, lines 30-31).

      Additionally, the anatomical data and findings are largely non-quantitative in nature. However, solid microscopy images are presented to support each claim. Additional quantification would strengthen the paper, specifically the quantification of projection density for each population and the proportion of each subpopulation that projects to their regions of interest.

      To rigorously quantify the projection density of each subpopulation would require a level of exhaustivity our study was not designed for. This is because during microscopy we focused efforts on imaging regions containing dense signals but did not exhaustively image regions receiving apparently weak or no input. While we considered including a semi-quantitative table of projection density, based on the data available we could not discriminate with confidence between, e.g., regions recipient of minimal input versus no input from VTA populations. Thus, while we stand by our descriptive statements we do not expand on those further.

      The authors should consider discussing the possibility that subpopulations of these cells could still be true interneurons especially if cells were looked at the single neuron level of resolution.

      We agree that some of the VTA populations we studied could include subpopulations that are bona fide interneurons. The identification of alternate markers or combinations of markers, or use of single-cell imaging approaches may indeed support this possibility in future. This is discussed in the context of currently available evidence on page 5 lines 32-34, page 11 lines 2-4, page 12 lines 2-11, and page 12 lines 15-16.

      Overall, the paper is well-written and important for the field and beyond.

      Thank you!

      Reviewer #2:

      Weaknesses:

      While the authors use several Cre driver lines to identify GABAergic projection neurons, they then use wild-type mice to show that projection neurons synapse onto neighboring cells within the VTA. This does not seem to lend evidence to the idea that previously described "interneurons" are projection neurons that collateralize within the VTA.

      We think the use of WT mice is a strength because it allows us to measure both GABA and non-GABA synapses made by VTA projections on to the same cells within VTA. However, we have also done this experiment targeting NAc-projecting VTA VGAT-Cre neurons, and VP-projecting VTA MOR-Cre neurons. Consistent with the WT dataset, we find that these defined projection neurons also make intra-VTA synapses. These data are now included as Figure 7.

      More broadly. Our review of the literature finds very little evidence to support the notion of a VTA interneuron as we define it: VTA neurons that makes only local connections. But the absence of evidence need not imply evidence of absence, thus we do not claim that all VTA neurons previously presumed to be interneurons must be projection neurons. We do express confidence in our findings that VTA projection neurons (that include GABA-releasing neurons) make local synapses in VTA. We argue that in the absence of compelling positive evidence for the existence of VTA interneurons, such as a selective marker, “we”, “the field”, should not presume their existence.

      Other suggestions:

      (1) While the authors present evidence that some projection neurons also synapse locally, there is no quantification as to the proportion of each neuronal subtype that collateralizes within the VTA. This would be a useful analysis.

      We agree this would be useful information. But our experiments were not designed to answer this question. Indeed, we have not conceived of a feasible method to discriminate between collateralizing and non-collateralizing VTA projection neurons at the single-cell level, thus we do not know how we would calculate such proportions.

      (2) There is significant interest in the molecular heterogeneity and spatial topography of the VTA. Additional analyses of the spatial topography of labeled projectors would be useful. For example, knowing if Pvalb+ projection neurons are distributed throughout the VTA or located along the midline would be a useful analysis.

      Prior studies and public databases (e.g., Allen brain atlas, GENSAT) allow one to visualize the location of VTA neurons positive for Pvalb and the other markers we investigated (Olson & Nestler, 2007). However, these label the entire population of neurons and thereby include those that project to any of the various projection targets. There are also studies that have used retrograde labeling approaches to map the distribution of labeled VTA cells projecting to one or another target (Beier et al., 2015; Lammel et al., 2008; Margolis et al., 2006). For example, finding that LHb-projecting neurons (a major target of Pvalb+ VTA neurons) are enriched in medial VTA (Root et al., 2014). From this evidence we might infer that Pvalb+ VTA neurons that project to LHb are likely to be medially biased. Future studies may more carefully map the intersection of specific projection targets for each VTA subpopulation.  

      Reviewer #3 (Recommendations For The Authors):

      Weaknesses:

      This study has a few modest shortcomings, of which the first is likely addressable with the authors' existing data, while the latter items will likely need to be deferred to future studies:

      (1) Some key anatomical details are difficult to discern from the images shown. In Figure 1, the low-magnification images of the VTA in the first column, while essential for seeing what overall section is being shown, are not of sufficient resolution to distinguish soma from processes. A supplemental figure with higher-resolution images could be helpful.

      We uploaded a higher resolution file for figure 1.

      Also, where are the insets shown in the second column obtained from? There is not a corresponding marked region on the low-magnification images. Is this an oversight, or are these insets obtained from other sections that are not shown?

      This was an oversight, we added the corresponding marked region to the low-magnification images.

      Lastly, there is a supplemental figure showing the NAc injection sites corresponding to Figure 5, but not one showing VP or PFC injection sites in Figure 6. Why not?

      We added a figure with histology examples for the VP and the PFC injection sites as done for Figure 5, included as Supplemental Figure 3.

      (2) Because multiple ChR2 neurons are activated in the optogenetic experiments, it is not clear how common is it for any specific projection neuron to make local connections. Are the observed synaptic effects driven by just a few neurons making extensive local collateralizations (while other projection neurons do not), or do most VTA projection neurons have local collaterals? I realize this is a complex question, that may not have an easy answer.

      This is a great question but, indeed, we don’t know the answer. As mentioned in response to Reviewer #2, we are not convinced there is a currently feasible way to discriminate between collateralizing and non-collateralizing cells at the single cell level.

      (3) There is something of a conceptual disconnect between the early and later portions of this paper. Whereas Figures 1-4 examine forebrain projections of genetic subtypes of VTA neurons, the optogenetic studies do not address genetic subtypes at all. I do realize that is outside of the scope of the author's intent, but it does give the impression of somewhat different (but related) studies being stitched together. For example, the MOR-expressing neurons seem to project strongly to the VP, but it is not addressed whether these are also the ones making local projections. Also, after showing that PV neurons project to the LHb, the opto experiments do not examine the LHb projection target at all.

      This too was raised by Reviewer #2. While addressing this question for all the populations we investigated feels redundant, we now include optogenetic data showing that NAc-projecting VTA VGAT-Cre and VP-projecting VTA MOR-Cre neurons also make local collaterals (Figure 7). We think this allows us to connect the two approaches to a greater degree. Based on our findings using a dual virus approach to express Syn:Ruby in each population of VTA projection neuron, we think it very likely that we’d continue to find similar results using optogenetics-assisted slice electrophysiology for each population.

      Other suggestions:

      (1) I appreciated the extensive and high-quality anatomical figures shown in Figures 2-4. However, the layout was sometimes left-to-right, and sometimes right-to-left, which felt distracting. At some point, the text refers to "Fig. 3KJ", i.e. with the letters being in backward alphabetical order, and Figures 3I and 3L do not appear mentioned anywhere in the main text, leading me to wonder if that text was intended to read "Fig. 3I-L".

      Thank you for noting this. We have harmonized the layout of Figures 2-4 and adjusted the in-text Figure call-outs.

      Also, the inset in Figure 3J appears to show local collaterals of NTS neurons in the VTA, since there is no soma in that inset. This is interesting, and worth reporting, but is not explained in either the main text or Figure legend.

      We added a more complete description in the result section (page 6 line 25-30).

      (2) Perhaps I missed it, but I could not find any mention of the intensity of the LED light delivered during the optogenetic experiments. While acknowledging that this can be variable, do the authors have at least a rough range?

      We have added this information to the methods, page 17 line 8.

      Editor's Note:

      Should you choose to revise your manuscript, please double check that you have fully reported all statistics including exact p-values wherever possible alongside the summary statistics (test statistic and df) and 95% confidence intervals.

      We confirm that we have fully reported all statistics including exact p-values wherever possible alongside the summary statistics (test statistic and df) and 95% confidence intervals.

      Note to Editor and Readers

      While reanalyzing our data for resubmission, we discovered that some of the short-latency optogenetic evoked postsynaptic currents (oPSCs) we detected were erroneously categorized. Specifically, some VTA cells that showed large outward currents (oIPSCs) when held at 0 mV, also had small inward currents when held at -60 mV. These small inward currents were initially categorized as oEPSCs, suggesting these VTA cells received input from populations of VTA projection neurons that released GABA and/or glutamate. However, the kinetics of these small inward currents were slow and aligned with the within-cell kinetics of the oIPSCs, indicating that these were very likely mediated by GABA<SUB>A</SUB> receptors. In one case the opposite was apparent, with a small PSC initially miscategorized as an oIPSC. These miscategorized oEPSCs and oIPSC were presumably detected because our holding potentials were not precisely identical to the reversal potentials for GABA<SUB>A</SUB> and AMPA receptors, respectively. For this reason, we removed these 14 oEPSCs and 1 oIPSCs from our analyses in the revised version. The revised dataset suggests that VTA glutamate projection neurons may be less likely to collateralize widely within VTA compared to GABA projection neurons. But, importantly, this correction does not affect any of our conclusions.

      Citations:

      Beier, K. T., Steinberg, E. E., DeLoach, K. E., Xie, S., Miyamichi, K., Schwarz, L., Gao, X. J., Kremer, E. J., Malenka, R. C., & Luo, L. (2015). Circuit Architecture of VTA Dopamine Neurons Revealed by Systematic Input-Output Mapping. Cell, 162(3), 622-634. https://doi.org/10.1016/j.cell.2015.07.015

      Lammel, S., Hetzel, A., Hackel, O., Jones, I., Liss, B., & Roeper, J. (2008). Unique properties of mesoprefrontal neurons within a dual mesocorticolimbic dopamine system. Neuron, 57(5), 760-773. https://doi.org/10.1016/j.neuron.2008.01.022

      Margolis, E. B., Lock, H., Chefer, V. I., Shippenberg, T. S., Hjelmstad, G. O., & Fields, H. L. (2006). Kappa opioids selectively control dopaminergic neurons projecting to the prefrontal cortex. Proc Natl Acad Sci U S A, 103(8), 2938-2942. https://doi.org/10.1073/pnas.0511159103

      Olson, V. G., & Nestler, E. J. (2007). Topographical organization of GABAergic neurons within the ventral tegmental area of the rat. Synapse, 61(2), 87-95. https://doi.org/10.1002/syn.20345

      Root, D. H., Mejias-Aponte, C. A., Zhang, S., Wang, H. L., Hoffman, A. F., Lupica, C. R., & Morales, M. (2014). Single rodent mesohabenular axons release glutamate and GABA. Nat Neurosci, 17(11), 1543-1551. https://doi.org/10.1038/nn.3823

    1. It has to be celebrated.   O this great beloved world and all the creatures in it.

      These lines tell us that our love and care should not just end with planet earth but should also extend to all living things it contains. That we should appreciate all the creatures that roams the earth with us, and we must celebrate their existence. For it is the planet’s ecosystem that sustains our needs and allows us the opportunity to live our lives to the fullest.

    2. O this great beloved world and all the creatures in it.  It has to be spread out, the skin of this planet.

      I feel these sentences express deep respect for our world and the life that surrounds it and calls it home, I believe it expresses a sense of love and belonging. The “great beloved world” shows admiration, while “all the creatures” is a way of showing inclusivity. The second sentence portrays an imagery of the Earth as being vast and fragile, asking us to deep reverence for the world and its creatures, highlighting a sense of love and interconnectedness. The phrase “great beloved world” suggests admiration and gratitude, while “all the creatures” emphasizes inclusivity. The second line evokes imagery of the Earth as something vast yet delicate, urging us to protect it and all within it. I feel it asks us to explore, appreciate, and protect the planet’s beauty and life.

    3. And sky - such an 0! overhead - night and day   must be burnished and rubbed   by hands that are loving   so the blue blazons forth   and the stars keep on shining   within and above   and the hands keep on moving.

      I thought it was interesting how the poet used the phrase “such an O!”, I had to read it a couple times to get the hang of it. I think the use of the exclamation is to highlight the interest and adoration the speaker has towards the sky. The mentioning of night and day signifies the skies constant involvement and presence. The words “burnished” and “rubbed” created an image of hands working to polish “the stars so they keep on shining”. I think it was quite clever and creative as it created a strong image in my head and to be completed with “the hands keep on moving”, implying that there needs to be constant work done by humans to ensure the quality and beauty of our bright days and beautiful nights.

    1. He could have been a mu ici n, or ·Co.........bob t our ~othe pointed to the sun, a d we bur ,ed bri· htly • o'-'L..&.

      I like this saying becuase it means that people could not be what they wanted to, and when there mom pointed to the sun it meant they had to work.

    1. Esto significa que cuando nosencontramos con un período largo, con incisos también extensos, nuestra memoria sesobrecarga, no puede retener todas las palabras y perdemos el hilo de la prosa

      Concuerdo totalmente, ya que me pasa que cuando hay muchas palabras complicadas o parráfos extensos pierdo el hilo de la lectura o de la idea principal del párrafo, por ello concuerdo que en la escritura a veces lo simple y claro es lo mejor.

    Annotators

    1. rural hom

      Esta fotografía me llamo la atención por la sencilles de la casa o el lugar en donde están, es un lugar bastante básico que parece tener solo lo necesario, esto me llamo la atención porque hoy en día a la gente le importa mucho como se presenta su casa, las decoraciones las ediciones caras y lo que otra gente piense se su hogar.

    1. Reviewer #2 (Public review):

      Summary:

      Marylin Alves de Almeida et al. developed a novel mouse cross via conditionally depleting functional SMN protein in the liver (AlbCre/+;Smn2B/F7). This mouse model retains a proportion of SMN in the liver, which better recapitulates SMN deficiency observed in SMA patients and allows further investigation into liver-specific SMN deficiency and its systemic impact. They show that AlbCre/+;Smn2B/F7 mice do not develop an apparent SMA phenotype as mice did not develop motor neuron death, neuromuscular pathology or muscle atrophy, which is observed in the Smn2B/- controls. Nonetheless, at P19 and P60, these mice develop mild liver steatosis, and interestingly, this conditional depletion of SMN in the liver impacts cells in the pancreas.

      Strengths:

      The current model has clearly delineated the apparent metabolic perturbations which involve a significantly increased lipid accumulation in the liver and pancreatic cell defects in AlbCre/+;Smn2B/F7 mice at P19 and P60. Standard methods like H&E and Oil Red-O staining show that in AlbCre/+;Smn2B/F7 mice, their livers closely mimic the livers of Smn2B/- mice, which have the full body knockout of SMN protein. Unlike previous work, this liver-specific conditional depletion of SMN is superior in that it is not lethal to the mouse, which allows an opportunity to investigate the long-term effects of liver-specific SMN on the pathology of SMA.

      Weaknesses:

      Given that SMA often involves fatty liver, dyslipidemia and insulin resistance, using the current mouse model, the authors could have explored the long-term effects of liver-specific depletion of SMN on metabolic phenotypes beyond P19, as well as systemic effects like glucose homeostasis. Given that the authors also report pancreatic cell defects, the long-term effect on insulin secretion and resistance could be further explored. This has been addressed in the revised manuscript. The mechanistic link between a liver-specific SMN depletion and apparent pancreatic cell defects has been made clearer.

      Discussion:

      This current work explores a novel mouse cross in order to specifically deplete liver SMN using an Albumin-Cre driver line. This provides insight into the contribution of liver-specific SMN protein to the pathology of SMA, which is relevant for understanding metabolic perturbations in SMA patients. Nonetheless, given that SMA in patients involve a systemic deletion or mutation of the SMN gene, the authors could emphasize the utility of this liver-specific mouse model, as opposed to using in vitro models, which have been recently reported (Leow et al, 2024, JCI).

      Comments on current version:

      No further suggestions. Previous recommendations have been addressed by the authors.

    2. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      This manuscript presents a comprehensive exploration of the role of liver-specific Survival Motor Neuron (SMN) depletion in peripheral and central nervous system tissue pathology through a well-constructed mouse model. This study is pioneering in its approach, focusing on the broader physiological implications of SMN, which has traditionally been associated predominantly with spinal muscular atrophy (SMA).

      Strengths:

      (1) Novelty and Relevance: The study addresses a significant gap in understanding the role of liver-specific SMN depletion in the context of SMA. This is a novel approach that adds valuable insights into the multi-organ impact of SMN deficiency.

      (2) Comprehensive Methodology: The use of a well-characterized mouse model with liver-specific SMN depletion is a strength. The study employs a robust set of techniques, including genetic engineering, histological analysis, and various biochemical assays.

      (3) Detailed Analysis: The manuscript provides a thorough analysis of liver pathology and its potential systemic effects, particularly on the pancreas and glucose metabolism.

      (4) Clear Presentation: The manuscript is well written. The results are presented clearly with well-designed figures and detailed legends.

      We thank the reviewer for their positive comments. They had some concerns for us to consider (see below). We provide a point-by-point response to their comments.

      Weaknesses:

      (1) Limited Time Points: The study primarily focuses on a single time point (P19). This limits the understanding of the temporal progression of liver and pancreatic pathology in the context of SMN depletion. Longitudinal studies would provide a better understanding of disease progression.

      We thank the reviewer for the suggestion. We extended our analysis to include P60 mice and performed both liver and pancreatic analyses at this time point to address this suggestion.

      (2) Incomplete Recombination: The mosaic pattern of Cre-mediated excision leads to variability in SMN depletion, which complicates the interpretation of some results. Ensuring more consistent recombination across samples would strengthen the conclusions.

      The variability in Cre-mediated excision is inherently stochastic, influenced by factors such as Cre expression levels, timing of recombination, and the accessibility of the target locus in individual cells. Achieving complete consistency across samples is particularly challenging, especially given the complexity of our breeding scheme, which occasionally results in litters without any animals of the desired genotype. Importantly, our study not only demonstrates that liver-specific SMN depletion results in liver alterations and pancreatic dysfunction but also highlights the limitations and challenges associated with this mouse model. By doing so, we aim to provide valuable insights for other researchers considering similar approaches in future studies.

      Reviewer #2 (Public review):

      Summary:

      Marylin Alves de Almeida et al. developed a novel mouse cross via conditionally depleting functional SMN protein in the liver (AlbCre/+;Smn2B/F7). This mouse model retains a proportion of SMN in the liver, which better recapitulates SMN deficiency observed in SMA patients and allows further investigation into liver-specific SMN deficiency and its systemic impact. They show that AlbCre/+;Smn2B/F7 mice do not develop an apparent SMA phenotype as mice did not develop motor neuron death, neuromuscular pathology or muscle atrophy, which is observed in the Smn2B/- controls. Nonetheless, at P19, these mice develop mild liver steatosis, and interestingly, this conditional depletion of SMN in the liver impacts cells in the pancreas.

      Strengths:

      The current model has clearly delineated the apparent metabolic perturbations which involve a significantly increased lipid accumulation in the liver and pancreatic cell defects in AlbCre/+;Smn2B/F7 mice at P19. Standard methods like H&E and Oil Red-O staining show that in AlbCre/+;Smn2B/F7 mice, their livers closely mimic the livers of Smn2B/- mice, which have the full body knockout of SMN protein. Unlike previous work, this liver-specific conditional depletion of SMN is superior in that it is not lethal to the mouse, which allows an opportunity to investigate the long-term effects of liver-specific SMN on the pathology of SMA.

      We thank the reviewer for their positive comments. They had some concerns for us to consider (see below). We provide a point-by-point response to their comments (review comments in black, our response in red).

      Weaknesses:

      Given that SMA often involves fatty liver, dyslipidemia and insulin resistance, using the current mouse model, the authors could have explored the long-term effects of liver-specific depletion of SMN on metabolic phenotypes beyond P19, as well as systemic effects like glucose homeostasis. Given that the authors also report pancreatic cell defects, the long-term effect on insulin secretion and resistance could be further explored. The mechanistic link between a liver-specific SMN depletion and apparent pancreatic cell defects is also unclear.

      We extended our analysis to include P60 mice and performed both liver and pancreatic analyses at this time point to address this suggestion. In addition, we discussed the liver-pancreas axis in the Discussion.

      Discussion:

      This current work explores a novel mouse cross in order to specifically deplete liver SMN using an Albumin-Cre driver line. This provides insight into the contribution of liver-specific SMN protein to the pathology of SMA, which is relevant for understanding metabolic perturbations in SMA patients. Nonetheless, given that SMA in patients involve a systemic deletion or mutation of the SMN gene, the authors could emphasize the utility of this liver-specific mouse model, as opposed to using in vitro models, which have been recently reported (Leow et al, 2024, JCI). Authors should also discuss why a mild metabolic phenotype is observed in this current mouse model, as opposed to other SMA mouse models described in literature.

      We appreciate the reviewer’s insightful comment. We have thoroughly addressed this suggestion in the Discussion section, particularly in lines 284-298; 309-322 and 334-359.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) Longitudinal Studies: Conducting studies at maybe one more time points postnatally to provide a clearer picture of how liver-specific SMN depletion affects tissue pathology over time.

      We extended our analysis to include P60 mice and performed both liver and pancreatic analyses at this time point to address this suggestion.

      (2) Functional Assays: Incorporate glucose tolerance tests, insulin sensitivity tests, and more detailed metabolic profiling to better understand the physiological consequences of liver-specific SMN depletion on glucose metabolism and pancreatic function.

      We sincerely thank the reviewer for this suggestion. We have included a full panel of metabolic hormones associated with glucose metabolism from animals at P19 and P60. These new data, along with additional figures, have now been provided in our revised manuscript.

      (3) Mechanism: Discuss the molecular pathways affected by SMN depletion in the liver and pancreas. Mechanistic studies including transcriptomic or proteomic analyses to identify dysregulated pathways will help.

      We appreciate the reviewer’s insightful comment. We have thoroughly addressed this suggestion in the Discussion section, particularly in lines 284-298 and 334-359.

      (4) Typos in the abstract: beta cells secret insulin and alpha cells produce gulcagon. 

      Thank you for catching this error. It has been corrected to reflect that insulin is produced by beta cells and glucagon by alpha cells.

      (5) Efficiency and specificity of the Alb-Cre: if possible, cross the Alb-Cre with the Rosa26 reporter line to test the efficiency and specificity of the Alb-Cre.

      We agree that this would provide valuable insights. However, initiating a new breeding program to generate the required genotypes would take over a year and is beyond the scope of this study. To address this in part, we performed Cre immunostaining of the liver, pancreas, and spinal cord at P19, as well as the liver at P60. These results, now included in Supplemental Figure 1, demonstrate liver-specific expression and variability across hepatocytes.

      Reviewer #2 (Recommendations for the authors):

      The title of this manuscript is potentially misleading. The manuscript largely investigates the involvement of SMN protein on peripheral organs such as the liver, muscles, neuromuscular junction, and the pancreas. Yet, the title could be interpreted that the peripheral nervous system or central nervous system is the main focus. The title should be edited to indicate key terms such as "motor neuron and peripheral tissue pathology".

      Thank you for pointing this out. We have revised the title to better represent the study’s focus. It is now “Impact of liver-specific survival motor neuron (SMN) depletion on central nervous system and peripheral tissue pathology”.

      Suggestions:

      Please clarify and explain clearly the various mouse lines (Smn2B/+, Smn2B/- and +/+; Smn2B/F7 ) used as controls as the nomenclature used is confusing. In addition, authors could consider the use of a wild-type mouse line to be used as a control to validate changes in AlbCre/+;Smn2B/F7 mice.

      We have now provided clarification on mouse line nomenclature in the Results section (lines 104–124). Full-body heterozygous mice (_Smn_2B/+) are used as controls due to their slightly reduced SMN protein levels and absence of phenotypic changes compared to wild-type mice.

      Given that the main phenotype implicated by the liver-specific depletion of SMN protein in AlbCre/+;Smn2B/F7 mice is pancreatic abnormalities (changes in alpha- and beta- cell numbers and blood glucose levels), authors should expand further on the pancreatic phenotype.  

      We added a full panel of metabolic hormones related to glucose metabolism in animals at P19 and P60. Furthermore, this has been discussed in detail in lines 284-298 and 334-344 of the Discussion.

      A pancreas-specific depletion of SMN would provide this current manuscript with a better understanding of the role of SMN in regulating SMA pathology and provide more definitive conclusions on the contribution of liver-specific SMN depletion on normal pancreatic function.

      We agree that this would be very informative. However, to do this would require initiation of a new breeding program that will take more than a year to arrive at the right genotypes. Although valuable, it is beyond the scope of the present study.

      The authors should also delineate the role of hepatic SMN in pancreatic function, and how the intrinsic liver-specific loss of SMN directly impacts the pancreas. Currently, literature demonstrates that the fatty liver phenotype in SMA patients is a primary SMN-dependent hepatocyte-intrinsic liver defect associated with mitochondrial and other hepatic metabolism implications (see Leow et al, 2024 J Clin Invest). Given that the authors describe that SMN protein levels are not altered in the pancreas of AlbCre/+;Smn2B/F7 mice at P19, the authors ought to clarify how pancreas development and function is impacted in this mouse model, whether in-utero or postnatally. This could potentially underscore the cross-talk between liver SMN and pancreas function.

      We have discussed the relationship between hepatic SMN and pancreatic function in the Discussion at lines 284-298 and 334-359.

      Authors should also perform some metabolic tolerance tests to both oral glucose and insulin at an older age (e.g. P60) to study their homeostasis in these mice. These would help to substantiate the authors' conclusion and provide the paper with a greater level of novelty.

      We thank the reviewer for this suggestion. A full panel of metabolic hormones related to glucose metabolism at P19 and P60 has been included, supported by additional figures that enhance the manuscript's novelty and depth.

      Authors mentioned in the Discussion in lines 238 to 240: "Altogether, our findings underscore the necessity of conducting further investigations at later time points to unveil potential modifications in other pathways and their repercussions on liver physiology". Please elucidate the effects of longer term liver-specific depletion of SMN beyond P19, such as the onset of NAFLD or a diabetic phenotype due to pancreatic dysfunctions.

      We extended our data to include P60 mice and performed liver and pancreatic analyses at these time points. The observed effects were transient, possibly due to the stochastic nature of Cre expression.

      In addition, while AlbCre/+;Smn2B/F7 mice had similar weight gain trends as controls, it does appear that AlbCre/+;Smn2B/F7 mice weigh more than their controls by P60 (Figure 9C). This data would provide more convincing evidence of the metabolic defects observed in these mice.

      As per the reviewer’s suggestion, we included new data (Figure 9D) showing % weight gain at P60 normalized to basal weight at P7. However, no statistically significant differences were detected.

      Other than protein quantification, authors should perform immunohistochemistry or in-situ hybridization of SMN and imaging of AlbCre/+;Smn2B/F7 organs to validate the loss of liver-specific SMN. It is unclear from western blots that the expression of SMN is only in hepatocytes.

      We thank the reviewer for the suggestion. Unfortunately, SMN antibodies have not produced reliable tissue immunostaining. To address this, we performed Cre immunostaining of the liver, pancreas, and spinal cord at P19, and the liver at P60, which demonstrated liver-specific expression. These results are now included in Supplemental Figure 1.

      Authors should consider re-wording lines 228 through 231: "While our current analysis did not reveal significant differences in AlbCre/+;Smn2B/F7 mice, the observed upward trend in transferrin and HO levels suggests ongoing changes in iron metabolism, which may not be fully manifested at P19". Alternatively, a higher number of mouse samples would allow them to qualify this statement. Authors should also consider comparing levels of liver biomarkers such as ALT and AST, to check for liver homeostatic function.

      We have removed speculative statements to avoid unsupported claims.

      Recommendations:

      The methods and additional details to generate the AlbCre/+;Smn2B/F7 should be explained better in section 2.1 of the Results. It is potentially confusing as to why these mice had to carry both 2B and F7 alleles. Additionally, the role of the F7 allele is not deliberately clear in the Introduction.

      Additional details are now included in the Introduction (lines 87-90) and the Results section (lines 104-124).

      Authors should refer to Leow et al 2024 (J Clin Invest) and discuss how their current findings compare with their hepatocyte-intrinsic SMN deficiency IPSCs model.<br /> We note a previous publication (Deguise et al 2021 Cell Mol Gastroenterol Hepatol) by the authors which characterized the Smn2B/- mouse model and its NAFLD/NASH features. From our understanding, the Smn2B/- mouse model appears to recapitulate SMA phenotype well, such as the early onset of hepatic steatosis and neurological conditions. As a follow-up to this publication, authors should discuss why this current study of a liver-specific SMN depletion is important and relevant to the study of SMA pathology.

      We thank the reviewer for the insightful suggestions. We have included a discussion of these findings and their relevance to the study of SMA pathology in lines 284-298 and 309-322.

      Minor corrections:

      Abstract (line 32) reads: "a decrease in insulin producing alpha-cells and an increase in glucagon producing beta-cells". The authors should clarify and correct as insulin producing beta-cells and glucagon producing alpha-cells.

      Thank you for catching the error. We corrected the description of insulin- and glucagon-producing cells.

      Please clarify the number and gender of mice used for weight tracking and motor function experiments up to P60 (Figure 9C). It would be inappropriate if male and female mice were plotted together. If so, authors should stratify data by gender.

      We thank the reviewer for the suggestion. Unfortunately, we did not stratify the animals by sex due to the unequal and insufficient number of males and females in our study. To address this, we normalized weight gain to each animal’s starting weight, and no significant differences were observed (now shown in Figure 9D).

      The number of figures should be reduced. We recommend merging Figures 1 and 2 (generation of AlbCre/+;Smn2B/F7 mouse line and validation) and Figures 3 and 4 (liver function). Figures 5 through 9 may be supplemental figures instead.

      We thank the reviewer for the suggestions. We merged Figures 1 and 2, and Figures 3 and 4, as requested. However, we would prefer to keep the other figures within the main results as they assess the impact of liver-specific depletion of SMN on other pathologies within the mouse model.

      Standardize the use of asterisks and reporting p-values in Figure 2. All other figures in the manuscript utilize asterisks, but Figures 2C', 2D' and 2E' use p-values across comparisons.

      P-values were included only when they approached statistical significance, providing additional clarity to the results.

      It is unclear what the white arrow in Figure 7A indicates.

      It is meant to point out the absence of an innervating axon. Please see Figure 5 legend, lines 801-802.

      Note spelling errors in Figures 8B and 8C: 'Muscle flber'.

      Thank you for catching this. We have corrected the typo to indicate muscle fiber instead.

      Please clarify if muscle fiber size should be indicated as µm2 instead of µ2 in Figures 8B and 8C, as written in Materials and Methods under line 394.

      Thank you for catching this. We corrected the typo to indicate µm2 instead.

    1. Author response:

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

      Reviewer 1:

      (1) The overall conclusion, as summarized in the abstract as "Together, our study documents the diversification of locomotor and oculomotor adaptations among hunting teleost larvae" is not that compelling. What would be much more interesting would be to directly relate these differences to different ecological niches (e.g. different types of natural prey, visual scene conditions, height in water column etc), and/or differences in neural circuit mechanisms. While I appreciate that this paper provides a first step on this path, by itself it seems on the verge of stamp collecting, i.e. collecting and cataloging observations without a clear, overarching hypothesis or theoretical framework.

      There are limited studies on the prey capture behaviors of larval fishes, and ours is the first to compare multiple species systematically using a common analysis framework. Our analysis approach could have uncovered a common set of swim kinematics and capture strategies shared by all species; but instead, we found that medaka used a monocular strategy rather than the binocular strategy of cichlids and zebrafish. Our analysis similarly could have revealed first-feeding larvae of all species go through a “bout” stage, which was previously proposed as important for sensorimotor decision making (Bahl et al., 2019), but instead we found that medaka and some cichlids have more continuous swimming from an early life stage. Finally, the rate at which prey capture kinematics evolves is not known. Our approach could have revealed rapid diversification of feeding strategies in cichlids (similarly to how adult feeding behavior evolves), but instead we found smaller differences within cichlids than between cichlids and medaka.

      (2) The data to support some of the claims is either weak or lacking entirely.

      Highlighted timestamps in videos, new stats in fig 1H and fig 2, updated supplementary figures now provide additional support for claims.

      - It would be helpful to include previously published data from zebrafish for comparison.

      We appreciate the suggestion. Mearns et al. (2020) provided a comprehensive account of prey capture in zebrafish larvae in an almost identical setup with similar analyses. We do not feel it is necessary to recount all the findings in that paper here. There are many studies on prey capture in zebrafish from the past 20 years, and reproducing these here would not add anything to that extensive pre-existing literature.

      - Justification is required for why it is meaningful to compare hunting strategies when both fish species and prey species are being varied. For instance, artemia and paramecia are different sizes and have different movement statistics.

      We added text explaining why different food was chosen for medaka/cichlids. There is no easy way to stage match fishes as evolutionarily diverged as cichlids, medaka, and zebrafish. Size is a reasonable metric within a species, but there is no guarantee that sizematched larvae of two different species are at the same level of maturity. Therefore, we thought the most appropriate stage to address is when larvae first start feeding, as this enables us to study innate prey capture behavior before any learning or experience-dependent changes have taken place. Given that zebrafish, medaka and cichlid larvae are different sizes when they first start feeding, it was necessary to study their hunting behavior to different prey items.

      - It would be helpful in Figure 1A to add the abbreviations used elsewhere in the paper. I found it slightly distracting that the authors switch back and forth in the paper between using "OL" and "medaka" to refer to the same species: please pick one and then remain consistent.

      Medaka is the common name for the japanese rice fish, O. latipes. Cichlilds do not have common names are only referred to by their scientific names. Since readers are more likely to be familiar with the common name, medaka, we now use medaka (OL) throughout the manuscript, which we hope makes the text clearer.

      - The conceptual meaning of behavioral segmentation is somewhat unclear. For zebrafish, the bouts already come temporally segmented. However in medaka for instance, swimming is more continuous, and the segmentation is presumably more in terms of "behavioral syllables" as have been discussed for example mouse or drosophila behavior (in the last row of Figure S1 it is not at all obvious why some of the boundaries were placed at their specific locations). It's not clear whether it's meaningful to make an equivalence between syllables and bouts, and so whether for instance Figure 1H is making an apples-to-apples comparison.

      We clarified the text to say we are comparing syllables, rather than bouts.

      - The interpretation of 1H is that "medaka exhibited significantly longer swims than cichlids"; however this is not supported by the appropriate statistical test. The KS test only says that two probability distributions are different; to say that one quantity is larger than another requires a comparison of means.

      Updated Fig 1H; boostrap test (difference of medians) and re plotted data as violin plots.

      (2) The data to support some of the claims is either weak or lacking entirely.

      Highlighted timestamps in videos, new stats in fig 1H and fig 2, updated supplementary figures now provide additional support for claims.

      - I think the evidence that there are qualitatively different patterns of eye convergence between species is weak. In Figure 2A I admire the authors addressing this using BIC, and the distributions are clearly separated in LA (the Hartigan dip test could be a useful additional test here). However for LO, NM, and AB the distributions only have one peak, and it's therefore unclear why it's better to fit them with two Gaussians rather than e.g. a gamma distribution. Indeed the latter has fewer parameters than a two-gaussian model, so it would be worthwhile to use BIC to make that comparison. The positions of the two Gaussians for LO, NM, and AB are separated by only a handful of degrees (cf LA, where the separation is ~20 degrees), which further supports the idea that there aren't really two qualitatively different convergence states here.

      Added explanation to text.

      - Figure S2 is unfortunately misleading in this regard. I don't claim the authors aimed to mislead, but they have made the well-known error of using colors with very different luminances in a plot where size matters (see e.g.

      https://nam12.safelinks.protection.outlook.com/?url=https%3A %2F%2Fwww.r-project.org%2Fconferences%2FDSC2003%2FProceedings%2FIhaka.pdf&data=05%7C02%7Cdme arns%40princeton.edu%7C17ae2b44f0f246f15ddd08dc9b8e2 01c%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7

      C638556282750568814%7CUnknown%7CTWFpbGZsb3d8ey

      JWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJ XVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Ll4J4Xo39JEtKb %2FNnRWNoyedZAu5aAOMq0lHJCwsfXI%3D&reserved=0).

      Thus, to the eye, it appears there's a big valley between the red and blue regions, but actually, that valley is full of points: it's really just one big continuous blob.

      Kernel density estimation of eye convergence angles were added to Figure S2. The point we wish to make is that there is higher density when both eyes are rotated invwards (converged) in cichlids, but not medaka (O. latipes). The valley between converged and unconverged states being full of points is due to (1) slight variation with placement of key points in SLEAP, which blurs the boundary between states and (2) the eye convergence angle must pass through the valley in order to become converged, so necessarily there are points in between the two extremes of eye convergence.

      - In Figure 2D please could the authors double-check the significance of the difference between LO and NM: they certainly don't look different in the plot.

      Thank for for flagging this. We realize the way we previously reported the stats was open to misinterpretation. We have updated figure 2C, D and F to use letters to indicate statistical groupings, which hopefully makes it clearer which species are statistically different from each other.

      - In Figure 2G it's not clear why AB is not included. It is mentioned that the artemia was hard to track in the AB videos, but the supplementary videos provided do not support this.

      The contrast of the artemia in the AB videos is sufficiently different from the other cichlid videos that our pre-trained YOLO model fails. Retraining the model would be a lot of extra work and we feel like a comparison of three species is sufficient to address the sensorimotor transformations that occur over the course of prey capture in cichlids.

      - The statement "Zebrafish larvae have a unique swim repertoire during prey capture, which is distinct from exploratory swim bouts" is not supported by the work of others or indeed the authors' own work. In Figure 4F all types of bouts can occur at any time, it's just the probability at which they occur that varies during prey capture versus other times (see also Mearns et al (2020) Figure S4B).

      The point is well taken that there probably is not a hard separation between spontaneous and prey capture swims based on tail kinematics alone, which is also shown in Marques et al. (2018). However, we think that figure 2I of Mearns et al., which plots the probability of swims being drawn from different parts of the behavior space during prey capture (eyes converged) or not (eyes unconverged), shows that the repertoire of swims during the two states is substantially different. Points are blue or red; there are very few pale blue/pale red points in that figure panel. Figure S4B is showing clustered data, and clustering is a notoriously challenging problem for which there exists no perfect solution (Kleinberg, 2002). The clusters in Mearns et al. incorporated information about transition structure, as this was necessary for obtaining interpretable clusters for subsequent analyses. However, a different clustering approach could have yielded different boundaries, which may have shown more (or less) separation of bout types during prey capture/exploratory swimming. Therefore, we have updated the text to say that zebrafish perferentially perform different swim types during prey capture and exploration, and re-interpreted the behavior of cichlids similarly.

      - More discussion is warranted of the large variation in the number of behavioral clusters found between species (11-32). First, how much is this variation really to be trusted? I appreciate the affinity propogation parameters were the same in all cases, but what parameters "make sense" is somewhat dependent on the particular data set. Second, if one does believe this represents real variation, then why? This is really the key question, and it's unsatisfying to merely document it without trying to interpret it.

      Extended paragraph with more interpretation.

      - What is the purpose of "hovers"? Why not stay motionless? Could it be a way of reducing the latency of a subsequent movement? Is this an example of the scallop theorem?

      Added a couple of sentences speculating on function.

      - I'm not sure "spring-loaded" is a good term here: the tension force of a coiled tail is fairly negligible since there's little internal force actively trying to straighten it.

      Rewrote this part to highlight that fish spring toward the prey, without the implication that tension forces in the tail are responible for the movement. However, we are not aware of any literature measuring passive forces within the tail of fishes. Presumably the notochord is relatively stiff and may provide an internal force trying to straighten the tail.

      - There are now several statements for which no direct evidence is presented. We shouldn't have to rely on the author's qualitative impressions of what they observed: show us quantitative analysis.

      * "often hover"

      * "cichlids often alternate between approaches and hover swims"

      * "over many hundreds of milliseconds"

      * "we have also observed suction captures and ram-like attacks"

      * "may swim backwards"

      * "may expel prey from their mouth"

      * "cichlid captures often occur in two phases"

      Added references to supplementary videos with timestamps to highlight these behaviors.

      - I don't find it plausible that sated fish continue hunting prey that they know they're not going to eat just for the practice.

      Removed the speculation.

      - In Figure 3 is it not possible to include medaka, based on the hand-tracked paramecia?

      The videos are recorded at high frame rate, so it would be a lot of additional work to track these manually. Furthermore, earlier in prey capture it is very difficult to tell by watching videos which prey the medaka are tracking, especially as single paramecia can drift in and out of focus in the videos. Since there is no eye convergence, it is very difficult to ascertain for certain when tracking a given prey begins. In Fig 4, it was only possible to track paramecia by hand since it is immediately prior to the strike and from the video it is possible to see which paramecium the fish targeted. Our analyses of heading changes was performed over the 200 ms prior to a strike, which we think is a conservative enough cutoff to say that fish were probably pursuing prey in this window (it is shorter than the average behavioral syllable duration in medaka).

      - Figure 3 (particularly 3D) suggests the interesting finding that LA essentially only hunt prey that is directly in front of them (unlike LO and NM, the distribution of prey azimuth actually seems to broaden slightly over the duration of hunting events).

      This is worthy of discussion.

      We offer a suggestion for the many instances of prey capture being initiated in the central visual field in LA later in the manuscript when we discuss spitting behavior. We have added text to make this point earlier in the manuscript. The increase in azimuthal range at the end of prey capture may be due to abort swims (e.g. supp. vid. 1, 00:21). The widening of azimuthal angles is present in LO and NM also and is not unique to LA.

      - The reference Ding et al (2016) is not in the reference list.

      Wrong paper was referenced. Should be Ding 2019, which has been added to bibliography.

      - I am not convinced that medaka exhibit a unique side-swing behavior. I agree there is this tendency in the example movie, however, the results of the quantification (Figure 4) are underwhelming. First, cluster 5 in 4K appears to include a proportion of cases from LA and AB. These proportions may be small, but anything above zero means this is not unique to medaka. Second, the heading angle (4N) starts at 4 degrees for LA and 8 degrees for medaka. This difference is genuine but very small, much smaller than what's drawn in the schematic (4M). I'm not sure it's justifiable to call a difference of 4 degrees a qualitatively different strategy.

      We have changed the text to highlight that side swing is highly enriched in medaka. Comparing 4J to 3B we would argue that there is a qualitative difference in the strategy used to capture prey in the cichlid larvae we study here and medaka. We agree that further work is required to understand distance estimation behaviors in different species. In this manuscript, we use heading angle as a proxy for how prey position might change on the retina over a hunting sequence. But as the heading and distance are changing over time, the actual change in angle on the retina for prey may be much larger than the ~8 degree shift reported here. The actual position of the prey is also important here, which, for reasons mentioned above, we could not track. Given the final location of prey in the visual field prior to the strike (Fig 4J), the most parsimonious explanation of the data is that the prey is always in the monocular visual field. In cichlids, the prey is more-or-less centered in the 200 ms preceding the strike. While it is true theat the absolute difference in heading is 4 degrees, when converted to an angular velocity (4N, right), the medaka (OL) effectively rotate twice as fast as LA (20 deg/s vs 40 deg/s), which we think is a substantial difference and evidence of a different targeting strategy.

      - 4K: This is referred to in the caption as a confusion matrix, which it's not.

      Fixed.

      - 4N right panel: how many fish contributed to the points shown?

      Added to figure legend (n=113, LA; n=36, OL). Same data in left and right panels.

      - In the Discussion it is hypothesized that medaka use their lateral line in hunting more than in other species. Testing this hypothesis (even just compared to one other species) would be fairly straightforward, and would add significant interest to the paper overall.

      We agree that this is an interesting experiment for follow up studies, but it is beyond the scope of the current manuscript as we do not have the appropriate animal license for this experiment.

      Reviewer 2:

      The paper is rather descriptive in nature, although more context is provided in the discussion. Most figures are great, but I think the authors could add a couple of visual aids in certain places to explain how certain components were measured.

      Added new supplemental figure (Supp Fig 2)

      Figure 1B- it could be useful to add zebrafish and medaka to the scientific names (I realize it's already in Figure A but I found myself going back and forth a couple of times, mostly trying to confirm that O. latipes is medaka).

      Added common names to 1B, sprinkled reminders of OL/medaka throughout text.

      Figure 1G. I wasn't sure how to interpret the eye angle relative to the midline. Can they rotate their eyes or is this due to curvature in the 'upper' body of the fish? Adding a schematic figure or something like that could help a reader who is not familiar with these methods. Related to this, I was a bit confused by Figure 2A. After reading the methods section, I think I understand - but I little cartoon to describe this would help. It also reminds the reader (especially if they don't work with fish) that fish eyes can rotate. I also wanted to note that initially, I thought convergence was a measure of how the two eyes were positioned relative to the prey given the emphasis given on binocular vision, and only after reading certain sections again did I realize convergence was a measure of eye rotation/movement.

      New supplemental figure explaining how eye tracking is performed

      Figure 3. It was not immediately clear to me what onset, middle, and end represented - although it is explained in the caption. I think what tripped me up is the 'eye convergence' title in the top right corner of Figure 3A.

      Updated figure with schematic illustrating that time is measured relative to eye convergence onset and end.

      The result section about attack swim, S-strike, capture spring, etc. was a bit confusing to read and could benefit from a couple of concise descriptions of these behaviors. For example, I am not familiar with the S strike but a couple of paragraphs into this section, the reader learns more about the difference between S strike vs. attack swim. This can be mentioned in the first paragraph when these distinct behaviors are mentioned.

      Added description of behavior earlier in text.

      Figure 4. Presents lots of interesting data! I wonder if using Figure 1E could help the reader better understand how these measurements were taken.

      New supplemental figure added, explaining how tail tracking is performed.

      I probably overlooked this, but I wonder why so many panels are just focused on one species.

      Added explanation to the text.

      Is the S-shaped capture strategy the same as an S strike?

      Clarified in text to say "S-strike-like". This is a description of prey capture from adult largemouth bass in New et al. (2002). From the still frames shown in that paper, the kinematics looks similar to an S-strike or capture spring. The important point we wish to make is that tail is coiled in an S-shape prior to a strike, which indicates this that a kinematically similar behavior exists fishes beyond just larval cichlids and zebrafish.

      At the end of the page, when continuous swimming versus interrupted swimming is discussed, please remind the reader that medaka shows more continuous swimming (longer bouts).

      Added "while medaka swim continuously with longer bouts ("gliding")".

      After reading the discussion, it looks like many findings are unique. For example, given that medaka is such a popular model species in biology, it strikes me that nobody has ever looked into their hunting movements before. If their findings are novel, perhaps they should state so it is clear that the authors are not ignoring the literature.

      We have highlighted what we believe to be the novelty of our findings (first description of prey capture in larval cichlids and medaka). To our knowledge, we are first to describe hunting in medaka; but there is an extensive literature on medaka dating back to the early 20th century, some of which is only published in Japanese. We have done our best to review the literature, but we cannot rule out that there are papers that we missed. No English language article or review we found mentions literature on hunting behavior in medaka larvae.

      Reviewer 3:

      More evidence is needed to assess the types of visual monocular depth cues used by medaka fish to estimate prey location, but that is beyond the scope of this compelling paper. For example, medaka may estimate depth through knowledge of expected prey size, accommodation, defocus blur, ocular parallax, and/or other possible algorithms to complement cues from motion parallax.

      Added sentence to discussion highlighting that other cues may also contribute to distance estimation in cichlids and medakas. Follow-up studies will require new animal license.

      None. It's quite nice, timely, and thorough work! For future work, one could use 3D pose estimation of eye and prey kinematics to assess the dynamics of the 2D image (prey and background) cast onto the retina. This sort of representation could be useful to infer which monocular depth cues may be used by medaka during hunting.

      Great suggestion for follow up studies. Bolton et al. and Mearns et al. both find changes in z associated with prey capture, and it would be interesting to see how other fish species use the full 3-dimensional water column during prey capture, especially considering the diversity of hunting strategies in adult cichlids (ranging from piscivorous species, like LA, to algar grazers).

      In Figure 4N, you use "change in heading leading up to a strike as a proxy for the change in visual angle of the prey for cichlids and medaka." This proxy makes sense, but you also have the eye angles and (in some cases) the prey positions. One could estimate the actual change in visual angle from this information, which would also allow one to measure whether the fish are trying to stabilize the position of the prey on a high-acuity patch of the retina during the final moments of the hunt. This information may also shed light on which monocular depth cues are used.

      As addressed in comment to reviewer 1, this would require actually manually tracking individual paramecia over hundreds of frames. It is not possible to determine exactly when hunting begins in medaka, and it is prone to errors if medaka switch between targets over the course of a hunting episode. This question is better addressed with psychophysics experiments in embedded animals where it is possible to precisely control the stimulus, but this requires new animal licenses and is beyond the scope of this paper.

      In Figure 5, you could place the prey object a little farther from the D. rerio fish for the S-strike diagram.

      Fixed.

      Figure 4F legend should read "...at the peak of each bout."

      Fixed.

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Dong et al. study the directed cell migration of tracheal stem cells in Drosophila pupae. The migration of these cells which are found in two nearby groups of cells normally happens unidirectionally along the dorsal trunk towards the posterior. Here, the authors study how this directionality is regulated. They show that inter-organ communication between the tracheal stem cells and the nearby fat body plays a role. They provide compelling evidence that Upd2 production in the fat body and JAK/STAT activation in the tracheal stem cells play a role. Moreover, they show that JAK/STAT signalling might induce the expression of apicobasal and planar cell polarity genes in the tracheal stem cells which appear to be needed to ensure unidirectional migration. Finally, the authors suggest that trafficking and vesicular transport of Upd2 from the fat body towards the tracheal cells might be important.

      Strengths:

      The manuscript is well written. This novel work demonstrates a likely link between Upd2JAK/STAT signalling in the fat body and tracheal stem cells and the control of unidirectional cell migration of tracheal stem cells. The authors show that hid+rpr or Upd2RNAi expression in a fat body or Dome RNAi, Hop RNAi, or STAT92E RNAi expression in tracheal stem cells results in aberrant migration of some of the tracheal stem cells towards the anterior. Using ChIP-seq as well as analysis of GFP-protein trap lines of planar cell polarity genes in combination with RNAi experiments, the authors show that STAT92E likely regulates the transcription of planar cell polarity genes and some apicobasal cell polarity genes in tracheal stem cells which appear to be needed for unidirectional migration. Moreover, the authors hypothesise that extracellular vesicle transport of Upd2 might be involved in this Upd2-JAK/STAT signalling in the fat body and tracheal stem cells, which, if true, would be quite interesting and novel.

      Overall, the work presented here provides some novel insights into the mechanism that ensures unidirectional migration of tracheal stem cells that prevents bidirectional migration. This might have important implications for other types of directed cell migration in invertebrates or vertebrates including cancer cell migration.

      Weaknesses:

      It remains unclear to what extent Upd2-JAK/STAT signalling regulates unidirectional migration. While there seems to be a consistent phenotype upon genetic manipulation of Upd2-JAK/STAT signalling and planar cell polarity genes, as in the aberrant anterior migration of a fraction of the cells, the phenotype seems to be rather mild, with the majority of cells migrating towards the posterior.

      We agree that the phenotype is mild, as perturbing JAK/STAT signaling in the progenitors specifically affects the coordinated migration of the cells rather than alters their direction or completely blocks migration. Our data indicate that inter-organ communication ensures coordinated behavior of the progenitor cells, although the differential responses exhibited by individual cells represent an interesting unresolved issue that awaits future in-depth investigation.

      While I am not an expert on extracellular vesicle transport, the data presented here regarding Upd2 being transported in extracellular vesicles do not appear to be very convincing.

      We performed additional PLA experiments which support the interaction between Upd2 and the core components of extracellular vesicles (revised Figure 8). Furthermore, we performed electron microscopy to visualize the Lbm-containing vesicles in fat body (Figure 8-figure supplement 1D).

      These data are now provided in the revised manuscript.

      Major comments:

      (1) The graphs showing the quantification of anterior (and in some cases also posterior migration) are quite confusing. E.g. Figure 1F (and 5E and all others): These graphs are difficult to read because the quantification for the different conditions is not shown separately. E.g. what is the migration distance for Fj RNAi anterior at 3h in Fig5E? Around -205micron (green plus all the other colors) or around -70micron (just green, even though the green bar goes to -205micron). If it's -205micron, then the images in C' or D' do not seem to show this strong phenotype. If it's around -70, then the way the graph shows it is misleading, because some readers will interpret the result as -205. Moreover, it's also not clear what exactly was quantified and how it was quantified. The details are also not described in the methods. It would be useful, to mark with two arrowheads in the image (e.g. 5 A' -D') where the migration distance is measured (anterior margin and point zero).

      Overall, it would be better, if the graph showed the different conditions separately. Also, n numbers should be shown in the figure legend for all graphs.

      We apologize for those inappropriate presentation and insufficient description and thank you for kindly pointing them out. We used different colors to represent different genotypes, and the columns were superimposed. we chose to show the quantification in different conditions separately in the revised Figures. The anterior migration distance for Fj RNAi is around 70 µm.

      We now provided detailed description in the revised methods. For migration distance measurement, we took snapshots at 0hr\ 1hr\ 2hr and 3hr, and measured the distance from the starting point (the junction of TC and DT) to the leading edge of progenitor clusters. The velocity formula: v=d (micrometer)/t (min). As you kindly suggested, we indicated the anterior margin and point zero in the corresponding panels. We have added n number in the legends.

      (2) Figure 2-figure supplement 1: C-L and M: From these images and graph it appears that Upd2 RNAi results in no aberrant anterior migration. Why is this result different from Figures 2D-F where it does?

      The fat body-expressing lsp2-Gal4 was used in Figure 2-figure supplement 1C-L and Figure 2D-F, while trachea specific btl-Gal4 was used in Figure 2-figure supplement 1K-L. The lsp2-Gal4-driven but not btl-Gal4-driven upd2RNAi causes aberrant anterior migration, suggesting that fat bodyderived Upd2 plays a role. We have further clarified this in the text.

      (3) Figure 5F: The data on the localisation of planar cell polarity proteins in the tracheal stem cell group is rather weak. Figure 5G and J should at least be quantified for several animals of the same age for each genotype. Is there overall more Ft-GFP in the cells on the posterior end of the cell group than on the opposite side? Or is there a more classic planar cell polarity in each cell with FtGFP facing to the posterior side of the cell in each cell? Maybe it would be more convincing if the authors assessed what the subcellular localisation of Ft is through the expression of Ft-GFP in clones to figure out whether it localises posteriorly or anteriorly in individual cells.

      We staged the animals, measured several animals for each genotype and provided the quantifications in the revised manuscript. The level of Ft-GFP is higher in the cells at the frontal edge. We tried to examine the expression of Ft-GFP at single-cell level. However, this turned out to be technically difficult because the tracheal stem cells are not regularly arranged as epithelial cells and the proximal-distant axis of the tracheal stem cells remains unclear. We thus decided to measure the fluorescence signal of groups of stem cells along the DT regardless of their individual polarity within cells.

      (4) Regarding the trafficking of Upd2 in the fat body, is it known, whether Grasp65, Lbm, Rab5, and 7 are specifically needed for extracellular vesicle trafficking rather than general intracellular trafficking? What is the evidence for this?

      In our experiments, knocking down rab5, rab7, grasp65 or lbm in trachea using btl-Gal4 did not cause abnormality in the disciplined migration, which excludes their intracellular contribution in the trachea (Figure 7-figure supplement 1). Perturbation of Grasp65 or Lbm in fat body increased intracellular upd2-containing vesicles, indicating that intracellular production is functional (Figure 6J). The Grasp65 is specifically required for Upd2 production. Lbm, Rab5 and Rab7 are important of vesicle trafficking. Our conclusion does not pertain to extracellular or intracellular compartment.

      (5) Figure 8A-B: The data on the proximity of Rab5 and 7 to the Upd2 blobs are not very convincing.

      The confocal images indicate the proximity of Rab5 and Rab7 to the Upd2 vesicles. We interpret the proximity together with the results from Co-IP and PLA data (Figure 8E-K).

      (6) The authors should clarify whether or not their work has shown that "vesicle-mediated transport of ligands is essential for JAK/STAT signaling". In its current form, this manuscript does not appear to provide enough evidence for extracellular vesicle transport of Upd2.

      Lbm belongs to the tetraspanin protein family that contains four transmembrane domains, which are the principal components of extracellular vesicles. We show that Lbm interacts with Upd2. The JAK/STAT signaling depends on the Upd2 in the fat body as well as vesicle trafficking machinery. Furthermore, we performed electron microscopy and show the presence of Lbm-containing vesicles in fat body (Figure 8-figure supplement 1D).

      (7) What is the long-term effect of the various genetic manipulations on migration? The authors don't show what the phenotype at later time points would be, regarding the longer-term migration behaviour (e.g. at 10h APF when the cells should normally reach the posterior end of the pupa). And what is the overall effect of the aberrant bidirectional migration phenotype on tracheal remodelling?

      We observed that the integrity of tracheal network especially the dorsal trunk was impaired, which may be due to incomplete regeneration (Figure 3-figure supplement1E-I).

      (8) The RNAi experiments in this manuscript are generally done using a single RNAi line. To rule out off-target effects, it would be important to use two non-overlapping RNAi lines for each gene.

      We validated the phenotype using several independent RNAi alleles.

      Reviewer #2 (Public review):

      Summary:

      This work by Dong and colleagues investigates the directed migration of tracheal stem cells in Drosophila pupae, essential for tissue homeostasis. These cells, found in two nearby groups, migrate unidirectionally along the dorsal trunk towards the posterior to replenish degenerating branches that disperse the FGF mitogen. The authors show that inter-organ communication between tracheal stem cells and the neighboring fat body controls this directionality. They propose that the fat body-derived cytokine Upd2 induces JAK/STAT signaling in tracheal progenitors, maintaining their directional migration. Disruption of Upd2 production or JAK/STAT signaling results in erratic, bidirectional migration. Additionally, JAK/STAT signaling promotes the expression of planar cell polarity genes, leading to asymmetric localization of Fat in progenitor cells. The study also indicates that Upd2 transport depends on Rab5- and Rab7-mediated endocytic sorting and Lbm-dependent vesicle trafficking. This research addresses inter-organ communication and vesicular transport in the disciplined migration of tracheal progenitors.

      Strengths:

      This manuscript presents extensive and varied experimental data to show a link between Upd2JAK/STAT signaling and tracheal progenitor cell migration. The authors provide convincing evidence that the fat body, located near the trachea, secretes vesicles containing the Upd2 cytokine. These vesicles reach tracheal progenitors and activate the JAK-STAT pathway, which is necessary for their polarized migration. Using ChIP-seq, GFP-protein trap lines of planar cell polarity genes, and RNAi experiments, the authors demonstrate that STAT92E likely regulates the transcription of planar cell polarity genes and some apicobasal cell polarity genes in tracheal stem cells, which seem to be necessary for unidirectional migration.

      Weaknesses:

      Directional migration of tracheal progenitors is only partially compromised, with some cells migrating anteriorly and others maintaining their posterior migration.

      Our results suggest that Upd2-JAK/STAT signaling is required for the consistency of disciplined migration. Although only a few tracheal progenitors display anterior migration, these cells lose the commitment of directional movement. We acknowledge that the phenotype is moderate.

      Additionally, the authors do not examine the potential phenotypic consequences of this defective migration.

      We examined the long-term effects of the aberrant migration and observed an impairment of tracheal integrity and melanized tracheal branches (Figure 3-figure supplement1E-I).

      It is not clear whether the number of tracheal progenitors remains unchanged in the different genetic conditions. If there are more cells, this could affect their localization rather than migration and may change the proposed interpretation of the data.

      We examined the progenitor cell number in bidirectional movement samples and control group. The results show that cell number does not exhibit a significant difference between control and bidirectional movement groups (Figure 3-figure supplement 1).

      Upd2 transport by vesicles is not convincingly shown.

      We performed additional PLA experiments to further support the interaction between Upd2 and the core components of extracellular vesicles. Furthermore, we performed electron microscopy and show the presence of Lbm-containing vesicles in fat body (Figure 8-supplement 1D). Additional experiments such as colocalization and Co-IP assay and better quantification are provided in the revised manuscript (see revised Figure 8).

      Data presentation is confusing and incomplete.

      We used different colors to represent different genotypes, and the columns were superimposed. we changed the graphs to show the quantification in different conditions separately. We revised data presentation to avoid confusing.

      Reviewer #3 (Public review):

      Summary:

      Dong et al tackle the mechanism leading to polarized migration of tracheal progenitors during Drosophila metamorphosis. This work fits in the stem cell research field and its crucial role in growth and regeneration. While it has been previously reported by others that tracheal progenitors migrate in response to FGF and Insulin signals emanating from the fat body in order to regenerate tracheal branches, the authors identified an additional mechanism involved in the communication of the fat body and tracheal progenitors.

      Strengths:

      The data presented were obtained using a wide range of complementary techniques combining genetics, molecular biology, quantitative, and live imaging techniques. The authors provide convincing evidence that the fat body, found in close proximity to the trachea, secrete vesicles containing the Upd2 cytokine that reach tracheal progenitors leading to JAK-STAT pathway activation, which is required for their polarized migration. In addition, the authors show that genes regulating planar cell polarity are also involved in this inter-organ communication.

      Weaknesses:

      (1) Affecting this inter-organ communication leads to a quite discrete phenotype where polarized migration of tracheal progenitors is partially compromised. The study lacks data showing the consequences of this phenotype on the final trachea morphology, function, and/or regeneration capacities at later pupal and adult stages. This could potentially increase the significance of the findings.

      Regarding your kind suggestion, we examined the long-term effects of the aberrant migration and observed the impairment of tracheal integrity and melanized tracheal branches (Figure 3-figure supplement1E-I).

      (2) The conclusions of this paper are mostly well supported by data, but some aspects of data acquisition and analysis need to be clarified and corrected, such as recurrent errors in plotting of tracheal progenitor migration distance that mislead the reader regarding the severity of the phenotype.

      We used different colors to represent different genotypes, and the columns were superimposed. we changed the graphs to show the quantification in different conditions separately. We thank you for kindly pointing it out.

      (3) The number of tracheal progenitors should be assessed since they seem to be found in excess in some genetic conditions that affect their behavior. A change in progenitor number could lead to crowding, thus affecting their localization rather than migration capacities, thereby changing the proposed interpretation. In addition, the authors show data suggesting a reduced progenitor migration speed when the fat body is affected, which would also be consistent with a crowding of progenitors.

      We examined the cell number in bidirectional movement samples and control group. We examined cell number and cell proliferation and observed that there was no significance between control and bidirectional movement groups (Figure 3-figure supplement 2).

      (4) The authors claim that tracheal progenitors display a polarized distribution of PCP proteins that is controlled by JAK-STAT signaling. However, this conclusion is made from a single experiment that is not quantified and for which there is no explanation of how the plot profile measurements were performed. It also seems that this experiment was done only once. Altogether, this is insufficient to support the claim. Finally, a quantification of the number of posterior edges presenting filopodia rather than the number of filopodia at the anterior and posterior leading edges would be more appropriate.

      We staged the animals, measured several animals for each genotype and provided the quantifications in the revised manuscript. The level of Ft-GFP is higher in the cells at the frontal edge. We tried to examine the expression of Ft-GFP at single-cell level. However, this turned out to be difficult due to the fact that the tracheal stem cells are not regularly patterned as epithelial cells and the proximaldistant axis of tracheal stem cells is not well defined. We thus decided to measure the fluorescence signal of groups of stem cells along the DT regardless of their individual polarity.

      (5) The authors demonstrate that Upd2 is transported through vesicles from the fat body to the tracheal progenitors where they propose they are internalized. Since the Upd2 receptor Dome ligand binding sites are exposed to the extracellular environment, it is difficult to envision in the proposed model how Upd2 would be released from vesicles to bind Dome extracellularly and activate the JAK-STAT pathway. Moreover, data regarding the mechanism of the vesicular transport of Upd2 are not fully convincing since the PLA experiments between Upd2 and Rab5, Rab7, and Lbm are not supported by proper positive and negative controls and co-immunoprecipitation data in the main figure do not always correlate to the raw data.

      We use molecular modeling to show that Upd2 and Lbm intermingle, and Upd2 is not entirely encapsulated in vesicles (Figure 8-supplement 1E). We performed PLA experiments using the animals not expressing upd2-Cherry as negative control (Figure 8 E-J). We corrected the Co-IP panel and apologize for this error.

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      Minor comments:

      (1) Figure 1-figure supplement 1: E: How was the migration velocity assessed? By live imaging individual cells or following the cell front of the group? Over what time period? Do the data points in the graph correspond to individual cells or the cell group? It would be important to show confocal images that go along with this quantification.

      We took snapshots of pupae at 0hr\ 1hr\ 2hr and 3hr, and measured the distance covered by the migrating progenitor cells from the start place (the junction of TC and DT) to the leading edge of progenitor groups. We then calculated the migration rate by v=d (micrometer)/t (min). As the progenitor cells revolve around and migrate along the DT, tracking single tracheoblast through intact cuticle is technically challenging. We have therefore measured the leading edge as a proxy to the whole cell group. We agree with you that time-lapse imaging is favorable for analysis of migration.

      (2) Figure 1-figure supplement 1: F: Why is there Gal80ts in the genotype? (and in Figure 1H). Also, what pupal age was used for this quantification?

      Expression of hid and rpr in L3 stage impaired fat body integrity and adipocyte abundance, and caused lethality. Gal80ts was used for controlling the expression of rpr.hid. The pupal at 0hr APF were used in EdU experiment.

      (3) Figure 2C: what is shown in the 6 columns (why 3 each for control and rpr/hid)?

      We conducted 3 replicates of each group for control and rpr.hid.

      (4) In the methods, several Drosophila stocks are listed as 'source:" from a particular person (e.g. Dr Ma). Please list the real source of this stock, e.g. Bloomington stock number, or the lab and publication in which the stock was originally made.

      We provide the information on these stocks in the revised methods.

      (5) The SKOV3 carcinoma cell and S2 cell work is not described in the methods.

      We added detailed description of this experiment in the revised method-Cell culture and transfection. 

      (6) Figure 6 (F) 'Bar graph plots the abundance of Upd2-mCherry-containing vesicles in progenitors.' What does abundance mean? What was quantified, the number of vesicles, or the mean intensity? This is also not mentioned in the methods.

      We counted the number of Upd2-mCherry-containing vesicles in fat body cells and trachea progenitors and added the description of measurement in the method.

      (7) There are a few language mistakes throughout the manuscript. E.g.

      (a) Line 117 and other places: Language: 'fat body' should be 'the fat body'.

      We thank you for pointing out these errors and corrected it accordingly.

      (b) Line 1276 Language mistakes: 'Video 1 3D-view of confocal image stacks of tracheal progenitors and fat body. Scale bar: 100 μm. Genotypes: UAS-mCD8-GFP/+;lsp2-Gal4,P[B123]-RFP-moe/+.' :stacks and genotypes should be singular.

      We fixed these errors and thank you for kindly pointing them out. We also proofread the entire manuscript to assure accuracy.

      (8) In general, it is hard to figure out the exact genotypes used in experiments. This is mostly not written very clearly in the figure legends. E.g. Figure 2: genotype for A-C missing in figure legend (is B from control animals?)

      We added genotypes in the figure legends. For Figure 2, A and C lsp2-Gal4,P[B123]-RFP-moe/+ for control, UAS-rpr-hid/+;Gal80ts/+;lsp2-Gal4,P[B123]-RFP-moe/+ for rpr.hid; B from control animals.

      Reviewer #2 (Recommendations for the authors):

      Major comments:

      (1) The phenotype resulting from Upd2 downregulation by RNAi is subtle and shown by unconvincing images. In addition, these phenotypes are analyzed using only one RNAi line.

      We used two independent alleles of upd2RNAi from THFC (THU1288 and THU1331), and observed similar phenotype. For RNAi experiments, we always use multiple independent alleles.

      (2) The authors should analyze the phenotypic consequences of directional migration changes. Is there an effect on tracheal remodeling?

      We observed that the integrity of tracheal network especially the dorsal trunk was impaired and that melanized tracheal branches were present, which may be due to incomplete regeneration (Figure 3figure supplement1E-I).

      (3) The number of tracheal progenitors should be quantified, as some genetic conditions may affect cell numbers, as is apparent in some panels.

      We examined cell number and cell proliferation and observed that there was no significance between control and bidirectional movement groups (Figure 3-figure supplement 1).

      (4) The data on PCP protein distribution are unconvincing, unquantified, and insufficient to support one of the main conclusions of the study, which is stated in the abstract: "JAK/STAT signaling promotes the expression of genes involved in planar cell polarity, leading to asymmetric localization of Fat in progenitor cells."

      We staged the animals, measured several animals for each genotype and provided the quantifications in the revised manuscript. The level of Ft-GFP is higher in the cells at the frontal edge. We tried to examine the expression of Ft-GFP at single-cell level. However, this turned out to be difficult due to the fact that the tracheal stem cells are not regularly patterned as epithelial cells and the proximaldistant axis of tracheal stem cells is not well defined. We thus decided to measure the fluorescence signal of groups of stem cells along the DT regardless of their individual polarity.

      Minor comments:

      (1) Language should be revised. In many places in the manuscript, starting in line 113, "fat body" should be "the fat body".

      Thank you for pointing out this error. We corrected it accordingly.

      (2) Genotypes used in experiments should be described.

      We added all the genotypes. We proofread the entire manuscript to complete the figure legends for genotypes.

      (3) Line 67, the reference to "The progenitor cells reside in Tr4 and Tr5 metameres and start to move along the tracheal branch" should include (Chen and Krasnow, Science 2014).

      We added the reference in the manuscript.

      (4) Line 1081, Figure 7 Legend. "Bar graph plots the abundance of Upd2-mCherry-containing vesicles" Abundance is the number of vesicles? The graph displays the average number of vesicles? Please explain and describe the quantification.

      The bar graph represents the number of Upd2-mCherry-containing vesicles in different conditions. We quantified the number of vesicles per area.

      (5) Figure 1 (I-J) What is shown on the panels? Progenitors marked with? This information is not present in the figure or figure legend. Same for Figure 2 (D-E).

      Figure 1I-J show the vector of migrating progenitors. We added the information in the legends. The tracheal cells were labeled by nls-mCherry in Figure 1I-J. In Figure 2D-E, the progenitors were marked with P[B123]-RFP-moe.

      (6) Figure 3 Q, Stat92E-GFP values in the graph are not well-explained. What do the numbers in the y-axis refer to?

      y-axis represents the intensity of Stat92E-GFP normalized to control. We have changed the y-axis label to ‘normalized Stat92E-GFP intensity’ in the legends.

      (7) In general, figures and figure legends must be revised. Sometimes stainings are not well-defined, some scale bars are missing and plots do not say what the values are.

      We apologized for inadequate information and have revised the figures and legends accordingly.

      Reviewer #3 (Recommendations for the authors):

      Several points should be addressed by the authors in order to improve their manuscript.

      Major points:

      (1) The phenotype obtained from decreasing the inter-organ signaling is quite discrete. It is further weakened by the fact that the images chosen to illustrate the measures are not really convincing. No image at 1h APF shows any clear anterior migration. Based on the scale, most of the images at 3h APF do not show a striking difference compared to the control, and in any case, stronger phenotypes would be missed anteriorly since they would thus be out of frame. In addition, at 3h APF, progenitors migrating anteriorly from Tr5 position get mixed with those migrating posteriorly from Tr4 so it is not clear how measurements were made. Given that most phenotypes are observed upon the use of RNAis, it is possible that phenotypes are weak due to persistent gene expression. Using null clones for dome, hop, or stat in progenitors could therefore aggravate the phenotypes and support further the significance of the study. Finally, assessing the consequences of compromised fat body-tracheal communication on trachea morphology, function, and regeneration later in pupal development and on adult flies would also help strengthen the importance of the findings.

      We agree with you that anteriorly migrated Tr5 progenitors adjoining Tr4 progenitor hinders measurements and that mutants may give stronger phenotype than RNAi lines. We only measured Tr4 progenitors (instead of Tr5) when assessing anterior migration. Thus, we performed experiments using mutant alleles, which gave aberrant migration of tracheal progenitors (Figure 3-figure supplement1A-D). We can now show that the integrity of tracheal network especially dorsal trunk was impaired, which may be due to incomplete regeneration (Figure 3-figure supplement1E-I).

      (2) Although the authors did not observe defects in tracheal progenitor proliferation, progenitors seem to be present in excess in some key genetic background (e.g, upon expression of rpr.hid, statRNAi, Rab-RNAi or in the presence of BFA). This excess could be the result of another mechanism than proliferation (recruitment of extra progenitors since it is not clear how they originate, defect in apoptosis...) and could impact the localization of progenitors, those being pushed anteriorly as a consequence of crowding. A proper characterization of tracheal progenitor number would thus help to discriminate between defects in migration or crowding. This point could also be addressed by performing individual tracking of tracheal progenitors, to find out whether each progenitor is indeed migrating in the wrong direction or if the movement assessed by the global tracking method that is used is just a consequence of progenitor excess.

      We examined the cell number in bidirectional movement samples and control group. The results show that there was no significance between control and bidirectional movement groups (Figure 3figure supplement 1). We also tried to follow every progenitor, but were unable to obtain convincing results with P[B123]-RFP-moe, as tracking single tracheoblast through intact cuticle is technically challenging.

      (3) Regarding the ChIP-seq experiment, an explanation of why choosing the "establishment of planar polarity" family should be provided since data indicate a quite low GeneRatio. Indeed, the "cell adhesion" family seems a more obvious candidate, which would be further supported by the fact that the JAK-STAT pathway has been shown to affect cell adhesion components such as ECadherin and FAK (Silver and Montell 2001, Mallart et al 2024). Also, have these known targets of JAK-STAT signaling been found in the ChIP-seq data? Since filopodia polarization is affected in tracheal progenitors when JAK-STAT signaling is decreased, the same question also applies to enabled, which is involved in filopodia formation and has been recently identified as a target of JAK-STAT signaling.

      As you kindly suggested, we tested a number of cell adhesion-related genes such as E-Cadherin (shg), fak, robo2 and enabled (ena). We did not observe an apparent aberrancy in the migration of tracheal progenitors (Figure 5-supplement 1J).

      (4) Data investigating PCP protein distribution is not convincing, not quantified, and not sufficient to draw one of the main conclusions of the study, which is even written in the abstract "JAK/STAT signaling promotes the expression of genes involved in planar cell polarity leading to asymmetric localization of Fat in progenitor cells."

      We better quantified the abundance of Ft in in the progenitors in the frontal edge and those lagging behind. The traces plot multiple replicates in the figures. The level of Ft-GFP is higher in the cells at the frontal edge.

      (5) Overall, the figures together with their caption and/or the material and methods section lack some important information for the reader to fully understand the data. In addition, some errors are found in multiple plots throughout the article and must be corrected. Here are some examples:

      According to your suggestion, we revised legends and methods section to include sufficient information.

      (a) Migration distance plots from Figure 3E do not match the data presented in the source data file. It seems that, when creating the plot, instead of superimposing the bars, bars were stacked. This should be corrected for all migration distance plots from Figure 3E onward, including in supplementary figures.

      We apologized for misleading representation. We revised it accordingly and show the quantification in different conditions separately.

      (b) The number of analyzed flies and/or clusters of tracheal progenitors from different flies should be stated for all quantification or observations made on images. This information is lacking for all migration distance plots, for progenitor migration tracking (Figure 1 I, J), for DIPF reporter in Figure 2J, for plot profiles (Figure 5G, J), for Upd2-Rab5/Rab7/Lbm co-detections, PLA, CoIP, and lbm-pHluorin experiments. This also applies to RNA seq, ChIP seq, and surface proteomics, for which the number of pupae and number of replicates is not indicated.

      We changed the graphs to show the quantification and n number in different conditions separately.

      We also added the n number of replicates in methods.

      (c) How quantifications were performed is not sufficiently explained. For example, the reference point for migration distance measurement is not defined, and neither is whether the measures were made on fixed or live imaging samples. In fluorescence intensity measurements and Upd2 vesicle counting, information on whether measures were made on a single z slice or on a projection of several z slices should be stated together with what ROI and which FIJI tool for quantification were used. For plot profiles, the same information regarding z slices misses together with how the orientation, the thickness, and the length of the line were chosen, and again the number of times the experiment was conducted should be mentioned and error bars should appear on graphs.

      We thank this reviewer for the suggestions which help clarify the methodology of our experiments and improve presentation of our data. We have made the changes according to the suggestions and modified our methods section and the related figures to incorporate these changes.

      For measuring the migration distance of tracheal progenitors, we took snapshots of living pupae at 0hr\ 1hr\ 2hr and 3hr APF, and measured the migration distance of tracheal progenitors from the start place (the junction of TC and DT) to the leading edge of progenitor groups.

      For the measurements of fluorescent intensity of stat92E-GFP and DIPF, we took z-stack confocal images of samples and quantified the fluorescent intensity using FIJI. Specifically, intensity was quantified for regions of interest, using the Analysis and Measurement tools. To quantify Upd2mCherry vesicles, z-stack confocal images of fat body were taken and the cell counting function of FIJI was used to measure the vesicle number.

      To quantify the fluorescent intensity of in vivo tagged Ds, Ft and Fj proteins, a single z slice was used. The expression level of the protein was assessed as the integrated fluorescent intensity normalized to area.

      For the measurement of Ft-GFP distribution, a single z slice of the progenitors immediately proximal to the DT was imaged. An arbitrary line was drawn along the migration direction from the starting TC-DT junction to the leading front (the length of the line corresponds to the distribution range of tracheal stem cell clusters). Then, fluorescent intensity along the line was automatically calculated with the imbedded measurement function of Zeiss confocal software.

      Minor points:

      (1) In several instances, the authors generalize that stem cells migrate to leave their niche, but this is not the case for all stem cells.

      The phenomenon that stem cells leave their niche when they are activated is commonly observed. We interpreted the general mechanism from our system of tracheal stem cells. We fully agree with you that it may not be the case for all stem cells. We modified the text accordingly.

      (2) Line 122 -a reference paper or an image showing the expression pattern of the lsp2-Gal4 driver is missing.

      We added the reference in the manuscript.

      (3) Line 136 - The term "traces of individual progenitors" is overstated and should be reformulated as the method used does not seem to be individual cell tracking.

      We rephrased accordingly in the revised manuscript.

      (4) Line 146 - Fat body and tracheal progenitors are qualified as interdependent organs, in which aspect do tracheal progenitors affect the fat body?

      Current knowledge suggests a close inter-organ crosstalk between trachea and fat body: The fly trachea provides oxygen to the body and influences the oxidation and metabolism of the whole body. When the trachea is perturbed, the body is in hypoxia, which causes inflammatory response in adipose tissue as an important immune organ (Shin et al., 2024).

      (5) Line 163 - Not all the genes tested are cytokines, so the sentence should be reformulated. In addition, in supplementary Fig2-1 C-J, the KD of hh seems to abolish completely tracheal progenitor migration, which is not commented on.

      According to your suggestion, we revised the description on information of the genes tested. We added comments in the revised manuscript regarding phenotypes of hh knockdown. 

      (6) Line 180 - Conclusion is made on Dome expression while using a dome-Gal4 construct, which does not necessarily recapitulate the endogenous pattern of dome expression, so it should be reformulated. Ideally, dome expression should be assessed in another way. Also, it is not clear whether GFP is present only in progenitors since images are zoomed.

      We revised statement and provided larger view of dome>GFP that shows an enriched expression in the tracheal progenitors (Figure 2-figure supplement 2E), an expression pattern that is consistent with FlyBase.

      (7) Line 199 - Is it upd-Gal4 or upd2-Gal4 that is used? Since the conclusion of the experiment is made on upd2, the use of upd-gal4 would not be relevant. If upd2-gal4 is used, it should be corrected. In general, the provenance of the Gal4 lines should be provided. In addition, a strong GFP signal in the trachea is visible on the image in Supplementary Figure 2-2F but not commented on and seems contradictory with the conclusion mentioning that fat body and gut are the main source of Upd2 production.

      We removed data obtained from the use of this irrelevant upd-Gal4 line.

      (8) Figures:

      -  Figure 1 G, H - Scale bar is missing.

      We added it accordingly.

      -  Figure 1 I, J - The information on the staining is missing.

      We added it in the revised manuscript.

      -  Figure 2A - Providing explanations of the terms "Count" and "Gene ratio" in the caption would be helpful for readers who are not used to this kind of data. In addition, the color code is confusing since the same color is used for the selected gene family and for high p-values (the same applies to other similar graphs).

      Gene ratio refers to the proportion of genes in a dataset that are associated with a particular biological process, function, or pathway. Count indicates the number of genes from input gene list that are associated with a specific GO term. We used redness to indicate a smaller p-value and a higher significance.

      -  Figure 2 B, C - What does the color scale represent? What do the columns in C correspond to, different time points, different replicates?

      The color scale represents the normalized expression. The columns in C correspond to different replicates of control and rpr.hid.

      -  Figure 2 F - The error bars on the 3h APF posterior bars are missing.

      We added error bars accordingly.

      -  Figure 2 G - The legend "Down-Stable-Up" is in comparison to what?

      The control group was generated from the reaction without H2O2. The comparison was relative to the control group.

      -  Figure 2 J - The specificity of the DIPF tool that has been created should be validated in other tissues displaying known JAK-STAT activity and/or in conditions of decreased JAK-STAT signaling. In addition, the added value of the tool as compared to the JAK-STAT activity reporter used later, which has been well characterized, is not obvious.

      We added the signal of DIPF in fat body and salivary gland, both of which harbor active JAK/STAT signaling (Figure 2-figure supplement 2F-H). As opposed to the well characterized Stat92E-GFP reporter that assays the downstream transcription activity, the DIPF reporter measures the upstream event of receptor dimerization.

      -  Figure 3 I-P - Reporter tool validation in Images I-L could be moved to supplementary data. In images M-P, staining of nuclei and/or membranes would be useful to assess cell integrity.

      We revised the figures accordingly.

      -  Figure 3Q and similar plots in the following figures do not explain the normalization performed and how it can be higher than 1 in control conditions.

      In these figures, we normalized the signal relative to control groups, e.g., The value of Stat92E-GFP in btl-GFP control group was set to 1 in the previous Figure 3Q (revised Figure 3-supplementary

      Figure B-J).

      -  Figure 4C - These representations lack explanations to be fully understood by a broad audience.

      The figure showing that Stat92E binding was detected in the promoters and intronic regions (the orange peaks) of genes functioning in distal-to-proximal signaling, such as ds, fj, fz, stan, Vang and fat2. We added the information in figure legend according to your suggestion.

      -  Figure 5 K,L - What is the x-axis missing, together with the method of tracking used?

      The x-axis refers to time of recording from a t stack series with a time interval of 5 min. We revised method section and provide detailed procedure of this experiment.

      -  Figures 6 and 8- The overall figures lack a wider view of the cells/tissues/organs and/or additional staining to understand what is presented.

      We showed preparation of fat body. In order to obtain the high resolution of vesicles, we used high magnification. We now added wider views of the tissues under investigation (e.g. Figure 6-figure supplement 1).

      -  Figure 6 D,E - The scale bar is missing.

      We added it accordingly.

      -  Figure 8 O-S - What is the blue staining?

      The blue staining shows DAPI-stained nuclei. We have added the information in the legend.

      -  PLA experiments can give a lot of non-specific background. What kind of controls have been used in Figure 8 F-J? Negative controls should be done on cells that do not express upd2-mCherry using both antibodies to detect non-specific background, which does not usually appear completely black.

      If possible, a positive control using a known protein interacting with Rab5-GFP should be included.

      We used the control samples without one of the primary antibodies in previous Figure 8. In the revised Figure 8, we conducted experiment as you suggested with controls that do not express upd2mCherry (Figure 8 E-J).

      -  Co-IP experiments - The raw data file for blots is quite hard to read through. Some legends are not facing the right lane and some blots presented in the main figure are difficult to track since several blots are presented in the raw data file. e.g.

      (a)  Raw blot for Figure 8 K: the band for mCherry in the IP anti-GFP blot (lane one in K) is not convincing, it is not distinguishable from other aspecific bands. On the reverse IP presented only in raw data, on the input from blot IB anti-mCherry, both lanes present exactly the same bands at 72kb when one of the lanes corresponds to extract from flies not expressing upd2-mCherry.

      We thank you for pointing out the incorrect labels. We apologized for the errors and corrected it accordingly.

      (b)  Raw blot for Figure 8 L: on the input blot IB anti-GFP, there is a band corresponding to Rab7-GFP in the lane of the extract from flies not expressing Rab7-GFP.

      We corrected it.

      (c)  Raw data for Figure 8 M: on the last blot, legends are missing above the input Ib anti-GFP blot.

      We added the missing legends in the figure.

      Shin, M., Chang, E., Lee, D., Kim, N., Cho, B., Cha, N., Koranteng, F., Song, J.J., and Shim, J. (2024). Drosophila immune cells transport oxygen through PPO2 protein phase transition. Nature 631, 350-359.

    1. Kwasy tłuszczowe omega-3 wydają się spowalniać procesy starzenia
      • Daily intake of 1g of omega-3 fatty acids can slow down aging, especially when combined with vitamin D and exercise - as demonstrated by a 3-year study on 777 Swiss seniors[1][2].

      • Epigenetic clocks were used to measure the pace of aging, showing up to 4 months of biological age reduction[1][3].

      • Additional benefits included:

        • 61% reduction in invasive cancer risk[4]
        • 10% reduction in falls[4]
        • 13% decrease in infection rates[4]
      • Sources of omega-3: fish, seafood, rapeseed and flaxseed oil, walnuts, supplements[7][9]

      Citations: [1] https://www.sci.news/medicine/omega-3-supplementation-biological-aging-13635.html [2] https://www.news-medical.net/news/20250204/Omega-3-fatty-acids-and-vitamin-D-slow-biological-aging-in-older-adults.aspx [3] https://www.nature.com/articles/s43587-024-00793-y [4] https://www.medonet.pl/leki-od-a-do-z/witaminy-i-mineraly,wystarczy-gram-dziennie--spowolnisz-starzenie-nawet-o-cztery-miesiace,artykul,86261609.html [5] https://www.eurekalert.org/news-releases/1072552 [6] https://www.national-geographic.pl/nauka/kwasy-omega-3-to-pigulka-mlodosci-zwlaszcza-w-polaczeniu-z-witamina-d/ [7] https://dzienniknaukowy.pl/kwasy-tluszczowe-omega-3-wydaja-sie-spowalniac-procesy-starzenia [8] https://translate.google.com/?prev=_t&hl=pl&ie=UTF-8&eotf=1&sl=en&tl=zh-CN [9] https://www.businessinsider.com/taking-omega-3-supplements-may-slow-down-aging-study-2025-2 [10] https://pubmed.ncbi.nlm.nih.gov/36629088/ [11] https://www.sciencedaily.com/releases/2025/02/250204132423.htm

    1. Angehörige des von Ellen Maske geleiteten zungenanden, D-O-G-E, haben sich Zugang zu Diensträumen der amerikanischen Behörde für Atmosphäre und Ozeane verschafft. Fachleute befürchten, kommen das in die Arbeit der Behörde zerstörerisch eingegriffen werden soll, kommen bevor die möglichen rechtlichen Schritte dagegen ergriffen werden können. Im für die neue Administration offenbar maßgeblichen Projekt 2025 wird eine radikale Verkleinerung dieser Behörde gefordert. Die sei für die amerikanischen Wirtschaftsinteressen schädlich. Schon länger versuchen Interessengruppen, die Behörde zu untersagen, ihre Daten zu publizieren und sie zu zwingen, die Daten stattdessen privaten Anbietern für kommerzielle Produkte zu überlassen. https://www.theguardian.com/us-news/2025/feb/04/doge-noaa-headquarters

    1. We are rapidly, of course, destroying all the natural systemsin the world, the balanced natural systems. We simply makethem unbalanced — but still natural

      defining natural -- with vs w/o humans in equation

    Annotators

    1. Author response:

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

      Public Reviews:

      Reviewer #1 (Public Review):

      Summary:

      Hahn et al use bystander BRET, NanoBiT assays, and APEX2 proteomics to investigate endosomal signaling of CCR7 by two agonists, CCL19 and CCL21. The authors suggest that CCR7 signals from early endosomes following internalisation. They use spatial proteomics to try to identify novel interacting partners that may facilitate this signaling and use this data to specifically enhance a Rac1 signaling pathway. Many of the results in the first few figures showing simultaneous recruitment of Barr and G proteins by CCR7 have been shown previously (Laufer et al, 2019, Cell Reports), as has signaling from endomembranes, and Rac1 activation at intracellular sites. The new findings are the APEX2 proteomics studies, which could be useful to the scientific community. Unfortunately, the authors only follow up on a single finding, and the expansion of this section would improve the manuscript.

      First of all, we would like to thank the reviewer for helping with the manuscript. The summary is mostly accurate except for the statement that simultaneous recruitment of barr and G protein to CCR7 has been shown before. It should also be noted that it has not been demonstrated that CCR7 activates G proteins from endosomes previously nor has the functional role of this signaling mechanism. However, that CCR7 activity at endomembranes is associated with Rac1 signaling was demonstrated in the Laufer et al. study as the reviewer correctly points out.

      Strengths:

      (1) The APEX2 resource will be valuable to the GPCR and immunology community. It offers many opportunities to follow up on findings and discover new biology. The resource could also be used to validate earlier findings in the current manuscript and in previous manuscripts. Was there enrichment of early endosomal markers, Barr and Gi as this would provide further evidence for their earlier claims regarding endosomal signaling? Previous studies have suggested signaling from the TGN, so it is possible that the different ligands also direct to different sites. This could easily be investigated using the APEX2 data.

      Thank you for your comment. We do in fact observe enrichment of TGN/Golgi markers in response to chemokine stimulation, which we now have highlighted in the manuscript (fourth paragraph on page 7).

      (2) The results section is well written and can be followed very easily by the reader.

      We are glad that the reviewer found the results section very readable.

      (3) Some findings verify previous studies (e.g. endomembrane signalling). This should be acknowledged as this shows the validity of the findings of both studies.

      This is correct. We have now included more discussion of previous work related to CCR7 signaling at endomembranes (thirdparagraph on page 10).

      Weaknesses:

      (1) The findings are interesting although the studies are almost all performed in HEK293 cells. I understand that these are commonly used in GPCR biology and are easy to transfect and don't express many GPCRs at high concentrations, but their use is still odd when there are many cell-lines available that express CCR7 and are more reflective of the endogenous state (e.g. they are polarised, they can perform chemotaxis/ migration). Some of the findings within the study should also be verified in more physiologically relevant cells. At the moment only the final figure looks at this, but findings need to be verified elsewhere.

      We thank the reviewer for raising this point and giving us an opportunity to elaborate in further detail. The major goal of our study was to investigate whether CCR7 activates G protein from endosomes, the underlying mechanism, and functions of this potential signaling mechanism. The reason we chose CCR7 as our model receptor was that it belongs to a group of GPCRs, the chemokine receptors, that most often have features associated with the ability to promote endosomal G protein activation (phosphorylation site clusters in the C-terminal region).

      Specific detection of G protein activation at distinct subcellular compartments is currently very challenging in truly endogenous systems despite new innovative biosensors that are available (not just related to CCR7, but GPCRs in general). To our knowledge, most if not all studies that detect direct activation of G protein at a specific compartment whether at the plasma membrane, endosome, Golgi, or other compartments, have overexpressed either the receptor, G protein, or both. This is why we choose the HEK293 cell system for most of our experiments, which are easy to manipulate. That being said, we did confirm major findings in an indirect manner using Jurkat T-cells, which express CCR7 endogenously and are physiological relevant. Our hope is that in the future we will be able to use highly sensitive biosensors to directly confirm our findings in such a cell system as the reviewer wisely suggests.

      (2) The authors acknowledge that the kinetic patterns of the signals at the early endosome are not consistent with the rates of internalisation. They mention that this could be due to trafficking elsewhere. This could be easily looked at in their APEX2 data. Is there evidence of proximity to markers of other membranes? Perhaps this could be added to the discussion. Similarly, previous studies have shown that CCR7 signaling may involve the TGN. Was there enrichment of these markers? If not, this could also be an interesting finding and should be discussed. It is also possible that the Rab5 reporter is just not as efficient as the trafficking one, especially as in later figures the very convincing differences in the two ligands are not as robust as the differences in trafficking.

      Excellent point. We have now highlighted the possibility of CCR7 being further trafficked to the trans-Golgi network (TGN) as possible explanation for the transient translocation of activated CCR7 to the early endosome in Fig. 1G-H (second paragraph on page 3).

      Furthermore, in the APEX2 experiment we observe enrichment of proteins involved in lysosomal trafficking (LAMP1, VPS16, VAMP7, WDR91, and PP4P1) by CCL19 stimulation at 25 min, and recycling endosomes/TGN markers (SNX6, RAB7L, and GGA) by CCL21 stimulation at 25 min. In addition to this, several markers of TGN/Golgi (SNX3, COG5, YIF1A, SC22B, and AP3S1) were enriched as well in response to both CCL19 and CCL21 stimulation. We have now included a statement in the manuscript, which describes the likely trafficking of CCR7 to the TGN/Golgi in response to CCL19 and CCL21 stimulation (fourth paragraph on page 7).

      (3) In the final sentence of paragraph 2 of the results the authors state that the internalisation is specific to CCR7 as there isn't recruitment to V2R. I'm not sure this is the best control. The authors can only really say it doesn't recruit to unrelated receptors. The authors could have used a different chemokine receptor which does not respond to these ligands to show this.

      The point with this control experiment was to demonstrate that the loss of NanoBiT signal in response to CCL19 in CCR7-SmBiT/LgBiT-CAAX expressing cells, but not in V2R-SmBiT/LgBiT-CAAX expressing cells, was a result of bona fide CCR7 internalization rather than potential artifactual effects of CCL19 on the NanoBiT system. Our intent was not to demonstrate specificity of CCL19 among chemokine receptors, which already has been thoroughly tested in previous studies. We have now modified the sentence (second paragraph on page 3) “Moreover, CCL19/CCL21-stimulation of receptor internalization to endosomes is specific to CCR7 as none of the chemokines promote internalization or trafficking to endosomes of the vasopressin type 2 receptor (V<sub>2</sub>R)-SmBiT construct (Fig. S1E-F)” to “Moreover, CCL19/CCL21-stimulation did not promote internalization or trafficking to endosomes of the vasopressin type 2 receptor (V<sub>2</sub>R)-SmBiT construct, which validates that these chemokines act specifically via the CCR7-SmBiT system (Fig. S1E-F).”

      (4) The miniGi-Barr1 and imaging showing co-localisation could be more convincing if it was also repeated in a more physiological cell line as in the final figure. Imaging of CCR7, miniGi, and Barr1 would also provide further evidence that the receptor is also present within the complex.

      We agree with the reviewer’s assessment. However, as mentioned above it is currently extremely challenging to detect endogenous G protein coupling/activation to endogenous receptors. In addition, we are not sure if overexpressing fluorophore-tagged receptor, miniG, and barr1 in a physiological-relevant cell line would provide truly physiological conditions as the expression of these proteins still would be artificially high. This is why we chose to conduct these mechanistic experiments in HEK293 cells and then indirectly verify key findings in an endogenous and physiological-relevant cell line.

      (5) The findings regarding Rac1 are interesting, although an earlier paper found similar results (Laufer et al, 2019, Cell Reports), so perhaps following up on another APEX2-identified protein pathway would have been more interesting. The authors' statement that Rac1 is specifically activated, and RhoA and Cdc42 are not, is unconvincing from the current data. Only a single NanoBiT assay was used, and as raw values are not reported it is difficult for the reader to glean some essential information. The authors should show evidence that these reporters work well for other receptors (or cite previous studies) and also need evidence from an independent (i.e. non-NanoBiT or BRET) assay.

      The major focus of the study was to investigate whether CCR7 can activate G protein after having been internalized into endosomes via formation of CCR7-Gi/o-barr megaplexes, and to dissect out potential functions of said endosomal G protein signaling. To do this, we used CCL19 and CCL21 which stimulate G protein to the same extent but differ in their ability of promote barr recruitment and receptor internalization with CCL19 being superior to CCL21. To this end, we found that CCL19 also promote endosomal G protein activation to a greater extent than CCL21, and therefore, we specifically looked for proteins enriched by CCL19 in our APEX experiment. This led us to some Rho GTPase regulators that were differentially enriched by CCL19 and CCL21. We agree that there were other interesting effectors related to CCR7 biology identified in the APEX experiment such as EYA2, GRIP2, and EI24. However, those proteins were enriched similar by CCL19 and CCL21 challenge, and thus, do not seem to be activated specifically at endosomes. Following the same argument, we also did not observe any difference in the activity of RhoA or Cdc42 when stimulated with CCL19 or CCL21, so we cannot conclude that these signaling proteins are activated specifically in endosomes. On the other hand, Rac1 was stimulated to a larger degree by CCL19 than CCL21, its activity was inhibited by the Gi/o inhibitor PTX and endocytosis inhibitors Dyngo-4a and PitStop2. CCR7-mediated Rac1 signaling was also inhibited by expression of a dominant negative dynamin mutant that inhibits receptor internalization, and Rac1 was not activated by an internalization-deficient CCR7-DS/T mutant. Finally, the involvement of Rac1 in CCR7 mediated chemotaxis of Jurkat T cells was also demonstrated. We believe that these findings together provide strong basis for the claim that endosomal Gi/o protein signaling by CCR7 activates Rac1.

      Following the reviewer’s suggestion, we have now included experiments to show that the activation of RhoA, Rac1, and Cdc42 by CXCR4 also can be detected by the NanoBiT biosensors (Fig. S7D-F). We have also added the appropriate references to the original studies where these biosensors were developed in the results section (first paragraph on page 8).

      (6) At present, the studies in Figure 7 do not go beyond those in the previous Laufer et al study in which they showed blocking endocytosis affected Rac1 signalling. The authors could show that Rac1 signalling is from early endosomes to improve this, otherwise, it could be from the TGN as previously reported.

      The major purpose of Figure 7 was to indirectly confirm findings from HEK293 cells experiments and to tie them to physiological functions. Our experiments using Jurkat T-cells show that CCL19 promote stronger chemotactic response than CCL21 despite similar Gi/o response. In addition, we showed that CCR7-mediated Gi/o activation, receptor endocytosis, as well as Rac1 activity, are required to drive chemotaxis. The Laufer et al. study did not investigate whether CCR7 activates G protein after having been internalized into endosomes via formation of CCR7-Gi/o-barr megaplexes, and thus, did not focus on functional outcomes of this signaling mechanism. Based on this, we believe our work provides new and valuable knowledge to the field.

      Reviewer #2 (Public Review):

      Summary:

      This manuscript describes a comprehensive analysis of signalling downstream of the chemokine receptor CCR7. A comprehensive dataset supports the authors' hypothesis that G protein and beta-arrestin signalling can occur simultaneously at CCR7 with implications for continued signalling following receptor endocytosis.

      We would like to thank the reviewer for helping with the manuscript. We agree on all points made and have now updated the manuscript accordingly.

      Strengths:

      The experiments are well controlled and executed, employing a wide range of assays using - in the main - CCR7 transfectants. Data are well presented, with the authors' claims supported by the data. The paper also has an excellent narrative which makes it relatively easy to follow. I think this would certainly be of interest to the readership of the journal.

      We appreciate the positive assessment of strengths.

      Weaknesses:

      Since the authors show a differential enrichment of RhoGTPases by CCR7 stimulation with CCL19 versus CCL21, I think that they also need to show that the Gi/o coupling of HEK-292-CCR7-APEX2 cells to both CCL19 and CCL21 is not perturbed by the modification. Currently, the authors only show data for CCL19 signalling, which leaves the potential for a false negative finding in terms of CCL21 signalling being selectively impaired. This should be relatively easy to do and should strengthen the authors' conclusions.

      We agree with the reviewer and have now included experiments to show that both CCL19- and CCL21-mediated CCR7-APEX2 stimulation leads to Gi/o activation (Fig. S4C). In addition, our proteomics experiments show strong effects of both CCL19 and CCL21 stimulation, which suggest that the receptor is activated by both ligands.

      The authors conclude the discussion by suggesting that their findings highlight endosomal signalling as a general mechanism for chemokine receptors in cell migration. I think this is an overreach. The authors chose several studies of CXC chemokine receptors to support their argument that C-terminal truncation or mutation of the C-terminal phosphorylation sites impairs endocytosis and chemotaxis (refs 40-42). However, in some instances e.g. at the related chemokine receptor CCR4, C-terminal removal of these sites impairs endocytosis but promotes chemotaxis (Nakagawa et al, 2014); Anderson et al, 2020). I therefore think that either the final statement needs to be tempered down or the counterargument discussed a little.

      We appreciate the reviewer highlighting this point. We have now modified the concluding sentence from “Thus, the findings from our study highlight endosomal G protein signaling by chemokine receptors as a potential general mechanism that regulates key aspects of cell migration” to “Thus, the findings from our study highlight endosomal G protein signaling by some chemokine receptors as a potential mechanism that regulates key aspects of cell migration.” We hope that the temper level of this sentence is more appropriate.

      References:

      Anderson, C. A. et al. A degradatory fate for CCR4 suggests a primary role in Th2 inflammation. J Leukocyte Biol 107, 455-466 (2020).

      Nakagawa, M. et al. Gain-of-function CCR4 mutations in adult T cell leukaemia/lymphoma. Journal of Experimental Medicine 211, 2497-2505 (2014).

      Recommendations for the authors:

      Reviewer #1 (Recommendations For The Authors):

      (1) The results section is well written, although the introduction needs more information on what is known about CCR7 trafficking and endomembrane signaling. I understand this is because the authors wanted to focus on GPCR signaling, but the study will equally be of interest to researchers in the immunology and chemokine fields, and therefore more CCR7-focussed discussion in the introduction would be useful. Similarly, the discussion would benefit from more discussion of previous studies of CCR7 trafficking and endomembrane signaling (in particular the Laufer et al paper) to acknowledge that many of the findings within this paper verify previous studies.

      We have now included additional immunology/endomembrane background information about CCR7 at the place where the receptor is introduced (first paragraph on page 3). We have also expanded our discussion of our work in relation to the Laufer et al. study (third paragraph on page 10).

      (2) On page 5, the authors state that 'The response to chemokine stimulation was not observed in mock transfected HEK293 cells'. Figure S4D does not have a legend so it is difficult to see what they mean by mock transfected. Do they mean not transfecting with anything or not with the receptor? The better control would be transfecting the reporters but not the receptor. This may have been done, but the wording needs clarifying and S4D needs a legend.

      Thanks for pointing this out. We believe the reviewer refers to Figure S2D and we have now highlighted/clarified the legend better. Mock transfected conditions refer to HEK293 cells transfected with the reporter, but not the receptor. This is written in the legend as “(D) Change in luminescence signal generated between SmBiT-barr1 and LgBiT-miniGi in response to 100 nM CCL19 or 100 nM CCL21 in mock transfected HEK293 cells (no CCR7)”, which we believe should be clear to the audience.

      (3) The validation of the APEX2 receptor construct relies on a single assay with one ligand. The authors should show that the receptor expresses at the cell surface, is internalised normally, and that both ligands activate the receptor.

      We have now included additional data to show that (1) the receptor is expressed at the cell surface, (2) that the CCR7-APEX2 recruits barr1 to the plasma membrane, (3) that this association leads to barr1 translocation to the early endosomes as an indirect measurement of receptor internalization, and (4) that both CCL19- and CCL21-stimulation inhibit forskolin induced cAMP production (Fig.S4A-C, and described in fifth paragraph on page 6).

      (4) The APEX2 section is very short, especially as this is novel data. It lacks some important information, e.g. when the authors state that 'we identified a total of 579 proteins', is this in total for both ligands, separately or were some shared? More information on each ligand separately and combined would make this clearer.

      We have now specified that the identified total proteins enriched from our APEX2 approach is when the cells are stimulated with either CCL19 or CCL21 (third paragraph on page 7). Furthermore, we have included a Venn diagram in Fig. S5C to show how many proteins were enriched by CCL19 or CCL21 stimulation and how many of those were shared at different time points.

      (5) The discussion would benefit from some further work. The current first two paragraphs just reiterate the introduction and don't discuss the current paper so could be removed completely. The Laufer et al study needs much more discussion as they report many of the findings of the current paper (signaling following endocytosis, Rac1 endomembrane signaling) five years ago. The APEX2 findings that are discussed, though interesting, are not followed up by further experimental evidence and there is little discussion of why the two ligands have different responses or what the physiological effects could be.

      We appreciate the reviewer’s effort in helping with the discussion. To this end, we have now expanded our discussion of the mentioned paper further as suggested (third paragraph on page 10). We agree that the findings from our APEX experiment are interesting, but the focus of this study relates to proteins enriched specifically at endosomes. Several of the most enriched proteins did not show this localization bias, which is why these proteins were not further investigated.

      Minor changes:

      (1) The authors should remove the word 'recent' at the start of the first sentence of the third paragraph. Endosomal signaling by GPCRs was described 15 years ago so cannot really be seen as recent anymore.

      We have now adjusted the manuscript accordingly.

      (2) Tukey defaulted to Turkey in some places.

      We thank the reviewer for pointing out these typos, which now have been corrected.

      Reviewer #2 (Recommendations For The Authors):

      Minor Points:

      (1) ACKRs do not couple to G proteins so it is peculiar to see them in this table. I would limit the table to the conventional CCR1-10, CXCR1-6 and XCR1. The ligand for XCR1 is XCL1 which is absent from the table.

      We have now modified the table accordingly.

      (2) CCL19 (formerly known as ELC) has been long known to be a more efficacious and potent ligand in chemotaxis assays (Bardi et al, 2001). This earlier reference should be added to the citations in the preceding statement on page 10.

      This is an important study showing that CCL19 is more efficacious than CCL21 in promoting chemotaxis and that this has been known for decades. We have now included the reference accordingly (reference 59 in second paragraph on page 11).

      (3) Figure 6, Panel Q. I think the legends for CCR7 and CCR7 delta ST might be flipped.

      We thank the reviewer for pointing out this error. We have now corrected the figure panel.

      (4) Figure S5 (or 5) might benefit from simple Venn diagrams showing the numbers of differentially enriched proteins following treatment with the two ligands at different time points.

      We have included a Venn diagram in Fig. S5C to show how many proteins were enriched by CCL19 or CCL21 stimulation and how many of those where shared.

      Reference:

      Bardi, G., Lipp, M., Baggiolini, M. & Loetscher, P. The T cell chemokine receptor CCR7 is internalized on stimulation with ELC, but not with SLC. European Journal of Immunology 31, 3291-3297 (2001).

  3. drive.google.com drive.google.com
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      [Q] Could this process truly be successful when including stakeholders across different generations?

    1. “Desafortunadamente, nuestros sistemas de evaluación siguen estando estrechamente ligados a la publicación de nuestros trabajos y a métricas controvertidas como el factor de impacto

      Esto depende las disciplinas, en Ciencias Sociales o Humanidades es posible hacer una carrera académica exitosa sin nunca haber publicado en revistas de "alto factor de impacto".

    Annotators

  4. inst-fs-iad-prod.inscloudgate.net inst-fs-iad-prod.inscloudgate.net
    1. confusion.

      I think that this means that people are getting confused and cannot accurately say what is surrealism as opposed to abstract art is because of the various styles the artists use. To be more accurate we should look at the historical background o of an art piece and decipher what the artist was trying to convey or understand.

    1. • 230(c)(1), which states that “[n]o provider or user of an interactive computer service shall be treated as the publisher or speaker of any information provided by another information content provider.”• 230(c)(2), which shields providers and users of an interactive computer service from civil liability with regard to any action that is “voluntarily taken in good faith to restrict access to or availability of material that the provider or user considers to be obscene, lewd, lascivious, filthy, excessively violent, harassing, or otherwise objectionable” or “taken to enable or make available to information content providers or others the technical means to restrict access” to such material.• 230(e)(3), which states, inter alia, that “no cause of action may be brought and no liability may be imposed under any State or local law that is inconsistent with this section.”

      what does section 230 meann

    1. Author response:

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

      Reviewer #1:

      The analysis of the dormancy rates is interesting and offers some intriguing questions related to the higher dormancy rate found for the L2 isolates and lower for the L3 ones. It will be interesting in the future to expand the data generated in this advanced in vitro plaAorm to in vivo studies.

      Indeed, an increased dormancy propensity of L2 isolates was previously reported in broth culture and associated to specific genetic polymorphisms. The opposite phenotype observed in the L3 isolates is indeed particularly intriguing and was not described to date. Hence, we fully agree that it would be very interesting to find out whether these phenotypes are also observed in vivo.

      The authors propose that ‘strains exhibiting greater proliferative capacity are more prone to induce macrophage apoptosis, thereby contributing to the extent of the granulomatous response.’ It would be interesting to know what happens if the macrophage apoptotic response is blocked.

      This is an interesting suggestion that would deserve a dedicated comprehensive investigation covering other cell death pathways. Even though the trend is significant, the correlation coefficient is rather low in this interaction, which looks a fortiori due to substantial inter-host variability in the apoptotic propensity of macrophages from individual donors to a given strain. In addition, such blocking experiments may require performing isolated macrophage infections that would fall outside of the scope of this study, or considering the extent and the contribution of the apoptosis of other cell subsets. 

      In contrast to macrophage apoptosis, T cell activation correlated with less replicative bacteria. Are these two findings related, ie, are the granulomas showing more (apoptotic) macrophages the ones with a lower percentage of activated T cells? This would shed light on what distinguishes granulomas that are protective from those that support bacterial growth. 

      Indeed, a significant negative correlation between macrophage apoptosis induction and T cell activation can be observed, specifically with activated CD4 T cells expressing CD38 (rS \= -0.36, p < 0.05) or CD69 (rS = -0.40, p < 0.01). We have added this additional result in the manuscript text (line 217).

      It would also be interesting to know the functional impact of blocking early CXCL9 or IL1b on the outcome of granulomatous response/bacteria growth.

      We have performed the suggested early blocking experiments and added the expected negative effect on granuloma formation upon neutralization of IL-1b (current Fig. 6E) in the revised version of the manuscript, and furthermore discussed the null effect on bacterial growth of the treatment with an anti-CXCL-9 specific antibody (current Fig. 6H).

      The authors acknowledge the absence of neutrophils in this model. However, this could be discussed in more detail, as neutrophils play an important part in TB pathogenesis as shown in different models of infection and human TB. 

      We concur and have expanded the importance of neutrophils in TB pathogenesis (including references) in the discussion section (line 260). 

      Related to neutrophils and TB pathogenesis, another important player is type I IFN. The multiplex assay used included IFN-alpha, was this molecule detected? If so, was there any difference in the levels of type I IFN detected among the different infections?

      We agree and that is why we had originally included IFN-α in our screen. However, this cytokine remained under the limit of quantification at both studied time points, preventing us to draw conclusions on the effect of Mtb strain diversity on the secretion of type I IFNs in in vitro granulomas.

      Reviewer #2:

      In Figure 1b/c, it is not clear what comparisons are being made to give the p-value annotations.

      In Figure 2a/b, it is not clear what comparisons are being made to give the p-value annotations.

      In Figure 3a, again it is not clear what comparisons are being made to give the p-value annotation.

      The p-values formerly present on the upper le] corner of the panels were resulting from either Friedman (Figures 1C, 2A and 3A) or Kruskal-Wallis (Figures 1B and 2B) tests and indicated whether there was a significant difference between the analyzed groups overall. To avoid confusion, those values have been removed to only leave the post-test comparison between specific groups.  

      In the results narrative related to Figure 1 (lines 93-103), the authors refer to lineage heterogeneity without providing any objective quantification of this - I suggest they do so, by providing variance or standard deviations. 

      Thank you very much for this relevant suggestion, we have now included the coefficients of variation as a quantitative measure of the within-lineage heterogeneity in the manuscript (line 97). 

      I also suggest the authors explain what the data points actually represent in this figure - do I assume each data point = cfu from a well of 'granuloma'? Are they all from the same donor PBMC? What is the sample N for each lineage? If the data are not from the same donor PBMC, I think more informative to present the results of paired statistical analyses, stratified by donor cells. In addition, the authors should include a summary table of the demographic characteristics of the donors (at least sex, ethnicity, and age). If the data are derived from a single donor, I'd advocate providing data from at least one further donor.

      In the new supplementary figure requested by Reviewer 3 Figure 1—figure supplement 1 (actual CFU data on days 1 and 8 p.i. used to calculate the growth rate) it is now indicated that bacterial load was quantified as CFU per well.

      Regarding the number of donors used, as stated in the Material and Methods section (current line 418) and depicted by the four different shapes used when data are grouped by individual infecting strain, all figures in our manuscript have been generated using PBMCs from 4 independent donors. For greater clarity, “n = 4” has now been included in the figure legends. Regarding the statistical analyses, paired statistical analyses stratified by donor were already performed in the original version of the manuscript whenever appropriate. 

      As stated in the methods section, the buffy coats used for PBMC isolation are anonymized so demographic data are unavailable.

      The premise of the analysis in Figure tic and the results narrative ("This finding suggests that an increased ability to enter dormancy is not necessarily associated with a more pronounced growth phenotype", line 132) is not clear to me. Why would increased dormancy relate to increased growth in the same context? I suggest this analysis be removed.

      We apologize for the confusion in our original statement. We now rephrased it as “This finding suggests that an increased tendency to remain in a metabolically active state is not necessarily associated with a more pronounced growth phenotype”.

      In Figure 3b, I think it may be more informative if the data points from the same donor were linked. Likewise in Figure 3c, I'd like to see a donor-paired statistical analysis.

      For all figures, the choice of using individual symbols to identify data points from the same donor but not connecting lines was made to provide a neater image. Nevertheless, we have now modified the figure linking the data points from the same donor. The statistical analysis performed is always donor-paired whenever appropriate. 

      The casual inference suggested in the results narrative between ‘macrophage apoptosis’ and granulomatous response line 173-175) is not tested directly by the experiment – I suggest the authors exclude this statement.

      Fair point, the statement has been removed.

      To what extent have the authors considered whether variation in T cell responses between lineages may be confounded by variation in Mtb reactive T cell frequencies in donor PBMC. Can this be disentangled at all? This should be acknowledged as a potential limitation of the study.

      We did characterize the presence of mycobacterial antigen-specific reactive T cells in the PBMCs from the investigated donors. To do so, we performed in vitro stimulations with purified protein derivative (PPD) or an ESAT-6/CFP-10 peptide pool and quantified the frequency of IFN-γ-positive CD4 T cells by flow cytometry. The percentage of IFN-γg-positive CD4 T cells recalled by PPD stimulation ranged from 0.02% to 0.13%, while no ESAT6/CFP-10 reactive T cells were detected. As such, we can akest that the PBMC donors never encountered Mtb even though some levels of memory recalled by PPD may be due to cross-reactivity with BCG or pre-exposure to non-tuberculous mycobacteria. We have now added a panel in Figure 5—figure supplement 2 representing the frequency of mycobacteria-specific CD4 T cells and, as suggested, discussed the impact on the extent of the T cell responses observed in granulomas in the revised version of the manuscript.  Nevertheless, the observed MTBC strain-specific trends are consistent across the donors, as depicted in Figure 5B and Figure 5—figure supplement 2A-B.

      Moreover, the experimental design does not really test cause and effect for the relationship between T cell proliferation/activation and bacterial growth. What is the impact of T-cell depletion from PBMC on bacterial growth?

      The increased TB susceptibility of HIV patients demonstrated that T cells play a critical part in the control of Mtb infection. We agree and did envisage such a depletion experiment. However, depleting T cells from PBMCs would imply removing up to 70% of the cells present in the specimen, which would lead to a situation from which results cannot be compared to the original sample and therefore would not be interpretable. 

      Reviewer #3:

      Data presentation:

      - In Figure 1 (replication rate), actual cumulative CFU means from each strain for both days 1 and 8 with statistical analysis should be presented as panels in this figure.

      Agreed. We are providing the requested representation of the data and the corresponding paired statistical analysis as supplementary material Figure 1—figure supplement 1.

      - In Figure 2 (dormancy), a panel comparing the mean number of bacteria that are single positive for either Auramine-O, Nile Red, or are double positive should be included for each strain, with statistical analysis. Representative photomicrographs of phenotypes from the staining should also be included. Electron microscopy could be conducted to compare the presence of intermediate lipid inclusions within organoidbound mycobacteria.

      As requested, percentages of single stained as well as double positive bacilli in each sample are now represented in Figure 2—figure supplement 1. In addition, we have now also followed the request and included a photomicrograph picturing representative Mtb staining phenotypes. Lastly, it would certainly be very elegant to visualize the presence of Mtb lipid inclusions within cellular aggregates by electron microscopy. However, we do not currently have the means for such investigations and the implementation of such a protocol under BSL3 conditions appears unrealistic in the context of this study.  

      - In Figure 3 (granulomatous response), the number, circularity, and size of immune aggregates are presented as "granuloma score" in which the mean ratio of size to circularity is divided by the number of inclusions. To their credit, in Supplementary Figure 2, the authors provide the data in a straighAorward manner. However, the granuloma score metric is reduced as the number of observed "granulomas" increases, which is counterintuitive. Additionally, circularity is not a definitive aspect of human granulomas (Wells et al., Am J Respir Crit Care Med, 2021, PMID: 34015247). I am skeptical that the "granuloma score" is an accurate predictor granulomatous inflammation. Is there precedent for this metric in the literature? If so, a reference should be provided. A high magnification inset of 1 representative granuloma from each strain should be included in Figure 3A.

      As requested, insets of a representative average granuloma for each strain have been included in Figure 3A. The formulation of the “granuloma score” has no precedent and cannot be referenced. By doing so, we meant to integrate within one single parameter the visual differences represented in the current Figure 3— figure supplement 2. We intentionally sought to assign the highest score to the massive aggregation that some strains may promote unlike some that trigger several small, dispersed and diffused aggregates.

      - In Figure 4 (macrophage apoptosis), a panel showing the percentage of dual Annexin V and 7-AAD positive cells should be included to provide the reader with the relative scope of ongoing apoptotic vs necrotic/secondary necrotic death in the model. If the data is readily available, including a control of uninfected PBMCs would also allow the reader to evaluate donor-dependent differences of in vitro cell death at baseline.

      No significant differences were observed in the percentage of dual Annexin V- and 7-AAD-positive macrophages (necrosis/secondary necrosis) between the MTBC strains at this time-point. Nevertheless, we have disclosed this result in the revised manuscript as Figure 4—figure supplement 2.

      - In Figures 5 and 6 (lymphocyte activation and soluble mediator secretion), panels showing unscaled data should be included. Panels depicting the unscaled immunoassay protein readings (pg/mL) by strain for CXCL9, granzyme B, and TNF with statistical analysis should be included in Figure 6.

      As requested, unscaled lymphocyte activation and soluble mediator data have been included as Figure 5— figure supplement 2 and Figure 6—figure supplement 1, respectively (replacing former supplementary figures 5 and 7). In addition, updated Figure 6G panel now depicts correlation analysis with the unscaled cytokine concentrations.

      The DosR-regulon:

      The authors hypothesize that differences in the prevalence of the dormancy metrics (acid-fastness or lipid inclusion prevalence, are due to strain-specific increases in expression of the DosR regulon within the model's hypoxic conditions (lines 107-114, 126-127). The claim that their model is equipped to evaluate dosR-dependent mycobacterial phenotypes was also previously proposed (Arbués et el., 2021) and should be tested. A comparison of the dosR-dependent gene expression of each strain in PBMC aggregates and broth culture by qRT-PCR would test this idea at a very basic level.

      We agree. Actually, a similar request was made during the revision of our first in vitro granuloma study for which such qPCR data were generated and presented in Fig. 1 D (PMID: 32069329). In addition, the work of Kapoor et al., who originally developed the in vitro granuloma model also demonstrated the induction of most of the DosR regulated genes by qPCR (PMID: 23308269). We trust that the reviewer will agree that this does not need to be repeated.

      The modern Beijing lineage strain L2C:

      The authors claim (Line 101-102) that the results of Figure 1 "confirm the higher virulence propensities of strains from modern lineages". From the data presented, it appears that strain L2C (Modern-Beijing) dominates the modern vs ancestral and inter/intra-lineage phenotypes of replication, dormancy, and apoptosis. Are significant differences between modern and ancestral lineages or between strains simply a facet of the distinct profile of L2C? Do the statistical differences disappear when the L2C group is excluded?

      Indeed, among the modern lineages’ isolates, L2C exhibits a hypervirulent profile in terms of bacterial replication. However, the difference between modern and ancestral strains remains statistically significant when L2C is excluded from the analysis (p = 0.002). That is also the case when we analyze the proportion of dormant bacteria. Exclusion of L2C strain results in a Kruskal-Wallis overall p = 0.005, and p = 0.0002 when we compare L2 vs. L3. Lastly, regarding the percentage of apoptotic macrophages, if we use L2B (instead of L2C) to compare, the difference is still significant vs. L1A (p = 0.008) although there is no longer a trend for L2A (p = 0.1).

      "Dormancy":

      Dormancy is definitively a non-replicative state, where bacterial growth is absent. The authors' findings and claims appear to be incompatible with that definition, which they acknowledge (Lines 130-135). The lack of correlation between growth and dormancy in their model is supported with reference to Figure 2C, a Spearman's analysis of dormancy ratio with growth rate (inclusive of all strains under consideration). The figure supports a model where "dormancy" and "growth rate" are disjunct but also appears to show high "dormancy" accompanying increasing "growth" in the L2C group. How are strains able to grow if they are in a non-replicative state? Are the "growth rate" assays actually measures of survival? Are there different rates of infectivity? Are the bacteria growing cellularly in the serum-rich ECM, etc. etc? We need to see the hard CFU and Nile Red, and Auramine-O data to contextualize these findings. Alternatively, could the accumulation of inclusions in the model not be a reliable dormancy metric (Fines et al., BioRxiv [Preprint], 2023, PMID: 37609245)?

      We fully agree. The Nile red profiles are always relative and only depict the proportion of the population that has entered a dormant state. Nevertheless, dormancy can be dynamic and bacteria may swi]ly resuscitate in that model. Furthermore, and as depicted in Figure 2—figure supplement 1, despite showing an increased tendency to enter a dormant-like state, a considerable population of lineage 2 bacilli still remains metabolically active and in a replicative state. The referred preprint is very interesting and we will follow it up closely.

      Specificity of responses to PBMC aggregation:

      The authors claim that their results "reveal a broad spectrum of granulomatous responses" (Line 73) but do not show any aggregation specificity of PBMC responses beyond the model's intrinsic metrics of area and circularity. To establish that their phenotypes such as lymphocyte activation, cytokine release, cell death, or mycobacterial acid-fastness/lipid inclusion prevalence, are aspects of the granulomatous response the authors could infect PBMCs from the same donors with the same strains and perform the same assays using established Mtb-PBMC models in which the cells do not aggregate. This would answer many important questions, for example, does the rate of macrophage infection account for variability in apoptosis percentage? Phagocytosis assay and quantification of stained intracellular mycobacteria within recently infected PBMCs could be conducted to determine if phenotypes are an aspect of granulomatous aggregation or due to strain-specific differences in cellintrinsic macrophage immunity. It would also be very informative to know what percentage of PBMCs and mycobacteria are granuloma-bound in the ECM.

      We are not aware of Mtb-PBMC models in which the cells do not aggregate. We previously compared PBMC infection models in the presence or absence of the collagen matrix and cells also spontaneously coalesced around infection foci (PMID: 34603299). Regarding the last point, the melting step of the collagen matrix requires enzymatic digestion and pipetting that dislocate the aggregates. Accordingly, we cannot distinguish the bacteria that would remain within the matrix compared to those replicating within cellular aggregates. However, we did resolve this question by demonstrating that the bacteria were not able to grow in the absence of cells in this culture condition (Supplementary material, PMID: 34603299)

      Minor recommendations

      - The term TNF-a should be replaced with TNF throughout the manuscript.

      We acknowledge that the term TNF-a can be interchangeable with TNF. However, we chose to use the TNFα terminology to differentiate it from lymphotoxin α, which is also referred to as TNF-β.

      - The authors cite studies conducted in murine and NHP models to support the claim that "understanding of immune protective traits in TB remains insufficient and yet dominated by data from mouse and non-human primate studies" (Lines 63-64) but ignore an abundance of data from other in vivo and in vitro models that have provided numerous valuable insights in the field of TB immunology. This line should be revised or omired.

      For us, the term “dominate” implies that these models are widely used, not that they are the only ones. Other models indeed provided additional relevant data. We are citing the lung-on-chip model of McKinney’lab and the in vitro granuloma model of Elkigton’s lab (line 66). We would be very happy to include more references upon further specifications even though we cannot build an extensive review here.

      - The authors claim that their model "encompasses, with the exception of neutrophils, all immune cell types involved in TB" (Lines 67-68). To support this claim, they should provide additional references or data demonstrating that the PBMC aggregates include, eosinophils, mast cells, dendritic cells, yolk-sac-derived alveolar macrophages, and Langhan's giant cells.

      With the aim of providing a more accurate and detailed information regarding the cell types present in the model, the sentence has been reformulated as: “The model encompasses all PBMC-derived cell types involved in TB immune responses, but lacks granulocytes (i.e. neutrophils, eosinophils, basophils and mast cells)” (line 260). Noteworthy, the presence of multinucleated giant cells was reported in Kapoor’s paper describing the in vitro granuloma model for the first time (PMID: 23308269).

      -  As an additional note, the title can be improved and made more broadly accessible by revising the use of the acronyms CXCL9, granzyme B, and TNF-α.

      To render the title more broadly accessible we propose to replace the listed acronyms by “soluble immune mediators”, but we remain opened to more appropriate and specific suggestions.

      Answers to the reviewers’ public comments

      Reviewer #1:

      First of all, we would like to thank the reviewers for their feedback and suggestions to improve our manuscript. To strengthen the findings of our study, we have performed and added results from IL-1b and CXCL9 blocking experiments evaluating the impact on the granulomatous response and bacterial load, respectively. In the revised version of the manuscript, while we discuss the null effect on bacterial growth of the treatment with an anti-CXCL-9 antibody and the potential reason behind it, we are now reporting a negative effect on the magnitude of granuloma formation upon neutralization of IL-1b that the correlation analysis had initially suggested.

      Reviewer #2:

      The revised version of our manuscript incorporates now all the points detailed in the private answers to the reviewer, including clarifications on the statistical tests performed, additional supplementary materials to transparently disclose the raw data behind the normalization approach, as well as flow cytometry data on the immune memory status of the blood donors. In addition, and as stated in the answer to reviewer #1, to test causal relationship between some host and pathogen traits, we have now performed and provided data and interpretation of IL-1b and CXCL9 blocking experiments.

      Reviewer #3:

      We are thankful and concur with these constructive comments and insights. We have now consistently revisited the statistics in the figures to improve clarity and included new supplementary figures reporting the raw data that were missing in the initial version of the manuscript. In addition, and as mentioned in the answers to reviewers #1 and #2, we have now performed and added IL-1β and CXCL9 blocking experiments to test causal relationship between specific host and pathogen traits. In particular, we are now reporting a negative effect on the magnitude of granuloma formation upon neutralization of IL-1β that the correlation analysis had initially suggested.

      More specifically, regarding the point that our method for bacterial collection calls into question whether all Mtb plated for CFU assay resided within granulomatous aggregates, we previously reported that Mtb growth strictly required the presence of human cells in our culture conditions (Supplementary material, Arbués et al, 2021, PMID: 34603299). In the presence of cells, our microscopy read-out does allow us to observe extra-cellular growth if infections are carried on beyond an 8-day limit, which we applied in the current study to exclude this particular caveat. 

      Concerning the apparently conflicting observation that those strains displaying an increased tendency to enter a dormant-like state are the ones exhibiting the highest replication rates, we would like to point out that a considerable population of bacilli still remains metabolically active and in a replicative state. For instance, and as depicted in Figure 2—figure supplement 1, despite showing an increased tendency to enter a dormant-like state, a considerable population of lineage 2 bacilli does remain metabolically active. Moreover, dormancy can be dynamic and bacteria may swi]ly resuscitate.

      Regarding the mentioned limitations of our study that we have discussed in the revised version of our manuscript, we fully concur that PBMC-based in vitro granuloma models lack tissue structure as well as some important stromal and immune cellular players. Nevertheless, we and others demonstrated the particular relevance of the 3-dimensional infection approach within a matrix of collagen and fibronectin by providing mechanistical insights into Mtb resuscitation previously associated to treatment with various immunomodulatory drugs (Arbués et al., 2020, PMID: 32069329; Tezera et al., 2020, PMID: 32091388).

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      Referee #2

      Evidence, reproducibility and clarity

      This article presents a study on a mutant form of RNA polymerase I (RNAPI) in yeast, referred to as SuperPol, which demonstrates increased rRNA production compared to the wild-type enzyme. While rRNA production levels are elevated in the mutant, RNAPI occupancy as detected by CRAC is reduced at the 5' end of rDNA transcription units. The authors interpret these findings by proposing that the wild-type RNAPI pauses in the external transcribed spacer (ETS), leading to premature transcription termination (PTT) and degradation of truncated rRNAs by the RNA exosome (Rrp6). They further show that SuperPol's enhanced activity is linked to a lower frequency of PTT events, likely due to altered elongation dynamics and reduced RNA cleavage activity, as supported by both in vivo and in vitro data.

      The study also examines the impact of BMH-21, a drug known to inhibit Pol I elongation, and shows that SuperPol is less sensitive to this drug, as demonstrated through genetic, biochemical, and in vivo approaches. The authors show that BMH-21 treatment induces premature termination in wild-type Pol I, but only to a lesser extent in SuperPol. They suggest that BMH-21 promotes termination by targeting paused Pol I complexes and propose that PTT is an important regulatory mechanism for rRNA production in yeast. The data presented are of high quality and support the notion that 1) premature transcription termination occurs at the 5' end of rDNA transcription units; 2) SuperPol has an increased elongation rate with reduced premature termination; and 3) BMH-21 promotes both pausing and termination. The authors employ several complementary methods, including in vitro transcription assays. These results are significant and of interest for a broad audience. Beyond the minor points listed below, my main criticism concerns the interpretation of data in relation to termination. While it is possible that the SuperPol mutation affects the wild-type Pol I's natural propensity for termination, it is also possible that premature termination is simply a consequence of natural or BMH-21-induced Pol I pausing. SuperPol may elongate more efficiently than the wild-type enzyme, pause less frequently, and thus terminate less often. In this light, the notion that termination "regulates" rRNA production might be an overstatement, with pausing as the primary event. Claiming a direct effect on termination by both the mutation and BMH-21 would require showing that with equivalent levels of pausing, termination occurs more or less efficiently, which would be challenging and should not be expected in this study. The authors address this point in the last two paragraphs of the discussion. My suggestion is to temper the claims regarding termination as a regulatory mechanism.

      Minor points

      • pp. 14-15: The authors note local differences in peak detection in the 5'-ETS among replicates, preventing a nucleotide-resolution analysis of pausing sites. Still, they report consistent global differences between wild-type and SuperPol CRAC signals in the 5'ETS (and other regions o fthe rDNA). These global differences are clear in the quantification shown in Figures 2B-C. A simpler statement might be less confusing, avoiding references to a "first and second set of replicates"
      • Figures 2A and 2C: Based on these data and quantification, it appears that SuperPol signals in the body and 3' end of the rDNA unit are higher than those in the wild type. This finding supports the conclusion that reduced pausing (and termination) in the 5'ETS leads to an increased Pol I signal downstream. Since the average increase in the SuperPol signal is distributed over a larger region, this might also explain why even a relatively modest decrease in 5'ETS pausing results in higher rRNA production. This point merits discussion by the authors.
      • A decreased efficiency of cleavage upon backtracking might imply an increased error rate in SuperPol compared to the wild-type enzyme. Have the authors observed any evidence supporting this possibility?
      • pp. 15 and 22: Premature transcription termination as a regulator of gene expression is well-documented in yeast, with significant contributions from the Corden, Brow, Libri, and Tollervey labs. These studies should be referenced along with relevant bacterial and mammalian research.
      • p. 23: "SuperPol and Rpa190-KR have a synergistic effect on BMH-21 resistance." A citation should be added for this statement.
      • p. 23: "The released of the premature transcript" - this phrase contains a typo

      Significance

      These results are significant and of interest for a basic research audience.

      This referee has expertise in RNA biology, Pol II transcription and termination.

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      Referee #1

      Evidence, reproducibility and clarity

      The study characterises an RNA polymerase (Pol) I mutant (RPA135-F301S) named SuperPol. This mutant was previously shown to increase yeast ribosomal RNA (rRNA) production by Transcription Run-On (TRO). In this work, the authors confirm this mutation increases rRNA transcription using a slight variation of the TRO method, Transcriptional Monitoring Assay (TMA), which also allows the analysis of partially degraded RNA molecules. The authors show a reduction of abortive rRNA transcription in cells expressing the SuperPol mutant and a modest occupancy decrease at the 5' region of the rRNA genes compared to WT Pol I. These results suggest that the SuperPol mutant displays a lower frequency of premature termination. Using in vitro assays, the authors found that the mutation induces an enhanced elongation speed and a lower cleavage activity on mismatched nucleotides at the 3' end of the RNA. Finally, SuperPol mutant was found to be less sensitive to BMH-21, a DNA intercalating agent that blocks Pol I transcription and triggers the degradation of the Pol I subunit, Rpa190. Compared to WT Pol I, short BMH-21 treatment has little effect on SuperPol transcription activity, and consequently, SuperPol mutation decreases cell sensitivity to BMH-21.

      I'd suggest the following points to be taken into consideration:

      Major points:

      1. The differences in the transcriptionally engaged WT Pol I and SuperPol profiles (Figure 2) are very modest, without any statistical analyses. What is the correlation between CRAC replicates? Are they separated in PCA analyses? Please, include more quality control information. In my opinion, these results are not very convincing. Similarly, the effect of BMH-21 on WT Pol I activity (Figure 7) is also very subtle and doesn't match the effect observed in a previous study [1]. Could the author comment on the reasons for these differences? These discrepancies raise concerns about the methodology. In addition, according to the laboratory's previous work [2], Pol I ChIP signal at rDNA is not significantly different in cells expressing WT Pol I and SuperPol. How can these two observations be reconciled? I would suggest using an independent methodology to analyse Pol I transcription, for example, GRO-seq or TT-seq.
      2. While the experiments clearly show SuperPol mutant increases nascent transcription and decreases the production of abortive promoter-proximal transcripts compared to WT Pol I. RPA135-F301S mutation has a minor impact on total rRNA levels, at least those shown in Figure 3B. Are steady-state rRNA levels higher in cells expressing SuperPol mutant? It would be interesting to know if SuperPol mutant produces more functional rRNAs.

      Minor points

      1. In general, the writing style is not clear, and there are some word mistakes or poor descriptions of the results, for example:<br /> On page 14: "SuperPol accumulation is decreased (compared to Pol I)". On page 16: "Compared to WT Pol I, the cumulative distribution of SuperPol is indeed shifted on the right of the graph."
      2. There are also issues with the literature, for example: Turowski et al, 2020a and Turowski et al, 2020b are the same article (preprint and peer-reviewed). Is there any reason to include both references? Please, double-check the references.
      3. In the manuscript, 5S rRNA is mentioned as an internal control for TMA normalisation. Why are Figure 1C data normalised to 18S rRNA instead of 5S rRNA?
      4. Figure 4 should be a supplementary figure, and Figure 7D doesn't have a y-axis labelling.
      5. In Figure 7C, BMH-21 treatment causes the accumulation of ~140bp rRNA transcripts only in SuperPol-expressing cells that are Rrp6-sensitive (line 6 vs line 8), suggesting that BHM-21 treatment does affect SuperPol. Could the author comment on the interpretation of this result?

      References

      1. Jacobs RQ, Huffines AK, Laiho M & Schneider DA (2022) The small-molecule BMH-21 directly inhibits transcription elongation and DNA occupancy of RNA polymerase I in vivo and in vitro. J. Biol. Chem. 298: 101450
      2. Darrière T, Pilsl M, Sarthou M-K, Chauvier A, Genty T, Audibert S, Dez C, Léger-Silvestre I, Normand C, Henras AK, Kwapisz M, Calvo O, Fernández-Tornero C, Tschochner H & Gadal O (2019) Genetic analyses led to the discovery of a super-active mutant of the RNA polymerase I. PLoS Genet. 15: e1008157

      Significance

      The work further characterises a single amino acid mutation of one of the largest yeast Pol I subunits (RPA135-F301S). While this mutation was previously shown to increase rRNA synthesis, the current work expands the SuperPol mutant characterisation, providing details of how RPA135-F301S modifies the enzymatic properties of yeast Pol I. In addition, their findings suggest that yeast Pol I transcription can be subjected to premature termination in vivo. The molecular basis and potential regulatory functions of this phenomenon could be explored in additional studies.

      Our understanding of rRNA transcription is limited, and the findings of this work may be interesting to the transcription community. Moreover, targeting Pol I activity is an open strategy for cancer treatment. Thus, the resistance of SuperPol mutant to BMH-21 might also be of interest to a broader community, although these findings are yet to be confirmed in human Pol I and with more specific Pol I inhibitors in future.

      My expertise is human Pol II and Pol III transcription regulation.

    1. Reviewer #1 (Public review):

      In this manuscript, the authors report that GPR55 activation in presynaptic terminals of Purkinje cells decrease GABA release at the PC-DCN synapse. The authors use an impressive array of techniques (including highly challenging presynaptic recordings) to show that GPR55 activation reduces the readily releasable pool of vesicle without affecting presynaptic AP waveform and presynaptic Ca2+ influx. This is an interesting study, which is seemingly well-executed and proposes a novel mechanism for the control of neurotransmitter release. However, the authors' main conclusions are heavily, if not solely, based on pharmacological agents that most often than not demonstrate affinity at multiple targets. Below are points that the authors should consider in a revised version.

      Major points:

      (1) There is no clear evidence that GPR55 is specifically expressed in presynaptic terminals at the PC-DCN synapse. The authors cited Ryberg 2007 and Wu 2013 in the introduction, mentioning that GPR55 is potentially expressed in PCs. Ryberg (2007) offers no such evidence, and the expression in PC suggested by Wu (2013) does not necessarily correlate with presynaptic expression. The authors should perform additional experiments to demonstrate the presynaptic expression of GPR55 at PC-DCN synapse.

      (2) The authors' conclusions rest heavily on pharmacological experiments, with compounds that are sometimes not selective for single targets. Genetic deletion of GPR55 would be a more appropriate control. The authors should also expand their experiments with occlusion experiments, showing if the effects of LPI are absent after AM251 or O-1602 treatment. In addition, the authors may want to consider AM281 as a CB1R antagonist without reported effects at GPR55.

      (3) It is not clear how long the different drugs were applied, and at what time the recordings were performed during or following drug application. It appears that GPR55 agonists can have transient effects (Sylantyev, 2013; Rosenberg, 2023), possibly due to receptor internalization. The timeline of drug application should be reported, where IPSC amplitude is shown as a function of time and drug application windows are illustrated.

      (4) A previous investigation on the role of GPR55 in the control of neurotransmitter release is not cited nor discussed Sylantyev et al., (2013, PNAS, Cannabinoid- and lysophosphatidylinositol-sensitive receptor GPR55 boosts neurotransmitter release at central synapses). Similarities and differences should be discussed.

      Minor point:

      (1) What is the source of LPI? What isoform was used? The multiple isoforms of LPI have different affinities for GPR55.